"Genetic Death": The Evolution Meat Grinder

You may be right. I'm not familiar with this guy but if creationist/ID'ers are saying faith and reason take's precedence over science to acquire knowledge then I don't buy that. Faith and reason had us believing that the earth was the center of the universe for a very long time.

If we go to the beginning of this controversy, we will find that Dr. Kenneth Miller was posed as the counterbalance to Dr. Behe( he of the "irreducable complexity" school. when searching the writings of Dr. Kenneth Miller, I found the following:

-
"True Knowledge comes only from a combination of faith and reason"

Shall we then remove Dr. Miller as a counterbalance to Dr. Behe?

Very well. Let us do so.

We are then left with( unless more worthies are brought into the fray) Dr. Behe who, as everyone knows, views God, according to Dr. Miller, as a "biochemical mechanic" and Charles Darwin, who concluded his "Origin of Species" with this sentence--
quote--

"There is grandeur in this view of life; with its several powers having been originally breathed by the Creator into a few forms or into one' and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most wonderful and most beautiful have been and are being evolved"

Rather, let us discuss the faith and resolution of President Bush, whose vision will surely lead us to victory in Iraq.

Mr Farmerman, who, I am sure is very accomplished in his field knows that the structure of the molecule and its functions have not been fully described or explained by modern chemistry. A learned Chemist at Berkeley, named Martin-Gordon I believe, wrote:

This experience coupled with the availability of standardizedbasis sets means that routine application of these methods to a
wide range of chemical problems is now possible for nonexperts.
With the proliferation of low cost workstations whose capability
nevertheless greatly exceeds minicomputers of the early 1980s,
electronic structure theory is in the fortunate position of having
a continually decreasing cost of entry! For readers who are
newcomers to this field, the good news is that it is easy to learn
more and to experiment with the capabilities (and inevitably
also the limitations!) of the standard theoretical model chem-
istries. The textbooks and reviews already cited (e.g., refs 11,
20, and 22) are a good place to begin, together with one of the
many program packages (and their tutorials!) which are avail-
able, both commercially and in the public domain.As I have stressed at various points throughout the article,this is nevertheless not a mature field in the sense of applied
linear algebra, where standard algorithms are well established.
Instead, almost all fundamental aspects of quantum chemistry
remain to varying degrees in a state of rapid development: this
includes the theoretical models, the algorithms used to imple-
ment them, the methods used to interpret them, and of course
by implication the problems to which they may be applied. The
future therefore appears full of challenges that when met will
transform the horizons of the field. Here is a summary of some
of the present issues that have been mentioned:(1) There are no completely satisfactory theoretical modelswhich are feasible. The most widely used methods for treating
molecules near their equilibrium geometries are not adequate
for global exploration of potential energy surfaces, due to being
unable to correctly describe bond breaking. Methods that can
correctly describe bond breaking are not formulated in a way
which meets the criteria of a theoretical model chemistry without
prohibitive cost. There is hence much scope for novel future
developments in the area of electron correlation, with this remark
applying even more strongly to excited states than for the ground
state.(2) Most widely used theoretical model chemistries havecomputational requirements which scale in an unphysical way
with the size of the molecule (to be specific, worse than the
quadratic scaling implied by Coulomb's law for distant electron-
electron interactions). While applications of self-consistent-
field methods to systems in the hundreds of atom region are
now possible, and will surely become routine in the near future,
much work is required to reformulate existing theories of
electron correlation to permit their application to the large
systems where much of the future of chemistry lies.


That is exactly what Dr. Behe is referring to. Behe says:

"Molecular evolution is not based on scientific authority. There is no publication in the scientific literature that describes how molecular evolution of any, real, complex, biochemical system either did occur or even might have occured."

I am not a chemist but the essay above by Dr. Martin Gordon at Berkeley seems to assert that we are a long way from understanding exactly how the molecule works.

What's your point?

My point? Even the most learned chemists and physicists do not fully understand the structure and nature of the atom and the molecule, much less how they evolved.

bern.
What dont you understand? Are you, by quoting this, insisting that Darwin was confessing his faith? or as I see, he was providing a short summary of his 3 points of "descent with modification"

His points were quite simple and quite powerful , when you cut out all the Victorian language

1 All life, whether its a fossil or living is connected by a single "nested" set of common features. Darwin didnt know a damn about molecular biology, but we' re certain that he'd be pleased that his point was upheld by the deep insights that DNA/RNA give us.

2THE history of life should proceed from the simple to the complex, and this should be preserved in the fossil record. Ditto, this point is made abundantly obvious

3From"The Descent of MAn"... we gather that the fossil record should reveal a progression of hominids from apelike to larger brained, upright, tool-making species(like us). There are a total of 1700 or so individual hominid specimens available to science now and these all fit into Darwins theory.

bern again. NO he doesnt. Hes stating that , by the principles of quantum chemistry we now can affix and predict (STATISTICALLY) how most reactions will proceed. In fact we count on it. Even in crystallography (which used to be my field) we had relied upon statistical reinforcement of the positions that crystal axes and reaction surfaces occupied. Arcane stuff like Braggs law , counts on it. Almost all of our chemical analyses equipment relies upon the quantum world. Hes actually talking about submolecular but not atomic reaction and correlation

AND THEN we proceed to the question Rosborne posted, What does this have to do with anything ? Its not even a good quote mine job.

Youre making the mistake of trying to logically connect the evolution of biological systems with physical chemistry. Its amazing that (You say) youve read Darwin and Behe , yet you dont have the usual questions that an open mind would possess. (Wheres Behes evidence? Why did Behe just stop at each point that he called Irreducible complexity, when by homology, he knew that same features with slightly different chemical reactions were proceeding in other species? how did Darwin intuit and then go on to experiment? Howd he make that leap? How did the principles like more species=more evolution , come about in his mind?How could he predict the genetic similarities and selection when he had a very simple minded view of early genetics? How did he put the concept of the imperfection of the fossil record as a reason for missing intermediates when less science minded men would just default to a god?)

So what?

You are the chemist, Mr. Farmerman. I am not. But I do know how to read.

quote( capitals mine)

"There are NO COMPLETELY SATISFACTORY THEORETICAL MODELS which are feasible. The most widely used methods for treating molecules near their equilibrium geometries are NOT ADEQUATE FOR GLOBAL EXPLANATION OF POTENTIAL ENERGY SURFACES, due to being unable to ADEQUATELY DESCRIBE BOND BREAKING"

I thought that scientists knew everything they needed to know about Molecules and their structure. Here we have an expert telling us that bond breaking cannot be adequately described.

and Behe states:

"None of the papers published in JME( The Journal of Molecular Evolution) during the entire course of its life has ever proposed a detailed model by which a complex biochemical system might have been produced in a gradual, step by step Darwinian fashion"

Is this true, Mr. Farmerman?

If it is not, can you please supply a link to a source which EXPLICITY proposes a detailed model by which a complex biochemical system might have been produced in a gradual step by step Darwinian fashion?

Thank you, sir!!!

Really? I thought Farmerman was a geologist.



No one said that. Look, I'm not going to quote the rest of your post and refute every single part of it, because there's no need. Basically, all your argument is boiling down to is, "there are gaps in the Theory of Evolution, so therefore it must not be correct."

Big deal.

There are gaps in our historical understanding of the Bible. Does that mean it is not correct?



So? That's what research chemists and physicists do all day. They find out the answers to these questions. Do you know how long a small research project takes (like identifying the role of a gene)? Go on, give me an estimate and let's see how well you understand science.

No, theyre talking about 2 different phenoms.

Wolf, that was my fiirst area, my geology is actually an outgrowth of P=chem and crystallography. I am a geo now.

Bern-you seem angry for some reason. The posts youve made that were , trying to make some connection between what is known v what is unknown are based upon 2 different and unrelated areas. Apples and Oranges dont you know. I find this quote from Morton a bit disarticulated for some reason.. Hes being vague and general so , unless you can provide me with a context and a meaning, Im gonna pass on this one.

However, there are enough good links available . Why not just type "chemical evolution" into google. Youll find that Melvin Calvin, also a faculty at Berkely had published a seminal work on the rise of living systems and its called "Chemical Evolution" .Its old (1970) , but its still a good starting place.

Bern, while indeed you are going at apples and oranges, let me offer you a couple of plums:

Try Polycyclic Aromatic Hydrocarbons and Lipids.

See also: A 1997 paper dealing with the diversity and inevitability of phospholipids (essentially, among the most basic building blocks of life on Earth) available here:
MOLECULAR BASIS FOR MEMBRANE PHOSPHOLIPID DIVERSITY: Why Are There So Many Lipids? (Note: 34 page .pdf download)

The abstract:

There are a series of competing theories concerning the rise of complex polymers of living molecules.

1RNA Firts-this was proposed by Altman and Cech in the mid 80's)
They theorized that RNA was first produced as both an enzyme and a substrate upon which other reactions could occur (Gave rise to the concepr of an RNA world)

2 Protein first -protenoids can form from amino acids at about 170 C

3 Clay catalysis of RNA and Proteins (This is a mix of 1ans 2 ) The interspatial distance bewteen clay "phylla" and base pairs in RNA is roughly the same. So clays can interact with the RNA and act as alkaline and zinc and Magnesium and iron donors and acceptors

NOTE-The above is what we know from lab studies that has grown out of the Miller Urey experiments of 1958. Weve learned that its doable to form enzymes, proteinoids, and RNA (see where were going?)
NOW the problem is actually deferred to the next step which is creating living molecules.

Forming Macroolecules (prior to life , macromolecules are complex megamers "super polymers"). Since the Gibbs free energy in catalysis of proteins into complex polymers is positive, and the substrate basis for clays or mineral "caves" or "Black smoker" environments are negative. The concept of formation of these megaers in clay horizons or mineral rich "soups' or near black smokers is doable by just standing around and not screwing with the reactions

Macromolecules toliving cells is where the "miracle happens"
Formation of prebionts--we dont really know yet

Formation of coacervates and microspheres-These are the formation of the cell walls that timbers last paper is a seminal report


SO, what do we know-We know that chemicals can form amino acids (weve done it)
we can form proteins and ultimately RNA from the reactions and processes Ive skimmed over (This all in Calvins book and the work by cechs and Altman)

We know how to go from proteins to complex polymers and 'macromolecules". The last step, the formation of a living cell is where the action is. AND, its not that we have no great idea. We have an overabundance of competing ideas, to which Doug Futuyama said (very wisely) "could it be that life had many pots in which it was brewed?"

We know that , from debunking Behes complex cascade of "enzymes in clotting" that we can remove a number of the mass of these compex ofther enzymes by creating "boutique mice" in which we can see blood clotting occur at a number of stages. Behe relies on a complx of "cascading enzymes" when its really not necessary. AS Eldgredge said'WE can play beautiful music with a small orchestra". Behe counts on the complex array of enzymes to make a point , when its actually more the fact that we, as a chemical plant are"incompetently designed" with leftover unimportant reactions preserved in our cells DNA switches. Blood clotting can occur with 25 or les of the fibrinogen precursors and does happen quite nicely in other "lower animals" So instead of Behe strengthening his points, the scientists looking at his logic , actually came up with new models for the origin of life
So the same may be true for the origins of life

So, the formation of lifes precursors can happen with relative ease in varied environments and through time the concept of acquiring entire genomes by prokaryotes and eukaryotes has "blended" the entire process into a simple cell plan. (This was first postulated by Carl Sagans wife back in the 70s when she was writing about Gaia theory)

Dear Mr. Timberlandko and Mr. Farmerman. I do appreciate your help. As an non-scientist, I can, obviously, get lost in discussions of science since I am not as versed in scientific terminology as I would like to be. But, as my dear departed father once told me--beware of "snow jobs" couched in esoteric terminology.

Since both of you are obviously very scientifically oriented, I hope I am not too brash if I ask that you supply me with material from what Dr. Behe references, namely---The Journal of Molecular Evolution.

Dr. Behe descibes this journal as "devoted exclusively to research aimed at explaining how life at the molecular level came to be."

Even as a non-scientist, I can deduce that this specialized professional journal(peer-reviewed, no doubt) is PRECISELY the vehicle for the answers to the questions being asked.

Dr.Behe states: "In fact, NONE of the papers published in JME over the entire course of its life has ever proposed a DETAILED MODEL by which a complex biochemical system might have been produced in a gradual, step by step Darwinian fashion".

Is this correct? If not, can either of you please reference any papers in the JME which contradicts Dr. Behe's claim? I would dearly love to read such an article or articles. I seek only for closure on this question.

Thank you, sirs!!!

Bern, what Behe's statement amounts to is that he doesn't accept any of the research which inconveniences his pet (and now soundly, roundly, and incontravertably discredited) theories. When science conflicts with belief, believers discount science. You want your basic snow job, just look to the nexus of ID-iocy/Creationism/Fundamentalist Christianity. Find any objective, empirical, external, independent validation for any of it - go ahead, try, and no rush, feel free to take all the time you need. We'll wait; we've been waiting millenia already, a few more centuries ain't gonna matter one way or the other.

The Darwinian model governs life. It does not, nor ever has , been a model for biochemical origins. When we talk about The atomic theory, we dont ask why the AT doesnt include biosystems? why should we then ask natural selection to address chemical origins?
Calvins book "Chemical Evolution' dsicusses the chemistry of the foundation of life, not on a Darwinian sense but on a reaction /interaction base.
He doesnt try to make the point that natural selection governs the formation of the first living polymer. (and he did win a Nobel Prize). I think that you are trying to make natural selection a big peach basket in which is contained everything about molecular bio, chemical origins, cosmology etc.

Dear Mr. O'Donnell. Scientists are making "discoveries" about the human genome and revising them every day.

Quote---Nature via Nurture ---Matt Ridley

"Genome discovery shocks scientists: genetic blueprint contains far fewer genes than thought--DNA's importance downplayed"

a new myth says Ridley--that "fewer genes implied more environmental influences" and second that 50,000 genes were "too few" to explain human nature where 100,000 would have been enough"

Ridley recounts his conversation with one of the leaders of the human genome project, Sir John Sulston--Sulston said:

"Just 11 genes, each coming in just two varieties( such as on or off), would be enough to make every human being in the world unique. There are more than 10 billion ways of flipping a coin 33 times. So, 50,000 is not such as small number after all. Two multiplied by itself 50,000 times produces a number larger than the total number of particles in the known universe."

Headlines such as those above sell papers but they are often wrong or misleading. Research continues. I hope to read a paper where, As Dr. Behe has written--" A detailed model by which a complex bio-chemical system might have been produced in a gradual step by step Darwinian fashion". 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".


There are more things in heaven and on earth than are dreamth of in your philosophy--Hamlet to Horatio.

There are fewer things in the cosmos than dreamt in the religionist's philosophy - timber to Bern