Request

22 views
Skip to first unread message

Zoe

unread,
Jul 20, 2005, 11:40:35 PM7/20/05
to
Following is a portion of a post in response to Howard Hershey, which
he has not answered. Can anyone else please provide an answer to the
following evolutionary scenario?

Can you trace the pathway of how chimps and humans manage to
produce offspring as they first separate from their common ancestor?

The common ancestor has, let's say, 23 pairs of chromosomes. A rare
"beneficial mutation" causes an offspring to be born with an extra
pair of chromosomes. He is the forerunner of the chimp. Where does
the human ancestor come in? Does the common ancestor also produce an
offspring with 23 pairs of chromosomes, but with some other rare
"beneficial mutation" that takes the offspring, now ancestor to
humans, in a different direction?

Here's your budding tree.


common ancestor Chimp ancestor (single individual)
_____________________/
\
Human ancestor (single individual)

Can you take it from there? What's the pathway? At this point, can
the chimp ancestor still interbreed with either the common ancestor or
with the human ancestor? It has to interbreed with something in order
to produce more offspring after its own kind, so where does the
partner come from?

If there is no reasonable and/or specific answer as to a possible
pathway for the above to happen, then why on earth do evolutionists
make such strong claims that it happened? And why do they lambast
anyone who dares to question their scenario?

Steven J.

unread,
Jul 21, 2005, 12:29:15 AM7/21/05
to

"Zoe" <muz...@aol.com> wrote in message
news:ho5ud1tiqh4h94opl...@4ax.com...

> Following is a portion of a post in response to Howard Hershey, which
> he has not answered. Can anyone else please provide an answer to the
> following evolutionary scenario?
>
> Can you trace the pathway of how chimps and humans manage to
> produce offspring as they first separate from their common ancestor?
>
> The common ancestor has, let's say, 23 pairs of chromosomes. A rare
> "beneficial mutation" causes an offspring to be born with an extra
> pair of chromosomes. He is the forerunner of the chimp. Where does
> the human ancestor come in? Does the common ancestor also produce an
> offspring with 23 pairs of chromosomes, but with some other rare
> "beneficial mutation" that takes the offspring, now ancestor to
> humans, in a different direction?
>
For a couple of reasons, it seems more likely that the last common ancestor
of humans and chimps had 24 pairs of chromosomes. First, chimps, gorillas,
and orangutans all have 24 pairs of chromosomes (which makes it seem more
likely that was the number of the last common ancestor of great apes, and
continued until it was reduced in the human lineage). Second, while all
chromosomes have a centromere in the center and telomeres at the end, human
chromosome two has a vestigial centromere and telomere embedded in the
chromosome itself, suggesting that it was formed by a fusion of two
chromosomes. Indeed, there are two separate chromosomes in chimps that are
very similar in sequence to two "halves" of human chromosome 2.

By the way, although you didn't explicitly ask, the okapi (a rare,
short-necked giraffe) species has individuals with 22 pairs of chromosomes,
23 pairs, and even 22.5 pairs (for 45 chromosomes in all -- in which case
two chromosomes from one parent must be paired with one -- fused --
chromosome from the other parent). So a mutation that produced the first
human with a chromosome 2 (rather than the ancestral chromosomes 2a and 2b)
would not have prevented that individual from mating successfully. Or, take
the case of Przewalski's horse and the domestic horse: domestic horses, like
their human breeders, have one fewer chromosome pairs than their wild
ancestors, due, apparently, to a chromosomal fusion -- but domestic and
Przewalski's horses can still interbreed to produce fertile offspring. In
other cases (e.g. "chromosomal races" of mice), having different chromosome
numbers reduces interfertility.

There is no reason to suppose that the difference in chromosome numbers
started with the last common ancestor; it may well have been much more
recent, long after the human line had separated from the chimp line.
There's no particular reason, for that matter, to suppose that the human
line started out with some particular beneficial mutation, rather than our
ancestors simply moving into a different part of Africa from Cheetah's
ancestors, so that they could no longer interbreed (geographical separation
prevented any new beneficial -- or neutral or harmful -- mutations in the
hominin line from entering the chimp gene pool).


>
> Here's your budding tree.
>
>
> common ancestor Chimp ancestor (single individual)
> _____________________/
> \
> Human ancestor (single individual)
>

No, surely the branching involved entire breeding populations -- one band,
or a few bands, of apes moving into a new territory far from the lands where
other members of their species lived. As noted, at the branch point, both
populations would have been apes of the same species; they wouldn't become
different species until *after* the branch point, after geographical
separation left them free to evolve in two different directions. Remember
that, just as there was no "first French speaker" struggling to make himself
understood in a nation of classical Latin speakers, so there was no "first
human" or "first chimpanzee," but only a gradual change over many
generations from the same ancestral species.


>
> Can you take it from there? What's the pathway? At this point, can
> the chimp ancestor still interbreed with either the common ancestor or
> with the human ancestor? It has to interbreed with something in order
> to produce more offspring after its own kind, so where does the
> partner come from?
>

Most evolutionists hold that most speciation events are "allopatric,"
meaning that they occur *after* the ancestral population has split into two
groups that could interbreed if they met, but which no longer meet up.
Afterwards, mutation, genetic drift, and selection to different environments
gradually change the populations into different species. No particular
mutation (unless you count polyploidy) is likely to produce a new species.
A better (though still oversimplified) approach would be to think of a
whole series of mutations, some beneficial, most neutral (but they still
made us different from chimps), that each made the bearer a tiny bit more
"human" (or, in the other lineage, a tiny bit more "chimp"). No single
gene would have made its bearer much different from other members of his
species, or unable to interbreed with them.

It doesn't seem likely that a modern human could (or at least would)
interbreed with a modern chimp, but presumably five million years ago, our
ancestors were just a tiny bit more "human" than the ancestors of modern
chimps. They probably could have produced fertile offspring with the chimp
ancestors, but as noted, they lived in different parts of Africa and no
longer met.

By the way, polyploidy is duplication of the entire genome; plants speciate
this way all the time, but it's rarer for animals (though there are strongly
supported examples for frogs, rodents, and other vertebrates; presumably,
they can't form a new species unless they can either reproduce
parthenogenically, or unless polyploidy happens often enough that eventually
it produces two members of the same species at the same time and place).
But this has nothing to do with how humans split off from apes.


>
> If there is no reasonable and/or specific answer as to a possible
> pathway for the above to happen, then why on earth do evolutionists
> make such strong claims that it happened? And why do they lambast
> anyone who dares to question their scenario?
>

-- Steven J.


Mike Dworetsky

unread,
Jul 21, 2005, 2:54:58 AM7/21/05
to
This is such a clear and readable explanation of the way in which species
diverge from a common ancestor that I would like to see it mounted as a Post
of the Month. "No first Frenchman" indeed.

--
Mike Dworetsky

(Remove "pants" spamblock to send e-mail)
"Steven J." <sjt195...@nts.link.net.INVALID> wrote in message
news:11du954...@corp.supernews.com...

zawa...@yahoo.com

unread,
Jul 21, 2005, 7:36:13 AM7/21/05
to
Seconded.
Ce qui? Aucun premier Français?


Cheezits

unread,
Jul 21, 2005, 10:19:51 AM7/21/05
to
"Mike Dworetsky" <plati...@pants.btinternet.com> wrote:
> This is such a clear and readable explanation of the way in which
> species diverge from a common ancestor that I would like to see it
> mounted as a Post of the Month. "No first Frenchman" indeed.

I agree. I had wondered about that chromosome question myself.

Sue
--
"It's not smart or correct, but it's one of the things that
make us what we are." - Red Green

John Harshman

unread,
Jul 21, 2005, 11:17:23 AM7/21/05
to
Zoe wrote:

> Following is a portion of a post in response to Howard Hershey, which
> he has not answered. Can anyone else please provide an answer to the
> following evolutionary scenario?
>
> Can you trace the pathway of how chimps and humans manage to
> produce offspring as they first separate from their common ancestor?
>
> The common ancestor has, let's say, 23 pairs of chromosomes. A rare
> "beneficial mutation" causes an offspring to be born with an extra
> pair of chromosomes. He is the forerunner of the chimp. Where does
> the human ancestor come in? Does the common ancestor also produce an
> offspring with 23 pairs of chromosomes, but with some other rare
> "beneficial mutation" that takes the offspring, now ancestor to
> humans, in a different direction?

There are several problems with this scenario already. First, you assume
that the common ancestor is a single individual when it's really a
population or species. Second, you assume this chromosomal mutation is
beneficial, for which there is no evidence. Third, you assume that the
mutation in question was a fission in the chimp line, when it was
instead a fusion in the human line. Fourth, you assume that the mutation
happened in the common ancestor, when it almost certainly happened some
time after the human and chimp lineages separated. Fifth, you assume
that this mutation had something to do with making us human, when it's
most likely to be irrelevant.

> Here's your budding tree.
>
>
> common ancestor Chimp ancestor (single individual)
> _____________________/
> \
> Human ancestor (single individual)

I'm afraid your ASCII graphics have misfired. But there is no single
individual involved here, just populations that become isolated
(geographically at first) and diverge from each other.

> Can you take it from there? What's the pathway? At this point, can
> the chimp ancestor still interbreed with either the common ancestor or
> with the human ancestor? It has to interbreed with something in order
> to produce more offspring after its own kind, so where does the
> partner come from?

The partner comes from other members of its population. At some time in
the past, the common ancestral species became split into two
populations, geographically isolated from each other. At this point they
began diverging. They may in fact have begun with slightly different
gene pools, because of locaal differences that already existed, as is
common in many species with large ranges. The environments in the two
now-isolated parts of the original species range may have been somewhat
different too, in which case selection would speed divergence. But in
any case, drift would cause divergence too. After a while, sooner if
selection is operating and later if only drift is operating, the
descendants, if put together, would no longer recognize each other as
potential mates. And that's speciation.

As for the chromosomal mutation, that's just one of the changes that
happened in the human lineage. It began as a single mutation in a single
individual, and for one reason or another increased in frequency in that
population until it reached fixation, and now all humans have only 46
chromosomes instead of 48.

Chromosomal fusion, by the way, does not prevent interbreeding with
other members of the population that have unfused chromosomes. If you
look on the web, you will find several examples of species with
chromosomal polymorphisms of this sort.

> If there is no reasonable and/or specific answer as to a possible
> pathway for the above to happen, then why on earth do evolutionists
> make such strong claims that it happened? And why do they lambast
> anyone who dares to question their scenario?

If their basis for questioning it is a complete misunderstanding of the
facts, then lambasting is entirely appropriate.

Zoe

unread,
Jul 23, 2005, 11:16:14 PM7/23/05
to
On Wed, 20 Jul 2005 23:29:15 -0500, "Steven J."
<sjt195...@nts.link.net.INVALID> wrote:

>
>"Zoe" <muz...@aol.com> wrote in message
>news:ho5ud1tiqh4h94opl...@4ax.com...
>> Following is a portion of a post in response to Howard Hershey, which
>> he has not answered. Can anyone else please provide an answer to the
>> following evolutionary scenario?
>>
>> Can you trace the pathway of how chimps and humans manage to
>> produce offspring as they first separate from their common ancestor?
>>
>> The common ancestor has, let's say, 23 pairs of chromosomes. A rare
>> "beneficial mutation" causes an offspring to be born with an extra
>> pair of chromosomes. He is the forerunner of the chimp. Where does
>> the human ancestor come in? Does the common ancestor also produce an
>> offspring with 23 pairs of chromosomes, but with some other rare
>> "beneficial mutation" that takes the offspring, now ancestor to
>> humans, in a different direction?
>>
>For a couple of reasons, it seems more likely that the last common ancestor
>of humans and chimps had 24 pairs of chromosomes. First, chimps, gorillas,
>and orangutans all have 24 pairs of chromosomes (which makes it seem more
>likely that was the number of the last common ancestor of great apes, and
>continued until it was reduced in the human lineage).

is this a principle, that majority determines which comes first? In
comparing genomes in species that are supposed to be related, if there
are more life forms with the same number of chromosomes, then is that
taken to mean, as a rule, they had to be ancestors to those with a
lesser number of chromosomes?

If not, then we can discard your first reason.

> Second, while all
>chromosomes have a centromere in the center and telomeres at the end, human
>chromosome two has a vestigial centromere and telomere embedded in the
>chromosome itself, suggesting that it was formed by a fusion of two
>chromosomes. Indeed, there are two separate chromosomes in chimps that are
>very similar in sequence to two "halves" of human chromosome 2.

this would appear, on its surface, to be a more convincing reason to
conclude that humans and chimps have a common ancestor (though you
have not yet addressed how fusion affects fertility or the parallel
meaning, if any, attached to chromosome fusion in mice.)

That said, the latest evidence in genome comparison between chimps and
humans reveal an 83% difference between chimp chromosome 22 and human
chromosome 21 (chimp chromosome 22 is said to be the ortholog of human
chromosome 21.) And even though there appears to be 99% similarity
between the DNA of humans and chimps, the recombination hot spots have
turned out to be almost completely different. Apparently, then, DNA
sequences, even though highly similar, do not determine biological
function.

It's like comparing the recipes for two cakes. They both use 99%
similar ingredients -- flour, sugar, butter, eggs. Does this
similarity mean that both cakes came from the same batter? Not
necessarily. Not even probably. The more reasonable assumption is
that both cakes were created in their own right, from different
recipes, but using similar ingredients.

>By the way, although you didn't explicitly ask, the okapi (a rare,
>short-necked giraffe) species has individuals with 22 pairs of chromosomes,
>23 pairs, and even 22.5 pairs (for 45 chromosomes in all -- in which case
>two chromosomes from one parent must be paired with one -- fused --
>chromosome from the other parent).

would you have references, by any chance, to studies that have
followed the interbreeding of these subspecies of opaki? Have they
tried to interbreed an opaki with 22 pairs of chromosomes with an
opaki that has 23 pairs of chromosomes? Or do opakis with 22 pairs of
chromosomes breed only with those that have 22 pairs of chromosomes,
and so on?

> So a mutation that produced the first
>human with a chromosome 2 (rather than the ancestral chromosomes 2a and 2b)
>would not have prevented that individual from mating successfully.

I'm not sure that that is a hard-and-fast conclusion, considering that
there is no evidence today that humans with chromosome 2 can
interbreed with chimps with chromosomes 2a and 2b. If they can't
today, why speculate that they could have at one time, unless you have
evidence that such a thing is possible?

> Or, take
>the case of Przewalski's horse and the domestic horse: domestic horses, like
>their human breeders, have one fewer chromosome pairs than their wild
>ancestors, due, apparently, to a chromosomal fusion -- but domestic and
>Przewalski's horses can still interbreed to produce fertile offspring. In
>other cases (e.g. "chromosomal races" of mice), having different chromosome
>numbers reduces interfertility.

if you are comparing the horse scenario to the human/chimp scenario,
you would need to explain why the domestic horse can still breed
successfully with their wild ancestor, the Przewalski horse, and yet
humans cannot breed with their supposed wild ancestor, the ape.

>There is no reason to suppose that the difference in chromosome numbers
>started with the last common ancestor; it may well have been much more
>recent, long after the human line had separated from the chimp line.
>There's no particular reason, for that matter, to suppose that the human
>line started out with some particular beneficial mutation, rather than our
>ancestors simply moving into a different part of Africa from Cheetah's
>ancestors, so that they could no longer interbreed (geographical separation
>prevented any new beneficial -- or neutral or harmful -- mutations in the
>hominin line from entering the chimp gene pool).
>>
>> Here's your budding tree.
>>
>>
>> common ancestor Chimp ancestor (single individual)
>> _____________________/
>> \
>> Human ancestor (single individual)
>>
>No, surely the branching involved entire breeding populations -- one band,
>or a few bands, of apes moving into a new territory far from the lands where
>other members of their species lived. As noted, at the branch point, both
>populations would have been apes of the same species; they wouldn't become
>different species until *after* the branch point, after geographical
>separation left them free to evolve in two different directions. Remember
>that, just as there was no "first French speaker" struggling to make himself
>understood in a nation of classical Latin speakers, so there was no "first
>human" or "first chimpanzee," but only a gradual change over many
>generations from the same ancestral species.

okay, so I'll redraw the ancestral lines as follows, according to your
explanation.

Chimp ancestor population (24chrm)
common ancestor (24 chrm) /_____________________
___________________________/
\
\
Human ancestor population (24chrm)

At this point, there is as yet no change in the genetic makeup of
either the chimp ancestor population or the human ancestor population.
The only change is in geographical location which prevents Population
A (containing a potential chimp ancestor) from interbreeding with
Population B (containing a potential human ancestor).

Right so far?

Okay, so focusing now on the human ancestor population:

Human ancestor population (24chrm)
______________________________ /??

What happens at this point? A fusion occurs in a single individual in
this population, supposedly, right? I take it that the proposed rare
beneficial mutations do not hit several members of the population at
the same time? Otherwise they wouldn't be rare.

Okay, so we now have a population of 24chrm members and one member's
chromosomes 2a and 2b fuse into a single chromosome, forming
chromosome 2 of the human ancestor's set of chromosomes.

Supposedly, this 23chrm member of the 24chrm population can continue
to interbreed with the 24chrm members, producing offspring that may or
may not carry this 23chrm set. How does selection work in this case?
Has it been demonstrated that Chromosome 2 in humans makes them
distinctly different from apes, and gives them a distinct selective
advantage? If not, it would be predicted that 23chrm members of the
population would not necessarily increase but instead, as, they
continue to interbreed, the 24chrm members will dominate because they
are more in abundance, and the supposedly advantageous and distinct
Chromosome 2 will die out and be lost to the population.

That would be one scenario. There's another. Looking at comparisons
of human chromosome 2 and chimp chromosomes 2a and b, except for where
the fusion supposedly occurs, the chromosomes appear to be physically
identical. Problem here is which direction to go in giving value to
the similarities.

If the similarities mean that both human chromosome 2 and chimps
chromosomes 2a and b will produce biological similarities, then what
is there to choose from, selection wise, in order to give the
advantage to Chromosome 2 in humans?

But if, as research reveals (as recently as February, 2005),
recombination hot spots on human chromosome 21, supposedly orthologous
to chimp chromosome 22, are 83% different, and 17% similar -- then
even though human Chromosome 2 and Chimp Chromosomes 2a and b appear
to be almost identical, this apparent similarity may not be real after
all.

See:

http://www.admin.ox.ac.uk/po/050214.shtml

>> Can you take it from there? What's the pathway? At this point, can
>> the chimp ancestor still interbreed with either the common ancestor or
>> with the human ancestor? It has to interbreed with something in order
>> to produce more offspring after its own kind, so where does the
>> partner come from?
>>
>Most evolutionists hold that most speciation events are "allopatric,"
>meaning that they occur *after* the ancestral population has split into two
>groups that could interbreed if they met, but which no longer meet up.
>Afterwards, mutation, genetic drift, and selection to different environments
>gradually change the populations into different species. No particular
>mutation (unless you count polyploidy) is likely to produce a new species.
>A better (though still oversimplified) approach would be to think of a
>whole series of mutations, some beneficial, most neutral (but they still
>made us different from chimps),

no, no, no, you can't claim neutral mutations as changes that make us
different from chimps. If humans become different, it would be
because change (or mutation, as you call it) has occurred. No change,
no difference. Neutral "mutations" cannot be counted to make a
difference between humans and chimps. So once again you are left with
trying to have the rare "beneficial" mutation carry the entire weight
of your evolutionary theory.

> that each made the bearer a tiny bit more
>"human" (or, in the other lineage, a tiny bit more "chimp"). No single
>gene would have made its bearer much different from other members of his
>species, or unable to interbreed with them.

in which case, selection has nothing to work on, does it?

>It doesn't seem likely that a modern human could (or at least would)
>interbreed with a modern chimp, but presumably five million years ago, our
>ancestors were just a tiny bit more "human" than the ancestors of modern
>chimps.

how can a life form be a tiny bit more human before it becomes human?

> They probably could have produced fertile offspring with the chimp
>ancestors, but as noted, they lived in different parts of Africa and no
>longer met.

I note the use of "probably" here.

snip>

Steven J.

unread,
Jul 24, 2005, 1:59:10 AM7/24/05
to

"Zoe" <muz...@aol.com> wrote in message
news:kt06e1hhsolj6fi6c...@4ax.com...
No, parsimony rather than simple majority rule determines which (probably)
came first. "Parsimony," in this case, means accounting for the observed
pattern with the fewest postulated entities -- in this case, mutations. If
the last common ancestor (LCA) of African apes had 23 chromosome pairs, then
we need two mutations -- one to give the gorillas 24 pairs, and one to give
the chimps 24 pairs -- to account for the observed distribution. If we
assume that the African ape LCA had 24 pairs, but the human-chimp LCA had 23
pairs, then we still need two mutations: one to reduce the number of pairs
after the human-chimp line splits from gorillas, and one to increase the
number of pairs in chimps after the human and chimp lines split. If we
assume that both the African ape and human-chimp LCA had 24 pairs, then we
need only one mutation to explain the difference (after the human-chimp
split). Of course, in some cases, parsimony will be *wrong* (nature isn't,
as far as anyone knows, trying to keep mutations to a minimum), but it seems
a good approximation most of the time.

>
> If not, then we can discard your first reason.
>
>> Second, while all
>>chromosomes have a centromere in the center and telomeres at the end,
>>human
>>chromosome two has a vestigial centromere and telomere embedded in the
>>chromosome itself, suggesting that it was formed by a fusion of two
>>chromosomes. Indeed, there are two separate chromosomes in chimps that
>>are
>>very similar in sequence to two "halves" of human chromosome 2.
>
> this would appear, on its surface, to be a more convincing reason to
> conclude that humans and chimps have a common ancestor (though you
> have not yet addressed how fusion affects fertility or the parallel
> meaning, if any, attached to chromosome fusion in mice.)
>
I thought I did address that issue. See below.

>
> That said, the latest evidence in genome comparison between chimps and
> humans reveal an 83% difference between chimp chromosome 22 and human
> chromosome 21 (chimp chromosome 22 is said to be the ortholog of human
> chromosome 21.) And even though there appears to be 99% similarity
> between the DNA of humans and chimps, the recombination hot spots have
> turned out to be almost completely different. Apparently, then, DNA
> sequences, even though highly similar, do not determine biological
> function.
>
When you say "83% difference," I'm not sure what you mean. If you mean that
83% of the genes have at least one nucleotide different between the two
species, that is perfectly consistent with a 99% sequence similarity between
the two chromosomes. Suppose (these figures are illustrative only; do not
assume they reflect actual measurements of the chromosome) that two
chromosomes in different species have 100 genes each. Suppose each gene has
300 nucleotides, and that for each gene two nucleotides differ between the
two species. That would mean that on this chromosome, 100% of the genes are
(slightly) different from their homologues in the other species, but that
overall sequence similarity is over 99%. But certainly minor differences in
DNA sequence can produce major changes in function, and certainly genes by
themselves do not determine everything that happens in an organism.

>
> It's like comparing the recipes for two cakes. They both use 99%
> similar ingredients -- flour, sugar, butter, eggs. Does this
> similarity mean that both cakes came from the same batter? Not
> necessarily. Not even probably. The more reasonable assumption is
> that both cakes were created in their own right, from different
> recipes, but using similar ingredients.
>
Actually, a sufficient similarity in composition (exact proportions of many
minor ingredients) may strongly indicate origin from the same batter. At
least, this line of reasoning is commonly used in forensic science for
bullet fragments and dirt samples. But in any case, a closer analogy to DNA
would be the exact wording of the recipes themselves -- especially if both
recipes shared the same mispellings of the same words in the same order, and
had bits of text that were alike but didn't seem to have anything to do with
the actual recipe (like, e.g. the pseudogenes and endogenous retroviruses
chimps and humans share).

By the way, why is it more reasonable, even if we don't know for sure, to
suppose that the cakes were created from different recipes and different
batter? Certainly a baker is capable of making one big batch of batter and
making lots of cakes from it. And a Creator, I would suppose, is perfectly
capable of making many species from a single ancestral population, as He
made (according to the Bible) many nations from one original human
population.


>
>>By the way, although you didn't explicitly ask, the okapi (a rare,
>>short-necked giraffe) species has individuals with 22 pairs of
>>chromosomes,
>>23 pairs, and even 22.5 pairs (for 45 chromosomes in all -- in which case
>>two chromosomes from one parent must be paired with one -- fused --
>>chromosome from the other parent).
>
> would you have references, by any chance, to studies that have
> followed the interbreeding of these subspecies of opaki? Have they
> tried to interbreed an opaki with 22 pairs of chromosomes with an
> opaki that has 23 pairs of chromosomes? Or do opakis with 22 pairs of
> chromosomes breed only with those that have 22 pairs of chromosomes,
> and so on?
>

Okapis have no known subspecies; the variant chromosome numbers do not
correspond to racial or habitat differences. And, apparently, they
interbreed freely with okapis with different numbers of chromosomes and
produce fertile offspring. Google turns up a few scholarly articles on
"chromosomal polymorphism" in okapis and other species, and this appears, in
okapis and some other species, to work like any other polymorphism (that is,
it no more affects interbreeding than the difference between, say, type A
and type O blood, or blue and brown eyes).


>
>> So a mutation that produced the first
>>human with a chromosome 2 (rather than the ancestral chromosomes 2a and
>>2b)
>>would not have prevented that individual from mating successfully.
>
> I'm not sure that that is a hard-and-fast conclusion, considering that
> there is no evidence today that humans with chromosome 2 can
> interbreed with chimps with chromosomes 2a and 2b. If they can't
> today, why speculate that they could have at one time, unless you have
> evidence that such a thing is possible?
>

There's no evidence that chimps with chromosomes 2a and 2b can interbreed
with gorillas with chromosomes 2a and 2b. They've spent seven million years
or more evolving in different directions (not just in obvious anatomical
ways, but in more subtle ones). For all either of us knows, hominins (the
human side of the human-chimp lineage) and panins (the chimp side) stopped
being interfertile before the chromosome fusion happened in the hominin
line. I doubt that chromosome number per se is much of a guide to
interfertility.

But again, horse subspecies with different numbers of chromosomes are
interfertile. Okapis with a rather recent mutation that produced a fused
chromosome are interfertile. I'm speculating that what is known to happen
in several species today could have happened in other species at other
times; it seems a safe enough speculation.


>
>> Or, take
>>the case of Przewalski's horse and the domestic horse: domestic horses,
>>like
>>their human breeders, have one fewer chromosome pairs than their wild
>>ancestors, due, apparently, to a chromosomal fusion -- but domestic and
>>Przewalski's horses can still interbreed to produce fertile offspring. In
>>other cases (e.g. "chromosomal races" of mice), having different
>>chromosome
>>numbers reduces interfertility.
>
> if you are comparing the horse scenario to the human/chimp scenario,
> you would need to explain why the domestic horse can still breed
> successfully with their wild ancestor, the Przewalski horse, and yet
> humans cannot breed with their supposed wild ancestor, the ape.
>

Well, I'm not sure it's been conclusively demonstrated that we *can't*
interbreed with chimps, but assuming that we can't, our ancestors split from
theirs about six million years ago; that's a lot of time to evolve barriers
to interbreeding (starting with we probably look a lot uglier and less sexy
to each other than the two horse subspecies do). The ancestors of
Przewalski's horse separated from those of modern horses much more recently
(60,000 years ago? 6000 years ago? more recently still -- perhaps not
until humans started domesticating horses?). Reproductively isolated
populations evolve intersterility by degrees, over time, and at varying
rates.

Please try to understand: there is no reason to suppose that the difference
in chromosome number caused he split between the hominin and panin lines, or
happened at the same time. Now, it's possible that it occurred in the
human-chimp LCA, and the 23-pair version simply died out among chimps and
survived and became "fixed" (present in 100% of the population) in humans.
If this is the case, then there was a time when it wasn't a peculiarly
"human" trait, any more than type A blood (which is also a polymorphism
present in both humans and chimps) is, and individuals with both chromosome
numbers could interbreed freely. Or perhaps, as I suggested in my earlier
post, the chromosomal polymorphism arose after the human-chimp split, and no
chimp ancestor ever had that particular chromosomal fusion. I don't know of
any strong reason to prefer either possibility.

Right, except that population A contains many potential (indeed, *actual*)
chimp ancestors, as population B contains many human ancestors. Some
individuals in either population will end up having no living descendants,
but others will be the ancestor (if they're in population A) of every
chimpanzee alive today), or (if they're in population B) of every human
who's ever lived (and every Neanderthal, _Homo erectus_, australopith, and
so on). There is no one single mutant individual who is the sole ancestor
and cause of modern humans.


>
> Okay, so focusing now on the human ancestor population:
>
> Human ancestor population (24chrm)
> ______________________________ /??
>
> What happens at this point? A fusion occurs in a single individual in
> this population, supposedly, right? I take it that the proposed rare
> beneficial mutations do not hit several members of the population at
> the same time? Otherwise they wouldn't be rare.
>

There's no reason to suppose the change was beneficial, rather than neutral.
There's been speculation that the change in chromosomal numbers was linked
to the emergence of some distinctively human trait (e.g. bipedalism), but
there's no evidence for that that I'm aware of. Again, note that
differences in chromosome numbers seem to make no difference to okapis; it's
simply another way individuals in a population can vary.

Now, if you have a neutral mutation (one that makes an individual neither
more nor less fit in that particular environment), then its survival in each
generation is a matter of pure chance. Most neutral mutations presumably
die out in short order, swamped by the more common (even if no better)
alleles at that locus. But mathematical models show that, from time to
time, by sheer dumb luck, a neutral mutation will become more and more
common in each successive generation, until it completely replaces the
original trait.

http://www.talkorigins.org/faqs/genetic-drift.html

Humans and chimps have identical amino-acid sequences for the enzyme
cytochrome-c, but the *genes* for cytochrome-c differ in one nucleotide
between the two species (this is possible because there are multiple
three-nucleotide codons for each amino acid). This is a "silent" mutation
(one with no phenotypic effect), and surely neutral. It presumably
originated as a mutation in one individual in one species, and just by sheer
dumb luck spread through that species over hundreds of generations. This
can also happen to traits that do make a difference, if the difference
doesn't affect chances of reproductive success. Perhaps the spread of the
fused chromosome was just a case of neutral drift.


>
> Okay, so we now have a population of 24chrm members and one member's
> chromosomes 2a and 2b fuse into a single chromosome, forming
> chromosome 2 of the human ancestor's set of chromosomes.
>
> Supposedly, this 23chrm member of the 24chrm population can continue
> to interbreed with the 24chrm members, producing offspring that may or
> may not carry this 23chrm set. How does selection work in this case?
> Has it been demonstrated that Chromosome 2 in humans makes them
> distinctly different from apes, and gives them a distinct selective
> advantage? If not, it would be predicted that 23chrm members of the
> population would not necessarily increase but instead, as, they
> continue to interbreed, the 24chrm members will dominate because they
> are more in abundance, and the supposedly advantageous and distinct
> Chromosome 2 will die out and be lost to the population.
>

As noted, this happens most of the time, with most neutral mutations, but
every so often you get an exception. Flip enough coins enough times, and
sooner or later one will come up "heads" over and over and over.


>
> That would be one scenario. There's another. Looking at comparisons
> of human chromosome 2 and chimp chromosomes 2a and b, except for where
> the fusion supposedly occurs, the chromosomes appear to be physically
> identical. Problem here is which direction to go in giving value to
> the similarities.
>
> If the similarities mean that both human chromosome 2 and chimps
> chromosomes 2a and b will produce biological similarities, then what
> is there to choose from, selection wise, in order to give the
> advantage to Chromosome 2 in humans?
>

Maybe nothing. Not all evolution is the result of natural selection. And
there are problems with describing selection pressures on populations
millioins of years ago. There's a lot that isn't known about how genes
interact with each other and the environment to build an organism, and it's
hard to say what the effect would be. Even if we could say what the effect
would be, there's still the problem of figuring out why it would be
advantageous (there are several competing theories of why bipedalism, or
larger brains, or thinning body hair, would benefit our ancestors).


>
> But if, as research reveals (as recently as February, 2005),
> recombination hot spots on human chromosome 21, supposedly orthologous
> to chimp chromosome 22, are 83% different, and 17% similar -- then
> even though human Chromosome 2 and Chimp Chromosomes 2a and b appear
> to be almost identical, this apparent similarity may not be real after
> all.
>
> See:
>

This article discusses differences between human and chimp chromosomes in
where "crossovers" (e.g. the two copies of chromosome 22 switching parts
with each other) take place. I explained above why having 83% of genes
different is compatible with having 99% of DNA sequences identical. I don't
see any reference to "83%" in the article, but if it refers to "hotspots,"
rather than to genes or nucleotides, then I still don't see why this is
incompatible with either 99% sequence identity between genes, or with
virtually identical functions for genes. Presumably, the differences that
produce different "hotspots" are small, local changes in noncoding DNA
(which affect where the chromosome is likely to break apart during mating,
not how the genes themselves work), not in the genes themselves.


>
> http://www.admin.ox.ac.uk/po/050214.shtml
>
>>> Can you take it from there? What's the pathway? At this point, can
>>> the chimp ancestor still interbreed with either the common ancestor or
>>> with the human ancestor? It has to interbreed with something in order
>>> to produce more offspring after its own kind, so where does the
>>> partner come from?
>>>
>>Most evolutionists hold that most speciation events are "allopatric,"
>>meaning that they occur *after* the ancestral population has split into
>>two
>>groups that could interbreed if they met, but which no longer meet up.
>>Afterwards, mutation, genetic drift, and selection to different
>>environments
>>gradually change the populations into different species. No particular
>>mutation (unless you count polyploidy) is likely to produce a new species.
>>A better (though still oversimplified) approach would be to think of a
>>whole series of mutations, some beneficial, most neutral (but they still
>>made us different from chimps),
>
> no, no, no, you can't claim neutral mutations as changes that make us
> different from chimps. If humans become different, it would be
> because change (or mutation, as you call it) has occurred. No change,
> no difference. Neutral "mutations" cannot be counted to make a
> difference between humans and chimps. So once again you are left with
> trying to have the rare "beneficial" mutation carry the entire weight
> of your evolutionary theory.
>

Of course I can argue that. As noted above, some neutral changes are
"silent," with no phenotypic effect. But a change can produce a quite
marked effect, and still be "neutral" (that is, can make reproductive
success in the given environment neither more nor less likely). There are
two vireo (a type of bird) species that humans can easily tell apart only by
eye color. There's no reason to suppose that one eye color is better than
the other for the birds, but the difference distinguishes the two species.
Of course, the change might be beneficial in one population, because of
sexual selection (female fashion-consciousness), but that's not quite the
same thing as getting food more easily, avoiding becoming food, or fighting
off infections better. Quite possibly some of the differences between
humans and chimps were sexually rather than "naturally" selected.

As argued above, the change in chromosome number was quite possibly a
"neutral" change, although it is clearly one of the differences between us
and chimps. Note that something like 90% of the genome is neither genes nor
regulatory sequences. A lot of the 100 million or so differences between
the human and chimp genomes almost certainly don't make any difference that
matters to us -- they are "information" if you're looking for differences
between human and chimp genomes, but if you're looking for "what makes us
human," they aren't "information" in whatever sense it is that creationists
have in mind when they speak of "new information."


>
>> that each made the bearer a tiny bit more
>>"human" (or, in the other lineage, a tiny bit more "chimp"). No single
>>gene would have made its bearer much different from other members of his
>>species, or unable to interbreed with them.
>
> in which case, selection has nothing to work on, does it?
>

Again, mathematical models suggest that very small differences in "fitness"
can give a trait a big advantage over time. So, for that matter, do actual
observations of microevolution in the wild: Grant's finches on the Galapagos
had small differences in beak size and shape that hardly made them different
species, or even different subspecies -- but made a real difference in
fitness.


>
>>It doesn't seem likely that a modern human could (or at least would)
>>interbreed with a modern chimp, but presumably five million years ago, our
>>ancestors were just a tiny bit more "human" than the ancestors of modern
>>chimps.
>
> how can a life form be a tiny bit more human before it becomes human?
>

I said "human" in scare quotes. Maybe their brains were a trifle larger.
Maybe they walked erect a little more often and more easily. Maybe they
just had that silent mutation in the cytochrome-c gene (if a human had a
mutation that reversed that change, we wouldn't regard that person as less
human, of course, which is why I put "human" in scare quotes). The point
is, some of their evolutionary changes had made their genes (and probably,
if we looked closely enough, their bodies) a bit more like ours.


>
>> They probably could have produced fertile offspring with the chimp
>>ancestors, but as noted, they lived in different parts of Africa and no
>>longer met.
>
> I note the use of "probably" here.
>

Well, yes.
>
> snip>
>
-- Steven J.


John Harshman

unread,
Jul 24, 2005, 9:53:25 AM7/24/05
to
Zoe wrote:

No, that's not a principle, but we can't discard his first reason. It's
not just numbers of species but the shape of the phylogenetic tree that
determines what came first. Since we know the tree (i.e. that chimps,
gorillas, orangutans, and gibbons are successively less closely related
to humans), we know what came first. Either 24 pairs came first (and
humans evolved 23), or chimps, gorillas, orangutans, and gibbons all
evolved 24 pairs independently from an ancestor with 23 pairs. Which
makes more sense to you?

>>Second, while all
>>chromosomes have a centromere in the center and telomeres at the end, human
>>chromosome two has a vestigial centromere and telomere embedded in the
>>chromosome itself, suggesting that it was formed by a fusion of two
>>chromosomes. Indeed, there are two separate chromosomes in chimps that are
>>very similar in sequence to two "halves" of human chromosome 2.
>
> this would appear, on its surface, to be a more convincing reason to
> conclude that humans and chimps have a common ancestor (though you
> have not yet addressed how fusion affects fertility or the parallel
> meaning, if any, attached to chromosome fusion in mice.)

Parallel meaning? Fusion doesn't affect fertility very much, and in some
cases it doesn't affect it at all. How's that?

> That said, the latest evidence in genome comparison between chimps and
> humans reveal an 83% difference between chimp chromosome 22 and human
> chromosome 21 (chimp chromosome 22 is said to be the ortholog of human
> chromosome 21.)

I'm afraid you will have to tell us where you got that number, and what
it means. You have misunderstood something seriously, but I don't know
what. Ah, looking below I find you do tell us. The 83% difference is in
the location of recombination hot spots, not sequence. This would be a
very silly measure of genetic difference. In fact, as the press release
says, it doesn't seem to involve genetic differences at all. The DNA
sequence itself is still 99% identical.

> And even though there appears to be 99% similarity
> between the DNA of humans and chimps, the recombination hot spots have
> turned out to be almost completely different. Apparently, then, DNA
> sequences, even though highly similar, do not determine biological
> function.

Now that's a bundle of non sequiturs. Explain what you think you mean by
that. Of course they determine biological function. What they apparently
don't do is determine the sites at which recombination happens. That's
one biological function, not "biological function".

> It's like comparing the recipes for two cakes. They both use 99%
> similar ingredients -- flour, sugar, butter, eggs. Does this
> similarity mean that both cakes came from the same batter? Not
> necessarily. Not even probably. The more reasonable assumption is
> that both cakes were created in their own right, from different
> recipes, but using similar ingredients.

This analogy has nothing at all to do with the similarity of DNA.
Further, the major evidence for common descent is not mere similarity,
but (have you heard this before?) nested hierarchy. Cakes just don't
display any such thing.

>>By the way, although you didn't explicitly ask, the okapi (a rare,
>>short-necked giraffe) species has individuals with 22 pairs of chromosomes,
>>23 pairs, and even 22.5 pairs (for 45 chromosomes in all -- in which case
>>two chromosomes from one parent must be paired with one -- fused --
>>chromosome from the other parent).
>
> would you have references, by any chance, to studies that have
> followed the interbreeding of these subspecies of opaki? Have they
> tried to interbreed an opaki with 22 pairs of chromosomes with an
> opaki that has 23 pairs of chromosomes? Or do opakis with 22 pairs of
> chromosomes breed only with those that have 22 pairs of chromosomes,
> and so on?
>
>> So a mutation that produced the first
>>human with a chromosome 2 (rather than the ancestral chromosomes 2a and 2b)
>>would not have prevented that individual from mating successfully.
>
> I'm not sure that that is a hard-and-fast conclusion, considering that
> there is no evidence today that humans with chromosome 2 can
> interbreed with chimps with chromosomes 2a and 2b. If they can't
> today, why speculate that they could have at one time, unless you have
> evidence that such a thing is possible?

Check out the mice, the shrews, and other species in which chromosomal
fusions are within-population polymorphisms.

>>Or, take
>>the case of Przewalski's horse and the domestic horse: domestic horses, like
>>their human breeders, have one fewer chromosome pairs than their wild
>>ancestors, due, apparently, to a chromosomal fusion -- but domestic and
>>Przewalski's horses can still interbreed to produce fertile offspring. In
>>other cases (e.g. "chromosomal races" of mice), having different chromosome
>>numbers reduces interfertility.
>
> if you are comparing the horse scenario to the human/chimp scenario,
> you would need to explain why the domestic horse can still breed
> successfully with their wild ancestor, the Przewalski horse, and yet
> humans cannot breed with their supposed wild ancestor, the ape.

Przewalski's horse is not the ancestor of domestic horses. It's a close
relative. The factors that allow or prevent interbreeding are complex,
but simple length of time apart is one of them. Humans and chimps have
been separated longer than the two horse species. Morphological
divergence is another, and we have diverged more than the horses.

You are still having problems with ASCII graphics, assuming this is
supposed to be a tree.

> Chimp ancestor population (24chrm)
> common ancestor (24 chrm) /_____________________
> ___________________________/
> \
> \
> Human ancestor population (24chrm)
>
> At this point, there is as yet no change in the genetic makeup of
> either the chimp ancestor population or the human ancestor population.
> The only change is in geographical location which prevents Population
> A (containing a potential chimp ancestor) from interbreeding with
> Population B (containing a potential human ancestor).
>
> Right so far?
>
> Okay, so focusing now on the human ancestor population:
>
> Human ancestor population (24chrm)
> ______________________________ /??
>
> What happens at this point? A fusion occurs in a single individual in
> this population, supposedly, right? I take it that the proposed rare
> beneficial mutations do not hit several members of the population at
> the same time? Otherwise they wouldn't be rare.

Right. But nobody says this fusion is beneficial, and nobody says it's
the first difference to become fixed in the human lineage.

> Okay, so we now have a population of 24chrm members and one member's
> chromosomes 2a and 2b fuse into a single chromosome, forming
> chromosome 2 of the human ancestor's set of chromosomes.
>
> Supposedly, this 23chrm member of the 24chrm population can continue
> to interbreed with the 24chrm members, producing offspring that may or
> may not carry this 23chrm set. How does selection work in this case?
> Has it been demonstrated that Chromosome 2 in humans makes them
> distinctly different from apes, and gives them a distinct selective
> advantage?

No. There's no reason to suppose it does.

> If not, it would be predicted that 23chrm members of the
> population would not necessarily increase but instead, as, they
> continue to interbreed, the 24chrm members will dominate because they
> are more in abundance, and the supposedly advantageous and distinct
> Chromosome 2 will die out and be lost to the population.

You need to read up on genetic drift. Chromosomal mutations happen with
a certain frequency. Most are lost. By chance, a few increase in
frequency and eventually become fixed. This could easily be such a case.

> That would be one scenario. There's another. Looking at comparisons
> of human chromosome 2 and chimp chromosomes 2a and b, except for where
> the fusion supposedly occurs, the chromosomes appear to be physically
> identical. Problem here is which direction to go in giving value to
> the similarities.
>
> If the similarities mean that both human chromosome 2 and chimps
> chromosomes 2a and b will produce biological similarities, then what
> is there to choose from, selection wise, in order to give the
> advantage to Chromosome 2 in humans?
>
> But if, as research reveals (as recently as February, 2005),
> recombination hot spots on human chromosome 21, supposedly orthologous
> to chimp chromosome 22, are 83% different, and 17% similar -- then
> even though human Chromosome 2 and Chimp Chromosomes 2a and b appear
> to be almost identical, this apparent similarity may not be real after
> all.
>
> See:
>
> http://www.admin.ox.ac.uk/po/050214.shtml

I really don't understand why you take this the way you do. As the press
release says, this doesn't mean the genomes are different. It means that
the location of recombination is under the control of some mechanism
that doesn't depend on the DNA sequence at that location. The DNA is
still 99% identical.

>>>Can you take it from there? What's the pathway? At this point, can
>>>the chimp ancestor still interbreed with either the common ancestor or
>>>with the human ancestor? It has to interbreed with something in order
>>>to produce more offspring after its own kind, so where does the
>>>partner come from?
>>>
>>
>>Most evolutionists hold that most speciation events are "allopatric,"
>>meaning that they occur *after* the ancestral population has split into two
>>groups that could interbreed if they met, but which no longer meet up.
>>Afterwards, mutation, genetic drift, and selection to different environments
>>gradually change the populations into different species. No particular
>>mutation (unless you count polyploidy) is likely to produce a new species.
>>A better (though still oversimplified) approach would be to think of a
>>whole series of mutations, some beneficial, most neutral (but they still
>>made us different from chimps),
>
> no, no, no, you can't claim neutral mutations as changes that make us
> different from chimps. If humans become different, it would be
> because change (or mutation, as you call it) has occurred. No change,
> no difference. Neutral "mutations" cannot be counted to make a
> difference between humans and chimps. So once again you are left with
> trying to have the rare "beneficial" mutation carry the entire weight
> of your evolutionary theory.

This depends on what you mean by "different". If you're talking about
that 1% difference in DNA sequence, then most of it is due to neutral
mutations. If you're talking about the differences in morphology, well
of course most of those neutral mutations have nothing to do with that,
and it must be the relatively few beneficial mutations that are mostly
responsible. (I'm hedging here because it's entirely possible for a
mutation with a phenotypic effect to be neutral too.)

>>that each made the bearer a tiny bit more
>>"human" (or, in the other lineage, a tiny bit more "chimp"). No single
>>gene would have made its bearer much different from other members of his
>>species, or unable to interbreed with them.
>
> in which case, selection has nothing to work on, does it?

Wrong. Selection works on individual variation within species, and it
can easily work on small differences. Big changes cana result from the
accumulation over time of little changes.

>>It doesn't seem likely that a modern human could (or at least would)
>>interbreed with a modern chimp, but presumably five million years ago, our
>>ancestors were just a tiny bit more "human" than the ancestors of modern
>>chimps.
>
>
> how can a life form be a tiny bit more human before it becomes human?

How can it not? I don't understand your objection here. We're talking
about intermediates. Do you deny even the logical possibility of
intermediate forms?

>> They probably could have produced fertile offspring with the chimp
>>ancestors, but as noted, they lived in different parts of Africa and no
>>longer met.
>
>
> I note the use of "probably" here.

Yes. That's because we don't know, and have no way of ever knowing,
exactly when reproductive isolatio evolved between the two lineages.

Zoe

unread,
Jul 24, 2005, 11:35:53 PM7/24/05
to
On Sun, 24 Jul 2005 00:59:10 -0500, "Steven J."
<sjt195...@nts.link.net.INVALID> wrote:

I see. I suppose that's a good speculative answer but not
sufficiently scientific to hang an evolutionary cap upon. Call it a
neutral position -- makes no difference one way or the other.

see:

http://genomebiology.com/researchnews/default.asp?arx_id=gb-spotlight-20040528-01

Begin quote:

'Sakaki said their analysis found about 68,000 insertions or
deletions. "That is almost one insertion/deletion every 470 bases," he
said. In addition, a small proportion of genes showed a relatively
higher rate of evolution than most other genes. "We haven't known what
proportion of the genes shows adaptive evolution. This study shows it
to be about 2 to 3%," he said.

'Early molecular comparisons between humans and chimpanzees suggested
that the species are very similar to each other at the nucleotide
sequence level - a difference of between 1.23% and 5%, Sakaki said.
The results reported this week showed that "83% of the genes have
changed between the human and the chimpanzee - only 17% are identical
- so that means that the impression that comes from the 1.2%
[sequence] difference is [misleading]. In the case of protein
structures, it has a big effect," Sakaki said.'

End quote.

I recognize that this is written from an evolutionary point of view,
so expect to find attempts to explain the differences in terms of
change and loss or gain. But, really now, if a difference between the
two is observed, there is nothing to say that the present difference
is a result of change over millions of years, or if the difference was
present from the time of origin.

Further in the article, Derek Wildman tries to hold onto the idea that
similarity must still mean relationship through a common ancestor, but
I'm betting that with further comparison between the chimp genome and
the human genome, this idea of relationship through a common ancestor
will continue to degrade.

> Suppose (these figures are illustrative only; do not
>assume they reflect actual measurements of the chromosome) that two
>chromosomes in different species have 100 genes each. Suppose each gene has
>300 nucleotides, and that for each gene two nucleotides differ between the
>two species. That would mean that on this chromosome, 100% of the genes are
>(slightly) different from their homologues in the other species, but that
>overall sequence similarity is over 99%.

Quoting further from the above link:

'Early molecular comparisons between humans and chimpanzees suggested
that the species are very similar to each other at the nucleotide
sequence level - a difference of between 1.23% and 5%, Sakaki said.
The results reported this week showed that "83% of the genes have
changed between the human and the chimpanzee - only 17% are identical
- so that means that the impression that comes from the 1.2%
[sequence] difference is [misleading]. In the case of protein
structures, it has a big effect," Sakaki said.'

End quote.

> But certainly minor differences in
>DNA sequence can produce major changes in function, and certainly genes by
>themselves do not determine everything that happens in an organism.

what are some other things, besides changes in genes, that are
suggested would cause the kind of changes in an organism that would
lead its population in a direction away from its old genus to a new
one?

>> It's like comparing the recipes for two cakes. They both use 99%
>> similar ingredients -- flour, sugar, butter, eggs. Does this
>> similarity mean that both cakes came from the same batter? Not
>> necessarily. Not even probably. The more reasonable assumption is
>> that both cakes were created in their own right, from different
>> recipes, but using similar ingredients.
>>
>Actually, a sufficient similarity in composition (exact proportions of many
>minor ingredients) may strongly indicate origin from the same batter. At
>least, this line of reasoning is commonly used in forensic science for
>bullet fragments and dirt samples.

we do not have access to exact proportions in biology. In forensic
science, there is access to the original firearm and the original
source of dirt for comparison purposes. Not so in biology.

> But in any case, a closer analogy to DNA
>would be the exact wording of the recipes themselves -- especially if both
>recipes shared the same mispellings of the same words in the same order, and
>had bits of text that were alike but didn't seem to have anything to do with
>the actual recipe (like, e.g. the pseudogenes and endogenous retroviruses
>chimps and humans share).

recipes aren't available biologically so the analogy falls apart at
this point.

But, again, similarity is not sufficient to indicate relationship
through a common ancestor, as is being seen in in the latest
chimp/human genome comparisons.

>By the way, why is it more reasonable, even if we don't know for sure, to
>suppose that the cakes were created from different recipes and different
>batter?

because, from experience, we know that cakes come from different
batters. There is not one single grand clearing house of cake batter
from which all cakes come.

> Certainly a baker is capable of making one big batch of batter and
>making lots of cakes from it.

yes, but there is no single common source of batter to all cakes.

> And a Creator, I would suppose, is perfectly
>capable of making many species from a single ancestral population, as He
>made (according to the Bible) many nations from one original human
>population.

but we don't think that cakes and cars come from the same batter or
assembly line, do we? There is no one common source of material to
all categories of things, just as there is no one common ancestor to
all categories of life forms.

>>>By the way, although you didn't explicitly ask, the okapi (a rare,
>>>short-necked giraffe) species has individuals with 22 pairs of
>>>chromosomes,
>>>23 pairs, and even 22.5 pairs (for 45 chromosomes in all -- in which case
>>>two chromosomes from one parent must be paired with one -- fused --
>>>chromosome from the other parent).
>>
>> would you have references, by any chance, to studies that have
>> followed the interbreeding of these subspecies of opaki? Have they
>> tried to interbreed an opaki with 22 pairs of chromosomes with an
>> opaki that has 23 pairs of chromosomes? Or do opakis with 22 pairs of
>> chromosomes breed only with those that have 22 pairs of chromosomes,
>> and so on?
>>
>Okapis have no known subspecies; the variant chromosome numbers do not
>correspond to racial or habitat differences. And, apparently, they
>interbreed freely with okapis with different numbers of chromosomes and
>produce fertile offspring. Google turns up a few scholarly articles on
>"chromosomal polymorphism" in okapis and other species, and this appears, in
>okapis and some other species, to work like any other polymorphism (that is,
>it no more affects interbreeding than the difference between, say, type A
>and type O blood, or blue and brown eyes).

so these scholarly articles to which you refer, do they mention having
tested the chromosomes of known parents to known offspring and having
discovered that the chromosome counts differ in the parents? Or is
the testing randomly done, without checking to see if those opaki with
same chromosome counts might tend to be attracted to each other, or
whether different chromosome-count opakis tend to repel each other?

>>> So a mutation that produced the first
>>>human with a chromosome 2 (rather than the ancestral chromosomes 2a and
>>>2b)
>>>would not have prevented that individual from mating successfully.
>>
>> I'm not sure that that is a hard-and-fast conclusion, considering that
>> there is no evidence today that humans with chromosome 2 can
>> interbreed with chimps with chromosomes 2a and 2b. If they can't
>> today, why speculate that they could have at one time, unless you have
>> evidence that such a thing is possible?
>>
>There's no evidence that chimps with chromosomes 2a and 2b can interbreed
>with gorillas with chromosomes 2a and 2b. They've spent seven million years
>or more evolving in different directions (not just in obvious anatomical
>ways, but in more subtle ones). For all either of us knows, hominins (the
>human side of the human-chimp lineage) and panins (the chimp side) stopped
>being interfertile before the chromosome fusion happened in the hominin
>line. I doubt that chromosome number per se is much of a guide to
>interfertility.

so it's just guesswork here at this point?

>But again, horse subspecies with different numbers of chromosomes are
>interfertile. Okapis with a rather recent mutation that produced a fused
>chromosome are interfertile. I'm speculating that what is known to happen
>in several species today could have happened in other species at other
>times; it seems a safe enough speculation.

okay, it's still speculation. Moving on...

okay.

so are you saying that many members of Population B got hit by the
same rare benefit mutation, or are you saying that many members of
Population B result from a single member getting hit by the rare
beneficial mutation and passing it down to offspring?

And I take it that Population A must have been hit with some other
kind of rare beneficial mutation in order for it to begin to exhibit
characteristics of chimpness?

> Some
>individuals in either population will end up having no living descendants,
>but others will be the ancestor (if they're in population A) of every
>chimpanzee alive today), or (if they're in population B) of every human
>who's ever lived (and every Neanderthal, _Homo erectus_, australopith, and
>so on). There is no one single mutant individual who is the sole ancestor
>and cause of modern humans.

well, it has got to start with a single member, unless you are
proposing that the same rare beneficial mutation hits many members of
the population at the same time or within a certain time frame?

>> Okay, so focusing now on the human ancestor population:
>>
>> Human ancestor population (24chrm)
>> ______________________________ /??
>>
>> What happens at this point? A fusion occurs in a single individual in
>> this population, supposedly, right? I take it that the proposed rare
>> beneficial mutations do not hit several members of the population at
>> the same time? Otherwise they wouldn't be rare.
>>
>There's no reason to suppose the change was beneficial, rather than neutral.

it has to be beneficial, according to your theory, in order to get
selected. If it's neutral, there's nothing to select.

>There's been speculation that the change in chromosomal numbers was linked
>to the emergence of some distinctively human trait (e.g. bipedalism), but
>there's no evidence for that that I'm aware of. Again, note that
>differences in chromosome numbers seem to make no difference to okapis; it's
>simply another way individuals in a population can vary.
>
>Now, if you have a neutral mutation (one that makes an individual neither
>more nor less fit in that particular environment), then its survival in each
>generation is a matter of pure chance. Most neutral mutations presumably
>die out in short order, swamped by the more common (even if no better)
>alleles at that locus. But mathematical models show that, from time to
>time, by sheer dumb luck, a neutral mutation will become more and more
>common in each successive generation, until it completely replaces the
>original trait.

so the entire evolutionary framework consists of sheer dumb luck. Not
very scientific or predictable, is it?

>http://www.talkorigins.org/faqs/genetic-drift.html
>
>Humans and chimps have identical amino-acid sequences for the enzyme
>cytochrome-c, but the *genes* for cytochrome-c differ in one nucleotide
>between the two species (this is possible because there are multiple
>three-nucleotide codons for each amino acid). This is a "silent" mutation
>(one with no phenotypic effect), and surely neutral. It presumably
>originated as a mutation in one individual in one species, and just by sheer
>dumb luck spread through that species over hundreds of generations. This
>can also happen to traits that do make a difference, if the difference
>doesn't affect chances of reproductive success. Perhaps the spread of the
>fused chromosome was just a case of neutral drift.

"presumably" "perhaps" "speculated" "sheer dumb luck" "seem to"
"there's no evidence" "pure chance" -- sorry, Steven, but none of this
sounds very scientific. And these terms are used in connection with
the central core of your theory. How is this expected to command
respect from any thinking but undecided person? Gravity, which many
like to have placed in the same category as evolutionary theory, does
not consist of a series of maybes and perhapses.

>> Okay, so we now have a population of 24chrm members and one member's
>> chromosomes 2a and 2b fuse into a single chromosome, forming
>> chromosome 2 of the human ancestor's set of chromosomes.
>>
>> Supposedly, this 23chrm member of the 24chrm population can continue
>> to interbreed with the 24chrm members, producing offspring that may or
>> may not carry this 23chrm set. How does selection work in this case?
>> Has it been demonstrated that Chromosome 2 in humans makes them
>> distinctly different from apes, and gives them a distinct selective
>> advantage? If not, it would be predicted that 23chrm members of the
>> population would not necessarily increase but instead, as, they
>> continue to interbreed, the 24chrm members will dominate because they
>> are more in abundance, and the supposedly advantageous and distinct
>> Chromosome 2 will die out and be lost to the population.
>>
>As noted, this happens most of the time, with most neutral mutations, but
>every so often you get an exception. Flip enough coins enough times, and
>sooner or later one will come up "heads" over and over and over.

your whole theory is built upon the flip of the coin. Still not a
scientific approach.

>> That would be one scenario. There's another. Looking at comparisons
>> of human chromosome 2 and chimp chromosomes 2a and b, except for where
>> the fusion supposedly occurs, the chromosomes appear to be physically
>> identical. Problem here is which direction to go in giving value to
>> the similarities.
>>
>> If the similarities mean that both human chromosome 2 and chimps
>> chromosomes 2a and b will produce biological similarities, then what
>> is there to choose from, selection wise, in order to give the
>> advantage to Chromosome 2 in humans?
>>
>Maybe nothing. Not all evolution is the result of natural selection.

but natural selection is a biggie, isn't it? What's left?

> And
>there are problems with describing selection pressures on populations
>millioins of years ago.

of course there are. So why the strident, dogmatic stance of so many
posters on TO -- excluding you, of course.

> There's a lot that isn't known about how genes
>interact with each other and the environment to build an organism, and it's
>hard to say what the effect would be. Even if we could say what the effect
>would be, there's still the problem of figuring out why it would be
>advantageous (there are several competing theories of why bipedalism, or
>larger brains, or thinning body hair, would benefit our ancestors).

thank you for a fair and impartial answer.

>> But if, as research reveals (as recently as February, 2005),
>> recombination hot spots on human chromosome 21, supposedly orthologous
>> to chimp chromosome 22, are 83% different, and 17% similar -- then
>> even though human Chromosome 2 and Chimp Chromosomes 2a and b appear
>> to be almost identical, this apparent similarity may not be real after
>> all.
>>
>> See:
>>
>This article discusses differences between human and chimp chromosomes in
>where "crossovers" (e.g. the two copies of chromosome 22 switching parts
>with each other) take place. I explained above why having 83% of genes
>different is compatible with having 99% of DNA sequences identical. I don't
>see any reference to "83%" in the article, but if it refers to "hotspots,"
>rather than to genes or nucleotides, then I still don't see why this is
>incompatible with either 99% sequence identity between genes, or with
>virtually identical functions for genes. Presumably, the differences that
>produce different "hotspots" are small, local changes in noncoding DNA
>(which affect where the chromosome is likely to break apart during mating,
>not how the genes themselves work), not in the genes themselves.

see the link above.

and selection works with phenotypic effect, I take it?

> But a change can produce a quite
>marked effect, and still be "neutral" (that is, can make reproductive
>success in the given environment neither more nor less likely).

I didn't think that is what was meant by neutral mutations. There are
two definitions that I see so far, used by evolutionists:

1) A mutation that has no effect on the Darwinian fitness of its
carriers.
2) A mutation that has no phenotypic effect.

Where is the "marked effect" in the above understanding of neutral
mutations?

> There are
>two vireo (a type of bird) species that humans can easily tell apart only by
>eye color. There's no reason to suppose that one eye color is better than
>the other for the birds, but the difference distinguishes the two species.

wait a minute. Does difference in eye color alone make a new species?
Then a blue-eyed human is a different species from a brown-eyed human?

>Of course, the change might be beneficial in one population, because of
>sexual selection (female fashion-consciousness), but that's not quite the
>same thing as getting food more easily, avoiding becoming food, or fighting
>off infections better. Quite possibly some of the differences between
>humans and chimps were sexually rather than "naturally" selected.

add "quite possibly" to the dictionary of evolutionary theory. So far
nothing scientific. What is scientific is the actual data. The
theory proposed in regard to the data, however, being based on maybes
and possiblies, is not scientific.

>As argued above, the change in chromosome number was quite possibly a
>"neutral" change, although it is clearly one of the differences between us
>and chimps. Note that something like 90% of the genome is neither genes nor
>regulatory sequences.

it would be expected that more than 90% of a cell's chromosomes (the
genome) would have its genes turned off and unrecognizable as genes
since only 3% or so of each cell's chromosomes have genes turned on to
code for the protein making of that particular cell type. This does
not mean that the noncoding material is junk. It just is not used for
that particular cell's purpose. And I would expect that when not
actively in use, the potential for gene formation sits around looking
for all the world like junk.

> A lot of the 100 million or so differences between
>the human and chimp genomes almost certainly don't make any difference that
>matters to us -- they are "information" if you're looking for differences
>between human and chimp genomes, but if you're looking for "what makes us
>human," they aren't "information" in whatever sense it is that creationists
>have in mind when they speak of "new information."

I'm not following you here.

>>> that each made the bearer a tiny bit more
>>>"human" (or, in the other lineage, a tiny bit more "chimp"). No single
>>>gene would have made its bearer much different from other members of his
>>>species, or unable to interbreed with them.
>>
>> in which case, selection has nothing to work on, does it?
>>
>Again, mathematical models suggest that very small differences in "fitness"
>can give a trait a big advantage over time.

"small differences" aren't the same as neutral differences, are they?

> So, for that matter, do actual
>observations of microevolution in the wild: Grant's finches on the Galapagos
>had small differences in beak size and shape that hardly made them different
>species, or even different subspecies -- but made a real difference in
>fitness.
>>
>>>It doesn't seem likely that a modern human could (or at least would)
>>>interbreed with a modern chimp, but presumably five million years ago, our
>>>ancestors were just a tiny bit more "human" than the ancestors of modern
>>>chimps.
>>
>> how can a life form be a tiny bit more human before it becomes human?
>>
>I said "human" in scare quotes. Maybe their brains were a trifle larger.
>Maybe they walked erect a little more often and more easily. Maybe they
>just had that silent mutation in the cytochrome-c gene (if a human had a
>mutation that reversed that change, we wouldn't regard that person as less
>human, of course, which is why I put "human" in scare quotes). The point
>is, some of their evolutionary changes had made their genes (and probably,
>if we looked closely enough, their bodies) a bit more like ours.

add "maybe" and scare quotes to the lexicon.

>>> They probably could have produced fertile offspring with the chimp
>>>ancestors, but as noted, they lived in different parts of Africa and no
>>>longer met.
>>
>> I note the use of "probably" here.
>>
>Well, yes.

thank you.

Zoe

unread,
Jul 24, 2005, 11:47:53 PM7/24/05
to

the shape of the phylogenetic tree is a subjective one, based on the
subjective opinions of the taxonomist and cladist, right?

> Since we know the tree (i.e. that chimps,
>gorillas, orangutans, and gibbons are successively less closely related
>to humans),

isn't this what is called assuming your conclusion? You say,
authoritatively, We know that these creatures are successively less
closely related to humans. How do we know this? By our phylogenetic
tree that we have subjectively made up.

> we know what came first. Either 24 pairs came first (and
>humans evolved 23), or chimps, gorillas, orangutans, and gibbons all
>evolved 24 pairs independently from an ancestor with 23 pairs. Which
>makes more sense to you?

if I were forced to embrace evolutionary theory, I would have to say
that fusion makes more sense than fission. But fission is just as
plausible within the evolutionary framework in which many life forms
emerge from a single common ancestor.


>
>>>Second, while all
>>>chromosomes have a centromere in the center and telomeres at the end, human
>>>chromosome two has a vestigial centromere and telomere embedded in the
>>>chromosome itself, suggesting that it was formed by a fusion of two
>>>chromosomes. Indeed, there are two separate chromosomes in chimps that are
>>>very similar in sequence to two "halves" of human chromosome 2.
>>
>> this would appear, on its surface, to be a more convincing reason to
>> conclude that humans and chimps have a common ancestor (though you
>> have not yet addressed how fusion affects fertility or the parallel
>> meaning, if any, attached to chromosome fusion in mice.)
>
>Parallel meaning?

if chromosome fusion is used as evidence of a split from a common
ancestor population, does chromosome fusion in mice also represent a
split from a common ancestor population, especially as mice and humans
are almost identical in their genetic makeup, as well?

>Fusion doesn't affect fertility very much, and in some
>cases it doesn't affect it at all. How's that?

too vague.

>> That said, the latest evidence in genome comparison between chimps and
>> humans reveal an 83% difference between chimp chromosome 22 and human
>> chromosome 21 (chimp chromosome 22 is said to be the ortholog of human
>> chromosome 21.)
>
>I'm afraid you will have to tell us where you got that number, and what
>it means. You have misunderstood something seriously, but I don't know
>what. Ah, looking below I find you do tell us. The 83% difference is in
>the location of recombination hot spots, not sequence. This would be a
>very silly measure of genetic difference. In fact, as the press release
>says, it doesn't seem to involve genetic differences at all. The DNA
>sequence itself is still 99% identical.

See:

http://genomebiology.com/researchnews/default.asp?arx_id=gb-spotlight-20040528-01

>> And even though there appears to be 99% similarity
>> between the DNA of humans and chimps, the recombination hot spots have
>> turned out to be almost completely different. Apparently, then, DNA
>> sequences, even though highly similar, do not determine biological
>> function.
>
>Now that's a bundle of non sequiturs. Explain what you think you mean by
>that. Of course they determine biological function. What they apparently
>don't do is determine the sites at which recombination happens. That's
>one biological function, not "biological function".

bring this up again AFTER reading the above link.

>> It's like comparing the recipes for two cakes. They both use 99%
>> similar ingredients -- flour, sugar, butter, eggs. Does this
>> similarity mean that both cakes came from the same batter? Not
>> necessarily. Not even probably. The more reasonable assumption is
>> that both cakes were created in their own right, from different
>> recipes, but using similar ingredients.
>
>This analogy has nothing at all to do with the similarity of DNA.
>Further, the major evidence for common descent is not mere similarity,
>but (have you heard this before?) nested hierarchy. Cakes just don't
>display any such thing.

every analogy breaks down sooner or later.

>>>By the way, although you didn't explicitly ask, the okapi (a rare,
>>>short-necked giraffe) species has individuals with 22 pairs of chromosomes,
>>>23 pairs, and even 22.5 pairs (for 45 chromosomes in all -- in which case
>>>two chromosomes from one parent must be paired with one -- fused --
>>>chromosome from the other parent).
>>
>> would you have references, by any chance, to studies that have
>> followed the interbreeding of these subspecies of opaki? Have they
>> tried to interbreed an opaki with 22 pairs of chromosomes with an
>> opaki that has 23 pairs of chromosomes? Or do opakis with 22 pairs of
>> chromosomes breed only with those that have 22 pairs of chromosomes,
>> and so on?
>>
>>> So a mutation that produced the first
>>>human with a chromosome 2 (rather than the ancestral chromosomes 2a and 2b)
>>>would not have prevented that individual from mating successfully.
>>
>> I'm not sure that that is a hard-and-fast conclusion, considering that
>> there is no evidence today that humans with chromosome 2 can
>> interbreed with chimps with chromosomes 2a and 2b. If they can't
>> today, why speculate that they could have at one time, unless you have
>> evidence that such a thing is possible?
>
>Check out the mice, the shrews, and other species in which chromosomal
>fusions are within-population polymorphisms.

have they checked the parents of particular offspring and found that
different-numbered genomes were able to interbreed? Or did they
simply test various members, found that some have a certain number
chromosome count, and others a different count, and assumed that
different counts could interbreed?

>>>Or, take
>>>the case of Przewalski's horse and the domestic horse: domestic horses, like
>>>their human breeders, have one fewer chromosome pairs than their wild
>>>ancestors, due, apparently, to a chromosomal fusion -- but domestic and
>>>Przewalski's horses can still interbreed to produce fertile offspring. In
>>>other cases (e.g. "chromosomal races" of mice), having different chromosome
>>>numbers reduces interfertility.
>>
>> if you are comparing the horse scenario to the human/chimp scenario,
>> you would need to explain why the domestic horse can still breed
>> successfully with their wild ancestor, the Przewalski horse, and yet
>> humans cannot breed with their supposed wild ancestor, the ape.
>
>Przewalski's horse is not the ancestor of domestic horses. It's a close
>relative.

well, Steven called it "ancestors." Could you and he come to some
agreement?

>The factors that allow or prevent interbreeding are complex,
>but simple length of time apart is one of them.

so would your theory predict that the Chinese race, living apart from
the Indian race, would eventually, over time, evolve the inability to
interbreed?

no, this is not a tree. This is the beginning of what could be a
tree. I'm waiting for you to tell me how this tree grows.

>
>> Chimp ancestor population (24chrm)
>> common ancestor (24 chrm) /_____________________
>> ___________________________/
>> \
>> \
>> Human ancestor population (24chrm)
>>
>> At this point, there is as yet no change in the genetic makeup of
>> either the chimp ancestor population or the human ancestor population.
>> The only change is in geographical location which prevents Population
>> A (containing a potential chimp ancestor) from interbreeding with
>> Population B (containing a potential human ancestor).
>>
>> Right so far?
>>
>> Okay, so focusing now on the human ancestor population:
>>
>> Human ancestor population (24chrm)
>> ______________________________ /??
>>
>> What happens at this point? A fusion occurs in a single individual in
>> this population, supposedly, right? I take it that the proposed rare
>> beneficial mutations do not hit several members of the population at
>> the same time? Otherwise they wouldn't be rare.
>
>Right. But nobody says this fusion is beneficial, and nobody says it's
>the first difference to become fixed in the human lineage.

so now evolutionary theory proposes that life forms evolve, not only
from selected beneficial mutations, but from harmful and/or neutral
mutations?

>> Okay, so we now have a population of 24chrm members and one member's
>> chromosomes 2a and 2b fuse into a single chromosome, forming
>> chromosome 2 of the human ancestor's set of chromosomes.
>>
>> Supposedly, this 23chrm member of the 24chrm population can continue
>> to interbreed with the 24chrm members, producing offspring that may or
>> may not carry this 23chrm set. How does selection work in this case?
>> Has it been demonstrated that Chromosome 2 in humans makes them
>> distinctly different from apes, and gives them a distinct selective
>> advantage?
>
>No. There's no reason to suppose it does.

so how does your mechanism of selected beneficial mutation work then?
If chromosome2 is the main piece of evidence that chimps and humans
come from a common ancestor, and yet this piece of evidence makes no
difference in the life form containing the fusion, what is there to
select?

>> If not, it would be predicted that 23chrm members of the
>> population would not necessarily increase but instead, as, they
>> continue to interbreed, the 24chrm members will dominate because they
>> are more in abundance, and the supposedly advantageous and distinct
>> Chromosome 2 will die out and be lost to the population.
>
>You need to read up on genetic drift. Chromosomal mutations happen with
>a certain frequency. Most are lost. By chance, a few increase in
>frequency and eventually become fixed. This could easily be such a case.

saying so doesn't make it so. Where's Deadrat when I need him. Maybe
he could draw up a mathematical formula that will demonstrate how
chance "beneficial" mutations that make no difference can get selected
for.

snip>

>>>It doesn't seem likely that a modern human could (or at least would)
>>>interbreed with a modern chimp, but presumably five million years ago, our
>>>ancestors were just a tiny bit more "human" than the ancestors of modern
>>>chimps.
>>
>>
>> how can a life form be a tiny bit more human before it becomes human?
>
>How can it not? I don't understand your objection here. We're talking
>about intermediates. Do you deny even the logical possibility of
>intermediate forms?

intermediate forms between an apple and a carrot? No. Intermediate
forms between a carrot and a snail? No. Intermediate forms between
a dinosaur and a bird? No.

>>> They probably could have produced fertile offspring with the chimp
>>>ancestors, but as noted, they lived in different parts of Africa and no
>>>longer met.
>>
>>
>> I note the use of "probably" here.
>
>Yes. That's because we don't know, and have no way of ever knowing,
>exactly when reproductive isolatio evolved between the two lineages.

I'm not asking for when it happened, but how it happened. So far, no
steps have been given other than probabilities and maybes.

John Harshman

unread,
Jul 25, 2005, 1:02:59 AM7/25/05
to
Zoe wrote:

No. You have been told about this before, but you never seem to listen.

>>Since we know the tree (i.e. that chimps,
>>gorillas, orangutans, and gibbons are successively less closely related
>>to humans),
>
> isn't this what is called assuming your conclusion? You say,
> authoritatively, We know that these creatures are successively less
> closely related to humans. How do we know this? By our phylogenetic
> tree that we have subjectively made up.

It's not subjective. We've been over this before.

>>we know what came first. Either 24 pairs came first (and
>>humans evolved 23), or chimps, gorillas, orangutans, and gibbons all
>>evolved 24 pairs independently from an ancestor with 23 pairs. Which
>>makes more sense to you?
>
> if I were forced to embrace evolutionary theory, I would have to say
> that fusion makes more sense than fission. But fission is just as
> plausible within the evolutionary framework in which many life forms
> emerge from a single common ancestor.

That makes no sense.

>>>>Second, while all
>>>>chromosomes have a centromere in the center and telomeres at the end, human
>>>>chromosome two has a vestigial centromere and telomere embedded in the
>>>>chromosome itself, suggesting that it was formed by a fusion of two
>>>>chromosomes. Indeed, there are two separate chromosomes in chimps that are
>>>>very similar in sequence to two "halves" of human chromosome 2.
>>>
>>>this would appear, on its surface, to be a more convincing reason to
>>>conclude that humans and chimps have a common ancestor (though you
>>>have not yet addressed how fusion affects fertility or the parallel
>>>meaning, if any, attached to chromosome fusion in mice.)
>>
>>Parallel meaning?
>
> if chromosome fusion is used as evidence of a split from a common
> ancestor population, does chromosome fusion in mice also represent a
> split from a common ancestor population, especially as mice and humans
> are almost identical in their genetic makeup, as well?

Where do you get your ideas? The mice in question are all a single
species, with many partially isolated populations, whose boundaries
change over time. Mice and humans are not almost identical in their
genetic makeup. Mice differ from humans much more than chimpanzees do,
by any measure you care to name.

>>Fusion doesn't affect fertility very much, and in some
>>cases it doesn't affect it at all. How's that?
>
> too vague.

What else do you need?

>>>That said, the latest evidence in genome comparison between chimps and
>>>humans reveal an 83% difference between chimp chromosome 22 and human
>>>chromosome 21 (chimp chromosome 22 is said to be the ortholog of human
>>>chromosome 21.)
>>
>>I'm afraid you will have to tell us where you got that number, and what
>>it means. You have misunderstood something seriously, but I don't know
>>what. Ah, looking below I find you do tell us. The 83% difference is in
>>the location of recombination hot spots, not sequence. This would be a
>>very silly measure of genetic difference. In fact, as the press release
>>says, it doesn't seem to involve genetic differences at all. The DNA
>>sequence itself is still 99% identical.
>
>
> See:
>
> http://genomebiology.com/researchnews/default.asp?arx_id=gb-spotlight-20040528-01

I saw it. I have no idea what you think it means.

>>>And even though there appears to be 99% similarity
>>>between the DNA of humans and chimps, the recombination hot spots have
>>>turned out to be almost completely different. Apparently, then, DNA
>>>sequences, even though highly similar, do not determine biological
>>>function.
>>
>>Now that's a bundle of non sequiturs. Explain what you think you mean by
>>that. Of course they determine biological function. What they apparently
>>don't do is determine the sites at which recombination happens. That's
>>one biological function, not "biological function".
>
>
> bring this up again AFTER reading the above link.

I read it already. What do you think it means?


>>>It's like comparing the recipes for two cakes. They both use 99%
>>>similar ingredients -- flour, sugar, butter, eggs. Does this
>>>similarity mean that both cakes came from the same batter? Not
>>>necessarily. Not even probably. The more reasonable assumption is
>>>that both cakes were created in their own right, from different
>>>recipes, but using similar ingredients.
>>
>>This analogy has nothing at all to do with the similarity of DNA.
>>Further, the major evidence for common descent is not mere similarity,
>>but (have you heard this before?) nested hierarchy. Cakes just don't
>>display any such thing.
>
>
> every analogy breaks down sooner or later.

Yours break down sooner rather than later.

The former. Of course, you understand that you can karyotype individuals
and find out if they are hybrids between different chromosome numbers.

>>>>Or, take
>>>>the case of Przewalski's horse and the domestic horse: domestic horses, like
>>>>their human breeders, have one fewer chromosome pairs than their wild
>>>>ancestors, due, apparently, to a chromosomal fusion -- but domestic and
>>>>Przewalski's horses can still interbreed to produce fertile offspring. In
>>>>other cases (e.g. "chromosomal races" of mice), having different chromosome
>>>>numbers reduces interfertility.
>>>
>>>if you are comparing the horse scenario to the human/chimp scenario,
>>>you would need to explain why the domestic horse can still breed
>>>successfully with their wild ancestor, the Przewalski horse, and yet
>>>humans cannot breed with their supposed wild ancestor, the ape.
>>
>>Przewalski's horse is not the ancestor of domestic horses. It's a close
>>relative.
>
>
> well, Steven called it "ancestors." Could you and he come to some
> agreement?

Possibly.

>>The factors that allow or prevent interbreeding are complex,
>>but simple length of time apart is one of them.
>
>
> so would your theory predict that the Chinese race, living apart from
> the Indian race, would eventually, over time, evolve the inability to
> interbreed?

If that were true, then yes it would. However, no human population has
ever been that isolated. There is no Chinese race and no Indian race,
just clinal variation from one point to another.

Your diagram communicates nothing to me.

>>> Chimp ancestor population (24chrm)
>>>common ancestor (24 chrm) /_____________________
>>>___________________________/
>>> \
>>> \
>>> Human ancestor population (24chrm)
>>>
>>>At this point, there is as yet no change in the genetic makeup of
>>>either the chimp ancestor population or the human ancestor population.
>>>The only change is in geographical location which prevents Population
>>>A (containing a potential chimp ancestor) from interbreeding with
>>>Population B (containing a potential human ancestor).
>>>
>>>Right so far?
>>>
>>>Okay, so focusing now on the human ancestor population:
>>>
>>>Human ancestor population (24chrm)
>>>______________________________ /??
>>>
>>>What happens at this point? A fusion occurs in a single individual in
>>>this population, supposedly, right? I take it that the proposed rare
>>>beneficial mutations do not hit several members of the population at
>>>the same time? Otherwise they wouldn't be rare.
>>
>>Right. But nobody says this fusion is beneficial, and nobody says it's
>>the first difference to become fixed in the human lineage.
>
> so now evolutionary theory proposes that life forms evolve, not only
> from selected beneficial mutations, but from harmful and/or neutral
> mutations?

Yes. Does that come as a surprise? Harmful mutations are of course
eliminated, unless they're so slightly harmful as to be effectively neutral.

>>>Okay, so we now have a population of 24chrm members and one member's
>>>chromosomes 2a and 2b fuse into a single chromosome, forming
>>>chromosome 2 of the human ancestor's set of chromosomes.
>>>
>>>Supposedly, this 23chrm member of the 24chrm population can continue
>>>to interbreed with the 24chrm members, producing offspring that may or
>>>may not carry this 23chrm set. How does selection work in this case?
>>>Has it been demonstrated that Chromosome 2 in humans makes them
>>>distinctly different from apes, and gives them a distinct selective
>>>advantage?
>>
>>No. There's no reason to suppose it does.
>
>
> so how does your mechanism of selected beneficial mutation work then?
> If chromosome2 is the main piece of evidence that chimps and humans
> come from a common ancestor, and yet this piece of evidence makes no
> difference in the life form containing the fusion, what is there to
> select?

Chromosome 2 is by no means the main piece of evidence. And nobody says
that the fusion was selected.

>>>If not, it would be predicted that 23chrm members of the
>>>population would not necessarily increase but instead, as, they
>>>continue to interbreed, the 24chrm members will dominate because they
>>>are more in abundance, and the supposedly advantageous and distinct
>>>Chromosome 2 will die out and be lost to the population.
>>
>>You need to read up on genetic drift. Chromosomal mutations happen with
>>a certain frequency. Most are lost. By chance, a few increase in
>>frequency and eventually become fixed. This could easily be such a case.
>
> saying so doesn't make it so. Where's Deadrat when I need him. Maybe
> he could draw up a mathematical formula that will demonstrate how
> chance "beneficial" mutations that make no difference can get selected
> for.

I'm telling you they don't get selected for, and they're not beneficial.
Drift, not selection. Neutral, not beneficial.

> snip>
>
>>>>It doesn't seem likely that a modern human could (or at least would)
>>>>interbreed with a modern chimp, but presumably five million years ago, our
>>>>ancestors were just a tiny bit more "human" than the ancestors of modern
>>>>chimps.
>>>
>>>
>>>how can a life form be a tiny bit more human before it becomes human?
>>
>>How can it not? I don't understand your objection here. We're talking
>>about intermediates. Do you deny even the logical possibility of
>>intermediate forms?
>
> intermediate forms between an apple and a carrot? No. Intermediate
> forms between a carrot and a snail? No. Intermediate forms between
> a dinosaur and a bird? No.

Well, of course the first two are silly. The third sort are found in
fair profusion in the fossil record, e.g. Archaeopteryx. But were were
talking about human ancestry, yes?

>>>>They probably could have produced fertile offspring with the chimp
>>>>ancestors, but as noted, they lived in different parts of Africa and no
>>>>longer met.
>>>
>>>
>>>I note the use of "probably" here.
>>
>>Yes. That's because we don't know, and have no way of ever knowing,
>>exactly when reproductive isolatio evolved between the two lineages.
>
>
> I'm not asking for when it happened, but how it happened. So far, no
> steps have been given other than probabilities and maybes.

That's because we will never, ever know the details. We see the results
of 6 million years of evolution in two lineages, and you're asking to
see the order in which all the many changes occurred. How would that
even be possible?

Steven J.

unread,
Jul 25, 2005, 2:33:57 AM7/25/05
to

"Zoe" <muz...@aol.com> wrote in message
news:4pm8e19ue3o131sju...@4ax.com...

> On Sun, 24 Jul 2005 00:59:10 -0500, "Steven J."
> <sjt195...@nts.link.net.INVALID> wrote:
>
I've snipped out older portions of our exchange, which can make this post a
bit confusing, but if we keep arguing this point without snipping out
anything, we're going to end up with posts the length of _Moby Dick_.
>
-- [snip]

>
>>No, parsimony rather than simple majority rule determines which (probably)
>>came first. "Parsimony," in this case, means accounting for the observed
>>pattern with the fewest postulated entities -- in this case, mutations.
>>If
>>the last common ancestor (LCA) of African apes had 23 chromosome pairs,
>>then
>>we need two mutations -- one to give the gorillas 24 pairs, and one to
>>give
>>the chimps 24 pairs -- to account for the observed distribution. If we
>>assume that the African ape LCA had 24 pairs, but the human-chimp LCA had
>>23
>>pairs, then we still need two mutations: one to reduce the number of pairs
>>after the human-chimp line splits from gorillas, and one to increase the
>>number of pairs in chimps after the human and chimp lines split. If we
>>assume that both the African ape and human-chimp LCA had 24 pairs, then we
>>need only one mutation to explain the difference (after the human-chimp
>>split). Of course, in some cases, parsimony will be *wrong* (nature
>>isn't,
>>as far as anyone knows, trying to keep mutations to a minimum), but it
>>seems
>>a good approximation most of the time.
>
> I see. I suppose that's a good speculative answer but not
> sufficiently scientific to hang an evolutionary cap upon. Call it a
> neutral position -- makes no difference one way or the other.
>
Note that molecular phylogeny uses the same techniques -- and many of the
same assumptions -- used in reconstructing "phylogenies" of, e.g. multiple
variant copies of the _Canterbury Tales_, or the gospels, or chain letters.
I would think you would appreciate explanations that prefer the fewest
number of assumptions about unobserved events.
>
-- [snip]

>
>>When you say "83% difference," I'm not sure what you mean. If you mean
>>that
>>83% of the genes have at least one nucleotide different between the two
>>species, that is perfectly consistent with a 99% sequence similarity
>>between
>>the two chromosomes.
>
> see:
>
> http://genomebiology.com/researchnews/default.asp?arx_id=gb-spotlight-20040528-01
>
> Begin quote:
>
> 'Sakaki said their analysis found about 68,000 insertions or
> deletions. "That is almost one insertion/deletion every 470 bases," he
> said. In addition, a small proportion of genes showed a relatively
> higher rate of evolution than most other genes. "We haven't known what
> proportion of the genes shows adaptive evolution. This study shows it
> to be about 2 to 3%," he said.
>
Now, if my math can be trusted, one insertion/deletion every 470 bases
amounts to a bit over one-fifth of one percent difference. If there are no
other differences in the genes besides those mentioned, then sequence
similarity between genes (as opposed to noncoding sequences) would be
something like 99.75%. Note that the authors distinguish between "adaptive
evolution" ("beneficial mutations") and, presumably, evolution that isn't
adaptive. If I'm reading this right, about 83% of the genes show *some*
difference (perhaps only one or two nucleotides altered), and about 3% of
genes show differences that resulted from beneficial mutations spreading
through natural selection, and the rest show differences that are inferred
to have arisen through neutral mutations that drifted to fixation. Of
course, this summary does not enable me to determine how they decided which
changes were adaptive and which were not.

>
> 'Early molecular comparisons between humans and chimpanzees suggested
> that the species are very similar to each other at the nucleotide
> sequence level - a difference of between 1.23% and 5%, Sakaki said.
> The results reported this week showed that "83% of the genes have
> changed between the human and the chimpanzee - only 17% are identical
> - so that means that the impression that comes from the 1.2%
> [sequence] difference is [misleading]. In the case of protein
> structures, it has a big effect," Sakaki said.'
>
Again, the point is not that the sequence similarity is smaller than
previous estimates had made it, much less that the evidence for human-chimp
common ancestry is weaker than had previously been thought. Rather, the
point is that 1% sequence difference doesn't mean that only 1% of genes are
different (in principle, one could make a 1% difference in 100% of the
genes, or that the differences produce only a 1% difference in phenotype.
There's an analogy offered by some creationist sites: the sentences "All
competent biologists accept common descent" and "Not all competent
biologists accept common descent" have very high sequence similarity, but
opposite meanings. But the analogy works better for evolutionists:
obviously, one of those sentences is a modified copy of the other, and they
show how minor modifications can at once reveal common ancestry and produce
large changes.

>
> End quote.
>
> I recognize that this is written from an evolutionary point of view,
> so expect to find attempts to explain the differences in terms of
> change and loss or gain. But, really now, if a difference between the
> two is observed, there is nothing to say that the present difference
> is a result of change over millions of years, or if the difference was
> present from the time of origin.
>
If all we had to study were humans and chimps, that would be more or less
true (although that vestigial centromere and telomere on chromosome 2 is
still very suggestive). But the strongest evidence for common descent is
not similarities between any two species, but the *nested hierarchy* of
similarities and differences for the huge number of known species.

If we had only two variant copies of some ancient manuscript, perhaps both
came from the hand of the original author, who revised his own first draft
slightly. But when we have dozens of copies, which naturally fall into
groups (sharing many similar readings), falling into larger groups (united
by a smaller number of readings shared by all the manuscripts in the larger
group) and so on, the idea that the original author didn't produce all these
copies, but that they were introduced gradually by different copyists at
different times, would become irresistable (especially if we already knew
about copyists and their errors).

Likewise, we know about mutations in living populations, and about the
nested hierarchies of related populations into which living species fall.
The overall pattern of life is simply a larger-scale version of the pattern
we see in populations *known* to be produced by common descent with
modification, whether cattle or silkworms or humans (or, for that matter,
families of languages and manuscripts).


>
> Further in the article, Derek Wildman tries to hold onto the idea that
> similarity must still mean relationship through a common ancestor, but
> I'm betting that with further comparison between the chimp genome and
> the human genome, this idea of relationship through a common ancestor
> will continue to degrade.
>

It has not "degraded" yet, so if it "degrades" in the future this will not
be a continuation of current trends. Noting that a lot of genes differ
between humans and chimps does not mean that the differences are at all
difficult to explain in terms of mutation and selection or drift, or even
that the number is greater than the theory of evolution (as opposed to
mathematically naive intuition) would lead us to expect.


>
>> Suppose (these figures are illustrative only; do not
>>assume they reflect actual measurements of the chromosome) that two
>>chromosomes in different species have 100 genes each. Suppose each gene
>>has
>>300 nucleotides, and that for each gene two nucleotides differ between the
>>two species. That would mean that on this chromosome, 100% of the genes
>>are
>>(slightly) different from their homologues in the other species, but that
>>overall sequence similarity is over 99%.
>
> Quoting further from the above link:
>
> 'Early molecular comparisons between humans and chimpanzees suggested
> that the species are very similar to each other at the nucleotide
> sequence level - a difference of between 1.23% and 5%, Sakaki said.
> The results reported this week showed that "83% of the genes have
> changed between the human and the chimpanzee - only 17% are identical
> - so that means that the impression that comes from the 1.2%
> [sequence] difference is [misleading]. In the case of protein
> structures, it has a big effect," Sakaki said.'
>
> End quote.
>

Zoe, the quoted passage and my own paragraph above do not contradict each
other in any respect. As noted above, "there is a 1.2% sequence difference"
is not the same thing as "1.2% of *genes* are different" -- 1.2% sequence
difference could mean that every single gene is, on average, 1.2% different
(which might produce no effects, or very profound effects, or about anything
in between), or it could mean that 1.6% of genes are 75% different from each
other, or some figure in between.


>
>> But certainly minor differences in
>>DNA sequence can produce major changes in function, and certainly genes by
>>themselves do not determine everything that happens in an organism.
>
> what are some other things, besides changes in genes, that are
> suggested would cause the kind of changes in an organism that would
> lead its population in a direction away from its old genus to a new
> one?
>

My point was that DNA, by itself, does nothing; only when combined with the
effects of the environment (which, for a gene, includes other genes, along
with ribosomes and other cellular systems) do genes produce any effects at
all. Changes outside the genes, if they could be inherited in some way
(e.g. taught by parents rather than passed on through sex cells), could
affect the way genes build an organism, or the selective pressures on genes,
or both. For example, if some ape *learns* to use a new food source (that
is, its genes are no different from those of other members of its species
who don't eat that food), and teaches its children to do likewise, this
could free the apes from some selective pressures (they wouldn't need to
compete so hard for older food sources), and create new selective pressures
(e.g. modifications in the digestive tract or other anatomical features to
enable them to better use the new food source).
>
-- [snip]


>
>>Actually, a sufficient similarity in composition (exact proportions of
>>many
>>minor ingredients) may strongly indicate origin from the same batter. At
>>least, this line of reasoning is commonly used in forensic science for
>>bullet fragments and dirt samples.
>
> we do not have access to exact proportions in biology. In forensic
> science, there is access to the original firearm and the original
> source of dirt for comparison purposes. Not so in biology.
>

We only know that it is the "original" firearm, or the "original" source of
dirt, based on the same sort of argument that you reject for genomes.


>
>> But in any case, a closer analogy to DNA
>>would be the exact wording of the recipes themselves -- especially if both
>>recipes shared the same mispellings of the same words in the same order,
>>and
>>had bits of text that were alike but didn't seem to have anything to do
>>with
>>the actual recipe (like, e.g. the pseudogenes and endogenous retroviruses
>>chimps and humans share).
>
> recipes aren't available biologically so the analogy falls apart at
> this point.
>

In the analogy, genes (or rather genomes) *are* the recipes. Certainly
genomes are available biologically.


>
> But, again, similarity is not sufficient to indicate relationship
> through a common ancestor, as is being seen in in the latest
> chimp/human genome comparisons.
>

I don't think you understand the latest human/chimp genome comparisons.
And, again, the argument for common descent is not based simply on
human/chimp similarities, but on the consistent ways in which we are more
similar to chimps than either of us is to gorillas, and so forth throughout
the nested hierarchy of life.


>
>>By the way, why is it more reasonable, even if we don't know for sure, to
>>suppose that the cakes were created from different recipes and different
>>batter?
>
> because, from experience, we know that cakes come from different
> batters. There is not one single grand clearing house of cake batter
> from which all cakes come.
>

Okay, you don't buy junk food. Good for you.

But we *do* know that living things come from other living things, that
reproduction is not quite perfect, and that mutations, natural selection,
and drift cause populations to evolve over time. We *do* know that
consistent nested hierarchies of inheritable traits result from branching
descent with modification, whether we're talking about breeds of domestic
animals, or viruses, or languages, and hand-copied biblical texts. There is
ample reason to infer that the nested hierarchy of life reflects a series of
more or less remote common ancestors.


>
>> Certainly a baker is capable of making one big batch of batter and
>>making lots of cakes from it.
>
> yes, but there is no single common source of batter to all cakes.
>

To paraphrase your own argument above, cake batter isn't available
biologically, so your analogy falls apart at this point.


>
>> And a Creator, I would suppose, is perfectly
>>capable of making many species from a single ancestral population, as He
>>made (according to the Bible) many nations from one original human
>>population.
>
> but we don't think that cakes and cars come from the same batter or
> assembly line, do we? There is no one common source of material to
> all categories of things, just as there is no one common ancestor to
> all categories of life forms.
>

Zoe, if you follow that analogy far enough, it implies that there is no
common Creator to all categories of life forms. If you don't follow it that
far, why should you expect me to follow it to imply that there is no common
ancestor to all known taxa?
>
-- [snip]


>
>>Okapis have no known subspecies; the variant chromosome numbers do not
>>correspond to racial or habitat differences. And, apparently, they
>>interbreed freely with okapis with different numbers of chromosomes and
>>produce fertile offspring. Google turns up a few scholarly articles on
>>"chromosomal polymorphism" in okapis and other species, and this appears,
>>in
>>okapis and some other species, to work like any other polymorphism (that
>>is,
>>it no more affects interbreeding than the difference between, say, type A
>>and type O blood, or blue and brown eyes).
>
> so these scholarly articles to which you refer, do they mention having
> tested the chromosomes of known parents to known offspring and having
> discovered that the chromosome counts differ in the parents? Or is
> the testing randomly done, without checking to see if those opaki with
> same chromosome counts might tend to be attracted to each other, or
> whether different chromosome-count opakis tend to repel each other?
>

I don't think they mention checking actual parentage for any okapis. I
doubt very much that okapis can tell how many chromosome pairs another
okapi has, but the presence of several okapis with odd numbers of
chromosomes strongly implies mating between okapis with different numbers of
chromosomes, at least in the past.
>
-- [snip]


>
>>There's no evidence that chimps with chromosomes 2a and 2b can interbreed
>>with gorillas with chromosomes 2a and 2b. They've spent seven million
>>years
>>or more evolving in different directions (not just in obvious anatomical
>>ways, but in more subtle ones). For all either of us knows, hominins (the
>>human side of the human-chimp lineage) and panins (the chimp side) stopped
>>being interfertile before the chromosome fusion happened in the hominin
>>line. I doubt that chromosome number per se is much of a guide to
>>interfertility.
>
> so it's just guesswork here at this point?
>

On some points, yes, it's pretty much guesswork. Are you hoping to argue
that if scientists don't know everything, they can't know anything, or that
all aspects of hominid phylogeny must be equally speculative (rather than
some parts virtually certain and others, as you note, mere guesswork)? Is
there any area of historical reconstruction of which this is true? It seems
to me that it is quite common to have the broad outlines of historical
events firmly established and amply supported by evidence, while the fine
details are sketchy and often poorly evidenced. It is the same with human
evolution.


>
>>But again, horse subspecies with different numbers of chromosomes are
>>interfertile. Okapis with a rather recent mutation that produced a fused
>>chromosome are interfertile. I'm speculating that what is known to happen
>>in several species today could have happened in other species at other
>>times; it seems a safe enough speculation.
>
> okay, it's still speculation. Moving on...
>

By "a safe enough speculation" I meant that we know, from experience, that
differing chromosome numbers, by themselves, do not lower interfertility
(although different chromosome numbers, plus other genetic and chromosomal
changes, will do this), so there is no reason at all to suppose that the
first hominid with 23 chromosome pairs would have any problems mating with
hominids of the same species, but with 24 pairs.
>
-- [snip of longish section that you did not challenge]


>
>>Right, except that population A contains many potential (indeed, *actual*)
>>chimp ancestors, as population B contains many human ancestors.
>
> so are you saying that many members of Population B got hit by the
> same rare benefit mutation, or are you saying that many members of
> Population B result from a single member getting hit by the rare
> beneficial mutation and passing it down to offspring?
>

Zoe, suppose a mutant ape (call him "Harvey") is born, long ago in Africa.
Suppose one of Harvey's two copies of chromosome 2a fused with a copy of
chromosome 2b, to produce fused chromosome 2. Harvey has 47 chromosomes
(since it inherited 23 chromosomes, including the fused chromosome, only
from one parent, and the "normal" 24 chromosomes from the other). This
mutation may be beneficial in some way, or purely neutral. Harvey grows up
and sires many ape babies, some of whom inherit its fused chromosome (others
inherit the unfused version, so some of its kids have 48 chromosomes and
some have 47). This goes on for many generations, until a generation comes
along in which two descedants of Harvey (both of whom have, unlike some of
Harvey's descendants, inherited this fused chromosome) mate and produce an
offspring with *two* copies of the fused chromosome. This sort of thing
goes on for many, many, many generations.

If the fused chromosomes are actually beneficial (maybe Harvey and some of
his descendants are smarter than the average ape), then apes with one copy
of the fused chromosome will mate more often and have more surviving
children (especially if the children have inherited the chromosome), and the
fused chromosome will spread through the population rapidly (in geological
time). If it is merely a neutral change, then it will be unlikely to spread
through the population -- but "unlikely" does not mean it will never happen,
and in some cases neutral mutations, over hundreds of generations, do spread
through the entire population. If the fused chromosomes produce a
deleterious effect -- if Harvey is dumber or clumsier than the average
ape -- the the fused chromosome will most likely go extinct in a few
generations (maybe just one, if Harvey dies without surviving offspring).
But then, since the fused chromosome did survive, presumably it wasn't
detrimental.

It works much the same for any mutation. There's no need for it to occur in
many members of the population at once (although it may -- some mutations
recur over and over). Note that even though, in the scenario above, every
member of the descendant population inherits Harvey's mutation, they aren't
the descendants of Harvey alone. They are, at least, the descendants of the
non-mutant (or at least, not carrying *this* particular mutation) female(s)
who bore Harvey's offspring. They are descendants of the males and females
who mated with Harvey's kids and grandkids. They are, in short, descended
from many of Harvey's contemporaries, and inherit, probably, many genes from
those contemporaries, even if not one copy of the unfused chromosomes 2a and
2b from those contemporaries has been passed on (if you have children, you
probably have alleles they didn't inherit -- since each child inherits only
a random half of your genes -- but they're still 100% your descendants).


>
> And I take it that Population A must have been hit with some other
> kind of rare beneficial mutation in order for it to begin to exhibit
> characteristics of chimpness?
>

There is no need for this to happen when it first branched off from
population B, but yes, in time, presumably mutants with favorable mutations
were born in population A on many occasions, over millions of years. Note,
by the way, that humans exhibit many characteristics of "chimpness" (Jared
Diamond wrote a book about our species called _The Third Chimpanzee_ --
bonobos are the second chimpanzee), and the human/chimp LCA presumably was
more chimplike than we are already.


>
>> Some
>>individuals in either population will end up having no living descendants,
>>but others will be the ancestor (if they're in population A) of every
>>chimpanzee alive today), or (if they're in population B) of every human
>>who's ever lived (and every Neanderthal, _Homo erectus_, australopith, and
>>so on). There is no one single mutant individual who is the sole ancestor
>>and cause of modern humans.
>
> well, it has got to start with a single member, unless you are
> proposing that the same rare beneficial mutation hits many members of
> the population at the same time or within a certain time frame?
>

No single mutation made us human, or a different species from the parents of
the mutant. We are descended from many, many individuals, most of them
"mutants" in the sense that some portion of some gene they have is slightly
different from any gene of either of their parents.
>
-- [snip]


>
>>There's no reason to suppose the change was beneficial, rather than
>>neutral.
>
> it has to be beneficial, according to your theory, in order to get
> selected. If it's neutral, there's nothing to select.
>

True. But in a sexually reproducing population, since only half the genes
get passed on to any offspring, if an organism has ten offspring, any given
gene has roughly 1 chance in 1024 of not being passed on at all. Likewise
any given gene has the same chance of being passed on to all ten offspring.
That sounds like tiny odds -- but apes have ca. 25,000 genes. Now, over
time and in a large population, favorable mutations will tend to spread
despite this, but some neutral variations will die out, and others will
spread to fixation, just by "chance," or, as it is technically known,
genetic drift.


>
>>There's been speculation that the change in chromosomal numbers was linked
>>to the emergence of some distinctively human trait (e.g. bipedalism), but
>>there's no evidence for that that I'm aware of. Again, note that
>>differences in chromosome numbers seem to make no difference to okapis;
>>it's
>>simply another way individuals in a population can vary.
>>
>>Now, if you have a neutral mutation (one that makes an individual neither
>>more nor less fit in that particular environment), then its survival in
>>each
>>generation is a matter of pure chance. Most neutral mutations presumably
>>die out in short order, swamped by the more common (even if no better)
>>alleles at that locus. But mathematical models show that, from time to
>>time, by sheer dumb luck, a neutral mutation will become more and more
>>common in each successive generation, until it completely replaces the
>>original trait.
>
> so the entire evolutionary framework consists of sheer dumb luck. Not
> very scientific or predictable, is it?
>

No, neutral drift consists of sheer dumb luck, which is a very different
matter from natural selection. Evolutionary theory encompasses both,
although evolutionists argue among themselves as to which explains more
genetic change over time (hardly anyone disputes that natural selection
explains *adaptive* change, but not all change is adaptive). Note that
sheer dumb luck is quite predictable, which is why Las Vegas casinos manage
to stay in business, and quite scientific, which is why probability and
statistics exist as branches of mathematics.


>
>>http://www.talkorigins.org/faqs/genetic-drift.html
>>
>>Humans and chimps have identical amino-acid sequences for the enzyme
>>cytochrome-c, but the *genes* for cytochrome-c differ in one nucleotide
>>between the two species (this is possible because there are multiple
>>three-nucleotide codons for each amino acid). This is a "silent" mutation
>>(one with no phenotypic effect), and surely neutral. It presumably
>>originated as a mutation in one individual in one species, and just by
>>sheer
>>dumb luck spread through that species over hundreds of generations. This
>>can also happen to traits that do make a difference, if the difference
>>doesn't affect chances of reproductive success. Perhaps the spread of the
>>fused chromosome was just a case of neutral drift.
>
> "presumably" "perhaps" "speculated" "sheer dumb luck" "seem to"
> "there's no evidence" "pure chance" -- sorry, Steven, but none of this
> sounds very scientific. And these terms are used in connection with
> the central core of your theory. How is this expected to command
> respect from any thinking but undecided person? Gravity, which many
> like to have placed in the same category as evolutionary theory, does
> not consist of a series of maybes and perhapses.
>

[a] Evolutionary theory does not consist of series of "perhapses and
maybes." On the other hand, reconstructions of specific evolutionary events
and series of events are like reconstructions of other historical phenomena.
Many histories of ancient empires and wars are full of such terms -- we have
the lists of kings and victories, the rough outlines of borders, the temples
and hymns to major gods, and the like, but the fine details of life,
religion, and politics are half guesswork. It is much the same with human
evolution; there is massive and firm evidence for the broad outlines of
phylogeny (and the *fact* of that phylogeny), but the details are, indeed,
rather speculative.

[b] No one knows what gravity *is*. There are detailed equations
describing how it works, but as to *why* it works that way, or whether
"gravitons" exist (theory predicts them, but they've never been detected),
and the like, are indeed "a series of maybes and perhapses." There's a lot
of math behind those maybes -- but then, there's more math than you seem to
grasp behind arguments over the relationships of extinct hominids.

[c] It seems to me that one can better command the respect of thinking and
undecided persons by frankly admitting when one did not know, or when the
evidence could be interpreted in many ways, or when the evidence was
absent -- this ought, I would think, increase the weight given to claims
that were not hedged about with such qualifications, because they *were*
strongly supported by evidence. I was going to make a snide comment about
thinking and undecided creationists here, but decided not to.
>
-- [snip]


>
>>As noted, this happens most of the time, with most neutral mutations, but
>>every so often you get an exception. Flip enough coins enough times, and
>>sooner or later one will come up "heads" over and over and over.
>
> your whole theory is built upon the flip of the coin. Still not a
> scientific approach.
>

Entire faculties of mathematical geneticists and molecular phylogenists will
be *so* sorry to hear (from someone who once argued that dividing by zero
gave meaningful results) that their fields of study are invalid and
unscientific.
>
-- [snsip]


>
>>Maybe nothing. Not all evolution is the result of natural selection.
>
> but natural selection is a biggie, isn't it? What's left?
>

Natural selection is a "biggie" when it comes to explaining adaptive changes
(changes that make organisms better able to find food, avoid becoming food,
and generally leave descendants). Not all changes are adaptive. Besides
natural selection there are, at least, sexual selection and genetic drift.


>
>> And
>>there are problems with describing selection pressures on populations
>>millioins of years ago.
>
> of course there are. So why the strident, dogmatic stance of so many
> posters on TO -- excluding you, of course.
>

Note that there are differences between "common descent" and mechanisms of
common descent. It is not unheard of to be able to say with immense and
justified confidence that something happened, and have only vague and
poorly-supported notions of *why* it happened. Think of the comments about
gravity above. Heck, think about the programming decisions of the major
television networks. For that matter, there is a difference between arguing
that natural selection *can* produce some effect, and showing that, in fact,
particular selective pressures *did* in fact produce that effect. I don't
think many of the posters who argue with you are strident and dogmatic about
the selective pressures at work in the past (although they may, perhaps, be
dogmatic about what selective pressures were *not* present -- see some
discussions of the "aquatic ape hypothesis").


>
>> There's a lot that isn't known about how genes
>>interact with each other and the environment to build an organism, and
>>it's
>>hard to say what the effect would be. Even if we could say what the
>>effect
>>would be, there's still the problem of figuring out why it would be
>>advantageous (there are several competing theories of why bipedalism, or
>>larger brains, or thinning body hair, would benefit our ancestors).
>
> thank you for a fair and impartial answer.
>

You're quite welcome.
>
-- [snip of matters dealt with, as best I can, above]


>
>>Of course I can argue that. As noted above, some neutral changes are
>>"silent," with no phenotypic effect.
>
> and selection works with phenotypic effect, I take it?
>

Yes, almost by definition.


>
>> But a change can produce a quite
>>marked effect, and still be "neutral" (that is, can make reproductive
>>success in the given environment neither more nor less likely).
>
> I didn't think that is what was meant by neutral mutations. There are
> two definitions that I see so far, used by evolutionists:
>
> 1) A mutation that has no effect on the Darwinian fitness of its
> carriers.
> 2) A mutation that has no phenotypic effect.
>
> Where is the "marked effect" in the above understanding of neutral
> mutations?
>

Any change that's obvious to an observer, but doesn't affect the organism's
odds of reproductive success.


>
>> There are
>>two vireo (a type of bird) species that humans can easily tell apart only
>>by
>>eye color. There's no reason to suppose that one eye color is better than
>>the other for the birds, but the difference distinguishes the two species.
>
> wait a minute. Does difference in eye color alone make a new species?
> Then a blue-eyed human is a different species from a brown-eyed human?
>

Difference in eye color is not the *only* difference between the two
species, I'm pretty sure, and I doubt it's the *cause* of speciation, but
it's the obvious difference. My point is that one species has one eye
color, and another species has another eye color, and there's no reason to
suppose that one eye color is an adaption to some aspect of the environment,
but it's an obvious (a "marked") difference. It's a visible analog to the
difference in chromosome numbers between humans and chimps. I could have
cited different color patterns seen in many "vicar" species (you remember
vicar species, I assume) to make the same point -- not all evolution is
adaption.

Note, although it's irrelevant to the exact point at hand, that differences
that cause speciation in one group of organisms might be irrelevant in
another. There are cichlid species that are kept separate, in the wild,
purely because they are different in color -- if you put them in an aquarium
under light that makes their colors indistinguishable, they will mate to
produce fertile offspring. It's quite conceivable that eye color alone
could make populations in *some* genus into separate species, even though it
obviously doesn't do that in humans.


>
>>Of course, the change might be beneficial in one population, because of
>>sexual selection (female fashion-consciousness), but that's not quite the
>>same thing as getting food more easily, avoiding becoming food, or
>>fighting
>>off infections better. Quite possibly some of the differences between
>>humans and chimps were sexually rather than "naturally" selected.
>
> add "quite possibly" to the dictionary of evolutionary theory. So far
> nothing scientific. What is scientific is the actual data. The
> theory proposed in regard to the data, however, being based on maybes
> and possiblies, is not scientific.
>

This has been dealt with above.


>
>>As argued above, the change in chromosome number was quite possibly a
>>"neutral" change, although it is clearly one of the differences between us
>>and chimps. Note that something like 90% of the genome is neither genes
>>nor
>>regulatory sequences.
>
> it would be expected that more than 90% of a cell's chromosomes (the
> genome) would have its genes turned off and unrecognizable as genes
> since only 3% or so of each cell's chromosomes have genes turned on to
> code for the protein making of that particular cell type. This does
> not mean that the noncoding material is junk. It just is not used for
> that particular cell's purpose. And I would expect that when not
> actively in use, the potential for gene formation sits around looking
> for all the world like junk.
>

You are confused, here. That 90% of the genome wasn't "turned on" in any
cell, ever. Actually, a rather higher percentage than that is never turned
on; to get to 10% you have to include DNA that is never transcribed into
proteins, but that seems to regulate which DNA is transcribed into proteins.


>
>> A lot of the 100 million or so differences between
>>the human and chimp genomes almost certainly don't make any difference
>>that
>>matters to us -- they are "information" if you're looking for differences
>>between human and chimp genomes, but if you're looking for "what makes us
>>human," they aren't "information" in whatever sense it is that
>>creationists
>>have in mind when they speak of "new information."
>
> I'm not following you here.
>

Most of the genetic differences between humans and chimps don't have any
effect on how we or chimps develop or behave. They are "silent" or
"neutral" mutations, and most of them are changes to DNA with no discernable
"function" except taking up space in the genome.
>
-- [snip]


>
>>Again, mathematical models suggest that very small differences in
>>"fitness"
>>can give a trait a big advantage over time.
>
> "small differences" aren't the same as neutral differences, are they?
>

No, and natural selection isn't the same as genetic drift.


>
>> So, for that matter, do actual
>>observations of microevolution in the wild: Grant's finches on the
>>Galapagos
>>had small differences in beak size and shape that hardly made them
>>different
>>species, or even different subspecies -- but made a real difference in
>>fitness.
>>>
>>>>It doesn't seem likely that a modern human could (or at least would)
>>>>interbreed with a modern chimp, but presumably five million years ago,
>>>>our
>>>>ancestors were just a tiny bit more "human" than the ancestors of modern
>>>>chimps.
>>>
>>> how can a life form be a tiny bit more human before it becomes human?
>

I'm going to address this again. _Ardipithecus ramidus_, whose spine
entered its skull at an angle in between the chimp and human angles, seems
to have been "a tiny bit more human" than the human-chimp LCA (assuming the
LCA had a fully-chimplike posture and gait). _Australopithecus_, with many
chimplike features but an erect gait and a brain that was large for a chimp
its size was "a tiny bit more human" than _Ardipithecus_. _Homo
rudolfensis_ was "a tiny bit more human" than the australopiths. _Homo
ergaster_ was "a tiny bit more human" than _H. rudolfensis_. If you don't
understand this, what about evolutionary theory can you hope to understand?
>
-- [snip of matters I tried to deal with above]
>
-- Steven J.


Steven J.

unread,
Jul 25, 2005, 3:11:31 AM7/25/05
to

"Zoe" <muz...@aol.com> wrote in message
news:6vn8e1h4rfl6ag833...@4ax.com...

> On Sun, 24 Jul 2005 13:53:25 GMT, John Harshman
> <jharshman....@pacbell.net> wrote:
>
-- [snip]

>
>>No, that's not a principle, but we can't discard his first reason. It's
>>not just numbers of species but the shape of the phylogenetic tree that
>>determines what came first.
>
> the shape of the phylogenetic tree is a subjective one, based on the
> subjective opinions of the taxonomist and cladist, right?
>
No, the shape of the phylogenic tree (at least among living ape species) is
not subjective; it is the tree that best fits the evidence. John Harshman
wrote a "post of the month" that explains the reasoning behind this and the
math that supports the given tree over all other possible trees. The
"subjective decisions" are things like whether to class humans, chimps, and
gorillas all in the genus _Homo_, or as separate genera in the subfamily
Homininae. How you label the various splits is a different matter from
deciding in which order, or approximately when, they occurred. Labelling
is subjective (within limits); the splits and their order is objective.

>
>> Since we know the tree (i.e. that chimps,
>>gorillas, orangutans, and gibbons are successively less closely related
>>to humans),
>
> isn't this what is called assuming your conclusion? You say,
> authoritatively, We know that these creatures are successively less
> closely related to humans. How do we know this? By our phylogenetic
> tree that we have subjectively made up.
>
No, the phylogenic tree is a conclusion which was not assumed, but inferred
from and strongly supported by the data. See Harshman's
http://www.talkorigins.org/origins/postmonth/apr05.html for more details.
The phylogenic tree isn't offered as evidence, but as a graphic
representation of what is deduced from the pattern of similarities and
differences in different species.

>
>> we know what came first. Either 24 pairs came first (and
>>humans evolved 23), or chimps, gorillas, orangutans, and gibbons all
>>evolved 24 pairs independently from an ancestor with 23 pairs. Which
>>makes more sense to you?
>
> if I were forced to embrace evolutionary theory, I would have to say
> that fusion makes more sense than fission. But fission is just as
> plausible within the evolutionary framework in which many life forms
> emerge from a single common ancestor.
>
What you need to decide is whether *one* fusion of chromosomes (in one
branch of the primate family tree) is more plausible than some combination
of of four fissions or fusions, all happening to the same chromosome, all in
the same closely-related group of species, while (despite how common
chromosome number changes would have to be in apes for this explanation to
be right) no other chromosomes in any ape species seem to have fused or
split.
>
-- [snip]

>
> if chromosome fusion is used as evidence of a split from a common
> ancestor population, does chromosome fusion in mice also represent a
> split from a common ancestor population, especially as mice and humans
> are almost identical in their genetic makeup, as well?
>
It is certainly assumed that different chromosomal races of _Mus musculus_
were descended from a common ancestral population of _Mus musculus_ -- that
is, that all house mice share, at some point, a common ancestor that was a
house mouse (even if that common ancestor didn't, at the time, live in
houses).

Zoe, you don't seem to be actually thinking about the evidence being
presented to you, or you just don't understand it. Chromosome fusion (or
fission, whichever) in mice isn't being offered as evidence that mice and
humans shared a common ancestor (*that* conclusion depends on the overall
fit of mice into the rodent nested hierarchy, and the fit of the rodent and
primate nested hierarchies into the overall mammal nested hierarchy,
including fossil species). It isn't being used, by itself, as evidence that
mice share common ancestors with anything (except other mice); it's being
used as evidence that differences in chromosome numbers can mean the
difference between different species, or different races in the same
species, or merely between different individuals in the same breeding
population.


>
>>Fusion doesn't affect fertility very much, and in some
>>cases it doesn't affect it at all. How's that?
>
> too vague.
>

How is it vague?
>
-- [snip]


>
>>Przewalski's horse is not the ancestor of domestic horses. It's a close
>>relative.
>
> well, Steven called it "ancestors." Could you and he come to some
> agreement?
>

John is the actual biologist and expert in molecular phylogenics. Assume
where we disagree on a question in biology (if, in fact, we actually are in
disagreement) that I am wrong and he is right.


>
>>The factors that allow or prevent interbreeding are complex,
>>but simple length of time apart is one of them.
>
> so would your theory predict that the Chinese race, living apart from
> the Indian race, would eventually, over time, evolve the inability to
> interbreed?
>

They don't live "apart" -- commerce and communication between the two
countries is ancient and continuing. How do you suppose that Buddhism -- a
religion that started in India -- became so common in China and other east
Asian lands? Gene flow between the two lands is not heavy, but neither is
it negligible, and different populations aren't likely to speciate as long
as they're exchanging genes with each other (although there's always
sympatric speciation to consider, I suppose).
>
-- [snip]


>
>>Right. But nobody says this fusion is beneficial, and nobody says it's
>>the first difference to become fixed in the human lineage.
>
> so now evolutionary theory proposes that life forms evolve, not only
> from selected beneficial mutations, but from harmful and/or neutral
> mutations?
>

Neutral drift (and "nearly-neutral drift") is thought to explain a lot of
nonadaptive evolution, yes.
>
-- [snip]


>
>>> how can a life form be a tiny bit more human before it becomes human?
>>
>>How can it not? I don't understand your objection here. We're talking
>>about intermediates. Do you deny even the logical possibility of
>>intermediate forms?
>
> intermediate forms between an apple and a carrot? No. Intermediate
> forms between a carrot and a snail? No. Intermediate forms between
> a dinosaur and a bird? No.
>

Carrots did not evolve into snails, or vice-versa; their last common
ancestor was a single-celled organism. Intermediate forms between nonavian
theropod dinosaurs and birds are embarrassingly abundant if you want to deny
that they are even logically possible: think _Archaeopteryx_,
_Sinosauropteryx_, _Microraptor_, _Confuciusornis_, etc. Why do you think
these cannot even conceivably be intermediate forms?


>
>>>> They probably could have produced fertile offspring with the chimp
>>>>ancestors, but as noted, they lived in different parts of Africa and no
>>>>longer met.
>>>
>>>
>>> I note the use of "probably" here.
>>
>>Yes. That's because we don't know, and have no way of ever knowing,
>>exactly when reproductive isolatio evolved between the two lineages.
>
> I'm not asking for when it happened, but how it happened. So far, no
> steps have been given other than probabilities and maybes.
>

You seem, at many places, to deny that it even *did* happen, so evidence
that it did happen is relevant and important, even if we can't provide you
with conclusive evidence as to how and why it happened.
>
-- Steven J.


Zoe

unread,
Jul 27, 2005, 9:51:12 PM7/27/05
to
On Mon, 25 Jul 2005 01:33:57 -0500, "Steven J."
<sjt195...@nts.link.net.INVALID> wrote:

snip>

>Note that molecular phylogeny uses the same techniques -- and many of the
>same assumptions -- used in reconstructing "phylogenies" of, e.g. multiple
>variant copies of the _Canterbury Tales_, or the gospels, or chain letters.
>I would think you would appreciate explanations that prefer the fewest
>number of assumptions about unobserved events.

the problem is not with the number of assumptions. It is with the
fact that parsimony is applied to a situation in which numbers are
irrelevant. Random mutations have no order governing them. They can
happen often or little or not at all, according to sheer dumb luck, as
you put it. So to try to apply a principle of order and "how it
should be" to random activity would be useless, I think.

>-- [snip]
>>
>>>When you say "83% difference," I'm not sure what you mean. If you mean
>>>that
>>>83% of the genes have at least one nucleotide different between the two
>>>species, that is perfectly consistent with a 99% sequence similarity
>>>between
>>>the two chromosomes.
>>
>> see:
>>
>> http://genomebiology.com/researchnews/default.asp?arx_id=gb-spotlight-20040528-01
>>
>> Begin quote:
>>
>> 'Sakaki said their analysis found about 68,000 insertions or
>> deletions. "That is almost one insertion/deletion every 470 bases," he
>> said. In addition, a small proportion of genes showed a relatively
>> higher rate of evolution than most other genes. "We haven't known what
>> proportion of the genes shows adaptive evolution. This study shows it
>> to be about 2 to 3%," he said.
>>
>Now, if my math can be trusted, one insertion/deletion every 470 bases
>amounts to a bit over one-fifth of one percent difference. If there are no
>other differences in the genes besides those mentioned, then sequence
>similarity between genes (as opposed to noncoding sequences) would be
>something like 99.75%.

if sequence similarity between genes were truly 99.75%, then
morphologically, we would be 99.75% similar to chimps. Reality is, we
are not 99.75% similar to chimps in our outward appearance. Outward
appearance is a result of those same genes that are considered to be
almost identical to chimps.

> Note that the authors distinguish between "adaptive
>evolution" ("beneficial mutations") and, presumably, evolution that isn't
>adaptive. If I'm reading this right, about 83% of the genes show *some*
>difference (perhaps only one or two nucleotides altered), and about 3% of
>genes show differences that resulted from beneficial mutations spreading
>through natural selection, and the rest show differences that are inferred
>to have arisen through neutral mutations that drifted to fixation. Of
>course, this summary does not enable me to determine how they decided which
>changes were adaptive and which were not.

is there even a way to determine if a change is adaptive versus a
result of some rare "beneficial" mutation?

>> 'Early molecular comparisons between humans and chimpanzees suggested
>> that the species are very similar to each other at the nucleotide
>> sequence level - a difference of between 1.23% and 5%, Sakaki said.
>> The results reported this week showed that "83% of the genes have
>> changed between the human and the chimpanzee - only 17% are identical
>> - so that means that the impression that comes from the 1.2%
>> [sequence] difference is [misleading]. In the case of protein
>> structures, it has a big effect," Sakaki said.'
>>
>Again, the point is not that the sequence similarity is smaller than
>previous estimates had made it, much less that the evidence for human-chimp
>common ancestry is weaker than had previously been thought. Rather, the
>point is that 1% sequence difference doesn't mean that only 1% of genes are
>different (in principle, one could make a 1% difference in 100% of the
>genes, or that the differences produce only a 1% difference in phenotype.
>There's an analogy offered by some creationist sites: the sentences "All
>competent biologists accept common descent" and "Not all competent
>biologists accept common descent" have very high sequence similarity, but
>opposite meanings. But the analogy works better for evolutionists:
>obviously, one of those sentences is a modified copy of the other, and they
>show how minor modifications can at once reveal common ancestry and produce
>large changes.

in what way does the fact that you have two sentences, one starting
with "Not all...." and the other starting with "All..." mean common
ancestry in your analogy? And why does one sentence necessarily have
to be a modified copy of the other? The one sentence quite obviously
comes from a completely different source than the other. One from
creationists, the other from evolutionists.

>> End quote.
>>
>> I recognize that this is written from an evolutionary point of view,
>> so expect to find attempts to explain the differences in terms of
>> change and loss or gain. But, really now, if a difference between the
>> two is observed, there is nothing to say that the present difference
>> is a result of change over millions of years, or if the difference was
>> present from the time of origin.
>>
>If all we had to study were humans and chimps, that would be more or less
>true (although that vestigial centromere and telomere on chromosome 2 is
>still very suggestive). But the strongest evidence for common descent is
>not similarities between any two species, but the *nested hierarchy* of
>similarities and differences for the huge number of known species.

a nested hierarchy would only be strong evidence if there are no other
nested hierarchies that form in the real world. To ignore the fact
that there are other nested hierarchies in the real world that are not
a result of common descent, and then claim that this one particular
nested hierarchy must be the result of common descent, is to impose an
undue burden upon the one evolutionary hierarchy.

For the evolutionary understanding of nested hierarchy, see:

http://www.lobue.com/enterprise_evolution/knowledge_hierarchy.html

by the above evolutionary admission, there are other nested
hierarchies besides the biological hierarchies.

Nested hierarchy is just another term for levels of organization. You
find levels of organization in many other fields besides biology.
None of these other fields draw the conclusion that, therefore, common
source or ancestry is indicated.

Take, for instance, the following hierarchy for all humans.

Using geographical boundaries. North America: USA: Florida: Seminole
County: Orlando: 100 East Street: Human: John Doe.

Using ecological boundaries. Biome: Community: Population: Human:
John Doe.

Lo, we have a twin-nested hierarchy.

Here's another twin-nested hierarchy.

Population: John Doe: organ systems: organs: tissues: cells:
chromosomes: DNA.

and

Population: John Doe: brain, nervous system: neuron: dendrites/axons:
synapse: neurotransmitters.

So, does the ability to recognize hierarchies and/or twin-nested
hierarchies mean anything more than we are able to classify things
hierarchically?

>If we had only two variant copies of some ancient manuscript, perhaps both
>came from the hand of the original author, who revised his own first draft
>slightly. But when we have dozens of copies, which naturally fall into
>groups (sharing many similar readings), falling into larger groups (united
>by a smaller number of readings shared by all the manuscripts in the larger
>group) and so on, the idea that the original author didn't produce all these
>copies, but that they were introduced gradually by different copyists at
>different times, would become irresistable (especially if we already knew
>about copyists and their errors).

are you proposing here that the first common ancestor was as complex
as an intelligently produced manuscript? Or has your analogy broken
down before it even started?

>Likewise, we know about mutations in living populations, and about the
>nested hierarchies of related populations into which living species fall.
>The overall pattern of life is simply a larger-scale version of the pattern
>we see in populations *known* to be produced by common descent with
>modification, whether cattle or silkworms or humans (or, for that matter,
>families of languages and manuscripts).

the principle of common descent does not hold when applied to all
other twin-nested hierarchies. Why should it hold just for biological
life forms?

>> Further in the article, Derek Wildman tries to hold onto the idea that
>> similarity must still mean relationship through a common ancestor, but
>> I'm betting that with further comparison between the chimp genome and
>> the human genome, this idea of relationship through a common ancestor
>> will continue to degrade.
>>
>It has not "degraded" yet, so if it "degrades" in the future this will not
>be a continuation of current trends. Noting that a lot of genes differ
>between humans and chimps does not mean that the differences are at all
>difficult to explain in terms of mutation and selection or drift, or even
>that the number is greater than the theory of evolution (as opposed to
>mathematically naive intuition) would lead us to expect.

well, the term used in the article was "misleading."

"... the impression that comes from the 1.2% [sequence] difference is
[misleading]."

What impression is this that is misleading, if not the impression that
we are so nearly identical to chimps that we must have come from a
common ancestor?

rather than speculate as to what the 1.2% difference means, it might
help to just take what Sakaki says at face value. He says that the
current impression is misleading.

>>> But certainly minor differences in
>>>DNA sequence can produce major changes in function, and certainly genes by
>>>themselves do not determine everything that happens in an organism.
>>
>> what are some other things, besides changes in genes, that are
>> suggested would cause the kind of changes in an organism that would
>> lead its population in a direction away from its old genus to a new
>> one?
>>
>My point was that DNA, by itself, does nothing; only when combined with the
>effects of the environment (which, for a gene, includes other genes, along
>with ribosomes and other cellular systems) do genes produce any effects at
>all. Changes outside the genes, if they could be inherited in some way
>(e.g. taught by parents rather than passed on through sex cells), could
>affect the way genes build an organism, or the selective pressures on genes,
>or both. For example, if some ape *learns* to use a new food source (that
>is, its genes are no different from those of other members of its species
>who don't eat that food), and teaches its children to do likewise, this
>could free the apes from some selective pressures (they wouldn't need to
>compete so hard for older food sources), and create new selective pressures
>(e.g. modifications in the digestive tract or other anatomical features to
>enable them to better use the new food source).

isn't that Lamarck? Wikipedia says that Lamarckism holds that traits
acquired (or diminished) during the lifetime of an organism can be
passed on to the offspring.

>-- [snip]
>>
>>>Actually, a sufficient similarity in composition (exact proportions of
>>>many
>>>minor ingredients) may strongly indicate origin from the same batter. At
>>>least, this line of reasoning is commonly used in forensic science for
>>>bullet fragments and dirt samples.
>>
>> we do not have access to exact proportions in biology. In forensic
>> science, there is access to the original firearm and the original
>> source of dirt for comparison purposes. Not so in biology.
>>
>We only know that it is the "original" firearm, or the "original" source of
>dirt, based on the same sort of argument that you reject for genomes.

I meant that we have access to the original firearm or dirt. We do
not have access to the original ancestors for comparison purposes.

>>> But in any case, a closer analogy to DNA
>>>would be the exact wording of the recipes themselves -- especially if both
>>>recipes shared the same mispellings of the same words in the same order,
>>>and
>>>had bits of text that were alike but didn't seem to have anything to do
>>>with
>>>the actual recipe (like, e.g. the pseudogenes and endogenous retroviruses
>>>chimps and humans share).
>>
>> recipes aren't available biologically so the analogy falls apart at
>> this point.
>>
>In the analogy, genes (or rather genomes) *are* the recipes. Certainly
>genomes are available biologically.

the genomes of the early ancestors are not available. We are
comparing the present DNA makeup with what is supposed to have been in
the common ancestor, aren't we?

>> But, again, similarity is not sufficient to indicate relationship
>> through a common ancestor, as is being seen in in the latest
>> chimp/human genome comparisons.
>>
>I don't think you understand the latest human/chimp genome comparisons.
>And, again, the argument for common descent is not based simply on
>human/chimp similarities, but on the consistent ways in which we are more
>similar to chimps than either of us is to gorillas, and so forth throughout
>the nested hierarchy of life.

not only is similarity not a good basis on which to conclude
relationship, but the classification itself is entirely subjective.

>>>By the way, why is it more reasonable, even if we don't know for sure, to
>>>suppose that the cakes were created from different recipes and different
>>>batter?
>>
>> because, from experience, we know that cakes come from different
>> batters. There is not one single grand clearing house of cake batter
>> from which all cakes come.
>>
>Okay, you don't buy junk food. Good for you.

I'm curious as to how you drew that conclusion.

>But we *do* know that living things come from other living things, that
>reproduction is not quite perfect, and that mutations, natural selection,
>and drift cause populations to evolve over time. We *do* know that
>consistent nested hierarchies of inheritable traits result from branching
>descent with modification, whether we're talking about breeds of domestic
>animals, or viruses, or languages, and hand-copied biblical texts. There is
>ample reason to infer that the nested hierarchy of life reflects a series of
>more or less remote common ancestors.

once again, the ability to classify objects based on similarity does
not necessarily mean common ancestry. If, as a rule, similarity
always meant relationship (not to mention common ancestry), then
evolutionists would have a point. "Looks like" is too superficial to
carry much weight.

>>> Certainly a baker is capable of making one big batch of batter and
>>>making lots of cakes from it.
>>
>> yes, but there is no single common source of batter to all cakes.
>>
>To paraphrase your own argument above, cake batter isn't available
>biologically, so your analogy falls apart at this point.

cake batter is an attempt to analogize your common ancestor. At that
point, it has not yet fallen apart. There is no single source of
batter to all cakes, just as there is no single common ancestor to all
life forms.

>>> And a Creator, I would suppose, is perfectly
>>>capable of making many species from a single ancestral population, as He
>>>made (according to the Bible) many nations from one original human
>>>population.
>>
>> but we don't think that cakes and cars come from the same batter or
>> assembly line, do we? There is no one common source of material to
>> all categories of things, just as there is no one common ancestor to
>> all categories of life forms.
>>
>Zoe, if you follow that analogy far enough, it implies that there is no
>common Creator to all categories of life forms.

there is a difference between the creator and the created. The
Creator is apart from the created. You can have a creator who is
common to all his creation. You don't have a creation that is common
to all other creation.

> If you don't follow it that
>far, why should you expect me to follow it to imply that there is no common
>ancestor to all known taxa?

because intelligence is known to create in a nested hierarchical
fashion. Created items are not known to organize themselves into such
patterns. It's as simple as that -- observation of how intelligence
(or mental activity) works, versus stupidity (or mindless activity).
In every area it works the same except when it comes to evolutionary
theory. Why is that? Is it a wish to not acknowledge a mind that
could be of superior intelligence to ours?

>-- [snip]
>>
>>>Okapis have no known subspecies; the variant chromosome numbers do not
>>>correspond to racial or habitat differences. And, apparently, they
>>>interbreed freely with okapis with different numbers of chromosomes and
>>>produce fertile offspring. Google turns up a few scholarly articles on
>>>"chromosomal polymorphism" in okapis and other species, and this appears,
>>>in
>>>okapis and some other species, to work like any other polymorphism (that
>>>is,
>>>it no more affects interbreeding than the difference between, say, type A
>>>and type O blood, or blue and brown eyes).
>>
>> so these scholarly articles to which you refer, do they mention having
>> tested the chromosomes of known parents to known offspring and having
>> discovered that the chromosome counts differ in the parents? Or is
>> the testing randomly done, without checking to see if those opaki with
>> same chromosome counts might tend to be attracted to each other, or
>> whether different chromosome-count opakis tend to repel each other?
>>
>I don't think they mention checking actual parentage for any okapis. I
>doubt very much that okapis can tell how many chromosome pairs another
>okapi has,

of course, they would not be expected to know the chromosome count of
each other -- leave that to be investigated by the researcher. But it
would be expected that the mere existence of differing chromosome
counts would produce differing kinds of proteins such that,
instinctively, the "same-counts" opakis would gravitate to each other.

> but the presence of several okapis with odd numbers of
>chromosomes strongly implies mating between okapis with different numbers of
>chromosomes, at least in the past.

has this been observed, is the question. Has it been investigated and
found that two parents of a particular offspring had different
chromosome counts?

>-- [snip]
>>
>>>There's no evidence that chimps with chromosomes 2a and 2b can interbreed
>>>with gorillas with chromosomes 2a and 2b. They've spent seven million
>>>years
>>>or more evolving in different directions (not just in obvious anatomical
>>>ways, but in more subtle ones). For all either of us knows, hominins (the
>>>human side of the human-chimp lineage) and panins (the chimp side) stopped
>>>being interfertile before the chromosome fusion happened in the hominin
>>>line. I doubt that chromosome number per se is much of a guide to
>>>interfertility.
>>
>> so it's just guesswork here at this point?
>>
>On some points, yes, it's pretty much guesswork. Are you hoping to argue
>that if scientists don't know everything, they can't know anything, or that
>all aspects of hominid phylogeny must be equally speculative (rather than
>some parts virtually certain and others, as you note, mere guesswork)?

no, but guesswork must be recognized as guesswork and not fact.

> Is
>there any area of historical reconstruction of which this is true? It seems
>to me that it is quite common to have the broad outlines of historical
>events firmly established and amply supported by evidence, while the fine
>details are sketchy and often poorly evidenced. It is the same with human
>evolution.

that's just it. What you consider to be broad outlines firmly
established, I have yet to see those broad outlines established by
anything more than maybe or probably.

>>>But again, horse subspecies with different numbers of chromosomes are
>>>interfertile. Okapis with a rather recent mutation that produced a fused
>>>chromosome are interfertile. I'm speculating that what is known to happen
>>>in several species today could have happened in other species at other
>>>times; it seems a safe enough speculation.
>>
>> okay, it's still speculation. Moving on...
>>
>By "a safe enough speculation" I meant that we know, from experience, that
>differing chromosome numbers, by themselves, do not lower interfertility

and that was my question. For those species that have differing
chromosome numbers, have they tested the parents to see if they indeed
had differeing chromosome numbers, or did they just test random
members of populations and conclude that therefore,
different-chromosome members were able to interbreeded and produce
fertile offspring?

>(although different chromosome numbers, plus other genetic and chromosomal
>changes, will do this), so there is no reason at all to suppose that the
>first hominid with 23 chromosome pairs would have any problems mating with
>hominids of the same species, but with 24 pairs.

until the above question is answered, there is every reason to
question whether some fantasized first hominid with 23 chromosomes was
able to interbreed with one with 24 pairs.

you do realize that the entire scenario you painted above is a
speculative one, containing no hard facts?

>It works much the same for any mutation.

and from the above speculative scenario it is concluded,
authoritatively, that, therefore, it woks much the same for any
mutation?

> There's no need for it to occur in
>many members of the population at once (although it may -- some mutations
>recur over and over). Note that even though, in the scenario above, every
>member of the descendant population inherits Harvey's mutation, they aren't
>the descendants of Harvey alone. They are, at least, the descendants of the
>non-mutant (or at least, not carrying *this* particular mutation) female(s)
>who bore Harvey's offspring. They are descendants of the males and females
>who mated with Harvey's kids and grandkids. They are, in short, descended
>from many of Harvey's contemporaries, and inherit, probably, many genes from
>those contemporaries, even if not one copy of the unfused chromosomes 2a and
>2b from those contemporaries has been passed on (if you have children, you
>probably have alleles they didn't inherit -- since each child inherits only
>a random half of your genes -- but they're still 100% your descendants).

supposition is not science. Until you can demonstrate that Harvey and
his kids followed the scenario that you painted for them, it remains a
just-so story used to prop up evolutionary theory.

>> And I take it that Population A must have been hit with some other
>> kind of rare beneficial mutation in order for it to begin to exhibit
>> characteristics of chimpness?
>>
>There is no need for this to happen when it first branched off from
>population B, but yes, in time, presumably mutants with favorable mutations
>were born in population A on many occasions, over millions of years. Note,
>by the way, that humans exhibit many characteristics of "chimpness" (Jared
>Diamond wrote a book about our species called _The Third Chimpanzee_ --
>bonobos are the second chimpanzee), and the human/chimp LCA presumably was
>more chimplike than we are already.

similarities are made to carry far more weight than they can truly
carry. Steven, so far, all you're giving me are presumptions.
Presumptions are not science.

>>> Some
>>>individuals in either population will end up having no living descendants,
>>>but others will be the ancestor (if they're in population A) of every
>>>chimpanzee alive today), or (if they're in population B) of every human
>>>who's ever lived (and every Neanderthal, _Homo erectus_, australopith, and
>>>so on). There is no one single mutant individual who is the sole ancestor
>>>and cause of modern humans.
>>
>> well, it has got to start with a single member, unless you are
>> proposing that the same rare beneficial mutation hits many members of
>> the population at the same time or within a certain time frame?
>>
>No single mutation made us human, or a different species from the parents of
>the mutant. We are descended from many, many individuals, most of them
>"mutants" in the sense that some portion of some gene they have is slightly
>different from any gene of either of their parents.

I didn't say that a single mutation made an ape human. I said that
the first single mutation has to hit a single individual, unless you
think that the same rare mutation hits many members of the population
at the same time.

>-- [snip]
>>
>>>There's no reason to suppose the change was beneficial, rather than
>>>neutral.
>>
>> it has to be beneficial, according to your theory, in order to get
>> selected. If it's neutral, there's nothing to select.
>>
>True.

true. You said "true." That answer is sufficient, so leave it at
that. What follows does not address what I just said.

probability and statistics has nothing to do with organization and
building and creating. It just says what are the chances of something
happening. Once the thing happens, probability and statistics can
only say what are the chances that such a thing can happen again. You
don't use probability and statistics to build something in an orderly
and methodical manner.

Explain to me how you build a digestive system via the mechanism of
blind, sheer dumb luck. Or make it easier. Explain how you would
build a cardboard box via the mechanism of sheer dumb luck.

>>>http://www.talkorigins.org/faqs/genetic-drift.html
>>>
>>>Humans and chimps have identical amino-acid sequences for the enzyme
>>>cytochrome-c, but the *genes* for cytochrome-c differ in one nucleotide
>>>between the two species (this is possible because there are multiple
>>>three-nucleotide codons for each amino acid). This is a "silent" mutation
>>>(one with no phenotypic effect), and surely neutral. It presumably
>>>originated as a mutation in one individual in one species, and just by
>>>sheer
>>>dumb luck spread through that species over hundreds of generations. This
>>>can also happen to traits that do make a difference, if the difference
>>>doesn't affect chances of reproductive success. Perhaps the spread of the
>>>fused chromosome was just a case of neutral drift.
>>
>> "presumably" "perhaps" "speculated" "sheer dumb luck" "seem to"
>> "there's no evidence" "pure chance" -- sorry, Steven, but none of this
>> sounds very scientific. And these terms are used in connection with
>> the central core of your theory. How is this expected to command
>> respect from any thinking but undecided person? Gravity, which many
>> like to have placed in the same category as evolutionary theory, does
>> not consist of a series of maybes and perhapses.
>>
>[a] Evolutionary theory does not consist of series of "perhapses and
>maybes."

well, those are the words used when describing it.

> On the other hand, reconstructions of specific evolutionary events
>and series of events are like reconstructions of other historical phenomena.
>Many histories of ancient empires and wars are full of such terms -- we have
>the lists of kings and victories, the rough outlines of borders, the temples
>and hymns to major gods, and the like, but the fine details of life,
>religion, and politics are half guesswork. It is much the same with human
>evolution; there is massive and firm evidence for the broad outlines of
>phylogeny (and the *fact* of that phylogeny), but the details are, indeed,
>rather speculative.

I'm afraid, from what you've described so far, the broad outlines are
also speculative.


>
>[b] No one knows what gravity *is*. There are detailed equations
>describing how it works, but as to *why* it works that way, or whether
>"gravitons" exist (theory predicts them, but they've never been detected),
>and the like, are indeed "a series of maybes and perhapses." There's a lot
>of math behind those maybes -- but then, there's more math than you seem to
>grasp behind arguments over the relationships of extinct hominids.

gravity is not in the same class as evolutionary theory. Making the
comparison doesn't fool anyone who is thinking outside the
evolutionary box.


>
>[c] It seems to me that one can better command the respect of thinking and
>undecided persons by frankly admitting when one did not know, or when the
>evidence could be interpreted in many ways, or when the evidence was
>absent -- this ought, I would think, increase the weight given to claims
>that were not hedged about with such qualifications, because they *were*
>strongly supported by evidence. I was going to make a snide comment about
>thinking and undecided creationists here, but decided not to.

very noble of you.

>-- [snip]
>>
>>>As noted, this happens most of the time, with most neutral mutations, but
>>>every so often you get an exception. Flip enough coins enough times, and
>>>sooner or later one will come up "heads" over and over and over.
>>
>> your whole theory is built upon the flip of the coin. Still not a
>> scientific approach.
>>
>Entire faculties of mathematical geneticists and molecular phylogenists will
>be *so* sorry to hear (from someone who once argued that dividing by zero
>gave meaningful results) that their fields of study are invalid and
>unscientific.

making fun of my dividing by zero doesn't work here because I made it
clear that I was thinking outside of the mathematical box. It turned
out to be quite an interesting mental exercise for me.

As to the part played by a flip of a coint. It would be observed that
systems are not put together by the mechanism of flipping coins. We
were discussing how systems are put together, whether by intelligence
or random activity. Coin flipping is random, and no one would dare to
say that coin flipping works for building systems -- except
evolutionists, I guess.

>-- [snsip]
>>
>>>Maybe nothing. Not all evolution is the result of natural selection.
>>
>> but natural selection is a biggie, isn't it? What's left?
>>
>Natural selection is a "biggie" when it comes to explaining adaptive changes
>(changes that make organisms better able to find food, avoid becoming food,
>and generally leave descendants). Not all changes are adaptive. Besides
>natural selection there are, at least, sexual selection and genetic drift.

none of these carry the weight you would like them to carry. Sorry.

>>> And
>>>there are problems with describing selection pressures on populations
>>>millioins of years ago.
>>
>> of course there are. So why the strident, dogmatic stance of so many
>> posters on TO -- excluding you, of course.
>>
>Note that there are differences between "common descent" and mechanisms of
>common descent. It is not unheard of to be able to say with immense and
>justified confidence that something happened, and have only vague and
>poorly-supported notions of *why* it happened.

in real science, one does not say, with immense and justified
confidence, that something definitely happened a certain way, when all
that supports such an idea are speculative notions on HOW it happened.

> Think of the comments about
>gravity above. Heck, think about the programming decisions of the major
>television networks. For that matter, there is a difference between arguing
>that natural selection *can* produce some effect, and showing that, in fact,
>particular selective pressures *did* in fact produce that effect. I don't
>think many of the posters who argue with you are strident and dogmatic about
>the selective pressures at work in the past (although they may, perhaps, be
>dogmatic about what selective pressures were *not* present -- see some
>discussions of the "aquatic ape hypothesis").

I find that the aquatic ape theory is another example of fantasy gone
haywire. There are no facts to support it, as far as I can see.

snip>

>>>Of course I can argue that. As noted above, some neutral changes are
>>>"silent," with no phenotypic effect.
>>
>> and selection works with phenotypic effect, I take it?
>>
>Yes, almost by definition.

and that is why chromosome 2 is the death knell to the chimp/human
relationship. If chromosome 2 is 99% identical to chromosomes 2a and
b in apes, then humans, phenotypically, should be 99% similar to apes.
We are not. So then you would have to say that the 1% difference is
what has caused the differences. Phenotypically, apes (or chimps) and
humans are NOT 1% different.

>>> But a change can produce a quite
>>>marked effect, and still be "neutral" (that is, can make reproductive
>>>success in the given environment neither more nor less likely).
>>
>> I didn't think that is what was meant by neutral mutations. There are
>> two definitions that I see so far, used by evolutionists:
>>
>> 1) A mutation that has no effect on the Darwinian fitness of its
>> carriers.
>> 2) A mutation that has no phenotypic effect.
>>
>> Where is the "marked effect" in the above understanding of neutral
>> mutations?
>>
>Any change that's obvious to an observer, but doesn't affect the organism's
>odds of reproductive success.

chromosome2 is not obvious to an observer, is it? It shouldn't get
selected.

>>> There are
>>>two vireo (a type of bird) species that humans can easily tell apart only
>>>by
>>>eye color. There's no reason to suppose that one eye color is better than
>>>the other for the birds, but the difference distinguishes the two species.
>>
>> wait a minute. Does difference in eye color alone make a new species?
>> Then a blue-eyed human is a different species from a brown-eyed human?
>>
>Difference in eye color is not the *only* difference between the two
>species, I'm pretty sure, and I doubt it's the *cause* of speciation, but
>it's the obvious difference.

eye color is an obvious difference that means nothing to the point you
were trying to make, I don't think.

> My point is that one species has one eye
>color, and another species has another eye color, and there's no reason to
>suppose that one eye color is an adaption to some aspect of the environment,
>but it's an obvious (a "marked") difference.

who said that eye color is an adaptation? I gave two reasons for
variation. One is variation as a result of recombination, just for
the sake of variation. And one is variation as a result of
adaptation, for the sake of coping with environmental stimuli.

> It's a visible analog to the
>difference in chromosome numbers between humans and chimps. I could have
>cited different color patterns seen in many "vicar" species (you remember
>vicar species, I assume) to make the same point -- not all evolution is
>adaption.

not all variation is adaptation, I agree.

>Note, although it's irrelevant to the exact point at hand, that differences
>that cause speciation in one group of organisms might be irrelevant in
>another. There are cichlid species that are kept separate, in the wild,
>purely because they are different in color -- if you put them in an aquarium
>under light that makes their colors indistinguishable, they will mate to
>produce fertile offspring. It's quite conceivable that eye color alone
>could make populations in *some* genus into separate species, even though it
>obviously doesn't do that in humans.

more speculation. We need hard facts -- evidence.

>>>Of course, the change might be beneficial in one population, because of
>>>sexual selection (female fashion-consciousness), but that's not quite the
>>>same thing as getting food more easily, avoiding becoming food, or
>>>fighting
>>>off infections better. Quite possibly some of the differences between
>>>humans and chimps were sexually rather than "naturally" selected.
>>
>> add "quite possibly" to the dictionary of evolutionary theory. So far
>> nothing scientific. What is scientific is the actual data. The
>> theory proposed in regard to the data, however, being based on maybes
>> and possiblies, is not scientific.
>>
>This has been dealt with above.

sorry, I'm afraid not, Steven.

>>>As argued above, the change in chromosome number was quite possibly a
>>>"neutral" change, although it is clearly one of the differences between us
>>>and chimps. Note that something like 90% of the genome is neither genes
>>>nor
>>>regulatory sequences.
>>
>> it would be expected that more than 90% of a cell's chromosomes (the
>> genome) would have its genes turned off and unrecognizable as genes
>> since only 3% or so of each cell's chromosomes have genes turned on to
>> code for the protein making of that particular cell type. This does
>> not mean that the noncoding material is junk. It just is not used for
>> that particular cell's purpose. And I would expect that when not
>> actively in use, the potential for gene formation sits around looking
>> for all the world like junk.
>>
>You are confused, here. That 90% of the genome wasn't "turned on" in any
>cell, ever.

and how did you decide this? In another cell, a different set of
genes are turned on. How do you know that this new set didn't come
from the 90% that was turned off and unrecognizable in another cell?

> Actually, a rather higher percentage than that is never turned
>on; to get to 10% you have to include DNA that is never transcribed into
>proteins, but that seems to regulate which DNA is transcribed into proteins.
>>
>>> A lot of the 100 million or so differences between
>>>the human and chimp genomes almost certainly don't make any difference
>>>that
>>>matters to us -- they are "information" if you're looking for differences
>>>between human and chimp genomes, but if you're looking for "what makes us
>>>human," they aren't "information" in whatever sense it is that
>>>creationists
>>>have in mind when they speak of "new information."
>>
>> I'm not following you here.
>>
>Most of the genetic differences between humans and chimps don't have any
>effect on how we or chimps develop or behave. They are "silent" or
>"neutral" mutations, and most of them are changes to DNA with no discernable
>"function" except taking up space in the genome.

so you can't count these neutral mutations as evolutionary. There is
nothing new or advantageous to select from. And you can't count the
harmful mutations, that's for sure. So you're back to building your
theory on some fantasized rare "beneficial mutations."

It's a rickety structure that won't stand up to the evidence.

>-- [snip]
>>
>>>Again, mathematical models suggest that very small differences in
>>>"fitness"
>>>can give a trait a big advantage over time.
>>
>> "small differences" aren't the same as neutral differences, are they?
>>
>No,

the answer is no. Adding anything more just muddies the answer.

> and natural selection isn't the same as genetic drift.
>>
>>> So, for that matter, do actual
>>>observations of microevolution in the wild: Grant's finches on the
>>>Galapagos
>>>had small differences in beak size and shape that hardly made them
>>>different
>>>species, or even different subspecies -- but made a real difference in
>>>fitness.
>>>>
>>>>>It doesn't seem likely that a modern human could (or at least would)
>>>>>interbreed with a modern chimp, but presumably five million years ago,
>>>>>our
>>>>>ancestors were just a tiny bit more "human" than the ancestors of modern
>>>>>chimps.
>>>>
>>>> how can a life form be a tiny bit more human before it becomes human?
>>
>I'm going to address this again. _Ardipithecus ramidus_, whose spine
>entered its skull at an angle in between the chimp and human angles, seems
>to have been "a tiny bit more human" than the human-chimp LCA (assuming the
>LCA had a fully-chimplike posture and gait). _Australopithecus_, with many
>chimplike features but an erect gait and a brain that was large for a chimp
>its size was "a tiny bit more human" than _Ardipithecus_. _Homo
>rudolfensis_ was "a tiny bit more human" than the australopiths. _Homo
>ergaster_ was "a tiny bit more human" than _H. rudolfensis_. If you don't
>understand this, what about evolutionary theory can you hope to understand?

what I understand is that a lot of speculative ideas are put forward
as fact. They are the ungrounded assumptions upon which evolutionary
theory teeters and totters.

Zoe

unread,
Jul 27, 2005, 9:55:22 PM7/27/05
to
On Mon, 25 Jul 2005 05:02:59 GMT, John Harshman
<jharshman....@pacbell.net> wrote:

snip>

zoe asked:

>> have they checked the parents of particular offspring and found that
>> different-numbered genomes were able to interbreed? Or did they
>> simply test various members, found that some have a certain number
>> chromosome count, and others a different count, and assumed that
>> different counts could interbreed?
>
>The former. Of course, you understand that you can karyotype individuals
>and find out if they are hybrids between different chromosome numbers.

karyotyping an individual does not tell you that two different
chromosome-numbered parents interbred. It simply tells you that the
individual ended up with too many or too few chromosomes. How does
this happen?

see:

http://gslc.genetics.utah.edu/units/disorders/karyotype/karyotypeinfo.cfm

Quote:

"How can cells end up with too many or too few chromosomes?

"Sometimes chromosomes are incorrectly distributed into the egg or
sperm cells during meiosis. When this happens, one cell may get two
copies of a particular chromosome, while another cell gets none."

End quote.

a different count of chromosomes, as seen in karyotyping, does not
mean that two parents with different counts interbred, but simply that
the chromosomes got incorrectly distributed during meiosis.

snip>

>>>The factors that allow or prevent interbreeding are complex,
>>>but simple length of time apart is one of them.
>>
>>
>> so would your theory predict that the Chinese race, living apart from
>> the Indian race, would eventually, over time, evolve the inability to
>> interbreed?
>
>If that were true, then yes it would. However, no human population has
>ever been that isolated. There is no Chinese race and no Indian race,
>just clinal variation from one point to another.

my point was, according to evolutionary ideas, if there are groups of
Chinese that have never been to India, and groups of Indians that
never went to China, would members of those particular groups, should
they ever meet after thousands of years, be unable to interbreed?

snip the rest of John's non-answers>

Zoe

unread,
Jul 27, 2005, 10:02:08 PM7/27/05
to

Okay, here's the core of John's argument:

--Quote:

"Here is a set of DNA sequences. They come from two mitochondrial
genes, ND4 and ND5. If you put them together, they total 694
nucleotides. But most of those nucleotides either are identical among
all the species here, or they differ in only one species. Those are
uninformative about relationships, so I have removed them, leaving 76
nucleotides that make some claim. I'll let you look at them for a
while.


[ 10 20 30 40 50]
[ . . . . .]
+ 1 2++ 3 11 +4 3 ++ 52+1 2615+4 14+ 3 3+6+
gibbon ACCGCCCCCA TCCCCTCCCT CAAGTCCTAT CCAATCTACT GTACTTTGCC
orangutan ACCACTCCCA CCCTTCCTCC TAAGACTCAC ACAACTCGCC ACACCTCGTC
human GTCATCATCC TTCTTTTTTT AGGAATTTCC TCTCTCCGTC ACGCTCTACT
chimpanzee ATTACCATTC CTTTTTTCCC CGGATTCTCC CTTCTTCATT ATGTCTCATT
gorilla GTTGTTATTA CCTCCCTTTC AAGAACCCCT TTCACCTATC GCGTCCCACT
[ 60 70 ]
[ . . ]
+++ +++1 + +? 2 + +++
gibbon CCTACAGCCC AGCCAAACGA CACTAA
orangutan CCTACCGCCT AGCCATTTCA CACTAA
human CCCCTTATTT TCTTGTCCGG TGACCG
chimpanzee TTCCTCATTT TCTTACTCAG TGACCG
gorilla TTCCTTATTC TTTCGCCTAG TGATTA

I've marked with a plus sign all those sites at which gibbon and
orangutan match each other, and the three African apes (including
humans) have a different base but match each other. These sites all
support a relationship among the African apes, exclusive of gibbon and
orangutan. You will note there are quite a lot of them, 24 to be
exact. The sites I have marked with numbers from 1-6 contradict this
relationship. (Sites without numbers don't have anything to say about
this particular question.) We expect a certain amount of this because
sometimes the same mutation will happen twice in different lineages;
we call that homoplasy. However you will note that there are fewer of
these sites, only 22 of them, and more importantly they contradict
each other. Each number stands for a different hypothesis of
relationships; for example, number one is for sites that support a
relationship betwen gibbons and gorillas, and number two is for sites
that support a relationship between orangutans and gorillas (all
exclusive of the rest). One and two can't be true at the same time. So
we have to consider each competing hypothesis separately. If you do
that it comes out this way:

hypothesis sites supporting
African apes (+) 24
gibbon+gorilla (1) 6
orangutan+gorilla (2) 4
gibbon+human (3) 4
gibbon+chimp (4) 3
orangutan+human (5) 2
orangutan+chimp (6) 2

I think we can see that the African ape hypothesis is way out front,
and the others can be attributed to random homoplasy. This result
would be very difficult to explain by chance."

--End quote.

Well, I'm not going to even consider the statistical test John applies
to his idea above, because already the above is based on a faulty
premise. You can have a faulty premise and everything works after
that, even unto the math and statistics, but the conclusion will still
be false, regardless of how well the math works, simply because the
premise itself was false.

What is John's premise in the above comparisons? That DNA sequences
that are alike mean relationship. He chooses 76 nucleotides that make
some "claim," as he puts it. The claim, I take it, is that these
sequences are unique to both humans and chimps. Armed with this
similarity, and the faulty premise that similarity must mean
relationship, he proceeds to show how much more similar the
human/chimp relationships are than any other primate.

Well, big whoopdeedoo.

I can decide that similarity between computer-generated characters
means that they are related, too. I can point out where the
similarities lie, and how much more similar certain computer-generated
characters are than others. That does not make the characters any
more related to each other, just by my setting up some unsupported
standard that says similarity means relationship.

First John needs to establish the validity of his premise, that
similarity HAS to mean relationship. He has not done so.

snip>

Steven J.

unread,
Jul 28, 2005, 12:54:26 AM7/28/05
to

"Zoe" <muz...@aol.com> wrote in message
news:io8ge1da66g48bj0b...@4ax.com...

> On Mon, 25 Jul 2005 01:33:57 -0500, "Steven J."
> <sjt195...@nts.link.net.INVALID> wrote:
>
-- [snip]

>
> the problem is not with the number of assumptions. It is with the
> fact that parsimony is applied to a situation in which numbers are
> irrelevant. Random mutations have no order governing them. They can
> happen often or little or not at all, according to sheer dumb luck, as
> you put it. So to try to apply a principle of order and "how it
> should be" to random activity would be useless, I think.
>
Zoe, if your statements above were true, why would there be -- how *could*
there be -- such a thing as a "mutation rate?" For that matter, how could
there be "hot spots" on chromosomes where mutations are more likely than at
other loci? "Random," with respect to mutations, does not mean that the
mutations occur for no reason, or that all mutations are equally likely, or
that there is no possibility of saying how likely a mutation is to occur.
It means simply that the causes of the mutations, and the causes that make
some traits beneficial and others harmful, are not related to one another.

For that matter, again, if random events had no order governing them, then
probability as a field of mathematics could not exist. Your position as
stated above is pure obstinant folly.
>
-- [snip]


>
> if sequence similarity between genes were truly 99.75%, then
> morphologically, we would be 99.75% similar to chimps. Reality is, we
> are not 99.75% similar to chimps in our outward appearance. Outward
> appearance is a result of those same genes that are considered to be
> almost identical to chimps.
>

There is no one-to-one mapping between genotype and phenotype. A tiny
alteration in a gene can have an immense effect on how the organism
develops, or, conversely, very large changes in multiple genes can have no
effect at all. It has been known for a long time (since well before the
discovery of genes) that tiny changes in developmental rates (e.g. how long
a particular structure continues to grow) can produce immense differences in
how an organism looks -- and tiny changes in development rates can result
from tiny changes in genes. OTOH, as noted, large sections of many proteins
(and hence the genes that code for them) can be replaced with completely
different sequences without affecting function. Consider how many genetic
disorders are the result of changing one amino acid in one protein (the
result of changing one nucleotide in one gene). Equally drastic effects
that are not disorders can be produced by equally small changes.


>
>> Note that the authors distinguish between "adaptive
>>evolution" ("beneficial mutations") and, presumably, evolution that isn't
>>adaptive. If I'm reading this right, about 83% of the genes show *some*
>>difference (perhaps only one or two nucleotides altered), and about 3% of
>>genes show differences that resulted from beneficial mutations spreading
>>through natural selection, and the rest show differences that are inferred
>>to have arisen through neutral mutations that drifted to fixation. Of
>>course, this summary does not enable me to determine how they decided
>>which
>>changes were adaptive and which were not.
>
> is there even a way to determine if a change is adaptive versus a
> result of some rare "beneficial" mutation?
>

"Beneficial" mutations are by definition "adaptive," since both "beneficial"
and "adaption" are diagnosed because they enhance the organism's chances of
surviving and reproducing in a particular environment. Not all adaptive
change is the result of mutations: it may be that the "fitter" or better
adapted alleles are already present in the population, and simply become
more common due to natural selection. "Adaptive" evolution simply means
that alleles that are more beneficial become more common, whether those
alleles arise from new mutations or have been present since the parent
population first evolved.
>
-- [snip]


>
>>Again, the point is not that the sequence similarity is smaller than
>>previous estimates had made it, much less that the evidence for
>>human-chimp
>>common ancestry is weaker than had previously been thought. Rather, the
>>point is that 1% sequence difference doesn't mean that only 1% of genes
>>are
>>different (in principle, one could make a 1% difference in 100% of the
>>genes, or that the differences produce only a 1% difference in phenotype.
>>There's an analogy offered by some creationist sites: the sentences "All
>>competent biologists accept common descent" and "Not all competent
>>biologists accept common descent" have very high sequence similarity, but
>>opposite meanings. But the analogy works better for evolutionists:
>>obviously, one of those sentences is a modified copy of the other, and
>>they
>>show how minor modifications can at once reveal common ancestry and
>>produce
>>large changes.
>
> in what way does the fact that you have two sentences, one starting
> with "Not all...." and the other starting with "All..." mean common
> ancestry in your analogy? And why does one sentence necessarily have
> to be a modified copy of the other? The one sentence quite obviously
> comes from a completely different source than the other. One from
> creationists, the other from evolutionists.
>

Actually, in the original example, both sentences came from a creationist;
when I retyped the sentences, both came from someone who accepted evolution.
But the point is that any reasonable person (must present company be
excluded?) would infer that one of those two sentences was the original, and
the other was derived by either adding or removing the initial "not."
>
-- [snip]


>
> a nested hierarchy would only be strong evidence if there are no other
> nested hierarchies that form in the real world. To ignore the fact
> that there are other nested hierarchies in the real world that are not
> a result of common descent, and then claim that this one particular
> nested hierarchy must be the result of common descent, is to impose an
> undue burden upon the one evolutionary hierarchy.
>

Strictly speaking, one can arrange any set of entities in a nested
hierarchy. Anyone who's ever written an outline for a paper, or tried to
sort books in a library, has arranged ideas or objects in a nested
hierarchy. Note, though, that for many sets of objects, there are multiple
equally valid hierarchical arrangements of the objects. A book on, e.g.
_The History of the Spread of the Great Plague_ might be filed under
"History," or "Epidemiology," or "Diseases." One can arrange automobiles in
many different nested hierarchies: arrange them by manufacturer (e.g. GM
cars, and within that category Dodges, Cadillacs, Chevrolets, etc.), or by
type of vehicle (e.g. sedans, and under sedans GM sedans, Ford sedans,
etc.), or by various other schemes. One can always get a nested hierarchy,
but the hierarchy one gets depends on the traits one selects to compare.

What makes biology interesting is that one can pick many different sets of
traits to compare, and get the *same* nested hierarchy. The most-cited
example is the hierarchy formed by comparison of anatomical features and
that formed by comparing genes and proteins (the "twin nested hierarchy),
but one can see the same thing just be comparing, say, anatomical features.
All organisms with one bone in the lower jaw and three in the middle ear
also have mammary glands, and none have feathers. There's no obvious
reason, assuming separate origins, for that feature -- why not bats with
feathers, or penguins with mammary glands? *Consistent* nested hierarchies
do not arise through known methods of design -- human engineers cross-copy
components into very different designs (e.g. CD players installed in both GM
sedans and Ford trucks). Nature does not: pterosaurs and bats, although
both used furry membranous wings, use different ways of modifying forelimbs
to produce those wings.


>
> For the evolutionary understanding of nested hierarchy, see:
>
> http://www.lobue.com/enterprise_evolution/knowledge_hierarchy.html
>

This is astonishing. You may just have found the worst explanation of what
evolutionists mean by "nested hierarchy" on the entire World Wide Web (this
is not to say that the explanation is useless for other purposes). I would
suggest, rather,

http://www.talkorigins.org/faqs/comdesc/CDhierarchy.html
http://www.talkorigins.org/faqs/comdesc/CDhierarchy.html
http://www.isss.org/hierarchy.htm


>
> by the above evolutionary admission, there are other nested
> hierarchies besides the biological hierarchies.
>
> Nested hierarchy is just another term for levels of organization. You
> find levels of organization in many other fields besides biology.
> None of these other fields draw the conclusion that, therefore, common
> source or ancestry is indicated.
>

Actually, a "nested" hierarchy has not merely levels of organization, but
the lower levels form parts of the higher levels, as, e.g. "primates" are
part of the "mammals," which are part of the "vertebrates."


>
> Take, for instance, the following hierarchy for all humans.
>
> Using geographical boundaries. North America: USA: Florida: Seminole
> County: Orlando: 100 East Street: Human: John Doe.
>

John Doe is not a geographical feature; he is not part of East Street, or
part of the geography of Seminole County. Note, furthermore, that [a] if
John Doe moves to California, he ceases to be part of Seminole County in any
sense, and [b] John Doe can, as you note below, be classified as part of a
quite different nested hierarchy. Again, you are ignoring the salient and
compelling nature of the consistent nested hierarchies in biology.


>
> Using ecological boundaries. Biome: Community: Population: Human:
> John Doe.
>
> Lo, we have a twin-nested hierarchy.
>

No, you have two quite different nested hierarchies containing the same
entity. Again, one can construct nested hierarchies for any set of objects
or ideas, but the distinctive feature of life is that it falls into pretty
much the same hierarchy no matter what traits one seeks to compare.


>
> Here's another twin-nested hierarchy.
>
> Population: John Doe: organ systems: organs: tissues: cells:
> chromosomes: DNA.
>
> and
>
> Population: John Doe: brain, nervous system: neuron: dendrites/axons:
> synapse: neurotransmitters.
>
> So, does the ability to recognize hierarchies and/or twin-nested
> hierarchies mean anything more than we are able to classify things
> hierarchically?
>
>>If we had only two variant copies of some ancient manuscript, perhaps both
>>came from the hand of the original author, who revised his own first draft
>>slightly. But when we have dozens of copies, which naturally fall into
>>groups (sharing many similar readings), falling into larger groups (united
>>by a smaller number of readings shared by all the manuscripts in the
>>larger
>>group) and so on, the idea that the original author didn't produce all
>>these
>>copies, but that they were introduced gradually by different copyists at
>>different times, would become irresistable (especially if we already knew
>>about copyists and their errors).
>
> are you proposing here that the first common ancestor was as complex
> as an intelligently produced manuscript? Or has your analogy broken
> down before it even started?
>

Extant manuscripts only let us reconstruct the *last* common ancestor, not
the first. Variant manuscripts of the gospels enable scholars to
reconstruct (with some uncertainty) the text from which they were all
derived, but they are less informative about the process by which the
gospels originated, or what earlier lost forms of the gospels might have
existed. The same problem exists with life: the last common ancestor need
not have been -- presumably was not -- the *first* common ancestor.


>
>>Likewise, we know about mutations in living populations, and about the
>>nested hierarchies of related populations into which living species fall.
>>The overall pattern of life is simply a larger-scale version of the
>>pattern
>>we see in populations *known* to be produced by common descent with
>>modification, whether cattle or silkworms or humans (or, for that matter,
>>families of languages and manuscripts).
>
> the principle of common descent does not hold when applied to all
> other twin-nested hierarchies. Why should it hold just for biological
> life forms?
>

As noted, sets of phenomena that fall into consistent nested hierarchies
(basically the same hierarchy is derived regardless of the set of traits
used for comparison) do not typically result except from common descent.
Designed things, like cars or airplanes, not only diverge into variant
designs, but as designers modify them they copy features from one line of
descent into some items from other lines of descent (e.g. one manufacturer
introduces windshield wipers, and soon others add them to their models).
Designers don't "reinvent the wheel," they just copy already existing wheel
designs. Life (e.g. different wing designs in birds, bats, and pterosaurs,
different thumb designs in primates and pandas, different box-camera eye
designs in cephalopods and vertebrates) reinvents the wheel all the time.
>
-- [snip]


>
> well, the term used in the article was "misleading."
>
> "... the impression that comes from the 1.2% [sequence] difference is
> [misleading]."
>
> What impression is this that is misleading, if not the impression that
> we are so nearly identical to chimps that we must have come from a
> common ancestor?
>

That surely cannot be the meaning intended by the author, who is clearly an
evolutionist. The "misleading impression" is that if only a tiny percentage
of the sequence is different, then only a tiny percentage of genes can be
different, or perhaps that if only a tiny percentage of the genotype
differs, the phenotypes likewise must be only slightly different.
>
-- [snip]


>
> rather than speculate as to what the 1.2% difference means, it might
> help to just take what Sakaki says at face value. He says that the
> current impression is misleading.
>

And he does *not* say that this casts any doubt on human-chimp common
ancestry, and indeed assumes such common ancestry in his analysis. You are
not taking his words at face value; you are trying to force-fit them into a
creationist framework.
>
-- [snip]


>
>>My point was that DNA, by itself, does nothing; only when combined with
>>the
>>effects of the environment (which, for a gene, includes other genes, along
>>with ribosomes and other cellular systems) do genes produce any effects at
>>all. Changes outside the genes, if they could be inherited in some way
>>(e.g. taught by parents rather than passed on through sex cells), could
>>affect the way genes build an organism, or the selective pressures on
>>genes,
>>or both. For example, if some ape *learns* to use a new food source (that
>>is, its genes are no different from those of other members of its species
>>who don't eat that food), and teaches its children to do likewise, this
>>could free the apes from some selective pressures (they wouldn't need to
>>compete so hard for older food sources), and create new selective
>>pressures
>>(e.g. modifications in the digestive tract or other anatomical features to
>>enable them to better use the new food source).
>
> isn't that Lamarck? Wikipedia says that Lamarckism holds that traits
> acquired (or diminished) during the lifetime of an organism can be
> passed on to the offspring.
>

Lamarckianism means one or more of the following:

[a] Changes to the phenotype (whether the result of injury, learning, or
whatnot) can alter the genotype; the contrary idea is called "Weismannism"
(oddly, this idea was held by both Lamarck and Darwin, and is not essential
to either theory, but the winners write the history books, and the
Darwinists and Weismannists won).

[b] There is an "evolutionary ladder" from "lower" to "higher" forms, and
different species (or "kinds") evolved from separately originating lineages
that climbed this ladder over time (so, e.g. monkeys do not share common
ancestry with humans, but have evolved the same way we did, but not so far
as we have). Evolution has the "goal" of reaching the top of the ladder,
and all lineages are climbing the same ladder, but are on different rungs.

[c] Populations are propelled up the evolutionary ladder by some innate
force that acts upon their "need" to evolve and become better. Another
force adapts them to local variants of the environment.

The idea that there might be nongenetic influences on development, and
nongenetic paths of inheritance, is not Lamarckian in any of these senses.
>
-- [snip]


>
>>In the analogy, genes (or rather genomes) *are* the recipes. Certainly
>>genomes are available biologically.
>
> the genomes of the early ancestors are not available. We are
> comparing the present DNA makeup with what is supposed to have been in
> the common ancestor, aren't we?
>

It seems to me that we are attempting to reconstruct (in some cases) the DNA
(or some of it) from common ancestors, based on comparisons of the DNA of
living species -- just as a Biblical textual critic attempts to reconstruct
the original wording of the Bible by comparing different surviving texts,
not (of course) the lost ancient manuscripts themselves.
>
-- [snip]


>
>>I don't think you understand the latest human/chimp genome comparisons.
>>And, again, the argument for common descent is not based simply on
>>human/chimp similarities, but on the consistent ways in which we are more
>>similar to chimps than either of us is to gorillas, and so forth
>>throughout
>>the nested hierarchy of life.
>
> not only is similarity not a good basis on which to conclude
> relationship, but the classification itself is entirely subjective.
>

You persistently confuse the subjective *labelling* branch points with the
methods used to determine the branch points themselves, which are not

subjective.
>
>>>>By the way, why is it more reasonable, even if we don't know for sure,
>>>>to
>>>>suppose that the cakes were created from different recipes and different
>>>>batter?
>>>
>>> because, from experience, we know that cakes come from different
>>> batters. There is not one single grand clearing house of cake batter
>>> from which all cakes come.
>>>
>>Okay, you don't buy junk food. Good for you.
>
> I'm curious as to how you drew that conclusion.
>

Because junk food is made from huge batches of batter from which thousands
and thousands of snack food items are made. All twinkies, in fact, come
from one single grand clearing house of twinkie ingredients. It was a joke,
Zoe.
>
-- [snip]


>
> because intelligence is known to create in a nested hierarchical
> fashion. Created items are not known to organize themselves into such
> patterns. It's as simple as that -- observation of how intelligence
> (or mental activity) works, versus stupidity (or mindless activity).
> In every area it works the same except when it comes to evolutionary
> theory. Why is that? Is it a wish to not acknowledge a mind that
> could be of superior intelligence to ours?
>

Well, in a sense, at least one created object -- language -- organizes
itself into nested hierarchies. Humans don't try to change their languages
into new languages (although they add new words and slang), so, e.g. the
change of Latin into Spanish, French, Italian, etc. is unplanned and more an
attribute of the way language works than of human design. Furthermore,
humans deliberately confuse, to some extent, the nested hierarchy into which
languages natural fall as they differentiate from one another, by borrowing
words, and even sounds and grammatical features from one language into
another. So we see in language how consistent nested hierarchies result
from undesigned change, while designed change produces violations of
consistent nested hierarchies. A similar argument applies, as noted, to
automobiles, televisions, and other artifacts of known designers.
>
-- [snip]


>
> of course, they would not be expected to know the chromosome count of
> each other -- leave that to be investigated by the researcher. But it
> would be expected that the mere existence of differing chromosome
> counts would produce differing kinds of proteins such that,
> instinctively, the "same-counts" opakis would gravitate to each other.
>

There's no reason to suppose the proteins would differ; the genes themselves
are not changed (at least not as the result of chromosome fusion or
fission); they are not even moved relative to the genes near them on the
chromosome. The effect is like combining two encyclopedia volumes into one,
or splitting one into two: it doesn't change the articles themselves.


>
>> but the presence of several okapis with odd numbers of
>>chromosomes strongly implies mating between okapis with different numbers
>>of
>>chromosomes, at least in the past.
>
> has this been observed, is the question. Has it been investigated and
> found that two parents of a particular offspring had different
> chromosome counts?
>

It has certainly been done with domestic horses and Pzewalski's horses; I do
not know if it has been done with okapis.
>
-- [snip]


>
>>(although different chromosome numbers, plus other genetic and chromosomal
>>changes, will do this), so there is no reason at all to suppose that the
>>first hominid with 23 chromosome pairs would have any problems mating with
>>hominids of the same species, but with 24 pairs.
>
> until the above question is answered, there is every reason to
> question whether some fantasized first hominid with 23 chromosomes was
> able to interbreed with one with 24 pairs.
>

As noted, it works with horses and mice of different chromosomal races, so
there is, in fact, no reason to question whether it would be possible with
the first hominin with 47 chromosomes (he would, I presume, have one copy
each of chromosomes 2a and 2b, and one copy of the fused chromosome 2).
>
-- [snip]

I was attempting to illustrate to you how a mutation occurring in a single
individual could become fixed (homozygous in 100% of the population) over
time. It was offered as an illustration, not as supporting data for a
theory.


>
>>It works much the same for any mutation.
>
> and from the above speculative scenario it is concluded,
> authoritatively, that, therefore, it woks much the same for any
> mutation?
>

No, from my knowledge of how mutations and inheritance work, I concluded
that it works much the same for any mutation. You have this bad habit (it
seems common in creationists, but that's no excuse) for mistaking
illustrations of conclusions (e.g. the above scenario, or the phylogenic
trees of primates, or a reconstruction of an "ape-man") with the evidence
from which the conclusions were drawn (and, of course, if the pictures or
stories were the evidence, then the conclusions would indeed be weakly
supported).
>
-- [snip]


>
>>No, neutral drift consists of sheer dumb luck, which is a very different
>>matter from natural selection. Evolutionary theory encompasses both,
>>although evolutionists argue among themselves as to which explains more
>>genetic change over time (hardly anyone disputes that natural selection
>>explains *adaptive* change, but not all change is adaptive). Note that
>>sheer dumb luck is quite predictable, which is why Las Vegas casinos
>>manage
>>to stay in business, and quite scientific, which is why probability and
>>statistics exist as branches of mathematics.
>
> probability and statistics has nothing to do with organization and
> building and creating. It just says what are the chances of something
> happening. Once the thing happens, probability and statistics can
> only say what are the chances that such a thing can happen again. You
> don't use probability and statistics to build something in an orderly
> and methodical manner.
>

Some orderly systems do, in fact, arise from purely stochastic processes,
but that is not my point.


>
> Explain to me how you build a digestive system via the mechanism of
> blind, sheer dumb luck. Or make it easier. Explain how you would
> build a cardboard box via the mechanism of sheer dumb luck.
>

I have distinguished between adaptive evolution (which I attribute to
natural selection of mutations), and nonadaptive evolution, which I have
attributed largely to genetic drift ("dumb luck"). Digestive systems are
adaptions. Please try harder to understand the arguments directed at you.
>
-- [snip of Zoe repeating "unfounded assumptions" and "guesses" a lot]

When you are prepared to think about the arguments presented to you, we can
continue.
>
-- Steven J.


Steven J.

unread,
Jul 28, 2005, 1:08:42 AM7/28/05
to

"Zoe" <muz...@aol.com> wrote in message
news:aqege1p8ialqf37vs...@4ax.com...

> On Mon, 25 Jul 2005 02:11:31 -0500, "Steven J."
> <sjt195...@nts.link.net.INVALID> wrote:
>
>>
>>"Zoe" <muz...@aol.com> wrote in message
>>news:6vn8e1h4rfl6ag833...@4ax.com...
>
-- [snip]

>
>>> isn't this what is called assuming your conclusion? You say,
>>> authoritatively, We know that these creatures are successively less
>>> closely related to humans. How do we know this? By our phylogenetic
>>> tree that we have subjectively made up.
>>>
>>No, the phylogenic tree is a conclusion which was not assumed, but
>>inferred
>>from and strongly supported by the data. See Harshman's
>>http://www.talkorigins.org/origins/postmonth/apr05.html for more details.
>>The phylogenic tree isn't offered as evidence, but as a graphic
>>representation of what is deduced from the pattern of similarities and
>>differences in different species.
>
> Okay, here's the core of John's argument:
>
-- [snip]

>
> Well, I'm not going to even consider the statistical test John applies
> to his idea above, because already the above is based on a faulty
> premise. You can have a faulty premise and everything works after
> that, even unto the math and statistics, but the conclusion will still
> be false, regardless of how well the math works, simply because the
> premise itself was false.
>
Two points need to be made here.

First, you have asserted many times that the phylogenic tree is
"subjective." Now, perhaps I've misunderstood you, but I took that to mean
that you felt that, even assuming common ancestry, there was no objective,
testable basis for preferring the conclusion that humans and chimps were
more closely related to each other than to orangutans, than for preferring
the conclusion that humans and orangutans were most closely related.
Clearly, there *is* an objective, testable basis for preferring some
phylogenic trees over others. Even if the premise of common descent is
false, the phylogeny is not purely subjective.

Second, don't you find it rather odd, if the premise of common descent is
false, that multiple lines of evidence converge on the same phylogeny?
Harshman picked a particular set of genes to compare, but one could reach
the same conclusion by examining other genes, or noncoding DNA sequences, or
proteins. If all the hominoid (ape + human) species are separately created,
why do they fall into the sort of pattern we would expect if they were
produced by braching descent from a common ancestor? If apes, or some apes,
are derived by descent with modification from an ape common ancestor, but
humans are separately created, why do comparisons consistently put humans
closer to African apes than to Asian apes -- and closer to chimps than to
gorillas?


>
> What is John's premise in the above comparisons? That DNA sequences
> that are alike mean relationship. He chooses 76 nucleotides that make
> some "claim," as he puts it. The claim, I take it, is that these
> sequences are unique to both humans and chimps. Armed with this
> similarity, and the faulty premise that similarity must mean
> relationship, he proceeds to show how much more similar the
> human/chimp relationships are than any other primate.
>

This is a meaning of "unique" which I have not previously encountered. The
sequences are found in both humans and other apes; homologues are probably
found in monkeys as well, and it would not surprise me to find them in many
other mammalian species.


>
> Well, big whoopdeedoo.
>
> I can decide that similarity between computer-generated characters
> means that they are related, too. I can point out where the
> similarities lie, and how much more similar certain computer-generated
> characters are than others. That does not make the characters any
> more related to each other, just by my setting up some unsupported
> standard that says similarity means relationship.
>
> First John needs to establish the validity of his premise, that
> similarity HAS to mean relationship. He has not done so.
>

Or you have not understood his argument.
>
> snip>
>
-- Steven J.


Zoe

unread,
Jul 30, 2005, 5:41:57 PM7/30/05
to
On Wed, 27 Jul 2005 23:54:26 -0500, "Steven J."
<sjt195...@nts.link.net.INVALID> wrote:

>
>"Zoe" <muz...@aol.com> wrote in message
>news:io8ge1da66g48bj0b...@4ax.com...
>> On Mon, 25 Jul 2005 01:33:57 -0500, "Steven J."
>> <sjt195...@nts.link.net.INVALID> wrote:
>>
>-- [snip]
>>
>> the problem is not with the number of assumptions. It is with the
>> fact that parsimony is applied to a situation in which numbers are
>> irrelevant. Random mutations have no order governing them. They can
>> happen often or little or not at all, according to sheer dumb luck, as
>> you put it. So to try to apply a principle of order and "how it
>> should be" to random activity would be useless, I think.
>>
>Zoe, if your statements above were true, why would there be -- how *could*
>there be -- such a thing as a "mutation rate?" For that matter, how could
>there be "hot spots" on chromosomes where mutations are more likely than at
>other loci? "Random," with respect to mutations, does not mean that the
>mutations occur for no reason, or that all mutations are equally likely, or
>that there is no possibility of saying how likely a mutation is to occur.
>It means simply that the causes of the mutations, and the causes that make
>some traits beneficial and others harmful, are not related to one another.
>
>For that matter, again, if random events had no order governing them, then
>probability as a field of mathematics could not exist. Your position as
>stated above is pure obstinant folly.

probability and statistics does not explain how a cardboard box is put
together. Neither does it explain how a certain number of chromosomes
are consistently found in any particular life form. It merely
predicts the chances of a single, discrete action occurring. These
threads have had to do with how systems are put together.

So now, are you saying that random events are credited with pulling
together a digestive system or a circulatory system or a cardboard
box? Or are you taking a fully-formed reproductive system and
applying your evolutionary theory of mutations to it? I am really
interested in the construction of the system, not in the mutations
that can happen to the construction.

>>
>-- [snip]
>>
>> if sequence similarity between genes were truly 99.75%, then
>> morphologically, we would be 99.75% similar to chimps. Reality is, we
>> are not 99.75% similar to chimps in our outward appearance. Outward
>> appearance is a result of those same genes that are considered to be
>> almost identical to chimps.
>>
>There is no one-to-one mapping between genotype and phenotype.

I didn't mean genotype and phenotype here, but a one-to-one mapping
between genes and morophology. A specific gene will always produce
the same specific protein or proteins, and if there is another gene
that is identical to it, that identical gene will also produce the
same results. So if the claim is that gene similarity was 99.75%
between chimps and humans, you would expect to find 99.75% similar
morphology.

> A tiny
>alteration in a gene can have an immense effect on how the organism
>develops, or, conversely, very large changes in multiple genes can have no
>effect at all.

references, please, for the claim that large changes in multiple genes


can have no effect at all.

> It has been known for a long time (since well before the
>discovery of genes) that tiny changes in developmental rates (e.g. how long
>a particular structure continues to grow) can produce immense differences in
>how an organism looks -- and tiny changes in development rates can result
>from tiny changes in genes. OTOH, as noted, large sections of many proteins
>(and hence the genes that code for them) can be replaced with completely
>different sequences without affecting function.

references, please?

> Consider how many genetic
>disorders are the result of changing one amino acid in one protein (the
>result of changing one nucleotide in one gene). Equally drastic effects
>that are not disorders can be produced by equally small changes.

examples of these equally drastic effects that are not disorders?

>>
>>> Note that the authors distinguish between "adaptive
>>>evolution" ("beneficial mutations") and, presumably, evolution that isn't
>>>adaptive. If I'm reading this right, about 83% of the genes show *some*
>>>difference (perhaps only one or two nucleotides altered), and about 3% of
>>>genes show differences that resulted from beneficial mutations spreading
>>>through natural selection, and the rest show differences that are inferred
>>>to have arisen through neutral mutations that drifted to fixation. Of
>>>course, this summary does not enable me to determine how they decided
>>>which
>>>changes were adaptive and which were not.
>>
>> is there even a way to determine if a change is adaptive versus a
>> result of some rare "beneficial" mutation?
>>
>"Beneficial" mutations are by definition "adaptive," since both "beneficial"
>and "adaption" are diagnosed because they enhance the organism's chances of
>surviving and reproducing in a particular environment. Not all adaptive
>change is the result of mutations: it may be that the "fitter" or better
>adapted alleles are already present in the population, and simply become
>more common due to natural selection. "Adaptive" evolution simply means
>that alleles that are more beneficial become more common, whether those
>alleles arise from new mutations or have been present since the parent
>population first evolved.

so how do you determine whether an adaptation is inherent or a result
of beneficial mutations? You haven't answered that yet.

you're excluding yourself, Steven? :-)

> would infer that one of those two sentences was the original, and
>the other was derived by either adding or removing the initial "not."

I did not assume that one of the two sentences was an original. In
the creationist worldview, one sentence could be original to them. In
the evolutionist worldview, the other sentence could be original to
them. They are simply original statements of belief, neither copying
the other.

>-- [snip]
>>
>> a nested hierarchy would only be strong evidence if there are no other
>> nested hierarchies that form in the real world. To ignore the fact
>> that there are other nested hierarchies in the real world that are not
>> a result of common descent, and then claim that this one particular
>> nested hierarchy must be the result of common descent, is to impose an
>> undue burden upon the one evolutionary hierarchy.
>>
>Strictly speaking, one can arrange any set of entities in a nested
>hierarchy.

which is what has been done for the biological world. Humans have
arranged biological life forms into hierarchies.

> Anyone who's ever written an outline for a paper, or tried to
>sort books in a library, has arranged ideas or objects in a nested
>hierarchy. Note, though, that for many sets of objects, there are multiple
>equally valid hierarchical arrangements of the objects. A book on, e.g.
>_The History of the Spread of the Great Plague_ might be filed under
>"History," or "Epidemiology," or "Diseases." One can arrange automobiles in
>many different nested hierarchies: arrange them by manufacturer (e.g. GM
>cars, and within that category Dodges, Cadillacs, Chevrolets, etc.), or by
>type of vehicle (e.g. sedans, and under sedans GM sedans, Ford sedans,
>etc.), or by various other schemes. One can always get a nested hierarchy,
>but the hierarchy one gets depends on the traits one selects to compare.

and the traits selected for biology is morphology and genetics, right?
Biology can also be classified into other hierarchies, using other
traits as standards, such as habits, location, size, mental abilities,
and so on.

All that hierarchies demonstrate is the ability of humans to
categorize and compare.

>What makes biology interesting is that one can pick many different sets of
>traits to compare, and get the *same* nested hierarchy.

as long as you are consistently categorizing the same items, whether
books or cars or life forms, you will always get nested hierarchies
for whatever traits are chosen to be used as a categorizing tool. For
any category chosen, you WILL get the same nested hierarchy because
you are dealing with the same category of things.

> The most-cited
>example is the hierarchy formed by comparison of anatomical features and
>that formed by comparing genes and proteins (the "twin nested hierarchy),

don't stop at "twin nested". You can get triple nested, too, or
quadruple nested. The ability to categorize in a hierarchical manner
doesn't demonstrate much, other than the ability to compare, since
anything else can be formed into several nested hierarchies, also.

>but one can see the same thing just be comparing, say, anatomical features.
>All organisms with one bone in the lower jaw and three in the middle ear
>also have mammary glands, and none have feathers. There's no obvious
>reason, assuming separate origins, for that feature -- why not bats with
>feathers, or penguins with mammary glands? *Consistent* nested hierarchies
>do not arise through known methods of design -- human engineers cross-copy
>components into very different designs (e.g. CD players installed in both GM
>sedans and Ford trucks). Nature does not: pterosaurs and bats, although
>both used furry membranous wings, use different ways of modifying forelimbs
>to produce those wings.

are you saying that similarity, wherever observed, must always be
evidence of common roots and never evidence of cross-copying? On what
basis do you decide that certain similarities cannot be the result of
cross copying and other similarities are the result of cross-copying?

I hope the basis isn't that: "There is no mind higher than ours,
therefore anything that has no human creator must be self created from
a common root."

>> For the evolutionary understanding of nested hierarchy, see:
>>
>> http://www.lobue.com/enterprise_evolution/knowledge_hierarchy.html
>>
>This is astonishing. You may just have found the worst explanation of what
>evolutionists mean by "nested hierarchy" on the entire World Wide Web (this
>is not to say that the explanation is useless for other purposes). I would
>suggest, rather,
>
>http://www.talkorigins.org/faqs/comdesc/CDhierarchy.html
>http://www.talkorigins.org/faqs/comdesc/CDhierarchy.html

same link

>http://www.isss.org/hierarchy.htm

these links say, just in detail, what my link says in brief. I
understand that nested hierarchies can be developed for just about
anything, and that includes biological life forms.

>> by the above evolutionary admission, there are other nested
>> hierarchies besides the biological hierarchies.
>>
>> Nested hierarchy is just another term for levels of organization. You
>> find levels of organization in many other fields besides biology.
>> None of these other fields draw the conclusion that, therefore, common
>> source or ancestry is indicated.
>>
>Actually, a "nested" hierarchy has not merely levels of organization, but
>the lower levels form parts of the higher levels, as, e.g. "primates" are
>part of the "mammals," which are part of the "vertebrates."

agreed, if these are the classification standards chosen.

>> Take, for instance, the following hierarchy for all humans.
>>
>> Using geographical boundaries. North America: USA: Florida: Seminole
>> County: Orlando: 100 East Street: Human: John Doe.
>>
>John Doe is not a geographical feature; he is not part of East Street, or
>part of the geography of Seminole County. Note, furthermore, that [a] if
>John Doe moves to California, he ceases to be part of Seminole County in any
>sense, and [b] John Doe can, as you note below, be classified as part of a
>quite different nested hierarchy. Again, you are ignoring the salient and
>compelling nature of the consistent nested hierarchies in biology.

I expect any nested hierarchy to be consistent as long as the
categorization is consistently of the same group.

>> Using ecological boundaries. Biome: Community: Population: Human:
>> John Doe.
>>
>> Lo, we have a twin-nested hierarchy.
>>
>No, you have two quite different nested hierarchies containing the same
>entity.

okay, so I'm not the greatest classifier, but it doesn't mean
twin-nested hierarchies cannot be drawn up for just about any set of
things.

> Again, one can construct nested hierarchies for any set of objects
>or ideas, but the distinctive feature of life is that it falls into pretty
>much the same hierarchy no matter what traits one seeks to compare.

actually, this is not a distinctive feature of life. It is a feature
of any group of things one chooses to categorize hierarchically.

snip what has already been answered>

>>>No, neutral drift consists of sheer dumb luck, which is a very different
>>>matter from natural selection. Evolutionary theory encompasses both,
>>>although evolutionists argue among themselves as to which explains more
>>>genetic change over time (hardly anyone disputes that natural selection
>>>explains *adaptive* change, but not all change is adaptive). Note that
>>>sheer dumb luck is quite predictable, which is why Las Vegas casinos
>>>manage
>>>to stay in business, and quite scientific, which is why probability and
>>>statistics exist as branches of mathematics.
>>
>> probability and statistics has nothing to do with organization and
>> building and creating. It just says what are the chances of something
>> happening. Once the thing happens, probability and statistics can
>> only say what are the chances that such a thing can happen again. You
>> don't use probability and statistics to build something in an orderly
>> and methodical manner.
>>
>Some orderly systems do, in fact, arise from purely stochastic processes,
>but that is not my point.
>>
>> Explain to me how you build a digestive system via the mechanism of
>> blind, sheer dumb luck. Or make it easier. Explain how you would
>> build a cardboard box via the mechanism of sheer dumb luck.
>>
>I have distinguished between adaptive evolution (which I attribute to
>natural selection of mutations), and nonadaptive evolution, which I have
>attributed largely to genetic drift ("dumb luck"). Digestive systems are
>adaptions. Please try harder to understand the arguments directed at you.

please, Steven, dearest, try harder to understand my question, which
is, again:

Explain to me how you build a digestive system via the mechanism of
blind, sheer dumb luck. Or make it easier. Explain how you would
build a cardboard box via the mechanism of sheer dumb luck.

snip>

>When you are prepared to think about the arguments presented to you, we can
>continue.

I've thought about the arguments, find them unpersuasive, so I shall
indeed continue on....to Creation Theory-6. :-)

Steven J.

unread,
Jul 31, 2005, 6:53:55 PM7/31/05
to

"Zoe" <muz...@aol.com> wrote in message
news:igsne1tsdue4nfr1b...@4ax.com...

> On Wed, 27 Jul 2005 23:54:26 -0500, "Steven J."
> <sjt195...@nts.link.net.INVALID> wrote:
>
-- [snip]

>
>>For that matter, again, if random events had no order governing them, then
>>probability as a field of mathematics could not exist. Your position as
>>stated above is pure obstinant folly.
>
> probability and statistics does not explain how a cardboard box is put
> together. Neither does it explain how a certain number of chromosomes
> are consistently found in any particular life form. It merely
> predicts the chances of a single, discrete action occurring. These
> threads have had to do with how systems are put together.
>
Zoe, I thought that we had established that, in fact, a "certain number of
chromosomes" is not found consistently in any particular species; there are
species with varying numbers of chromosomes in different individuals.
Heredity explains (to the extent that heredity is understood) why, in
general, chromosome counts don't vary wildly from parent to offspring or
individual to individual within a species.

>
> So now, are you saying that random events are credited with pulling
> together a digestive system or a circulatory system or a cardboard
> box? Or are you taking a fully-formed reproductive system and
> applying your evolutionary theory of mutations to it? I am really
> interested in the construction of the system, not in the mutations
> that can happen to the construction.
>
No, I am not saying that random events are credited with putting together a
digestive system (at least, not by themselves); random events in combination
with natural selection (reproduction, variation, and differential
reproductive success) put complex structures together.

>
>>>
>>-- [snip]
>>>
>>> if sequence similarity between genes were truly 99.75%, then
>>> morphologically, we would be 99.75% similar to chimps. Reality is, we
>>> are not 99.75% similar to chimps in our outward appearance. Outward
>>> appearance is a result of those same genes that are considered to be
>>> almost identical to chimps.
>>>
>>There is no one-to-one mapping between genotype and phenotype.
>
> I didn't mean genotype and phenotype here, but a one-to-one mapping
> between genes and morophology. A specific gene will always produce
> the same specific protein or proteins, and if there is another gene
> that is identical to it, that identical gene will also produce the
> same results. So if the claim is that gene similarity was 99.75%
> between chimps and humans, you would expect to find 99.75% similar
> morphology.
>
What is your definition of "phenotype," and how does "phenotype" differ from
"morphology?" Now, to be sure, to a biologist "phenotype" includes behavior
(a pointer's tendency to point at birds is as much part of its phenotype as
the shape of its ears), and may even include results of that behavior
(Richard Dawkins has argued for treating, e.g. beaver dams and termite
mounds as part of the phenotypes of these species), but it's basically "what
the genes build, directly or indirectly, in a given environment."

http://w3.fiu.edu/milesk/genetics.htm

Let's take a simple case and question: are chihuahuas and St. Bernards 99+%
similar in morphology (note that not merely size, but proportions and even
toe number may vary between these breeds)? Domestic dogs differ from grey
wolves by only about 0.2% of their mitochrondrial DNA (and mitochrondrial
DNA mutates faster and is more variable than nuclear DNA, which is what we
were comparing with humans and chimps above), so the degree of genetic
difference between any two dog breeds must be very tiny indeed. I'm not
sure how you'd quantify the difference between, e.g. the St. Bernard and the
chihuahua, or a greyhound and a dachsund, but I think you'd easily come up
with less than 99.9% similarity in appearance, for all that their genetic
similarity can be that great.


>
>> A tiny
>>alteration in a gene can have an immense effect on how the organism
>>develops, or, conversely, very large changes in multiple genes can have no
>>effect at all.
>
> references, please, for the claim that large changes in multiple genes
> can have no effect at all.
>

http://globin.cse.psu.edu/html/huisman/variants/contents.html

There are over 1000 documented variants in human hemoglobin. Granted, many
of these produce very marked and generally deleterious phenotypic effects
(e.g. sickle-cell anemia, thalassemia, etc.), but others have no apparent
difference in function from normal human hemoglobin. Or consider this:
there is a gene, Pax-6, which triggers eye development in fruit flies.
Humans also have a form of Pax-6 (which controls development of the iris of
the human eye), which is not identical to the fruit fly version, but
experimenters have induced fruit fly eyes to grow on fruit fly wings by
introducing *human* Pax-6 genes into the wings (there are, of course,
already fruit fly Pax-6 genes in the wings, but they are deactivated).
Evidently, fruit flies could develop normally if some of their genes were
replaced by their human homologues, which implies, again, that large changes
in multiple genes could have little or no noticeable effect. The large
variations in sequence between cytochrome-c in various species, together
with the similarity in function of the enzyme in different species, likewise
suggests that changes in genes don't map one-to-one directly to changes in
morphology or behavior.


>
>> It has been known for a long time (since well before the
>>discovery of genes) that tiny changes in developmental rates (e.g. how
>>long
>>a particular structure continues to grow) can produce immense differences
>>in
>>how an organism looks -- and tiny changes in development rates can result
>>from tiny changes in genes. OTOH, as noted, large sections of many
>>proteins
>>(and hence the genes that code for them) can be replaced with completely
>>different sequences without affecting function.
>
> references, please?
>

The classic examples of small changes in genes producing large phenotypic
effects are things like four-winged fruit flies (the rear wings are produced
by a single mutation modifying the growth of the halteres behind the
front -- and in normal flies, only -- wings), or achondroplasty in humans or
dogs (a mutation that shortens the limbs).

It is well-known that some homologous proteins between different species are
very different in sequence (e.g. the aforementioned cytochrome-c, or the
even more widely varying fibrins, while others (e.g. the histones that form
the backbones of chromosomes) differ very little between species. And I've
mentioned that there are variants in hemoglobin within the human species,
some of which don't seem to have much in the way of effects. The inference,
of course, is that nearly all alterations to histones prevent them from
working properly, while hemoglobin and cytochrome-c can vary much more
without affecting function.

http://alpha2.bmc.uu.se/~lars/biowww/Proteinevol.html


>
>> Consider how many genetic
>>disorders are the result of changing one amino acid in one protein (the
>>result of changing one nucleotide in one gene). Equally drastic effects
>>that are not disorders can be produced by equally small changes.
>
> examples of these equally drastic effects that are not disorders?
>

Does
http://www.hindu.com/thehindu/seta/2002/03/07/stories/2002030700060300.htm
count? It involves a mutation that drastically reduces the number of pairs
of legs in a species of shrimp, without so far as I can tell actually
crippling the shrimp.

http://www.talkorigins.org/faqs/mutations.html#Q2 has a list of favorable
mutations in various species, which would certainly seem to answer your
request.

You weren't asking that question. With bacteria or fruit flies, watching
evolution in real time, one can sequence individuals at the start and end of
the experiment and spot the mutations. In the case of humans and chimps,
one can only note that certain alleles that are ubiquitous in humans are
unknown in chimps, and infer that either humans or chimps have experienced a
mutation since the LCA.
>
-- [snip example of difference between Zoe logic and Earth logic]

But pretty clearly ear bones and mammary glands are not the same things.
Having hair and having a single (left) aortic arch (as opposed to having two
aortic arches like many reptiles, or a single right arch like birds) are not
the same thing either. So why, if you create a category of all vertebrates
that have three bones in the inner ear, have you also, automatically,
created a category of all vertebrates with mammary glands, a single left
aortic arch, and fur?

If I create a category of all cars with automatic transmissions and four
doors, that will not the the same as, or entirely contain, or be entirely
contained within, a category of, e.g. "all Ford cars with CD players."
Consistent nested hierarchies which arise independently from comparisons of
many different sets of traits are not found in designed artifacts.


>
>> The most-cited
>>example is the hierarchy formed by comparison of anatomical features and
>>that formed by comparing genes and proteins (the "twin nested hierarchy),
>
> don't stop at "twin nested". You can get triple nested, too, or
> quadruple nested. The ability to categorize in a hierarchical manner
> doesn't demonstrate much, other than the ability to compare, since
> anything else can be formed into several nested hierarchies, also.
>

The point, again, is that living things fall into *one* nested hierarchy,
regardless of the features chosen in order to arrange that hierarchy. That
is a product of branching descent with inheritance and modification, and
only of such a process.


>
>>but one can see the same thing just be comparing, say, anatomical
>>features.
>>All organisms with one bone in the lower jaw and three in the middle ear
>>also have mammary glands, and none have feathers. There's no obvious
>>reason, assuming separate origins, for that feature -- why not bats with
>>feathers, or penguins with mammary glands? *Consistent* nested
>>hierarchies
>>do not arise through known methods of design -- human engineers cross-copy
>>components into very different designs (e.g. CD players installed in both
>>GM
>>sedans and Ford trucks). Nature does not: pterosaurs and bats, although
>>both used furry membranous wings, use different ways of modifying
>>forelimbs
>>to produce those wings.
>
> are you saying that similarity, wherever observed, must always be
> evidence of common roots and never evidence of cross-copying? On what
> basis do you decide that certain similarities cannot be the result of
> cross copying and other similarities are the result of cross-copying?
>

I was talking, in this case, about *dissimilarity*. Pterosaurs and bats
clearly aren't examples of cross-copying, because their shared features are
all shared with the larger category of amniote vertebrates, and their
derived features -- e.g. wings and other flight adaptions -- are different
from each other. Just as a tape player in one truck isn't cross-copied from
a CD player in another, so bird, bat, and pterosaur wings don't seem to be
examples of cross-copying. Conversely, we see that small, insect-eating
birds have the same basic wing structure as large birds like eagles (or
ostriches, for that matter), while small, insect-eating bats have the same
basic wing structure (as well as many other anatomical similarities to)
large fruit bats. If wings aren't cross-copied between bats and birds in
similar ecological niches, and both bats and birds fall into the consistent
nested hierarchies expected from common descent, isn't it reasonable to
ascribe the shared wings of bats to common roots? Indeed, the various
creationists who speak of a "bat kind" seem to accept this reasoning.
>
-- [snip]
>
-- Steven J.


John Harshman

unread,
Aug 1, 2005, 1:11:26 AM8/1/05
to
Zoe wrote:

I'm afraid all that is irrelevant, since we're not talking about
aneuploidy (which is what the snippet is discussing), but fusions.
Karyotyping can tell you whether the offspring has inherited the unfused
state from one parent and the fused state from another.

>>>>The factors that allow or prevent interbreeding are complex,
>>>>but simple length of time apart is one of them.
>>>
>>>
>>>so would your theory predict that the Chinese race, living apart from
>>>the Indian race, would eventually, over time, evolve the inability to
>>>interbreed?
>>
>>If that were true, then yes it would. However, no human population has
>>ever been that isolated. There is no Chinese race and no Indian race,
>>just clinal variation from one point to another.
>
> my point was, according to evolutionary ideas, if there are groups of
> Chinese that have never been to India, and groups of Indians that
> never went to China, would members of those particular groups, should
> they ever meet after thousands of years, be unable to interbreed?
>
> snip the rest of John's non-answers>

It wasn't a non-answer. Read it and try to understand. It doesn't matter
whether anyone travels between China and India, as long as there is a
chain of interbreeding populations in between -- which there is. What
you may have been trying to say, and it's hard to tell, is that if there
were total isolation between China and India for a long enough period,
the inhabitants would become different species. And that's true, though
how much time would be required is unclear.

ErikW

unread,
Aug 1, 2005, 3:17:58 AM8/1/05
to

No. If he were to type out all nucleotide positions in that sequence it
would take too much space. So he excluded all nucleotides that are not
different between all species because they don't make any claim about
relationships. (That they make no claim means that they are not
informative, i.e. have no information to contribute to this particular
question.) What remains after pruning out nucleotide positions that do
not make any claim are those that contain differences that are shared
between two or more species in the table since they have the necessary
information. The claims that the postitions make are different for
different positions and he included all of them. (It's all written in
the quote you presented above. I got the impression that you
misunderstood it, however.)

> Armed with this
> similarity, and the faulty premise that similarity must mean
> relationship, he proceeds to show how much more similar the
> human/chimp relationships are than any other primate.
>
> Well, big whoopdeedoo.

You might want to consider another claim of his from that post: "By
itself, this is pretty good evidence for the African ape connection.
But if I did this little exercise with any other gene I would get the
same result too."

Something worth thinking about.

Zoe

unread,
Aug 3, 2005, 9:41:11 PM8/3/05
to
On Sun, 31 Jul 2005 17:53:55 -0500, "Steven J."
<sjt195...@nts.link.net.INVALID> wrote:

>
>"Zoe" <muz...@aol.com> wrote in message
>news:igsne1tsdue4nfr1b...@4ax.com...
>> On Wed, 27 Jul 2005 23:54:26 -0500, "Steven J."
>> <sjt195...@nts.link.net.INVALID> wrote:
>>
>-- [snip]
>>
>>>For that matter, again, if random events had no order governing them, then
>>>probability as a field of mathematics could not exist. Your position as
>>>stated above is pure obstinant folly.
>>
>> probability and statistics does not explain how a cardboard box is put
>> together. Neither does it explain how a certain number of chromosomes
>> are consistently found in any particular life form. It merely
>> predicts the chances of a single, discrete action occurring. These
>> threads have had to do with how systems are put together.
>>
>Zoe, I thought that we had established that, in fact, a "certain number of
>chromosomes" is not found consistently in any particular species; there are
>species with varying numbers of chromosomes in different individuals.
>Heredity explains (to the extent that heredity is understood) why, in
>general, chromosome counts don't vary wildly from parent to offspring or
>individual to individual within a species.

Steven, I'm talking about the usefulness of probability and statistics
in explaining how a cardboard box is put together or in determining
how chromosomes are consistently the same for any group of life forms.
It isn't useful for these purposes, is it?

>> So now, are you saying that random events are credited with pulling
>> together a digestive system or a circulatory system or a cardboard
>> box? Or are you taking a fully-formed reproductive system and
>> applying your evolutionary theory of mutations to it? I am really
>> interested in the construction of the system, not in the mutations
>> that can happen to the construction.
>>
>No, I am not saying that random events are credited with putting together a
>digestive system (at least, not by themselves); random events in combination
>with natural selection (reproduction, variation, and differential
>reproductive success) put complex structures together.

and this is the process that has not yet been explained by posters to
TO -- not one. Please describe a scenario, based on facts, not
fantasy, of how a digestive system comes together through random
events in combination with natural selection. And you cannot use
reproduction, variation, and differential reproductive success unless
you are willing to concede that the machinery was already in place,
fully functioning, after which comes along your mutations and
selection.

So, okay, we have a simple common ancestor consisting of a single
functioning cell (and even that is a generous given) that replicates
(we know not how that started). Take it from there and describe a
realistic scenario, using factual, scientific observations, as to how
this single cell develops a digestive system, based on random
mutations and selection.

Can't do it? Then evolutionists need to be a little humbler about
their position. To say "We know the digestive system evolved," but go
silent when the question of "how?" is asked, is to ask thinking minds
to take your word on faith.

So, here we go.

A single cell exists, replicating itself repeatedly. Along comes a
random "beneficial mutation." What happens next, based on your
selection principle? How does the digestive system develop?

>>
>>>>
>>>-- [snip]
>>>>
>>>> if sequence similarity between genes were truly 99.75%, then
>>>> morphologically, we would be 99.75% similar to chimps. Reality is, we
>>>> are not 99.75% similar to chimps in our outward appearance. Outward
>>>> appearance is a result of those same genes that are considered to be
>>>> almost identical to chimps.
>>>>
>>>There is no one-to-one mapping between genotype and phenotype.
>>
>> I didn't mean genotype and phenotype here, but a one-to-one mapping
>> between genes and morophology. A specific gene will always produce
>> the same specific protein or proteins, and if there is another gene
>> that is identical to it, that identical gene will also produce the
>> same results. So if the claim is that gene similarity was 99.75%
>> between chimps and humans, you would expect to find 99.75% similar
>> morphology.
>>
>What is your definition of "phenotype," and how does "phenotype" differ from
>"morphology?"

phenotype has to do with group characteristics, psychological and
anatomical, resulting from both heredity and environment. It refers
to characteristics of organisms collectively, or a group of organisms
having like characteristics.

Morphology has to do with individual characteristics, the form and
structure of individual animals and plants.

>Now, to be sure, to a biologist "phenotype" includes behavior
>(a pointer's tendency to point at birds is as much part of its phenotype as
>the shape of its ears), and may even include results of that behavior
>(Richard Dawkins has argued for treating, e.g. beaver dams and termite
>mounds as part of the phenotypes of these species), but it's basically "what
>the genes build, directly or indirectly, in a given environment."
>
>http://w3.fiu.edu/milesk/genetics.htm
>
>Let's take a simple case and question: are chihuahuas and St. Bernards 99+%
>similar in morphology (note that not merely size, but proportions and even
>toe number may vary between these breeds)? Domestic dogs differ from grey
>wolves by only about 0.2% of their mitochrondrial DNA (and mitochrondrial
>DNA mutates faster and is more variable than nuclear DNA, which is what we
>were comparing with humans and chimps above), so the degree of genetic
>difference between any two dog breeds must be very tiny indeed. I'm not
>sure how you'd quantify the difference between, e.g. the St. Bernard and the
>chihuahua, or a greyhound and a dachsund, but I think you'd easily come up
>with less than 99.9% similarity in appearance, for all that their genetic
>similarity can be that great.

nuclear DNA produces morphological similarity. MtDNA has to do with
energy transfer, not morphological similarities. So why are you using
MtDNA as an example of morphological similarity?

>>> A tiny
>>>alteration in a gene can have an immense effect on how the organism
>>>develops, or, conversely, very large changes in multiple genes can have no
>>>effect at all.
>>
>> references, please, for the claim that large changes in multiple genes
>> can have no effect at all.
>>
>http://globin.cse.psu.edu/html/huisman/variants/contents.html

want to summarize or quote the section from this that describes very
large changes in multiple genes having no effect at all? Giving me
this link is tantamount to someone asking me a Biblical question and I
throw the whole Bible at them and say, "there's your reference."

>There are over 1000 documented variants in human hemoglobin. Granted, many
>of these produce very marked and generally deleterious phenotypic effects
>(e.g. sickle-cell anemia, thalassemia, etc.), but others have no apparent
>difference in function from normal human hemoglobin.

reference and quote, please? Not the whole library, but something
specific that you have read in the above.

> Or consider this:
>there is a gene, Pax-6, which triggers eye development in fruit flies.
>Humans also have a form of Pax-6 (which controls development of the iris of
>the human eye), which is not identical to the fruit fly version, but
>experimenters have induced fruit fly eyes to grow on fruit fly wings by
>introducing *human* Pax-6 genes into the wings (there are, of course,
>already fruit fly Pax-6 genes in the wings, but they are deactivated).
>Evidently, fruit flies could develop normally if some of their genes were
>replaced by their human homologues, which implies, again, that large changes
>in multiple genes could have little or no noticeable effect.

I