Re: [asa] Amazing Proteins

Hi Steve,

It may be a few days before I can reply (I'm up against a Friday deadline),
but I wanted you to know I found your reply to be quite helpful and
thought-provoking. Thanks.

Mike

----- Original Message -----
From: "Stephen Matheson" <smatheso@calvin.edu>
To: <asa@calvin.edu>
Sent: Tuesday, May 13, 2008 11:18 PM
Subject: Re: [asa] Amazing Proteins

> Hello Mike--
>
> First, my apologies for getting ahead of you on the fine-tuning thing. I
> agree with you that the question is interesting in its own right, and I'm
> happy to discuss it without any further comments about what it might mean
> for a design/fine-tuning debate. I hope my formatting below is clear
> enough...
>
> Mike: "As I explained before, I see the RNA world as something that would
> support the notion that proteins are superior design material, given that
> the RNA world was replaced/enslaved by the world saturated with proteins."
>
> Do we know that? It looks to me like RNA/DNA are running things, using
> proteins as slaves. This is not to say that proteins are not "superior
> design material"; that may well be the case depending on how one defines
> the relevant terms. It's just to say that I'm not so sure that the RNA
> world "lost".
>
> Steve: "Second, you claim that "evolution has been quite successful
> because of proteins," but we all know that you can't produce a comparative
> study that justifies this conclusion."
>
> Mike: Consider it a hypothesis or speculation, not a conclusion. For
> starters, do you think lateral gene transfer has been a crucial factor in
> the success of microbial evolution?
>
> Okay. I like hypotheses, even speculations. And I'm not sure why you
> ask, but yes I do think that lateral gene transfer has been a factor in
> bacterial evolution -- how crucial, I don't know.
>
> Steve: "Specifically, I note that you have no solid basis for asserting
> that protein-based life is superior to other formats, most of which we
> likely can't even imagine."
>
> Mike: Do you have a solid basis to assert there is a better format?
>
> Nope. That's irrelevant, though, because I'm not asserting that there
> *is* a better format. I'm asserting that there are surely formats --
> unexamined, even unimagined, perhaps spectacularly numerous -- that could
> undergird what we would recognize as "life", and I'm pretty confident that
> some of those formats would outperform proteins. It seems to me that
> those who envision -- and are currently working to create --
> nanotechnologies of various kinds are envisioning non-protein formats for
> machinery that is (often) already known in the protein world.
>
> Steve: "It is certainly possible that protein-based life is superior (from
> an evolutionary standpoint, at least) to most or all other options, and
> that this explains why life as we know it is protein-based. But there is
> at least one other explanation for the emergence of a protein format in
> the absence of others, and it arises from the consideration of contingency
> in the trajectory of evolution."
>
> Mike: I wasn't able to fully grasp your point here as it seems only to
> explain why life does not continually spontaneously generate and not why
> proteins are biological universals. Perhaps it would help if you could
> better flesh out your explanation for the disappearance of ribo-organisms.
>
> The basic point is that abiogenesis should be viewed as a competition like
> any other competition in biological evolution, but with one factor
> magnified dramatically. That factor is contingency, or the influence of
> earlier events on the trajectory (and even the possibility) of later
> events. In the case of very early life, we should probably assume that
> the competition is not so much a war or struggle, but a race. The winner,
> if you will, achieves metabolism (however crude), such that the resulting
> (proto)organisms don't just replicate, but they actively alter the
> environment. And hence the winner doesn't just live: the winner acquires
> the ability to destroy the rest of the competition. This is the point of
> the quote from The Beak of the Finch, still readable below. It's like a
> game of King of the Hill, where the first one up the hill gets hold of
> weapons and advantages that are practically insurmountable. The rest of
> the competitors can no longer just tinker with a lit!
>
> tle replication here and a little interaction there. They need to get to
> the top of the hill without being eaten. This is now, today, impossible.
> That's how the thinking goes.
>
> And this means that the winner need not be the best. The winner was the
> fastest to reach the top of the hill, and that could have resulted from
> galactic superiority, but it could also have resulted from mere speed or,
> of course, from stochastic mechanisms (better known as sheer dumb luck).
> If we re-run the race, then perhaps we'd get a significantly different
> outcome.
>
> Is that a little clearer?
>
> Steve
>
> ----- Original Message -----
> From: "Stephen Matheson" <smatheso@calvin.edu>
> To: <asa@calvin.edu>
> Sent: Sunday, May 11, 2008 10:27 PM
> Subject: Re: [asa] Amazing Proteins
>
>
>> Hello Mike--
>>
>> I think I have gleaned the gist of your question from these two excerpts:
>>
>> "I think a better way of saying it is that evolution has been quite
>> successful because of proteins. After all, there doesn't seem to be much
>> evidence that the blind watchmaker can do all that much without the help
>> of
>> proteins."
>>
>> "I don't argue that proteins are essential for evolution. I am
>> suggesting
>> that evolution has been quite successful because of proteins. After all,
>> why don't you have other data points to point to?"
>>
>> I think others have noted that you seem to be constructing a fine-tuning
>> argument, or at least a claim regarding an instance of fine tuning. I
>> don't care for fine-tuning arguments myself, and I won't address the
>> merits or utility of such discussions here. Instead, I want to point to
>> what I see as some very significant weaknesses in your premises,
>> weaknesses that make your idea unworthy of serious further consideration.
>>
>> First, you claim that "there doesn't seem to be much evidence that the
>> blind watchmaker can do all that much without the help of proteins."
>> This
>> type of argument (from ignorance) is so vacuous and fallacious that it
>> damages your credibility as a commentator. The best you can say is "we
>> don't know", which is lame enough, but in this case there are some solid
>> ideas about non-protein chemistries that may underlie the origin of life.
>> Catalytic RNA itself is a solid rejoinder to your challenge, but even if
>> there were no ideas at all regarding alternative (or primitive) chemical
>> bases for life, the "lack of evidence" claim is a thoroughly unsound
>> basis
>> for concluding anything in an area about which we know so little.
>>
>> Second, you claim that "evolution has been quite successful because of
>> proteins," but we all know that you can't produce a comparative study
>> that
>> justifies this conclusion. Specifically, I note that you have no solid
>> basis for asserting that protein-based life is superior to other formats,
>> most of which we likely can't even imagine.
>>
>> Finally, you are overly impressed by the current absence of other
>> chemistries. In fact, this absence is the only observation you can
>> produce in support of your idea, and I gather that you favor the
>> conclusion that protein-based life out-competed other formats (or that
>> the
>> other formats never even existed) by virtue of surpassing excellence. It
>> is certainly possible that protein-based life is superior (from an
>> evolutionary standpoint, at least) to most or all other options, and that
>> this explains why life as we know it is protein-based. But there is at
>> least one other explanation for the emergence of a protein format in the
>> absence of others, and it arises from the consideration of contingency in
>> the trajectory of evolution. If you have a copy of Jonathan Weiner's The
>> Beak of the Finch, check out page 301, where he discusses this very
>> question. "Possession, as we say, is nine-tenths of the law," he begins,
>> referring to biological niches, such as the Galapagos Islands upo!
>>
>> n the arrival of the first finches. When self-duplicating molecules
>> first
>> arose, they could "grow at their own pace," because "all paths lay open."
>> But once "life" got off the ground, some paths started to disappear --
>> they were blocked by already-successful replicators with a head start.
>> Here's the key paragraph:
>> "In the laboratories, the trial soups are kept hermetically sealed, or
>> each experiment would be cut short before it got interesting because the
>> new molecules in the soup would be scavenged by bacteria. The waiting
>> Pyrex ponds are sterile as the seas and shorelines of this planet before
>> life began. But in the ocean, of course, as fast as molecules make their
>> first gestures toward life, they are devoured. Creation in the sea has
>> never stopped, but the niche of life is taken."
>>
>> Yes, proteins are cool, really cool. But don't put so much stock in your
>> inability to imagine better paths, and don't make the mistake of assuming
>> that protein-based life dominates today due to victory in a planetary
>> round-robin tournament.
>>
>> Steve Matheson
>>
>>
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>>
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Received on Tue May 13 23:54:54 2008