Surprising Similarities between Genetic and Computer Codes

_{March 29, 2013

Evolution, Genetics}

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Here’s what we read in this PhysOrg blurb:

It may seem logical, but the surprising part of this finding is how universal it is. “It is almost expected that the frequency of usage of any component is correlated with how many other components depend on it,” said Maslov. “But we found that we can determine the number of crucial components – those without which other components couldn’t function – by a simple calculation that holds true both in biological systems and computer systems.” For both the bacteria and the computing systems, take the square root of the interdependent components and you can find the number of key components that are so important that not a single other piece can get by without them.

” crucial components . . . without which other components couldn’t function . . . ”

Sounds a lot like “irreducible complexity,” doesn’t it? I wonder what that square root figure turns out to be. That would represent the amount of specified complexity required simply for life to begin, hence, completely outside of Darwinian mechanisms.

Comments

OT: Ants follow Fermat's principle of least time - April 1, 2013 Excerpt: Ants have long been known to choose the shortest of several routes to a food source, but what happens when the shortest route is not the fastest? This situation can occur, for example, when ants are forced to travel on two different surfaces, where they can walk faster on one surface than on the other. In a new study, scientists have found that ants behave the same way as light does when traveling through different media: both paths obey Fermat's principle of least time, taking the fastest route rather than the most direct one. http://phys.org/news/2013-04-ants-fermat-principle.htmlbornagain77_{April 1, 2013
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OT: The Bible Series Finale Sneak Peek - video http://www.youtube.com/watch?feature=player_embedded&v=CG_onGkRy6Q Of semi-related note to God 'making a way' for us through Jesus, I just caught a glimpse of a severely compromised Exodus account on the Military channel. Yet, contrary to these many 'compromised' accounts of the Hebrew Exodus from Egypt on TV, there is actually very strong archeological evidence supporting the Biblical narrative that has recently come to light: Exodus Revealed - Startling Evidence For The Hebrew Exodus From Egypt - documentary video http://vimeo.com/39498729 The Exodus Case Interviews with Lennart Moller - video http://www.prophecyinthenews.com/the-exodus-case-interviews-with-lennart-moller/ Here is a small portion of the video footage showing the coral encrusted remains of Egyptian chariots in the Red Sea at the proposed Nuweiba crossing,,, Seems the Charlton Heston depiction in the movie, 'The Ten Commandments', was not that far off the mark of what really happened after all! THE REAL EXODUS - A SMALL PORTION THE SUPPRESSED EVIDENCE - video http://www.youtube.com/watch?v=Xqf6t_DnmGYbornagain77_{March 31, 2013
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OT: Dr. Sewell, I've been hoping for some time that we could have a discussion of your ideas, but it seems that most of your recent posts have comments closed. Would it be possible to open the comments on your latest thread so we can discuss the issues (or perhaps start a new thread)? Thanks,Eric Anderson_{March 30, 2013
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And though they referred to horizontal gene transfer in the physorg write up (a very elaborate process in and of itself), it seems they forgot to mention the fact that a large percentage of totally unique ORFan genes are now being found in every new genome sequenced:
ORFan Genes Challenge Common Descent - Paul Nelson - short version - video https://vimeo.com/17135166 Estimating the size of the bacterial pan-genome - Pascal Lapierre and J. Peter Gogarten - 2008 Excerpt: We have found >139 000 rare (ORFan) gene families scattered throughout the bacterial genomes included in this study. The finding that the fitted exponential function approaches a plateau indicates an open pan-genome (i.e. the bacterial protein universe is of infinite size); a finding supported through extrapolation using a Kezdy-Swinbourne plot (Figure S3). This does not exclude the possibility that, with many more sampled genomes, the number of novel genes per additional genome might ultimately decline; however, our analyses and those presented in Ref. [11] do not provide any indication for such a decline and confirm earlier observations that many new protein families with few members remain to be discovered. http://www.paulyu.org/wp-content/uploads/2010/02/Estimating-the-size-of-the-bacterial-pan-genome.pd Genes from nowhere: Orphans with a surprising story - 16 January 2013 - Helen Pilcher Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these "orphan genes" are high achievers (are just as essential as 'old' genes),,, But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn't be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven't-quite the opposite, in fact.,,, The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, "the probability that a functional protein would appear de novo by random association of amino acids is practically zero".,,, Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing. http://ccsb.dfci.harvard.edu/web/export/sites/default/ccsb/publications/papers/2013/All_alone_-_Helen_Pilcher_New_Scientist_Jan_2013.pdf Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm
bornagain77_{March 29, 2013
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Here's the main paper and the supplemental information to the paper:
Universal distribution of component frequencies in biological and technological systems - February 19, 2013 Excerpt: Bacterial genomes and large-scale computer software projects both consist of a large number of components (genes or software packages) connected via a network of mutual dependencies. Components can be easily added or removed from individual systems, and their use frequencies vary over many orders of magnitude. We study this frequency distribution in genomes of approx. 500 bacterial species and in over 2 million Linux computers and find that in both cases it is described by the same scale-free power-law distribution with an additional peak near the tail of the distribution corresponding to nearly universal components. We argue that the existence of a power law distribution of frequencies of components is a general property of any modular system with a multilayered dependency network.,,, http://www.pnas.org/content/early/2013/03/21/1217795110.abstract Please note the quarter power scaling that is indicated on the last graph of the supporting information page: Supporting Information http://www.pnas.org/content/suppl/2013/03/22/1217795110.DCSupplemental/pnas.201217795SI.pdf
Related notes:
The predominance of quarter-power (4-D) scaling in biology Excerpt: Many fundamental characteristics of organisms scale with body size as power laws of the form: Y = Yo M^b, where Y is some characteristic such as metabolic rate, stride length or life span, Yo is a normalization constant, M is body mass and b is the allometric scaling exponent. A longstanding puzzle in biology is why the exponent b is usually some simple multiple of 1/4 (4-Dimensional scaling) rather than a multiple of 1/3, as would be expected from Euclidean (3-Dimensional) scaling. http://www.nceas.ucsb.edu/~drewa/pubs/savage_v_2004_f18_257.pdf “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection." Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79 https://uncommondescent.com/evolution/16037/ 4-Dimensional Quarter Power Scaling In Biology - video http://www.metacafe.com/w/5964041/ What Is The Genome? It's Certainly Not Junk! - Dr. Robert Carter - video - (Notes in video description) http://www.metacafe.com/w/8905583 Comparing genomes to computer operating systems - Van - May 2010 Excerpt: we present a comparison between the transcriptional regulatory network of a well-studied bacterium (Escherichia coli) and the call graph of a canonical OS (Linux) in terms of topology,,, http://www.ncbi.nlm.nih.gov/pubmed/20439753 Venter: Life Is Robotic Software - July 15, 2012 Excerpt: “All living cells that we know of on this planet are ‘DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,” said (Craig) Venter. http://crev.info/2012/07/life-is-robotic-software/
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