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Yet another triumph of evolution

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The Biological Frontier of Physics
Rob Phillips and Stephen R. Quake
May 2006, page 38

… The cell’s nanometer-scale machines are mostly protein molecules, although a few are made from RNA, and they are capable of surprisingly complex manipulations. They perform almost all the important active tasks in the cell: metabolism, reproduction, response to changes in the environment, and so forth. They are incredibly sophisticated, and they, not their manmade counterparts, represent the pinnacle of nanotechnology. Yet scientists have no general theory for their assembly or operation.


It is surely one of the triumphs of evolution that Nature discovered how to make highly accurate machines in such a noisy environment.

"Single-molecule biophysics techniques, which create new ways to observe, study, and characterize macromolecular machines ... are providing exactly the sort of data needed to address some of the problems we have described in this article." This is just one of several same-minded statements I could have quoted. They talk about "macromolecular machines." To our Darwinist friends, two challenges: (1) the authors have recognized a 'machine' without knowing, assuming, or querying about the 'origin' of the machine. The machines are 'recognizable'. We don't have to 'know' who 'built' the machine. (2) when you look out at Nature (NOT under a microscope), where do you see naturally occurring machines? [Remember, the scientists are saying that the nano-world machines of the cell are vastly beyond the nano-technology we now posses. Yet we make all kinds of machines. Ergo, macro-level machines are easier to construct than nano-level machines; but we don't see any naturally occurring 'macro'-level machines. How do you answer?] PaV
but so ridiculous on more detached inspection that years from now they could reply “come on, you can’t believe, after reading the entire paragraph, that we were really serious?”
I can even now hear their cries of "quote mining," as the future Darwinian minority resorts to quoting ID'ers to prop up their religious convictions. Mung
From the article:
As the characteristic size approaches that of biological macromolecules, all the energies [thermal, chemical, mechanical, and electrostatic] converge. The convergence is remarkable, since the energies range over 20 orders of magnitude as object size scales from subatomic to macroscopic; its existence is an opportunity for complex physical phenomena and processes that are evidently utilized by life. Broadly speaking, the interplay between thermal and deterministic forces is what gives rise to the rich behavior of molecular machines...
Something else to factor into cosmological fine-tuning.
It is surely one of the triumphs of evolution that Nature discovered how to make highly accurate machines in such a noisy environment.
Funny! This guy's good! (Really: If the editors of "Physics Today" expect their publication to be taken seriously on the subject, they are going to to have to stop allowing indefensible lines that.)
Information flow in the central dogma is likewise often presented as a cartoon: a series of directed arrows showing that information moves from DNA to RNA to proteins, and from DNA to DNA. But information also flows from proteins to DNA because proteins regulate the expression of genes by binding to DNA in various ways. Though all biologists know that interesting feature of information flow, central-dogma cartoons continue to omit the arrow that closes the loop.
If it's a closed loop, where does the new information come from? ;-)
...scientists have made tremendous progress in discovering and cataloging the molecules that form the basis of life. In what respect is their pursuit intellectually distinct from the "stamp-collecting" mindset of the pre-molecular era?
DaveScot, you were consulted for this article? j
I must second others that the article is Very interesting. I have no direct evidence, but the conspiracy theorist in me suspects the authors are secretly pro-ID (hence the choice of cover photo with the flagellum), and even the apparent brief bows to the "triumph of evolution" sound almost tongue-in-cheek hilarious to me -- as if they knew that such phrasing was necessary to get the article published by the true believers, but so ridiculous on more detached inspection that years from now they could reply "come on, you can't believe, after reading the entire paragraph, that we were really serious?" SCheesman
Despite evolutionary magic statements, I enjoyed the article. They bring many emerging realities to bear on the subject of systems biology and in terms I could understand. Noted one of the contributors is a HHMI appointee within range of a new mandate for cross-discipline grant studies. One of the more interesting lines besides the words "stamp collecting" is the following: "Understanding collective effects in the cell will require merging two philosophical viewpoints. The first is that life is like a computer program: An infrastructure of machines carries out arbitrary instructions that are encoded into DNA software. The second viewpoint is purely physical: Life arises from a mixing together of chemicals that follow basic physical principles to self-assemble into an organism. Presumably, the repertoire of available behaviors is more limited in the latter. The two viewpoints are complementary, not incompatible: Either one could best describe cell behavior, depending on the particular situation." They leave out direct design inference. But, a computer program is designed and they recognize two philosophical viewpoints must merge into a holistic approach in order for research to expand for predictable patterns. The two views are complimentary in fact required. Materialist will have to recognize it eventually. However, where telic reasoning engulfs materialism, the opposite is not true. A protein "vector" though determinant in direction say by thermal cause still cannot realize higher logic or ascend to thought processes outside its designed purpose let alone self realization. It is only one part of many and therefore purposeless on its own. Besides physics, thermal and fluid dynamics, or mechanical engineering; an industrial manufacturing engineer should get great kicks out of the cell manufacturing plant efficiency in movement of component parts as a big picture. Plus in the article they recognized the energy efficiency which should eventually have impact for us all. The motor's directional change due to thermal fluctuation right before 50seconds and the recognition of convergence along energy levels is intriguing as well. For my simple mind - its quite stunning. "It is surely one of the triumphs of evolution that Nature discovered how to make highly accurate machines in such a noisy environment." They utilize the word "marvelous" too. Now that's just marvelous! ;-) Fearfully and wonderfully made! Rightfully so they are amazed at the intricate weavings of life. What I'm curious to know is if thermal fluctuation is also responsible for the double helix twisting and how this also might be related to folding and topology. The directional change of the motor is a strange bird. Is there analagous examples elsewhere in nature? Bird migration? Fish? Snowbirds in Florida, hehe. Plus with irreversible processes and Pi, its a curious thing to see if or how equations might be arranged to account for such motions in a fluid environment of information exchange. The hopping effect from "one strand to another" is a curious look at possible new hiearchial storage/retrieval processes and differential equations in use with storage algorithms of a 3D form. Does the organic spiral offer the most energy efficient storage method? No wonder IBM is planting millions into this arena. They see the writing on the wall - highly self-efficient storage technology with 90% energy ratings on minute levels of charge. And I'll say it anyway, though everyone will think my thoughts nuts. The double helix at the center of our galaxy twisting due to magnetic forces in cicular momentum is something to look at imh - unorthodox logic. I'm not saying its a full application or analogy. But that energy/diffusion or thermal flux and magnetic/spin are seen everywhere in nature in micro/macro scales. Black holes recently - old ones are seen as the most energy efficient systems. When a hurricane/tornado comes thru there is a rapid heat dissipation/coolant exchange. The application of spiral forms for energy efficient propulision systems posted here not long ago also shows real mechanical proof sets for better thermal flows and oddly enough noise reduction. It acts as a natural buffer. And the reason I'd think this way is a Designer would make all things simple as possible between spatial worldviews. I tried to find the info posted about spiral systems and ended up finding this info just now about spiral technology for image storage: http://portal.acm.org/citation.cfm?id=1082184&dl=ACM&coll=ACM to coool, cool beans.... it gives a whole new meaning to made in His image. Michaels7
Farshad: I sincerely apologize. Overexposure to those who repudiate anything which is not the strictest orthodoxy has caused my "irony recognition filter" to become clogged. Sorry. tinabrewer
Tina, being a new-age spiritualist I'm well aware of what neo-paganism is (or is not). My analogy was an *ironic* look at the Darwinian view. While Darwinists overtly reject any intelligent causation it seems that they are unconsciously worshiping some sort of god of nature who is able to create any complex life form out of nothing. They always talk about wonders and endless powers of mother-nature without any need for real scientific evidence. They act and speak as though nature is their god. Farshad
Um, Farshad, I hate to be the one to break this to you, but paganism is the original form of belief in intelligent causation, and bears absolutely no resemblance to Darwinism or materialism. Pagans, in their uncorrupted form, believe in the active participation, by non-material entities, in the formation and development of life on earth, and as such are well within the ID 'big tent'. Paganism would be a big step up from this empty materialism, and probably far closer to the truth... tinabrewer
Article:"It is surely one of the triumphs of evolution that Nature discovered how to make highly accurate machines in such a noisy environment." Nature discoverd! Nature designed! Nature made! Nature developed! Nature created! Nature planned! Who art thou worshipful Nature? Release your mask! Let us know thee! Is Darwinism another form of neo-paganism? Article:"One marvelous example is DNA polymerase, a molecular copying machine only 13 nanometers in size, capable of copying DNA molecules with an intrinsic error rate approaching one part per million" Not to mention all those precise error-correction mechanisms that cooperate the copying process. We must simply assume all of these nano-machines are evolved and the Darwinian mechanisms is the only alternative. The gods of mutation and selection at work! Farshad
Apart from the obligatory genuflection to Darwin the article is really quite interesting. Mung
"It is surely one of the triumphs of evolution that Nature discovered how to make highly accurate machines in such a noisy environment." The greater the obstacles to their theory, the greater the triumph it enjoys! The less plausible it becomes, the more certainly it occured. What a powerful force faith is! russ
From the article: "...despite the field's reputation as a soft science, nearly all of biology is now ripe for quantitative analysis of the sort that physicists are used to..." Its about time physicists got more involved in these areas of biology. They will shine a light where Darwinists have only been ducking and diving and it can only reinforce the points ID has been making for a long time now,IMO. PS look at the front cover of that issue: part of a cell with a ... flagellum! antg

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