Tuesday, July 31, 2007

Relative Sizes

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.

Monday, July 30, 2007

Repetitive DNA

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.

Sunday, July 29, 2007

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

Saturday, July 28, 2007

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.

Thursday, July 26, 2007

Why are there variations in Genome Size?

The genome size varies considerably from one species to another. The enormity of the c. 40 000-fold range in genome size have intrigued scientists for over half a century. Scientists have asked how and why genomes vary so extensively and whether it matters. But recent findings have extended a paleogenomics dimension to these questions. By using the size of fossil dinosaur bone cells as proxies for genome size, they have attempted to trace the evolution of genome size in reptiles over 200 million years. By analyzing currently available sequence data from a range of reptiles and birds, they have aimed to shed light on the genomic makeup of dinosaur genomes.

Size doesn't matter
Back in the later 1940's estimates of genome size were made, but as data increased, it soon became clear that there was a huge disparity between organismal complexity and genome size. In other words, a complex animal does not guarantee a large genome. In fact, the lowly liverwort has 18 times as much DNA as we have, and the slimy, dull salamander known as Amphiuma has 26 times our complement of DNA'.

Where does Genome size diversity come from?
Since then, there has been much progress in understanding the molecular basis behind how genomes vary so extensively in size. It is now widely accepted that genome size diversity arises from differences in the amount of non-coding repetitive DNA (e.g. pseudogenes, retrotransposons, transposons satellite repeats, and so on.).

Where does the size of the Genome come from?
The actual genome size of an organism is determined by the differential activity of mechanisms generating increases such as retrotransposon amplification, polyploidy, segmental duplications or generating decreases like illegitimate and unequal recombination, or differences in double-strand break repair in the DNA amount.

Wednesday, July 25, 2007

The Out of Nowhere Gene

New genes have been for decades believed to created from existing genes. New research that some new genes pop up Out of Nowhere. Researchers studying the Drosophilia fruit fly have discovered a gene without peers.

A new gene, called hydra, exists in only a small number of species of Drosophila fruit flies. Research indicates that the gene was created roughly 13 million years ago, when it is believed that the melanogaster subgroup species diverged from a common ancestor.

In addition to the appearance of new gene, some early evidence also shows that this new gene is functional i.e. not "junk" DNA. and may express itself as a protein involved in late stages of sperm cell development (spermatogenesis). Other scientists working with functional genes in any species also are expressed in male testes and appear related to spermatogenesis.

One problem that the researchers are working on is how the hydra gene was created. They believe that it came out of nowhere. Some speculate that the gene may have developed from a piece of DNA junk called a transposable element which some refer to as a "jumping gene". It may have been inserted into the genome by a virus. These transposons are known to copy and insert themselves into DNA sequences. One theory is that when a transposon sits next to a gene it carries part of the gene sequence it was next to and then if it jumps to a new location it inserts that gene sequence in the new location. Current thinking is that transposable gene elements appear to have no function or may be harmful and are eliminated by natural selection, however, other researchers believe that some transposons may be a source for creating new functional genes as well.

Tuesday, July 24, 2007

Genetic variation and Genetic stability

Scientists from the Max-Plank institute and from the Salk Institute and the university of Chicago have identified which genes are prone to variation and which are stable and do not have modification. They have developed a method to sift out whole genomes for all the environmental fixes and addendums accumulated over time. What the scientists are after is the regions that are currently targeted by natural selection or have been so during the evolutionary past.

This is an exciting prospect because it lends itself to a further accumulation of evidence about how evolution works. The entire genome isn't affected, only parts of it. Scientists studying the plant the mustard weed Arabidopsis thaliana have been able to identify genetic variations in 23 strains.

Why study arabidopsis?
About 10 years ago Arabidopsis was adopted by plant scientists as an easily manipulated model for other plants because it is simple to grow in the laboratory, has a short life cycle and a small genome. Arabidopsis only has about 120 million base pairs of DNA. Compared to corn, which might have as many as 2.5 billion base pairs of DNA and the human genome with roughly 3 billion pairs, one can study it more easily.

Effects on genes
Plants are under constant threat from heat, cold, high acidity or salinity, or pathogens such as viruses and leaf-munching insects. So how do plants survive? Plants mobilize physiological and biochemical defenses for their survival. Scientists expected certain classes of genes to be highly variable due to natural selection in different environments. And now two different studies revealed precisely which gene family members indeed were shaped by evolution. In general, genes that don't change over time are under strong negative selection because they perform important housekeeping functions, while genes that vary widely such as disease resistance genes are under strong positive selection.

Monday, July 23, 2007

Out of Africa - the evolution of the Elephant

Approximatly 50-60 million years ago, mammals with the approximate size of current day pigs, were the roots of the proboscideans from which modern representatives evolved from. Based on both morphological and biochemical evidence, the manatees, dugongs, and hyraxes are the closest living relatives of the today's elephants. It is amazing to consider that given the different sizes, external appearances and the fact that they occupy completely different habitats they are all related to one another.

It has been shown that mammoths are more closely related to Asian than to African elephants. This research is the result of using the mitochondrial genome sequence, together with sequences from two African elephants, two Asian elephants, and two woolly mammoths.

The complete mitochondrial genom sequencing of the mastodon (Mammut americanum) was recently announced. This is a recently extinct relative of the living elephants that diverged about 26 million years ago.

How was the mitochondrial sequence obtained?
The sequence was obtained from a tooth dated to 50,000--130,000 years ago. The mastodon becomes the third extinct taxon for which the complete mitochondrial genome is known, joining the woolly mammoth, and several species of Moa, the giant flightless Australasian bird.

Some Results
Researchers used the mastodon data as a calibration point, lying outside the Elephantidae radiation (elephants and mammoths). This has allowed them to estimate the time of divergence of African elephants from Asian elephants and mammoths at about 7.6 million years ago, and the time of divergence between mammoths and Asian elephants at roughly 6.7 million years ago.

Common Cause for divergence?
The dates found in these divergences are very similar to the divergence time for humans, chimpanzees, and gorillas. This raises the possibility that the speciation of mammoths and elephants and of humans and African great apes had a common cause.


Saturday, July 21, 2007

Six Mechanisms of Evolution

Evolution is the process by which modern organisms have descended from ancient ancestors. Evolution is responsible for both the similarities we see across all life and the amazing diversity of that life — but exactly how does it work?

Here are some of the major factors at play:
Natural selection includes variation, differential reproduction, and heredity
Descent and the genetic differences that are heritable and passed on to the next generation;
Mechanisms of change include mutation, migration (gene flow), genetic drift, and natural selection as
Genetic Variation
genetic drift
The random nature of and the effects of a reduction in genetic variation
Coevolution how different species can affect each other’s evolution

Friday, July 20, 2007

The Tree of Life

Bacteria - Traits

  • single, circular chromosome
  • Contain operons Many of the genes in E. coli are always turned "on". Others, however, are active only when their products are needed by the cell, so their expression must be regulated.
  • Do not have Introns: This is the portion of a gene that is transcribed into RNA but is removed during the formation of the mature RNA molecule. Found in rRNA and tRNA genes as well as in genes encoding proteins. Most eukaryotic genes have introns; most genes in bacteria and archeans do not.
  • bacterial-type membrane transport channels
  • Many metabolic processes including:
  1. energy production
  2. nitrogen-fixation
  3. polysaccharide synthesis

Eukaryotic Features

DNA replication machinery
histones are the chief protein components of chromatin. They act as spools around which DNA winds, and they play a role in gene regulation.
nucleosome-like structures

  • Transcription machinery
    RNA polymerase
    TATA-binding protein (TBP)
  • Translation machinery
    initiation factors
    ribosomal proteins
    elongation factors
    poisoned by diphtheria toxin

Conclusions from this collection of traits

Many traits found in the bacteria first appeared in the ancestors of all the present-day groups.
The split leading to the archaea and the eukaryotes occurred after the bacteria had gone their own way.
However, the acquisition by eukaryotes of mitochondria (probably from an ancestor of today's rickettsias) and chloroplasts (from cyanobacteria)occurred after their line had diverged from the archaea.

Thursday, July 19, 2007

Islamic Creationist and a Very Expensive Book

Harun Yahya, a Turkish citizen has produced numerous books, videos and DVDs on science and faith, in particular what he calls the “deceit” inherent in the theory of evolution. But his latest book, “Atlas of Creation,” is turning up, unsolicited, in mailboxes of scientists around the country and members of Congress, and at science museums in places like Queens and Bemidji, Minn.

Expensive Book
At 11 x 17 inches and 12 pounds, with a bright red cover and almost 800 glossy pages, most of them very will illustrated and designed, “Atlas of Creation” is probably the largest and most beautiful creationist book to challenge Darwin’s theory. Production costs alone must have been very high, and if sold openly would easily garner $90 or more.

Mailing costs were another thing. The book was shipped by a company called SDS Worldwide, which has an office in Illinois with everything prepaid and labeled. It was distributed all over the country and reports have shown that it was distributed in France and Britain as well.


As with most creationist theories, the author glosses over the facts, the fossil record, the DNA record, the anthropological record. He does not do a very good job of addressing the very topics that other creationists have had to contend with. Some creationist dismiss evolution, but at least they do so attempting to address the issues that evolutionists challenge them with.

Irreducible complexity is, if nothing else, a concept that needs to be met face on, not ignored. Evolutionists and creationist can at least quarrel over such a concept, the same is with the DNA record. But this book does nothing to even address the Creationists claims. As a critique of Darwin, it is not very good. As a creationist book it is not very good either.

Wednesday, July 18, 2007

Skulls and Questions about the Out of Africa theory

A study published in the July 17 issue of Nature makes the case that the Origin of humans occured somewhere in south - central Africa. There is a lot of genetic variation in that region as found by looking at 4500 male fossil skulls. And as one moves away from Africa the genetic variation and skull variation ceases to be significant.


However, John Hawks a researcher from the University of Wisconsin-Madison says the paper is “mistaken" and has flaws. The biggest flaw is that the current research is largely based on skull variability. Hawks claims that one can’t find the origin of people by measuring the variability of their skulls.

He maintaines that differences in skull features are related to genetics, but genetic variation depends on how much mixing occurs with other populations. The argument for the skull variation theory is that it is a significant element in showing how features were distributed on earth. But Hawks believes that the research into the Out-of-Africa theory is based on flawed assumption from genetics papers of 10 to 15 years ago, and those assumptions wrong.

So how do you account for the skull variability and distance explanation?

One scenario is that Africa is large and ecologically diverse so cranial variation is a function of that environments. In diverse environments which would support a variety of foods such as roots, the inhabitants would need bigger and stronger jaw muscles, and in turn larger areas for muscle attachments.

In another part of the paper he notes that correcting for climate is not a good idea. Climate is the most important feature that is related to skull size. So by correcting for climate, as the researchers have done they are subtracting a major component of variability.

This debate is not over.

The Nature journal:

Tuesday, July 17, 2007

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

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.

Monday, July 16, 2007

Accuracy of Fossils and Dating Methods

Fossils provide a record of the history of life. Any attempt to make a claim about evolution always comes back at some point to the geologic time scale. But if you are going to be looking at time scales that are that old how do you get the dates? Where are the dates coming from and how is the measurement occurring? How does the fossil record work with the geologic time scale. The answer is that you use radioactive carbon dating to get the dates. But this is only the most current method. But other methods have also been used to date the fossil record.

The Fossils Sequence Record

It was the study of rock layers in England near the beginning of the 19th century that lead to the study of paleontology and from there to the study of fossils. Early geologists, at the end of the 18th and early 19th century noticed how fossils appeared in certain sequences: some fossil assemblages were always found below other assemblages, not above. This meant that the ones below were older than the ones on top.

It took a canal surveyor circa 1800, William Smith in England, who noticed that he could map out great tracts of rocks on the basis of their contained fossils. The sequences he saw in one part of the country could be matched precisely with the sequences in another. This lead to the recognition of one of the principles of geology, i.e., stratigraphy, older rocks lie below younger rocks and that fossils occur in a particular, predictable order.

The next step was for geologists began to build up the stratigraphic column. And this gave us the familiar list of divisions in the geologic time scale -- Jurassic, Cretaceous, Tertiary, and so on. Most importantly, it was recognized that each time-unit was characterized by the appearance of particular fossils. The scheme worked all round the world, without fail.

The next observation occurred when geologists noted how fossils became more complex through time. At the oldest, or deepest layer of rock there was no record of fossils, but then they noticed that simple sea creatures were found at the next higher level, then more complex ones like fishes at the next higher level and so on. Next came life on land, then reptiles, then mammals, and finally humans. One fact was soon clear, no dinosaur record could be found to coincide with a human fossil record.

So it was apparent that there was some kind of 'progress' going on. It was all clear when in 1859 Charles Darwin published his "On the Origin of Species". The 'progress' shown by the fossils was a documentation of the grand pattern of evolution through long spans of time. The accuracy of the fossil record using the stratigraphy method has been well documented. The order of appearance in a sequence is well documented, but that is not all.

Phylogeny, mathematics, and other methods used to date fossils.

Biologists now have at their disposal a variety of independent means to look at the history of life. Besides the order of fossils in the rocks, another method is the use phylogenetic trees.
Phylogenetic trees are used to show how all the species of particular groups of plants or animals relate to each other. They are drawn up mathematically, using lists of morphological (external form) or molecular (gene sequence) characters.

What is noteworthy is that modern phylogenetic trees derive no input from stratigraphy, scientific comparisons between tree shape and stratigraphy can be used to confirm the fossil record. The majority of test cases show good agreement, so the fossil record accordingly relates the same story as the molecules enclosed in living organisms.

Techniques used for Absolute Dating

All of this gets us to one of the most important physical techniques, radioactive Dating. Carbon dating in geology may be relative or absolute. One does relative dating by observing fossils sequences using the stratigraphical method. One records which fossil is younger and which is older. The discovery of a different means, one for which absolute dating is possible occurred in the early 20th century. The methods are based on radioactive decay.

Certain naturally occurring elements are radioactive, and they break down or decay at well-known predictable rates. Chemists can measure the half-life of these elements, which is the time it takes for half of the radioactive parent element to break down into the stable daughter element. Then by comparing the two proportions of parent to daughter elements in the rock sample, and knowing the half-life, the absolute age can be calculated.

Carbon Dating

Carbon-14 dating is the best-known absolute dating technique. This is the one preferred by archaeologists prefer to use. But there is a problem, the half-life of carbon-14 is only 5730 years, so the method cannot be used for materials older than about 70,000 years. (After 70,000 the element is stable, it doesn't decay any longer.)

A second technique involves the use of isotopes. An isotope is an atom having the same number of protons in its nucleus as other varieties of the element but has a different number of neutrons. Radiometric dating using one of the following isotope series, such as rubidium/strontium, thorium/lead, potassium/argon, argon/argon, or uranium/lead can be used. All have a very long half-life, ranging from 700 million years to 48.6 billion years. Subtle differences in the relative proportions of the two isotopes can give good dates for rocks of any age.

Different Isotopes can be used for cross-referencing dates

When radiometric dating was first used around 1920, it showed that the Earth was hundreds of millions, or billions, of years old. Since then, geologists have made many tens of thousands of radiometric age determinations, using the different isotope pairs and scientists have refined the earlier estimates. This is important, for the accuracy of a fossil is not dependent on one finding; other checks are possible.

Now a day's there is only a 1% chance of error occurring with the current dating technology. In fact new geologic time scales are published every few years, providing the latest dates for major time lines. One important result is that some older dates may change by a few million years up and down, but the younger dates are very stable.

A good example occurs with the work on the boundary mark known for about 50 years now as the Cretaceous-Tertiary boundary. This boundary marks the end of the dinosaur's period, which was 65 million years ago. Repeated retests, using more sophisticated techniques and equipment have not shifted that date. It continues to be accurate to within a few thousand years. With modern, extremely precise methods the error bars are often only 1% or so.
Conclusion: The strict rules of the scientific method ensure the accuracy of fossil dating.

The fossil record is fundamental to an understanding of evolution. The first technique used was stratigraphy, looking at the sequence of fossils as the appeared in geologic formations. Other methods were also developed, Phylogenetic trees of species, mathematical models, carbon dating and radioactive isotope dating were also developed. These different techniques do not contradict one another, but in fact support the timeline that has been identified. Fossils do tell the evolutionary story of live on earth.

Evidence of Evolution Shown in 1 year Changes

One of the most problematic elements of having skeptics of evolution believe is the long time tables needed to account for the changes. Indeed, many skeptics simply cannot fathom the million year time tables needed for changes to occur as evidence.

However, there is now evidence that changes have occured that took place in about a year's time frame. The species was the Samoan island butterfly, commonly known as the Blue Moon or Great Eggfly butterfly, which had nearly disappeared by 2001. Researchers went back in 2005, and noted the same female/male ratio. However by the end of 2006, however, the number of males had recovered.

The culprit that was responsible for the near elimination of the male Hypolimnas bolina butterfly was a parasite called Wolbachia. This parasite was killing male butterfly embryos. But according to researchers, it appears that the butterflies evolved rapidly to develop more suppressor genes that helped protect the males against the parasites.

Within 10 generations that spanned less than a year, the proportion of males of the Hypolimnas bolina butterfly on the South Pacific island of Savaii jumped from a paltry 1 percent of the population to about 39 percent. This is evidence that parasites can be major drivers in evolution.

Saturday, July 14, 2007

Universal Common Descent

Are all living things commonly related? One scientific approach called universal common descent tries to answer that question. It is the hypothesis that all living, earth bound organisms are genealogically related. In other words, all existing species originated gradually by biological, reproductive processes on a geological timescale. Modern organisms come from a common gene pool; they are the genetic descendants of some original species. That species could have been found in one location, but it may also have been found in multiple locations around the earth.

Genetical "gradualness" is a mode of biological change that is dependent on population phenomena. To be sure, it is not a statement about the tempo of evolution modification. Genetically gradual events instead are changes which occur within the range of biological variation that is normally expected between two consecutive generations. On a geological timescale morphological change may appear fast but nevertheless still be genetically gradual. How does this impact macroevolutionary events? Gradualness is not a mechanism of evolutionary change, but it imposes severe constraints on possible macroevolutionary events. Likewise, the requirement of gradualness necessarily restricts the possible mechanisms of common descent and adaptation

How are Microevolutionary theories related to Macroevolutionary theories?
Microevolutionary theories are gradualistic explanatory mechanisms that biologists use to account for the origin and evolution of macroevolutionary adaptations and variation. These mechanisms include such concepts as natural selection, genetic drift, sexual selection, neutral evolution, and theories of speciation.

The Basic Mechanisms of Evolution

Natural Selection
This is a process in which some individuals have genetically-based traits that will improve survival chances or reproduction abilities thus having more offspring which in turn will survive to reproductive age than other individuals. Now as the offspring also carry the genes with these traits, this process gives the genes with these advantageous traits to become more common in populations and the genes with disadvantageous traits to become less common in populations.

Genetic Drift
Some individuals in each generation may leave behind a few more descendents and their genes than other individuals. The genes of the next generation will be the genes of the “lucky” individuals. This does not necessarily mean that they are healthier or “better” individuals. That, is genetic drift. It is a random effect. Some genes survive, others don't. It happens to all populations—there’s no avoiding it. Genetic drift affects the genetic makeup of the population through an entirely random process. It is a mechanism of evolution, it doesn’t work to produce adaptions.

Sexual Selection
Sexually acting on an organism’s ability to obtain or successfully copulate with a mate. This process may produce traits that seem to decrease an organism’s chance of survival, while increasing its chances of mating. It is a “special case” of natural selection.
Sexual selection is often powerful enough to produce features that are harmful to the individual’s survival. Think Peacock, for example. It's colorful and extravagant tail feathers are as likely to attract predators as well as interested members of the opposite sex.

Neutral Evolution
If we look around it might appear that everywhere we look, we will see evidence of natural selection - where organisms seem to make do pretty well to their environments; they have adapted successfully. But the neutral theory of molecular evolution suggests that most of the genetic variation in populations is the result of mutation and genetic drift and not selection.

A species is a group of individuals that actually or potentially interbreed in nature. So a species would be the biggest gene pool possible under natural conditions.
Now speciation is a lineage-splitting event that produces two or more separate species. Imagine that you are looking at a tip of the tree of life that constitutes a species of beetle. Move down the phylogeny to where your beetle twig is connected to the rest of the tree. That branching point, and every other branching point on the tree is called a speciation event. And it is at that point where genetic changes have resulted in two separate beetle lineages. Previously there had just been one lineage.

Thursday, July 12, 2007

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.

Wednesday, July 11, 2007

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.

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 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 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.

Tuesday, July 10, 2007

If there is Intelligent Design - Why are there Useless Limbs?

Vestigial Organs or Organs that do not have a purpose pose a challenge to the Intelligent Design argument. Vestigiality is a term which describes characteristics of organisms such as anatomical structures which have lost all or most of their original function in a species through evolution. Here are 10 examples:

#1. The Wings on Flightless Birds: The ostrich
In 1798, a French anatomist, √Čtienne Geoffroy St. Hilaire, traveled to Egypt where he witnessed and wrote about a flightless bird whose wings appeared useless for soaring.

That bird was an ostrich, but he described it as a "cassowary", a term then used to describe various birds of ostrich-like appearance. Ostriches and cassowaries are among several birds that have wings that are vestigial.
Besides the cassowary, other flightless birds with vestigial wings are the kiwi, and the kakapo.

Wings are complex structures that are specifically adapted for flight and those belonging to these flightless birds are no different. They are, anatomically speaking, rudimentary wings, but they could never be used to give these bulky birds flight. The wings are not completely useless, as they are used for balance during running.

#2. Hind Leg Bones in Whales
For over 100 million years the only vertebrates on Earth were water-dwelling creatures, with no arms or legs, or so biologists believe. But at some point these "fish" began to develop hips and legs and eventually were able to walk out of the water, giving the earth its first land lovers.

Once the land-dwelling creatures evolved, some mammals moved back into the water. Biologists estimate that this happened about 50 million years ago, and that this mammal was the ancestor of the modern whale.

Despite the apparent uselessness, evolution left traces of hind legs behind, and these vestigial limbs can still be seen in the modern whale. Cases have been found where whales have rudimentary hind limbs in the wild, and examples are found in baleen whales, humpback whales, and in many specimens of sperm whales.

#3. Goose Bumps and Body Hair
Do you ever get goose bumps? Smooth muscle fibers that give humans "goose bumps" they are the erector pili. If the erector pili are activated, the hairs that come out of the nearby follicles stand up and give an animal a larger appearance that might scare off potential enemies and a coat that is thicker and warmer. Humans, though, don't have thick furs and our strategy for several thousand years has been to take the fur off other warm looking animals to stay warm. And the rest of that hair, though, is essentially useless as is the Erector Pili.

#4. The Human Tailbone
These fused vertebrae bones are the only vestiges that are left of the tail that other mammals still use for balance, communication, and in some primates, as a prehensile limb.

As our ancestors were learning to walk upright, their tail became useless, and it slowly disappeared. It has been suggested that the coccyx helps to anchor minor muscles and may support pelvic organs. However, there have been many well documented medical cases where the tailbone has been surgically removed with little or no adverse effects.

#5. The Blind Fish
The Astyanax Mexicanus is a species of fish known which dwells in caves deep underground off the coast of Mexico: it is blind.

The pale fish has eyes, but as it is developing in the egg, the eyes begin to degenerate, and the fish is born with a collapsed remnant of an eye covered by a flap of skin. These vestigial eyes probably developed after hundreds or even thousands of years of living in total darkness.

Now how do we know that eye is degenerate, but the fish can still be able to see? Can we test this evolutionary phenomenon. That the fish, under the right conditions could see?

Well to have the experiment a control subject is needed. And there is such a fish. In fact such a fish of the same species live right above, near the surface, where there is plenty of light. These fish have fully functioning eyes.

So to test if the eyes of the blind Mexicanus could function if given the right environment, scientists removed the lens from the eye of the surface-dwelling fish and implanted it into the eye of the blind fish. The results showed that after eight days or so an eye began to develop beneath the skin. By two months the fish had developed a large functioning eye with a pupil, cornea, and iris. The blind fish could now they see.

#6. Wisdom Teeth in Humans
Wisdom teeth, humans have become remnants from their large jawed ancestors. But regardless of how much they are despised, the wisdom teeth remain, and force their way into mouths regardless of the pain inflicted. Two reasons are possible to explain why the wisdom teeth have become vestigial. The first is that the human jaw has become smaller than its ancestors' and the wisdom teeth are trying to grow into a jaw that is much too small.

The second reason may have to do with dental hygiene. Thousand years ago, it might be common for an 18 year old man to have lost several, if not all of his teeth, and the incoming wisdom teeth would prove useful. Now with better dental hygiene it's possible to keep one's teeth for a lifetime.

#7. The Sexual Organs of Dandelions
Dandelions, like all flowers, have the stamen and pistil, the sex organs necessary for sexual reproduction, but they do not use them. Instead dandelions reproduce without fertilization. They clone themselves, and they are quite good at it. Look at any lawn for the proof.

#8. Fake Sex in Virgin Whiptail Lizards
Lizards of the genus Cnemidophorus exhibit certain vestigal behavior. Since only females exist in several species of the lizards of the genus Cnemidophorus, how to they propagate the species? The females reproduce by parthenogenisis. They don't need the males. Parthenogenisis is a form of reproduction in which an unfertilized egg develops into a new individual. Females just produce clones of themselves as a form of reproduction.

So why do the females try to copulate? Despite the fact that it is unnecessary and futile, the lizards still like to try, and occasionally one of the females will start to "act like a male" by attempting to copulate with another female. The lizards evolved from a sexual species and the behavior to copulate like a male -- to engage in fake sex is a vestigial behavior. So the sexual copulation behavior is present in a species, but is expressed in an imperfect form, in this case, is as a useless act. This is an example of vestigial behavior.

#9. Male Breast Tissue and Nipples
Both men and women have nipples because in early stages of fetal development, but in the early stages an unborn child is effectively sexless. Thus nipples are present in both males and females. In the later stages of fetal development when testosterone causes sex differentiation in a fetus does the sex of a fetus become apparent. Mammary glands are present in all mammals, male and female. And male nipples are vestigial; they may perform a small role in sexual stimulation and a small number of men have been able to lactate.

#10.The Human Appendix
The human appendix is a small pouch attached to the large intestine where it joins the small intestine. It does not directly assist digestion. Biologists believe it is a vestigial organ left behind from a plant-eating ancestor. In plant-eating vertebrates, the appendix is much larger and its main function is to help digest a largely herbivorous diet. This is not useful in Humans who consume plants and animals.

These are 10 examples of biological functions and artifacts that promote the idea that Intelligent Design is not intelligent. If it were intelligent, that is well designed, why are these vestigial elements present. And they are present on mammals, plants, birds, and fish, there is even vestigial behavior.

Monday, July 9, 2007

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.

Sunday, July 8, 2007

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.

Thursday, July 5, 2007

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:

Wednesday, July 4, 2007

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.

Tuesday, July 3, 2007

BioGeography and Evolution

Biogeography was central to Darwin's logic when he summarized his findings from five years of collecting evidence around the world as a passenger on the HMS Beagle. He realized that animal and plant species, though diverse, were more similar to each other on the same continent.

So what is BioGeography? It is the study of the distributions of plants and animals over the surface of the Earth spatially and temporally. The spatial component describes and explains the distributions of one or more species over the world. The temporal component is used to explain the changing distributions of organisms over time, either in the short term or over geological time.

For example Australian species were more similar to each other than they were to South American species. But such geographic diversity also played out on local island groups such as those of the Archipelago Galapagos in the South Pacific. The famous Darwin finches were his prime exhibit in formulating the theory of evolution.

How does this idea work?
Species will change over time in go in a different direction if they are isolated from each other over long periods of time. Now remember that time periods in evolution are very, very long. They are measured in geological time, for example in MYA or million years ago.
Fossil records together with the theory on plate tectonics and continental drift support the idea of speciation, which come from a long lasting period of geographic isolation.

What is speciation? Speciation is the process of evolving two different species from a founder species as the result of an event that caused separation of the founder population into two isolated populations. Consequently, individuals from one population cease to reproduce with individuals from the other population. Their similarities will continue to exist, but their differences will start to become apparent.

Sunday, July 1, 2007

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.