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Does handed DNA and protein prove Intelligent Design?

Post of the Month: July 2008


Subject:    | Summary of Origin of Life Problems 3 - Revisit
Date:       | 14 Jul 2008
Message-ID: |

apobetics wrote:
>> Amino Acids

>> 1. Amino acids are necessary for life, but they do not form
>> spontaneously, or naturally.

>> 2. The amino acids formed by Miller were a mixture of D- and L- amino
>> acids yet D- amino acids are poisonous to living organisms. Miller
>> would need to demonstrate how the first life could use both D- and L-
>> amino acids and later change into only L- amino acids.

>> For all intents and purposes amino acids must be ruled out as
>> naturally forming on their own. Amino acids are a prima facia evidence
>> of a supernatural Designer which is the real primary axiom - "In the
>> beginning God created amino acids".

Devil's Advocaat wrote:
> And I would like to make the following response.

> Hundreds of naturally occurring amino acids have been isolated and
> identified, the majority of which are never found in living organisms.
> The cell walls of many bacteria contain D-alanine and D-glutamic acid
> in their structure. Even some of the proteins produced by cone snails
> contain D-amino acids. To suggest that amino acids cannot form
> "spontaneously, or naturally" ignores the fact that chemical reactions
> are not chance events, and emphasises the creationist idea that "X
> cannot have happened by chance, therefore X must have been
> deliberately created".

> Now coming to the part that "apobetics" didn't obtain from Carl
> Werner's "Evolution: The Grand Experiment". "apobetics" claims that
> "Amino acids are a prima facia evidence of a supernatural Designer".

> But what does he mean by "prima facia evidence"? The actual phrase I
> believe he should have typed in is "prima facie", which means "on its
> first appearance" or "by first instance", and in legal circles refers
> to something that appears on first examination to be self evident from
> the facts. This doesn't mean that the thing is confirmed by the facts,
> as "apobetics" seems to think from his posting. "apobetics" is one of
> many who oppose the theory of evolution simply because it doesn't fit
> in with their worldview. To him and others if his ilk I have only this
> to say: "necessitas probandi incumbit ei qui agit".

The classic paper was of course Stanley Miller's 1953 paper

Miller, Stanley L., 1953 "A Production of Amino Acids Under Possible Primitive Earth Conditions" Science vol. 117:528-529

With a bit more information included in:

Miller, Stanley, Harold C. Urey 1959 "Organic Compound Synthesis on the Primitive Earth" Science vol 139 Num 3370: 254-251

Miller showed that a very simple set up that mimicked some key aspects of the early Earth could rapidly produce amino acids, among other things.

This result has been one of the most often repeated (and confirmed) experiments I have ever encountered. In spite of this, creationists regularly claim that it is invalid. Jonathan Wells, a fellow of the creationist "Discovery Institute" claims to have refuted the Miller/ Urey experiment (and all of what he called Darwinist "icons.")

But, the atmosphere is not the only synthesis location. For example

Amend, J. P. , E. L. Shock 1998 "Energetics of Amino Acid Synthesis in Hydrothermal Ecosystems" Science Volume 281, number 5383, Issue of 11 Sep , pp. 1659-1662.

Blank, J.G. Gregory H. Miller, Michael J. Ahrens, Randall E. Winans 2001 "Experimental shock chemistry of aqueous amino acid solutions and the cometary delivery of prebiotic compounds" Origins of Life and Evolution of the Biosphere 31(1-2):15-51, Feb-Apr

Chyba, Christopher F., Paul J. Thomas, Leigh Brookshaw, Carl Sagan 1990 "Cometary Delivery of Organic Molecules to the Early Earth" Science Vol. 249:366-373

Engel, Michael H., Bartholomew Nagy, 1982 "Distribution and Enantiomeric Composition of Amino Acids in the Murchison Meteorite", Nature , 296, April 29, , p. 838.

Matthews CN. 1992 Hydrogen cyanide polymerization: a preferred cosmochemical pathway. J. Br. Interplanet Soc. 45(1):43-8

Schoonen, Martin A. A., Yong Xu 2001 "Nitrogen Reduction Under Hydrothrmal Vent Conditions: Implications for the Prebiotic Synthesis of C-H-O-N Compounds" Astrobiology 1:133-142

Creationist liars also like to insist that without a reducing atmosphere, there could be no amino acid production. I think it was totally fitting that the last publication of Stanley Miller, 55 years after his ground breaking article, demonstrated that under a neutral atmosphere, or even with trace free oxygen, ample amino acids could form in the presence of common minerals such as calcite.

H. James Cleaves & John H. Chalmers & Antonio Lazcano & Stanley L. Miller & Jeffrey L. Bada 2008 "A Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres" Orig Life Evol Biosph 38:105-115

So amino acids are easy and plentiful on a pre-life (abiotic) Earth.

Regarding chirality (which creationists like to pontificate about without the slightest idea of what it means), there is actually no problem at all.

Pasteur discovered that most amino acids came in two forms which can be identified by how they refract light. We label theses L- (for levo or left) and D- (for dextro, or right). The interesting thing is that life on Earth uses the L form of amino acids, and hardly ever uses the D- form. A solution of just one form is called "chiral" and a mix of forms about 50/50 is called racimic. The kinds (L or D) are called enantomers.

The nucleic acid bases I mentioned earlier are also found in L- and D- forms, only in this case life on Earth only uses the D- form.

Creationists like to present this as a profound mystery that is supposed to "prove" that they are correct. I want to mention a neat instance where both left and right amino acids are used in a living thing. It seems very rare, but it does happen. Next time a creationist claims to be an "expert" and that amino acid chirility "proves" something supernatural, you can gob-smack-em. The protein is called Gramicidin A and it has 8 L-amino acids, 6 D-amino acids, and one glycine which is an amino acid that is neither L- or D- in its structure. I have found that even many biologists will bet an "adult beverage" that all proteins are exclusive L- amino acids.

Before we go forward another couple of basic chemical facts need to be added to the discussion. First, L- amino acids will randomly convert to D- amino acids over time, and D- forms will convert to L- forms. This is called "racimization" because eventually you will end up with equal amounts of L- and D- amino acids. The rate that this occurs at varies with the amino acid, and its surroundings. The fastest conversion happens to amino acid molecules all by themselves in hot water. Under cold, dry conditions when the amino acids are attached to one another, or better yet, if they are also attached to a mineral, racimization can be very slow. Very, very slow.

This means that if there is even a tiny advantage one way or the other, the favored form will become the dominant form. The advantage comes from a surprising direction: outer space.

Cronin, J. R. & Pizzarello, S., 1999. Amino acid enantomer excesses in meteorites: Origin and significance. Advances in Space Research 23(2): 293-299.

Service, RF, 1999. Does life's handedness come from within? Science 286: 1282-1283.

Antonio Chrysostomou, T. M. Gledhill,1 Fran‡ois M‚nard, J. H. Hough, Motohide Tamura and Jeremy Bailey 2000 "Polarimetry of young stellar objects -III. Circular polarimetry of OMC-1" Monthly Notices of the Royal Astronomical Society Volume 312 Issue 1 Page 103 - February

Michael H. Engel and Bartholomew Nagy, 1982 "Distribution and Enantiomeric Composition of Amino Acids in the Murchison Meteorite", Nature , 296, April 29, , p. 838.

Jeremy Bailey, Antonio Chrysostomou, J. H. Hough, T. M. Gledhill, Alan McCall, Stuart Clark, Fran‡ois M‚nard, and Motohide Tamura 1998 Circular Polarization in Star- Formation Regions: Implications for Biomolecular Homochirality Science 1998 July 31; 281: 672-674. (in Reports)

Chyba, Christopher F. 1997 Origins of life: A left-handed Solar System? Nature 389, 234- 235 (18 Sep 1997)

Engel, M. H., S. A. Macko 1997 Isotopic evidence for extraterrestrial non- racemic amino acids in the Murchison meteorite. Nature 389, 265 - 268 (18 Sep) Letters to Nature

That should do for that. The next question is can the advantage of L- amino acids be conserved in the formation of more complex molecules called "peptides?" Yep.

Schmidt, J. G., Nielsen, P. E. & Orgel, L. E. 1997 Enantiomeric cross- inhibition in the synthesis of oligonucleotides on a nonchiral template. J. Am. Chem. Soc. 119, 1494-1495

Saghatelion A, Yokobayashi Y, Soltani K, Ghadiri MR, 2001"A chiroselective peptide replicator", Nature 409: 797-51, Feb

Singleton, D A,& Vo, L K, 2002 "Enantioselective Synthsis without Discrete Optically Active Additives" J. Am. Chem. Soc. 124, 10010-10011

Yao Shao, Ghosh I, Zutshi R, Chmielewski J. 1998 Selective amplification by auto- and cross-catalysis in a replicating peptide system. Nature. Dec 3;396(6710):447-50.

And there seems to be other L- selection advantages as well. For example:

Hazen, R.M., T.R. Filley, and G.A. Goodfriend. 2001. Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality. Proceedings of the National Academy of Sciences 98(May 8):5487.

So chirility doesn't seem to be a big problem. This is far different from the way creationists present this. They cite a few out of date reports and then falsely claim that chiral life is impossible by natural means.

There are larger arguments for a racemic origin of life.

Edward Trifonov (2004) confirmed two ideas, that the earliest amino acids were those easiest to form abiotically, that codons and aa's organized contemporaneously to form short ogliomers (what he didn't cite was the notion that oligomers can form spontaneously, are "selected" merely by being stable, and that RNAs (or Lacanzo and Miller's PNAs) imprint and replicate "successful" short peptides.) Trifonov wrote, "The amino-acid chronology itself is a quintessence of natural simplicity and opportunism: use first those amino acids that are available. When done with all codons, take from those amino acids that have too many."

The fact is that there are a growing list of short proteins with D- aa's, (most of the ones I know of are bacterial membrane components but there are also examples from yeasts to humans). Add to this, most bacteria have evolved enzymes that convert L-aa's to D-aa's for the same Miller/prebiotic amino acids. Again even we humans have enzymes to use D-aa's.


  1. ancient first cells were using racemic L- and D- aa's because they were readily available,
  2. biological and biochemical events reduced the availability of D- aa's,
  3. bacteria evolved racemases to maintain/sustain their existing metabolic pathways as attested by L- to D- amino acid racemases found even in humans. Ergo: The chirality "problem" in OOL isn't a problem.

Trifonov, Edward N. 2004 "The Triplet Code From First Principles" Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 22, Issue Number 1,

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