Cope's rule and bacterial evolution
Perplexed in Peoria
Cope's rule or Cope's law. Wikipedia has a nice explanation:
http://en.wikipedia.org/wiki/Cope's_law
Whether the rule stands up to scrutiny or not, it is interesting
because of its somewhat paradoxical combination of a direction
to micro-evolution superposed on a macro-evolutionary trend in
the opposite direction. Most species get bigger over time,
but big species tend to go extinct and it is the little species
which branch prolifically producing new species. So the
number of species in each size range stays constant.
Cute idea, even if it isn't really true.
I found out about the following research on an ID website, but
it seems legit:
A. Mira, et al., "Deletional bias and the evolution of bacterial
genomes", Trends in Genetics 17 (2001), 589.
I haven't read it, but the idea seems to be a kind of Cope's rule
for bacterial evolution. But in this case, the bacteria aren't
trending larger, they are trending SIMPLER. Their genomes are
getting smaller. They are optimizing by discarding rarely needed
functionality and thereby gaining a competitive edge in a
narrowly specialized niche. But, in doing so, they risk eventual
extinction.
And of course, counter to this micro-evolutionary trend, there
is the macro-trend. It is the generalist bacteria with the
relatively large genomes which branch and produce new bacterial
species.
Extrapolating backward we can imagine that the LUCA (Last Universal
Common Ancestor) was the most versatile and generalist micro-organism
of them all, and had the biggest genome. ;-)
The idea may not be as crazy as it sounds. And, in any case,
it, too, is a cute idea.
William Morse
$1...@darwin.ediacara.org:
> There is an old idea about mammal and dinosaur evolution known as
> Cope's rule or Cope's law. Wikipedia has a nice explanation:
> http://en.wikipedia.org/wiki/Cope's_law
>
> Whether the rule stands up to scrutiny or not, it is interesting
> because of its somewhat paradoxical combination of a direction
> to micro-evolution superposed on a macro-evolutionary trend in
> the opposite direction. Most species get bigger over time,
> but big species tend to go extinct and it is the little species
> which branch prolifically producing new species. So the
> number of species in each size range stays constant.
>
> Cute idea, even if it isn't really true.
Perhaps I am being naive, but as I understand it Cope's rule is more an
observation than a prediction. It is fairly easily explained:
Niches are characterized by available energy, so that small species will
have more individuals than big species.
The likelihood of a species surviving an extinction event is proportional
to the absolute size of the remaining population, but the likelihood of
an individual surviving an extinction event is independent of the
population size (i.e. the event kills 90% of the population of both large
and small species).
A change in size (in either direction) is a common way of invading or
creating a new niche - it is fairly easy to accomplish developmentally
yet it causes a large change in interactions with other species.
So what we expect to see is a regular loss of large species after
extinction events, followed by a recreation of the large species to fill
the otherwise vacant niches. Becoming smaller is another option to invade
or create a niche, but the small species all survived the extinction
event.
> I found out about the following research on an ID website, but
> it seems legit:
>
> A. Mira, et al., "Deletional bias and the evolution of bacterial
> genomes", Trends in Genetics 17 (2001), 589.
>
> I haven't read it, but the idea seems to be a kind of Cope's rule
> for bacterial evolution. But in this case, the bacteria aren't
> trending larger, they are trending SIMPLER. Their genomes are
> getting smaller. They are optimizing by discarding rarely needed
> functionality and thereby gaining a competitive edge in a
> narrowly specialized niche. But, in doing so, they risk eventual
> extinction.
>
> And of course, counter to this micro-evolutionary trend, there
> is the macro-trend. It is the generalist bacteria with the
> relatively large genomes which branch and produce new bacterial
> species.
The same two options should exist for new niches - you can get smaller or
you can get larger. The problem for bacteria is that the larger option is
limited by competition with eukaryotes (and may also be limited by
physical and chemical factors based on cell organization - I suspect this
but don't know enough about cellular biology). Meanwhile the smaller
option requires specialization in order to gain a competitive edge. In
the case of bacteria, however, the populations are already so large that
survival of species during an extinction event is no longer related to
size. Survival is instead related to survival of the niche - and in this
aspect the generalist will have a survival edge. (Note that generalists
also have a survival edge among eukaryotes.)
Yours,
Bill Morse
g
"Perplexed in Peoria" <jimme...@sbcglobal.net> wrote in message
news:dsl3qe$tnq$1...@darwin.ediacara.org...
>
> I haven't read it, but the idea seems to be a kind of Cope's rule
> for bacterial evolution. But in this case, the bacteria aren't
> trending larger, they are trending SIMPLER. Their genomes are
> getting smaller. They are optimizing by discarding rarely needed
> functionality and thereby gaining a competitive edge in a
> narrowly specialized niche. But, in doing so, they risk eventual
> extinction.
>
> And of course, counter to this micro-evolutionary trend, there
> is the macro-trend. It is the generalist bacteria with the
> relatively large genomes which branch and produce new bacterial
> species.
Not only are bacteria accused of decomplexification but, also, viruses.
The same thing bugs me about lots of biological comments as bothers me about
ID comments, and there may not be more than five other sbe readers who will
'git' this, but I'll say it for sake of you and them:
Making an observation of (or about) a phenomenon in a biological setting is
good DESCRIPTIVE science. No problem with that.
Arguing, on the other hand, for why that is a very utilitarian for bacteria
or viruses (or any other individuals or species to do) is purely
speculative.
Until and unless some mechanism is found whereby a phenomenon occurs (be it
increasing in size or complexity, or be it shedding of genes or excess
complexity or be it any other "quasi-strategic fortuity availance" (QSFA)
then any implication that the QSFA is being done because it is advantageous
is
at least as unscientific as the ID positing of "G-d did it" (GDI).
I cannot over-emphasize that I am NOT trying to say QSFA is "wrong" or GDI
is "wrong." I'm not saying one is right and the other wrong. I'm not
saying both are right. All I am saying is that they are two equally
non-scientific assignations in absence of empirical evidence: the former
conceptually putting the reins in the hands of a deity, and the latter
putting the reins in the hands of organisms themselves.
Bio-evo theorists are applying a double standard if they condemn the ID view
(putting the deity in the gaps) yet turn right around and insinuate that
bacteria or viruses dispose of gene baggage they can do without (by farming
out such things as replication of themselves to cells), or that complex
phenotypes mold themselves to avail themselves of niches, or increase their
capacity to tolerate some challenge.
I am trusting you to spare me the "it's just a metaphor, for crying out
loud" sermon because I believe you and I have come to understand mutually
that my objections are not just biologist bashing... but biologist plugging
(as in plugging for one's favorite pro football team). And I would wish to
see my favorite science team -- or, okay, one of them -- avoid the
APPEARANCE of assuming a double standard.
One poster recently (it does not matter who) sought to persuade me that the
fact that H. sapiens cannot make their own ascorbic acid is because... now
get this... because... vitamin C is abundant in their diet under most
circumstances -- some exceptions being onboard a ship at sea in the 1600s or
at the Arctic Circle anytime, where Eskimos used to get it by eating the
contents of the stomachs of seals).
The fact that H. sapiens could get along without making their own ascorbic
acid does NOT explain how, nor why -- as the case may be -- any of our
anthropoid ancestors had it and lost it, nor why they never developed it.
It actually says nothing more, actually, than that we don't have it and have
managed to reach a large population size... period.
By the same token, merely demonstrating that it is mathematically POSSIBLE
for a single mutation, in a single individual, to become spread throughout
an entire population does not explain that it actually DID happen.
As I have indicated elsewhere, repeatedly, a mutation need not be
advantageous to spread. Neither, just because it is harmful, need it get
weeded out. In neither case is "selection" a sole and decisive factor.
In the case of a mutation which deprived of an organism's ability to
synthesize its own ascorbic acid, in an environment where ascorbic acid is
plentiful in the diet, this did not yield any huge advantage. To say it is
energy conservation by default, in saving the energy that would be required
to make ascorbic acid when none was needed, is ONCE AGAIN to pose that a
population would proactively do what is necessary to make such a miniscule
energy saving. There are many traits in humans that have not been dumped in
order to save such a small amount of energy expenditure.
On the disadvantage side of the mutation (causing ascorbic acid not to be
produced) there may be a question as to whether some individuals were
overdosing, just as humans are over-dosing on sugars in their diet today. I
hope humans will not, as a result, lose the capacity to convert starches to
sugars, due to the fact that so much sugar is available in most humans'
daily diet. (I will stipulate that if it were to happen, it might take a
million years or more, so I'm not just summonsing a short-range view. Nor
am I meaning to imply that we may not be gravitating in that direction in
increments to small to measure. Maybe we are.)
But this is getting long. So let me wrap up by saying that just because an
organism makes a change, and that change provides some benefit, that does
NOT prove the organism made the change as a result of the fact it foresaw
that it would be "nice."
All I would suggest is that, when biologist (one of my favorite teams) make
a comment along the lines of saying, for example, that "viruses are
disposing of their excess baggage," they qualify that by making the
disclosure, "... but we do not know yet exactly why or how..." (Or if we do
know exactly why and how, as supported by an abundance of empirical
evidence, then let us say that, and produce our evidence.)
Otherwise, we make the same mistake (or appearance thereof) as the ID'ers,
of substituting our own eclectic "choice of cause" for theirs, to fill the
potholes in our knowledge.
g
g
"g" <gill...@earthlink.net> wrote in message
news:dt561p$1br5$1...@darwin.ediacara.org...
> Otherwise, we make the same mistake (or appearance thereof) as the ID'ers,
> of substituting our own eclectic "choice of cause" for theirs, to fill the
> potholes in our knowledge.
>
> g
BUT, I should have added... Nothing above is intended to contradict the
following:
A. That the total biotic mass/energy index of a population would
participate in a formula for quantity of evolutionary pressure;
B. That the number of replications on average per individual per unit of
time (in combination with A, above) would impact quantity of pressure;
C. That number of errors on average per individual unit per unit of time
(in combination with A and B) would impact quantity of diversification
pressure;
And, the higher the total index, of A and B and C, above, working together,
would be filtered by the total of all abiotic filters (the unique complex of
all abiotic mass and energy brought to bear such that it would not increase
or decrease it, but would affect how it is distributed as to increased
diversification, neither increase nor decrease diversification, or decrease
diversification.
(I am not through with this, by any means, but am in process of trying to
think through all the ins and outs and pros and cons of it. Therefore, this
is not posed as an argumentation but as a disclosure of
where I am in trying to make sense of it as of this time. So objections
fine, if they point to fallacies or oversights in it. Pointing me to
existing models that approach from an entirely different angle would not
help me work through this one and determine whether I should trash it or
fine tune it.)
g
an...@sci.sci
> and thereby gaining a competitive edge in a narrowly specialized niche.
> But, in doing so, they risk eventual extinction.
> And of course, counter to this micro-evolutionary trend, there
> is the macro-trend. It is the generalist bacteria with the
> relatively large genomes which branch and produce new bacterial
> species.
> Extrapolating backward we can imagine that the LUCA (Last Universal
> Common Ancestor) was the most versatile and generalist micro-organism
> of them all, and had the biggest genome.
Or maybe there was no single LUCA. Did you ever consider that possibility?
You talk like it's been mathematically proven there must have been a
single LUCA, and all we need to do is figure out how it was.
What if there were a whole bunch of separate common ancestors, each in
a tiny eco-niche where it originated. It was totally sloppy in just
about everything regarding security, because it didn't come into
contact with the others elsewhere. For example, it'd leak out DNA and
protein products indiscriminately and then take them back in later,
from its neighbors rather from itself most usually, but it didn't
matter because neighbors were brothers. Cellular structure helped
concentrate biochemical pathways to make them more efficient, but
cellular structure weren't used to defend the genome against neighbors.
(Earlier there might have been adhesion on particles of clay, or
adhesion on metallic surfaces, instead of enclosure in a membrane, to
hold enzymes close together to make pathways more efficient. But later
enclosure in membranes gave good-enough close-holding combined with
much better freedom of motion during reactions, so was an improved
tradeoff, hence the takeover from adhesion to enclosing.)
These early forms of life were not very good at filling eco-niches
worldwide. Most of the ocean was devoid of life. Only in those very fea
places *most* hospitable for life was there any yet. There were huge
gaps between adjacent eco-niches that had life in them.
As the surface of the Earth cooled and tektonic plates moved around and
fissures opened and closed and modulated intensity, ecological niches
expanded and contracted and moved around. From time to time two
eco-niches of *different* kinds of life would get close enough together
that some DNA leaking from one would get into the other, the first
instances of horizontal gene flow (HGF). Depending on the environment,
selection pressure might merge genomes, or have one drive the other to
extinction, or favor cells which happened to be able to defend against
invasion of alien DNA. Most likely most parts of each genome would be
kept while a few parts would be eliminated as redundant and not as good
as their counterparts.
As eco-niches split apart, a single genome would remain in *both*
parts, separate from each other, allowing divergence of genomes to
occur. Meanwhile more meetings of formerly-separate genomes would
happen. The combination of natural selection and merging of disparate
genomes resulted in overall better fitness of the surviving genomes, so
they now occupied a larger portion of the ocean, and encounters between
adjacent genomes became more and more common, until eventually nearly
all of the eco-niches had merged to form a single eco-niche that
spanned the globe. So instead of separate genomes in separate
eco-niches, there was a graduation of genome from one kind of
environment to another kind of environment, with constant leakage of
DNA in both directions. At this point there would be advantage to
defending against invasion of alien DNA, to avoid this
cross-environment pollution that kept diluting any local natural
selection that had occured. So there was now selection pressure to
develop cell walls that blocked nearly all intake of alien DNA, and
also to block nearly all leakage of DNA since once it leaks out it can
no longer ever come back in. Those genomes which survived this time,
i.e. those which indeed chanced into reasonably good (but not perfect,
just good enough) protection against HGF, thereby became the very first
true quasispecies/strains/clades of cellular life, the LUCAs of all
present-day life. Prior to that "clade" was meaningless. Now (ignoring
a low level of HGF which continued occurring) we had true clades at the
cellular level.
Now tack on the scenerio I discussed a few weeks ago, where these first
true clades (ignoring low-level HGF) were not prokaryotes, only
pre-prokaryotes, (ur-karyotes as some call them) but eventually merged
their genomes in various combinations to yield three true prokaryote
clades, which were so immensely successful that they drove all
remaining ur-karyotes to extinction, and how one of the three clades
developed much more advanced cytostructure than the other two (not
discussed specifically in my earlier posting), evolving to form the
very first pre-eukaryotes, which later used their cytostructure to
invent mitosis, whereupon we'd consider them true eukaryotes despite
them not yet having mitochondria endosymbionts.
As to when the RNA-or-whatever to DNA takeover happened amidst that
complicated sequence: My best guess is very shortly before the merging
of the ur-karyotes to the three clades of prokaryotes. DNA replicase,
and the genetic code, is what made those three clades so much more
successful than the remaining ur-karyotes, driving ur-karyotes extinct.
Transcription and reverse transcription already existed in the
ur-karyotes, which is how DNA was created (as archival storage because
RNA was too fragile), and how DNA was retrieved to restore RNA later
from the backup (when regulatory machinery detected that RNA had gotten
degraded, or constantly in parallel so no detection of RNA damage would
be needed, but then the RNA genome would have a mix of restored
ancestral sequences and the very latest evolved sequences which would
slow the effective rate of evolution). After the DNA takeover,
retro-transcription was no longer needed, so most genomes eventually
lost that capability, but some viruses found it a wonderful tool so
they kept it. Since the genetic code actually works on RNA not DNA,
perhaps I should re-phrase the above. The genetic code and
transcription both directions between RNA and DNA was already in place,
and DNA replicase was invented as a way of making backups of backups,
which immediately made RNA-to-DNA transcription almost unnecessary, but
because cell fission was still synchronized with RNA replicase, RNA
replicase was still necessary for cell fission. That moment when cell
fission became synchronized with activity of DNA replicase (instead of
with RNA replicase as before) is the defining moment of the DNA
takeover, when both RNA replicase and RNA-to-DNA transcription became
no longer useful.
I think I've just convinced myself that RNA-world was the immediate
predecessor of our current DNA-world. So where I said whatever-or-RNA,
you can now replace that with a firm *RNA*. (I hope you don't mind
these train-of-thoughts articles I write, where you can observe my
actual train of thoughts as I conceive new ideas. If I ever become
famous for any of these hairbrained ideas of mine, and somebody wonders
where I got the ideas from, just look here, if Google preserves their
archive of newsgroups all that time, which is not guaranteed!)
.
an...@sci.sci
diffusion from already-filled places to just-previously-empty places,
and the apparently-opposite trend in bacteria is just the same.
Regarding animal species, where Cope's rule applies:
> Niches are characterized by available energy, so that small species will
> have more individuals than big species.
So with sudden collapse of ecosystem during an extinction event, total
energy is decreased for all niches, so the large-animal niches no
longer have enough energy to support a breeding population, so they go
extinct:
> So what we expect to see is a regular loss of large species after
> extinction events, followed by a recreation of the large species to fill
> the otherwise vacant niches.
Agreed. Cope's rule is simply restoring the vacated large-animal
niches, which takes millions of years to gradually increase size of
previously small-size animals.
Now in the other case:
> The problem for bacteria is that the larger option is limited by
> competition with eukaryotes (and may also be limited by physical and
> chemical factors based on cell organization ...). Meanwhile the smaller
> option requires specialization in order to gain a competitive edge. In
> the case of bacteria, however, the populations are already so large
> that survival of species during an extinction event is no longer
> related to size. Survival is instead related to survival of the niche -
> and in this aspect the generalist will have a survival edge.
Agreed. Specialized bacteria lose their niche, and die out wholescale,
while generalists are greatly reduced but still find some niche or two
to survive, so they don't go extinct. Then after the extinction event
is finished, and the ecosystem is rebounding, and many destroyed niches
are finally re-appearing, the new generalist niches are simply refilled
by colonization from neighboring simialr niches, while the specialized
niches are refilled by some of the generalist bacteria evolving to
eventually fill them, discarding all unnecessary parts of their
genomes.
Are you going to be remembered as "The Newton of ecosystem-related evolution"?
(And I'll be remembered as the MickeyMouse Sorcerer________Newton's apprentice?)
.
Perplexed in Peoria
"William Morse" <wdm...@twcny.rr.com> wrote in message news:dt5615$1bfp$1...@darwin.ediacara.org...
Bill,
Your response raises some interesting implicit epistemological issues.
Gil's response speaks directly to epistemology. Hence the change in
direction and thread title, which is further explained by this parable:
A team of Martian scientists is observing a rural village on Earth.
They notice that the youngsters in the village tend to grow in size,
becoming too large for their britches. They also notice that when
the young reach a certain age, they frequently catch the first bus
out of town, join the navy, and leave their old wardrobe behind as
hand-me-downs for their younger siblings. Finally, they notice that
there is a continuing supply of new small youngsters.
The first Martian scientist has a hypothesis. All three observations
can be explained by the buses. The departure of the older Earthlings
leaves behind a 'britches vacuum', which induces younger Earthlings to
grow so as to fill them. And this vacuum, in turn, causes the apparent
spontaneous generation of very small Earthlings to fill the smallest
vacant britches.
The second Martian says that the first has cause and effect backward.
It is the spontaneous appearance of new small Earthlings which creates
a "britches pressure" forcing each cohort to the next larger size of
britches.
The third Martian (actually not ethnically Martian; she is a post-doc
from Titan) claims that the growth is caused by something internal to
the Earthlings; that the growth, the appearance of small Earthlings, and
the departure of large ones are actually three separate phenomena with
three separate explanations.
The other two both scorn this hypothesis, pointing out that it violates
the principle of explanatory economy. They also point out that if the
three phenomena are separate, that would mean that the apparent steady
state is something of a fluke. However, since the Martian scientific
tradition emphasizes respect for specialists, and since there is a
support team of epistemological specialists available in orbit, they
radio up for advice. "Is one hypothesis to be preferred?, they ask.
"What kinds of observations would support one hypothesis over another?
And is this all this hypothesis generation just 'speculation'?"
The parable ends at this point because the entire point of the story
is to invite you to put yourselves in the shoes (figuratively speaking)
of the Martian epistemologists. You may object that it is difficult
to do this since you already know which of the three scientists was
right. But this is no different from the usual situation in which an
Earthling scientist and generalist, attempting to do his own epistemological
thinking, tries to ignore his own preconceptions about the validity of
his own hypotheses and adopt an objective, neutral epistemological stance.
I tell this parable, in part, because the story I heard regarding Cope's
rule is that the long-term growth of the size of the typical organism
in a population is driven by things like sexual competition among males
or territorial exploitation of resources - not by "niche vacuums" or
"niche pressure".
So, what advice would I give as an epistemologist? Well, I would tell
the Martians to seek data as to whether the apparent 'steady state' is real,
or just an assumption. I would point out that the 'vacuum' and 'pressure'
hypotheses can probably only be distinguished internally by looking
at situations in which the steady state is disturbed, so that pressures
or vacuums are particularly large. I would urge that they investigate
more closely whether there is indeed a law of "conservation of britches"
as they seem to assume. And I would quote the great Earthling scientist
Lewontin to point out that all three hypotheses would benefit from
further attention to issues of mechanism. But I would not like to call
the hypotheses 'mere speculation'. To the contrary, I would urge the
scientists to continue to generate these hypotheses, and even to elaborate
them, because the whole question of what kind of observations to make
can only be driven by hypothesis.
The epistemological issues here interest me mostly because I see the
same kinds of issues arising in my area of greatest interest - OOL.
What kind of weight should be given to claims of explanatory economy
in evaluating competing hypotheses? However, our cynical postdoc
from Titan might well point out that I am not really interested in
achieving epistemological objectivity. I just want to know how to
structure my arguments so as to convince others to my viewpoint.
an...@sci.sci
> (be it increasing in size or complexity, or be it shedding of genes or
> excess complexity or be it any other "quasi-strategic fortuity
> availance" (QSFA) then any implication that the QSFA is being done
> because it is advantageous is at least as unscientific as the ID
> positing of "G-d did it" (GDI).
Note: This kind of debate really belongs in talk.origins.
Maybe the moderator can cross-post there to start miagration to there?
Anyway, do you agree that sometimes the mechanism that replicates DNA
occasionally slips backwards (causing a short repeat) or forwards
(causing a point or short-sequence deletion) mutation? So there's your
mechanism for introducing longer or shorter sequences into the genomes
of the population of various cells in a clade.
Do you furthermore agree that any fatal mutations are eliminated within
a single generation, so only non-fatal mutations survive over multiple
generations? Likewise disadvantageous though not-immediately-fatal
mutations will die out in a few generations? Do you furthermore agree
that if by chance one of these indel mutations is an advantage, either
in trimming down a too-long genome, or in enhancing a genome by adding
something new, the clade with the mutation has a good chance of
producing more members than the clade without the mutation,
exponentially more over long time spans, and driving the non-mutated
clade to extinction as soon as the mutated clade has grown large enough
to exhaust all resources of the shared niche? So there's your mechanism
for evolving toward better fitness via either trimming a too-large
genome down to more efficient size, or enlarging the genome if that
results in some improvement.
How exactly are these mechanisms no better than GDI?
Re GDI vs. Darwinian mutation+selection:
> the former conceptually putting the reins in the hands of a deity,
> and the latter putting the reins in the hands of organisms themselves.
I don't know what you mean by reins here. With mutation+selection, its
the environment, the circumstances affecting the individual, that
determines which directions of change are favorable and which
directions are unfavorable. Mutation simply tries lots of different
directions at random, and selection is what we call the differential
survival due to the environment. If we use the metaphor of "reins", at
best it's the environment that holds the reins, but it's not reins in
the sense of deliberately directing evolution, it's more analagous to a
minefield, whereby some directions of wandering immediately hit a mine
and are blown up, while other directions get so far from any high
density of mines that they allow much more freedom of wandering with
few deaths thereby allowing those populations to grow without the
severe attenuation of growth caused by frequent hitting of mines. There
aren't any reins pulling individuals away from mines. It's just that
any individual who happens to wander far from mines thereby achieves a
nice safe place to raise children, and grandchildren, etc., so after
much time the families living in the densest parts of the minefields
become rare while the families living away from mines become common.
> Bio-evo theorists are applying a double standard if they condemn the
> ID view (putting the deity in the gaps) yet turn right around and
> insinuate that bacteria or viruses dispose of gene baggage they can do
> without
All we say is that they randomly dispose of one bit or another of their
genome, and if they dispose of an essential part they die promptly,
while if they dispose of something they don't happen to need they have
more offspring than any brothers without that mutation. What part of
that do you dispute??
> or that complex phenotypes mold themselves to avail themselves of
> niches, or increase their capacity to tolerate some challenge.
Nobody except misunderstanderers-of-Lamarck would make any such claim.
You are using a strawman here.
> And I would wish to see my favorite science team -- or, okay, one of
> them -- avoid the APPEARANCE of assuming a double standard.
In this case, appearance is entirely in the perverted mind of the beholder.
> One poster recently ... sought to persuade me that the fact that H.
> sapiens cannot make their own ascorbic acid is because... vitamin C is
> abundant in their diet under most circumstances
Slight correction to your parahprase of what somebody else said:
For several million years in the *past*, our ancestors all lived in
abundant tropical rain forests in Africa, eating fruit which contained
lots of vitamin C. It is only starting about four million years ago,
during a period of drought, that our ancestors moved out of the
fruit+rain-forests, and learned of our need to take special measures
to get enough vitamin C, and it had been such a long time since we had
a working gene to make it that a simple mutation or two couldn't get it
back to working again.
> The fact that H. sapiens could get along without making their own
> ascorbic acid does NOT explain how, nor why -- as the case may be --
> any of our anthropoid ancestors had it and lost it
Have you ever heard of "point mutation"?? You don't need a deletion event.
A simple point-change in a DNA base is sufficient to disable a working
enzyme in a biochemical pathway. That was an advantage, because too
much vitamin-C is slightly toxic, and we already had more than enough
in our fruit diet and actually needed to spend energy excreting it. The
mutation saved us both the energy needed to make it and some of the
energy needed to excrete it.
> By the same token, merely demonstrating that it is mathematically
> POSSIBLE for a single mutation, in a single individual, to become
> spread throughout an entire population does not explain that it
> actually DID happen.
That's correct. It's a matter of chance whether any particular kind of
mutation will actually happen during a given span of time (although
it's inevitable that *every* kind of mutation will eventually happen if
a clade survives forever, and nearly inevitable during a span of five
billion years from the first animals to the end of the Sun's lifetime).
Our ancestors had only about 50 million years in the rain forests, so
some of them lost their vitamin-C synthesis ability and some retained
it, as a matter of chance. Our particular clade lost it. More info:
<http://www.grisda.org/origins/12096.htm>
The standard comprehensive reference on comparative physiology
(Prosser 1973) states that ascorbic acid is synthesized in adequate
amounts by most vertebrates, though required in the diet of man,
monkeys, and guinea pig. ...
In the last half of the decade three comprehensive papers on
mammals appeared, all by Birney et al. (1976, 1980) and Jenness et al.
(1980). They could detect the critical synthesizing enzyme for
ascorbic acid in only 1 of the 34 species (6 families) of bats
studied, and there only a trace was present. ...
The article goes on to discuss how vitamin-C is made in the liver or
kidney (or neither) in different clades of animals. Then it concludes:
Is this pattern produced by degenerative loss of synthetic
capability? The evidence indicates that it is. ...
> To say it is energy conservation by default, in saving the energy
> that would be required to make ascorbic acid when none was needed, is
> ONCE AGAIN to pose that a population would proactively do what is
> necessary to make such a miniscule energy saving.
You're attacking a strawman. Nobody claims any life proactively changes
its genome. We all (except Creationists and IDiots) say life randomly
chances into various changes, and there's a bias toward keeping the
good changes and discarding the bad changes.
> I hope humans will not, as a result, lose the capacity to convert
> starches to sugars, due to the fact that so much sugar is available in
> most humans' daily diet. (I will stipulate that if it were to happen,
> it might take a million years or more, so I'm not just summonsing a
> short-range view. Nor am I meaning to imply that we may not be
> gravitating in that direction in increments to small to measure. Maybe
> we are.)
In this case you're almost exactly correct. It would take a very very
long time, both for significant chance of such a mutation happening and
lasting enough generations to avoid prompt extinction, and then for
such multi-copy new allelle to spread through the population.
> ... just because an organism makes a change, and that change provides
> some benefit, that does NOT prove the organism made the change as a
> result of the fact it foresaw that it would be "nice."
That's the misunderstood-Lamarck strawman again.
> when biologist (one of my favorite teams) make a comment along the
> lines of saying, for example, that "viruses are disposing of their
> excess baggage," they qualify that by making the disclosure, "... but
> we do not know yet exactly why or how..." (Or if we do know exactly
> why and how, as supported by an abundance of empirical evidence, then
> let us say that, and produce our evidence.)
There are multiple mechanisms already known for deleting small sections
of a genome. I mentionned forward-slippage of the DNA copying mechanism
earlier. Another is accidental cutting of a DNA chain in two places and
losing the middle place and accidently splicing the two end pieces back
as if whole again. The best we can demonstrate when looking at before
and after sequences of a mutated virus is that a particulr sequence
which was present is now gone. There's no way we can run time back and
look at the actual deletion event in an electron microscope to
determine for sure which of the two or more known mechanisms actually
was responsible for that particular event. You're asking for miracles!
> Otherwise, we make the same mistake (or appearance thereof) as the
> ID'ers, of substituting our own eclectic "choice of cause" for
> theirs, to fill the potholes in our knowledge.
IMO that's a completely unfair judgement on biologists. The biologist
demonstrates, in the lab, several ways that deletions actually do
happen. The biologists go to a lot of trouble and expense to sequence
the virus at various times, and they discover a difference, of the
deletion type, between two successive sequences they have measured. The
biologist then says a deletion seems to have happened, probably by one
of the known and demonstrated mechanisms, possibly by a new mechanism
not yet discovered. The IDiot never demonstrates G_d doing any
deletions, yet claims GDI for sure, dismissing all the evidence the
biologist has already shown as to various known biochemical mechanisms
that could have been responsible.
How can you possibly equate biologist = IDiot?
.
Perplexed in Peoria
<an...@sci.sci> wrote in message news:dt86sa$2u0h$1...@darwin.ediacara.org...
> > PiP:
> > Extrapolating backward we can imagine that the LUCA (Last Universal
> > Common Ancestor) was the most versatile and generalist micro-organism
> > of them all, and had the biggest genome.
>
> Or maybe there was no single LUCA. Did you ever consider that possibility?
Sure. How could I not consider it when there are big names like
Woese and Margulis promoting it and leveler heads like Doolittle
taking it seriously.
> You talk like it's been mathematically proven there must have been a
> single LUCA, and all we need to do is figure out how it was.
I continue to think that the idea of a single LUCA (with only occasional
HGT since then and only a very few cases of endosymbiosis) is the most
fruitful hypothesis to drive research. In fact, I doubt that complete
fusion of genomes was particularly important at any time since protein
synthesis and the unpartitioned cytoplasm.
[snip long speculation along conventional lines]
> If I ever become
> famous for any of these hairbrained ideas of mine, and somebody wonders
> where I got the ideas from, just look here, if Google preserves their
> archive of newsgroups all that time, which is not guaranteed!)
Well, I didn't notice any "hairbrained ideas" in this posting which
could make you famous. I've heard almost all of those ideas before.
In any case, you don't become famous just for having ideas. You need
to back the ideas up with fact and argument and convince a lot of
other people that you are correct.
Everyone's favorite example of a vindicated "crackpot" these days is
Wegner, but he had to write quite a large number of good scholarly
papers on his ideas just to keep them in the collective consciousness
until a revised version of his ideas came to prominence in the 1960s.
an...@sci.sci
> HGT since then and only a very few cases of endosymbiosis) is the most
> fruitful hypothesis to drive research.
I respectfully disagree. IMO it's completely unknown at this time
whether the various highly-conserved genes we track across all three
domains co-evolved all the way back to a single LUCA or whether they
criss-crossed or otherwise followed different whole-cell trajectories
during the very early days. We should not pre-judge this question
and direct all our research as if it were true. Instead we should
draw evolutionary trees for each gene separately and then compare them
to see which co-evolved together how far back and where such
co-evolution ceases further back indicating a merging of those parts of
the genomes at that point. Then we can effectively consider evidence
for the very distant evolutionary history to judge how many different
early common ancestors yielded genes we can trace to the present day.
> In fact, I doubt that complete fusion of genomes was particularly
> important at any time since protein synthesis and the unpartitioned
> cytoplasm.
Except for endosymbiosis where two or more complete genomes merged into
a single cell but remained in separate organelles within the cell, and
only later most/all of the genes from one organelle miagrated to
another, for example most of the mitochondrial DNA, and all of the
spindle DNA, right? I'm not claiming that two genomes ever instantly
merged into a single organelle. All I'm claiming is endosymbiosis as
above, with DNA only gradually miagrating from one location to another
within the cell, or direct horizontal-gene flow from one cell to
another completely different cell, where only a small amount of DNA
flows during any single event, but over hundreds of milions of years
most/all of the DNA could get copied from each single clade to most/all
of the other clades.
> Well, I didn't notice any "hairbrained ideas" in this posting which
> could make you famous. I've heard almost all of those ideas before.
Yeah, but when you heard them before, did you think those people with
those same ideas were crackpots who thought it was possible to build
perpetual motion devices and travel back in time to change history, or
did you think those people were bright kids who needed funding and a
thesis advisor so they could perhaps develop their ideas into actual
science?
.
Perplexed in Peoria
<an...@sci.sci> wrote in message news:dufmkq$lho$1...@darwin.ediacara.org...
> > I continue to think that the idea of a single LUCA (with only occasional
> > HGT since then and only a very few cases of endosymbiosis) is the most
> > fruitful hypothesis to drive research.
>
> I respectfully disagree. IMO it's completely unknown at this time
> whether the various highly-conserved genes we track across all three
> domains co-evolved all the way back to a single LUCA or whether they
> criss-crossed or otherwise followed different whole-cell trajectories
> during the very early days. We should not pre-judge this question
> and direct all our research as if it were true. Instead we should
> draw evolutionary trees for each gene separately and then compare them
> to see which co-evolved together how far back and where such
> co-evolution ceases further back indicating a merging of those parts of
> the genomes at that point. Then we can effectively consider evidence
> for the very distant evolutionary history to judge how many different
> early common ancestors yielded genes we can trace to the present day.
Well, exactly that has been done by Peer Bork's group, as described
in the posting today by RKS - "A New Tree Of Life Allows A Closer Look
At The Origin Of Species". And they are far from the first group to
do so. I posted recently about some papers by various groups which
built trees involving some horizontal gene transfer for the
aminoacyl-tRNA-synthetases. So far, it looks as though HGT definitely
happened, but it doesn't destroy the basic tree pattern. No doubt
such studies will continue for decades.
> > In fact, I doubt that complete fusion of genomes was particularly
> > important at any time since protein synthesis and the unpartitioned
> > cytoplasm.
>
> Except for endosymbiosis where two or more complete genomes merged into
> a single cell but remained in separate organelles within the cell, and
> only later most/all of the genes from one organelle miagrated to
> another, for example most of the mitochondrial DNA, and all of the
> spindle DNA, right?
Right. Except that the 'spindle' is not generally believed to be
derived from an endosymbiont. But Margulis was right once, so maybe
she will be eventually proved right again. I remain agnostic on that
idea.
> I'm not claiming that two genomes ever instantly
> merged into a single organelle. All I'm claiming is endosymbiosis as
> above, with DNA only gradually miagrating from one location to another
> within the cell, or direct horizontal-gene flow from one cell to
> another completely different cell, where only a small amount of DNA
> flows during any single event, but over hundreds of milions of years
> most/all of the DNA could get copied from each single clade to most/all
> of the other clades.
I agree that transfers like that happen. I deny that 'most/all DNA'
is transferred to 'most/all clades'. But this is a question that will
rapidly yield to experiment over the next few years. There is little
point to our debating it here.
> > Well, I didn't notice any "hairbrained ideas" in this posting which
> > could make you famous. I've heard almost all of those ideas before.
>
> Yeah, but when you heard them before, did you think those people with
> those same ideas were crackpots who thought it was possible to build
> perpetual motion devices and travel back in time to change history, or
> did you think those people were bright kids who needed funding and a
> thesis advisor so they could perhaps develop their ideas into actual
> science?
Well, 'those people' were Lynn Margulis and Carl Woese. Not exactly
'bright kids'. I volunteered to advise them, and help turn their ideas
into science, but they turned me down. ;-)