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

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.

New Route For Heredity Bypasses DNA

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

Greenland: Oldest DNA Shows Warmer Planet

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.

DNA is a vestige of formation of liquid crystal order

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.

Is Junk DNA really Junk?

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.

Stopping Cancer Cells From Reading Their Own DNA

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 Chromosome Breaking

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.

Molecular evolution

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.

The Chloroplast Genome

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

The Mitochondrial Genome

What does the genome of human mitochondria look like?

It contains 16,569 base pairs of DNA organized in a closed circle.

These encode:

• 2 ribosomal RNA (rRNA) molecules
• 22 transfer RNA (tRNA) molecules (shown in the figure as yellow bars; two of them labeled)
• 13 polypeptides.

The 13 polypeptides participate in building several protein complexes embedded in the inner mitochondrial membrane.

• 7 subunits that make up the mitochondrial NADH dehydrogenase
• 3 subunits of cytochrome c oxidase
• 2 subunits of ATP synthase cytochrome b

All these gene products are used within the mitochondrion, but the mitochondrion also needs proteins encoded by nuclear genes. These proteins are synthesized in the cytosol and then imported into the mitochondrion.

Mitochondrial DNA and Human Evolution

"Where do we come from?" This has been one of the fundamental questions asked by humans for thousands of years. Is it philosophical? Religious? Anthropological? Depending on your view point it determines how you look for the answer. From an anthropolical viewpoint physical anthropologists have been looking for answers by studying morphological characteristics of bones or skeletons that have been uncovered, such as skull shape, of the fossilised remains of our human and proto-human ancestors.

Molecular Anthropology - New study
Molecular anthropologists have been comparing the DNA of living humans of diverse origins to build evolutionary trees. Because mutations occur in our DNA at a regular rate and will often be passed along to our children these differences or polymorphisms, as they are termed, show that on a genotypical level make us all unique and analysis of these differences will show how closely we are related. But using these techniques, however, have led to opposing views on how modern humans evolved from our archaic ancestors.

Two competing theories

The two main hypotheses agree that Homo erectus evolved in Africa and spread to the rest of the world around 1 - 2 million years ago; it is regarding our more recent history where they disagree.

1) Multi-regional evolution
This theory suggests that modern humans evolved from archaic forms, such as Neanderthal and Homo erectus. They originated concurrently in different regions of the world supported by physical evidence, such as the continuation of morphological characteristics between archaic and modern humans. But this is the minority view.

2) Out of Africa view
This view holds that modern humans evolved in Africa before colonizing the world. The recent African origin view holds that modern humans evolved once in Africa between 100 - 200 thousand years ago. Subsequently modern humans colonised the rest of the world without genetic mixing with archaic forms supported by the majority of genetic evidence. This is now the majority view.

Which theory is right?

One way to answer this is by looking at mitochondrial DNA. While DNA is present inside the nucleus of every cell of our body it is the DNA of the cell's mitochondria that has been most commonly used to construct evolutionary trees.

What is Mitochondrial DNA?
This is DNA found outside of the cell nucleus. They are inherited only from the mother, which allows tracing of a direct genetic line. They also have their own genome of about 16,500 bp. Each contains 13 protein coding genes, 22 tRNAs and 2 rRNAs. Fewer samples is required vecause they are present in large numbers in each cell. And they have a higher rate of substitution that is mutations where one nucleotide is replaced with another than nuclear DNA making it easier to resolve differences between closely related individuals. They don't recombine. Mitochnondrial DNA doesn't recombine with other Mitochondrial DNA. The process of recombination which occurs in nuclear DNA mixes sections of DNA from the mother and the father creating a strained genetic history.

So Mitochondrial DNA tells us what?
The out of Africa theory has support from Mitochondrial DNA. But these conclusions have been criticised for a lack of statistical support. This is due to the fact that a small section of the Mitochondrial DNA called the D-loop, about 7% of the genome has been used for the studies. Statistically, the out of Africa theory is not well founded. Here is why. Three main problems with data from the D-loop section have been identified:
back mutation - sites that have already undergone substitution are returned to their original state
parallel substitution - mutations occur at the same site in independent lineages
rate heterogeneity - there is a large difference in the rate at which some sites undergo mutation when compared to other sites in the same region; data shows evidence of 'hot spots' for mutation.
But there has been a study that has fixed some of these problems. First the mitochondrial genome is one of the first genomes to be sequenced in its entirety. However it was not until recently that technological advances allowed large sequences to be obtained easily and a study of any appreciable size using whole genomes was undertaken. There were some clear advantages.

First the D-loop was evolving at a much higher rate. And this greater length of the complete genome allowed for the analysis of twice as many informative polymorphic sites (sites that show the same polymorphism in at least two sequences). Second the numbers of back- and parallel mutations found outside of the D-loop were practically zero. So this had no effect. And finally the rate of evolution of the rest of the genome was even between different genes and also between the different gene complexes; it was also even between different sites

Conclusions
The phylogenetic tree reconstructed with this latest dataset of complete mitochondrial genomes provides support to the 'recent African origin' theory. Chronologically speaking by determining the substitution rate of the genomic sequences, it is possible to derive dates for points on the tree and build a chronology of events in the evolution and migration of our species.

The most important date, in relation to the competing evolutionary theories, is the time when all the sequences coalesce into one -- the 'mitochondrial Eve.' That date about 171,500 years ago fits very well with that proposed in the recent African origin hypothesis.

On the other hand, in order to accept multi-regionality, a much older date would have had to be used; this would represent the common ancestor of Homo erectus and not Homo sapiens.

DNA and Genome transfer from one Bacterial Species to Another

Scientists are now able to take the genetic material from one bacterial species and transfer it to another, basically swapping their Genomes. The implications for synthetic custom - built bugs is astonishing.

The experiment marks the attempt to re-engineer a living cell with a view to one day developing micro-organisms that were different than how nature designed them. Some could be used for biofuels, cleaning up toxic waste, sequestering carbon or other applications.

Transplanting the entire genome from one species to another and having it work is the equivalent of taking a MacIntosh computer and making it a PC by inserting a new piece of software.

For the first time it is possible to insert an intact genome into a host organism and have that second organism express the original-foreign DNA.

But what is next? To create a synthetic genome and then transplant that one into a host organism.

From an evolutionary perspective, it would indicate that if man could do something like this, it would be possible for it to also occur in nature. In other words, the variation that we see in nature, may have come about with the co-mingling of genomes from different species.

The Tree of Life: Archaea, Bacteria, and Eukaryota

If we are to talk about evolution, then we first have to talk about what kind of life exists on earth. The tree of life is made up of three distinct branches. The Eukaryota, Bacteria, and Archaea.

Eukaryotes
The eukaryotes include animals (humans), plants and fungi and a rich variety of micro-organisms also known as protists. The protists include parasites which can be biologically speaking very successful and they can compromise the environment of entire countries. The Eukaryotes are identified and distinguished from other forms of life by the presence of nuclei and the presence of a cytoskeleton.


Bacteria
Bacteria are microscopic organisms whose single cells do not have a membrane-bounded nucleus nor other membrane-bounded organelles like mitochondria and chloroplasts. Another group of microbes, the archaea, meet these criteria but are so different from the bacteria in other ways that they must have had a long, independent evolutionary history since close to the dawn of life.

Bacteria are maligned because of the human and animal disease they cause. However, some, like the actinomycetes, produce antibiotics such as streptomycin and nocardicin. Others have different functions. They live symbiotically in the guts of animals (including humans) or elsewhere in their bodies, or on the roots of certain plants, converting nitrogen into a usable form. They are seen everywhere. For instance, bacteria give the tangy taste in yogurt and the sour in sourdough bread. Bacteria are responsible for the break down of dead organic matter. The are also an important base of the food web in many environments. Life on earth may be complex but it appears that this was the basis of all early life. The oldest fossils known, nearly 3.5 billion years old, are fossils of bacteria-like organisms.

Archaea
Archaea are microbes and most live in extreme environments. Those that do are called extremophyles. Other Archaea species are not extremophiles and live in ordinary temperatures and salinities.

When these microscopic organisms were first discovered in 1977, they were considered bacteria. It became apparent however, that they were not when their ribosomal RNA was sequenced. The sequencing showed that they were not closely relationed to the bacteria but were instead more closely related to the eukaryotes.

Archaea are a much different and simpler form of life. They may also be the oldest form of life on Earth. Because they requires neither sunlight for photosynthesis as do plants, nor oxygen as to animals. Archaea absorbs CO2, N2, or H2S and gives off methane gas as a waste product the same way humans breathe in oxygen and breathe out carbon dioxide.

Archaeans may be the only organisms that can live in extreme habitats such as extremely hot thermal vents or hypersaline water. They appear to be extremely abundant in environments that are hostile to all other life forms.

The Helicase Enzyme and its effect on DNA replication

How do the two DNA strands separate? Is is active or passive? Is there some internal mechanism or is there some force from the outside?

Cornell University researchers have found that an enzyme called Helicase is the active force behind the unravelling of the two DNA strands.

This is a significant find because it explains how the separation occurs, from an outside force; but it also shows that defects in helicases can influence many human diseases, from a tendency or predisposition to cancer to premature aging.

The research occured by tying down the two strands separately and introducing the helicase enzyme. They found that the separation occured very quickly and they were able to measure the tension of the strand using a laser beam.

One effect on this is that the process of replication is understood, so one can see the effect it can have on genetic mutations. If the enzyme makes a poor separation, the DNA copy will not be a replica of the original. Hence a mutation will occur.
http://www.sciencedaily.com/releases/2007/07/070703172500.htm

DNA Polymerase and Genome stability

Why are genomes unstable? What factors in the environment can cause a DNA strand to be replicated? Well the answer comes from the fact that an enzyme called DNA polymerase epsilon plays a significant role in replicating DNA in higher organisms such as yeast and perhaps even humans.

An enzyme is a protein that acts as a catalyst for chemical reactions. A protein is a molecule made up of a sequence of amino acids. They are the unit molecular building blocks of proteins. They occur in a certain sequence. And there are 20 main amino acids in the proteins of living things, and the properties of a protein are determined by its particular amino acid sequence.
In 1953 Watson and Crick first described the structure of DNA, they also pointed out that the two DNA strands, referred to as leading and lagging, pair with each other to form the now familiar double helix.

Researchers at the Umeå University in Sweden found that in baker's yeast, the primary role in replicating the leading strand of DNA was the enzyme called DNA polymerase epsilon. This enzyme was found to be a key determinant providing genome stability and it also is responsible for cellular responses to DNA damage resulting from exposures to environmental stress.

In the mid 50's researchers discovered the first enzymes capable of replicating DNA. This is an important process required to make new genomes for cell division. So the enzymes, called DNA polymerases, were shown to copy the two DNA strands in only one of two possible directions. One strand of the double helix must be replicated first by a dedicated leading strand polymerase, then it was followed by replication from the lagging strand by a different polymerase.

In lower organisms like the E. coli bacteria one DNA polymerase can accomplish both tasks. But with humans and related higher organisms, such as baker's yeast, the DNA polymerase function is more complicated. Some discoveries, which emerged from the human genome project, indicate that the human genome encodes at least 15 DNA polymerases that can copy DNA. Their tasks appear to be different. Some are thought to perform genomic replication, but others operate under special circumstances, such as to repair DNA damage resulting from environmental exposures.

Which came first? The Egg came first

This is one of those questions which is supposed to confound evolutionists because it gets to the heart of the matter so quickly.

Chickens lay eggs. Chickens come from eggs. Without the egg, there would be no chicken. Without the chicken there would be no egg.

So which came first? The chicken or the egg.

If the chicken evolved it had to evolve from something. But if that's the case, wouldn't it have evolved from an egg? But the egg already has all of its own genetic material so it couldn't have changed or mutated. It would be in a state of finality...so it can only produce one animal, the chicken. So the chicken couldn't have evolved from an other species only from the egg. And the egg already has all of the genetic material necessary to create a chicken. So the chicken and egg are already in their final states of development. Moreover, they are already in their first state of development. The chicken can only lay chicken eggs, the chicken eggs can only produce chickens. So there is no way that the chicken or egg could have evolved.

That argument only works because it assumes that the egg genetic material cannot be modified. The answer is that it can. There can be many contributing factors that mutate or change the egg. Radiation, external temperature variations, missing genetic cell instructions, protein development that did not work right, RNA carrying instructions that are not fully implemented in creating proteins. And if these variations continue over a long period of time a small instruction change can have large effects over time.

The egg is very fragile from an external point of view, but also internally. The chicken did come from an egg, but the first egg did not come from a chicken. No it came from an animal closely resembling a chicken, but the egg is a genetic mutation. And over a long period of time the egg's genetic material took on a form that we recognize today - the Chicken.

What this means is that over long period of time, there are no static life forms, all have the capacity to mutate and change.

For a different take see:
http://www.word-detective.com/howcome/chickenoregg.html

The Origins of the domesticated cat

This was a great story I came across. It's about the origin of the domesticated cat. Like many of you, I was under the impression that it was Egypt that domesticated the cat but that notion is wrong.

The domesticated cat came from the Fertile Crescent in the Middle East about 130,000 years ago when wildcats moved into villages. Scientists have discovered five modern genetic lines to the wildcat species. It shows that domestication came from the cats wanting to be with humans. Humans used them for mice patrol; they did not hunt cats, but tolerated them. The work bolsters the notion that cats became useful to humans when agriculture started forcing people to protect grain stores from rodents.

As species go Wildcats are single Old World. And five subspecies lived in Europe, sub-Saharan Africa, China, Central Asia, and the Near East. So researchers collected genetic material from almost a thousand cats, both wild and domestic, from three continents. What they were able to find was that the common ancestors of all domesticated cats lived in the Near East some 130,000 years ago.

Irreducible Complexity and Digital Organisms

What is irreducible complexity? When you have a system in biology such that the
intermediate step creates an apparently USELESS system and ONLY the FINAL step results in a USEFUL system. (From Michael Behe) That is what is meant by irreducible complexity.

For example, one not taken from nature. If you build a house. The separate parts don't add up individually into anything meaningful. At different stages, the parts are intermediate. When all of the parts are complete, you have a house.

But is there any way for a complex system to evolve?
Some recent findings a physicist at Caltech wanted to know if he could teach digital organisms how to add, when they didn't know how. Ok, what is a digitial organism? A digital organism is a self-replicating computer program that mutates and evolves. They are used as a study tool of the dynamics of Darwinian evolution. They can be used to test or verify specific hypotheses or mathematical models of evolution. This is closely related to the area of artificial life.

So what happened? At first he presented numbers to them at recurring timed intervals. They were not able to do anything at first. However, each time a digital organism replicated,on occasion one of its command lines might mutate. These mutations allowed an organism to process one of the numbers in a simple way. Thus an indifferent organism might acquire the ability simply to read a number, for example, and then produce an identical output. This would change to characteristic of the organism, from indifference to attentive.

In followups one of the things the scientist did was to reward the digital organisms by speeding up the time it took them to reproduce. If an organism could read two numbers at once, he would speed up its reproduction even more. And if they could add the numbers, he would give them an even bigger reward.

Within six months, the organisms were able to perform many number operations. They were able to evolve on order but the astonding fact was that they evolved in ways that were not initially programmed like taking input, storing it, manipulating it, and producing output.

See http://discovermagazine.com/2005/feb/ for a full story.

The Reptile to Mammal link

Noteworthy items: The period is from the Permian to the Triassic. Here are some of the evolutionary marks from fully reptile to mamalian-reptiles.

1. The switch in teeth appearance. From peg like to differentiated teeth of mammals - incisors, molars, canines.
2. The switch in jaws appearance. From 5 bones to 1 bone the dentary. In the reptilian past and present, the jaw joint lies between the articular bone at the back of the lower jaw, and the quadrate bone in the skull. But in mamals In mammals the jaw joint is between the dentary and the squamosal element of the skull.
3. The switch in the middle ear. In reptiles, as in amphibians and fishes, there is a single hearing bone, the stapes. But in mammals, including humans, have three ear bones, hammer, anvil, and stirrup or stapes.

OK. So here it is folks. More evidence that evolution can be traced and predicted. It is not an empty scientific proposition.