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Biologist James Shapiro comments. Curious to hear what knowledgeable readers think of this. (D'o not comment unless you are knowledgeable about the relevant biology and/or the relevant philosophical issues.)
For years Shapiro has been banging on about the inadequacy of neo-Darwinism to explain evolution. He is regarded as a crank by most evolutionists I know because his alternative views are almost teleological and are totally without biological support. Rather than criticize them in detail, I'll give a few links to places where I give my beefs about Shapiro's views in detail (I'm an evolutionary biologist at the University of Chicago. Have a look at these:
https://whyevolutionistrue.com/2024/03/26/nautilus-disses-genes/
https://whyevolutionistrue.com/2012/12/02/james-shapiro-gets-evolution-wrong-again/
https://whyevolutionistrue.com/2012/08/22/james-shapiro-goes-after-natural-selection-again-twice-on-huffpo/
https://whyevolutionistrue.com/2012/04/07/jim-shapiro-continues-his-misguided-attack-on-neo-darwinism/
https://whyevolutionistrue.com/2012/12/05/james-shapiro-in-his-attempts-to-forge-a-new-evolutionary-paradigm-is-reduced-to-going-after-my-commenters-2/
That should get you started.
As someone in evolutionary/developmental biology and philosophy of biology, the short answer is that Shapiro's ideas about evolution are not taken very seriously within the contemporary evolutionary biology community. The article claims that "living organisms alter their own heredity" in a way that is inconsistent with the neo-Darwinian principle that evolution proceeds by random small mutations and natural selection. Leaving aside the fact that he is criticizing an outdated version of evolutionary theory, the evidence invoked to support this claim is the existence and importance of mobile transposable elements. But changes in transposable elements are also "random" in the sense relevant to standard evolutionary theory, i.e. random with respect to their possible adaptive value. They are also molecular mechanisms rather than organism-scale processes, and are in effect just another way of producing genetic variation. Claiming that "organisms" alter their heredity misleadingly implies that the genetic material is being altered by the organism itself, or that transposable elements are influenced by the organism's exercise of purposive agency. If you see his other writings, it's clear that this is the claim he ultimately is aiming at, but it is a claim for which there is no compelling evidence.
I guess I’d like to add to the current comments by noting that I see nothing wrong with the biological facts mobilized – error prone replication, error prone repair mechanisms, mobile genetic elements – his description of those is fine as far as they go; what bothers me is the leap from those things happen to some criticism of evolutionary theory I don’t entirely understand. But basically these accidents as he calls them, random mutations, were never miracles, so of course there is a mechanistic explanation, and I don’t see how characterizing mobile elements or other mechanisms as a genome editing itself adds anything – what mechanism isn’t done by the self? I agree with the teleological bent to the article noted by Jerry Coyne – there may be biases in what/where mutations are introduced depending on the mechanism involved, but that doesn’t mean they were introduced just to make the organism more fit, which I feel like is being implied (and of course most aren’t beneficial)
It is a principle of evolutionary theory that genetic mutation is "random". But it is very important to understand what that means, as "random" can have a variety of meanings. In evolutionary biology, the meaning is this: Mutations are random in the sense that the probability of a mutation occurring is independent of whether or not it would be adaptive. It does *not* mean that mutations are uncaused. All sorts of things cause genetic mutations– including McClintock's transposable elements (which are, themselves, mutations). It does *not* mean that all mutations are equiprobable. Mutation rates vary among different kinds of organisms (e.g., higher in mammals than bacteria), among different genes, and among different places in the same gene. It *does* not mean that mutations of every possible effect on the characteristics of an organism are possible. A winged-horse like Pegasus is improbable because the developemental system of tetrapods and their fish ancestors has produced four limbs for almost as long as there have been backboned animals– a 3rd pair of legs to turn into wings is not readily available in the "mutational space" for horses.
Once one understands the meaning of "random", Shapiro's objections and examples dissolve. There are no known cases where the "need" for an adaptive feature has been shown to increase the rate of adaptive mutations– that is what would be needed to show that mutations are not random in the sense of evolutionary. There are conditions that are known to increase mutation rates, but they do not induce mutations that are adaptive to the conditions rather than just induce more mutations in general.
I coincidentally covered this topic in my evolutionary biology class this week.
Definitely not coming to the rescue of Shapiro or implying anything about purposeful agency, but now seems like a good time to point out how wild it is that an equine stop-codon got repurposed as a functioning amino acid. At least it disrupts the naive view about how to read phylogeny out of a genetic sequence.
(Not boasting knowledge of anything, Brian.)
The remarkable thing about these comments is the hostility Shapiro's piece evokes. As far as I can see there is nothing he says that implies "teleology" in the offensive sense of change explained by the fact that it is adaptive. It is another question why this would be so offensive, but it is true that there are no generally accepted processes that have this character. The "principle" that genetic mutation is random, in the sense well explained by Gregory Mayer, is plausible enough, but still has a rather dogmatic feel to it. The title "living organisms alter their own heredity" obviously triggers fears of teleology, or even worse, Lamarckism, but actually says no more than is clearly documented in Shapiro's article: there are major (not gradual) endogenous changes in genomes. Indeed, genomes are clearly far more active and interesting entities than the static strings of functionally fixed information still imagined by some orthodox evolutionists. Whether such changes are immediately adaptive or just provide more complex and structured selective targets for evolution than the traditionally assumed point mutations is another question.
Genomes have been evolving as long as the organisms they live in, and it would be extraordinary if they had not acquired novel and almost certainly adaptive properties, as Shapiro illustrates they have. Even if they have not acquired Lamarckian capacities, they have surely contributed to the evolvability of organism lineages. It is remarkable that the feeling that they contravene deeply entrenched dogma has encouraged many evolutionist to ignore their obvious importance.
Genetic mutation, and hence genetic variation, may be random. But phenotypic variation is not—it is biased or “facilitated.” This is one of the most important insights of evolutionary developmental biology. It also helps recover the kernel of truth in Shapiro’s agential perspective—not by denying the randomness of mutation, but by showing how organisms shape its phenotypic expression and genomic consequences.
Morphological space is not isotropic: organisms do not express all possible phenotypes with equal probability. Through phenotypic plasticity, developmental accommodation, and niche construction, development biases variation toward functional, adaptive outcomes. Organisms can thus attain and maintain viability despite a range of internal and external perturbations.
Organisms may be powerless with respect to when mutations occur, but not with respect to their genomic and phenotypic effects. They actively shape those effects through genome rearrangement, gene regulation, and the modulation of developmental pathways. Development does not passively transmit mutation to morphology; it absorbs, redirects, or deflects mutational impacts in structured—often functional—ways.
These processes are molecular—this is not magic—but they are no less organismal for that. Developmental dynamics often exhibit functional invariance across molecular realizations. The adaptive value of an ontogenetic outcome may be incidental to the molecular configuration that realizes it, but not to the structure of the developmental phase space, which is partially shaped top-down by the organism’s own self-organizing, self-regulatory activity.
On this view, Shapiro’s claim that organisms alter their heredity need not be interpreted as saying that they choose or induce adaptive mutations, but rather that they partly shape those mutations’ adaptive significance.
I am and Evolutionary Biologist and has fate would have it I am updating my lecture to be given tomorrow on Transposons.
I am very proud to say that Dr. Margaret Kidwell (see link below) was one of my mentor and was a pioneer in the study of transposable elements. I know that she and every other Evolutionary Biologist I know would strongly disagree with the paper mentioned above.
The author seems to think that Darwinian evolution only works on single nucleotide substitutions (SNPs) i.e., a single change in the DNA. For example a change in the DNA from CCC to TCC would alter the amino acid in the protein. While these SNPs are very important and are widely studied, they are not the only type of mutation that natural selection can act on.
There is a large body of literature on the evolution of transposons. I always prefer to start with a few early seminal studies. For that look here: Genome Res
. 2009 Aug;19(8):1419-28. doi: 10.1101/gr.091678.109. Epub 2009 May 28.
Transposons can create large changes in the genome. But all are subject to natural selection. A very small number of these changes increased individual fitness – they are adaptive- and natural selection has maintained them over evolutionary time- the example cited in the paper under discussion. BUT most of the changes (mutations) caused are deleterious or decrease fitness and natural selection has removed them. That is to say that the individual in which these mutations occurred did not reproduce. That we do not see the negative impacts of transposable elements in specie today is evidence of natural selection- it is NOT proof that negative transposable elements (TE) events do not occur.
When I was a first year graduate student I attended a symposium and heard a talk by Dr. Maxine Singer on her work on TEs. She described how she was brought into study the factor IIX gene of a child who had hemophilia- yet his parents did not. She found that a transposable element had inserted into the child's gene- and the TE was the cause of the disease.
Transposable elements generate variation- natural selection acts on that variation.
Maxine Singer: https://circulatingnow.nlm.nih.gov/2024/03/07/maxine-singer-a-life-in-research-and-advocacy/
Margaret Kidwell: https://en.wikipedia.org/wiki/Margaret_Kidwell
https://genetics.arizona.edu/margaret-kidwell-endowment
Response to Jerry Coyne, Posted February 19, 2012 http://whyevolutionistrue.wordpress.com/2012/02/18/a-colleague-wrongfully-disses-modern-evolutionary-theory/#comment-186010
Jerry Coyne Fails to Understand Yet Again
Posted April 10, 2012 http://www.huffingtonpost.com/james-a-shapiro/jerry-coyne-fails-to-unde_b_1411144.html
Natural Genetic Engineering and Natural Selection: Perplexing Delusions of Certain Neo-Darwinist Advocates
Posted April 23, 2012 http://www.huffingtonpost.com/james-a-shapiro/natural-genetic-engineeri_b_1442309.html
How Natural Genetic Engineering Solves Problems in Protein Evolution
Posted: 05/24/2012 http://www.huffingtonpost.com/james-a-shapiro/genetic-engineering_b_1541180.html
The Distinct Roles of Selection, Horizontal Transfer and Natural Genetic Engineering in Dangerous Superbug Evolution Posted: 08/29/2012
http://www.huffingtonpost.com/james-a-shapiro/the-distinct-roles-of-sel_b_1831996.html
Mobile DNA Repeats and Transcriptional Formatting of the Mammalian Genome in Evolution Posted: 09/22/2012
http://www.huffingtonpost.com/james-a-shapiro/mobile-dna-repeats-and-tr_b_1906135.html
The Evolutionary Importance of Horizontal DNA Transfer into Animal Germ Lines Posted: 10/03/2012
http://www.huffingtonpost.com/james-a-shapiro/the-evolutionary-importan_b_1936059.html
Why the 'Gene' Concept Holds Back Evolutionary Thinking
Posted: 11/30/2012 http://www.huffingtonpost.com/james-a-shapiro/why-the-gene-concept-hold_b_2207245.html
Inconvenient Truths: Why Are Self-Styled Defenders of Evolution so Resistant to Lessons From Molecular Genetics?
Posted: 12/04/2012 http://www.huffingtonpost.com/james-a-shapiro/inconvenient-truths-why-a_b_2228277.html
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