A paper by a member of the Department of Physics and Astronomy, Rutgers University, offered the following significance statement:
Proteins are the prime example of self-organized networks, as they have benefited from extensive natural (Darwinian) selection. Here, we quantify the dynamical shapes of dynein as they have evolved through interactions with water films. The interactions are long-range and are easily identified, and their improvement by evolution varies with the functions of parts of this molecular motor. It appears that evolution has brought human dynein close to a dynamical critical point, indicative of intelligent design. – Self-organized networks: Darwinian evolution of dynein rings, stalks, and stalk heads, J. C. Phillips, PNAS April 7, 2020 117 (14) 7799-7802; first published March 23, 2020 https://doi.org/10.1073/pnas.1920840117 (paywall)
Well! Intelligent design? Never mind that author Phillips also identifies the cause of these networks as as “extensive natural (Darwinian) selection.” Soon there was a letter from Eugene V. Koonin et al., decrying such suspected heresy:
No waves of intelligent design – August 18, 2020
“In summary, it is unfortunate when observations on simple patterns in biological sequences are overinterpreted to overthrow the fundamental tenets of evolutionary biology. Invoking intelligent design in an attempt to buttress unjustified generalizations on evolution is non sequitur writ large.” – No waves of intelligent design, Eugene V. Koonin, Yuri I. Wolf, Mikhail I. Katsnelson Proceedings of the National Academy of Sciences 2020 117 33
Phillips, presumably preparing for the upcoming struggle session, writes back to say (it’s mostly paywalled but you can read this part for free):
I am grateful to Koonin et al. (1) for highlighting the question of whether positive Darwinian evolution occurs at the molecular level, or only neutral evolution (generally accepted). In a series of papers, I have displayed evidence for positive Darwinian evolution of proteins, using a new hydropathic method based on statistical physics (self-organized criticality) (2) and (synchronizable) network theory (3, 4). While the main structural features of proteins have been formed over long times, the recent evolution of many proteins shows features evolving with function in a way not explained by conservation of the protein fold. A classic example is hen egg white, whose peptide backbone has remained …
A scout sent us a copy of the whole thing, titled “Evolution of proteins is Darwinian.” Thus, we can also provide, starting from the truncated sentence in the last paragraph above,
A classic example is hen egg white, whose peptide backbone has remained almost unchanged from chicken to human, but whose sequences have evolved to perform new functions (5, 6). In other words, conservation of protein fold (neutral evolution) does not explain positive Darwinian evolution of protein function.
Granted that protein functions are complex, what obvious reason is there to suppose that Darwinian evolution can be analyzed from protein amino acid sequences alone? None, but even so, it appears to have happened, and this is where the tools of physics (2) and mathematics (3) apply. – Reply to Koonin et al.: Evolution of proteins is Darwinian J. C. Phillips, Proceedings of the National Academy of Sciences 2020 117 33
Now here’s the abstract:
Abstract: Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin, and dynein. Their positive Darwinian evolution enables them to approach optimized functionality (self-organized criticality). Dynein has three distinct titled subunits, but how these units connect to function as a molecular motor is mysterious. Dynein binds to tubulin through two coiled coil stalks and a stalk head. The energy used to alter the head binding and propel cargo along tubulin is supplied by ATP at a ring 1,500 amino acids away. Here, we show how many details of this extremely distant interaction are explained by water waves quantified by thermodynamic scaling. Water waves have shaped all proteins throughout positive Darwinian evolution, and many aspects of long-range water–protein interactions are universal (described by self-organized criticality). Dynein water waves resembling tsunami produce nearly optimal energy transport over 1,500 amino acids along dynein’s one-dimensional peptide backbone. More specifically, this paper identifies many similarities in the function and evolution of dynein compared to other cytoskeleton proteins such as actin, myosin, and tubulin.
It’s possible that what Phillips means by “positive Darwinian selection” is random selection that looks a lot like design. The sin is in actually using words that imply that that IS what it looks like.
Been in the news business fifty years. These flaps signify unease within the orthodoxy. And just when it looks like they’ve hammered everything into submission, another bulge appears. – O’Leary for News
Notice, by the way, that only Koonin’s attack on the paper is free to the public, not the paper or the reply to Koonin. Not saying that it proves anything. But it is just so typical.