E squared – the Evolution of Evolution

Darwin’s prescription for evolution involved just blind variation + natural selection as if evolution were inevitable and all that was required was a collection of objects that are able to reproduce themselves imperfectly.  We know now that it is not at all inevitable.  The mode of variation is crucially important to making evolution possible.  Some systems can support evolution while others cannot.  In real biological systems, evolution works unaccountably well.  Is this just a lucky accident?

For example, imagine trying to “evolve” a software program to alphabetize lists of words.  Say you have a program that does the job tolerably well – it works, but it’s slow and inefficient.  To simulate mutation, we change one letter of the program at a time and we ask “better or worse?”  If the program now works better, we keep the change; otherwise we keep the original.  If we do this long enough, can we make a better and better computer program?

It may not surprise you to hear that for all standard computer languages, this procedure won’t work at all.  So we might try to enhance the workability of the model by simulating sex.  Imagine breaking apart and recombining pieces from a number of very similar programs, all of which can alphabetize a word list. But this is not a practical way to create a better computer program, either.  Even if this whole evolutionary process is realized in software that runs at many gigaflops, the program could go on for many times the life of the Universe without ever creating a better algorithm.*

Computer languages do not constitute an evolvable system.  Living systems, on the other hand, have evolvability.  How lucky for us!



We might not be satisfied attributing the evolvability of life to “luck”.  Perhaps at the dawn of life, a lot of proto-living systems began in many different forms, but it was only a few that happened to be evolvable, and those are the ones that survived.  In other words, evolvability evolved.  But the truth is larger than this and far stranger.  The evolution of evolvability has been an ongoing process, interwoven with the “normal” evolution of fitness, and continuing all through the history of life.

We know this because there are traits that are obviously highly-evolved, but they offer no selective advantage whatsoever, in the traditional sense of survival and reproduction – their only advantages are in the long-range prospects for adaptive change.  How did evolvability traits manage to evolve, without ever offering a selective advantage to the individual carrying that trait, but only to its great, great grandchildren?

The genome is organized like a bureacracy, with command-and-control genes at the top and implementation genes underneath.  In the 1990s, it was discovered that a single gene could be inserted into a fruit fly’s DNA that would cause the ectopic appearance of an entire eye or a wing or a leg on a part of the body where it does not belong.  The term invented for this was hox genes and they perform a function similar to calling a subroutine in a computer algorithm, or a homeowner hiring a contractor to work on his house, or a general issuing an order down the chain of command.

How did the genome come to be organized hierarchically?  This feature offers no advantage in fitness for the individual.  It does, however, contribute to the rate of increase of fitness over evolutionary time.

The advantage of such a system is not that it makes it easier for the body to construct an eye or a leg – it doesn’t.   The advantage is that it permits evolutionary experimentation.  Using HOX genes, the placement of limbs or organs can be optimized in an evolutionary trial-and-error process.  Without having to re-invent the eye or the kidney each time, different body parts can be moved around to create “endless forms most beautiful and wonderful” that Darwin described.  As a way to design any particular organ for one animal, it is a very inefficient way to go; but as a system that can flexibly experiment with legs or wings or eyes or kidneys, hox genes are a brilliant invention.  Did I say “invention”?  Of course, they’re not an invention at all – merely a product of evolution.  But this is a kind of evolution that expands on the traditional “survival of the fittest”.  The idea that ‘evolution = blind variation + natural selection’ has become untenable.

How does evolution manage to give the impression of being “smart”?  There is a chicken-and-egg problem here.  You need an evolvable system to get started with evolution.  You need a highly evolvable system in order to select for evolvability.  So evolvability is a property that is needed in order to create itself.  Think “bootstrapping”.

Besides hierarchical organization of the genome, there are additional ways in which life is optimized for evolution.  The most obvious and prominent is sex, to which we’ll return presently (gives me something to look forward to).  Some places in the DNA are thousands of times more likely to mutate than others, and these hot spots always correspond to opportunities for experimentation.  Meanwhile, genes that control the core metabolism common to all life are tucked away safely beyond the reach of mutation 

Genes are not coded into the DNA as contiguous segments**, but are spread out over smaller units (“transposable elements“) that have to be cut and spliced together to make each single protein.  This is a complex and inefficient process, adding time and energy and potential for errors.  The benefit is that this system promotes evolvability, because functional segments of protein can be cut and spliced in new ways to try out new possibilities without having to evolve them from scratch.

The maintenance of diversity is a major ingredient in evolvability, and it is predominantly appropriate and useful diversity that persists.  How does this come about?

Darwin and the Sources of Variability

Through Darwin’s career, the missing piece in his theory, the mystery that he recognized but never resolved was the maintenance of diversity.  Natural selection cannot work in a uniform population.  It requires diversity as a kind of raw material, which it “consumes” as the less-fit are selected out.

Variability is governed by many unknown laws, more especially by that of correlation of growth. Something may be attributed to the direct action of the conditions of life. Something must be attributed to use and disuse. The final result is thus rendered infinitely complex…These facts seem to be very perplexing, for they seem to show that this kind of variability is independent of the conditions of life. (Origin of Species, First Edition, 1859)

A partial response to this mystery came with Mendel’s understanding of genetics and the mechanism of sexual inheritance.  But it remains true in the 21st Century that when we estimate the rate at which selection collapses diversity and the rate at which useful new diversity is generated by mutation and recombination, we cannot escape concluding that the gain in diversity ought to fail by many orders of magnitude to keep up with its loss.  150 years after Darwin, we still fail to account for the maintenance of diversity in nature.

Evolvability and Sex

The vast majority of species shares genes between consenting adults, mixing and matching in a never-ending quest for new combinations.  Bacteria are promiscuous, floating their genes out into the environment in the form of “plasmids“, and constantly pick up new genes, without regard to their origin.  Single-celled protists swap genes through a process of “conjugation”, actually merging and re-shuffling their genetic identities.  This is sex without reproduction, in which two individuals come together and scramble their genomes.  The two individuals that emerge from the process are re-shuffled combinations of the two original cells.

Almost all multi-celled organisms include some kind of sexual reproduction.  And yet, sex is not at all adaptive in the traditional sense.  For individual fitness, sex is a disaster.  If we cloned ourselves instead of requiring male + female to reproduce, we could be (at least) twice as fit.  The most efficient way to reproduce is simple cloning, and if the most successful individuals reproduced (rapidly!) via cloning, the entire population would, within a few generations, consist in copies of this one type alone.  The advantage of sex comprises only a contribution to evolvability.

By chance, I was witness to the dawn of evolvability theory.

In 1980 I was a grad student and teaching assistant, working for physics Prof David Layzer of the Harvard Astrophysical Observatory.  Layzer is a broadly-cultured man, a musician and a scholar of many sciences.  The course that I taught with him that year was offered to non-science majors, tying together ideas about the behavior of collections of similar objects, from molecules in a gas to animals in a population to galaxies in the Cosmos.  That same year, Layzer wrote a paper entitled Genetic Variation and Progressive Evolution, which he succeeded in getting published in the high-profile journal, American Naturalist.  Layzer was writing for biologists, while thinking like a physicist.  Suppose there were a gene, he mused, that offered no fitness advantage whatever, but which promoted the gradual increase in fitness of offspring and offsprings’ offspring over evolutionary time.  Could such a gene be selected in a Darwinian process.  “Yes”, was what Layzer concluded, and proferred a mathematical proof.

 Layzer’s paper and the ideas within it were roundly ignored, both because he was ahead of his time and because Layzer didn’t speak the language of biologists.  It was not until sixteen years later that a Yale biologist and an AI expert from Hawaii paired up to describe the same ideas in language that a biologist might appreciate.  They were not aware of Layzer’s precedent, and arrived at their ideas completely independently.  This seminal paper of Gunter Wagner and Lee Altenberg put evolvability on the map, and sparked a revolution in evolutionary thinking.  Well, perhaps I overstate the situation; though the paper has been widely cited and the issue recognized, these ideas have yet to affect the foundations of evolutionary theory in a way that logically must follow.


There can be no doubt that without evolvability adaptations, evolvability could never have evolved.  In other words, evolvability promotes itself in a positive feedback loop, or bootstrapping process.  The further evolution of evolvability progresses, the more rapid is further progress in evolvability [sic].

This idea gives us greater respect for evolution, the foundation and basis for life.  Evolution is not a simple process that is bound to happen, beginning whenever some chemical happens to catalyze its own synthesis and proceeding inexorably onward and upward from there.  Evolution as we know it has required this further action of exponentially increasing its own effectiveness, a process that modern evolutionary science can barely describe, let alone understand.

Evolvability and Group Selection

Most evolutionary biologists strain at the gnat of ‘group selection’ but they swallow whole the camel of evolvability.  What I mean by this is that multi-level selection theory (MLS) is well-grounded in traditional evolutionary theory, and requires only a modest theoretical step beyond kin selection.  For historic and cultural reasons going back to the 1960s, many evolutionary biologists categorically dismiss the body of MLS research, insisting that the “selfish gene” is a one-size-fits-all explanation for all evolutionary processes.

Evolvability, in contrast, is an irriducibly radical concept.  It requires group selection on a vast scale that dwarfs MLS accounts.  Evolution of evolvability is a story of how evolution came to be smart, or at least give the illusion of being smart.

A simple yet controversial idea from MLS is that local geography ties together fate of a local animal community, which can be described as having a collective fitness, and which experiences Darwinian selection as a unit.  But evolution of evolvability (E2) goes far beyond this, requiring that selection work on entire lineages that last over many generations required for significant evolution to take place.  Somehow, during all that time, the fittest individuals don’t manage to crowd out those that are collectively good evolvers, though much less fit (by the traditional definition)

Evolvability and Aging

You’ll have to wait until next week.

* There’s a science devoted to evolving computer programs in this way, and it is called genetic algorithms. The process can work when the rules are carefully defined to make sure that pieces of different programs must fit together in a way that makes logical sense.

**in higher life, but not bacteria

22 thoughts on “E squared – the Evolution of Evolution

  1. You’re certainly asking interesting questions. My own image for NeoDarwinism is to imagine gradually introducing typos into The Hungry Caterpillar and expecting to get War and Peace. It does not seem plausible. Which might simply be my lack of imagination.

    I’m always slightly disappointed when this kind of questioning does not include any mention of Lynn Margulis. Arguably the most significant moment for life on earth is when a free living bacteria that had learned to metabolise the molecular poison oxygen was swallowed by a complex cell (probably the result of a previous symbiosis) and gave us complex oxygen breathing eukaryote cells. Margulis showed how this happened. It’s in all introductory biology texts now, but has never really been given appropriate prominence by NeoDarwinists who have invested in selfish genes rather than cooperative genes. And yet where would we be without it? she also showed that it continued to happen.

    What if evolution is more like modern programming than we think? We tend to think of programmers writing code from scratch. But what most people these days do is use libraries of classes and functions (in C++ for example) to stitch together an app which does the job on more or less any platform – apps that can run on my phone, my PC, and e-book. This is similar to Margulis’s view of evolution with bacteria providing libraries of genes representing the possibility of exploiting new metabolic pathways.

    Our loosely symbiotic micro-flaura masses ca. 3 million genes to our 25k. We know that a lot of our DNA is viral in origin. Margulis explained viruses as cut down bacteria – stripped of all but essentials. Indeed the very largest viruses resemble the very simplest bacteria.

    I can imagine how we might take the characters and story line of The Hungry Caterpillar (THC) and combine it with other children’s books to create more complex plots and interactions. Certainly a little Darwinian variation would help in this process, but we need to add functionality and bulk up – symbiotic combination is one option that gets over-looked

    Symbiosis has played a huge part in our evolution. I think your point about hierarchies in genes also points towards acting together rather than competing as the essential mechanism.

    Arguable Darwin saw the world as a man of the post-Napoleonic War period. His class dominated the rest of Britain and more or less the whole world. They conquered and pillaged and became fabulously wealthy. And his class already had well rehearsed notions of hierarchy, fitness to rule, rationalisations for exploitation. Their triumph over Napoleon and the world was only the “natural” outcome of being superior. Darwinism incorporates this view, and projects it onto the natural world. I think this kind of Darwinistic thinking infects UK politics at present.

  2. You’re correct that “evolving” a sorting program by making bitwise changes to source files isn’t practical. Making bitwise changes to the compiled binary would be more successful, though probably still not practical. But computer programmers do use evolution (genetic algorithms, simulated annealing, neural networks, etc.) on a pretty regular basis. A neural network, for example, can be seen as simply a “program” that evolves to perform as well as possible on some classification problem or other.

    Even source code development is becoming evolutionary in nature. In git, developers create different “branches” of code, and merge beneficial mutations back and forth between them.

    These all support your ultimate point: these work well because the mechanism of variation is built from the beginning to encourage positive variations. Just saying that we comp geeks aren’t so evolutionarily hopeless as this piece seems to suggest. 🙂

    • Yes – you understood my meaning perfectly. There’s a footnote about genetic algorithms at the bottom of the post. But my point was exactly as you stated: the system is only capable of evolution if you deliberately build that into the rule system. Evolvability doesn’t come for free.

  3. I came to this field only because The Selfish Gene book really made me uncomfortable. It is just so wrong from a holism point of view that is so typical in Chinese culture. After that, I worked out the technical detail, but there is still one thing I never understand. Why are there so many evolutionary biologists that are so excited about the idea of selfish genes even if the name itself is so misleading? Why did selfishness and conflict become the focus of so many “smart” evolutionary biologists and become dominant in evolutionary biology? Why are there so many evolutionary biologists comfortable living with the idea that selfishness is how evolution works?

    In Chinese culture, believing that selfishness is how life works is really something deeply frowned upon in the well-educated. The reason is simple, there are thousands of years of well documented history that frequently shows the completely unselfish part of human nature. There are always a group of social elite that are willing to sacrifice their life for the people — not necessarily kins. If one believes that psychology is part of biology, one has to believe that evolution works beyond kin selection. For me, altruism and higher-level selection are just so natural that I cannot believe in anything else. This is the only reason I believed that higher-level selection could work despite individual-level selection and took so much effort to prove it. I hope that Michael can make the decision faster so that it can come out faster.

    But the question still remains. Why did the Western world get on the wrong path at the first place? I think there are also famous unselfish people in the West, but why have so many evolutionary biologists abandoned the idea? I came up with one hypothesis. Maybe because traditional western culture was merged with religion, but science works against religion. So, when some scientists, especially evolutionary biologists, tried to devoice themselves from religion, they also abandoned all their tradition. Altruism is so deeply intertwined with religious doctrine in the West that it is too tempting for those evolutionary biologists who want to distinguish themselves from religion to not abandon altruism and cooperation.

    Maybe as someone grown up in the West, you can better explain to me what went wrong for those evolutionary biologists to get lost in the wrong direction.

    • Hi, Jiang-Nan –
      I agree that the whole evolutionary community took a wrong turn with the “selfish gene” idea. The reasons for this are historical, I believe. It has a lot to do with the personality of R.A. Fisher, a brilliant mathematician who believed passionately in eugenics, and invented a lot of clever and useful statistical techniques. Before Fisher, Darwinian evolution was a qualitative theory, and no one thought that you could write down a formula for fitness or calculate how it changes in a population. to his credit, Fisher offered a clear and basic quantitative model for how evolution works. The problem is that the predictions of the model don’t agree with what we find in nature, and that most evolutionary naturalists were just too cowed by the mathematics to question the theory based on its wrong predictions.

      • I do not think eugenics is the problem. Even I myself believe in some sort of eugenics, since there are clearly many adaptive traits that many persons have failed to inherit. Everyone is flawed in many ways and detrimental mutations accumulate in every generation. Neither do I believe that Fisher alone can be the problem. The problem is why so many evolutionary biologists followed him. It does not seem that Fisher’s theory is perfect. It is extreme reductionism and logically flawed due to oversimplification. It is a disaster when applying his theory to something like the existence of sex. I saw this at the very first time I read The Selfish Gene in my second year of college. I am not super smart and I just like to examine things carefully. But still, so many (western) evolutionary biologists followed him without a second thought (some eastern biologists followed this simply because of the historical tradition of learning from the west). When something influences such a large portion of the population, I tend to find the reasons in the culture rather than in a single person. And, since this topic is so related to ethics, I cannot accept a simple answer from just methodology. In the west, there were the breakup from religion and the (often brutal) sudden colonization expansion, both of which tended to distort any view from the more moderate tradition.

        • Yes – very well said! I agree with your politics as well as your science.

          It’s true that our culture has an inordinate influence on evolutionary science. Fisher lived in the age of the robber-baron. Here’s a quote about capitalism from his book on Evolutionary Genetics:

          The private possession of property, representing as in this system it must do, the accumulation of services already performed to other members of the society, and the effective means of calling upon equivalent return services in the future, shall be rigorously protected. In the theory of this system each individual is induced, by enlightened self-interest, to exert himself actively in whatever ways may be serviceable to others, and to discover by his ingenuity new waysor improved methods of making himself valuable to the commonwealth Such individuals as succeed best in performing valuable services will receive the highest rewards, including, in an important degree, the power to direct the services of other in whatever ways seem to them most advantageous. Those, on the contrary, who fail most completely to perform socially advantageous actions have the least claim upon the wealth and amenities of the community. In theory they may perish of starvation… {Fisher, 1930 #29 p 202}

          Later in the century, we had the era of Ronald Reagan and Margaret Thatcher. Just when pure capitalism was being touted as the one perfect economic system, at the same time the selfish gene was supposed to explain everything about evolution.

  4. A couple of issues with some of the ideas that you are promoting: First – you are correct that sexual reproduction is less efficient than asexual reproduction, but the major advantage that trumps this, as Highlighted by Matt Ridley in The Red Queen, is protection against susceptibility to disease. Cloned offspring might improve fitness, but if a disease comes along that is detrimental to that particular genetic combination, the whole lineage dies out. At least with sexual reproduction, genes can benefit by hitching a ride with others that make them immune to a new disease strain. The other issue, in your section on group selection, is that you make the mistake of indicating surprise that the fittest ‘individuals’ don’t come to crowd out the rest of the group. The problem with this is that individuals are not the unit of selection. The genes are. The major problem with group selection theory is that there is not a distinct unit of selection upon which evolution can act. If the characteristics of one group lead it to outperform another group and it then grows larger by attaining more members, the characteristics of that group have changed (even if only slightly). If the group splits in two (or more), the subgroups are not identical copies of the original. They are unique and are thus acted upon differently by selection pressures. The only tenable unit of selection that has been defined is a the gene, and contrary to what you have said, many brilliant scientists have shown that the ability to replicate is sufficient to produce evolution from the simplest molecules to the most complex life forms.

    • >> The major problem with group selection theory is that there is not a distinct unit of selection upon which evolution can act!

      I don’t see why this is a problem. In my research, I use “viscous simulations” to investigate evolution in a population that is arrayed on a 2D grid. Usually there is one individual per site, and each individual is characterized by some traits involving survival and fertility, and there are nearest-neighbor interactions in all directions along the grid. (See for example, Mitteldorf and Wilson 2000 http://www.mathforum.org/~josh/ecoopvsc.pdf)

      In these simulations, we commonly see no permanent group structure, but constantly shifting boundaries between regions of selfish behavior and regions of cooperation. Still, this structure is far more supportive of the evolution of altruism than “selfish gene” models would lead you to believe.

      In some sense, it is certainly true that what makes the models work is the common descent of neighbors that are contributing altruistically to one another’s fitness. And yet, the relationships are so intricate and difficult to trace (even in these simple cellular automata) that they defy analysis in terms of Hamilton’s Rule.

    • >> many brilliant scientists have shown that the ability to replicate is sufficient to produce evolution from the simplest molecules to the most complex life forms.

      Please give some examples of who has said this. It’s my impression that people who investigate the subject almost all have come to the conclusion that evolvability is not a given; that some replicating systems are capable of evolution and others are not*.

      *What I mean by this is that the probability of evolving more sophisticated systems from simple ones is vanishingly small, even in a geological time frame.

      • >>In these simulations, we commonly see no permanent group structure, but constantly shifting boundaries between regions of selfish behavior and regions of cooperation. Still, this structure is far more supportive of the evolution of altruism than “selfish gene” models would lead you to believe.

        This very phenomenon is actually outlined by Dawkins in the book The Selfish Gene. Again, it appears as though you are referring to the individuals as units of selection, and you seem to be making the suggestion that altruism would be unlikely to evolve in a population of individuals. If this is truly how you are approaching the problem, this constitutes a misunderstanding of the selfish gene theory. The theory, taking the gene as the unit of selection, predicts the evolution of altruism based on the probability that copies of the genes for altruism exist in other members of the population. Thus, the selfish behavior of the genes (promoting fitness of copies of themselves in others) promotes altruism at the level of the individual. The opening paragraph of the paper you referenced states that altruism is a fundamental problem for evolutionary biology, but this hasn’t been the case for decades. The theory of reciprocal altruism has been in play since the late 60’s. Paired with kin selection theory, provide two strong models for the evolution of altruism that have received considerable empirical support.

        The easy example of an individual who has provided strong logical / empirical arguments that self-replication with mutation is a sufficient condition to give rise to evolution is Richard Dawkins. His argument has been echoed by the likes of Cosmides & Tooby, Buss, Pinker, and others. The key point is that even if the probability of a random mutation which increases the complexity and fitness of an organism is vanishingly small, multiple opportunities increase the probability according to the formula: p-hat = 1 – (1-p)^n, where p is the probability of the event, n is the number of opportunities the event has to occur, and p-hat is the updated probability of the event occurring at least once at some point over the set of n opportunities. Even probabilities which are extremely remote in the context of the human lifetime become extremely probable in a geological timescale through multiple opportunities.

        • Come on, The Selfish Gene is garbage! Before you argue that the gene is the basic unit of selection, clearly define a gene first. Don’t simplify, define a gene in actual biology. Given sexual recombination, given transposition, given introns, given regulatory elements, given everything, define a gene first. Remember that, you and me have more than 95% identity in our genome, does this mean that you should treat me mostly as yourself? If not, how do you determine how much you will treat me as yourself according to the selfish gene theory?

          Second, why does there have to be a “unit” of natural selection? Why a unit? What is a unit? Something independent of others? Then can you draw a boundary for a “gene” to make it independent? Can’t evolution happen on a larger and dynamic scale with multiple component evolving together? Why do you need to draw a boundary that only exist in your mind?

          • I didn’t realize that I was backed into a corner. Surely nobody is advocating that we can’t define a gene? Seeing as how the human genome has been sequenced, and behavioral geneticists have identified a host of genes that are implicated in very specific functions, I think we can safely move past the point that genes, as a sequence of proteins that occupy a specific space on a specific chromosome, do in fact exist. I also would agree wholeheartedly with the statement above from Josh that the function of genes is context dependent, and that much more often, a host of genes work in combination to code for a specific trait. This is no argument against selfish gene theory though. The reason that selection at the level of the group, or at the level of the individual doesn’t work is that replication does not occur at those levels. Groups and individuals represent distinctly unique combinations of traits. Even if the group or the individual outperforms all competitors in a specific time and in a specific context, that specific combination of traits is lost once the group changes or once the individual dies. Genes, however, make exact copies of themselves and as such, their ability to outperform other genes (by having more copies of themselves made) persists across generations. As such, genes are subject to selection pressures because their ability to outperform rival alleles matters, whereas the ability of an individual or group to outperform other individuals or groups does not lead to a proliferation of clone individuals or groups. These unique bundles of traits only exist for a finite period of time, regardless of how well they perform.

            I’m not really sure I understand why there is such opposition to the selfish gene theory? Am I missing something?

        • When backed into a corner, advocates of the Selfish Gene define it as meaning that altruism can only evolve when the benefit of the altruistic trait falls preferentially on others that carry the same trait. Well, that’s something we can all agree on. In fact, it’s the starting point for most MLS (multi-level selection) analysis.

          Something else we can agree on, perhaps, is that epistasis is the rule rather than the exception. In other words, most genes have an effect on fitness that is dependent on context, and the vast majority of biological functions are realized through the interrelation of many, many genes working in concert.

          • “altruism can only evolve when the benefit of the altruistic trait falls preferentially on others that carry the same trait”
            True for qualitative trait but false for quantitative trait such as longevity. For quantitative trait, being the same is rare, which also shows the limit of the selfish gene theory.

  5. Reciprocal altruism is a very narrow function because it depends on the ability of each individual to recognize others who have helped him in the past. This is a capacity that is limited to mammals. Kin selection involves preferential treatment dependent on descent from a common ancestor. This is a broader mechanism and includes, for example, social insects.

    But MLS goes further to recognize other bases for the evolution of altruism. Geographic proximity is a common one. Plants may be altruists by this definition, and their benefits may fall on others that are not necessarily even of the same species, let alone sharing a common recent ancestor. Altruism may also evolve in communities that share a common food source or a common pollinator. Sentinel behavior can evolve in communities of animals that share a common predator, and again the altruism can cross species boundaries.

    I’ve written about selection at the ecosystem level. Entire ecosystems are co-evolved for demographic homeostasis. http://mathforum.org/~josh/PRLS4Oikos.pdf

    • I wouldn’t disagree with any of the statements above, but I don’t think that any of that goes against selfish gene theory. Reciprocal altruism, symbiotic as well as parasitic relationships; all of these are predicted and can be explained by selfish genes. Regardless of how we define the terms, the theory still readily explains what we actually observe in nature.

      • >>The reason that selection at the level of the group, or at the level of the individual doesn’t work is that replication does not occur at those levels.

        Are you familiar with the study at Binghamton on artificial ecosystem-level selection? http://www.pnas.org/content/97/16/9110.short Yes, whole communities can replicate themselves. It’s a little funky, and fidelity is not 100%. But if you’re honest you have to say that about any of these replicators: Genes replicate themselves, but not in isolation. (Sexual) individuals only replicate themselves with a great deal of mixing and confounding.

        >>I’m not really sure I understand why there is such opposition to the selfish gene theory?

        Some people interpret selfish gene theory in a narrower way and use it to make predictions. The case I’m most familiar with is aging. There is diverse and abundant evidence (documented at http://tinyurl.com/byd27ts) that aging is an adaptation in its own right, selected for its own sake. Dawkins, among others, has refused to look at this evidence because he knows as a matter of theory that this could not be the case. I say that if the theory predicts that aging cannot evolve as an adaptation, then we need to re-evaluate the theory.


        If you define the Selfish Gene broadly enough, then you can get anything out of it. I was surprised to see you mention the Red Queen mechanism because, to my mind, that’s the epitome of a group effect. We’re talking about selection for diversity – diversity isn’t even a property of an individual, but only of a community.

        • >>Some people interpret selfish gene theory in a narrower way and use it to make predictions.

          Am I misreading your intent here? Theories are supposed to lead to predictions, that’s how their merit is judged according to the scientific process. The prevailing theories are the ones whose predictions are best supported by evidence. Most theories will eventually be eclipsed by something better, but unless I am missing something, there is a solid body of evidence which supports the selfish gene theory, and I don’t know of any examples where a direct prediction of the theory has been shown to be false (please point me in the right direction if I am mistaken)

          So – In your aging paper, if I label the 4 major theories that you allude to as 1, 2, 3, and 4, I would say that I am most familiar with #3, and it is what I would say would be the theory favored by the selfish gene theory (I wasn’t quite sure if you were indicating that #1 or #3 was the prominent theory of our time, but my impression is that it is #3). The slight hesitation with the way you have phrased it is that I would hesitate to say that the tradeoffs are “inescapable”, which seems to be the main crux of your argument against it. The way I understand the position, it is that genes which have deleterious effects earlier in life are selected out because they have a much more pronounced effect on reproductive success. The selection pressure for genes that have deleterious effects later in life is weaker because offspring are more likely to have been produced and so the genes that have the negative effects later are more likely to have already been passed on to the next generation by the time they pose a cost to the parent. There would be some weak selection pressure because of differences in parental investment, but nothing nearly as strong as the pressure faced prior the age of reproductive maturity. Anyway, based on that understanding, I feel that it is a plausible theory, though as far as I know, there isn’t a ton of empirical work that has explored it to date.

          The theory that you support, #4, is interesting, and I want to read through it again. I don’t in any way have an opposition to a theory of aging as an adaptation. I’m in favor of what ever theory is best at predicting and explaining the world we live in. However, the one part that strikes me at this point is that the theory is based on the assumption that selection happens at the group level. Am I wrong or does the theory fall apart if this assumption turns out to be untrue? If that is the case, I have a hard time with it because I am far from convinced that group selection is possible, but I would definitely be open to further discussion. Let me know if I am going astray anywhere.

  6. Hi Russ,

    No, you cannot move beyond the definition of genes yet. Attention that “the human genome” is not called the human “gene” project. You say that a gene is “a sequence of proteins”, meaning that you do not have the correct definition of genes even at the level of current consensus. How about miRNAs or enhancers? Do you call them genes? Also attention that the concept of genes in molecular biology is completely different from population genetics. You cannot just interchange the ideas. Why not? Because the selfish gene theory need to draw a narrow boundary for genes! Beyond a narrow boundary, things become messy for the theory because of sex and the “unit” becomes ambiguous. If you draw a loose boundary for genes, then using this logical you cannot argue against group selection.

    “Genes, however, make exact copies of themselves”. No, this is not true. First of all, most genes do not make copies of themselves, proteins like polymerases do that. Most genes are just survival materials rather than things that desperately replicate as portrayed in the selfish gene theory. They can be replicated but they do not actively replicate themselves. So do not confuse ideas. Second, genes do not necessarily get being copied exactly. There are things called mutation and sex. For some sequences at mutation hotspots, genes help the survival of their alleles rather than themselves because they eventually get mutated. The reproduction of the individual they are in is the survival of their alleles.

    “Groups and individuals represent distinctly unique combinations of traits… specific combination of traits is lost once the group changes or once the individual dies.” No. This is only the definition from the selfish gene point of view. You can actually define a group as a genome pool. Change of the group only slightly change the genome pool, especially for recombination. Neither does recombination change a lot for individuals. Always remember that your children and you is not just of zero-identity or 50% identity; you actually share more than 99% identity! You are all human beings! So, groups can replicate, just with some small changes, the same as the mutations in gene replication. So, the selfish gene theory is no better than group selection in this logic.

    “Why there is such opposition to the selfish gene theory?” Again, because it is garbage! For several reasons! First, it is extreme reductionism but contradicts itself in its methodology. It reduces everything to the gene but the gene can further be reduced into nucleotides. This gives it problematic boundary issues. Second, it is logically flawed as I showed you above. Third, it is arrogance. It seeks to be a universal theory in evolution and criticizes everything else, but in reality, it only covers a small aspect in evolution. Fourth, it is publicly misleading and makes the theory of evolution ugly! Yes, there is some sort of reciprocity (or feedback?) for the existing mode of most genes, but why do Dawkins call this selfish?! What is his motive at the first place? I am sometimes ashamed of telling others what I study because of the book The Selfish Gene! Am I someone just full of selfish ideas in everything? No body really likes the theory except for a small group of orthodox evolutionary biologists and people feeling comfortable of being selfish! So, the selfish gene theory is rotted in its core and disgusting on its surface. And this is exactly what we define garbage. Yes, it is garbage!

  7. I am trying to wrap my mind around group selection and how that can occur. The only thing I can think of is the extinction of a group. Yes, that species died. It obviously was not fit. Since almost every species that ever existed is now extinct, maybe that is the basis of evolution? 😉

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