Re: Genes and Development Conference

Tim Ikeda (
Sat, 03 Apr 1999 12:19:17 -0500

BH> Hello Tim. I appreciate your comments a great deal but am a
BH> little confused. I believe that everybody knows (including
BH> Goodwin) that everybody knows that there are factors involved
BH> in addition to the genetic programs. I thought it clear enough
BH> from the quote that the point of contention is the relative
BH> importance of the genetic program.

Hi Brian. Thanks for your reply. I was particularly strident
in my last letter on the subject but I do understand that the
topic was partially a debate over the relative importance of
particular components.

I think Goodwin frames the problem incorrectly. Arguing over the
"relative importance" of any particular part of a nested control
system is a waste of time, IMO.

BH> I'm sure there are a wide range of views as to how important
BH> this is. At one extreme one has the selfish gene (I recall
BH> Dawkins saying that organisms are just survival machines
BH> constructed by genes) and at the other end people like Goodwin.
BH> I'm happy to hear what you say about "most of the biochemists
BH> you've encountered". It seems to me quite often that what laymen
BH> like myself hear the most about are the extreme views (Dawkins or
BH> Goodwin) and not enough about the middle of the roaders which
BH> hopefully make up most scientists.

That's because the "middle" is boring. The "middle" takes flak from
both sides. Kinda like being a TE or an agnostic, no?

In his book, Michael Behe mentioned that some of his biochemist
colleagues were surprised when told just how little we knew about
the actual steps involved in the evolution of biochemical systems.
I mentioned to him that I had not had similar experiences and that
most of the biochemists I knew understood the difficulties involved
in that sort of work.

So either I am extremely lucky in having only friends that are
exceptionally well-informed about the shortcomings of current
biological understanding, or I'm learning that people with
axes to grind aren't telling the whole story.

BH> Nevertheless, I do not believe that the view that
BH> development is most predominantly (but not exclusively) directed
BH> by a genetic program is a strawman. Goodwin gives several quotes
BH> in his book supporting this view, for example:

[...good examples of scientists suffering from cranial-rectal
inversion syndrome removed...]

I've seen similar statements peppering the literature as well.
There's no doubt that some believe it (or did believe it at one
time). However, I think the when backed into a corner and really
probed on the specifics, even those people quoted would probably
admit that their comments were a tad overstated (I'd hope). What
I find to be foolish are attempts to quantify what proportion of
developmental control is genetic or "extra-genetic". They're
*both* important. You can't have one without the other. I think
that if someone (anyone) sits still and thinks about the problem,
this becomes apparent. Genes are just parts of the whole organism.
Take the example of cloning, where a nucleus is transferred from
one cell type into another, which "resets" the developmental clock
in the process. What changed? Probably not the DNA sequence. DNA
is simply one of the many intermediate players in the whole process.
The reason there has been so much focus on genes is that they are
much easier to study. (Sequencing is easy, understanding the
context is hard).

This problem is not confined to development, but runs across
areas like metabolism as well (Heck, if we're going to assign
claims of priority, people studying metabolism recognized the
problem very early). Knowing gene sequences aren't going to tell
us all we need to know about how cells sense and respond to changes
in their environments. We understand that metabolism is regulated
at many levels in a huge interconnecting network of which genes
are just one component.

For example, there are now many technologies that allow us to
monitor changes in the levels of the different mRNAs in a cell.
We can subject a culture to various changes in conditions
(nutrient availability, temperature, addition of antibiotics &
etc.) and see which genes are activated or repressed in response.
The hope is that with this information, one would be able to
determine what functions/genes are involved in a particular response
and figure out how the signals propagate through metabolism. The
harsh reality is that so much change happens that it's practically
impossible to distinguish signal from noise. Worse still, it's
likely that the signals you're interested in propagated long before
any response is reflected as a change in mRNA levels. On top of
and woven within the "genetic program" are many other layers of
"non-genetic" responses. (Aside: The technology still has its uses,
specially in well-defined systems or in situations where you'd like
to test a particular hypothesis).

BH> Just to check if one had to really dig for such quotes, I took
BH> a look at <The Shape of Life> by Rudolf A. Raff. All I had to
BH> do was look in the index under "gene" and then the subtopic
BH> beneath "assuming primacy in developmental biology" which led
BH> me to the following:
BH> "Genes are important because they are the controllers and
BH> executers of developmental processes." -- Raff

Yes, taken at face value, Raff's statement is ridiculous. Genes
can't execute anything. I've seen similar statements made re:
genes and metabolism as well.

TI>These people (Goodwin et al.) make grandiose statements about
TI>where their "new" paradigms will take them in answering the
TI>mysteries of life -- but inevitably their concepts are absorbed
TI>and assimilated (or spit out) without the predicted bloodbath
TI>of a violent revolution. Hardcore biochemists are like the Borg,
TI>and as difficult to impress.
BH> Yes, well this is often what happens. But I personally believe
BH> that science is enriched by this process and that people like
BH> Goodwin are needed for this enrichment, even if they turn out to
BH> be wrong. It is the rare individual that will risk everything by
BH> doing something really daring. Reminds me of something Einstein
BH> said. Something to the effect that most scientists are like
BH> carpenters who look for the thinnest section in the board and
BH> then drive a great number of nails through it.

Sure, there's nothing like putting your cajones on the line as
a motivator. However, adding to Einstein's metaphor, if you're
going to nail through thick sections, you'd better be sure you
start that nail straight. And there's no sense adding unnecessary
flourishes to your swing that make it more difficult to hit the
nail. Essentially, and without the added ornamentation, what
Goodwin and many others are trying to do is understand what non-
genetic (non-DNA) components drive morphological development. Over
the years we've accumulated evidence that such factors can be
extremely important -- so this doesn't come as much of a shock to
me or most biochemists that I know. What really separates Goodwin
is how big of a role these extragenetic factors have and how they
may be altered over time. The stuff about "Darwinism", and
supplanting evolution is rhetorical garbage, IMO. Yes, that
*might* happen, but that's way, way downstream.

I'm glad Goodwin et al. are out there. I just get tired of
reading what I consider to be "science by fiat" approaches.
It's one thing to try staking out a new area or a new approach
for research. It's a different thing to make the claim that
the new approach will revolutionize or overturn a great deal
of what has been done before, especially when you've got nothing
to show for it yet. In this respect Goodwin is making exactly the
same errors as those colleagues he criticizes.

I suspect that part of the problem comes from the need to make broad
generalizations in review articles that cover an entire discipline
in biology. You've got to gloss over most things just to make it
under the page limit (or to keep the talk under an hour). But the
tendency then, when you're trying to present a new approach, is to
only present the "extreme" views and downplay the intermediate
opinions. That makes for more interesting reading and increases the
contrast. But it's easy to take it too far, especially when you're
fired up about the idea.

[...My make-believe situation removed...]
BH> A humorous story Tim, but I believe you're erecting your own
BH> strawman :).

Yes! That's exactly what I was doing. Actually, I was resurrecting
your question to ID'ers about "forms without histories" rather than
what I suspect would be Goodwin's real position. Strawman are so darn
easy to construct and much less messier than real life. That's why I
don't like review articles (on things like developement) when I see
strawmen embedded in the arguments. In the case of genetic vs.
extra-genetic influences in evolution, neither influence changes

Tim Ikeda (despam address before use)