1. Mathematics

Sal,I like the way you think. If the numbers
don’t add up, somethin’s not right.

You’ll find lots of them that do at:

http://www.hereoisreal.com
more at:
http://www.bloglines.com/blog/hereoisreal

Zero

ID connoisseurs would perceptively note here that these strong statements about “junk DNA”’s function seem to contrast with the shyness of ID advocates regarding the attributes, goal and identity of the Designer (why couldn’t She be a compulsive junk collector, as far as Her critters’ genomes go, after all?). But ID advocates have of course at least two good reasons to support this view: first, the admission of a careless or incompetent Designer would constitute a bad P.R. move with the movement’s religious supporters, and second, if uniquely identifiable junk DNA elements, like pseudogenes, are indeed non-functional, then their observed transmission along evolutionary lines (see for instance this paper) is powerful evidence of common descent, with which most ID advocates have yet to make peace.

May I inquire 1) how does ID explain pseudogenes? 2) has ID’s ‘predictions’ been falsified and what does this mean for ID?

Of course, this could benefit from some actual data to show that the inference of common design explains the data equally well (or better?)
Since there is no design hypothesis, how can it explain the data better I wonder?

Explain how you calculated the following:

IDC: Common design
E: Evidence of ortologis

P(IDC|E)=P(E|IDC)*P(IDC)/P(E)

Looking forward to your calculations David. When can we expect them?

Spalog

The term ’spalog’ (pronounced [spailog]) denotes a 3-D structure that is spatially similar, to a specified extent, to another 3-D structure. This term is strictly about spatial similarity and implies nothing about evolutionary relatedness and functional properties of structures.

Defined by Alexander Varshavsky

See also: homolog, ortholog, paralog, pseudoortholog, pseudoparalog, sequelog, xenolog
————–
Ortholog

An equivalent gene in different organisms, based on similarity of genetic sequence and the degree of correlation of conserved sequences. Functional genes in animals such as mice have been used to help find the similarly functional genes in humans – the human orthologs of the animal gene. The idea of conserved sequences generally relies on the assumption that organisms share a common genetic ancestry, but is equally well explained by the inference of common design.
Ortholog>
————-
Sequelog

Defined by Alexander Varshavsky

When you mentioned the phrase “paradox of purpose” it really caught my attention. We do see strong functional analogies, but these are very hard to quantify objectively.

A missile has a guidance system, but so does a monarch butterfly, at least in terms of functional analogy between human engineered systems and natural systems.

However, what is less subjective, and operationally useful are structural analogies between engineered systems and natural systems. Where the paradox of purpose is most evident are in these structural analogies. For example, the flagellar motor, looks structurally like a motor in the engineering sense:

Flagellum motor

Because of the structural similarities, we are inclined to think they exist for similar reasons (they have purpose). I think that’s where one line can be drawn. There is no requirement to say they are teleological because they look structurally like those things which are manufactured for a purpose. This demarcation of pure structure analysis is the bulk of CSI analysis. It is the “D” part of ID. For example, we can structurally demonstrate analogies between computers and cells, between communication and information systems and the genetic code, etc.

The “I” part of ID argues that analogy in complex structure implies analogy in mode of origin, namely intelligence. This of course is the area of extreme contention between EBers and IDers.

Salvador

(1) Stretching back to Darwin and Owen there is a tradition in biology of distinguishing biological “analogy” (e.g., the wings of hummingbirds and butterflies) from biological “homology” (e.g., the wings of birds and the flippers of penguins). Biological homology might be a philosophical analogy in some sense, but it is best to be ultra-clear about it.

(2) I think Alan overplays the problem that biological analogy/homoplasy causes for biologists. To pick his own example, no one is confused by similarities in the wings of birds and insects. And a vast number of other cases, including all of the impressive cases of convergence cited in textbooks, are quite clear.

In reality, the difficulties arise if a taxonomist is working with a group of relatively closely-related organisms. These organisms will already share many features due to common ancestry, and then the question becomes whether or not certain specific recently-evolved features — bumps on bones or something — are a shared ancestral feature, or evolved twice as sister species in similar environments made similar adaptations. This is a much different situation than convergence between dolphins and sharks, or some such.

I quoted Lewontin at the other weblog:

It is not possible to do the work of science without using a language that is filled with metaphors. Virtually the entire body of modern science is an attempt to explain phenomena that cannot be experienced directly by human beings, by reference to forces and processes that we cannot perceive directly because they are to small, like molecules, or too vast, like the entire known universe, or the result of forces that our senses cannot detect, like electromagnetism, or the outcome of extremely complex interactions, like the coming into being of an organism from its conception as a fertilized egg. Such explanations, if they are to be not merely formal propositions, framed in an invented technical language, but are to appeal to the understanding of the world that we have gained through ordinary experience, must necessarily involve the use of metaphorical language.

If I might give my ranking of the analogies in science with #1 being the strongest in terms of acceptance as “valid”:

1. Mathematics
2. Physics and Chemistry
3. Engineering
4. Biological Structure
5. Biological Function
6. historical hypotheses

#1 and #2 are so central to science they are adopted as articles of faith. Given analgous experimental conditions, we expect analogous experimental results.

#3 is defensible because we have access to the designers themselves (engineers). They can answer questions about analogies if we pose them, like “Is each car analogous to another? That’s what you had in mind, right?” And so, in that sense there is no ambiguity if the analogy was intended or not.

#4 is accepted practice, we see structural similarities and build hierarchical relationship where the most analogous creatures are grouped together. This was accpeted before and after Darwin.

#5 deals with something a bit more esoteric. For example we say creatures “see”, yet the same function is achieved with structurally different architecutres.

#6 finally we have analogies related to historical events. We try to project the present back into the past and hope we have a good picture. We hope we can extrapolate some analogies in the present back to the past….

EB and ID theories are most strongly at variance in #6.

D (design theories) deal mostly with structural similarities in objects described by #3 and #4. One could take 98% of Dembski’s Design Inference and apply it to purely structural analyses. That is, his work in that book can actually be used to measure the quality of structural analogies with no reference to intelligence. As I said, it’s consistent with the word “design” as when biologists used the word.

Dembski’s later work and I (intelligence theories) No Free Lunch dealt more with #6.

Behe’s work arguable dealt with #5 and #6. Irreducible Complexity deals with functional analogies.

At least that’s kind of my perception of things.