Home » Intelligent Design, News, Origin Of Life » Both genetics-first and metabolism-first origin of life models” strain scientific credibility.”

5 Responses to Both genetics-first and metabolism-first origin of life models” strain scientific credibility.”

1. 1

   bornagain77November 29, 2011 at 7:53 am

   As to this question:

   “What Might Be a Protocell’s Minimal ‘Genome?

   Actually a paper came out recently with a ‘surprising’ result as to what would be needed for a ‘Minimal Genome’:

   Life’s Minimum Complexity Supports ID – Fazale Rana – November 2011
   Excerpt page 16: The Stanford investigators determined that the essential genome of C. crescentus consisted of just over 492,000 base pairs (genetic letters), which is close to 12 percent of the overall genome size. About 480 genes comprise the essential genome, along with nearly 800 sequence elements that play a role in gene regulation.,,, When the researchers compared the C. crescentus essential genome to other essential genomes, they discovered a limited match. For example, 320 genes of this microbe’s basic genome are found in the bacterium E. coli. Yet, of these genes, over one-third are nonessential for E. coli. This finding means that a gene is not intrinsically essential. Instead, it’s the presence or absence of other genes in the genome that determine whether or not a gene is essential.,,
   http://www.reasons.org/files/e.....011-11.pdf

   ,,,Another nail in the coffin for the genetic reductionism model of neo-Darwinism!!!:

   Further notes:

   “An earlier study published in 1999 estimated (not proven) the minimal gene set to fall between 265 and 350. A recent study making use of a more rigorous methodology estimated the essential number of genes at 382.”
   John I. Glass et al., “Essential Genes of a Minimal Bacterium,” PNAS, USA103 (2006): 425-30.

   Jack T. Trevors – Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8
   “No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes programmed?”
   http://www.biomedcentral.com/c.....2-2-29.pdf

   First-Ever Blueprint of ‘Minimal Cell’ Is More Complex Than Expected – Nov. 2009
   Excerpt: A network of research groups,, approached the bacterium at three different levels. One team of scientists described M. pneumoniae’s transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation.
   “At all three levels, we found M. pneumoniae was more complex than we expected,”
   http://www.sciencedaily.com/re.....173027.htm

   There’s No Such Thing as a ‘Simple’ Organism – November 2009
   Excerpt: In short, there was a lot going on in lowly, supposedly simple M. pneumoniae, and much of it is beyond the grasp of what’s now known about cell function.
   http://www.wired.com/wiredscie.....s-of-life/

   Simplest Microbes More Complex than Thought – Dec. 2009
   Excerpt: PhysOrg reported that a species of Mycoplasma,, “The bacteria appeared to be assembled in a far more complex way than had been thought.” Many molecules were found to have multiple functions: for instance, some enzymes could catalyze unrelated reactions, and some proteins were involved in multiple protein complexes.”
   http://www.creationsafaris.com.....#20091229a

   etc.. etc.. etc..
2. 2

   Eric AndersonNovember 29, 2011 at 12:35 pm

   Does anyone know whether most, or any, of these minimal-complexity studies looks at whether the organisms survive and reproduce for multiple generations with only the alleged minimal genome in place?

   My understanding was that most, or at least some, of these studies come to their conclusions about which genes are required by performing knockouts. There are, however, good reasons to take knockout results with a grain of salt. Further, non-coding DNA can perform many critical roles, so looking at essential “genes” only misses a huge part of the picture.

   It seems it would be possible to remove the genetic material from a single-celled organism, replace it with a DNA sequence consisting only of the “required” genes and see if the organism in fact is able to survive and reproduce successfully. If that occurs, then one could say that, *given an already-constructed and living organism* this particular gene set of genes x1 . . . xn is the minimal set required. Does anyone know if such an experiment has been done?
3. 3

   bornagain77November 29, 2011 at 5:17 pm

   Eric Anderson, gpuccio, or some of the other Docs on UD, could probably give you a far better answer, but as far as I know the experiments have not been ‘rigorously’ performed yet.;

   notes:

   Minimal genome should be twice the size – 2006
   Excerpt: “Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath. “This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product. “When you knock out one gene, the genome can compensate by using an alternative gene. “But when you repeat the knock out experiment by deleting the alternative, the genome can revert to the original gene instead. “Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments.
   http://www.news-medical.net/ne.....16976.aspx

   Mouse Genome Knockout Experiment
   http://www.uncommondescent.com.....ent-374647

   John I. Glass et al., “Essential Genes of a Minimal Bacterium,” PNAS, USA103 (2006): 425-30.
   Excerpt: “An earlier study published in 1999 estimated the minimal gene set to fall between 265 and 350. A recent study making use of a more rigorous methodology estimated the essential number of genes at 382.,,, Given the evolutionary path of extreme genome reduction taken by M. genitalium, it is likely that all its 482 protein-coding genes are in some way necessary for effective growth in its natural habitat”
   http://www.pnas.org/content/103/2/425.full

   It is interesting to note that Dr. Stephen Meyer used the very conservative number of 250 for his estimate:

   Signature in the Cell – Book Review – Ken Peterson
   Excerpt: If we assume some minimally complex cell requires 250 different proteins then the probability of this arrangement happening purely by chance is one in 10 to the 164th multiplied by itself 250 times or one in 10 to the 41,000th power.
   http://www.spectrummagazine.or.....ature_cell

   As well, years ago Fred Hoyle arrived at approximately the same number, one chance in 10^40,000, for life spontaneously arising. From this number, Fred Hoyle compared the random emergence of the simplest bacterium on earth to the likelihood “a tornado sweeping through a junkyard might assemble a Boeing 747 therein”. Fred Hoyle also compared the chance of obtaining just one single functioning protein molecule, by chance combination of amino acids, to a solar system packed full of blind men solving Rubik’s Cube simultaneously.

   Professor Harold Morowitz showed the Origin of Life ‘problem’ escalates dramatically over the 1 in 10^40,000 figure when working from a thermodynamic perspective,:

   “The probability for the chance of formation of the smallest, simplest form of living organism known is 1 in 10^340,000,000. This number is 10 to the 340 millionth power! The size of this figure is truly staggering since there is only supposed to be approximately 10^80 (10 to the 80th power) electrons in the whole universe!”
   (Professor Harold Morowitz, Energy Flow In Biology pg. 99, Biophysicist of George Mason University)

   Dr. Morowitz did another probability calculation working from the thermodynamic perspective, with a already existing cell, and came up with this number:

   DID LIFE START BY CHANCE?
   Excerpt: Molecular biophysicist, Horold Morowitz (Yale University), calculated the odds of life beginning under natural conditions (spontaneous generation). He calculated, if one were to take the simplest living cell and break every chemical bond within it, the odds that the cell would reassemble under ideal natural conditions (the best possible chemical environment) would be one chance in 10^100,000,000,000. You will have probably have trouble imagining a number so large, so Hugh Ross provides us with the following example. If all the matter in the Universe was converted into building blocks of life, and if assembly of these building blocks were attempted once a microsecond for the entire age of the universe. Then instead of the odds being 1 in 10^100,000,000,000, they would be 1 in 10^99,999,999,916 (also of note: 1 with 100 billion zeros following would fill approx. 20,000 encyclopedias)
   http://members.tripod.com/~Black_J/chance.html

   Further notes

   “a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.” – R. C. Wysong

   ‘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

   of note: The 10^12 bits of information number for a bacterium is derived from entropic considerations, which is, due to the tightly integrated relationship between information and entropy, considered the most accurate measure of the transcendent quantum information/entanglement constraining a ‘simple’ life form to be so far out of thermodynamic equilibrium. For calculations, from the thermodynamic perspective, please see the following site:

   Molecular Biophysics – Information theory. Relation between information and entropy:
   Excerpt: Linschitz gave the figure 9.3 x 10^12 cal/deg or 9.3 x 10^12 x 4.2 joules/deg for the entropy of a bacterial cell. Using the relation H = S/(k In 2), we find that the information content is 4 x 10^12 bits. Morowitz’ deduction from the work of Bayne-Jones and Rhees gives the lower value of 5.6 x 10^11 bits, which is still in the neighborhood of 10^12 bits. Thus two quite different approaches give rather concordant figures.
   http://www.astroscu.unam.mx/~a.....ecular.htm
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   Eric AndersonNovember 29, 2011 at 5:45 pm

   Thanks bornagain77. These are helpful citations. Just a couple of quick thoughts:

   “Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath. “This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product.

   This is only a part of the issue. As I mentioned on another thread, the most we can say about a knockout, is that it appears the particular gene is not needed at this particular stage in the organism’s life. It doesn’t mean the gene wasn’t needed in a prior stage or won’t be needed at a later stage. There are a huge number of processes that occur in building the organism in the first place, many of which may not be needed later. That information must be somewhere, i.e., in DNA.

   “An earlier study published in 1999 estimated the minimal gene set to fall between 265 and 350. A recent study making use of a more rigorous methodology estimated the essential number of genes at 382.,,, Given the evolutionary path of extreme genome reduction taken by M. genitalium, it is likely that all its 482 protein-coding genes are in some way necessary for effective growth in its natural habitat”

   If, as it appears from their statement, they are referring only to protein-coding genes, it doesn’t even being to address what is needed for life. Having all the necessary genes doesn’t give us life anymore than having a CDROM gives us a functional computer. There have to be mechanisms to locate, retrieve, transcribe, translate, build, breakdown, etc. Gene knock out experiments typically don’t address any of that. The DNA necessary for simple life must include not only the minimal set of protein-coding genes for ongoing metabolic function, but also all instructions necessary to access and use those genes, as well as the information to build the organism in the first place.

   I agree with you that Meyer’s use of 250 proteins is almost certainly optimistically low. My take is that he understands that, but is willing to concede the point and go with this low estimate in order to make a larger point: even with a low estimate for what is needed for life, you don’t get even close to making it happen by chance with the probabilistic resources of the known universe.
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   bornagain77November 29, 2011 at 8:04 pm

   Programming of Life – video playlist:
   http://www.youtube.com/playlis.....F11E2FB840