Stangelove:
just for discussion, here is a very simple citation in favour of the importance of modeling. It is from the first chapter of a manual of statistics (Statistics for Research With a Guide to SPSS, 2nd.Edition).
“The conceptualization and operationalization of variables
Where do variables come from? Why do we choose to study particular variables and not
others? The choice of variables to investigate is affected by a number of complex factors, three
of which I will emphasize here.
1. Theoretical framework. Theories are ways of interpreting the world and reconciling
ourselves to it, and even though we may take for granted that a variable is worthy of
research, it is in fact often a highly charged selection process that directs one’s attention to
it. We may be working within an established theoretical tradition that considers certain
variables to be central to its world-view. For example, Marxists consider ‘economic class’
to be a variable worthy of research, whereas another theoretical perspective might consider
this variable to be uninteresting. Analyzing the world in terms of economic class means
not analyzing it in other ways, such as social groups. This is neither good nor bad:
without a theory to order our perception of the world, research will often become a jumble
of observations that do not tie together in a meaningful way. We should, though,
acknowledge the theoretical preconceptions upon which our choice of variables is based.”

I think hat subjectivity, conceptualization and modeling are constantly present in scientific research. In statistics, if you want to analyze the correlation between two variables, you have usually to decide first which, in your model, is the indipendent one. That is sometimes obvious, other times much less obvious, and it may critically depend on you pre-existing model of the phenomenon.
More in general, modeling phenomena according to obligatory naturalistic mechanisms is a choice that has deep consequences on how one tends to make research or to intepret the existing data.
The same problem is very obvious in sciences of men’s behaviour (psychology, sociology, psychotherapy, etc.), where fundamental beliefs about what a mind is or can be, or about free will or determinism, are very likely to deeply influence theories and research. For instance, a position of dependance from the theory of strong Artificial Intelligence will shut out a lot of models, leaving space only for purely algorithmic ones. That’s very important, because I think that strong AI has a role, corresponding to that of strict darwinism in biology, in supporting a purely naturalistic model of mind and brain in pshychological and mental disciplines.
For instance, a mahematician and physic like Roger Penrose, who does not believe in strong AI, has generated a complex model of non algorithmic mental functions, based on his interpreation of Godel’s theorem (that model is obviously rejected by most, but it is very interesting and it is seriously debated. After all, I believe Penrose still has is job, and maybe that proves that mathematicians and physics are much more tolerant than biologists. Or am I being too optimistic?).

Patrick:
thanks for the link. I had already read that very interesting work, even in its extended form. The analysis is very complex, and the conclusions rather undefined and problematic, but it remains an extremely provocative article. I hope there is some follow-up on the same theme.

I think we’ve both reached the point where we’re just plain ol’ arguing. And somehow I haven’t been able to get across my point effectively to you. And likewise I don’t get your point very well. Our previous comments stand for themselves. I’ll move on to more interesting threads.

“They were able to restore sight in blind fish with different gene regulation induced artificially.” So an intelligent designer (man this time) had to change the gene regulation so the fish could see again. Hmmm….

“Where exactly in this loss of functionality is this new information you’re talking about?” An eye that can’t see sounds like a loss in functionality to me. What would you call it?

When’s the last time your nicitating membrane had a function? When’s the last time ostriches flew? When’s the last time whales walked on land? You’re throwing out these numbers, 4.5 million, 7 million, 20 million, as if they somehow disprove something. It does prove that you’re capable of looking up stuff. And for that I applaud you. But what do those numbers show? That it happened a long time ago. To which I reply, “So?”

I equated the idea of “CAREFUL COORDINATION” with new information. Is that wrong to do?

Yes. This has to do with changes in the regulation of one gene during development. They were able to restore sight in blind fish with different gene regulation induced artificially. Where exactly in this loss of functionality is this new information you’re talking about?

And as I said before other scientists have posited that this change might be due to a responsive mechanism. Other senses are supposedly enhanced in addition to the loss of sight. Sounds Lamackian to me…but whatever, I cannot even remember where I read that.

I don’t need to further speculate on things I know nothing about.

Funny, you’re perfectly willing to do just that in your next paragraph:

Why is it a stretch of logic to think that one of our common ancestors with the chimps had a tail? Just look at most other primates and land mammals. It does not have to be our most previous ancestor that was tailed for us to retain it’s mark.

So, you’re claiming that this reversion to conserved tail information comes from an ancestor from before Ardipithecus ramidus–over 4.5 million years ago? Unfortunately Sahelanthropus tchadensis, dated at around 7 million years, is just a skull so we cannot tell if it had a tail. Or we can go back 20 million years ago to Proconsul heseloni, which lived in the trees of dense forests in eastern Africa. Proconsul is said to have had features that closely link it to the common ancestor of humans—for example, the lack of a tail. But fine, you go ahead and believe that if you want.

I honestly know nothing about this. I’ve never even heard of mammary glands in armpits. I don’t need to further speculate on things I know nothing about.

Patrick: “Besides, if the bony tail is evidence that we evolved from tailed creatures, why also bother to insist that we evolved from a common ancestor with pan troglodytes, which doesn’t have tails? Just exactly who is stretching logic here?”

Why is it a stretch of logic to think that one of our common ancestors with the chimps had a tail? Just look at most other primates and land mammals. It does not have to be our most previous ancestor that was tailed for us to retain it’s mark.

It was previously discussed here that cavefish were descended from sighted fish. Let’s take that assumption at face value. Now, you point out that “blindness results from the CAREFUL COORDINATION of gene expression”. That sounds like to me that the cavefish has more genes being expressed than the sighted fish. I equated the idea of “CAREFUL COORDINATION” with new information. Is that wrong to do? Hence, under the assumption that these fish descended from sighted fish, that new information had to come from somewhere.

Now we can consider that assumption false. If the new information is CSI, then doesn’t the theory if ID require that the designer blinded these fish, or designed them with useless eyes to begin with?

If you see some holes in my logic, point ‘em out.

http://www.dimaggio.org/Archiv.....humans.htm

Human “tails”…aka disarrangements that occurred during embryological development. I also highly doubt these “tails” are extra-embryonic features (“scaffolding” is just a common term I used for this discussion). That interpretation of the data is only a possibility with the whale leg; don’t attempt to confuse the two in an attempt to make a bad argument. I don’t believe the precise genetic basis for these examples of “tail” growth in humans is known, but I’d say the best bet is Hox (homeobox) genes. Mutations in these genes cause alterations in the development of the axial skeleton (vertebral column and ribs) and limbs, among other things. The Pax-6 regulatory group–which is about 130 amino acids long–shares a 94% similarity between humans and insects. They are conserved across all animal phyla, with similar or homologous functions (you can argue over the cause of this–designer reuse or common descent–later). Mutations in these regulatory gene sets can cause biological components to not be built (an animal losing their hind legs). They can result in more than the correct number of elements being built (as in the case of Hox-4.6 in chickens which create an extra “thumb”). They can even result in the construction of components in the wrong places. Ultimately, manipulations to these genes can only result in the rearrangement of elements already present in the biological development plan for a given organism. If I wanted to give someone’s child a tail, we’d need to know the exact pattern of expression of the correct gene(s) and how to achieve it by artificially engineering promoter-gene fusions and inserting them into the genome of an embryo. Otherwise you’d end up with these useless extensions as seen in the above pictures.

But let’s ask some questions. Some human females are born with mammary glands under the armpits; does this mean they’re regressing to an earlier mammalian stage? After all, some mammals have mammary glands in their armpits. Does a second nipple on my right breast mean I’ve generated CSI? Of course not. Besides, if the bony tail is evidence that we evolved from tailed creatures, why also bother to insist that we evolved from a common ancestor with pan troglodytes, which doesn’t have tails? Just exactly who is stretching logic here?

Also, you should read this:

http://www.uncommondescent.com.....chives/875

Obviously I’m in the search for the truth, not some tired attempt to defend an old framework. Whether humans came from pan troglodyte, or another route through convergent evolution, or were specially created…I don’t care. I just want to make certain it’s true.

I cannot see the sciencenow link on cave fish, but I can read what you posted about it. It seems to be saying that the “micro-evolution” of the blind eyes of the cave fish was the result of NEW information, not a degeneration of existing information. Would ID then require to say that designer went out of his way to make these fish blind? Or perhaps the new information isn’t CSI?

“Of course they’re interpreting this evidence in an evolutionary framework, claiming it as ”rudimentary hind limbs” present during development. Another interpretation would be to consider this structure as temporary ”scaffolding” (extra-embryonic) that is ”normally” removed as the creature grows.”

I don’t know much about whale development. But a similar vestige closer to home, the human tail, has been more closely studied. http://www.ncbi.nlm.nih.gov/en.....t=Abstract

The “scaffolding” argument loses alot of weight when the vestige is found to be 13cm long and outside of the body. “Scaffolds” rarely contain blood vessels, nerve tissue, muscles, sweat glands, hair follicles, etc. One really has to stretch the logic to suggest that these are anything other than vestigial tails from our primate heritage.

Thanks for the link on gpuccio’s assertion. I heard a similar argument about convergence of the charge/mass ratio of the electron. Millikan’s data from his famous oil-drop experiment was a little off at first. All of the subsequent data from other scientists repeating the experiment caused the ratio to asymptotically approach the value accepted today. It goes to show you that scientists are humans, too.