Tuesday, January 31, 2006

Re: Improbability of Abiogenesis Calculations (A Response to Ian Musgrave)


Thanks for your message. As I usually do when I get a message of general interest, I am copying my reply to my blog CreationEvolutionDesign, minus your personal identifying information.

----- Original Message -----
From: AN
To: ...
Cc: Stephen E. Jones
Sent: Sunday, January 29, 2006 8:09 PM
Subject: Improbability of Abiogenesis Calculations (A Response to Ian Musgrave)

AN>Dear Sir,
>I'm neither a professional biologist nor an Evolution Theory expert. While I wandered in talkorigins.com and read some of their articles. I focused on one of the articles that I analysed throughly and eventually I convinced myself that I have enough scientific backup to write a response.

I regret that I don't have time to read your attached response, and anyway I have a rule not to click on attachments from people I don't know, in case it contains a virus. So this reply of mine is entirely my own.

AN>The original Article is: Lies, Damned Lies, Statistics,and Probability of Abiogenesis Calculations. Like most of Neo-Darwinists Ian Musgrave's weapon is to blame scientists who don't believe in their theory as liars.

Actually to be fair to Musgrave (who I have heard of but don't know - or can't remember - anything about him), the saying, "there are lies, damned lies and statistics" is an old one, being attributed to Mark Twain and Benjamin Disraeli, and I cannot see that Musgrave used the term "lies" (or its cognates) in the actual article.

AN>As far as I analysed his claims, it seems he must be the one who plays dangerous games with probability and statistics.

I will comment on only one part of Musgrave's paper, since it contains with the fundamental error (committed by almost the entire field of abiogenesis) of missing the whole point):

"The myth of the "life sequence" Another claim often heard is that there is a "life sequence" of 400 proteins, and that the amino acid sequences of these proteins cannot be changed, for organisms to be alive. This, however, is nonsense. The 400 protein claim seems to come from the protein coding genome of Mycobacterium genetalium, which has the smallest genome currently known of any modern organism [20]. However, inspection of the genome suggests that this could be reduced further to a minimal gene set of 256 proteins [20]. Note again that this is a modern organism. The first protobiont/progenote would have been smaller still [4], and preceded by even simpler chemical systems [3, 10, 11, 15]. " (Ian Musgrave, "Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations," The Talk.Origins Archive, December 21, 1998)

The fundamental point that Musgrave (along with most most evolutionists and indeed most creationist/IDists arguing with them) misses (as I pointed out in my two-part post "The Minimal Cell 1/2" and 2/2), is that the problem is not the `blind watchmaker' origin of life's individual building blocks (i.e. amino acids/proteins or nucleic acids/RNA/DNA), difficult though that is, but the much greater problem of the origin of a fully self-sustaining, self-reproducing, cell, i.e. a Von Neumann machine.

A quote by Princeton biophysicist Harold F. Blum makes this point, that the problem is "how a self-replicating machine came into existence," not just the origin of the "a mixture of chemicals":

"The living machine is clearly not just a mixture of chemicals, yet there seems to be widespread belief that, once the proper molecular compounds were there, life would appear, whether on the earth, on Mars, or elsewhere in the universe. This no more follows, I may point out at the risk of being thought overly facetious, than that an automobile, 1962 model, might spring spontaneously from a mixture of all the chemical species from which it is composed. ... As the late John von Neumann pointed out ... we are trying to understand how a self-replicating machine came into existence; this poses problems that are indeed difficult to formulate in our imagination, and should not be passed over too lightly." (Blum H.F., "Time's Arrow and Evolution," [1951], Harper Torchbooks: New York NY, Second Edition, 1955, Revised, 1962, pp.178G-178H)

It is in fact far, far more of a problem than Fred Hoyle's analogy of a whirlwind blowing through a junkyard producing a fully assembled Boeing 747:

"The popular idea that life could have arisen spontaneously on Earth dates back to experiments that caught the public imagination earlier this century. If you stir up simple nonorganic molecules like water, ammonia, methane, carbon dioxide and hydrogen cyanide with almost any form of intense energy, ultraviolet light for instance, some of the molecules reassemble themselves into amino acids, a result demonstrated about thirty years ago by Stanley Miller and Harold Urey. The amino acids, the individual building blocks of proteins can therefore be produced by natural means. But this is far from proving that life could have evolved in this way. No one has shown that the correct arrangements of amino acids, like the orderings in enzymes, can be produced by this method. No evidence for this huge jump in complexity has ever been found, nor in my opinion will it be. Nevertheless, many scientists have made this leap-from the formation of individual amino acids to the random formation of whole chains of amino acids like enzymes-in spite of the obviously huge odds against such an event having ever taken place on the Earth, and this quite unjustified conclusion has stuck. In a popular lecture I once unflatteringly described the thinking of these scientists as a "junkyard mentality". As this reference became widely and not quite accurately quoted I will repeat it here. A junkyard contains all the bits and pieces of a Boeing 747, dismembered and in disarray. A whirlwind happens to blow through the yard. What is the chance that after its passage a fully assembled 747, ready to fly, will be found standing there? So small as to be negligible, even if a tornado were to blow through enough junkyards to fill the whole Universe." (Hoyle F., "The Intelligent Universe," Michael Joseph: London, 1983, pp.18-19)

The analogy would be of the whirlwind producing Boeing's 747 factory (which BTW I have visited near Seattle), but that it would have to also include all the factories that produce all the components from their raw materials that the Boeing 747 factory assembles together, because that is what the simplest free-living cell does.

I have added the above to a new section of my "Problems of Evolution" book outline, sections PE "Cell ... It is far more a problem than Hoyle's whirlwind in a junkyard assembling a Boeing 747." I have also added the following quotes under sections PE 8.5."The minimal cell", sub-sections PE 8.5.2 "Minimum number of genes" and PE 8.5.4. "Minimum number of gene products (proteins, RNAs)," respectively:

"Mycoplasma genitalium has the smallest genome of any organism that can be grown in pure culture. It has a minimal metabolism and little genomic redundancy. Consequently, its genome is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. Using global transposon mutagenesis, we isolated and characterized gene disruption mutants for 100 different nonessential protein-coding genes. None of the 43 RNA-coding genes were disrupted. Herein, we identify 382 of the 482 M. genitalium protein-coding genes as essential, plus five sets of disrupted genes that encode proteins with potentially redundant essential functions, such as phosphate transport. Genes encoding proteins of unknown function constitute 28% of the essential protein-coding genes set. Disruption of some genes accelerated M. genitalium growth." (Glass J.I., et al., "Essential genes of a minimal bacterium," Proceedings of the National Academy of Sciences, USA, Vol. 103, No. 2, January 10, 2006, pp.425-430)

"In July 1995 the entire DNA sequence of the bacterium Haemophilus influenzae, 1.8 million base-pairs, was elucidated, followed three months later by the sequence of a second parasitic bacterium. In April 1996 the complete sequence (12 million base-pairs) of yeast was announced, and in August 1996 the first complete sequence of a free-living bacterium, Methanococcus, which has 1.7 million base-pairs and about 1700 genes, perhaps close to the minimum necessary for independent life." (Patterson C., "Evolution," [1978], Cornell University Press: Ithaca NY, Second edition, 1999, p.23).

AN>Attached you will find my attempt to write a response. I don't have a web site to post it and of course it may contain calculation errors and scientific misconceptions as well but I hope it will be of your interest.

Thanks again, but see above on my rule of not opening attachments from people I don't know. Also, it is my long-standing policy to not get involved in private discussions on creation, evolution, design topics. If you think your paper may have "calculation errors and scientific misconceptions," then may I suggest you join an Internet discussion group like CreationEvolutionDebate (not to be confused with my now-terminated group CreationEvolutionDesign) and post your response there, where it will be webbed on the group's archives. I am sure the evolutionist members of that group would be only to happy to correct any errors or misconceptions (real or imaginary) in it! If you can put up with evolutionists' insults (a big "if"), then from personal experience of 5+ years on evolutionist-dominated lists, it is a great way to learn about creation, evolution and design issues and to have one's position `refined in the fire', all for free!

AN>Best Regards
Senior Software Engineer

Stephen E. Jones, BSc (Biol)
"Problems of Evolution"

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