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 23:19:23 2008