I wrote: [...]
>> For example, if a protease's specificity
>>changes so that it now hydrolyzes a different substrate, is that
>>considered a new function or simply a modification of a previously
>>existing one? If a mutation permits a "new" sugar to be harvested
>>by a cell for metabolism, is this a new function?
>
>Clearly not.
??? Those were previously existing functions, then?
> as Spetner points out a generalization of an existing
>function is a loss of information, not an increase (his example is
>instructive...it takes more information to tell you how to get to
>my house than it does to tell you how to get to my town, or state,
>etc., so a loss of specificity is nothing more than a loss of
information.)
I'm a bit confused by this response and maybe I've missed something.
I thought we were talking about "information" as identified by the
acquisition of new functionality, and I provided several examples
of how this might be achieved. Perhaps I overlooked the word,
"specificity". Yet I still don't see how one could toss out these
examples of new and altered function simply because they may
(or may not) have reduced the specificity of an enzyme for a
specific substrate.
I can see some potential pitfalls here, which are related to how one
defines information and in what context the various measures are used.
For example, I have seen "information" being discussed is many ways.
One area is the study of specificity in enzyme mechanisms from the stand-
point of thermodynamics (probably statistical thermodynamics). Here,
people examined how binding energies and reaction specificities change in
response to modifications around the binding sites of substrates. Protein
folding has also been described in possibly related terms. So here,
information was used as a term in the thermodynamic description of reactions
or folding specificities.
In a separate area, I have also seen "information" used in genomics to
describe patterns of sequence. And further still, I have seen the term
come up (with the accompaniment of some derision), in discussions of
metabolic and regulatory pathways.
There's just one hitch: All the uses of "information" are not equivalent.
There are no simple or good interconversion factors between applications.
They are all depend entirely on context.
This is how I can understand how someone like Spetner might try to claim
that a reduction in enzyme specificity that opened up a new pathway for
the organism is actually tallied as a loss of information. From the
narrowly defined standpoint of enzyme thermodynamics, perhaps it was.
But what does this mean for genomics? Nothing. Or metabolism? It's
quite different. And in terms of selection in the lab? It's is big
plus. So again, the question is: "What's the context?" Well, context
is everything in biology it seems.
We can look at the housefinding problem from another perspective.
Does it necessarily matter that evolution find one particular house
or is it sufficient that it simply can find your house among the
many which it can also find? The thing is, finding new houses by
expanding territories are the changes which are very possibly the
major routes by which new functions (and yes, "information") are
acquired in evolution.
>>> In this context, Lee Spetner (Not by Chance!) has made a (in my
>>> opinion) compelling case for the absence for any evidence for the
>>> addition of new information in the whole history of the study of
>>> biological organisms.
>>
>>Interesting. What is his method and metric for quantifying "information"
>>in this context? For example, I would have thought that the capture
>>of bacteria as mitochondria and plastids in eukaryotes would result
>>in the addition of new "information" to the merged organisms (Well,
>>perhaps that's one of the more dramatic, "one-shot" examples).
>
> He limits his consideration to what has been demonstrated or claimed
> from research, and does not give consideration to what people may
> have speculated to have happened, so he has nothing to say about that.
If he disputes changes which alter the specificity of an enzyme, or
possibly dimisses gene duplication & transposition, and also
limits his survey to only those _very few_ systems which have been
actively monitored in a lab,...
... then I really don't believe he's going to find much that suits
his fancy. Without read his book, I can't say he's "stacking the deck",
but I do wonder.
FWIW - The acquistion of endosymbiotic bacteria in eukaryotes has
been observed in the lab. See Kwang W. Jeon, ed. - _International Review
of Cytology - Supplement 14: Intracellular Symbiosis_ NY, Academic
Press 1983. Pg 29 is the start of his article: "Integration of
bacterial endosymbionts in amoebae". I know he's carried this work
further, discussing it at a recent (or soon to be) Gordon conference in
Switzerland.
[...]
>>I've seen functions arise in bacteria that weren't originally in the
>>bugs -- Even "irreducibly complex" functions. Chemostats and other
>>continuous culturing methods are wonderful for this sort of work
>>in metabolism. Well... provided you can get >1E10 of your organisms
>>into the growth chamber.*
>
> True, these claims have been made many times, but I think he carefully
> covers every known claim, and I think rather compellingly demonstrates
> them not to represent de novo generation of new information. At least
> I was impressed with his approach.
I checked for Lee's name on the web while looking for Amazon.com.
Now I remember Spetner! He's one of the early people (along with Hoyle)
who tried to make the case that the Archaeopteryx fossils were faked,
wasn't he? Well, his new book should be an interesting read -- I'll try
browsing it at a Christian bookstore.
Regards,
Tim Ikeda (tikeda@sprintmail.com)