Re: Request
- From: John Harshman <jharshman.diespamdie@xxxxxxxxxxx>
- Date: Sun, 14 Aug 2005 14:39:43 GMT
Zoe wrote:
> 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.
That's where the tree comes in. As you recall, humans are more closely
related to chimps than chimps are to gorillas, gorillas are more closely
related to chimps and humans than to orangutans, etc. So there was no
common ancestor of gorillas, chimps, et cetera, unless et cetera
includes humans. And that's why three fissions would be needed if the
ancestor of the great apes had 23 chromosomes. One fission in the
ancestor of orangutans (after splitting from the human/chimp/gorilla
line), one in the ancestor of gorillas (after splitting from the
chimp/human line), and one in the ancestor of chimps (after splitting
from the human line).
> 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.
Except that there was no such differentiation into "various species of
apes" unless you include humans in that group. This differentiation has
nothing to do with chromosome number, either. And it's not
"hypothesized"; the evidence is overwhelming.
> 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's not unknown. It's an unavoidable inference from the phylogenetic tree.
> 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.
No, it's nothing like that. We sequence DNA from actual organisms. That
tells us what their relationships are to each other. The chromosome
thing is a necessary consequence of those relationships. Conveniently,
the human chromosome in question shows the marks of fusion, in that it
has telomeres in the interior of the chromosome at just the spot they
would be expected, given a fusion.
> 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.
No, it's just that you don't understand what "random" means. Not in
statistics or in biology. In statistics, "random" means that you can't
tell in advance what outcome you are going to get, like picking a number
out of a bag. But the bag doesn't have to have one each of every number.
It could have 10 ones, 5 twos and 1 three, for example. If you pick out
of this bag, you are very unlikely to pull a three as opposed to a one.
But the draw is still random. This is called a distribution. There can
be any distribution, and as long as the pick from that distribution is
not selecting a result based on anything other than its frequency in the
bag, the pick is random.
Now, in biology we have a restricted meaning with regard to mutation.
What "random" means in that context is merely that mutations do not
happen with regard to the current needs of the organism.
> 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.
People make use of randomness all the time, even in design. At the
simplest level, they sometimes flip a coin. And when you put a pot of
water on the stove to boil, you rely on the random collisions of atoms
to help make your tea. An evolutionary concept of God's creation is
similar to the latter: he sets up initial conditions -- big bang, first
cell, whatever -- such that known processes like random mutation and
natural selection will eventually produce the result he wants, while he
goes off to read a book until the pot boils.
>>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.
Sometimes it does, sometimes it doesn't. If people exhibit mental
activity, then they also certainly resort to trial and error quite
frequently.
>>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.
Why would this be different from the way anyone else would approach
science, or at least a small subset of science?
> 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.
Would you consider all the animals with incomplete digestive systems to
be analogous to doodles? It seems to have taken life quite a while to
figure out that having distinct entrances and exits in the system would
be a good idea.
>>>>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.
This is not actually true, if you're talking about natural languages.
They fall into a real, nested hierarchy. You would have to pick your
traits very carefully to avoid it. Or do you not believe that French and
Spanish are descended from Latin?
> 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.
I'd like to see you try. (I don't know what you mean here by "twin or
triple-nested", by the way.)
>>>>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.
Yes it has, dozens of times. It's not the similarity per se. It's the
nested hierarchy.
>>>>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.
>
> 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.
If the trunk were reduced to the size of a glove compartment, we might
well call it vestigial. There is certainly a bit of subjectivity in how
reduced you need a function to be before you apply the term. Your main
idea, however, requires the denial of homology. You need to assume that
the coccyx has nothing to do at all with the tails of other vertebrates,
despite its detailed anatomical and developmental similarities, and that
nested hierarchy again.
>>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?
Two reasons. First, the nested hierarchy again. We just don't see nested
hierarchies being produced by human design. Second, humans use
functional templates. If your object needs to roll, you put wheels on
it. If it needs to fly, you don't take a wheel and bang it into shape to
be a wing; instead, you install a wing, a completely new structure for
the completely new function. That's just not what we see in the history
of life. We see old structures being turned to new and quite different
purposes.
>>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.
>
> "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."
You need to read a bit further. From the same source: "However, most
physicians and scientists believe the appendix lacks significant
function, and that it exists primarily as a vestigial remnant of the
larger cellulose-digesting cecum found in our herbivorous ancestors."
>>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.
>
> 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?
You are picking and choosing little bits of your reference and ignoring
anything you don't like. That's called quote mining.
>> 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.
No it doesn't. A successful template works for the same purpose in many
contexts. Under the template theory, we would expect bird wings, bat
wins, and insect wings to all have the same structure. Instead, we find
that bird wings and theropod forelimbs have the same structure, rather
different from bat wings, and entirely unrelated to insect wings.
>> 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.
>
> 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.
Those are hardly designs at all. They're simple concepts at best. At any
rate, you seem to be making up the nature of mental activity to fit your
own template, and it doesn't seem to have anything to do either with
real mental activity or real living things.
> 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.
No idea what that meant. "Overarching system"?
> <snip inability to explain how selected mutations cause evolution>
You mean "snip your inability to understand what Steven is saying".
.
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