Re: Stereotypes and reputations

From: Pim van Meurs <pimvanmeurs@yahoo.com>
Date: Sat Aug 06 2005 - 00:31:23 EDT

Cornelius Hunter wrote:

> Ted, Pim and Tim (after this I'll probably have to bow out of the
> discussion for awhile):

Don't worry, we will keep the flame going for when you return, these are
interesting topics and any help we can provide to address some of the
confusion surrounding evolutionary theory to readers of this groups
seems to serve a useful function.

>> You may also
>> want to comment on other possible assumptions that someone else might
>> perhaps make. I hope this is clear enough to move the conversation in a
>> potentially very helpful direction.
>
>
> Conversation? Not sure I would so dignify this thread. Lies, invective
> and abuse don't usually qualify as such. More problematic it seems to
> me is lack of engagement in preference of stultifying repetition. For
> example, we have this:

More unsupported accusations and assertions I notice.

>> Yes, God can create animals that way but why? Unless the mechanisms
>> used inevitably lead to nested hierarchies.
>
>
> I have already explained that I do not share these theological
> presuppositions, but the questions persist as though they represent
> universal criteria that all creationists must answer. Sorry, but
> unlike you I have not assumed the job of so rationalizing divine action.
>
I understand, creationism is, unlike evolutionary science, not
interested in addressing the mechanisms, methods. Of course, God can
create any way He wants, so why can He not have created via evolutionary
mechanisms, as the evidence so strongly show and why does one have to
reject one of the strongest evidences of His actions, namely common
descent? I do not understand this neither as a scientist nor as a
Christian (yes, contrary to your guess both Glenn and I are Christians.
In fact we both share the burden of a young earth creationist past.)

> Or again,
>
>> Although CH without any evidence suggests that "Manufactured objects
>> can fall into an hierarchical pattern." he provides no logical or
>> scientific argument to support this claim. In fact, I doubt that such
>> an argument can be made.
>
>
> *Of course* objects can be manufactured to fall into a hierarchical
> pattern. This is trivial. More repetition of questions that have been
> answered mutliple times:

Conveniently, the term nested has been dropped here but perhaps CH can
explain with some examples. Perform a cladistic analysis on manufactured
goods. As Douglas Theobalt, in his excellent response to Camp showed,
Hunter's claims are based on a misunderstanding as to the nature of
nested hierarchies and cladistic analysis.

See http://www.talkorigins.org/faqs/comdesc/camp.html

Camp quoted Hunter

[quote]Consider a group of vehicles, beginning with a small economy car
and increasing in size to larger cars and to minivans and large-sized
vans. One could quantify several aspects of the vehicle designs, such as
tire size, steering mechanism, engine size, number of seats and so
forth. Presupposing the evolutionary paradigm and searching for
parsimonious relationships, we would find that most of the design
measures suggest the same relationship. The smaller vehicles have
smaller tires, manual steering, smaller engines, and fewer seats. The
larger vehicles have larger tires, power steering, larger engines, and
more seats. In other words, the groupings suggested by the different
design measures (tire size, steering mechanism, engine size, etc.) tend
to be similar. But of course, the family of automobiles did not evolve
from one another via random mutations. The groupings of the design
measures are a natural result of engineering and have nothing to do with
Darwinian evolution. How then can Penny's results provide "strong
support" for evolution? (Hunter, 40.)[/quote]

As Douglas however shows, this example by Hunter is erroneous

[quote]
Hunter's example is erroneous for another reason—he has chosen
characters that are not independent. This is a big "no-no" in cladistic
analysis, and it is a rudimentary issue that is addressed early on in
any introductory text on phylogenetic analysis. When using characters of
organisms in a cladistic analysis, biologists attempt to use characters
that are as functionally and developmentally independent of one another
as possible. For instance, the size of an animal is only one character.
Of course larger animals will in general have larger bodies, larger
legs, and larger heads, just as in Hunter's example larger cars have
larger tires, larger engines, etc. To be valid, "largeness" cannot be
counted more than once. The very easy solution, which is regularly used
by biologists, is to measure the /relative/ sizes of different
characters. For instance, having a femur/tibia ratio of 3 is a different
character from having a femur/tibia ratio of 1/2, regardless of the
overall length of the bones. Biologists know that they must normalize
for size, and instead they concentrate on structural details. Hunter's
example is thus a straw man.

Penny's analysis (Penny /et al/. 1982
<http://www.talkorigins.org/faqs/comdesc/camp.html#Penny_etal1982>) used
five genes, four of which are functionally independent; thus, the result
that trees made from several different independent genes match with
statistical significance is indeed extremely strong support for common
descent. For Hunter's analogy to be valid, he would have to claim that
phylogenetic trees made only with cars' steering wheels will match
phylogenetic trees made only with cars' tires and trees made only with
cars' headlights and trees made only with cars' engines and trees made
only with cars' transmissions. Such a claim would be false, since cars
with similar tires (e.g. similar width/diameter ratio, manufacturers,
tread, color, materials, etc.) do not generally also have similar
engines (e.g. similar manufacturer, injection systems, cylinder
arrangement, orientation, etc.), or headlights (e.g. similar shape,
brightness, manufacturer, bulb type, position, number, etc.), or
transmissions, or steering wheels.

Thus, Hunter's analogy is false
<http://www.intrepidsoftware.com/fallacy/falsean.htm> for multiple
reasons. Hunter's example of how cars' characters can be analyzed to
infer a phylogeny is quite different from how real organisms' characters
are analyzed by biologists when inferring a phylogeny.

[/quote]

I hope that this help put to rest the confusion about nested hierarchies
and manufactured goods.

>
>> So far the vaste amount of evidence supporting CD is extremely well
>> explained by evolutionary theory. If CH has an alternative
>> explanation, then please present it. But given the focus of CH on
>> 'disproving' CD, I doubt that such an explanation could be forthcoming.
>>
>> Thus my question becomes, why focus on trivial puzzles and ignore the
>> vaste amount of evidence in favor of CD?
>>
>> CH believes that minor violations of a tree structure are evidence
>> against common descent when in fact the mechanisms that create such
>> vines are understood and the tree (with vines) can be reconstructed.
>> The reason that it has become so hard to disprove CD is because of
>> the overwhelming evidence supporting it. Not to mention the lack of
>> any competing explanation.
>
>
> But there are no such known mechanisms. Pim has explained the problem,
> unaware the solution he envisions does not exist.

See below, there ARE known mechanisms. And did CH not quote with
approval, Woese and Doolittle and yet he does not accept their argument?
That's confusing.

> There are no known mechanisms for the various problems I've described
> (vines and hubs with rapid transfers is not a known mechanism, for
> instance, but then again, I've already explained this).

Nope, you have merely stated this. Explanation requires a bit more effort.

> Nonhomologous genes and development have no known mechanisms, unless
> you want to count "and then a miracle happened." These are not
> "trivial puzzles" and until this is understood there can be no moving
> on to alternative explanations.
>
Your statement that they have no known mechanisms defies logic as I have
explained. At most they are a puzzle and so far other than asserting,
you have shown no logical argument to support your claims. I understand
that 'a miracle happens' is a common argument in creationist circles but
in science we rather admit that there are puzzles, instead of letting
our ignorance guide us to unwarranted conclusions or assertions

>
>
>
> Pim:
>
>>
>> CH: False, gradual evolution can include accelerated mutation rates.
>>
>> I have no idea what you are objecting to. Accelerated mutation rates
>> are still gradual just faster. In fact evolutionary theory explains
>> accellerated rates quite easily. Check out evolvability.
>
>
> This is circular. Evolution does not "explain" accelerated mutation
> rates, it assumes accelerated mutation rates because they are
> required, among other just-so stories, to try to explain awkward data,
> such as how highly conserved proteins originally evolved.

Evolutionary theory in fact does explain accelerated mutation rates as
it increases evolvability. Come on Cornelius, you may call these just so
stories but that hardly makes them unscientific. They are called
hypotheses amongst those involved in scientific inquiry.
You seem to be upset that evolutionary theory finds succesful
explanations and mechanisms that match the actual data. Such is the
burden of science.

>> They'll always add something else and the worst case, in my opinion,
>> is invoking the G-bomb: An agent that has no definable or
>> classifiable characteristics. You'll never alter the views of someone
>> who invokes a mechanism with no boundary conditions. Personally, I'm
>> not interested in discussions with or about such potentially
>> irrational ideologues. It becomes a stereotypical caricature. But for
>> most others, at some point the modifications get to be too much (but
>> YMMV). For you, Cornelius, it appears that there can be 'too much'.
>> That demonstrates that r ejection is possible and serves as a
>> reminder that thresholds clearly vary between people.
>
>
> That's funny, I thought I was the one pointing out scientific
> problems. There are massive scientific problems with evolution, but
> you dismiss them because the "G-bomb" is unacceptable to you. Then you
> cast me as being credulous.
>
You keep saying that there are masssive scientific problems with
evolution and yet you fail to present them. When you are presented with
vaste evidence supportive of common descent, you decide to ignore it
because you believe that there are some 'massive scientific problems
with evolution'. Yet, so far your examples show minor puzzles,
additional mechanisms and misunderstanding on your part. While I can
understand avoidance to deal with the data, after all the data are quite
impressive, I fail to understand why you cannot present your case in a
coherent, supported manner. Instead you argue without much evidence that
there are massive problems for evolution. So far the examples you
provided us with and the quotes from evolutionists have failed to
support your thesis.
For instance, the Cambrian explosion, or the horizontal gene transfer
examples of Woese and Doolittle, supported by additional recent
evidence. You claim that horizontal gene transfer is not observed, but
on the contrary such transfer is observed. I am sure you are familiar
with plasmid transfer? Bacterial sex so to speak... A fascinating
finding which helps resolve the issue of problems with certain trees.
The latest data show a tree with vines, where the vines are horizontal
transfer of genetic information. Imagine how evidence shows how genetic
data is transfered horizontally and then vertically. Recent data so far
suggests that horizontal gene transfer is a minor component but
nevertheless, it supports Woese and Doolittle's viewpoint that
horizontal gene transfer does play a role.

For those interested in the sex life of the bacteria see for instance

http://www.chennaionline.com/science/BiotechCorner/14biotech.asp

Or for evidence that horizontal gene transfer happens see

http://www.i-sis.org.uk/hgthappens.php

Or check out
http://scholar.google.com/scholar?hl=en&lr=&sa=X&oi=scholart&q=plasmid+horizontal+gene+transfer

Then we come to the issue of convergence, while convergence is no
problem for common descent, it does present a puzzle for evolutionary
theory. Namely that is the mechanism(s) through which such convergence
takes place. As I have argued, given the many constraints involved, it
is not surprising that similar solutions are found for similar
environmental pressures.

As I showed, Kaufmann has shown how in self organization, limited amount
of limit cycles arise. In other words, despite the countless options,
only a few are viable options under self organization. Powerful stuff
that helps understand these concepts of convergence in a scientific manner.

Thus the 'similarity' between the marsupial and mammalian wolf, while to
experts quite shallow, may appear to the unfamiliar observer as a strong
similarity shows how similar but not too similar solutions have evolved.
While these present no problems for Common Descent, they do deserve an
explanation by evolutionary theory. And as I showed, evolutionary theory
has presented some very plausible explanations. Only time will tell
which one(s) will end up being correct.

Needless to say, while evolutionary theory has explanations,
predictions, and mechanisms, all Hunter has is... what exactly?..

Perhaps CH can finally address the following fact?

[quote] As seen from the phylogeny in Figure 1
<http://www.talkorigins.org/faqs/comdesc/phylo.html#fig1>, the predicted
pattern of organisms at any given point in time can be described as
"groups within groups", otherwise known as a /nested hierarchy/. The
only known processes that specifically generate unique, nested,
hierarchical patterns are branching evolutionary processes. Common
descent is a genetic process in which the state of the present
generation/individual is dependent only upon genetic changes that have
occurred since the most recent ancestral population/individual.
Therefore, gradual evolution from common ancestors must conform to the
mathematics of Markov processes and Markov chains
<http://en.wikipedia.org/wiki/Markov_chain>. Using Markovian
mathematics, it can be rigorously proven that branching Markovian
replicating systems produce nested hierarchies (Givnish and Sytsma 1997
<http://www.talkorigins.org/faqs/comdesc/section1.html#GivnishSytsma1997>;
Harris 1989
<http://www.talkorigins.org/faqs/comdesc/section1.html#Harris1989>;
Norris 1997
<http://www.talkorigins.org/faqs/comdesc/section1.html#Norris1997>). For
these reasons, biologists routinely use branching Markov chains to
effectively model evolutionary processes, including complex genetic
processes, the temporal distributions of surnames in populations (Galton
and Watson 1874
<http://www.talkorigins.org/faqs/comdesc/section1.html#GaltonWatson1874>),
and the behavior of pathogens in epidemics.[/quote]

If he disagrees. all he needs to do is provide the necessary evidence.
Douglas Theobalt provides all the necesary references. CAn we expect the
same from Hunter when he attempts to reject these claims?

1. Evolutionary processes produce nested hierarchies
2. The only processes that specifically generate unique, nested,
hierarchical patterns are branching evolutionary processes.

In Christ
Received on Sat Aug 6 00:34:44 2005

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