Thursday, September 21, 2006

Reply to Nanosplit

I had two comments on the last post, and wanted to devote a whole post to a response. The first was a mild expression of skepticism by CalvinDude, which I respect...hell, I consider myself a skeptic too, nothing wrong with a little skepticism. However, the question is -- what makes us skeptical, and how skeptical can we be and remain reasonable?

How much evidence [for human evolution] is ever enough, and is your "bar of skepticism" set as high towards your religion as towards paleoanthropology? Isn't skepticism about witholding belief until suitable evidence substantiates it? What position does CalvinDude stand on in order to say that the evidence from evolutionary science is not yet sufficient to garner his belief? Is he standing on admitted ignorance? Or in some creationist myth?

Is he saying, "I don't know, and I don't know if science does either," or "I already believe and know X, and since scientific evidence contradicts X, I remain skeptical of science"? If X is based on solid evidence, and so is science, then fine, stay skeptical, but if X = the Hebrew creation myth...then...I'm afraid this is called "dogmatism", and not "skepticism".

Next, a more critical comment from nanosplit:
Like every claim in the past this too will turn out to be b.s.
Heres the question--How does matter give rise to coded information? How does information evolve? How does personality evolve?
And you got the arrogance to say your not in la la land. Dig a little deeper pal.
My reply in full follows:
Dear nanosplit,

Your questions were entirely based on arguments from ignorance -- posturing that if I don't know the answer to a question, that this means the question is either: 1) unanswerable via science, or 2) answered by your religion by default.

Since you have yet to demonstrate (nor your religion) any grasp of answering the sorts of questions you've posed to me in intelligible terms (saying, "God did it!" is not an explanation), I must laugh at the idea of (2). So, all you've done here is attempt to posit that these sorts of questions are out of the scope of science's powers, which I strongly disagree with, but, even if you're right, what does that mean? Should we throw our hands up in the air and go back into caves with stones and flints? Should we abandon the pursuit of knowledge via science, and go back to your ancient superstitions? Should we sprinkle bird blood on lepers again (via Leviticus 14) instead of using modern medicine?

Q: What knowledge has your religion, your faith, your set of dusty scrolls of unknown origins and unknown authorship, ever given to the world?

A: Nothing. Nothing. Nothing.

On to your comment:

Like every claim in the past this too will turn out to be b.s. [nanosplit is here referring to the "claim" that a beautifully-preserved afaresnis child was found]

Man, I agree! Over a thousand of those common creationist claims have turned out to be complete and utter bullshit! The good news is that TalkOrigins has compiled all of this utter bullshit into one big stinking pile, called "The Index to Common Creationist Claims". Even better news is that the paperback version of this index is almost available!

Wait...you were talking about creationist claims, right? Cause after all, the claims and evidence of human evolution have grown and solidifed over time, so if you're referred to hominid evolution...then I guess you'd be a dishonest person, and you're not one of those, right?

Heres the question--How does matter give rise to coded information?

I'll answer your question, after seemingly contradicting the question itself.

First, you need to understand that "code" is a very human concept. And, like the "code" of human language, there are physical limitations upon the interplay of gene and genetic code. Consider your vocal cords -- they always fall into a range of lengths and sizes. Thus, human beings could only possibly make certain sounds, and so language is restricted to those sounds.

In the same way, the laws of physics and chemistry restrict the "genetic code" to be what it is, within a range of possibilities. Consider, for instance, that AAU/AAC did not HAVE to code Asp. However, due to thermodynamics and energy efficiency, a forty-six-letter system is completely out of the question for correspondence between gene and code. And so we might start to ask some preliminary questions: why are there 20 amino acids? Why do we have a triplet system? Are those two interconnected? [Take a wild guess]

Now, can you tell me, using solely physical laws, what "coded information" means? For starters, which of the following two sequences contains "more" information, and how do you go about determining it?

Sequence 1: cag tgt ctt ggg ttc tcg cct gac tac gag acg cgt ttg tct tta cag gtc ctc ggc cag cac ctt aga caa gca ccc ggg acg cac ctt tca gtg ggc act cat aat ggc gga gta cca agg agg cac ggt cca ttg ttt tcg ggc cgg cat tgc tca tct ctt gag att tcc ata ctt

Sequence 2: tgg agt tct aag aca gta caa ctc tgc gac cgt gct ggg gta gcc act tct ggc cta atc tac gtt aca gaa aat ttg agg ttg cgc ggt gtc ctc gtt agg cac aca cgg gtg gaa tgg ggg tct ctt acc aaa ggg ctg ccg tat cag gta cga cgt agg tat tgc cgt gat aga ctg

Please use your 'procedure', whatever it may be, to measure the 'genetic information' content of these two sequences. Please write down the step-by-step process by which you measured the 'genetic information' content of these two sequences, being as clear and/or specific as you can.

I'll hold my breath waiting...

Now, since I know that you are not an expert, I'll do you one better -- read what the experts write about this sort of question, and/or actually send it off to your favorite pseudoscientist, aka "Creation Scientist", and have them answer it for you.

I'll hold my breath waiting on that one, as well...

Now, since the methodology by which we establish information is crucial to answering the question of "how matter gives rise to it", then I think you ought to qualify your question, and tell me exactly what it is you really want me to answer for you.

Short of that (since you won't be able to do this), I'll get into a more general approach to save you some face:

You do understand that the nucleic acid triplet system has nothing to do with a "CODE", in the sense that as it developed, the coevolution (it had to happen over time and a piece at a time) of gene and code wasn't "fixed" to some syntax, don't you? It's just chemistry, my silly creationist friend, and "CODE" is what humans try to make to help them understand it. The laws of thermodynamics give a range of possibilities within which the evolution (of everything, including of the components of transcription and translation) takes place, and it can do no other. Now, the code that we observe, as I pointed out above, is not some "had to be this way" necessity -- indeed, we can imagine life existing with 20 amino acids, or 10, or 100. Life would certainly be different, but it would still exist. And so can we say that our system is one out of a number of chance possibilities? Yes and no.

We can imagine life existing with our triplet system, a different triplet system (different letters for each AA), a possible quartet system, or even just a two-digit code. The code that exists is the result of deterministic physical laws, but run the whole thing over again, with slightly different conditions, and not only should we not expect the same result, but I can guarantee a different one. So in that sense, chance does play a part in the way that our code developed. But chance also plays a part in the way that each animal develops from the moment of fertilization on.

Don't believe me? Well, perhaps I shouldn't be surprised, since you've probably never taken a university course on biochemistry (I have a BS in it from Virginia Tech).

However, since we pointed out already that there are restrictions, the determination of the code via chemistry and physics wasn't "purely random" in that sense. For one thing, we have to consider whether or not we're discussing a "metabolism first" approach, since using certain metabolites restricts the sort of molecules that would end up making up our code. Indeed, DNA is composed of these nucleotides that you're familiar with, but is that also necessary? Could it have been, say, sulfates rather than phosphates that connect the bases? Or could it have been all purines, or all pyrimidines, or different ones? Yes. It could.

So when we even start to look at *how* to answer these questions, we see that it gets quite complex to attempt to give an answer

Now, to answer your question, here are two really good peer-reviewed papers on the origin of the genetic code, if you are actually interested in some testable, practical models to answer your question:
1) Selection, history and chemistry: the three faces of the genetic code (1999)
2) The origin of the genetic code: theories and their relationships, a review (2005)

The major models are (from paper #2):

1. The stereochemical theory
2. The physicochemical and ambiguity reduction theories
3. The coevolution theory

Please note that these models are not mutually exclusive and represent three different possibilities for "driving forces" that we know from chemistry and physics that certainly did play a role in at least part of the development of the "code". The question is how much for each one, and whether or not one is dominant.

Quoting the second paper:

(Model 1.) The stereochemical theory claims the origin of the genetic code must lie in the stereochemical interactions between anticodons or codons and amino acids (Crick, 1968). The theory suggests, for example, asparagine must have been codified by the codons AAU or AAC as asparagine is somehow stereochemically correlated with these codons. Several models have been proposed which indeed seem to define a stereochemical relationship between anticodons or codons and amino acids (Gamow, 1954, Pelc and Welton, 1966, Welton and Pelc, 1966, Dunnill, 1966, Woese, 1967, Black, 1973, Black, 1995, Melcher, 1974, Nelsestuen, 1978, Balasubramanian et al., 1980, Marlborough, 1980, Hendry et al., 1981, Shimizu, 1982, Yarus, 1991 and Szathmary, 1993).


(Model 2.) The physicochemical theory claims that the force defining the origin of the genetic code structure was the one that tended to reduce the deleterious effects of physicochemical distances between amino acids codified by codons differing in one base (Sonneborn, 1965 and Woese et al., 1966). In particular, Sonneborn (1965) identified the selective pressure reducing the deleterious effects of mutations as the force defining the amino acid allocations in the genetic code table (Ardell and Sella, 2001 and Sella and Ardell, 2002). Whereas, Woese et al. (1966) maintained that the driving force defining genetic code organization must lie in a selective pressure tending to reduce the translation errors of the ancestral genetic message.

A similar theory is the ambiguity reduction hypothesis. This theory claims that group codons differing in one base were assigned to groups of physicochemical similar amino acids, and the genetic code reached its current organization through the lowering of the ambiguity in the coding within and between groups of amino acids (Woese, 1965 and Fitch and Upper, 1987). Only one study conducted on 300 tRNAs sequences specific for 8 amino acids (Fitch and Upper, 1987) is in favour of the ambiguity reduction theory (Woese, 1965 and Fitch and Upper, 1987). Other and equivalent analyses are in favour of the coevolution theory (Di Giulio, 1992a, Di Giulio, 1994a, Di Giulio, 1995, Chaley et al., 1999 and Bermudez et al., 1999).


(Model 3.) The coevolution hypothesis of the origin of the genetic code (Wong, 1975) suggests that the origin of the genetic code should be sought in the biosynthetic relationships between amino acids. In particular, this hypothesis maintains that early on in the genetic code few amino acids (perhaps five) were codified: the precursors (Wong, 1975). As the other amino acids arose biosynthetically from these precursors, part or all of the codon domain of the precursor amino acid was passed to the product amino acids (Wong, 1975).

The mechanism through which the precursor amino acids passed part or all their codon domain to the precursor amino acids is postulated by the coevolution theory as occurring on tRNA-like molecule on which this theory suggests the biosynthetic transformation between amino acids took place (Wong, 1975). If the biosynthetic pathways linking up the amino acids took place on tRNA-like molecules, then a tRNA-like molecule bearing a product amino acid evolving from the biosynthetic transformation of a given precursor amino acid must clearly have recognized some of codons belonging to the precursor. Therefore, this molecule was able to evolve naturally towards a tRNA specific for that particular product amino acid and its reassigned codons.



You will have to follow up with references to the specific papers for detailed evidence of each model, and a discussion of how the evidence supports the model. That is assuming that you actually want to know...

Now, there are some answers to your question. What do you do with these answers? Ignore them and continue to present argumentum ad ignorantium attacks on the validity of science and evolutionary theory? Yes, you will. Because the truth is, you don't want science to answer these questions, you want to believe that they are rendered unknowable by some divine action, that since God is involved, that man cannot know such things. Well, the church has said this for generations, and all the while, the church's God has shrunk and shrunk in size. It used to be that the church opposed anatomical studies on human beings, saying that the workings of the body are "divine" and shouldn't be messed with.

Every fence of ignorance the church has erected, science has torn down. Thankfully. And your prospects are getting any brighter in the area of genetics.

To your next (God of the gaps) question:
How does information evolve?

If you're one of the creationists who thinks that you understand information theory and that it somehow refutes evolutionary theory, please allow Mark Chu-Carroll to correct you HERE.

You'll note he takes on information theory directly in opposition to Dembski's silliness in many different posts, but hits the nail on the head in posts like this one: creationists don't understand information theory, and real mathematicians never have and never will use it as the basis of a challenge to evolution.

Contrary to your muddled way of looking at things, disorder in a string of characters actually produces more information for coding systems -- explained here.

And now, for your last God-of-the-gaps-question:
How does personality evolve?

Ask Freud, Jung, Spotnitz and Sullivan. What do I look like, a freaking psychologist? I'm a chemist, for heaven's sake!

If you're interested in one component of personality, in particular, then altruism is a good one to study, since we observe it in other animals. A new book just came out on this very question -- The Altruism Equation: Seven Scientists Search for the Origins of Goodness. See a review of the book HERE

Now, it's my turn to ask questions:

Assuming that matter is not the fundamental substance of our universe, and that it cannot explain the questions you've asked above--
How does some invisible, immaterial, "spirit" substance contribute to any of the questions you've asked above? How does it interact with matter?
Why is it that I can take away specific parts of your brain and alter specific parts of your personality (language, long-term memory [amnesia], short-term memory, impulse control, erratic behaviors, compulsivity...etc), if the personality is not, itself, a function of the brain?

Should you recognize that your system of belief proffers you absolutely nothing, nil, in the way of answers to these same questions, why consider it a "superior answer"? God apparently didn't find it necessary to explain anything to you in the Bible concerning the workings of the physical world, so why not leave that to the physicists and chemists, and not your local preacher, who likely knows diddly-squat-shit in the way of science? Just leave him to his mystical ramblings and inanities.

And now to your last comment:
And you got the arrogance to say your not in la la land. Dig a little deeper pal.

What I say is that creationists are wallowing in ignorance and ignoring what we know to be reality. It is quite different to say, 1) that a body of knowledge is solid and contradicts your religious myths, and 2) that I have the answer to every question, and I know everything personally, or that this body of knowledge (science) is complete, absolute, and total. I never said (2), just (1). Now, which of us, on the other hand, claims to know God and what God wants and says and does? Which of us claims that they know the way to gain admission into God's heaven? Which of us thinks that the other is damned for eternity, since the other doesn't believe that kissing divine ass is a logical belief? What kind of arrogance does that require?

When you don't profess to have any answers yourself, appealing to ignorance is a dangerous thing. Dig a little deeper, and you might realize you aren't even standing on anything [faith?] at all.
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