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

From: Schwarzwald <schwarzwald@gmail.com>
Date: Thu Jun 18 2009 - 01:36:53 EDT

Heya all,

Just to pop in briefly here, I'd have to agree with Mike about the validity
of comparing "life's machines" with "man-made machines". Pointing out that
life's machines "look different" does nothing to persuade me personally, and
as someone who really enjoys reading up on modern/future technology (along
with esoteric past technology) it's hard to fathom why anyone would put
stock in it. Especially in an age where A) "life's machines", from the
bacterial level up to the bodily level, are many times looked to as a
guide/inspiration for our own creations, B) whatever crude level our
technology is comparatively at now, creating our own machines on those
levels (and drastically, purposefully altering existing ones) is on the
rise, and C) evolutionary principles have been and are used explicitly in
human design.

In other words, there's a danger of a "skepticism of the gaps" being at work
here - the unspoken suggestion that the things we see happening in nature
could not be the result of a mind. I'm not a fan of this strategy, or the
God of the gaps strategy - frankly, the latter seems like a safer bet by
far.

On Wed, Jun 17, 2009 at 3:07 PM, Nucacids <nucacids@wowway.com> wrote:

> 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.
>
>
>
> http://designmatrix.wordpress.com/2009/01/18/the-amazing-proteins/
>
>
>
> 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
> advanced/sophisticated.
>
>
>
> Mike
>
>
>
>
>
>
> 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" <nucacids@wowway.com>
>> 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 Thu Jun 18 01:37:12 2009

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