A Dynamic Fitness Landscape

_{June 8, 2007

Intelligent Design}

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Behe’s focus and where he finds major problems with chance and necessity is in nano-molecular cellular machinery rather than the gross anatomical level such as scales becoming feathers or limbs turning into wings. That is also where I find the NeoDarwinian explanations most deficient. In that context could someone please describe for me the “dynamic fitness landscape” that could drive the evolution of this:

Good luck.

Comments

...or this just another bit of fantastic speculation?
Now you're asking LM to step outside his personal area of expertise. I think that's unfair.Mung_{June 9, 2007
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Larry Moran Your link doesn't even begin to give a detailed evolutionary sequence for topoisomerase. First of all, you make a huge unsupported leap in supposing a precursor. Topoisomerases evolved from such nickases. Do topoisomerases share a large portion of sequence with endonucleases? And what was used to solve the supercoiling problem before there was a topoisomerase? If topoisomerase is missing altogether can DNA still be replicated? If not then it follows that endonucleases and topoisomerases, along with all other critical enzymes involved in DNA replication, must have appeared together otherwise the DNA replication process doesn't work. Then you talk of ligases performing part of the function of topoisomerases and speculate that a gene fusion event brought the two functions together. Do topoisomerases share sequence information with ligases? Do you have any concrete examples of two complex enzymes performing disparate tasks just fusing together at the coding gene level where the protein product then performs the function of both the other enzymes or this just another bit of fantastic speculation?DaveScot_{June 9, 2007
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magnan - I hope you don't mind that I don't have an educated response to your excellent post. I am just sitting here with a smile on my face saying WOW!! and reading on Wikipedia about Brownian motors and adenosine triphosphate and microtubules and cytoskeletons and...sagebrush gardener_{June 8, 2007
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One of the things to keep in mind is the nanometer scale. There could be many millions of topoisomerase molecules hovering all around the coils of DNA. How they know when to cut, unwind, & splice could be very simple - they just cut & splice all the time and if there's no tension no unwinding takes place and there's no harm done. Just a guess. But hey, guesswork like this is de rigueur in evolutionary biology - if you can imagine something it's as a good as a fact!DaveScot_{June 8, 2007
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sagebrush gardener: "...So what forces are causing the enzymes, proteins, DNA, etc. to go to the right place at the right time and do their jobs?" I agree the intricacies of these subcellular machines are fascinating. You bring up an interesting question. If you try to get down to the basic mechanisms driving such intracellular processes as transport, DNA helix unwinding, etc. it is mostly the action of molecular "motors" or progressive enzymes, driven by energy derived from the hydrolysis of ATP. Binding energies of the ATP molecule are released to free energy by catalytic enzymes with the addition of water molecules. The deeper question, which I had never looked into before, is precisely how this energy is transformed into force and work in moving the molecular motor. There are a lot of different types of molecular motors, but they mostly seem to move unidirectionally along some sort of macromolecular "track" or substrate. Apparently the precise mechanisms are mostly unknown for certain at present, with several competing models. Also, the actual mechanism seems to be different between different motors. The competing models seem to mostly boil down to two: a "power stroke ratchet" hypothesis and a "Brownian ratchet" hypothesis. With the power stroke model the released molecular binding energy to force transduction mechanism is the irreversible structural change in shape of the motor protein macromolecule as it is hydrolyzed. The motor molecule conforms or holds on to a macromolecular track that is shaped in such a way that the structural change to the motor molecule forces it forward along the track by one step. With the "Brownian ratchet" model, apparently the idea is that the random thermal motions of the substrate or "track" are rectified by the periodic changes in shape of the motor molecule. The "motor" can only move forward and by one step at a time, and its dynamics are tuned to the average Brownian thermal vibrations of the substrate so that these motions tend to jog the motor forward a step at a time at a certain average rate. In this case it is not clear to me just how the ATP binding energy gets transformed into work. What causes these processes to be carried out in such a coordinated way, each at the right time? I can only think of some general answers. This apparently is through the collective "intelligence" of the cell as a whole, where all the various functional organelles, the nucleus, transport molecular machines, structural systems, etc. etc. collectively work together as a sort of incredibly intricate robot mechanical data processor and controller.magnan_{June 8, 2007
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Are any of those thousands of hits on Chu-Carroll Behe on a reputable widely read non-evolution oriented site the general public might read and if so is it supportive of CarrollÃ¢â‚¬â„¢s diatribe?
No, except maybe reader screeds at Amazon. And oddly enough the number Google of hits has gone down to 14,000 from an earlier 26,400. What does Chu-Carroll do at Google anyway?Jehu_{June 8, 2007
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This and other videos of nano-molecular cellular machinery are fascinating. But I am puzzled about something. In all of these videos the amazing stuff "just happens". The nano-machines glide across the screen as if guided by an unseen hand, performing their functions like little robots. But physical actions, especially complex procedures like these, don't "just happen" without force and direction. So what forces are causing the enzymes, proteins, DNA, etc. to go to the right place at the right time and do their jobs?sagebrush gardener_{June 8, 2007
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This is already poor stuff - the muddled version of his explanation of common descent; his presentation of a shallow tautological form of natural selection; and his ignorance of any source of genetic diversity other that mutation.
Is there some correlation between being an angry young man and spreading lies? The patenetly false nature of Chu-Carrol's statement can be found in the very first chapter of Behe's book, pp. 10-11.Mung_{June 8, 2007
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Out of curiosity... Are any of those thousands of hits on Chu-Carroll Behe on a reputable widely read non-evolution oriented site the general public might read and if so is it supportive of Carroll's diatribe? I glanced at the first few dozen and none of them satisfy both conditions. There are three general categories I saw: 1) Popular Darwinian apologist blogs who support Carroll. 2) Popular Darwinian skeptic blogs who don't support Carroll. 3) Obscure blogs with little readerships. Wake me up when the New York Times or Nature or some other widely read reputable outlet publishes a review of The Edge of Evolution. Carroll's review has no impact on those already committed to a position and a negative impact on those few fence sitters who happen to read it due to its sophomoric derogatory tone i.e. Mark Chu-Carroll "the angry young man". :lol:DaveScot_{June 8, 2007
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I totally think that nano machinery is a huge, huge prb for Darwinoids and the like, but I think that the expression of these nano molecular changes is far more difficult to explain ie how all these little changes in a cell communicates to all other cells and than all these together form an amazing phenotype from a "random" genotype change. If SSBPs can pop up from nowhere, produce amazing functions hey why not, eyeballs too?jpark320_{June 8, 2007
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See A State of Extreme Cognitive Dissonance for an outline of the answer to your question.Larry Moran_{June 8, 2007
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I don't think it is possible that random chance formed the topoisomerase, regardless of much pixie dust the dyanmic fitness landscape was able to sprinkle on it. The Darwin lobby may have a point about dynamic fitness landscapes theoretically preventing genes from being stuck at a local maximum, however, I think this point is de minimus. According to Kimura, most mutations are neutral. The majority may in fact be actually near neutral and slightly deleterious. Which means most evolution must happen by a random walk. How a dynamic fitness landscape saves the day for evolution is lost on me. I think that argument is more of a placebo than an actual cure for Darwinism. Yet, the "Chu-Carroll" "Behe" counter on Google is now up to 26,400 hits. The Chu-Carroll placebo is in high demand.Jehu_{June 8, 2007
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