"Genetic Death": The Evolution Meat Grinder

Darwin once wrote a letter to Hooker . In it he said.
"If (and a big if indeed) we could conceive in some warm little pond with all sorts of Ammonia and Phosphoric salts-light, heat, electricity etcpresent , that a protein compound was chemically formed, ready to undergo more complexchanges, at the present day such matter would be instantly devoured, or absorbed, which would not have been the case before living creatures were formed
henrietta makes hardly any progress..."

In another letter in 1882 (the year he died) he wrote to a colleague and confessed

"You expressed quite correctly... where you said I intentionally left the question of the Origin of Life uncanvased ... and only dealt with the the manner of succession. I have met with no evidence that seems , in the least trustworthy, in favor of so-called Spontaneous Generation.... I believe ...that the principle of continuity renders it probable that the principle of life will hereafter be shown to be a part of, or consequence, of some general law..."

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I think I understand what you are saying, sirs. But, all I asked for was a very simple thing. I asked for an article from the JOURNAL OF MOLECULAR EVOLUTION that, as Behe's stated, "proposed a detailed model by which a complex biochemical system might have been produced in a gradual, step by step Darwinian fashion.

I really have no problem, despite the musings of SJ Gould, accepting the "fossil record". The brilliant Steven Pinker, in his great book, "The Blank Slate" is quite persuasive in his defense of evolution. He excoriates Behe with these words--"He takes every phenomenon which evolutionary history HAS NOT YET FIGURED OUT and chalks it up to design by default."

If the incredibly erudite Steven Pinker agrees that evolutionary history has NOT YET FIGURED OUT EVERY PHENOMENON, who am I to disagree?

I remain skeptical!!!

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Bern

Quote:

That would be so much more satisfying to me than the enormous logical leaps taken by the brilliant scientist, the late Stephen J. Gould in books such as "Dinosaur in a Haystack".

. Im not sure what you mean about the enormous leaps in logic that Gould made.

Hes talking about coding genes, those between the stop codons. Between thee are miles o introns or junk DNA. The new thinking is that this stuff isnt junk because it follows that the older specie have more of it and it could be that which records evolution of that species.

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Mr. Farmerman and Mr. Timberlandko. I thank you for providing the material. Since I am not a scientist, I read such material very slowly. However( and please correct me if I am wrong--show me please) I do not think any of your offerings reach the criterion established by Dr. Behe--namely--" a d e t a i l e d model by which a complex biochemical system might have been produced in a gradual step by step Darwinian fashion"

I have referenced the eruidte scholar and student of the Way the Mind Works--Dr. Stephen Pinker who, as you may have read indicated, after strongly disagreeing with Behe, that indeed there exist "phenomenon(s) whose evolutionary history has not been figured out."

I don't believe that Pinker's statement can be overlooked.

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Please excuse the double post on Gould!!!!

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Bernard wrote-

Quote:

. But, as my dear departed father once told me--beware of "snow jobs" couched in esoteric terminology.

It might be dependent on ancestry then.

Those fortunate enough to have fathers,or surrogate fathers, who successfully transmitted such wisdom to their son, or surrogate son, tend to be sympathetic to ID and IC, Darwin himself, if the quotes so kindly provided by fm,who's wallet I hope has ceased to ache,is anything to go by, and those who haven't had such luck will believe any old fanny-adams that any old oily flatterer lards him over with.

(A pyramid sale so to speak. An upside down one balanced on the last fraction of uncertaintitty known to man.)

Is that what you meant Bern?

(I think the punctuation is correct.If it isn't try it over again and see if you can get the facial expression which is an integral part of the meaning.)

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Mr. Spendius- Are you making a comment on the substance of the thread or do you merely wish to append a footnote.?If so, please advise.

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Punctuated Equilibrium was developed to provide some understanding of an artifact of fossilization or Darwins "imperfection of the GEologic Record"

Subsequent sampling of Gould and Eldredges own sample sites in the HAmilton group have provided data that the "long periods of stasis without evolution did not occur here as there was evidence of a series of transitional froms that were missed at that particular fossil field site.

HAve you read "Structure of Evolutionary Theory"? Inside Gould doesnt attempt to defend Punctuated equilibrium as an exclusive mechanism because he knows that many environmental conditions have occured quickly in the past and evolution gas kept pace with changes clearly shown if the fossil reord.

his comments of spandrel constraints are an attempt to rectify "exaptation pools" to accomplish macroevolution, because microevolution, the cumulative accumulation of smaller changes cuts down the exaptive capability when times get tough. He failed in his book , to discuss the co-exitence of more or less adapted species side-by-side with more primitive forms as a niche gets changed by some catastrophe. The actual loss of a species as a final non-adaptive act is not without precedent in the fossil record. Look at hominids, or how bout Neanderthal? He was perfectly adapted to an Ice Age but lost out to sapintis as the world melted.

Gould is not a God of evolution. He was a very wordy and sometimes confusing witer who like to hear himself spout off many times. He chose very complex phrases over plain talk and was always criticized by his editors. Its one of the reasons that hed stopped writing technical papers.

However, throughout "Structure..." he says repeatedl that PE is not a "replacement mechanism" its another possible mechanism.

STill ,no matter what the status of his work in review. Lets not try to extend Goulds meanings and use them for quote mining for Creationist rhetoric.
Turn to page 1295 and read to the end. Then read chapter 12. There He dismisses overarching conclusions from an imperfect fossil record. He sorta argues with himself.

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BernardR wrote:

I think I understand what you are saying, sirs. But, all I asked for was a very simple thing. I asked for an article from the JOURNAL OF MOLECULAR EVOLUTION that, as Behe's stated, "proposed a detailed model by which a complex biochemical system might have been produced in a gradual, step by step Darwinian fashion

Ohwhuthuhell - ya ask for one article from the Journal of Molecular Evolution proposing a detailed model by which a complex biochemical system might have been produced in a gradual, step by step 'Darwinian' fashion, therewith implying that if so provided, you'll shut up about it, right? OK, here ya go:

Quote:

Evolution of the Cytochrome c Oxidase Proton Pump (Note: 13 page .pdf download)
Musser, S.M. and Chan, S.I.
J Mol Evol (1998) 46:508-520

Abstract

The superfamily of quinol and cytochrome c terminal oxidase complexes is related by a homologous subunit containing six positionally conserved histidines that ligate a low-spin heme and a heme-copper dioxygen activating and reduction center. On the basis of the structural
similarities of these enzymes, it has been postulated that all members of this superfamily catalyze proton translocation by similar mechanisms and that the CuA center found in most cytochrome c oxidase complexes serves merely as an electron conduit shuttling electrons from ferrocytochrome c into the hydrophobic core of the enzyme. The recent characterization of cytochrome c oxidase complexes and structurally similar cytochrome c:nitric oxide oxidoreductase complexes without CuA centers has strengthened this view. However, recent experimental evidence has shown that there are two ubiquinone (ol) binding sites on the Escherichia coli cytochrome bo3 complex in dynamic equilibrium with the ubiquinone(ol) pool, thereby strengthening the argument for a Q(H2)-loop mechanism of proton translocation [Musser SM et al. (1997) Biochemistry 36:894-902]. In addition, a number of reports suggest that a Q(H2)-loop or another alternate proton translocation mechanism distinct from the mitochondrial aa3-type proton pump functions in Sulfolobus acidocaldarius terminal oxidase complexes. The possibility that a primitive quinol oxidase complex evolved to yield two separate complexes, the cytochrome bc1 and cytochrome c oxidase complexes, is explored here. This idea is the basis for an evolutionary tree constructed using the notion that respiratory complexity and efficiency progressively increased throughout the evolutionary process.

There ... a published JME paper that satisfies the structure of your request - now, what about your end of the bargain, or do you feel now is the time to redefine terms, or perhaps to renegotiate the bargain?

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Bernard-

Gunga wrote this in the first post-

Quote:

This basic pipeline/genetic-death scheme is also the thing which Hitler and the other nazis were seeing in evolutionism. They were simply taking Charles Darwin at his word and, granted they were a bunch of **** and were guilty of a whole lot of ****, they were NOT guilty of any sort of a breakdown in basic logic. They were assuming that if the rise of a new and supposedly better racial stock GUARANTEED the extinction of the old stock, then they were not doing the members of the old stock any favors by prolonging the agony. Similarly, when asked about the firebombing raids over Japan, Curtis LeMay replied that you're not doing a dog with a cancerous tail any favors by cutting the tail off in slices.

That's the substance of the thread.

And Yes I was adding a comment with that in mind. It may have been a bit allusive but non the worse for that.

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I am very sorry, Mr. Timberlandko, but since I am not a scientist, I cannot adequately respond to what I am sure you will agree is a very difficult paragraph to decipher. I cannot understand what step by step mechanisms are involved. I do not understand that your paragraph produces a "detailed model".

Can you please provide a "precis" or, at the very least, a translation into layman's terms of the exact detailed model referred to in the paragraph which might have been produced in a step by step fashion?

I do not wish to be repititious but I really must refernce the erudite Steven Pinker who does admit that there are phenomenons whose evolutionary history have not been yet figured out.

It is such statements which prevent me from discarding my "skepticism".

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That you might not understand the science is no reason to go with more easily understood pseudoscience.

Here's another from JME - no direct link, sorry; gotta be a subscriber, but here's the abstract:

Quote:

Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution
Melandez-Hevia E, Waddell TG, Cascante M, Journal of Molecular Evolution 1996; 43: 293-303.
Abstract

The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into a single-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.

From Nature, Vol 423, 8 May 2003, a precis of a much lengthier article which appeared in JME earlier that year:

Quote:

The evolutionary origin of complex features (Note: 6 page .pdf download)
Richard E. Lenski*, Charles Ofria, Robert T. Pennock & Christoph Adami§
* Department of Microbiology & Molecular Genetics, Department of Computer Science & Engineering, and Lyman Briggs School & Department of Philosophy,
Michigan State University, East Lansing, Michigan 48824, USA
§ Digital Life Laboratory, California Institute of Technology, Pasadena, California 91125, USA

AbstractThese findings show how complex functions can originate by random mutation and natural selection.

So - is Behe correct in his assertion pertaining to the available literature?

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Mr Farmerman" I know that SJ Gould is no longer here to defend himself but he really made many mistakes according to other theorists.

Richard Dawkins- In his fine book-"Unweaving the Rainbow' Critques Gould thusly and fiercely:

"Gould's eternally unresolved questions( UNRESOLVED QUESTIONS???) in paleontology are three in number: Does time have a directional arrow> Is the driving motor of evolution internal or external? Does evolution proceed gradually or in jumps? Historically, he finds examples of palentologists who have espoused all eight possible combinations of answers to these three questions, and he satisfies himself that they STRADDLE the Darwinian Revolution as though it had never happened. But he manages this feat only by FORCING ANALOGIES between schools of thought, which, carefully examined, have no more in common than blood and wine, or helical orbits and helical DNA....Is natural selection externalists or internalist? It depends whether you are talking about adaptation to the external environment or co-adaptation of the parts to each other."

It would seem that Dr. Behe would be an "internalist". Behe searches for the "DETAILED model by which a COMPLEX biochemical system might have been produced in a gradual STEP BY STEP Darwinian fashion.

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BernardR wrote:

I do not wish to be repititious but I really must refernce the erudite Steven Pinker who does admit that there are phenomenons whose evolutionary history have not been yet figured out.

It is such statements which prevent me from discarding my "skepticism".

There will always be "phenomenons" whose evolutionary history have not yet been figured out yet. The list of possible phenomena are almost endless.

Perhaps your skepticism is unassailable by what most of us consider a vast preponderance of evidence. In which case its not skepticism you're dealing with, but denial.

What *would* it take to give you confidence in evolutionary theory? If someone proved out just one of the molecular sequences step by step, would that do it, or would you simply hitch your wagon to the next molecule which hadn't yet been explored?

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Bern, everybody had problems with Gould. I posted my concerns of a number of his pet projects. However, thats what science does. It dounts itself until all doubts can be answered . Then it moves on to new ones.
In line with what ros said, you seemto be using the quotes as play off of each other and you admittedly dont know what theyre about.

The evolution of krebs cycle has been an issue since the late 60's as well as the adenosine energy series.
I put the discussion re: molecularorigins in as simple a fashiona sI could..you ignore and move on t another quote mine .
Oh well, Im taking a few days offd so Im not doing anything valuable anyway
As far as your Behe and Gould comprisons, there are none. Gould wasnt dealing with IDers, hed been amazed at how they loudly champion their cause and base it on nothing. Behe comes along, gives the IDers something to use (for a while at least) , but the substance of Behes work and Goulds , rarely touched.

Once more--did you read the" Structure of Evolutionary Theory"?

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I am afraid that you misunderstand me. I don't have a problem with great sections of evolutionary theory. Neither does Dr. Behe, if I understand him correctly. I do not wish to be repititious since I have posted Dr. Behe's query several times already.

Nothing that I have read on this thread is persuasive. Indeed, I read the last article you presented, Mr.Timberlandko and I must admit that the part that caught my eye was the section which said--'Many important questions remain open"-- I will not replicate those questions since they are in your article.

When will we have the answers to those questions so we may have closure?

I do not wish to go off the topic but I must give additional reasons of why my skepticism remains.

Mortimer Adler, one of my favorite writers and, in my mind, a great American thinker, wrote:

"At one extreme clearly belonging to the sphere of truth, is mathematics, and associated with it, the exact sciences. Placing these disciplines in the sphere of truth does not mean that at any time there is perfect agreement among all experimental scientists about everything in their fields....But it does mean that, when they do disagree, we expect them to be able to resolve their disagreements by recourse to rational processes employing the methods and techniques of their disciplines."

As I have stated repeatedly, I am not a scientist but I do know that the "experimental method" cannot fully apply to the theoretical conjecture of how complex biochemical systems might have been produced in a gradual step by step Darwinian fashion.

Statements about the detailed model of a complex biochemical system which evolved eons ago must be deduced by trained scientists as speculation and theory.

A wonderful case in point is the current controversy about "the Big Bang" Did it or did it not occur? There are theorists on both sides and, indeed, examination of the Universe leads to wonderful theorizing but, as far as I can determine, no hard and fast answer.

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I might indeed be tempted to go along with "a vast preponderance of evidence". But, as the article so graciously provided on the Krebs cycle notes--for one-"Why and how did the full pathway emerge from there"?

As long as such questions remain, there is indeed room for skepticism( not, as I replied, about many of the ideas on evolution which even Dr. Behe embraces but on the ultimate questions concerning the DETAILED model. Dr.,Behe raises some other interesting questions--

"How did the photosynthetic reaction center develop?

"How did intramolecular trasnsport start?

"How did cholesterol biosynthesis begin?

Could these questions be some of the questions referred to by Dr. Pinker?

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Gunga-

HELP!!!

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"Genetic Death": The Evolution Meat Grinder

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