The origin(s) of replication and translation

[The Barbarian]

(Barbarian shows that bob has misrepresented the views of yet another real scientist)

(bob attempts to change the subject)

Do you conider "scenarios" to be science?

Yep. Why? Because he advanced a testable claim, based on evidence. I know how much you hate the "e word", but that's what science is based on. The issue, however was your blatant misrepresentation of the man's views:

So why did Koonin submit this article for publication and risk the scorn of the peer reviewers? I submit that he did this because he considers the rise of replication-transcription an impenetrable "mystery".

Note that he not only doesn't think that, he proposes a mechanism, and shows how it can be tested.

Also, I noticed that you failed to provide a link so that we could see the date of Koonin's proposed "scenario".

Biol Direct. 2007 May 31;2:14

Doesn't matter. If you didn't know his opinions on the matter, you had no right to make up a position for him. As you see, this paper is the same date as the one you cited, so you have no excuse at all.

Furthermore, even earlier, Koonin had written:
Comparative analysis of the diversity of genomic strategies and organizations of viruses and cellular life forms has the potential to open windows into the deep past of life's evolution, especially, with the regard to the origin of genome replication systems. When complemented with information on the evolution of the relevant protein folds, this comparative approach can yield credible scenarios for very early steps of evolution that otherwise appear to be out of reach.
Biol Direct. 2006 Dec 18;1:39

 

[Johnny]

Shameful.

 

[bob b]

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life
Eugene V Koonin
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

Biology Direct 2007, 2:15 doi:10.1186/1745-6150-2-15

The electronic version of this article is the complete one and can be found online at: http://www.biology-direct.com/content/2/1/15

Received 10 May 2007
Accepted 31 May 2007
Published 31 May 2007

© 2007 Koonin; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Background

Recent developments in cosmology radically change the conception of the universe as well as the very notions of "probable" and "possible". The model of eternal inflation implies that all macroscopic histories permitted by laws of physics are repeated an infinite number of times in the infinite multiverse. In contrast to the traditional cosmological models of a single, finite universe, this worldview provides for the origin of an infinite number of complex systems by chance, even as the probability of complexity emerging in any given region of the multiverse is extremely low. This change in perspective has profound implications for the history of any phenomenon, and life on earth cannot be an exception.

Hypothesis

Origin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial) solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe, i.e., that a coupled system of translation and replication emerged by chance, and became the breakthrough stage from which biological evolution, centered around Darwinian selection, took off. A corollary of this hypothesis is that an RNA world, as a diverse population of replicating RNA molecules, might have never existed. In this model, the stage for Darwinian selection is set by anthropic selection of complex systems that rarely but inevitably emerge by chance in the infinite universe (multiverse).

Conclusion

The plausibility of different models for the origin of life on earth directly depends on the adopted cosmological scenario. In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable. Therefore, under this cosmology, an entity as complex as a coupled translation-replication system should be considered a viable breakthrough stage for the onset of biological evolution.

Reviewers

This article was reviewed by Eric Bapteste, David Krakauer, Sergei Maslov, and Itai Yanai.

 

[bob b]

I agree with Johnny that it was quite shameful of Barb to post from a different article that I had never seen and imply that I was deceitful in misrepresenting Koonin's views.

Apparently Koonin was covering his *** by writing the 2nd article with a colleague.

Also note that the claim is made that "only some aspects" of the theory would be subject to experimental verification.


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On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
Yuri I Wolf1 and Eugene V Koonin1
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Corresponding author.
Yuri I Wolf: wolf@ncbi.nlm.nih.gov; Eugene V Koonin: koonin@ncbi.nlm.nih.gov
Received May 10, 2007; Accepted May 31, 2007.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Background
The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a "frozen accident" or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies. Here we combine the results of comparative genomics of translation system components, data on interaction of amino acids with their cognate codons and anticodons, and data on catalytic activities of ribozymes to develop conceptual models for the origins of the translation system and the genetic code.

 

[The Barbarian]

Bob once again shows his sense of ethics by changing Koonin's words:

Also note that the claim is made that "only some aspects" of the theory would be subject to experimental verification.

In fact, Koonin didn't say that. He said some aspects were amenable to being tested, without saying whether or not others could be, or might be in the future.

Several aspects of this scenario are amenable to experimental testing.

"Amenable" means agreeable to, or compliant. In short, easy to test. But bob, in his rush to redeem himself, came up with a new falsehood. The quote is, quite simply, a fabrication in the tradition of Answers in Genesis. Take a genuine quote, and add or subtract just enough to change the meaning. And be sure to put it in quote marks, so people will think it's a genuine quote.

Koonin does not, and apparently never did, believe what bob attributed to him.

When are you going to learn, bob?