Re: Request
- From: "Steven J." <sjt1957NOSPAM@xxxxxxxxxxxxxxxxxxxx>
- Date: Fri, 19 Aug 2005 22:31:18 -0500
"Zoe" <muze10@xxxxxxx> wrote in message
news:pcr7g1tfrhlq4g17f49gj34h8i6kq18qt3@xxxxxxxxxx
> On Sun, 14 Aug 2005 20:41:45 -0500, "Steven J."
> <sjt1957NOSPAM@xxxxxxxxxxxxxxxxxxxx> wrote:
>
> Steven, just so you know, I am not trying to be obstinate in my
> responses to your posts. I truly come from a different world view and
> have legitimate questions about yours. When I fail to agree with your
> explanation, it is not because I see that you are right but refuse to
> acknowledge it. It is because there are still questions in my mind
> that haven't been answered persuasively. To me, there are other
> reasonable and legitimate ways of viewing the data.
>
I'm not sure that sheer cluelessness counts as a worldview, but I'll try to
be open-minded, here.
>
-- [snip]
>
>>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.
>
> you got it coming and going, I see. Similarities mean relationship.
> Dissimilarities mean relationship. And the unsupported premise for
> "dissimilarity means relationship" is that differences must mean that
> change has occurred over time, and the more change there is, the more
> time must have passed. The conclusion based on this premise is that
> degree of difference correlates with placement on a timeline.
>
Actually, neither similarities nor dissimilarities by themselves mean
relationship, but we'll discuss that in more detail, below, when we get to
nested hierarchies. Beyond that, it's hard to believe (but I suppose
that's just an argument from incredulity) that you don't see my point. My
cousins and my brothers are both relatives, but my cousins are more distant
relatives, and, oddly, one could in principle tell this (by, e.g. seeing
which ones of us looked more like my father, or testing our DNA for various
markers). Molecular anthropologists use genetic comparisons to tell when
various human groups split off from one another and determine, e.g. that
Polynesia was settled from Malaysia, not from South America, because their
genetic markers are closer to those of Malaysians than South American
Indians. Now, if a molecular anthropologist pointed out that, despite this,
Polynesians and South American Indians were, in fact, both human, would you
accuse him of arguing that "dissimilarities mean relationship?" Even within
related groups, some are more closely related than others. Techniques much
like those used to determine degrees of relationships among different human
populations can be used to determine degrees of relationships among
different species.
>
> Shouldn't the premise first be validated that differences between two
> objects must invariably mean (1) that those differences are a result
> of change in the original, and (2) that the more the difference, the
> older the object?
>
Why should I validate that premise? I'm not arguing either of those
premises. We're discussing change *from* the original, in branching lines
of descendants of that original, and no line of descendants of that original
is older than any other. Rather, lines of descent branch at different
times, and taxonomists and systematists try to reconstruct the order of
branchings. Note that
>
> Likewise, in the case of the similarity principle used for
> relationship, shouldn't the premise first be validated that similarity
> between two objects must invariably mean (1) that those similarities
> are a result of relationship, and (2) that the more similar the
> objects, the more closely related?
>
In the statements above, replace "object" with "person" or "human being,"
and examine the resulting question. Please do not, just yet, digress into
an argument that we haven't shown that humans are related to other species;
we both accept that humans are related to other humans, and that it is
possible, using genetic and other tests, to be more specific in many cases
about who is related to whom, and which groups are more closely related to
other groups. There are, of course, creationists who deny this: they hold
that different "races" have separate origins and do not share common
ancestors, but I think we both agree that these are bad creationists. But
the arguments for common descent of widely separated human populations apply
also to show common ancestry of humans and other species, and the methods by
which we can show, e.g. that Native Americans are related to east Asians
more closely than to, e.g. Arabs, apply also to the question of whether
humans are more closely related to chimps than either species is to
orangutans.
>
> If there are numerous exceptions to the premise that
> similarity/dissimilarity means relationship, then you don't have a
> valid premise at all but just some made-up rules that fit a pet idea.
>
> Anyway .... okay, so now we're talking about dissimilarities. If you
> use the assumption that the more dissimilarities there are, the
> further removed the relationship and therefore, the earlier in time,
> then this undermines Richardson's blairgenealogy link that purports to
> show relationship through mutations of the Y-chromosome.
>
> Quote:
>
> "It is possible for two distant cousins to match exactly on all
> markers while two brothers might not match exactly."
>
If, as appears, you are quoting http://blairgenealogy.com/dna/dna101.html ,
then the point is that two distant cousins might have inherited an unmutated
copy of their how-ever-many-greats-grandfather, while a brother of one of
those cousins experiences a new mutation, making his Y-chromosome a little
different. Similar problems arise for different species: if, as is
commonly inferred, humans are more closely related to chimps than to
gorillas, it is still possible for, e.g. a mutation to have occurred in the
chimp line *after* that chimp line split off from the human line, while
humans inherit unchanged the gene of the human/gorilla/chimp LCA.
Comparison of that single gene would imply that humans are more closely
related to gorillas than to chimps (and genes like that exist, and other
genes -- where, presumably, the *human* lineage underwent a mutation --
imply a closer chimp-gorilla relationship). You need to compare many
different characters and genetic loci and see the overall pattern of
similarities and differences. The "multiple nested hierarchies" are not
quite identical, although they are very similar, precisely because of this
random nature of mutations.
>
> End quote.
>
> That would be saying, then, that one brother is further removed from
> the common ancestor than the other one is, because there were
> differences between them. Your principle of dissimilarity should be
> consistent for all dissimilarities, otherwise it is not a principle at
> all, but just a willy-nilly rule that is applied to whatever suits the
> fancy.
>
I would be saying no such thing about the two brothers. All reconstructions
of phylogeny depend on probabilities. Comparing one gene, in three
individuals, tells you next to nothing about which two are most closely
related, for the reasons mentioned above: distantly related individuals, or
species, might have inherited unchanged some gene from a common ancestor,
while a close relative has undergone a recent drastic mutation. Comparing
multiple genes and multiple different individuals (or species), with
comparisons to "outgroups" (populations thought to be only very distantly
related) gives better results.
>
-- [snip]
>
>>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.
>
> since the mechanism of genetics is copying, there has to be a
> one-to-one mapping of genotype to morphology. If the sequences are
> the same, then the protein produced will be the same. If there are
> slight variations so that the protein differs, I don't know how you
> can even begin to say that similar sequences mean relationship. You
> no longer have anything to work with. What looks like similar
> sequences are really not producing similar results so even if chimp
> DNA looks almost 99% similar, the fact is that those sequences are
> producing different results, meaning they're really not similar after
> all.
>
"Morphology" means, well, the shape of the organism and its parts; it isn't
usually understood (and I certainly did not mean it) to include amino acid
sequence in proteins. Morphology doesn't map one-to-one with genotype,
because it doesn't map one-to-one with proteins. Sometimes (I think we've
covered this before) different sequences of amino acids can produce
identical effects, while, conversely, minor changes in a protein can have
quite drastic effects on morphology.
Of course, given the degeneracy (redundancy) of the genetic code, one can
have exactly the same protein coded for by different genetic sequences. If
there up to six different three-nucleotide codons for some amino acids, even
identical proteins need not imply identical genes behind them (there is a
minor example known for humans and chimps: although our cytochrome-c is
identical, the gene for that enzyme differs between humans and chimps at one
nucleotide).
>
-- [snip]
>
> I do wish you would answer my questions directly. I asked why you
> hsve a specialized meaning of random instead of the meaning given in
> the regular dictionary. Why not use a different term to avoid
> confusion?
>
If every English-speaking biologist on the planet uses "random" in this
sense to refer to mutations, and every popularization (other than
creationist tracts) uses "random" in this sense to refer to mutations, then
wouldn't it be *more* confusing if I invented some entirely novel term? I'm
using a standard English word in one of its standard English senses (note,
in case you've never noticed, that most English words have multiple
meanings, depending on context). "Random" does not mean, even in casual
nonbiological use, "uncaused," or "falling into no discernable pattern." It
is very common in English to state that " X is random with respect to Y;"
all this means is that knowing Y won't help you figure out what X is,
although knowing any number of other things might help you figure out what X
is. Thus, astrological signs are random with respect to personality type
(or vice-versa), but this does not mean that either astrological signs or
personality types happen for no reason or according to no pattern.
"Mutations are random with respect to fitness" means that knowing what
mutations will benefit an organism does not help you figure out what
mutations will happen (note: this does not mean that such mutations cannot
happen, or even that they are unlikely to happen; that is one of the things
that knowing what mutations would be beneficial won't tell you).
>
>> 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.
>
> when this happens, does the meaning of random change from "equally
> likely to happen" to "less and less like to happen, depending on what
> you're looking for"?
>
The meaning of "random" remains constant: if I'm playing craps and I my
"point" (the number I'm trying to roll again, before a seven comes up), and
the guy next to me has six for his "point," his chances of rolling five are
exactly the same as mine; the outcome of the dice roll is "random."
>
>>"Random" also has a common meaning of "unrelated to whatever purpose
>>something is needed for."
>
> in short, random also has a common meaning of purposeless, right?
>
That is not what I said. It might, in fact, be the case that a random
mutation, or a random dice roll, or a random meeting in the park, is
purposeless, but I would hope you could distinguish between "X has no
purpose" and "the purpose, if any, of X does not depend on Zoe's personal
purposes."
>
-- [snip]
>
>>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.
>
> I did not say random activity is not part of design. I meant that you
> do not construct anything by random activity alone. Evolutionary
> theory claims that things are constructed by random activity alone.
> It tries to insert selection as the non-intelligent answer for the
> necessity of intelligence, but selection's choices themselves have to
> be random since it is based on random activity.
>
No, this is wrong. Selection is based on what traits best enable the
organism to find food, avoid becoming food, resist parasites and diseases,
mate and reproduce, and so forth. These things are not random with respect
to "design;" what we see as "design" in biology is defined by the ability to
meet these needs. Take the simplest example: survival of bacteria exposed
to antibiotics is certainly not "random" with respect to antibiotic
resistance, and, conversely, odds for survival and spread of genes for
antibiotic resistance is not random with respect to the presence of
antibiotics. The color of peppered moths most likely to escape predation is
hardly random with respect to the color of the bark on which they rest, even
though mutations that produce new color patterns are random.
>
> snip>
>
>>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?
>
> how do you recommend that intelligence should behave, if not in
> figuring out how to create something?
>
An omniscient Designer, by definition, does not have to figure out anything;
He already knows the solution to every problem.
>
>>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.
>
> if you set up laws by which you run your household, because you know
> these laws are for the best good of your household, you still have to
> figure out how to work within these laws in order to accomplish
> certain goals. You might lay down the law that your children should
> be in bed by 9:00 p.m. You also want to show them a fun DVD that is
> three hours long. You work within the constraints of your own laws by
> planning to start the showing at 6:00 p.m. so that your 9:00 p.m. law
> will not be violated. Working within the confines of laws that you
> have established because you know this is the best way to run your
> household does not invalidate your "figurings."
>
Children have set bedtimes because they have physiological needs (and so do
the parents) that the parents do not get to choose and can alter only to a
limited extent. There is a "best way to run a household" because you don't
get to design all aspects of your own household from scratch; most of it is
a given beyond your control. An omnipotent parent could cause children not
to need sleep (either permanently or for that one night), or, indeed, cause
a three-hour DVD to play in 30 minutes. Parents establish the laws of their
household within the context of laws of nature that they do not establish,
but constrain them as strongly as the they do the children.
>
> On a more critical level, there are laws of the universe established
> that cannot be broken (unlike the 9:00 p.m. ruling). These laws make
> the universe what it is. To change them or break them would mean
> changing the equilibrium of the universe. So in order to maintain
> law, it must be figured out how to create within the boundaries of
> these laws. In this way a designer is constrained by his own laws of
> physics, not because of limited knowledge, but because of total
> knowledge of what would happen if the laws were not operating as they
> should.
>
But that is the point: the Designer is not stuck with the universe as it is;
He could have made it with other properties.
>
> And that is why God will not change His laws to save you. He had to
> find another way to do so.
>
>>> 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?
>
> you can choose to use traits such as geographical locations
> (communities, ghettos) or types of literature, and those very same
> languages will no longer fall into a nested hierarchy.
>
The English language is spoken in ghettos, in suburbs, in isolated valleys
in the mountains. Where the language is spoken is not a trait of the
language in the same sense that, e.g. vocabulary is, or grammar, or the
sounds used to make the language (all these vary from place to place, of
course; in linguistics as in biology there is a problem deciding where to
draw dividing lines: when are two dialects really two different languages,
or two subspecies really two different species?).
>
>> 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.
>
> what traits are you using to construct the nested hierarchy?
>
I thought the reference to "words, sounds, and grammar rules" was rather a
giveaway about the traits I was using.
>
>>> 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?
>
> let's take a hierarchy for all knitted products.
>
> There is a common "language" running through all knitted items. The
> pearl stitch and the knit stitch. Out of those two stitches come an
> immense variety of patterns. The patterns can be arranged
> hierarchically according to (1) use of the end product, (2) according
> to patterns used, (3) according to materials used. Sweaters can be a
> category in which uses might be for deep winter, fall weather, or just
> plain clothing. Patterns can be categorized by, for instance,
> cable-stitch patterns for adult sweaters; straight knitted stitches
> for sweaters for babies. Materials would be heavier wools or cotton
> for adults, or soft, fine wools for babies. A triple-nested hierarchy
> can be developed for knitted items, using the traits of: use,
> patterns, material. And all three traits would be found to be present
> for all knitted items. Does this consistency mean relationship? Of
> course not. They relate only in classification, not in the origins of
> the knitted materials.
>
But you get very different hierarchies when you categorize by, variously,
end product, or pattern, or materials. If all sweaters were cable-stitched
wool, for example, while all knit caps were straight-knitted cotton, then
you might have a consistent nested hierarchy. But what you have, in fact,
is a pattern where any end-product can be made of any material using any
stitching pattern. If, as I noted in a previous post, we found bats had
feathers, or that pelicans had mammary glands, then we would have the sort
of *inconsistent* nested hierarchy in life that we have in human artifacts
like knitted ware.
The point of the "twin nested hierarchy" is that, even though there is no
necessity for it, a nested hierarchy based on genes or proteins falls into
much the same pattern as one formed by examining morphological traits.
Indeed, as Harshman and Richardson showed, you can construct a nested
hierarchy using one set of genes (or noncoding DNA, which is not expressed
as proteins), and then use a different set of DNA sequences from the same
set of species, and get the same hierarchy. This is just the opposite of
your knitting example.
>
-- [snip]
>
>>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,
>
> isn't "more like" the same as similar? You are using similarity as a
> basis for concluding relationship.
>
I am using similarity as a basis for concluding similarity. Or is your
objection to any attempt to come up with an explanation for why the
similarity exists in the first place? Creationism offers no reason for God
to make the world in this fashion (as opposed to some other function), but
common descent offers an explanation why we see this pattern rather than
other possible patterns.
>
>>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?
>
> I don't have all the answers, and I don't want to get into the global
> flood right now except to say that Mesopotamia, Sumeria, Africa, all
> fit into the account of the starting over of life forms in this area
> of the world called the cradle of civilization.
>
>>Common descent (we are all in Africa because that's
>>where our last common ancestor lived) explains this.
>
> as does a starting over of life in this area explains it.
>
Then why are there no kangaroos in Africa? Didn't the marsupials "start
over" in this area also, on your account?
>
>> 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.
>
> separate creation would not have taken place at the point where life
> started over after a global flood. Common descent within species
> would resume.
>
-- [snip]
>
>>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).
>
> I don't tell nature how it should be. Nature should be studied for
> what it is. What you see is what you get.
>
Okay, I see I was correct above. Your objection is to the whole concept of
theories; you don't think there's any point to trying to explain things.
>
>> 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.
>
> you seem to think that the only conclusion that can be drawn when
> there are differences between species is that the function was lost.
> Again, this seems to be a preconceived notion and a premise that has
> no supporting evidence.
>
Zoe, you aren't reading for comprehension. But then, you aren't *thinking*
for comprehension. I'm beginning to think that incomprehension is that
"different worldview" of which you earlier spoke.
>
-- [snip of deliberate obliviousness]
>
-- Steven J.
.
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