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

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.
Annalen der Physik und Chemie, 88, Leipzig

Saturday, July 21, 2012

Rabbi Adam Jacobs, July 2012 in Algemeiner

As of Sunday the 22, Algemeiner has blocked the rest of my comments from appearing.

After about 16 hours, this post was finally seen. There was typically stupid reply which I appended below with my response.

I judge the quality of someone's thinking partly by how well they can handle the simple facts they use to build their argument. These minor features, rather than being trivial reflect the care and grounding of an argument. Adam Jacobs stumbles at the starting line.

With the title, Intelligent Design In Language," my BS detector was in high from the start. When Jacobs wrote, "Isaac Mozeson, a Ph.D. in linguistics from NYU," my first thought was, "If he was From NYY, Where did he go?" A simple Google check revealed that Dr. Mozeson A) never received a doctorate in linguistics, B) he never held an academic appointment in linguistics, C) he never published in a professional linguistics journal. He is a promoter of biblical literalism, and claims to have "discovered" that all human languages derive from what he has variously termed Hebrew, biblical Hebrew, proto-Hebrew, pre-Hebrew, and most recently "Edenic." For a direct example of his thinking see, "COULD PRE-HEBREW BE THE SAFA AHAT OF GENESIS 11:1 ?"

In that essay, the core failure of Mozeson's reasoning is exposed- he assumes from biblical arguments that all languages, and all humanity originated as presented in Genesis. Any counter evidence is to be disregarded as the result of magical intervention given in Gen. 11:6, 9.

But, lets return to Rabbi Jacobs. He wrote, "Ever wonder where the name gopher came from? No one seems to know, but we do know the quality of the creature – he’s a digger, and as it happens, the Edenic word for digging is “khofer.” This raised some serious issues about Jacobs' education. I should have thought a Rabbi should know that "khofer" does not mean "to dig." I had supposed that a Rabbi would know the Hebrew verb pronounced "ko fer" כפר in the Bible, eg the Leningrad Codex, meant "to cover" (see Gen. 6:14). But, let's leave Hebrew for the moment. The third gross error by Jacobs is that "No one seems to know (the origin of the name gopher given in North America to small burrowing rodents). This showed that Rabbi Jacobs was at best very lazy, too lazy to use the Oxford English Dictionary, or the Webster's Unabridged. (The origin of this particular use of the phoneme "go fer" comes from the French word for "honeycomb" first used in English for a fried bread now popularly called a "waffle." Early Francophone settlers called the intricate shallow burrows made by Geomys sp., and Thomomys sp. "gophers."

Three strikes. Yer out!

Added July 22, 2012

Aharon Ben David
July 22, 2012
12:09 am

I might suggest that you judge the quality of an argument, by the argument (and not by the relatively extraneous points you take issue with). Whatever Mozeson assumes and whatever his degree do not have any direct impact on the quality of the argument presented here.

You have, therefore, only offered one potentially valuable critique re: the word Gopher. “Khofer” does however mean dig (chet, pey, reish)as I just checked in the Reuben Alcalay dictionary. The French waffle connection seems like a stretch to me. Khofer/digger seems much more direct and accurate.

Reply, so far blocked by Algemeiner;

Aharon Ben David, Your comment is a perfect example of why those uneducated in linguistics should not attempt linguistic analysis. My point regarding the Isaac Mozeson's literature degree was that this Rabbi Adam Jacobs is incapable of correctly making even minor points of fact.

This was not your only error.

The Reuben Alcalay dictionary was intentionally limited to the modern Hebrew language decided upon by the Hebrew Language Academy, plus new words invented by the Hebrew language popular press principally from Israel in just the last 60 years. It is absurd to claim that this dictionary is of help understanding 3 to 4 thousand year old lexicons. It is this arrogant ignorance that is central to Isaac Mozeson's effort.

Read this out loud;

He was a janglere and a goliardeys,

And that was moost of synne and harlotries.

Wel koude he stelen corn, and tollen thries;

And yet he hadde a thombe of gold, pardee.

A whit cote and a blew hood wered he.

A baggepipe wel koude he blowe and sowne,

And therwithal he broghte us out of towne.

That is in English a mere 600 years ago. Mozeson claims to have reconstructed a proto-Hebrew he calls "Edenic" that is the mother tongue of all human language well over 10,000 years old. My specific example of this incompetence, "ko fer," was selected by Rabbi Jacobs. He made the error that an early biblical attested meaning of "כפר" was "digging" and that this was in anyway related to the modern English meaning of "Gopher" referring to members of the genus Thomomys. For the truthful derivation of this in English, I directed you to the Oxford English Dictionary, or Webster's Unabridged. You obviously ignored the obvious. As for the actual biblical meaning of "כפר" you should start with the older bits of the Torah. And if you do, you will find that "dig" isn't in the ancient biblical lexicon.

Sunday, July 15, 2012

I have rarely ever seen a worse mess

My news feeder came up with this the other day, "Darwin's Evolution theory obsolete?", hosted by "Allvoices" which calls itself, "the world's premier platform for citizen journalism."

It is such a crow's nest of paranoid right-wing fanaticism, and creationist twaddle that I won't even begin to try and untangle it. I know that clicking on the page feeds a fraction of a penny to the lunatic who wrote it, but it is such a freak show that I posted the link anyway. There is probably something I should say about the quality of "information" on the internet, but it seems inadequate.

In other news, local fishing remains slow, and my attempts to make anything clear to creationists on The Nation's Creationism and education thread have come to naught.

Tuesday, July 10, 2012

I found an excellent pro-science site

"Letters to Creationists" I was serching around for material to use in a debunking of some bullshit about the Grand Canyon by Andrew Snelling. This was as good, or better, than what I would have done.