Re: [asa] Amazing Proteins

I think you're overlooking a vast number of -ases, at least many of which
are not proteins.
Dave (ASA)

On Thu, 15 May 2008 10:26:32 -0400 "Nucacids" <nucacids@wowway.com>
writes:
> 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 19:19:44 2008