The Kinesin Motor: A Stunning Example of Cellular Nanotechnology

_{Jonathan McLatchie

August 15, 2011

Intelligent Design}

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One of the most amazing examples of cellular nanotechnology is a molecular motor protein known as kinesin. Kinesin is responsible for transporting molecular cargo — including chromosomes (e.g. during cell division), neurotransmitters and other important material — along microtubule tracks from one region of the cell to another. Read More>>

Comments

Nick @16: "This can be useful if the protein has some weak activity that allows the bacterium to eat a new food molecule, or break down a new antibiotic or whatever." Fair enough. In which case there would be selective pressure to maintain the additional expression of that protetin. So either you get to choose the neutral approach, or you get to assume that there was a selective advantage conferred by having a duplicate protein, which then turned out to be not such an important advantage after all. In any event, what about the coding question. Isn't it the case that cooption must involve taking on complete coding sequences (and regulatory mechanisms, etc., but we'll leave that aside for the moment)?Eric Anderson_{August 18, 2011
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"if we can’t rely on sequence similarity to demonstrate common ancestry" How did you reach that conclusion? "we can come up with other hypothetical ways of showing common ancestry." I think all the data in the references I provided are sequence based. "And comparing a bunch of kinesin’s with each other told us about how they came about in the first place?" Yes. Read the above references. Or http://pages.uoregon.edu/joet/pubs.htm Or http://en.wikipedia.org/wiki/Molecular_phylogeneticsDrREC_{August 17, 2011
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DrREC, It's nice to know if we can't rely on sequence similarity to demonstrate common ancestry we can come up with other hypothetical ways of showing common ancestry. And comparing a bunch of kinesin's with each other told us about how they came about in the first place?Mung_{August 17, 2011
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Genetic algorithms are designed, or did you not know that? And the reason their output appears to be designed is because it is. By inference, so are living organisms.Mung_{August 17, 2011
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So for you, selection is the effect, not the cause?Mung_{August 17, 2011
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I'm all for gradual pathways, especially more probable ones -- as long as more probable translates into even possible Do we know how often auto-inhibition evolves, from empirical research?material.infantacy_{August 17, 2011
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“Also, there is a lot of evidence that gene duplicates can themselves be selected even before they start acquiring mutations and altering binding and function.” That is an interesting point. I guess the question that jumps out immediately is what is doing the selecting. Presumably it is not a survival advantage that is being selected for.
Why do you say that? The selective advantage is typically that more copies of the gene increases the dosage of the protein. This can be useful if the protein has some weak activity that allows the bacterium to eat a new food molecule, or break down a new antibiotic or whatever. Standard mutation/selection. Later on, point mutations can improve the secondary activity of the protein, such that it becomes the primary activity. The duplicate genes are then not needed and are lost through drift or selection -- except for the new gene with the new function. (And, by the way, this is how new genetic information comes about, thus falsifying the ID claim that only intelligence can produce new information.)NickMatzke_UD_{August 16, 2011
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Nick @12: "Only very vaguely, if we are talking about the flagellum. E.g. there is no particular requirement that a bacterium acquire a protein-coding sequence from an outside source, although that is often known to happen. Your description is leaving out within-genome gene duplication and cooption which are very likely the major processes." I was thinking of cooption in my description of the process. Wouldn't cooption primarily work by obtaining a coding sequence? In other words, if bacterium B coopts a protein from bacterium A, aren't we really saying that it obtained the coding sequence necessary to manufacture that protein? Presumably if B subsumes one of A's existing proteins to within B's cell membrane it won't give B the ability to replicate A's protein unless B has the sequence and the machinery to do so? Same would go for a protein complex or a complete system. Even if B could somehow use the protein/protein complex/system, it would not pass that information on the the next generation without instructions for doing so. "Also, there is a lot of evidence that gene duplicates can themselves be selected even before they start acquiring mutations and altering binding and function." That is an interesting point. I guess the question that jumps out immediately is what is doing the selecting. Presumably it is not a survival advantage that is being selected for. Would this be some kind of pre-programed selection or front-loading process, or when you say duplicates can be selected without function, do you just mean that duplicates can sometimes remain in the population for a time if they are neutral (i.e., they weren't selected for, but just weren't weeded out)? "And, there is no requirement that the evolution of the flagellum or most other systems had to happen by linking in one protein at a time in sequence. E.g. it looks like the flagellum evolved by linking several preexisting multiprotein subsystems with nonflagellar functions." Agreed. I was just trying to describe the process roughly. So cooption could theoretically work by grabbing single proteins or multiprotein subsystems (or, I presume, whole systems). These would then be integrated into the new bacterium, together with the instructions for building it in the next generation.Eric Anderson_{August 16, 2011
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"miracle force called chance and necessity?" Let's not cloud the air. Forget chance and necessity. The observation is genetic diversity + differential reproduction -> non-random outputs that LOOK in hindsight, as if they were designed, or intended. This is directly observable in genetic algorithms, directed evolution and nature. My core claim is demonstrable. "While you’re at it, please explain why OOL research, or any other research for that matter, would be summarily terminated or adversely affected due to a working hypothesis of design" Depends-which working hypothesis of design?DrREC_{August 16, 2011
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material.infancy- Others have set the bar at the probabilistic resources of life on earth, or even the universe. Ask Kairosfocus. 20^12 isn't getting you there-especially when not all 12 residues are constrained, and show advantages independent of the others (partial function). I'd accept these thresholds, but the calculations that exceed them inevitably ignore evolution--the consider an all at once scenarion, but not gradual pathways that are much more probable.DrREC_{August 16, 2011
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Why is direct observation now subsumed by the mystical powers of an apparently miracle force called chance and necessity? Why is that which we plainly observe, not to be trusted over a mystical force -- chance/necessity -- that has been posited, but its efficacy never demonstrated? I need to prove true what we plainly observe, yet you and yours are under no practical burden to even demonstrate that what you proclaim as truth is subject to scrutiny, even in the slightest. Impressive positioning! Explain to everyone here why there are no substantive obstacles to the hypothesis that life arose strictly by chance and necessity. While you’re at it, please explain why OOL research, or any other research for that matter, would be summarily terminated or adversely affected due to a working hypothesis of design.material.infantacy_{August 16, 2011
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Some reply.
Not as impressive as your response to my question about numbers indicative of design. Allow me to quote your reply:

So if a sequence complexity like 20^12 "is [not] going to produce numbers that scream for design," what numbers would?material.infantacy_{August 16, 2011
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NM: "Do you really think kinesin has no relatives?" MI: "I have relatives." Some reply. BUT, it proves a point-you could cluster your family tree into a hierarchy, and learn a great deal about inherited traits. You can do the same thing for the kinesins, and learn a great deal about their evolution. Like these scientists did: http://www.biomedcentral.com/1471-2148/10/110 http://valelab.ucsf.edu/publications/1998kulljmusrescellm.pdfDrREC_{August 16, 2011
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"I don’t need to. The telic nature of living systems is apparent." Apparent? Some rubric for science. The miasma theory of disease was apparent for centuries.DrREC_{August 16, 2011
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"selection" is a function of the differential reproduction of those bearing more or less advantageous traits. More efficient kinesin=advantage. Do you not get this, or are you being willfully obtuse?DrREC_{August 16, 2011
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"didn’t the cell need its Fed Ex vesicle delivery service and highways to move the Kinesin delivery trucks on right from the beginning?" Um, no. Non-Eukaryotes generally lack vesicles, microtubules and kinesins. Kinesins also function, albeit inefficiently without the auto-inhibition mechanism.DrREC_{August 16, 2011
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Is that more or less the proposed pathway?
Only very vaguely, if we are talking about the flagellum. E.g. there is no particular requirement that a bacterium acquire a protein-coding sequence from an outside source, although that is often known to happen. Your description is leaving out within-genome gene duplication and cooption which are very likely the major processes. Also, there is a lot of evidence that gene duplicates can themselves be selected even before they start acquiring mutations and altering binding and function. And, there is no requirement that the evolution of the flagellum or most other systems had to happen by linking in one protein at a time in sequence. E.g. it looks like the flagellum evolved by linking several preexisting multiprotein subsystems with nonflagellar functions.NickMatzke_UD_{August 16, 2011
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Nick @8: Thanks for the link. I have great respect for Mike Gene's careful approach to these issues (and was one of the early individuals to buy his book). If I am understanding the situation as Mike describes it, one of the challenges evolution has to overcome in order to successfully build a new structure by co-option (the current preferred hypothesis for the evolution of the bacterial flagellum) is the issue of continuity (roughly speaking, that the various parts had to have been in existence in more ancient organisms). Based on prior understanding, Mike had assigned a certain "Discontinuity Score" to the flagellum based on the lack homologous proteins (meaning, no continuity from more ancient organisms). Based on more recent work, including the work you have done, Mike is now of the opinion that there are homologous proteins for all, or almost all, of the proteins in the flagellum. Therefore, Mike concludes that discontinuity, in and of itself, is not a show-stopper for the co-option hypothesis and that this hurdle has been overcome. So, assuming all the necessary proteins not only exist, but are available in the right place at the right time (no discontinuity), is the current proposed evolutionary co-option pathway roughly (just speaking in broad terms) as listed below: - Bacterium (B) obtains a protein-expressing sequence of genetic material from another bacterium or other source - B integrates that genetic material into its own genome - B alters its expression machinery to express the protein in a controlled fashion (or its expression machinery is already be able to do so) - the expressed protein becomes integrated into cellular mechanisms so as to perform a new or improved function - the new (improved) function confers a selective advantage - over time the new B (B') becomes fixed in the population (or at least in a large enough sub-population to allow the next steps to take place) - the above process repeats for the next protein, and so on. Is that more or less the proposed pathway?Eric Anderson_{August 16, 2011
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Okay, you put it here.kairosfocus_{August 16, 2011
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Rube sez: But, er, er, er, didn't the cell need its Fed Ex vesicle delivery service and highways to move the Kinesin delivery trucks on right from the beginning? And, the ATP Synthase battery system needed for each kinesin walking truck -- talk about star wars! -- step.kairosfocus_{August 16, 2011
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These and these; with these too. And many more behind them.kairosfocus_{August 16, 2011
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Fair Comment: Given that Dr Matzke knows or should know the actual state of the discussion, this seems to be a willful strawmannish misrepresentation of the problem raised by Behe, to provide in-lit, detailed, technical documentation of origin of IC systems; from those who are too often providing only just so stories with few if any actual points of evidence on observation as opposed to inferences presented as facts. Literature bluffing, aka hurling the elephant by in effect implying that a mass of technical lit documents what on diligent search it does not: detailed observationally anchored cases of origin of IC systems on chance plus necessity Darwinian mechanisms, is a fallacy. Judge Jones should never have allowed that stunt of piling up journals in his court room -- that is the worst form of generalised appeal to claimed authority, in the teeth of a challenge to warrant claims on merits of fact and reason. (Case -- literally from a textbook -- in point of inferences presented as observed facts on the unobservable deep past, here.)kairosfocus_{August 16, 2011
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MI has something to say to this, but cross posted here.kairosfocus_{August 16, 2011
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I love how ID/creationists think this is an argument
Which are we, ID proponents or creationists?
Do you really think kinesin has no relatives?
I have relatives.
Why do you think anyone who is well-informed about the actual science and methods of evolutionary biology should take you at all seriously when you armchair critics won’t even bother to get vaguely informed about the most basic data you would need to even begin to have an informed discussion of the evolutionary history of this system.
Darwinian gnostic bluster, that. How an astonishingly sophisticated living system functions and replicates and self-modifies says nothing of how it came to be. That’s the armchair consensus, anyhow.
This goes for Jonathan M. also, only ten times more strongly, since he exhibits some actual ability to read science, and yet bizarrely refuses to do any serious investigation of the evolutionary literature and sequence databases which are relevant to even the most basic discussion of the kinds of question he is interested in (or claims to be interested in, at least).
You couldn’t go 3 rounds with Jonathan M.
Imagine if someone proclaimed the origin of the moon was an unexplainable mystery, without bothering to read any of the literature or look at any of the data on the geology and chemistry of the moon. If you were a scientist who studied moon geology and chemistry, what would you think of such a person?
Have you read SITC?
Now you know how evolutionary biologists feel...
The feelings of evolutionary biologists is not at issue.
...about IDists/creationists virtually every time they write some breezy post along the lines of “X is complicated and functional, and I’m not going to bother to research the evolutionary explanations at all, therefore it’s obvious design is the best explanation!”
X is complex, and functional, and interdependent, if by X you mean practically every protein and its corresponding coded representation in DNA. This functional, integrated complexity is beyond the realm of chance by many orders of magnitude multiplied many times over; and the role of necessity is completely unestablished. Design is the best explanation. You’re welcome to demonstrate otherwise.material.infantacy_{August 16, 2011
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Dr Matzke: You have been corrected over and over and over again on the improper conflation of design thought and Biblical creationism. Why do you insist on what you know or should know is not correct? Do you not see the implications of such rhetoric in light of duty to truth and to fairness? (Have you not even taken notice of the latest thread here at UD where the creationist objection to ID that it is not doing what they are interested in, was raised?) GEM of TKIkairosfocus_{August 16, 2011
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Vid here at youtube.kairosfocus_{August 16, 2011
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F/N: Folks, forget the idea hitman comments and watch the vid, listening to the explanation. The vid literally speaks for itself and is quite a show-tell. Then, ask yourself: how could a cell get along without something like this, from the outset, as well as without something like the ATP Synthase rotary action ATP energy battery molecule factory, the Ribosome and mRNA-tRNA system, the Golgi post-office, the intracellular highway system that Kinesin is using, and notice the trick on traffic direction? And so on. Insist on solid empirical evidence not mere Lewontinaian just-so stories and a priori materialism in a lab coat. Remember, Kinesin is part of a targetted dispatch system in the cell, and reflects a much wider context of integrated sophisticated nanomolecular technology, a system that is an inspiration and challenge to engineers. (Remember, a self-replicating factory would be a techno-econ breakthrough that would transform our planetary economy and the space colonisation project that is the real challenge of the century ahead.) And, let us never ever forget that just 500 - 1,000 bits of functional info would be well beyond the search capacity of blind chance and necessity on the gamut of our observed cosmos. As in, notice also how there has been ever so much dodging the force of the log-reduced, simplified Dembski Chi metric and its application to real world bio cases: Chi_500 = I*S - 500, bits beyond the solar system PTQS threshold Unless, you are willing to argue and show how life was in effect written into the basic physics of the cosmos. Which would exponentiate the power of the cosmological design inference on fine tuning. Imagine, a cosmos fine-tuned for C-chemistry, cell based life and PROGRAMMED to produce such life in the right environment just finetuned for? Talk about monkeying with the physics of the cosmos! Ole Sir Fred Hoyle is looking over the balcony of heaven, shaking his head and laughing! Denton -- remember, this is 1986, 25 years ago! -- is proving more and more apt by the day:
To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometers in diameter [[so each atom in it would be “the size of a tennis ball”] and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the port holes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings we would find ourselves in a world of supreme technology and bewildering complexity. We would see endless highly organized corridors and conduits branching in every direction away from the perimeter of the cell, some leading to the central memory bank in the nucleus and others to assembly plants and processing units. The nucleus itself would be a vast spherical chamber more than a kilometer in diameter, resembling a geodesic dome inside of which we would see, all neatly stacked together in ordered arrays, the miles of coiled chains of the DNA molecules. A huge range of products and raw materials would shuttle along all the manifold conduits in a highly ordered fashion to and from all the various assembly plants in the outer regions of the cell. We would wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison. We would see all around us, in every direction we looked, all sorts of robot-like machines . . . . We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of components, error fail-safe and proof-reading devices used for quality control, assembly processes involving the principle of prefabrication and modular construction . . . . However, it would be a factory which would have one capacity not equaled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours . . . . Unlike our own pseudo-automated assembly plants, where external controls are being continually applied, the cell's manufacturing capability is entirely self-regulated . . . . [[Denton, Michael, Evolution: A Theory in Crisis, Adler, 1986, pp. 327 – 331.]
And,the objections like the above -- remember, from NCSE's former chief idea hitman! -- are turning into inadvertent demonstrations of the power of the inference to design on observed functionally specific complex organisation and linked information. GEM of TKIkairosfocus_{August 16, 2011
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Oh good, no infinite detail required? Excellent. Real science is about testable hypotheses. And we have those for the evolution of the flagellum and many other complex systems. And, as it happens, the evolutionary explanation of the flagellum has passed several tests -- even tests that the one IDist who has bothered to get familiar with the details of the relevant evidence, Mike Gene, found surprising. http://designmatrix.wordpress.com/2009/03/28/evolution-of-bacterial-flagellum/NickMatzke_UD_{August 16, 2011
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Nick, no-one is asking for infinite or near-infinite detail from evolutionists. We're asking for something that isn't laughable, something that can even be analyzed in a serious way. We certainly are not looking for "gee this can happen in two steps" a la DrRec above, and we are certainly are not looking for "assume step A, then assume B, then assume C, and viola, we can now get to D," which was the level of detail provided by someone (who shall remain unnamed) in an article trying to "explain" the evolution of the bacterial flagellum.Eric Anderson_{August 15, 2011
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And let's not have the "we demand infinite/near-infinite detail from evolutionists before we'll believe anything" response. That's just a cheap rhetorical trick. No one requires infinite detail in any other branch of history or science. And IDists hypocritically provide *absolutely no details whatsoever* about their proposed "explanation". And before someone drops the "just-so story" line -- c'mon, "ID did it" is the most vague, useless, untestable just-so story you can come up with.NickMatzke_UD_{August 15, 2011
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