The Non-Linearity of the History of Science

As I mentioned in my last post, in a history of biology course I am sitting in on we were discussing Cuvier, and if we were discussing Cuvier, we were probably also discussing catastrophism vs. Lyell’s uniformitarianism. Which is true.

The story that is frequently told about this debate and its influence upon Darwin is, as is usual, simpler and a lot less interesting than what actually happened.

Catastrophism was a geological theory that claimed that the planet had experienced large-scale… catastrophes… that completely changed the world rather quickly. No one living at the time, or for the past few thousand years, had ever experienced these kinds of events. Frequently catastrophism was linked to Biblical events such as Genesis and Noah’s Flood (and in the future, Armageddon), but there were scientific reasons to believe catastrophism was true (but I am not currently aware of them). Cuvier avoided Biblical talk in his own catastrophic ideas, arguing for more regional (rather big regions, mind you, but not global) disasters that didn’t wipe out the entirety of existence.

The English geologist, Charles Lyell, constructed the theory of uniformitarianism – a theory very much opposed to catastrophism. Lyell argued that catastrophism was unscientific, but Stephen Jay Gould, in an essay in Ever Since Darwin points out that Lyell was attacking Biblical catastrophism which is somewhat of a strawman. I don’t know the details here so I can’t tell you what the scientific evidence was for or against catastrophism .

Lyell’s uniformitarianism postulated that processes acting today are the same processes that acted yesterday. Instead of mountains rising or canyons furrowing rather suddenly, as the catastrophists believed, Lyell argued that everyday earthquakes and river erosion acting gradually were sufficient to explain these natural formations.

As is typically said in histories of science, Lyell’s uniformitarianism paved the way for Darwin’s theory of evolution.* Special Creation can be construed as a biological form of catastrophism – God, in six days, created all of the life that now exists today, and is an event that we do not experience in our daily lives. Evolution, on the other hand, is obviously not catastrophist as the process happens all around us on a continuous basis, even today. We can explain what happened yesterday by examining what is happening today.

There is an aspect of Lyell’s uniformitarianism that is frequently ignored, however, and it formed a rather large part of Lyell’s worldview. Gould called this tenet the “dynamic steady-state.” It is almost like the Law of Conservation of Mass and Energy, but applied to geology. In regards to land mass, Lyell believed the size of today’s landmass is the same as yesterday’s; the distribution may have changed, but the total amount has remained. Because climate wasn’t “conserved” due to the landmasses moving about the globe, he was able to accept some form of transmutation of species. (Because the continents moved around, Lyell had a cyclical view of history in which biological eras, such as “the age of reptiles” and “the age of mammals,” would also cycle.)

Leaving out the dynamic steady-state in the history of Lyell’s impact on Darwin’s theory of evolution is misleading. The typical story casts the catastrophists in a negative light, even though they were correct about a linear history of the planet. Darwin had to abandon a major tenet of Lyell’s theory to construct his own theory of evolution. The idea of “progress” was “in the air” in Darwin’s time, so I have no idea if the catastrophists’ beliefs regarding linear time influenced him at all, but it would be interesting to check whether or not that is the case. But in any case, there wasn’t a simple jump from uniformitarianism to Darwin’s theory of evolution; instead, Darwin had to eliminate one of the central tenets of Lyell’s theory in order for his to make any sense.

(As for which school of thought is true, modern geology is a mixture of both. Canyons and mountains are generally formed by uniformitarian processes, but asteroids slamming the earth and causing mass extinctions is clearly a catastrophic event. Depressingly, one of the lectures by the creationist Terry Mortenson I saw last spring was focused on disproving uniformitarianism and proving catastrophism. As with all false dichotomies, neither is exclusively true and the answer is somewhere in the middle. The dichotomy is especially false because Mortenson labels modern geology as exclusively uniformitarian when in reality, it’s he who is the oddball extremist.)

The Historical Importance of Modularity

I am currently sitting in on a graduate philosophy of biology seminar and the theme of this semester’s seminar is evo-devo and we recently discussed the concept of modularity. I’m also sitting in on a history of biology course and we have talked a little about the early 19th century French scientist, Georges Cuvier. While attending the seminar, I was delighted to make a historical link between the two! (And oddly enough, one of the works we read in the seminar was a chapter from a book on modularity co-authored by Gunther Wagner which opens with the same link I had made.)

In my posts about the Spencer-Weismann debates, one of Spencer’s anti-Darwinian arguments I focused on can be called the “correlation of parts.” It was an idea articulated earlier by Cuvier, who said (as quoted by Wikipedia),

Today comparative anatomy has reached such a point of perfection that, after inspecting a single bone, one can often determine the class, and sometimes even the genus of the animal to which it belonged, above all if that bone belonged to the head or the limbs. … This is because the number, direction, and shape of the bones that compose each part of an animal’s body are always in a necessary relation to all the other parts, in such a way that – up to a point – one can infer the whole from any one of them and vice versa.

This article from the Academy of Natural Sciences quotes another passage from Cuvier:

Every organized being forms a whole, a unique and closed system, in which all the parts correspond mutually, and contribute to the same definitive action by a reciprocal reaction. None of its parts can change without the others changing too; and consequently each of them, taken separately, indicates and gives all the others.

The parts of an animal are so thoroughly integrated, that changing a single part – without proportionately modifying everything else involved as well – would produce a non-working animal. The correlation of parts prevented Cuvier from accepting Lamarckian evolution, or transmutation, in principle.

The correlation of parts later became an argument for Lamarckian evolution against Darwinian evolution,* as exemplified by Herbert Spencer. (I wonder if there has been any study on this shift in the principle’s use?) He believed, like Cuvier, that frequently a feature of an organism is tightly linked to a multitude of other parts and it would be very unlikely for all these parts to simultaneously vary to the appropriate magnitudes and directions required by neo-Darwinian evolution that prohibits the inheritance of acquired characteristics.

For example, an elk’s antlers are supported by thick skulls and strong back and neck muscles. If an elk were to gain an extra point to the rack through continued growth, increasing its weight, its muscles would be strained to keep the head up and the animal wouldn’t survive. However, in Lamarckian evolution, the muscles that the buck strengthens over its lifetime are passed on to its offspring. Over generations, the muscles would continue to strengthen to the point where extra growth in the rack could be supported. Thus the correlation of parts showed that pure Darwinian evolution couldn’t work in elk antlers, but Lamarckism could – according to Spencer, anyway.**

So, historically, according to some, evolution (or specifically, Darwinian evolution) couldn’t work because of the correlation of parts. I think the concept of modularity easily resolves this.

A module can be loosely defined as a semi-autonomous individual part or process. (I have written about modularity before in a previous post.) An example of modular part is the assortment of lobster appendages: they act and move mostly separate from the rest of their body. A modular process is exemplified by the development of the appendages themselves: each appendage develops indepently of the others, and these appendages are specified and created by modular genetic networks and pathways. Additionally, these modular structures, processes, and genetic networks can evolve freely from the rest of the organism-at-large.

Modularity answers Cuvier’s and Spencer’s objections to evolution. Yes, an organism may be well-integrated, but it is also built of semi-autonomous modules. A part or process of an organism can vary without the rest of the organism falling apart! Spencer argued that if Lamarckian inheritance, which sidesteps the correlation of parts, weren’t true, then evolution couldn’t happen, but perhaps he was half-right: modularity (which also sidesteps the correlation of parts), not Lamarckian inheritance, is what allows evolution to happen.

* I am obviously omitting Darwin’s views on the topic, but given what I read in Gould’s The Structure of Evolutionary Theory, his views seem a bit muddy and complicated. Perhaps I will investigate Darwin’s views on the correlation of parts at a later date, but here I am focusing on correlation of parts vs. modularity.

** I don’t understand why Spencer excludes the possibility of later fluctuations or mutations that could arise after the weight increase in the antlers. He also doesn’t mention how the skull would thicken as a result of Lamarckian processes. I don’t think Spencer’s argument works at all given his framework, but it still illustrates the use of the principle of correlation of parts as an argument against Darwinian evolution.

Ants and Their Castes in the Spencer-Weismann Controversy

Ant (Wikipedia)

Ants are evolutionarily weird and are quickly rising in my favorite organisms list.  The same evolutionary principles apply to ants as they apply to us, of course, but because ants are haplodiploid, live in large colonies, and have a caste system, biologists have to apply the same principles differently – it isn’t exactly intuitive. Ants (and other insects such as bees and termites) are frequently the subjects of hot debate when it comes to kin selection, but their role in evolutionary disputes is over a century old. Charles Darwin discussed them in The Origin of Species, but they were later the center of the controversy between Herbert Spencer and August Weismann.

As discussed in my last post, Herbert Spencer was a Lamarckian who believed in “inheritance of acquired characteristics” and thought natural selection was “inadequate” for explaining how organisms have evolved. August Weismann contested this; he was known as an “ultra-Darwinian” who believed natural selection explained all biological traits and thought Lamarckism was dead wrong. He believed this because of his idea, called the “Weismann barrier,” which postulated an organism’s hereditary material is contained exclusively in reproductive cells (sperm and eggs) called the germ line. With the barrier, there would be no way for the environment or acquired traits developed in the soma (any cell not sperm/egg) to directly influence the germ line because they were totally isolated from each other. Because their respective biological theories were being questioned in their entirety by the opponent and because neither theory was completely accepted by the scientific community at the time, the stakes were high. Were acquired characteristics actually inherited? Could natural selection explain all traits? What was the role of the environment in modifying traits? Was the Weismann barrier even real?

The “Controversy” began with Spencer’s “The Inadequacy of Natural Selection” and “Prof. Weismann’s Theories” in 1893, followed by Weismann’s response, “The All-Sufficiency of Natural Selection.” Spencer then published “A Rejoineder to Prof. Weismann” and a brief follow-up called “Weismannism Once More.”

The ants were not initially discussed by Spencer, but brought up by Weismann as an example of where he thought Lamarckism faltered, specifically in the evolution and maintenance of their famous caste system. In the caste system, individuals are divided into classes within the colony: typical castes are the queen along with various workers such as soldiers and caretakers (of the larvae). A special quality of the worker class is that they do not reproduce – only the queen and the males do. Weismann exploited this feature to attack Lamarckism for all it was worth.

Weismann observed that worker ants have reduced reproductive organs, eyes, and wings (“retrogressive”). Because they don’t need them, these reductions may have occurred because of inherited disuse (a Lamarckian argument). As Weismann points out, the argument has one problem: the workers don’t reproduce! They can’t directly transmit their reduced organs (315-316)! Such morphological (and also instinctual) changes occurred after the evolution of the castes themselves, he argues, and thus cannot explain the caste system (328-331).

August Weismann (Wikipedia)

Weismann also makes a point regarding reduced wings: even if workers reproduced, wings can’t degenerate through disuse because wings are perfectly formed before use and deteriorate because of use. Additionally, eyes in the workers can’t have degenerated through disuse because workers still use their eyes! Instead, Weismann argues, the atrophy of worker ant eyes favors his theory of panmixia: highly developed eyes are superfluous for the worker ants and are not maintained by selection (317). [2] [3]

In “The Inadequacy of Natural Selection,” Spencer argued that selection could not produce complex morphological changes because such complexity would require all of the involved traits to vary to similar degrees and in parallel directions. For example, evolving the ability to jump would require many concurrent variations in the skeletal, muscular, and nervous/instinctual systems. In Paleyesque fashion, Spencer lists over two pages of required variations, arguing that the probability of having dozens of traits vary in the right degrees and in the right directions is extremely low. Natural selection wouldn’t even be able to act on the ability to jump. Instead, “using” one’s jump ability strengthens the muscles together – no variation in the isolated germ plasm is necessary – and these acquired changes are what gets passed on to the offspring. (I don’t know how skeletal changes would work though…)

Pheidole megacephela - the big-headed ant referenced by Weismann. Yeah, weird as hell. (Photo by Hirotami T. Imai and Masao Kubota, from Japanese Ant Image Database.)

Weismann adopts the list-as-many-connected-traits-as-possible argumentation style for the ants, but to argue against Lamarckism. In addition to degenerated organs, worker ants have specialty traits not found in the sexual castes such as thorns and larger heads and jaws (“progressive”). “Many parts must have varied simultaneously and in harmony with one another.” He piles on, in Paleyesque fashion, all of the variations required to produce such morphological changes. But Lamarckism can’t handle all of these necessary variations; because workers are sterile, the acquired characters are not passed on to the offspring! Lamarckism can’t work here.

Instead of using “inheritance of acquired characters” to explain the castes, Weismann believes his germ plasm theory is sufficient, arguing that castes are differentiated by multiple “determinants” (similar to what we would call chromosomes, I presume) within the germ plasm (325-326). Selection then acts on the workers through selection on the queen who carries inactivated worker determinants (i.e., kin selection). Weismann seems prescient, eh?

He admits proving this hypothesis to be true is nearly impossible because the sheer number of ants in a single colony and the nearly infinite amount of minute variations involved would be impossible to study closely. However, according to Weismann, because Lamarckism is inadequate for explaining ant castes, “that it is necessary for us to accept the principle of natural selection. It alone can explain the adaptations of organisms without assuming the help of a principle of design” (319). We know Lamarckism and design are false, so selection, the only alternative, must be the solution to the ant caste system.

Not surprisingly, Spencer doesn’t think Weismann has refuted Lamarckism at all. Instead, Spencer offers his own evidence that selection is inadequate in explaining the ant caste system. He begins his argument with observations of wasps and extrapolating those to ants.

Spencer argues that social insect castes can be explained without selection. [4] He first invokes Haeckel’s concept of heterochrony – social insect development does not recapitulate phylogeny (Haeckel’s biogenetic law [5]), but has instead been reordered to reflect behavioral development. According to Spencer, just as girls play with dolls (maternal instinct) before having children (sexual instinct), queen-wasps progress from “building cells and feeding larvae” (maternal) to exclusively laying eggs (sexual). He argues that worker-wasps are undeveloped queen-wasps – their development was arrested before the sexual stage could arrive. (655). “Thus interpreting the facts, we have no occasion to assume any constitutional difference between the eggs of worker-wasps and the eggs of queens” and that “the larva of a worker-wasp can be changed into the larva of a queen-wasp by special feeding” (656). Additionally, he notes that malnutritioned eggs produce males. Feeding/nutrition – an environmental inductor – controls the caste system in waps, according to Spencer, and not information emanating from Weismann’s germ plasm.

Herbert Spencer (Wikipedia)

Although Spencer has been examining the wasps, he assumes ants develop similarly, applying the “arrested development” (658) argument to the rest of Weismann’s objections. For example, Weismann said that the worker caste has less developed eyes than the queen ants, but because the workers don’t reproduce, the Lamarckian argument of disuse can’t apply to them. Spencer replies that yes, disuse cannot apply here, but because eyes are among the latest organs to develop (larvae are blind), “arrested development” by lack of feeding leaves worker ants with underdeveloped eyes – they were prevented from fully forming (658)! Spencer says “arrested development” takes care of Weismann’s wing argument as well. Furthermore, many species show intermediate classes which under Weismann’s scheme would imply more and more determinants, but with Spencer’s “arrested development,” they are no surprise (659). [4]

He again applies the “arrested development” argument to explain away Weismann’s Amazon ant objection, that larger heads and jaws of the soldier class evolved after the caste system evolved and because they can’t reproduce, those features are not explained by Lamarckism. Spencer simply counters the objection by claiming the Amazon ants are most likely descended from ants that resemble the soldier-caste. He seems to believe that all ants with caste systems derive from an ancestral warrior species as he provides us with some intriguing ant/human sociology:

[The ancestors] must have had marked powers of offence and defence. Of predacious creatures, it is the more powerful which form societies, not the weaker. Instance human races. Nations originate from the relatively warlike tribes, not from the relatively peaceful tribes. Among the several types of individuals forming the existing ant community, to which, then, did the ancestral ants bear the greatest resemblance? They could not have been like the queens, for these, now devoted to egg-laying, are unfitted for conquest. They could not have been like the inferior class of workers, for these, too, are inadequately armed and lack strength. Hence they must have been most like these Amazon-ants or soldier-ants, which now make predatory excursions – which now do, in fact, what their remote ancestors did (663).

Thus Spencer bypasses Weismann’s objection that the soldier caste can’t transmit their acquired characteristics: they didn’t need to do so because they inherited them! “It is not that the soldier-ants have gained these traits,” he argues, but “the other castes have lost them” as “early arrest of development causes absence of [soldier traits] in the inferior workers; and from the queens they have slowly disappeared by inheritance of the effects of disuse” (663).

Spencer provides us with a Lamarckian framework for caste evolution. Not only does he claim that classical Lamarckian use/disuse inheritance is involved, but he also adds direct stimulation by the environment to explain how castes can form. (I think the latter is an underappreciated aspect of Lamarckism that I only just read about in Peter Bowler’s The Eclipse of Darwinism, but Spencer appears to find it an incredibly important aspect.) Weismann, on the other hand, also provides us with a useful framework in which to understand how the germ plasm theory and Lamarckian theory were distinct and at the time, completely opposed. We are left with no clear answer, however. As the paleontologist Henry Fairfield Osborn wrote about the controversy:

In fact, the reason these papers, interesting and able as they are, leave no final verdict in the mind is that neither meets the tests of scientific truth. When we look beneath the surface and recover from the first blinding effects of the brilliant style which characterizes both attack and reply, we see that both set forth mainly the modes in which nature may be supposed to act, rather than the mode in which nature does act. Nature, if anything, is illogical in many of her forms (313).

This discussion, at least in its theoretical phase, has reached its climax in this controversy (315).

In the end, and as with most false dichotomies, the answer to caste differentiation lies somewhere in the middle between Spencer and Weismann. Weismann’s barrier concept turned out to be correct, at least in many animals (to the exclusion of the rest of life… over 99% of it) – the germ cells are isolated from the somatic cells – but the barrier doesn’t rule out Spencer’s environmental influence on development either.

Caste differentiation is still a topic of debate over a century later. A study from just this past April found the protein responsible for queen development in bees that is found in “royal jelly.” When this “royal jelly” containing the protein is given to bee larvae, a queen bee results. Fascinatingly, when this protein is fed to flies – which have no castes – “queen flies” with large body sizes and ovaries come about. However, a neat 2008 review by Anderson et al. (PDF) points out that historically, environmental factors (as argued by Spencer) were shown to be the dominant form of caste determination (and involved more than just feeding, but season, temperature, and others) but that, at least in some ant species, genetic factors (Weismannian) have recently been shown to play a large role as well. Of course, genetics and environment do not act independently, but concurrently, and also act upon each other. Both Weismann and Spencer were right; they just didn’t know it!

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[1] Panmixia is different from the economical hypothesis that traits may be lost because of the excess energy it costs to develop and maintain them. Instead, panmixia holds that selection has been removed allowing the trait to be reduced due to lack of maintenance.

[2] Weismann says Spencer accepts the giraffe’s neck as a result of selection because “the process appears easy to imagine” (320). A topic for future investigation.

[3] Weismann also applies panmixia to caste-specific behaviors (333).

[4] Here is an example of where I have trouble understanding why Spencer believes selection has no role to play in ant castes. Why couldn’t selection have produced the environmentally induced development? Is this an error/oversight on Spencer’s part, or me not properly understanding the debate (especially without the knowledge scientists have developed since)?

[5] So far, Spencer seems to not be applying Haeckel’s biogenetic law – ontogeny recapitulates phylogeny – but alludes to it when discussing ant wings: “Wings are late organs insect phylogeny, and therefore will be among those most likely to abort where development is prematurely arrested” (658).

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History:

Osborn, Henry Fairfield. “The Discussion Between Spencer and Weismann.”Psychological Review 1 (1894): 312-315.

Spencer, Herbert. “Appendix B. The Inadequacy of Natural Selection, Etc., Etc.” The Principles of Biology. Revised and Enlarged Edition. Vol. 1. New York: D. Appleton and, 1898. 602-91.

Weismann, August. “The All-Sufficiency of Natural Selection.” Contemporary Review 64 (1893): 309-338.

Science:

Anderson, Kirk E., Timothy A. Linksvayer & Chris R. Smith. “The causes and consequences of genetic caste determination in ants (Hymeonoptera: Formicidae)” (PDF). Myrmecological News 11 (2008): 119-132.

Kamakura, Masaki. “Royalactin induces queen differentiation in honeybees.” Nature 473 (2011): 478–483. doi:10.1038/nature10093

Wait. What? Herbert Spencer was a Lamarckian?

While reading Peter J. Bowler’s The Eclipse of Darwinism, I was surprised to find out that the “social Darwinist”* Herbert Spencer was actually more Lamarckian than Darwinian. He apparently expressed Lamarckian views prior to the 1859 publication of The Origin of Species, and while he accepted Darwinian explanations and the theory of natural selection, Spencer believed Lamarckism – defined (here) as the inheritance of acquired characteristics through use/disuse – was the more important of the two theories. In fact, in his article, “The Inadequacy of Natural Selection,” Spencer states quite strongly that “either there has been inheritance of acquired characters, or there has been no evolution” (621).

Why did this “social Darwinist” think natural selection was inadequate? I think it can be boiled down to his belief that Darwinism couldn’t explain non-adaptive features and features that varied so finely that selection couldn’t detect them, as evidenced by his example of “skin discriminativeness,” or what we would now call tactical acuity.

Figure 1.

It is trivially true that your fingertips are more sensitive than the skin anywhere else on your body. In a series of experiments, Weber took a compass (the geometrical kind) and tested at what minimum distance a subject could detect the compass’s two points. For example, subjects could detect the two points 1/12 inch apart on their forefinger, but the points had to be 2.5 inches apart to be detected separately on the subject’s back. The rest of the body parts fell somewhere between 1/12 inches and 2.5 inches. (My MSPaint Figure 1 shows the “skin discriminativeness” Weber found among body parts.)

Why this distribution of tactical acuity? Why doesn’t all skin show the same acuity? According to Spencer, if this distribution is to be explained by natural selection, then there must be some kind of fitness benefit to having more sensitive fingertips and having one’s “thigh near the knee be twice as perceptive as the middle of the thigh” (604), but he is unable to offer one. Furthermore, he argues, would people with a more sensitive “thigh near the knee” survive and reproduce more than those who don’t? He thinks it unlikely – selection can’t see differences so miniscule.

Spencer notes that blind people, especially those who read Braille, as well as typesetters, show higher tactile acuity than normal. He claims this is “clear proof” that skin discriminativeness is an acquired trait (605) and suggests that when the skin touches objects, additional nerve growth is stimulated which increases tactile acuity (647). This explains why the back has the least sensitive skin – it just touches clothes – whereas the stomach has slightly more as it is explored by the hands more frequently. The nose is more sensitive than the forehead because we rub our nose more, and our palms are less sensitive than our fingertips because the fingertips manipulate while the palms merely help grasp. The more used a body part is, the higher tactile acuity it shows.

Spencer thinks his argument is solidified when he brings up the tip of the tongue. Weber found that the tongue tip has double the sensitivity of the fingertips, but Spencer doesn’t think the increased sensitivity is because of some selective advantage. He argues that food is moved by the body of the tongue, not the tip, and while the tip is used in making some sounds, people can get by with less sensitive tongues. Instead, much like skin sensitivity, Spencer believes the tongue tip’s acuity is a result of constant environmental stimulation – the tongue is continually exploring the mouth and teeth. There is no adaptive function for having a tongue that can sense two points 1/24 inches apart, according to Spencer.

So now we have a standard Lamarckian explanation of tactile acuity: the more use, the more nerve growth, the more acute.** His argument is also non-adaptive and very much not (ultra)Darwinian.

Spencer’s argument was challenged by at least three people: the neo-Darwinians Alfred Russell Wallace and August Weismann as well as psychologist James McKeen Cattell. The dispute with Wallace is rather uninteresting: Wallace claims skin sensitiveness is a result of natural selection and Spencer disagrees but both claim the facts are on their side (646). Weismann points out that the other apes use the tongue as “an organ of touch,” but Spencer still disputes that selection could detect such fine-scale differences (like between 1/24 inches and 1/20 inches). Spencer further points out that Weismann’s argument is “suicidal” because it refutes Weismann’s own theory of panmixia – that traits may be lost because selection on the trait is removed – which has apparently not taken place in the human tongue as it is still extremely sensitive (665). Cattell points out that “relatively great accuracy of discrimination can be quickly acquired by ‘increased interest and attention. … Practice for a few minutes will double the accuracy of discrimination, and practice on one side of the body is carried over to the other’” (666). Spencer dismisses this challenge, claiming that those studies actually showed that the subjects were only able “to learn to discriminate between the massiveness of a sensation produced by two points and the massiveness of that produced by one, and to infer one point or two points accordingly” (666). While Spencer’s pro-Lamarckian arguments seem weak, being based on crude experiments and hearsay, he was able to handily refute his opponents as well.

However, the most problematic part of Spencer’s argument in my mind is the issue of heredity. For some reason, Wallace and Weismann never address the issue. James McKeen Cattell does challenge Spencer on this point, but Spencer leaves this problem unanswered. Was proving heredity not as essential in this period as it is today? Spencer apparently felt he showed that acquired traits were inheritable in Factors of Organic Evolution (which I have yet to read), but he didn’t even attempt to show that increased tactile acuity was.

So yes, Spencer was indeed a Lamarckian. In addition to skin discriminativeness, he thought the reduced size of the little toe in humans, the evolution of jumping, and the antlers of the Irish elk were Lamarckian features. Perhaps I should have known this already, but it seems strange that a man known for “social Darwinism” was actually a Lamarckian. He did accept Darwinian explanations for some features, but he thought natural selection was well, inadequate. He believed that Darwinism couldn’t explain non-adaptive traits, traits that varied in minuscule gradations, and traits that required parallel variations in other traits. Lamarckism filled those gaps in Spencer’s eyes.

* Eric Michael Johnson has a great series of posts on why “social Darwinism” is such a problematic term and also discusses some of Herbert Spencer’s beliefs, called “Deconstructing Social Darwinism.”

** A question I am interested in is: Was Spencer right or wrong on this point?  According to this study, “Tactile Spatial Acuity Enhancement in Blindness: Evidence for Experience-Dependent Mechanisms,” blind people do outperform the non-blind in tactile acuity and that touch is “the trigger for tactile spatial acuity enhancement.” They say the results suggest “the action of underlying experience-dependent neural mechanisms such as somatosensory and/or cross-modal cortical plasticity” but I have no idea what that means. Is this nerve growth or something else?

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Spencer, Herbert. “Appendix B. The Inadequacy of Natural Selection, Etc., Etc.” The Principles of Biology. Revised and Enlarged Edition. Vol. 1. New York: D. Appleton and, 1898. 602-91. Print.

When the developmental context changes, so do the master controllers

In my last post, I mentioned that I was reading Cycles of Contingency: Developmental Systems and Evolution and while I will highlight its major themes in a later post, I wanted to again briefly focus on one of its essays that I found fascinating. Developmental biologist H. Frederik Nijhout’s essay “The Ontogeny of Phenotype” (based on a 1997 paper) primarily argues that developmental pathways cannot be isolated from their genetic background, i.e., context matters, and the integration of developmental networks are also not cast in stone. There is a potential and remarkable fluidity to developmental systems that I was not previously aware of.

Fig. 1: A protein gradient can pattern the anterior-poster axis by activating or repressing genes where it is high in concentration. Image from Wikipedia.

In a computer model, Nijhout and Paulsen created a diffusion gradient (Fig. 1) with six “genes” controlling six different aspects of the gradient. The gene that produces the diffusion molecule (source), the molecule’s rate of diffusion and rate of decay, the time at which the gradient is “read” (T-end) and the threshold of activation, and the background rate of production of the molecule. Each gene has two alleles: a high and low value. They assigned the gradient a “phenotypic value” that can range from zero to one and is an abstract measure of the interactions among the six genes. (The exact nature of the phenotypic value is not crucial, I don’t think.)

Fig. 2: A. Response of the phenotype to selection. B. Response of the genes to selection. C. Genetic correlations of the genes to the phenotype during selection. From Fig. 5 of Nijhout & Paulsen (1996) and Fig. 11.6 of Nijhout (137).

With selection, the phenotypic value predicably falls from a high ~17 to a low 2 (Fig. 2A). There isn’t too much excitement here but that’s because the “phenotype” is hiding all of the dynamics going on behind-the-scenes…

As Fig. 2B shows, not all the genes respond the same to selection. Source and T-end react immediately: their allele frequencies are zero by generation 8 while the other four allele frequencies remain high. Diffusion subsequently falls to zero, followed by the other three in a progression of precipitous drops. While the phenotype fell deterministically toward zero, the six genes responded erratically.

Fig. 2C shows the correlation between each gene and the phenotype. The correlations follow from 1B: at first Source is most receptive to change by selection and most highly correlated with the phenotype, followed by the other five genes, which provides us an intriguing idea: there is no single “master” gene controlling this developmental system. The master gene, the one gene most highly correlated with phenotype and modifies the developmental system as it itself changes, shifts from one gene to another throughout the course of selection. Furthermore, variation with a single gene may not always have large effects on the phenotype – only sometimes (Fig. 2C). It’s the context – the genetic background – that matters.

This is a computer model and I wonder if any similar work has been done on living organisms, if the project would even be feasible. None of the articles on Google Scholar that cite this paper seem to have done so. I don’t see how though!- the dynamics of a “simple” diffusion gradient provide a much more complicated picture than I had previously thought. Why didn’t Sean B. Carroll talk about this in Endless Forms Most Beautiful?

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Nijhout, H., & Paulsen, S. (1997). Developmental Models and Polygenic Characters The American Naturalist, 149 (2) DOI: 10.1086/285996

Nijhout, H. F. “The Ontogeny of Phenotypes.” Cycles of Contingency: Developmental Systems and Evolution. Comp. Susan Oyama, Paul E. Griffiths, and Russell D. Gray. Cambridge, MA: MIT, 2001. 129-40.

“Niche construction” before “niche construction” was cool?

One of the most useful aspects of being aware of the history of science is that much like literature and the arts, one can trace the historical origins of ideas and make connections among various thinkers who lived at different times. Last week’s post was a great example of such a connection: the arguments of Gould & Lewontin were articulated over 70 years before 1979 by TH Morgan, and more astoundingly, William Bateson (who even nailed down the idea of a “spandrel”). While there may be no link between Gould & Lewontin and Morgan & Bateson, this example shows us that biologists have had to argue against adaptationism since at least 1903. We can see a clear historical trend.

I came across another example in Lewontin’s 1983 essay, “Gene, Organism and Environment.” [1] While originally published in From Molecules to Man, I read this essay in Cycles of Contingency: Developmental Systems and Evolution (2001) (which I will blog about later). Lewontin’s central argument is that evolution by natural selection, still under the controlling influence of Darwin and Mendel, is too frequently said to be a process of “autonomous” environmental forces acting on the internal genetics of the organism; the internal and external operate in separate domains. Lewontin believes we should instead view the organism and environment as reciprocal influences upon each other – they evolve in tandem. This gives us the idea of niche construction: ”organisms do not adapt to their environments; they construct them out of the bits and pieces of the external world” (64). Frequent examples include beaver dams (building a physical structure that lasts generations) and the chemical changes to the soil enacted by earthworms.

A beaver dam - an example of an organism constructing its own environment. From: SewerDoc (Flickr) (click image to go to his page).

I find this idea to be an entirely new way of thinking about how evolution works. The book this is compiled in, Cycles of Contingency, is all about dissolving the barriers and false dichotomies biologists have constructed over the years (such as nature/nurture and genes/environment) and Lewontin’s niche construction falls right in place here.

While Lewontin is attacking the status quo of evolutionary population genetics (as articulated by the Modern Synthesis) which perpetuates the internal/external dichotomy, it is important to examine what some of the major Synthesis thinkers may have actually thought. In my history major paper, I had the chance to read some of the work by scientists like Dobzhansky, Fisher, and Wright, and luckily enough, what I read may have some bearing on the issue (and by “may” I mean “this is why I am writing the post”).

According to Lewontin, the orthodox view is that “the history of life is then the history of the coming into being of new forms that fit more and more closely into these preexistent niches” (63).

This actually matches something Dobzhansky wrote in a 1974 essay titled “Chance and Creativity in Evolution:” [2]

Evolution creates new living systems to occupy the ecological niches that are available and accessible. As pointed out above, not even minuscule ecological niches are disregarded if they are accessible. New ecological niches constantly arise. This is why evolution has not become stalled or terminated (Dobzhansky 330).

Evolution by natural selection allows populations to fit to newly accessible niches (Dobzhansky believes mutation isn’t important in this regard), but Lewontin, of course, would respond that this is also partly due to the fact that organisms construct the niches in which they occupy. No wonder there is a “marvelous fit of organisms to their environments” (Lewontin 63)!

So far, Lewontin’s portrayal of orthodoxy seems accurate, but the Synthesis thinkers were not monolithic in their worldviews or scientific beliefs. A scientist that may have had a rudimentary sense of niche construction was RA Fisher.

Lewontin points out a way in which organisms may construct their environment:

(4) Organisms create a statistical patten of environment different from the pattern in the external world.

It might be objected that the notion of organisms constructing their environments leads to absurd results. After all, hares do not sit around constructing lynxes! But in the most important sense they do. … The biological properties of lynxes are presumably in part a consequence of selection for catching prey of a certain size and speed, i.e., hares. Second, lynxes are not part of the environment of moose while they are of hares, because of biological differences between moose and hares. (Lewontin 64).

(While the first sentence may seem cryptic, I think the different “statistical pattern of environment” is illustrated by the moose: moose are physically in the same environment as the lynx and hare, but play no part in lynx/hare biology. In this sense, the lynx and hare have constructed an environment with no moose in it.)

It seems that, to Lewontin, evolutionary arms races are a form of niche construction: the environment of the lynx, which includes the hare, evolves because of the lynx. While this example may seem trivial, Lewontin’s portrayal of the scenario lends it a new light as coevolution – one species indirectly constructs the other –  but RA Fisher [3] may have agreed with him already:

Just where does the theory of natural selection place the creative causes which shape evolutionary change? In the actual life of living things; in their contacts and conflicts with their environments, with the outer world as it is to them; in their unconscious efforts to grow, or their more conscious efforts to move (Fisher 17).

“Contacts and conflicts with their environments, with the outer world as it is to them” sounds an awful lot like the different “statistical pattern of environment” argument from Lewontin. Fisher even gives a similar example to illustrate his point:

The timid antelope has played its part in the creation of the lion, and species long extinct must have left indelible memorials in their effects on species still surviving. Who knows if the mammals would ever have evolved, but for the creative activity of the dinosaurs! (Fisher 18-19).

This example is almost exactly the same one given by Lewontin, only 33 years earlier.

At this point, I doubt there was an intellectual link between Lewontin’s niche construction and Fisher’s proto-niche construction (and “proto” may even be too strong of a prefix). However, I don’t know how widespread Fisher’s antelope/lion argument was at the time – was this an original thought by Fisher or was he articulating a belief held widely by other biologists?

Whatever the case, the evolutionary theory we have inherited didn’t incorporate the ideas of niche construction. For example, Lewontin argues that the adaptive landscape completely changes when we take into account niche construction – populations no longer “climb mountain peaks” but are “walking on trampolines;” frequency-dependent selection becomes the norm, rather than a “complication of marginal interest” (Lewontin 65). So it seems that in the end, even though Fisher had some idea of niche construction, he didn’t transmit those ideas in any meaningful way as a founder of population genetics.

I am not trying to establish too much here or make any grandiose claims. I just wanted to point to an example of how being well-read in the history of science (not that I am particularly well-read… yet) helps you make links between various lines of thought from different historical periods. It makes your science much richer when you know the intellectual history of the science itself.

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[1] Lewontin, Richard. “Gene, Organism and Environment.” In Cycles of Contingency: Developmental Systems and Evolution, edited by Susan Oyama, Paul E. Griffiths, and Russell D. Gray, 59-66. Cambridge, MA and London: The MIT Press, 2001.

[2] Dobzhansky, Theodosius. “Chance and Creativity in Evolution.” In Studies in the Philosophy of Biology: Reduction and Related Problems, edited by Francisco José Ayala and Theodosius Grigorievich Dobzhansky, 307-38. Berkeley and Los Angeles: University of California Press, 1974.

[3] Fisher, Ronald Aylmer, Sir. “Creative Aspects of Natural Law.” In The Eddington Memorial Lecture: Cambridge University Press, 1950.

Allele Origination by Intergenic Recombination (Adaptive Recursion IV)

New alleles are normally said to arise from mutations, but recombination can be just as potent. Recombination relies on new mutations, of course, but its shuffling power increases the number of possible allele combinations. Biologists Jeffrey Feder and Sebastoam Velez found that the Jamaican click beetles use recombination to generate their unique bioluminescent polymorphisms, but this recombination is between two different, but related, genes, and creates a novel allele cycling system.

Fig. 1: A) Dorsal organs. B) The colors of the green and yellow-green dorsal alleles. C) Ventral organ. D) The colors of the yellow-green, yellow, and orange ventral alleles. From Stolz et al. (2003).

First, a brief review of how bioluminescence works in the Jamaican click beetle, Poryphorus plagiophthalamus. The species has two sets of bioluminescent organs – a pair of dorsal organs and a single ventral organ, and each set’s color is controlled by its own luciferase locus. Within an individual the two sets can be different colors but what makes the species unique, however, is that each organ shows polymorphisms within the species. Related species exhibit only a single color in the ventral locus and another color in the dorsal locus – in P. plagiophthalamus, one can find green or yellow-green dorsal alleles (dGR, dYG) and yellow-green, yellow or orange ventral alleles (vYG, vYE, vOR) (Fig. 1). These alleles are differentiated by point mutations in luciferase that increase or decrease the wavelength.

Gene trees of luciferase indicate that vOR is derived from vYE with only three base substitutions differentiating the two. vYE in turn is derived from vYG (which itself is most likely derived from vGR, as seen in other Poryphorus species). However, Feder and Velez found a (relatively) novel form of allele generation: gene conversion through intergenic recombination, or the imposition of one gene’s sequence (say dorsal) onto another gene’s sequence (ventral). If the right portion of the sequence is converted, a new color allele can be generated.

Stolz et al. first found evidence of intergenic recombination in 2003. Due to most of the found mutations occurring in exon 4 of luciferase (as well as a couple in 1 and 5) and none in exons 2 and 3, the authors could compare evolutionary trees of the exons against each other (Fig. 2).

Fig x: Gene trees of exons in luciferase. On the left, exons 2 & 3 which are not involved in the color phenotype, show different relationships than the color exons 1, 4-7 on the right. On the right, dGR is closely related to vOR/vYE, whereas it is less related on the left. From Stolz et al. (2003).

When they compared the trees, they found incongruence: exons 1, 4-7 in vOR/vYE and dGR (on the right) were more closely related to each other than to exons 2 and 3 (on the left). Because the dorsal and ventral alleles have actually been separated for millions of years, the only way they could be “more related to each other” sequence-wise is by an intergenic recombination event, effectively homogenizing the two genes, which also means that while dorsal and ventral organs are genetically controlled independently, they have not always evolved independently.

The 2003 study did not investigate the effects of intergenic recombination much further but the evolutionary implications were clarified in a 2009 study by Feder and Velez. It turns out that intergenic recombination is relatively common in Poryphorus, being found in several other species. However, due to the polymorphic nature of bioluminescent color in P. plagiophthalamus, intergenic recombination plays a unique role in allele generation.

First, the evidence of recombination. Reconfirming some results in the 2003 study, Feder and Velez found that the dYG and vYG alleles were more closely related to each other than to any other alleles in P. plagiophthalamus (Fig. 3). Also, dYG + vYG/vYE/vOR are nested within a clade containing dGR (Fig. 3). When the dorsal and ventral alleles “should be” nested separately, these results are highly unusual and indicative of intergenic recombination.

Fig. 3: In the red box, the dorsal yellow-green (dYG) allele is more related to the ventral alleles than it is to the dorsal green (dGR) allele. This tree indicates that the ventral alleles are derived from dGR through dYG. From Feder and Velez (2009).

Looking at specific mutations, Feder and Velez were able to construct an evolutionary history of intergenic recombination and allele origins. Evolving from the green allele, the yellow-green allele has two affecting mutations: base-pair 671 has a T->C substitution resulting in a wavelength shift of 14-nm longer (i.e., yellower); base-pair 967 has an A->G transition, shifting wavelength 2-nm longer. Both mutations are found in both dYG and vYG and were likely derived only once, not independently (parsimoniously-speaking) . This is further evidenced by both mutations occurring within sequences already suggested as sites of gene conversion and also by the existence of a silent mutation only found in the dYG/vYG alleles (Feder and Velez 2009).

Because 671C is found in the ventral luciferase locus of both P. plagiophthalamus and P. mellifluous, it is likely that 671C originated in the ventral locus and was later converted over to the dorsal locus in P. plagiophthalamus. The authors propose that 967G, on the other hand, originated in the dorsal locus because dYG is associated with higher genetic diversity and because dYG is more common in Jamaica than is vYG.

Given this evidence, the evolutionary history that Velez and Feder construct is as follows (Fig. 4): the 671C mutation converted from vYE to dGR where it became associated with 967G, causing dGR to mutate to dYG because of the longer wavelength shift. A subsequent dorsal-to-ventral conversion event mutated vYE to vYG. Thus P. plagiophthalamus exhibits a unique system of allele generation: color cycling through intergenic recombination (Fig. 4). Dorsal-to-ventral conversions cause the ventral locus to shift toward shorter wavelengths whereas ventral-to-dorsal conversions cause the dorsal locus to shift toward longer wavelengths. However, the dorsal-to-ventral exchange (longer-to-shorter wavelengths) may be selected against because of possible ongoing selection towards vOR. Here, selection’s role is stopping the cycle from being completely fulfilled.

Fig. 4: The proposed color allele cycling system in P. plagiophthalamus. Dorsal->ventral conversions shift the ventral locus toward green, but due to mutation and subsequent selection towards orange, ventral->dorsal conversions shift the dorsal locus towards longer wavelengths. This cycle is driven by mutation, recombination, and selection. From Feder and Velez (2009).

I find this allele generating system to be incredibly cool. The authors note that intergenic recombination may play similar roles in other biological systems, such as “pathogen-resistant genes in plants, the major histocompatibility complex in mammals, Glutatione S-Transferase genes in Drosophila, silk genes in spiders, and tRNA genes in yeast,” but after reading (or trying to read) those papers, the Jamaican click beetle’s use of intergenic recombination seems to be the simplest.

We have also seen intergenic recombination in the mammalian Y chromosome. The Y chromosome contains multiple copies of many genes that show very high sequence similarity to each other. Thus the Y genes are homogenized through intergenic recombination unlike the polymorphisms of P. plagiophthalamus. This is because the Y’s multiple copies are all fulfilling the same selective purpose – evolving concurrently – whereas the beetle’s dorsal and ventral loci are being pushed in different directions by selection, maintaining different colors. Here, intergenic recombination creates alleles opposed to selective pressures and so polymorphism is maintained. Thus the same mechanism, intergenic recombination, can result in either homogenization of genes or cycling of new alleles – both are neat, but the latter’s dynamism is fascinating!
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Feder JL, & Velez S (2009). Intergenic exchange, geographic isolation, and the evolution of bioluminescent color for Pyrophorus click beetles. Evolution; international journal of organic evolution, 63 (5), 1203-16 PMID: 19154393

Stolz U, Velez S, Wood KV, Wood M, & Feder JL (2003). Darwinian natural selection for orange bioluminescent color in a Jamaican click beetle. Proceedings of the National Academy of Sciences of the United States of America, 100 (25), 14955-9 PMID: 14623957

“Spandrels” before “spandrels” were cool

In 1979, Stephen Jay Gould and Richard Lewontin famously attacked what they called the “Adaptationist Program.” They accused evolutionary biologists and sociobiologists of concocting “just-so stories” in which scientists would claim a particular trait, an adaptation, was a result of natural selection without rigorously testing their hypotheses. If they did test the claim and it turned out the claim was false, the scientist would create another just-so story, rarely questioning whether the trait was an adaptation or possibly a byproduct or fixed by non-adaptive processes. Most readers are familiar with this argument, so I won’t expand any further.

Upon reading material for my history major paper, I came across some arguments by the biologists T.H. Morgan and William Bateson that seemed oddly familiar…

T.H. Morgan in Evolution and Adaptation (1903):

They [Darwinians] have contented themselves, as a rule, with pointing out that certain structures are useful, and this has seemed to them sufficient proof that the structures must have been acquired because of their value (462).

Morgan was an experimental biologist which is evident in his argument: speculations about evolution and adaptations weren’t enough. This argument continues over a century later with disputes over evolutionary psychology studies that sometimes make large, sweeping arguments based on poor or little experimental evidence. Sociobiology was one of the targets of Gould and Lewontin, but Morgan was making similar arguments against the natural historians of his day.

Even more eerily though, William Bateson, in “Heredity and Variation in Modern Lights” (1909), wrote

By suggesting that the steps through which an adaptative mechanism arose were indefinite and insensible, all further trouble is spared. While it could be said that species arise by an insensible and imperceptible process of variation, there was clearly no use in tiring ourselves by trying to perceive that process. This labour-saving counsel found great favour. All that had to be done to develop evolution-theory was to discover the good in everything, a task which, in the complete absence of any control or test whereby to check the truth of the discovery, is not very onerous. The doctrine “que tout est au mieux” was therefore preached with fresh vigour, and examples of that illuminating principle were discovered with a facility that Pangloss himself might have envied, till at last even the spectators wearied of such dazzling performances.

I trust that readers familiar with the Spandrels paper will catch the parallel immediately: Bateson accused Darwinian selectionists of being Panglossian in 1909! 70 years before Gould & Lewontin launched their famous attack, Bateson had made an identical argument (although the former put it more eloquently and forcefully).

Thankfully, Gould was aware of this. Biologist Donald Forsdyke notes on his website that in the 1993 book dedicated to the ‘Spandrels’ paper, Understanding Scientific Prose, that

Gould conceded that “I did not know about Bateson’s invocation of Voltaire when I wrote ‘Spandrels,’ but the convergence is scarcely surprising, as Dr. Pangloss is a standard … form of ridicule.” To criticize the adaptionist program Bateson had introduced, not spandrels, but “toolmarks, mere incidents of manufacture, benefiting their possessor not more than the wire-marks on a sheet of paper, or the ribbing on the bottom of an oriental plate renders these objects more attractive to our eyes.” Furthermore, examples of the doctrine that all is for the best “were discovered with a facility that Pangloss himself might have envied.

Not only did Bateson make an argument about Dr. Pangloss, he even had “spandrels”! As is frequently the case, new ideas are rehashes of older ones, whether intentional or not. The famous phrases, “those who cannot remember the past are condemned to repeat it” and “plus ça change, plus c’est la même chose,” even apply to the sciences. It pays off to know your history (which Gould certainly understood).

How to test for selection (Adaptive Recursion III)

Before my unintended break from blogging, I had started writing about the work by Stolz, Feder, and Velez on bioluminescent color in the Jamaican click beetle, Poryphorus plagiophthalamus (here and here). In this organism are two sets of bioluminescent organs – a dorsal pair and a single ventral organ. Not only can the two sets of organs differ in color within an organism, but – and this is what makes the species special – the colors can be polymorphic within the species. By that I mean within a population, one can find green and yellow-green dorsal organs in addition to yellow-green, yellow, and orange ventral organs. Variation of bioluminescent color within the population is apparently unheard of, even within the rest of the Poryphorus genus. The polymorphism of bioluminescent color provides a simple system for evolutionary and ecological study (as I point out in my first post about the species).

Fig 1: (A) Paired dorsal light organs of P. plagiophthalamus. (B) Allele colors in dorsal organs: green (dGR) and yellow–green (dYG). (C) Ventral light organ of a yellow bioluminescing beetle. (D) Allele colors in ventral organ: green (vYG), yellow (vYE), and orange (vOR). From Stolz et al. (2003).

Instead of outlining the entire series of studies like I had intended, I want to extract two larger themes out of the papers – how biologists test for selection on DNA sequences and how the different color alleles in the beetles arose (and I promise, this is a really cool system of allele origination!).

I ask the first question because the authors employ several tests to detect selection and when writing about these studies for a mini-review in my evolution course, I stumbled in this area. I resolved to figure this out for personal education purposes and because I have yet to find a good source that explains these tests in a readily understandable way, I decided to blog about it. For this reason, if I make any mistakes, please point them out! I am writing about this topic to teach myself something I didn’t learn in any of my classes!

I also want to note that readers probably won’t come out understanding evolution in Jamaican click beetles after reading this post. I look at the selection tests out of order and I don’t discuss in much detail the resulting selective scenario the authors propose. (The post about allele origination will be chock-full of click beetle biology, however!)

The three tests I examine are the QTL sign test, the McDonald-Kreitman test, and substitution rate ratios.

QTL Sign Test

(Apparently) developed by Allen Orr, the QTL sign test helps detect whether selection may or may not have acted upon quantitative traits at the molecular level. QTL means “quantitative trait locus” – basically a gene whose alleles affect the phenotype in a quantifiable way and is not necessarily an on/off system. Additionally, a quantitative trait is frequently affected by multiple loci (or polygenic). A quantitative (and not on/off) trait such as weight is not controlled by a single gene – there is no “gene for weight”; instead, weight is a culmination of multiple genes that happen to act upon weight.

Scientists first pick a quantitative trait to examine based on how strong of a difference there is between two phenotypes, R. After QTL mapping in which the affecting loci/nucleotides are found, the QTLs can be given a plus or minus sign for positive or negative effects, respectively; a higher (plus) or lower (minus) weight, for example. When the distribution of plus/minus loci is determined, a statistical test can be performed to infer the likelihood of that given distribution appearing by chance, or in this case, how likely the difference in phenotypes (R) is to have evolved neutrally (Figure 1; left, shows what a neutral distribution could look like). If the found probability is less than 0.05, the null hypothesis (neutral evolution) can be safely rejected. Selection probably played some role.

Stolz et al. use a QTL sign test to find whether or not diversifying selection is acting on the bioluminescence of the dorsal and ventral organs. Luciferase in the click beetles is a great example of a QTL: the detected mutations do not turn luciferase on or off, but instead shift the produced light’s wavelength by several nanometers up (plus) or down (minus).

A difference between a typical QTL analysis and the analysis performed on click beetles is that we are looking at point mutations within a single gene, rather than multiple loci. Stolz et al. thus call their analysis a QTN test – a quantitative trait nucleotide test – but the same principles of QTL apply: bioluminescent color is affected by multiple mutations, not just a single one, and they each have quantitative effects.

Stolz et al. looked at the divergence between the dGR and vYE alleles, assuming these two alleles to be the ancestral and least-derived states of the loci (for reasons not explained here). The difference between phenotypes (R), wavelength in this case, is 31 nanometers. Nine fixed non-synonymous substitutions contribute to this difference and the nine nucleotides in vYE increase wavelength (and are assigned ‘plus’ status) (Figure 1; right). The probability of finding nine plus mutations and zero minus mutations was 0.039 – low enough to reject the null hypothesis of neutral evolution. This finding provides evidence that selection is acting on bioluminescent color.

Figure 1: On the left is an example of a neutral distribution of plus and minus nucleotides - there is no detectable directional selection. On the right is a recreation of the data from Stolz et al. (2003) with nine plus mutations of varying strengths. The number line only indicates the order of the nucleotides in the gene; it has no implications of genetic distance.

McDonald-Kreitman Test

A well-known way to detect selection at the molecular level is the McDonald-Kreitman (M-K) test. The test compares the ratios of synonymous and non-synonymous fixed differences between species and polymorphic differences within a species. This may sound a bit complicated at first, but it makes sense – let me explain.

A synonymous (s) site is where a base substitution has no effect on the translated codon (hence synonymous; same amino acid = same “word”), and a non-synonymous (n) site is where the translated codon does change. A polymorphic (P) site is one which shows variation within the species whereas a fixed (D) site shows no variation within the species but is different compared to a related species.

This is how the M-K test works to detect selection: under neutral evolution, selection is not acting and thus differences should only be attributable to the mutation rate. Furthermore, because they are only affected by the mutation rate, the ratios of non-synonymous to synonymous differences (n/s) should be equal between fixed (Dn/Ds) and polymorphic (Pn/Ps) categories. Additionally, the ratio between fixed and polymorphic (D/P) sites should be equal between synonymous and non-synonymous categories. Basically, all ratios should divide to 1 (Table 1) and any divergence from 1 indicates selection may be acting. If D > P or n>s, then directional selection is presumed to be acting upon the sequence.

Table 1: An example of neutrality in a McDonald-Kreitman test; all ratios divide to 1.
	Fixed (D)	Polymorphic (P)
Synonymous (s)	13	4
Non-synonymous (n)	13	4

As with the QTL sign test, the McDonald-Kreitman test used on the beetles is slightly different – instead of testing between species differences, they tested the differences between the ventral and dorsal loci. (These loci have diverged for over a million years and can presumably be treated as “different species.”)

Let us first look at a region of luciferase that does not affect color (non-color region). (Table 2).

Table 2: McDonald-Kreitman test for the non-color region of luciferase.
	Fixed (D)
Synonymous (s)	13
Non-synonymous (n)	16
The non-color region of luciferase shows a similar table to Table 1. This 2×2 contingency table has a p-value of 0.845, an indication of neutrality.

The ratios of synonymous/non-synonymous in both fixed and polymorphic columns are either the same or close to being the same (Dn/Ds ≈ Pn/Ps). The “fixed” ratio confirms the site is selectively neutral – the non-synonymous sites are being fixed at the same rate as synonymous sites. Furthermore, Ds/Ps ≈ Dn/Pn.

Now let’s look at the coding region of luciferase (Table 3).

Table 3: McDonald-Kreitman test for the color region of luciferase.
	Fixed (D)	Polymorphic (P)
Synonymous (s)	1	6
Non-synonymous (n)	16	6
There is an excess in Dn and a deficit of Ds in the color region. P-value = 0.011.

There is an excess of fixed non-synonymous sites which indicates the presence of selection. However, Stolz et al. note that Ds is low compared to the rest of the numbers in the table (and in Table 2) which they claim is “atypical of directional selection” (emphasis mine). They exclude codon bias as a possible explanation and also note that this “paucity” of silent fixations is abnormal within the Poryphorus genus. They conclude that intergenic recombination may have cleared any differences between the two loci (reducing both Ds and Dn) and rapid selection subsequently increased Dn. (Don’t worry; intergenic recombination will make a lot more sense in a later post.)

Thus, much like the QTL sign test, the McDonald-Kreitman test looks for divergence from the neutral model in the distribution of base substitutions, inferring the presence of selection if the divergence is strong enough.

Substitution Rate Ratios

Similar to the M-K test, substitution rate ratios look at the difference between synonymous and non-synonymous substitutions between two sequences, but it doesn’t bother to examine fixed and polymorphic differences. In this way, the test is simpler.

The test comes down to two ratios: the number of synonymous substitutions per synonymous site (dS) and the number of non-synonymous substitutions per non-synonymous site (dN). If dN = dS, then the sequences are undergoing neutral evolution (similar to the reasoning in the M-K test). If dN/dS > 1, positive selection; if dN/dS < 1, purifying selection. (dN/dS is often denoted as ω.)

In the color region of luciferase, dN = 0.0217 and dS = 0.0062 (errors omitted). Thus, dN/dS = 3.49. In the non-color region, dN = 0.0023 and dS = 0.058; dN/dS = 0.040. The two dN/dS ratios were significantly different (P = 0.0013). Because dN/dS in the color region is much higher than 1, positive selection is inferred to be acting. (Stolz et al. make no mention of why the non-color region has such a low dN/dS ratio, however. The value indicates purifying selection is rather strong here, so while the non-color region may not be important in determining bioluminescent color, I would presume it codes for an essential structural component of luciferase.)

Other Indirect Tests

The three tests discussed here by no means exhaust the ways one can test for selection. Not only are there other statistical tests one can employ, but there are other indirect ways of detecting selection in a genetic sequence. For example, a reduction of local nucleotide diversity may indicate a selective sweep. As selection drives an allele towards fixation, selection further removes diversity in the surrounding sequence due to hitchhiking. This pattern was found in the ventral orange allele in the Jamaican click beetle: nucleotide diversity in vOR was 0.00046 and in vYE, vOR’s presumed ancestor, diversity was 0.00129. While this isn’t particularly rigorous, it serves as another piece of evidence that selection is acting upon luciferase in the Jamaican click beetles.

This post serves as a (hopefully) basic overview of how molecular biologists can test for selection on DNA sequences. There are many other tests and there are a host of problems associated with each one that I haven’t even begun to explore. I can never stress enough that I am not an expert in this area – I am only providing my understanding of the material in hopes of being corrected by those who know more than me as a way to teach myself evolutionary concepts and, if correct, hopefully teach others in a similar boat as mine.

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Orr HA (1998). Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data. Genetics, 149 (4), 2099-104 PMID: 9691061

Stolz U, Velez S, Wood KV, Wood M, & Feder JL (2003). Darwinian natural selection for orange bioluminescent color in a Jamaican click beetle. Proceedings of the National Academy of Sciences of the United States of America, 100 (25), 14955-9 PMID: 14623957

Source I used to understand selection tests: Genetics of Populations by Philip Hedrick (Google Books)

Favorite Arguments from Paley I: Day & Night

Busy busy busy! To buffer against the death of my blog, my next few posts will focus on various arguments from Paley that I am particularly fond of (aside from the few arguments I discussed in my previous post). The first argument I chose is not related to intelligent design as we normally think of it; instead, Paley’s awe towards the relation of living organisms to the cycles of day and night evokes a wider sense of design in the universe than the narrowly constructed “God must have designed the bacterial flagellum.” Paley sees design in the construction of the heavens itself. As Paley points out, this relation is quite wondrous!