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On Deciphering the Signature

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September 12, 2011 Tags: Design

Today's entry was written by Darrel Falk. You can read more about what we believe here.

On Deciphering the Signature

Steve Meyer has responded to Dennis Venema’s review1 of his book Signature in the Cell in the September 2011 issue of Perspectives on Science and the Christian Faith (PSCF) (63:171-182). Although, Dennis has ably responded (63:183-192), I would like to address one specific aspect of Meyer’s response, especially since it relates to the final paragraph of my initial essay regarding the book and Dennis’s six part series on the BioLogos website.

BioLogos has dealt fairly extensively with what we thought was the basic premise of Signature in the Cell. I had read the book carefully and I know Dennis did as well before we responded. I sincerely thought that the heart of Meyer’s argument is summarized in the following three quotes from the book:

1. “So the discovery of the specified digital information in the DNA molecule provides strong grounds for inferring that intelligence played a role in the origin of DNA. Indeed, whenever we find specified information and we know the causal story of how that information arose, we always find that it arose from an intelligent source. It follows that the best, most causally adequate explanation for the origin of the specified, digitally encoded information in DNA is that it too had an intelligent source. Intelligent design best explains the DNA enigma” (p. 347, emphasis added).

2. “Since, as argued in Chapters 8 through 15, intelligence is the only known cause of large amounts of specified information, the presence of such information in the cell points decisively back to the action of a designing intelligence” (p. 382, emphasis added).

3. “Because we know intelligent agents can (and do) produce complex and functionally specified sequences of symbols and arrangements of matter, intelligent agency qualifies as an adequate causal explanation for the origin of this effect. Since, in addition, materialistic theories have proven universally inadequate for explaining the origin of such information, intelligent design now stands as the only entity with the causal power known to produce this feature of living systems.” (p. 386, emphasis added).

So we at BioLogos have always thought that if mainstream science demonstrated an increase in “complex specified information” (CSI) without needing to invoke supernatural intervention, Meyer’s assertion that “intelligence is the only known source of such information in the cell” will have been refuted at the scientific level. It sure seemed to me that this is what he said in the above quotes.

With that in mind, we’ve put a great deal of effort into showing a number of cases in the lab and in nature where scientific data have provided very strong evidence for increased CSI which is entirely consistent with how we scientists would define “natural explanations.” All this time, starting with my first essay almost two years ago, we sincerely thought we were engaging Meyer’s book on Meyer’s terms.

But now, in his PSCF article, Meyer states that arguments based on examples of increased CSI don’t count if they occur after life began on Earth.

Signature in the Cell argues, first that no purely undirected physical or chemical process—whether those based upon chance, law-like necessity, or the combination of the two—has provided an adequate causal explanation for the ultimate origin of the functionally specified biological information. In making that claim, I specifically stipulate that I am talking about undirected physical and chemical processes, not processes (such as random genetic mutation and natural selection) that commence only once life has begun. Clearly material processes that only commence once life has begun cannot be invoked to explain the origin of information necessary to produce life in the first place) (pp. 173-174, Perspectives on Science and Christian Faith, Sept. 2011, emphasis added).

Since I had read the book very carefully, and have gone over it many times since, I was amazed that I could have missed this stipulation. Again, he says: “I specifically stipulate that I am [not] talking about … processes (such as random genetic mutation and natural selection) that commence only once life has begun.”

Did he really specifically stipulate that? Have we been barking up the wrong tree all this time? While we knew the main focus of Meyer's book was the origin of life (not mechanisms of evolution), his argument clearly stated, we thought, that no large increase in CSI (Complex Specified Information) had ever been demonstrated without the need to invoke intelligence. Period.

I went back through my well-marked up copy of the book again, re-examining each section in which he wrote about increased CSI. Despite my best efforts, I could not find the stipulation he mentions in the PSCF article. Still, thinking I had missed it, I spent $15 for an electronic version of the book—one that would allow me to identify every time the word “mutation,” or natural selection” appeared—anything that would help me find his stipulation. I couldn’t find it.

Actually I thought Meyer was pretty clear and highly specific in his book. Consider this scientific challenge on page 429:

If, for example, someone successfully demonstrated that "large amounts of functionally specified information do arise from purely chemical and physical antecedents," then my design hypothesis, with its strong claim to be the best (clearly superior) explanation of such phenomena, would fail.

Find a case where a large amount of CSI has accumulated without needing to invoke intelligence, and his argument, Meyer said, fails. This is a strong statement, clearly worded, and there is no hint of Meyer’s stipulation that it doesn’t count if life has already begun. In Dennis Venema's BioLogos blog series, he showed many cases where there were large increases in CSI (whole genome duplication, for example) without needing to invoke that supernatural intervention was necessary to create it. Chromosomes, the cell division machinery, and nucleotides are “purely chemical and physical antecedents.” The information content in the genome, Venema showed, quadrupled early in vertebrate history through material processes that we know and understand well. Did this not meet the scientific criteria that Meyer specifically called for?

I don’t know how misunderstandings like this happen. I believe that Stephen Meyer, who I consider to be a friend and colleague, thinks the stipulation exists in his book and that he worded it clearly. I assume he thinks it was implied in some overarching statement that I have not been able to find. I also think he believes he was clear. Unfortunately, clear he was not. I’ve looked thoroughly and I have not been able to find his stipulation.

In post after post, we have set out to demonstrate the scientific case we thought Meyer called for. Then in the end, it sure seems to us, that the rules changed, even though Steve feels they were written in his book all the way along.

Still, let’s move on. Let’s play by the new rule and let’s define it carefully.

So here’s the rule as I now understand it: If large increases in CSI can be demonstrated without the need to invoke an external intelligence, “then [Meyer’s] design hypothesis with its strong claim to be the best (clearly superior) explanation of such phenomena, would fail.”

Having stated the rule, we have to make two exceptions (Meyer himself made Exception #1 clear in Chapter 13; Exception #2 is the new stipulation we've been discussing):

Exception 1. We can’t count large increases in CSI which develop as a result of computer programs because minds designthe program parameters.

Exception 2. We can’t count large increases in CSI which develop in the history of life, because DNA was necessary to set those processes in motion.

So what can we count? Until he clarified the existence of Exception #2, I thought any general increases in CSI would count. However, it is now very hard for me to imagine any increase in information that would not be categorized within either Exception 1 or Exception 22. The only thing left that doesn’t fit into one of these two exceptions is the origin of life itself. The point of the book, I thought, was to bring other examples of increased CSI to bear on this very question.

With Meyer’s exceptions and the inability to bring general CSI increases to bear on the origin of life question, we also no longer have “positive3 experiments [which] provide causal adequacy of intelligent design” (p. 335, emphasis added).

So what are we left with? Are we not simply left with the question of whether the origin of life experiments show that information-rich molecules will arise in a test tube from chemicals off the shelf? Dr. Meyer, I think, says no, for reasons that are no longer clear to me other than that he’s given up on the science. I, on the other hand say, “Wait a while. Let the science play itself out before a scientifically based decision is made.” To be frank though, I am a little concerned that even if the right mix of materials is found to produce molecules that can spontaneously assemble in a manner that gives rise to complex specified information, Dr. Meyer or those who follow him will say, “Sorry, you can’t count that because it took a mind to create the conditions and it took a mind to mix them together in a test tube.” And with that we’ll have a new stipulation which most likely was in some manner implied in Signature in the Cell to begin with.4

The interesting thing about this is that Steve Meyer and I are probably really in almost the same exact position when it comes to our core beliefs. Obviously as fellow Christians, we both believe that there is a Mind behind the process. We both think that the history of life with its constant increase in complex specified information is a product of the activity of God. We both stand amazed at the majesty of creation and our love for the Creator who is personally involved not only in our own individual lives but those of our families and faith communities as well. We differ primarily in one regard. Steve thinks he has shown through scientific analysis that this Mind we both believe in must have been present and supernaturally active in the creation of information. I think the Mind (God) was present, but I can’t put the existence of God into a scientific experiment to demonstrate God's activity. Furthermore, unlike Steve, I have no pre-conceived ideas about whether God's,supernatural activity was necessary for creation of information. God, as I see it, may have chosen to create information bearing molecules indirectly through God’s natural activity in a manner that is analogous to the development of a baby or the growth of a tree from a seed.

In the end, our difference is simple, he thinks that the test tubes won’t ever deliver information rich molecules and I think it is too early to say. He has declared the matter more or less settled on the basis of scientific analysis. I consider the matter fully unsettled. But the most important thing of all has been settled and on this we both agree. This Mind we speak of is God’s Mind--God's Holy Spirit. That Spirit not only fills all of creation, but more specifically that Spirit fills us with his Presence and envelopes us in his love. This is cause for celebration and, with "sandals off," we each bow our heads in humble worship. Truly, we--all of us--are standing on holy ground.

Notes

1. Perspectives in Science and Christian Faith 62:276
2. Note to Steve: Does not the human brain count within Exception #2? After all, it arose in the history of life and its development depends upon DNA. If so, you might need an exception to the exception.
3. The term “positive” is used 21 times in the book. It is clearly important to the author that the evidence for intelligence associated with the origin of DNA be viewed not as absence of contrary evidence, but rather a piece of convincingly positive evidence that hinges upon the fact that CSI in general, can’t be built without a mind.
4. I’m really not trying to be facetious here. I really do think that’s what would happen. I can almost draft the stipulation now.


Darrel Falk is former president of BioLogos and currently serves as BioLogos' Senior Advisor for Dialog. He is Professor of Biology, Emeritus at Point Loma Nazarene University and serves as Senior Fellow at The Colossian Forum. Falk is the author of Coming to Peace with Science.


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Bilbo - #64774

September 16th 2011

Open,

Also, you point out major differences between prokaryotic and eukaryotic repair mechanisms.  Do we know that the latter evolved by Darwinian processes from the former, or do we just assume that they did so?


Kirk Durston - #64778

September 16th 2011

Glen Davidson wrote, “because evolution simply evinces no evidence of intelligence working, ... Just thought I’d add to your disanalogy to emphasize the importance of evolution as an explanation for facts that ID generally ignores—for good reason.”

 

Glen, the revision of existing code is not what Meyer and I are talking about. I believe that Meyer is talking about how the code got there in the first place. It is the elephant in the room. To say that ‘evolution simply evinces no evidence of intelligence working’ is to ignore the elephant ..... where does the functional information come from to begin with? It is an empirical fact that intelligence can produce functional information. I’m afraid the intelligence option is the only serious, testable, empirical candidate we have on the table. Some hold forth a promissory note with the hope that science will discover a non-intelligent method to produce functional information, but until science does, we only have one candidate on the table right now .... we know intelligence can produce functional information.

 

I would say that ID science explains the facts (current observations of genetic change) far better than Darwinian theory when it comes to what is going on with the software of life. ID theory holds that the functional information for life was frontloaded in the past, possibly in several, unique multiple packages, and everything unpacked from there. There has been no tweaking since, so the functional information will slowly run down. Darwinian theory states that we started with zero functional information and steadily increased to what we have today. Thus we have two competing core predictions:

 

1.  DarPred: functional information steadily increases over time

 

2. IntelPred: functional information steadily deteriorates over time

 

I would suggest that science is pointing in the direction of IntelPred on this prediction and DarPred is consistently being falsified. There is evidence that the entire prokaryote genome is slowly deteriorating (see Mira, A.; Ochman, H.; Moran, N.A. 2001, Deletional bias and the evolution of bacterial genomes, Trends Genet, 17, (10) 589-96.) There is evidence that the drosophila genome is also deteriorating (see Petrov, D.A.; Hartl, D.L. 1998, High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups, Mol Biol Evol, 15, (3) 293-302.) A colleague of mine tells me that his own research is indicating that the arabidopsis genome is also running down. So a core prediction of ID is being verified and its competing prediction DarPred is being falsified.

 

The primary point that I am making, and that I think Meyer is making (as I said earlier, I have not read his book, just the response above) is that functional information is a fingerprint of intelligence (see my hypothesis in my initial post). When we look at life, the fingerprints of an intelligent origin are all over the genomes of life. The hypothesis I advanced in my first post states that functional information is a unique characteristic of intelligence. So if we find the genomes of life covered with the fingerprints of intelligence, we have good, empirical reason to conclude that life had an intelligent origin. This is no different from forensic science.

 

 


Glen Davidson - #64780

September 16th 2011

Glen, the revision of existing code is not what Meyer and I are talking about.”

br>
It was what Beaglelady was talking about.  It also is what Meyer was talking about, only not being the slightest bit upfront about it, rather conflating the two throughout the book.
br>
 I believe that Meyer is talking about how the code got there in the first place.  It is the elephant in the room.”
br>
There’s nothing new about abiogenesis being an issue, nor about the origins of other aspects of life that may not have appeared immediately.  Unfortunately, Meyer also conflates what are likely evolutionary developments of information with abiogenesis, which is not acceptable.  Anyway, there are indications of the evolution of the code, mentioned at the beginning of my Amazon review of SITC:
br>
http://tinyurl.com/3hog6ur
br>
And, importantly, there’s no indication of intelligence affecting life at any stage, throughout evolution and to the beginning of life, aside from our slight manipulations of life.
br>
It is an empirical fact that intelligence can produce functional information.”
br>
It can also produce nonsense.  What of either?
br>
I’m afraid the intelligence option is the only serious, testable, empirical candidate we have on the table.”
br>
How is it testable or empirical?  Or even a reasonable hypothesis, given that no identifiable effects of intelligence, such as rationality and forethought, are to be found in life?
br>
 we know intelligence can produce functional information.”
br>
And?  The issue is not “functional information,” it’s the origin of life.  Obscuring that fact is a common tactic we get from ID proponents, and there’s absolutely no indication that even today intelligence could produce life de novo, or that it would do so today, let alone that it could and would billions of years ago.
br>
Glen Davidson
http://tinyurl.com/mxaa3p

Genomicus - #64830

September 19th 2011

Glen Davidson:
“Anyway, there are indications of the evolution of the code…”

Yea, but the ‘indications’ are rather weak and the bulk of the scenarios on how the genetic code could have arisen through non-teleological mechanisms ignore the problem of how the genetic code got to be so optimal in the pattern of which codons code for what amino acids. The default explanation for the origin of the genetic code is not non-teleology. The default explanation is teleology, because, putting the genetic code aside for the moment, every single code is the product of a mind. Just because one might have a non-teleological explanation for, say, a metallic pyramid-shaped object floating in space doesn’t mean that that’s how that object arose.

And,
importantly, there’s no indication of intelligence affecting life at
any stage, throughout evolution and to the beginning of life, aside from
our slight manipulations of life.”

Actually, there are clues that intelligence manipulated parts of life during its history. The bacterial flagellum, for example, is a pretty nice chunk of evidence that some intelligence(s) manipulated life in the past, because the presence of extremely specified molecular machines all point to a teleological origin.

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Glen Davidson - #64857

September 20th 2011

“Yea, but the ‘indications’ are rather weak and the bulk of the scenarios on how the genetic code could have arisen through non-teleological mechanisms ignore the problem of how the genetic code got to be so optimal in the pattern of which codons code for what amino acids.”

At least we have indications of the evolution of the code.  Your side has no evidence for design of it.

And what’s so optimal about it?  I think that something so old and ubiquitous could be expected to be fairly efficient, but apparently later amino acids like pyrrolysine and selenocysteine are kludged into the code.  No apparent foresight there, nor even a clever redesign as one might expect of an intelligent agent.

“The default explanation is teleology, because, putting the genetic code aside for the moment, every single code is the product of a mind.”

Please, the mere fact that both Morse code and the genetic code can be called “codes” doesn’t mean that they’re more than barely comparable.  One is based upon clearly human activity, and the other has nothing to do with human creation.  Pretending that “God” is a logical inference because it’s clearly not human isn’t thought, it’s wishful thinking.

“The bacterial flagellum, for example, is a pretty nice chunk of evidence that some intelligence(s) manipulated life in the past, because the presence of extremely specified molecular machines all point to a teleological origin.”

How?  What’s teleological about it, what indicates anything but the usual slavishly derivative nature that evolution predicts and intelligence would not be expected to do?

Glen Davidson
http://tinyurl.com/mxaa3p


Glen Davidson - #64781

September 16th 2011

Continuing from above:


I would say that ID science explains the facts (current observations of genetic change) far better than Darwinian theory when it comes to what is going on with the software of life.”
br>
Only if you don’t bother with matching up cause and effect, as real science does.
br>
ID theory holds that the functional information for life was frontloaded in the past, possibly in several, unique multiple packages, and everything unpacked from there.”
br>
ID apologetics comes up with events willy-nilly, without bothering to explain anything.  Real theories effect entailments, not mere flights of fancy like ID does.
br>
The primary point that I am making, and that I think Meyer is making (as I said earlier, I have not read his book, just the response above) is that functional information is a fingerprint of intelligence (see my hypothesis in my initial post).”
br>
I have read his book, and found it to be very improper in how it hides facts until after the “discussion” of their relevant context is already past.  And functional information is not a fingerprint of intelligence until that is determined to be the case.  That you and Meyer merely assume it prior to even asking the questions that could determine it indicates that you are interested in shoring up your beliefs, not in investigating the issues.
br>
The hypothesis I advanced in my first post states that functional information is a unique characteristic of intelligence.”
br>
That’s not a scientific hypothesis, as it’s not based upon observation.  It’s based merely upon a strain of apologetics that dearly wishes it were so.
br>
The fact that you don’t look for the fingerprints of intelligence that we actually recognize in archaeology and which we would recognize in alien machines, notably rationality, indicates that you wish merely to redefine “design” to fit the facts of life, rather than to properly look for real indicators of intelligence.

Kirk Durston - #64783

September 16th 2011

Glen Davidson, from reading your comments above, it appears that you are engaged at an emotional level, but not at an intellectual level. To make your contribution more productive, I would suggest that you read those first three papers on functional information/functional complexity, as well as the one by Abel and Trevors on sequence complexity. We can then discuss the subject of functional information and biopolymers more knowledgeably and productively and with a little more depth.


Glen Davidson - #64784

September 16th 2011

Glen Davidson, from reading your comments above, it appears that you are engaged at an emotional level, but not at an intellectual level.”

br>
As much evidence is given for that as for all of the rest of your presuppositional apologetics.
br>
I have no reason to respond further to such unreasoning attacks.
br>
Glen Davidson
http://tinyurl.com/mxaa3p

beaglelady - #64787

September 16th 2011

Glen Davidson, from reading your comments above, it appears that you are
engaged at an emotional level, but not at an intellectual level.


In other words, Glen actually read the book!

As for the “software of life” being front-loaded, why would that be? Was the master programmer planning to leave the company all along, perhaps leaving junior programmers the task of running the show, timidly commenting out code they don’t really understand?


Kirk Durston - #64819

September 19th 2011

What Venema and other contributors to Biologos such as Randy Isaac need to do when writing about the kind of information found in the genomes of life, is to stay current with the science. Old notions of information as laid out by Claude Shannon, Kolmogorov and others do not distinguish between meaningless gibberish and functional information. But for biology, it makes a great deal of difference whether a sequence is functional or not; that is an important point that Szostak laid out. That is precisely why ‘functional information’ was proposed by Jack Szostak in 2003 and that is where the attention of subsequent papers is shifting to (for a simple, non-technical and easy to read one-page article, see
Szostak, J.W. 2003, Functional information: Molecular messages, Nature,
423, (6941) 689. ). Venema’s belief that duplication results in an increase in information reveals that he is either not current with the concept of functional information in biopolymers as laid out in the current scientific literature, or he does not understand it. His refutation of Meyer’s discussion of CSI, therefore, does not succeed.


Genomicus - #64831

September 19th 2011

Another response to Glen Davidson:

How
is it testable or empirical?  Or even a reasonable hypothesis, given
that no identifiable effects of intelligence, such as rationality and
forethought, are to be found in life?”

Well, actually, rationality and forethought are definitely found in parts of life. The genetic code has exact aspects of rationality: it is an optimal code. It is a well-designed code, so as to minimize the harm of deleterious mutations. And it has aspects of foresight: the genetic code is able to be implemented in fruit flies, apes, bacteria, mice, fish, reptiles, birds, bees, etc. In other words, when the genetic code first appeared in life, it was “right from the start.”

Also, consider the bacterial flagellum: it is clearly designed rationally. In fact, its rational design is a bit difficult to explain using non-teleological mechanisms. And yes, I know you’re going to respond with the same tired ole’ arguments about pseudogenes, introns, inverted retinas, etc. But this argument ignores the possibility that only parts of life arose through a teleological mechanism.

Anyways, the point is this: features of life do display signs of rational design and foresight.

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John - #64839

September 19th 2011

The genetic code has exact aspects of rationality: it is an optimal code.”

br>
Well, actually, it isn’t.
br>
“It is a well-designed code,...”
br>
Well, actually, it isn’t. I can easily get you to praise one feature of the code as well-designed, but you won’t be able to explain why the same feature is lacking in another aspect of the code. You will simply conclude that I am an evil person for pointing this hypocrisy out to you.
br>
”... so as to minimize the harm of deleterious mutations.”
br>
Sorry, but that phrase makes no sense. If a mutation is deleterious, by definition it causes harm.
br>
“And it has aspects of foresight: the genetic code is able to be implemented in fruit flies, apes, bacteria, mice, fish, reptiles, birds, bees, etc. In other words, when the genetic code first appeared in life, it was “right from the start.” ”

So how do you explain the exceptions to its universality?
br>
“Also, consider the bacterial flagellum: it is clearly designed rationally.”
br>
No, it clearly isn’t. Moreover, you’ve never considered “the bacterial flagellum” as there is more than one. What you are doing is deliberately deceptive. You are claiming that you’ve considered a flagellum when in reality you’re only regurgitating hearsay ABOUT one of the bacterial flagella.
br>
Why not consider the other one? What about eukaryotic flagella? 

Glen Davidson - #64858

September 20th 2011

“Well, actually, rationality and forethought are definitely found in parts of life. The genetic code has exact aspects of rationality: it is an optimal code. It is a well-designed code, so as to minimize the harm of deleterious mutations.”

What does optimization (and by what criteria could the genetic code even be considered to be optimal?) have to do with rationality and forethought?  Bird wings are exceedingly well optimized for each bird species’ lifestyle, and they remain merely modified dinosaur forelimbs.  Optimization is not possible in all evolutionary cases, yet in other cases it’s more or less the norm.

“so as to minimize the harm of deleterious mutations.”

Oh, so the fact that it’s more tolerant of mutations than it might be is somehow the mark of a designer, rather than the expectation of evolution?  As usual, ID supplies no evidence, it merely tries to take good aspects of life and pretend that this means “design.”

“And it has aspects of foresight: the genetic code is able to be implemented in fruit flies, apes, bacteria, mice, fish, reptiles, birds, bees, etc. In other words, when the genetic code first appeared in life, it was “right from the start.” “

The genetic code is evolvable.  Huh, I wonder how this points to foresight or rationality?  Indeed, why do we have two slightly different genetic codes, one in the nucleus and one in our mitochondria?  Evolution gives us a very good endosymbiotic with extensive modification scenario for this, while it looks rather unlike what an actual designer would effect.

And where was the foresight in coding for pyrrolysine and selenocysteine?  These kludges work, but only as one would expect of evolution, not of some exceedingly intelligent being.

“Also, consider the bacterial flagellum: it is clearly designed rationally.”

Said like a true IDist.  No evidence for design, it’s just “clear” that it was “designed rationally.”  Why the many homologies, then?  Why would any designer take code for something else, rework it extremely, and yet leave the remnants of its ancestry behind?  It would require extreme intelligence to do that—no human is capable of any such feat today—and yet beginning from first principles would almost certainly be the better idea.

More importantly, what was the bacterial flagellum designed for?  To infect humans?  To live in warm little ponds?  To serve as viral hosts?  Why doesn’t the general lack of purpose of bacteria, along with their adaptations, concern you?  Bacterial flagella were designed in order to eat the dead, infect humans, and keep viruses replicating, or what?  Notably, the patterns of feeding by bacteria fit what one would roughly expect from evolution, and seem to serve no purpose of some supreme mind.

Why do the flagella of archea, eukarya, and bacteria all diverge markedly, as expected by evolution?  Possibly eukarya do better with our flagella, but surely archea would do well with bacterial flagella, and vice versa.  Whether or not these two fairly different flagella arose from a common ancestor isn’t certain, but, in any case, they are quite different, when there is no design reason for this to be so, only evolutionary reasons for it.

“And yes, I know you’re going to respond with the same tired ole’ arguments about pseudogenes, introns, inverted retinas, etc.”

No, you already ignored my point, that flying vertebrates don’t share any common design, rather are modifications of their ancestors forelimbs.  You also happily ignore the fact that the same is true of archeal, bacterial, and eukaryotic flagella.  The patterns are clearly evolutionary, not due to functional design.

“Anyways, the point is this: features of life do display signs of rational design and foresight.”

You haven’t done the least to back up that claim.  The patterns are evolutionary as expected, and we do not see deviations from those patterns as would be expected from design.

Glen Davidson
http://tinyurl.com/mxaa3p


Genomicus - #64856

September 20th 2011

Well, actually, it isn’t. I can easily
get you to praise one feature of the code as well-designed, but you
won’t be able to explain why the same feature is lacking in another
aspect of the code. “

Feel free to point out exactly where the genetic code displays irrational design.

So how do you explain the exceptions to its universality?”

Oh, so some life doesn’t use the genetic code? What do these life forms you speak of use? Maybe a molecule built around di-nucleotide codons instead of codons made up of three nucleotides?
  I venture to guess that you’re talking about life forms that have effectively reassigned which codons code for which amino acids. However, this only strengthens the case for the statement I made that the genetic code can be used by all types of life forms, from unicellular bacteria to multicellular animals like whales. The code can even be modified to fit a population’s specific needs; it can be modified to the point where a population can, through the elegance of the Darwinian mechanism, reassign which codons code for which amino acids. The genetic code is still universal though, in the sense that all organisms use tri-nucleotide codons which prescribe amino acids to construct proteins. And the same four bases are used in every single organism.

No, it clearly isn’t. Moreover, you’ve
never considered “the bacterial flagellum” as there is more than one.
What you are doing is deliberately deceptive. You are claiming that
you’ve considered a flagellum when in reality you’re only regurgitating
hearsay ABOUT one of the bacterial flagella.”


I’m talking about the core components shared by all bacterial flagella. The structural arrangement of the core components shared by all bacterial flagella is a rational design. Not only does Darwinian evolution have difficulty accounting for the origin of the core structure, it also has difficulty in explaining the rational design that is seen in the core components of bacterial flagella.


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Papalinton - #64862

September 20th 2011

Kirk Durston:  “I believe that Meyer is talking about how the code got there in the first place. It is the elephant in the room. “


Oh Dear!  Right from the get-go of this thread the ‘god of the gaps’ has raised its head above the parapet.  The code didn’t just pop in there.  It isn’t the elephant in the room you teleologically imagine it to be. The ‘code’ [for want of a better word] was gradually accreted,  bit by bit, through every trial and countless errors being made as the earliest  self-replicating success of the naturally-derived organism evolved and accumulated and coalesced miniscule other bits that gave it a greater chance of success to continue replicating while other simultaneous trials simply fizzled out.  And this process has been seamlessly going on for billions of years.  We know the end product of the evolutionary process was successful as we, today,  stand as testament to its replicative history.  It is simple as that. 

And we know that replication is both an organic and inorganic natural occurrence. If inorganic material can replicate naturally [formation of crystals, compounds, etc] then the process of replication is perfectly normal to apply to organic compounds. Indeed organic/inorganic compounds are simply varying descriptors of the range of natural chemical processes that produce the environment we find ourselves in.

There is far more transcendent meaning and deep value for this world and our existence and relationship in it through what humanity has discovered, than spinelessly and cravenly forfeiting the story of our origins to some other-world agency.

Genomicus - #64866

September 20th 2011

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Response to Glen Davidson:

>> At least we have indications of the evolution of the code. <<

Not really. Keep in mind that experimental support for the hypothesis that, for example, ribozymes could function in a pre-biotic context (e.g., as catalysts) does not mean that ribozymes did function in a pre-biotic context. What actual evidence do you have that the genetic code did evolve through a non-teleological mechanism? I would be interested in seeing this evidence. I am not aware of any phylogenetic evidence whatsoever that would indicate that the genetic code evolved from some sub-optimal, simpler code – and phylogenetic evidence would offer the most persuasive argument in favor of viewing the genetic code as evolved. That there are no simpler, sub-optimal precursor genetic codes that predate the current genetic code is interesting, to say the least.

 

>> And what’s so optimal about it? <<

 

From Freeland et al., 2000:

“Here, we show that if theoretically possible code structures are limited to reflect plausible biological constraints, and amino acid similarity is quantified using empirical data of substitution frequencies, the canonical code is at or very close to a global optimum for error minimization across plausible parameter space.”

 

In other words, the genetic code is optimal in its error minimization capability. Consider what would happen if, for example, the four codons that code for glycine were arbitrary. In other words, instead of GGU, GGC, GGA, and GGG coding for glycine, what if GGG, AGU, CAU, and UUC were the codons that encoded glycine. In such a situation, synonymous mutations would be extremely rare, and non-synonymous point mutations would be extremely common, increasing the likelihood that a mutation in any one of the codons that (hypothetically) encoded glycine would result in a radically different amino acid. This would mean that protein folds would be constantly disrupted by just about every single point mutation. In the above scenario, the genetic code is not optimal. Of course, as the peer-reviewed literature has argued, the real genetic code is extremely optimal in the context of error minimization.

 

Oh, but it goes deeper than that. The abstract of a peer-reviewed paper by Itzkovitz and Alon (2007) states that:

“DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These ‘parallel codes’ include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.”

 

Thus, the optimality of the genetic code extends deeper than the level of error minimization: the identity of the stop codons further optimizes the genetic code. Of course, the non-teleologists can always argue that all of this surprising optimality arose through processes like random mutation and natural selection. But there are severe obstacles for that supposition. The teleological explanation is much better. The argument that we teleologists have no evidence that the genetic code was designed by a teleological mechanism is as absurd as suggesting that since we have no evidence that, say, a hypothetical metallic, pyramid-shaped object floating in space was intelligently designed, then we should conclude that it was produced by non-teleological mechanisms.(contd)


 

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Glen Davidson - #64871

September 20th 2011

>> At least we have indications of the evolution of the code. <<
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Glen Davidson - #64872

September 20th 2011

>> At least we have indications of the evolution of the code. <<
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Glen Davidson - #64873

September 20th 2011

>> At least we have indications of the evolution of the code. <<
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Glen Davidson - #64874

September 20th 2011

I’ll try again, but obviously this hasn’t been working well for me.
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>> At least we have indications of the evolution of the code. <<
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Glen Davidson - #64877

September 20th 2011

>> At least we have indications of the evolution of the code. <<
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John - #64917

September 22nd 2011

“Keep in mind that experimental support for the hypothesis that, for example, ribozymes could function in a pre-biotic context (e.g., as catalysts) does not mean that ribozymes did function in a pre-biotic context.”


Are you keeping in mind the experimental support for the RNA World hypothesis in the realm of the most important ribozyme in your body?

Clearly your hero Meyer couldn’t explain it because his book conceals it from the reader. I don’t buy that it was an error.

Do you know to which ribozyme I refer?

“What actual evidence do you have that the genetic code did evolve through a non-teleological mechanism? I would be interested in seeing this evidence.”

Please stop with the falsehoods. You aren’t interested in seeing any evidence. You’re only interested in hearsay.

“From Freeland et al., 2000:

“Here, we show that if theoretically possible code structures are limited to reflect plausible biological constraints, and amino acid similarity is quantified using empirical data of substitution frequencies, the canonical code is at or very close to a global optimum for error minimization across plausible parameter space.””

br>

How can you claim to be interested in evidence when you are lazily quote-mining abstracts?

br>

They go on to write,

Although significantly better codes do exist under some assumptions, they are extremely rare and thus consistent with reports of an adaptive code: previous analyses which suggest otherwise derive from a misleading metric. However, all extant, naturally occurring, secondarily derived, nonstandard genetic codes do appear less adaptive. The arrangement of amino acid assignments to the codons of the standard genetic code appears to be a direct product of natural selection for a system that minimizes the phenotypic impact of genetic error.”

span class=“Apple-style-span” style=“font-family: arial, helvetica, sans-serif; font-size: 14px; line-height: 20px; “>

font class=“Apple-style-span” face=“arial, helvetica, sans-serif”>What you are doing is simply sleazy.

 

“In other words, the genetic code is optimal in its error minimization capability.”

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But that doesn’t mean that it isn’t the product of natural selection.

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“Of course, as the peer-reviewed literature has argued, the real genetic code is extremely optimal in the context of error minimization.”

br>

But the people (literature doesn’t argue, people do) who produce the evidence don’t conclude intelligent design. What makes someone like you, with a severe allergy to evidence, better informed?

 

“Of course, the non-teleologists can always argue…”

br>

The non-teleologists don’t merely argue, they test hypotheses empirically. Why doesn’t your side have sufficient faith to do the same?


Genomicus - #64867

September 20th 2011

Response to Glen Davidson:

>> I think that something so old and ubiquitous could be expected to be fairly efficient… <<

 

Yes, of course. But what is your proposed pathway for how the genetic code got to be so efficient *and* your answer to why this Darwinian pathway failed to leave any phylogenetic trace of this evolution?

 

>> but apparently later amino acids like pyrrolysine and selenocysteine are kludged into the code… <<

 

The addition of the amino acids pyrrolysine and selenocysteine does not refute the fact the genetic code is optimal. Those amino acids merely indicate that Darwinian evolution can tinker with an already-existing, optimal genetic code. As Freeland et al., 2000, note, “all extant, naturally occurring, *secondarily* derived, *nonstandard* genetic codes do appear less adaptive…” (emphasis added).

 

>> Please, the mere fact that both Morse code and the genetic code can be called “codes” doesn’t mean that they’re more than barely comparable.  One is based upon clearly human activity, and the other has nothing to do with human creation. <<

Yea, except that:

 

  1. If     SETI scientists detected a metallic, pyramid-shaped object floating in     space, they would conclude that an intelligence designed that object, even     though that object is clearly not based upon human activity. Why would the     SETI scientists conclude intelligent design in the above example?
  2. If we     found a lengthy English message encoded in a sequence of DNA (DNA     cryptographers have all the techniques to do that), we would conclude that     that message was not just an appearance of a message, but that message was     actually the product of a mind, even though no one observed that message     being placed there. Furthermore, what if we detected this hypothetical     message in DNA sequences that were several million years old? This removes     the objection that would conclude design in the above case because humans     are a known candidate for the design of that message. But if we found a     hypothetical, lengthy English message encoded in genes that had been     around for millions of years, we would still conclude that that message     was intelligently designed. Why?

 

>> How?  What’s teleological about it, what
indicates anything but the usual slavishly derivative nature that evolution
predicts and intelligence would not be expected to do?<<



Teleological mechanisms are the only known mechanisms that are capable of
producing molecular machines of the same level of functional specificity as the
core structure of the bacterial flagellum. And Darwinian evolution has not
substantially tinkered with the IC core of the bacterial flagellum.

References:

Freeland, et al. Early Fixation of an Optimal Genetic Code. Molecular Biology and Evolution, 2000, 17:511-518.

 Shalev
Itzkovitz and Uri Alon. The genetic code is nearly optimal for allowing
additional information within protein-coding sequences. Genome Res.,
2007, 17: 405-412.


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Genomicus - #64869

September 20th 2011

Response to Glen Davidson:

>> What does optimization (and by what criteria could the genetic code even be considered to be optimal?) have to do with rationality and forethought?  Bird wings are exceedingly well optimized for each bird species’ lifestyle, and they remain merely modified dinosaur forelimbs. <<

 

 

 Optimization has to do with rationality, because a rational designer would not design a sub-optimal code, so that takes care of your first question. You are suddenly shifting the topic of discussion when you argue that “Optimization is not possible in all evolutionary cases, yet in other cases it’s more or less the norm.” That’s not the *point* of our current discussion. The point is not whether Darwinian processes can produce optimal systems. The point is that, earlier, you stated that “no identifiable effects of intelligence, such as rationality and forethought, are to be found in life” and my example of the optimal properties of the genetic code is a direct answer to that argument of yours. Life *does* display signs of rationality, and one sign of rational design is that the system will be optimal so that it will perform its function in an efficient manner. The genetic code is optimal in its error minimization design, which means that its function of coding for stable, functional protein folds can be efficiently carried out – and so that genetic code does show signs of rational design.

 

>> Oh, so the fact that it’s more tolerant of mutations than it might be is somehow the mark of a designer, rather than the expectation of evolution? <<

Again, Glen, you’re shifting the topic of the discussion. The discussion is *not* whether evolution can explain the optimal properties of the genetic code. The point is whether there are signs of rational design in life, and the genetic code does show such signs in its optimal properties. Anyways, please point out where in the literature (prior to the full elucidation of its properties) Darwinian evolution predicted that the genetic code would be optimal. Darwinian evolution seems to be predicting everything these days.

 

 

>> The genetic code is evolvable.  Huh, I wonder how this points to foresight or rationality?  Indeed, why do we have two slightly different genetic codes, one in the nucleus and one in our mitochondria? <<

All organisms use the same nucleotide bases that are found in the genetic code. That populations can, through Darwinian evolution, reassign which codons code for what amino acids says nothing about the basic structure of the genetic code. I mean, what if the first genetic code had just 8 codons, so that it could code for a maximum of 8 amino acids? It is very unlikely then that complex metazoan life forms could evolve in such a situation.

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Genomicus - #64870

September 20th 2011

>> Said like a true IDist.  No evidence for design, it’s just “clear” that it was “designed rationally.”  Why the many homologies, then? <<

 Well, actually there aren’t that many homologies. Ten flagellar components are homologous to ten components found in the type III secretory system (TTSS), but we can take those homologues off the table since it’s pretty clear that the TTSS is younger than the flagellum, so the TTSS could not be a precursor to the flagellum. Then there’s the flagellar motor proteins, MotA/B, which are most homologous to TolQ/R. But the homology here might have been expected since both groups of proteins are membrane complexes, and membrane proteins often have similar patterns of amino acids. The flagellar proteins FliR, FliQ, FliP, FliK, FliI, FliF, FliE, FlhA, and FlhB seem to be essential to flagellar function and have no homologous counterparts that also pre-date the flagellar system. This means that out of ~20 flagellar proteins that are essential to flagellar function, 9 of them have no homologous precursor proteins. FliC and FlgL are homologous to each other, but they only share homologies with each other (well, FliC is homologous to a TTSS protein, but the TTSS is not a precursor system that pre-dates the flagellum), so if, for example, FlgL arose from FliC, we still have the problem that FliC has no known homologous counterpart that pre-dates the system. This increases the 9 original proteins to 10. So this means that ~50% of the core flagellar components have no known precursor homologues. The other 50% of the core flagellar components do have homologues with precursor systems, but the significance of those homologues is debatable. For example, FliG is shares only about 20% sequence similarity with MgtE, and this level of sequence similarity is in the “twilight zone” which means that it’s not certain if this is a significant homology.

 

>> Why would any designer take code for something else, rework it extremely, and yet leave the remnants of its ancestry behind?  It would require extreme intelligence to do that—no human is capable of any such feat today—and yet beginning from first principles would almost certainly be the better idea. <<

 

Well, an intelligent designer(s) has only a few thousand possible protein folds to work with, and since it is largely the protein fold that determines the function of a protein, an intelligence would be pretty much forced to re-use protein folds that are used in other biological systems. So we find that the flagellar components have a number of structural (i.e., similar protein fold) homologies with other systems, but the flagellar components don’t have too many homologues that both pre-date the system and share sequence similarity with the flagellar components.

 

>> More importantly, what was the bacterial flagellum designed for? <<

To provide motility to bacteria.

 

>> Why do the flagella of archea, eukarya, and bacteria all diverge markedly, as expected by evolution?  Possibly eukarya do better with our flagella, but surely archea would do well with bacterial flagella, and vice versa. <<

 That’s pretty debatable, actually, considering that archea have a different cellular structure than bacterial flagella. This would actually be a pretty neat research question: if you put a bacterial flagellum into organisms belonging to archea. Would those organisms function and use the bacterial flagella? My guess is ‘no.’<input id=“gwProxy” type=“hidden”><!—Session data—><input id=“jsProxy” type=“hidden”><div id=“refHTML”>
John - #64884

September 21st 2011

Genomicus:

“Well, actually there aren’t that many homologies.”

Have you looked for yourself, or are you regurgitating hearsay?

“Ten flagellar components are homologous to ten components found in the type III secretory system (TTSS), but we can take those homologues off the table since it’s pretty clear that the TTSS is younger than the flagellum, so the TTSS could not be a precursor to the flagellum.”

Why is the flagellum more special than the TTSS, Genomicus? Doesn’t going either direction kill the most basic argument of IDCreationists, who lack sufficient faith in their hypotheses to test them empirically?

”...This means that out of ~20 flagellar proteins that are essential to flagellar function, 9 of them have no homologous precursor proteins.”

Um…so what? How do you explain the other 11? What new evidence would demonstrate that you are wrong?

“The other 50% of the core flagellar components do have homologues with precursor systems, but the significance of those homologues is debatable.”

Why debatable? Why not testable?

“For example, FliG is shares only about 20% sequence similarity with MgtE, and this level of sequence similarity is in the “twilight zone” which means that it’s not certain if this is a significant homology.”

Good thing we have structural homology to consider, but I’m betting that you’re afraid to consider that—the evidence, I mean, not hearsay.

Glen Davidson - #64875

September 20th 2011

>> At least we have indications of the evolution of the code. <<
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Glen Davidson - #64876

September 20th 2011

I seem unable to respond.  Probably all right, since the usual games of ID are with what Genomicus has replied.
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Glen Davidson
http://tinyurl.com/mxaa3p

Glen Davidson - #64878

September 20th 2011

>> At least we have indications of the evolution of the code. <<
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beaglelady - #64887

September 21st 2011

What is happening to your posts, Glen? Are you pasting in a long post and having most of it disappear?  This is a terrible editor!


Glen Davidson - #64892

September 21st 2011

I don’t know.  In the last attempt I took half of a post near the limit, and I was at 21000+ characters—and nothing posted.  So I gave up.

The commenting software now is terrible.

Glen Davidson
http://tinyurl.com/mxaa3p


beaglelady - #64899

September 21st 2011

The commenting software now is terrible.

Not very intelligently designed, is it?


Ashe - #64891

September 21st 2011

 membrane proteins often have similar patterns of amino acids.

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do you have a reference? 
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 ” The flagellar proteins FliR, FliQ, FliP, FliK, FliI, FliF, FliE, FlhA, and FlhB seem to be essential to flagellar function and have no homologous counterparts that also pre-date the flagellar system. ”
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FliI and the beta subunit of F1F0-ATP synthetase has 30% homology.  It probably evolved from a primitive type III export system.
 

Kirk Durston - #64893

September 21st 2011

 

 

 

 


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Response to Paplinton:

 

I want to respond to two things, the ‘god of the Gaps’ idea, and the creative story on how the functional information for a given protein family is supposed to have arisen.

 

To label my argument for ID in biological life as a case of the ‘god of the gaps’ is either,

  1. a complete failure to grasp the argument from intelligence at even its most basic level or, if the argument is grasped, it is
  2. a dishonest, misrepresentation of the actual argument.

A ‘god of the gaps’ argument occurs when one makes the leap from ‘we have no testable, verifiable explanation for X’ to the conclusion, ‘therefore, God did X’.

 

If you will read just a few lines more of the very post from which you have quoted, you will observe that we do, in fact, have an empirical, testable explanation for the origin of functional information ..... intelligence. Every time you write a post you are demonstrating that intelligence can produce functional information. It follows that it is irrational to try to argue that intelligence cannot produce functional information, for the very act of constructing the argument is self refuting if it contains any functional information at all. So, rather than a ‘god of the gaps’ leap, we have the following ....

  1. The genomes of life contain a large amount of functional information.
  2. It is an empirical fact that intelligence can produce a large amount of functional information.
  3. Therefore, we have reason to believe that the functional information encoded within the genomes of life may have been produced by intelligence.

This is a standard form of an argument that is used throughout science that proceeds as follows:

  1. We observe effect Y.
  2. It is an empirical fact that Z can produce Y.
  3. Therefore, we have reason to believe that Y may have been produced by Z.

Note, that evidence should not be confused with proof; perhaps Y can also be produced by something unknown.

 

Now to the creative story as to how self replication with occasional errors produced the functional information coding for, say, a protein family. Essentially, what you are referring to is an evolutionary search engine that works through replication and mutation. Protein structure is determined by physics, so what an evolutionary search engine must do is search sequence space to find sequences that physics permits to fold into a stable 3D structure that also, hopefully, has a function within the evolving organism. The assumption in the creative story is that an evolutionary search engine is powerful enough to find all the thousands of protein families we observe today. Of course, science demands we must test this, otherwise, all we have is a creative story. To start with, it is helpful to know at least two things:


a. the probability of finding any sequence at all, in a single trial, that codes for an average protein

b. the total number of trials available for the search engine.

 

Since science is about testable, verifiable and falsifiable propositions, the oft repeated creative story you suggested needs to be tested, so let us start with (a) and (b). What are your estimates? I can certainly provide numbers, but since you are the one making the claim, I’d like to see your numbers and how you got them, then we can proceed from there. Science is about data, equations, numbers, so let us move beyond the creative story into the testing phase. What are your numbers?

 

 

 

 


Genomicus - #64900

September 21st 2011

John:

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>> Have you looked for yourself, or are you regurgitating hearsay? <<

Yes, I have. Specifically, I’m citing Pallen and Matzke’s 2006 paper that lists the homologues of flagellar components.

 

>> Why is the flagellum more special than the TTSS, Genomicus? Doesn’t going either direction kill the most basic argument of IDCreationists, who lack sufficient faith in their hypotheses to test them empirically? <<

I’m not sure what you mean by ‘special,’ but the flagellum is interesting because there are no plausible Darwinian pathways to account for the origin of the core components of bacterial flagella. On the other hand, the TTSS could have plausibly evolved from the flagellar export apparatus. Only a few truncating mutations, some tinkering here and there, and the TTSS could evolve from the flagellum.

 

>> Um…so what? How do you explain the other 11? What new evidence would demonstrate that you are wrong? <<

 Well, at most 11/20 of the core flagellar components do have homologues. But six of these proteins (FlgBCEFGK) only share homology with each other, so the cooption scenario doesn’t apply for these four proteins. Instead, gene duplications (and possibly protein fusions) must be invoked. For starters, this means that one of these proteins is the ‘first’ protein from which the other proteins originated, either directly or indirectly. So, this increases the number to 10 core flagellar components that have no homologues that pre-date the system. The Darwinian explanation for the shared homology between these six proteins is gene duplication, and perhaps protein fusion events.  Let us briefly consider the logistics of this scenario. FlgG and FlgF are about the same length, FlgF being ~251aa in length and FlgG being ~260aa in length. FlgC and FlgB are also similar in length, each being about 135aa in length. Finally, FlgE is 400-450aa in length, and FlgK is about 550aa in length. Thus, if the bulk of these proteins formed by gene duplication, we would expect that proteins of approximately the same size would be more similar to each other than to the other flagellar proteins. For example, in the gene duplication model, FlgG and FlgF would be expected to be more similar to each other than to the other flagellar proteins. This is because both of them are about the same size, implying that one arose from the other via gene duplication. How does this expectation fare with sequence analysis? Well, a cursory sequence analysis (using ClustalW 2.1) reveals that the alignment score of FlgG and FlgF is 26, while the alignment score between FlgG (~260) and FlgC (~130aa) is higher, the score being 29. Thus, the notion that the homology observed between FlgBCEFGK is explained by non-teleological gene duplication doesn’t seem to match our expectations – although note that I just performed a cursory analysis. Further sequence analyses would reveal if the gene duplication model fits the observations. But at the moment, the observations just don’t seem to fit the Darwinian expectations (continued below).

    
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John - #64919

September 22nd 2011

Me: >> Have you looked for yourself, or are you regurgitating hearsay? <<

Genomicus: “Yes, I have. Specifically, I’m citing Pallen and Matzke’s 2006 paper that lists the homologues of flagellar components.”


WHAT??? 

Genomicus, is English not your native language? On what planet would citing a review even slightly resemble “looking for yourself”?

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