The Language of God: Size Doesn't Matter

The Language of God, Chapter 5

By B.J. Marshall

In this section, Collins describes how "the study of genomes leads inexorably to the conclusion that we humans share a common ancestor with other living things" (p.133-4). There are a lot of ideas in this chapter to unpack, so I'd like to start by reviewing Collins' material on DNA at a high level: size and broad similarity. It would be my hope that, even if Creationists only heard some of the material in this chapter, they would quickly see the flaws in Intelligent Design.

First, to lay some groundwork: There is a common misconception made particularly among Creationists that atheism necessarily follows from believing in evolution. This argument is as logically flawed as saying that atheism necessarily follows from believing in gravity, eschewing the entirely-poorly publicized view of Intelligent Falling. Granted, I think evolution poses difficult challenges to theism, but evolution is not theism's death knell. Atheism is a lack of a belief in god(s); the strongest form of atheism takes it one step further to declare "there are no gods." That's basically it. One could hypothetically be an atheist and still believe in the Tooth Fairy, The Loch Ness Monster, or the efficacious treatment of homeopathy. Or, more to the point of evolution, an atheist could believe in Intelligent Design so long as the designing was done intelligently by some space-faring aliens. So long as you don't believe in a god, you're an atheist; this is despite all the other nonsense you might believe. Of course, Collins wants you to see that, too. He's trying to harmonize science and religion, so it would do him no good whatsoever to make all these compelling assertions about the validity of evolution if he thought you were going to jump ship and become an atheist.

Now, that being said, Collins called the genome "the book written in the DNA language by which God spoke life into being" (p.123). Although we still don't know how abiogenesis occurred, Collins appears to be incorrect in waxing poetic about DNA's crucial role. It appears that RNA, acting as simple enzymes, might have paved the way for life to begin. But even beyond waxing poetic, Collins treats DNA as something sacred, as "uncovering this most remarkable of all texts was both a stunning scientific achievement and an occasion of worship" (p.3). And, although Collins has admonished his readers to steer clear of god-of-the-gaps arguments, he states that "DNA... seems an utterly improbable molecule to have 'just happened'" (p.91). Indeed, Collins confesses that he is "in awe of this molecule" (p.102) and regards the "digital [sic] elegance of DNA" as "deeply satisfying" (p.107). (Since DNA is based on four letters, it's really a Quaternary system.) It's probably that deep sense of awe that one can only get through belief in god.

Regarding the size of the genome, Collins makes the observation that a surprisingly small portion of it actually codes for proteins. There are only about 20,000-25,000 protein-coding genes in the human genome. Collins states that the total amount of DNA used by those genes to code for protein is about 1.5-2.0% of the total genome. Collins notes that some observers have been insulted at this. Surely as monarchs of the animal kingdom, we should be special! Well, these observers contend, perhaps "our complexity arises not from the number of separate instruction packets, but from the way they are utilized. Perhaps our component parts have learned how to multitask" (p.125). He disappointingly never expounds on whether genes can multitask, so we're left wondering. Answer: at least some can.

To quell the righteous indignation of some, Collins offers an analogy by way of the language used to write books. He goes on to say the average educated English speaker has a vocabulary of about 20,000 words. (Actually, that is a very low estimate, as Stephen Pinker in "The Language Instinct" points out that the average high school graduate knows about 45,000 words; it might even be 60,000 if you count proper names.) Collins says these words can be used in simple ways (owner's manual) or really complex ways (James Joyce's Ulysses). Unfortunately, I think the analogy fails in a way that subverts Collins' intent. If you want to bring the faithful around to seeing how evolution (unplanned, no ultimate goal, no creator) works, then it doesn't do well to relate it to a construct (language) whose entire function hinges on the intent of, and usage by, intelligent actors. I think I would have offered the reader an analogy of chemistry: you got some protons, neutrons, and electrons to form a few basic building blocks. From different combinations of these, you get the periodic table. For the theoretical physicists in you all, you could even punt to the different vibrations of strings a la Superstring Theories.

Regarding the similarities, Collins mentions that humans are all about 99.9% the same DNA-wise. This certainly makes me feel better, since my hometown was jokingly known for its residents meeting their future spouses at family reunions. He points out that this fits well with the fossil record, which places us in East Africa about 100,000-150,000 years ago to a common set of founders about 10,000 in number. Now, before you get all antsy, making your way to AnswersInGenesis (I can't bring myself to link to it) to refute the fossil record, I want to tell you we will disregard for now this line of evidence; we're really interested in seeing how Collins can back up his claim that DNA alone is sufficient to demonstrate evolution.

Back to just DNA. Here's a nifty table!

Animal Protein Coding Genes Random Segments between Genes
Chimpanzee 100% 98%
Dog 99% 52%
Mouse 99% 40%
Chicken 75% 4%
Fruit Fly 60% ~0%
Roundworm 35% ~0%

The significance of that table is this: If you asked a computer to construct a tree of life based solely on similarities of DNA sequences of multiple organisms, you'd get (courtesy of this site):

Tree of Life, made only through DNA evidence

The DNA similarities also show that genetic mutations that do not have deleterious effects on survival will accumulate over time - the stuff quite arrogantly dubbed "junk DNA." Indeed, mutations in coding regions of genes are observed far less frequently, since the deleterious effects of these are more pronounced.

If these genomes, Collins asks, were created by some intelligent designer, why would these particular features appear? Collins poses more challenges to Creationists, and we'll address them in the next posts.

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December 31, 2010, 5:13 pm • Posted in: The ObservatoryPermalink23 comments
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The Case for a Creator: Information Wars

The Case for a Creator, Chapter 9

How likely is the spontaneous origin of life? In chapter 9, Stephen Meyer likens it to one of those tornado-in-a-junkyard scenarios that creationists love so much:

"Imagine trying to generate even a simple book by throwing Scrabble letters onto the floor. Or imagine closing your eyes and picking Scrabble letters out of a bag. Are you going to produce Hamlet in anything like the time of the known universe?" [p.229]

Obviously, the answer is no. Almost as obviously, however, this is not a question that bears on the origin of life.

Let's see how Meyer's facile comparison holds up if we put some actual numbers on it. I downloaded Hamlet from Project Gutenberg and did a character count on the text file. Not counting spaces, punctuation or the copyright notice, I came up with a total of 129,839 characters. Since the alphabet has 26 letters, it takes a minimum of 5 bits to specify any single letter, which means that Hamlet has (129,839 x 5) = 649,195 bits of information.

To contrast to this, consider the smallest known genome: Carsonella ruddii, a bacterium that lives in the guts of leaf-eating insects called psyllids. It has only about 160,000 base pairs of DNA, coding for 182 proteins. But since there are only 4 base pairs in DNA, it takes only 2 bits to specify each one, which means that Carsonella's genome contains (160,000 x 2) = 320,000 bits of information: less than half of Hamlet! And Carsonella is the smallest modern genome. The very first life, which was probably little more than a self-replicating hypercycle of molecules, would have been smaller still.

Obviously, this analogy is still rigged in Meyer's favor: neither evolution nor the laws of chemistry are very much like picking Scrabble tiles out of a bag. The laws of English are such that the vast majority of possible arrangements of letters are meaningless gibberish, but this is not true of proteins and DNA. Because a protein's function is defined by its shape, virtually every possible string of amino acids potentially "means something" in a way that random combinations of English letters don't. In the primordial sea, there would have been billions of different molecules drifting around, bumping up against each other, interacting in countless ways. Until we know the smallest possible interacting set of molecules that could be called alive - and we don't know that, at least not yet - there's no basis for any claim about how likely it would have been for such a thing to arise by chance.

"There's a minimal complexity threshold... There's a certain level of folding that a protein has to have, called tertiary structure, that is necessary for it to perform a function. You don't get tertiary structure in a protein unless you have at least seventy-five amino acids or so. That may be conservative. Now consider what you'd need for a protein molecule to form by chance.

First, you need the right bonds between the amino acids. Second, amino acids come in right-handed and left-handed versions, and you've got to get only left-handed ones.

Creationists are fond of invoking this "handedness" problem (the technical term is "chirality"). It refers to the fact that certain organic molecules like sugars and amino acids naturally come in two stable configurations that are mirror images of each other, like your left and right hand. Most living things use only left-handed amino acids and right-handed sugars, and creationists often suggest that no natural force could produce this bias.

But, in fact, there's a wide variety of natural mechanisms that can sort molecules by chirality. Some common crystals, such as calcite, selectively absorb molecules of one handedness on one crystal face and the other handedness on the opposing face. (The chirality of all modern life may simply be because that vital first set of chemical reactions occurred on one side of a rock rather than another.) Circularly polarized ultraviolet light also selectively destroys molecules of one handedness. (The Murchison meteorite, which contains amino acids produced in the early solar system, has an imbalance of left-handed amino acids, and some scientists feel it's for precisely this reason. See also.) There's also a chemistry principle called "majority rule" in which certain reactions that begin with a weakly chiral mixture can produce products that are strongly chiral. Some scientists even believe that the laws of physics are not completely symmetric and one chirality is energetically favored over the other. Any of these mechanisms, or several of them in combination, could plausibly be why life has one chirality and not the other. We don't know the true cause for certain - but it's not that we have no idea how it could have happened; it's that we have too many candidates and can't choose among them!

"Third, the amino acids must link up in a specified sequence, like letters in a sentence.

Run the odds of these things falling into place on their own and you find that the probabilities of forming a rather short functional protein at random would be one chance in a hundred thousand trillion trillion trillion trillion trillion trillion trillion trillion trillion trillion. That's a ten with 125 zeroes after it!" [p.229]

There's no explanation of how Meyer got these numbers (again, footnotes are absent just where they'd be most helpful). But I strongly suspect he's committing the poker player's fallacy again: assuming that only one amino acid sequence can provide the function he wants. His mention of "a specified sequence" implies as much. But in any plausible origin-of-life scenario, there wouldn't be one miracle sequence, but a large number of functionally equivalent sequences. We already know this to be true in modern life: a large percentage of mutations are neither positive nor negative but neutral, having no effect on the overall shape or functioning of the protein.

But if Meyer's numbers are right, it should be easy to prove in an experiment: just generate some organic molecules at random and see what happens. If he's correct, nothing interesting or useful will ever emerge. Well, unlike creationists comfortably ensconced in their armchairs, real scientists do run experiments like this. From a Usenet post by the biologist Howard Hershey:

Random syntheses of 50 nucleotide long RNAs generates certain specific selectable functional ribozyme (RNA enzyme) activities relevant to biological functions that would be needed for an ur-organism (RNA ligases, terminal transferases, etc.) in the range of once every 1014-1017 molecules (a mole of molecules is about 1023, so it is a virtual certainty that you will have a number of molecules with the needed activities in a millimole of such randomly generated RNA (you would certainly be able to hold this in a thimble). Moreover, ALL these activities would be present in the SAME millimole of RNA.

For technical details, see this similar paper from the journal Science: "Structurally Complex and Highly Active RNA Ligases Derived from Random RNA Sequences". The authors say, "The fact that such a large and complex ligase emerged from a very limited sampling of sequence space implies the existence of a large number of distinct RNA structures of equivalent complexity and activity."

To put this in layman's terms: a thimbleful of randomly generated RNA sequences contains numerous enzymes with an interesting variety of biologically relevant abilities. This is a far cry from Meyer's "ten with 125 zeroes after it". Either nature is pulling a prank on us by defying the odds every single time, or else the ID advocates' calculations are based on unrealistic assumptions. Note that these RNA enzymes were only 50 nucleotides long - shorter than Meyer's "minimal complexity threshold" of 75 amino acids or more - and yet were still able to perform biologically interesting functions. And for any plausible origin-of-life scenario, we're not talking about a thimbleful of molecules, but a whole planet's worth.

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March 26, 2010, 5:39 am • Posted in: The ObservatoryPermalink49 comments
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The Case for a Creator: Soup's On!

The Case for a Creator, Chapter 9

Chapter 9 is ostensibly about the origin of biological information, but what it's really about is the origin of life. We've discussed this in part in an earlier chapter, but Meyer has some other objections to raise.

First up, Strobel raises the question of the "prebiotic soup" - the dilute broth of organic molecules that's believed to have existed in the Earth's oceans before the origin of life, a fitting stage for many kinds of complex chemical reactions. This is a plausible environment for abiogenesis to take place, so Meyer tries to sow some doubt:

"I hear scientists talk a lot about this prebiotic soup," I said. "How much evidence is there that it actually existed?"

"That's a very interesting issue," he replied. "The answer is there isn't any evidence... If this prebiotic soup had really existed... it would have been rich in amino acids. Therefore, there would have been a lot of nitrogen, because amino acids are nitrogenous. So when we examine the earliest sediments of the Earth, we should find large deposits of nitrogen-rich minerals... Those deposits have never been located." [p.227]

There's no footnote for this, and I find it a puzzling and implausible argument. Earth today contains billions of tons of organic molecules locked up in life. But the Earth is a closed system. Aside from negligible contributions by comets and meteorites, the atoms on this planet today are the same ones that were here when it was first formed. As I mentioned in an earlier post, we know from Miller-Urey-type experiments that organic molecules like amino acids readily form in the presence of a source of energy. How could there not have been a prebiotic soup? What does Meyer imagine all those molecules were doing prior to the origin of life? (Then again, as I pointed out in chapter 4, Meyer appears to be a believer in the young-earth mythology - so maybe the alternative he's really trying to push is the Garden of Eden.)

Meyer also fails to qualify his mention of "earliest sediments". The earliest sediments, if by that he means sedimentary rocks of the same age as the origin of life, do not exist: erosion and plate tectonics tend to destroy and recycle the very oldest rocks. Most of the oldest surviving rocks that we possess are zircons, tiny mineral grains that form in igneous and metamorphic rocks. Zircons can be radiometrically dated, and some are known that are over 4 billion years old, but they don't offer any clues as to when life got started.

The oldest geologic evidence of life is significantly later. There are fossil stromatolites about 3.45 billion years old in rocks from the Warrawoona Group of Western Australia, which is the oldest clear evidence of living things. More controversially, there are rocks from Greenland about 3.85 billion years old that may contain "chemofossils". Living things concentrate the C-12 carbon isotope, rather than the slightly heavier C-13. These rocks show that same altered ratio, which could be a chemical marker left by early life. Evidence this subtle is still being debated by the scientific community, and given the extensive recycling of the Earth's oldest rocks, it's not reasonable to expect "large deposits" of nitrogen-rich minerals dating back to the origin of life to have survived.

Meyer has only one source to back up all of this, and it's a real laugh riot:

"In fact, Jim Brooks wrote in 1985 that 'the nitrogen content of early organic matter is relatively low - just .015 percent.' He said in Origins of Life: 'From this we can be reasonably certain that there never was any substantial amount of 'primitive soup' on Earth when pre-Cambrian sediments were formed; if such a soup ever existed it was only for a brief period of time.'" [p.227]

Strobel labels this an "astounding conclusion", but what he should be more astounded by is how far Meyer had to stretch to find a source for this claim. Wanting to verify this, I did a search for Jim Brooks' Origins of Life, only to find that it's long out of print according to several online booksellers. But more comical is that Strobel cites the publisher of this book as "Lion" - which I found out is Lion Hudson, which is, in fact, a Christian publishing house. A twenty-year-old, out-of-print book by a Christian publisher - that's the most reliable source that could be found to back up these assertions! Couldn't Meyer find even one actual scientific source to quote-mine?

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March 8, 2010, 1:21 pm • Posted in: The ObservatoryPermalink11 comments
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