Steve Meyer, Signature in the cell:
Sometimes critics point out that some functional amino acid chains, such as peptide hormones, have fewer than 150 amino acids. Some peptide hormones, for example, are just a few tens of amino acids long, though some are much longer. And there are also some proteins that are shorter than 150 amino acids. Critics ask: “Couldn’t such molecules have arisen by random chemical interactions and then evolved into longer functional molecules?” Functional proteins (including all enzymes) depend upon complex folds, or “tertiary structures.” Attaining tertiary structures in proteins requires about 50 properly sequenced amino acids for the simplest structures and many more (typically hundreds) for more common structures. These thresholds of minimal function vary from protein to protein. Just because one protein fold or tertiary structure may need just 50 specifically sequenced amino acids does not mean that another can form with that few. Most can’t. The protein equivalent of a ruler may form with only 50 amino acids, but the hammer and saw may need 150, the wrench 200, and the drill 300. Many of the functions that a minimally complex cell requires depend upon these longer proteins. Thus, the presence of some shorter proteins does nothing remove the need for many larger proteins in the origin of life. There are physical reasons that short proteins with small tertiary structures can’t be gradually transformed into larger tertiary structures. Short proteins typically exhibit a hydrophilic exterior. To build a larger structure around them, at least some of this hydrophilic exterior would have to become interior to the larger structure. But this requires, among other things, that a region of hydrophilic surface become hydrophobic, which in turn requires many simultaneous amino acid changes. Having a short protein to start with contributes little or nothing toward building a larger one. The same probabilistic hurdles have to be overcome in sequencing. In any case, it is important to distinguish between peptides that function without a folded structure at all and proteins that function only with a folded structure. The former (which includes for example short peptide hormones) are functional only by virtue of binding to larger folded protein structures. But this implies that these shorter molecules have no function—and no selective advantage—apart from the prior existence of much larger protein molecules. Thus, citing functional peptide hormones as a starting point for evolution begs the question as to the origin of the larger protein molecules that give them functional significance. It only pushes the problem back to where it started—to the problem of explaining the origin of large functionally specified proteins by random happenstance. Indeed, absent long functional protein molecules—and, realistically, a minimally complex self-reproducing cell—there would be no context to confer functional significance or advantage on either unfolded peptide hormones or shorter proteins (for that matter).