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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,,,
To Model the Simplest Microbe in the World, You Need 128 Computers - July 2012
Excerpt: Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That's a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,,
The bioengineers, led by Stanford's Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What's fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell's lifecycle processes.,,,
,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore's Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that's only a fraction of what will eventually be required to consider the simulation realistic.,,,
Excerpt: DNA computers will work through the use of DNA-based logic gates. These logic gates are very much similar to what is used in our computers today with the only difference being the composition of the input and output signals.,,, With the use of DNA logic gates, a DNA computer the size of a teardrop will be more powerful than today’s most powerful supercomputer. A DNA chip less than the size of a dime will have the capacity to perform 10 trillion parallel calculations at one time as well as hold ten terabytes of data. The capacity to perform parallel calculations, much more trillions of parallel calculations, is something silicon-based computers are not able to do. As such, a complex mathematical problem that could take silicon-based computers thousands of years to solve can be done by DNA computers in hours.
The physics of going viral: Researchers measure the rate of DNA transfer from viruses to bacteria - June 27, 2012
Excerpt: E. coli cells contain roughly 3 million proteins within a box that is roughly one micron (1,000 nanometers) on each side. Less than 10 nanometers separate each protein from its neighbors. "There's no room for anything else," Phillips says. "These cells are really crowded."
'The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica."Carl Sagan, "Life" in Encyclopedia Britannica: Macropaedia (1974 ed.), pp. 893-894
3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009
Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.
Do you believe Richard Dawkins exists?
Excerpt: DNA is the best information storage mechanism known to man. A single pinhead of DNA contains as much information as could be stored on 2 million two-terabyte hard drives.
Programming of Life - Biological Computers - video
Human DNA is like a computer program but far, far more advanced than any software we've ever created.
Bill Gates, The Road Ahead, 1996, p. 188
Astonishing DNA complexity demolishes neo-Darwinism - Alex Williams
Excerpt: Not only has the ENCODE project elevated UTRs out of the ‘junk’ category, but it now appears that they are far more active than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes.
Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift – creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors – it surely would have killed us. Since Haldane’s dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation – but has obtained identical results.
John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 159-160
Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.
John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162
Majestic Ascent: Berlinski on Darwin on Trial – David Berlinski – November 2011
Excerpt: The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. “A critique of neo-Darwinism,” the Dutch biologist Gert Korthof boasted, “can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science.”
By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian.
“The failure to recognize the full implications of this particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology." Wyatt Gibbs, The Unseen Genome: Gems among the Junk, Scientific American, November 2003, pp 45-53
Junk DNA Found To Have High Level Function
Multidimensional Genome - Dr. Robert Carter - video