What are the fundamentals of evolutionary biology?

by Matthew Cobb

Dan Graur, who is Professor of Biology and Biochemistry at the University of Houston,  describes himself on Tw*tter as “A Very Angry Evolutionary Biologist, a Very Angry Liberal, and an Even Angrier Art Lover”. His Tumblr says he ‘has a very low threshold for hooey, hype, hypocrisy, postmodernism, bad statistics, ignorance of population genetics and evolutionary biology masquerading as -omics, and hatred of any kind.’
Anyway, yesterday he tw**eted a link to a document containing what he called ‘All of evolutionary biology in 12 paragraphs, 237 words and 1,318 characters’. Here they are for your delectation. I’ve made some comments at the end – feel free to chip in (you too, Dan!).
1.Evolutionary biology is ruled by handful of logical principles, each of which has repeatedly withstood rigorous empirical and observational testing.
2. The rules of evolutionary biology apply to all levels of resolution, be it DNA or morphology.
3. New methods merely allow more rapid collection or better analysis of data; they do not affect the evolutionary principles.
4. The only mandatory attribute of the evolutionary processes is a change in allele frequencies.
5. All novelty in evolution starts as a single mutation arising in a single individual at a single time point.
6. Mutations create equivalence more often than improvement, and functionlessness more often than functionality.
7. The fate of mutations that do not affect fitness is determined by random genetic drift; that of mutations that do affect fitness by the combination of selection and random genetic drift.
8. Evolution occurs at the population level; individuals do not evolve. An individual can only make an evolutionary contribution by producing offspring or dying childless.
9. The efficacy of selection depends on the effective population size, an historical construct that is different from the census population size, which is a snapshot of the present.
10. Evolution cannot create something out of nothing; there is no true novelty in evolution.
11. Evolution does not give rise to “intelligently designed” perfection. From an engineering point of view, most products of evolution work in a manner that is suboptimal.
12. Homo sapiens does not occupy a privileged position in the grand evolutionary scheme.
I think the main thing that’s not quite right about this is 5, “All novelty in evolution starts as a single mutation arising in a single individual at a single time point”. While this is essentially true, it misses out two of the most significant novelties in the history of life, which were not created by mutation, but instead by instances of predation that went wrong and instead produced symbiosis, with one kind of cell living inside another.

The first such event took place around 2 billion years ago, somewhere in the ocean. Prior to that moment, all life had consisted of small organisms called prokaryotes which had no cell nucleus or mitochondria (these are the tiny cellular structures that help provide you and me and giraffes and mushrooms with energy). Everything changed when one unicellular life-form, known as an achaebacterium, tried to eat another, called a eubacterium. On this one occasion the eubacterium survived inside its would-be predator and became trapped, losing many of its genes to its host and eventually turning into a molecular powerhouse – the mitochondrion – that produced energy from chemical reactions and was used by the new eukaryotic cell. These new eukaryotic life-forms were a weird hybrid, composed of two different organisms. They were our ancestors.

A second, similar, event occurred around a billion years ago, when a eukaryotic cell, complete with mitochondria, engulfed a eubacterium that had long ago evolved the trick of acquiring energy from sunlight, through photosynthesis. Predation went wrong again, and another form of symbiosis eventually appeared. This gave rise to algae and eventually plants, in which small organelles called chloroplasts, the descendants of the intended eubacterial victim, turn light into energy for the benefit of the eukaryotic host.

What happened after these events took place was entirely down to natural selection, following the kind of processes that Dan describes above. But the source of the novelty – and pace his point 10 above, these were truly novel organisms – was not mutation, but an incredibly unlikely pair of events.

It is striking that these two acts of predation gone wrong were able to open up the potential of life in ways that genetic mutation + natural selection have not been able to do in 3.5 billion years of evolution. Life on Earth without mitochondria – prokaryotic life – is limited to the microscopic because of the physical limits imposed on the transport of matter, energy and information from the environment into the inside of the organism. In the absence of an additional, powerful energy source, prokaryotic life cannot carry out those operations beyond certain tiny physical dimensions. The co-option of the energy-producing mitochondria first enabled eukaryotic cells to grow large, and then, eventually, to become multicellular. Mutation and natural selection were not able to do this. Similarly, no eukaryotic organism has on its own mastered the trick of evolving photosynthesis; the only way the ancestors of plants were able to do this was through symbiosis with photosynthetic bacteria.

Other people have pointed this out on Tw*tter; Dan’s response was to redefine ‘mutation’ in point 5 as ‘any heritable change’. Which is fine, but would have been clearer had he said so from the outset

What do you think of Dan’s list? Is it useful, either for students, for the lay person, or for clarifying differences within evolutionary biology? Could it give rise to testable hypotheses?

58 Comments

  1. John Willis
    Posted February 22, 2016 at 11:13 am | Permalink

    It looks basically great in terms of evolution = genetic change (in allele frequencies) over time. But there’s nothing about speciation and its converse common ancestry. One could completely understand and agree with everyone of his points, but not understand or agree that humans are related to dogs, redwoods, morels, and E. coli.

    Without common ancestry of all of currently living species, there would not even be a cohesive field of biology, with common principles/facts about central dogma, genetics, cell devision, metabollism, etc. – nothing in biology makes sense except in the light of evolution!

  2. Craw
    Posted February 22, 2016 at 11:17 am | Permalink

    I would like to see variants of this list, and variants of the variants, developed over time with the more appealing lists driving out the others in posts and books and notes.

  3. David Duncan
    Posted February 22, 2016 at 11:20 am | Permalink

    I’ve never really understood the rationale behind point 12. Although other organisms are better at some things than us we have learned so much about the universe, done so many things, like putting men on the moon, consciously developed antibiotics, and so on that I’m tempted to think we are special, in some sense.

    • GBJames
      Posted February 22, 2016 at 11:34 am | Permalink

      We are all special in our differences. In other words, none of us are special.

    • Stephen
      Posted February 22, 2016 at 11:40 am | Permalink

      We think those things are special. I doubt that orcas, oak trees, Paramecia, just to name a few, do. Whose estimate of importance is “correct”?

      • Posted February 22, 2016 at 3:29 pm | Permalink

        The ability to destroy all living things seems pretty special from any organism’s point of view …

        /@

        • Posted February 22, 2016 at 5:06 pm | Permalink

          Which then puts us on a level with asteroids. : )

          • Posted February 22, 2016 at 5:52 pm | Permalink

            🤔💡Oh, yes, because they’re consequences of terrestrial evolution too …

            /@

    • Gordon Davisson
      Posted February 22, 2016 at 8:14 pm | Permalink

      We are special in some ways, but not the ways that evolution is concerned with. As far as the “grand evolutionary scheme” is concerned, we’re just another branch of the family tree.

      BTW, relevant Calvin & Hobbes: http://www.gocomics.com/calvinandhobbes/2009/12/10

      • Posted February 23, 2016 at 12:41 am | Permalink

        Of course; every species alive today is the culmination of 3.5B years of evolution (ignoring a few thousand years of selective breeding of some species by us).

        /@

  4. Bill Gilliland
    Posted February 22, 2016 at 11:32 am | Permalink

    Does the acquisition of mitochondria and chloroplasts have to be predation gone wrong? Couldn’t they have also started as parasitism by the incipient endosymbionts, where the much smaller bacteria took up residence in a larger host cell, which then over time evolved into a more mutualistic symbiosis?

    • Torbjörn Larsson
      Posted February 22, 2016 at 12:37 pm | Permalink

      I was too hasty when I initially browsed the thread, I missed your comment before I posted my similar comment way down below. FWIW I added some other possible detail, among them a recent reference to the pre-mitochondrion phylogeny as likely a parasite!

  5. GBJames
    Posted February 22, 2016 at 11:32 am | Permalink

    I have two quibbles.

    1) Regarding #8. “An individual can only make an evolutionary contribution by producing offspring or dying childless.” This seems to ignore the role of kin selection where an individual might influence the frequency of alleles by interacting with those with shared genes.

    2) Regarding #10. “There is no true novelty in evolution.” When a mutation generates some new allele of a gene, isn’t that truly novel? Hasn’t the only “mandatory” feature of evolution (change in frequency of alleles) been satisfied?

    • Mark R.
      Posted February 22, 2016 at 11:43 am | Permalink

      I interpreted #10 as: evolution has no skyhooks, only cranes.

      • GBJames
        Posted February 22, 2016 at 11:48 am | Permalink

        I guess it all hinges on what qualifies as “true” novelty.

        I’m down with the “no skyhooks” point. But I don’t think #10 is well articulated. If there wasn’t novelty there could be no evolution since there would be nothing to act upon.

        • Mark R.
          Posted February 22, 2016 at 11:53 am | Permalink

          “If there wasn’t novelty there could be no evolution since there would be nothing to act upon.”

          Good point. I agree that #10 needs a little more clarification.

          • Posted February 23, 2016 at 4:57 am | Permalink

            Agreed…. number 10 needs restatement and improvement.
            Given that there exists a genotype which defines a phenotype, a mutation in a genotype can create “something that never existed before” because such a thing had never been “built” before in the phenotype. Thereby Evolution provides a vehicle for “invention” although this type of invention is randomly produced. Although the “invention” is built on a modification of the genotype the functionality at phenotype level is indeed novel

    • Charlie Jones
      Posted February 22, 2016 at 11:51 am | Permalink

      I am also concerned about “10. Evolution cannot create something out of nothing; there is no true novelty in evolution.” as well. It seems that a lot of new features acquired by life over the past 500 Myr or so indeed arose from modified duplicated genes or repurposed genes, but what if we go back 3.5 or 4 billion years ago, when life was just beginning? Was one gene formed at random on a clay mineral template, sucked into a proto-cell, and then all new genes in all subsequent bacteria and archea are mutated duplicates of this one?

      • Posted February 22, 2016 at 12:06 pm | Permalink

        As far as I know, the only something from nothing event in all of science is the inflationary big bang.

        • Somite
          Posted February 22, 2016 at 12:26 pm | Permalink

          And even that event is probably from something to something else

          • Posted February 22, 2016 at 12:37 pm | Permalink

            It’s an interesting definitional question. Quantum events can reasonably be said to come from nothing. And Inflation erased information about what might have preceded, so, even if it might have made sense to say that something “caused” Inflation, said something doesn’t exist for any meaningful definition of the word. Division by zero, effectively…all answers are equally valid, and so therefore no answer is valid.

            Causality is a notion of extremely limited utility. Is the water boiling because of the heat added to it from the stove, or because you want a cup of tea? You can use causality as a tool for forward projection and planning…if I want a cup of tea, then I should set the pot on the stove, and so on. But inverting it and looking backwards…well, why do you want a cup of tea, and shouldn’t that be the “true” cause? And so on.

            b&

            >

      • Mark Joseph
        Posted February 22, 2016 at 8:27 pm | Permalink

        Once there was nothing but cyanobacteria. Now there are giraffes with recurrent phayrngeal nerves, malaria parasites with fantastically complex lifecycles, pandas with elongated sesamoid bones, humans with their light-sensitive cells on the wrong side of the retina, and cephalopods with their light-sensitive cells on the correct side of the retina.

        So, either the second half of #10 is just plain wrong, or I am not grasping the meaning of the phrase “true novelty”.

    • BobTerrace
      Posted February 22, 2016 at 12:18 pm | Permalink

      I understood #10 to mean that the building blocks (bases) are still the same. Just reconfiguration takes place.

  6. Posted February 22, 2016 at 11:35 am | Permalink

    Number 8 was true in the past. In the future, individuals can make contributions by genetic engineering. Perhaps some would not describe this as evolutionary, but I would.

    • Torbjörn Larsson
      Posted February 22, 2016 at 12:46 pm | Permalink

      I think genetic engineering, if it isn’t combined with a legislation enforcing it, would rather be a mutation. If people do it for remedies or for vanity, say, it is unlikely to take (be fixed by selected or drift) in the population.

  7. Mark R.
    Posted February 22, 2016 at 11:49 am | Permalink

    From Dan’s tw**t: “Mutation is any heritable change.”

    I’ve never thought of it like that; what a simple and succinct definition.

  8. DrBrydon
    Posted February 22, 2016 at 11:51 am | Permalink

    I am afraid I don’t appreciate the importance of the distinction made in #9 between effective population size and census population size.

    • GBJames
      Posted February 22, 2016 at 12:01 pm | Permalink

      I think the point is that it doesn’t matter if the census population is very large if the effective (reproductive) population is small. The distribution of alleles within the effective population is the only thing that would change over time.

      • Mark Sturtevant
        Posted February 22, 2016 at 3:03 pm | Permalink

        And to add something to that: effective population size is about the allelic diversity in the population. There are large populations that are like small populations in terms of genetic diversity b/c of a historical crash. Their evolution is more governed by genetic drift than by natural selection.

  9. HBB
    Posted February 22, 2016 at 12:00 pm | Permalink

    I think item 3 is a bit of an overstatement. We should at least leave open the possibility that new discoveries with new methods could lead to modifications of the principles in item 1. For example, although they did not really pan out in terms of changing evolutionary principles, new discoveries in epigenetics looked like they had that potential, at least at first.

  10. Marilee Lovit
    Posted February 22, 2016 at 12:02 pm | Permalink

    As a student myself, I like the list a lot, with Matthew’s additions. I look forward to reading other comments on this post.

  11. Mark Sturtevant
    Posted February 22, 2016 at 12:05 pm | Permalink

    Very interesting, and a pretty useful list from Dan.
    I too jumped on #5, in that at times an upswing in fitness does not always emerge after a single mutation. Sometimes this happens after an earlier, effectively neutral or slightly deleterious mutation is combined with a 2nd mutation. There are different examples of this, and ironically Larry Moran has a post about this sort of thing today.
    But I think it is a good list overall, and I would rather not add a lot of extra #s to it lest it become overly long.

    • Wayne Tyson
      Posted February 25, 2016 at 1:39 am | Permalink

      I’d be interested in your revision of the statement.

      WT

  12. Mark Sturtevant
    Posted February 22, 2016 at 12:11 pm | Permalink

    The meaning of #1 would be a bit clearer if it said that evolution has been fully supported by rigorous observation and testing. Saying that it has ‘withstood’ those tests is correct, but this could be misunderstood by laypersons who do not understand that we try to disprove our hypotheses and theories by testing them.

    • Wayne Tyson
      Posted February 25, 2016 at 1:38 am | Permalink

      How would you modify the statement?

      WT

  13. Somite
    Posted February 22, 2016 at 12:14 pm | Permalink

    Loved the list.

    I noticed however, it avoids mentioning that genes are the units of selection as opposed to groups of individuals.

    • Torbjörn Larsson
      Posted February 22, 2016 at 12:42 pm | Permalink

      It is a good list, and you did a good catch!

      (Unless it is implicit in the discussion about mutations, but if so it isn’t very clear IMO.)

    • John Scanlon FCD
      Posted February 24, 2016 at 10:52 am | Permalink

      There’s nothing to stop selection from acting on groups; it’s just too weak to oppose selection on entities that multiply orders of magnitude faster, and also can’t explain adaptations of individual bodies.

      • Wayne Tyson
        Posted February 25, 2016 at 1:35 am | Permalink

        Can you clarify a bit? What is “it” in the context of your sentence?

        If you mean physiological adaptation (bigger lungs at higher altitude), does this mean that you believe that it is due to genetic change within and individual organism or that physiological adaptation is due to genetic characteristics of the individual organism?

        WT

        • John Scanlon FCD
          Posted February 27, 2016 at 8:23 am | Permalink

          Sorry, I didn’t realise that was unclear: “it” referred to “selection acting on groups”.

    • Wayne Tyson
      Posted February 25, 2016 at 1:36 am | Permalink

      How would you modify the list?

      WT

  14. Posted February 22, 2016 at 12:25 pm | Permalink

    8. Evolution occurs at the population level; individuals do not evolve. An individual can only make an evolutionary contribution by producing offspring or dying childless. [emphasis added]

    I take issue with the part I emphasized. An individual can also make quite significant evolutionary contributions by influencing the breeding and survival of others. All of agriculture is the result of humans directing the reproduction and death of other organisms, and it’s long been a staple of human society to apply similar principles to ourselves. Arranged marriages? Infanticide (especially of the children of rivals)? Jealous spouses murdering rivals and potential rivals?

    …and not just humans. We observe these same behaviors in lots of other species.

    And, of course, that’s before we consider the possibilities of cloning and other methods of generational reproductive manipulation. Or, for that matter, does gene therapy, especially if it gets into the germ line, constitute change in allele frequency? If so, that’s evolution in a single individual in the individual’s lifetime. And, if that’s the case, shouldn’t the same be defined for those rare natural instances of similar change?

    Most interesting times we live in, indeed….

    b&

    • Wayne Tyson
      Posted February 25, 2016 at 1:27 am | Permalink

      I would like to hear/read Graur’s response.

      Ben, do you believe Graur’s statement to be invalid or just too narrow–or?

      WT

  15. revelator60
    Posted February 22, 2016 at 12:28 pm | Permalink

    On an off-topic but still evolution-related note, the renown literary critic George Scialabba has just published a positive review of Faith Versus Fact:
    http://inference-review.com/article/good-for-nothing
    (“Good for nothing” refers to intelligent design, not the book!)

  16. Torbjörn Larsson
    Posted February 22, 2016 at 12:30 pm | Permalink

    I would quibble with listing #10-12 in a summary. Those seem unnecessary corollaries solely noted to clarify and parry religion. Possibly #11 is a useful observation, but then I would drop the references to religion.

    Or at least #10 seems to fit with #11 & 12. “Something out of nothing” is a religious deepity when they try to conjure up an argument from nothing. (Because religionists don’t see the need to define and test for “nothing”.)

    Re endosymbionts, I don’t know about plasmids but couldn’t mitochondria be much the opposite of being part of “unlikely … events”?

    Maybe there is a later phylogeny, but Wang & Wu found the pre-mitochondrion to be an energy (ATP) stealing parasite of a clade that today insert itself into eukaryote cells. [ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110685 ] Then – whether or not the archaebacteria repeatedly tried to eat its associated parasite, or it evolved the ability to insert itself into the host it siphoned ATP out of – there seem to have been room for a gradual evolutionary trajectory towards the pre-mitochondrion managing the host interior.

    Why rely on lucky accidents when gradualism is so much more likely and seem to carry the majority of evolutionary processes?*

    *If the rarity of the endosymbiosis seem to be a problem, I note there are now similar captures known among prokaryotes. Even a triple one where the gene transfer has gone in both directions, toward the inner and the outer cell!

    Remains to explain why it evolved only once. But so did the elephant trunk, and I am not sure that uniqueness is seen as a lucky accident?

  17. Christopher Bonds
    Posted February 22, 2016 at 12:54 pm | Permalink

    “A Very Angry Evolutionary Biologist, a Very Angry Liberal, and an Even Angrier Art Lover”. His Tumblr says he ‘has a very low threshold for hooey, hype, hypocrisy, postmodernism, bad statistics, ignorance of population genetics and evolutionary biology masquerading as -omics, and hatred of any kind.’

    . . . sounds like my kind of guy!

  18. BogiT
    Posted February 22, 2016 at 1:29 pm | Permalink

    Right, but this rare event of predation gone wrong is the result of a mutation that allowed pray to escape digestion or a mutation that reduced the ability of host to process engulfed organism.

  19. Merilee
    Posted February 22, 2016 at 1:41 pm | Permalink

    Sub

  20. sensorrhea
    Posted February 22, 2016 at 1:47 pm | Permalink

    You meant archaebacterium but you left out the first r.

  21. RossM
    Posted February 22, 2016 at 3:34 pm | Permalink

    Evolution should be placed into its wider scientific background. Physics shows clearly that the universe is 13.8 billion years old and the Earth is 4.5 billion years old. Once you start to understand the solid factual basis of deep time, evolution is a small detail.

    • John Scanlon FCD
      Posted February 24, 2016 at 10:58 am | Permalink

      Of course deep time and the chemical composition of the biosphere are important, but evolution would still be true if those numbers were different; historically they are much more recent discoveries, and rely on whole branches of physics and chemistry that have little role in understanding how life evolves.

  22. KD
    Posted February 22, 2016 at 10:03 pm | Permalink

    The first thing that occurs to me is the strong suspicion that morphological aberration leads to genetic aberration. That is to say that changes in morphology can result in changes in genetics.

    The reason I would say such a silly thing is that we know clearly from cancer that morphological changes often precede genetic changes in cells. The genetic change seems to be an effect, not a cause.

    I think we are going to figure these mechanisms out because we won’t get too far in understanding cancer if we don’t.

    If morphology can impact genetics, this would also demonstrate the importance of epigenetics to long-term evolutionary change.

    I have seen a Japanese study demonstrating morphological variations leading to genetic variations in species of plants. However, I am not really qualified to judge.

    Anyways, if my suspicions are true, the person who can figure out the biochemistry will be in a position to make some money.

    From the web:

    http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-11-5

    A growing body of work suggests that phenotypic plasticity strongly influences the origin of novel phenotypes [17–19, 30–44]. The earliest support comes from classic work by Waddington [45, 46], Schmalhausen [47] and Baldwin [48]. Waddington showed that artificial selection of a phenotype that initially appears only in a few organisms after non-genetic perturbations, can easily result in the trait’s genetic determination [46, 49]. More recently, other researchers have made the same observation for diverse traits and different species [37, 38, 42]. Artificial selection can thus turn an alternative into a native phenotype. In addition, many observations in wild populations suggest that in multiple cases an ancestral alternative phenotype may have facilitated the evolution of new, genetically fixed adaptive traits [17–19, 30–36, 40]. The phenotypes where plasticity may have facilitated adaptation are very diverse. They include gill surface area in cichlid fishes [33], pigmentation patterns in the crustacean Daphnia melanica [34], and head size in the snake Notechis scutatus [35], to name but a few. Despite an abundance of candidate examples, plasticity’s importance for adaptive evolution is not universally accepted [50, 51]. We still do not know whether existing observations from artificial selection experiments or from wild populations are rare oddities or hint at general principles of evolution [39, 43, 44, 52, 53].

  23. KD
    Posted February 22, 2016 at 10:23 pm | Permalink

    The other thing that is interesting is the work on social cooperation in yeast populations and its impact on the fitness of yeast colonies.

    If you take a view of the organism as an organic clock, then it is pretty clear that clocks cannot communicate each other or synchronize their behavior with each other.

    If the level of social cooperation confers survival value in systems as simply as yeast colonies, then there is an entirely different dimension beyond the biology of any particular organism in understanding the development of life: the relationships between the living organisms as manifested in networks of social cooperation (and punishment of shirkers).

    In other words, primitive hierarchical social orders almost all the way down.

    Also, communication or at least primitive memetics requires on one level an awareness of the other, and self-awareness as manifest in imitation. [Of course, when I say self-awareness, I am referring to reflexivity as manifested in observable behavior.]

  24. Posted February 23, 2016 at 5:18 am | Permalink

    I don’t agree with this statement in number 11 -“From an engineering point of view, most products of evolution work in a manner that is suboptimal.”
    There is a misconception about what “optimal” means. Most people think it means “works best functionally” and I think Dan is addressing and using this definition. But it is sloppy thinking mathematically. Optimality is seeking ANY particular mathematical criteria.. and yes.. Evolution does not seek maximised functionality. But it DOES seek optimal ADAPTIVENESS. This is ultimately what produces greatest fitness – on a conceptional “fitness plane” evolution is seeking adaptive peaks – it is seeking optimality. There may be several such peaks on a fitness plane, and at some time the optimisation search may lead to getting “trapped” on a local fitness peak that is not the maximum peak. But the mathematics is still seeking optimisation.
    A further point – adaptiveness involves MULTIPLE factors which often have to be traded off against each other – growth for root structure in a tree is paid for partly by growth that was possible in tree height. Both things contribute to fitness – but there is an ADAPTIVE optimum in this tradeoff, and that is what Evolution seeks.

  25. Wayne Tyson
    Posted February 25, 2016 at 12:54 am | Permalink

    Context is everything.

    Wayne Tyson

  26. Wayne Tyson
    Posted February 25, 2016 at 1:19 am | Permalink

    Graur and Cobb have answered my prayers–getting at the core of evolution/evolutionary biology in clear, concise statements. I, although I acknowledge that they are ‘as high above [me] as heaven is hell’ (as Judge Roy Bean might say), share their anger, but try to keep it to myself. The challenge is to keep remembering, as Ray Gilmore would say, that “the suspension of judgment is the highest exercise in intellectual discipline.

    WT

  27. Wayne Tyson
    Posted February 25, 2016 at 1:21 am | Permalink

    Organisms do what they can, when they can, where they can.

    WT


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