Re: [asa] RE: (irreducible complexity and evolution) design and the nature of science (was: Re: [asa] Re: Gingerich on TE and ID)

From: Nucacids <>
Date: Wed Jun 17 2009 - 15:07:27 EDT

Hi Bill,

Here’s how Adam Wilkins, editor of BioEssays, puts it:

“In closing, it is worth considering for a moment the question of how well
the “machine” metaphor when applied to molecular complexes actually holds
up. . . the articles included in this issue demonstrate some striking
parallels between artifactual and biological/molecular machines. In the
first place, molecular machines, like man-made machines, perform highly
specific functions. Second, the macromolecular machine complexes feature
multiple parts that interact in distinct and precise ways, with defined
inputs and outputs. Third, many of these machines have parts that can be
used in other molecular machines (at least, with slight modification),
comparable to the interchangeable parts of artificial machines. Finally, and
not least, they have the cardinal attribute of machines: they all convert
energy into some form of “work.””

When studying molecular machines, molecular biologists approach them much as
an engineer might approach an unknown machine – they engage in structural
and functional decomposition of a system. Genetics can be used to define
the number of essential parts (through knock-outs) of the system and maybe
identify subsystems. Biochemical purification and characterization of the
parts can help define the function. Both genetics and biochemistry can be
used to determine which parts interact. Function is often found at the
interface of the parts and depends on coordinated movement of the parts
because some part extracts energy from ATP hydrolysis and/or an ion
gradient. NMR studies and X-ray crystallography allow scientists to see the
parts and then employ the form-function relationship as a guide.

Oh, and for the other point discussed in this thread, yes, proteins are
different from man-made material. But I would argue that proteins represent
a superior design material to anything than man uses.

There are thus two ways to explain the differences between man-made machines
and life’s machines:

1. Man-made machines are designed while life’s machines are not.

2. Man-made machines are primitive/crude while life’s machines are


> Mike:
> In thinking of certain protein processes as molecular machines what
> structural algorithm was used? That's vague, but, for example, we speak
> of cars as composed of functional parts. Hence, there is a functional
> analysis (break down) of the car. Typically, machines are analyzed
> according to functional units.
> But there may be other types of analysis (e.g., structural).
> What kinds of analyses have been employed in speaking of protein processes
> as machines?
> Once such an analysis is in place, one can then begin thinking of a number
> of things.
> 1) what parts are essential
> 2) what parts might be interchangable
> 3) what are the requirements of the parts in accordance with the type of
> analysis
> 4) etc.
> thanks,
> bill
> On Wed, 17 Jun 2009 14:30:50 -0400, "Nucacids" <>
> wrote:
>> It is not organisms that are analogous to machines; certain protein
>> complexes are analogous to machines. It was not the IDM that came up
>> with
>> the analogy; molecular biologists came up with the analogy (the term
>> 'molecular machine' emerged from science). And this analogy has proven
>> itself to be very useful to science:
>> "The articles in this special issue of Molecular BioSystems focus on this
>> fascinating area of multi-protein complex chemistry, biochemistry and
>> molecular biology. They reveal that the Alberts paradigm of thinking of
>> these complexes as highly interactive, tightly regulated biochemical
>> machines has held up well over the years and guided many of the important
>> studies that have elucidated their mechanism of action."
>> - Rise of the machines: Bruce Alberts and the biochemistry of
>> multi-protein complexes. Mol. BioSyst., 2008, 4, 1043-1045
>> Mike

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Received on Wed Jun 17 15:07:57 2009

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