Science and Evolution

What Makes Us Human

2009-09-11T08:33:00.000-05:00

It is understood that in the field of molecular evolution new genes can only evolve from duplicated or rearranged versions of preexisting genes. Furthermore, it seemed unlikely that evolutionary processes could produce a functional protein-coding gene from what was once inactive DNA.

But that view is changing as some evidence suggests that this phenomenon does in fact occur. It has been found that genes have arisen from non-coding DNA in yeast,flies, and also primates. No such genes had been found to be unique to humans until now, and the discovery raises questions about how these genes might make humans different from other primates.

One gene was identified in chronic lymphocytic leukemia. This is the first evidence for entirely novel human-specific protein-coding genes originating from ancestrally noncoding sequences. A non-coding sequence involves RNA (ncRNA) is a molecule that is not translated into a protein.In other words, a gene that was once dormant is now active.

The consequence of the finding is that while many coding sequences exist, there are some that are dormant in primates, but become active in humans. This makes us different

Flu in U.S. found resistant to main antiviral drug: Evolution in Action

2009-03-09T06:33:00.000-05:00

Virtually all the flu in the United States this season is resistant to the leading antiviral drug Tamiflu, and scientists and health officials are trying to figure out why.
The problem is not yet a public health crisis because this has been a below-average flu season so far and the chief strain circulating is still susceptible to other drugs — but infectious disease specialists are worried nonetheless.
Last winter, about 11 percent of the throat swabs from patients with the most common type of flu that were sent to the Centers for Disease Control and Prevention for genetic typing showed a Tamiflu-resistant strain. This season, 99 percent do.
"It's quite shocking," said Dr. Kent Sepkowitz, director of infection control at Memorial Sloan-Kettering Cancer Center in New York. "We've never lost an antimicrobial this fast. It blew me away."
The single mutation that creates Tamiflu resistance appears to be spontaneous, and not a reaction to overuse of the drug. It may have occurred in Asia, and it was widespread in Europe last year.

Resistance appeared several years ago in Japan, which uses more Tamiflu than any other country, and experts feared it would spread.
But the Japanese strains were found only in patients already treated with Tamiflu, and they were "weak" — that is, they did not transmit to other people.
"This looks like a spontaneous development of resistance in the most unlikely places — possibly in Norway, which doesn't use antivirals at all," Monto said.
Dr. Henry Niman, a biochemist in Pittsburgh who runs recombinomics.com, a Web site that tracks the genetics of flu cases around the world, has been warning for months that Tamiflu resistance in H1N1 was spreading.
He argues that it started in China, where Tamiflu use is rare, was seen last year in Norway, France and Russia, then moved to South Africa (where winter is June to September), and back to the northern hemisphere in November.

This is another example of evolution in action. Mutations occur which change the DNA features of a virus, where it was resistant to drugs, is not so now.

Neanderthal Timeline

2008-12-28T12:42:00.000-06:00

The Neanderthal (Homo neanderthalensis) or Neandertal was a species of the Homo genus that inhabited Europe and parts of western Asia. The first proto-Neanderthal traits appear in Europe as early as 350,000 years ago. By 130,000 years ago, full blown Neanderthal characteristics had appeared and by 50,000 years ago, Neanderthals disappeared from Asia, although they did not reach extinction in Europe until 33,000 to 24,000 years ago, perhaps 15,000 years after Homo sapiens had migrated into Europe.

LUCA:Last Universal Common Ancestor

2008-12-25T18:58:00.000-06:00

In trying to find the elements necessary for the origin of life, another question of importance is "what was the last universal original ancestor of life?"

A 3.8-billion-year-old organism was not the creature usually imagined. In LUCA, the prevailing belief is that it was a heat-loving or hyperthermophilic organism; like those odd organisms living in the hot vents along the continental ridges deep in the oceans today, above 90 degrees Celsius .
However, the new data suggests that LUCA was actually sensitive to warmer temperatures and lived in a climate below 50 degrees.

The research compared genetic information from modern organisms to characterize the ancient ancestor of all life on earth. Researchers identified common genetic traits between animals, plant, bacteria, and used them to create a tree of life with branches representing separate species. These all stemmed from the same trunk – LUCA, the genetic makeup that we then further characterized.

The RNA Connection to the Origin of Life
What this means is that in the origin of life question an important step has taken place towards reconciling conflicting ideas about LUCA. In particular, they are much more compatible with the theory of an early RNA world, where early life on Earth was composed of ribonucleic acid (RNA), rather than deoxyribonucleic acid (DNA).

RNA is particularly sensitive to heat and is unlikely to be stable in the hot temperatures of the early Earth. But the data indicate that LUCA found a cooler micro-climate to develop, which helps resolve this paradox and shows that environmental micro domains played a critical role in the development of life on Earth.

RNA and the Origin of Life

2008-12-23T18:24:00.000-06:00

What were the conditions necessary for the formation of life? Some scientists believe that RNA was responsible for the development. RNA, the single-stranded precursor to DNA, normally expands one nucleic base at a time, growing sequentially like a linked chain. The problem is that in the primordial world RNA molecules didn't have enzymes to catalyze this reaction, and while RNA growth can proceed naturally, the rate would be so slow the RNA could never get more than a few pieces long (for as nucleic bases attach to one end, they can also drop off the other).

The RNA mechanism to overcome this thermodynamic barrier has been studied by incubating short RNA fragments in water of different temperatures and pH. Under an acidic environment and temperature lower than 70 degrees Celsius, the RNA pieces ranging from 10-24 in length could naturally fuse into larger fragments. This was generally accomplished within 14 hours.

The operation involved the RNA fragments which came together as double-stranded structures then joined at the ends. The fragments did not have to be the same size, but the efficiency of the reactions was dependent on fragment size in which case the larger the better until an optimal efficiency is reached around 100 and then it drops again.

The researchers note that this spontaneous fusing, or ligation, would a simple way for RNA to overcome initial barriers to growth and reach a biologically important size; at around 100 bases long, RNA molecules can begin to fold into functional, 3D shapes.

RadioActive Dating - Potassium-Argon

2008-12-20T12:03:00.000-06:00

Potassium-Argon dating

The element potassium (symbol K) has three nuclides, K39, K40, and K41. Only K40 is radioactive; the other two are stable. K40 can decay in two different ways: it can break down into either calcium or argon. The ratio of calcium formed to argon formed is fixed and known. Therefore the amount of argon formed provides a direct measurement of the amount of potassium-40 present in the specimen when it was originally formed.

Because argon is an inert gas, it is not possible that it might have been in the mineral when it was first formed from molten magma. Any argon present in a mineral containing potassium-40 must have been formed as the result of radioactive decay. F, the fraction of K40 remaining, is equal to the amount of potassium-40 in the sample, divided by the sum of potassium-40 in the sample plus the calculated amount of potassium required to produce the amount of argon found. The age can then be calculated from equation (1).

In spite of the fact that it is a gas, the argon is trapped in the mineral and can't escape. (Creationists claim that argon escape renders age determinations invalid. However, any escaping argon gas would lead to a determined age younger, not older, than actual. The creationist "argon escape" theory does not support their young earth model.)

The argon age determination of the mineral can be confirmed by measuring the loss of potassium. In old rocks, there will be less potassium present than was required to form the mineral, because some of it has been transmuted to argon. The decrease in the amount of potassium required to form the original mineral has consistently confirmed the age as determined by the amount of argon formed.

Human Migration From Asia To Americas

2008-12-18T12:28:00.000-06:00

Finding A new set of ideas on migration to North America have been proposed. One idea is a hypothesis that seems to map the peopling process during the pioneering phase and well beyond, and another is that at the same time there was much more genetic diversity in the founder population than was previously believed.
The Conventional View

Questions about human migration from Asia to the Americas have perplexed anthropologists for decades, but as scenarios about the peopling of the New World come and go, the big questions have remained. One questions is do the ancestors of Native Americans derive from only a small number of “founders” who trekked to the Americas via the Bering land bridge? Also, how did their migration to the New World proceed? And was climate change involved; did the climate have anything to do with their migration? And finally what took them so long?

Changing the Conventional View

A phylogeographic analysis of a new mitochondrial genome dataset allows scientists to draw several conclusions.

30,000 years ago - clades

First, the ancestral population on its way to the Americas paused in Beringia long enough for specific mutations to accumulate. These mutations separate the New World founder lineages from their Asian sister-clades. (A clade is a group of mitochondrial DNAs (mtDNAs ) that share a recent common ancestor. Sister-clades would include two groups of mtDNAs that each share a recent common ancestor and the common ancestor for each clade is closely related.)

Another way to express this is the ancestors of Native Americans who first left Siberia for greener pastures perhaps as much as 30,000 years ago, came to a standstill on Beringia – a landmass that existed during the last glacial maximum that extended from Northeastern Siberia to Western Alaska, including the Bering land bridge – and they were isolated there long enough – as much as 15,000 years – to maturate and differentiate themselves genetically from their Asian sisters.

Lineages are distributed quickly not gradually
Founding lineages or haplotypes are uniformly distributed across North and South America instead of exhibiting a nested structure from north to south. So after the Beringian standstill, the initial North to South migration occured in a swift pioneering process, not a gradual diffusion.

Bi-directional Migrations to North America then Back to Beringia

The DNA data also suggest a lot more going back and forth than was previously suspected of populations during the past 30,000 years in Northeast Asia and North America. The dataset analysis shows that after the initial peopling of Beringia, there were a series of back migrations to Northeast Asia as well as forward migrations to the Americas from Beringia. There was a bi-directional gene flow between Siberia and the North American Arctic.

Using Mitochondrial datasets from populations in the Americas and East Asia
The investigation of the pioneering phase in the Americas, a research team, a group of geneticists from around the world, pooled their genomic datasets and then analyzed 623 complete mitochondrial DNAs (mtDNAs) from the Americas and Asia, including 20 new complete mtDNAs from the Americas and seven from Asia.

What Mitochondrial DNA data reflects

Mitochondrial DNA, that is, DNA found in organelles, rather than in the cell nucleus, is considered to be of separate evolutionary origin, and is inherited from only one parent – the female. The dataset sequence was used to direct genotyping from 20 American and 26 Asian populations.

The Discovery 3 New Sub-Clades
The team identified three new sub-clades that incorporate nearly all of Native American haplogroup C mtDNAs – all of them widely distributed in the New World, but absent in Asia; and they defined two additional founder groups, which differ by several mutations from the Asian-derived ancestral clades.

Disconnect in migration dates
Did the migration occur quickly or slowly? Migration may have occured 30,000 years ago, but the earliest archeological evidence is that it occurred only 15,000 years ago.

The point of departure places Homo sapiens at the Yana Rhinoceros Horn Site in Siberia as early as 30,000 years before the present, but the earliest archaeological site at the southern end of South America is dated to only 15,000 years ago.

Two possible scenarios
First the ancestors of Native Americans peopled Beringia before the Last Glacial Maximum, but remained locally isolated – likely because of ecological barriers – until entering the Americas 15,000 years before the present (the Beringian incubation model, BIM).

The second is that the ancestors of Native Americans did not reach Beringia until just before 15,000 years before the present, and then moved continuously on into the Americas, being recently derived from a larger parent Asian population (direct colonization model, DCM).

The conclusion of the study
The team set out to test the two hypotheses: one, that Native Americans’ ancestors moved directly from Northeast Asia to the Americas; the other, that Native American ancestors were isolated from other Northeast Asian populations for a significant period of time before moving rapidly into the Americas all the way down to Tierra del Fuego.

The data supports the second hypothesis: The ancestors of Native Americans peopled Beringia before the Last Glacial Maximum, but remained locally isolated until entering the Americas at 15,000 years before the present. So they moved into the Americas quickly.

Genome Sequence of Neanderthal Man

2008-12-13T15:40:00.000-06:00

Were Neanderthals and Humans connected at some time in the past? This question is still up for debate, but recently the complete mitochondrial genome of a 38,000-year-old Neanderthal has been sequenced.

At the Max-Planck Institute for Evolutionary Anthropology in Germany scientists have reconstructed the genome sequence. They sequenced the Neanderthal mitochondria—powerhouses of the cell with their own DNA including 13 protein-coding genes—nearly 35 times over. This coverage allowed them to sort out those differences between the Neanderthal and human genomes resulting from damage to the degraded DNA extracted from ancient bone versus true evolutionary changes.

This new sequence and its analysis confirms that the mitochondria of Neanderthals falls outside the variation found in humans today and it provides no evidence of integration between the two lineages although it remains a possibility. It also shows that the last common ancestor of Neanderthals and humans lived about 660,000 years ago, give or take 140,000 years.

The new sequence revealed that the Neanderthals have fewer evolutionary changes overall, but a greater number that alter the amino acid building blocks of proteins. This means that the Neanderthals had a smaller population size than humans do, which makes natural selection less effective in removing mutations.

That notion is consistent with arguments made by other scientists based upon the geological record. Anthropologists argue there were a few thousand Neanderthals that roamed over Europe 40,000 years ago. That smaller population might have been the result of the smaller size of Europe compared to Africa. Another geological issue was that the Neanderthals also would have had to deal with repeated glaciations.

Single Main Migration Across Bering Strait

2008-12-02T21:39:00.000-06:00

Did a relatively small number of people from Siberia who trekked across a Bering Strait land bridge some 12,000 years ago give rise to the native peoples of North and South America?

Researcher working with an international team of geneticists and anthropologists, have produced new genetic evidence that's likely to hearten proponents of the land bridge theory. The study, is one of the most comprehensive analyses so far among efforts to use genetic data to shed light on the topic.

The researchers examined genetic variation at 678 key locations or markers in the DNA of present-day members of 29 Native American populations across North, Central and South America. They also analyzed data from two Siberian groups. The analysis shows:

genetic diversity, as well as genetic similarity to the Siberian groups, decreases the farther a native population is from the Bering Strait -- adding to existing archaeological and genetic evidence that the ancestors of native North and South Americans came by the northwest route.

a unique genetic variant is widespread in Native Americans across both American continents -- suggesting that the first humans in the Americas came in a single migration or multiple waves from a single source, not in waves of migrations from different sources. The variant, which is not part of a gene and has no biological function, has not been found in genetic studies of people elsewhere in the world except eastern Siberia.

The researchers say the variant likely occurred shortly prior to migration to the Americas, or immediately afterwards.

The Genetic Markers for North American Populations originate in East Asia
There is reasonably clear genetic evidence that the most likely candidate for the source of Native American populations is somewhere in east Asia, the research concludes. If there were a large number of migrations, and most of the source groups didn't have the variant, then you would not see the widespread presence of the mutation in the Americas.

Studies with Genetic Markers

Researchers studied the same set of 678 genetic markers used in the new study in 50 populations around the world, to learn which populations are genetically similar and what migration patterns might explain the similarities. For North and South America, the current research breaks new ground by looking at a large number of native populations using a large number of markers.

The pattern the research uncovered -- that as the founding populations moved south from the Bering Strait, genetic diversity declined -- is what one would expect when migration is relatively recent. There has not been time yet for mutations that typically occur over longer periods to diversify the gene pool.

The study also found that:

The study's findings hint at supporting evidence for scientists who believe early inhabitants followed the coasts to spread south into South America, rather than moving in waves across the interior.

Assuming a migration route along the coast provides a slightly better fit with the pattern that are seen in genetic diversity.

Populations in the Andes and Central America showed genetic similarities.

Populations from western South America showed more genetic variation than populations from eastern South America.

Among closely related populations, the ones more similar linguistically were also more similar genetically.

RadioActive Carbon Dating

2008-11-26T09:25:00.000-06:00

The radiocarbon dating method was developed in the 1940's by Willard F. Libby and a team of scientists at the University of Chicago. It subsequently evolved into the most powerful method of dating late Pleistocene and Holocene artifacts and geologic events up to about 50,000 years in age.

Carbon Dating Carbon has unique properties that are essential for life on earth. Familiar to us as the black substance in charred wood, as diamonds, and the graphite in “lead” pencils, carbon comes in several forms, or isotopes. One rare form has atoms that are 14 times as heavy as hydrogen atoms: carbon-14, or 14C, or radiocarbon. Carbon-14 is made when cosmic rays knock neutrons out of atomic nuclei in the upper atmosphere. These displaced neutrons, now moving fast, hit ordinary nitrogen (14N) at lower altitudes, converting it into 14C. Unlike common carbon (12C), 14C is unstable and slowly decays, changing it back to nitrogen and releasing energy. This instability makes it radioactive.

We can take a sample of air, count how many 12C atoms there are for every 14C atom, and calculate the 14C/12C ratio. Because 14C is so well mixed up with 12C, we expect to find that this ratio is the same if we sample a leaf from a tree, or a part of your body. The C-14 within an organism is continually decaying into stable carbon isotopes, but since the organism is absorbing more C-14 during its life, the ratio of C-14 to C-12 remains about the same as the ratio in the atmosphere. When the organism dies, the ratio of C-14 within its carcass begins to gradually decrease. The rate of decrease is 1/2 the quantity at death every 5,730 years. That is the half-life of C-14. Obviously, this works only for things which were once living. It cannot be used to date volcanic rocks, for example. The rate of decay of 14C is such that half of an amount will convert back to 14N in 5,730 years (plus or minus 40 years). This is the “half-life.” So, in two half-lives, or 11,460 years, only one-quarter of that in living organisms at present, then it has a theoretical age of 11,460 years. Anything over about 50,000 years old, should theoretically have no detectable 14C left. That is why radiocarbon dating cannot give millions of years. In fact, if a sample contains 14C, it is good evidence that it is not millions of years old.

Because the decay rate is logarithmic, radiocarbon dating has significant upper and lower limits. It is not very accurate for fairly recent deposits. In recent deposits so little decay has occurred that the error factor (the standard deviation) may be larger than the date obtained. The practical upper limit is about 50,000 years, because so little C-14 remains after almost 9 half-lives that it may be hard to detect and obtain an accurate reading, regardless of the size of the sample.

The ratio of C-14 to C-12 in the atmosphere is not constant. Although it was originally thought that there has always been about the same ratio, radiocarbon samples taken and cross dated using other techniques like dendrochronology have shown that the ratio of C-14 to C-12 has varied significantly during the history of the Earth.

This variation is due to changes in the intensity of the cosmic radiation bombardment of the Earth, and changes in the effectiveness of the Van Allen belts and the upper atmosphere to deflect that bombardment. For example, because of the recent depletion of the ozone layer in the stratosphere, we can expect there to be more C-14 in the atmosphere today than there was 20-30 years ago. To compensate for this variation, dates obtained from radiocarbon laboratories are now corrected using standard calibration tables developed in the past 15-20 years.

When reading archaeological reports, be sure to check if the carbon-14 dates reported have been calibrated or not.

The major developments in the radiocarbon method up to the present day involve improvements in measurement techniques and research into the dating of different materials. Briefly, the initial solid carbon method developed by Libby and his collaborators was replaced with the Gas counting method in the 1950's. Liquid scintillation counting, utilising benzene, acetylene, ethanol, methanol etc, was developed at about the same time.

Today the vast majority of radiocarbon laboratories utilise these two methods of radiocarbon dating. Of major recent interest is the development of the Accelerator Mass Spectrometry method of direct C14 isotope counting.

In 1977, the first AMS measurements were conducted by teams at Rochester/Toronto and the General Ionex Corporation and soon after at the Universities of Simon Fraser and McMaster. The crucial advantage of the AMS method is that milligram sized samples are required for dating. Of great public interest has been the AMS dating of carbonacous material from prehistoric rock art sites, the Shroud of Turin and the Dead Sea Scrolls in the last few years.

The development of high-precision dating (up to ±2.0 per mille or ±16 yr) in a number of gas and liquid scintillation facilities has been of similar importance (laboratories at Belfast (N.Ireland), Seattle (US), Heidelberg (Ger), Pretoria (S.Africa), Groningen (Netherlands), La Jolla (US), Waikato (NZ) and Arizona (US) are generally accepted to have demonstrated radiocarbon measurements at high levels of precision).

The calibration research undertaken primarily at the Belfast and Seattle labs required that high levels of precision be obtained which has now resulted in the extensive calibration data now available. The development of small sample capabilities for LSC and Gas labs has likewise been an important development - samples as small as 100 mg are able to be dated to moderate precision on minigas counters with similar sample sizes needed using minivial technology in Liquid Scintillation Counting.

The radiocarbon dating method remains arguably the most dependable and widely applied dating technique for the late Pleistocene and Holocene periods.

Figure: The "Curve of Knowns"

The first acid test of the new method was based upon radiocarbon dating of known age samples primarily from Egypt (the dates are shown in the diagram by the red lines, each with a ±1 standard deviation included). The Egyptian King's name is given next to the date obtained. The theoretical curve was constructed using the half-life of 5568 years. The activity ratio relates to the carbon 14 activity ratio between the ancient samples and the modern activity. Each result was within the statistical range of the true historic date of each sample.

Other forms of Radioactive Dating

There are various other radiometric dating methods used today to give ages of millions or billions of years for rocks. These techniques, unlike carbon dating, mostly use the relative concentrations of parent and daughter products in radioactive decay chains. For example, potassium-40 decays to argon-40; uranium-238 decays to lead-206 via other elements like radium; uranium-235 decays to lead-207; rubidium-87 decays to strontium-87; etc. These techniques are applied to igneous rocks, and are normally seen as giving the time since solidification.

Rubidium occurs in nature as two isotopes: radioactive Rb-87 and stable Rb-85. Rb-87 decays with a half-life of 48.8 billion years to Sr-87. This half-life is so long that the Rb-Sr method is normally only used to date rocks that are older than about 100 million years.

Neutral Evolution and the Shape of Our Genome

2008-11-25T09:58:00.000-06:00

Finding: There is a growing body of evidence which shows that many of the genetic bits and pieces that drive evolutionary changes do not confer any advantages or disadvantages to humans or other animals.

The conventional view
The basic belief of evolution was that all random genetic changes that manage to stick around have some selective advantage on the species.

But a study concludes that we are what we are largely due to random changes that are completely neutral. This study reinforces and highlights the equal, and in some cases greater, importance of neutral genetic drift.

Repeat Elements
Repeat elements are fragments of DNA containing the same repetitive sequence of chemical base pairs several hundred times. Experiments demonstrate that repeat elements rose to prominence without offering any benefits to the organism it inhabits. They are one of the major architectural markers of the human genome, and they make up over 40 percent of our genome,

Numts or Copies of mitochondrial sequences found in DNA portions

One type of repeat element was found while looking at genes associated with Bardet Biedl syndrome, a rare disorder. Researchers found portions of DNA that had been copied from the mitochondria, the energy-making apparatus of human cells that has its own small genome. These mitochondrial sequences are known as numts.

More Numts as the species gets more sophisticated
The whole human genome, has more than 1200 such pieces of mitochondrial DNA of various lengths embedded into chromosomes. While chimps have a comparable number, mice and rats only have around 600 numts. Since they increase in frequency as species advance, it suggested there was some evolutionary purpose to keeping them around.

But none of these numts contained an actual gene to make a protein that does anything, nor did they seem to control the function of any nearby genes. These numts are a neutral part of our genome. If anything, they may be mildly negative since long repeat sequences can be unstable or get inserted inside genes and disrupt them.

The researchers believe they have uncovered a possible reason why these potentially damaging but mostly neutral bits of DNA accumulate over time by comparing the sequences of human numts with those in different animals. How closely the different species' sequences match can provide an estimate of when that particular sequence got inserted into the ancestor of the human genome.

Numts became embedded roughly when primates emerged: 54 Million years ago
Calculations made about the location and structure of the numts revealed that most numts became embedded in our genome over a 10-million-year period centered roughly 54 million years ago -- right around the time when the first primates emerged. When new species emerge, their numbers and therefore their genetic differences are very small. The consequences are that this creates a genetic bottleneck during which any changes in the genome will either get eliminated quickly or spread to the whole population quickly.

Numts expanded because they were not eliminated - they were not detrimental

Numts, being "neutral," were generally at low levels in ancient mammals, but during the primate emergence 54 million years ago, they accumulated and spread through the small early primate populations precisely because they were not detrimental enough to be eliminated. Then, as these populations expanded, numts reached stable but higher frequencies.

Radioactive Dating: Rubidium-Strontium

2008-11-22T12:07:00.000-06:00

Rubidium-Strontium dating:The nuclide rubidium-87 decays, with a half life of 48.8 billion years, to strontium-87. Strontium-87 is a stable element; it does not undergo further radioactive decay. (Do not confuse with the highly radioactive isotope, strontium-90.) Strontium occurs naturally as a mixture of several nuclides, including the stable isotope strontium-86.

If three different strontium-containing minerals form at the same time in the same magma, each strontium containing mineral will have the same ratios of the different strontium nuclides, since all strontium nuclides behave the same chemically. (Note that this does not mean that the ratios are the same everywhere on earth. It merely means that the ratios are the same in the particular magma from which the test sample was later taken.) As strontium-87 forms, its ratio to strontium-86 will increase. Strontium-86 is a stable element that does not undergo radioactive change. In addition, it is not formed as the result of a radioactive decay process. The amount of strontium-86 in a given mineral sample will not change. Therefore the relative amounts of rubidium-87 and strontium-87 can be determined by expressing their ratios to strontium-86: Rb-87/Sr-86 and Sr87/Sr-86 We measure the amounts of rubidium-87 and strontium-87 as ratios to an unchanging content of strontium-86.

Because of radioactivity, the fraction of rubidium-87 decreases from an initial value of 100% at the time of formation of the mineral, and approaches zero with increasing number of half lives. At the same time, the fraction of strontium-87 formed increases from zero and approaches 100% with increasing number of half-lives. The two curves cross each other at half life = 1.00. At this point the fraction of Rb87 = Sr87 = 0.500. At half life = 2.00, Rb87 = 25% and Sr87 = 75%, and so on.

Radioactive Dating: Uranium-Lead

2008-11-12T12:28:00.000-06:00

The uranium-lead method is the longest-used dating method. It was first used in 1907, about a century ago. The uranium-lead system is more complicated than other parent-daughter systems; it is actually several dating methods put together.

Natural uranium consists primarily of two isotopes, U-235 and U-238, and these isotopes decay with different half-lives to produce lead-207 and lead-206, respectively. In addition, lead-208 is produced by thorium-232. Only one isotope of lead, lead-204, is not radiogenic.

The uranium-lead system has an interesting complication: none of the lead isotopes is produced directly from the uranium and thorium. Each decays through a series of relatively short-lived radioactive elements that each decay to a lighter element, finally ending up at lead. Since these half-lives are so short compared to U-238, U-235, and thorium-232, they generally do not affect the overall dating scheme. The result is that one can obtain three independent estimates of the age of a rock by measuring the lead isotopes and their parent isotopes. Long-term dating based on the U-238, U-235, and thorium-232 will be discussed briefly here; dating based on some of the shorter-lived intermediate isotopes is discussed later.

The uranium-lead system in its simpler forms, using U-238, U-235, and thorium-232, has proved to be less reliable than many of the other dating systems. This is because both uranium and lead are less easily retained in many of the minerals in which they are found. Yet the fact that there are three dating systems all in one allows scientists to easily determine whether the system has been disturbed or not.

Using slightly more complicated mathematics, different combinations of the lead isotopes and parent isotopes can be plotted in such a way as to minimize the effects of lead loss. One of these techniques is called the lead-lead technique because it determines the ages from the lead isotopes alone. Some of these techniques allow scientists to chart at what points in time metamorphic heating events have occurred, which is also of significant interest to geologists

Intelligent Design ... by the numbers

2008-11-10T09:19:00.000-06:00

The most endearing element of Intelligent Design is that the universe is so fine tuned that only a designer with a purpose could have made it so.

If the structure of the atom was changed just so...If the energy property of the quarks was altered just so slightly...every thing would be different. The Universe as we know it would not exist. And life would not exist.

OK...Let's see.

The Dimensions of the Game
Let's talk about baseball. Many baseball purists think that the game is perfect. It is the perfect team sport and the perfect individual sport. Defense vs. Offense. And if you change the dimensions of the game, it would be different.

Think of it. The bases are 90 ' ft from each other. This accounts for the batting averages being what they are. The majority of baseball players have a batting average between 250 and 275. The really good batters will have an average above 280 and up to 340. Very few if any will have a yearly batting average above 350. In the last 60 years only one player has had an average above 400. It is very hard to get a hit given the dimensions of the game.

Now suppose you changed the dimensions only a little bit. Instead of the base path at 90', you changed them to 89' and 10". That's only two inches. But that would be enough to change the batting averages. Not much but you would affect the close calls. Now instead of missing the close call base hit by 2" you make it by 2". Batting averages would go up from 250 to 275; the outstanding hitters will have averages above 350 to 380.

Changing the dimensions of the game make a change in the game. But it is still baseball. Ohter adjustments may be made to favor the picture. 5 balls will equal a walk; 2 stikes equal a strike out. Change the dimensions to favor the batter, and you change other rules to favor the picture.

But it is still baseball. The game has changed, because the rules have changed. But it is baseball.

The Structure of the Universe
Well that's what the universe is like. If you change the rules so that this universe will produce a set of atoms with a certain atomic structure, you can have different molecular structures that would adjust to the different chemical rules, and hence different physical rules. The table of periodic elements would look different, but you would still have a table of periodic elements.

Fine Tuning
So the fine tune tinkering would not necessarily be unique. In fact, if you have a universe with the basic laws of F=MA and Shroedingers equation.

You have this universe. Now you can take this universe and change it by tinkering with the rules. But you would get a different universe. However, there is nothing to say that it couldn't evolve life and consciousness. If it did that, if it allowed that, then you would have a universe like ours. It would permit life and consciousness. But it would not be unique.

The Arguement for Design does it show a necessary universe?
The result is that if any universe can create the conditions of life and consciousness, it undermines the argument of design. This is a finely tuned universe, but so is any universe that can create the conditions of life and consciousness. There is nothing special; this is a condition of nature and not necessarily unique. If it is not necessarily unique then the uniqueness factor is not the necessary factor to make you believe in a designer. That is unless you believe that the designer is nature, in the sense that God is nature via Spinosa.

A necessary universe is a unique universe. A universe which can create life and consciousness is necessary only if there is no other way to create those elements; only if life and consciousness can only be created in one universe. If any universe or a great number of possible universes can create life and consciousness then those conditions are ubiquitous; they are pan-universal. So the universe is not unique among universes. It is not unique, and if it is not unique, it is not necessary.

The Hap Map Project?

2008-09-21T18:51:00.000-05:00

The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors.

The Project is a collaboration among scientists and funding agencies from Japan, the United Kingdom, Canada, China, Nigeria, and the United States. All of the information generated by the Project will be released into the public domain.

The goal of the International HapMap Project is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. By making this information freely available, the Project will help biomedical researchers find genes involved in disease and responses to therapeutic drugs.

In the initial phase of the Project, genetic data are being gathered from four populations with African, Asian, and European ancestry. Ongoing interactions with members of these populations are addressing potential ethical issues and providing valuable experience in conducting research with identified populations.

Creationism and Snapshots of the Universe

2008-09-16T12:48:00.000-05:00

One problem that Creationism has (among many) is that it is a snapshot of the state of the Universe. By that I mean that any changes to the underlying structure cannot be made because time and space and the elements have already been spelled out by the Creator.

One way of looking at this is the notion that when the Creator made the universe he could have made a less than perfect creation or a perfect creation.

If the creation is less than perfect, end of story. There is no need to pursue creationism or Intelligent design as a model for the universe.

If the creation is perfect, as creationists believe, then in Liebniz' words, this is the "best of all Possbile worlds."

Well is it? I for one don't think it is because it could be improved by getting rid of cancer or diabeties. In other words, the universe doesn't meet the condition of being perfect if there are flaws. So the snapshot that was taken didn't really occur.

Creationism, Evolution and the Peppered Moth

2008-08-22T23:26:00.000-05:00

Finding: The Peppered Moth has been used as an example of evolution in action. Recent controversy about the precise mechanism used to change the appearance of the Peppered Moth has allowed creationists to argue that Evolutionists have used an incorrect and fraudulent example of evolution. but new research has confirmed the actual environmental process used by evolution to change the appearance of the Peppered Moth.

An Example of Evolution in Action
For decades, the peppered moth was the textbook example of evolution in action, unassailable proof that Darwin got it right.

Recently, though, the peppered moth's status as an icon of evolution has been under threat. Emboldened by legitimate scientific debate over the fine details of the peppered moth story, creationists and other anti-evolutionists have orchestrated a decade-long campaign to discredit it - and with it the entire edifice of evolution.

These days you're less likely to hear about the peppered moth as proof of evolution than as proof that biologists cannot get their story straight.

Recent Controversy
The peppered moth now counts among the anti-evolutionists' most potent weapons. In the past few years it has helped them get material critical of evolution added to high-school science lessons in Ohio and Kansas, although the material has now been removed. In 2000, the authors of the widely used school textbook Biology reluctantly dropped the peppered moth in direct response to creationist attacks. The latest edition features the beaks of Galapagos finches instead.
Now, though, biologists are fighting back. Majerus recently finished an exhaustive experiment designed to repair the peppered moth's tattered reputation and reverse the creationists' advances. The preliminary results are out, and Majerus says they are enough to fully reinstate the moth as the prime example of Darwinian evolution in action.

The Peppered Moth Evolutionary Story
The textbook version of the peppered moth story is simple enough. Before the mid-19th century, all peppered moths in England were cream coloured with dark spots. In 1848, however, a "melanic" form was caught and pinned by a moth collector in Manchester. By the turn of the 20th century melanic moths had all but replaced the light form in Manchester and other industrial regions of England. The cause of the change was industrial pollution: as soot and other pollutants filled the air, trees used by peppered moths as daytime resting places were stripped of their lichens then stained black with soot. Light-coloured moths that were well camouflaged on lichen-coated trees were highly conspicuous on blackened trees. Melanic moths, in contrast, were less easily spotted by predatory birds and so survived longer, leaving more offspring than the light forms. As melanism is heritable, over time the proportion of black moths increased.
As with all textbook examples, however, this is a simplified account of decades of field work, genetic studies and mathematical analyses carried out by dozens of researchers. It also draws disproportionately on the flawed work of one biologist, Bernard Kettlewell of the University of Oxford.

1950 Experiments
In the 1950s Kettlewell carried out a series of classic experiments that cemented the peppered moth's iconic status. These were designed to test a hypothesis first proposed that the rise in melanism was a result of natural selection caused by differential bird predation.

Kettlewell carried out experiments in 1953 and 1955 in polluted woodland in Rubery, near Birmingham, and unspoiled woodland in rural Dorset. In the mornings he dropped hundreds of marked moths, both light and melanic, on tree trunks, where they quickly took up resting positions. In the evenings he used moth traps to recapture them. In Birmingham, he recaptured twice as many dark as light moths. In Dorset, he found the opposite, recapturing more light moths. The obvious conclusion was that light moths were more heavily predated than dark moths in Birmingham, and vice versa in Dorset.

During these experiments Kettlewell also directly observed robins and hedge sparrows eating peppered moths. As expected, the birds noticed and ate more light-coloured moths on soot-covered trees, and more melanic ones on lichen-covered trees. This was a breakthrough, as hardly anyone in Kettlewell's time believed that birds ate moths.

Kettlewell's experiments were accepted as proof that the rise of the melanic moth was a case of evolution by natural selection, and that the agent of selection was bird predation. The peppered moth quickly found its way into textbooks, often accompanied by striking photographs of light and dark moths resting on lichen-covered and soot-stained bark.

Problems with the Experiments
But in truth there were problems with Kettlewell's experiments. Perhaps the most significant was that he released moths onto tree trunks. Although moths occasionally choose trunks as a daytime resting place, they prefer the underside of branches. Kettlewell also let his moths go during the day, even though they normally choose their resting place at night. And he released more moths than would naturally be present in an area, which may have made them more conspicuous and tempted birds to eat them even if they wouldn't normally. These problems were familiar to evolutionary biologists, many of whom tried to resolve them with experiments, but were not given a general airing until 1998, when Majerus pointed out the flaws in Kettlewell's work in his book Melanism: Evolution in action.

The Origins of the Controversy
In November 1998, Nature published a review of his book by evolutionary biologist Jerry Coyne of the University of Chicago. In it, Coyne wrote a sentence that would come back to haunt him: "For the time being we must discard Biston as a well-understood example of natural selection in action." He did not mean to imply that the peppered moth was not an example of evolution by natural selection, merely that the fine details were still lacking. "I wasn't very clear. The key was well-understood."

But to anti-evolution organisations such as the Discovery Institute, they took the criticism of the Kettewell experiments. Coyne's words were taken out of context and were selectively quoting him and Majerus they managed to portray the textbook version of events as hopelessly flawed, and with it the entire theory of evolution. They also pointed at the textbook pictures - which are often staged with dead specimens - and proclaimed that the science behind those pictures was staged too.

Out of the Frying Pan into the Fire
In 2000 Majerus embarked on a large experiment designed to iron out the problems with Kettlewell's work. But things took a turn for the worse when in 2002, journalist Judith Hooper published a popular science book called Of Moths and Men: Intrigue, tragedy & the peppered moth. She accused Kettlewell of manipulating his data to prove his hypothesis. Hooper's book is not a creationist text, but creationists seized on it anyway as evidence that Kettlewell was a fraud.

Promlems with Hooper's Book
Numerous historians and scientists pointed out that Hooper's book is littered with factual errors, not least the accusation that Kettlewell forged his data. There is no evidence he did so. Coyne himself wrote a scathing review of Hooper's book in which he accused her of unfairly smearing Kettlewell and concluded that "industrial melanism still represents a splendid example of evolution in action". It is fair to say that this accurately represented the views of the vast majority of evolutionary biologists at the time, but by then the damage had been done.

Reworking the Experiments
Meanwhile, Majerus was steadily working through his experiment in his own garden in Cambridge. He started by identifying 103 branches that were suitable resting places for peppered moths, ranging in height from 2 to 26 metres, many of them covered in lichen. For seven years, every night from May to August, he placed nets around 12 randomly chosen branches and released a single moth into each net. Around 90 per cent were light-coloured to reflect the natural frequencies of the two forms around Cambridge.

The moths took up resting positions overnight, usually on the underside of the branch. At sunrise the next morning Majerus removed the nets and 4 hours later checked to see which moths were still there. His assumption was that, as peppered moths spend the whole day in their resting position, any that disappeared between sunrise and mid-morning had almost certainly been spotted and eaten by birds.

Because he was able to watch some of the branches from his house through binoculars, he also observed the moths being eaten by many species of bird - including robins, blackbirds, magpies and blue tits. As expected, the birds were better at spotting the dark moths than the camouflaged light ones, he says.

Majerus addressed all the flaws in Kettlewell's experiments. He let moths choose their own resting positions, he used low densities, he released them at night when they were normally active, and he used local moths at the frequencies found in nature.

Majerus presented his preliminary results at a meeting of evolutionary biologists at the University of Uppsala in Sweden. He said that over the seven years, 29 per cent of his melanic moths were eaten compared with 22 per cent of light ones. This was a statistically significant difference.

As in many parts of the UK, pollution in Cambridge has declined since the adoption of clean air acts in the 1950s, and melanic moths are becoming increasingly rare, declining from 12 per cent of the population in 2001 to under 2 per cent today. According to Majerus, his results show that bird predation is the agent of this change. Birds were better at spotting dark moths than light ones, ate more of them and reduced the percentage of black moths over time. It provides the proof of evolution.

There is no doubt that the peppered moth's colour is genetically determined, so changes in the frequencies of light and dark forms demonstrate changes in gene frequencies - and that is evolution. What's more, the direction and speed at which this evolution occurred can only be explained by natural selection.

Anti-evolutionists continue to suggest there is, of course, but as far as Majerus and others are concerned their claims have been debunked and the peppered moth should be reinstated as a textbook example of evolution in action. Not just to teach children either, but also as a direct rebuttal of anti-evolutionism. The peppered moth story is easy to understand because it involves things that we are familiar with: vision and predation and birds and moths and pollution and camouflage and lunch and death. That is why the anti-evolution lobby attacks the peppered moth story. They are frightened that too many people will be able to understand.

Some problems with Intelligent Design

2008-08-22T13:58:00.000-05:00

Is this the only way that life could have originated?

Intelligent design advocates make the case that the universe is finely tuned, so much so that if you changed some small feature, the gravitational constant, or the mass of the proton, then the universe would be different, and life could not have been formed. They conclude that the intelligent construction of the universe, so finely tuned, creates proof that the universe was created by an intelligent creator. In other words, the intelligent creation is the result of an intelligent creator. The universe is intelligently designed, so there must be an intelligent creator, or God.

Let's look at this arguement. The main thrust of the argument is that because the universe, with it's natural construction of atoms has resulted in an organized table of periodic elements, and one of them, carbon, is the foundation of life, this natural construction could not have occured if the resulting organization weren't put into place to begin with.

Let's see.

Let's talk about Baseball. In baseball, the home plate is 90 feet from first base. Batters have their entire careers built around getting to first base as soon as possible after they hit the ball.

Good batters will get there about 30% of the time. Bad batters will get there about 20% of the time. Most batters will fall in between those two percentages.

Now let's change the dimensions of the ball field. Now say that the distance is not 90 feet but 89 feet. That means that more players will get to first base. Averages my go up so the the best hitters are over 35% and the worst hitters are now batting over 25%. The statistics have changed and the players will have to adjust their game to the new dimensions.

Or suppose the length is not 90 feet but 91 feet. The opposite will occur. More players will be out. Batting averages will drop, so that the best hitters are now batting around 25%; the worst hitters are batting around 15%. Again the statistics change, and the players have to adjust to the new dimensions.

But in both cases the game of baseball is still recognized. The conditions change but the game is still there. So let's take this kind of argument and apply it to the universe.

Universe #1

About 13 to 15 billion years ago, the big bang occurred. And let's say that one of the results of the big bang was that certain rules, and physical laws and constants were created that made the universe the way that it is. Let's call the rules and conditions by a simple term: "C" which the constant for the speed of light.

One result of the rules is periodic table of elements. There are 92 naturally occuring, and about 26 man-made.

We also know that element # 6 is carbon. And carbon is the foundation of life.

Universe #2:
Now let's suppose that in Universe #2, there was a big bang as well. But this time the constant of the universe is 1.1C. It is just a little bit bigger than C is in our universe. One of the consequences is that there are 134 naturally occurring elements. Carbon is one of them, but in this universe, element #48, our "Cadmium" is responsible for life, not carbon. Again in this universe there was a naturally occuring structure built around how the atoms were arranged. Life was not pre-ordained to start with Carbon, but with a different element.

Universe #3.
Universe #3 is like universe #2 and Universe #1. But in universe #3, the constant is .98C, smaller than universe #1. As a result there are only 58 naturally occuring elements, and element #18, "Argon" creates life. And again with this universe, the atoms arranged in such away that the properties of the periodic table result in a very different configuration for what constitutes matter.

In all three universes, we see that it is not necessary to invoke a special design, or even that the design in one is unique. This means that an intelligent design in which there is only one way to create life, doesn't have to be.

New Method Of Selecting DNA Microarray-based Genomic Selection (MGS),

2008-07-22T19:11:00.000-05:00

Finding: Microarray-based Genomic Selection (MGS), is a research protocol that allows scientists to extract and enrich specific large-sized DNA regions, then compare genetic variation among individuals using DNA resequencing methods. Sequencing can be done by a small staff of researchers...it is inexpensive and not labor intensive.

The new technology will allow researchers to more easily discover subtle and overlooked genetic variations that may have serious consequences for health and disease.

Problem in genetic investigation
DNA sequencing platforms do not have a simple, inexpensive method of selecting specific regions to resequence; this has been a serious barrier to detecting subtle genetic variability among individuals.

The goal of most human genetics researchers is to find variations in the genome that contribute to disease. Despite the success of the human genome project and the availability of a number of next-generation The Emory scientists believe that goal will be much more obtainable thanks to MGS.

MGS uses DNA oligonucleotides (probes) arrayed on a chip at high density (microarray) to directly capture and extract the target region(s) from the genome. The probes are chosen from the reference human genome and are complementary to the target(s) to capture. Once the target is selected, resequencing arrays or other sequencing technologies can be used to identify variations.

The Emory scientists believe MGS will allow them to easily compare genetic variation among a number of individuals and relate that variation to health and disease.

The human genome project focused on sequencing just one human genome--an amazing technological feat that required a very large industrial infrastructure, hundreds of people and a great deal of money. The question since then has been, can we replicate the ability to resequence parts of the genome, or ultimately the entire genome, in a laboratory with a single investigator and a small staff" The answer is now 'yes.'"

Geneticists have found many different types of obvious gene mutations that are deleterious to health, but more subtle variations, or variations located in parts of the genome where scientists rarely look, may also have negative consequences but are not so easily discovered.

Other methods for isolating and studying a particular region of the genome, such as PCR and BAC cloning (bacterial artificial chromosomes) are comparatively labor intensive, difficult for single laboratories to scale to large sections of the genome, and relatively expensive, says Dr. Zwick.

Whereas typical microarray technology measures gene expression, MGS is a novel use of microarrays for capturing specific genomic sequences. For the published study, a third type of microarray--a resequencing array--was used to determine the DNA sequence in the patient samples.

The logic behind the resequencing chip is that you design the chip to have the identity of the base at every single site in a reference sequence. You use the human genome reference sequence as a shell and you search for variation on the theme. This alternative new technology allows a regular-sized laboratory and single investigator to generate a great deal of data at a cost significantly less than what a sequencing center would charge.

Importance Of Gene Regulation For Common Human Disease

2008-06-20T16:12:00.000-05:00

Finding: A new study shows that common, complex diseases are more likely to be due to genetic variation in regions that control activity of genes, rather than in the regions that specify the protein code.

Where are the regions?
This result comes from a study of the activity of almost 14,000 genes in 270 DNA samples collected for the HapMap Project. The authors looked at 2.2 million DNA sequence variants (SNPs) to determine which affected gene activity. They found that activity of more than 1300 genes was affected by DNA sequence changes in regions predicted to be involved in regulating gene activity, which often lie close to, but outside, the protein-coding regions.

The challenge of large-scale studies that link a DNA variant to a disease
We predict that variants in regulatory regions make a greater contribution to complex disease than do variants that affect protein sequence. This is the first study on this scale and these results are confirming our intuition about the nature of natural variation in complex traits.
One of the challenges of large-scale studies that link a DNA variant to a disease is to determine how the variant causes the disease: our analysis will help to develop that understanding, a vital step on the path from genetics to improvements in healthcare.

What the HapMap does
Past studies of rare, monogenic disease, such as cystic fibrosis and sickle-cell anaemia, have focused on changes to the protein-coding regions of genes because they have been visible to the tools of human genetics. With the HapMap and large-scale research methods, researchers can inspect the role of regions that regulate activity of many thousands of genes.

The HapMap Project established cell cultures from participants from four populations as well as, for some samples, information from families, which can help to understand inheritance of genetic variation. The team used these resources to study gene activity in the cell cultures and tie that to DNA sequence variation

Scientists found strong evidence that SNP variation close to genes - where most regulatory regions lie - could have a dramatic effect on gene activity. Although many effects were shared among all four HapMap populations, they also shown that a significant number were restricted to one population.

What about the house keeping genes?
They also showed that genes required for the basic functions of the cell - so-called housekeeping genes - were less likely to be subject to genetic variation. This was exactly as one would expect: you can't mess too much with the fundamental life processes and we predicted we would find reduced effects on these genes.

The study also detected SNP variants that affect the activity of genes located a great distance away. Genetic regulation in the human genome is complex and highly variable: a tool to detect such distant effects will expand the search for causative variants. The authors note, however, that the small sample size of 270 HapMap individuals is sensitive enough to detect only the strongest effects.

Happenstance mutations matter

2008-06-17T08:18:00.000-05:00

Scientists show that happenstance mutations matter

Finding: In experiments on bacteria grown in the lab, scientists found that evolving a new trait sometimes depended on previous, happenstance mutations. Without those earlier random mutations, the window of opportunity for the novel trait would never have opened. History might have been different.

Evolutionist Stephen Jay Gould once suggested that the if the evolution of life were “wound back” and played again from the start, it could have turned out very differently.

Though not firmly conclusive, the new research adds a real-world case study of evolution in action to the decades-old debate stirred by Gould’s thought experiment. British paleontologist Simon Conway Morris and others argued that only a few optimal solutions exist for an organism to adapt to its environment, so even if the clock were wound back, environmental pressures would eventually steer evolution toward one of those solutions — regardless of the randomness along the way.

What the scientists did
Scientists obviously can’t turn back the hands of time, but Richard Lenski and his colleagues at Michigan State University in East Lansing did the next best thing. Lenski’s team watched 12 colonies of identical E. coli bacteria evolve under carefully controlled lab conditions for 20 years, which equates to more than 40,000 generations of bacteria. After every 500 generations, the researchers froze samples of bacteria. Those bacteria could later be thawed out to “replay” the evolutionary clock from that point in time.

The evolution of a nutrient absorption ability
After about 31,500 generations, one colony of bacteria evolved the novel ability to use a nutrient that E. coli normally can’t absorb from its environment. Thawed-out samples from after the 20,000-generation mark were much more likely to re-evolve this trait than earlier samples, which suggests that an unnoticed mutation that occurred around the 20,000th generation enabled the microbes to later evolve the nutrient-absorption ability through a second mutation, the researchers report in the Proceedings of the National Academy of Sciences.

By way of contrast with another control group
In the 11 other colonies, this earlier mutation didn’t occur, so the evolution of this novel ability never happened.

Put populations in the same environment and see what happens
This is a direct empirical demonstration of Gould-like contingency in evolution. You can’t do an exact replay in nature, but scientists were able to literally put all these populations in virtually identical environments and show that contingency is really what had occurred.

What was the mutation that occured?
The next step will be to determine what that earlier mutation was and how it made the later change possible. If the first mutation didn’t offer any survival advantage to the microbes on its own, it would make the case airtight that Gould was right. That’s because a mutation that doesn’t improve an organism’s ability to survive and reproduce can’t be favored by evolution, so whether the microbe happens to have that necessary mutation when the second evolutionary change occurs becomes purely a matter of chance. Thus the first mutation must have improved the chance of the organisms survival.

The first mutation gave the microbes a survival advantage. The growth rate and the density of bacteria in the colony jumped up after the second mutation, but not after the first one. The first mutation may have set the stage for what was to come, the second mutation took advantage of the change.

BAC: Super-Sized Inserts

2008-05-26T20:04:00.000-05:00

Bacterial Artificial Chromosomes (BAC) have been developed to hold much larger pieces of DNA than a plasmid can. BAC vectors were originally created from part of an unusual plasmid present in some bacteria called the F’ plasmid.

The F’ plasmid allows bacteria to have “sex” (well, sort of: F’ helps bacteria give its genome to another bacteria but this only happens rarely when bacteria are under a lot of stress). F’ had been studied extensively and it was found that it could hold up to a million basepairs of DNA from another bacteria. Also, F’ has origins of replication and bacteria have a way to control how F’ is copied.

Mitochondrial Eve

2008-05-16T10:34:00.000-05:00

'Mitochondrial Eve' Research: Humanity Was Genetically Divided For 100,000 Years
A Picture of the Ancient Past
Finding:
Based on Anthroopological genetic research, researchers believe that about 60,000 years ago, modern humans started the journey to populate the world. However, relatively little is known about the demographic history of our species over the previous 140,000 years in Africa.

The current study focuses on Africa and refines the understanding of early modern Homo sapiens history. These early human populations were small and isolated from each other for many tens of thousands of years.

The research was based on a survey of African mitochondrial DNA (mtDNA) and is the most extensive survey of its kind. It included over 600 complete mtDNA genomes from indigenous populations across the continent.

How Old Was “Mitochondrial Eve”?

MtDNA, inherited down the maternal line, was used in 1987 to discover the age of the “Mitochondrial Eve,” the most recent common female ancestor of everyone alive today. This work has since been extended to show unequivocally that “Mitochondrial Eve” was an African woman who lived sometime during the past 200,000 years.

Recent data suggests that Eastern Africa went through a series of massive droughts between 90,000 and 135,000 years ago. It is possible that this climate shift contributed to the population splits. What is surprising is the length of time the populations were separate — for as much as half of our entire history as a species.

The study shows that tiny bands of early humans, forced apart by harsh environmental conditions, coming back from the brink to reunite and populate the world. Truly an epic drama, written in our DNA.

Last Common Ancestor Of Neanderthals And Humans

2008-04-28T13:14:00.000-05:00

Finding: Fossil Found In Europe, 1.2 Million Years Old

That's 500,000 years older than the previous oldest known humanlike fossils from the area. The new find bolsters the view that Homo reached Europe not long after leaving Africa almost 2 million years ago.

It seems probable that the first European population came from the region of the Near East, the true crossroads between Africa and Eurasia, and that it was related to the first demographic expansion out of Africa.

The researchers tentatively classified the new fossil as an earlier example Homo antecessor (Pioneer Man), the species represented by the previous oldest fossils and thought to be the last common ancestor of Neanderthals and modern humans.

Early Human Populations Evolved Separately For 100,000 Years

2008-04-06T11:55:00.000-05:00

Finding:
A team of Genographic researchers and their collaborators have published the most extensive survey to date of African mitochondrial DNA (mtDNA). Over 600 complete mtDNA genomes from indigenous populations across the continent were analyzed by the scientists. Analyses of the extensive data provide surprising insights into the early demographic history of human populations before they moved out of Africa, illustrating that these early human populations were small and isolated from each other for many tens of thousands of years.

MtDNA, inherited down the maternal line, was used to discover the age of the famous 'mitochondrial Eve' in 1987. This work has since been extended to show unequivocally that the most recent common female ancestor of everyone alive today was an African woman who lived in the past 200,000 years. Paleontology provides corroborating evidence that our species originated on this continent approximately 200,000 years ago.

The migrations after 60,000 years ago that led modern humans on their epic journeys to populate the world have been the primary focus of anthropological genetic research, but relatively little is known about the demographic history of our species over the previous 140,000 years in Africa. The current study returns the focus to Africa and in doing so refines our understanding of early modern Homo sapiens history.

There is strong evidence of ancient population splits beginning as early as 150,000 years ago, probably giving rise to separate populations localized to Eastern and Southern Africa. It was only around 40,000 years ago that they became part of a single pan-African population, reunited after as much as 100,000 years apart.

Recent paleoclimatological data suggests that Eastern Africa went through a series of massive droughts between 135,000-90,000 years ago. It is possible that this climatological shift contributed to the population splits. What is surprising is the length of time the populations were separate - as much as half of our entire history as a species.

Two Explosive Evolutionary Events Shaped Early History Of Multicellular Life

2008-03-14T08:20:00.000-05:00

The Avalon Explosion suggests that more than one explosive evolutionary event may have taken place during the early evolution of animals. Using rigorous analytical methods, scientists have identified another explosive evolutionary event that occurred about 33 million years earlier among macroscopic life forms unrelated to the Cambrian animals.

The Cambrian explosion event refers to the sudden appearance of most animal groups in a geologically short time period between 542 and 520 million years ago, in the early Cambrian Period. Although there were not as many animal species as in modern oceans, most (if not all) living animal groups were represented in the Cambrian oceans.

Methodology

To test whether other major branches of life also evolved in an abrupt and explosive manner, Virginia Tech scientists analyzed the Ediacara fossils: the oldest complex, multicellular organisms that had lived in oceans from 575 to 542 million years ago; that is, before the Cambrian Explosion of animals. What was notable was that the Ediacara organisms do not have an ancestor-descendant relationship with the Cambrian animals, and most of them went extinct before the Cambrian Explosion.

This group of organisms -- most species -- seems to be distinct from the Cambrian animals. But how did those Ediacara organisms first evolve? Did they also appear in an explosive evolutionary event, or is the Cambrian Explosion a truly unparalleled event. 50 characters were identified and mapped the distribution of these characters in more than 200 Ediacara species. These species cover three evolutionary stages of the entire Ediacara history across 33 million years. The three successive evolutionary stages are represented by the Avalon, White Sea, and Nama assemblages (all named after localities where representative fossils of each stage can be found).

The earliest Avalon stage was represented by relatively few species. These earliest Ediacara life forms already occupied a full morphological range of body plans that would ever be realized through the entire history of Ediacara organisms. In other words, major types of Ediacara organisms appeared at the dawn of their history, during the Avalon Explosion. Then Ediacara organisms diversified in White Sea time and then declined in Nama time. But, despite this notable waxing and waning in the number of species, the morphological range of the Avalon organisms were never exceeded through the subsequent history of Ediacara.

The process involved adapting quantitative methods that had been used previously for studying morphological evolution of animals, but never applied to the enigmatic Ediacara organisms. "We think of diversity in terms of individual species. But species may be very similar in their overall body plan. For example, 50 species of fly may not differ much from one another in terms of their overall shape -- they all represent the same body plan. On the other hand, a set of just three species that include a fly, a frog and an earthworm represent much more morphological variation. We can thus think of biodiversity not only in terms of how many different species there are but also how many fundamentally distinct body plans are being represented.

The approach combined both those approaches. In addition, the method relies on converting different morphologies into numerical (binary) data. This strategy allows us to describe, more objectively and more consistently, enigmatic fossil life forms, which are preserved mostly as two-dimensional impressions and are not understood well in terms of function, ecology, or physiology.

Scientists are still unsure what were the driving forces behind the rapid morphological expansion during the Avalon explosion, and why the morphological range did not expand, shrink, or shift during the subsequent White Sea and Nama stages.

The evolution of earliest macroscopic and complex life also went through an explosive event before to the Cambrian Explosion. It now appears that at the dawn of the macroscopic life, between 575 and 520 million years ago, there was not one, but at least two major episodes of abrupt morphological expansion.

New Route For Heredity Bypasses DNA

2008-02-23T20:06:00.000-06:00

A group of scientists in Princeton's Department of Ecology and Evolutionary Biology has uncovered a new biological mechanism that could provide a clearer window into a cell's inner workings.

What's more, this mechanism could represent an "epigenetic" pathway -- a route that bypasses an organism's normal DNA genetic program -- for so-called Lamarckian evolution, enabling an organism to pass on to its offspring characteristics acquired during its lifetime to improve their chances for survival. Lamarckian evolution is the notion, for example, that the giraffe's long neck evolved by its continually stretching higher and higher in order to munch on the more plentiful top tree leaves and gain a better shot at surviving.

The research also could have implications as a new method for controlling cellular processes, such as the splicing order of DNA segments, and increasing the understanding of natural cellular regulatory processes, such as which segments of DNA are retained versus lost during development. The team's findings will be published Jan. 10 in the journal Nature.
Princeton biologists Laura Landweber, Mariusz Nowacki and Vikram Vijayan, together with other members of the lab, wanted to decipher how the cell accomplished this feat, which required reorganizing its genome without resorting to its original genetic program. They chose the singled-celled ciliate Oxytricha trifallax as their testbed.

Ciliates are pond-dwelling protozoa that are ideal model systems for studying epigenetic phenomena. While typical human cells each have one nucleus, serving as the control center for the cell, these ciliate cells have two. One, the somatic nucleus, contains the DNA needed to carry out all the non-reproductive functions of the cell, such as metabolism. The second, the germline nucleus, like humans' sperm and egg, is home to the DNA needed for sexual reproduction.
When two of these ciliate cells mate, the somatic nucleus gets destroyed, and must somehow be reconstituted in their offspring in order for them to survive. The germline nucleus contains abundant DNA, yet 95 percent of it is thrown away during regeneration of a new somatic nucleus, in a process that compresses a pretty big genome (one-third the size of the human genome) into a tiny fraction of the space. This leaves only 5 percent of the organism's DNA free for encoding functions. Yet this small hodgepodge of remaining DNA always gets correctly chosen and then descrambled by the cell to form a new, working genome in a process (described as "genome acrobatics") that is still not well understood, but extremely deliberate and precise.
Landweber and her colleagues have postulated that this programmed rearrangement of DNA fragments is guided by an existing "cache" of information in the form of a DNA or RNA template derived from the parent's nucleus. In the computer realm, a cache is a temporary storage site for frequently used information to enable quick and easy access, rather than having to re-fetch or re-create the original information from scratch every time it's needed.

"The notion of an RNA cache has been around for a while, as the idea of solving a jigsaw puzzle by peeking at the cover of the box is always tempting," said Landweber, associate professor of ecology and evolutionary biology. "These cells have a genomic puzzle to solve that involves gathering little pieces of DNA and putting them back together in a specified order. The original idea of an RNA cache emerged in a study of plants, rather than protozoan cells, though, but the situation in plants turned out to be incorrect."

Through a series of experiments, the group tested out their hypothesis that DNA or RNA molecules were providing the missing instruction booklet needed during development, and also tried to determine if the putative template was made of RNA or DNA. DNA is the genetic material of most organisms, however RNA is now known to play a diversity of important roles as well. RNA is DNA's chemical cousin, and has a primary role in interpreting the genetic code during the construction of proteins.

First, the researchers attempted to determine if the RNA cache idea was valid by directing specific RNA-destroying chemicals, known as RNAi, to the cell before fertilization. This gave encouraging results, disrupting the process of development, and even halting DNA rearrangement in some cases.

In a second experiment, Nowacki and Yi Zhou, both postdoctoral fellows, discovered that RNA templates did indeed exist early on in the cellular developmental process, and were just long-lived enough to lay out a pattern for reconstructing their main nucleus. This was soon followed by a third experiment that "… required real chutzpah," Landweber said, "because it meant reprogramming the cell to shuffle its own genetic material."

Nowacki, Zhou and Vijayan, a 2007 Princeton graduate in electrical engineering, constructed both artificial RNA and DNA templates that encoded a novel, pre-determined pattern; that is, that would take a DNA molecule of the ciliate's consisting of, for example, pieces 1-2-3-4-5 and transpose two of the segments, to produce the fragment 1-2-3-5-4. Injecting their synthetic templates into the developing cell produced the anticipated results, showing that a specified RNA template could provide a new set of rules for unscrambling the nuclear fragments in such a way as to reconstitute a working nucleus.

"This wonderful discovery showed for the first time that RNA can provide sequence information that guides accurate recombination of DNA, leading to reconstruction of genes and a genome that are necessary for the organism," said Meng-Chao Yao, director of the Institute of Molecular Biology at Taiwan's Academia Sinica. "It reveals that genetic information can be passed on to following generations via RNA, in addition to DNA."

The research team believes that if this mechanism extends to mammalian cells, then it could suggest novel ways for manipulating genes, besides those already known through the standard methods of genetic engineering. This could lead to possible applications for creating new gene combinations or restoring aberrant cells to their original, healthy state

Oxygen: The Clue To First Appearance Of Large Animals

2008-02-02T19:50:00.000-06:00

The sudden appearance of large animal fossils more than 500 million years ago – a problem that perplexed even Charles Darwin and is commonly known as “Darwin’s Dilemma” – may be due to a huge increase of oxygen in the world’s oceans.

In 2002 researchers found the world’s oldest complex life forms between layers of sandstone on the southeastern coast of Newfoundland. This pushed back the age of Earth’s earliest known complex life to more than 575 million years ago, soon after the melting of the massive “snowball” glaciers. New findings reported today shed light on why, after three billion years of mostly single-celled evolution, these large animals suddenly appeared in the fossil record.

A huge increase in oxygen following the Gaskiers Glaciation 580 million years ago corresponds with the first appearance of large animal fossils on the Avalon Peninsula in Newfoundland.
Now for the first time, geochemical studies have determined the oxygen levels in the world’s oceans at the time these sediments accumulated in Avalon. Studies show that the oldest sediments on the Avalon Peninsula, which completely lack animal fossils, were deposited during a time when there was little or no free oxygen in the world’s oceans. Immediately after this ice age there is evidence for a huge increase in atmospheric oxygento at least 15 per cent of modern levels, and these sediments also contain evidence of the oldest large animal fossils.

The close connection between the first appearance of oxygenated conditions in the world’s oceans and the first appearance of large animal fossils confirms the importance of oxygen as a trigger for the early evolution of animals, the researchers say. They hypothesize that melting glaciers increased the amount of nutrients in the ocean and led to a proliferation of single-celled organisms that liberated oxygen through photosynthesis. This began an evolutionary radiation that led to complex communities of filter-feeding animals, then mobile bilateral animals, and ultimately to the Cambrian “explosion” of skeletal animals 542 million years ago.

Genome Pictures

2008-01-23T21:11:00.000-06:00

Bones From French Cave Show Neanderthals, Cro-Magnon Hunted Same Prey

2008-01-21T20:59:00.000-06:00

Finding: A 50,000-year record of mammals consumed by early humans in southwestern France indicates there was no major difference in the prey hunted by Neanderthal and Cro-Magnon.

Research findings counter the idea proposed by some scientists that Cro-Magnon, who were physically similar to modern man, supplanted Neanderthals because they were more skilled hunters as a result of some evolutionary physical or mental advantage.

The new study suggests Cro-Magnon were not superior in getting food from the landscape. Archeoligists could detect no difference in diet, the animals they were hunting and the way they were hunting across this period of time, aside from those caused by climate change.

The takeover by Cro-Magnon does not seem to be related to hunting capability. There is no significant difference in large mammal use from Neanderthals to Cro-Magnon in this part of the world. The idea that Neanderthals were big, dumb brutes is hard for some people to drop. Cro-Magnon created the first cave art, but late Neanderthals made body ornaments, so the depth of cognitive difference between the two just is not clear.

Bears, Caves, and Cro-magnon
The study also resurrects a nearly 50-year-old theory first proposed by Finnish paleontologist Björn Kurtén that modern humans played a role in the extinction of giant cave bears in Europe. Cro-Magnon may have been the original "apartment hunters" and displaced the bears by competing with them for the same caves the animals used for winter den sites.

The cave has a rich, dated archaeological sequence that extends from about 65,000 to about 12,000 years ago, spanning the time when Neanderthals flourished and died off and when Cro-Magnon moved into the region. Neanderthals disappeared from southwestern France around 35,000 years ago, although they survived longer in southern Spain and central Europe.
The researchers were most interested in the transition from the Middle to Upper Paleolithic, or Middle to Late Stone Age.

Neanderthals occupied Grotte XVI as far back as 65,000 years ago, perhaps longer. Between 40,000 and 35,000 years ago, people began making stone tools in France, including at Grotte XVI, that were more like those later fashioned by Cro-Magnon. However, human remains found with these tools at several sites, were Neanderthal, not Cro-Magnon. Similar tools but no human remains from this time period were found in Grotte XVI and people assumed to be Cro-Magnon did not occupy the cave until about 30,000 years ago.

The researchers examined more than 7,200 bones and teeth from large hoofed mammals that had been recovered from the cave. The animals – ungulates such as reindeer, red deer, roe deer, horses and chamois were the most common prey – were the mainstay of humans in this part of the world, according to Grayson.

He and Delpech found a remarkable dietary similarity over time. Throughout the 50,000-year record, each bone and tooth assemblage, regardless of the time period or the size of the sample involved, contained eight or nine species of ungulates, indicating that Neanderthals and Cro-Magnon both hunted a wide variety of game.

The only difference the researchers found was in the relative abundance of species, particularly reindeer, uncovered at the various levels in Grotte XVI. At the oldest dated level in the cave, reindeer remains accounted for 26 percent of the total. Red deer were the most common prey at this time, accounting for nearly 34 percent of the bones and teeth. However, as summer temperatures began to drop in Southwestern France, the reindeer numbers increased and became the prey of choice. By around 30,000 years ago, when Cro-Magnon moved into the region, reindeer accounted for 52 percent of the bones and teeth. And by around 12,500 years ago, during the last ice age, reindeer remains accounted for 94 percent of bones and teeth found in Grotte XVI.

Grayson and Delpech also looked at the cut marks left on bones to analyze how humans were butchering their food. They found little difference except, surprisingly, at the uppermost level, which corresponds to the last ice age.

It is possible that because it was so cold, people were hard up for food. The bones were very heavily butchered, which might be a sign of food stress. However, if this had occurred earlier during Neanderthal times, people would have said this is a sure sign that Neanderthals did not have the fine hand-eye coordination to do fine butchering.
In examining the Grotte XVI record, the researchers also found a sharp drop in the number of cave bears from Neanderthal to Cro-Magnon times.

Cave bears and humans may have been competing for the same living space and this may have led to their extinction. He added that it is not clear if the decline and eventual extinction of the bears was driven by an increase in the number of humans or increased human residence times in caves, or both.

If we can understand the extinction of any animal from the past, such as the cave bear, it gives us a piece of evidence showing the importance of habitat to animals. The cave bear is one of the icons of the late Pleistocene Epoch, similar to the saber tooth cats and mammoths in North America. If further study supports the argument, we finally may be in a position to confirm a human role in the extinction of a large Pleistocene mammal on a Northern Hemisphere continent.

Biogeographic distributions

2008-01-14T22:01:00.000-06:00

I. Three important principles:
How do these principles support descent with modification?
A. Environment cannot account for either similarity or dissimilarity, since similar environments can harbor entirely different species groups
B. "Affinity" (=similarity) of groups on the same continent (or sea) is closer than between continents (or seas)
C. Geographical barriers usually divide these different groups, and there is a correlation between degree of difference and rate of migration or ability to disperse across the barriers.

Disjoint locations for the same extant species: Is this evidence for creation? Note that Evolution proposes Single Centers for the origins of species, so Discontinuous Distributions need to be explained.
A. this means that a method of dispersal must be proposed.
1. Changes in climate or geology must have affected migration (i.e., by first allowing migration and then preventing migration)
2. Darwin designed tests of a priori assumptions
3. Although "accidental", dispersal is not really random (and thus allows very specific predictions about distributions in some cases)

B. Case study: Similarity of flora and fauna at mountain summits (is this evidence for independent creations or something else?)
1. Evidence is clear for recent glaciation
2. Migrations are easily visualized in the gradual advances and retreats of glaciers
3. Because mountain tops retain a colder climate, some cold-adapted, northern species would be retained on mountain tops (and thus isolated during glacial retreat)
4. Also explains why such mountain-top species are most closely related to species living due north
5. Isolation poses an opportunity for change, esp. if it means a change in its interspecific associations
6. Assumption of the scenario: Circumpolar distribution is uniform (presently the case)
7. Secondary assumption: Similar situation for subarctic species

C. Many difficulties remain to be solved, esp. the very distinct, but distantly related forms in the Southern hemisphere (e.g., marsupial versus placental mammals)
1. These species are too distinct to be explained by the recent glaciation
2. Darwin postulates an earlier glaciation, because he did not know about plate tectonics
3. With plate tectonics, many (if not all) of these kinds of problems are soluble.

Fresh water distributions
Because freshwater is isolated, you might expect restricted ranges, however, this is not the case just the opposite, they often have distributions even broader than terrestrials: How can this be explained? Three cases to consider:
A. Distribution of Fish
B. Distribution of Shells (molluscs)
C. Distribution of Plants (often very wide ranges)
In all cases, dispersal of freshwater organisms depends largely on animal (esp. bird) transport
Distribution of species on oceanic islands
Darwin considered this evidence as especially strong in its support of descent with modification
A. The total number of species on oceanic islands is small compared to the number on an equal area of continent
B. Proportion of endemic species is very high
C. Oceanic islands are missing entire Classes
D. Endemic species often possess characters that are adaptive elsewhere, but are useless characters on the island
E. Endemic species often show (new) adaptive traits not possessed by any of their relatives
F. Batrachians are universally absent (except one frog in New Zealand)
G. Terrestrial mammals are not found on any island >300 miles from mainland
H. But arial mammals are found on such islands, and many of these are endemic
I. Also a correlation between the depth of the sea separating islands inhabited by mammals and the degree of "affinity" (classification) between these species
J. "The most striking and important fact" (p. 397) is the affinity of these island species to those of the nearest mainland, without being actually the same species
K. Within an archipelago, species are more closely related to each other than to those on the mainland (but still distinct from each other)
L. The principle applies widely that island inhabitants are most closely related to the inhabitants of a region from which colonization is possible
M. According to this principle, it must be the case that at some former time, a single parental species covered both ranges (i.e., the migration event itself)N. Darwin draws a parallel between Time and Space in the "Laws of Life"

Greenland: Oldest DNA Shows Warmer Planet

2008-01-07T08:08:00.000-06:00

Greenland: Scientists studying the glaciers probed two kilometers and recovered the oldest plant DNA. Their studies also showed that the earth was much warmer hundreds of thousands of years ago than is generally believed.

Using the DNA of trees, plants and a variety of insects from underneath the southern Greenland glacier estimated to date from 500,000 to 900,000 years ago.

So what is the prevailing view that a forest of this kind could only have existed in Greenland as recently as 2.4 million years ago. This means that if the area supported these plants and insects, it was warmer than previously thought.

The DNA samples showed that the temperature may have reached 50 degrees Fahrenheit in the summer and 1 degree F in the winter.

Another finding showed that during the last period between ice ages, between 116,000-130,000 years ago, temperatures were on average 9 degrees F higher than now, so the glaciers on Greenland did not completely melt away.

How trees changed the world

2007-12-24T23:00:00.000-06:00

Finding: A nearly completly preserved tree dating 385 million years ago from the Gilboa Forests was found. It came from the first forests on Earth.

The Gilboa tree dates from the middle of the Devonian period (416 to 359 million years ago), a time of explosive evolutionary action among land plants. During this period trees evolved from small, primitive forms that would have barely brushed your ankle into genuine trees up to 30 metres tall. And with the evolution of trees, they and all the other plants - hitherto confined to marshy environments - went on to conquer the surface of the planet.

The First Forests
These first forests changed the face of the Earth. Early land plants had already started leaking oxygen into the atmosphere, creating soils and providing food and shelter for animals, and the evolution of trees upped the pace of change. They weathered rocks, made soils deeper and richer, created complex habitats and changed the climate beyond recognition. By the end of the Devonian, an ecologically modern world had appeared. Discoveries such as the Gilboa tree are bringing stunning new insights into how the foresting of the world came about.

Plants in the Ordovician Period
Plants first colonised land in the Ordovician period, around 465 million years ago (see Chart). By the early Devonian they had developed many of the features of modern plants, including a protective waxy cuticle, vascular plumbing for transporting water and nutrients, and pores called stomata to draw in carbon dioxide. But there were many differences from modern plants too. Seeds had yet to evolve - early land plants instead reproduced by way of spores. Wood, large leaves and deep roots were unknown. Few plants were taller than a few centimetres.

The Rhynie ecosystem
The best place to catch a glimpse of this primitive terrestrial forest is in the hills around the village of Rhynie in Aberdeenshire, UK. Here the finely crystallized quartz of the Rhynie chert preserves in extraordinary detail an entire ecosystem that was engulfed and petrified by silica-rich waters from a volcanic spring 410 million years ago. The fossil plants still stand upright, and even their cells remain visible. Tiny creatures such as insects, centipedes, mites, harvestmen and spider-like trigonotarbids are preserved in great detail. Some still cling to the stems on which they lived and died.

Originally, Rhynie wouldn't have been recognisable as a modern environment. Every plant would have been on a small scale - knee height and lower. However, by the late Devonian, plants are on a scale that humans are used to. You can walk around a woodland and identify a tree canopy layer, a shrub layer and a herbaceous layer. Now the whole environment looks more modern.

Prototaxites
The Rhynie landscape was not entirely devoid of large living things, however. Dotted here and there were featureless columns standing up to 6 metres high and a metre wide at the base. When first described in 1857, from fossils found in Quebec, they were identified as conifer trunks and named Prototaxites. However, studies into the structure of their "wood" soon revealed that they were not trees. Various alternatives were proposed, including giant algae, lichen and fungi, but the identity of Prototaxites remained uncertain.

Last year a research team University of Chicago decided to settle matters. They measured the ratio of different carbon isotopes in Prototaxites fossils to reveal whether they were making a living from photosynthesis or by eating rotting matter as fungi do today. The results clearly showed that Prototaxites was a fungus. It was both tougher and stronger

And there was more. The isotopes also revealed that some Prototaxites were probably living off microbial crusts composed of bacteria, algae and lichens. These crusts still exist today but are confined to places where vascular plants can't grow, such as deserts. What Prototaxites shows is that there were large patches of the early Devonian landscape with no vascular plants. This means that plants didn't conquer the land as quickly and completely as scientists once assumed.

The Rise of the Forests
With large patches of land still free of vascular plants, clearly an upgrade of their plumbing and support systems was needed for the terrestrial conquest to continue. This was achieved through "secondary growth", the evolution of tougher and stronger tissues to carry water and nutrients up longer stems. Once these were in place, plants were able to grow much bigger. It was these advances that allowed the trees of the Gilboa forest to reach their full height of 8 meters or more. The foresting of the Earth had begun.

The appearance of trees changed the rules of the game, with evolutionary scramble for height, for light to power photosynthesis, and for prime positions to disperse spores. Once it became possible to be a tree, then the race is on for size and dominance. If you look at modern ecosystems, the trees that are dominant hog the light space of the environment. The goal is to be at the top and collect the most light.

The Gilboa Forest
So what was the Gilboa forest like? Its trees, known as cladoxylopsids, looked a bit like tree ferns, although they are not related. Their trunks were long and slender, with a bulbous base and shallow roots. They did not have leaves, instead sporting a goblet-shaped crown of branches and thread-like branchlets. These were probably green to carry out photosynthesis. In other words it must have looked like a strange, giant bottle brush.

Gilboa, 385 million years ago, was a warm, wet flood plain 10 degrees south of the equator. Since the cladoxylopsids lacked leaves, the forest would have been airier and brighter than any modern forest. There was a diverse understorey that included club mosses and ferns, but the only animal inhabitants were arthropods, including insects, centipedes and mites. It would also have been wet underfoot: as with today's ferns and mosses, cladoxylopsid spores could only be fertilised on wet surfaces, so the trees were confined to flood plains.

World Wide Representation
Cladoxylopsids achieved worldwide success: fossils of their crowns (which until the Gilboa tree were thought to be complete plants) have been found in Europe, China and the Americas. However, in many respects they were primitive, and lurking in their shadows was a group of plants that would soon put them in the shade.

Other Plant Developments
These were the archaeopterids, relatives of the conifers. At the time of the Gilboa forest, archaeopterids were no bigger than shrubs, but their lineage soon made some key evolutionary advances, including wood, deep roots and large leaves. By 370 million years ago, a fully fledged tree, Archaeopteris, had emerged from the archaeopterid ranks.

With the trunk of a conifer and fern-like leaves, Archaeopteris reached 30 metres - as tall as a mature oak - and dominated late Devonian forests all over the world. Its wooden trunk permitted it to grow much taller than the cladoxylopsids. There is a stronger material around, per mass, than wood says a leading researcher in the chemical make-up of fossil plants. Wood also led to the formation of the first complex soils. Soil humus is, by and large, lignin, the polymer that makes wood tough.

The Decline of CO2 Levels and the Rise of Deep Roots
Archaeopteris was also the first plant to evolve deep roots. Roots eat away at rocks, burrowing into and dissolving them with acids in pursuit of nutrients. Over an immense period of time the weathered material gets washed into the oceans, where it combines with dissolved CO2 to form sediments that are eventually subducted into the Earth's interior by tectonic activity. This process removed huge amounts of CO2 from the oceans and atmosphere, with profound consequences for the climate. Between the beginning and end of the Devonian, levels of the gas plummeted by up to 95 per cent. Greenhouse conditions vanished, to be replaced by an ice age that at its peak 300 million years ago saw glaciers approaching the tropics.

Deep Roots and Large Leaves
But oddly it was the climatic upheaval brought about by roots that appears to have driven the next great innovation - large leaves. These first appeared 390 million years ago, but only became widespread with Archaeopteris 15 million years later. The stripping of CO2 from the Devonian atmosphere helped to remove an obstacle that had been inhibiting the evolution of large leaves.

Although large, flat leaves are very efficient at capturing sunlight for photosynthesis, they are difficult to keep cool. To prevent overheating, leaves need to release water vapour through their pore-like stomata - the plant equivalent of sweating. The problem is the number of stomata is regulated by a genetic switch that responds to CO2 levels in the atmosphere: the more CO2, the lower the stomatal density. If that genetic switch was already in place in the Devonian, high CO2 levels would have prevented plants from evolving large leaves. If large leaves had appeared then they would have cooked.

Only with falling levels of CO2, and improvements in roots and vascular systems to supply cooling water, could plants evolve the high stomatal densities that make large leaves viable. Studies on fossil leaves have so far supported this idea: earlier leaves were smaller and had far fewer pores than later ones, and only after CO2 levels fell did large leaves become abundant.

The Rise of Seeds
Archaeopteris had one more innovation to offer. It evolved a method of reproduction that partially freed trees from the flood plains that had confined the cladoxylopsids. Male and female cladoxylopsid spores were the same size, and fertilisation could only occur on wet ground where nutrients were readily available to nourish the embryo. In contrast, female Archaeopteris spores were larger than male ones and stored a food supply for the embryo. From this beginning, seeds evolved.

Seed plants - the grasses, flowers, shrubs and trees that are everywhere today - are thought to have descended from Archaeopteris and its relatives. With the evolution of seeds, plants could now spread to all sorts of places that had previously been out of bounds. Seeding freed plants from a reproductive necessity on water. Seeds allow trees to occupy and colonise drier environments.

Where Do Trees Colonise?
One of the most difficult places for trees to colonise was the uplands. In 2003, scientists discovered the oldest-known fossils of mountain plants, in Blanche Brook, a remote river in Newfoundland. Hundreds of giant trees lying in the a remote part of the river bed. The trees turned out to be 305 million years old, from the late Carboniferous. Known as cordaitaleans and standing up to 50 metres tall, they were seed plants related to conifers and looked a bit like monkey puzzle trees.

What about the Carboniferous Sporing vs Seeds?
Elsewhere in the Carboniferous, however, sporing plants still held sway. In the swampy lowland rainforests, Archaeopteris and the cladoxylopsids were overshadowed by giant club moss and horsetail trees that towered above the seed plants jostling for space below. In modern forests the opposite is true, with seed-bearing trees dominating the sporing ferns, mosses and horsetails of the understorey. It's like the world was turned upside down. Spores prevailed over seeds for the last time.

Organic Carbon and Coal
These late Carboniferous lowlands are noted for the sheer fecundity of their tree and plant fossils. Much of Europe, Asia and North America were near the equator and were blanketed by huge tracts of rainforest. Tectonic forces meant that the basins where the rainforests grew were slowly subsiding. This process, coupled with regular flooding, led to colossal amounts of organic carbon being buried. Much of the world's coal reserves formed in this 20-million-year period.

Then around 300 million years ago, a catastrophic earthquake caused one coal forest in what is now Illinois to slump below sea level, where it was rapidly buried. Low-oxygen conditions preserved a 1000-hectare expanse of this forest floor in near-pristine condition. The forest floor now forms the ceiling of the Riola and Vermilion Grove coal mines in Illinois.

The Ancient Rainforest
Scientists conducted the largest ever study of this ancient forest. The coal that had been mined out used to be the soil of the ancient rainforest, so as you walked around looking up you could see roots hanging down just above your head, and you could see giant fallen trees complete with their roots, trunk and crown.

You can see the roots of an ancient rainforest hanging down just above your head.
Spectacular 40-metre club mosses and shorter tree ferns monopolised the Illinois forest. There is really nothing today that looks anything like the giant club mosses. They probably grew much closer together than do trees in a modern rainforest because they don't have large canopies, so you don't have a lot of shadow cast by the trees. The forest would also have been greener than its modern counterpart, as the abundant club mosses had green scale-like leaf cushions all over their trunks and branches.

Swampworld and Tectonic Forces
Swampworld was not to last. As tectonic forces dragged the world's landmasses together to form the supercontinent Pangaea, the climate changed. Dryer, harsher conditions set in, and by the end of the Carboniferous the coal swamps had disappeared from most of the world. The mighty sporing trees could no longer find the water they needed to reproduce, and seed plants gained the upper hand. The reign of modern plants had truly begun.

'Wall Of Africa' Allowed Humanity To Emerge

2007-12-22T18:47:00.000-06:00

Finding: The accelerated uplift of mountains and highlands stretching from Ethiopia to South Africa blocked much ocean moisture, converting lush tropical forests into an arid patchwork of woodlands and savannah grasslands that gradually favored human ancestors who came down from the trees and started walking on two feet -- an energy-efficient way to search larger areas for food in an arid environment.

Scientists long have focused on how climate and vegetation allowed human ancestors to evolve in Africa. Now, University of Utah geologists are calling renewed attention to the idea that ground movements formed mountains and valleys, creating environments that favored the emergence of humanity.

Tectonics

Tectonics or the movement of Earth's crust may have been ultimately responsible for the evolution of humankind. This includes the movements of Earth's crust, its ever-shifting tectonic plates and the creation of mountains, valleys and ocean basins. It also includes the 3,700-mile-long stretch of highlands and mountains also known as "the Wall of Africa." It parallels the East African Rift valley, where many fossils of human ancestors were found.

As a topic about the influence on human evolution tectonics has been discussed since at least 1983. But much of the previous discussion of how climate affected human evolution involves global climate changes, such as those caused by cyclic changes in Earth's orbit around the sun, and not local and regional climate changes caused by East Africa's rising landscape.

However, 0ver the last 7 million years the crustal movement or tectonism in East Africa, the landscape drastically changed. That landscape controlled climate on a local to regional scale. That climate change spurred human ancestors to evolve away from the ape line.

Hominins (the new scientific word for humans (Homo) and their ancestors, including Ardipithecus, Paranthropus and Australopithecus) split from apes on the evolutionary tree roughly 7 million to 4 million years ago. The earliest undisputed hominin was Ardipithecus ramidus 4.4 million years ago. The earliest Homo arose 2.5 million years ago, and our species, Homo sapiens, almost 200,000 years ago.

A Force from within the Earth

The geological or tectonic forces shaping Africa begin deep in the Earth, where a "superplume" of hot and molten rock has swelled upward for at least the past 45 million years. This superplume and its branching smaller plumes help push apart the African and Arabian tectonic plates of Earth's crust, forming the Red Sea, Gulf of Aden and the Great Rift Valley that stretches from Syria to southern Africa.

As part of this process, Africa is being split apart along the East African Rift, a valley bounded by elevated "shoulders" a few tens of miles wide and sitting atop "domes" a few hundreds of miles wide and caused by upward bulging of the plume.

The East African Rift runs about 3,700 miles from the Ethiopian Plateau south-southwest to South Africa's Karoo Plateau. It is up to 370 miles wide and includes mountains reaching a maximum elevation of about 19,340 feet at Mount Kilimanjaro.

The rift "is characterized by volcanic peaks, plateaus, valleys and large basins and freshwater lakes," including sites where many fossils of early humans and their ancestors have been found, says Nahid Gani (pronounced nah-heed go-knee), a research scientist. There was some uplift in East Africa as early as 40 million years ago, but "most of these topographic features developed between 7 million and 2 million years ago."

A Wall Rises and New Species Evolve

The Wall of Africa started to form around 30 million years ago, recent studies show most of the uplift occurred between 7 million and 2 million years ago, just about when hominins split off from African apes, developed bipedalism and evolved bigger brains.
Nature built this wall, and then humans could evolve, walk tall and think big.

Is there any characteristic feature of the Wall that drove human evolution?

The answer is the variable landscape and vegetation resulting from uplift of the Wall of Africa, which created a topographic barrier to moisture, mostly from the Indian Ocean and dried the climate. Contrary to those who cite global climate cycles, the climate changes in East Africa were local and resulted from the uplift of different parts of the wall at different times.

The change from forests to a patchwork of woodland and open savannah did not happen everywhere in East Africa at the same time, and the changes also happened in East Africa later than elsewhere in the world.

The Rise of the Wall

Studies of the roughly 300-mile-by-300-mile Ethiopian Plateau, which is the most prominent part of the Wall of Africa indicated the plateau reached its present average elevation of 8,200 feet 25 million years ago. New analysis shows that the rates at which the Blue Nile River cut down into the Ethiopian Plateau, creating a canyon that rivals North America's Grand Canyon.
The conclusion: There were periods of low-to-moderate incision and uplift between 29 million and 10 million years ago, and again between 10 million and 6 million years ago, but the most rapid uplift of the Ethiopian Plateau (by some 3,200 vertical feet) happened 6 million to 3 million years ago.

Other research has shown the Kenyan part of the wall rose mostly between 7 million and 2 million years ago, mountains in Tanganyika and Malawi were uplifted mainly between 5 million and 2 million years ago, and the wall's southernmost end gained most of its elevation during the past 5 million years.

The Time Frame of the Wall development and Human evolution

Clearly, the Wall of Africa grew to be a prominent elevated feature over the last 7 million years, thereby playing a prominent role in East African aridification by wringing moisture out of monsoonal air moving across the region. That period coincides with evolution of human ancestors in the area.

The earliest undisputed evidence of true bipedalism (as opposed to knuckle-dragging by apes) is 4.1 million years ago in Australopithecus anamensis, but some believe the trait existed as early as 6 million to 7 million years ago.

The shaping of varied landscapes by tectonic forces -- lake basins, valleys, mountains, grasslands, woodlands could also be responsible, at a later stage, for hominins developing a bigger brain as a way to cope with these extremely variable and changing landscapes in which they had to find food and survive predators.

For now the lack of more precise timeframes makes it difficult to link specific tectonic events to the development of upright walking, bigger brains and other key steps in human evolution.

Evolution With A Restricted Number Of Genes

2007-12-20T19:54:00.000-06:00

Finding: RNA polymerase II is highly conserved through evolution, with many of its structural characteristics being conserved between bacteria and humans. The development of higher forms of life would appear to have been influenced by RNA polymerase II. This enzyme transcribes the information coded by genes from DNA into messenger-RNA (mRNA), which in turn is the basis for the production of proteins.

Single-Cell Organisms and the Problem of Complexity
Single-cell organisms were already in existence 500 million years ago, with several thousand genes providing different cellular functions. Further developments seemed dependent on producing even more genes.

It would appear that for a highly developed organism like a human, this form of evolution would have resulted in several million genes. But researchers were surprised to learn, following publication of the human genome, that a human only has around 25,000 genes – not many more than a fruit fly or a worm with approximately 15,000 to 20,000 genes.

It would appear that, over the last 500 million years, other ways to produce highly complex organisms have evolved. Evolution has simply found more efficient ways to use the genes already there. But what could have made this possible?

Is there an answer? Yes - it involves the RNA
New results represent a piece of the puzzle and shed new light on to the purpose of an unusual structure in RNA polymerase II.

They build on earlier observations that gene expression is not just regulated by binding of the enzyme to the gene locus to which it is recruited, but also during the phase of active transcription from DNA into RNA. During this phase, parts of the newly synthesised RNA may be removed and the remaining sequences combined into new RNA message. This ‘splicing’ of RNA occurs during gene transcription, and in extreme cases, can produce RNAs coding for several thousand different proteins from a single gene.

How it Works - The Development of CTD
But what was the development that permitted this advance in gene usage? The RNA polymerase II has developed a structure composed of repeats of a 7 amino-acid sequence. In humans this structure – termed “carboxyterminal domain” or CTD – is composed of 52 such repeats. It is placed exactly at the position where RNA emerges from RNA polymerase II. In less complex organisms the CTD is much shorter: a worm has 36 repeats, and yeast as few as 26, but many single-cell organisms and bacteria have never developed an obvious CTD structure.

Although the requirement of CTD for the expression of cellular genes in higher organisms is undisputed, the molecular details for the gene-specific maturation of RNAs is still largely enigmatic. Research groups have now shown a differential requirement for phosphorylation of the amino acid serine at position 7 of CTD in the processing and maturation of specific gene products.

These results provide the groundwork for the discovery of further pieces of the CTD puzzle and thus enlarge our knowledge of gene regulation. Given its fundamental importance, understanding the mechanism of gene regulation is essential if we are to understand cancer and other diseases at the molecular level and develop new therapies.

Losses Of Long-established Genes Contribute To Human Evolution

2007-12-18T20:39:00.000-06:00

Finding: While it is well understood that the evolution of new genes leads to adaptations that help species survive, gene loss may also afford a selective advantage. A group of scientists has investigated this less-studied idea, carrying out the first systematic computational analysis to identify long-established genes that have been lost across millions of years of evolution leading to the human species.

The idea that gene losses might contribute to adaptation has been kicked around, but not well studied.

To find gene losses a software program called TransMap. The program compared the mouse and human genomes, searching for genes having changes significant enough to render them nonfunctional somewhere during the 75 million years since the divergence of the mouse and the human.

Genes can be lost in many ways. This study focused on losses caused by mutations that disrupt the open reading frame (ORF-disrupting mutations). These are either point mutations, where events such as the insertion or substitution of a DNA base alter the instructions delivered by the DNA, or changes that occur when a large portion of a gene is deleted altogether or moves to a new place on the genome.

Using the Dog Genome
The dog genome was used as an out-group to filter out false positives because the dog diverged from our ancient common ancestor earlier than the mouse. So if a gene is still living in both dog and mouse but not in human, it was probably living in the common ancestor and then lost in the human lineage.

Using this process, they identified 26 losses of long-established genes, including 16 that were not previously known.

The gene loss candidates found in the study do not represent a complete list of gene losses of long-established genes in the human lineage, because the analysis was designed to produce more false negatives than false positives.

The study compares multiple genomes
Next they compared the identified genes in the complete genomes of the human, chimpanzee, rhesus monkey, mouse, rat, dog, and opossum to estimate the amount of time the gene was functional before it was lost. This refined the timing of the gene loss and also served as a benchmark for whether the gene in question was long-established, and therefore probably functional, or merely a loss of a redundant gene copy. Through this process, they found 6 genes that were lost only in the human.

The ACYL3 Protein - A loss From many to none
One previously unknown loss, the gene for acyltransferase-3 (ACYL3), was particularly important. This is an ancient protein that exists throughout the whole tree of life. Multiple copies of the ACYL3 gene are encoded in the fly and worm genomes. In the mammalian clade there is only one copy left, and somewhere along primate evolution, that one copy was lost to the primate clan.

Next it was found that this gene contains a nonsense mutation in both human and chimp, and it appears to still look functional in rhesus. Further, they found that the mutation is not present in the orangutan, so the gene is probably still functional in that species. On the evolutionary tree leading to human, on the branch between chimp and orangutan sits gorilla. Knowing if the gene was still active in gorilla would narrow down the timing of the loss.

The gorilla DNA sequence showed the gene intact, without the mutation, so the loss likely occurred between the speciation of gorilla and chimpanzee.

Other Functional Losses
Acyltransferase-3 was not the only lost gene that doesn't have any close functional homologues in the human genome. A highlight of the research was that they were able to find a list of these orphan losses. Some of them have been functional for more than 300 million years, and they were the last copies left in the human genome. While the copies of these genes remaining in the human genome appear to be nonfunctional, functional copies of all of them exist in the mouse genome.

These orphan genes may be interesting candidates for experimental biologists to explore. It will be interesting to find out what was the biological effect of these losses. Once their function is well characterized in species that still have active copies, we could maybe speculate about their effects on human evolution.

Human Ancestors More Primitive That Once Thought

2007-12-12T19:40:00.000-06:00

Finding: A team of researchers has determined through analysis of the earliest known hominid fossils outside of Africa, recently discovered in Dmanisi, Georgia, that the first human ancestors to inhabit Eurasia were more primitive than previously thought.

The fossils, dated to 1.8 million years old, show some modern aspects of lower limb morphology, such as long legs and an arched foot, but retain some primitive aspects of morphology in the shoulder and foot. The species had a small stature and brain size more similar to earlier species found in Africa.

The earliest known hominins to have lived outside Africa in temperate zones of Eurasia did not yet display the full set of derived skeletal features the researchers conclude.

What this means
The new evidence shows how this species had the anatomical and behavioral capacity to be successful across a range of environments and expand out of Africa.

This research shows that the limb proportions and behavioral flexibility which allowed this species to expand out of Africa were there at least 1.8 million years ago.

Dmanisi is the site of a medieval village located about 53 miles southwest of Tbilisi, Georgia on a promontory at the confluence of the Mashavera and Phinezauri rivers.

New Insights Into The Evolution Of The Human Genome

2007-12-10T22:30:00.000-06:00

Which came first, the chicken genome or the egg genome?

Finding: The answers provide the first evolutionary history of the duplications in the human genome that are partly responsible for both disease and recent genetic innovations.

This work marks a significant step toward a better understanding of what genomic changes paved the way for modern humans, when these duplications occurred and what the associated costs are -- in terms of susceptibility to disease-causing genetic mutations.

Researchers have answered a similar vexing genomic question: Which of the thousands of long stretches of repeated DNA in the human genome came first? And which are the duplicates?

Genomes have an ability to copy a long stretch of DNA from one chromosome and insert it into another region of the genome. Segmental duplications hold many evolutionary secrets and uncovering them is a difficult biological and computational challenge with implications for both medicine and our understanding of evolution.

Evolutionary History
Researchers have created the first evolutionary history of the duplications in the human genome that are partly responsible for both disease and recent genetic innovations. This marks an important step toward a better understanding of what genomic changes paved the way for modern humans, when these duplications occurred and what the associated costs are - in terms of susceptibility to disease-causing genetic mutations.

In the past, the highly complex patterns of DNA duplication -- including duplications within duplications -- have prevented the construction of an evolutionary history of these long DNA duplications. To crack the duplication code and determine which of the DNA segments are originals (ancestral duplications) and which are copies (derivative duplications), the researchers looked to both algorithmic biology and comparative genomics.

Identifying the original duplications is a prerequisite to understanding what makes the human genome unstable. Researchers modified an algorithmic genome assembly technique in order to deconstruct the sequence of repeated stretches of DNA and identify the original sequences. The belief is that perhaps there may be something special about the originals, some clue or insight into what causes this colonization of the human genome.

This is the first time that we have a global view of the evolutionary origin of some of the most complicated regions of the human genome. The researchers tracked down the ancestral origin of more than two thirds of these long DNA duplications.

Special Findings:
First, researchers suggest that specific regions of the human genome experienced elevated rates of duplication activity at different times in our recent genomic history. This contrasts with most models of genomic duplication which suggest a continuous model for recent duplications. Second, a large fraction of the recent duplication architecture centers around a rather small subset of "core duplicons" -- short segments of DNA that come together to form segmental duplications. These cores are focal points of human gene/transcript innovations.

Not all of the duplications in the human genome are created equal. Some of them -- the core duplicons -- appear to be responsible for recent genetic innovations the in human genome. Researchers uncovered 14 such core duplicons.

In 4 of the 14 cases, there is compelling evidence that genes embedded within the cores are associated with novel human gene innovations. In two cases the core duplicon has been part of novel fusion genes whose functions appear to be radically different from their antecedents.

Results suggest that the high rate of disease caused by these duplications in the normal population may be offset by the emergence of newly minted human/great-ape specific genes embedded within the duplications. The next challenge will be determining the function of these novel genes.

Mathematical Algorithms and Biological construction
Research applied their expertise in assembling genomes from millions of small fragments -- a problem that is not unlike the "mosaic decomposition" problem in analyzing duplications that the team faced.

Over the years researchers applied the 250-year old algorithmic idea first proposed by 18th century mathematician Leonhard Euler (of the fame of pi) to a variety of problems and demonstrated that it works equally well for a set of seemingly unrelated biological problems including DNA fragment assembly, reconstructing snake venoms, and now dissecting the mosaic structure of segmental duplications.

DNA is a vestige of formation of liquid crystal order

2007-11-26T19:50:00.000-06:00

Finding: Scientists have discovered liquid crystals of ultrashort DNA molecules immersed in water, providing a new scenario for a key step in the emergence of life on Earth.

The research team found that surprisingly short segments of DNA, life's molecular carrier of genetic information, could assemble into several distinct liquid crystal phases that "self-orient" parallel to one another and stack into columns when placed in a water solution.

Life is widely believed to have emerged as segments of DNA- or RNA-like molecules in a prebiotic "soup" solution of ancient organic molecules.

The conventional View Random formation of DNA is not possible.
If the formation of molecular chains as uniform as DNA by random chemistry is essentially impossible, then what are the effective ways for simple molecules to spontaneously self-select, "chain-up" and self-replicate.

What the study shows
In a mixture of tiny fragments of DNA, those molecules capable of forming liquid crystals selectively condense into droplets in which conditions are favorable for them to be chemically linked into longer molecules with enhanced liquid crystal-forming tendencies.

Even tiny fragments of double helix DNA can spontaneously self-assemble into columns that contain many molecules. From the collection of ancient molecules, short RNA pieces or some structurally related precursor emerged as the molecular fragments most capable of condensing into liquid crystal droplets, selectively developing into long molecules.

What are Liquid Crystals?
Liquid crystals are organic materials related to soap that exhibit both solid and liquid properties. They are commonly used for information displays in computers, flat-panel televisions, cell phones, calculators and watches.

What affects liquid crystals?
Most liquid crystal phase molecules are rod-shaped and have the ability to spontaneously form large domains of a common orientation, which makes them particularly sensitive to stimuli like changes in temperature or applied voltage.

RNA and DNA are chain-like polymers with side groups known as nucleotides, or bases, that selectively adhere only to specific bases on a second chain. Matching, or complementary base sequences enable the chains to pair up and form the widely recognized double helix structure. Genetic information is encoded in sequences of thousands to millions of bases along the chains, which can be microns to millimeters in length.

Such DNA polynucleotides had previously been shown to organize into liquid crystal phases in which the chains spontaneously oriented parallel to each other. Researchers understand the liquid crystal organization to be a result of DNA's elongated molecular shape, making parallel alignment easier, much like spaghetti thrown in a box and shaken would be prone to line up in parallel.

How short is short?
A series of experiments were conducted to see how short the DNA segments could be and still show liquid crystal ordering. The team found that even a DNA segment as short as six bases, when paired with a complementary segment that together measured just two nanometers long and two nanometers in diameter, could still assemble itself into the liquid crystal phases, in spite of having almost no elongation in shape.

What does this mean?
Structural analysis of the liquid crystal phases showed that they appeared because such short DNA duplex pairs were able to stick together "end-to-end," forming rod-shaped aggregates that could then behave like much longer segments of DNA. The sticking was a result of small, oily patches found on the ends of the short DNA segments that help them adhere to each other in a reversible way -- much like magnetic buttons -- as they expelled water in between them.

Columnar Stacking is possible if the nanoDna can form duplexes
The experiments provided direct evidence for the columnar stacking of the nano DNA pieces in a fluid liquid crystal phase. The key observation with respect to early life is that this aggregation of nano DNA strands is possible only if they form duplexes. In a sample of chains in which the bases don't match and the chains can't form helical duplexes, we did not observe liquid crystal ordering.

Complementary and noncomplementary DNA segments
Additional tests by the team involved mixed solutions of complementary and noncomplementary DNA segments. The results indicated that essentially all of the complementary DNA bits condensed out in the form of liquid crystal droplets, physically separating them from the noncomplementary DNA segments.

Significance for DNA molecules
The significance is that small molecules with the ability to pair up the right way can seek each other out and collect together into drops that are internally self-organized to facilitate the growth of larger pairable molecules.

DNA is a vestige of formation of liquid crystal order
The liquid crystal phase condensation selects the appropriate molecular components, and with the right chemistry would evolve larger molecules tuned to stabilize the liquid crystal phase. If this is correct, the linear polymer shape of DNA itself is a vestige of formation by liquid crystal order.

Environmental Setting Of Human Migrations In The Circum-Pacific Region

2007-11-24T13:52:00.000-06:00

Finding: The expansion of modern human populations into the circum-Pacific region occurred in at least four pulses, in part controlled by climate and sea level changes in the Late Pleistocene and Holocene epochs. Modern humans migrated into eastern Asia via a southern coastal route.

A new study adds insight into the migration of anatomically modern humans out of Africa and into Asia less than 100,000 years before present (BP).

Phase 1 45,000 to 40,000 BP Stable climate and sea level

The initial "out of Africa" migration was thwarted by dramatic changes in both sea level and climate and extreme drought in the coastal zone. A period of stable climate and sea level 45,000-40,000 years BP gave rise to the first major pulse of migration, when modern humans spread from India, throughout much of coastal southeast Asia, Australia, and Melanesia, extending northward to eastern Russia and Japan by 37,000 years BP.

33,000 to 16,000 BP Climate change - sea level and cold climate change
The northward push of modern humans along the eastern coast of Asia stalled north of 43° N latitude, probably due to the inability of the populations to adjust to cold waters and tundra/steppe vegetation.

The ensuing cold and dry Last Glacial period, ~33,000-16,000 year BP, once again brought dramatic changes in sea level and climate, which caused abandonment of many coastal sites.

Phase 2 16,000 to 8,000 BP Climate Warming

After 16,000 years BP, climates began to warm, but sea level was still 100 m below modern levels, creating conditions amenable for a second pulse of human migration into North America across an ice-free coastal plain now covered by the Bering Sea.

Phase 3 8,000 to 6,000 BP climate stabilization

The stabilization of climate and sea level in the early Holocene (8,000-6,000 years BP) supported the expansion of coastal wetlands, lagoons, and coral reefs, which in turn gave rise to a third pulse of coastal settlement, filling in most of the circum-Pacific region.

A drop in sea level in the western Pacific in the mid-Holocene (~6,000-4,000 year BP), caused a reduction in productive coastal habitats, leading to a brief disruption in human subsistence along the then densely settled coast.

Phase 4 3,500 to 1,000 BP

This disruption may have helped initiate the last major pulse of human migration in the circum-Pacific region, that of the migration to Oceania, which began about 3,500 years BP and culminated in the settlement of Hawaii and Easter Island by 2000-1000 years BP.

Gene comparison between Human and mammals

2007-11-23T21:31:00.000-06:00

Finding: By comparing portions of the human genome with those of other mammals, researchers have discovered almost 300 previously unidentified human genes, and found extensions of several hundred genes already known.

Behind the discovery
The fundamental is the idea that as organisms evolve, sections of genetic code that do something useful for the organism change in different ways.

What is the human genome?
The complete sequence of the human genome was accomplished several years ago. That means that the 3 billion or so chemical units, called bases, that make up the order of the genetic code is known. What is not known is the identification of the exact location of all the short sections that code for proteins or perform regulatory or other functions.

The genes make proteins...the basic chemical component needed for building cells. More than 20,000 protein-coding genes have been identified. This finding is important because it shows there still could be many more genes that have been missed using current biological methods. These existing methods are very effective at finding genes that have a wide expression but may miss those that are expressed only in certain tissues or at early stages of embryonic development.

Using evolution for gene discovery
This method involves using evolution to identify these genes. Gene comparision follows evolution; it has been doing this experiment for millions of years. There are many similarities between genes of the two species. The differences can be identified. Using a computer is the microscope to observe the results.

Four different bases -- commonly referred to by the letters G, C, A and T -- make up DNA. Three bases in a row can code for an amino acid (the building blocks of proteins), and a string of these three-letter codes can be a gene, coding for a string of amino acids that a cell can make into a protein.

Conserved genes
Siepel and colleagues set out to find genes that have been "conserved" -- that are fundamental to all life and that have stayed the same, or nearly so, over millions of years of evolution.
The researchers started with "alignments" discovered by other workers -- stretches up to several thousand bases long that are mostly alike across two or more species.

Over millions of years, individual bases can be swapped -- C to G, T to A, for example -- by damage or miscopying. Changes that alter the structure of a protein can kill the organism or send it down a dead-end evolutionary path. But conserved genes contain only minor changes that leave the protein able to do its job. The computer looked for regions with those sorts of changes by creating a mathematical model of how the gene might have changed, then looking for matches to this model.

Migration of Early Humans From Africa Aided By Wet Weather

2007-11-21T15:56:00.000-06:00

Finding: Migrations out of Africa 200,000 to 150,000 was dependent on the the wet climate in the presently hyper-arid Saharan-Arabian desert.

Conventional thinking
This migration was dependent on the occurrence of wetter climate in the region. There is good evidence that the southern and central Saharan-Arabian desert experienced increased monsoon precipitation during this period (200,000 to 150,000), but there is no unequivocal evidence for a corresponding rainfall increase in the northern part of the migration corridor, including the Sinai-Negev land bridge between Africa and Asia.

Passage through this "bottleneck" region would have been dependent on the development of suitable climate conditions.

Uranium series dating method - Speleothems
Scientists a reconstruction of paleoclimate in the Negev Desert based on absolute uranium series dating of carbonate cave deposits (speleothems). Speleothems only form when rainwater enters the groundwater system and vegetation grows above a cave.

Today the climate in the Negev Desert is very arid and speleothems do not form, but their presence in a number of caves clearly indicates that conditions were wetter in the past. Scientists have dated 33 speleothem samples from five caves in the central and southern Negev Desert.

Increased Rainfall in the central and Southern Negev Desert
The ages of these speleothems show that the last main period of increased rainfall occurred between 140,000 and 110,000 years ago. The climate during this time consisted of episodic wet events that enabled the deserts of the northeastern Sahara, Sinai, and the Negev to become more hospitable for the movement of early modern humans.

Wet periods in the North and South parts of the Saharan-Arabian desert
The simultaneous occurrence of wet periods in the northern and southern parts of Saharan-Arabian desert may have led to the disappearance of the desert barrier between central Africa and the Levant.

The humid period in the Negev Desert between 140,000 and 110,000 years ago was preceded and followed by essentially unbroken arid conditions; thus creating a climatic "window" for early modern human migration to the Levant.

Evolution Is Deterministic, Not Random -- Multi-species Study

2007-11-15T09:14:00.000-06:00

Finding: Biologists in an international team have concluded that developmental evolution is deterministic and orderly, an not the random sequence operation many previously believed based on a study of different species of roundworms.

If organs do not change, how does evolutionary development work in those organs?

Enter the study involving the female copulatory and egg-laying organ, the vulva, found in nearly 50 species of roundworms. The conventional wisdom is that because the vulva does not significantly change across species, one might predict that there would be little variation in vulva development. But that is not the case. Researchers found a lot of developmental variation. They concluded that this variation, since it did not affect the final adult vulva, could not have evolved in a random, fashion.

The research team looked at more than 40 characteristics of vulva development, including cell death, cell division patterns, and related aspects of gonad development. They plotted the evolution of these traits on a new phylogenetic tree, which illustrates how species are related to one another and provides a map as to how evolutionary changes are occurring.

Unidirectional changes

Their results showed an even greater number of evolutionary changes in vulva development than they had expected. But they found that evolutionary changes among these species were unidirectional in nearly all instances.

The decline of cell divisions

For example, they concluded that the number of cell divisions needed in vulva development declined over time instead of randomly increasing and decreasing.

The decline of number of rings

In addition the number of rings used to form the vulva consistently declined during the evolutionary process.

These results demonstrate that, even where you might expect evolution to be random, it is not.

Tiny DNA Molecules Show Liquid Crystal Phases, Pointing Up New Scenario For First Life On Earth

2007-11-13T23:21:00.000-06:00

Finding: Scientists have discovered some unexpected forms of liquid crystals of ultrashort DNA molecules immersed in water, providing a new scenario for a key step in the emergence of life on Earth.

Short segments of DNA, life's molecular carrier of genetic information, could assemble into several distinct liquid crystal phases that "self-orient" parallel to one another and stack into columns when placed in a water solution.

Life is widely believed to have emerged as segments of DNA- or RNA-like molecules in a prebiotic "soup" solution of ancient organic molecules.

Since the formation of molecular chains as uniform as DNA by random chemistry is essentially impossible, scientists have been seeking effective ways for simple molecules to spontaneously self-select, "chain-up" and self-replicate. The new study shows that in a mixture of tiny fragments of DNA, those molecules capable of forming liquid crystals selectively condense into droplets in which conditions are favorable for them to be chemically linked into longer molecules with enhanced liquid crystal-forming tendencies, he said.

Tiny fragments of double helix DNA can spontaneously self-assemble into columns that contain many molecules. Our vision is that from the collection of ancient molecules, short RNA pieces or some structurally related precursor emerged as the molecular fragments most capable of condensing into liquid crystal droplets, selectively developing into long molecules.

Liquid crystals -- organic materials related to soap that exhibit both solid and liquid properties -- are commonly used for information displays in computers, flat-panel televisions, cell phones, calculators and watches. Most liquid crystal phase molecules are rod-shaped and have the ability to spontaneously form large domains of a common orientation, which makes them particularly sensitive to stimuli like changes in temperature or applied voltage.

RNA and DNA are chain-like polymers with side groups known as nucleotides, or bases, that selectively adhere only to specific bases on a second chain. Matching, or complementary base sequences enable the chains to pair up and form the widely recognized double helix structure. Genetic information is encoded in sequences of thousands to millions of bases along the chains, which can be microns to millimeters in length.

Such DNA polynucleotides had previously been shown to organize into liquid crystal phases in which the chains spontaneously oriented parallel to each other, he said. Researchers understand the liquid crystal organization to be a result of DNA's elongated molecular shape, making parallel alignment easier, much like spaghetti thrown in a box and shaken would be prone to line up in parallel.

Teams at CU-Boulder and University of Milan began a series of experiments to see how short the DNA segments could be and still show liquid crystal ordering. The teams found that even a DNA segment as short as six bases, when paired with a complementary segment that together measured just two nanometers long and two nanometers in diameter, could still assemble itself into the liquid crystal phases, in spite of having almost no elongation in shape.

Structural analysis of the liquid crystal phases showed that they appeared because such short DNA duplex pairs were able to stick together "end-to-end," forming rod-shaped aggregates that could then behave like much longer segments of DNA. The sticking was a result of small, oily patches found on the ends of the short DNA segments that help them adhere to each other in a reversible way -- much like magnetic buttons -- as they expelled water in between them.

A key characterization technique employed was X-ray microbeam diffraction combined with in-situ optical microscopy, carried out with researchers from Argonne and Brookhaven National Laboratories. The experiments provided direct evidence for the columnar stacking of the nano DNA pieces in a fluid liquid crystal phase.

The key observation with respect to early life is that this aggregation of nano DNA strands is possible only if they form duplexes. In a sample of chains in which the bases don't match and the chains can't form helical duplexes, we did not observe liquid crystal ordering.

Subsequent tests by the team involved mixed solutions of complementary and noncomplementary DNA segments. The results indicated that essentially all of the complementary DNA bits condensed out in the form of liquid crystal droplets, physically separating them from the noncomplementary DNA segments.

It means that small molecules with the ability to pair up the right way can seek each other out and collect together into drops that are internally self-organized to facilitate the growth of larger pairable molecules.

In essence, the liquid crystal phase condensation selects the appropriate molecular components, and with the right chemistry would evolve larger molecules tuned to stabilize the liquid crystal phase. If this is correct, the linear polymer shape of DNA itself is a vestige of formation by liquid crystal order.

Fantasy Hero's and Intelligent Design

2007-11-06T09:07:00.000-06:00

A lot of Intelligent design proponents question the slow and methodical evolutionary march to sophistication. They believe that sophistication came all at once, that it was designed that way...because the designer knew before hand what the final design was to look like, so there was no need for an intermediary step.

OK. Prove it!

This reminds me of the time when I was young and believed in superheroes and superhuman feats. If you start with the comic book heroes like Superman, The Fantastic Four and the like they all had extra-ordinary gifts and abilities. I soon realized that such fantasy powers couldn't come true. So I substituted those comic book fantasy powers for other fantasy powers, like hitting .500 in baseball, or throwing 6 touchdowns per game without an interception, or carrying a ball for an average of 8 yards per carry. It soon dawned on me why most hitters were hitting .260, why most Quarterbacks throw only 2 touchdowns passes and also throw picks; and that most runners only have a 2.5 yard per carry average. Reality bites.

The intelligent design argument is much like believing in the fantasy world of the comic books. It is a fine world, but reality bites. If you want to produce a scientific basis for Intelligent design, as a viable alternative to Evolution, I and most other scientists would be glad to listen.

So develop a scientific theory of Intelligent Design...prove it!.

Simple to complex then simple to complex

2007-11-04T21:13:00.000-06:00

There has been one rule that evolutionary biologists felt they could cling to: the amount of complexity in the living world has always been on the increase. Now even that is in doubt.

The Tree of Life
In recent years, genetic analysis has forced biologists to consider the possibility that organisms such as the sea squirt might have lost some of the complexity of their ancestors. Yet even now, few recognise the full implications of loss as a key player in evolution. The entire tree of life has been built on the assumption that evolution entails increasing complexity. So, for example, if two groups of animals were considered close because both had a particular prominent feature, then someone discovered a third, intermediate line that lacked that feature but shared many other aspects of the two groups, traditional phylogenists would conclude that the feature had arisen independently in the two outlying groups, by a process known as convergent evolution.

They often did not even consider the alternative explanation: that the feature in question had evolved just once in an ancestor of all three groups, and had subsequently been lost in the intermediate one. Now a handful of molecular biologists are considering that possibility.

Instead of simply looking to see whether two species share certain genes, the new approach involves taking the "molecular fingerprint" of different types of cells. It identifies the unique combination of transcription factors - molecules that control which of a cell's genes are turned on and when - that specify the make-up of a cell, including the molecular signals it transmits and receives.

If two groups of organisms share the same type of cells, with the same molecular fingerprint, giving rise to similar features in both, then it is extremely unlikely that these features evolved twice. So any intermediate groups of organisms that lack that feature would most likely have lost it during the course of evolution. Only now, with the ability to explore at the molecular level how morphological features have been lost, gained and modified over time, is the true extent of evolutionary loss coming to light.

Finding: In genetic variation - an ancestor may develop certain traits, only to be followed by generations of child variants that lose the trait, and then redevelop the trait.

500 million year old Jellyfish

2007-11-02T21:46:00.000-05:00

Finding: Using "fossil snapshots" found in rocks more than 500 million years old, three University of Kansas researchers have described the oldest definitive jellyfish ever found. This is significant because the fossil record is biased against soft-bodied life forms such as jellyfish, because they leave little behind when they die. That means that scientists are still working to solve the evolutionary development of many soft-bodied animals. But now they have a clear picture of what the soft-body form looked like when it comes to Jelly-Fish.

Here is what happened: researchers describe four types of cnidarian fossils preserving traits that allow them to be related to modern orders and families of jellyfish. The specimens are about 200 million years older than the oldest previously discovered jellyfish fossils.

Rapid Species diversification
Research jellyfish the group describes, found in Utah, offer insights into the puzzle of rapid species diversification and development that occurred during the Cambrian radiation, a time when most animal groups appear in the fossil record, beginning roughly 540 million years ago. The fossil record reveals much less about the origin and early evolution of animals such as jellyfish than it does about animals with hard shells or bones.

The Problem resolution:
The fossil record is full of circular shaped blobs, some of which are jellyfish. That's one of the reasons the fossils we describe are so interesting, because you can see a distinct bell-shape, tentacles, muscle scars and possibly even the gonads. The jellyfish left behind a film in fine sediment that resembles a picture of the animal. Most jellyfish do not leave such a clear impression behind because they are often preserved in coarse sand.

With the discovery of the four different types of jellyfish in the Cambrian, however, provide enough detail to assert that the types can be related to the modern orders and families of jellyfish. The specimens show the same complexity. That means that either the complexity of modern jellyfish developed rapidly roughly 500 million years ago, or that the group is even older and existed long before then.

The jellyfish described in the article are also unique because they push the known occurrence of definitive jellyfish back from 300 million to 505 million years, a huge jump, and show more detail than anything previously described that is younger.

Dawn Of Animal Vision Discovered

2007-10-29T23:07:00.000-05:00

Finding: By peering deep into evolutionary history, scientists at the University of California, Santa Barbara have discovered the origins of photosensitivity in animals. 600 Million Years.

The scientists studied the aquatic animal Hydra, a member of Cnidaria, which are animals that have existed for hundreds of millions of years. The scientists looked at light-receptive genes in cnidarians, an ancient class of animals that includes corals, jellyfish, and sea anemones.

Not only are we the first to analyze these vision genes (opsins) in these early animals, but because we don't find them in earlier evolving animals like sponges, you can put a date on the evolution of light sensitivity in animals.

Now there is a time frame for the evolution of animal light sensitivity. We know its precursors existed roughly 600 million years ago.

There are only a handful of cases where scientists have documented the very specific mutational events that have given rise to new features during evolution.

Anti-evolutionists often argue that mutations, which are essential for evolution, can only eliminate traits and cannot produce new features. Such claims are simply wrong. Specific mutational changes in a particular duplicated genes (opsin) allowed the new genes to interact with different proteins in new ways. Today, these different interactions underlie the genetic machinery of vision, which is different in various animal groups.

Hydras are predators, and the authors speculate that they use light sensitivity in order to find prey. Hydra use opsin proteins all over their bodies, but they are concentrated in the mouth area, near the tip of the animal. Hydras have no eyes or light-receptive organs, but they have the genetic pathways to be able to sense light.

A map of Human Global Migration

2007-10-29T14:39:00.000-05:00

Palaeontologists, archaeologists and geneticists are piecing the migration picture.

As a coherent picture emerges, however, new mysteries arise. It is looking likely that our species appeared far earlier than previously suspected - and remained in Africa for tens of thousands of years before going global. It could be said that humans were all dressed up and going nowhere.

Why the delay? Yet when our ancestors finally flocked onto the world stage, their spread was remarkably rapid. What caused them to explode out of Africa when they did? What circumstances suddenly allowed those early humans to smash down their boundaries like no species before or since?

Map of Neanderthal Geography

2007-10-26T14:47:00.000-05:00

Neanderthals have been at the centre of many of the most intense debates in palaeoanthropology ever since the discovery of their bones spawned the field 150 years ago. A popular caricature portrays them as beetle-browed brutes, but this is far from the truth. Neanderthals were sophisticated stone-tool makers and made razor-sharp knives out of flint. They made fires when and where they wanted, and seem to have made a living by hunting large mammals such as bison and deer. Neanderthals also buried their dead, which, fortunately for researchers, increases the odds of the bones being preserved.

Bones and artefacts leave a whole range of questions wide open, though. How exactly are Neanderthals related to us? Did our ancestors interbreed with them, and if so, do modern Eurasians still carry a little Neanderthal DNA?

Just how "human" were they? There's only one way to be sure: By sequencing their entire genome we can begin to learn more about their biology. What's more, if we can answer the genetic questions we might solve the biggest mystery of all: why did Neanderthals die out while modern humans went on to conquer the globe?

Duplication and Division of Labor - The Mechanics of Evolution

2007-10-15T19:41:00.000-05:00

Finding: Evolution works by gene duplication and division of labor.

Researchers at the University of Wisconsin-Madison have provided an exquisitely detailed picture of natural selection as it occurs at the genetic level.

Two scientists document how, over many generations, a single yeast gene divides in two and parses its responsibilities to be a more efficient denizen of its environment. The work illustrates, at the most basic level, the driving force of evolution.

This is how new capabilities arise and new functions evolve. This is what goes on in butterflies and elephants and humans. It is evolution in action.

The work is important because it provides the most fundamental view of how organisms change to better adapt to their environments. It documents the workings of natural selection, the critical idea first posited by Charles Darwin where organisms accumulate random variations, and changes that enhance survival are "selected" by being genetically transmitted to future generations.

The new study replayed a set of genetic changes that occurred in a yeast 100 million or so years ago when a critical gene was duplicated and then divided its nutrient processing responsibilities to better utilize the sugars it depends on for food.

One source of newness is gene duplication

When you have two copies of a gene, useful mutations can arise that allow one or both genes to explore new functions while preserving the old function. This phenomenon is going on all the time in every living thing. Many of us are walking around with duplicate genes we're not aware of. They come and go.

Two genes can be better than one because redundancy promotes a division of labor. Genes may do more than one thing, and duplication adds a new genetic resource that can share the workload or add new functions. For example, in humans the ability to see color requires different molecular receptors to discriminate between red and green, but both arose from the same vision gene.

The difficulty, he says, in seeing the steps of evolution is that in nature genetic change typically occurs at a snail's pace, with very small increments of change among the chemical base pairs that make up genes accumulating over thousands to millions of years.

To measure such small change requires a model organism like simple brewer's yeast that produces a lot of offspring in a relatively short period of time. Yeast, Carroll argues, are perfect because their reproductive qualities enable study of genetic change at the deepest level and greatest resolution because researchers can produce and quickly count a large number of organisms. The same work in fruit flies, one of biology's most powerful models, would require "a football stadium full of flies" and years of additional work, Carroll explains.

The process of becoming better occurs in very small steps. When compounded over time, these very small changes make one group of organisms successful and they out-compete others.

The new study involved swapping out different regions of the yeast genome to assess their effects on the performance of the twin genes, as well as engineering in the gene from another species of yeast that had retained only a single copy.

Retracing the Steps of evolution
The work shows in great detail how the ancestral gene gained efficiency through duplication and division of labor. They became optimally connected in that job. They're working in cahoots, but together they are better at the job the ancestral gene held. Natural selection has taken one gene with two functions and sculpted an assembly line with two specialized genes.

Is Junk DNA really Junk?

2007-10-12T12:21:00.000-05:00

The discovery of the structure of DNA led to the idea that genomes are merely a series of DNA sequences, or genes, that code for proteins. Yet a paradox soon emerged: some relatively simple creatures turned out to have much larger genomes than more complex ones. Why would they need more genes?

What does DNA code for? Genetic traits and proteins. So do simple creatures need larger DNA structures? They don't. It rapidly became clear that in animals and plants, most DNA does not code for proteins. Early in studies of the Genome. 98 per cent of our DNA is of the non-coding variety. But even back in the 1970s it was obvious that not all non-coding DNA is junk. There is a certain kind of regulatory DNA. Certain sequences for which certain proteins bind can boost or block the expression of genes nearby. Such DNA is important.

This feature has been discovered over the years. Tiny bits of non-coding DNA have turned out to have a regulatory role or some other function. It was believed until recently that such sequences were only a small-part of non-coding DNA. Only in the past decade, as the genomes of more and more species have been sequenced and compared, has the bigger picture begun to emerge.

Conservation of Genes
Even though it is 450 million years since the ancestors of pufferfish and humans parted ways, everyone expected that we would still share many of the same genes - as proved to be the case. Most of the protein-coding DNA in different vertebrates is very similar or "conserved". The surprise was that even more of the non-coding DNA is conserved, too. Why did this occur?

DNA is constantly mutating due to copying mistakes and damage from chemicals and radiation. Specific sequences will be conserved only if natural selection weeds out any offspring with changes in these sequences. This will happen only if the changes are harmful, so researchers are convinced that all the conserved non-coding DNA must do something important. Why else would evolution hang on to it?

Those regions really challenge our understanding of biology. Biologists trying to find out what conserved non-coding DNA does, so scientists recently added extra copies of some of these sequences to mice. It's like taking a few extra pages and stapling them into a book.

Ultra-conserved
Copies of the "ultra-conserved" sequences that are almost exactly the same, base for base, in the mouse, rat and human. Nearly half of the sequences the team tested boosted gene expression in specific tissues, especially genes involved in nervous system development, the team reported last year.

This suggests that much of the conserved non-coding DNA is needed to make a brain cell, say, different from a skin cell. However, conserved DNA still accounts for only a tiny proportion of the genome. Even counting the 1.2 per cent of coding DNA, the human sequences found in other mammals add up to just 5 per cent. What's the other 95 per cent for?

One possibility is that some of the DNA whose sequence is not conserved might be conserved in a different sense. Regulatory sequences are essentially binding sites for proteins, so what matters is their three-dimensional structure. And while the conventional view is that the 3D structure of DNA is closely related to its sequence, scientists have found evidence that some regulatory regions share similar structures even though their sequences are different. Looked at this way, the total amount of conserved DNA could be much higher.

The RNA transcription factor
Another line of evidence suggesting that some non-conserved DNA has a function comes from looking at which DNA sequences get transcribed into RNA. It used to be thought that, with a few exceptions, most RNAs were produced as the first step in making proteins.

Protein-coding genes contain vast stretches of non-coding DNA called introns, which make up a quarter of our genome. These introns are transcribed into RNA but immediately edited out of the "raw" RNA. The resulting "processed" RNAs represent just 2 per cent of the genome.
A few years ago, however, scientists showed that far more than 2 per cent of the genome gets transcribed into RNA. The latest estimates are that 85 to 97 per cent of the entire genome is transcribed into raw RNA, resulting in processed RNAs representing 18 per cent of the genome.

Clearly, most of this RNA is non-coding, or ncRNA. So what is it for? While some of the very small ncRNAs have a big role in the control of gene expression most ncRNA remains mysterious.

Science and Falseability

2007-10-07T14:59:00.000-05:00

Science works on several principles. The most important is the search for truth. The duplication of experiments to verify a claim as true. But also is the possibility of showing that something that is claimed to be true is actually false. That is the falsibility criteria. Here are some examples:

The Ptolemaic system of astronomy made some very important claims about how the solar system was structured. That Earth was the center of the solar system...maybe even the universe. It claimed that the stars and the planets orbited around the Earth.

These were scientific claims and as such were subject to verification. As astronomers grew interested in the stars, they becan to examine these claims. Leonardo Da Vince, Gallileo, Kepler, Copernicus, Tyco Brahe and Issac Newton were scientists that researched and found that these claims were false. The earth was not the center of the solar system, the sun was.

The claim was falsifiable. That was important. As a scientific claim it was wrong. It was shown to be wrong, and several astronomers, physicists, and mathematicians were able to verify the experiments that showed how the claim was false, and a new claim was true.

This is the essence of science.

Can the same be said about Evolution? Can it be shown to be falsifiable? This is a critical claim. Because if it cannot be falsifiable then it is like Intelligent Design, a philosophical claim that cannot be verified, or denied.

One way to show that evolution is false would be to show that there are no variations in the human or animal kingdom. But that is not the case. Just recently there was a sad case of an Indian girl that was born with four arms and four legs. This example shows that there are genetic variations possible. But there have to be other tests to show that evolution works. Evolution as a function of genetic mutation.

One experiment would be to expose cells to radiation. If there are no genetic mutations as a result of the experiment then genetic mutation might be suspect as a vehicle of evolution. But as it is there are many cases of radiation leading to genetic mutation. This however is the falsifiability condition.

DNA microarray

2007-09-28T20:14:00.000-05:00

A DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array) is a collection of microscopic DNA spots, commonly representing single genes, arrayed on a solid surface by covalent attachment to chemically suitable matrices.

DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system. Qualitative or quantitative measurements with DNA microarrays utilize the selective nature of DNA-DNA or DNA-RNA hybridization under high-stringency conditions and fluorophore-based detection. DNA arrays are commonly used for expression profiling, i.e., monitoring expression levels of thousands of genes simultaneously, or for comparative genomic hybridization.

Microarray technology is often used for gene expression profiling. It makes use of the sequence resources created by the genome sequencing projects and other sequencing efforts to answer the question, what genes are expressed in a particular cell type of an organism, at a particular time, under particular conditions?

For instance, they allow comparison of gene expression between normal and diseased (e.g., cancerous) cells. There are several names for this technology - DNA microarrays, DNA arrays, DNA chips, gene chips, others. Sometimes a distinction is made between these names but in fact they are all synonyms as there are no standard definitions for which type of microarray technology should be called by which name.

Microarrays exploit the preferential binding of complementary nucleic acid sequences. A microarray is typically a glass slide, on to which DNA molecules are attached at fixed locations (spots or features). There may be tens of thousands of spots on an array, each containing a huge number of identical DNA molecules (or fragments of identical molecules), of lengths from twenty to hundreds of nucleotides. The spots on a microarray are either printed on the microarrays by a robot, or synthesized by photo-lithography (similar to computer chip productions) or by ink-jet printing. There are commercially available microarrays, however many academic labs produce their own microarrays.

Microarrays that contain all of the about 6000 genes of the yeast genome have been available since 1997. The latest generations of commercial microarrays represent the entire human genome, more than 30,000 genes, on two microarrays.

Genetic Carrying Handles: Cloning Vectors

2007-09-25T19:54:00.000-05:00

In order to clone a gene, its DNA sequence must be attached to some kind of carrier, also made of DNA, that can take it into the cell. Biologists call these carriers vectors. A vector acts like a handle for the DNA, and it also contains other tools such as an origin of replication and a selective marker.

The origin of replication is a sequence of DNA that the host cell recognizes that allows it to make more copies of the clone DNA sequence. This origin sequence is where the cell begins copying the vector and the attached clone DNA. The selective marker is a specific DNA sequence that is used by biologists to tell if the clone has entered the cell, and they are usually genes that confer antibiotic resistance to the cell.

The most common media used for this process is actually very similar to chicken soup, but the carbohydrate agarose is added to convert the media into a semi-solid substance, since bacterial colonies are much easier to detect on a semi-solid surface. Agarose is much like gelatin, but it comes from seaweed and unlike gelatin, most bacteria cannot digest it. Antibiotics are often added to the media, to kill any cells that do not possess the antibiotic resistant selective marker gene, which is in the clone DNA. This way, biologists can ensure that all the remaining cells have in fact taken up the clone DNA and its vector.

These cells are called transfected cells. Antibiotics are not the only way to identify transfected cells. Biologists sometimes use selective markers that turn cells a different colour or even to make them glow. Common proteins that do this include luciferase, which makes fireflies glow or green fluorescent protein, which comes from certain species of jellyfish. Green fluorescent protein also comes in other colours!

Bacterial artificial chromosome

2007-09-23T19:42:00.000-05:00

A bacterial artificial chromosome (BAC) is a DNA construct, based on a fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually E. coli. F-plasmids play a crucial role because they contain partition genes that promote the even distribution of plasmids after bacterial cell division. The bacterial artificial chromosome's usual insert size is 150 kbp, with a range from 100 to 300 kbp. A similar cloning vector, called a PAC has also been produced from the bacterial P1-plasmid.

BACs are often used to sequence the genetic code of organisms in genome projects, for example the Human Genome Project. A short piece of the organism's DNA is amplified as an insert in BACs, and then sequenced. Finally, the sequenced parts are rearranged in silico, resulting in the genomic sequence of the organism.

Bats and Humans share a common Gene for communication

2007-09-19T12:53:00.000-05:00

Finding: The FOXP2 gene found in humans and bats allows human language evolution and bat echo location.

Discoveries that mutations in the FoxP2 gene lead to speech defects and that the gene underwent changes around the time language evolved both implicate FOXP2 in the evolution of human language.

No genetic variation exists among many vertebrates
Recently, patterns of gene expression in birds, humans and rodents have suggested a wider role in the production of vocalisations. But many reports have established that FOXP2 shows very little genetic variation across even distantly related vertebrates - from reptiles to mammals -- providing few extra clues as to the gene's role.

Genetic Variation does exist with echo locating bats
A new study, undertaken by a joint of team of British and Chinese scientists, has found that this gene shows unparalleled variation in echolocating bats. The results, appearing in a study report that FOXP2 sequence differences among bat lineages correspond well to contrasting forms of echolocation.

Bats like people need coordination of mouth and face for communication
Like speech, bat echolocation involves producing complex vocal signals via sophisticated coordination of the mouth and face. The involvement of FOXP2 in the evolution of echolocation adds weighty support to the theory that FOXP2 functions in the sensory-motor coordination of vocalisations.

New Method Can Reveal Ancestry Of All Genes Across Many Different Genomes

2007-09-18T19:43:00.000-05:00

Finding: A new method has been developed that can reveal the ancestry of all genes across many different genomes. First applied to 17 species of fungi, the approach has unearthed some surprising clues about why new genes pop up in the first place and the biological nips and tucks that bolster their survival.

The problem
The wheels of evolution turn on genetic innovation as new genes with new functions appear, allowing organisms to grow and adapt in new ways. But deciphering the history of how and when various genes appeared, for any organism, has been a difficult and largely intractable task. Having the ability to trace the history of genes on a genomic scale opens the doors to a vast array of interesting and largely unexplored scientific questions. Although the principles laid out in the study pertain to fungi, they could have relevance to a variety of other species as well.

What we know
It has been recognized for decades that new genes first arise as carbon copies of existing genes. It is thought that this replication allows one of the gene copies to persist normally, while giving the other the freedom to acquire novel biological functions. Though the importance of this so-called gene duplication process is well appreciated it is the grist for the mill of evolutionary change the actual mechanics have remained murky, in part because scientists have lacked the tools to study it systematically.

Genes from 17 different species
Driven by the recent explosion of whole genome sequence data, the authors of the new study were able to assemble a natural history of more than 100,000 genes belonging to a group of fungi known as the Ascomycota. From this, the researchers gained a detailed view of gene duplication across the genomes of 17 different species of fungi, including the laboratory model Saccharomyces cerevisiae, commonly known as baker's yeast.

Methodology - Synergy
The basis for the work comes from a new method termed "SYNERGY", which first author Ilan Wapinski and his coworkers developed to help them reconstruct the ancestry of each fungal gene.

By tracing a gene's lineage through various species, the method helps determine in which species the gene first arose, and if -- and in what species -- it became duplicated or even lost altogether. SYNERGY draws its strength from the use of multiple types of data, including the evolutionary or "phylogenetic" tree that depicts how species are related to each other, and the DNA sequences and relative positions of genes along the genome.

Perhaps most importantly, the method does not tackle the problem of gene origins in one fell swoop, as has typically been done, but rather breaks it into discrete, more manageable bits. Instead of treating all species at once, SYNERGY first focuses on a pair of the most recently evolved species -- those at the outer branches of the tree -- and works, two-by-two, toward the more ancestral species that comprise the roots.

From this analysis scientists were able to identify a set of core principles that govern gene duplication in fungi. The findings begin to paint a picture of how new genes are groomed over hundreds of millions of years of evolution.

History of Bacteria evolution

2007-09-17T19:54:00.000-05:00

Finding: The evolutionary history of bacteria has been worked out.

Unlike other organisms that tend to pass their genes on to the next generation of their own species, bacteria often exchange genetic material with totally unrelated species a process called lateral gene transfer.

Researchers did not believe that they could work out the evolutionary history of bacteria. But now, thanks to the availability of sequenced genomes for groups of related bacteria, and a new analytical approach, researchers at have been able to demonstrate that constructing a bacterial family tree is indeed possible.

Here is how they do it
Scientists propose an approach that begins by scouring genomes for a set of genes that serve as reliable indicators of bacterial evolution. This method has important implications for biologists studying the evolutionary history of organisms by establishing a foundation for charting the evolutionary events, such as lateral gene transfer, that shape the structure and substance of genomes.

In this study, the researchers chose the ancient bacterial group called gamma Proteobacteria, an ecologically diverse group (including Escherichia coli and Salmonella species) with the most documented cases of lateral gene transfer and the highest number of species with sequenced genomes.

Why use bacteria at all?
Bacteria promise to reveal a wealth of information about genomic evolution, because so many clusters of related bacterial genomes have been sequenced--allowing for broad comparative analysis among species--and because their genomes are small and compact.

The results support the ability of their method to reconstruct the important evolutionary events affecting genomes. Their approach promises to elucidate not only the evolution of bacterial genomes but also the diversification of bacterial species events that have occurred over the course of about a billion years of evolution.

Human - Chimpanzee split occured 5-7 million years ago

2007-09-16T10:54:00.000-05:00

Finding- New research indicates that the split between chimpanzees and humans occured 5 to 7 million years ago. This improves the time differential which previously had a 10 million year range 3-13 million years. Now the differential is 2 million years.

How it was done:
Scientists analyzed the largest data set yet of genes that code for proteins and also used an improved computational approach that they developed, which takes into account more of the variability -- or statistical error--in the data than any other previous study. Gene studies are needed to address this problem because the interpretation of the earliest fossils of humans at the ape/human boundary are controversial and because almost no fossils of chimpanzees have been discovered.

The science team examined 167 different gene sequence sets from humans, chimpanzees, macaques, and mice.

No previous study has taken into account all of the error involved in estimating time with the molecular-clock method. The new statistical technique is a multifactor bootstrap-resampling approach.

Nucleotide arrangement
The scientists estimated the time of divergence between species by studying the sequential arrangement of nucleotides that make up the chain-like DNA molecules of each species. The number of mutations in the DNA sequence of a species, compared with other species, is a gauge of its rate of evolutionary change.

Calibration - rate of one species with that of another species
The minimum time of divergence
By calibrating this rate with the known time of divergence of a species on another branch of the tree-like diagram that shows relationships among species, scientists can estimate the time when the species they are studying evolved. In this case, the calibration time the scientists used was the split of Old World monkeys -- including baboons, macaques, and others -- from the branch of the phylogenetic tree that led to humans and apes, which fossil studies have shown is at least 24 million years ago. Using this calibration time, the team estimated that the human-chimp divergence occurred at least 5 million years ago, proportionally about one-fifth of the calibration time.

Other supporting evidence
The maximum time of divergence
This time is consistent with the findings of several research groups that have used the molecular-clock method to estimate the split of humans and chimpanzees since the first attempt in 1967. But this is only a minimum estimate, because it was based on a minimum calibration time. To obtain a maximum limit on the human-chimp divergence, the team used as a calibration point the maximum estimate, based on fossil studies, of the divergence of Old-World monkeys and the branch leading to humans -- 35 million years ago. Calculations using this date yielded a time for the human-chimp split of approximately 7 million years ago, which again was proportionally about one-fifth of the calibration time.

What else can be gathered from knowing the origin of the divergence?
Besides knowing when we divereged, a fact worth knowing, this divergence time also has considerable importance because it is used to establish how fast genes mutate in humans and to date the historical spread of our species around the globe.

Knowing the timescale of human evolution, and how we changed through time in relation to our environment, could provide valuable clues for understanding the evolution of intelligent life.

This research does not pinpoint the precise time of the split, it tells us that proportional differences on branches in family trees should be considered when proposing new times. For example, we now know that a 10-to-12-million-year human-chimp split would infer a divergence of Old World monkeys from our lineage that is too old (50-to-60-million years ago) to reconcile with the current fossil record of primates.

What then is the next step?
Although some additional improvement is possible by including more genes and more species, the greatest opportunity now for further narrowing this estimate of 5-to-7-million years will be the discovery of new fossils and the improvement in geologic dating of existing fossils.

Chimp-sized Hominid Walked Upright On Two Legs Six Million Years Ago

2007-09-15T19:40:00.000-05:00

Finding: When did hominids begin to walk upright? Recent fossil evidence suggests that a chimp size hominid walked upright on two legs in Kenya's Tugen Hills, over 6 million years ago. That is about 3 million years earlier than "Lucy," the most famous early biped in our lineage.

How the finding occured:

A U.S. research team responsible for analysis of the CT scans of the internal structure of the fossil bone was responsible there is now solid evidence of the earliest upright posture and bipedalism securely dated to six million years.

The fossil the team studied is part of a left thighbone unearthed nearly four years ago by Senut and Pickford at their dig in the Kenyan Lukeino Formation. The fragment includes the intact head of the left thighbone -- the ball that is inserted into the hip socket joint -- plus the bony neck that connects the ball to the thighbone shaft as well as part of the thighbone shaft.
Measurements show that the fossil bone is about the same size as a chimpanzee's. However, CT scans of the interior of the bone reveal that the neck connecting the ball to the shaft is thinner on top than it is on the bottom, a sign the researchers say that the individual from which it came walked on two legs.

How does this compare to modern day apes and humans?

In present day chimps and gorillas, the thicknesses in the upper and lower parts of that bone are approximately equal. In modern humans, the bone on top is thinner than on the bottom by a ratio of one to four or more. The ratio in this fossil is one to three.

The key is the ratio

The ratio in the fossil is evidence for transition to an upright posture and habitual bipedal gait the researchers argue. In addition, because walking upright is the essential mark of a hominid, the ratio is functional evidence that the bones fossilized at Lukeino were from hominids.

Early Man Could Walk but not Run - No Achilles tendon

2007-09-14T11:39:00.000-05:00

Finding: The earliest humans almost certainly walked upright on two legs but may have struggled to run at even half the speed of modern man.

A new study proposes that if early humans lacked an Achilles tendon, as modern chimps and gorillas do, then their ability to run would have been severely compromised.

Research supports the belief that the earliest humans used efficient bipedal walking rather than chimp-like 'Groucho' walking. But if, as seems likely, early humans lacked an Achilles tendon then whilst their ability to walk would be largely unaffected our work suggests running effectiveness would be greatly reduced with top speeds halved and energy costs more than doubled.

Efficient running would have been essential to allow our ancestors to move from a largely herbivorous diet to the much more familiar hunting activities associated with later humans. What we need to discover now is when in our evolution did we develop an Achilles tendon as knowing this will help unravel the mystery of our origins.

Why Genes Of One Parent Are Expressed Over Genes Of The Other: New Ideas In Genomic Imprinting

2007-09-12T20:05:00.000-05:00

Finding: Genetic imprinting arises from an 'epigenetic memory' that makes preferences. It appears that imprinting evolved in a stepwise, adaptive way, with each gene or cluster becoming imprinted as the need arose.

How we come to express the genes of one parent over the other is now better understood through studying the platypus and marsupial wallaby -- and it doesn't seem to have originated in association with sex chromosomes.

New research has shed light on the evolution of genomic imprinting, in which specific genes on chromosomes that have been inherited from one parent are expressed in an organism, while the same genes on the chromosome inherited from the other parent are repressed.

Imprinting arises from some kind of 'epigenetic memory' -- modifications to the DNA from one parent, such as the way the chromosomal material is packaged, that do not allow particular genes to be expressed. The reasons why imprinting evolved are not understood. It is known, however, that different patterns of imprinting occur in different classes of mammals, with some classes of mammals exhibiting the phenomenon and others not. Because the evolutionary relationship between mammals is well documented, patterns of imprinting in the different genomes can provide important clues about the evolution of imprinting.

One theory is that imprinted genes arose from sex chromosomes, which can be epigenetically 'shut down' to control the dosage of genes. Another idea is that imprinting arose from an ancestral chromosome that was itself imprinted.

The results of the distribution studies suggest that imprinted genes were not located on an ancestrally imprinted chromosome, nor were they associated with sex chromosomes. Rather it appears that imprinting evolved in a stepwise, adaptive way, with each gene or cluster becoming imprinted as the need arose.

The study is also important because despite its evolutionary importance, the platypus remains cytogenetically under-characterised. By linking specific sequences to particular chromosomes, the researchers have pinpointed important markers on the platypus genome.

Extra Gene Copies Were Enough To Make Early Humans' Mouths Water

2007-09-06T11:22:00.000-05:00

Finding: humans carry extra copies of the salivary amylase gene and starches may have been the food that made population growth possible.

What does this mean?
Humans have many more copies of this gene than any of their ape relatives and they use the copies to flood their mouths with amylase, an enzyme that digests starch. The finding bolsters the idea that starch was a crucial addition to the diet of early humans, and that natural selection favored individuals who could make more starch-digesting protein.

If one works - make more, don't wait for improvement to occur
Extra gene copies are an easy way for evolution to ramp up expression of a protein, why wait for chance mutations to improve gene function? Natural selection can favor duplicate copies of a gene that already works well, and enzyme production will increase.

Other primates eat mainly ripe fruits containing very little starch. A new ability to supplement the diet with calorie-rich starches could have fed our large brains and opened up new food supplies that fueled our unrivaled colonization of the planet, Dominy said.

How the research was done

The researchers sampled saliva from 50 European-American undergraduates and found as many as 15 copies of the amylase gene per person. By comparison, all 15 chimpanzees they sampled had exactly 2 copies each. Students with more copies of the gene also had higher concentrations of the enzyme in their spit.
Diet -Next, studies involving groups of humans with differing diets took place. They found a similar correspondence between the amount of starch in a group's diet and the average number of amylase gene copies its individuals possessed.
The Yakut of the Arctic, whose traditional diet centers around fish, had fewer copies than the related Japanese, whose diet includes starchy foods like rice. The same pattern existed for two Tanzanian tribes--the Datog, who raise livestock, and the Hadza, who primarily gather tubers and roots. The Hadza had more copies of the gene than the Datog.
Even though they're closely related genetically and live close to each other geographically, still there are big differences in the average number of copies in these populations. Geography and relatedness are not driving these differences. It's diet.
In pondering human origins anthropologists have long been stumped by the sudden, nearly simultaneous increases in our brain size, body size, and geographic range, while other apes changed little. Early humans simply must have found some source of better nutrition to make it all possible.

The big mystery in paleoanthropology
The big mystery of paleoanthropology is what changed? Why did our earliest human ancestors deviate from the pattern we see in living apes to evolve this incredibly large brain, which is very energetically expensive to maintain, and to become a much more efficient bipedal organism?

Starch - not meat
For years, the answer was thought to be the growing importance of meat in the diet, as early humans learned to hunt. But even when you look at modern human hunter-gatherers, meat is a relatively small fraction of their diet. They cooperate with language, use nets; they have poisoned arrows, even, and still it's not that easy to hunt meat. To think that, two to four million years ago, a small-brained, awkwardly bipedal animal could efficiently acquire meat, even by scavenging, just doesn't make a whole lot of sense.

Some anthropologists have begun to suspect the new source of food consisted of starches, stored by plants in the form of underground tubers and bulbs--wild versions of modern-day foods like carrots, potatoes, and onions. Once early humans learned to recognize tuber-forming plants, they opened up a food source unknown to other apes.

Starches and the Homo Erectus
Tubers may have been especially critical for the first widely successful humans, known as Homo erectus, who may have learned to cook with fire. Since this idea was proposed, about a decade ago, researchers have been looking for evidence to support or refute it--no easy task for a theory that concerns highly perishable food consumed two million years ago. But in work earlier this year, scientists found that animals eating tubers and bulbs produce body tissues with an isotopic signature that matches what has been measured in early fossilized humans.

The new discovery is a separate line of evidence pointing to the importance of starch in human beginnings. When early humans mastered fire, cooking starchy vegetables would have made them even easier to eat, he added. At the same time it would have made extra amylase gene copies an even more valuable trait.

We roast tubers, and we eat French fries and baked potatoes," Dominy said. "When you cook, you can afford to eat less overall, because the food is easier to digest. Some marginal food resource that you might only eat in times of famine, now you can cook it and eat it. Now you can have population growth and expand into new territories.

Genome Study Shines Light On Genetic Link To Height

2007-09-04T21:19:00.000-05:00

Finding: Inheriting the 'C'-containing copy of the HMGA2 gene -- a 'C' written in the DNA code instead of a 'T' often makes people taller: one copy can add about a half centimeter in height while two copies can add almost a full centimeter.

Why do tall people get to be tall?
Nearly a century ago it was thought that many genes likely influence how tall a person grows, but little progress was made to find the genes, until now.

Methodology
Using a new "genome-wide association" method, the research team searched the human genome for single letter differences in the genetic code that appear more often in tall individuals compared to shorter individuals. By analyzing DNA from nearly 35,000 people, the researchers zeroed in on a difference in the HMGA2 gene -- a 'C' written in the DNA code instead of a 'T'. This gene change can account for the difference in tallnes.

The study is the first convincing result that explains how DNA can affect normal variation in human height. Height is a complex trait, involving a variety of genetic and non-genetic factors, it can teach us about the genetic framework of other complex traits -- such as diabetes, cancer and other common human diseases.

In addition to being a textbook example of a complex trait, height is a common reason children are referred to medical specialists. Although short stature by itself typically does not signal cause for concern, delayed growth can sometimes reflect a serious underlying health condition.

DNA accounts for 90% of growth
Nearly 90% of the variation in height among most human populations can be attributed to DNA. The remainder is due to environmental and lifestyle factors, such as nutrition. Although a few genes have been uncovered through studies of rare, single-gene stature disorders, most do not seem to be associated with height in the general population. Recent advances, including the completion of the HapMap project and the availability of large-scale research tools, enabled the scientists to take a systematic approach to understand how common genetic differences can impact a person's height.

After scrutinizing the initial data, the scientists identified a single letter change -- known as a single nucleotide polymorphism or SNP -- in the HMGA2 gene as the most promising result. They collaborated with additional researchers to study this SNP through a second phase of analysis that encompassed nearly 30,000 individuals: adults and children from the Avon Longitudinal Study of Parents and Children (ALSPAC) and the Exeter Family Study of Childhood Health (EFSOCH),

Unlike most other complex traits, height is something that can be easily defined and measured in very large numbers of people. Soon the scientific community will have access to many more large-scale genomic data sets, making it feasible to identify additional genes involved in height."

What the Gene does
While surprisingly little is known about how genes hardwire humans for growth, some initial clues have already surfaced as a result of the HMGA2 discovery. The gene is active in the first months of fetal growth and shuts off shortly before birth, suggesting it orchestrates growth-related events early in human development. Moreover, it appears to influence the overall longitudinal growth of the skeleton, as scientists found that the T-to-C change in the gene's DNA sequence correlates with an increased length of both the limbs and spine in young children. HMGA2 has also been implicated in certain forms of cancer. Thus, further studies may help dissect the relationship between normal growth and the deranged growth central to cancer.

A new way to study evolutionary paths

2007-09-03T21:30:00.000-05:00

Finding: There is a new way to shed light on macroevolutionary research.
A team of scientists developed a novel methodological approach in evolutionary studies. Using the method they named 'genomic phylostratigraphy', its authors shed new and unexpected light on some of the long standing macroevolutionary issues, which have been puzzling evolutionary biologists since Darwin.

Problems with using Fossils
The only direct method of research in evolutionary history involves analyzing the fossil remains of once living organisms, excavated in various localities throughout of the world. However, that approach often cannot provide the full evolutionary pathway of some species, as it requires uncovering of many fossils from various stages of its evolutionary history. As the fossil record is imperfect, the evolution research fundamentally hinges on luck factor in discovering the adequate paleontological sites.

New Approach - Snapshots of the evolutionary path
However, the RBI team proposed a novel and interesting approach to bypass this obstacle. Namely, they suggested that the genome of every extant species carries the ‘snapshots’ of evolutionary epochs that species went trough. What's even more important, they also developed the method which enables evolution researchers to readily convert those individual 'snapshots’ into the full-length 'evolutionary movie' of a species.

The approach on flies
Applying their new methodology on the fruit fly genomic data they tackled some of the most intriguing evolutionary puzzles - some of which distressed even Darwin himself. First, they demonstrated that parts of the living organism exposed to the environment – so called ‘ectoderm’ - are more prone to evolutionary changes. Further, they explained the evolutionary origin of the ‘germ layers’, the primary tissue forms that form during the first days after the conception of a new animal, and from which subsequently all other tissues are developed. Finally, they discovered the potential genetic trigger for the 'Cambrian explosion', a major global evolutionary event on the planet, when some 540 million years ago almost all animal forms known today suddenly 'appeared'.

Ancient Pig DNA Study Sheds New Light On Colonization Of Europe By Early Farmers

2007-09-02T16:37:00.000-05:00

Finding: The earliest domesticated pigs in Europe, which many archaeologists believed to be descended from European wild boar, were actually introduced from the Middle East by Stone Age farmers.

The research involved mitochondrial DNA from ancient and modern pig remains. Its findings also suggest that the migration of an expanding Middle Eastern population, who brought their 'farming package' of domesticated plants, animals and distinctive pottery styles with them, actually 'kickstarted' the local domestication of the European wild boar.

While archaeologists already know that agriculture began about 12,000 years ago in the central and western parts of the Middle East, spreading rapidly across Europe between 6,800 -- 4000BC, many outstanding questions remain about the mechanisms of just how it spread. This research sheds new and important light on the actual process of the establishment of farming in Europe.

Many archaeologists believe that farming spread through the diffusion of ideas and cultural exchange, not with the direct migration of people. However, the discovery and analysis of ancient Middle Eastern pig remains across Europe reveals that although cultural exchange did happen, Europe was definitely colonised by Middle Eastern farmers.

A combination of rising population and possible climate change in the 'fertile crescent', which put pressure on land and resources, made them look for new places to settle, plant their crops and breed their animals and so they rapidly spread west into Europe.

The domestic pigs that were derived from the European wild boar must have been considered vastly superior to those originally from Middle East. In fact, the European domestic pigs were so successful that over the next several thousand years they spread across the continent and even back into the Middle East where they overtook the indigenous domestic pigs. For whatever reason, European pigs were the must have farm animal.

The Orchid may have been around 84 million years

2007-08-29T23:44:00.000-05:00

Finding: The Orchid survived the great extinction 65 million years ago, and flourished to over 25,000 species.
Which came first the mammal or the flower? Well it looks like flowermay have ruled after the dinosaurs died out. So say researchers who have discovered the first fossil orchid, a 15 to 20-million-year-old pollen specimen encased in amber, in the Dominican Republic.

The Orchidaceae family boasts the largest of all flowering plants, but it is poorly understood, because until now there has been no fossil record of its history. Previous speculations put the plants' first appearance at about 45 million years ago.

Harvard University researchers and colleagues compared genetic information from the fossilised Meliorchis caribea with modern-day plants and reconstructed an evolutionary tree. It suggests that the first orchids bloomed about 84 million years ago.

Those that survived the mass extinction 65 million years ago then rapidly proliferated, leading to today's 25,000 or so species.

The Orchid family

Orchidaceae or the Orchid family is the largest and most diverse of the flowering plant (Angiospermae) families, with over 800 described genera and 25,000 species.

Orchids, like the grasses and the palms, which they resemble in some ways—for instance the form of their leaves—are monocotyledons. They have one cotyledon, or embryonic leaf, in contrast to the two of most flowering plants.

Orchids are world wide in distribution, occurring in every habitat, except Antarctica and deserts. The great majority are to be found in the tropics, mostly Asia, South America and Central America. They are found above the Arctic Circle, in southern Patagonia and even on Macquarie Island, close to Antarctica.

I'm here & I'm not going away: World's Oldest Bacteria Found Living In Permafrost

2007-08-28T14:13:00.000-05:00

Finding: A research team has for the first time ever discovered DNA from living bacteria that are more than half a million years old. Never before has traces of still living organisms that old been found.

What significance does this have?

The exceptional discovery can lead to a better understanding of the aging of cells and might even cast light on the question of life on Mars. All cells decompose with time. But some cells are better than others to postpone the decomposing and thus delay aging and eventually death. And there are even organisms that are capable of regenerate and thereby repair damaged cells. The DNA of these cells are very interesting to the understanding of the process of how cells break down and age.

How the discovery was made

The research team, which consists of experts in, among other things, DNA traces in sediments and organisms, have found ancient bacteria that still contains active and living DNA. So far, it is the oldest finding of organisms containing active DNA and thus life on this earth. The discovery was made after excavations of layers of permafrost in the north-western Canada, the north-eastern Siberia and Antarctica.

Near Death
The project is about examining how bacteria can live after having been frozen down for millions of years. Other researchers has tried to uncover the life of the past and the following evolutionary development by focusing on cells that are in a state of dead-like lethargy.

Still active
We, on the other hand, have found a method that makes is possible to extract and isolate DNA traces from cells that are still active. It gives a more precise picture of the past life and the evolution towards the present because we are dealing with cells that still have a metabolistic function -- unlike "dead" cells where that function has ceased.

After the fieldwork and the isolation of the DNA, the researchers compared the DNA to DNA from a worldwide gene-bank in the US to identify the ancient material. Much in the same way the police compares fingerprints from a crime, the researchers were able to place the DNA more precisely and to place it in a context.

Impact on Darwinian evolution
There is a very long way, of course, from our basic research towards understanding why some cells can become that old. But it is interesting in this context to look at how cells break down and are restored and thus are kept over a very long period. The researchers' methods and results can be used to determine if there was ever life on Mars the way we perceive life on earth.
And then there is the grand perspective in relation to Darwin's evolution theory. It predicts that life never returns to the same genetic level. "But our findings allows us to post the question: are we dealing with a circular evolution where development, so to speak, bites its own tail if and when ancient DNA are mixed with new?

Come Together: Social Habits Of Cells May Hold Key To Fighting Diseases

2007-08-28T13:45:00.001-05:00

Finding: Research into Systems Biology have discovered that networking in living cells may determine whether a cell cause diseases.

Scientists in Manchester are working to change the social habits of living cells -- an innovation that could bring about cleaner and greener fuel and help fight diseases such as cancer and diabetes.

As part of a new £18 million project spanning six countries, The Manchester Centre for Integrative Systems Biology at The University of Manchester will spearhead important new research into an emerging field of science and engineering known as Systems Biology*.
Scientists have recently discovered that networking in living cells may determine whether a cell causes diabetes or cancer or helps to maintain our health.

By adjusting and modifying the way cells network, researchers believe it's possible to adjust the behaviour of living cells and reduce the chances of disease occurring.

Using this approach Manchester researchers working on the Systems Biology of Microorganisms (SysMO) research programme will also drive a project that looks at how the yeast used in the production of beer and bread can be turned into an efficient producer of bioethanol.
Other work to be carried out in Manchester includes the investigation of 'lactobacilli'. Some of these occasionally turn into flesh-eating bacteria or cause human diseases such as strep throat and rashes, whereas others are completely safe and are used in the production of cheeses and yoghurts.

It's hoped the work will lead not only to greater understanding of how 'wrong' networks lead to disease, but also to the production of drugs and other foods more efficiently and safely.
Academics will also look at 'pseudomonads' -- soil bacteria that may make people ill but can also be used to degrade nasty compounds in the environment, or to create compounds now being made by chemical industries.

Thermophilic Organisms
Researchers will also focus on 'thermophilic' organisms that live naturally in hot springs, and examine how their networks enable them to survive high and varying temperatures. It's hoped that this research will reveal how to make any living organism cope better with extreme conditions. It may also lead to better performance of detergents and cosmetics.

This is a unique opportunity to begin to understand how networking contributes to the functioning of living cells inside and outside our bodies. It enables us to integrate the best groups from six European countries and will address four concrete issues of energy, the disease-benefit balance, white biotechnology and robustness.

What is Systems Biology?
Systems Biology combines molecular biology and mathematics, which have traditionally been seen as the equivalents of fire and water. This type of research is still viewed as controversial by some in the scientific community.

But researchers involved in SysMO believe this approach will allow them to obtain a very large set of mathematical equations that describe living cells. This may then allow those cells to be engineered in a number of ways, with numerous benefits in the field of medicine and in the commercial world.

A new Approach to bioscience
Systems biology is a new approach to bioscience that combines theory, computer modelling and experiments. It is revolutionising how bioscientists think and work and will make the outputs on their work more useful, and easier to use in industry and policymaking. Instead of using the traditional biology approach of observation and experiment, systems biology uses computer simulations and modelling to process results, design new, more quantitative experiments and generate predictive solutions

Ancient bacteria could point to life on Mars

2007-08-27T18:35:00.000-05:00

Finding: Harsh conditions ok for the survival of Bacteria
Ancient bacteria are able to survive nearly half a million years in harsh, frozen conditions, researchers said on Monday in a study that adds to arguments that permafrost environments on Mars could harbor life. The findings also represent the oldest independently authenticated DNA to date obtained from living cells and could offer clues to better understand ageing.

How long can it live?
"When it can live half a million years on Earth it makes it very promising it could survive on Mars for a very long time," Willerslev said. "Permafrost would be an excellent place to look for life on Mars."

Where did the bacteria live?
The international team, which also included researchers from the United States, Canada, Russia and Sweden, tested the microbes living up to 10 meters deep in permafrost collected from Northern Canada, the Yukon, Siberia and Antarctica.

Repair operations
When a cell dies, its DNA fragments into pieces but the samples studied were all very long strands -- evidence the cells were able to continuously repair genetic material and remain alive.

These cells are active cells repairing DNA to deal with continuous degradation of the genomes. It is the same thing with humans.

What is the mechanism of repair
The scientists do not yet know the mechanism driving the continuous repair but the cells survived by eating nutrients like nitrogen and phosphate lodged in the permafrost.
This is interesting because the temperature on Mars is much colder with more stable temperatures, representing an even better environment to sustain this kind of life, he added.
While most scientists think our neighbor in the solar system is lifeless, the discovery of microbes on Earth that can exist in environments previously thought too hostile has fuelled debate over extraterrestrial life.

Researchers had known these microbes could survive for a long time without food but until now there was little agreement on how long they could live. Knowing this, and eventually pinpointing the key to this longevity, may also help scientists better understand the ageing process, he added.

It is interesting to see why some cells can survive for a very long time, that can be a key for understanding ageing.

One Species, Many Genomes

2007-08-26T21:11:00.000-05:00

Finding: Adaptation to the environment may produce many genomes for the same species

Adaptation to the environment has a stronger effect on the genome than anticipated. Faster growth, darker leaves, a different way of branching - wild varieties of the plant Arabidopsis thaliana are often substantially different from the laboratory strain of this small mustard plant, a favorite of many plant biologists.

Discovering which detailed differences distinguish the genomes of strains from the polar circle or the subtropics, from America, Africa or Asia is being investigated for the first time by research teams from Tübingen, Germany, and California. The results were surprising: The extent of the genetic differences far exceeds the expectations for such a streamlined genome, as the scientists write in Science magazine.

To track down the variation in the genome of the different Arabidopsis strains, the researchers compared the genetic material of 19 wild strains with that of the genome of the lab strain, which was sequenced in the year 2000. Using a very elaborate procedure, they examined every one of the roughly 120 million building blocks of the genome.

For their molecular sleuthing they used almost one billion specially designed DNA probes. The result of this painstaking analysis: on average, every 180th DNA building block is variable. And about four percent of the reference genome either looks very different in the wild varieties, or cannot be found at all. Almost every tenth gene was so defective that it could not fulfill its normal function anymore!

From one - many
Results such as these raise fundamental questions. For one, they qualify the value of the model genomes sequenced so far. There isn’t such a thing as the genome of a species. The insight that the DNA sequence of a single individual is by far not sufficient to understand the genetic potential of a species also fuels current efforts in human genetics.

Still, it is surprising that Arabidopsis has such a plastic genome. In contrast to the genome of humans or many crop plants such as corn, that of Arabidopsis is very much streamlined, and its size is less than a twentieth of that of humans or corn—even though it has about the same number of genes. In contrast to these other genomes, there are few repeats or seemingly irrelevant filler sequences. That even in a minimal genome every tenth gene is dispensable, has been a great surprise.

What does the analysis show?
Detailed analyses showed that genes for basic cellular functions such as protein production or gene regulation rarely suffer knockout hits. Genes that are important for the interaction with other organisms, on the other hand, such as those responsible for defense against pathogens or infections, are much more variable than the average gene. The genetic variability appears to reflect adaptation of local circumstances. It is likely that such variable genes allow plants to withstand dry or wet, hot or cold conditions, or make use of short and long growing seasons.

Such genome analyses of unprecedented details will allow a much better understanding of local adaptation, and this was indeed one of the main reasons for conduction the study. By extending these types of studies to other species we hope to help breeders to produce varieties that are optimally adapted to rapidly changing environmental conditions.

New methods - Direct Sequencing

How environment and genome interact is also the goal of new methods. While the technology used so far can only identify genes that have changed or are lost relative to the reference genome, direct sequencing of the genome of wild strains will allow the detection of new genes. The plan is to decipher the genomes of at least 1001 Arabidopsis varieties. A new instrument, with which the entire genome of a plant can be read in just a few days, is already available. Still missing are the computational algorithms to interpret the anticipated flood of data.

How Snakes Survive Starvation and still grow

2007-08-25T20:30:00.000-05:00

Finding: Snakes are efficient users of their metabolism even lowering it to survive without food.
Starving snakes employ novel survival strategies not seen before in vertebrates, according to research conducted by a University of Arkansas biologist. These findings could be used in conservation strategies to determine the health of snake populations.

These animals take energy reduction to a whole new level.
While scientists knew that some snake species could survive for up to two years without a meal, no studies have examined the physiological changes that take place when a snake goes for prolonged periods without food. Scientists three snake species – the ball python, the ratsnake and the western diamondback rattlesnake – to study their responses to prolonged periods without food.

The 62 snakes studied went about six months without eating – a time period that could well be duplicated in the wild, where food supplies can be scarce. Scientists then looked at physiological, compositional and morphological changes in the snakes.

Low energy demands and can grow even without food
The results showed that the snakes could lower their standard metabolic rates, some by up to 72 percent.

Snakes already had low energy demands. Scientists now know that they can go lower.
Another surprising finding: The snakes continued to grow despite the lack of food – a counterintuitive finding, but a measurement that again does not appear in the research literature.

Meaning what?
This suggests that there must be a strong selective advantage to growing longer. It also means the snakes have become extremely efficient in their ability to use available resources.

To illustrate the strategies employed by snakes to combat starvation, look at an economic analogy of supply and demand.

When you’re cut off from resources, you are an organism that still needs to expend energy. The “demand” end is met by decreasing their metabolic rate. The “supply” end must be met by frugal use of resources they have at hand for energy, which comes from within.
The body composition of snakes includes water, ash, protein, fats and carbohydrates. Scientists found that the snakes used up selected fat stores first during starvation, but he also found crucial differences between the snake species. The ratsnakes, which typically have a more abundant rodent supply in their natural environment, began to break down proteins faster than the pythons or rattlesnakes.

The protein use was higher in the snakes less well adapted to starvation. Snakes are relatively new on the world scene, having been around for about 100 million years. Yet they currently comprise about half of all reptile species.

Snakes appear to be very evolutionarily successful. Understanding the physiology that allows them to succeed in low-energy environments will help scientists further their understanding of the snakes’ evolution and their adaptation to their current ecosystems.

Why Were Prehistoric Insects Huge?

2007-08-25T12:28:00.000-05:00

Finding: More than 300 million years ago, there was 31 to 35 percent oxygen in the air. That means that the respiratory systems of the insects could be smaller and still deliver enough oxygen to meet their demands, allowing the creatures to grow much larger.

A recent study was conducted to help determine why insects, once dramatically larger than they are today, have seen such a remarkable reduction in size over the course of history. Insects breathe through a network of air filled tubes that deliver oxygen directly to the cells. These tracheal tubes, especially in the leg, take up more room in larger beetles.

There were hundreds of ideas to explain the small size, but none of them could be proven. One theory was that it was an insect’s respiratory system that limited its size. So a study was launched an extensive study using beetles and fruit flies.

The study, much of which was performed at Illinois’ Argonne National Laboratory, involved the examination of various beetles’ respiratory systems, using new x-ray beam technology to help determine how they breathe.

It's not just genes that sets us apart

2007-08-24T12:15:00.001-05:00

U.S. geneticists believe they know why humans are so different from chimps, although sharing most of the same genes: it's how the genes are used.

After studying the regulatory sequences adjacent to 6,280 genes in the DNA of chimps, humans and the rhesus macaque, scientists determined the differences center mainly on traits involving brains and diet. It's rather like the same set of notes being played in very different ways.

Positive selection, the process by which genetic changes that aid survival and reproduction spread throughout a species, has targeted the regulation of many genes known to be involved in the brain and nervous system and in nutrition.

Although many studies have looked for significant differences in the coding regions of genes relating to neural system development and failed to find any, the Duke team believes its study is the first to take a genome-wide look at the evolution of regulatory sequences in different organisms.

The Chimp Genome Reveals A Retroviral Invasion In Primate Evolution

2007-08-23T19:20:00.000-05:00

What functions are done in DNA?
It's been known for a long time that only 2%-3% of human DNA codes for proteins. Much of the rest of our genomes is often referred to as junk DNA. It consists of retroelements: genomic elements that are transcribed into RNA, reverse-transcribed into DNA, and then reinserted into a new spot in the genome. Human endogenous retroviruses make up one class of these retroelements. Retroviruses can insert themselves into the host's DNA in either soma (nonreproductive cells) or the germline (sperm or egg).

If the virus invades a nonreproductive cell, infection may spread, but viral DNA will die with the host. A retrovirus is called endogenous when it invades the germline and gets passed on to offspring. Because endogenous retroviruses can alter gene function and genome structure, they can influence the evolution of their host species. Over 8% of our genome is made of these infectious. It is these remnants infections that scientists believe occurred before Old World and New World monkeys diverged (2.5 billion years ago).

Are there any retrovirus in other animals but not found in Humans?
In a new study scientists scanned finished chimpanzee genome sequence for endogenous retroviral elements, and found one called PTERV1 that does not occur in humans. Searching the genomes of a subset of apes and monkeys revealed that the retrovirus had integrated into the germline of African great apes and Old World monkeysbut did not infect humans and Asian apes (orangutan, siamang, and gibbon). This undermines the notion that an ancient infection invaded an ancestral primate lineage, since great apes (including humans) share a common ancestor with Old World monkeys.

Are the sequences common to an ancestor?
Scientists have found over 100 copies of PTERV1 in each African ape (chimp and gorilla) and Old World monkey (baboon and macaque) species. They compared the sites of viral integration in each of these primates and found that few if any of these insertion sites were shared among the primates. It appears then that the sequences have not been conserved from a common ancestor, but are specific to each lineage.

What is PTERV1?
PTERV1 contains three structural genes: gag, pol, and env and regulatory sequences called long terminal repeats (LTRs). To further explore the evolutionary history of the retroviral elements, the scientists compared the sequences of gag and pol, as well as the LTR sequences, for each infected primate species. The sequence history, they discovered, did not comport with the established evolutionary history of the primates themselves. Divergence between macaque and baboon was significantly greater than between gorilla and chimp even though slightly more evolutionary time separates gorilla and chimp than macaque and baboon.

What does a retrovirus produce?
When a retrovirus reproduces, identical copies of LTR sequences are created on either side of the retroviral element; the divergence of LTR sequences within a species can be used to estimate the age of an initial infection. Scientists estimate that gorillas and chimps were infected about 34 million years ago, and baboon and macaque about 1.5 million years ago. The disconnect between the evolutionary history of the retrovirus and the primates, they, could be explained if the Old World monkeys were infected by "several diverged viruses" while gorilla and chimpanzee were infected by a single, though unknown, source.

Not all primates are infected
As for how this retroviral infection bypassed orangutans and humans, the authors offer a number of possible scenarios but dismiss geographic isolation: even though Asian and African apes were mostly isolated during the Miocene era (spanning 24 to 5 million years ago), humans and African apes did overlap.

It could be that African apes evolved a susceptibility to infection, for example, or that humans and Asian apes evolved resistance. A better understanding of the evolutionary history and population genetics of great apes will help identify the most likely scenarios. And knowing how these retroviral elements infiltrated some apes while sparing others could provide valuable insights into the process of evolution itself.

Human Ape Split may have occurred 13 million years ago

2007-08-22T11:32:00.000-05:00

Ten million-year-old fossils discovered in Ethiopia show that humans and apes probably split six or seven million years earlier than widely thought, according to landmark study released Wednesday.

The handful of teeth from the earliest direct ancestors of modern gorillas ever found -- one canine and eight molars -- also leave virtually no doubt, the study's authors and experts said, that both humans and modern apes did indeed originate from Africa.

The near total absence to date of traces on the continent of apes from this period had led many scientists to conclude that the shared line from which humans and living great apes emerged had taken a long evolutionary detour through Eurasia.

The Last common ancestor - out of Africa
But the study, published in the British journal Nature, demonstrates that the Last Common Ancestor (of both man and ape) was strictly an African phenomenon. Tthe fossils are viewed as "a critically important discovery," a view echoed by several other scientists who had read the paper or seen the artifacts.

The most startling implication of the find, the scientists agree, is that our human progenitors diverged from today's great apes -- including gorillas, orangutans and chimpanzees -- several million years earlier than widely accepted research based on molecular genetics had previously asserted.

The trail in the hunt for physical evidence of our human ancestors goes cold some six or seven million years ago.

The anthropological past
Orrorin was discovered in Kenya in 2000 and nicknamed "Millennium Man" and it goes back 5.8 to 6.1 million years, while Sahelanthropus, found in 2001 later in Chad, is considered by most experts to extend the human family tree another one million years into the past.

Beyond that, however, fossils of early humans from the Miocene period, 23 to five million years ago, disappear. Fossils of early apes especially during the critical period of 14 to eight million years ago were virtually non-existant -- until now.

"We know nothing about how the human line actually emerged from apes," the authors of the paper noted.
But the new fossils, dubbed "Chororapithecus abyssinicus" by the team of Japanese and Ethiopian paleoanthropologists who found them, place the early ancestors of the modern day gorilla 10 to 10.5 million years in the past, suggesting that the human-ape split occurred before that.

The line: Orangutan, Gorrilla, Chimpanzee - Human

There is broad agreement that chimpanzees were the last of the great apes to split from the evolutionary line leading to man, after gorillas and, even earlier, orangutans.

Conventional scientific wisdom, based on genetic "distances" measured by molecular geneticists, had placed the divergence between chimps and humans some five to six million years ago. Orangutans are thought to have parted company with our ancestors 13 to 14 million years ago.
"If the new discovery is in the gorilla lineage, then this will definitely substantially push back the split time between apes and humans," Halie-Selassie at Kent State told AFP.

When did the split take place?
The scientists leading the team that found the fossils calculated that the human-orangutan split could easily have been as old as 20 million years.

They determined that the teeth belonged to gorilla ancestors based on unique shared characteristics of the molars, which had evolved for a diet of fibrous foods such as stems and leaves.

The match is not exact, however, and could prompt some scientists to challenge the findings.
The teeth fragments, found in barren scrubland some 170 kilometres (100 miles) east of Ethiopia's capital Addis Ababa, almost went unnoticed.
Asfaw recalled the chance discovery.

"It was our last day of field survey in February 2006, and our sharp-eyed field assistant, Kampiro, found the first ape tooth, a canine," he said.
"He picked it up and showed it to me, and I knew that this was something new -- Ethiopia's first fossil great ape."

How close are we to creating artificial life?

2007-08-21T21:17:00.000-05:00

Around the world, a few scientists are trying to create life from scratch ...they're getting closer.
Some experts expect an announcement within 3 to 10 years from someone in the now little-known field of "wet artificial life."

That first cell of synthetic life—made from the basic chemicals in DNA— i.e., creating protocells has the potential to shed new light on our place in the universe, this will remove one of the few fundamental mysteries about creation in the universe and our role.

It's going to be a big deal and everybody's going to know about it, we're talking about a technology that could change our world in pretty fundamental ways—in fact, in ways that are impossible to predict.

Several scientists believe man-made life forms will one day offer the potential for solving a variety of problems, from fighting diseases to locking up greenhouse gases to eating toxic waste.
Bedau figures there are three major hurdles to creating synthetic life:

A container, or membrane, for the cell to keep bad molecules out, allow good ones, and the ability to multiply.
A genetic system that controls the functions of the cell, enabling it to reproduce and mutate in response to environmental changes.
A metabolism that extracts raw materials from the environment as food and then changes it into energy.

some of the steps under way will be : creating a cell membrane then getting nucleotides, which are the building blocks of DNA to form a working genetic system.

His idea is that once the container is made, if scientists add nucleotides in the right proportions, then Darwinian evolution could simply take over. It's a cleaver ploy we may not be smart enough to design things, but we let evolution do the hard work and then we figure out what happened.

One scientist is attacking that problem by going outside of natural genetics. Normal DNA consists of four bases—adenine, cytosine, guanine and thymine (known as A,C,G,T)—molecules that spell out the genetic code in pairs. Instead of 4 pair, one scientist is trying to add eight new bases to the genetic alphabet.

DNA Replication Behavior- from Low to High

2007-08-20T11:53:00.000-05:00

DNA replication is considered the heart of the DNA process. Recent findings by scientists at the Genome Institute of Singapore (GIS) may be paving the way for more efficient analyses and tests related to the replication of cells, and ultimately, to the better understanding of human biology, such as in stem cell research.

Where does duplication occur?
Faithful duplication of the genome ensures that daughter cells inherit a complete set of genetic materials identical to parent cells. This duplication occurs in the section of the cell cycle known as the S-phase. Extensive research on the budding yeast revealed that the replication process is started at hundreds of origins in the S-phase.

Is the replication process efficient?
Many previous studies focused on the replication timing and initiation sites, but not on the efficiency. So it was believed that the replication efficiency decreased as the S-phase progressed.
But now they know better. In a recently published paper scientists described how they were able to determine the replication timing and efficiency at the various loci in the genome. Now replication efficiency is low at the beginning of the S-phase, but the efficiency increased at the later stage of this phase.

Genes changes linked to an organism's survivability

2007-08-19T11:39:00.000-05:00

Studies from biologists have found that a simple interaction between just two genes determines the patterns of fur coloration that camouflage mice against their background, protecting them from many predators. The work marks one of the few instances in which specific genetic changes have been linked to an organism's ability to survive in the wild.

What does the research show?
The work shows how changes in just a few genes can greatly alter an organism's appearance. It also illuminates the pathway by which these two genes interact to produce distinctive coloration. The result is that now there's reason to believe this simple pathway may be evolutionarily conserved across mammals that display lighter bellies and darker backs, from mice to tuxedo cats to German Shepherds.

What was studied?
Researchers studied Peromyscus, a mouse that is the most widespread mammal in North America. Within the last several thousand years, these mice have migrated from mainland Florida to barrier islands and dunes along the Atlantic and Gulf coasts, where they now live on white sand beaches. In the process, the beach mice's coats have become markedly lighter than that of their mainland brethren.

What did the research show?
Nature provides a tremendous amount of variation in color patterns among organisms, ranging from leopard spots to zebra stripes; these patterns help individuals survive. But it has been difficult to understand how these adaptive color patterns are generated. The research helped identify the genetic changes producing a simple color pattern that helps camouflage mice inhabiting the sandy dunes of Florida's Gulf and Atlantic coasts. These 'beach mice' have evolved a lighter pigmentation than their mainland relatives, a coloration that helps camouflage them from predators that include owls, herons, and hawks.

Previous research has shown that such predators, all of which hunt by sight, will preferentially catch darker mice on the white sand beaches, providing a powerful opportunity for natural selection to evolve increased camouflage.

Which Genes were involved?
Through a detailed genomic analysis, researchers identified two pigmentation genes, for the melanocortin-1 receptor (Mc1r) and an agouti signaling protein (Agouti) that binds to this receptor and turns it off. Conclusion: A single amino-acid mutation in Mc1r gene can weaken the receptor's activity, or a mutation in the Agouti gene can increase the amount of protein present without changing the protein's sequence, also reducing Mc1r activity and yielding lighter pigmentation.

Research findings
What do the genes do? Both genes affect the type and amount of melanin in individual hairs. If both genes are turned on, the mouse is dark in color. If a mutation occurs, which changes either gene this leads to a somewhat blonder mouse, but when the combination of mutations occur in both genes this produces a mouse very light in color.

Does temperature affect evolution?

2007-08-19T00:59:00.001-05:00

Where does evolution occur in a temperate area or in a hot area?
It turns out that new species originate more frequently in temperate regions than in the tropics. Steamy and wet they may be, but tropical hotspots of biodiversity are not the hottest as far as evolution is concerned. Scientists looked at pairs of "sister" species - pairs that evolved from an immediate common ancestor - and estimated how long ago the sisters diverged from each other.

In hot areas
Near the equator, sister species split on average about 3.4 million years ago, whereas those in temperate regions split roughly 1.7 million years ago. It is true that tropical zones do host a greater species diversity, but that's because fewer species have gone extinct there.

In cold areas
In very high latitudes - above the Arctic Circle - the sister species split even more recently, with none of those reviewed separating more than a million years ago.

Dramatic climatic changes in temperate regions over the past hundreds of thousands of years may have driven evolution harder.

Retracing Evolution With First Atomic Structure Of An Ancient Protein

2007-08-17T14:54:00.001-05:00

Can you show any evidence of evolution by looking at the atomic structure of a protein? Scientists say yes. They have determined for the first time the atomic structure of an ancient protein. This reveals in detail how genes evolved their functions.

Recreating ancient progenitors of protein
The workhorses of the cell are proteins. But a detailed study showing how proteins have evolved has not been possible and has eluded evolutionary biologists. This was due because ancient proteins have not been available for direct study. So scientists used state-of-the-art computational and molecular techniques to re-create the ancient progenitors of an important human protein.

Looking at the Atoms
The challenge: can you use only the atoms of ancient proteins to trace changes in the atomic architecture? Two different groups of scientists worked together to trace how changes in the protein's atomic architecture over millions of years caused it to evolve a crucial new function -- uniquely responding to the hormone that regulates stress.

The ultimate level of detail
This is the ultimate level of detail and you can see exactly how evolution tinkered with the ancient structure to produce a new function that is crucial to our own bodies today.
The researchers focused on the glucocorticoid receptor (GR), a protein in humans and other vertebrates that allows cells to respond to the hormone cortisol, which regulates the body's stress response. The scientists' goal was to understand the process of evolution behind the GR's ability to specifically interact with cortisol.

How it was done
Scientists used computational techniques and a large database of modern receptor sequences to determine the ancient GR's gene sequence from a time just before and just after its specific relationship with cortisol evolved. The ancient genes existed more than 400 million years ago -- were then synthesized, expressed, and their structures determined using X-ray crystallography, a state-of-the art technique that allows scientists to see the atomic architecture of a molecule.

Results
The structures allowed the scientists to identify exactly how the new function evolved. They found that just seven historical mutations, when introduced into the ancestral receptor gene in the lab, recapitulated the evolution of GR's present-day response to cortisol. They were even able to deduce the order in which these changes occurred, because some mutations caused the protein to lose its function entirely if other "permissive" changes, which otherwise had a negligible effect on the protein, were not in place first.

In evolutions playground, Humans left chimps behind

2007-08-16T15:34:00.001-05:00

What is the difference between humans and chimps?
MICRO-RNA, the snippets of RNA that control gene expression, could be the difference.

Variation between individuals, in traits ranging from pigment to behaviour, is the raw material of evolution. The difference can be down to very subtle changes: the genes involved may code for exactly the same proteins but make them at other places and times. So could micro-RNA be the determining factor?

What do Micro-RNA's do?
Micro-RNAs are a mere 22 nucleotides long and block the messenger RNA that translates DNA into protein. This allows them to fine-tune gene expression. Micro-RNA has only recently been studied because it was discovered withing the last few years. But it has been shown to determine what cell types form, and, for example, whether sheep become muscular or puny.

Now, researchers at the Hubrecht Laboratory in Utrecht, the Netherlands, have combed painstakingly through the RNA in human and chimp brains, and found 447 new micro-RNAs, more than doubling the number discovered so far. Some were expressed very rarely.

What accounts for the differences between Chimps and Humans?
The brain has 10,000 cell types, so it is possible because of all these micro-RNAs. Many were unique to chimps and humans, and some only to humans. So while we share most of our DNA with chimps, the small genetic changes through Micro RNA that fine-tune its expression might account for the radical differences in our brains. This is the playground of evolution.

Why Are There So Many More Species Of Insects? Because Insects Have Been Here Longer

2007-08-15T07:14:00.000-05:00

J. B. S. Haldane once famously quipped that "God is inordinately fond of beetles." Results of a study suggest that this fondness was expressed not by making so many, but rather by allowing them to persist for so long.

In a study appearing in the American Naturalist, scientists show that many insect groups like beetles and butterflies have fantastic numbers of species because these groups are so old. In contrast, less diverse groups, like mammals and birds, are evolutionarily younger.

This is a surprisingly simple answer to a fundamental biological puzzle. They accumulated data from molecular phylogenies (which date the evolutionary relationships among species using genetic information) and from the fossil record to ask whether groups with more species today had accumulated species at faster rates.

Animals as diverse as mollusks, insects, spiders, fish, amphibians, reptiles, birds, and mammals appear to have accumulated new species at surprisingly similar rates over evolutionary time. Groups with more species were simply those that had survived longer. Their analyses thus identify time as a primary determinant of species diversity patterns across animals.

Given the unprecedented extinction rates that the Earth's biota are currently experiencing, these findings are also quite sobering. We are rapidly losing what it has taken nature hundreds of millions of years to construct, and only time can repair it.

Stopping Cancer Cells From Reading Their Own DNA

2007-08-14T17:01:00.001-05:00

There are three primary ways of treating cancer at present, and these have fundamentally changed little in 30 years. If there are tumours, surgery can be used to cut out the cancerous tissue, It the cells are malignang, then radiation therapy is the method. Chemotherapy is used to keep the cancerous cells from dividing. But a new approach using a molecular technique to prevent interference in the DNA copy metric.

The approach uses the information from tumor cells and block them from copying DNA sequences. This will cut off the genetic information flow that tumours need to grow.

The enzyme called Topoisomerase IB plays a key role in some of the molecular metric involved in the processes of DNA and RNA copying during cell division. These are responsible for reading the genetic code and making sure it is encoded correctly in the daughter cell. In healthy cells this process works normally, but in cancer cells it does not work well at all. If one can specifically target these molecular metrics in cancer cells one can prevent the cancer cells from growing into a larger tumor.

This molecular copying metric is constructed largely out of proteins. It works by effectly walking along the DNA double helix reading the genetic code so that it can be copied accurately into new DNA during division. Other components is responsible for slicing and assembling the DNA itself.

Genetic evidence for evolution

2007-08-13T17:22:00.001-05:00

If there is evolution, is there any evidence for it at the genetic level?

The answer is yes. Scientists who have been studying genetic changes occurring in the human genome over the last 15,000 to 100,000 years, have found that over this relatively short period of time the human genome has changed by as much as 10 percent.

Evidence withing the Human Genome
A scientific study identifies small, gradual changes (microevolution) that demonstrate species divergence from a common ancestor millions of years ago (macroevolution). The study makes human-to-human comparisons throughout the complete human genome instead of comparing a human to mice or chimpanzees. By this procedure humans can be seen changing over time, due to our ancestors being exposed to – among other selective pressures – different climates as they spread across the globe.

Evidence for Change
Early humans had problems digesting lactose after the age of one. Lactose is an enzyme found in milk. Befor the domestication of animals (about 20,000 years ago) humans could not digest milk after infancy. But some time after humans began migrating and domesticating animals, humans began to develop a gene that allowed us to tolerate consuming milk into adulthood. In other words as humans have populated the world, there has been strong selective pressure at the genetic level for mutations that allow digestion of a new food source or tolerate infection by a pathogen that the population may not have faced in a previous environment.

Trilobite variation declined after the Cambrian Explosion

2007-08-12T12:00:00.000-05:00

From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on. So a highly variable species will evolve more rapidly than others.

Is that statement true?

Paleontologists for decades have suspected that highly variable species evolved more rapidly than others, and several studies have approached questions pertaining to it--but this is the first to convincingly document it in any group.

Most studies have focused on the variability that occurs between species rather than within them, but one recent study analyzed 982 species of trilobites, ancient relatives of spiders and horseshoe crabs.

When did Trilobites live?
Trilobites have been extinct for over 250 million years. They were once the most common creatures in the world's oceans. They ranged in size from nearly microscopic to more than a foot long, though most of the 17,000 known species measured from one to four inches. They were very diverse.

Trilobites were among the creatures that emerged 500 million years ago, during what paleontologists call "the Cambrian explosion," or "the Cambrian radiation." Before this time, life on Earth was limited mostly to bacteria, algae, single-celled organisms and only the simplest animal groups. But during the Cambrian Period, more complex creatures with skeletons, eyes and limbs emerged with amazing suddenness.

What does the research show?

So the question is what fueled the Cambrian radiation, and why was that event so singular? The answer: It appears that organisms displayed "rampant" within-species variation in the 'warm afterglow' of the Cambrian explosion, but not later.

A study focused on actively evolving characteristics during the Cambrian time. The trilobite head alone displayed many different characteristics. There were differences in ornamentation, number and placement of spines, and the shape of head segments. Overall, approximately 35 percent of the 982 trilobite species exhibited some variation in some aspect of their appearance that was evolving. But more than 70 percent of early and middle Cambrian species exhibited variation, while only 13 percent of later trilobite species did so.

Conclusion: There's hardly any variation in the post-Cambrian. Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn't vary in the post-Cambrian trilobites.

Why does variation withing a species decline through time?
Paleontologists have proposed two ideas to account for why variation within species declined through time.

1)Ecological. In the very early Cambrian seas, fewer organisms existed than today, which meant that they faced less competition for food. You didn't really have to be tightly specialized to make a living in the Cambrian. But as evolution gave rise to more varieties of organisms, ecological communities became more diverse. You had to be very fine-tuned to your particular niche to make a living and to beat out competitors for a limited resource. More organizms in the ocean meant that there must be more genetic variation in order to survive.

2) The genomic hypothesis offers a second explanation for the decline of within-species variation over time. According to this idea, internal processes in the organism were the key factors. Various developmental processes interact with one another to control the growth and formation of body parts as any organism progresses from egg to adult.

It's been suggested that early on in evolutionary history, in the Cambrian Period, the degree to which these different developmental processes interacted with each other within the organism was a lot less. As a result, the constraints on what the final organism looked like were relatively low.

A Complete primate gene study

2007-08-11T10:43:00.001-05:00

U.S. scientists have completed what's believed the most comprehensive assessment of gene copy number variations across human and non-human primate species.

A study provides an overview of genes and gene families that have undergone major copy number expansions and contractions during approximately 60 million years of evolutionary time.

Primates first appeared on Earth about 90 million years ago, and today roughly 300 primate species exist. To survey the differences in gene copy number among those species, researchers used DNA microarrays containing more than 24,000 human genes to perform comparative genomic hybridization experiments. DNA comparisons were made using samples from humans with those of nine other primate species: chimpanzee, gorilla, bonobo, orangutan, gibbon, macaque, baboon, marmoset, and lemur. This allowed them to identify specific genes and gene families that, through evolutionary time, have undergone lineage-specific copy number gains and losses.
The scientists said they discovered differences potentially associated with cognition, reproduction, immune function, and susceptibility to genetic disease.

Shrinking Genomes

2007-08-10T21:12:00.000-05:00

Scientists generally believe that insertions of retroelements, or"jumping genes," once established in a population, are irreversible and are maintained throughout evolution. This unidirectional theory of retroelement evolution, which calls for ever-expanding genome size, is challenged by work that appears in the September issue of Genome Research.

Deletion of Genome elements from Rhesus to Humans
Researchers performed a whole-genome comparison of the human, chimpanzee, and Rhesus monkey sequences, and they identified 37 instances where a retroelement was present in Rhesus (a more primitive primate species) but absent in either humans or chimpanzees. This indicated that these retroelements had been deleted during the evolution of the more recent primate species.

Mediation by short identical sequences
Intriguingly, the scientists further demonstrated that these deletions were mediated by short identical sequences that flank the retroelements. They extended the study to random, non-retroelement sequences and showed that deletions caused by short identical DNAsequences were a widespread genomic phenomenon. In fact, thousands of insertion-deletion sequence differences between the human and chimpanzee genomes were likely mediated by short identical sequences.

The work strongly suggests an important role for short, non-adjacent, identical segments of DNA in genomic deletions and it lends insight into deletion mechanisms that help to counterbalance genome expansion in primates.

Conclusion: Genes don't get bigger with more complex species, they get smaller.

Ecological Biogeography

2007-08-09T11:54:00.001-05:00

Unlike historical biogeographers, ecological biogeographers make extensive use of current population information. They study the ways in which species develop and interact in the presence of other species and different environments. Many ecological biogeographers mimic Darwin: they study island communities as a type of experimental system to test hypotheses about species development.

Much of ecological biogeography is concerned with species richness, the number of different species an area supports. In specific, ecological biographers have developed the species richness equilibrium model.

The model begins with an uninhabited "island" that can be either a literal island or an area of like habitats completely surrounded by unlike habitats. All species available to colonize the new area are called the "species pool." As more and more new species enter the new area, the species pool becomes smaller and smaller, and the immigration rate (the probability that any given species moving into the area will be a new species) decreases.

At the same time, the island becomes more and more crowded and supplies become scarce, causing the extinction rate to increase. The point at which the extinction rate and the immigration rate balance is called the equilibrium point. The model predicts that changes in extinction and immigration rates will tend toward the equilibrium point, which is different for every island, depending on resources and degree of separation from other areas. This is shown graphically in the figure below.

Historical biogeographers

2007-08-08T17:41:00.001-05:00

Historical biogeographers also make use of a tool called an area cladogram. This diagram is made by taking a taxonomic tree, which shows various species and their relatedness, and replacing the species names with the geographic location in which those species are found. This new tree allows scientists to determine how the differences in environments have effected the evolutionary history of different species of common origin. A sample area cladogram is shown below:

The Dynamics Of Transcription In Living Mammalian Cells

2007-08-07T15:26:00.000-05:00

Transcription is the transfer of DNA’s genetic information through the synthesis of complementary molecules of messenger RNA. It forms the basis of all cellular activities. But the dynamics of the process is not well understood. Scientist do not know how efficient it is or how long it takes. But researchers at the Albert Einstein College of Medicine have measured the stages of transcription in real time. Their unexpected and surprising findings have fundamentally changed the way transcription is understood.

The study focused on the ensyme responsible for transcription, RNA polymerase II. During transcription, numbers of RNA polymerase II molecules assemble on DNA and then synthesize RNA by sequentially recruiting complementary RNA nucleotides.

3 phases of Transcription

To visualize the transcription process, the researchers used living mammalian cells, each of which contained 200 copies of an artificial gene that they had inserted into one of the cell’s chromosomes. Then, by attaching fluorescent tags to RNA polymerase II, they were able to closely monitor all three phases of the transcription process:

binding of the enzyme molecules to DNA,
initiation (when the enzyme links the first few RNA nucleotides together) and
elongation (construction of the rest of the RNA molecule).

The result of the observation
As they observed the RNA polymerase II molecules attaching to DNA and making new RNA, they saw many cases where enzyme molecules attached — and then promptly fell off.

Transcription is inefficient
During the first two phases the transcription process is really inefficient. It turns out that only one percent of polymerases that bind to the gene actually remain on to help in synthesizing an RNA molecule.

Transcription may be inefficient for a reason. All the factors needed for transcription have to come together at the right time and the right place, so there’s a lot of falling off and adding on of polymerases until everything is precisely coordinated.

The researchers observed that

the binding phase of transcription lasted six seconds and
initiation phase lasted 54 seconds.
the elongation phase lasted 517 seconds (about eight minutes).

Pausing and Elongation
The “lead” polymerase on the growing polymerase II enzyme sometimes “paused” for long periods, retarding transcription in the same way that a Sunday driver on a narrow road slows down all traffic behind him.
But in the absence of pausing, elongation proceeded much faster — about 70 nucleotides synthesized per second — than has previously been reported.

These two phenomena — pausing and rapid RNA synthesis during elongation — may be crucial for regulating gene expression. Once the ‘paused’ polymerase starts up again, in a very short time you could synthesize a new batch of messenger RNA molecules that might suddenly be needed for making large amounts of a particular protein.

Biogeorgraphic Distributions

2007-08-06T15:58:00.001-05:00

The geographic distributions of species can be of a number of types
Consider the distribution of three species of toucans in the genus Ramphastos.
• Endemic distributions
Two of the species, R. vitellinus and R. cluminatus , have endemic distributions: they are limited to a particular area. Endemic distributions can be more or less widespread.
• Cosmopolitan distributions
The extreme case of species that are found on all continents of the globe are called cosmopolitan. The pigeon, for example, is found on all continents except Antarctica; on a strict definition, the pigeon (pictured opposite) might not be allowed to be cosmopolitan, but the term is usually intended less strictly - and the pigeon is called a cosmopolitan species.
• Disjunct distributions
Other species, like R. ariel , are not confined to a single area, but are distributed in more than one region with a gap between them: these are called disjunct distributions.
Maps can be drawn for a taxonomic group at any Linnaean level: just as species have geographic distributions, so too do genera, families, orders. Biogeography aims to explain the distributions of the higher taxa too, in addition to those of species; and different explanatory processes are often appropriate at different levels.
Short-term movements of individuals influence the distributions of populations and species, whereas slower acting geological processes may control the biogeography of higher taxa.

Genetic Chromosome Breaking

2007-08-05T16:54:00.000-05:00

Researchers in genome stability have observed that many kinds of cancer are associated with areas where human chromosomes break. Its been hypothesized, but not proven, that slow or altered replication led to the chromosomes breaking.

But now a study at Tufts University two molecular biologists have used yeast artificial chromosomes to prove that hypothesis. They found a highly flexible DNA sequence that increases fragility and stalls replication, which then causes the chromosome to break.

Cancer Causing Areas
The area in question is an area that has a tumor suppressor gene -- a gene whose absence can cause tumors. If you delete that gene or delete part of that gene so it doesn't work anymore, that can lead to tumors. The fact that there is fragility in the same region that this gene is located is a bad coincidence. Fragility can cause deletions and deletions can cause cancer, so you want to understand the fragility because that might be what's causing cancer.

DNA structure leads to fragility
Past research had predicted the flexibility of the DNA helix in this particular common fragile site by calculating the twist angle between consecutive base pairs and found that there were several points of high flexibility, suggesting that the flexibility was connected to the fragility.
Freudenreich and Zhang used yeast artificial chromosomes to test this idea because it allowed them to look at the region in a more detailed way than looking at human chromosomes and to monitor the replication process. They expect the results will be similar when tested in human cells based on previous research using yeast chromosomes.

How the research was conducted
Two regions of predicted high flexibility, plus a region near a cancer cell breakpoint and a control region were tested to see whether any of these regions could cause breakage of a yeast chromosome. They found that one did. This is the first known sequence element within a human common fragile site shown to increase chromosome breakage. What is intriguing is that the sequence that breaks, in addition to being flexible, is predicted to form an abnormal DNA structure." The result is that when replication stalls, chromosomes can break.

How did the chromosomes break?
From past studies, they hypothesized that breakage was connected to replication. Replication is just the duplication of DNA in side the cells as they divide, the DNA inside those cells must duplicate. The research showed that the chromosomes were breaking because replication was stalled.

The problem arises when they do not heal correctly and instead are deleted or rearranged, Cancer cells almost always have some sort of deletions or rearrangements. Something is wrong with their chromosomes that then messes up the genes that are in those areas.

Replication process stalled
The researchers also noticed that this particular sequence was an AT-rich region, where the DNA was composed mostly of the bases adenine (A) and thymine (T), rather than the other bases cytosine (C) or guanine (G). Freudenreich and Zhang found the longer the AT-repeat, the more the replication process was stalled, something they would like to follow up on with further research.

Some researchers believe that the longer the repeat, the more the abnormal the DNA structure forms, and the more fragile the chromosome becomes. What is still up in the air is whether people with longer repeats are more prone to deleting that tumor suppressor gene and getting cancer as a result. Does this correlation between chromosome breaks and cancer has a medical consequence.

BioGeorgraphy and Range Limitations?

2007-08-03T09:31:00.000-05:00

What factors limit the geographic range of a species?
Ecological factors
The distributional limits of a species are set by its ecological attributes:

• Fundamental niches
If a species is able to tolerate a certain range of physical factors such as temperature, humidity, and so on and it has the capacity in theory live anywhere within these tolerance limits, this is its fundamental niche.

• Realized niches - Competing species
However, if there are competing species that occupy part of this range the competition may be too strong to permit both species to exist. The near extinction of the red squirrel in Britain due to competition from the grey squirrel is a good example. Each species' realized niche will be smaller than its physiology makes possible. In other words each species will occupy a smaller range than it otherwise would in the absence of competition.

Genetic Factors Strongly Shape How Peers Are Chosen

2007-08-02T15:43:00.001-05:00

The company we keep may be more influenced by genetics than previously thought. Researchers report that as individuals develop, genes become more important in influencing how they choose their peer groups. The findings offer insight into which individuals may be at risk for future substance use or other externalizing behaviors such as conduct and antisocial personality disorder.

The study involved 1,800 male twin pairs from mid-childhood to early adulthood, between 1998 and 2004.

Through a series of interviews, researchers found that genetic factors increasingly impact how male twins make choices as they mature and develop their own social groups. Their finding include that the path from genes to behaviors like drug use and antisocial behaviors is not entirely direct or biological. Rather an important part of this pathway involves the genetics, which influences our own social environment, which in turn impacts on our risk for a whole host of deviant behaviors. Results demonstrate clearly that a complete understanding of the pathway from genes to antisocial behaviors, including drug abuse, has to take into account self-selection into deviant versus benign environments. The effects of peers in adolescence can be quite powerful, either encouraging or discouraging deviant behaviors. Peers also provide access to substances of abuse.

Molecular evolution

2007-08-01T12:38:00.001-05:00

Molecular evolution is the process of evolution at the scale of DNA, RNA, and proteins.

Some of the key topics that spurred development of the field have been

the evolution of enzyme function,
the use of nucleic acid divergence as a "molecular clock" to study species divergence,
and the origin of non-functional or junk DNA.

Recent advances in genomics, including whole-genome sequencing, high-throughput protein characterization, and bioinformatics have led to a dramatic increase in studies on the topic. In the 2000s, some of the active topics have been the role of gene duplication in the emergence of novel gene function, the extent of adaptive molecular evolution versus neutral drift, and the identification of molecular changes responsible for various human characteristics especially those pertaining to infection, disease, and cognition.

Relative Sizes

2007-07-31T06:55:00.000-05:00

In reality, however, many tiny individual units called cells make up these objects and almost all other components of plants and animals. The average human body contains over 75 trillion cells, but many life forms exist as single cells that perform all the functions necessary for independent existence. Most cells are far too small to be seen with the naked eye and require the use of high-power optical and electron microscopes for careful examination.

Repetitive DNA

2007-07-30T08:42:00.000-05:00

Repetitive DNA studies of many organisms has revealed that a large proportion of eukaryotic genomes consists of repetitive DNA.

For example in the kangaroo rat

the sequence (AAG) is repeated 2.4 billion times,

the sequence (TTAGGG) is repeated 2.2 billion times and

the sequence (ACACAGCGGG) is repeated 1.2 billion times.

What it does is unclear. These are called junk DNA sequences.

Note that junk is stuff you don't throw away because it might be useful some day;
garbage is stuff you don't want so you throw it away.

These sequences might have some function we don't know about so they have been called junk DNA. The fact that such sequences seem to accumulate in genomes has lead to the notion that repetitive DNA is selfish DNA, since the sequence makes additional copies of itself within the genome decoupled from the reproduction rate of the host.

The Chloroplast Genome

2007-07-29T09:02:00.000-05:00

The genome of the chloroplasts found in Marchantia polymorpha contains 121,024 base pairs in a closed circle.

A chloroplast is the organelle that carries out photosynthesis and starch grain formation. It is a chlorophyll-containing organelle in plants that is the site of photosynthesis.

These make up some 128 genes which include:

duplicate genes encoding each of the four subunits (23S, 16S, 4.5S, and 5S) of the ribosomal RNA (rRNA) used by the chloroplast
37 genes encoding all the transfer RNA (tRNA) molecules used for translation within the chloroplast.

Some of these are represented in the figure by black bars.
4 genes encoding some of the subunits of the RNA polymerase used for transcription within the chloroplast (the blue ones)
a gene encoding the large subunit of the enzyme ribulose bisphosphate carboxylase oxygenase (RUBISCO)

9 genes for components of photosystems I and II
6 genes encoding parts of the chloroplast ATP synthase
genes for 19 of the ~60 proteins used to construct the chloroplast ribosome