Monday, July 04, 2011

Mr. Benedict misrepresents Manfred Eigen

Manfred Eigen, won the Nobel Prize in 1967 for his work measuring extremely fast chemical reactions brought about by energy pulses. Though proud to use the term evolution, his models of the origin of life are not based on chance but on self-organizing chemical reactions that cycle to higher and higher levels. He is also the author of Eigens Paradox that explains a critical problem in positing cycles of RNA that lead to DNA.

Mr. Benedict has this problem; he doesn’t have any idea of what “random” or “chance” or “random chance” mean in probability theory, chemistry, or how they might apply in evolutionary theory, or studies of the origin of life. When I have taught statistics and probability at the college level, I had the advantage of very intelligent students committed to learning. I doubt that this is currently the situation.

One of the greatest philosophical advances of all time was the notion that real life should be the basis for our understanding of the universe. This was in direct contradiction of Platonic ideas of some “perfect” reality which was beyond the perception of humanity. But, this appeal to reality is what makes science ‘work.’ In this specific context of the “Eigen’s Paradox,” we can default to real physical data which trumps philosophical speculation. The particular result I have in mind is;

Ádám Kun, Mauro Santos & Eörs Szathmáry
2005 “Real ribozymes suggest a relaxed error threshold” Nature Genetics 37, 1008 - 1011 Published online: 28 August 2005 | doi:10.1038/ng1621

Abstract: The error threshold for replication, the critical copying fidelity below which the fittest genotype deterministically disappears, limits the length of the genome that can be maintained by selection. Primordial replication must have been error-prone, and so early replicators are thought to have been necessarily short. The error threshold also depends on the fitness landscape. In an RNA world, many neutral and compensatory mutations can raise the threshold, below which the functional phenotype, rather than a particular sequence, is still present. Here we show, on the basis of comparative analysis of two extensively mutagenized ribozymes, that with a copying fidelity of 0.999 per digit per replication the phenotypic error threshold rises well above 7,000 nucleotides, which permits the selective maintenance of a functionally rich riboorganism with a genome of more than 100 different genes, the size of a tRNA. This requires an order of magnitude of improvement in the accuracy of in vitro–generated polymerase ribozymes. Incidentally, this genome size coincides with that estimated for a minimal cell achieved by top-down analysis, omitting the genes dealing with translation.


PointsOfInterest said...

Dr Hurd. I have read a bit of your blog and while I don't pretend to understand all of it as I am not a scientist I do have a question for you. Do you suppose that whatever started the spark of life would have created it with an intelligent design that would allow life to evolve to better survive the environment in which it finds it's self? I do realize that life has evolved and everything that I have read about, that I understand of course, makes a certain amount of sense to me. Perhaps you can shed some light on this for me? I do apologize for the method of contact but I did find your name on the Knoxville News Sentinel comments section talking about evolution and was inspired to seek more information. Thank you in advance for your time.

Gary S. Hurd said...

I want to appologise to "points of interest" for the delay in their comment showing up on Stones and Bones. It was automatically sent to the "spam" file. I don't know why.

The best way I can think of to tell a purely chemical reaction from 'life' is that the chemistry of life is a) cyclic, and b) capable of evolution. I see nothing in the origin of life that requires a supernatural manipulator.

If you are looking for a justification of your belief in the supernatural, then you simply cannot look to the sciences. There seems to be no reason that an external, willful 'creator' is required. There are a fair number of physicists (more than a handful anyway) who think that there is a strange consistency, and apparent precision to cosmological constants. They think there is a consequent justification to the idea that these constants are artificial, implying a creator. An example would be;

McGrath, Alister E.
2009 "A Fine-Tuned Universe" Louisville: Westminster John Knox Press

And here is a counter argument;

Susskind, Leonard
2005 "The Cosmic Landscape: String Theory and the Illusion of Intelligent Design" New York: Little and Brown Publishers

PointsOfInterest said...

Well perhaps I should clarify a bit Doctor. First the question I posted to you is not so much a validation of God. It was more a question of doesn't it make sense that whatever created life on this planet did it with a thought to evolution?

I am not convinced by teachings of the Bible as they were written, for the most part, by people who were not there. So I tend to think that whatever created life, a biological accident, higher power, whatever, did it with evolution in mind.

I don't pretend to understand thermodynamics or the whole of the fossil record, but what I do understand of it does point to evolution being the logical course.

I realize that my understanding is basic at best which is why I contacted you for more information. I do have the desire to understand more of it.

Gary S. Hurd said...

I think I understand your question. Is the capacity for evolution inherent to life?

I would say yes. Nothing that is incapable of evolution can said to be alive. But, if evolution is an inherent property of any and all living things (and presumably everywhere in the universe, too) is there a need for a creator? From my study of the basic chemistry of life, I would say no; there is no need for any intervention to create life.

Something could exist that does act in some way to increase the likelihood that life exists on some particular planet, or another. Over 30 years ago, I tried to sell a science fiction story with that as a background idea. It was called "You can't get there from here," and the idea was that we find out that there is no way for humans to leave the solar system. So, we send "life ships" that find a suitable planet and start life there. And then, we get a visit from the "people" who started life on Earth. (3.5 billion years ago as we know now, when I wrote the story I left the exact "when" vague).

PointsOfInterest said...

So as I understand it, the universe is made up of matter and energy. Matter is described as having mass and takes up volume. So going by the law of for every action there is an equal and opposite reaction, would I be safe in saying that the big bang destroyed matter and then reconstructed that matter into what we now know to be our solar system or even universe.

In the reconstruction of the matter into something that we know now is it possible that the "instructions" of the matter were somehow lost, as if caught in the event horizon of a black hole? There by being built back into a brew that caused the forming of life on Earth?

Probably far off base I know but is it something that is workable as a theory? I am certainly not trying to rewrite the laws of physics just to get a better understanding of how we got here and could we be somewhere else?

Gary S. Hurd said...

The best on-line sources for information on the origin of the universe are;

Ned Wright's Cosmology Tutorial

The Berkely Cosmology Group"

and, the best introduction is;

NASA Cosmology:The Study of the Universe

I was think this morning that nearly all good books on the origin of life have a section on the question of what is life? The best introduction to this was by Iris Fry, "The Emergence of Life on Earth: A Historical and Scientific Overview" (2000 Rutgers University Press). Her presentation makes the connection of how our advances in understanding what life is has led to changes in how we think life originated.

Gary S. Hurd said...

PS: Fry's book is a bit dated on the current origin of life research. For example, the prebiotic chemistry of the nucleotides is much clearer now, and the role of minerals in the origin of life is now seen as critically important.

PointsOfInterest said...

Thank you doctor for your time. You have certainly given me some things to digest and to work with in my search for some answers. I certainly go appreciate it, as I point out here.