Re: [asa] Amazing Proteins

Hi Steve,

"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."

I'm sorry, but you are merely trying to anticipate where I am going when I
myself am not sure where I am going with this. My whole line of inquiry
originated from something Francis Crick said in response to Monod's insight
about allostery. I'm simply feeling things out from there.

"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."

Such is life. But you err here in confusing an observation for an argument.
It is simply an empirical fact (AFAIK) that there is little evidence that
the blind watchmaker can do all that much without the help of proteins. It
was my hope that those who believed otherwise would be stimulated to provide
such evidence if it existed. Y'see, I am sincerely interested in whether or
not the blind watchmaker is the success it is largely because of the design
material it uses. In fact, the more I think about it, the more interesting
it becomes.

"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."

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.

"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."

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?

"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."

Do you have a solid basis to assert there is a better format?

"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."

This is one very commonly held view.

"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."

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.

-Mike

----- 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 Mon May 12 00:37:50 2008