Note:  This is a very long question about Behe and Intelligent design.  The
question is a few pages down (look for the indented material)

I study medicine, and I am in the second year this year. I am a lot interested
on questions about creation/evolution. I am a Christian and take seriously me
faith in God, and also where it is based. I heard of Behe’s book ?Darwin?s Black
Box?  If I had to choose just one of the examples of that book to use as an argument
for design, the blood coagulation would definitely be the one.  But reading
it a question came to my mind, to which I can?t answer based on my current knowledge.
Actually it is a scenario on how that system (or even the other systems) might have
evolved.

 Before beginning, I want to let you know that I don?t take pleasure in being
a cynic or being uselessly skeptical just for making myself look smart, or anything
like that. This is a sincere doubt that came to my mind as I was reading the
book. I don?t like shallow answers from people who don?t share my views, so
for that same reason I don?t like to give them shallow answers for questions
they ask me. These questions came to my mind as I asked myself  ?If I were an
evolutionist what would I say? How would I answer to this challenging argument??
So if I want to build a case for intelligent design, using an argument from
that book I believe I need to clear up my thought about it first.

 So now I can share my thought. I thought: Imagine we have a kind of animal.
Also imagine that it has (among many others) a gene, called gene A.  Gene A
codes for protein A which has its function in the cell. Then a duplication happens.
So now we have two genes A which code for the same protein. But one of the two
genes is mutated.  Let?s call it now gene B. Now the protein it codes for is
different from protein A, and thus doesn?t have its function.  In fact now that
protein doesn?t have any function at  all. Let?s call it protein B.  But nothing
happens to the animal which inherited it.  In fact protein A is produced and
makes it?s job as normally. So the mutation doesn?t result in a damage for the
animal and it can keep on living as the one who hasn?t that mutation. It is true
that is doesn?t even result in any advantage, but it doesn?t even result in
a damage.  It is neutral.  So the animal can live and reproduce normally.  It
seems to me that there is no reason why it should not be like this.  Now the mutant
animal has its offspring which produce both protein A and protein B. These mutants
for now don?t have any advantage over their normal  cousins. Even if further
mutations happened to gene B it won?t affect the viability of their descendents (since
protein B didn?t have any job, so it?s change won?t have any negative result
on the animal)  So after some time we will have a whole specie of animals which
have the same probability of survival, but in which specie there is a lot of
polymorphism about what we called protein A (after a lot of time in some it became
protein C, in some others protein D, in some others protein E, in some it?s
still protein A, and so on)

 Now what can happen over time is that the same thing happens with other genes
(so they duplicate, one of the two accumulates mutations, but still no damage
is done to the animal which still got the other gene for producing its protein
as before the duplication, and so the other mutated protein will keep on changing
without affecting the animal).  So after a while the animal happens to have
a lot of proteins which till that moment don?t interact and do nothing in the
cell. But after one final mutation on one of the useless proteins they all can
interact and so the system is formed.  The proteins which till that time were
sitting around doing nothing, now interact and form a system. NOW this animal
and it?s descendants do have an advantage over the other animals of the same species.
Natural selection can act NOW.  Now this will require a lot of time and a lot
of luck, to be sure, but it?s not impossible. Every interaction (as a result
of a final mutation) that would do a damage to the animal will be lost with the
death of that animal.

So only the advantagious or the neutral mutations would continue to be transferred,
until some useful interactions happens.  My point is: there is no reason why
neutral mutations can?t stay on the animal and be transmitted to the offspring.
It?s true that natural selection selects advantages, and eliminates disadvantages,
but it doesn?t eliminate neutralities (it is neutral to neutral mutations),
so they can stay.  

In the Rube Goldberg example, in chapter 4, Michael Behe said that  ??suppose the
string were attached to a dollar bill and directly to the canon, which would
then blast the rooster when picked up the bait.  A Darwinian transformation
of that simpler system into the more complex system in the cartoon would require
gradually repositioning the canon, pointing it to a different direction?Clearly,
however the system therefore would be out of commission much of the time, so
a step by step Darwinian transformation is not possibile.?

 Now the point of my question (or scenario) is that you can put TWO dollar bills
both attached directly to two different but identical canons. Then while you
used one for blasting the rooster, you could make experiments with the other  ca
non until a satisfactory result came (the telephone pole falls on the head of
the victim). After that you use  just this model while the other, used just in
the time of producing this final model, now is not much preferred and is thrown
away.  So you have the transformation of the dollar bill- string- canon system
in a more complex one and also in the mean time you didn?t have to not punish
Rooster Foghorn for being so annoying.  But an objection might arise: well also
the simpler system (dollar bill- string- canon) is also irreducibly complex.
How did THAT arise? How did the animal manage to survive before that ?simpl
e? system evolved? As an evolutionist I would make the assumption that that
system evolved BEFORE the blood circulation system evolved. So you have a primitive
blood coagulation system that is perfectly working in a small part of that population
(remember that above assumption was that there was a lot of polymorphism of some
neutral proteins) before having any blood system at all in that species. So
the individual that had this system  already in them had more probability for survival
only after the evolution of blood arose.  It?s a bit speculative, I know, but
why not? After all if evolution is blind then things don?t need to go in a certain
sequence of events.  That was what I would have said if I were an evolutionist. What
would you answer as a creationist?

 Answer: 

          You raise a question which I have actually thought about a lot.  It is
certainly true that all complexspecies have a lot of genetic material which appears
to be unused at this time, although just because geneticists do not know any
particular function for a seemingly dormant gene, does not mean that it actually
serves no function. I am prepared to accept the hypothesis that there are some
chunks of human DNA which are, in essence, "junk" (exons vs intron
s, as you know)
and which at least appear to be unexpressed.  It is also true that mutations which
occur in the unused portions of the DNA can be temporarily neutral simply because
that portion of DNA/gene is not being expressed in the cells of that organism.

           I would agree with you that Behe’s model is a bit too simple in that
it appears to ignore the possibility of neutral but unexpressed change later on
being expressed when it becomes beneficial.  I would say that this argument (which Behe
appears to ignore, but which I bet he would acknowledge if you talked to him
personally) could explain certain fairly small changes, such as color adaptations
and other things which one might label as "microevolution."  You certainly could accuse Behe
of temporarily shoving under the rug possible mechanisms which could allow for
certain small and advantageous changes to occur which would allow for sufficient
variation to occur to for small jumps in enzyme function.  I assume Behe does this in
order to keep his arguments simple enough to be understood by a general audience.

           Having acknowledged that Behe’s picture is probably too simplified,
I nevertheless agree with his conclusion.  There are types of changes which had to occur
to go from bacteria to human beings which involve too large a leap of complexity to
be reduced to believable changes which could happen in believable numbers of
generations by believable rates of mutations by believable actual enzymes.  In the end,
it comes down to mathematics and probability.  What you propose as a Rube Goldberg examp
le and as a parallel protein evolution example is possible in principle, but
the question is whether it is possible given the known laws of probability,
independent selection, rates of actual mutation and so forth.  At this point, to be
honest, I am outside my range of expertise, so am forced to rely on the mathematicians
to do such calculations, but from what I have seen, the argument for irreducible
complexity still holds true.  There are amounts of change which have occurred which involve
jumps that simply could not occur if one applies known rates of mutation and
mechanism of DNA expression and so forth.  Atheists do not accept the hypothesis of
irreducible complexity simply because to accept this hypothesis would require them
to throw out their atheistic presuppositions which happen to be the basis of
their entire belief systems.  I do not expect most evolutionists to give up their presuppositions
easily.

           My conclusion, from all I have seen, is a somewhat uncomfortable
mixture of paradigms.  I wish it all presented a simple and clearly defendable scientific
picture, but as I see it this is not the case.  I see a natural system for gradual
and small amounts of change created by God. I see God’s hand in allowing there
to be just enough uranium and other radioactive elements in the earth’s crust
to both allow for plate tectonics (and therefore a sufficiently mineral-rich crust) and
also to allow for a rate of mutation which can produce small adaptations to
environmental pressures.  In other words, God, in his wisdom, created a natural system
which produces a relatively low level of "evolution".  However, I still see God’s hand poking
into the process at various times for various reasons which are way beyond my
ability to understand or explain.  Given the fossil record and the clear and
unavoidable (unavoidable in my opinion–I will leave you to decide for yourself)
evidence for irreducible complexities (such as in blood protein chemistry and in the
functioning of the eye and in the functioning of aerobic metabolism and so forth),
I see God somehow miraculously intervening in the process at different times
for various reasons.

           I understand that this will appear to be an extremely convenient argument
to the atheistic evolutionist, but that is what I see when I look at what we
can observe from biochemistry and from the fossil record.  

            It is an interesting analogy that this fits the model of human history
as we can see it as well.  God normally lets events take their own course, with his
finger interceding behind the scenes, but at certain times in human history,
God has directly intervened in dramatic ways, such as in sending Jesus, in having
Jesus raise people from the dead, in having Moses and the people of Israel cross
the Sea of Reeds on dry ground, in setting the people of Israel free from Egypt
and so forth.  What appears to be the case with evolution of species is consistent
with God and human history–God setting up a system which from the outward,
human perspective, runs itself, but God intervening at various points and for
various reasons according to his own great wisdom and plan..

           I really appreciate the work of Behe and Johnson and others who try
to put this pictures into mathematical and scientifically understandable terms. 
To be honest, I would not want to be in their place.  They are trying to present a
perfectly reasonable and even at times compelling argument to two groups who
will not ever accept their work, no matter how compelling.  Atheists, almost without exc
eption, will not accept their work because they are working under a paradigm
which completely rejects divine explanation before they even look at the evidence.  C
onservative creationists will reject the work of the intelligent design people
as well, as they reject the possibility that the earth is old and do not even
consider the scientific evidence for age.  Intellectual blinders are a problem which
it is very difficult to overcome!

 John Oakes, PhD