Neutral Evolution and the Shape of Our Genome

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

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

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

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

Numts or Copies of mitochondrial sequences found in DNA portions

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

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

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

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

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

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

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

Simple to complex then simple to complex

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

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

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

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

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

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

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.