Wesley:
>I think that's a non sequitur. Monophyly of life on earth
>does not imply singularity of abiogenesis. See the
>restoration at the end of this post.
My point was not that monophyly implies a singular
abiogenesis event. My point is that there are two
schools of thought with regards to abiogenesis (it
was likely and it was unlikely) and these schools
point in different directions.
Now, both schools make different predictions. If
abiogenesis was likely, it would seem that it
would have happened many times (likely things
happen often). If it was unlikely, it would have
happened one (or a very few) time. Thus,
monophyly is an *expected* pattern of unlikely
abiogenesis. It doesn't refute the "abiogenesis
was likely" view, but it is not as expected from such
views (it has to be rescued with ad hoc explanations).
Furthermore, I would add that the intractability of
abiogenesis also better fits with the "abiogenesis was
unlikely" event. Abiogenesis may have happened due
to a set of unlikely historical contingencies and it is
almost impossible to uncover and recreate them.
If abiogenesis was a likely event, it would seem
reasonable to expect far more progress in this field
(just recreate the appropriate conditions and the
chemistry takes care of the rest). If you ask me, the
view which states that life arose once because it
was such an unlikely event is far more parsimonious
than the view which claims it was likely but then
seeks to account for the monophyletic nature of
life through vague, ad hoc accounts.
MB>One can, of course, raise ad hoc scenarios where the first
MB>life forms outcompete subsequent life forms, but these are
MB>easily canceled out by other ad hoc scenarios where this
MB>would not happen.
Wesley:
>Only if we all agree that all such ad hoc scenarios are
>equiprobable. I don't see that as happening any time soon.
Since the "abiogenesis was unlikely" view does not
depend on such scenarios, it is not bogged down with
trying to figure out which scenario is more probable given
the stark lack of data needed to address those questions.
MB>If a self-replicating system arose, I agree this would decrease the
MB>likelihood of another self-replicating system arising *IF* the
MB>original uses the resources needed to generate the other.
WRE>So far, so good.
MB>But this doesn't effect *different* life forms from arising.
WRE>Hmm. I don't see how this can be supported. Sequestration of
WRE>significant chemical resources surely will have an effect on
WRE>other abiogenesis events, whether they would result in similar
WRE>results or not. Also, to accept the assertion as given one
WRE>must ignore the possible products of such chemical systems,
WRE>which may inhibit the formation of other self-replicators.
MB>All of this is possible. And given that abiogenesis is
MB>largely imaginary, we can invent scenarios that go either
MB>way. For example, sequestration may prevent other life
MB>forms from arising *nearby*, but the earth is a huge
MB>laboratory. If sequestration is thus to be significant,
MB>these primitive systems must have been quite efficient very
MB>early on and the raw resources provided by the planet must
MB>have been scarce.
Wesley:
>I'm not sure I buy that. As Mike points out later, this
>question hinges on whether the rate of abiotic production
>exceeds the rate at which some self-replicator sequesters
>resources. It's a common intro biology problem to figure
>out how long it would take for even slow-reproducers, like
>elephants, to reproduce beyond earthly resources.
Yes, but exponential growth curves will not help unless
we have information about many other relevant dynamics.
1. What is the rate of self-replication and how does it
compare to the rate of degradation of self-replicators?
(This is especially relevant to the RNA world as the
functional group important in RNA catalysis also makes
RNA a very unstable molecule).
2. What is the rate of abiogenesis given the "appropriate
conditions?"
3. What components of the abiotic "soup" does the self-replicator
actually need/use?
4. What does the self-replicator really sequester from the
prebiotic soup? (i.e., what do the left-overs look like
and can they be used to spawn another type of self-replicator?)
If the *net* rate at which replicators replicate is slow, and the
entire planet is churning out abiotic material, and the rate of
abiogenesis is high (implied by the "abiogenesis is likely"
explanation), there might be a significant window for
multiple appearances of life. In fact, given that abiogenesis
is envisioned to have taken place in local environments (to
get away from the dilution problem), there could have been
billions of mini-labs spread about the planet and many could
have been effectively isolated from each other for a very long
time. These could have spawned very different life forms that
would have later have emerged to compete with each in the way
elephants compete with mosquitoes.
The complexity issue is also relevant. If many different parts are
needed to form a self-replicator, this would again be a better
fit with the "abiogenesis was unlikely" view. An abiogenesis
was likely view would more naturally predict self-replicators
with a small number of independent parts. But taking a small
number of parts from the pool of abiotic material logically
means even more left-overs.
MB>If, on the other hand, the primitive systems were not
MB>efficient (and I see no reason to think they would be) and
MB>the earth was providing plenty of abiotic material (a
MB>common assumption), there would seem to have been plenty of
MB>abiotic precursors to go around. And since inhibitory
MB>byproducts would quickly dilute out through diffusion and
MB>degradation, newly forming systems on the other side of the
MB>planet would appear to me to be quite safe.
WRE>Well, I guess we will have to agree to disagree on this point.
MB>For example, supposedly a self-replicating system arose that uses
MB>L-amino acids. Why didn't one arise that uses D-amino acids?
WRE>Modern organisms predominantly utilize L-amino acids. In the
WRE>(rare) cases where a D-amino acid is used, there seems to be
WRE>a specific conversion process to go from an L-amino precursor
WRE>to a D-amino acid. This situation, though, does not constrain
WRE>the initial self-replicating system to exclusive use of L-amino
WRE>acids.
MB>Given this initial self-replicating system is entirely
MB>hypothetical, I don't see how we can put any constraints on
MB>it.
WRE>But we seem to be having fun trying.
Yep.
WRE>The instantiation of the biochemistry needed to
WRE>generate amino acids from other chemical precursors may have
WRE>come later, and with it the observed reliance upon one set of
WRE>amino acids rather than their chiral opposite numbers. Even
WRE>based upon consideration of biochemical systems made from
WRE>mixtures of amino acids of both L- and D- chirality, one could
WRE>argue that self-selective effects could lead such systems to
WRE>accentuate any imbalance in the proportion of chiral isomers
WRE>utilized until either L- or D- isomers were predominantly or
WRE>exclusively utilized.
MB>Yes. Let's say a population of self-replicating systems
MB>begins to favor the L-isomers and begins to predominate.
MB>But if a competing population begins to favor the D forms,
MB>it will quickly carve out its own niche so it is no longer
MB>competing with the L forms. This is how evolution
MB>typically works. Why would these initial life forms all
MB>jockey for the same niche? Why wouldn't they simply
MB>specialize along different trajectories to avoid direct
MB>competition and stake out their own niches?
Wesley:
>Hmm. I thought that we were discussing the scenario where one
>self-replicator precedes any other, not some scenario where
>multiple simultaneously produced self-replicators interact.
Well, I wasn't. I interpreted Bertvan's point to mean that
if abiogenesis was likely, multiple life forms would have
arisen "simultaneously" (in a geologic sense). If someone
is going to argue abiogenesis was likely, it doesn't make
much sense to argue it only happened in one place unless
the conditions needed to make abiogenesis likely were themselves
unlikely to happen (which would mean abiogenesis was
unlikely).
But even if we discuss the scenario you envision, my point
remains. A single population that used both D and L amino
acids could spawn two populations where one specializes in
using L while the other specializes in using D. If a population
of replicators became good at using L, such that its self-replication
rate exceeds the original population that uses both, then clearly
mutations which allowed a sub-population to start choosing D might
be favorable. It would cut itself off from the superior L forms
and seek out a safe niche.
WRE>The existence of specific conversion mechanisms in modern
WRE>organisms to make the odd D-amino acid from a L-amino acid
WRE>is suggestive that at some point there might have been such
WRE>mechanisms to convert a surplus of free D-amino acids to
WRE>their L-amino acid counterparts.
MB>What makes you think these conversion mechanisms did not
MB>arise long after the origin of life?
Wesley:
>What makes Mike think that my argument is sensitive to that?
I suppose it depends on how seriously we are take the suggestive
element behind the claim about what might have happened. If
the conversion mechanism is essentially "modern," I
don't see how it would shed any light on the state of
affairs prior to these modern mechanisms.
[snip]
WRE>If no such dependence is necessary,
WRE>then an initial self-replicator which scavenges both L- and
WRE>D-amino acids would reduce available amino acids to non-useful
WRE>levels for other self-replicator productions wherever the
WRE>first one reached.
MB>Do you have one little piece of data to support this claim?
Wesley:
>About as much as for claims of multiple abiogenesis events
>having happened.
I don't think there were multiple abiogenesis events. I
simply maintain that multiple abiogenesis events are
what we would expect from the "abiogenesis was likely"
hypothesis.
>Maybe more. After all, we can observe the
>behavior of modern self-replicating systems as to how they
>utilize available resources.
Yes indeed, and what we observe often is that such systems
seek to avoid direct competition with other by seeking out
their own niches. The view that one primordial life form would
drive all other primordial life forms doesn't make much sense
to me. Bacteria clearly have a higher fitness than eukaryotes,
yet eukaryotes evolved from them. And some eukaryotes lost
their mitochondria yet were not driven to extinction by those
that didn't. Mammals didn't drive reptiles into extinction,
reptiles didn't drive amphibians into extinction, amphibians
did not drive fish into extinction, etc. I don't view evolution as a
process where all life forms are competing for the same spot. To me,
most of evolution looks like life forms making do with whatever they
can, thus avoiding direct competition whenever possible. Thus, I don't
understand why the existence of some original primordial
organism would preclude any other form of life from
existing.
MB>What if the global rate of formation of amino acids is many
MB>times greater than the rate at which this primitive
MB>self-replicator sucks them up?
Wesley:
>Self-replicators have this property of often following an
>exponential growth curve. I think that the suggestion that
>abiotic production could match or exceed this is not very
>likely.
Without the relevant data (see above), what you think is not
likely stems merely from hand-waving. The need to rely on
hand-waving is something that comes from the notion
that abiogenesis was likely.
MB>What's more, life uses only a small subset of all possible
MB>amino acids (only 20; and some of these are thought to have
MB>been acquired into life after its appearance). Given that
MB>abiogenesis experiments produce many other kinds of amino
MB>acids not used by life (often in greater concentrations),
MB>why didn't a life form appear that used these amino acids?
WRE>Why, indeed?
MB>Who knows? But it is a problem for the view of chemical
MB>determinism.
Wesley:
>Is it? It doesn't appear to be much of a problem if what
>I've seen so far typifies the objections.
Really? It does appear to be much of a problem if what I've
seen so far typifies the responses the objections.
WRE>Question: How many of these non-biological amino
WRE>acids are present in, say, our modern oceans? Our modern
WRE>lakes? Marine hydrothermal vents? If they are not present
WRE>in useful concentrations, why aren't they there?
MB>Many would argue that the oxygenic atmosphere has
MB>essentially shut down abiotic amino acid synthesis.
Wesley:
>That pretty much corresponds to my point about the products
>of an early self-replicator affecting the conditions that
>could give rise to others.
I doubt very much the self-replicators were pumping out
oxygen, as oxygenic photosynthesis is a highly evolved
trait particular to a highly evolved lineage of eubacteria
(and their chloroplast descendents). If all you mean is
that this represents a vague example of how some
by-product might have possibly prevented the
abiogenesis of another life form, two can play the
possibility claim and I can thus argue that some
byproducts could have possibly *enhanced* the likelihood
of abiogenesis (as one organism's dung is often another's
dinner).
WRE>Possible answer: Non-biological amino acids may have been
WRE>*used* by an early self-replicator, but not simply grabbed
WRE>and incorporated into protein structure. These may have
WRE>been processed into other, more useful, chemical products.
MB>And unless they were very, very good at using these and
MB>there were very few amino acids to begin with, I don't
MB>see this as likely.
Wesley:
>This will have to be another point upon which we will disagree.
Agreed. But I still don't see how this explains why more
prevalent non-biological amino acids were excluded from
proteins in favor of the more rare biological amino acids.
WRE>Second possible answer: Perhaps these non-biological amino
WRE>acids also commonly have R-groups that interfere with protein
WRE>stability. If so, then these amino acids would make
WRE>relatively unpalatable "leftovers" for a second or further
WRE>self-replicating system.
MB>If this is the answer, the implications are mind-boggling.
MB>For what this means is that the twenty biological amino
MB>acids are essentially the only ones that can form stable
MB>(and thus functional) proteins. This then means that the
MB>universal use of these twenty amino acids is NOT evidence
MB>of a universal common ancestor (as is commonly claimed).
Wesley:
>Really? I don't recall that the mere similarity of amino acids
>used is *commonly* claimed as evidence for common descent.
>Some examples would be useful. If it is commonly used (and
>established as such), I would join Mike in arguing that it
>should not be.
Since I don't feel like paging through a stack of old texts,
I'll gladly withdraw the claim that this is commonly claimed
(if I stumble across one of these claims, I'll post it).
But *I* will make this claim. That all life forms use the same
set of twenty amino acids is indeed evidence of monophyly.
The notion that non-biological amino acids would not
be incorporated because of some negative effect on protein
stability is simply not supported in light of all the work
being done on peptide/protein design using unnatural
amino acids. I'll pick it up here in the next reply.
Mike