January 26, 2011 | David F. Coppedge

Evolutionists Admit It’s About Mistakes

Evolution by Mistake” is the headline of an article about evolution on Science Daily.  Can the protagonists get mistakes to create eyes, wings, and brains?
    The rest of the headline reads: “Major Driving Force Comes from How Organisms Cope With Errors at Cellular Level.”  Right off the bat, a tension seems set up between errors, which are directionless and purposeless, and how organisms cope with them, which at first glance seems a matter of design and purpose (as in a corporate security policy or anti-virus software).  But this is not an appeal to intelligent design.  “Charles Darwin based his groundbreaking theory of natural selection on the realization that genetic variation among organisms is the key to evolution,” the opening sentence declared.  The tip of the hat to Darwin means they intend to explain all of the wonders of the living world by descent with modification from bacteria to man.  Can they pull it off with “evolution by mistake”?
    Like Darwin, Joanna Masel and Etienne Rajon at University of Arizona (smiling at the whiteboard in a photo), recognize the exquisite adaptation of organisms to their environment.  “But exactly how nature creates variation in the first place still poses somewhat of a puzzle to evolutionary biologists,” the article admitted.  That may appear strange to readers who thought Darwin or the neo-Darwinists had that issue wrapped up long ago.
    Masel and Rajon “discovered the ways organisms deal with mistakes that occur while the genetic code in their cells is being interpreted greatly influences their ability to adapt to new environmental conditions – in other words, their ability to evolve.”  They are implying that ability to evolve will lead to innovation (wings, eyes, brains), because later, the phrase “how nature creates innovation” appears.  Can they get from errors to innovation?  If so, they need to do it without personifying evolution, so readers had best forgive this line that mixes up personified evolution with intelligent design:

Evolution needs a playground in order to try things out,” Masel said  “It’s like in competitive business: New products and ideas have to be tested to see whether they can live up to the challenge.”

Overlooking that slip, they delved into the details of their idea:

In nature, it turns out, many new traits that, for example, enable their bearers to conquer new habitats, start out as blunders: mistakes made by cells that result in altered proteins with changed properties or functions that are new altogether, even when there is nothing wrong with the gene itself.  Sometime later, one of these mistakes can get into the gene and become more permanent.

Keep your eyes on the ball.  The reader wants to see innovation, like an eye, or a wing, or a brain, where it didn’t exist before.  So far we have blunders that alter proteins.  The gene was fine, but something happened downstream.  “Sometime later, one of these mistakes can get back into the gene,” they claimed.  Any evidence?  None in the article.
    They next distinguished between global and local solutions.  The global solution, they said, is “to avoid making errors in the first place, for example by having a proofreading mechanism to spot and fix errors as they arise.”  Something “watches over the entire process,” they said, begging the question again of how an entire process that watches for errors and fixes them could itself be a product of mistakes.  Regardless, global solutions are about preserving integrity of the genome, not innovating wings, eyes, and brains.  Innovation will have to be local:

The alternative is to allow errors to happen, but evolve robustness to the effects of each of them.  Masel and Rajon call this strategy a local solution, because in the absence of a global proofreading mechanism, it requires an organism to be resilient to each and every mistake that pops up.
    “We discovered that extremely small populations will evolve global solutions, while very large populations will evolve local solutions,” Masel said.  “Most realistically sized populations can go either direction but will gravitate toward one or the other.  But once they do, they rarely switch, even over the course of evolutionary time.”

This paragraph is full of strategy – another ostensibly purposeful concept.  If an organism has a strategy to allow some errors to creep in, but then “evolve robustness” to their effects, did that strategy itself evolve by mistake?  They didn’t say.
    Next, they introduced a contrast between “regular variation, which is generally bad most of the time, since the odds of a genetic mutation leading to something useful or even better are pretty slim,” (see online book for calculation), “and what they call cryptic variation, which is less likely to be deadly, and more likely to be mostly harmless.”  Even so, a poison pill and a placebo are not likely to produce wings, eyes, and brains.  If you have an antidote to the poison pill, or a process to avoid swallowing it in the first place, it won’t kill you, but the placebo (cryptic variation), even if it is “mostly harmless,” contains no power to innovate.  You are not likely to get a third eye from it. 

So how does cryptic variation work and why is it so important for understanding evolution?
    By allowing for a certain amount of mistakes to occur instead of quenching them with global proofreading machinery, organisms gain the advantage of allowing for what Masel calls pre-selection: It provides an opportunity for natural selection to act on sequences even before mutations occur.

The critical reader of this paragraph is going to want to know not just whether their theory can produce innovation from mistakes, but how their theory itself arose from mistakes.  In other words, they talked about cryptic variation working, about importance, about understanding, about strategies of allowing some mistakes but not others – who or what decides?  They swept right past the question of how “global proofreading machinery” could ever arise from mistakes, to the grand fallacy (see Weinberg’s Corollary) of pre-selection as “an opportunity for natural selection to act”.  Is natural selection a person?  Does it have a plan?  How would natural selection have any precognition of the need for an eye, a wing, or a brain?
    A mistake that leads to a misfolded protein, they admitted, could be “very toxic to the organism.”  Creationists would agree that “In this case of a misfolded protein, selection would favor mutations causing that genetic sequence to not be translated into protein or it would favor sequences in which there is a change so that even if that protein is made by accident, the altered sequence would be harmless.”  Purifying selection (eliminating mistakes) and compensating selection (tolerating mistakes) are not controversial: unless you avoid taking the poison pill, or have no antidote, you die without passing on your genes.  Having those protections still won’t give you a wing, an eye, or a brain.  But if you just had the opportunity to get them, wouldn’t you want them?

Pre-selection puts that cryptic variation in a state of readiness,” Masel said.  “One could think of local solutions as natural selection going on behind the scenes, weeding out variations that are going to be catastrophic, and enriching others that are only slightly bad or even harmless.
    “Whatever is left after this process of pre-selection has to be better,” she pointed out.  “Therefore, populations relying on this strategy have a greater capability to evolve in response to new challenges.  With too much proofreading, that pre-selection can’t happen.

Masel’s wording recalls Darwin’s personified depiction of his theory: “Natural selection is daily and hourly scrutinizing, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life.”  But even Darwin might have balked at the idea of pre-selection, that natural selection would keep harmless variations in a junkyard for scrutinizing later.  Masel argued that “the organism doesn’t pay a large cost for it, but it’s still there if it needs it.
    How big a junkyard can an organism afford to keep around?  Masel and Rajon recognized the cost of error correction:

Avoiding or fixing errors comes at a cost, they pointed out.  If it didn’t, organisms would have evolved nearly error-free accuracy in translating genetic information into proteins.  Instead, there is a trade-off between the cost of keeping proteins free of errors and the risk of allowing potentially deleterious mistakes.

The accuracy of error correction is indeed surprisingly high, but there is also a cost of hanging onto useless junk.  All the junk has to be copied every time a cell divides, and transported in a dynamic environment where the need to eat, eliminate, defend and adapt are ever present.  It may be that some organisms carrying around huge genomes are at a disadvantage and are headed for extinction.  Maybe they still need time to sift through their junk for parts of eyes, wings, and brains.
    The authors ended on a biomimetic theme.  Engineers, too, may want to imitate the practice of evolution by mistake:

“We find that biology has a clever solution.  It lets lots of ideas flourish, but only in a cryptic form and even while it’s cryptic, it weeds out the worst ideas.  This is an extremely powerful and successful strategy.  I think companies, governments, economics in general can learn a lot on how to foster innovation from understanding how biological innovation works.

Most entrepreneurs, while admitting the value of brainstorming, trial and error, and even “evolutionary algorithms” (10/04/2005, 04/18/2009) will recognize that what they do has purpose and intent.  The same cannot be said of mistakes in yeast cells that Masel and Rajon studied.
Paper View
It might be said in the authors’ defense that the popular press had to oversimplify and personify their ideas for the lay public; the original paper in PNAS is where the goods are.1  A look at the abstract, though, shows a strong requirement: “The local solution requires powerful selection acting on every cryptic site and so evolves only in large populations.”  Yet the local solution is the only one pregnant with innovating potential, because “Strongly deleterious effects can be avoided globally by avoiding making errors (e.g., via proofreading machinery) or locally by ensuring that each error has a relatively benign effect.”  If large populations with mistakes of “relatively benign effect” is the best one can hope for, will wings, eyes, and brains follow?
    In the body of the paper, the words innovate or innovation are nowhere to be found.  The stem improve is only found in reference to “improved proofreading machinery,” which they assume already existed.  There are equations about fitness, but with apparently no linkage to innovation: “components of fitness associated, respectively, with the expression of cryptic sequences, with deleterious sequences becoming permanently expressed through new mutations and with the cost of proofreading during protein synthesis.”  But cryptic sequences, remember, are only variations that do not kill the organism.  They are mistakes that are tolerated and kept in store.  Other mentions of fitness concern deleterious mutations, loss of function, and null fitness, except where additive fitness is offered hopefully: “Fitness in the additive scenario depends on the total concentration of all deleterious products within the cell and on their toxicity.”  It sounds more like a bomb shelter than a lab for innovation.  The authors use fitness primarily as a measure of mutations that assimilate in a population without getting edited out.  The last paragraph sums it up:

Our core result is that a solution acting at many sites at once evolves in small populations, and local solutions at each independent site evolve in large populations, whereas either outcome is possible in populations of intermediate size.  Local solutions, associated with large populations, have both higher mean fitness and greater evolvability.

Again, though, the authors never linked “higher mean fitness” with anything better than assimilation of harmless mutations.  In fact, what they present as a “positive feedback loop” is merely a loophole for mutations to escape the scrutiny of the editing machines: “This positive feedback loop between accuracy and the proportion of cryptic sequences that are strongly deleterious would ultimately lead to the evolution of an infinitely small error rate if avoiding errors did not come at a cost, resulting in a trade-off between the cost of expressing deleterious sequences and the cost of accuracy.”  Tolerance for harmless mutations was never linked to the innovation of wings, eyes, or brains, or anything even simply adding a new function to a cell – no matter how small – except for one vague reference in a table to “subfunctionalization” (split of functions between copies)2 or “neofunctionalization” (no examples provided; cf. 10/24/2003).
    Apparently, then, all the authors hope for is the opportunity for evolution to work its magic (see 01/23/2011): “The local solution facilitates the genetic assimilation of cryptic genetic variation and therefore substantially increases evolvability” – i.e., the opportunity to innovate.  But they cannot assume that evolvability entails the ability to innovate new organs of extreme perfection without begging the very question Darwin’s original idea proposed 150 years ago.3  They lead the reader to hope that evolution may “tinker” with the assimilated junk: “cryptic sequences that are not strongly deleterious may tinker with rather than destroy function and so contribute to adaptation.”

1.  Etienne Rajon and Joanna Masel, “Evolution of molecular error rates and the consequences for evolvability,” Proceedings of the National Academy of Sciences, published online before print January 3, 2011, doi: 10.1073/pnas.1012918108 PNAS January 3, 2011.
2.  On subfunctionalization, see 06/20/2005, 07/26/2006, 10/17/2007, and 01/03/2011.  Note that the word neofunctionalization begs the question whether natural selection is capable of producing new function. 3.  For previous attempts to explain “evolvability,” see 08/04/2004, 10/04/2005, 10/16/2006 bullet 3, 02/05/2007, 10/17/2007 bullet 4, 03/20/2008 commentary, 02/18/2009, and 01/05/2010.

It may seem like this long entry was like a cruel cat playing with its captive mouse, or the hangman letting the victim draw his own rope, but it was necessary to give them all the space they wanted before showing there is no escape.  They chose to bounce on the cat’s paws; they built their own gallows.  We wanted them to have the space to make their case and try to escape, but they should have known it was doomed from the start.  Can you get wings, eyes, and brains by mistake?  Intuitively, none of us could ever believe that.  Yet academia presents that weird idea as unquestionable scientific truth.
    OK, give it your best shot.  Here you had it – one of the most optimistic explications of evolutionary innovation you could ever find, by trained Darwin Party sophists, letting us all know why our intuitions are misguided.  And all they could do was tell us the old “If you build it, they will come” theory of evolution (03/29/2007, 10/31/2010, 11/29/2010 commentaries).  Merely give Tinker Bell the tools (08/30/2006, 11/29/2010), and wings, eyes, and brains are sure to follow.  Impressed by the song and dance?
    This series of remakes about evolvability is like American Idol with never a star.  It didn’t help change the judges’ decision when they tiptoed offstage with a little biomimetics flower toss.  Entrepreneurs, before taking their business advice, realize that this weird science show would probably never have been produced without your tax money from the National Institutes of Health.  The government always has your business interest in mind.

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