DNA, Where did the code come from?

I TOLD you to spare me the 'eddies' argument but you had to do it

You write of this molecule as if it's prior existence and impact on biology were a fact, which is fine since you have not tried to tell us it is a fact and when specifically asked you acknowledged it no longer exists.

Leadfoot Quote:
"I TOLD you to spare me the 'eddies' argument but you had to do it"


If thats the way you act, sticking your fingers in your ears and yelling "I cant hear youuu, I cant hear youu"

Setanta wrote:

Leadfoot wrote:
." . . I don't see any exceptions in the universe unless I take 'biology as natural' as an act of faith and I seem incapable of doing that with anything."


Set replied:
Ah-hahahahahahahahaha . . .

You can't beat this place for free entertainment . . . usually from unintentional comedy . . .

FBM quips:
It's mind-boggling sometimes, innit? How the faith twists the words to the point that they condemn themselves, I mean

Quote:

You write of this molecule as if it's prior existence and impact on biology were a fact, which is fine since you have not tried to tell us it is a fact and when specifically asked you acknowledged it no longer exists.

Sez who? These things happen, caincha see? There's probably billions of them popping up every damn day. We just don't notice because we just assume they were there yesterday, ya know?

One of these days a few hundred will spring up in a hermetically-sealed test tube and then we'll have the proof, I figure.

...I don't see any exceptions in the universe unless I take 'biology as natural' as an act of faith and I seem incapable of doing that with anything.

Neo-Darwinism does not provide a satisfactory explanation for evolution and however resilient it may prove to criticism, it must eventually give way to a more realistic theory. This can only occur if we abandon the reductionistic and mechanistic ‘paradigm of science’, which neo-Darwinism so faithfully reflects.

Published in The Ecologist Vol. 20 No. 2, March–April 1990

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Decades ago, Haldane predicted that facts would soon emerge which would show that natural selection was not an adequate explanation of evolution. Waddington had similar thoughts. As he said at the 1969 Beyond Reductionism Anspach Symposium, “I think that we are going to see extraordinary changes in our ideas about evolution quite soon.” [1]

Yet, although the deficiencies of neo-Darwinism have become increasingly apparent in recent years, and criticism has mounted on almost every front, it remains the official scientific explanation for evolution.

My feeling, indeed my conviction, is that a realistic and coherent theory of evolution will be proposed and accepted only once a clean break is made, not only with neo-Darwinism, but also with the sacrosanct ‘paradigm of science’, which paints a very distorted view of the world. Let us see why....

Conclusion

It is the thesis of this article that in order to understand evolution, one must reject the neo-Darwinist thesis and indeed the ‘paradigm of science’ itself that this thesis so faithfully reflects. We must also see evolution and life processes in general as displaying precisely the opposite features to those that they are held to display by neo-Darwinists and mainstream scientists in general.

•Rather than being atomistic they are highly organised and hierarchical.
•Rather than being mechanistic and hence passive and non-creative, they are living dynamic and creative.
•Rather than being random they are ordered and highly purposive.
•Rather than being geared to perpetual flux in the direction of some mysterious undefined goal which is usually referred to as ‘progress’, they are highly conservative and seek at all costs to preserve their stability.
•Rather than being brought about by some single physical event or ’cause’ that preceded them in time and hence managed by some atomistic, mechanical and external force, they are self-regulating and subject to the influence of their past and of the hierarchy of spatio-temporal systems of which they are part.
•Rather than being explicable in quantitative terms, which assumes their atomistic and mechanistic nature, they can only be understood in the qualitative language appropriate for expressing their highly sophisticated capacity for creativity, improvisation and innovation.

Of course, to adopt such a view of life processes and of evolution, the overall life process, would, among many other things, force us to reconsider very radically our attitude to the living world and what we are doing to it (Edward Goldsmith the late environmentalist, author, & philosopher)

Biology today is at a crossroads. The molecular paradigm, which so successfully guided the discipline throughout most of the 20th century, is no longer a reliable guide. Its vision of biology now realized, the molecular paradigm has run its course. Biology, therefore, has a choice to make, between the comfortable path of continuing to follow molecular biology's lead or the more invigorating one of seeking a new and inspiring vision of the living world, one that addresses the major problems in biology that 20th century biology, molecular biology, could not handle and, so, avoided...

The most pernicious aspect of the new molecular biology was it reductionist perspective, which came to permeate biology, completely changing its concept of living systems and leading then to a change in society's concept thereof.

We cannot proceed further without clarifying and discussing what is meant by reductionism. The stakes here are high because the concept is deeply woven into the fabric of modern biology, and biology today has hit the wall of biocomplexity, reductionism's nemesis. Thus, a topic that previously had been left for the philosophers and scientific dilettantes has suddenly become a very real and global issue for the practicing biologist.

Biology's march into reductionism began in earnest with the “rediscovery” of the gene in the early 20th century. And the molecular dissection of the cell, which had begun with physiology being redefined (in part) on the level of enzymology, really took off with the advent of (molecular) genetics....

The pinnacle of fundamentalist reductionism in biology was reached with the Watson-Crick structure of DNA. This structure, which clearly revealed the mechanism of gene replication, was hailed by molecular biologists as fundamentally solving the problem of the gene—a conclusion reified by the fact that once the Watson-Crick structure became known, most or all of the molecular biology coterie originally involved with the problem effectively packed their intellectual bags and moved on to “other great problems in Biology”.

It is most interesting that molecular biologists declared the problem of the gene to be solved before the mechanism of translation (the core of gene expression) was at all understood—which, of course, was anathema to the classical biologist, who understood the gene to be defined by the genotype-phenotype relationship, by gene expression as well as gene replication. (I shall examine the implications of this signal, defining point in molecular biology's history further below.)

The molecular cup is now empty. The time has come to replace the purely reductionist “eyes-down” molecular perspective with a new and genuinely holistic, “eyes-up,” view of the living world, one whose primary focus is on evolution, emergence, and biology's innate complexity. (Note that this does not mean that the problems worked on in any new representation of biology will not be addressed by customary molecular methodology; it is just that they will no longer be defined from molecular biology's procrustean reductionist perspective.)

Nearly 40 years ago the physicist-philosopher David Bohm exposed the fundamental flaw in the mechanistic reductionist perspective (5): “It does seem odd… that just when physics is… moving away from mechanism, biology and psychology are moving closer to it. If the trend continues… scientists will be regarding living and intelligent beings as mechanical, while they suppose that inanimate matter is too complex and subtle to fit into the limited categories of mechanism.”

Thus, molecular biology, with its fundamentalist reductionistic mechanistic perspective, was faced with a difficult if not impossible task in developing a comprehensive understanding of biology. Not seeing the forest for the trees (and not caring what a tree was in any case), molecular biology took the only approach open to it: it clear-cut the forest. In other words, it dispensed with all those aspects of biology that it could not comprehend or effectively deal with.

Any educated layman knows that evolution is what distinguishes the living world from the inanimate. If one's representation of reality takes evolution to be irrelevant to understanding biology, then it is one's representation, not evolution, whose relevance should be questioned.

Let's stop looking at the organism purely as a molecular machine. The machine metaphor certainly provides insights, but these come at the price of overlooking much of what biology is. Machines are not made of parts that continually turn over, renew. The organism is....

If they are not machines, then what are organisms? A metaphor far more to my liking is this. Imagine a child playing in a woodland stream, poking a stick into an eddy in the flowing current, thereby disrupting it. But the eddy quickly reforms. The child disperses it again. Again it reforms, and the fascinating game goes on. There you have it! Organisms are resilient patterns in a turbulent flow—patterns in an energy flow. A simple flow metaphor, of course, fails to capture much of what the organism is. None of our representations of organism capture it in its entirety....

Twenty-first century biology will concern itself with the great “nonreductionist” 19th century biological problems that molecular biology left untouched. All of these problems are different aspects of one of the great problems in all of science, namely, the nature of (complex) organization.

I received my doctorate in biophysics from Yale University in the spring of 1953, just in time to celebrate the greatest achievement of the molecular era, the solving of the double-stranded structure of DNA....The genetic code became for me the looking glass through which I entered the world of real biology. Like many molecularists of the day, I was taken by the code, and at first I emulated their cryptographic approach to the problem.

The clash came, however, over the issue of gene expression. Classical biologists naturally considered that process fundamental too. But for the molecularist, gene expression would be a fundamental biological process only if it too could be explained in simple molecular terms—for example, as the result of specific recognition of amino acids by corresponding oligonucleotides—and it was indeed along such lines that molecularists first sought to explain gene expression....

As we all know, once cracked, that code did not lead to a fundamental explanation of gene expression (translation). The code seemed to be merely an arbitrary correspondence table between the amino acids and corresponding trinucleotides. There seemed to be no simple physical-chemical interactions underlying the mechanism of gene expression (or that suggested the mode of its evolution). Could it be just another one of evolution's many “historical accidents”? Could there be nothing fundamental about it? That's how the molecularists saw it: outside of its structure, the only fundamental aspect of “the gene” was its mode of replication....

No other single issue has exposed the difference between the molecular and classical perspectives more clearly than this one. Should the problem of translation be treated as just another (idiosyncratic) molecular mechanism (as it now is), or is that problem central, and thus fundamental, to the nature of the cell. As we shall see, biology today continues to live with this unresolved problem.

Here was the real problem of the gene, how the genotype-phenotype relationship had come to be. Translation, far from being just another relatively uninteresting study in biological idiosyncrasy, actually represented one of a new class of deep evolutionary questions, all of which had to be formulated and addressed on the molecular level.

Carl Woese, one of the giants of contemporary biology, passed away a day before New Year’s Eve (see the NY Times obituary). Woese, an American microbiologist from the University of Illinois, revolutionized our understanding of life with the discovery of a new domain of living organisms, the Archaea, and the creation of a universal tree of life made of three main branches (Bacteria, Archaea and Eukarya) (Woese, 1990

Twentieth century bacteriology was a prime example of a science not seeking to define itself, letting itself instead be defined by external influences. The discipline had never sought to frame the overarching questions that synthesize and define a field. Quite the contrary: when such questions happened to come along, microbiologists either shied away from them or papered them over with guesswork.

There was one occasion (perhaps the only one) on which the “lack of a concept of a bacterium” was recognized and denounced as the “abiding scandal” of bacteriology (45). But, rather than use this insight to begin a much-needed dialog within the field, the authors concocted a guesswork solution to settle the matter then and there, thereby removing the question/problem from the
arena of discourse.

Enter the infamous “procaryote.” Not only did this bit of thimblerig appear to settle the immediate issue (see below), but it forever changed the course of microbiology. In retrospect the “procaryote” episode (see discussion below) was microbiology's historical nadir.

For the sake of trying to understand what microbiology (bacteriology) is today and where it is (should be) going, we need to go into this strange juncture in the field's course in some detail. I have come to see the whole unfortunate episode and its outcome as the product of the clash between the classical (home-grown) perception of biology and the fundamentalist reductionism introduced by molecular biology. Bacteriology was effectively shattered by this encounter and did (does) not have the “self-awareness” to pull itself back together—although there is now hope.

One thing that makes this juncture so interesting and important is that it may well have represented a genuine fork in the road for 20th century biology, and the “road not taken” might have led (as mentioned above) to a more inclusive, a more “biological” kind of biology than the harsh molecular reductionist regimen that was actually followed—though we shall never know.

The critical period is the decade surrounding 1960. Microbiology's search for a natural classification of bacteria, the key to bacteriology as an organismal discipline, had clearly reached an impasse; classical approaches to a natural bacterial taxonomy could not crack the problem. Some leading microbiologists had thrown up their hands about a natural classification, their frustration rising to the level of toying with the defeatist notion that bacterial phylogenies are inherently unknowable.

The implications of this for bacteriology were far reaching—a whole new approach to the stalled problem of the natural relationships suddenly became possible. But microbiology was no longer willing to fight the battle. All it now wanted was to leave the past and defeat behind and recast the field in a new, more productive (reductionist) way. Microbiologists were of no mind to hear, much less embrace, Crick's prescient proclamation:

Quote:

“Biologists should realize that before long we shall have a subject which might be called ′protein taxonomy'—the study of amino acid sequences of proteins of an organism and the comparison of them between species. It can be argued that these sequences are the most delicate expression possible of the phenotype of an organism and that vast amounts of evolutionary information may be hidden away within them.”

The crisis came for microbiology in 1962, when the term (and concept) “procaryote” slithered onto the scene (45). The procaryote was invoked in order once and for all to overcome (actually, obscure) the impasse over bacterial phylogenetic relationships and to provide microbiology with its long-needed “concept of a bacterium.

All bacteria, it was asserted, are procaryotes....This meant that the concept of a bacterium could be gained without having to know the natural relationships among bacteria. Consequently, the question of their relationships could be finally dispensed with, or so it seemed

If it wasn't clear at the time, it is more than clear today that this “procaryote” prescription for gaining the critical “concept of a bacterium” doesn't work. Regardless of the fact that there have never been any facts to support the monophyly of the bacteria, a concept of a group of organisms cannot be gained simply by knowing differences between that group and some other (unrelated) organismal group; it requires knowing both differences and similarities within the group. Why, as scientists, biologists then and now (21, 29) accepted the procaryote-eucaryote argument at face value is a mystery. ...

So, what are we now to conclude about the “procaryote episode”? The meaning of the term procaryote that appeared in 1962 seems to have no historical justification. In 1962 the term meant that all bacteria shared the “distinctive structural properties associated with the procaryotic cell…,” which allowed us “therefore [to] safely infer a common origin for the whole group in the remote evolutionary past…”

This entire strange period in microbiology's history can be rationalized as an attempt to bury the old microbiology (along with its past failures) in order to remake the field along more progressive (read reductionist) molecular lines. Unfortunately, the process left microbiologists knowing less about what bacteriology is than before, and the field became the technological playground for other biological disciplines and for medical and related practical concerns.


What are we now to do? Obviously, it is not scientifically appropriate (one might even say ethical) to teach the procaryote concept any more. At the same time, given the ingrained nature of the term procaryote, it is not useful (not to mention feasible) suddenly to discard it. The way out of this conundrum may be to redefine the term once again.

The procaryote episode makes one leery: are there other guesswork explanations woven into biology's conventional wisdom that also mask important unanswered questions and so impede progress? We should look particularly at evolution, where conjecture is necessarily the mainstay of defining and understanding issues. Remember, it is not guesswork per se that is anathema; it is guesswork, conjecture, and the like that masquerade as problem-solving, interest-ending fact and so violate scientific norms.

The 19th was biology's defining century. There, for the first time, biology's great problems lay scientifically outlined and assembled, with all of them effectively in early stages of development.... some [problems] (like the natures of the gene and of the cell) cried out for dissection, analysis in terms of their parts,[ whereas others (such as evolution and morphogenesis and the significance of biological form in general) were holistic, metaphysically challenging, not fundamentally understandable as collections of parts.

The 19th century as a whole had a reductionistic world view, if for no other reason than because of the outlook of classical physics. Physics at that time saw a fundamentally reductionistic world, in which ultimate explanation lay completely in the properties and interactions of atoms...Biologists of the 19th century were no exception to the reductionist zeitgeist, but theirs tended to be an empirical, analytical reductionism, not a metaphysical one: one would be hard put to explain evolution and the problem of biological form in reductionist terms alone....

But the physics and chemistry that entered biology (especially the former) was a Trojan horse, something that would ultimately conquer biology from within and remake it in its own image. Biology would be totally fissioned, and its holistic side would be quashed. Biology would quickly become a science of lesser importance, for it had nothing fundamental to tell us about the world. Physics provided the ultimate explanations....

In the last several decades we have seen the molecular reductionist reformulation of biology grind to a halt, its vision of the future spent, leaving us with only a gigantic whirring biotechnology machine. Biology today is little more than an engineering discipline. Thus, biology is at the point where it must choose between two paths: either continue on its current track, in which case it will become mired in the present, in application, or break free of reductionist hegemony, reintegrate itself, and press forward once more as a fundamental science.

The latter course means an emphasis on holistic, “nonlinear,” emergent biology—with understanding evolution and the nature of biological form as the primary, defining goals of a new biology. Society cannot tolerate a biology whose metaphysical base is outmoded and misleading: the society desperately needs to live in harmony with the rest of the living world, not with a biology that is a distorted and incomplete reflection of that world.

Society needs to appreciate that the real relationship between biology and the physical sciences is not hierarchical, but reciprocal: physics↔biology. Both physics and biology are primary windows on the world; they see the same gem but different facets thereof (and so inform one another).

Society cannot tolerate a biology whose metaphysical base is outmoded and misleading:

OK, wiseass--you claim that you are incapable of "doing that" (an act of faith) with anything--yet you believe in god, capisce? If you need an explanation of that, you must not be a native speaker of English. Parse that, sucker.

Woese: Remember, it is not guesswork per se that is anathema; it is guesswork, conjecture, and the like that masquerade as problem-solving, interest-ending fact and so violate scientific norms.

was the source of this little diversion my use of the term prokaryotes with Leadfoot? Im wondering where you are going.