Friday, July 27, 2012

Creationist physicist Nathan Aviezer

Physicist Nathan_Aviezer has recently replied to a critical review of his work on creationism written 13 years ago by Mark Perakh.

Perakh devoted a page or two to the "paradox of the origin of life" as proposed by Aviezer. Specifically, he quoted Aviezer "...the(sic) life could not develop from inanimate matter because inanimate matter contains neither proteins nor nucleic acids." In his reply to Perakh, Aviezer reiterates this "paradox" writing, "My second example concerns the chicken-and-egg paradox relating to the origin of life. I explained (p. 68, In the Beginning) that all living cells contain both nucleic acids and proteins and that life is quite impossible without both. The paradox lies in the fact that proteins are produced only by nucleic acids and that nucleic acids can exist only in the presence of proteins. Since neither molecule can exist without the other, there is a paradox: how did nucleic acids and proteins come into existence? This paradox is often compared to the famous “chicken-and-egg paradox.” Since chicken eggs come only from chickens and chickens come only from chicken eggs, how did chickens and chicken eggs come into existence?"

Aviezer insisted his superficial treatment of the origin of life was drawn from "leading scientists" (emphasis in the original). His cited experts were David G. Smith, editor-in-chief of The Cambridge Encyclopedia of Earth Sciences (1981), Professor Frank Shu of the University of California, and Professor Jean Audouze, General Editor of "The Cambridge Atlas of Astronomy" (1982). Aviezer then hides behind these "authorities" accusing Perakh of "calling “absurd” the discussion of respected men of science." This is a fraud that should be addressed prior to exploding Aviezer's scientific claims about the origin of life.

I have found over the years that creationists discussing OOL have no idea at all of the available literature. Aviezer is no exception. His citation of the 30 year old work edited by David G. Smith is unimpressive. Further, a literature search shows no original work by DG Smith on the topic. I found the selection of Aviezer's remaining experts rather amusing as like Aviezer and Perakh, they are physicists. Physicists are the smartest of all scientists, and are experts at all things. Just ask Aviezer. (Surgeons have a similarly high opinion of themselves). Frank Shu, a theoretical physicist at Cal Berkeley has a distinguished career spanning over 40 years. But looking at his major interests, such as "SELF-SIMILAR COLLAPSE OF ISOTHERMAL SPHERES AND STAR FORMATION" (1977), or "Planetesimal Formation by Gravitational Instability" (2002), I find nothing on the origin of life. He also conducted research on the formation of chondrites, which in a very abstract way could have relevance to OOL. His 30 year old undergraduate book, "The Physical Universe: An Introduction to Astronomy" (1982) did have a short chapter on origin of life research. And as this was the work cited by Aviezer, we can understand his lack of familiarity with OOL research.

Jean Audouze specialized in stellar nucleosynthesis, the origin of elements heavier than lithium. See for example his, "The First Generation of Stars: First Steps toward Chemical Evolution of Galaxies" 1995. This is at least of some interest to OOL as we need heavy elements to exist as a precursor to any life form. But, it has nothing relevant to any modern study of OOL, or biological evolution.

So, Alviezer lacking any knowledge about origin of life research makes some assertions that insurmountable problems "prove" the existence of the supernatural, and the literal interpretations of various (but not all) biblical texts. A brief review of some recent research debunking Aviezer's claims follows.

The 1970s discovery of ribozymes, small RNAs that are catalytic, a nucleic acid enzyme, resulted in the "RNA world" hypothesis. This proposed that prebiotic RNAs were both metabolic, and a template of molecular memory. Leslie Orgel in 2004 was doubtful about any straight forward solutions, in spite of noting, “The demonstration that ribosomal peptide synthesis is a ribozyme-catalyzed reaction makes it almost certain that there was once an RNA World.” For an early demonstration of spontaneous hypercycles directly related to OOL, see Lee, et al (1997). An exciting RNA example published in 2009 was "Self-sustained replication of an RNA enzyme" (Lincoln et al).

Powner et al (2009) have demonstrated that simple chemical stock when reacted under realistic prebiotic conditions will produce ample activated ribonucleotides. They allowed readily available minerals to react with the organics, in this case the key feature was inorganic phosphorus added to the reaction. The key feature of Powner et al is that they used a more prebiotically natural mixture of organic and inorganic chemistry. This eliminates Aviezer's insistence that only living systems can produce nucleotides. (Actually, his "vitalism" idea was dispensed with by Wöhler in 1828).

Creationists also insist that RNAs must be "highly complex." This "complexity" notion is the core concept of the Intelligent Design creationist argument, and is operationalized as having an exact sequence that cannot have happened randomly. Just two papers are adequate to dismiss this argument; “Isolation of new ribozymes from a large pool of random sequences” and “Structurally complex and highly active RNA ligases derived from random RNA sequences." These papers also expose the foolishness of creationist’s calculations of “probabilities” for the origin of life such as used by Aviezer, and Intelligent Design creationists William Dembski, and Stephen Meyer. We are told by creationists that RNAs must be large to be active. This was known to be false over 13 years ago with the publication of, “A small catalytic RNA motif with Diels-Alderase activity.” It was further refuted two years ago by, “Multiple translational products from a five-nucleotide ribozyme.” We were told by creationists that many nucleotides, in complex patterns were necessary for the origin of life. This was debunked a decade ago by, "A ribozyme composed of only two different nucleotides." However, we can have spontaneous complexity too, as shown by Derr et al (2012).

Ribozymes, can be combined with equally natural lipid vesicles such as those studied by David Deamer of the University of California since the mid 1980s. He found meteoric amphipilic compounds which spontaneously form vesicles similar to phospholipid membranes. This research was reviewed in Deamer et al (2002), and Deamer (2011). Ribozymes, combined with equally natural lipid vesicles are extremely close to life, if in fact not "living" in the modern sense of complex cells. They would be "living" in the sense of a sustainable molecular system capable of Darwinian evolution. There are two major events necessary for the early evolution of modern cells; the shift to DNA as the principle cellular "memory," and the transition to amino acid enzymes rather than ribozymes. This goes well beyond the scope of this comment, but readers might be interested in Trifonov 2004, and Woese 2002.

For additional information on OOL research, see my "Short Outline of the Origin of Life.

Bartel, DP, JW Szostak,
1993 “Isolation of new ribozymes from a large pool of random sequences” Science 10 September 1993: Vol. 261 no. 5127 pp. 1411-1418
DOI: 10.1126/science.7690155

Burckhard Seelig and Andres Jgschke
1999 “A small catalytic RNA motif with Diels-Alderase activity” Chemistry & Biology Vol 6 No 3

Deamer, David W., JASON P. DWORKIN, SCOTT A. SANDFORD, MAX P. BERNSTEIN, and LOUIS J. ALLAMANDOLA
2002 “The First Cell Membrane” ASTROBIOLOGY Volume 2, Number 4, 371-381

Derr, Julien, Michael L. Manapat, Sudha Rajamani, Kevin Leu, Ramon Xulvi-Brunet, Isaac Joseph, Martin A. Nowak, Irene A. Chen
2012 “Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences” Nucl. Acids Res. (2012) doi: 10.1093/nar/gks065

Ekland, EH, JW Szostak, and DP Bartel
1995 "Structurally complex and highly active RNA ligases derived from random RNA sequences" Science 21 July 1995: Vol. 269. no. 5222, pp. 364 - 370

Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR,
1997 “Emergence of symbiosis in peptide self-replication through a hypercyclic network.” Nature, 390: 591-4

Lincoln et al.
2009 Self-Sustained Replication of an RNA Enzyme. Science, Jan 8, 2009 Vol. 323 no. 5918 pp 1229-1232; DOI: 10.1126/science.1167856

Orgel LE.
2004 “Prebiotic chemistry and the origin of the RNA world” Crit Rev Biochem Mol Biol. Mar-Apr; 39(2):99-123. DOI: 10.1080/10409230490460765

Powner, Matthew W., Be´atrice Gerland & John D. Sutherland
2009 “Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions” Nature Vol; 459, 239-242 doi:10.1038/nature08013
102. Reader, J. S. and G. F. Joyce
2002 "A ribozyme composed of only two different nucleotides." Nature vol 420, pp 841-844.

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

Turk, Rebecca M., Natayliya V. Chumachenko, Michael Yarus
2010 “Multiple translational products from a five-nucleotide ribozyme” PNAS vol. 107 no. 10 4585-4589

Woese, Carl
2002 “On the evolution of Cells” PNAS Vol. 99 13:8742-8747, June 25

Wöhler, F.
1828 ON THE ARTIFICIAL PRODUCTION OF UREA
Annalen der Physik und Chemie, 88, Leipzig

2 comments:

Torbjörn Larsson, OM said...

On the RNA world I would add, as I noted over on The Panda's Thumb, that modern genome/protein methods now reach down through the DNA UCA before domain diversification all the way to the RNA/protein world by way of protein fold families.

It turns out that the RNA/protein world is ~ 20 % of a fold clock proxy, the DNA UCA another ~ 20 %, and first after comes diversification into domains. ["The evolution and functional repertoire of translation proteins following the origin of life", Goldman et al, Bio Dir 2010; and similar works.] In other words, ~ 50 % of cell history (by proxy) happened before the ancestors of modern cells evolved.

To contribute more references here, the existence of a DNA UCA is itself tested by phylometabolic methods.

On a trophic level, a robust and doubled autotrophic CO2 metabolism before diversification tests a common root. The robustness further tests that early cell regulation of metabolism and growth, the latter which would have acted as a parasitic drain on the autocatalytic cores of carbon metabolism, was less evolved as would be expected out of an RNA world and/or chemical evolution. [“The Emergence and Early Evolution of Biological Carbon-Fixation, Braakman et al, PLoS Comp Bio 2012.]

Similarly a non-stereosymmetric lipid membrane biosynthesis before diversification tests a common root. [“Ancestral lipid biosynthesis and early membrane evolution”, Peretó et al, TRENDS in Bio Sci 2004.]

And on the ribozymes I would add that we now know that the chemical selection promotes catalysts. Which implies that pre- to protobiotic pathways could within reach for testability! Yes, it really seems so, as the following toy model shows:

DNA-protein cell machinery, RNA or ATP biosynthesis before the first membranes, the first enzymes are examples of (not fully exclusive) common evolutionary chicken-and-egg problems. Luckily such problems conveniently bottleneck possible pathways to a smaller set.

Bottom up, chemical network enzymes are a natural outcome in newer scenarios. High-temperature reactions seems to be much faster than orthodox theory believed from scant data. This temperature dependence gives a self-selection for enthalpic pre-proteinous enzymes. ["Impact of temperature on the time required for the establishment of primordial biochemistry, and for the evolution of enzymes", Stockbridge et al, PNAS, 2010.]

Now looking top down, we see that pathways meet. The first modern metabolic networks originated with purine metabolism, and specifically with the gene family of the P-loop-containing ATP hydrolase fold. ["The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture", Caetano-Anollés et al. PNAS, 2007; "Rapid evolutionary innovation during an Archaean genetic expansion", David et al, Nature, 2010.]

That is, ATP sits at the intersection between a cooling and/or hydrothermal vent active Earth premetabolism and nucleotide protometabolism. (Which compound seems to later have been exaptated by modern proteinous metabolic genes as coenzyme/energy currency.) Minimum change of traits picks ATP use before RNA evolution

Note that this is an (informal) test of a phylogenetic pathway. Abiogenesis is actually slightly testable today as far as I can see.

To solve the new chicken-and-egg problem between RNA and coenzymes in metabolism, it turns out ATP, CoA et cetera coenzyme's synthesis can be easily RNA-catalyzed by polyphosphate activation. ["RNA-Catalyzed CoA, NAD and FAD Synthesis from Phosphopantetheine, NMN, and FMN", Huang et al, Biochem 2000.] Finally there is also recent implications of selection of RNA in its enhanced enzymatic capability in the presence of iron under anoxic conditions, as on the primeval Earth.

Gary S. Hurd said...

Thanks for your remark. I have the next few days filled, but I'll try to read your citations as soon as I ca. It is currently a very active time in Origin Of Life research.