Re: Request


"Zoe" <muze10@xxxxxxx> wrote in message
news:aj7tf1ddp8oc80isq40kg517p2f7v0in4m@xxxxxxxxxx
> On Wed, 10 Aug 2005 00:35:48 -0500, "Steven J."
> <sjt1957NOSPAM@xxxxxxxxxxxxxxxxxxxx> wrote:
>
> zoe asked:
>
>>> What is the source information for chromosome fission or fusion?
>>>
>>> Apparently, the basis on which you decide that the last common
>>> ancestor was more likely to have 24 chromosomes is because all apes
>>> except humans have 24 chromosomes. You conclude that there is more of
>>> a chance for fusion rather fission because there are (present tense)
>>> more populations of 24's available for the random fusing mutation, and
>>> less of a chance for the random fissioning mutation to hit a single
>>> population of 23's. But the probability is calculated on what exists
>>> today and not on the original population, which is what I think should
>>> be used.
>
>>No, that is not the basis. The basis is this: if the last common ancestor
>>(LCA) of great apes had 23 pairs of chromosomes, then at least three
>>fissions (of the exact same chromosome, at the exact same place on that
>>chromosome) had to take place (once in the line leading from the LCA to
>>orangutans, and once again in the line leading to gorillas after the
>>African
>>apes split off, and once yet again in the chimp line after the
>>human-chimp
>>split).
>
> why would there have to be three fissions? You're forgetting about
> inheritance. You can have a member of a 23-chromosome population get
> hit by your mutation, supposedly causing fission. That member should
> now be the LCA of populations with 24 chromosomes. If the first small
> population of 24's does not get decimated by the abundance of 23's
> (most likely to happen within your worldview), then you now have your
> growing population of 24's which, according to your theory,
> differentiated into gorillas, chimps, et cetera.
>
The difficulty with this scenario, as I explained in the post to which you
are replying, is that orangutans differentiated from African apes *before*
African apes (including humans) differentiated from each other, and that
among African apes, gorillas differentiated from chimps/humans *before*
humans differentiated from chimps. This is based on comparisons of many,
many different DNA sequences and proteins, all of which show African apes
are more different from (and therefore, on the assumption of common descent,
split off from our family line before) orangutans than any of the African
apes are from each other, and most of which show that gorillas are more
different from humans and chimps than humans and chimps are from each other.

Never mind, just for the moment, that you don't accept such facts as
arguments for a literal tree of descent; just recall that evolutionists
accept them, and cannot suppose that one species (with 24 chromosome pairs)
could give rise to chimps, gorillas, and orangutatans without being
ancestral to humans (with 23 chromosome pairs) as well.

You are, by the way, correct to suppose that it was unlikely that the
chromosomal fusion would spread through the population and become fixed.
But then, there's no reason to suppose that the chromosomal fusion is
special, or beneficial, or important to anything (like erect posture, or
large brains, or whatnot) that make us human. It's just one of the neutral
mutations that happened to accumulate in the line leading up to us. Neutral
mutations are common, and some of them, by sheer chance, are going to become
fixed. Oddly, the ID proponent William Dembski makes a good point about
this: he warns us of the distinction between hitting a target with an arrow
("specification"), and drawing a target around wherever the arrow happened
to hit. The 23-chromosome-pair arrangement is just where, for us, the arrow
happened to hit.
>
> If you insist that the 24-chromosome population was more likely to
> start first, then you still have to explain how the first 24's
> differentiated into your hypothesized various species of apes. Your
> explanation for this differentiation could have taken place just as
> well before a fusion occurs, as after a fission occurs. It has
> nothing to do with parsimony.
>
You don't seem to understand my argument.
>
> So I don't see how probability and statistics has an answer to
> something that you have no idea which came first, 23 or 24. How can
> odds be placed on an unknown? It is not known if your "history" of
> ape chromosomes is even a reality. It's like saying, let's suppose
> that fairies exist and they have a human-like form. Now we can
> sequence DNA from humans and then we'll know what fairies' DNA was
> like.
>
First of all, it's not very much like that at all. We're hardly saying
"let's suppose chimpanzees and gorillas exist," or even "let's suppose
australopiths and ardipithecenes existed" (although we can directly examine
the genes of chimps and gorillas, which is not possible for extinct apes).
You seem quite obstinate in your refusal to learn anything or revise your
thinking here.

Second, as I've explained to you, there is no one-to-one mapping of genotype
onto phenotype, and no reason, in terms of genetics, for fairies to have
humanlike genomes simply because they have humanlike phenotypes.
>
> large snip of non-answers>
>
>>By the way, while I don't think it's important to this discussion,
>>"mutations are random" does *NOT* mean "all mutations are equally likely,"
>>or "all mutations are equally likely to be selected"
>
> isn't that the meaning of "random"? Why the specialized meaning of
> random in evolutionary theory then? Might as well use a different
> term.
>
John Harshman has already answered this (and your other points as well), but
let me try again. If I toss one six-sided die, I get a random result with
every possible outcome equally likely. But if I toss two six-sided dice, I
get a random outcome in which some outcomes (2 and 36) have only a 1 in 36
chance of happening, while another (7) has a 1 in 6 chance of occurring.
"Random" also has a common meaning of "unrelated to whatever purpose
something is needed for." If, e.g. I am on the streets and ask "random
strangers" for the time, that does not mean I am asking people who have no
reason to be on the street, or who might as well be in some other city, but
people who I have no particular reason to suppose know the correct time or
wish to tell me what it is.
>
> snip>
>
>>>>also suspect that you have neither the intention nor the ability to tell
>>>>us
>>>>how "intelligence" (other, perhaps, than human intelligence) implements
>>>>any
>>>>"design" or change in design in living organisms.
>>>
>>> I cannot make a digestive system, so I cannot tell you how to do it.
>>> But if I were to try to recreate something that works like the
>>> digestive system, I certainly would not try to do it by random
>>> mutations. Would you? I would take note of the steps taken in a
>>> what-you-see-is-what-you-get system, and attempt to copy those, as far
>>> as possible. And that would be a useful, scientific venture, learning
>>> from nature, copying its processes, rather than speculating on its
>>> history.
>>>
>>Why would you not use random mutations?
>
> would you? Observation of how mental activity behaves in the real
> world would tell you that things are not constructed through random
> activity. So if creation theory contends that the digestive system is
> not the result of random activity, this contention correlates well
> with how mental activity behaves.
>
In the real world, I note that genetic algorithms (attempts to
computer-model "Darwinian" evolution) are quite common design tools. So is
"brainstorming" -- sitting around and tossing out ideas more or less at
random. Later on, of course, one will have to go through these ideas, weed
some out and refine others -- but random activity is, in fact, a common
design tool.
>
>> If you don't know how to make a
>>digestive system, making lots of copies of an initial cell, varying them
>>in
>>small ways, and seeing which ways move you closer to a digestive system,
>>might be a better idea than trying to dream up a complete digestive system
>>from scratch.
>
> trial and error is a tool of mental activity if a creator has not yet
> figured out how to make something. But unlike random mutations that
> have no idea that they want to make a digestive system, mental
> activity knows what it wants to make, and it plans and dreams and
> works towards its goal.
>
>> Note that, before there are any digestive systems, you can't
>>very well copy one that already exists (since none do).
>
> my mention of copying had to do with how a creationist would approach
> science. They would copy nature, and learn how to use the principles
> seen in nature to create new things.
>
> But back before digestive systems existed on this earth, if you had to
> make a digestive system from scratch, I would hope you would put your
> mind to the task and figure out how best to approach it. You'd be
> fired on your first day on the job if you were caught sitting around
> idly doodling on your pad, hoping that something would come together
> on its own....which is the principle upon which evolutionary theory is
> based.
>
One hopes you are never put in charge of designing, well, anything,
anywhere, ever.

Of course, there's an interesting question here: why would the Intelligent
Designer of Life need to figure out how to put together a digestive system?
A problem with "intelligent design" as an explanation for biological
complexity was noted as far back as William Paley (1743 - 1805, the founder
of ID theory): an omnipotent designer doesn't *need* complicated systems
("contrivance," in Paley's term) to accomplish some goal. A Designer Who
can do anything can make a chunk of granite see, or digest food. Only a
designer constrained by the laws of physics and limited knowledge of the
universe has to "figure out" things and build complicated systems to
accomplish tasks.
>
> snip>
>
>>>>You have, in the consistent nested hierarchy of homologies,
>>>
>>> you have yet to demonstrate that nested hierarchies always mean common
>>> descent. If they do not always mean common descent, then on what
>>> basis do you decide that only the nested hierarchies of nature mean
>>> common descent?
>>>
>>I have argued that *consistent* nested hierarchies -- seen if families of
>>hand-copied manuscripts, families of languages, and clades of living
>>organisms -- imply common descent. Your supposed counterexamples involve
>>sets of entities that fall into very different hierarchies depending on
>>what
>>traits one chooses to examine and compare.
>
> there's the key: "Depending on what traits one chooses to examine and
> compare."
>
> Families of languages would not fall into a nested hierarchy if you
> chose other traits for comparison than the ones you have chosen to
> use. Those same languages that seem to fall into a nested hierarchy
> would not appear hierarchical if you chose to classify them according
> to other traits.
>
Can you give some examples here? To be sure, consistent nested hierarchies
are produced by branching descent with only "vertical" (from parent to
offspring) inheritance; one can mess up such nested hiearchies with
"lateral" transfer, and "lateral" transfer is common in languages. They can
borrow vocabulary, sounds, even grammatical features from each other. But
for all that, natural spoken languages (not to be confused with means of
*writing* those languages -- some languages have multiple writing systems)
fall into families nested in larger families, and the same pattern arises
when comparing many different sets of words, sounds, and grammar rules.
>
> Depending on the traits you choose to use for comparison you can get a
> nested hierarchy and even twin or triple-nested hierarchy, or none --
> all for the same groups.
>
Example, please?
>
>>>> in biogeography,
>>>
>>> why does biogeography mean common descent, unless there is a
>>> preconceived notion in place?
>>>
>>If, e.g. the various genera of the hominoids are not related, why do the
>>two
>>living genera most genetically similar to humans share a continent with
>>[a]
>>the greatest genetic diversity of humans (indicating humans have lived on
>>that continent longer than they've lived on other continenets), and [b]
>>with
>>the australopiths, the extinct great ape genus most similar to our own
>>genus
>>_Homo_.
>
> this, again, is the as-yet-unsupported premise that similarity means
> relationship. On what basis do you decide that similarity must means
> relationship for only biological life forms, but nowhere else? So
> far, this question has not been answered by anyone.
>
No, you don't seem to be paying any attention to my argument. I am not
*assuming* that humans are related to other African apes. I am noting that
we are, anatomically and genetically, more like chimps and gorillas than any
of us is like any other species, and anatomically, at least, the same goes
for the australopiths, and I'm asking, if these species all arose
separately, or if they all migrated from Noah's Ark, how did they all end up
in Africa together? Common descent (we are all in Africa because that's
where our last common ancestor lived) explains this. Separate creation
would make it rather unlikely that similar but separately created "kinds"
would end up close together (and close to fossils of similar, extinct
species) so often.
>
> snip>
>
>>>>in vestigial structures at the genetic and morphological level,
>>>
>>> the term "vestigial structures" is a term arising out of preconceived
>>> notions. Some may call the appendix vestigial, but there are uses for
>>> the appendix. Some may call the tailbone vestigial, but there are
>>> uses for the tailbone...and so on. To call something vestigial
>>> because it seems to have no use is a misunderstanding of and
>>> egotistical dismissal of structures that are really not vestigial at
>>> all.
>>>
>>"Vestigial structures" are defined as having *reduced* function, not *no*
>>function, and can be recognized without regard to evolutionary notions.
>
> and what is the standard for reduced function? You have to first
> know the function of the supposed "vestige" in order to say its
> function has been reduced. It's too superficial to look at a
> similar-looking organ in another life form and decide that, therefore,
> this "vestigial" organ is indeed meant to function the same way as the
> other, but it's just not functioning anymore.
>
So you are arguing that comparative anatomy is not possible?
>
> You might as well look at the trunk of a car and call it vestigial
> because the tray of a pickup truck seems to perform a similar
> function, just more extensively.
>
>>Indeed, they can be recognized where evolution is rejected as an
>>explanation: the shortened simplified limbs of a thalidomide baby are
>>vestigial according to definition (that is, they lack some of the function
>>of homologous structures in related or allied organisms), but the
>>vestigial
>>limbs aren't caused by any genetic change (the genes are unchanged), and
>>therefore cannot be an example of evolution. However, when vestigial
>>features are not the result of developmental derangement, it is reasonable
>>to ask why they share so many details of structure with organs with which
>>they do not share details of function, in species otherwise very similar
>>to
>>the one with the vestigial structure.
>
> human creators use the same template for many different purposes. If
> mental activity is evidenced in the use of templates, why doesn't the
> similarity of structures not cause you to see mental activity here,
> also?
>
>>Saying that the appendix is vestigial does not mean it does nothing; it
>>means that it occupies the location and shares embryological and
>>anatomical
>>features with the caecum, a pouch used to digest leaves in many monkeys.
>
> no, no, no. The cecum or caecum in the monkey has its counterpart in
> the cecum or caecum of the human. Its counterpart is NOT the
> appendix. See:
>
> http://en.wikipedia.org/wiki/Caecum
>
> "Cecum or caecum is a pouch connected to the large intestine between
> the ileum and the colon. It is separated from the ileum by the
> ileocecal valve (ICV) or Bauhin's valve, and is considered to be the
> beginning of the large intestine and part of the colon.
>
"Carnivores, whose diet contains little or no plant material, have a reduced
caecum, often partially or wholly replaced by the vermiform appendix. The
appendix is a branch of the caecum."

I stand corrected, slightly. The caecum has its counterpart in the part of
the caecum that monkeys have, and we don't. You still have the question of
why we have this blockage- and infection-prone extension of the caecum,
instead of simply the smaller caecum (which could easily accomodate patches
of lymphatic tissue). A clearly example, I think, is the plantaris tendon;
it occurs in most (but not all) humans and all nonhuman apes. In nonhuman
apes it connects to the foot bones and enables the ape to clench its feet
into fists. In humans, its attachments are highly variable and it doesn't
help us move any part of our body. Again, this seems a moderately odd
feature, unless we inherited it (and lost part of its function, unless you
can grasp baseballs with your feet) from a common ancestor with nonhuman
apes.
>
> "Its primary function is to absorb water and salts from undigested
> food. It has a muscular wall that can knead the contents to enhance
> absorption.
>
> "The cecum is present in mammals, birds, and some reptiles."
>
>>Since it doesn't digest leaves in humans, why does it have this location
>>and
>>these traits?
>
> the appendix is not even designed to have supposedly digested leaves.
> It has a lymphatic function and seems well placed in an area that most
> needs it.
>
It's well placed, if its function were to digest leaves (for which,
admittedly, it does not seem well designed at all).
>
> See:
>
> http://www.betterhealth.vic.gov.au/bhcv2/bhcarticles.nsf/pages/Lymphoma?OpenDocument
>
> "The lymphatic system is part of the immune system, which defends the
> body against infection. It consists of lymph nodes connected by lymph
> vessels, which branch out into all parts of the body except the brain
> and spinal cord. The lymphatic system also includes the bone marrow,
> spleen, thymus gland, tonsils, adenoids and APPENDIX (caps mine.)"
>
> What better area to place an organ of the lymphatic system than at a
> point where bacteria are likely to be present?
>
Someplace where vagrant bits of undigested food can't block it off, and
start a fatal infection? Just a suggestion.
>
>> Why does the human tailbone, whatever its uses, share so many
>>homologies to actual tails in other primates (and other mammals)?
>
> based on how mental activity behaves, it is evident that a successful
> template works for many different purposes.
>
>> Vestigial
>>structures are simply an extreme case of the problem of "parahomology:"
>>similar designs for dissimilar functions. It's one thing to use commn
>>design for common purposes, but what logic (other than evolutionary logic,
>>in which the function of a structure can evolve over time, without erasing
>>all traces of the structure's history) is there to common design for
>>different purposes (especially when there is also -- consider bat, bird,
>>and
>>pterosaur wings -- different design for common purposes).
>
> I suggest a study of how mental activity behaves when creating items,
> and you will get your answer as to common design for different
> purposes and different design for common purposes.
>
I take this to be handwaving, rather than an answer.
>
> Reducing this to basics, a rectangle is a common design used for many
> different purposes. Or a circle is a different design for common
> purposes.
>
> snip meanderings>
>
>>>>> 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?
>>>>>
>>>>It becomes a multicellular organism.
>>>
>>> could you be a little less vague? So you think that a single cell
>>> becoming multicellular is how a digestive system forms? Have you
>>> accounted for the changes in DNA sequences that are needed to produce
>>> the particular types of proteins needed to construct an esophagus, a
>>> stomach, duodenum, jejunum, small intestines, and all the attendant
>>> parts that make a digestive system work?
>>>
>>Multicellularity preceeds specialization of the cells in question. For
>>that
>>matter, formation of a digestive system preceeds all those specialized
>>subcomponents you mention.
>
> I'm afraid that formation of an overarching system to hold a digestive
> system precedes even the digestive system, not to mention the
> specialized subcomponents.
>
> <snip inability to explain how selected mutations cause evolution>
>
-- Steven J.


.

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