BWE
Posts: 1902
Joined: Jan. 2006
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This article, A New Biology for a New CenturyHere
Edit, damn thing submitted on its own I swear.
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| Quote | 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. Machines are stable and accurate because they are designed and built to be so. The stability of an organism lies in resilience, the homeostatic capacity to reestablish itself. While a machine is a mere collection of parts, some sort of "sense of the whole" inheres in the organism, a quality that becomes particularly apparent in phenomena such as regeneration in amphibians and certain invertebrates and in the homeorhesis exhibited by developing embryos.
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. But the flow metaphor does begin to show us the organism's (and biology's) essence. And it is becoming increasingly clear that to understand living systems in any deep sense, we must come to see them not materialistically, as machines, but as (stable) complex, dynamic organization. |
And I think he is attempting to create a broader blur between the organism, the population and the biosphere in general.
| Quote | Enter the "era of the genetic code," when theoreticians and experimentalists alike were racing to see who would be first to "crack the code of life" (16, 22, 24, 30, 43). 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. Needless to say, classically trained biologists did not see it this way: in that translation (the heart of gene expression) was not yet understood, "the problem of the gene" could not possibly be completely (not to mention fundamentally) solved. 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.
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 (55). But that approach didn't have a biological "feel" to it. Wasn't it wrong to consider the codon assignments in cryptographic isolation? Weren't they just a superficial but important manifestation of something deeper and more interesting, i.e., how translation evolved? 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.
Universal evolutionary problems of this kind can be approached only in the context of a universal phylogenetic framework, and in the mid-1960s, when I set out to study the evolution of translation, no such framework existed. Animal and plant phylogenies were reasonably fleshed out, but the huge and overwhelming bacterial world was effectively virgin phylogenetic territory. A massive job lay ahead merely to establish a framework within which to begin operating. |
And here is where I need to defer to someone elses expertise:
| Quote | A heavy price was paid for molecular biology's obsession with metaphysical reductionism. It stripped the organism from its environment; separated it from its history, from the evolutionary flow; and shredded it into parts to the extent that a sense of the whole—the whole cell, the whole multicellular organism, the biosphere—was effectively gone. Darwin saw biology as a "tangled bank" (12), with all its aspects interconnected. Our task now is to resynthesize biology; put the organism back into its environment; connect it again to its evolutionary past; and let us feel that complex flow that is organism, evolution, and environment united. The time has come for biology to enter the nonlinear world.
From a theoretical point of view, one thing can be said about evolution with fair assurance: it is a complex, dynamic process. But it is only now, in the context of computer algorithms, fractals, and chaos mathematics, that we are beginning to get a useful feeling for what that means (33, 51), and it means that evolution is a bumpy road to who knows where. "Bumpy" implies that evolution, as a complex dynamic process, will encounter critical points in its course, junctures that result in phase transitions (drastic changes in the character of the system as a whole) (19, 26, 33, 51). "Who knows where" implies that the outcomes of these transitions, saltations, are not predictable a priori. Biologists now need to reformulate their view of evolution to study it in complex dynamic-systems terms.
When one starts looking for major evolutionary saltations, they are not all that hard to identify (48). It is immediately apparent that one of them is the development of language(s). Human language is a development that has set Homo sapiens worlds apart from its otherwise very close primate relatives, adding new dimensions to the phase space within which human evolution occurs. Another good critical-point candidate is the advent of (eucaryotic) multicellularity. Here too the saltation is accompanied by a qualitatively new world of possibilities.
Next comes the evolution of the eucaryotic cell itself. While biologists have traditionally seen this as a step (saltation) beyond the stage of bacterial cells, I do not. The idea that eucaryotic cell structure is the product of symbioses among bacteria, and so represents a higher stage than that of the bacterial cell, goes back a good century and a half, but there has been no effort to seriously rethink the matter in the light of modern biological knowledge. Nowhere in thinking about a symbiotic origin of the eucaryotic cell has consideration been given to the fact that the process as envisioned would involve radical change in the designs of the cells involved. You can't just tear cell designs apart and willy-nilly construct a new type of design from the parts. The cells we know are not just loosely coupled arrangements of quasi-independent modules. They are highly, intricately, and precisely integrated networks of entities and interactions. Any dismantling of a cell design would not reverse the evolution that brought it into existence; that is not possible. To think that a new cell design can be created more or less haphazardly from chunks of other modern cell designs is just another fallacy born of a mechanistic, reductionist view of the organism.
But what about the mitochondrion; isn't that a direct counterexample of what has just been said? No, it is not. Evolving the mitochondrion through (endo)symbiosis is fundamentally different from evolving the eucaryotic cell in this way. Whereas the latter process would involve a disruptive dismantling of the preexisting eucaryotic cellular design, acquisition of a mitochondrion does not significantly perturb the eucaryotic cell's basic organization, which is in essence the same with or without the mitochondrion's presence. I take it as a general rule in biology that the more complex, integrated, and specific a cell design becomes, the more intolerant of change that design is. For modern cells, the changes possible in their designs (other than degeneration) are all of a trivial, but not necessarily unimportant, nature. (Granted, the organization of the mitochondrial endosymbiont is radically changed during its evolution, but that change is a degeneration to a far simpler "cell-like" design, and the mitochondrial design could never evolve back to the level of complexity that its free-living [bacterial] ancestor had.)
In the remote evolutionary past lies the RNA world (18) or, as I call it, the era of nucleic acid life (57), an evolutionary stage whose existence is here taken for granted. The transition that gave rise to this era must have been one of the great evolutionary saltations, as was the transition(s) from that era ultimately to the world of the (proteinaceous) cells as we know them. Somewhere along the line there had to have occurred a saltation that we could call the "coding threshold," where the capacity to represent nucleic acid sequence symbolically in terms of a (colinear) amino acid sequence developed, a development that would generate a truly enormous new, totally unique evolutionary phase space. |
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Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far
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