john hawks weblog

Slate has an interesting slide-show by Jon Lackman about efforts to resurrect the quagga. The quagga was either a species or subspecies of Plains zebra, living in South Africa until the mid-19th century, when it was hunted to extinction. Here's the only known photograph:

The Quagga

The slideshow discusses the history and the present attempts to breed a quagga-like zebra back into being.

In 1971, taxidermist Reinhold Rau realized that the quagga's genes had not been forever lost. Zebras had occasionally interbred with quagga over the millenniums, and some of the descendants of these pairings still roamed South Africa. Rau surmised that he could retrace evolution's trail by mating the most quagga-looking zebras he could find and then mating certain of the offspring. In each generation, quagga genes will be further concentrated -- so that eventually, Rau believes, two zebras will produce a real quagga.

The slideshow has a picture of one of the more recent foals, named Henry, which really is quagga-like in its coloration. Of course, there is more to a species than its pelage, and since we know very little about any possible quagga-specific behaviors, there is no way to select for them in living zebras.

Then the slideshow includes this interesting tidbit:

A popular 19th-century theory held that men and animals inherit traits not just from their parents but also from their mother's first partner. This supposed phenomenon was called "the taint of the quagga" because it was said to have been discovered in the animal. The taint was alluded to by journalists of the era and in the writings of Goethe, Strindberg, Ibsen, and Zola. It reinforced the taboo of miscegenation and encouraged men to keep their women under lock and key.

Google brings this passage from chapter 11 of Darwin's "The variation of animals and plants under domestication":

Turning now to the animal kingdom. If we could imagine the same flower to yield seeds during successive years, then it would not be very surprising that a flower of which the ovarium had been modified by foreign pollen should next year produce, when self-fertilised, offspring modified by the previous male influence. Closely analogous cases have actually occurred with animals. In the case often quoted from Lord Morton, a nearly purely-bred Arabian chestnut mare bore a hybrid to a quagga; she was subsequently sent to Sir Gore Ouseley, and produced two colts by a black Arabian horse. These colts were partially dun-coloured, and were striped on the legs more plainly than the real hybrid, or even than the quagga. One of the two colts had its neck and some other parts of its body plainly marked with stripes. Stripes on the body, not to mention those on the legs, are extremely rare, -- I speak after having long attended to the subject, -- with horses of all kinds in Europe, and are almost unknown in the case of Arabians. But what makes the case still more striking is that in these colts the hair of the mane resembled that of the quagga, being short, stiff, and upright. Hence there can be no doubt that the quagga affected the character of the offspring subsequently begot by the black Arabian horse. Mr. Jenner Weir informs me of a strictly parallel case: his neighbour Mr. Lethbridge, of Blackheath, has a horse, bred by Lord Mostyn, which had previously borne a foal by a quagga. This horse is dun with a dark stripe down the back, faint stripes on the forehead between the eyes, plain stripes on the inner side of the fore-legs and rather more faint ones on the hind-legs, with no shoulder-stripe. The mane grows much lower on the forehead than in the horse, but not so low as in the quagga or zebra. The hoofs are proportionally longer than in the horse, -- so much so that the farrier who first shod this animal, and knew nothing of its origin, said, "Had I not seen I was shoeing a horse, I should have thought I was shoeing a donkey."

Karl Pearson, in his Life of Francis Galton, runs across a letter from Galton to Darwin mentioning the "Quagga taint", and adds this:

The Quagga case, as indeed all instances up-to-date, of so-called telegony can now be dismissed from consideration. They depend essentially on (i) observation of variation within the pure breed not being sufficiently wide, or (ii) the assertions of kennel-men and others endeavouring to screen their responsibility for unplanned matings (Pearson 159).

The Galton letter is part of a series reporting his experiments in transfusing blood into rabbits to see whether "foreign gemmules" in the blood might influence the rabbits' offspring. They are fascinating to read, considering the difficulty of determining whether traits sported in the offspring are variations common within a given breed or not. Galton's (and others') immediate purpose, of course, was to look for the locus of inheritance, and he was looking for evidence of a blood effect.

May 12, 1870: My Dear Darwin, Good rabbit news! One of the latest litters has a white forefoot. It was born April 23rd, but as we did not disturb the young, the forefood was not observed till to-day. The little things had huddled together showing only their backs and heads, and the foot was never suspected. The mother was injected from a grey and white and the father from a black and white. This, recollect is from a transfusion of only 1/8th part of alien blood in each parent; now, after many unsucccessful experiments, I have greatly improved the method of operation and am beginning on the other jugulars of my stock. Yesterday I operated on 2 who are doing well to-day, and who now have 1/3rd alien blood in their veins. On Saturday I hope for still greater success, and shall go on...until I get at least one-half alien blood. The experiment is not fair to Pangenesis until I do (quoted in Pearson 160).

Today, these kinds of experiments -- uncovering latent phenotypic variation by intensively breeding in a particular genetic background -- illustrate canalization and other epistatic effects. They are just as useful in uncovering these complex mechanisms today as they once were in obfuscating germline inheritance for Galton and so many others.

References:

Pearson K. 1924. The Life, Letters and Labours of Francis Galton. Volume 2. Cambridge University Press, Cambridge UK. Online at galton.org

Dienekes came up with his own set of predictions for next year. I have to say I love this one:

At least one paper from the Genographic project in a venue other than National Geographic about some obscure people that no one has heard about but everyone will talk about for days. The paper will have a feel-good message about the unity of mankind.

I wish I had thought of it!

Yesterday I ran across this paper by Thomas Flatt in Quarterly Review of Biology, which is a really thorough review of the concept of canalization from its origins to its recent resurgence. Really thorough in this case means that it repeats the same things in several different ways, which is sometimes helpful.

Here's a definition:

Canalization is the reduced sensitivity of a phenotype to changes or perturbations in the underlying genetic and nongenetic factors that determine its expression (see also Meiklejohn and Hartl 2002; De Visser et al. 2003). Canalization is a relative term, and can thus only be defined as a matter of comparison. Thus, a phenotype P is more canalized than another phenotype P* if P remains relatively invariant when the single- or multilocus genotype G, which determines P, is exposed to different environments (environmental canalization) or located in different genetic backgrounds (genetic canalization): P is "resilient," "robust," or "insensitive" to genetic and/or environmental changes or perturbations. Canalization can therefore be recognized by observing that most genetic or environmental changes leave the phenotypic expression of G, and thus the phenotype P, invariant; the expression of G is changed such that specific phenotypic changes (P -> P*) are induced only in some genetic backgrounds or environments (or combinations of genetic backgrounds and environments). Consequently, a canalizing allele or genotype G reduces the phenotypic variation of a trait across a range of genetic backgrounds and environments relative to a noncanalizing allele or genotype G*, and a canalized trait P exhibits a restricted range of phenotypic variation across genetic backgrounds and environments as compared to a noncanalized trait P* (Meiklejohn and Hartl 2002) (Flatt 2005:288).

OK, that's an eyeful. In a nutshell, a more canalized phenotype is one that changes less in response to changes in environment, changes in genetic background, or both.

The definition is complexified by the need to consider behavioral or physiological phenotypes. The paper considers the example of homeotherms, who maintain a single body temperature in a range of environmental ambient temperatures. In this case, the single body temperature is a stable phenotype (upon which much else depends), but it is maintained by diverse physiological mechanisms that are active at different levels and at different times. In this way, canalization is a result of substantial physiological buffering.

Why is canalization important? The intro to the review has this:

Canalization is highly relevant for evolutionary biology. For example, it implies that phenotypes may be stable around their fitness optimum despite genetic and environmental change (e.g., Rendel 1967). By keeping phenotypic variation low, canalization may constrain phenotypic evolution (e.g., Charlesworth et al. 1982; Maynard Smith et al. 1985) and provide a microevolutionary mechanism for character stasis (e.g., Stearns 1994). Canalization also allows genetic variation that is phenotypically not expressed to accumulate. This cryptic variation can lead to the appearance of new phenotypes when development is "decanalized," for instance by environmental stress, thereby allowing evolutionary change (e.g., Rutherford and Lindquist 1998) (Flatt 2005:288).

That is pretty abstract, since it only hints at the adaptive value of canalized phenotypes. What we really would like to know is why some phenotypes would be more canalized than others. The answer could include lots of mechanisms. For one thing, it might be adaptive to have a phenotype that was less vulnerable to environmental modification -- i.e., had less environmental variance. For another as described below, canalization could simply result from the reduction of pleiotropy that results from modularization of genetic or developmental pathways.

Here's one practical application: If you want to find the relationships among a group of species, it is most sensible to choose characters that have a clean distribution of variation --- they should vary relatively little within species, but relatively much between species. Characters that have a great deal of within-species variation are often less useful, because they will often remain polymorphic even within relatively distantly related species.

But a character that has a lot of between-species variation and relatively little within-species variation is exactly the kind of character that may result from canalization. These features may reflect adaptive canalization that differs among a group of species; they may reflect some kinds of developmental constraints on one or more developmental modules. In any event, we should be aware that the kinds of characters that tend to be most useful for phylogenetic reconstruction will have certain evolutionary characteristics.

This section is relevant to me, so I'm including it:

Modularity of development may contribute to canalization (Stearns 1989b; Maynard Smith 1998; Hartwell et al. 1999; Stern 2000). Changes in the organism in one of its parts should not compromise other achievements: independent functions should be coded independently so that the change of one function does not interfere with other optimized functions (G P Wagner and Altenberg 1996). Modularity can be a way to achieve this independence of functions. The significance of modularity for canalization is that perturbing one module does not necessarily perturb the development of the whole organism: the embedding of particular functions into distinct modules allows for phenotypic change by altering connections among the modules while the core function of a given module remains unchanged (G P Wagner and Altenberg 1996; Hartwell 1999; Stern 2000; Schank and Wimsatt 2001). First, if deleterious mutations are highly pleiotropic (but see Stern 2000), then these mutations are likely to have a negative effect on many traits. If gene networks have a modular structure, however, then genetic change in one of the modules does not necessarily influence the others (Bonner 1988). Thus, by restricting pleiotropy, modularity allows some modules to continue to function when others change (Schank and Wimsatt 2001). Second, random mutations of a given phenotypic effect are likely to be more deleterious in complex organisms consisting of many traits as compared to simpler organisms with less traits (Fisher 1930; Orr 2000). Fisher (1930) suggested that mutations of small phenotypic effect are more likely to be favorable than mutations with large effects. In a topological model, he showed that the probability of approaching (or deviating from) the fitness optimum is higher (or smaller) if a mutation has a small phenotypic effect than if it has a large phenotypic effect. In the latter case, a mutation is more likely to go beyond the optimum or to deviate from it more strongly than if the mutation has only a small phenotypic effect. For the same intuitive reason, random mutations of a given phenotypic effect are more likely to disrupt a complex than a simple organism (Orr 2000). It would therefore be evolutionarily advantageous to reduce the number of independent traits by bundling them into modules (Orr 2000) (Flatt 2005:299-300).

The review does not link this topic of modularity and canalization to evo-devo, but it seems like a fertile topic to me. The presence of different canalized pathways that might be alternated by genetic switches of various kinds is also a very interesting topic.

References:

Flatt T. 2005. The evolutionary genetics of canalization. Q Rev Biol 80:287-316. Full text (subscription).

Stephen Jay Gould famously made the false thumb of the giant panda one of his hallmark examples of the structural vagaries of adaptation. His original essay, "The Panda's Peculiar Thumb" is available online, courtesy of the Unofficial SJG Archive.

Now, a PNAS paper by Manuel Salesa and colleagues reports evidence of a false thumb in a Miocene relative of the red panda:

The "false thumb" of pandas is a carpal bone, the radial sesamoid, which has been enlarged and functions as an opposable thumb. If the giant panda (Ailuropoda melanoleuca) and the red panda (Ailurus fulgens) are not closely related, their sharing of this adaptation implies a remarkable convergence. The discovery of previously unknown postcranial remains of a Miocene red panda relative, Simocyon batalleri, from the Spanish site of Batallones-1 (Madrid), now shows that this animal had a false thumb. The radial sesamoid of S. batalleri shows similarities with that of the red panda, which supports a sister-group relationship and indicates independent evolution in both pandas. The fossils from Batallones-1 reveal S. batalleri as a puma-sized, semiarboreal carnivore with a moderately hypercarnivore diet. These data suggest that the false thumbs of S. batalleri and Ailurus fulgens were probably inherited from a primitive member of the red panda family (Ailuridae), which lacked the red panda's specializations for herbivory but shared its arboreal adaptations. Thus, it seems that, whereas the false thumb of the giant panda probably evolved for manipulating bamboo, the false thumbs of the red panda and of S. batalleri more likely evolved as an aid for arboreal locomotion, with the red panda secondarily developing its ability for item manipulation and thus producing one of the most dramatic cases of convergence among vertebrates.

So not only is there the bamboo grasping story, there is also the climbing carnivore story. Incidentally, red pandas are much cuter than giant pandas, and they hardly get any attention at all.

The noble red panda

UPDATE (1/6/06): I just saw that Carl Zimmer blogged this story long before I did. It's a good story.

References:

Salesa MJ, Anton M, Peigne S, Morales J. 2006. Evidence of a false thumb in a fossil carnivore clarifies the evolution of pandas. Proc Nat Acad Sci USA Online early access. Abstract

This is pretty clever:

Although fish are neutrally buoyant, they still have to push water out of the way to move forward, he said. That water raises the surface -- a phenomenon that is often imperceptible as it may be spread across an entire lake, stream or ocean.

"The water can only go up because the bottom and sides of the channel are rigid," Bejan said. "That bulge, however undetectable, is the fish's footprint."

Fish must, therefore, work against gravity to lift an amount of water equal to their own mass for each body length they move forward.

"It puts fish in the same physical realm as runners and fliers."

That's from an article about similarities in locomotor dynamics across swimmers, runners, and flyers. A bunch of engineers showed that common physical principles explain relationships between body mass and speed, stride (or wingbeat) frequency, and muscle force.

On the other hand:

"From simple physics, based only on gravity, density and mass, you can explain within an order of magnitude many features of flying, swimming and running," added James Marden, professor of biology at Penn State. "It doesn't matter whether the animal has eight legs, four legs, two, even if it swims with no legs."

I'm fairly sure that my own running speed is within an order of magnitude of almost everything with legs, regardless of its size. So a lot of biological interest is cruising beneath the radar of physical constraints. But these relations may explain why some mouse-elephant type allometries are relatively similar between fish, mammals, and birds.

UPDATE (1/2/06): A reader e-mails: "Am I missing something? Sure fish have to push water out of the way as they move forward, but that water has a perfectly good place to go: into the space the fish just vacated! There might be some small vertical displacement of water, but it's an entirely local phenomenon that has no effect on the surface."

That seems like a good point to me. You might as well say that cars have to push air uphill in order to move forward (albeit with much less mass). Hmmm....

As surely as night follows day, we have this story from CNN on the real island giant animals that evolved in a King-Kong-like fashion.

Animals sometimes follow exotic evolutionary trajectories on islands because of a lack of predators or competitors. That's the essential truth of the story. It certainly explains the killer mice:

On remote Gough Island in the South Atlantic, "monster mice" are eating albatross chicks alive, threatening rare bird species on the world's most important seabird colony.

The house mice -- believed to have made their way to Gough decades ago on sealing and whaling ships -- have evolved to about three times their normal size.

But you can't shoehorn these cases into a universal "islands breed giants and dwarfs" rule. Consider:

The huge Indian Ocean island of Madagascar -- the setting of another 2005 Hollywood blockbuster -- has also given rise to plenty of natural oddities.

These included massive elephant birds that stood over 9 feet 10 inches in height and lemurs that weighed 176 pounds and more.

Yes, and mouse lemurs, and dozens of species of every intermediate size. The point is that the island created opportunities that might have been filled by other animals in a larger landmass.

A reader sent me a reference to a 2001 PNAS paper by Gary Burness, Jared Diamond, and Timothy Flannery that examines the relation of land area to body size of top carnivores and herbivores. There's no mechanism in the paper to relate the two, but there does seem to be an empirical relationship between the areas of islands and continental landmasses of different sizes and the sizes of their largest animals.

Ectotherms in the empirical data get larger than endotherms, also. So taking everything together, there shouldn't be either dinosaurs or gigantogorillas on Skull Island, but if there were either, they should be dwarfish in size, and the dinosaurs should be plenty larger than the giant gorilla.

And of course, they shouldn't exist in populations of single individuals!

CNN has this part covered, also:

Seemingly the last of his kind, King Kong also reflects another phenomenon of islands -- their disturbingly high rate of extinction, especially when humans land on them.

Many island species have evolved in a predator-free environment -- producing things like flightlessness in birds -- which makes them easy prey for meat-eating intruders.

Such was the fate of Madagascar's elephant birds as well as the famed dodo of Mauritius.

According to the World Conservation Union, close to 800 species have become extinct since 1500, when accurate historical and scientific records began.

While the vast majority of extinctions since that time have occurred on islands, over the past 20 years continental extinctions have become as common.

Scientists say this is partly because continental habitats are being diced up by human activities -- a process that is creating what some biologists term "virtual islands."

King Kong's real-life relatives are marooned on one of these "islands" on East Africa's Virunga mountain range, home to the last of the world's roughly 700 mountain gorillas.

I think the most interesting aspect of Skull Island is the way it exaggerates the scale of the man-nature conflict. Clearly the fauna of the island could never exist. But to make a nature capable of thwarting humans, even for a short time, it takes predators of gigantic proportions. Even in 1933, the real gorillas wouldn't stand a chance.

It is notable that in later movies featuring giant animals, like Godzilla and Them, they are frequently products of human agency -- especially our abuse of poorly understood forces of nature like radioactivity.

As I write this, by the way, the television has "Speed Buggy" encountering a giant island gorilla named "King Zilla".

References:

Burness GP, Diamond J, Flannery T. 2001. Dinosaurs, dragons, and dwarfs: the evolution of maximal body size. Proc Nat Acad Sci USA 98:14518-14523. Full text

This course is a broad, interdisciplinary introduction to the evolution
of the brain and mind. This inquiry is focused on humans, with
comparisons drawn from primates and other mammals. The pursuit of an evolutionary account of the mind depends on answering several fundamental philosophical and empirical questions.

From an empirical perspective, the course addresses the following questions:

• How does the structure of the brain impact the function of the mind?
• What variation in mental function occurs among present-day humans?
• What delineates the variation between species in brain structure and function?
• What is the nature of the systematic structure of mental functioning?
• To what extent is the variation in mental function inherited genetically?
• What were the minds of ancient people and fossil hominids like?

To answer these questions, different functions of the mind are reviewed in a comparative context. The mental functions that are shared between humans and other mammals broadly are differentiated from those that set humans apart, including language, consciousness, self-awareness, culture, and many others. The foundations of these advanced cognitive features are explored in the mental lives of other creatures. Several models will be presented for the evolution of such characteristics from simpler neural and psychological structures. In addition, direct evidence from the fossil and archaeological records is considered as a possible indication of the sequence of human mental evolution.

From a philosophical perspective, the course also pursues several other questions:

• Is the mind coextensive with the brain, and does it include significant non-brain elements?
• What part does culture play in the determination of human minds, and does culture present a significant non-evolutionary mechanism of change?
• Are minds and mental representations commensurable between individuals?
• How do developmental changes in the brain and mind impact individuality, and does such an impact have social and evolutionary consequences?

While the empirical questions may yield to observation and experiment, these philosophical problems ultimately can be answered only through the application of logic. Nevertheless, their answers may significantly inform our understanding of the nature of mental evolution, by delineating boundary conditions for evolutionary change of the mind while highlighting other causes of change.

Together, these two bases of inquiry present a broad perspective on the biology of the mind. The subject matter is spread across the four cross-listed fields and others, including philosophy, computer science, genetics, and paleontology. This interdisciplinary base creates a demanding learning experience, recognized by the high level of the class, challenging written assignments, guest lectures by experts in their respective fields, and both primary and secondary readings. No students in the class can be expected to be expert in all the areas covered, and for this reason the course presents some introductory material important to the interdisciplinary understanding of the issues. For some students such material will be old hat, but please understand that students in different majors may never have been exposed to the fundamental concepts of your field, and may be unable to proceed without them. Almost certainly there will be other course components that are new to you but old hat to someone else.

The interdisciplinary nature of the course also ensures that every student may get something different out of it. Although the course goes through a systematic survey of issues related to the biology of the mind, the learning experiences of different students and what they take away to their respective fields may be very different. For this reason, the written assignments in the course attempt to promote dialogues between students in different fields and to allow the fuller development of individual perspectives.

I'm sure you've seen the story:

A team of Dutch and Mauritian scientists discovered the bones in a swampy area near a sugar plantation on the south-east of the island.

The bones were said to have been recovered from a single layer of earth, with the prospect of further excavations to come.

Sections of beaks and the remains of dodo chicks were thought to be among the find.

What more can I say? Oh, yeah: now begins the dodo genome project.

Burt Humburg and Ed Brayton have a very readable account of the Dover trial in Skeptic magazine, available now online. The article goes over the recent history of jurisprudence related to evolution in education, the ins and outs of the defense and plaintiffs' preparation for the trial, and the testimony of the key witnesses.

This seems like a key passage for those who find themselves on school boards pondering creationism:

Aralene "Barrie" Callahan, a Dover school board member at the time the ID policy was adopted, and Bryan Rehm, a former physics teacher at Dover High School would testify that prior to the adoption of the ID policy, members of the school board had spoken openly of wanting to balance the teaching of evolution with material advocating "creationism." This testimony helped tie the school board's actions to the actions struck down in Edwards.

Mrs. Callahan testified, and showed her handwritten notes from key school board meetings and board retreats in 2003 and 2004, that school board President Alan Bonsell and chair of the curriculum committee William Buckingham had repeatedly spoken in favor of creationism explicitly, something both men denied.

Take good notes. You can't count on your opponents to be truthful.

And according to many accounts, this was the most dramatic moment:

In the face of multiple witnesses, newspaper reports and even videotaped evidence, William Buckingham had a difficult time explaining his denials during deposition that he had never said anything about creationism. Both he and Alan Bonsell had been asked in depositions about where the money had come from to purchase the dozens of copies of the Pandas book; both testified that they didnÕt know where the money had come from, but that it was not taxpayer money. But under cross examination, it was revealed that Buckingham had raised the money at his church, wrote a check out of his own account for $850 and gave it to Bonsell, who then gave it to his father to purchase the books. This inconsistency angered the judge so much that he interrupted the attorneys and began to question Bonsell himself, demanding an explanation for why he had not mentioned this when asked directly about it.

If you didn't follow the trial, this is a great review. Highly recommended.

Check out the judge's opinion if you are interested. Ann Althouse cites from the text, including this portion:

The citizens of the Dover area were poorly served by the members of the Board who voted for the ID Policy. It is ironic that several of these individuals, who so staunchly and proudly touted their religious convictions in public, would time and again lie to cover their tracks and disguise the real purpose behind the ID Policy.

Of course people may support many kinds of public initiatives for religious reasons, and there's nothing wrong with that. But in the case of Intelligent Design, there is no possible justification that is non-religious, except for unalloyed ignorance. Not even lies -- and the Dover trial revealed plenty -- can hide the fact that ID is a religious viewpoint and not science.

I'm keeping Althouse's emphases in the next passage:

With that said, we do not question that many of the leading advocates of ID have bona fide and deeply held beliefs which drive their scholarly endeavors. Nor do we controvert that ID should continue to be studied, debated, and discussed. As stated, our conclusion today is that it is unconstitutional to teach ID as an alternative to evolution in a public school science classroom. Those who disagree with our holding will likely mark it as the product of an activist judge. If so, they will have erred as this is manifestly not an activist Court. Rather, this case came to us as the result of the activism of an ill-informed faction on a school board, aided by a national public interest law firm eager to find a constitutional test case on ID, who in combination drove the Board to adopt an imprudent and ultimately unconstitutional policy. The breathtaking inanity of the Board's decision is evident when considered against the factual backdrop which has now been fully revealed through this trial. The students, parents, and teachers of the Dover Area School District deserved better than to be dragged into this legal maelstrom, with its resulting utter waste of monetary and personal resources.

The Panda's Thumb, naturally, has much more.