16 Responses to “A Scenic Shot”

1. keiths Says:
   November 25th, 2007 at 10:40 pm

   Yes, and that rabbit appears a bit queasy after his gondola ride.

Comment by keiths — November 25, 2007 @ 10:40 pm

2. Thought Provoker Says:
   November 26th, 2007 at 1:49 am

   Hi Mike,

   I finished reading your book (first pass).

   In anticipation of discussion, I did a little digging into the origins of the genetic code and found ORIGINS OF THE GENETIC CODE: The Escaped Triplet Theory…

   There is very significant evidence that cognate codons and/or anticodons are unexpectedly frequent in RNA-binding sites for seven of eight biological amino acids that have been tested. This suggests that a substantial fraction of the genetic code has a stereochemical basis, the triplets having escaped from their original function in amino acid"“binding sites to become modern codons and anticodons. We explicitly show that this stereochemical basis is consistent with subsequent optimization of the code to minimize the effect of coding mistakes on protein structure. These data also strengthen the argument for invention of the genetic code in an RNA world and for the RNA world itself.

   Had you heard of this?

Comment by Thought Provoker — November 26, 2007 @ 1:49 am

3. Guts Says:
   November 26th, 2007 at 3:10 am

   Looks like Mike is on a much deserved vacation.

Comment by Guts — November 26, 2007 @ 3:10 am

4. Bradford Says:
   November 26th, 2007 at 8:06 am

   Hi TP. That issue has been discussed at TT albeit not as a result of a specific blog entry focused on it in particular. It came up during commentary related to another matter. This was blogged about elsewhere although there is much more to say about it. I'll wait for Mike to weigh in before saying more.

Comment by Bradford — November 26, 2007 @ 8:06 am

5. Alan Fox Says:
   November 26th, 2007 at 10:44 am

   [delurk]So, is it Venice or not? We lurkers demand to know. [/delurk]

Comment by Alan Fox — November 26, 2007 @ 10:44 am

6. kornbelt888 Says:
   November 26th, 2007 at 2:07 pm

   "Can you guess the city?"

   Knott's Berry Farm?

Comment by kornbelt888 — November 26, 2007 @ 2:07 pm

7. Wonders For Oyarsa Says:
   November 26th, 2007 at 3:36 pm

   Unless there are other places with signs to the Rialto bridge, I'm betting the rabbit is in Venice.

   Who'd have guessed Venice has echoes of design?

Comment by Wonders For Oyarsa — November 26, 2007 @ 3:36 pm

8. chunkdz Says:
   November 26th, 2007 at 6:06 pm

   Easy… Las Vegas. About half a mile from the Eiffel Tower.

Comment by chunkdz — November 26, 2007 @ 6:06 pm

9. Guts Says:
   November 26th, 2007 at 6:11 pm

   I loves me some chunkdz

Comment by Guts — November 26, 2007 @ 6:11 pm

10. Rock Says:
    November 27th, 2007 at 12:14 pm

    Isn't that Guadalajara after the flood? Is that rabbit passed out? And Mike Gene oughta fire his agent. Who the hell releases a book and then goes on vacation?! (I'm available BTW and I'm a barracuda.)

    And don't we call down upon our own heads von Neumann's curse when we start talking about codes as "arbitrary" maps. "Arbitrary" codes are for cryptographers, who are attempting to invoke the curse upon eavesdroppers and adversaries.

    There is nothing "arbitrary" about the design of the genetic code. It is a marvel of simplicity and effectiveness. And what it was plainly designed to do is evolve. The genetic code is the catalyst of evolution. It is an evolutionary algorithm.

    Food for thought, Thought Provoker:

    On the Hypercube Structure of
    the Genetic Code
    http://arxiv.org/PS_cache/cond...

Comment by Rock — November 27, 2007 @ 12:14 pm

11. MikeGene Says:
    November 27th, 2007 at 5:40 pm

    Yep, it's Venice (too bad it wasn't a contest). Nope, I'm not there on vacation; someone sent me the pic. Yep, I know about some of Yarus' work. Nope, I have not yet read through that review paper (yet). And nice link, Rock.

Comment by MikeGene — November 27, 2007 @ 5:40 pm

12. Rock Says:
    November 29th, 2007 at 5:59 pm

    As you can see, Thought Provoker (attempting, in vain (?) to get anyone interested), a simple, but physicochemically relevant, weighting of the nts reveals all sorts of interesting patterns (and exasperating departures from those patterns).
    Traditional representations, i.e., the Crick-Watson "code" in its usual tabular form, reveals no, and rather obscures, patterns that may well be explained in purely design-theoretic terms (in terms of the algebraic construction of codes).

    E.g., one can plainly see that the genetic code is a mosaic of codes, a multi-code, and not exclusively a ternary code (but also binary, quaternary, etc.). So there really is no such thing as the genetic code. It is genetic codes.

    Of more interest (I'm sure) to the IDers and fellow-travelers is that there is no "naturally selected" origin to the "code" as it forms a circuit.

Comment by Rock — November 29, 2007 @ 5:59 pm

13. Bradford Says:
    November 29th, 2007 at 6:22 pm

    Rock writes:

    And don't we call down upon our own heads von Neumann's curse when we start talking about codes as "arbitrary" maps. "Arbitrary" codes are for cryptographers, who are attempting to invoke the curse upon eavesdroppers and adversaries.

    There is nothing "arbitrary" about the design of the genetic code. It is a marvel of simplicity and effectiveness. And what it was plainly designed to do is evolve. The genetic code is the catalyst of evolution. It is an evolutionary algorithm.

    Whether there is an arbitrary mapping between codons and amino acids is not determined by whether or not the code is designed to evolve although perhaps you did not intend that meaning. The question is what generates the mapping. What causes a particular codon to acquire the mapping it has? The knee jerk response has been some form of selection. But how would selection operate to generate a code prior to a point in time when the elements of a code have function? The fundamental difficulty with tracing causal routes to a code or codes has been an insistence that the greater complexity exhibited by codes can be explained by reductionism pointing to the chemical properties of individual constituent molecules as the causal generator of the code itself. It is a failure of reductionism and infers a causal pathway from greater to lesser complexity. But that in turn violates an article of faith.

Comment by Bradford — November 29, 2007 @ 6:22 pm

14. Rock Says:
    November 30th, 2007 at 6:17 pm

    What I have observed is designers carefully, and quite "naturally" (I dare say), non-arbitrarily selecting those elements most suited to their purposes (designs).

    Bradford offers a "theory" of "arbitrary" design, based on no observations.

Comment by Rock — November 30, 2007 @ 6:17 pm

15. Bradford Says:
    November 30th, 2007 at 10:31 pm

    Rock:

    Bradford offers a "theory" of "arbitrary" design, based on no observations.

    It's true I did not catch the designer in the actual act of mapping but I have observed some things. First, the alternative explanation, is dependent on some sort of chemical causality i.e. chemical properties of biochemicals led to a deterministic mapping. That itself is an extraordinary claim. It says that under certain conditions chemical reactions will produce a system with specified mappings between codons and amino acids. Based on the very well known chemical properties of amino acid side chains we are in a position to point out real examples of proteins that bind to DNA. There are a variety of amino acids found at such binding sites and include a broader range of aa-codon interactions than would be observed in the genetic code mappings.

    What I have observed is designers carefully, and quite "naturally" (I dare say), non-arbitrarily selecting those elements most suited to their purposes (designs).

    Look at the code we are using to communicate (the English language represented by alphanumeric symbols) and tell me why specific letter to sound to word to meaning links are necessary for communication purposes. By reversing m with n we would produce a different appearance to the coding without altering the meaning. That suggests arbitrariness does it not? On a biochemical level the same is suggested.

Comment by Bradford — November 30, 2007 @ 10:31 pm

16. Rock Says:
    December 8th, 2007 at 6:53 pm

    The discussion, so far, tends to highlight (to my mind) the differenvce between design science and natural science and (ID-)creationism.

    Designers design things, whereas as creationists and evolutionists only have to figure out if their theories match designs that exist.

    As a designer I have to make it exist, and that involves selecting material elements of the design that (seem to me) most suited to it actualization.

    There is a fundamental difference between these "inverse" problems.

    Bradford? Is there a "fundamental difference," as I said?

Comment by Rock — December 8, 2007 @ 6:53 pm

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