My feeling about science news reports is decidedly mixed. On the one hand, I read most of the main news services in order to keep up with research outside of my own discipline. On the other hand, I would say that about once every two or three days I find a story so silly that it makes me physically uncomfortable. This is one of those.

Evolution’s new wrinkle: proteins with ‘cruise control’ act like adaptive machines

It opens:

A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.

The research, which appears to offer evidence of a hidden mechanism guiding the way biological organisms respond to the forces of natural selection, provides a new perspective on evolution, the scientists said.

Organisms do not “respond to natural selection”. Natural selection is the differential survival and reproduction of individuals within a population. It is a population level process and it is not interchangeable with “challenges to organism survival”. If all organisms in a population are able to respond to a challenge such that there is no differential survival and reproductive success, then there is no natural selection.

It continues:

The researchers — Raj Chakrabarti, Herschel Rabitz, Stacey Springs and George McLendon — made the discovery while carrying out experiments on proteins constituting the electron transport chain (ETC), a biochemical network essential for metabolism. A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.

“The discovery answers an age-old question that has puzzled biologists since the time of Darwin: How can organisms be so exquisitely complex, if evolution is completely random, operating like a ‘blind watchmaker’?” said Chakrabarti, an associate research scholar in the Department of Chemistry at Princeton. “Our new theory extends Darwin’s model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness.”

Adaptive evolution is the result of natural selection — the differential survival and reproduction of randomly varying individuals on the basis of heritable characteristics. This differential survival and reproduction is, by definition, non-random. Again, organisms do not evolve, populations do.

And then it says:

The work also confirms an idea first floated in an 1858 essay by Alfred Wallace, who along with Charles Darwin co-discovered the theory of evolution. Wallace had suspected that certain systems undergoing natural selection can adjust their evolutionary course in a manner “exactly like that of the centrifugal governor of the steam engine, which checks and corrects any irregularities almost before they become evident.” In Wallace’s time, the steam engine operating with a centrifugal governor was one of the only examples of what is now referred to as feedback control. Examples abound, however, in modern technology, including cruise control in autos and thermostats in homes and offices.

The essay is the one presented by Lyell and Hooker to the Linnean Society in 1858, along with one by Darwin. Here is the full paragraph:

Wallace (1858):

The hypothesis of Lamarck—that progressive changes in species have been produced by the attempts of animals to increase the development of their own organs, and thus modify their structure and habits—has been repeatedly and easily refuted by all writers on the subject of varieties and species, and it seems to have been considered that when this was done the whole question has been finally settled; but the view here developed renders such an hypothesis quite unneccessary, by showing that similar results must be produced by the action of principles constantly at work in nature. The powerful retractile talons of the falcon- and the cat-tribes have not been produced or increased by the volition of those animals; but among different varieties which occurred in the earlier and less highly organized forms of these groups, those always survived longest which had the greatest facilities for seizing their prey. Neither did the giraffe acquire its long neck by desiring to reach the foliage of the more lofty shrubs, and constantly stretching its neck for the purpose, but because any varieties which occurred among its antitypes with a longer neck than usual at once secured a fresh range of pasture over the same ground as their shorter-necked companions, and on the first scarcity of food were thereby enabled to outlive them. Even the peculiar colours of many animals, especially insects, so closely resembling the soil or the leaves or the trunks o which they habitually reside, are explained on the same principle; for though in the course of ages varieties of many tints may have occurred, yet those races having colours best adapted to concealment from their enemies would inevitably survive the longest. We have also here an acting cause to account for that balance so often observed in nature,—a deficiency in one set of organs always being compensated by an increased development of some others—powerful wings accompanying weak feet, or great velocity making up for the absence of defensive weapons; for it has been shown that all varieties in which an unbalanced deficiency occurred could not long continue their existence. The action of this principle is exactly like that of the centrifugal governor of the steam engine, which checks and corrects any irregularities almost before they become evident; and in like manner no unbalanced deficiency in the animal kingdom can ever reach any conspicuous magnitude, because it would make itself felt at the very first step, by rendering existence difficult and extinction almost sure soon to follow. An origin such as is here advocated will also agree with the peculiar character of the modifications of form and structure which obtain in organized beings—the many lines of divergence from a central type, the increasing efficiency and power of a particular organ through a succession of allied species, and the remarkable persistence of unimportant parts such as colour, texture of plumage and hair, form of horns or crests, through a series of species differing considerably in more essential characters. It also furnishes us with a reason for that “more specialized structure” which Professor Owen states to be a characteristic of recent compared with extinct forms, and which would evidently be the result of the progressive modification of any organ applied to a special purpose in the animal economy.

Wallace was talking about the consequences of randomly determined variants that had a change in one feature without a compensatory change in some other feature, namely that they would not survive. There is nothing in this that implies that individual organisms are changing in response to challenges or that species are directing their evolution.

It goes on, but I will jump forward:

The research, published in a recent edition of Physical Review Letters, provides corroborating data, Rabitz said, for Wallace’s idea. “What we have found is that certain kinds of biological structures exist that are able to steer the process of evolution toward improved fitness,” said Rabitz, the Charles Phelps Smyth ’16 Professor of Chemistry. “The data just jumps off the page and implies we all have this wonderful piece of machinery inside that’s responding optimally to evolutionary pressure.”

The authors sought to identify the underlying cause for this self-correcting behavior in the observed protein chains. Standard evolutionary theory offered no clues. Applying the concepts of control theory, a body of knowledge that deals with the behavior of dynamical systems, the researchers concluded that this self-correcting behavior could only be possible if, during the early stages of evolution, the proteins had developed a self-regulating mechanism, analogous to a car’s cruise control or a home’s thermostat, allowing them to fine-tune and control their subsequent evolution. The scientists are working on formulating a new general theory based on this finding they are calling “evolutionary control.”

…

Various researchers working over the past decade, including some at Princeton like George McClendon, now at Duke University, and Stacey Springs, now at the Massachusetts Institute of Technology, fleshed out the workings of [ATP], finding that they were often turned on to the “maximum” position, operating at full tilt, or at the lowest possible energy level.

Chakrabarti and Rabitz analyzed these observations of the proteins’ behavior from a mathematical standpoint, concluding that it would be statistically impossible for this self-correcting behavior to be random, and demonstrating that the observed result is precisely that predicted by the equations of control theory. By operating only at extremes, referred to in control theory as “bang-bang extremization,” the proteins were exhibiting behavior consistent with a system managing itself optimally under evolution.

Based on this story, it is challenging to determine just how this is differs from evolution in the usual sense. Looking at the original paper, it appears that what the authors are arguing is that 1) the constituent proteins in the electron transport chain are tuned to an extreme, 2) that this extreme is not related to the function of the proteins as would be “visible” to natural selection on the grounds of electron transport capability, 3) that the proteins in the network are optimized for redox potential, which has no consequences for the organism and therefore cannot have evolved through normal selection, and 4) that something else, i.e. self organization, is involved in producing the extreme features of the proteins. The rest is mathemagic, so someone else can wade through it and see if the argument makes sense if they like.

I am not actually concerned with whether the calculations are correct. As it so often is, the issue is about press releases and the hype and sloppy descriptions of both ideas and history that they (and, too often, the people interviewed) present.

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Update:

PZ weighs in.

People have been having trouble finding the article. It’s here.

The authors have another paper in the bastion of bad biology, arXiv, that quotes directly from Wallace (here). Don’t blame the story author, these guys lifted that out of context by their own selves.