Slicing and Dicing Falk: Part One
by BradfordStephen Meyer, author of Signature in the Cell wrote Response to Darrel Falk’s Review of Signature in the Cell. From the article:
Nevertheless, in his recent review on the Biologos website, Prof. Darrel Falk characterizes me as merely a well-meaning, but ultimately unqualified, philosopher and religious believer who lacks the scientific expertise to evaluate origin-of-life research and who, in any case, has overlooked the promise of recent pre-biotic simulation experiments.
I've seen no evidence that Meyer does not understand the biochemistry or cellular processes of which he alludes to in Signature in the Cell. I have not seen anyone point out specific errors that would indicate a lack of understanding. Citing the promise of recent experiments refers to a subjective assessment of what might be rather than confirmation of what is. It's the difference between speculation and solid scientific theory.
On the basis of two such experiments, Falk suggests I have jumped prematurely to the conclusion that pre-biotic chemistry cannot account for the origin of life. Yet neither of the scientific experiments he cites provides evidence that refutes the argument of my book or solves the central mystery that it addresses. Indeed, both experiments actually reinforce—if inadvertently—the main argument of Signature in the Cell.
Meyer is correct.
The central argument of my book is that intelligent design—the activity of a conscious and rational deliberative agent—best explains the origin of the information necessary to produce the first living cell. I argue this because of two things that we know from our uniform and repeated experience, which following Charles Darwin I take to be the basis of all scientific reasoning about the past. First, intelligent agents have demonstrated the capacity to produce large amounts of functionally specified information (especially in a digital form). Second, no undirected chemical process has demonstrated this power.
Properties can be attributed to conscious intelligence which include a capacity to manipulate the symbols of coded languages to confer meaning. Biological meaning equates to function. The relevant language is found expressed through a genetic code.
Hence, intelligent design provides the best—most causally adequate—explanation for the origin of the information necessary to produce the first life from simpler non-living chemicals. In other words, intelligent design is the only explanation that cites a cause known to have the capacity to produce the key effect in question.
The only natural phenomenon known to fix the specific effect alluded to, to a cause having the capacity to generate that effect is conscious intelligence. Reduction to underlying chemical properties of cellular constructs does not yield the causal linkage.
Nowhere in his review does Falk refute this claim or provide another explanation for the origin of biological information. In order to do so Falk would need to show that some undirected material cause has demonstrated the power to produce functional biological information apart from the guidance or activity a designing mind. Neither Falk, nor anyone working in origin-of-life biology, has succeeded in doing this.
True.
Thus, Falk opts instead to make a mainly personal and procedural argument against my book by dismissing me as unqualified and insisting that it is “premature” to draw any negative conclusions about the adequacy of undirected chemical processes.
Falk's focus on Meyer's qualifications reflects the weakness of his position. When you are dealing from strength, you welcome challenges easily refuted by citing facts and reason. If Meyer were arguing that extra-cellular formation of amino acids was implausible Falk would cite evidence refuting that position. He would not need to focus on the educational background of the antagonist.
In a follow-up post I'll pick up where I left off on Meyer's article.
January 28th, 2010 at 11:30 pm
Bradford wrote:
You have an awfully short memory, Bradford.
Comment by olegt — January 28, 2010 @ 11:30 pm
January 28th, 2010 at 11:44 pm
So an organism with a functionally sequenced genome contributes junk to the genome of another organism with a functionally sequenced genome and this constitutes a refutation of precisely what? Did you ever watch what a toddler can do to the functionally sequenced letters on a scrabble board? It does not have much relevance to the causal origin of the scrabble sequencing.
Comment by Bradford — January 28, 2010 @ 11:44 pm
January 28th, 2010 at 11:49 pm
Bradford,
That's not the problem Nick pointed out. If you insist on an allegory, he faults Meyer for arguing that a scrabble board messed up by a toddler is still densely packed with information.
Comment by olegt — January 28, 2010 @ 11:49 pm
January 29th, 2010 at 12:33 am
The protein coding genes are. Let me direct your attention to the trial of Truther, accused of having murdered the keeper of all some hold sacred. While testifying in his own defense he explained that the real murderer was observed by him fleeing the murder scene by taking a taxi from it to the airport. The prosecutor, in his summation, told the jury that Truther's testimony was impeached by evidence that this alleged real murderer was observed to have littered the lawn of an adjacent park with peanut shells contained in a brown bag he held. Since Truther did not include this in his story he must be an incompetent witness whose entire testimony should be dismissed. During deliberations juror Dim Wit agrees with the prosecutor and explains that you can't trust the story of a man who left garbage out of his story. Juror Half Wit senses the consensus of those around him and nods his assent. Juror Common Sense then points out that the evidence linking the real murderer to the crime is not impacted by Truther's omission. Common sense wins the day.
Comment by Bradford — January 29, 2010 @ 12:33 am
January 29th, 2010 at 3:31 am
Bradford — eh?
olegt — Actually, the right analogy would be that I argued that a scrabble board that was over 50% just one tile repeating over and over again, like "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", or a short sequence repeating over again "THETHETHETHETHETHETHETHETHETHETHETHETHETHETHE" — could not be "densely packed with information", according to Meyer's own arguments. Thus Meyer refuted himself on that point.
Comment by nickmatzke — January 29, 2010 @ 3:31 am
January 29th, 2010 at 9:49 am
OK, back to biology. Meyer wrote the following, but if anyone else had written it, would it not be equally true?
Comment by Bradford — January 29, 2010 @ 9:49 am
January 29th, 2010 at 12:38 pm
The repetitive sequences Meyer represents as aiding indexing, bracketing, rheostat, quantity control regulation.
The protein coding sequences are the "dense" regions of the genetic information. When Meyer refers to the "vast majority" he is referring to the coding regions
Matzke misrepresents Meyers comment about the "vast majority" as if Meyer was referring to the entire genome, when in fact meyer was referring to the base sequences.
It is also possible that information can be densely packed in some regions (such as coding regions) even though other parts may not be packed.
For example, a computer disk may have sectors highly compressed data versus regions of repetive empty regions filled with zeros or noise (the non data storing regions). Try drilling holes in these regions and see if the disk will still function! They have a purpose even though they don't immediately code for data.
So it is quite possible that portions of the genome like disk can have densely packed regions of incompressible information and Meyer argues this signals design. That is why he said:
The signal is the dense regions and the noise is the errors in the repetitive sequences. Much like the dense packing of information on a CD ROM and long "noise" of empty sequences where no data resides.
At issue is not Meyer's understanding of the genome by matzke's willingness to misrpresent Meyer as not understanding the architecture of the genome.
Regarding the repetitive sequences, Meyer qualified them as being the result of "rule, algorithm or general law".
It is possible a repetitive sequence not the result of "rule, algorithm, or general law" to be informative in the shannon sense (surprisal value), but not informative in the kolmogorov algorithmic sense. For example we may say a CD rom has a capacity of 700megs data (this is a shanon measure), but the files on the CD occupy only 50 megs (this is a rough algorithmic measure saying we have really not much more that 50 megs of data assuming the empty regions are roughly compressible to 0 bits).
Finally, reading a CD you'll encounter large regions of repetitive "ZEROS" and then regions of densely packed sequences. The large repetitive "ZEROS" in a CD could hardly argue for the lack of intelligent design in the CD, but Matzke and friends seem quite willing to use this flimsy argument of repetitive sequences to argue against intelligent design in the genome.
Comment by Salvador T. Cordova — January 29, 2010 @ 12:38 pm
January 29th, 2010 at 12:59 pm
Meyer:
Isn’t it interesting that Falk, like olegt, has to rely on fallacious arguments and reasoning to defend his position. That type of reasoning is supposed to convince a skeptic like me?
Again let’s turn the table and apply Dr. Falk’s logic to Dr. Falk. Let’s compare, for example, Dr. Falk’s educational background with Dr. Meyer’s.
Here is a synopsis of Falk’s a cv from the Biologos website:
Here is Dr. Meyer’s:
From just this I could argue that since Cambridge is a much more prestigious university than any of the schools that Dr. Falk attended, and that Meyer is eminently more qualified to write a book, critical essays and talk about the origin of life than Falk. Falk is clearly out of his league here (cheap shot) and should pay due deference (condescension) to someone with that kind of educational background. But once again, that whole line of reasoning is fallacious.
In the same way Falk’s critique of Meyer’s book is fallacious because he makes it about Meyer rather than Meyer’s book.
In my opinion if you have a good argument you don’t have to rely a fallacious reasoning to advance or defend it.
You are living on a different planet if you think you can make ID arguments go away with a dismissive wave of the hand.
Comment by JOHN_A_DESIGNER — January 29, 2010 @ 12:59 pm
January 30th, 2010 at 5:26 pm
Sal — bwa ha ha! The very quotes you post support my interpretation of Meyer, not yours. Meyer says "the genome" not "the protein coding genome". He even specifically includes "even the many sequences that do not code for proteins" as being dominated by functional sequence.
Here's the full quote again:
Your position seems to be that because Meyer is so clearly wrong to say that the "vast majority" of the genome contains functional sequence, he must not have said that. But he did. Too bad.
Comment by nickmatzke — January 30, 2010 @ 5:26 pm
January 31st, 2010 at 1:23 am
Nick,
I stand corrected. Sorry, you are correct, with respect to Meyer's referring to the entire genome.
Meyer's was indeed referring to the entire genome. However, you're characterization is still suspect.
Functional sequence does not imply that the sequence is non-repetitive. A repetitive sequence can be functional as I pointed out with the example of the "repetitive" sequences on a CD, but moreso with DNA.
In DNA the repetitive sequences can have function but not as coding for proteins.
Repetitive sequences in the context of Meyer's other discussion with repetitive sequences was with reference to self-ordering laws.
See Sternberg's writings on repetitive sequences. Do you think the majority of repetitive sequences are non-functional merely because they don't code for proteins.
One of Sternberg's first publsihed forays into the topic was in the Annals of the NY Academy of Sceinces:
http://www.ncbi.nlm.nih.gov/pu...
But it may not be that junk-DNA is for coding of proteins, but for other functions:
Gee, Nick, does DNA have to code for something to be functional? Yes, or no?
By the way, the sequence is functional if it yields certain physical properties which facilitate its abilty to create knots.
What if someone argued a pair of pliers is not functional nor designed because it cannot decode the Data on a CD ROM. To say DNA is non-functional merely because it does not directly code for something is an similarly flimsy argument.
By, the way, alternatively spliced DNA regions with multiple-meanings in a sea of repetitive elements is a compelling case for design. The presense of repetitive data in a CD-ROM does not negate the intelligent design of non-repetitive data on the CD-ROM, so it is a flimsy argument to say repetitive DNA negates the design hypothesis, especially if repetitive DNA is functional.
At best, one is left to making uncharitable readings of Meyer's work in an attempt to argue against his points.
So, Nick, are you going to argue that the majority of the genome is functionless?
Comment by Salvador T. Cordova — January 31, 2010 @ 1:23 am
January 31st, 2010 at 1:25 pm
Here are some bits of "evidence that Meyer does not understand the biochemistry…"
In Fig. 9.1, p. 206 of Signature in the Cell, illustrating the formation of a protein from amino acids, the nitrogens in the amide linkages of the resultant protein all have an extra hydrogen. The reactants are glycine molecules, but the product protein is a chain of generic amino acids: H's have been transformed into R's.
On the same page Meyer says amino acids "form peptide and nonpeptide bonds with roughly equal probability." What are these nonpeptide bonds? He does not say. The most plausible explanation I can think of is that he is referring to the two different "resonance" structures that can be drawn for the amide linkage. The one with the double bond between the C and N would be, I suppose, what he calls a peptide bond because it implies a planar arrangement for the amide linkage which is necessary for the helical structure of proteins. The other with the double bond between C and O would be the nonpeptide bond because it does imply a planar amide linkage. But these are two different, inadequate representations of the actual linkage between two amino acids. The actual structure of the amide linkage is planar, a sort of average of the two representations with the pi part of the double bond extending over the three atoms, O, C, and N. So there is only one way, not two different ways, in which the amide linkage can be formed (excluding reactions with the side chains). And then Meyer's probability of (1/2) raised to the 149th power should really be 1.
Comment by jospbevak — January 31, 2010 @ 1:25 pm
January 31st, 2010 at 2:13 pm
[...] of Signature in the Cell wrote Response to Darrel Falk’s Review of Signature in the Cell. A prior post focused on the first few paragraphs. Continuing with the article: Falk first cites a scientific [...]
Pingback by Slicing and Dicing Falk: Part Two - Telic Thoughts — January 31, 2010 @ 2:13 pm
January 31st, 2010 at 2:52 pm
By the way Nick, if I were you, I wouldn't be too quick to attempt refutations by suggesting others don't understand something, lest it be used against you.
Let me remind the readers of a pretty good take down of some writings you co-authored in 2004 in response to Meyer's article on the origin of biological information.
http://www.discovery.org/a/224...
It would more kind of me to say you misunderstood the subject matter and relevent literature and resorted to faulty logic rather than attribute what you wrote to willful distortion and dishonest arguments and other nefarious motives.
Perhaps it is better to stick to the arguments put forward by Meyer rather than try to make inferences about his level of understanding. That leads to needless sideshows, unless of course a sideshow is one's best defense because one lacks substantive counter-arguments to Meyer's thesis.
Comment by Salvador T. Cordova — January 31, 2010 @ 2:52 pm
January 31st, 2010 at 7:01 pm
OK, Sal, so you admit error and now agree that Meyer actually was referring to the entire genome. Now we just have to get you to agree that repetitive sequence cannot have dense information content — Meyer himself says at numerous points that repetitive sequences have low information.
But Meyer asserts that the genome is densely packed with information, despite being ~50% repetitive:
The sorts of "functions" you cited, Sal, are not sequence-specific, they just depend on a certain bulk of DNA. Meyer says information = specific function sequence. If any old sequence will do, there is not much information there.
And in fact, that 50% of the genome (and probably more) is repetitive elements that are just the kind of thing that is known to accumulate by mutation.
Comment by nickmatzke — January 31, 2010 @ 7:01 pm
February 1st, 2010 at 11:14 am
nickmatzke-
You are misrepresenting what Meyer is saying. He explains what he is talking about in the pages after your quote-mine 462-77
For one the densely packed information is that one gene can code for more than one product- messages within messages.
He also discusses SINEs and LINEs, which he states have a function.
Comment by ID guy — February 1, 2010 @ 11:14 am
February 1st, 2010 at 11:37 am
You mean like this?
Disulfide bonds? Hydrogen bonds?
Comment by ID guy — February 1, 2010 @ 11:37 am
February 1st, 2010 at 12:19 pm
I try to admit my errors when I think I've made one. I admit my error regarding "vast".
Are you willing to admit error when you're wrong?
I've not seen many if any retractions from you when you make errors, such as your 2004 GME offerings. Are you prepared to admit error in case you make a mistake?
Wrong. Different seqences may not result in proper physical properties (such as the ease of making knots). You might not want to make that argument. Also, if the reading and decoding machinery is optimized to read and write such sequences, you might not want to reconsider your claim.
50% repetitive is not completely repetitive. Meyer was referring to completely repetitive sequences. His examples of repetitive show the entire sequence as repetitive. Are you saying the entire genome is repetitive?
Even in meyer's example, of jones and smith there is the repetitive sequence "555". That is 27% of the string being repetitive. Are you going to argue that Meyer is improperly calling the string complex or that the string is not really complex because 27% of the string is repetitive?
A phone number like 1-800-800-8000 has repetition, but it is functionally specific. Try calling the number several time if you doubt its specificity.
Functional information is not the same as algorithmic or shanon information. For example, a screw might be considered to have high functional information (due to high specificity), even though it can be described in an algorithmically simple way. Same with a VLSI circuit.
You conveniently left out Meyer's discussion of functional specificity on pages 109 and 110.
You also failed to point out Meyer's examples of repetitive are completely repetitive, while yours are cherry picked.
To your credit, I'd recommend the presentation in Signature be re-vised. However, your claim that Meyer's doesn't understand the existence of SINEs and LINEs is weak since he describes their funciton and their importance in creating organization on page 468.
If repetitive sequences serve as Bar Codes, then like the "repetitive" number "555", they are part of a complex sequence, and thus one can't really argue the sequnce on the whole is non complex. One can even argue the information is densely packed because of specific function.
By your line of argumentation, a 700 meg CD ROM containing only 50 megs of data is not complex because of the abundance of zeros.
Comment by Salvador T. Cordova — February 1, 2010 @ 12:19 pm