> From: "Howard J. Van Till" <hvantill@novagate.com>
> To: asa@calvin.edu
> Subject: FW: What Creation lacks
> Date: Mon, 29 Oct 2001 19:31:04 -0500
>
> Following is a note I received from a biologist friend who is not on the
> listserve but has followed some of our recent discussion on the archives. I
> post it with his permission.
>
> Howard Van Till
>
> *************************
>
> I have followed the discussions on evolution on this site on and off for
> several years now. Now seems like an appropriate time to comment on two
> recent discussions that, to me, seem to be related---what does creation
> lack and the universality of the genetic code.
>
> Evidence suggests that the genetic code is (at least at the level of
> the first two bases) a real code. That is, you could encode the same
> message in many different ways depending on how the (presumably random)
> assignments are made in the code. In the actual genetic code UUU is
> assigned Phe, CCC is assigned Pro, AAA is assigned Lys, etc. I believe the
> evidence indicates that you could construct any organism using an entirely
> different code: for example, UUU could be Lys, AAA could be assigned Pro,
> etc. In an actual code there is no design in assigning the various
> relationships in the code. In cryptography the code for Day 1 has no
> connection with the code for Day 2 or the code for Day 3 and so on.
The actual genetic code definitely has some non-random features. It is
minimally error-prone (minimal possible chances of mutations producing
lethal stop codons), coordinated with the possibility of transfer RNA
frequencies in given tissues regulating relative transcription rates of
particular genes, possibly connected to amino acid metabolism pathways,
etc.
Some recent papers showing that the genetic codons are not randomly
assigned:
Di Giulio M., Medugno M. "The level and landscape of optimization in the
origin of the genetic code." Journal of Molecular Evolution 52 (2001),
372-382.
O'Sullivan J.M., Davenport J.B., Tuite M.F. "Codon reassignment and the
evolving genetic code: problems and pitfalls in post-genome analysis."
Trends in Genetics 17 (2001), 20-22.
Conticello S.G., Pilpel Y., Glusman G., Fainzilber M. "Position-specific
codon conservation in hypervariable gene families." Trends in Genetics
16 (2000), 57-59.
McVean G.A.T., Hurst G.D.D. "Evolutionary lability of context-dependent
codon bias in bacteria." Journal of Molecular Evolution 50 (2000),
264-275.
Freeland S.J., Knight R.D., Landweber L.F., Hurst L.D. "Early fixation
of an optimal genetic code." Molecular Biology and Evolution 17 (2000),
511-518.
Ronneberg T.A., Landweber L.F., Freeland S.J. "Testing a biosynthetic
theory of the genetic code: fact or artifact?" Proceedings of the
National Academy of Sciences USA 97 (2000), 13690-13695.
Di Giulio M., Medugno M. "The robust statistical bases of the
coevolution theory of genetic code origin." Journal of Molecular
Evolution 50 (2000), 258-263.
> We do not find significant differences in the genetic code for different
> organisms in life on this planet. The code that a mouse employs is just
> like its parents because the mouse inherits its genes and its translation
> mechanisms for the code from its parents. If there was a super genetic
> engineer, such a person could presumably make a mouse virtually identical
> to the mouse we see today using a genetic code entirely unrelated to the
> actual genetic code we find in organisms today. But mice have essentially
> the same code as humans and as trees and as fruit flies and as mushrooms,
> and as bacteria. Why is this so? If they were unrelated to each other
> there would be no reason for them to have this genetic code similarity.
A null hypothesis for design need not be random. It will not be random
if the codon assignments have some correlations with functional
features, as suggested above.
> The
> fact that they are same is evidence for evolution--inheritance of the
> genetic code from a common ancestor. It is probably the strongest evidence
> that links bacteria to fungi to plants to animals¯-that is why it is cited
> so often. Evidence of similar structures in anatomy and for similar
> biochemical pathways that are cited as evidence for a common ancestor are
> dismissed by antievolutionists as resulting from common design. (I
> personally find this a weak argument.) But with the genetic code this
> common design argument doesn't work. It is invalid because the assignment
> of codons to certain amino acids isn't designed.
We can't be sure it isn't designed because the assignment isn't random.
> The genetic code
> assignments would be an obvious place for an intelligent designer to insert
> evidence for discontinuities in the history of life.
Would he want to do that? Theological reasons (human freedom for a faith
decision) suggest that he probably wouldn't.
> (The Discovery
> Institute itself endorses this concept and in fact makes this argument, and
> DeHaan proposes something like it could exist in a recent post: "I think
> the stages are not hard to discern--prebiotic, unicellular life on earth;
> complex metazoan life, sentient life in the image of God.") Thus, if an
> intelligent designer wished to provide evidence that bacteria were
> different than complex multicellular organisms, that designer could use two
> entirely different genetic codes to construct such organisms. An
> evolutionist would be hardpressed to explain that by common ancestry. But
> different genetic codes are not the case here on Earth however; bacteria
> and humans have the same genetic code. (If a unicellular organism is found
> deep in the earth and it has an entirely different code than the one we
> have found in all organisms so far, I am quite confident few, if any,
> biologists will suggest that this new organism would have a common ancestor
> with all the organisms we know today.)
>
> So is the genetic code universal? The answer is no. Certain ciliates and
> some mitochondrial DNA have slightly different codon assignments involving
> the STOP codons, the Met codon, the Arg, codons, and a few others.
> However, the differences appear in only a few codons and there is no doubt
> that all the variants are all very similar to the so-called universal
> genetic code. The genetic code makes 64 assignments of codons to amino
> acids¯either most or all of the time ( I haven't researched this
> thoroughly) only 1 to 4 of these 64 codons vary from organism to organism,
> the rest remaining unchanged.
>
> Why aren't all the genetic codes exactly the same? The Discovery Institute
> discussion found on one of the links in a post about two weeks ago on this
> list indicates that these differences are the work of an intelligent
> designer who is providing us with evidence of discontinuities in the
> history of life.
I believe they are mistaken here - for the theological reason mentioned.
> According to the Discovery Institute, the reason ciliates
> have a different code is because they were formed separately in some manner
> from the rest of the organisms. They could not have developed from a common
> ancestor because their genetic code is different. Their proposal is that
> the designer is sending us a message of a discontinuity here. The
> evolutionary view is that the genetic code has evolved at a few sites
> (evident in mitochondria and ciliates), but has remained almost unchanged
> over billions of years.
The evolutionary interpretation of these observations looks reasonable.
> On October 18 and on additional posts on this list
> David Campbell provided some ideas to how this evolution might have
> happened. Also, I would add, there are known suppressor mutations that can
> be isolated today in bacteria where a codon is actually read differently
> due to a mutation in the tRNA. These are sick bacteria but they do survive
> in the lab.
>
> So I see this as a straightforward question: Why is there is a near
> universal genetic code with slight variations? It is not common design, it
> is not even the common use of the same code for everything, since there are
> these variations.
We cannot tell that it is not common design. All such claims presume to
know the mind of the Creator.
> We have three possible answers, I think:
> (1) The code evolved from a common ancestor since it appears in all life
> today
> (2) The intelligent designer made the different codes to show us
> discontinuities, but did not chose to make the variants obviously different
> at all 64 codons, but just a few at most.
> (3) It is necessary for a ciliate or a mitochondrion to have the particular
> code it does in order to function as it does.
>
> I don't think there is any evidence for (3). I find (2) to be unacceptable
> because that is counter what I believe an intelligent designer would do if
> that designer was intelligent. An intelligent designer would not make only
> slight variations to keep us guessing about an evolutionary possibility.
> I find (1) to be plausible.
How about a combination of some of each of the 3 answers? Such as: The
Creator made the code evolve according to his design, assigning the
normal code according to certain functional principles, and the
exceptional modifications according to special requirements. And:
Couldn't there be reasons why the Creator would not want to prove us his
existence on a scientific level?
> In summary, I think the near universal genetic code with its small
> variations poses significant problems for the intelligent design
> and the discontinuous positions.
>
> Al Koop
>
> koopa@gvsu.edu
>
> Department of Biology
> Grand Valley State University
> Allendale, MI 49501
I think the genetic code poses no problems for either intelligent design
theory or discontinuous creationism. On the other hand, I think an
intelligent designer poses no problems for continuous evolution and an
evolution of the genetic code. The problems with evolution are not
theological but scientific, with the insufficiency of the known
evolutionary mechanisms.
Peter Ruest
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