Posted by: Mr. C | May 7, 2008

Enzymes, DNA, Darwin, and Design

Douglas Axe has written a fascinating article about one of the building blocks of life and how it points to a designer. Here is a link to the original article.

The full text follows:

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Leaping into Trouble — April 3rd, 2008 by Douglas Axe

Darwinists have always recognized the existence of an intuitive barrier that prevents many of us from joining them. Human understanding of complex things is strongly shaped by our experiences with human technology. You don’t have to be an engineer to appreciate in some way the extraordinary difficulty of getting physical systems to perform extraordinary tasks. Technology doesn’t just happen. It only comes with sizable investments of genius and diligence, along with more than a little patience.

So Darwin’s suggestion that genius and diligence are optional if patience is plentiful is a stretch for most of us. Richard Dawkins put it this way:

It took a very large leap of imagination for Darwin and Wallace to see that, contrary to all intuition, there is another way and, once you have understood it, a far more plausible way, for complex ‘design’ to arise out of primeval simplicity. A leap of the imagination so large that, to this day, many people seem unwilling to make it. [1]

I doubt anyone, Dawkins included, would generally recommend sweeping aside all intuition to accommodate leaps of imagination, particularly when the intuition is your own and the leap is not. If Darwinism really is plausible, it must instead be the case that Darwin leapt to something of substance—something that really explains how, contrary to our intuitions, the remarkable gadgets we see in biology can be chalked up to mindless inevitability. What exactly is this explanation? It needs to be compelling, whatever it is, since the intuition we’re being asked to abandon is so tied to real-world experience—the very stuff of science.

About forty years ago, plant physiologist Frank Salisbury posed the question in terms of the origin of enzymes, the intricately folded protein chains that do all of life’s chemistry. Appearing in thousands of distinct natural forms, each form suited to a well-defined function or set of functions, these tiny workhorses have proven to be technological wonders not just inside cells but in laboratories as well. Much of today’s advanced technology for manipulating and analyzing DNA depends on them. Genomes don’t get sequenced without them. Whole companies are devoted to purifying them and selling them. [2] Do little marvels like that really just happen if we wait long enough? Long before the age of genomics, Salisbury put the question this way:

In reasonable time intervals, is mutation by random rearrangement of nucleotides [i.e., DNA bases] likely to produce an enzyme… Will there be an enzyme (gene) for selection to act on? [3]

Here’s the problem. Enzymes, like all proteins, are built within cells by linking amino acids together into long chains. There are 20 different amino acids, any one of which could potentially be placed at any position along the chain. But the actual chain sequences are anything but arbitrary. Rather, cells use elaborate machinery to link the amino acids according to the precise sequence specifications contained in genes. And because the protein chains are typically hundreds of amino acids long, the cellular machinery is hitting a very tight design specification every time a protein is made. So, even if we grant that some changes to these specifications are tolerable, the mere existence of a production line tuned to such precision implies that the precision is needed. If so, enzymes are much more complicated than they should be if they just happened. A short word might surface in your alphabet soup by chance, but a paragraph won’t.

In response to Salisbury, eminent British biologist John Maynard Smith offered an analogy along the lines of alphabet soup, starting with this succession of words:

WORD -> WORE -> GORE -> GONE -> GENE.

“This is an analogue of evolution,” he wrote, “in which the words represent proteins; the letters represent amino acids; the alteration of a single letter corresponds to the simplest evolutionary step, the substitution of one amino-acid for another; and the requirement of meaning corresponds to the requirement that each unit step in evolution should be from one functional protein to another.”[4] It’s an analogy worth considering because, despite its simplicity, it does capture the crucial aspect of different functions arising from different sequences.

Maynard Smith reasoned that for evolution to work, all functional proteins must be interconnected by stepwise changes in a manner analogous to four-letter words. But does his succession of words really illustrate Darwinian evolution? And is it really reasonable to think that proteins are analogous to four-letter words in this respect?

Actually, there appears to be a significant problem with the illustration itself. For a succession of changes to illustrate an adaptive process, each one has to provide not just function but function that is helpful in the sense of advancing a principal objective. For Darwinism, the principal objective is reproductive success. New functions are only adaptive if they advance that objective. Language has communication as a principal objective. While these objectives are very different, both imply that functions are very unlikely to be helpful simply by virtue of being new.

For example, imagine needing to communicate something with a vocabulary restricted to four-letter English words. “NEED HELP CALL COPS”, might be the desired message. As a further restriction, suppose you’re granted your first word but have to construct the rest of your message from single-letter variants of that word or subsequent ones. Suppose also that adding a word is permissible only if it advances your communication objective as is. It becomes apparent that your objective needs to be met with your first word—the one given to you—because these constraints virtually preclude adding anything to it. “HELP” on its own is much better than “HELP KELP” or “HEAP HELP”.

Furthermore, if letters correspond to amino acids, as Maynard Smith suggested, then biological functions that require several protein chains, each consisting of hundreds of amino acids, are more like lengthy messages than short words. If Darwin’s approach has trouble finding the words to summon the police, just imagine how much trouble it would have dispatching the police—to a particular location, prepared to deal with particular circumstances.

Of course, we should keep in mind that the exchange between Salisbury and Maynard Smith took place in 1969, when molecular biology was in its infancy. The genetic code, used by cells to build proteins according to the sequence information in genes, had just been cracked; only a few protein structures were known [5]; and the beginnings of the boom in DNA technology were still years away. But did the huge scientific discoveries of the subsequent decades strengthen Maynard Smith’s case? Have we found that protein structures, and therefore sequences, are mostly accretions of junk, with just a handful of amino-acid residues forming the equivalent of his four-letter words?

Quite the opposite. I was present in 1997 when the champagne was uncorked at the MRC Centre in Cambridge in honor of John Walker. He was to share the Nobel Prize in chemistry that year with Paul Boyer and Jens Christian Skou for his work on the structure of the enzyme complex that uses pH gradients to drive ATP synthesis. Known as F-type ATPase, this molecular machine is built of dozens of protein chains of seven specialized types. Boyer was not exaggerating when he described it as “aF-type ATPase image splendid molecular machine”. [6] With design elegance and miniaturization wholly unrivaled in human technology, the F-type ATPase is a double energy transducer, first converting gradient energy into rotational energy, and then using the rotational energy to make ATP, the chemical energy currency used in all life—all in a package 1/500 the size of a small pollen grain.

There is no junk here. The ATPase is made not of four amino acids but four thousand—more like an essay than a paragraph (much less a word). Could it have started out much smaller? Not much, in view of the two sections that have to be coupled for it to work. Like an essay, it might withstand trimming in some places, and some of the parts might be reworded if we knew the rules of composition for proteins. Typos can be tolerated to an extent, as with essays. But none of this explains how random single-letter changes can produce new essays, whether from scratch or from existing essays on other subjects. According to intuition, there’s only one way to get an essay.

So, Maynard Smith’s beautiful analogy ends up supporting the design intuition that troubles Darwinism so. And the funny thing is, it’s awfully hard to find an analogy that doesn’t do that. Maybe that’s why so many people are unwilling to leap along with Darwin’s imagination. And maybe that’s why the leapers keep resorting to the same arguments, long after their flaws are known.

The year that we toasted Walker’s achievements, geneticist Graham Bell’s excellent monograph on natural selection came out. [7] Upon receiving my copy and glancing at the contents, I immediately turned to section 10, titled: “Very improbable structures readily arise through the cumulation of small alterations.” That would certainly solve the problem, if structural innovations could morph themselves into existence, one adaptive frame at a time. So, was Bell going to deliver the goods that no one else seemed to be able to deliver? Was the long awaited violation of the design intuition finally going to be revealed?

I’m afraid not. Bell took his argument straight from Maynard Smith:

WORD -> WORE -> GORE -> GONE -> GENE.

Evidently three decades of huge advances in molecular biology hadn’t improved the case for the leap.

What about the design intuition, though? If proposed justifications for the leap always come up short, often validating the design intuition instead, doesn’t that indicate something more substantive than an intuition? Many would argue that it does, and you have to admit that their position has something potent in its favor. It’s called common sense. No leap required.


[1] Dawkins R (1986) The Blind Watchmaker. Penguin Books.
[2] http://www.neb.com/nebecomm/about.as
[3] Salisbury FB (1969) Natural selection and the complexity of the gene. Nature 224: 342-343.
[4] Maynard Smith J (1970) Natural selection and the concept of a protein space. Nature 225: 563-564.
[5]http://pdbbeta.rcsb.org/pdb/statistics/contentGrowthChart.do?content=molType-protein&seqid=100
[6] http://www.ncbi.nlm.nih.gov/pubmed/9242922
[7] Bell G (1997) Selection—The Mechanism of Evolution. Chapman & Hall.

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