A new paper in Proceedings of the National Academy of Sciences shows how a functional protein (an antifreeze protein in the blood of an Arctic fish) can be assembled out of scraps of genome that have no function at all. Moreover, the protein doesn’t become functional—e.g., being secreted into the fish blood to keep it from freezing—until the very last step of gene assembly, so the sequence looks “irreducibly complex”. But, contra the IDers, we can construct a perfectly naturalistic evolutionary sequence by looking at DNA in relatives and putative ancestors. This shows that the appearance of “irreducible complexity”—the existence of an adaptation that doesn’t seem to function until all its parts are in place—does not require a Behe-ian creationist Designer, but can arise from natural processes. But we already knew that.
Click on the segment below to read the paper; the reference is at bottom and the pdf is here.
The molecular mechanism and reconstruction of the evolutionary path is complicated, but I’ll try to present it in a stepwise fashion. (Remember that this is complex and I may get some stuff wrong; but I’ll do my best). Zhuang et al. used known phylogenies of fish related to the two “antifreeze” fish in the family Gadidae, a group of codfish. These codfish have functional antifreeze glycoproteins (AFGPs) that act to keep their blood from freezing when the cod swim in super-cold polar waters. The proteins do this by keeping ice crystals from forming and acting as sites of nucleation that could turn the fish into popsicles.
The fish’s AFGPs consist of three bits: the antifreeze protein itself, which consists of repeats of the amino acid sequence threonine-alanine-alanine (Thr-Ala-Ala), a second secretory protein that gives a signal to the genome to enable the antifreeze protein to be secreted into the blood, and a promoter region that is necessary to allow the DNA sequence to be transcribed into RNA (which then makes the antifreeze protein).
What’s remarkable about this configuration is that every bit of it, including the two proteins themselves and the promoter sequence, was cobbled together via translocations and duplications of DNA (this happens passively in the genome) until all the elements were in place. And the “functional” gene couldn’t function right up to the very end, when the promoter sequence moved to the right place to allow the protein-coding region to produce an RNA transcript. This entire series of steps was reconstructed by sequencing the DNA of relatives that don’t have functional AFGPs, so we could see the evolutionary order in which things were assembled, and where the functional bits originally came from.
Here’s how it occurred; this is Figure 4 from the paper, and I give its caption:
The evolutionary stages posited (and supported by sequence and phylogenetic analysis) are A-F. First, there is a sequence of GCAGCAGCA in an ancestor, a sequence that would normally code for repeated alanines, but wasn’t functional (this is found in a relative). It expanded through duplication: A —>B.
Then, a mutation from a guanine to a cytosine base in another ancestor converted one Ala-Ala-Ala sequence to a Threonine-Alanine-Alanine amino acid triplet, which itself expanded through successive duplications (B —>C). The gene now had four Thr-Ala-Ala units, but was still nonfunctional. But this was to be the core of the functional protein in the future; it’s the dark blue bit seen in C through F above.
Another part of the genome had a nonfunctional sequence that could serve as the secretory protein to get the dark blue protein secreted into the blood. A deletion of a single nucleotide (C—>E) rendered it capable of producing a signal protein (the purple bit in D-F). But the entire system was still nonfunctional because it lacked a promoter region.
Finally, the system became functional when the protogene moved to a location near a nonfunctional DNA region that could serve as a promoter for the nascent gene. Now a gene producing a repeated Thr-Ala-Ala protein could function and secrete it into the blood.
Further, natural selection could now act on the functioning gene to make it more effective, simply by selecting for those genes that had even more duplications of the Thr-Ala-Ala segment, so we had a big protein of repeated units that could act as an antifreeze in fish blood (E—>F). (More repeats = better antifreeze protection.)
It’s a bit more complicated than this, but this is the essence of how the final protein came to be. And it’s not speculation, because all the bits can be found in other species or posited in ancestors, and so this reconstruction is fairly sound. Moreover, it involves processes known to operate in the DNA: the moving of bits around by translocation, duplication of sequences, etc. No divine intervention is required to do this, even though the protein isn’t functional until it’s put together with the secretory protein and the promoter.
One might ask this reasonable question: “Well, if the nascent antifreeze protein is just sitting there and not doing anything before it becomes active, why isn’t it inactivated by mutations?” That’s a good question, and one answer is that the process took place reasonably quickly so that mutations (which are, after all, rare) didn’t have time to turn the dark blue protein core into gibberish. And once that core formed, duplication of the Thr-Ala-Ala would be rapid, promoted by natural selection because more repeats confer greater antifreeze activity.
So here we have an “irreducibly” complex system, functional as an antifreeze system only at the very end, but one that formed purely through natural and well-known genomic processes. No God or alien designer required. It’s a good example of how hard work (sequencing and phylogenetic reconstruction) can dispel the objection “we don’t understand how this irreducibly complex system formed, so God must have done it.”
The whole paper, besides being a really lovely piece of work, is a slap in the face of IDers like Michael Behe—a fish slap like the one below:
Zhuang, X., C. Yang, K. R. Murphy, and C.-H. C. Cheng. 2019. Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids. Proceedings of the National Academy of Sciences 116:4400-4405.