Re: [asa] How big a deal is homology?

The assertions that the "junk" DNA sequences sometimes actually have
function misses a converse point. Among multiple functional options,
things with close evolutionary relationships typically have similar
options. Although computer programing provides good analogies,
language is an example that is even more familiar to any audience. As
a rule, there are many different ways to say something. For example,
"methinks it is a weasel" and "the object in question appears to
represent one of the small terrestrial members of the family
Mustelidae" convey the same information with no word in common.

Certain genes occur in a wide variety of organisms, if not all known
organisms. In a few cases, versions from one organism have been
transferred into another without ill effect. There is no functional
reason known why the DNA sequence coding for, e.g., 18S rRNA or
cytochrome oxidase I in humans ought to be more like that of a
chimpanzee than that of a gibbon or a tarsier or a mouse or a cow or a
kangaroo or a chicken or a toad... except to the extent that the code
affects details that mesh with other molecules that also show the same
pattern of similarity. There's not a single blueprint for these
molecules that God would have to follow across the board. Rather,
within the range of options, the particular ones chosen follow the
pattern expected from evolution. Such patterns are not confined to
genetic similarity. Pterosaurs, birds, and bats demonstrate three
different ways to transform a vertebrate forearm into a wing. Whales
swim with an up and down bending of the body (hence tail fins extend
to either side), derived from terrestrial ancestors that had improved
terrestrial locomotion abilities by restricting side-to-side body
motion. Side-to-side bending of the body, as in salamnders, is not
only inefficient versus just moving the limbs in a front-to-back
pattern but also compresses the lungs. However, fish and most
crocodiles use a side-to-side bending of the body. Yet other swimmers
derived from land ancestors with limited body motion and strong limbs
rely on the limbs for propulsion, like human swimmers as well as
penguins, sea turtles, plesiosaurs, etc.

Then there are the regions that have function not tightly related to
sequence. Although it's true that these are not totally "junk", their
sequences are largely unconstrained. Much intron or spacer DNA falls
into this category. The ends need to identify themselves as ends of
the part to cut out or ignore, a certain approximate length may be
needed, and there may be occasional conserved motifs, generally of
unknown function, but as a whole the sequence appears free to vary.
I've worked with a calmodulin intron in snails. Although the
sequences from lymnaeids and planorbids (two closely related families)
show recognizable similarity at the beginning and end, I can't align
most of the middle. I can't find any meaningful similarity to
versions from distantly related snails, nor to paralogous versions
from the same snails. Species within a genus have similar sequences,
and sequences from closely related (based on morphology) genera are
relatively similar though not as close as within-genus comparisons.
ITS1 and 2 show similar patterns (for different species; they haven't
worked for the lymnaeids and planorbids that I am interested in).

An analogy from teaching arises. How do I tell if someone has
plagarized a paper? It's obvious if he was dumb enough to simply copy
something verbatim. On the other hand, I had a couple of students
last fall who reported on the same species of invertebrate and had a
couple of very similar sentences. A much more likely interpretaion of
this is that they both found a couple of the same facts, ultimately
deriving from the same source [websites often draw on each other in
complex ways, so the exact trail to the source is probably rather
tortuous], and independently worked them into sentences in the context
of each report. In between these would be the subtle cheater who
copies something but changes enough to avoid a direct match. All of
this is constrained by the fact that all reports about the same topic
will have some similarities. The question then becomes, are the
similarities no more than would be expected based on the common topic
and perhaps the use of some common sources, or is there copying of
extraneous detail that indicates a stronger dependence on a particular
source? Thus, my graduate advisor thinks that someone copied an entry
from one of his bibliographies because he mistook the German phrase
for "reprint from" as part of the journal title, and the subsequent
citation exactly matched his mistake. Similar factors arise in many
other fields, e.g., Jdg 12:6. The functionally unnecessary patterns
of genetic similarity accord with evolutionary expectations.

Two versions of the question of ID-like intervention-style miracles
can be made. Is it possible to rule out the possibility that God has
occasionally acted in a way not described by natural laws to produce a
particular outcome in the creation of organisms? Not by scientific
evidence. Is it necessary to invoke such actions to explain the
observed patterns? No, nothing is known in the course of organismal
origins that clearly cannot be explained within known natural laws.
Asserting that there is no good example within evolution that will
stand up as an example of ID does not require a process or other view
that restricts God's ability; it merely asserts that there is no good
evidence that indicates that God has acted in that way within the
course of evolution.

If God has chosen to work through the ordinary means of natural laws,
then we should expect to see the "sloppy programming", because the
laws of nature are unable to plan. Furthermore, the random spare bits
of DNA provide lots of material for evolution to work with without
harming the really important bits. The Bible has much more to say
about God's working out of His plan through human history than the
history of life, yet human history is definitely a mess without clear
directions evident to the theologically uninformed observer.

Although there are patterns of breaks in zoology, etc., they are
defined post hoc. Whatever changes happened relatively early in
evolution will now be expected to define major divisions merely
because of the long-term historical contingency. For example, many of
the Cambrian arthropods look sufficiently shrimplike that the average
person wouldn't notice that it was unusual. However, all more modern
arthropods (not counting mutant fruit flies but counting trilobites)
fall into only a few categories based on the number, position, and
type of appendages and segments. Some of the Cambrian forms fall
outside the later categories and thus appear to represent either
dead-end lineages equivalent to the few surviving groups or forms
originating before the major lineages were established. On the other
hand, no one has trouble distinguishing butterflies and ants, yet both
are holometabolous insects, relatively close in the overall scheme of
arthropods. Barnacles look sufficiently unlike standard crustaceans
that it took a while of study into the 1800's to place them, and many
parasitic barnacles don't even look like barnacles. However, the
larvae fit clearly into a particular group of crustaceans. In turn,
the crustaceans and insects are relatively closely related within
arthropods. Another example comes from the contrast between
traditional classifications, e.g. that in the Bible, with modern
biological classifications. Flying things, creeping things, big land
animals, and swimming things provide handy categories, but they do not
match well with current biological divisions. There are no gaps that
match well with the four Biblical categories, because looking for
biological gaps was not a major component of the development of the
categories.

>To my engineers' eye, evolution has the hallmarks of design
and Dembski's tests are all wet because he is looking for greedy
optimization and that's not how intelligent designers do our job.<

Dembski's and other ID tests to me seem to be efforts to find ways in
which biochemical complexity resembles some human-designed things,
with little regard for type I or type II error. Many things created
by the action of natural law are quite complex.

-- 
Dr. David Campbell
425 Scientific Collections
University of Alabama
"I think of my happy condition, surrounded by acres of clams"
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