Signature in the Cell

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December 28, 2009 Tags: Design

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

Signature in the Cell

I believe there is a Mind who was before all things and through whom all things are held together (Colossians 1:17): I believe that Mind is the intelligence behind all that exists in the universe. Hence, I believe in intelligent design. Does that by definition then, place me in the Intelligent Design (ID) movement?

No.

The recent book, Signature in the Cell , by ID movement leader Stephen C. Meyer, illustrates why.

Meyer holds a Ph.D. in philosophy from the University of Cambridge and is an expert in the philosophy of science. Admittedly, I am only an amateur in his area of expertise, but there were times as I was reading his book, when I was enthralled by the highly articulate explanation of how the tools of scientific logic enable us to become quite certain about the cause of natural events in the distant past. Similarly, his discussion of attempts to meaningfully define science was outstanding. He showed how the term has taken on new meaning based on practice. Today, as it is carried out by almost all practitioners, science has become synonymous with methodological naturalism. Meyer may have been overly optimistic when he wrote, “recently however, this [definition] has begun to change as more scientists are becoming interested in the evidence for intelligent design” (p. 437). Still, I enjoyed his discussion of the political and philosophical maneuvers of those with a vested interest in how this term ought to be defined. This is Stephen Meyer at his best. He is very effective in communicating philosophical issues to a general audience. Perhaps it is no surprise then, that a world-class philosopher, Thomas Nagel of New York University, recommended Signature in the Cell to The Times Literary Supplement as one of the best books of 2009.

It is important to emphasize, however, that the Intelligent Design movement is not purported to be philosophical or religious in nature. The leaders, including Stephen Meyer, emphatically declare this is a scientific movement and it needs to be judged on the quality of its science, not its philosophy or theology. So Meyer has expanded his extensive reading list to include numerous journal articles and books within the field of biochemistry, molecular biology and genetics. His purpose has been to assess the quality of the scientific interpretations of the data as it relates to the origin of the information inside of cells. He has reached the conclusion that the sciences of biochemistry, molecular biology and genetics have come to a dead end and that the only reasonable scientific explanation now is that the information inside of a cell is the product of an external mind.

Many scientists think that as life began, its source of information was found in RNA molecules. There are specialized reasons for this, which are not germane to the point I want to make. Suffice it to say, however, that Meyer suggests that the two different conditions for making two of the key building blocks that characterize an RNA molecule are incompatible (p. 303). In other words, the conditions under which one building block could have been synthesized on the early earth would have resulted in the destruction of the second building block, and vice versa. Since there is no way that both could have been produced simultaneously on a primitive earth, Meyer declares that RNA could not arise without the input of a mind. As he was writing these words, however, some elegant experiments were taking place at the University of Manchester that showed there is a way, a very feasible way that both building blocks could have been produced through natural processes.1

In Chapter 14, as Stephen Meyer brings his discussion about the feasibility of RNA’s role as the early storehouse for cellular information to a conclusion, he recalls a twenty year old conversation with a philosophy professor about origin-of-life-research: “The field is becoming increasingly populated by cranks. Everyone knows everybody else’s theory doesn’t work, but no one is willing to admit it about his own.” Following this statement, Meyer fast-forwards into the present, and writes of his own assessment of the field twenty years later: “I found no reason to amend these assessments” (p. 322). As a geneticist, I am taken aback by this assessment. The work he had just been discussing is the work of Jack Szostak who was awarded the Nobel Prize a few weeks ago. I’ve heard Dr Szostak speak a number of times. He is no crank. He is widely regarded as a brilliant mind. Read his Scientific American article for yourself (seefootnote, below), you’ll see he is also very frank about the strengths and weaknesses of his current thoughts about life’s origins. Also, his work is by no means at a standstill. Only a philosopher, I suppose, or someone else quite naïve about how science proceeds at a lab bench would be able to make such an assessment.

Immediately prior to Meyer’s assessment about cranks in the field of origin-of-life-research, he had also been discussing the work of Gerald Joyce of The Scripps Research Institute. I have also been privileged to hear Dr. Joyce speak on at least three occasions. He, like Szostak, is widely regarded by biochemists and molecular biologists as brilliant. Like Szostak, I find that his discussion of the strengths and weaknesses of the RNA world model is cautious. He knows there are many unanswered questions, but he has made great strides at answering some of them. At the time of writing Signature of the Cell, Dr. Meyer correctly concluded that no RNA molecule had ever been evolved in a test tube which could do more than join two building blocks together. However, while the book was in press, Gerald Joyce and Tracey Lincoln published an article in Science in which they demonstrated that evolved-RNA can take on a second function, the all-important replication activity. In just 30 hours their collection of RNA molecules had grown 100 million times bigger through a replication process carried out exclusively by evolved RNA molecules. So another dead-end pronouncement by Meyer was breached even while the book was in press.

I want to give one more example which demonstrates Meyer’s disappointing tendency to reach premature conclusions based on his unsuccessful attempt to move from philosophy into genetics, biochemistry and molecular biology. Dr. Meyer evaluates the work of the population geneticist, Michael Lynch of Indiana University. He points out the Lynch has proposed that “the structure of the genome can be explained by a neutralist theory of evolution based mainly on genetic drift” (p. 470). Meyer concludes in just a sentence or two that Lynch is wrong and that genetic drift is less likely than natural selection. Again, I am very puzzled by this conclusion in what is purported to be a science book which is examining scientific data. Lynch is one of the finest population geneticists in the world. What experiment or calculation has Stephen Meyer done to put himself in a position to tell Michael Lynch which of two possible scenarios is more likely? Yet he does this in a single sentence.

Signature in the Cell is by most accounts considered to be a highly successful book. From a philosophy perspective, it is considered by at least one leading philosopher to be one of the best books of 2009. From a religious perspective, Meyer, on the basis of this book, has just been declared “Daniel of the Year” by the widely read evangelical periodical World Magazine. From the public persona perspective it has sold very well—Amazon.com had it on one of its top ten lists for the 2009 best sellers.

However, the book is supposed to be a science book and the ID movement is purported to be primarily a scientific movement—not primarily a philosophical, religious, or even popular movement. Meyer argues throughout the book that his theory about the origin of information is scientific, not religious. He makes it clear that he wants it to be considered on its scientific merits alone. I am comfortable with this. Let it be evaluated on the basis of its science. Like him, I believe in intelligent design. However, I am also a scientist. So I need to evaluate this book in the way that he calls all of us to do, as a work of science. I must consider whether this philosopher, this Christian brother, this best-selling author, and this leading debater has been successful at analyzing the data of the world’s leading scientists—people who have given their careers full time for many years to asking (and answering) very sophisticated questions about whether material causes have created information.

There is no question that large amounts information have been created by materialistic forces over the past several hundred million years. Meyer dismisses this without discussing it. What about at the very beginning, 3.5 billion years ago? Everyone doing the science, Meyer notwithstanding, would say the jury is still out. There are some very elegant feasibility experiments going on at the present time. However, it is far too early for a philosopher to jump into the fray and declare no further progress will be made and that this science is now dead. If the object of the book is to show that the Intelligent Design movement is a scientific movement, it has not succeeded. In fact, what it has succeeded in showing is that it is a popular movement grounded primarily in the hopes and dreams of those in philosophy, in religion, and especially those in the general public. With all due respect for the very fine people associated with the ID movement, many of whom I have met personally and whose sincerity I greatly appreciate, our hopes and dreams need to be much bigger than this. The science of origins is not the failure it is purported to be. It is just science moving along as science does—one step at a time. Let it be.

1. See this Scientific American article for an outstanding description of this and other recent developments, which show that what Stephen Meyer declared to be a dead end is still an extremely active and exciting area of scientific research. Even as he was declaring that no further progress would be made, the problem had been solved.


Darrel Falk is former president of The BioLogos Foundation. He transitioned into Christian higher education 25 years ago and has given numerous talks about the relationship between science and faith at many universities and seminaries. He is the author of Coming to Peace with Science.

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cist - #1317

December 29th 2009

“You might be right but numbers on IBM Mainframes are held and processed in HEX representation. Its quicker than in bites.  In this case information is held in 4 bites as a whole.”

Hi VMartin,

HEX representation is used to address computer memory in general, not just in IBM mainframes. Nothing is processed in HEX, it is all processed in binary electrical on and offs under the hood at the transistor to gate level to jk flip flops to registers in CPU’s and what not. HEX is just a natural intuitive way of addressing memory if you have a 32-bit platform means you have 32-bit integer memory addresses or 4 bytes per slot which also implies base 2 ^ 32 possible address space. Notice here that the number of addresses is calculated based on the base 2 system. HEX is simply a 4 byte representation of 32-bits, but 32-bits are still processed via the CPU ALU or whatever logic circuit at some clock rate (HZ). Another thing to note is that HEX and OCTAL are powers of 2, they naturally map out from a base 2. 8 HEX digits are 32 bits long (0xEEEEEEEE), which means 4 bits per HEX digit.


cist - #1318

December 29th 2009

contd…

If there was a missing base system link in computing, it would be the DNA base 4 system.  We use base 2 system, the rest are just representations of the same base 2 system. So if DNA is not a representation, that means it actually uses a base 4 architecture, which means lots of problems for Darwinian Evolution if you think about it. No engineer would be dumb enough to choose a base 4 system because the engineering requirement exceeds a base 2 by several orders of magnitude, this implies that whatever happened with DNA happened for a extremely specific reason rather than just going for a base 2 counterpart. You have to think deeply about this as I have to understand the magnitude of the problem.


cist - #1320

December 29th 2009

What VMartin is referring too is that majority of evolutionary development of new body plans (phyla) has terminated, with little left except deterioration and subsequent extinction. The fact is we observe deterioration of the genome. If deterioration means evolution in the same way “scientists” mean evolution from one species to another, then I’m Elvis Presley.


Brian - #1322

December 29th 2009

Darrel Falk @ #1308

Thanks for the reply. 

First, thanks for the clarification; there are several statements from the article that are testable, and therefore scientific.  For example: “Ribose, along with three closely related sugars, can form from the reaction of two simpler sugars that contain two and three carbon atoms, respectively.”  The problem of course, is that such examples are also quite trivial.  The big-picture claims, the important claims like the ones I quoted at 1281, are unverifiable statements of faith. 

Second, I’d like to direct your attention to the paragraph in which Szostak discusses how his team “evolved” ribozymes (quotes are in the original).  He says, “we selected…, and we made copies…, and once again we singled those out… we were able to produce ribozymes….”  Do you not find it interesting that when evolution is demonstrated, it is done through the goal-directed manipulation of the material by an intelligent agent—the one thing that is expressly forbidden by all advoctes of the theory?  This example supports intelligent design, not undirected blind-watchmaker evolution.


Brian - #1323

December 29th 2009

Continued…

Third, just for the record, I have no doubts about the enthusiasm, level of engagement or work ethic of any of the researchers involved. 

Conclusion:  I am one of those people who you say you want to influence, but I’m an educated professional.  Arguments to “please trust me” aren’t going to cut it—especially when the support that you yourself provide is as thin as it is.  This article, like so many other popular evolution pieces, essentially says, “Through a lot of hard work and intelligent intervention, we can create one brick-like structure.  Therefore, its reasonable to believe that the Empire State Building evolved through blind-watchmaker mechanisms.” 

You’ll have to forgive me for being a little skeptical.


John Kwok - #1325

December 29th 2009

VMartin -

May I recommend reading eminent vertebrate paleobiologist Donald Prothero’s superb “Evolution: What the Fossils Say and Why It Matters”? Or take a look here at this website devoted to the American Museum of Natural History’s “Extreme Mammals” special exhibition, which is on display there through January 3rd, before it departs for a nationwide tour:

http://www.amnh.org/exhibitions/extrememammals/index.php

Both provide extensive evidence demonstrating that there’s been a lot of mammalian evolution since the Eocene.


VMartin - #1330

December 29th 2009

cist-

I only remember studying once Assembler that I read that HEX representation (or packed decimal ) is used in micropocessor as the best imaginable solution regarding efficiency. I forgot details. Of course you have to know seeing F that it is HEX 15 or 1111.
But your hypothesis about base 4 of genetic code sounds quite original. On the other hand many codes are degenarate - 64 codes for 20 aminoacids is too much.  What do you think?


John Kwok.

Professor Davison put in clearly in his blog entry - “Evolution is finished”, so I am not going to
repeat all his arguments especially when he is banned here. It is quite a suprising fact, considering all abusive posts here like from Dan, who presents himself as a scientist with 30 years experience and yet doesn’t know how to tell apart elements and their isotopes. Mutation of viruses can be percieved as evolution also only in the bizarre neodarwinian definition of “evolution”.


John Kwok - #1332

December 29th 2009

Dan,

I am by training a former invertebrate paleobiologist, so my own knowledge of molecular biology is limited. But Dan is absolutely right with respect to viruses and viral vaccines. May I suggest that if you don’t accept evolution as valid, that you don’t take a flu shot (since flu vaccine development does rely upon our current understanding of evolution)? May I also suggest that you look up research by Yale University virologist Paul Turner? I think he would strongly differ with your observation, so replete in its breathtaking inanity.


Bilbo - #1339

December 29th 2009

Darrel,

You, as other RNA -world proponents, fail to mention that all the prebiotic experiments are carried out with purefied chemicals, in very carefully sequenced reactions…something that never would have happened in pre-biotic conditions.  The agnostic chemist Robert Shapiro has said this over and over ad nauseam, apparently to no avail. 

So continue to believe in the RNA-world.  But it is a religious faith that carries you on, not a scientific one.


VMartin - #1340

December 29th 2009

John Kwok.

1)
I have no doubt that in a neodarwinian mind mutation of viruses prove evolution. Boldly extrapolating such mutations the darwinian mind has no problem in creating fantastic images that exactly such mutations also led evolution from an ancient fish to man.

2)
“Intellectually-challenged fools” are actually those whose deteriorated minds have accepted darwinism as a valid explanation of mystery of origin of man.

Accusing professor Davison of not understanding evolution etc… reminds me past times when those who opose communism in Russia were labeled as not understanding marxisms and were even locked in insane asylums.

This fanatical approach against their critics have darwinists and communists obviosly common.


nd - #1341

December 29th 2009

VMartin (#‘1314): this discussion isn’t really about thermodynamics, so I won’t take up any more bandwidth after this. Briefly: if the second law were to show that modern biology is wrong, every physicist would proclaim this with delight from the rooftops! Biologists (or “stamp collectors” as we prefer to call them) simply couldn’t stop us. The fact is, however, that thermodynamics and evolution are perfectly compatible. I know that you don’t agree, but your comments about thermodynamics suggest that you don’t really know much about it. Be honest - can you state its zeroth, first, and third laws? Do you know how thermodynamic temperature is defined, or what a heat engine is? Can you define enthalpy, Gibbs and Helmholtz free energies? All of these topics (apart from the third law) were covered in the first term of my undergraduate Physics degree, so they are not particularly advanced. If you can’t answer these questions, accept that you don’t know enough about thermodynamics and either learn about it or use other arguments. There is no shame in not knowing everything - there are plenty of topics discussed above that I (as a physicist) would not engage with, because I know that I do not know enough about them.


Dan - #1342

December 29th 2009

Biblo says, to Darrel Falk:

“So continue to believe in the RNA-world.  But it is a religious faith that carries you on, not a scientific one.”

I see no evidence that Dr. Falk “believes” in the RNA-world.  It is a scientific possibility, and it is worth scientific investigation.  Those investigations might or might not confirm the possibility.

This is in contrast to those like Dr. Meyer who claim, on flimsy basis, that the RNA-world hypothesis could never lead to anything fruitful.


VMartin - #1344

December 29th 2009

nd-

These arguments repeat here again and again. We critics of darwinism do not understand
science etc… I wonder if Margulis or Pholginghorne dismissing darwinism do not understand science as well.


I didn’t say anything about 3rd law. I simply claimed that living organisms violate the law of entropy which claims that “energy systems have a tendency to increase their entropy rather than decrease it”. It is also known as the 2nd law. I think every one can see it in ontogeny. I am not the first who
claim this. If all those who claim it do not understand “science” and by “science” is also meant neodarwinism it’s fine with me. I am in a good company.


VMartin - #1345

December 29th 2009

John Kwok wrote he is a Deist. Frankly I am quite surprised by some Deists and Christians here who embrace neodarwinism. Actually I am from Eastern Europe, Slovakia and never heard
of this intellectual combination: Christain-neodarwinist. Sounds like Christian-atheist to me in the first hearing.

Guys do you think that spirit exists?
Do you think that human spirit is an epiphenomenon of matter, of darwinian evolution?
Or it was bestowed upon us by God and is immortal? In the second case is it in accordance with neodarwinism?


William N. Kerney - #1346

December 29th 2009

Ernst Mayr tells us that evolution is believed only because other ideas are rejected.

The greatest triumph of Darwinism is that the theory of natural selection, for 80 years after 1859 a minority opinion, is now the prevailing explanation of evolutionary change. It must be admitted, however, that it has achieved this position less by the amount of irrefutable proofs it has been able to present than by the default of all the opposing theories

Ernst Mayr, Toward a New Philosophy of Biology, (Cambridge, MA: Harvard University Press, 1988), 192.

  Once Lenski tested for evolution it turned out that evolution was falsified.

http://www.pnas.org/content/105/23/7899


KBryan - #1350

December 29th 2009

“So there is one simple question to be addressed.  Is the science at a dead end?  Has Dr. Meyer demonstrated this or not? “

No, and no. For an excellent overview of the recent research in abiogenesis, see Robert Hazen’s book _Genesis: The Scientific Quest for Life’s Origins_ or his Teaching Company course on the same material:

http://www.teach12.com/ttcx/CourseDescLong2.aspx?cid=1515

http://www.amazon.com/Genesis-Scientific-Quest-Lifes-Origins/dp/0309094321/

Meyer’s arguments are well thought out and well presented, but they’re rehashing the old God-of-the-Gaps.


John Kwok - #1352

December 29th 2009

@ VMartin -

Your questions are irrelevant, since they do not pertain at all to science. I am interested in discussing excellent science and seeing it taught in science classrooms only wihtout any “accompanying” mendacious intellectual porn like Intelligent Design creationism and other flavors of creationism.


Dan - #1357

December 29th 2009

VMartin “claimed that living organisms violate the law of entropy which claims that “energy systems have a tendency to increase their entropy rather than decrease it”. It is also known as the 2nd law.”

Wrong again.  For one thing ... what is an “energy system”?  For a second ... the second law in entropy form pertains to isolated systems, and your quote omits that.  For a third ... the second law deals with what happens, not what “tends to happen.”

Finally, this is a perverse way to approach the second law.  The best way is by saying “a warm body heats a cold body”.  I admit that this is logically equivalent to “the entropy of an isolated system always increases” (as is proven in, for example, Fermi’s book “Thermodynamics”) but the logical chain between the two is very long and involves a lot of calculus.  Better to start with the simple statement “a warm body heats a cold body”.

It is not a violation of the second law for a person to eat bread and use it to get warm, any more than it’s a violation for a piece of wood to burn and get warm.


Dan - #1358

December 29th 2009

I see that VMartin holds many misconceptions about thermodynamics.  I recommend Jearl Walker’s “Fundamentals of Physics”.  This is the text I use when teaching introductory thermodynamics.  (In the senior-level course I use Dan Schroeder’s book.  But I also like Fermi’s golden oldie “Thermodynamics”.)


Dan - #1359

December 29th 2009

William N. Kerney claims “Ernst Mayr tells us that evolution is believed only because other ideas are rejected.”

In fact, no one believes in evolution.  To believe means to hold absolutely on the basis of faith.  Scientists don’t believe in evolution, or in atomic theory, or even in the round-earth theory.

Instead, we hold these ideas tentatively, and on the basis of evidence.  Every scientist I know is willing to give up evolution, or atomiticity, or the round-earth theory, provided someone provides evidence.

As Darrel Falk describes so well, Meyer provides no such evidence.


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