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On Reading the Signature: A Response to Stephen Meyer

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January 29, 2010 Tags: Christian Unity

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

On Reading the Signature: A Response to Stephen Meyer

Dr. Meyer is a philosopher, not a scientist. He is eminently qualified as a philosopher. He has studied at one of the world’s greatest universities and has earned its highest degree. Dr. Meyer is also an expert in communication. Like a number of his colleagues—Phillip Johnson, Michael Behe, William Dembski and, dare I say, Ben Stein—he is a master at communicating with his audiences. His book, Signature in the Cell, is a communicative masterpiece. It is because of his skill as a communicator that he and his colleagues have been able to move mountains.

I do not believe, as Dr. Meyer asserts, that he is unqualified—quite the opposite. He is likely more qualified as a philosopher than I am as a scientist. Furthermore, I guarantee you that if I was venturing into his discipline, I would have little of value to say. Dr. Meyer has ventured into my discipline, biology. He is not highly qualified as a biologist, but he’s ventured in anyway. Fair enough. Since he is a great communicator, we should be able to analyze the quality of his arguments.

This brings me to my next point. I believe that Dr. Meyer and his colleagues are sincere. P.Z. Myers, Jerry Coyne, and John Kwok notwithstanding, these people are not out to deceive, they sincerely believe that the mountain they are trying to knock down is a figment of our imagination. The evolutionary paradigm has come about, they believe, through methodological naturalism. When scientists investigate natural processes assuming there is nothing else at work, Meyer and his colleagues believe the scientists get an incomplete picture of how the natural world works. Again, fair enough. Let us be fair too. Let’s keep an open mind.

Are you ready for my next point? Dr. Meyer and his colleagues have a view of reality which is very similar to my own. I assume, for example, that the following Scripture is as central to their existence as it is to mine:

For I am convinced that neither death nor life, neither angels nor demons, neither the present nor the future, nor any powers, neither height nor depth, nor anything else in all creation, will be able to separate us from the love of God that is in Christ Jesus our Lord. - Romans 8:38, 39

So even if I disagree profoundly with what Stephen Meyer and his colleagues conclude, I must be careful. If this Scripture is true for them too, and if they really are never separated from the love of God, then I must not separate myself from them. If I did, if I pulled away, I would be separating myself from that which matters most of all in life, staying close to God’s love. Dr. Meyer and his colleagues are smart, they are sincere, and we are all bound together within the love of God.

All of this just brings me to my next point: You can be smart, sincere, and loved, but you can also be very wrong about the interpretation of scientific data. Even smart people are sometimes wrong, especially when they venture into a new discipline, such as would happen if I, heaven forbid, tried to venture into philosophy. On page 107 of Signature in the Cell, Meyer describes “specified complexity.” DNA, he says on page 109, contains “specified complexity” because

it contains “alternative sequences or arrangements of something that produce a specific effect.” Although DNA does not convey information that is received, understood, or used by a conscious mind, it does have information that is received and used by the cell’s machinery to build the structures critical to the maintenance of life.

In Meyer’s response to my review, he made a very strong statement. I am amazed that someone who is really smart and equally sincere could make it, but here it is

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. 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. (Emphasis added)

What is he saying here? First of all he says that intelligent agents are known to produce specified complexity. Of course. But look at what he says next: “no undirected chemical process has demonstrated this power.” Surely he doesn’t mean this. Consider the generation of antibody diversity for example. When a bacterium invades the body, a process results in a whole lot of random rearrangements of DNA sequence, and this eventually produces trillions of highly specific antibodies which specifically recognize and bind to the invading bacterial cells. The antibodies are highly specified. They bind only to that one type of bacteria. We go from a state of lower complexity to higher complexity—higher specified complexity! The process that generates this specified complexity is pure chemistry. A set of random processes have generated the highly specified information required to fight the bacterial infection. Surely none of us would believe there is a little “intelligent being” in the body directing the body step-by-step to make the correct antibody. We know it doesn’t work that way. The universe of biology is full of examples of random processes giving rise to specified information. Interested readers are referred to the outstanding book, Complexity: A Guided Tour by Melanie Mitchell for a marvelous discussion of how complexity, including specified complexity in living and non-living systems can emerge without the specific design-input of an intelligence.

Now at this point, Dr. Meyer might step in and remind me of our common belief that there is a Mind who established life’s processes, a Mind whose presence is necessary to sustain the laws of the universe. Sure. We both accept that. But that’s beside the point. There are “undirected chemical processes” that produce functionally specified information. If he wants to beg the question by saying that there is a Mind that created the DNA which would ultimately cause the random processes—fine. But, if he does this, I would go back further and argue that if he is going to beg the question this way, he needs to be willing to beg the question all the way back—there could also have simply been a Mind who established the system so that DNA arose through natural undirected processes. We just don’t know how it worked. And that’s my point. The data is simply not in yet. I emphasize again, all that Dr. Meyer has done is identified an area of science that still has many unanswered questions. For sure, it is simply far too early to jump in and say: “Stop the game. You’ve lost. We’ve won. Game’s over!” This, in my opinion, is silly. Let’s just wait and see.

Just because I believe Steve Meyer and his colleagues are really smart, really sincere, and really have integrity does not mean that they cannot also be really wrong. My one hope and prayer—given that they have the first three qualities—is that the day will come when they admit the fourth holds true as well. In the meantime, I will hold them up in prayer and I know they’ll do the same for us.

I would like to thank my colleagues, Kathryn Applegate at The Scripps Research Institute, and John Oakes of Grossmont Community College for helpful comments in my preparation of this response.

We will soon publish a second response from Stephen Meyer. This one will be a follow-up to Francisco Ayala’s post of several weeks ago.


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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Nick Matzke - #3680

January 30th 2010

“The evolutionary definition of randomness is that “one of the central tenets of Darwinian evolution is that mutations are random with respect to the needs of the organism in coping with its environment””

Do you have any evidence that the mutations in the immune system cells of a rabbit developing immunity to virus A are guided towards target A?  And that the mutations in a different rabbit are guided towards a different virus B?

No.  The mutations are random.  Most of them don’t work.  Only 1/3 joinings of two antibody segments even produces a sequence that is read in-frame.  10^16 trials to generate a few good binders is not an efficient strategy.  Diseases killed rabbits (and us) all the time before modern medicine, when the immune system wasn’t fast enough.

It is true that the mutation *rate* is nonrandom, and that the immune system genes have various mechanisms to increase the rate of mutations in the developing antibody receptors.


Nick Matzke - #3681

January 30th 2010

But—*because* the process is nonintelligent—most of the mutations don’t work.  Only those few that have stronger binding proliferate.  It’s process with random trials followed by nonrandom selection, based on binding specificity.

As for the origin of the adaptive immune system’s RAG, RSS, etc., the evolutionary explanation is well-established, well-tested, and deeply embarassing to e.g. Behe at the Kitzmiller trial.  See:

Andrea Bottaro, Matt A Inlay & Nicholas J Matzke (2006). Immunology in the spotlight at the Dover ‘Intelligent Design’ trial. Nature Immunology 7, 433 - 435 doi:10.1038/ni0506-433

...and many more links:
http://www.indiana.edu/~ensiweb/evo.imm.html

But even if you (inappropriately assuming your conclusion) decide that the immune system was intelligently designed to be able to evolve specified complex sequences through random mutation and natural selection, but you refuse to believe that other forms of random mutation and natural selection cannot evolve new specified complex sequences, you’ve still got problems, because we have direct evidence that the evolution of new genes with new functionally specified sequences is easy and common for natural evolution.


Nick Matzke - #3683

January 30th 2010

E.g.:

Long et al. (2003), “The origin of new genes: glimpses from the young and old.” Nature Reviews Genetics. Freely available on google scholar, although pointing a link to google seems to be interpreted as spam…


Jonathan Bartlett - #3686

January 30th 2010

Nick -

The formation of new genes is easy *with information*.  It is not easy *in the absence of information*.  Most interesting mutations that have been found, were later found to be guided by highly specific mechanisms.  That doesn’t mean that they are 100% specific - I don’t know anyone who is claiming that.  But the question is - which side does it lean to?  Sure, it takes a lot of trials to find the right mutations within the 400 base pairs that has to be searched, but that’s several orders of magnitude easier than the 4,000,000,000 base pairs that would have to be searched without the information.  If the information was wrong, the answer would never be found, because it was searching the wrong area.  The other thing to keep in mind is that the problem is exponential.  So, if we are searching for 3 base pairs,  then the search space is 1 in 4*10^6 for the first case, and 4 * 10^30 for the second case.  That’s 24 ORDERS OF MAGNITUDE DIFFERENCE. 

In addition, remember that, because of the C region, these genes already know how to properly attach to the B cell.  Thus, the entire pathway, save one piece, already exists, and the organism is setup to search for that piece in very specific ways.


Jonathan Bartlett - #3687

January 30th 2010

Nick -

If information is in the driver seat, then it isn’t natural selection.  Natural selection is the shorthand for the modern synthesis because “natural selection” was assumed to be the driving component of innovation and direction of evolution.  However, as has been pointed out, information reduces the search space by 3,999,999,600 base pairs, and selection takes care of the remaining 400 (though the analogy to natural selection is tenuous, because it is a program, not a struggle for life, that tells whether or not the given sequence should be selected).  So, clearly, in this case, it is not “evolution by natural selection” but “evolution by information inside the organism”.  Sure, some sort of selection has a role, but it is comparatively small.  Therefore, to call this an instance of “evolution by natural selection” would be quite absurd, given how small of a role that selection of any sort plays.


Nick Matzke - #3688

January 30th 2010

Where you are getting your search space of 4 billion nucleotides from?  That’s just bizarre.  We are talking about the abilities of a natural process of trial and error to generate functionally specific sequence.  Creationists always through up chaff about the immune system, and totally ignore the mass of scientific literature showing (a) how it is a (unguided!) mutation and selection process, and (b) how the adaptive immune system itself evolved.  Scientists aren’t going to take you seriously if you just ignore the hard work produced and published by thousands of them over decades.

But like I said, if you don’t like the immune system, you still lose, because various experiments and natural examples show that the evolution of specific binding sites doesn’t require searching that big a space of variation.  It’s just not that hard.  See references here:
http://pandasthumb.org/archives/2007/10/full-text-of-th.html


Jonathan Bartlett - #3693

January 31st 2010

“Where you are getting your search space of 4 billion nucleotides from?”

The size of the human genome.

“totally ignore the mass of scientific literature”

I summed up the scientific literature.  How is that the same thing as ignoring it?

“(a) how it is a (unguided!) mutation and selection process”

Again, you have not told us why we should think that a narrowing of the search space from 4,000,000,000 nucleotides to 400 should be considered unguided.

“if you don’t like the immune system”

Don’t like it?  I love it!  I just think that your description of it is misleading.

“evolution of specific binding sites doesn’t require searching that big a space of variation”

That’s correct—when there is information already in the cell telling it how best to mutate, it narrows the search space.  That is specifically what the research of Dembski and Marks shows.  If it doesn’t search that big of a space, then it is evolution by information, not evolution by natural selection.


Nick Matzke - #3694

January 31st 2010

The only way the search space would be 4 billion nucleotides would be if 4 billion specified nucleotides were required to bind an antigen.  But actually you only need 50 amino acids or so to achieve binding, and not even all of those have to be specified.  Not even the ID guys claim what you claim. 

PS The size of the human genome is ~3.5 billion nucleotides, and probably 90%+ of it is non-specified sequence, i.e. structural or junk.

PPS: If you don’t address the literature I referenced showing that binding sites and new genes are easy to evolve, and thus information is easy to evolve, then there is no reason for the scientific community to take your argument seriously.


Jonathan Bartlett - #3695

January 31st 2010

“The only way the search space would be 4 billion nucleotides would be if 4 billion specified nucleotides were required to bind an antigen.”

This is incorrect on several levels.  I am not talking about creating a whole new binding site.  I’m only talking about the much simpler procedure of finding the 3 or so base pairs that need to be modified to achieve a new binding from a similar one in somatic hypermutation.  The search space, for neo-Darwinism, is the whole genome.  Why?  Because, if natural selection is true, then “mutations are random with respect to the needs of the organism in coping with its environment” (Templeton).  For selection to be the primary cause the mutational mechanism should be random with respect to which base pairs need to be modified.  But it is not.  It is focused, out of the whole genome, on the 400 base pairs that might be useful.  Therefore, the primary cause for the mutation is information, which tells the cell which subset of the 4,000,000,000 base pairs in the genome need to be searched.

And, as I’ve said, genes are very easy to evolve, if the cell already has the information to tell it where to look.  Thus, it is evolution by information, not evolution by natural selection.


Nick Matzke - #3696

January 31st 2010

Ah.  Well that makes a little more sense.  The mutations are still random though, there are just more of them in the hypermutating regions.  If you decide to call the hypermutating region specification “information”, you still have to acknowledge that the specified sequence that produces an antibody binding site to a particular is not encoded anywhere in the hypermutation location specification.  That information, the particular sequence that produces the binding site, has been generated by the mutation-selection process, it didn’t exist before in that genome, and thus a natural, unintelligent random-mutation and selection process can generate new information.

The same process can happen anywhere, it just takes generations for organisms, instead of days/weeks for immune system cells.  Which everyone knew already.

I suppose you’re now going to argue that it is just inconceivable that evolution could produce a high-muation region in the right part of the genome in a certain cell line?  1 in 3.5 billion is just so wildly improbable we have to ignore the scientific explanations in the library, and conclude IDdidit?


hmm - #3698

January 31st 2010

Mike Gene wrote:

“Doesn’t antibody production give us reason to think that the origin of specified complexity/information does not require a mind?”

I don’t think so. First, it is an example of raising the complexity/information, but not of the origin of it. Second, I don’t believe that anything could exist without God. That’s why I believe that also antibody production requires a mind of God to exist and to work. And (because I don’t favor God of the Gaps theology, and see need for Him only in some places, but not in the others) I don’t see any evidence for the claim that origin of specified complexity in our world wouldn’t require a mind.

Nick Matzke wrote:

“Do you have any evidence that the mutations in the immune system cells of a rabbit developing immunity to virus A are guided towards target A?  And that the mutations in a different rabbit are guided towards a different virus B? No.  The mutations are random.”

Of course nobody knows what the plan (of God) is. And it may be impossible to show evidence for guiding without knowing what the (God’s) purposes are. But ignorance of the purposes is not the proof for the claim that mutations are not guided at all. It is just argument from ignorance.


Mike Gene - #3702

January 31st 2010

To balance things out here, I should mention that Professor Jerry Coyne had a tantrum about this thread.  He lashed out against Darrel as follows:

“But BioLogos, in its shameful pandering to religion, is simply an embarrassment to the community of biologists.  In their insistence that faith and science are mutually reinforcing, and their unwillingness to entertain any evidence to the contrary, people like Falk are impediments to the advance of rationality.  As Szostak says, “belief systems based on faith are inherently dangerous, as they leave the believer susceptible to manipulation when skepticism and inquiry are discouraged.””

http://whyevolutionistrue.wordpress.com/2010/01/28/accommodationists-vs-creationists-we-all-lose/

Coyne is confused.  He possesses this primitive, tribalistic mindset that essentially states, “If you are not an enemy of my enemy, you are my enemy.”  It is this form of extremism, coupled to reliance on emotional rhetoric and simplistic stereotypes,  that are “are impediments to the advance of rationality.”


Mike Gene - #3703

January 31st 2010

I should also point out that while Coyne uncritically embraced the sentiments of Dr. Szostak (since they echo Coyne’s hatred of religion), I think it important to apply critical thinking across the board.  I did this with Szostak’s comment (someone who values critical thinking had to do it).  See the fourth comment (and follow-ups) in this thread:

http://biologos.org/blog/signature-in-the-cell-a-follow-up/

How is it that such intelligent and successful scientists can come to embrace such irrational positions?


Nick Matzke - #3710

January 31st 2010

Hi Mike—in the other thread, Szostak said:

However, I suspect I must part company with you in that I believe that science and religion actually are irreconcilable. In my view a scientific world view is one based on continuous questioning and therefore a search for more and better evidence and theories; faith in the unknowable plays no role. I think that belief systems based on faith are inherently dangerous, as they leave the believer susceptible to manipulation when skepticism and inquiry are discouraged.

in response to Szostak, you said:


Nick Matzke - #3711

January 31st 2010

Oh, the rich irony of Dr. Szostak’s final paragraph.  His ham-handed perceptions of religion and religious people are clearly rooted in stereotype, as, contrary to his understanding, the journey of faith is filled with continuous questioning and a search for a better understanding.  Take this issue itself.  Many Christians continually question the relation between Christianity and evolution (and all that both entail) in an attempt to reach reconciliation.  Yet Dr. Szostak has declared all such efforts to be doomed as he “believes” they “actually are irreconcilable.”  What happened to his spirit of continuous questioning?

Isn’t it fair to say that much of his position is probably motivated by (a) experience with the anti-science attitudes of fundamentalists and perhaps certain other religious groups, and (b) his personally being unconvinced by theistic arguments, thus he puts them in the same category as other wrong beliefs, like homeopathy and whatnot?


Nick Matzke - #3712

January 31st 2010

I disagree with much of Szostak’s position, but I think we have to say it is fairly easy to see how a scientist could end up taking his position, after lots of provocation from fundamentalists and the like, and lots of claims about confidence in theism (from fundamentalists and nonfundamentalists) without the kind of empirical support that a scientist would hope to see in other areas.


Jonathan Bartlett - #3714

January 31st 2010

“the specified sequence that produces an antibody binding site…is not encoded anywhere in the hypermutation location specification…[it] has been generated by the mutation-selection process”

Yes

“and thus a natural, unintelligent random-mutation and selection process can generate new information.”

No. It has an unintelligent *component*.  The process as a whole is directed by information.  That a small amount of information can be produced is part of ID (see No Free Lunch, or pretty much anything by Dembski, for a quantification).

“The same process can happen anywhere, it just takes generations for organisms, instead of days/weeks for immune system cells.”

It can happen anywhere *where there is information to limit the search*.  You keep forgetting that part.

“it is just inconceivable that evolution could produce a high-muation region in the right part of the genome in a certain cell line?”

Well, it could, if it had adequate information.  But that would require more, not less, information.  See Dembski’s “Searching Large Spaces”.

As I’ve said, this is evolution by information, not evolution by natural selection.  Natural selection plays a role, but it is greatly overshadowed by information’s role.


Gregory Arago - #3715

January 31st 2010

Jonathan,

I’m getting the impression that you are giving to ‘information’ some kind of ‘agent-like’ force. Do you know if the concept duo ‘information selection’ has been considered in biology? You speak of ‘evolution by information,’ in contrast to ‘evolution by natural selection.’ Has there been a published article in a natural scientific or philosophy of biology journal on this topic?

Personally I’m unconvinced by N. Matzke’s pejorative label ‘fundamentalist.’ In my view and experience one can be a ‘fundamentalist’ and also ‘pro-science.’

As a former basketball player, I believe that every beginner should learn ‘fundamentals.’

If Szostak or Coyne or Matzke dismiss the value of theological or philosophical knowledge, that is their prerogative, their loss. Just because they are ‘scientists’ is no reason for me to respect them as ‘holistic’ thinkers, as persons.

WIth curiosity,
Gregory


beaglelady - #3717

January 31st 2010

Nick Matzke,

It’s good to see you here!


Nick Matzke - #3718

January 31st 2010

No. It has an unintelligent *component*.  The process as a whole is directed by information.

 
What’s the directing information in the case of a new gene evolving by mutation and natural selection acting on a gene duplicate?  I would say mutation and selection are providing the information, there.

That a small amount of information can be produced is part of ID (see No Free Lunch, or pretty much anything by Dembski, for a quantification).

I’ve read everything of Dembski’s.  Nowhere is there an explanation of why, or how, an information-building process has a memory, such that adding up to 150 bits is possible, but adding 1 more bit (or 100, or 1000, etc.) later on is impossible, because the system “remembers” that it already hit the limit of 150 bits.


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