>> DNAunion: By saying this, are you suggesting that the individual
components of a bacterium used to be capable of living independently, but
once incorporated into bacteria, they lost that ability? For example, were
ribosomes once free-living entities, and at that ancient time, ;bacteria; did
not have ribosomes (but later acquired them through symbiosis)?
>>Thadley: Yes, with the caveat that such a free-living entity would not be
"just" a ribosome but a ribosome plus something else. Likewise, these
hypothetical ancient bacteria, would not be "just" bacteria without
ribosomes, but cells functioning with something else. (My excuse for so many
hypotheticals would be that science hasn't yet ruled out the chemical
possibility of replicators simpler than bacteria.) Of possible relevance, I
just noticed this abstract on PubMed "Early evolution: prokaryotes, the new
kids on the block." which argues that the ribosome had a prior function
before protein synthesis (
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_u
ids=10497339&dopt=Abstract).
**********************
DNAunion: Thanks for the reference: I found the abstract (listed below) very
provocative, since it seems to go against conventional wisdom in at least 2
ways, and have purchased a copy of the article through www.bmn.com.
(However, it too relies on a RNA replicase arising by purely natural
processes, which is a big assumption, and one that the scientific experiments
have not, and do not, support).
"Prokaryotes are generally assumed to be the oldest existing form of life on
earth. This assumption, however, makes it difficult to understand certain
aspects of the transition from earlier stages in the origin of life to more
complex ones, and it does not account for many apparently ancient features in
the eukaryotes. From a model of the RNA world, based on relic RNA species in
modern organisms, one can infer that there was an absolute requirement for a
high-accuracy RNA replicase even before proteins evolved. In addition, we
argue here that the ribosome (together with the RNAs involved in its
assembly) is so large that it must have had a prior function before protein
synthesis. A model that connects and equates these two requirements
(high-accuracy RNA replicase and prior function of the ribosome) can explain
many steps in the origin of life while accounting for the observation that
eukaryotes have retained more vestiges of the RNA world. The later derivation
of prokaryote RNA metabolism and genome structure can be accounted for by the
two complementary mechanisms of r-selection and thermoreduction. Copyright
1999 John Wiley & Sons, Inc" (Early Evolution: Prokaryotes, the New Kids on
the Block, Poole A, Jeffares D, & Penny D, Bioessays 1999 Oct 21:10 880-9)
***************
[…]
>>>DNAunion: Symbiosis is a method by which *preexisting* life becomes more
complex. I would still like for you to *clearly* state how you are proposing
symbiosis assisted the origin of the very first cells.
>>>Thadley: What is needed first is several plausible replicators of any
kind. Then, some degree of divergent evolution followed by competition among
strains. I can't give you a step by step scenario, though, but I don't
think its nonexistence is obvious.
***************
DNAunion: That is the assumed scenario, but I don't see the symbiosis in it.
Your statements suggest simple competition, not the combining of separate
living entities into a new whole where each benefits. Perhaps you simply
left such comments out inadvertently.
***************
>>>DNAunion: Points 1 & 2 taken together -- there truly IS SOMETHING that
can arrange matter in complex and organized ways, and (2) there truly IS
NOTHING that opposes matter's being arranged in organized and complex ways --
indicate that all natural reactions would lead irreversibly toward greater
complexity and organization.
>>>Thadley: Oh, I see. Let me backtrack and reject (2), since there are
clearly many processes that "unarrange" matter.
*********************
DNAunion: Thanks, rejecting (2) has been my main point throughout this
series of exchanges on entropy. Someone (I have lost track who, FMAJ? Chris
Cogan?) stated to the effect that there is nothing that opposes matter's
being arranged in complex and organized ways. I said that such a statement
is wrong because there is something that does so (but it can be "overcome").
**********************
[…]
>>>DNAunion: As far as the simpler-than-bacteria self-replicators, they are
still only designed; none have been shown to arise under prebiotically
plausible conditions (and many leaders in OOL research express grave doubts
that ever will - at least RNA replicases).
>>>Thadley: What are the latest obstacles? It might depend on who you read.
****************
DNAunion: The largest obstacle is that RNA itself is not currently a
prebiotically-plausible molecule. No RNA obviously means no RNA replicase.
Another is that even assuming methods of producing the "dream" pool of RNA
polynucleotides, Orgel and Wright estimated that for 2 RNA replicases to
arise (an RNA replicase cannot copy itself and so if only 1 appeared, when it
"died", so would all hopes of sustained evolution) would require a mass of
RNA molecules greater than that of the entire Earth: not just the thin veneer
of the biosphere, but the entire Earth; core, mantle, and all! And their
assumption was based on the further assumption (which seems low to me,
personally) that a mere 40-mer could function as an RNA replicase. In
addition, there is the potential problem of Eigen's error
catastrophe/threshold, which in simple terms states that there is an inverse
relationship between the error rate in copying and the maximum length of a
"genome" (that is, the less accurate the copying of nucleotides is, the
shorter the maximum number of nucleotides that could be in the replicator).
Keep in mind that no RNA replicase (an all-RNA, RNA-dependent RNA-polymerase)
has been found in in vitro evolution experiments aimed at creating them: and
there have been several such experiments, and they have started with some
10^15 RNA molecules (that is a million billion RNA molecules). There is also
the problem of enantiomeric-cross inhibition: the poisoning of chain
elongation when both the L- and D-enantiomers are incorporated.
******************
>>>Thadley: At the very least, there is a great deal of molecular data that
certainly hints at some sort of complex chemical history, whether the
ultimate location of that is terrestrial or not.
http://imbs.massey.ac.nz/Research/MolEvol/Farside/ANT_RES.HTM
*******************
DNAunion: I noticed that the above link took me to a page written by the
same scientists you referenced earlier (from the abstract I posted from your
link). However, their scenario still seems to start from a preexisting RNA
world, without explaining how it first arose: this demonstrates the
acceptance of assumptions as valid starting points in OOL research (not that
I know of a way to get around doing such). And again, their scenario goes
against conventional OOL wisdom by proposing prokaryotes as being derived
from eukaryotes, instead of the other way around. I will have to wait until
I can read their published work to determine if I personally find their
arguments more reasonable than the mainstream.
********************
>>>DNAunion: And even if a self-replicator arose, how would symbiosis of
preexisting simple life forms explain the use of ribosomes by all cells,
since ribosomes are neither free-living nor living at all, and no material I
have read proposes that they ever were?
>>>Thadley: I'm using living and replicating in the same way.
*******************
DNAunion: Okay. But then I don't see how you are proposing symbiosis in the
origin of replication.
*******************
[…]
>>>DNAunion: A little off the subject, but somewhat related Margulis has
stated to the effect (and I agree) that it is a bigger leap going from amino
acids to a bacterium than it is going from a bacterium to a human: that is,
prebiotic chemical evolution is more difficult than subsequent biological
evolution (the real quote can be found at www.pansermia.org, but I don't know
exactly where at that site it is). If the smaller, easier leap (for the
first cells to evolve into humans) took about 4 billion years, then wouldn't
the larger, harder leap (for prebiotic chemical evolution to produce the
first cells) take much longer than 4 billion years? Yet the maximum windows
now being discussed are on the order of 200 million years, with the average
hovering around 50 million, with some even less.
>>>Thadley: I see the origin of life as sort of a black box with us having
the occasional barest glimpses into its interior. Processes we can observe
will always be seem to be easier to understand than processes we can only
guess at, so I'm not sure I'd agree with the implication that amino acids to
bacteria is really a qualitatively larger leap. Maybe quantitatively, yes.
***************
DNAunion: I see no reason to disallow the drawing of conclusions based on
our *current* knowledge. I think Margulis's statement is accurate based on
what prebiotic experiments have revealed. One can always hold out *hope*
that some new breakthrough will show the way, but I don't think we should
base our current conclusions on things we hope will be discovered in the
future.
***************
>>>Thadley: Let me ask this. Do you think we should stop researching
naturalistic methods of the origin of life?
**********
DNAunion: No. OOL researchers should continue their work (assuming that
more pressing scientific issues are not being negatively impacted due to lack
of funding being spent on OOL research). But I would like to see - and think
it is their obligation to use - words like "assume", "could be that",
"hypothetically", etc. scattered throughout OOL material, clearly indicating
that a purely-natural OOL is not scientific fact, but rather an unsupported
assumption.
***********
>>>Thadley: Do we know enough now about the origins of life to conclude it
didn't happen naturalistically 4 billions years ago on Earth?
*************
DNAunion: To *conclude*? Sure we do, because conclusions are not the same
as fact. I and others can *conclude* that life as complex as the simplest
autonomous bacterium could not have arisen by purely natural processes here
on Earth, in the amount of time available and under the conditions thought to
have existed, and no science says we are wrong. Those that assume a
purely-natural OOL on Earth can also *conclude* that it happened, and that
hoped-for future developments will show them to be correct after all. As far
as stating as fact, I don't believe either side has the evidence to do so.
OOL researchers clearly have not "proven" their position, and anti-OOL-ists
would have to "prove" a negative in science: something virtually impossible
to do.
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