Re: Request


"Zoe" <muze10@xxxxxxx> wrote in message
news:igsne1tsdue4nfr1b8rgd1he8hq6cjtq3i@xxxxxxxxxx
> On Wed, 27 Jul 2005 23:54:26 -0500, "Steven J."
> <sjt1957NOSPAM@xxxxxxxxxxxxxxxxxxxx> 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.
>
>>>> 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 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]
>
>>> 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.
>
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.


.

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