Re: [asa] Amazing Proteins

Hi Steve,

"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.)"

I too am unwilling to make that claim. And my motivation is largely
curiosity (I'm a slow learner, but a constant learner). My original and
primary focus on this issue is to question what degree that evolution on
this planet has been indebted to protein activity. I like Dawkins' metaphor
of the blind watchmaker, because I think it clear that random variations and
selection can act as a very effective designer-mimic. But the blind
watchmaker would also mimic a designer in another regard - what designers
can build is limited by their building material and tools. The primary
building material and tools of the blind watchmaker on this planet have been
proteins. Take them away and substitute something else in their place and I'm
not sure the blind watchmaker could do something analogous to what it has
done. So I ask myself whether proteins are more background material or
leading players.

A secondary line of inquiry that has fallen out of this is the "proteins as
superior design material" hypothesis...

"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."

Again, I don't "think this," I'm exploring this. And no, it would not be
just that. It's also an appreciation for what we do have. And it's not
just a laundry list of functions and stories that showcase the amazing
proteins (as I think many take all of this for granted), but an appreciation
for why proteins can do this (here, I'm thinking along the lines of Monod).

"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."

Here you show a wisdom that I greatly appreciate and respect. Yes, it's
about seeing the same thing from a different perspective (I call this
Duck/Rabbit). In the end, this whole issue boils down to perspective. In
fact, that is what annoys me about the yin-yang of the ID Movement and the
New Atheist movement. These questions cannot be answered to the
satisfaction of all precisely because it's about perspective. While both
sides claim it is about "the evidence," evidence itself is dependent on
perspective. It has been fun talkin' with ya about this.

-Mike Gene

----- Original Message -----
From: "Stephen Matheson" <smatheso@calvin.edu>
To: <asa@calvin.edu>
Sent: Friday, May 16, 2008 12:04 AM
Subject: 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
>

>
>

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Received on Fri May 16 11:11:38 2008