Evolution and Creation an Honest Question

[blutoski]

You dogmatically assert that you are entirely familar with the theory of evolution, but it's obvious that if your knowledge ever rose above "layman's level" (which I doubt), it certainly hasn't done so since most of the current practitioners of evolutionary biology were alive.

Somebody mentioned Asimov... one of his quotes is: "the true test of a man's honesty is not his tax return; it's the zero adjust on his bathroom scale."

What this means is: the worst type of dishonesty is trying to fool oneself. I have a feeling that hammegk is just having difficulty finding the right niche of expertise. I sympathize! There are so many interesting ideas out there with fields of study, bodies of literature, &c. It took me a long time to determine where I should concentrate my efforts.

Me: I'm an immunologist with a psychology degree on the side. Paradoxically, I tend to shy away from the immunology-related threads (because I have the same debates all the time in the real-world). But my biochem/microbi background gives me some confidence that I can constructively contribute to evolution threads. However, I'm not an expert in geology, zoology, physiology, genetics, or biochem, so I look forward to experts from these fields contributing. I had to learn my limits.



hammegk: you have a flair for metaphysics. Science is not metaphysics, although it adopts certain assumptions from that field. Science stands in the middle, between philosophy and engineering. This is my advice: teach metaphysics to the scientists, but learn science from them.

 

[Hellbound]

Hammy:

I equate it wirth dishonesty, as you've repeatedly told people that you had no need to learn more.

To be fair, it is refreshing to see you actually learning some of the information that's been relatively common for some time now, concering evolution and abiogenesis. Which is pretty much what everyone has been urging you to do since you're first comments about it.

 

[sphenisc]

Each nucleic (there are five) acid has at least eight chirality points.

I think each nucleic acid base is planar (so not chiral), which is why they 'stack' so well in DNA.

When attached to a [deoxy]ribose molecule to form a nucleoside, there are [4]3 chiral centres.

http://courses.cm.utexas.edu/biverson/ch310n/spring2006/MOTD Fl05/Chiral.html

The addition of a phosphate group doesn't add any more chiral centres, so I'm at a loss as to how you get eight.

[I'm assuming by nucleic acid you meant either a base, nucleoside or nucleotide.]

Can you clarify your calculation?

Thanks

 

[drkitten]

eta:
Awesome odds indeed, iff any of the alternates can be demonstrated to be 'life'. However, I suggest the burden of proof for that assertion rests with you.

Absolutely. Fortunately, that burden of proof has been met. (subject to the usual handwaving provision that "proof" in science simply means "the preponerance of the evidence suggest that there are no significant alternatives"). The alternatives you have suggested thus far have been investigated in detail and found not to be viable or significant.

You're obviously not familiar with the experiments. That's not my problem. If you are really "making an effort to become better informed," then you need to read up on them. The talk.origins page you dismissed earlier has a pretty good bibliography that you can use as a starting point, and there are any number of experts here who can suggest further reading when you finish with them.

But the fact that you are unaware of the evidence does not negate it, or invalidate the conclusions drawn from it. If your only exposure to a trial is the opening statements, you'll probably not understand the decision that the jury came to all the evidence. But that's your ignorance, not their dogmatic-mindedness.

Until that proof is incontrovertible, your ID opponents will just note what you admit are the incredible odds of random occurence.

So what? My ID opponents are also notable, not only to their reliance on dogma over evidence, but also for their willfulness in not seeking out evidence, misrepresent evidence when presented with it, or simply outright ignoring it.

Why do you bring this up? Are you suggesting that you yourself are one of my "ID opponents" and similarly remaining deliberately ignorant of recent advances? Or are you suggesting that the standard of scientific discourse should be that proofs should be so incontrovertible as to convince even those people who remain unaware of them?

 

[drkitten]

I think each nucleic acid base is planar (so not chiral), which is why they 'stack' so well in DNA.

When attached to a [deoxy]ribose molecule to form a nucleoside, there are [4]3 chiral centres.

Can you clarify your calculation?

Back of the envelope calculation, based on blutoski's statement that there are 512 different ways to make each ribose molecule (which in turn implies 8 points of left/right symmetry). I cheerfully admit that I didn't dig up the molecular structure myself to check. My bad.

 

[sphenisc]

Back of the envelope calculation, based on blutoski's statement that there are 512 different ways to make each ribose molecule (which in turn implies 8 points of left/right symmetry). I cheerfully admit that I didn't dig up the molecular structure myself to check. My bad.

That's right, pass the buck.

Blutoski, any comment on the 512 figure?

Thanks

 

[drkitten]

That's right, pass the buck.

Absolutely.

But there are a number of equally good combinatoric arguments that I could use (that don't even specifically involve chirality). Hammy's talk.origins link
provides a couple of good examples.

The DNA used by living organisms is synthesized using only four nucleosides (deoxyadenosine, deoxythymidine, deoxycytidine, and deoxyguanosine) out of the dozens known (at least 102 occur naturally and many more have been artificially synthesized).

A more-interested combinatorist than myself could calculate the probability of two independent abiogenesis events independently choosing the same four cards from a deck of 102 or more cards. My same envelope back tells me that the odds are on the order of 10,000,000:1 against.

Similarly,

In all known organisms, enzymatic catalysis is based on the abilities provided by protein molecules (and in relatively rare, yet important, cases by RNA molecules). There are over 390 naturally occurring amino acids known (Voet and Voet 1995, p. 69; Garavelli et al. 2001); however, the protein molecules used by all known living organisms are constructed with the same subset of 22 amino acids.

My envelope is not large enough for me to calculate the odds of drawing the same 22-card hand from a 390-card deck.

Similarly, the universality (or near-universality) of the genetic code. The genetic code is a mapping from the space of all (64) codon triplets to the space of (22) amino acids. Yet

All known organisms, with extremely rare exceptions, use the same genetic code for this. The few known exceptions are, nevertheless, simple and minor variations from the "universal" genetic code (see Figure 1.1.1) (Lehman 2001; Voet and Voet 1995, p. 967), exactly as predicted by evolutionary biologists based on the theory of common descent, years before the genetic code was finally solved (Brenner 1957; Crick et al. 1961; Hinegardner and Engelberg 1963; Judson 1996, p. 280-281).

What's the chance of independently duplicating the genetic code in two different abiogenesis events? 22^64:1 against, according to my poor overburdened envelope.

Similarly,

For example, the fundamental metabolic systems in living organisms are glycolysis, the citric acid cycle, and oxidative phosphorylation. In all eukaryotes and in the majority of prokaryotes, glycolysis is performed in the same ten steps, in the same order, using the same ten enzymes (Voet and Voet 1995, p. 445).

What's the chance of independently reinventing the same ten enzymes (out of the entire space of possible enzymes) in the same order?

And our hypothetical multiple abiogenesis event would need not only to have managed one of these difficult tasks, but all four of these. So take all these outlandish odds, and multiply them together,..... and now tell me to take seriously the possibility that this happened twice.

 

[drkitten]

duplicate post due to network wierdness, ignore

 

[sphenisc]

Absolutely.

A more-interested combinatorist than myself could calculate the probability of two independent abiogenesis events independently choosing the same four cards from a deck of 102 or more cards. My same envelope back tells me that the odds are on the order of 10,000,000:1 against.

There seems to be a hidden assumption of equal probability in here.

Similarly, the universality (or near-universality) of the genetic code. ...
What's the chance of independently duplicating the genetic code in two different abiogenesis events? 22^64:1 against, according to my poor overburdened envelope.

I think the combinatronics for mapping 64 codons onto 22 amino acids is more complicated than that, but anyway, not all possible ways of mapping are equally good. The present genetic code is near-optimal in a number of ways and ,hypothetically, may be the result of convergence from a number of sub-optimal starting points.

 

[drkitten]

There seems to be a hidden assumption of equal probability in here.

Is there? I'm sorry -- I didn't mean to hide it.

 

[blutoski]

Is there? I'm sorry -- I didn't mean to hide it.

And that's why I chose chirality as a favourite. Isomers/enantiomers are thermodynamically equivalent in a sterile environment.

I'll get back to the list about the chirality of polymerized nucleotides. 8 chiral centers was a conservative estimate, which is why I prefaced it with "at least". I just stopped counting at 8. I'm at work right now, so it'll have to wait until this evening when I can get home and either dust off the CPKs or locate a citation.

 

[blutoski]

Do you assert these self-replicators qualify as life?

Unnecessary. The question is: do we have a common ancestor. It is accepted that this may be an ancestral structure that spans biochemistry/biology boundary.

 

[drkitten]

eta:
KevinM: I am unqualified to address the accuracy of the author -- who appears to be a Christian as you are -- as he attempts to address many questions opponents of neo-Darwinism consider.

http://www.evanwiggs.com/articles/reasons.html#primer

"Attempts" is right.

The article cited is standard Creationist clap-trap, including most of the classic errors through willful ignorance.

He starts by quibbling over definitions, asserting without evidence that there is a distinction between micro- and macro- evolution, insists that only experimentally-falsifiable conjectures can be accepted (which throws out most of archeology as a science; I guess the Egyptian kings never existed), asserts that "evolution is a religious philosophy," tells the old lie that mutations can only lose information, and falls back on the good old standby of Irreducible Complexity, ignoring the fact that Behe's data was known to be wrong at the time he originally published it.

He uses the standard argument about the improbabiliy of assembling a protein from scratch, ignoning the fact that evolution does not operate "from scratch," but on the basis of incremental modifications, and gives the standard mis-argument against Dawkin's "weasel" example.

His discussion of chirality is factually wrong. He misrepresents the experiments with Spiegelman's monster, and relies heavily on out-of-context quotation and untraceable citations ("the chairman of a recent National Academy of Sciences committee").

His information theory is simply wrong out of the box and replicates all the errors of William Dembski. He makes the standard misrepresentation of thermodynamics and the difference between an open and closed system, presents long-discredited cosmological theories from second-rate speculative journals as though they were fact, and cites the traditional conspiracy of scientists to keep "doubt and dissent" from being tolerated -- a "growing dogmatic mindset that is alien to the spirit of free scientific inquiry."

He draws unwarranted extrapolations from the extra-solar planets that have been discovered. For example, all the known extrasolar planets are heavy planets with high orbital eccentricity, because only those planets will cause enough of a disturbance in the solar position to be noticeable.
"We have only seen about 200 extra solar planets and they are all gas giants, orbiting much too close to their suns." He concludes, however, that "it appears that the solar system is unique," because all the planets we've found appear to be of the only type we are equipped to find.

He makes the standard "why are there still short-period comets around" arguments, dismissing the observations of the Oort cloud and the Kuiper belt as "pure speculation."


If I had wanted to pick an example of factually inaccurate, agenda-driven, and simply bad science, I would have been hard-pressed to find a better one than this. If this is the quality of scholarship to which you are recommended in support of your views, I suggest that your views are probably wrong.

 

[hammegk]

If I had wanted to pick an example of factually inaccurate, agenda-driven, and simply bad science, I would have been hard-pressed to find a better one than this. If this is the quality of scholarship to which you are recommended in support of your views, I suggest that your views are probably wrong.

Thanks for at least reading through an xian fudamentalist article and commenting on what must be tripe from the view of human secularism -- basically that god does not exist, or if god does exist he'she'it is meaningless.

Your ID opponents of every hue in some way or another choose to disagree with that secular viewpoint.


We return to epsilon, and the not-a-naturalist wants to know how you explain the philosophical meaning of any value you assign to epsilon greater than zero.

Evolution is at -- and will always be at -- the cutting edge of this epistemologically-unsolveable debate.


I greatly appreciate the expansion of my knowledge base gleaned from the comments many have made in this thread.

 

[drkitten]

Thanks for at least reading through an xian fudamentalist article and commenting on what must be tripe from the view of human secularism -- basically that god does not exist, or if god does exist he'she'it is meaningless.

Your ID opponents of every hue in some way or another choose to disagree with that secular viewpoint.

Of course he chose to disagree with that viewpoint.

But in order to do, he had to misrepresent, manufacture, and ignore evidence.

We return to epsilon,

No, we don't. Not yet. Before that, I want to know on what basis you assign any evidentiary value to that document whatsoever, given that there's not a single paragraph in it that accurately represents the experimental evidence.

This "discussion" is rather like a discussion about the original colonization of the United States. Except that one person is telling the "narrative" based on history books and scholarship, and the other discussant is telling the "narrative" based on J.R.R. Tolkien's Lord of the Rings trilogy. I see no reason to give fiction -- which is all your "citation" amounts to -- any legitimate scientific standing.

And if you have no counterevidence to offer that isn't fiction, then you have no basis to dispute whatever epsilon those familiar with the evidence assign.

 

[blutoski]

And that's why I chose chirality as a favourite. Isomers/enantiomers are thermodynamically equivalent in a sterile environment.

I'll get back to the list about the chirality of polymerized nucleotides. 8 chiral centers was a conservative estimate, which is why I prefaced it with "at least". I just stopped counting at 8. I'm at work right now, so it'll have to wait until this evening when I can get home and either dust off the CPKs or locate a citation.

Here's my results:

• chances of getting the same 5 nucleotides with 3 chiral centers each 2 times independently: one in 1,073,741,824
• chances of getting the same 5 nucleotides with 3 chiral centers each 3 times independently: one in 35,184,372,088,832
• chances of getting the same 5 nucleotides with 3 chiral centers each 4 times independently: one in 1,152,921,504,606,850,000
• chances of getting the same 5 nucleotides with 3 chiral centers each 5 times independently: one in 37,778,931,862,957,200,000,000

And so on.

 

[drkitten]

Here's my results:

• chances of getting the same 5 nucleotides with 3 chiral centers each 2 times independently: one in 1,073,741,824
• chances of getting the same 5 nucleotides with 3 chiral centers each 3 times independently: one in 35,184,372,088,832
• chances of getting the same 5 nucleotides with 3 chiral centers each 4 times independently: one in 1,152,921,504,606,850,000
• chances of getting the same 5 nucleotides with 3 chiral centers each 5 times independently: one in 37,778,931,862,957,200,000,000

And so on.

Thank you. I think you just qualified as "a better combinatorist than myself."

 

[blutoski]

Thank you. I think you just qualified as "a better combinatorist than myself."

Excel did the heavy lifting.

I also recalculated for the credible criticism that perhaps it is imortant that all the riboses have the same configuration. Works out to one in:

64 (two events)
512 (three events)
4096 (four events)
32768 (five events)

respectively

So, if we assign a 99% confidence interval, two identical independent abiogenesis events are possible, with this relatively generous nucleotide model.

 

[hammegk]

Of course he chose to disagree with that viewpoint.

But in order to do, he had to misrepresent, manufacture, and ignore evidence.

From your worldview, you must be correct in that assessment. Many others are not so sure, and never could be convinced for many possible reasons and personality traits, that all the points raised in that screed have no merit.

You continue to ignore that real-world problem.

No, we don't. Not yet. Before that, I want to know on what basis you assign any evidentiary value to that document whatsoever, given that there's not a single paragraph in it that accurately represents the experimental evidence.

If that were an answer to our disagreement, there would be no disagreement; the best I can say, with little regard to that specific document, my epsilon is greater than zero.

This "discussion" is rather like a discussion about the original colonization of the United States. Except that one person is telling the "narrative" based on history books and scholarship, and the other discussant is telling the "narrative" based on J.R.R. Tolkien's Lord of the Rings trilogy. I see no reason to give fiction -- which is all your "citation" amounts to -- any legitimate scientific standing.

Again, from a naturalist's scientific view, you must be correct. Yet, your characterization of the opponents work as 'fiction' may as well work against you as for you, assuming you have interest in converting the 'non-believers'.

And if you have no counterevidence to offer that isn't fiction, then you have no basis to dispute whatever epsilon those familiar with the evidence assign.

Unfortunately, that comes across to many as another sermon requiring belief, although to you it's simple fact. I have no particular interest in your value other than to ask what a non-zero value means to you, and how you do not inadvertently slip into some form of philosophical dualism. I agree that 100% naturalism is a logically defensible position.


I will ask for clarification on the question of why rna/dna/life is necessarily a nested hierarchy for cladistics rather than -- at particular points -- a fait-accompli as is the table of elements. I suspect you will invoke epsilon in your answer.

 

[drkitten]

From your worldview, you must be correct in that assessment. Many others are not so sure, and never could be convinced for many possible reasons and personality traits, that all the points raised in that screed have no merit.

You continue to ignore that real-world problem.

Fair enough. I will no longer ignore that problem.

Attention, everyone. It has come to my attention that hammegk is "not so sure" whether statements known to the speaker to be untrue are less likely to be true than statements supported by experimental evidence.

It has come to my attention that hammegk is "not so sure" whether statements made in total and deliberately willed ignorance are less likely to be true than statements based upon reason and evidence.

It has come to my attention that hammegh is "not so sure" whether a deliberate misreading and misquotation of a text is less likely to reflect the authorial knowledge and intention than a correct one.

Furthermore, he has stated that he "never could be convinced" otherwise, "for many possible reasons."

I therefore urge all of you to take these direct admissions of fraud, chicanery, ill-faith, and willful ignorance into account when evaluating any of his writings, as he has declared himself forthrightly to be deliberately nothing more than an uneducated and uneducatable troll, intent only on disrupting the educational mission of the JREF.

I will ask for clarification on the question of why rna/dna/life is necessarily a nested hierarchy for cladistics rather than -- at particular points -- a fait-accompli as is the table of elements.

Ask away. Feel free to fictionalize any answer you like, since the mere matter of factual accuracy is by your own admission irrelevant to the truth value of the answer.