Monday, October 29, 2007

Dawn Of Animal Vision Discovered

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

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

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

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

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

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

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

A map of Human Global Migration

Palaeontologists, archaeologists and geneticists are piecing the migration picture.

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

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

Friday, October 26, 2007

Map of Neanderthal Geography

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

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

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

Monday, October 15, 2007

Duplication and Division of Labor - The Mechanics of Evolution

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

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

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

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

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

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

One source of newness is gene duplication

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

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

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

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

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

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

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

Friday, October 12, 2007

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.

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.

Sunday, October 7, 2007

Science and Falseability

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

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

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

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

This is the essence of science.

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

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

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