Evolution 2.0

Chimpanzee handEvolutionary science needs debugging. Apparently, there are a few issues that cannot be resolved with any precision when one asks questions like: What makes a human different from a chimp? Apparently, at the level of genetic sequences, systematic errors creep into any analysis, distorting our ancestry.

Now, researchers from the European Molecular Biology Laboratory’s European Bioinformatics Institute have revealed the source of these systematic errors in comparative genetic sequencing and have devised a new computational tool that avoids these errors and provides accurate insights into the evolution of DNA and protein sequences. Their work suggests that sequence turnover is much more common than assumed.

“Evolution is happening so slowly that we cannot study it by simply watching it,” explains Nick Goldman, group leader at EMBL-EBI, “we learn about the relationships between species and the course and mechanism of evolution by comparing genetic sequences.”

At the core of the evolutionary process are random changes in the DNA of all living things, incorrect copying of a single DNA base, or substitution, the loss of a base by deletion, and the inadvertent insertion of a new base. Such changes can lead to functional and structural changes in genes and proteins. If those mutations confer a reproductive advantage on the individual concerned then they will be carried on to the next generation. The accumulation of enough mutations over the course of many generations leads to the formation of new species. Reconstructing the history of these mutation events reveals the course of evolution.

Genetic mutationsTo compare two DNA sequences, researchers first align them by matching different sequences that share common ancestry. Insertions and deletions are then marked as gaps. This computationally draining process, originally designed for analysing proteins hence its limitations, is usually carried out progressively from several pairwise alignments. However, scientists cannot judge whether a particular length difference between two sequences is a deletion in one or an insertion in the other sequence. For correct alignment of multiple sequences, distinguishing between these two events is crucial, which is where those systematic errors creep in.

“Our new method gets around these errors by taking into account what we already know about evolutionary relationships,” explains Ari Löytynoja, who developed the new computational tool in Goldman’s lab. “Say we are comparing the DNA of human and chimp and cannot tell if a deletion or an insertion happened. To solve this our tool automatically invokes information about the corresponding sequences in closely related species, such as gorilla or macaque. If they show the same gap as the chimp, this suggests an insertion in humans.”

The team’s work (published in the June 20 issue of Science) suggests that insertions are much more common than previously assumed, while deletion numbers have been overestimated. Now, that tools are being developed to reveal such issues our understanding of evolution can only become clearer.

6 thoughts on “Evolution 2.0”

  1. The so-called theory of evolution is one of those ideas that, while it may appeal to our sense of the obvious, seems to have little in the way of scientific evidence to back it up. Yet it is widely believed to be true. In fact, most scientists seem to accept it as fact. But if you read any amount of evolutionary literature, you’ll find it laced with speculation.

    But science is supposed to keep us from kidding ourselves about how the real world works, is it not? To me, using speculation as a foundation for belief is terribly unscientific.

    The meager scientific evidence that seems to support the evolution idea can be explained in terms of dauermodifications, a concept embarrassing to evolutionists because it demonstrates the inviolability of the genetic material while allowing for wide adaptation to environmental conditions. Here’s a bit of discussion from chapter One of “Science and Faith” by Arthur C. Custance, PhD.

    “But in the past few years a renewed interest in the possibility of another pathway whereby the environment might have a direct influence upon an organism responding in an inheritable way has led to the conclusion that there are probably carriers of inheritable material in the cytoplasm of the cell and not merely in the nucleus. These carriers, which have been termed Plasmagenes, are responsive to the direct action of the environment. This responsiveness appears to be somewhat delayed, so that the environmental pressure must be held constant over several generations to influence the plasmagenes. That the response of these extra-nuclear genes can be inherited through succeeding generations is demonstrated by the fact that the effect persists even when the original stimulus is removed. If the environment gradually reverts to its original nature, the modified organisms will continue to retain their altered form for several generations, and then they too revert.”

    The full text can be accessed at http://www.custance.org/old/sci-faith/4ch1-4.html or simply Google “Dauermodifications.”

  2. No, no legs.

    But I did hear from a friend that they put a typewriter in one of the Petri dishes. After 12,000 or so generations, they had reproduced the entire works of Shakespeare.

  3. Good question. There are several other species that have bigger genomes than ours, there’s no reason to think that there weren’t organisms in the past that were more verbose too.

  4. I have a question: given scientists seem to think much of the so-called Junk Code is now actually functional code, of sorts, are we (and I reference all life today) genetically more verbose (in terms of raw DNA) than the animals of the distant past?

  5. Here’s a related story out of Michigan State University:

    Twenty years ago, evolutionary biologist Richard Lenski of Michigan State University in East Lansing, US, took a single Escherichia coli bacterium and used its descendants to found 12 laboratory populations.

    The 12 have been growing ever since, gradually accumulating mutations and evolving for more than 44,000 generations, while Lenski watches what happens.
    Profound change

    Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

    But sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.

    Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity.

    New Scientist

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