Engineering at Its Finest: Bacterial Chemotaxis and Signal Transduction

_{Jonathan McLatchie

September 19, 2011

Intelligent Design}

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ID theorists have long urged that the case for design is both a positive and scientific argument, based on standard principles of abductive scientific reasoning. Key to the detectability of design are particular characteristics that intelligent agents often leave behind as hallmarks of their activity. We know that intelligent causes are the only category of explanation with the ability to visualize, and ultimately actualize, a complex and functionally specified end goal. Hence, presented with a complex and functionally integrated system in nature, we can infer that some measure of conscious or rational deliberation was employed in its development.

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I'm not an expert, this is just my guess/opinion. But it seems like two things that organic chemotaxis has is signal transduction and somewhat controllable motility. If you can sense chemicals but you can't control your movement, what good is sensing the chemicals? And if you can control your movement but have no sensation of your environment, what good is the movement? That seems like a basic irreducibly complex feature. Also, that is extremely simplistic as sensation requires a host of proteins (each of which are extremely complex themselves). The movement itself requires lots of complex "equipment". Then there is the whole question of how does it KNOW how to behave this way or that way, depending on what it senses? Say an environment as food and poison. How is an organism "programmed" to behave in a way that will, on average, drive it to greater densities of food and away from densities of poison? Something tells me this is not a trivial process, as nothing in biology ever seems to be. You seem to portray organic chemotaxis as a step above random drift when it seems like a complex, brilliant mechanism, even upon a cursory glanceuoflcard_{September 21, 2011
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That’s pretty funny, considering I’m the one saying that these sorts of systems came about through descent with modification, and you’re the one proposing that they just miraculously appeared through magic. The standard of you and other commentators seems to be “evolution must provide an infinitely detailed explanation, and ID must provide absolutely no detail at all, including not even explaining which chemotaxis systems were designed when, despite the fact that they are extremely variable in composition across bacteria. Evolution doesn’t provide infinite detail, therefore clearly the best explanation is ItMustaBeenAMiracle!”,
Apparently I am a "miracle" worker as I am typing this out. After all, I am creating specified, functional, complex information, and it's not due to any natural process like neo-Darwinian mechanisms. If you agree with this, going by the logic in your comment, then it is a miracle that these words are forming on my screen. And if, by miracle, I click this "POST COMMENT" button, you will miraculously read and comprehend the message.uoflcard_{September 21, 2011
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Nick, you are missing the point. It’s only the irreducible part that can’t be reduced.
Someone please say what "the irreducible part" is for chemotaxis. JonathanM's opening post doesn't even try, and neither has anyone else. Yet the assertion has been made. Chemotaxis just ain't as hard as you guys think. Anything microscopic is already moving passively through Brownian motion, and anything that biases Brownian movement in the appropriate direction can cause chemotaxis. It's been awhile since I reviewed this topic, but one thing I can remember is that things like nonliving vesicles can exhibit chemotaxis under pretty simple conditions.NickMatzke_UD_{September 20, 2011
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Nick,
“evolution must provide an infinitely detailed explanation
No one expects such an explanation in every single case. But the premise that variation and selection can build any such system does require at least one such explanation. Without such an explanation, the premise is an untested hypothesis. You can't make such a claim and expect to get away without testing it except in the bizarro world of evolutionary science. Your claim is about the mechanism. That is why you must demonstrate it. ID must demonstrate the claims that it makes, not the ones it doesn't. When you read a book, do you need to know whether the content was produced with a pen and paper, crayons, on a typewriter, a computer, or by dictation, or some unknown medium, to know that it was generated by an author? Of course not. The mechanism is irrelevant. But if you claim that some natural process produced a book or some other seemingly designed artifact, the question logically changes. How specifically did it happen? A vague, untested answer won't do. Which part of that is so difficult to understand? As usual you have time to throw a few rocks - nothing wrong with that - but mysteriously none to defend the hypothesis which is at the core of your belief system. Are you ever going to get to that?ScottAndrews_{September 20, 2011
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Nick, Variablity does not refute IC.Joseph_{September 20, 2011
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NickMatzke:
That’s pretty funny, considering I’m the one saying that these sorts of systems came about through descent with modification, and you’re the one proposing that they just miraculously appeared through magic.
ID is OK with descent with modification, Nick. ID just claims it is directed by internal programming.
The standard of you and other commentators seems to be “evolution must provide an infinitely detailed explanation, and ID must provide absolutely no detail at all, including not even explaining which chemotaxis systems were designed when, despite the fact that they are extremely variable in composition across bacteria. Evolution doesn’t provide infinite detail, therefore clearly the best explanation is ItMustaBeenAMiracle!”
Well, Nick, it's like this- we have direct observational evidence of designing agencies creating complex, multi-part systems. We don't have any evidence of blind, undirected processes doing so. Therefor yours is an extraordinary claim and as such requires extraordinary evidence.
But, let’s not get distracted. JonathanM is the one who raised the claim that this system is “irreducibly complex”. This claim typically means that the system is supposed to be an all-or-nothing proposition.
Wrong again, as usual. With a targeted search we don't need an all-or-nothing scenario.Joseph_{September 20, 2011
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OT: Here is a good link for the video playlist of the recently released video 'Programming Of Life'; Programming of Life - video playlist: http://www.youtube.com/playlist?list=PLAFDF33F11E2FB840bornagain77_{September 20, 2011
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Nick you complain that this following 'unfair' burden of proof has been placed on you:
The standard of you and other commentators seems to be “evolution must provide an infinitely detailed explanation,
No Nick, I don't want an 'infinitely detailed explanation' for how a molecular machine, such as the Flagellum, came about, I want just a single simple demonstration that what you posit for all these molecular machines, which greatly surpass man-made machines in engineering parameters of efficiency and power, can come about by purely material processes. For you to jump up and down, pointing to severely tortured sequence similarities, or for you to stamp your feet badmouthing any who dares disagree with you when you say, without a actual demonstration, that such wondrously elegant molecular machines can happen without intelligent intervention, does nothing at all, as far as empirical science is concerned, to actually demonstrate that such wondrous machines can come about by purely material processes. And frankly Nick, though you accuse IDists of invoking 'magic', by pointing out the obviously reasonable need for intelligence to explain these machines, the fact is that for someone, such as you, to a-priori believe that such a plethora of sophisticated molecular machines can come about by purely material processes, without even a single simple demonstration that it can actually be done by such purely material processes, is the very definition of believing in 'magic'!!! notes:
in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system. "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologist The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,, ‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,, Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,, ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines http://www.metacafe.com/watch/5302950/ “The response I have received from repeating Behe's claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.” David Ray Griffin - retired professor of philosophy of religion and theology Michael Behe - Life Reeks Of Design - 2010 - video http://www.metacafe.com/watch/5066181 List of 40 Irreducibly Complex Molecular Machines which Defy Darwinian Claims http://creationbydesign.wordpress.com/2010/06/15/list-of-40-irreducibly-complex-molecular-machines-which-defy-darwinian-claims/ Simplest Microbes More Complex than Thought Excerpt: The smallest, simplest cells are prokaryotes.,,,One of the papers in Science to which PhysOrg referred said that some 200 molecular machines are found in this little microbe. http://www.creationsafaris.com/crev200912.htm#20091229a The Closest Look Ever At The Cell's Machines - 2006 Excerpt: The study combined a method of extracting complete protein complexes from cells (tandem affinity purification, developed in 2001 by Bertrand Séraphin at EMBL), mass spectrometry and bioinformatics to investigate the entire protein household of yeast, turning up 257 machines that had never been observed. It also revealed new components of nearly every complex already known. http://www.sciencedaily.com/releases/2006/01/060123121832.htm Molecular Biology Animations - Demo Reel http://www.metacafe.com/w/5915291/ Powering the Cell: Mitochondria - video http://www.youtube.com/watch?v=RrS2uROUjK4 Articles and Videos on Molecular Motors http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMzlkNjYydmRkZw&hl=en
bornagain77_{September 20, 2011
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That's pretty funny, considering I'm the one saying that these sorts of systems came about through descent with modification, and you're the one proposing that they just miraculously appeared through magic. The standard of you and other commentators seems to be "evolution must provide an infinitely detailed explanation, and ID must provide absolutely no detail at all, including not even explaining which chemotaxis systems were designed when, despite the fact that they are extremely variable in composition across bacteria. Evolution doesn't provide infinite detail, therefore clearly the best explanation is ItMustaBeenAMiracle!" But, let's not get distracted. JonathanM is the one who raised the claim that this system is "irreducibly complex". This claim typically means that the system is supposed to be an all-or-nothing proposition. I pointed out that the facts just don't support this for chemotaxis. The response so far? Irrelevancies and attempts to change the subject. Par for the course.NickMatzke_UD_{September 19, 2011
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One mutation, one part knock out, it can’t swim. Put that single gene back in we restore motility.
That's an incredibly fragile argument, especially since there are many different bacteria with subsets of the iconic flagellum genes. different subsets. Some motile, some not. If irreducible complexity really hinges on requiring all or none of the proteins, the concept is dead.Petrushka_{September 19, 2011
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Nick, you are missing the point. It's only the irreducible part that can't be reduced.Petrushka_{September 19, 2011
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Nick, You would have everyone's full attention if you could refute Jonathan's conclusion by describing how natural selection accounts for such developments. You could demolish his argument by providing yours. Instead, your objection calls attention to your inability to do so. The trouble isn't that your explanation isn't good. It's that you don't have one at all. It's like telling a child that babies from from storks. It only holds up as long as you avoid giving details. Eventually you have to admit that you don't know where storks get babies and no one has ever seen a stork deliver a baby, and then you cave in like an extra on Law and Order.ScottAndrews_{September 19, 2011
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Bacteria undoubedly developed these processes through the epigenetic codes, not Darwin's random chance mutations and then natural selection. Epigenetics does not look at all passive as Darwinism presents, and suggests strongly that those codes were there from the beginning of life, that is, by intelligent design. See James Shapiro's new book, a revelation.turell_{September 19, 2011
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We have to keep something in mind when presenting these kinds of arguments. Never ever underestimate the imagination of evolutionists!kuartus_{September 19, 2011
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This article fails to mention that signal transduction is much more variable than the flagellum (which itself has quite a bit of functional variability. Some flagellated species have dozens of signal transduction proteins tied to the flagellar system; some have 10; some have a few; and some have none. How can one assert IC if this is the case? How could JonathanM have missed this huge and obvious biological fact, if he is claiming to give a well-researched account of the system?NickMatzke_UD_{September 19, 2011
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Another day, another extremely bad day to be a neo-Darwinists. Very well researched and written Jonathan, I especially liked your closing comment;
The bacterial flagellum represents not just a problem of irreducible complexity. Rather, the problem extends far deeper than that. What we are now observing is the existence of irreducibly complex systems within irreducibly complex systems. How random mutations, coupled with natural selection, could have assembled such a finely set-up system is a question to which I defy any Darwinist to give a sensible answer.
And Jonathan, to male it even more inexplicable to the materialistic framework of neo-Darwinism, this following paper found 'spooky' quantum action in the Flagellum;
INFORMATION AND ENERGETICS OF QUANTUM FLAGELLA MOTOR Hiroyuki Matsuura, Nobuo Noda, Kazuharu Koide Tetsuya Nemoto and Yasumi Ito Excerpt from bottom page 7: Note that the physical principle of flagella motor does not belong to classical mechanics, but to quantum mechanics. When we can consider applying quantum physics to flagella motor, we can find out the shift of energetic state and coherent state. http://www2.ktokai-u.ac.jp/~shi/el08-046.pdf
Since a 'non-local' cause is required to explain quantum action (A. Aspect), the implications as to what this means are very deep and not at all friendly to current neo-Darwinian precepts! a few more notes of interest:
Bacterial Flagellum - A Sheer Wonder Of Intelligent Design - video http://www.metacafe.com/watch/3994630 Bacterial Flagellum: Visualizing the Complete Machine In Situ Excerpt: Electron tomography of frozen-hydrated bacteria, combined with single particle averaging, has produced stunning images of the intact bacterial flagellum, revealing features of the rotor, stator and export apparatus. http://www.sciencedirect.com/science/article/pii/S096098220602286X Bacterial Flagella: A Paradigm for Design – Scott Minnich – Video http://www.vimeo.com/9032112 Ken Miller's Inaccurate and Biased Evolution Curriculum - Casey Luskin - 2011 Excerpt: One mutation, one part knock out, it can't swim. Put that single gene back in we restore motility. ... knock out one part, put a good copy of the gene back in, and they can swim. By definition the system is irreducibly complex. We've done that with all 35 components of the flagellum, and we get the same effect. - Scott Minnich http://www.evolutionnews.org/2011/07/ken_millers_inaccurate_and_bia048321.html
bornagain77_{September 19, 2011
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As Jonathan Wells states in Unlocking the Mystery of Life: "It's irreducible complexity all the way down"Alan_{September 19, 2011
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