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Oh yeah, I forgot god's will is to stay the same forever. Don't ever try to better yourself for then god will not love you anymore. You know, god kind of sounds like a wife beater.

OK, I admit I have been wrong. I have seen the light and
His Name is the Flying Spaghetti Monster (Wikipedia entry).

The Revelation

The Pesto Manifesto

The Carbonara Compromise: Pastafarianism for the Atkins Diet set

FSM has a posse

FSM bumper sticker logo

I'm sure that you will all recant your previous wicked ways and join me in the undeniable glory of He Who Is Covered In Marinara Sauce.

May you be forever touched by His Noodly Appendage.
RAmen.

Humor. Please tell me you've escaped from the nursery and hijacked your parents computer.. if not.. please seek a sense of ... humor.

I ask a question, get a non-response. This happens several times over, what do you expect? Me just to say, "oh, its okay, you can say anything you like without backing it up."

NAG wrote:

Humor. Please tell me you've escaped from the nursery and hijacked your parents computer.. if not.. please seek a sense of ... humor.

I ask a question, get a non-response. This happens several times over, what do you expect? Me just to say, "oh, its okay, you can say anything you like without backing it up."

Oh come on.. these weren't questions, they were insulting, inflammatory statements.. however Sassy posted a good article.. C.S Lewis's book is a good read.. if you have the time.

The NYTime sis running a multipart series on Intelligent Design. In Explaining Life's Complexity, Darwinists and Doubters Clash is of some interest, mostly because of this excerpt.

Other studies that intelligent design theorists cite in support of their views have been done by Dr. Axe of the Biologic Institute.

In one such study, Dr. Axe looked at a protein, called penicillinase, that gives bacteria the ability to survive treatment with the antibiotic penicillin. Dr. Meyer, of the Discovery Institute, has referred to Dr. Axe's work in arguing that working proteins are so rare that evolution cannot by chance discover them.

What was the probability, Dr. Axe asked in his study, of a protein with this ability existing in the universe of all possible proteins?

Penicillinase is made up of a strand of chemicals called amino acids folded into a shape that binds to penicillin and thus disables it. Whether the protein folds up in the right way determines whether it works or not.

Dr. Axe calculated that of the plausible amino acid sequences, only one in 100,000 trillion trillion trillion trillion trillion trillion - a number written as 1 followed by 77 zeroes - would provide resistance to penicillin.

In other words, the probability was essentially zero.

Dr. Axe's research appeared last year in The Journal of Molecular Biology, a peer-reviewed scientific publication.

Dr. Kenneth R. Miller, a professor of biology at Brown University and a frequent sparring partner of design proponents, said that in his study, Dr. Axe did not look at penicillinase "the way evolution looks at the protein."

Natural selection, he said, is not random. A small number of mutations, sometimes just one, can change the function of a protein, allowing it to diverge along new evolutionary paths and eventually form a new shape or fold.

I'm pretty sure that the paper in question is

Mutagenesis studies and alignments of homologous sequences have demonstrated that protein function typically is compatible with a variety of amino-acid residues at most exterior non-active-site positions. These observations have led to the current view that functional constraints on sequence are minimal at these positions. Here, it is shown that this inference assumes that the set of acceptable residues at each position is independent of the overall sequence context. Two approaches are used to test this assumption. First, highly conservative replacements of exterior residues, none of which would cause significant functional disruption alone, are combined until roughly one in five have been changed. This is found to cause complete loss of function in vivo for two unrelated monomeric enzymes: barnase (a bacterial RNase) and TEM-1 beta-lactamase. Second, a set of hybrid sequences is constructed from the 50 %-identical TEM-1 and Proteus mirabilis beta-lactamases. These hybrids match the TEM-1 sequence except for a region at the C-terminal end, where they are random composites of the two parents. All of these hybrids are biologically inactive. In both experiments, complete loss of activity demonstrates the importance of sequence context in determining whether substitutions are functionally acceptable. Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular. Homologues sharing less than about two-thirds sequence identity should probably be viewed as distinct designs with their own sets of optimising features.

Axe DD (2000) "Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors." J Mol Biol 301:585-95

Interesting reading, though it hasn't been cited much.

jerwin wrote:

The NYTime sis running a multipart series on Intelligent Design. In Explaining Life's Complexity, Darwinists and Doubters Clash is of some interest, mostly because of this excerpt.

Interesting article.. thanks
It would seem that the intelligence is somehow programmed into the process.. (?) in that the protein doesn't just randomly try all possible foldings.. but is encouraged somehow to only try ones likely to be successful.

I think on a larger scale, this is what faith and religions try to accomplish when properly executed, for societies.. encourage successful choices to ensure survival. Can't argue with results.. comparing American(Christian foudation) culture vs. USSR (religionless, materialistic)... which made better choices?.. which folded their "proteins" more successfully?

cbaines wrote:

jerwin wrote:

The NYTime sis running a multipart series on Intelligent Design. In Explaining Life's Complexity, Darwinists and Doubters Clash is of some interest, mostly because of this excerpt.

Interesting article.. thanks
It would seem that the intelligence is somehow programmed into the process.. (?) in that the protein doesn't just randomly try all possible foldings.. but is encouraged somehow to only try ones likely to be successful.

I don't think you read the article.

At any rate, I like the spirit of what you said ... it would seem that Protestant evangelicalism and evolutionary science needn't conflict. It's just a question of balancing things out.

I think on a larger scale, this is what faith and religions try to accomplish when properly executed, for societies.. encourage successful choices to ensure survival. Can't argue with results.. comparing American(Christian foudation) culture vs. USSR (religionless, materialistic)... which made better choices?.. which folded their "proteins" more successfully?

Just out of curiosity, what the HELL are you talking about?

Either I need to investigate new citation databases, but it seems that Axe has mostly been ignored, except by Dembski, Meyer and the like.

The only serious paper I can see is Alex C.W. May (2002) "Definition of the tempo of sequence diversity across an alignment and automatic identification of sequence motifs: Application to protein homologous families and superfamilies" Protein Science, 11:2825-2835. which might yet prove to be interesting reading.

Last edited by jerwin (2005-08-24 12:00 pm)

I thought Hank might be able to comment.

ShnickyShnack wrote:

I think on a larger scale, this is what faith and religions try to accomplish when properly executed, for societies.. encourage successful choices to ensure survival. Can't argue with results.. comparing American(Christian foudation) culture vs. USSR (religionless, materialistic)... which made better choices?.. which folded their "proteins" more successfully?

Just out of curiosity, what the HELL are you talking about?

Not to mention the whole USSR = no religion is kind of a fallacy.

jerwin wrote:

I thought Hank might be able to comment.

I acutally sort of like this forum for this discussion.  It is nice and relaxed.  I used to post to talk.origins a fair amount, but I got really tired of the flood of posts that I had to keep track of and the major nuts that also posted there on topics completely unrelated to evolution and/or cosmology.

Dr. Axe calculated that of the plausible amino acid sequences, only one in 100,000 trillion trillion trillion trillion trillion trillion - a number written as 1 followed by 77 zeroes - would provide resistance to penicillin.

This sort of "calculation" always kills me.  Calculations like this always rely on the spontaneous arrival on the scene of a protein just like the one in hand.  Now, the esteemed Dr. Axe (I love that name, by the way!) has a good point in his actual article.  That is, one cannot just assume that all residues in a protien are interchangable. Such substitutions have to be tested (and, as he points out in his introduction, they have been in some systems).  Saying just that would be enough, and would be instructive.

But, just because in the past certain residues were seen by scientists as open to mutation with minimal effect, does not mean that they, in fact, are.  That sort of thing has to be tested, which was done ably by Dr. Axe.

Now, just because semi-random changes cause loss of function:

a) it does not mean that all changes cause lack of function
b) it does not mean that there aren't other combinations of changes that provide similar function
c) it does not mean that the current amino acid sequence is the only one that will "work" among the myriad choices available

Also, even according to Dr. Axe, there are residues that can be changed without radical change in function.  In his own words:

Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular. Homologues sharing less than about two-thirds sequence identity should probably be viewed as distinct designs with their own sets of optimising features.

In other words, some residues that were thought of as being non-important are, in fact, important.  However, this can't be taken, even by the wording of the article, to mean that ALL residues are important to function.  According to that wording, there is "wiggle room" of about 1/3 sequence identity, by Dr. Axe's calculations.

In terms of intelligence, if there is an intelligence behind all of this (and I personally believe that there is, but I cannot prove it) then the natural selection process is an EXTREMELY intelligent choice, because it finds solutions to complex problems that would be virtually impossible to design otherwise.  In other words, the Designer is using an amazingly powerful algorithm for design.

And we humans have just begun to catch onto that fact, and have begun to use the same in our computing, chemical designing, and engineering.  Many of the "naturally selected" designs that come out of those three (and other) fields have a low probability of existing when compared to the entire spectrum of possible designs.  But natural selection finds them very, very quickly.

Same deal with proteins.  Since there are ~20 possible residues at each location in protein, and since proteins can have several hundred such residues, there is a VAST array of possibilities.  But, again, using natural selection in the lab, new proteins with improved or radically altered function can be created from that myriad choices.

Basically, even though there are an almost infinite number of possibilities, natural selection has been found time and time again to move to one of the best choices in that array quite quickly.

OK, I just browsed the Xiojun et al. paper.  This is the abstract:

Pressured by antibiotic use, resistance enzymes have been evolving newactivities. Does such evolution have a cost? To investigate this question at the molecular level, clinically isolated mutants of the b-lactamase TEM-1 were studied. When purified, mutant enzymes had increased activity against cephalosporin antibiotics but lost both thermodynamic stability and kinetic activity against their ancestral targets, penicillins. The X-ray crystallographic structures of three mutant enzymes were
determined. These structures suggest that activity gain and stability loss is related to an enlarged active site cavity in the mutant enzymes. In several clinically isolated mutant enzymes, a secondary substitution is observed far from the active site (Met182 ! Thr). This substitution had little effect on enzyme activity but restored stability lost by substitutions near the active site. This regained stability conferred an advantage in vivo. This pattern of stability loss and restoration may be common in the evolution of new enzyme activity.

Note that the authors were using the exact same protein as discussed by Axe.  They found that there were mutations at the active site that altered function, but mutations elsewhere that restored that function.  In other words, the "design space" for any given protein is so huge, that there are also probably a fair number of "solutions" to various challenges.  And, any one of these "solutions" could be grasped onto by natural selection.

Axe has written another (earlier) paper
Douglas D. Axe, Nicholas W. Foster, and Alan R. Fersht (1996) "Active barnase variants with completely random hydrophobic cores" PNAS 93(11): 5590-5594

The central structural feature of natural proteins is a tightly packed and highly ordered hydrophobic core. If some measure of exquisite, native-like core packing is necessary for enzymatic function, this would constitute a significant obstacle to the development of novel enzymes, either by design or by natural or experimental evolution. To test the minimum requirements for a core to provide sufficient structural integrity for enzymatic activity, we have produced mutants of the ribonuclease barnase in which 12 of the 13 core residues have together been randomly replaced by hydrophobic alternatives. Using a sensitive biological screen, we find that a strikingly high proportion of these mutants (23%) retain enzymatic activity in vivo. Further substitution at the 13th core position shows that a similar proportion of completely random hydrophobic cores supports enzyme function. Of the active mutants produced, several have no wild-type core residues. These results imply that hydrophobicity is nearly a sufficient criterion for the construction of a functional core and, in conjunction with previous studies, that refinement of a crudely functional core entails more stringent sequence constraints than does the initial attainment of crude core function. Since attainment of crude function is the critical initial step in evolutionary innovation, the relatively scant requirements contributed by the hydrophobic core would greatly reduce the initial hurdle on the evolutionary pathway to novel enzymes. Similarly, experimental development of novel functional proteins might be simplified by limiting core design to mere specification of hydrophobicity and using iterative mutation-selection to optimize core structure.

Ah, the power of randomness!