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Proteins by Accident? Replying to a Critic of The Information Enigma

Douglas Axe

Axe Protein.jpg

Stephen Meyer and I appear in a new video from Discovery Institute, The Information Enigma, that shows how the information in DNA and proteins provides strong evidence for intelligent design. At the YouTube channel for the Center for Science & Culture, the video has generated some spirited discussion, which is good.

One commenter, who goes by the name ExtantFrodo2, has risen to the defense of Darwinism by enlisting several familiar Darwinian arguments, all of which make the evolutionary invention of new functional proteins sound much easier than it really is. The heavy use of arguments along these lines makes a response worthwhile, I think.

This excerpt from one of ExtantFrodo2’s comments expresses the evolutionary thinking well:

The proteins are simply shapes. Mutation makes the shapes different. Different shapes are new tools. Some are bad & cause death to the organism. Others have no affect. Very rarely one shape turns out to be useful somewhere in the cell. It’s only a metaphor to call it ‘information’. DNA is a mutable template (or jig) that is cast into protein. Change the template & you change the protein. The protein may be more effective, less effective, or even completely changed (frame-shift and/or critical linkage points like di-sulfide bonds). Furthermore mutations often occur on copies or duplicates of a gene, so no former functionality (protein production) need be lost at all. As the jig or mold is transformed by mutation it produces different proteins that interact with the environment (and the cell) in new & different ways.

The first misconception here has to do with protein shapes. Since proteins are long flexible chains of linked amino acids, it’s somewhat surprising that they can have fixed three-dimensional shapes at all. A strand of beads, for example, has no fixed shape. Why would a strand of amino acids be different?

In fact, the vast majority of possible protein chains are like strands of beads — lacking any fixed shape. Life, however, makes critical use of a very special subset of the possibilities. These special proteins are coaxed into forming precise shapes by the sequence of amino acids along their chains. The process triggered by this coaxing, where a floppy protein chain rapidly acquires a well-formed structure, is known as folding.

To give you an idea of how special these folding sequences are, the Journal of Molecular Biology paper referred to in the video estimates the proportion of chains that fold to be in the range of one in 1050 to one in 1074, depending on the complexity of the fold.

Even for simple folds, this means fewer than one in a trillion trillion trillion trillion amino acid sequences forms any well-defined shape at all. So the idea that every protein sequence has a shape is not at all accurate.

Secondly, the related idea that mutations merely change the shapes of proteins is equally inaccurate. The highly cooperative nature of protein folding means that it tends to be all-or-nothing. A particular protein sequence either forms structure A or it doesn’t, and likewise for structure B. So for a series of mutations to convert a protein from forming structure A to forming structure B, they would first have to undo the A structure (producing a chain with no well-defined structure) and then stabilize the B structure.

In other words, changing the structure of a protein isn’t nearly as easy as changing the shape of a lump of clay. The clay always has a shape, and with a little imagination we can even say the shape always represents something (which is all we ask of a lump of clay).

Proteins are different. Only highly exceptional proteins even have a shape, and these shapes are therefore fragile. Mutations are tolerated to a modest extent, after which all shape is lost.

Finally, the idea that it isn’t hard to stumble upon things that are good for something, while very popular in evolutionary circles, doesn’t explain the origin of exquisite things. Sure, the blobs of solder and scraps of metal or plastic you find on the floor of a workshop can be used for something — this one a straight edge (in a pinch), that one a makeshift coaster, maybe a paperweight over there. But this make-do approach clearly doesn’t work for impressive things — not for the things we humans set out to make, and still less for the far more exquisite things we see in life.

Such things never happen by accident.

Douglas Axe

Maxwell Professor of Molecular Biology at Biola University
Douglas Axe is the Maxwell Professor of Molecular Biology at Biola University, the founding Director of Biologic Institute, the founding Editor of BIO-Complexity, and the author of Undeniable: How Biology Confirms Our Intuition That Life Is Designed. After completing his PhD at Caltech, he held postdoctoral and research scientist positions at the University of Cambridge and the Cambridge Medical Research Council Centre. His research, which examines the functional and structural constraints on the evolution of proteins and protein systems, has been featured in many scientific journals, including the Journal of Molecular Biology, the Proceedings of the National Academy of Sciences, BIO-Complexity, and Nature, and in such books as Signature in the Cell and Darwin’s Doubt by Stephen Meyer and Life’s Solution by Simon Conway Morris.



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