Re: [asa] Amazing Proteins

Hi Steve,

Let me begin by clarifying that I am not arguing that proteins *are*
superior design material. But I am indeed flirting with this hypothesis.
That means I am probing and feeling it out. So let me try to focus on the
core issues here.

"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"."

I don't think it is a question of certainty, as you don't have to be sure of
something in order to tentatively propose or explore it. And one problem
here is that the RNA world tends to be a vague and fuzzy concept. 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).

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.

  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?

  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?

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.

Is there another equally parsimonious explanation?

"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."

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

So let's compare hypotheses.

Hypothesis A: Protein-based life is superior to other formats.

Hypothesis B: There could be many other life formats that are superior to
proteins.

Hypothesis A can be supported with circumstantial evidence. Since we are
not omniscient, we can never be sure. But we can compare proteins to other
macromolecules in terms of functional versatility coupled to simplicity of
synthesis and in this case, they excel over lipids, carbohydrates, and
nucleic acids. And this then leads to the most important point - Hypothesis
A is falsifiable. As you mentioned, nanotechnologists could design a
superior format. Or we could find a better format on another planet. But
how does one falsify Hypothesis B?

So while Hypothesis A can be supported by circumstantial evidence and is
falsifiable, Hypothesis B seems rather vacuous, essentially an unfalsifiable
belief about possibilities.

"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."

It will always be possible to design something that surpasses proteins by
one metric or another. What we need is a format that can a) generate a
wider range of functions while b) not entailing a more complicated mode of
synthesis. The metric is not one function or another - it's the success of
evolution itself. Remember, all the various diverse functions cited in the
opening essay stem from the same basic manufacturing process. Life did not
need to evolve different synthesis processes for different functions. It's
much smarter than that.

"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 little 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."

Yes, the key word is perhaps. Perhaps this is what happened. Perhaps not.
But two elements of the story stand out to me, giving it an ad hoc taste in
my mouth: a) why only one hill and b) why are proteins at the top of the
kill?

The Earth is a pretty big place, more so for microscopic proto-cells. If
there are so many possible design materials to stumble upon by contingency,
why should the winner of one hill be of relevance to another hill? Going
back to our bush of PLRBCLs, the ability of one lineage to reach the
proteins at the top of the hill would not necessarily be relevant to
countless other lineages in the process of enslaving one of those other
spectacularly numerous formats. You only get eaten if your format is food.

In the end, I would agree that the arguments you make prevent anyone from
concluding, with any sense of certainty, that proteins are superior design
material. But they don't really damage that hypothesis either. On the
contrary, these type of objections actually make me think the hypothesis A
*might* be on the right track. Don't worry, I'm not prepared to declare the
hypothesis as some type of position to declare, but it does, IMO, merit more
thought and exploration. So that's what I will do.

-Mike Gene

----- 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 Thu May 15 10:27:38 2008