Tag Archives: Evolution

One Iguana Two Iguanas: Children’s evolutionary biology book, with lizards!

The land and marine iguanas of the Galapagos Islands are famous. Well, the marine iguanas are famous, and the land iguanas, representing the ancestral state for that clade of two species, deserve a lot of credit as well. The story of these iguanas is integral with, and parallel to, the story of the Galapagos Islands, and of course, that story is key in our understanding of and pedagogy of evolutionary biology, and Darwin’s history. Continue reading One Iguana Two Iguanas: Children’s evolutionary biology book, with lizards!

How to choose the sex of your baby.

In order to make such a momentous decision, I insist that you learn the very interesting evolutionary biology behind it.

Start with this paragraph:

But for modern medical science, a baby’s sex would remain unknown until birth. But many mothers today know long beforehand whether a baby will be male or female. Routine ultrasound scans reveal fetal genitals a third of the way through pregnancy, and genetic tests identify sex even earlier. Yet basic questions remain. Is a baby’s sex like coin tossing, or can the male:female ratio be skewed? If sex bias occurs, does it happen through sperm sorting before fertilization or mortality differences in the womb after conception?

Then, CLICK HERE to read the rest of the story, by Robert Martin, expert on such things.

The Early Bird Crushes The Egg

Model I birds, the kind that lived during the Age of the Other Dinosaurs, may not have brooded their eggs. Today, birds sit on their eggs in such a way that the adult bird’s down surrounds the ovoids, and warmth from the adult can keep the eggs at a constant temperature. Depending on the bird, you may find additional intersting adaptaitons. For example, Penguins use their own feet as a nest, placing the egg there. One adult broods the egg for a long period (days, in some species) and then swaps with the other adult, with the swapping being very ritualized in some cases. Like this egg swqap between parent Adelie penguins (Tip: this video does not show the actual swap): Continue reading The Early Bird Crushes The Egg

Sexual Selection Up To Date: A Taste for the Beautiful

A Taste for the Beautiful: The Evolution of Attraction is a popular science book written by an actual expert on the field, addressing the ways in which the world of animals is shaped by sexual selection.

One of Darwin’s major contributions to the panoply of theoretical and observational work we call “evolution” was to recognize, describe, and model sexual selection. Continue reading Sexual Selection Up To Date: A Taste for the Beautiful

Darwin Quotes, Assembled

From Janet Browne, the author of Charles Darwin: A Biography, Vol. 1 – Voyaging and other works about Charles Dawin, The Quotable Darwin.

Quotes by Charles Darwin are not just the stuff of memes. Even the fake quotes. They can be the center of long arguments, or at least, they can significantly augment the arguments. For example, did you know that while Darwin never used the term “missing link” he did talk about missing links quite a bit, missing links are central to his thinking about evolution, and all those writers of today who claim that we must never speak of missing links are misguided? Continue reading Darwin Quotes, Assembled

ALERT: Two very good deals on two very good books

Every single regular reader of this blog has read or intends to read Stephen Jay Gould’s The Panda’s Thumb: More Reflections in Natural History. I just noticed that the Kindle version of it is available for $1.99, and I assume this is temporary. I already had the book on dead-tree matter, but I picked this up because ebooks are searchable! You will want one two.

Every single regular reader of this blog SHOULD want to read, or should have already read, Mary Doria Russell’s excellent binary set including The Sparrow: A Novel and Children of God. (The Sparrow is first, COG second.)

Right now, and I assume very temporarily, The Sparrow is also avaialble for $1.99.

A quick word about the Sparrow series. It has been classified as science fiction. Others have said, no, it is not science fiction, it is philosophy and spirituality. A lot of church groups read it because of its religious meaning and implications.

That is really funny because there isn’t a drop of religiosity in this series. There is a priest, but it is a priest mainly operating in a post-religion world. This series is primarily anthropology fiction, which happens to be set in a science fiction theme, and if anything, it deconstructs the central role of religious institutions and makes them look as potentially lame and potentially nefarious and as potentially impotent as the other institutions. Or, really, as products of human behavior as anthropologists understand it, the outcome of a mix of self interested behavior, bonding or revulsion, racism and in-group vs. out-group thinking, the power of institutions, ritual, tradition, class, and exploitation. Set, of course, in the background of co-evolution of morphology of predator and prey. There is also a linguistic theme addressing meaning creation (or lack there of: ouch), development of mind and behavior, language learning, and so on.

You have to read them, and now you can get one of them for two bucks! (Unfortunately COG seems regular price.)

Let me add this too, just noticed it, could be of interest for two bucks: The Science of Star Wars: The Scientific Facts Behind the Force, Space Travel, and More!.

Understanding Michele Bachmann in the context of Human Evolution

The only thing harder to understand than Michele Bachmann is the Republican Party. Bachmann is hard to understand in this way: How can a person with her mind be an elected member of congress? The Republican party is hard to understand in this way: How can a party that is trying to become more rather than less relevant keep putting Michele Bachmann on the podium in places like the National Party Convention and, most recently, at CEPAC?

I can’t explain any of this, but I can at least redescribe the problem in reference to a theoretical construct for the evolution of the human mind. I endeavor to do this for three reasons: 1) To have a chance to briefly discuss these theoretical ideas; 2) To try to place Michele Bachmann and the Republicans (and by minor extension, by the way, Sarah Palin) in at least a descriptive, if not explanatory, context; and 3) because I get to use the word “meta” a million times throughout this essay. No, no, not really. The third reason is because I feel this nagging need to make the link between the fact that Michele Bachmann should not be in Congress with the fact that not only is she actually in Congress, but was recently re-elected to congress. Specifically, I will assert that there is not always cognitive dissonance where one thinks one sees it. Michele Bachmann was re-elected because she represents the majority of her constituents quite effectively.

There is a theory that what makes a good story is meta-osity. A story about a person and another person interacting is too simple. A story like this but where one of the people is secretly manipulating the interaction is a bit interesting. A story like this but where, unknown to the manipulator, there is a larger scale manipulation going on is a novel that might sell. And so on.

There is another theory that presumes this first theory to be essentially correct, and that the human mind is actually an evolved organ designed to manage these meta-meta-meta states. The reason for this is that much of the important stuff in life is meta-meta. Ultimately, in a human society where food- and sex-competitive apes are violating the basic tenets of competition by living side by side and cooperating and sharing within groups, reproduction and survival are socio-political meta-meta matters.

My personal “belief” (read: informed hunch) is that this is essentially true, but the proximate mechanism for the human mind being able to do this is a pretty simple (yet biologically costly) genetically mediated neuro-developmental process overlapping with and followed by a culturally and experientially mediated neuro-developmental process, with a large part of that arising during the unique (compared to other apes) human developmental phase we all “childhood.” (See The Symbolic Species: The Co-Evolution of Language and the Brain by Terry Deacon for a run down on this approach.)

Which leads me to Michele Bachmann, who recently said:

I just wondered that if our founders thought taxation without representation was bad, what would they think of representation WITH taxation?

Uffda. To put this in context, just spend a minute and a half reviewing this speech at CPAC:

[sorry to report, this speech seems to have disappeared from the internet]

OK, well, putting it in context didn’t help, did it? But along side the other statements made here and elsewhere by Bachmann, we are starting to see a pattern.

You know about Michel Bachmann’s other problems. The Blue Scare scenario comes to mind. Bachmann called for the investigation of all elected Democrats in the federal system for Unamerican-ness. If you don’t agree with me you must be the enemy, and I must fear you. All of us who fear you must treat you all the same and throw bricks at you, as children might do. And so on.

Now let’s talk about what all this means. Bachmann’s statement (above) about taxes is an example of not understanding even the first level of meta, the most basic nuance, of the original slogan. Bachmann’s placement of all people who disagree with her in the same category, so that enemies and colleagues of a different party are all the same, is an example of the inability to go beyond the most basic of relationships. Bachmann is unable to see that we can disagree with our colleague, but join our colleague to disagree with a third party (meta) and sometimes ally with a third party to disagree with yet another third party (meta meta) and sometimes find influence among allies in a distant third party to effect change in a colleague (meta meta meta).

(By the way, that this analysis is valid is underscored by Bachmann’s insistence that actual card-carrying Republicans who happen to disagree with her are not “real” Republicans.)

Bachmann does not get even the simplest nuance. In politics, she is just a dog barking at the shadows behind the fence, and everything is a shadow behind the fence.

We can show that many animals including dogs have this level of capacity and not much more. A meta-X level, where you have one set of complexities on top of basic relationships, is clearly a generalized primate capacity and may even be found in some social birds, but is not well developed in dogs or other carnivores.

The next level of meta … meta-meta-x … is probably exclusively human, and if Homo erectus was around today, perhaps we’d be saying “Oh, H. erectus can do that. Sort of.” (I’m guessing at that.)

Beyond this, the next level of meta … meta-meta-meta-x … is what most humans can do when they try and have certain experience or training, and that very smart people do a lot of, and real smart people are probably doing all the time. Most people probably achieve meta-meta-X much of the time, but probably mainly in regards to certain aspects of their life but not others. (Again, I’m guessing.) Meta-osity is a general feature of thought and thus could be conceived of as independent of empirical realities, but I don’t think this is the case. I think there is a real relationship between physicality and thought process. So a person may be meta-meta-X or even meta-meta-meta-X about the novels they read and their family relationships, but little else. A different person may be meta-meta-meta-X about their workplace relationships and the stuff they do as an engineer, or teacher, or crane operator, but be meta-X at best when it comes to politics. And I think, in fact, that this is exactly what frequently happens. It may be in the interest of certain politicians to keep the conversation at a meta-X (or lower) level.

Ideally, in careers, and especially careers that are important to other members or elements of society, we would like to see people be at least meta-meta-X, especially those in charge of important things. For example, physicians should be meta-meta-meta-X, if possible, regarding the workings of the body in relation to disease, personal behavior, treatment options, and so on.

Examples of meta-meta-meta-X thinkers in politics include Bill Clinton, Barney Frank, Newt Gingrich, Adlai Stevenson and Al Franken. One imagines Ted Kennedy, clearly a meta-meta-meta-X thinker, relaxing by sailing on Nantucket Sound, where to succeed he merely needs to achieve meta-X thinking regarding winds, currents, sails, and ropes. Meanwhile, the captain of the Nantucket Ferry, who in her job driving a modern ship rarely has to go beyond meta-X, enriching her own life by engaging in BBC style crime dramas on TV and playing chess with her buddy the Harbor Master in Harwich Port.

Examples of meta-meta-X political thinkers who did well because they were in the right place at the right time might include George Bush Senior, Harry Truman, and George Washington. Examples of meta-X thinkers who probably didn’t apply the meta to the X in their political lives might be …. Hmmm, hard to come up with too many examples of this. Most people at that level would never get far beyond student council. Let’s see, who would be a good examp…

Oh,right, how could I forget!?!? … Michele Bachmann!

Here’s the thing. The objective of a politician might be to manage the thinking of others such that you get those other people to do what you wish them to do: fund your campaign and vote in your favor. It is much much easier to do this if you keep the public level of discourse as meta-free as possible. Newt Gingrich is on my list of meta-meta-meta-X thinkers, but he was a master at engendering the populous with a penchant for non-meta reasoning. For example, Gingrich successfully gained support from the masses by promising to bring to the floor a vote on each of ten allegedly key Republican issues (the famous “Contract with America”). However, a) the House (where Gingrich promised to do this) has weak rules for bringing something to vote, and b) bringing something to vote does not equal passing it or, really, even actually voting on it. So, you see, it would be trivially easy to keep this “contract.” It was not logical to infer that the Contract with America was a meaningful political construct that would have real results, but it became an effective rallying point for the first midterm election during Clinton’s first term. The Contract with America was a dog barking at a shadow behind the fence and nothing more. (Expect this dog to be barking again in about a year from now.)

The re-casting of stakeholders in a given issue as “taxpayers” is often a de-meta-fication of the issue at hand. The conflation of 1960s radicalism with 21st century terrorism with being black, or being a democrat, or being from Chicago, or whatever, is de-meta-fication of a person’s (Obama’s) entire career and philosophy. Claiming that the fact that Soviet/Russian bombers would fly over Alaska on their way to bomb the rest of America makes the governor of Alaska a foreign policy expert is the de-meta-fication of so, so many things.

Years of training have converted much of the Republican base to a pack of dogs, chained to an ideological stake in a dusty gloomy yard, always ready to bark at the movement of shadows beyond the tall fence that surrounds them. Michele Bachmann’s congressional district is demographically as close as any district can be to this Republican ideal. This is why Bachmann can be who she is, get re-elected, and continue to be invited to speak at major Party gatherings. Michelle Bachmann is not Newt Gingrich. She does not grasp the overarching strategy. She is not a simpleton’s face hiding a brilliant political mind. She is just the simpleton. I doubt she is even taking marching orders from anyone. Michele Bachmann is merely one of the dogs, among many, barking at the shadows moving behind the fence.

Michele Bachmann is the best possible representative for her district.


The Origin of the Chicken

From whence the humble chicken? Gallus gallus is a domesticated chicken-like bird (thus, the name “chicken”) that originates in southeast Asia. Ever since Darwin we’ve known that the chicken originated in southeast Asia, although the exact details of which one or more of several possible jungle fowls is the primal form has been debated. The idea that more than one wild species contributed to the early chicken has been on the table for a long time, though perhaps not as long as the chickens themselves have been on the table

Notice the yellow legs on this chicken. If you pluck out the feathers, you’ll notice that the skin is yellow as well. But if you go find, say, a crow, and pluck its feathers, it will be grayish in color. Or maybe black, I don’t know, it’s been a while since I’ve defeathered a crow. The point is, that some birds are yellow, some are not.ResearchBlogging.orgThere is a gene that is expressed in certain tissues that produces an enzyme that cleaves the carotenoid molecules that provide the yellow color. If there is no functional copy of this gene (if the individual is homozygotic for the broken version) then this cleaving does not happen, and you get a yellow bird (depending on other factors we shall ignore).In short, new research confirms as previously thought that the red jungle fowl (Gallus gallus) is ancestral to the modern chicken, as Darwin suspected. But this research also suggests that another bird, the grey jungle fowl (Gallus sonneratii) also contributed to the chicken’s genome, providing the yellow color we see on this chicken’s legs.The research, reported in PLoS Genetics, gives us two results. One is the first characterization of the process of pigmentation mentioned above, and the second is a new family tree for this bird.

Many bird species possess yellow skin and legs whereas other species have white or black skin color. Yellow or white skin is due to the presence or absence of carotenoids. The genetic basis underlying this diversity is unknown. Domestic chickens with yellow skin are homozygous for a recessive allele, and white skinned chickens carry the dominant allele. As a result, chickens represent an ideal model for analyzing genetic mechanism responsible for skin color variation. In this study we demonstrate that yellow skin is caused by regulatory mutation(s) that inhibit expression of the beta-carotene dioxygenase 2 (BCDO2) enzyme in skin, but not in other tissues. Because BCDO2 cleaves colorful carotenoids into colorless apocarotenoids, a reduction in expression of this gene produces yellow skin. This study also provides the first conclusive evidence of a hybrid origin of the domestic chicken. It has been generally assumed that the red junglefowl is the sole ancestor of the domestic chicken. A phylogenetic analysis, however, demonstrates that though the white skin allele originates from the red junglefowl, the yellow skin allele originates from a different species, most likely the grey junglefowl. This result significantly advances our understanding of chicken domestication.

Here is the phylogenetic tree that the authors of this paper present:i-a782d8d10ab087febef2b5b4a719fe02-chicken_tree.jpgClick here for a much larger image (84kb)You will read in press reports that “Darwin got it wrong” when it comes to chickens. Let’s have a look at what he said and see how wrong he was. Darwin addressed the two major theories of his time. One is a multiregional theory, much like the now discredited version of human evolution, where each kind of chicken was domesticated from a different wild form. The other is that all descended from one ancestor, Gallus gallus bankiva, also known as Gallus bankiva.Darwin uses chickens in a big way in developing his ideas about evolution. Chickens were perhaps as important as pigeons for examining breed characteristics. Therefore, he wrote quite a bit about chickens. In the end, he favored the single origin hypothesis, but he also describes the primordial species of his choosing … the red jungle fowl … as much more diverse in character than it is generally characterized today…

… Gallus bankiva, has a much wider geographical range than the three previous species; … This species varies considerably in the wild state. Mr. Blyth informs me that the specimens, both male and female, brought from near the Himalaya, are rather paler coloured than those from other parts of India; whilst those from the Malay peninsula and Java are brighter coloured than the Indian birds. I have seen specimens from these countries, and the difference of tint in the hackles was conspicuous. The Malayan hens were a shade redder on the breast and neck than the Indian hens. The Malayan males generally had a red ear-lappet, instead of a white one as in India; but Mr. Blyth has seen one Indian specimen without the white ear-lappet. The legs are leaden blue in the Indian, whereas they show some tendency to be yellowish in the Malayan and Javan specimens. In the former Mr. Blyth finds the tarsus remarkably variable in length. According to Temminck20 the Timor specimens differ as a local race from that of Java. These several wild varieties have not as yet been ranked as distinct species; if they should, as is not unlikely, be hereafter thus ranked, the circumstance would be quite immaterial as far as the parentage and differences of our domestic breeds are concerned. The wild G. bankiva agrees most closely with the blackbreasted red Game-breed, in colouring and in all other respects, except in being smaller, and in the tail being carried more horizontally. But the manner in which the tail is carried is highly variable in many of our breeds,…(Darwin 1868:233)

What we see here (my emphasis added) is evidence that skin color varied across different populations of this species.The study at hand asserts:

On the basis of observed character differences and cross-breeding experiments, Darwin concluded that domestic chickens were derived solely from the red junglefowl, though this was later challenged by Hutt [1], who stated that as many as four different species of junglefowls may have contributed to chicken domestication. Molecular studies of mtDNA and retroviral insertions have supported Darwin’s view. A study that analyzed both repeat nuclear elements and mitochondrial sequences found evidence that grey and Ceylon junglefowls may hybridize with domestic chickens, but did not provide evidence that these two species have contributed to chicken domestication. To date, no studies have compared gene sequences associated with a specific phenotype found in domestic chickens across numerous wild junglefowls and domestic breeds….We searched for the causal mutation … This analysis revealed a surprisingly high sequence diversity between the two groups (0.81%), well above the genome average for chicken (~0.5%) [15] and approaching the sequence divergence between chimpanzee and human (1.2%). We therefore included three other species of junglefowls in the sequence comparison: grey (G. sonneratii), Ceylon (G. lafayetii), and green (G. varius) junglefowls. This step was also motivated by the fact that grey and Ceylon junglefowls have red or yellowish legs which implies deposition of carotenoids and a Y/Y genotype…In contrast, mtDNA sequences from the same samples showed the expected pattern in which domestic chickens cluster with red junglefowl within a clade well separated from other junglefowls

The grey and red jungle fowl have, at present, disjunct ranges, but that may be a product of recent ecological changes, including human alterations of habitats. Also, in the early days of chicken domestication, there is no reason to suspect that a single origin would be followed by immediate isolation from wild forms, and in fact, all the available evidence including that reported here suggests the contrary.I think the truth of the matter is that Darwin did not really get the origin of the chicken wrong … he had it substantially right. Rather, Darwin had a better idea of variation in the wild forms than we may appreciate today, and he leaned a bit more towards a simpler history at the start than we tend to today. That’s not bad considering that all of the modern theory about origins of domesticated forms post dates, and often derives from, Darwin.In other words, Newton understood gravity, so today we can design an airplane. But if Newton designed and airplane that did not fly, would that mean that he got gravity wrong?I think not.

(More on Darwin here)Darwin, C. R. 1868. The variation of animals and plants under domestication. London: John Murray. First edition, first issue. Volume 1.Eriksson, J., Larson, G., Gunnarsson, U., Bed’hom, B., Tixier-Boichard, M., StrÃ?¶mstedt, L., Wright, D., Jungerius, A., Vereijken, A., Randi, E., Jensen, P., Andersson, L., Georges, M. (2008). Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken. PLoS Genetics, 4(2), e1000010. DOI: 10.1371/journal.pgen.1000010

Darwin and the Voyage: 10 ~ Rheas and the Birth of Evolutionary Theory

Everyone knows about Darwin’s Finches, of the Galapagos Islands. But of course, Darwin made observations of birds throughout his travels on The Beagle. Here, I present a number of passages from The Voyage that include some of these observations. Continue reading Darwin and the Voyage: 10 ~ Rheas and the Birth of Evolutionary Theory

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.

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.