Re: [asa] Amazing Proteins

Hello Mike--

This is fun and stimulating. Let me also be clear that I'm not arguing *against* proteins being "superior design material," and in fact I, like you, am quite impressed by their excellence. I'm not as taken with the hypothesis, for reasons I've tried to explain, but that doesn't mean I think it's not worth probing.

"While the term 'RNA World' means different things to different people, I'll interpret it to mean a population of protein-less, RNA-based, cellular life forms (PLRBCL)."

RNA-based *cellular* life forms?! Wow, that sure isn't anything *I* would propose. It seems possible, but I wouldn't *assume* it as a jumping-off point for a theory.

"So let's suppose the PLRBCLs create and enslave proteins and thus account for the fact that proteins are now biological universals. But two questions come to my mind."

I'm not excited about how the reasoning is structured. The supposition is so loaded already. Cellular, RNA-based life "creates and enslaves proteins"?!

"1.. The "RNA World" did not enslave proteins. A particular lineage of PLRBCLs acquired them as part of a larger bush of PLRBCLs. In other words, the protein-based lineage simply shared a common ancestor with the rest of
the RNA bush. So what happened to all the other lost lineages? Why did they all disappear?"

I've explained before why I'm not enthused about your competition/disappearance narrative. This looks a lot like a strawman here. I think I know the answer you're fishing for: that proteins are superior to RNA. But the logic is tortured, even if the conclusion (proteins excel) is correct.

"2.. If a cell composed of lipids, carbohydrates, and RNA was capable of creating and enslaving a fourth class of biological molecules, why haven't cells with lipids, carbohydrates, nucleic acids, and proteins been able to create and enslave a fifth class of biological macomolecules? If life and the blind watchmaker can add a fourth class of biological macromolecules to the cell's economy and architecture, why not a fifth?"

Again, a strawman created by assuming something extraordinary, and in this case asking questions that I find silly. Mike, I just don't see the utility of asking about things that haven't happened, in the way you are going about it. Your point is that proteins are great. Your assertion, that there would be more biological macromolecules participating if they could make things better, is strikingly simplistic. Applied to other areas of inquiry, I think this reasoning would be evidently nonsensical. Why, if marsupials can float on logs, is there only one indigenous North American marsupial species? Is it because marsupials belong in Australia, or because they're uniquely suited to life in Australia? Or might it be due to historical factors, contingent events that render certain possibilities fantastically improbable? You seem eager to conclude that "whatever is, is right" or more precisely that whatever is, is best. I just don't buy it, and pointing at the absence of !
 things you can't even begin to imagine is a very poor basis for theory-building. In my opinion.

"The hypothesis of protein superiority offers a very parsimonious explanation for both facts. All the other PLRBCL lineages could not compete against the superior protein-based life forms because proteins greatly enhanced the
functional versatility and evolvability of such life. And since proteins are superior design material, there is no fifth class of macromolecules (reachable by protein-based life ) that can be added to further enhance the functional versatility and evolvability of life, so there is nothing for the blind watchmaker to select."

I hope it's clear why I reject both the premise ("facts"??) and the conclusion.

Steve: "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."

Mike: Okay, so you are confident that something unimagined is possible. Sure, anything is possible. But where's the evidence?

Neither of us has "evidence" of the sort that would make sense of that challenge. We have a biosphere full of life, and we have a cosmos full of potential. Mike, I've tried very hard to make my position clear, and it's been fun but I think we're done. I consider my position to be a conservative one: I know that the creation is full of astonishing possibilities, because I know a bit about atoms and bonds, and I know that structures previously undreamed-of have been mass-produced and put into people's hands and homes. So I'm unwilling to claim that Earth's life format is necessarily excellent compared to other possibilities. (And I'm not motivated, theologically or psychologically, to suspect that it ought to be so excellent.) You are making a different choice: you think that what we have is somehow likely to be the best we could have, based solely on the fact that we don't have what we don't have. I can't understand why you prefer that choice, but I sure can't prove it !
 to be incorrect. "Parsimonious" is the last term I'd use to describe your preference, but I think that's because I see the cosmos very differently than you do.

If you'd like me to comment/respond on the subject of King of the Hill and the race to become alive, let me know. Otherwise, I think we're done, though I look forward to fruitful discussions in the future. Best regards,

Steve Matheson

----- 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

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Received on Fri May 16 00:05:58 2008