Question: Bio-Informatics Results Supporting Ongoing Evolution
8
gravatar for Monzoor
7.1 years ago by
Monzoor310
Monzoor310 wrote:

Is there a nice review paper that summarizes bio-informatics proofs to support the notion that evolution is true and evolution is indeed in progress ?

publication evolution • 2.3k views
ADD COMMENTlink modified 7.1 years ago by Martijn Van Iersel550 • written 7.1 years ago by Monzoor310
4

Yes. Experimental evolution is performed frequently over human times scales in microbial species, and coupled with next generation sequencing can provide in silico proof of evolutionary change. See for example http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html and the large body of work by Rich Lenski and co-workers: http://myxo.css.msu.edu/PublicationSearchResults.php?group=aad

ADD REPLYlink written 7.1 years ago by Casey Bergman17k

Just one final commment. Is it that all the arguments presented above help us in 'inferrring' that evolution is in progress. Can we cite (any real time event) or perform an experiment to show that we (or for that matter any living being) are evolving. My query may seem preposterous, but this is the exact question my students have asked me. All my students currently blame it on "inference"

ADD REPLYlink written 7.1 years ago by Monzoor280
12
gravatar for Joachim
7.1 years ago by
Joachim2.8k
San Francisco, California
Joachim2.8k wrote:

I might be wrong, but I do not think that the primary goal of bioinformatics is to prove that evolution takes place. The question whether evolution did happen/happens/will be happening has been more or less settled before bioinformatics became popular.

Are you perhaps looking for informatics/computer science applications that are related to research in evolution? If so, go to http://www.ncbi.nlm.nih.gov/pubmed and simply search for 'evolution', one of the first results is the paper 'Why do humans have chins? Testing the mechanical significance of modern human symphyseal morphology with finite element analysis.', which uses finite element analysis -- something that can be modelled and simulated very well in software. I am sure you could find more papers related to modelling/simulation if you narrow down your question to a few key points.

Otherwise, the references given here should be sufficient: http://en.wikipedia.org/wiki/Evolution

Of course, if you have a very distinct opinion about evolution to start with, you will find this web-page much more appealing: http://www.conservapedia.com/Evolution

ADD COMMENTlink written 7.1 years ago by Joachim2.8k
10
gravatar for Suk211
7.1 years ago by
Suk2111.0k
state college
Suk2111.0k wrote:

Statistical distribution of amino acid sequences: a proof of Darwinian evolution

ADD COMMENTlink written 7.1 years ago by Suk2111.0k

I thought this was a very interesting paper, a great one to quote for the question asked.

ADD REPLYlink written 7.1 years ago by Daniel Swan13k

Read through this paper yesterday. Hmm that gets me thinking. I somehow was an evolution sceptic. However my scepticism stems from scientific reasoning. Not religious though ..

Thanks to one and all for your valuable inputs

ADD REPLYlink written 7.1 years ago by Monzoor280

"We have proved that the distribution of amino acids, dipeptides and tripeptides is statistical which confirms that the evolutionary biodiversity development model is subject to the theory of independent events." I wish they didn't word it like this but I would need to read it carefully to understand the core idea.

ADD REPLYlink written 6.7 years ago by Aleksandr Levchuk3.1k
6
gravatar for Neilfws
7.1 years ago by
Neilfws47k
Sydney, Australia
Neilfws47k wrote:

It's important to realise that biological scientists accept evolutionary theory because multiple lines of evidence support it. Some of these stem from bioinformatics analysis, many do not. As Joachim pointed out, we've been addressing these questions for a long time (at least since the 1850s) and a PubMed search will return the results: currently 163 067 articles with the word "evolution" in title/abstract. As to whether evolution is "in progress" this is not a separate issue: the word itself implies an ongoing process.

Having said that, some of the best evidence for evolution comes from what may be called bioinformatics approaches. Identifying the same gene in several species by sequencing it implies that those species share a common ancestor (leaving aside issues of homologs, orthologs and paralogs). Using differences in gene sequence to cluster those species into a phylogenetic tree demonstrates the degree of relatedness. And modelling the rate of change in the gene sequence - molecular clocks - gives an estimate of when species diverged.

ADD COMMENTlink written 7.1 years ago by Neilfws47k
5
gravatar for Khader Shameer
7.1 years ago by
Manhattan, NY
Khader Shameer17k wrote:

Already nice answers, I would like to share my thoughts from the perspective of the protein evolution.

Understanding of evolutionary aspects of proteins are accelerated by several bioinformatics approaches. For example protein sequence classification (protein families, clans, protein domains) and protein structural classification (domain, family, superfamily, folds etc) are two areas where bioinformatics contributed to the understanding of evolution of protein structure and function.

Two popular bioinformatics resources based on such concepts are:

  • SCOP database provides structural and evolutionary relationships between proteins with structural data.
  • Pfam database provides data about evolutionarily conserved elements within proteins.

I would like to point you to couple of interesting article about the evolution of protein families across sequence and structure space.

Structural and functional constraints in the evolution of protein families

Protein families and their evolution-a structural perspective.

Evolution of protein structures and functions.

ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by Khader Shameer17k

Just one final commment. Is it that all the arguments presented above help us in 'inferrring' that evolution is in progress. Can we cite (any real time event) or perform an experiment to show that we (or for that matter any living being) are evolving. My query may seem preposterous, but this is the exact question my students have asked me.

ADD REPLYlink written 7.1 years ago by Monzoor280

Yes. Experimental evolution is performed frequently over human times scales in microbial species, and coupled with next generation sequencing can provide in silico proof of evolutionary change. See for example http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html and the large body of work by Rich Lenski and co-workers: http://myxo.css.msu.edu/PublicationSearchResults.php?group=aad

ADD REPLYlink written 7.1 years ago by Casey Bergman17k

You can do a quick analysis using a protein fold or protein domain that is present in lower-to-higher organism and discuss their relative length, sequence composition and other aspects from the perspective of evolution.

ADD REPLYlink written 7.1 years ago by Khader Shameer17k

Yep. Nice suggestion. Thank you

ADD REPLYlink written 7.1 years ago by Monzoor280
2
gravatar for Martijn Van Iersel
6.4 years ago by
Netherlands
Martijn Van Iersel550 wrote:

The E. coli long-term evolution experiment is a nice example of real experimental data for ongoing evolution. In this experiment, different E. coli populations are followed for more than 50000 generations, and the appearance and spread of genetic adaptations is shown.

ADD COMMENTlink written 6.4 years ago by Martijn Van Iersel550
1
gravatar for Yuri
6.6 years ago by
Yuri1.5k
Bethesda, MD
Yuri1.5k wrote:

A new article with nice experimental data on bacterivorous protist species just came out in "Ecology Letters" (June 14, 2011):

ADD COMMENTlink written 6.6 years ago by Yuri1.5k
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