Tag Archives: Genetics

Mammals and the KT Event

A very important and truly wonderful paper in Nature described a tour-de-force analysis of the Mammalian Evolutionary Record, and draws the following two important conclusions:

  1. The diversification of the major groups of mammals occurred millions of years prior to the KT boundary event; and
  2. The further diversification of these groups into the modern pattern of mammalian diversity occurred millions of years later than the KT boundary event.

Continue reading Mammals and the KT Event

The Three Necessary and Sufficient Conditions of Natural Selection

Natural Selection is the key creative force in evolution. Natural selection, together with specific histories of populations (species) and adaptations, is responsible for the design of organisms. Most people have some idea of what Natural Selection is. However, it is easy to make conceptual errors when thinking about this important force of nature. One way to improve how we think about a concept like this is to carefully exam its formal definition. Continue reading The Three Necessary and Sufficient Conditions of Natural Selection

The Modes of Natural Selection

There many ways of dividing up and categorizing Natural Selection. For example, there are the Natural Selection, Sexual Selection and Artificial Selection, and then there is the Modes of Selection (Stabilizing, Directional, and Disruptive) trichotomy.We sense that these are good because they are “threes” and “three” is a magic number. Here, I’m focusing on the Mode Trichotomy, and asking that we consider that there are not three, but four modes of Natural Selection. This will cause tremors throughout the Evolutionary Theory community because Four is not a magic number, but so be it. Continue reading The Modes of Natural Selection

Biology of Color Preference

Color is funny. Anthropologists have long known that different cultures have different relationships, linguistically and in day to day practice, to the color spectrum. For example, the Efe Pygmy Hunter-Gatherers of the Ituri Forest describe things as white, black, or red, and that’s it. They live in a world of green, so it does not get a mention. Going with the model for “Eskimos” having a hundred words for snow because snow is so important in their environment, one would expect that the Efe would have a hundred words for green. On the other hand, the Efe Hunter-Gatherers must have a fairly primitive culture, compared, say, to those of us living in Coon Rapids Minnesota, that of course they have fewer words for different colors.

Of course, this is all a bunch of hooey. First, we don’t call them “Eskimos.” We call them “Inuit.” “Eskimo” is a bad word. It would be like calling the Irish “Drunken Leprechauns.” Second, the “fact” that the Inuit have a hundred words for snow is simply not true. It is an Urban Legend. Third, the great variation in something — any thing — does not necessarily demand a rich lexicon to describe it. You — yes, you — rely heavily on computers, right? Many computer users presumably need to have a concept of “memory” and the memory their computers use — related to the choices you make when buying or using a computer, where and how you store your documents, etc. But this concept is often appallingly simplified. I know many people who can’t distinguish between storage of data on a hard drive from storage of data in RAM. And there are many kinds of hard drive and many kinds of RAM. And then there is processor cache, video memory, and so on. There are probably over two dozen kinds of memory, it matters to any computer user, and most computer users have either one word for memory or two. (“Memory” or “Hard drive” and “Memory”)

Finally, if the Efe are Primitive, then I’m a monkey’s uncle. Indeed, both are untrue. The Efe are far from primitive and I’m a monkey’s great great great …. great great nephew, not uncle. The Efe have one of the largest brain to body ratios of any people. I’ve never met an Efe man who knew fewer than four different languages. I’ve never met an Efe who was not very smart. I can’t say any of these things for the population living in Coon Rapids, or even Edina, Minnesota.

So why do the Efe not seem to even have a word for the color green?

I can think of two answers to that question. One is that they do but have not bothered to teach this to us. I spent years living with them, and there were basic, day to day things that I learned right up to the last day I was with them. Sure, linguists presumably asked them about this, but that means little considering that only a handful of linguists have actually worked with them. The other explanation is that this is a stupid question. We only think that one needs a large number of words for the color green (if you are an Efe) because we mistakenly think the Inuit have a hundred words for snow.

Then there is the issue of gender and color. I am not color blind, but I am a man. Therefore I have only a few words for color. Let’s see. There’s black and white, green red and yellow, and pretty much that’s it. OK, maybe purple as well. Brown is a form of lightish black. I am not color blind. I’m simply not that interested.

Boys = blue, girls = pink. We know this because these are the colors of clothing, decorations and wall paper or paint in nurseries, etc. Anthropologists will tell you that this blue/pink gender thing is cultural, and that you can find exceptions to it, even reversals, if you look around the world and across history. For instance, the color association with the emperor of Rome was some girley color like purple.

A current study in the journal Current Biology claims to have found a non-culturally generated (but nonetheless culturally modified) gender difference in color preference.

The long history of color preference studies has been described as “bewildering, confused and contradictory”. Although recent studies … tend to agree on a universal preference for ‘blue’, the variety and lack of control in measurement methods have made it difficult to extract a systematic, quantitative description of preference. Furthermore, despite abundant evidence for sex differences in other visual domains, and specifically in other tasks of color perception … there is no conclusive evidence for the existence of sex differences in color preference. This fact is perhaps surprising, given the prevalence and longevity of the notion that little girls differ from boys in preferring ‘pink’. Here we report a robust, cross-cultural sex difference in color preference, revealed by a rapid paired-comparison task. Individual color preference patterns are summarized by weights on the two fundamental neural dimensions that underlie color coding in the human visual system. We find a consistent sex difference in these weights, which, we suggest, may be linked to the evolution of sex-specific behavioral uses of trichromacy.Anya C. Hurlberta and Yazhu Linga. “Biological components of sex differences in color preference.” Current Biology. Volume 17, Issue 16, 21 August 2007, Pages R623-R625.

I think the study design is good and the results convincing, that there is a sex difference in color preference along one aspect of the way color is perceived. Here is what the difference looks like in the figure the researchers provide:Color Preference

As implied in the summary, this difference corresponds to male-female differences in visual processing. This is believable.

The ultimate (evolutionary) explanation that the researchers give is weaker. It is a fairly typical post-hoc Environment of Evolutionary Adaptedness argument. Females prefer or are more perceptive of red because they are gathering berries found in a background of green leafy stuff. Or, alternatively, females evolved to be sensitive to social signals (blushing).

We speculate that this sex difference arose from sex-specific functional specializations in the evolutionary division of labour. The hunter-gatherer theory proposes that female brains should be specialized for gathering-related tasks and is supported by studies of visual spatial abilities. Trichromacy and the L-M opponent channel are ‘modern’ adaptations in primate evolution thought to have evolved to facilitate the identification of ripe, yellow fruit or edible red leaves embedded in green foliage. It is therefore plausible that, in specializing for gathering, the female brain honed the trichromatic adaptations, and these underpin the female preference for objects ‘redder’ than the background. As a gatherer, the female would also need to be more aware of color information than the hunter. This requirement would emerge as greater certainty and more stability in female color preference, which we find. An alternative explanation for the evolution of trichromacy is the need to discriminate subtle changes in skin color due to emotional states and social-sexual signals; again, females may have honed these adaptations for their roles as care-givers and ’empathizers’ .

Why do I say this is a weak post-hoc argument? For the simple reason that a reversal of their findings could be equally well explained. The game sought by hunter-gatherers is distinguished from a green foliage-rich background by its reddish-brown hue. Most meat actually collected by male hunter-gatherers is not from shooting an animal dead with an arrow, but by wounding it and following an often very subtle blood (red) trail. Also, among the Efe, men gather wild fruit about as often as do women, and the food women gather from the wild tends to be either green or underground. If the Efe were the forager culture used to represent the human past by modern evolutionary psychologists, many of the ultimate, evolutionary, explanations attached to various findings would be very different.

Regarding the blushing: Since white skin against which blushing is most obvious is a recent mutation (and a rather harmful one at that), I think this argument can be rejected out of hand. Nonetheless, this is a good piece of research, well done, and of great interest.


HURLBERT, A., LING, Y. (2007). Biological components of sex differences in color preference. Current Biology, 17(16), R623-R625. DOI: 10.1016/j.cub.2007.06.022

Hybrids of Blind Fish Can See

The loss of sight in cave dwelling species is widely known. We presume that since sight in utter darkness has no fitness value, the mutation of a gene critical to the development of the sense of sight is not selected against. Over time, any population living in darkness will eventually experience such mutations, and these mutations can reach fixation.

i-c627cc83bac50a2981e1f62b7bb0f1d3-cave_fish.jpg
Astyanax mexicanus: Top is the surface, sighted form, bottom is the cave-dwelling, blind form. From the Jeffery Lab.

Beyond this, we may hypothesize that a mutation “turning off” sight could be beneficial. By definition, an adaptation (such as sight) has a cost. When a trait that is adaptive is no longer adaptive, individuals with that trait “turned off” should experience an increase in fitness. It may also be the case, however, that such an increase in fitness is so small that it may be irrelevant. This line of thinking needs further investigation and what one finds in such an investigation may vary a lot from system to system. For example, a mutation that simply causes a particular protein to no longer be produced in what would have been a small quantity would save the individual with that mutation the use of a few tens of thousands of amino acids over some fixed period of time. This would have very little fitness value. But if a system is exploitable by a pathogen — such as a receptor site on a cell used by a common virus — turning that gene off may have enormous benefits. But this is a bit of a digression from the research at hand.

Borowsky, in his paper “Restoring sight in blind cavefish,” provides a test case for how we think evolution works. In Mexico, the species Astyanax mexicanus, is known to exist in 29 distinct populations. Genetic studies indicate that the turning off of the sense of sight in these fish has involved a deleterious (as in loss of function) of genes in at least three different lineages, or to put it a different way, sightlessness has evolved three or more separate times in these Mexican blind cavefish.When Borowsky cross breeds some of these cavefish, crossing them between these populations, he gets a certain percentage of fish that have functional, if not fully developed, eyes.This should not be at all surprising. Several different genes are involved in the development of sight, so by cross breeding strains that have experienced mutations in different genes, one would expect a certain number of offspring to have a set of functioning genes sufficient to make the sense of sight develop at least to some extent. When Borowsky breeds the blind cavefish with the non-blind version of this fish (“surface fish”) he gets restoration of the sense of sight in all of the offspring.

F1 hybrids between surface fish and cave fish have smaller eyes than surface fish, but are fully visual, even into adulthood … Thus, one surface allele at each of the population-specific eye loci is sufficient for restoring vision.

This is also expected, although not necessarily inevitable (This depends on the dosage required for each genetically coded step in the development and function of sight).

It seems to me that one could test the hypothesis mentioned above that turning off any fitness-free gene is adaptive. If simple production of unused proteins is costly, the rate at which particular genes are found to be turned off should be correlated with that cost. Perhaps the genes coding for longer proteins, or proteins that are produced more often in a particular system, should be more likely turned off. Or, some measure of the total mass of amino acids turned into proteins when a gene functions, should be correlated to the likelihood of having a gene turned off. At a most basic level, one would need to show that the mutant genes are in fact turned off and are not simply producing a non-functional protein.In short, this study (and others by this and other research teams) demonstrates in empirical reality what is expected from commonly held evolutionary theory. Creationists often cite blind cave dwelling organisms as evidence against evolution, because, they say, it is “devolution.” This point of view is absurd, and relies on a teleological view of, in this case, teleost (bony fish) evolution.

Darwin wrote about cave blindness and disuse, and through various observations notes the potential complexity of the problem:

It is well known that several animals, belonging to the most different classes, which inhabit the caves of Styria and of Kentucky, are blind. In some of the crabs the foot-stalk for the eye remains, though the eye is gone; the stand for the telescope is there, though the telescope with its glasses has been lost. As it is difficult to imagine that eyes, though useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse. In one of the blind animals, namely, the cave-rat, the eyes are of immense size; and Professor Silliman thought that it regained, after living some days in the light, some slight power of vision. In the same manner as in Madeira the wings of some of the insects have been enlarged, and the wings of others have been reduced by natural selection aided by use and disuse, so in the case of the cave-rat natural selection seems to have struggled with the loss of light and to have increased the size of the eyes; whereas with all the other inhabitants of the caves, disuse by itself seems to have done its work.[On the Origin of Species…, 1859, pp 137-138]

You might be wondering how these fish got into these caves to begin with. I can’t describe the exact process for the fish studied in this paper, but there is a general way in which this can happen. Underground lakes or streams in caves may be connected to each other during less arid periods, in some cases running from the deeps of large lakes that later try up almost entirely. In this way, a continuous population in a river or lake is broken into relict populations that are separate from each other and perhaps living in habitats that are different from the original, continuous habitat, and possibly different from each other as well. Under these conditions evolution’s just gotta happen.


BOROWSKY, R. (2008). Restoring sight in blind cavefish. Current Biology, 18(1), R23-R24. DOI: 10.1016/j.cub.2007.11.023

Hopeful Monsters and Hopeful Models

A hopeful monster is a mutant born with a genetically determined and large novel trait (compared to its parents) which confers enhanced fitness on that individual. This enhanced fitness increases the likelihood that the new mutant gene that determines this trait will be passed on and spread throughout the evolving population, so in a single generation a rapid process of speciation is initiated. For example, a fish with a mutation that causes both its eyes to grow on one side of its head could become the flounder of a new generation of flatfish. Well, just for the halibut, it might be fun to further examine this notion.

The hopeful monster idea is attractive for three reasons. First, we already know that some of the most profound differences between larger scale taxonomic groups (like the phyla) are about aspects of body plan that are controlled by early stages in embryonic development. So, if a simple mutation in one of those stages can cause a taxon that has a certain number of limbs to give rise to a new species with a totally different number of limbs, then that would be cool.

The second reason is that the fossil record seems to have the property whereby many species stay roughly similar for long periods of time, then suddenly, there is lots of evolutionary change. You’ve heard of this, it’s called “punctuated equilibrium.” If hopeful monsters — also called saltational (dancing, leaping) evolution — occurred generally, we might postulate that these moments of dramatic change, these punctuations, are moments in time where for some reason a lot of hopeful-monstering was going on all at once. That would be cool.

The third reason that this is an attractive idea is just that it would be cool, especially if you are the guy who discovers the next hopeful monster.

Olivia Judson recently wrote a column talking about the Hopeful Monster idea. She proposes that the idea, which has been mostly discredited and put aside as not possible, or at least, so unlikely as to not be a factor in explaining overall patterns in evolution, is coming back. Her column, “The Monster is back, and its Hopeful” … is here.The article is interesting, but she does not really provide any new information that would lead one to suspect that we should be rethinking the unlikelihood of hopeful monstering. She gives a few examples of single, possibly small genetic changes that have huge (perhaps) phenotypic effects, within populations, that she suggests could be analogs for hopeful monster events.

One of these I want to discuss in more detail in a moment is the loss of feathers on a chicken over the neck and head. This, she suggests, is analogous to vultures having naked heads and necks (a presumed adaptation). So, a population of carrion eating eagles could give rise to a hopeful monster gene that produces a carrion eating vulture.O

livia Judson’s article has been read and taken to task by Jerry Coyne, a blogless curmudgeon who happens to be an expert on this topic, and who is friends of Carl Zimmer. Zimmer has given Coyne a spot on The Loom (Zimmer’s Blog) to respond to Judson. This post is here.

Coyne explains how Judson is totally wrong. The hopeful monster idea has been thrown out, and in fact its debunking happened some time ago. Nobody believes this crazy idea now, and what the heck is she doing bringing this up again.

I want to say a couple of things about both bits of writing, but especially Coyne’s.

First, I think Judson’s column is unconvincing and very fluffy, and I agree with Coyne’s critique that this kind of looks like a journalist getting readers more than the heralding of a new way of looking at evolution. However, it is a column in a newspaper and Judson is acting as a journalist, so maybe this approach can be forgiven. Regarding Judson’s examples, I think they are all reasonable examples of a genetic mutation that could indeed arise and spread in a population, but they are not species- or (and this is very important) higher taxa-determining differences. A vulture is different from an eagle for a very large number of reasons, and the naked head is only one of them, perhaps not even the most important. If a population of naked-headed eagles arose, then we’d have a subspecies of “truly bald” instead of “looks bald” eagles. They would not really be hopeful monsters.

On the other hand, I think that Coyne’s treatment of Judsons’s paper is a bit heavy handed and rather sanctimonious. And given this holier than thou attitude (which may well be justified, but I’m just sayin…) it is appropriate to hold him to a very high standard of perfection.

Coyne mentions that the naked-necked chickens are an example of a mutation in a domestic animal (true) and that mutations occur in domestic populations with great frequency compared to wild populations (maybe) and that these mutations only persist because the animals are coddled in their domestic setting.

This last part may often be true, and I think I agree with that. But not for the naked necked chickens. Naked necked chickens are common in the African tropical rain forest. They are not coddled. They are not kept in coops, they are not provided with water, they are not fed. Maybe they are kept from predators a little, but in fact, that is hard to argue since they are often eaten by eagles, hawks, snakes, civets, wild cats, and so on. It is even possible that in that setting, where they do eat some carrion, and where there is a high parasite load, that the naked neck and head are adaptive (though I’m not advocating for that idea, it is merely a tenable hypothesis).

So, I agree with Judson that the naked necked chicken, a simple genetic mutation, may be a good example of a one-shot trait that need not have arisen feather by feather over generations of time. But I disagree that a naked necked chicken is a hopeful monster. As hopeful as such a trait may be, it just isn’t that monstrous.

Now, if you try eating one of these chickens, that that is a different story. They are as tough as buffalo hide. Truly monstrous, as cuisine.

Natural Genetic Variation in Maize Nutritional Quality

Blogging on Peer-Reviewed ResearchThey always told you to eat your carrots, to improve your eyesight. Well, a deficiency of vitamin A (found in carrots, and lots of other foods) causes eye disease in a lot of children. In areas where Maize (corn) is a significant staple, there can be a problem because maize varies a great deal in how much vitamin A it can provide via precursor molecules. A new study in Science explores this relationship. Continue reading Natural Genetic Variation in Maize Nutritional Quality

Genome Size, Adaptations, Constraints, Exaptations, Aptations, and so on…

There is a discussion on the internet about Junk DNA, that includes a discussion at Sandwalk (Larry Moran’s blog) … I made a comment there about genome size that was responded to by T.R. Gregory. I started to write my response in Larry’s Little Box, but realized that it would not fit. So it is here: Continue reading Genome Size, Adaptations, Constraints, Exaptations, Aptations, and so on…

Moran, Gregory, Give me a Break!

Well, it is a good thing that I have a thick skin and a good sense of humor, or I would be very put off by Larry Moran and probably T. Ryan Gregory as well.Apparently, I stepped into an ongoing partially ad hominem debate over “Junk DNA” centering on the work of John Mattick and his research group. In this post, I’d like to provide a clarification of my “position” on Junk DNA, and I’ll spend a moment admonishing my colleagues for being dorks. Continue reading Moran, Gregory, Give me a Break!

Genes are only part of the story: ncRNA does stuff

Blogging on Peer-Reviewed ResearchYou know that organisms develop, grow, and function in part because genes code for proteins that form the building blocks of life or that function as working bioactive molecules (like enzymes). You also know that most DNA is junk, only a couple percent actually coding for anything useful. Most importantly, however, you know that everything you know is wrong. Right? Continue reading Genes are only part of the story: ncRNA does stuff