Re: [asa] Molecular Biology and Design

From: Nucacids <>
Date: Wed Dec 31 2008 - 14:45:14 EST

Hi Dave,

Well then, there is a certain irony of dismissing someone as "only an engineer" since engineering concepts played, and continue to play, crucial roles in molecular biology.


In a 1998 scientific essay about molecular machines, Bruce Alberts offered a most interesting acknowledgment at the end of his article. Alberts stated that he was indebted "to Jonathan Alberts for his explanation of how engineers analyze machines." A biologist is seeking engineering explanations to better understand biology?


In March 2002, John Doyle, an engineer from the California Institute of Technology published an article entitled "Reverse Engineering of Biological Complexity" in the journal Science.14 Biologists have recently begun to appreciate a "systems-level" of analysis15 as they have accumulated such massive amounts of molecular information about the cell. Doyle notes that "systems-level design has been at the core of modern engineering, motivating its most sophisticated theories in controls, information, and computation." He then highlights many of the insights from modern engineering and how they would apply to biology, ending his article by noting, "Biologists and engineers now have enough examples of complex systems that they can close the loop and eliminate specious theories. We should compare notes."


Then there is:


Robust perfect adaptation in bacterial chemotaxis through integral feedback control.


Integral feedback control is a basic engineering strategy for ensuring that the output of a system robustly tracks its desired value independent of noise or variations in system parameters. In biological systems, it is common for the response to an extracellular stimulus to return to its prestimulus value even in the continued presence of the signal-a process termed adaptation or desensitization. Barkai, Alon, Surette, and Leibler have provided both theoretical and experimental evidence that the precision of adaptation in bacterial chemotaxis is robust to dramatic changes in the levels and kinetic rate constants of the constituent proteins in this signaling network [Alon, U., Surette, M. G., Barkai, N. & Leibler, S. (1998) Nature (London) 397, 168-171]. Here we propose that the robustness of perfect adaptation is the result of this system possessing the property of integral feedback control. Using techniques from control and dynamical systems theory, we demonstrate that integral control is structurally inherent in the Barkai-Leibler model and identify and characterize the key assumptions of the model. Most importantly, we argue that integral control in some form is necessary for a robust implementation of perfect adaptation. More generally, integral control may underlie the robustness of many homeostatic mechanisms.


Of course, being an engineer does not make one an expert in biology. But then again, neither does being a biologist automatically make one on expert in evolution.


However, my point is simply that the depth and breadth of the similarities between engineering and molecular biology is reasonable basis for a suspicion that life was designed.



  I wasn't questioning your statements. Just asking (sort of tongue-in-cheek) for clarification wherever it may be available.

  You see, when I am in a state science standards committee, and someone stands up and says that another person's testimony is invalid and must be ignored because that person is "only an engineer" then I think the process of government is being gerrymandered.
  Nevermind that the critic herself has a degree, not in science, but in "science education", and the subject of the criticism [the alleged engineer] has published over 300 scientific papers and is a polymer chemist who gives his grad students assignments on polymer formation as part of a hypothetical abiogenesis process on a hypothetical primitive earth.

  So, my guess is its very relevant to public policy whether engineers do or don't have something to valid to say in their fields of expertise.

  Also, please let me quote from another thread:

  Bernie replied: > Why is that important, when you have universes

  constantly popping into existence, the vast majority of them being
  non-viable? If this has been going on forever (new universes
  constantly being produced), why is probability important or even
  considered? If you get a fraction of universes viable from an almost
  infinite set, that's a lot of universes!<

  Bernie has a very valid question. But as far as I know, and I get this from my biochem books, molecular biology is based quite a bit on probability calculations.

  One book discusses why we think, for example, that two organism are related based on coding for producing a certain protein sequence. Some sequences are so unlikely to have arisen in two places independently that scientists assume there was only one origin, but that 60 million years later the coding was inherited by two otherwise unrelated lineages that we now know were descended from that common organism. Thus they look for common descent. And that is quite reasonable. Its one of the main reasons to believe in common descent (and to believe in evolution). But if probability is an insufficent basis for the assumption (because an infinite number of trials produces an infinite sample set) there is no reason to believe in the connection between the organisms.

   So, I agree, the molecular clock idea is kind of important to the science.

  Now, to be fair to Bernie (or anyone), the sample set within one universe is not the same as all the samples in all the universes, unless one evalulates the partition functions. One needs to look at the Boltzmann factor for an infinite set of universes that contains various distributions of universes that contain life. I don't know how to do that. BUT someone who wants to draw a conclusion about the worthlessness of the probabilities had best do the calculations on a model with a set of proposed ensembles.
  I think that needs to be done formally.

  Meanwhile we have probability in our one known universe. Molecular biology works here - and the question is whether probabilistic concepts work here. I think they certainly do.

  Best Regards,
  David Clounch

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Received on Wed Dec 31 14:45:37 2008

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