Natural Selection, Specification and Common Ancestry
by BradfordBiological specification always denotes function.1 Biological changes are said to occur when genomic changes become fixed by natural selection. Change can be traced to a prior condition in which a biological function existed because it had selective value i.e. it conferred function which enhanced reproductive fitness. Mutations, which change protein properties, correlate to new functions or enhance already existing ones. There is a symmetry between protein properties and biological function. As one moves along a timeline encompassing a process, one can map different proteins to their respective functions. Natural selection gives rise to the changing events and connects them in the timeline. The match-up between proteins and their functions constitutes a physical specification which is linked to a specified quality. In the case of living things the quality that is specified in advance is… the ability to propagate genes in reproduction.2
Timelines have a starting point. That would involve a biological entity able to replicate itself. Once that condition is present it is assumed that natural selection sufficiently explains subsequent changes. Yet more than an unknown starting point needs to be recognized. A symmetry break between physical properties and function is noted as is the insufficiency of natural selection based theories to bridge a gap between a prebiotic environment and a biological reproducing entity. At one point in time there is no self-replicator and no specification criteria. Then there is both. That is the moment correlating to initial front loading. The difference between IDists and their critics is the belief by the former that intelligence accounts for loading of the replicating information storage unit.
But it may also be that natural selection is credited with more of a role than merited even when biological organisms are present. At least the logic that common ancestry requires natural selection is doubtful according to the PNAS paper: Did Darwin write the Origin backwards? The abstract:
After clarifying how Darwin understood natural selection and common ancestry, I consider how the two concepts are related in his theory. I argue that common ancestry has evidential priority. Arguments about natural selection often make use of the assumption of common ancestry, whereas arguments for common ancestry do not require the assumption that natural selection has been at work. In fact, Darwin held that the key evidence for common ancestry comes from characters whose evolution is not caused by natural selection. This raises the question of why Darwin puts natural selection first and foremost in the Origin.
Reference:
1. Intelligent Design; William A. Dembski; Page 149; InterVarsity Press; 1999.
2. Ibid.
July 2nd, 2009 at 7:20 am
Who is it that claims that common ancestry requires natural selection? I have never come across such a claim, indeed, the abstract itself says: "arguments for common ancestry do not require the assumption that natural selection has been at work"
Comment by The Pixie Again — July 2, 2009 @ 7:20 am
July 2nd, 2009 at 7:59 am
Here is a simple simulation showing how random variation can lead to drift, fixation, extinction, and the phylogenetic tree.
Zachriel's Nest of Letters
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Comment by Zachriel — July 2, 2009 @ 7:59 am
July 2nd, 2009 at 10:53 am
If there is in fact a prior specification. In biology function follows form (sort of an anti-Sullivan analysis).
There's a lot of statistical analysis (ht Zachriel) on what genomes might look like as a result random mutation within reproductively isolated populations. Geneticists use randomness as a null model; departure from the null is taken as an indication of selection.
IMHO a lot of confusion about reductionism and emergent properties would disappear if we talked about behavior rather than properties. A classic anti-reduction argument is "Nothing in the properties of hydrogen or the properties of oxygen gives us the properties of water". But the behavior of the atoms in a molecule consisting of two hydrogens and one oxygen — particularly the polar charge distribution, owing to the lone electron pair in the oxygen — can show us a lot about the behavior of water.
Comment by John Wendt — July 2, 2009 @ 10:53 am
July 2nd, 2009 at 11:34 am
JW:
You make a good point but what is it about codon sequences that confer knowledge of their behavior? Is it the molecular structure of nucleic acids? You get that same basic structure when mutations make biological mush out of functional sequencing.
Comment by Bradford — July 2, 2009 @ 11:34 am
July 2nd, 2009 at 6:22 pm
The behavior of a protein or a ribozyme is determined by its electrical shape, which is determined by the folded sequence of its components. Folding is controlled by interactions of the components with each other, with water, and sometimes with metal ions. Typically only a few positions in the sequence are important to the relevant parts of the electrical shape, so there are lots of opportunities for random mutation.
For a ribozyme the concept of "codon" doesn't arise: RNA is just the complement of DNA. For a protein, component sequence follows the sequence of DNA, but indirectly. DNA doesn't have anything like a codon; "codon" is a concept we attach to the process for convenience. The ternary nature of protein production comes from the elongation factors in the ribosome that move the mRNA three nucleotides each time an amino acid is attached to the growing polypeptide. The correspondence between these "virtual codons" and the corresponding amino acids is controlled by the enzymes that attach an amino acid to the proper tRNA.
So the structure of nucleotides is instrumental for ribozymes, but incidental for proteins.
Comment by John Wendt — July 2, 2009 @ 6:22 pm
July 2nd, 2009 at 6:37 pm
I don't want a semantic struggle so let's cite something more specific. A change in a single nucleotide within DNA can result in a protein that has an amino acid alteration. That in turn can result in radical phenotypic change. DNA is still the polymer it was before the mutation. Virtually identical but with a "behavioral" effect that is profound for the organism. We call some of these mutation alterations diseases. You wax eloquently about folding, electrical shape etc. But it is not the chemical behavior of the altered DNA that is significant. Rather it is the effect that change has within a system and that effect in turn results from a coding convention mapping sequences of DNA to amino acids.
Comment by Bradford — July 2, 2009 @ 6:37 pm
July 3rd, 2009 at 9:01 am
Then why inject semantics into chemistry? It's convenient, but remember it's chemistry from beginning to end.
All convenient semantic constructions that aren't in the DNA or the RNA.
Comment by John Wendt — July 3, 2009 @ 9:01 am
July 3rd, 2009 at 12:35 pm
I didn't John. I should have kept it simple and just pointed out that you were wrong.
Information for the genetic code is stored in a sequence of three nucleotide bases of DNA called base triplets, which act as a template for which messenger RNA (mRNA) is transcribed. A sequence of three successive nucleotide bases in the transcript mRNA is called a codon.
Comment by Bradford — July 3, 2009 @ 12:35 pm
July 3rd, 2009 at 12:52 pm
Bradford,
If we are all about accuracy then isn't John technically correct in pointing out that DNA and RNA don't understand codons? Then are just polymers, only the tRNA understands codons, even the ribosome only knows that the word length is three characters. Saying that DNA is a series of condons is correct only by semantics of the definition and has nothing to do with the chemistry. Saying DNA is made of codons incorrectly implies that DNA has/understands some sort of semantics which in fact are just labels we use for our own convenience.
Comment by Todd Berkebile — July 3, 2009 @ 12:52 pm
July 3rd, 2009 at 12:59 pm
Yes, if that is his point but then it would be a strawman. He wrote:
Codons are not figments of the imagination. They are real and not simply a convenient term.
Comment by Bradford — July 3, 2009 @ 12:59 pm
July 3rd, 2009 at 1:31 pm
They are real simply because they are defined to be real. I read John's statement simply as meaning DNA doesn't "understand" codon, DNA is not shaped by or behaviorally influenced by codons. If I defined a "bodon" as a series of two nucleotides in an RNA strand than it would be just a real to claim DNA is made of bodons. This definition tells us nothing about the nature of DNA so I fail to see how it is anything more than a convenient term. Terms like chromosome and gene and genome also are convenient for discussing DNA but they don't effect the nature of DNA either.
Comment by Todd Berkebile — July 3, 2009 @ 1:31 pm
July 3rd, 2009 at 1:33 pm
That's not what he wrote.
Comment by Bradford — July 3, 2009 @ 1:33 pm
July 3rd, 2009 at 1:47 pm
Those are not the exact words he wrote, but is that not the meaning of what he wrote? You said yourself that you do not want to argue semantics so obviously it is finding the meaning that is important, not the specific words spoken.
Comment by Todd Berkebile — July 3, 2009 @ 1:47 pm
July 3rd, 2009 at 2:29 pm
Wrong about what? You seem intent on "coding", "convention", and "mapping", which are all useful for characterizing the process; but they aren't in the chemistry.
Note that according to your link DNA doesn't have codons; they're called "base triplets". That's purely semantic.
Added: I see that Todd has made my point for me.
Comment by John Wendt — July 3, 2009 @ 2:29 pm
July 3rd, 2009 at 2:42 pm
It's relevant to the scientific reality.
Comment by Bradford — July 3, 2009 @ 2:42 pm
July 3rd, 2009 at 2:56 pm
Continuing after an interruption:
RNA polymerase adds ribonucleotides one at a time; there's nothing in either the DNA or the RNA that goes by threes. Three-ness comes only from the ribosome, and "mapping" comes only from the aminoacyl tRNA synthetase that matches a particular tRNA with a particular amino acid. All very distributed.
If you want to call codons "real", I don't actually have any objection. Just don't go on to say that "codons mean code, and a code needs a coder".
Unless of course you can tell us something about this hypothetical coder, for instance how he manages to move molecules into positions they couldn't assume naturally.
'.
Comment by John Wendt — July 3, 2009 @ 2:56 pm
July 3rd, 2009 at 3:04 pm
A code exists whether you like it or not.
Unless of course you can tell us something about how molecules are moved into positions in prebiotic environments…
Comment by Bradford — July 3, 2009 @ 3:04 pm
July 3rd, 2009 at 3:44 pm
We can tell you huge amounts about that, what do you want to know? There's convection, buoyancy, Brownian motion, dispersion, combustion, sedimentation, surface tension, hydrophobic effects, electrostatic effects, van der Wall forces, etc etc etc. Why on this very site on numerous occasions people have even linked articles showing how specific complex molecules can be formed naturally.
Oh, sorry, your question was rhetorical, meant to distract from your inability to answer John's question. Sorry, for a moment there I thought you wanted to learn about chemistry.
Comment by Todd Berkebile — July 3, 2009 @ 3:44 pm
July 3rd, 2009 at 4:06 pm
You don't have diddly on the origin of life and if you don't know that you need a better education.
Comment by Bradford — July 3, 2009 @ 4:06 pm
July 3rd, 2009 at 6:31 pm
Bradford wrote:
That wasn't an impressive argument. We also don't know how general relativity connects with quantum mechanics. But it doesn't mean that we have no idea about gravity.
Comment by olegt — July 3, 2009 @ 6:31 pm
July 3rd, 2009 at 7:11 pm
It wasn't intended to be. Did you notice how uninterested your side of the aisle is in substantive discussions? Good at personal attacks, setting up straw men, presuming superior knowledge and at juvenile antics. The reference to the Cap and Trade legislation is a case in point. The issue isn't even over global warming and the evidence for it. You're intelligent and reasonably objective. To accurately evaluate the bill's value one needs to assess the strength of scientific evidence for a regulatory impact on climate and balance that with some inevitable harmful economic effects. It's stuff like this that interests me Olegt. If a commenter is into games then why not get a Wii?
Comment by Bradford — July 3, 2009 @ 7:11 pm
July 3rd, 2009 at 7:32 pm
When were we talking about the origin of life? This is just more distraction and ducking the question. You know nothing about the origin of your theoretical designer and yet insist you can study the design. Yet biologists know nothing unless they can solve the problem of the origin of life? Double standard much?
Comment by Todd Berkebile — July 3, 2009 @ 7:32 pm
July 3rd, 2009 at 7:43 pm
We do know quite a bit about the nature of advanced intelligence and can make valid inferences based on that. I doubt there will ever be an empirical resolution of the issue but that is all the more reason not to presume a default position on the origins matter.
Comment by Bradford — July 3, 2009 @ 7:43 pm
July 3rd, 2009 at 7:49 pm
We know even more about chemistry and biology, but apparently we aren't allowed to make valid inferences based on that because those inferences clash with your metaphysics.
Comment by Todd Berkebile — July 3, 2009 @ 7:49 pm
July 3rd, 2009 at 8:00 pm
You can make inferences but make sure to distunguish them from sound scientific theories.
Comment by Bradford — July 3, 2009 @ 8:00 pm
July 3rd, 2009 at 8:26 pm
Bradford wrote:
What does cap and trade have to do with the subject of this thread? What does the origin of life have to do with cap and trade or the current topic?
I'm totally confused, Bradford. Enlighten me.
Comment by olegt — July 3, 2009 @ 8:26 pm
July 3rd, 2009 at 8:51 pm
Yeah. That was in another thread.
Comment by Bradford — July 3, 2009 @ 8:51 pm
July 4th, 2009 at 11:46 am
So we're back to god-of-the-gaps. Go figure.
I know you're tired of that, because you have no answer. I confess that I get tired of hearing it, especially when there's actually a lot of science in what you call "gaps". But it gets me to bone up on what we do know, which is s lot, and that's rewarding.
Somebody above mentioned Brownian motion. There are lots of molecules rattling around; with millions of years and a great many moles, even very improbable things can happen from time to time.
I give you substantive discussion, i.e. biochemistry, and you say "It was designed", or "The code exists". No substance at all.
Of chemistry and biology, yes, obviously.
We know about human intelligence; but every time we try to make inferences from that, like "That's bad design", or "Why would the Designer do it that way", you say "How do you know how the Designer would have done it?", or "Maybe the Designer has other reasons". Still no substance.
Anyway, "intelligence" has never done anything at all, as far as we can tell. Intelligent agents do things, and as far as we have ever seen they need some sort of energy to do them. In a chemical reaction every molecule moves according to the laws of Coulomb and Newton; that's what we call "natural". To make a reaction happen in an unnatural way requires that something or someone apply energy to particular molecules, to deflect them from the trajectories they would naturally take. Humans supply energy with muscle or machines (which can trace their ancestry to human muscle forging metal). Where does the Designer's energy come from, and how does he apply it to particular molecules? If you can't give at least a plausible explanation of that, we have to say that "design" as you envision it is impossible.
We have theories with moving parts, which allows us to make testable hypotheses. Some of them turn out to be good, some are bad. But even the bad ones can point to experiments and maybe better theory. (Mike Gene says he can make testable hypotheses starting from "If there is a designer…". Somehow he always seems to arrive at the same conclusions we get when we start from "Given what we know about biochemistry…". Ockham's Razor applies.)
"Some unknowable Designer did it" has no moving parts, so how can we work with it?
There's a nascent hypothesis in evolutionary biology based on the idea that change in development is caused more by changes in gene expression than in genes themselves. Not everone agrees, but note the discussion.
This somewhat contradicts the Modern Synthesis, but then the MS never had a good notion of how genes shape growth, let alone how change in a gene changes growth. So this is more an increase in detail than a change in the theory. And there's a lot of testableness.
Comment by John Wendt — July 4, 2009 @ 11:46 am
July 4th, 2009 at 12:04 pm
You'd make a good reporter. Biased and erroneous accounts. Yep, a perfect fit for the American media. You're the one who screwed up on codons
When are you going to demonstrate this? Memorizing facts is one part of studying a discipline. Work on the reasoned application of knowledge. That's where you're falling down.
Comment by Bradford — July 4, 2009 @ 12:04 pm
July 4th, 2009 at 12:10 pm
When referring to genetics, "code" just means correspondence between sets. What you mean by "code"?
Comment by Zachriel — July 4, 2009 @ 12:10 pm
July 4th, 2009 at 12:12 pm
Correpondence between nucleotide groups and protein amino acids.
Comment by Bradford — July 4, 2009 @ 12:12 pm
July 4th, 2009 at 12:12 pm
Throw in some stop commands for good measure.
Comment by Bradford — July 4, 2009 @ 12:12 pm
July 4th, 2009 at 12:17 pm
Yes, a correspondence can be drawn. So what?
Comment by Zachriel — July 4, 2009 @ 12:17 pm
July 4th, 2009 at 12:22 pm
The so what is how underlying laws of physics and chemistry explain the formation of that biological system.
Comment by Bradford — July 4, 2009 @ 12:22 pm
July 4th, 2009 at 1:25 pm
I don't get it. Protein production is ternary, and that's somehow for our "convenience"?
I also understood that in the nested hierarchy of formal languages, DNA-sequences belong to the class of extended context-free grammars.
For our convenience?
Comment by Rock — July 4, 2009 @ 1:25 pm
July 4th, 2009 at 2:52 pm
Quotes from Bradford:
Didn't I hear somebody say something about "personal attacks", hmm? What did I get wrong in the chemistry?
That's how I realized that the "genetic code" is a convenient human construct that abstracts the chemistry, rather than a thing in and of itself. Similarly, reasoned application of chemical knowledge tells me that DNA isn't actually, nor does it actually have, "information": in conjunction with one of the RNA polymerases DNA forms a transient holoenzyme that catalyzes the addition of one ribonucleotide to a string, based on the combined electrical shapes of the DNA, the polymerase, and one of the four biological nucleotides. We call that "biological information" as a convenience, but we need to remember that it's chemistry.
Where's your reasoned application of knowledge?
Comment by John Wendt — July 4, 2009 @ 2:52 pm
July 4th, 2009 at 4:34 pm
From Rock:
The ternary-ness comes from the elongation factors in the ribosome; there's nothing about "three" in the DNA or the mRNA. The "convenience" comes in calling the suite of chemical event sequences a "code".
Further thoughts: Some stretches of DNA produce a piece of RNA that becomes part of a ribosome, or a tRNA. Does this DNA contain codons? If it does, why do we say that? If it doesn't, then codons are nothing more than a reflection of the eventual fact that a particular piece of RNA becomes part of the protein production process. IOW the codon-ness is reflected back to the DNA, rather than being an as-such part of the DNA.
Suppose that a stretch of DNA that once coded for protein suffers a mutation in its TATA box, and so is no longer transcribed into RNA. Does this DNA still have codons? Go the other way: A non-coding stretch of DNA sits in the right relation to a stretch that mutates into a TATA box, so that this stretch begins to be transcribed. Its polypeptide probably won't fold into a protein; but does the newly-transcribable stretch of DNA acquire codons just because its RNA transcript binds to a ribosome?
I haven't though it out thoroughly, but right now I have a feeling that only the existence of that hierarchy lets us call DNA sequences a "language" at all.
Comment by John Wendt — July 4, 2009 @ 4:34 pm
July 4th, 2009 at 6:47 pm
Fine. Hold that view. But until you are able to demonstrate actual biochemical pathways backing up your views with empirical evidence as to how functional nucleic acids could form in prebiotic conditions, you are left with a personal opinion.
Information can be assessed independently of your belief in chemical sufficiency. Your attachment to naturalism is evident and so too is your faith in undemonstrable biochemical pathways based on it.
Comment by Bradford — July 4, 2009 @ 6:47 pm
July 4th, 2009 at 6:55 pm
You're making a circular argument. Noone is taking issue with the fact that chemical reactions lead to protein synthesis. Your insistence that this necessarily indicates the sufficiency of chemical origin pathways to coding components is your personal view, not to be confused with solid empirical data.
Comment by Bradford — July 4, 2009 @ 6:55 pm
July 4th, 2009 at 9:06 pm
The obvious elephant in the room is that "something or someone" DID in fact "apply energy to particular molecules, to deflect them from the trajectories they would naturally take", and that this "deflection" ultimately created life. The difference between us is not one of evidence (lots of things can do this – including intelligent agents), but of personal belief and bias. If you are not a believer in God, you'll interpret all evidence as supportive of the creative force being "something". If you believe in God, the evidence will support the creative force being "someone". Ockham's Razor has nothing to do with it since we witness both phenomena in the real world. The believers assumption is that God is a non-physical omniscient entity who is able to manipulate molecules to his liking. The specific prediction I have made based on this assumption is that no one will ever clearly delineate how "something" made any of the components of life.
Comment by Daniel Smith — July 4, 2009 @ 9:06 pm
July 5th, 2009 at 7:08 pm
So we're back to god-of-the-gaps. Surprise, surprise.
From the New York Times:
A very small sample of the RNA-world literature:
That's a lot more than "diddly".
Comment by John Wendt — July 5, 2009 @ 7:08 pm
July 5th, 2009 at 7:20 pm
Bradford and I have discussed this before, Bradford apparently doesn't believe that progress towards a goal provides any justification for accepting the validity of that goal. So while we try to understand how a natural OOL could occur Bardford denies that all the progress made makes a natural OOL more plausible. So much for Mike’s plausibility building methods outlined in the DM, I guess those can only be used to support the “god did it” hypothesis. "Science makes great progress towards understanding OOL," we say. "Do you know the final answer?," asks Bradford. "No," we freely admit. "Then you don't know diddly," Bradford repeatedly concludes. Apparently you are only allowed to draw logical inferences that support Bradford's metaphysical viewpoints.
Comment by Todd Berkebile — July 5, 2009 @ 7:20 pm
July 5th, 2009 at 10:09 pm
Todd:
It's not the metaphysics you need to concern yourself with. You don't have the empirical muscle needed to sustain the contention that life arises in prebiotic conditions. Sorry about that as the assumption of it is a vital part of your metaphysics.
Comment by Bradford — July 5, 2009 @ 10:09 pm
July 6th, 2009 at 12:38 am
Well, the fact that life exists and that despite thousands of years of searching there is zero evidence of any potential designers is all empirical evidence, but as I've admitted many times we don't yet have complete theory for natural OOL. There are lots of gaps in our knowledge for you to cling to and there always will be. However the lack of knowledge supports no theory including special creation.
Comment by Todd Berkebile — July 6, 2009 @ 12:38 am
July 6th, 2009 at 12:45 am
Zero evidence of a watchmaker, blind or sighted. When I see absolute descriptors like zero I suspect blinding viewpoint bias.
There are lot's of gaps where you can insert your materialistic bias.
Comment by Bradford — July 6, 2009 @ 12:45 am
July 6th, 2009 at 12:56 am
There is massive evidence of a blind watchmaker. For example, there is all of biology, physics, chemistry, etc. But please, share all the latest empirical findings about god if you think they are more than zero.
Inserting a null hypothesis makes a lot more sense than inserting invisible sky fairies.
Comment by Todd Berkebile — July 6, 2009 @ 12:56 am
July 6th, 2009 at 1:01 am
Biology, chemistry and physics do not predict that cells arise in prebiotic environments.
Inserting false assertions of what I believe makes you look like an ass, not a reasonable debator.
Comment by Bradford — July 6, 2009 @ 1:01 am
July 6th, 2009 at 1:15 am
Oh, you know everything there is to know about all these fields? Sounds like someone has their cart before the horse. The universe is a big place, if a molecule is one in a trillion there are 10^68 of them in the universe but Bradford can predict the results of 13 billions years of interstellar history.
So now you want to deny that you think god did it? Denying god just to win an Internet debate, tsk tsk.
Comment by Todd Berkebile — July 6, 2009 @ 1:15 am
July 6th, 2009 at 1:34 am
I don't insert God into gaps of knowledge. The point of the OP I linked to was that God is credited as the source of natural penomenon- both that which we have knowledge of and that we do not. In any case God and fairy are defined differently as a fair minded person would acknowledge. I don't mind your atheism so much as I mind your dishonest debating tactics. You need to study the approach of an atheist like Bradley Monton and mature a bit if you want to have civil exchanges. You apparently lack the interest in that at this time. You're gone.
Comment by Bradford — July 6, 2009 @ 1:34 am
July 7th, 2009 at 2:23 pm
You know, JW, chemistry bears an “uncanny” resemblance to coding. If I recall correctly (and I’m sure you will correct me—you are a chemist?), modern chemistry really began with the recognition of the existence of a chemical element; that elements are distinguishable by common properties, such as mass, weight, volume, density, etc.; and that elements combine in definite mathematical proportions.
If anyone didn’t know what a “code” is before, I just told you!
A code is a finite set of elements, related by common properties that vary amongst the elements (including mass, weight, volume, density, etc.), and which are combined according to a set of rules (grammar) that are summarized in terms of definite mathematical proportions (such as in the case of the DNA-code, ~3/1).
Let’s say I am a code-designer (not God) and I restrict myself (for the purposes of practical application) to the set of chemical elements. Am I also restricted to use chemistry’s grammatical rules?
Comment by Rock — July 7, 2009 @ 2:23 pm
July 11th, 2009 at 10:48 am
Rock writes:
There is evidence that the association between codons, anticodons and some amino acids are sterochemical in nature:
Yarus M, JG Caporaso & R Knight (2005). Origins of the genetic code: the escaped triplet theory. Ann. Rev. Biochem. 74: 179-198
Comment by KC — July 11, 2009 @ 10:48 am
July 17th, 2009 at 2:50 pm
Sorry, KC. And, JW. I wasn’t trying to “turn the tables” on you (Bradford). Just trying to nudge you into thinking a bit differently about the same subject.
Acceding to JW’s argument, I have to reject the codon escape (and codon capture) theory, because it admits the existence of a “code.” There is no code. It’s all chemistry.
The “new and improved” stereochemical theory is based on the auxiliary hypothesis that subsequent “code-optimization” has overwritten or “erased” most of the trace of a previous chemical evolution phase.
It’s all chemistry. There is no alternative. We should rather say that the chemistry has evolved to the point that the complexity of the purely chemical interactions have exceeded our analytical abilities to parse.
IOW, despite the press resleases, biologists haven't "cracked the code."
There is no subsequent phase of "code" evolution. It's chemical evolution.
Bradford and I have argued the point often…
Comment by Rock — July 17, 2009 @ 2:50 pm
July 18th, 2009 at 9:38 am
Sorry about not responded punctually. (Has everyone left the room?) Once the topics drop off the page I lose track of them.
I’m big fan of Yarus and his team, for them proving that we are not all “Little Churchills” (LOL). And I was previously familiar with (many) attempts to divine (so to speak) the inverse map, the “protein code” or “protein recognition code,” i.e., short DNAprotein binding motifs. Mixed results, but basically the same as what Yarus et al have reported. John Wendt may be correct (?) that a common preconception about the “code” (or coding in general) may be misleading us. Our analyses may be confounded by the existence of multiple overlapping codes, e.g., the existence of which is very strongly suggested by this and much more research, done independently, as in the search for the protein code. When I was in college I was taught that there is one code (“universal”) and it was “non-overlapping.” I was taught wrong.
Biologists have just begun to “crack the code.” It is proving far more complex then we might have earlier imagined.
I am also a big fan of David Harel. Here’s one reason why
http://www.wisdom.weizmann.ac.il/~dharel/SCANNED.PAPERS/DoConsideredOd.pdf
LOL
But I thought I’d just throw this out there, not that its topical (I’ve forgotten what the topic is or was), but because its fun, and even though the biologists make fun of it, I take DNA-numerology half-seriously. It makes me wonder… (I think Arthur Hunt once told me that this kinda stuff is crazy, or I was crazy to take it seriously. No problem for me. I rank pretty high on the Crackpot Index. But who said that science is never just plain crazy! Science and engineering have built the world. Take a look around you and tell me there isn’t something crazy going on! LOL)
Beauty is in the genes of the beholder*
*With apologies to Watson and Crick.
http://www.wisdom.weizmann.ac.il/~dharel/SCANNED.PAPERS/BeautyIsInTheGenes.pdf
Comment by Rock — July 18, 2009 @ 9:38 am
July 18th, 2009 at 9:52 am
I'm a biology buff. You can't understand modern biology without chemistry, and you can't understand modern chemistry without quantum physics.
True; but chemistry has come a very long way since.
The essence of an element is the atomic number, i.e. the number of protons in the nucleus. Weight (a proxy for mass) is determined by the number of protons plus a number of neutrons that is almost always at least as great as the number of protons. The number of protons determines (in the neutral atom) the number of electrons. Electrons arrange themselves in shells, in ways that are described by solutions of the Schroedinger equation.
Definite-proportions follows from the atomic nature of elements. (Noteworthy that "atoms" were controversial until about 1900.) Compounds arise when atoms share electrons in order to fill electron shells, as determined, again, by quantum mechanics. The distances between atoms are also determined by the QM of chemical bonds, which, with atomic mass, determines density. The shape of a molecule is determined by atoms arranging themselves in minimum-energy configurations.
That's a strange sort of definition. Commonly, a code is an association between sets of objects, such that elements of one set can be used to refer to the other, maybe for secrecy, or for economy. (Before WWII,when cable communication was expensive, commercial codes were common, consisting of a list of possibly-complex standard messages, each represented by a number. One writer remembered his time at a shipping company: one day he got a message that said "61387". With visions of sultry spies and international intrigue, he looked in the code book, to find "What facilities have you for the handling of heavy equipment?")
Associations of a generic code can be entirely arbitrary. The associations in the genetic code are determined by aminoacyl-transfer RNA synthetases.
Definite proportions are definitely not needed for a code. For maximum coding efficiency, Huffman codes use shorter codes for more frequent elements. A fixed-length genetic code is about 70% efficient. The 3/1-ness of the genetic code comes about because of the way tRNAs mate to mRNA.
No. Your code can be as arbitrary as you like. The genetic code is chemistry, and so follows the principles of chemistry.
Tried that; nothing happens. All ID can say is "It looks designed", or "I can't think how it could have happened naturally", therefore "there must be a Designer". Nothing about how the Designer can move particular molecules into particular places, especially since that requires energy, for which there is no apparent source.
From a recent article:
It's convenient to call the system a "code". What we object to is the conclusion that "code" requires an "intelligent coder".
From a less-recent article:
Key phrase:
This is consistent with the hypothesis that the first life contained fewer than 20 amino acids, with others added after synthesis machinery had evolved.
At any rate, ID doesn't seem to have one that does any work.
There's a growing realization that developmental processes are controlled by a great number of genes, with a great deal of redundancy. No particular sense of consistency, though. Figuring it out will take a great deal of experiment and analysis. Saying "It was designed" just sweeps the problem under the infinite rug.
True. But we know how to work on it. ID says "study the design". Biology and biochemistry study the organism, and have found a great many ways to avoid have go invoke an indescribable entity.
Comment by John Wendt — July 18, 2009 @ 9:52 am
July 18th, 2009 at 10:12 am
A number of crackpot ideas have become mainstream, like heliocentrism and endosymbiosis. But, as they say about hang gliding, you're talking to the survivors. Most out-of-the-box ideas just fade away. Success is usually the result of a lot of work.
Comment by John Wendt — July 18, 2009 @ 10:12 am
July 20th, 2009 at 4:25 pm
"Tried that; nothing happens."
‘Nuff said, JW. I thought you were a chemist. But you are not a scientist.
My mistake.
Comment by Rock — July 20, 2009 @ 4:25 pm