Signature in the Cell

The Origin of Information

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The Nature of Information

Information is central to all living systems, and is responsible for assembling the proteins that are essential to life and reproduction. Being a biochemist and taking many courses in molecular biology as well, I knew this already. But information, in and of itself, is mysterious…and that is something I hadn’t really thought about.

“Evolutionary biologists have failed to realize that they work with two more or less incommensurable domains: that of information and that of matter…the gene is a package of information, not an object. The pattern of base pairs in a DNA molecule specifies the gene. But the DNA molecule is the medium, it’s not the message.” Williams, Natural Selection, 11

Consider: if I fax a form to my bank, what I put into the machine and what comes out on the other end is not the same thing. They are different sheets of paper with different ink—the form can even be stored digitally. The actual information has nothing to do with ink or wood pulp or electrons on a hard drive. Information is completely different from “dust or particles,” and that seems to be the crux of the intelligent design argument.

This is something I had never considered before reading Signature in the Cell. It shows my ignorance of history and philosophy, for this was the dominant worldview for centuries. It was the understanding of Plato, Aristotle, Roman Stoics, Jewish philosophers such as Moses Mainonides, Christian philosophers such as Thomas Aquinas, and most of the founding scientists in the scientific revolution from 1300-1700 that mind was the primary source of reality. Material either issues from or is shaped by (or both) a pre-existing intelligence. This ignorance on my part is not surprising, though, if you think about it, since materialism dominates the modern university.

So, does information have anything to do with the DNA molecule? Or does it have everything to do with the order of the nucleotides? It is such an interesting insight to consider when reviewing data and articles on origin of life—does this experiment or result solve a material problem (producing amino acids or nucleotides in a test tube) or an information problem (the cause or mechanism of specific ordering of nucleotides)? And as I read more about origin of life, the more this delineation should be at the forefront of my mind.

What is Information?

Overall, I was really pleased with the amount of information and definitions on information in this book. What is information? Here are two definitions:

  1. The communication or reception of knowledge or intelligence
  2. The attribute inherent in and communicated by alternative sequences or arrangements of something that produces specific effects.

The first definition is sort of generic and intuitive, and deals with what people do all the time: “Turn right on Oak St.” “I like you a lot.” “I loathe you and all you represent.” Knowledge is passed from one being to another, and the other can take whatever action they see fit. A right turn, a kiss, or a firm uppercut. The second definition gets into more detail of the “language” of information—sequences or arrangements that produce an effect. It’s the arrangements that have an effect, and therefore the arrangements are a cause. This definition seems more applicable to software or DNA code.

Shannon Information Theory

Not only does information communicate knowledge or an effect, there can be a varied amount of information. According the Shannon Information Theory, information and uncertainty are inversely proportional. The more information in a sentence, the more uncertainty it reduces. Consider the following:

“Someone stole my wallet.”

“A tall light-skinned man with blonde hair, pimples on his nose, a tattoo of a mermaid on his left forearm, wearing blue denim jeans and a yellow tee-shirt stole my wallet, and he ran that way…”

In the first sentence, you could be looking for anyone. The second sentence obviously provides more information and reduces the uncertainty of exactly who stole my wallet (because I want it back, I have bills to pay and mouths to feed). Here are the categories of information:

  1. Order redundancy – ABCABCABCABC etc. This kind of information is compressible and, because of its regularity, carries little information.
  2. Mere complexity – ALWIWOCZNVDWIQSAOA. This information is not compressible. It is complex, but not specific to any particular function and conveys no information (assuming no hidden code). An example from the biological world would be random polypeptides or polymers that serve no biological function.
  3. Specific complexity – “TIME AND TIDE WAIT FOR NO MAN”. This information is also complex and not compressible. It clearly serves a function, though, or communicates a message. Biological examples include functional DNA and proteins. This is a synonym for specified information or informational content.

It is this specified complexity that Intelligent Design theorists are most interested in. What qualifies DNA as information-rich is that fact that the code in DNA is translated (via RNA) into a protein that performs a function.

Yes, one can perform experiments to try to imitate what happened in the “primordial soup.” But these experiments have to do with the dust and particles, and have nothing to do with the generation of information. That is what is essential to understanding where intelligent design is coming from. Suppose it can be discerned how nucleotides came together, formed the unfavorable bond at the ribose backbone, and then formed long enough chains—that is still not the same as explaining the origin of the information formed.

Signature of Controversy, part 2

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Dishonesty. And some religion…

David Klinghoffer’s article in this book, titled “Scared to Read Signature in the Cell?”, sums up the Darwinian atheist activism against SitC. He details how Coyne, Fletcher, P.Z. Myer, and even hordes of Amazon.com pseudo-reviewers have not read the book and simply trash it. How can a person of reason truly review or comment on something they have not read??  Not just to comment, but to post comments such as, “religious speculation,” “a stinker,” and “drivel.” It is completely intellectually dishonest.

How am I to respect evolution with disciples such as these? Do I throw out evolution because of this? Or do I learn what the evidence is, how it applies to our observation of nature, and assign it a place. Natural selection does occur, on a limited observable scale. There is hard evidence for common descent. There is no evidence for the generation of biological information by natural means.

But I don’t think they are scared to read the book. I think it is the religion of philosophical naturalism that drives these people. This is not my idea. I have heard Nancy Pearcey speak on this in her book, Total Truth. As british chemist John C. Walton wrote:

It is an amusing irony that while castigating students of religion for believing in the supernatural, [Fletcher] offers in its place an entirely imaginary “RNA world” the only support for which is speculation!

Klinghoffer concludes:

Alas, carelessness and dishonesty are hallmarks of the Darwinian propagandists. Hordes of whom, by the way, have been trying to overwhelm Signature’s Amazon page . They post abusive “reviews” making, again, little pretense of having turned a single page even as they then try to boost their own phony evaluations by gathering in mobs generated by email lists and clicking on the Yes button at the question, “Was this review helpful to you?” Per Amazon’s easily exploited house rules, this has the effect of boosting the “review” to enhanced prominence. It’s a fraudulent tactic, and sadly typical.

Is it really so? Can these people seriously, seriously, not detect their loathsome dishonest behaviour? Can they not see how hate taints their minds and body, degenerating their reasoning, and dehumanizing them into the true products of their theory of evolution, mere animals?

Signature of Controversy, part 1

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Ok, it is a bit frustrating to get into a conversation that has been going on for years. Intelligent design for me is now less about learning what the theory is, but rather what everyone thinks about it. I’m going to try and reserve opinion and judgement, in general. I think I will just try and chronicle the dialogue as I see it detailed in Signature of Controversy. (And I still need to summarize the notes I took on Signature in the Cell (SitC) and write a post!)

First, there is Franciso Ayala (“one of Biology’s living legends”) who supposedly reviewed SitC. I agree with Meyer and Klinghoffer; it doesn’t appear that Ayala actually read the book. Dr. Darrel Falk had asked Ayala to review the book (Falk’s review is found here). Meyer does respond to both Falk and to Ayala, but Meyer’s response to Ayala is prefaced by Falk, who says Ayala was responding to Falk’s essay, not SitC. But the review by Ayala clearly states that BioLogos sent him a copy of SitC . Huh. And Falk said he asked Meyer to respond only to Ayala’s philosophical and theological concerns. (“We will now take a moment to refrain from the whole purpose of BioLogos… Your handcuffs, sir.”) Double huh. Klinghoffer points out that Ayala opens his salvo on Meyer by claiming his main premise is an argument against chance…which it isn’t…and isn’t mentioned by Falk…whose essay he was supposedly responding to. Triple huh. Jay Richards also agrees that Ayala could not have read Meyer’s book. There was apparently a commentary from Falk on Ayala’s review, but it has been  (perhaps wisely) brought down. Quadruple…oh never mind.

Secondly, there is Jerry Coyne. I have seen his name and his book Why Evolution Is True, and he has a blog where he has written posts attacking Meyer’s book. I would like to peruse his site and see what he writes and stands for. From what I have seen though, just briefly, he is an opinionated militant atheist. From Signature of Controversy, Klinghoffer cites that in one particular post, Coyne accuses Meyer of lying. That particular post has been deleted, though.  Klinghoffer points out some of the things Coyne has gotten wrong about Meyer, yet Meyer is a “lying liar.” Huh.

Next, there was a back and forth attack by Stephen Fletcher against Thomas Nagel for selecting SitC as one of the Times Supplement Books of the Year. Fletcher’s argument is based on evidence data in favor of the RNA world theory of life’s origins. (This is a theory I would like to know more details about.) His claim (and the claim made by Falk, essentially) is that scientific developments have “overtaken Meyer’s book.” 

From one study Flether cites experiments leading to the synthesis of a pyrimidine ribonucleotide (an RNA molecule). Meyer’s criticism of this experiment is the same he has made in his book: it is only a letter and does not explain the origin of the “words” and “sentences” in DNA; and the molecule was synthesized in steps, selecting only R-isomers, purifying intermediates from impurities and cross reactions. Scientists had to intervene, adding “active intelligence” to the “unguided” process. This is the problem I am learning about experiments concerning our origins. A scientist always intervenes, and it doesn’t explain the origin of the code.

David Berlinski also responds to Fletcher.

If experiments conducted in the here and now are to shed light on the there and then, they must meet two conditions: They must demonstrate in the first place the existence of a detailed chemical pathway between RNA precursors and a form of self-replicating RNA; and they must provide in the second place a demonstration that the spontaneous appearance of this pathway is plausible under pre-biotic conditions….

Questions of pre-biotic plausibility remain. Can the results of Powner et al. be reproduced without Powner et al.? It is a question that Powner raises himself: “My ultimate goal,” he has remarked, “is to get a living system (RNA) emerging from a one-pot experiment.”

Let us by all means have that pot, and then we shall see further.

Review of Signature in the Cell

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Signature in the Cell: DNA and the Evidence for Intelligent DesignSignature in the Cell: DNA and the Evidence for Intelligent Design by Stephen C. Meyer

My rating: 5 of 5 stars

An excellent summary for the case for Intelligent Design (ID). Meyer answers critics who label ID as unscientific, citing Stephen Jay Gould, who described evolutionary biology, geology, paleontology, etc. as “historical sciences.” Meyer explains how the theory of ID fits these parameters.

Clearly, the biological information contained in DNA is code-like, so much so that people like Dawkins and Crick have to remind scientists that it only “appears” that way. In his first premise, Meyer recounts a thorough history of the search for life’s origin and how each theory has yielded no results on how the genetic code evolved. For his second premise, he demonstrates that the only known cause for the generation of information (specified complexity) is an intelligent agent. We look at cave paintings and chipped flint and scientists determine that some sort of intelligence produced this work. SETI searches the galaxies for patterns of information that designate intelligence. Every one of us creates information daily.

The conclusion of Meyer’s argument is an inference that, as the only known cause of information, intelligence was the cause of the rise of DNA. This inference, incidentally, is the same logic used by Darwin himself (the observation of micro-evolution and the inference that chance and natural selection, stretched back over time, determined the origin of species).

One point I found interesting was the discussion of the predictions of evolution and ID concerning “junk DNA.” ID predicts non-protein coding sequences should perform biological functions. It shouldn’t be useless or junk. The model of natural selection predicts a genome “riddled with useless information, mistakes, and broken genes.” Scientists have labeled this area between genes as junk (“gene deserts”) and proof against design, but research coming out of the ENCODE Project (http://www.genome.gov/10005107#al-1) are showing these parts of the genome are in fact highly functional. As Philip Kitcher said, “Intelligent Design has deep roots in the history of cosmology, and in the earth and life sciences.” Kitcher’s argument against ID is this supposed inability to explain “junk DNA,” yet clearly, ID can be a guiding principle and theory.

This is a book for those that truly want to understand the theory of intelligent design. There is a hard break that scientists use (methodological naturalism) which excludes anything supernatural from being considered as scientific. This book explains, step by step (sometimes a bit too slowly, perhaps), why ID is a viable theory that only invokes intelligence as a causal agent. There are, of course, theistic implications, but there are anti-religious implications from evolutionary theory as well. Meyer’s approach, however, is completely evidence based. Meyer quotes Antony Flew, a long time atheist who now accepts ID, asserting, we must “follow the evidence wherever it leads,” regardless of the implications.

View all my reviews

Debate concerning Alfred Russel Wallace

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I am almost finished with reading and taking notes on Signature in the Cell, and have found a great source of information for furthering my knowledge at Evolution News and Views. Already I have seen names quoted in the is book (James Shapiro, William Dembski), and see that there will be an on-line debate  between Michael Shermer (editor of Skeptic magazine and Discovery Institute’s Michael Flannery. The debate is concerning Alfred Russle Wallace. This man apparently shares credit with Darwin for the theory of evolution, but then came to embrace Intelligent Design. There is an movie made about his life by Flannery.

I also saw that there is a discussion going between a number of people, sparked by an aritcle by Dembski that asks, “Is James Shapiro a Design Theorist?” Perhaps here is where one can find links to all those involved.

I want to see the movie and read Shermer’s criticism, but I am trying to work diligently to finish Signature first. I wanted to capture some of the links here for future reference.

Through the clouds and into the melee

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Yesterday I posted my surprise at this article by Dennis Venema criticizing Meyer’s “Signature in the Cell.” I finished the review and made some notes for when I read Meyer’s book. I got the impression that, however civil Venema would like to think himself, he really had a low opinion of Meyer. One comment states that his assessment of Meyer’s grasp of molecular/cellular biology was introductory college level. I did a quick check on Wikipedia and Meyer has a degree in physics and earth science from Whitworth College and a Ph.D. in history and philosophy of science. Hmm, ok, maybe there is some truth to that assessment as he is not a bench scientist, but entry level?

So, clearly there is a divide between “evolutionary creationists” and proponents of intelligent design. I have done some searching and found some blogs on BioLogos from Venema, as well as others discussing Meyer’s work. There are forums, blogs, comments…the mental picture of my situation, coming upon all of dialogue and argument, was when Harry Potter, riding with Hagrid, pops out from the clouds into the mayhem of death eaters chasing his other selves. Clearly I have a lot to read and consider, and a lot to learn.

Here is an interview with Venema. He sounds like an interesting person, and I think it is fortuitous that I printed his review of Signature a month ago and chose now to read it. Venema has written a lot on BioLogos and it will be good to read both him and Meyer’s Signature and decide for myself what it is I believe.

In general, I am undecided. Well, I am convinced the universe, the world and life as we know it could not come about randomly. I do lean toward an intelligent design approach. I am for discovery and for weighing the facts.

Part II: Here is a review by Darrel Falk in which the same critique is given in a more balance approach. He highlights the admirable qualities as well as the failures in argument, and ultimately seems to fault Meyer on an “unsuccessful attempt to move from philosophy into genetics, biochemistry and molecular biology.” I thought that phrase very pointed and witty. He, in essence, praised it in its philosophical and religious context, but Meyer claims he wants to be judged on its scientific merit. And so he is judged.

Part III: Ok, here is an article concerning Meyer’s treatment by BioLogos. And a response to Venema. Clearly there is melee…

Humility is required

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Today was a full day of small-scale purification at work, which afforded me ample snippets of time in order to read. I perused Saturday’s Wall Street Journal and also was able to read one of the articles I had printed from the American Science Affiliation. The article was by Dennis Venema and was a review of a book I have just purchased and want to read, Signature in the Cell by Stephen C. Meyer. The author is a proponent of Intelligent Design, and I believe coined the phrase, I think.

The title of this short post became clear to me as I read Venema’s article. First, it was a critical review of the book and pointed out the flaws in Meyer’s arguments. I was not really expecting that. It was not done out of disrespect, but out of scientific necessity. I had assumed that Signature was going to be a source of authority for me and that it would be flawless. Also, this article strained my scientific knowledge base. It made me feel ignorant. Which I am. But with the amount of reading and application I have been doing, I…well, I obviously started to think highly of myself…and I did feel my pride deflated. I realized, again, that my self-education is going to require work (not just reading) and serious thought and a certain level of mastery of subjects.

So, as was presented in “A Thomas Jefferson Education,” George Wythe had his students write an essay every day. I don’t think I can do that, since I am not really at this full-time, but I think I will use this blog to essay about what I am learning, and of course, these sorts of meditations.