Complexity of gene codes (Introduction)

by David Turell , Sunday, August 15, 2010, 18:37 (5023 days ago) @ David Turell


> http://www.sciencemag.org/cgi/content/summary/329/5993/740-Here are selected paragraphs from the above article:-Human Evolution: 
Tracing Evolution's Recent Fingerprints
Ann Gibbons 
 -
"For Rasmus Nielsen, it was a revelatory moment. He was analyzing the frequency of different mutations in the genomes of Tibetans living at high altitude, searching for adaptations that allow them to thrive in thin air. His team's analysis had generated a graph in which most of the mutations were clustered together. But two stood apart, indicating they existed in almost all Tibetan highlanders but not in their close relatives, the Han Chinese. The high frequency of the mutations showed that this was a radical example of rapid evolution, with strong natural selection acting on a single gene. It was the most radical of a flurry of recent discoveries of human genes that evolution has strongly favored, a process called positive selection. They now realize, however, that plenty of positive selection exists, but it is subtler and harder to trace than originally anticipated. Using new statistical methods, they have found many less dramatic mutations that, for example, also help highland Tibetans survive at high altitude. A growing number of researchers now think it is rare for a particular mutation to spread rapidly to most people within a population, as was the case with the Tibetan gene. "There have been a bunch of papers that show very consistently selection across a lot of our genome, but of a type that doesn't leave these massive footprints," says Gilean McVean, a population geneticist at the University of Oxford. -Seeking selection 
Many researchers have argued that most of the obvious differences between humans today are the result of recent positive selection rather than mutations that accumulated randomly over time. All living humans are remarkably similar genetically because we all descended from a small founder population that arose in Africa about 200,000 years ago. As these modern humans moved around and, eventually, out of Africa in the past 80,000 years or so, they evolved genetic differences that helped them adapt to new climates, digest novel foods, and fight off new illnesses and parasites. -
With the sequencing of the complete human genome for the first time a decade ago, researchers were able to get a better handle on how selection has shaped the genome. Several large-scale projects used different methods to identify millions of single-nucleotide polymorphisms (SNPs) from across the genomes of people in different populations in Europe, Asia, and Africa. By comparing SNPs at the same sites in individuals from different populations, researchers could detect those where positive selection had driven a mutation to high frequencies in a population. 
 The identification of so many regions of the genome under positive selection prompted some researchers to conclude that evolution had accelerated as humans spread around the globe and adapted to new challenges.
 
Soft sweeps 
Yet McVean and others were convinced that positive selection had shaped much of the genome but lay beneath the radar of methods used to detect it. Consequently, earlier this year Pritchard and his colleagues proposed an alternative to strong selection on single new mutations. In Current Biology, they argued that selection on more than one gene at once could allow a new trait—increased height—to sweep more rapidly through a group. -
 While several teams are developing new methods to identify polygenic soft sweeps, others are working to pinpoint more precisely the DNA under positive selection. Sabeti's team was able to home in on 64 regions containing just a single gene, which narrows the search for a SNP that may boost an adaptive trait. 
Many groups are also ramping up efforts to do functional studies of the gene variants they have identified. Finally, many researchers are looking forward to the complete genomes of 1000 individuals in the 1000 Genomes Project.
As researchers look forward to scanning these new data sets, they say that the key question is no longer how much positive selection is in the genome."-
Think about it. Geneticists are now showing us that the genome is responding actively to environmental pressures, not passively as Darwin expected. This is done at the RNA level, methylation of DNA, SNP's, etc. Watson/Crick DNA is a copy code for the raw material of life, not a very effective code for rapid evolutionary advances. This is an obvious conclusion. Many other layers of the genome are operative to allow these rapid advances. Chance mutation and natural selction are a totally passive mechanism. Scientists are discovering much more beyond Neo-Darwinism.