If ID were true, what would that tell us about the designer's motives?

Some time back, a creationist by the name of Pitman made the following
claim:

"The argument of nested hierarchy as evidence for the common descent-
only hypothesis is based entirely on the notion that "No intelligent
designer would have done it that way."

I had written a reply, but did not send it at the time.

In reality, the argument of nested hierarchy can be used as evidence
both for the standard evolutionary model of descent with and by
modification *and* for intelligent design. After all, the intelligent
designer that creationists propose could easily produce a nested
hierarchy and sequence patterns just like those seen in organisms.
Intelligent agents that are omnipotent gods can do whatever they
want. Moreover, *if* the nested hierarchy points to an intelligent
designer, this actually gives us insight into "why" God would produce
this pattern (based on analogy with "why" known intelligent agents,
namely humans, are known to produce the same pattern). I am not sure
that creationists will like the reason, but that is not my problem.

The descent model is based on the fact that the pattern one *does*
observe is one that is (largely) consistent with the expectations of a
*vertically branching historical* process. Vertically branching
historical processes of change in organisms will *necessarily* produce
largely consistent nested hierarchies (a specific pattern of
branching) for all the protein or other sequences that retains the
same function throughout the biota that contains it. That is, the
statistically determined optimal branching pattern for cytochrome c
must be roughly the same as the statistically optimal branching
*pattern* for rRNA and the statistically optimal branching pattern for
many other proteins or nucleotides. Much of this with the *same*
function in all the organisms that have it. Because the pattern is
based on proteins or sequences (say rRNA or cytochrome c) with the
*same* function in all the organisms that have it, the differences
between these sequences must be (at least nearly) functionally
irrelevant (neither strongly selected for nor strongly selected
against). And there is experimental evidence to support that idea
that, despite the sequence differences, the cytochrome c of any given
organism can function as a cytochrome c in any other organism. This,
of course, is more true when the protein or function in question does
not involve the co-evolution of other proteins that associate with
it. And some sites do affect minor features like optimal temperature
range. But, for proteins, by and large, the enzymatic function and
the enzymatic structure is unchanged despite, sometimes, even so much
sequence change that sequence homology is barely detectable.

What this means is that the pattern of branching one obtains from
looking at each protein or sequence that performs a particular
function across a broad sweep of the biota is NOT a matter of
*functional necessity*. For any *one* protein, one can always get a
best fit nested pattern by applying the statistical methods that find
the pattern that produces minimal chains of changes in sequence, even
if the changes were completely random because they have no
*functional* relevance. However, *if* the pattern of changes in
sequence were random, this statistically determined minimal pathway is
highly unlikely to be *significantly* different from many other
possibilities. If the pattern found to be minimal was being simply
imposed on a random distribution of differences, we would expect the
chosen minimal sequence to barely be able to poke its head above the
mass of other possibilities.

Most of the time, however, the observed best fit pattern stands out as
a distinctly isolated and highly significant pattern (there may be a
couple of highly correlated sequences that differ in one or a few
sites). But even more important for the hypothesis of this pattern
being produced by a mechanism of historical descent with branching
modification, in most cases the pattern produced by *different*
proteins or sequences is essentially the same or very similar! Now,
as I said, for any one protein, one expects *some* particular
branching pattern to be the most likely one. But for the *same*
branching pattern of organisms to pop up time after time after time
after time is not due to chance. That this pattern largely coincides
with the branching pattern based on morphology (differing primarily in
the spots where the morphological evidence was weakest) also tells us
that the branching pattern picked up as the minimal pathway is not due
to chance.

So *if* the observed vertical branching pattern is not due to chance
and (because the differences are in places that don't affect
*function*) the differences are not due to *functional* requirements,
what could they be due to? They clearly could be due to history
(specifically the history of accumulation in separate lineages of
'copying errors)? One test would be to see if the amount of
difference reflects time since divergence rather than degree of
morphological difference. For example, humans diverged from chimps
about 5-7 million years ago. Certain frog species on either side of
the Atlantic started diverging from each other 30-40 million years ago
(when the Atlantic Ocean separated S.A. from Africa). Humans look
quite different from chimps (almost every bone differs), yet the frogs
look quite similar. So, if the accumulated differences are due to
time since divergence rather than amount of morphological
dissimilarity, I would expect 5-6X as much difference between the two
frog sequences than between humans and chimps. They are. What this
means is that one possible explanation of the observed branching
pattern is historical branching descent, just as evolution would
propose.

So the *evidence* is certainly consistent with most of the difference
between organisms being the consequence of historical descent. But is
there an alternative explanation that could also explain this pattern
so consistent with *real* historical descent?

Yes. Any sharp (and particularly an omnipotent) intelligent designer
*could* generate sequence changes that would produce exactly the same
result as the common descent explanation without *real* common descent
being the explanation. Moreover, we have actual experience with
respect to the motivations of all the known intelligent agents who
have ever produced such an *appearance* of common descent without it
being *actual* common descent. Namely, we have observed intelligent
agents produce such evidence specifically for the express intent of
deceiving or defrauding some other intelligent agent.

People have been presenting bogus lineages (the appearance of common
descent without the reality) to pass themselves off as Count X or Duke
Y or to pretend to be related to actress Z for many years. These
intelligent agents have forged documents, created fake documents, aged
them so that they would appear old. In short they used all the tricks
and deceptions so blithely described in the Gossean belly button
defense. But, in every case I know about, the intent was to
intentionally deceive some target.

The fact is that we have no evidence of any intelligent designer who
*purposely* produces such ersatz evidence of ancient historical
processes without having 'defrauding some poor sucker' as his or her
intention. So if the evidence, which so clearly points to common
descent, is actually evidence of *intentional* or *intelligent*
design, then it is clear evidence (by analogy to the way that known
intelligent agents work) of an intelligence attempting to deceive us.
That is, if some designer, 6000 years ago *intentionally* created a
design whereby he *independently* created and manufactured each and
every protein of each and every organism and *intentionally* did so in
just such a way that all of these sequences produced a pattern that is
consistent with ancient branching lineages and not with function, then
we also know his or her motives --- fraud and deception.

The problem, as I see it, is not that a supernatural designer could
not produce whatever pattern we could possibly observe. It is that
the pattern he did produce is consistent with branching common descent
over long millions of years and not consistent with the pattern one
would expect if an intelligent designer *without fraud and deception
on his or her mind*. It clearly would have been just as easy for an
intelligent designer capable of producing all life in one fell swoop
some 6000 years ago to have produced organisms and their proteins in
ways that differ solely based on functional requirements (or not at
all).

That means, to me, that creationists have to choose between a
'designer' that works in a scrutable and obvious (and non-dishonest)
way (i.e., one who works via evolutionary common descent, as the
evidence supports) or a 'designer' who is engaged in fraud and
deception, one who intentionally produces sequence patterns whose only
reasonable purpose seems to be to lead us to the evolutionary idea of
branching common descent. Atheists and agnostics, of course, can
choose to think there is no 'designer' at all. The choice of whether
there is or isn't a 'designer' is a matter of personal faith. Whether
you think that designer worked through evolution or by magical poofing
some 6000 years ago depends upon whether or not you think the designer
is honest or is trying to deceive us.

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