Tag Archives: Evolution

Culture influences brain function

People from different cultures use their brains differently to solve the same visual perceptual tasks, MIT researchers and colleagues report in the first brain imaging study of its kind.

This is not that surprising, but it is very interesting research. We already knew, for instance, that people who read and write different “kinds” of languages … pictographic vs. non-pictographic … use different regions of their brain for this function, and thus are differentially affected by strokes or other damage. Continue reading Culture influences brain function

The Origin of Syphilis

Blogging on Peer-Reviewed ResearchSyphilis is first clearly seen in Europe in 1495, when it appeared as a plague (though it was not “the plague” … Yersinia pestis) among Charles VIII’s troops. When these troops went home shortly after the fall of Naples, they brought this disease with them, staring an epidemic. The level of mortality in Europe was truly devastating. Is it the case that syphilis was brought to Europe by Columbus and his men just prior to the plague-like outbreak of 1495?

The origin of syphilis has been debated for years, really since the actual 1495 event itself. Some researchers have asserted that syphilis is present in the writings of Hippocrates, placing it squarely in the old world thousands of years prior to Columbus. Others, as suggested above, have argued that Columbus brought syphilis over to the Old World . A third (Crosby’s “combination theory”) asserts, essentially, that syphilis is both an Old World and New World disease, and that the history of the disease is complicated by the innately complex relationship between any pathogen and human populations with variable immunities, both of which tend to evolve.

A new paper is being published as we speak in PLoS Neglected Tropical Diseases, by Harper et al , called “On the Origin of the Treponematoses: A Phylogenetic Approach.” Studiously ignoring Crosby’s discussion (and I’m sure there is some unseemly story of academic infighting to explain that), the paper examines the Old World vs. New World origins hypotheses.Here is the author’s summary from the paper:


For 500 years, controversy has raged around the origin of T. pallidum subsp. pallidum, the bacterium responsible for syphilis. Did Christopher Columbus and his men introduce this pathogen into Renaissance Europe, after contracting it during their voyage to the New World? Or does syphilis have a much older history in the Old World? This paper represents the first attempt to use a phylogenetic approach to solve this question. In addition, it clarifies the evolutionary relationships between the pathogen that causes syphilis and the other T. pallidum subspecies, which cause the neglected tropical diseases yaws and endemic syphilis. Using a collection of pathogenic Treponema strains that is unprecedented in size, we show that yaws appears to be an ancient infection in humans while venereal syphilis arose relatively recently in human history. In addition, the closest relatives of syphilis-causing strains identified in this study were found in South America, providing support for the Columbian theory of syphilis’s origin.


The authors looked at 21 strains of the bacterium Treponematoses pallidum and conducted a detailed genetic (phylogenetic) study of these genomes to come to the conclusion that syphilis originates in the new world. However, a commentary on the paper, published along side it in PLoS, brings the conclusion into question. The commentary by Lukehart and Norris notes that the genetic data from the New World (which the main paper’s authors assert points to a New World origin) is weak. In addition, there are problems, partly outlined in the commentary and partly fairly obvious to anyone who reads the paper, that the issue of evolutionary change in both the pathogens and the humans who harbor them has not been sufficiently taken into account.In my view, a detailed phylogenetic study such as the one presented here is fundamentally important, but is very unlikely on its own to definitively answer the question of origin and evolution of syphilis.Need more research…

Updated: See The Science Behind Pre-Columbian Evidence of Syphilis in Europe: Research by Documentary, by Armelagos, Zuckerman, and Harper, on “Science by documentary” and “Science by press release”

This article discusses the presentation of scientific findings by documentary, without the process of peer review. We use, as an example, PBS’s “The Syphilis Enigma,” in which researchers presented novel evidence concerning the origin of syphilis that had never been reviewed by other scientists. These “findings” then entered the world of peer-reviewed literature through citations of the documentary itself or material associated with it. Here, we demonstrate that the case for pre-Columbian syphilis in Europe that was made in the documentary does not withstand scientific scrutiny. We also situate this example from paleopathology within a larger trend of “science by documentary” or “science by press conference,” in which researchers seek to bypass the peer review process by presenting unvetted findings directly to the public. © 2012 Wiley Periodicals, Inc.

See: Syphilis May Have Spread Through Europe Before Columbus.

Summary: A recent study conducted at the University of Zurich now indicates that Europeans could already have been infected with this sexually transmitted disease before the 15th century. In addition, researchers have discovered a hitherto unknown pathogen causing a related disease. The predecessor of syphilis and its related diseases could be over 2,500 years old.

Lukehart S, Mulligan C, Norris S (2008) Molecular Studies in Treponema pallidum Evolution: Toward Clarity? PLoS Negl Trop Dis 2(1).Harper KN, Ocampo PS, Steiner BM, George RW, Silverman MS, et al. (2008) On the Origin of the Treponematoses: A Phylogenetic Approach. PLoS Negl Trop Dis 2(1): e148. doi:10.1371/journal.pntd.0000148

PKU: An exploration of a metabolic disease

Phenylketonuria (fee-null-keet-o-noo-ria), mercifully also known as “PKU” (pee – kay – you) is a disorder in which phenylalanine, an essential amino acid, is not broken down as it normally would be by an enzyme (phenylalanine hydroxylase) and thus accumulates (in the form of phenylpyruvic acid) in the body. Normally, Phenylalanine hydroxylase coverts phenylalanine into tyrosine, another amino acid, which has a number of different functions.

This is bad because buildup of phenylpyruvic acid has several negative effects, the most important being to interfere with normal development of neural tissues. Continue reading PKU: An exploration of a metabolic disease

Charles Darwin Bicentennial – Iguanas, a “most disgusting, clumsy lizard…

…They are as black as the porous rocks over which they crawl & seek their prey as from the Sea. — Somebody calls them “imps of darkness”. — They assuredly well become the land they inhabit. — When on shore I proceeded to botanize & obtained 10 different flowers; but such insignificant, ugly little flowers, as would better become an Arctic, than a Tropical country. — The birds are Strangers to Man & think us him as innocent as their countrymen the huge Tortoises. Little birds within 3 & four feet, quietly hopped about the Bushes & were not frightened by stones being thrown at them.” [Darwin’s Beagle Diary (1831-1836)].

And thus we get a hint of Darwin’s impressions of the Galapagos, and in particular, that Island’s marine iguanas.

The Iguana family is Iguanidae, but most Iguana’s you’ve cuddled in the pet store are members of the genus Iguana (and most likely species Iguana iguana.) The Galapagos Islands have two or three species of iguana: The Land Iguana is Conolophus subcristatus and Conolophus pallidus, or perhaps is actually the subspecies Conolophus subcristatus pallidus. The marine iguana is Amblyrhynchus cristatus.

The two genera of iguana on the Galapagos seem able to interbreed, though they otherwise also seem to make good, distinctive species. (No, it is not really true that inability to inbreed is “THE biological definition of species….” it is more complex than that. A topic for another time, perhaps.) The phylogenetic relationship among the Galapagos iguanas and continental iguanas is similar to that among the finches and other Galapagos animals… complex and more complex because of the apparent fact that while the oldest of the Galapagos islands is about four million years old, earlier islands, perhaps going back twice that age, formerly existed but are now eroded down below sea level. One wonders what will happen next ice age (or what happened last ice age) when a 120 -150 meter drop in sea level exposes some of these islands! The point is that these volcanic islands have a complex history, and it is likely that the islands themselves have a complex relationship to the distant continent. Again, the topic of another post perhaps.

The following passages from Darwin (1839) Continue reading Charles Darwin Bicentennial – Iguanas, a “most disgusting, clumsy lizard…

Charles Darwin Bicentennial – A Tangled Bank

Last Darwin Post I gave you the famous “Tangled Bank” quote, in which Darwin links the concept of selection to the concept of ecology and thus derives “grandeur in this view of life.”

This is a theme of much of Darwin’s writing in The Origin, and in fact, the Phrase “Tangled Bank” shows up much earlier in the volume.

In the case of every species, many different checks, acting at different periods of life, and during different seasons or years, probably come into play; some one check or some few being generally the most potent, but all concur in determining the average number or even the existence of the species. In some cases it can be shown that widely-different checks act on the same species in different districts. When we look at the plants and bushes clothing an entangled bank, we are tempted to attribute their proportional numbers and kinds to what we call chance. But how false a view is this! Every one has heard that when an American forest is cut down, a very different vegetation springs up; but it has been observed that ancient Indian ruins in the Southern United States, which must formerly have been cleared of trees, now display the same beautiful diversity and proportion of kinds as in the surrounding virgin forest. What a struggle must have gone on during long centuries between the several kinds of trees, each annually scattering its seeds by the thousand; what war between insect and insect—between insects, snails, and other animals with birds and beasts of prey—all striving to increase, all feeding on each other, or on the trees, their seeds and seedlings, or on the other plants which first clothed the ground and thus checked the growth of the trees! Throw up a handful of feathers, and all must fall to the ground according to definite laws; but how simple is the problem where each shall fall compared to that of the action and reaction of the innumerable plants and animals which have determined, in the course of centuries, the proportional numbers and kinds of trees now growing on the old Indian ruins!

(Darwin, C. R. 1869. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. London: John Murray. 5th edition. Pages 86-87)

This is a fantastic example of Darwin’s breadth of interest and integrated mind. He makes explicit reference to the fact that selection is context dependant (“widely-different checks act on the same species in different districts”). He is explicit about the fact that chance is NOT the operative force in organizing nature (a fact that creationists seem to ignore when they speak of the unlikelihood of a tornado passing through a junkyard creating a Boeing 747 and http://gregladen.com/wordpress/?p=264such hogwash). Continue reading Charles Darwin Bicentennial – A Tangled Bank

Parasitic Birds and The Red Queen Effect

The Avian Brood Parasites

The Avian Brood Parasites

Brood parasitic birds lay their eggs in the nests of other birds (the “hosts”) who then raise them as their own. Examples of parasitic birds includes the cuckoo, cow birds, widow (“whyda”) birds, honeyguides, and even the South American Black-headed Ducks. Brood parasitism is virtually a world wide phenomenon.

Many interspecific brood parasites are obligate for this strategy … this is the only way they raise their own young. There are many variants (beyond the scope of this post). Intraspecific parasitism is known in many colonially nesting birds.

The Red Queen effect is a concept now widely known by aficionados of biology. The phrase is from Alice Through the Looking Glass, but the biological concept was first developed by Leigh Van Valen, a biologist at the University of Chicago.

While the Red queen and Alice are discussing chess, the following dialog and events ensue: Continue reading Parasitic Birds and The Red Queen Effect

Models of Sexual Selection

Darwin was puzzled by exaggerated traits. (Aren’t we all, really?) For example, why would a widow bird male have a tail so long that he could scarcely fly away from predators? Indeed, speaking of birds:

What a contrast is presented between the sexes by the polygamous peacock or pheasant, and the monogamous guinea-fowl or partridge! Many similar cases could be given, as in the grouse tribe, in which the males of the polygamous capercailzie and black-cock differ greatly from the females; whilst the sexes of the monogamous red grouse and ptarmigan differ very little. Amongst the Cursores, no great number of species offer strongly – marked sexual differences, except the bustards, and the great bustard (Otis tarda), is said to be polygamous. With the Grallatores, extremely few species differ sexually, but the ruff (Machetes pugnax) affords a strong exception, and this species is believed by Montagu to be a polygamist. Hence it appears that with birds there often exists a close relation between polygamy and the development of strongly-marked sexual differences. On asking Mr. Bartlett, at the Zoological Gardens, who has had such large experience with birds, whether the male tragopan (one of the Gallinaceæ) was polygamous, I was struck by his answering, “I do not know, but should think so from his splendid colours.”

Darwin, C. R. 1871. The descent of man, and selection in relation to sex. London: John Murray. Volume. 1. 1st edition. Pages 269-270

I don’t want to give a comprehensive (or bullet proof) “definition” of sexual selection. Instead, I want to lay out a few key ideas and suggest a way to think of models of sexual selection.

Darwinian Sexual Selection.
Females possess a built in aesthetic Continue reading Models of Sexual Selection

The Evolution of Human Diet

Chimp, Australopith and
Human Teeth Compared.

The evolution of human diet followed a major zig (as in zig-zag) in a wholly unexpected direction, followed by the most significant biological innovation to ever occur among multi celled animals: The invention of cooking. I’m actually going to point you to two papers on this topic, and provide a brief summary of the ideas here.

Let’s start with the bold assumption that humans evolved from a chimpanzee-like animal. This is tantamount to saying that the last common ancestor of chimpanzees and humans was, essentially, pretty much like a chimpanzee. At another time, I’ll write a post on why this is a good assumption, but for now lets just go with it. Some large percentage of human evolution experts like this assumption, a bunch of others hate it (which is the usual pattern for most ideas in human evolution).

A mammal’s diet is reflected in physiological attributes that can be discerned from the fossil record. Body size, the nature of the teeth and associated muscles, possibly the shape of the mouth’s cavity, and even the overall size and shape of the gut may be closely connected with diet.

If we draw a direct line from a presumed chimpanzee-like ancestor to modern humans, Continue reading The Evolution of Human Diet

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.

In Stabilizing Selection the extremes of a trait are selected against and the mean value of the trait remains the same. Mutations constantly introduced into the population tht produce traits out at the extremes are selected against. In Directional Selection the values of a trait at one end of the distribution are selected against and/or values at the other end are selected for, so that the distribution of values, and it’s mean, move in one direction. In Disruptive Selection the average values are selected against so that the distribution of the trait becomes bimodal.

That was pretty simple, but Continue reading The Modes of Natural Selection

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.

In this post, we will do the following:

  • Discuss historical and contextual aspects of the term “Natural Selection” in order to make clear exactly what it might mean (and not mean).
  • Provide what I feel is the best exact set of terms to use for these “three conditions,” because the words one uses are very important (there are probably some wrong ways to do it one would like to avoid).
  • Discuss why the terms should be put in a certain order (for pedagogical reasons, mainly) and how they relate and don’t related to each other.

When you are done reading this post you should be able to:

  • Make erudite and opaque comments to creationists that will get you points with your web friends.
  • Write really tricky Multiple Choice Exam Questions if you are a teacher.
  • Evolve more efficiently towards your ultimate goal because you will be more in control of the Random Evolutionary Process (only kidding on this third one…)

Continue reading The Three Necessary and Sufficient Conditions of Natural Selection

Of skinks and monkeys

I was recently looking at a practice AP biology test question on evolution, and sparing you the details, I found it interesting that two of the four parts dealt with genetic variation and speciation in such a way that it was difficult to tell them apart. As expected, students who answered these questions got confused as well, and tended to give perfectly good answers to Part B, but unfortunately, this was their answer to Part A. By the time they got to Part B they seemed a little confused, perhaps realizing that there was some overlap and conflation of concepts.

Inter and intra-specific variation is probably patterned such that the sum of variation among several species is greater than the partitioned variation within a given species. That’s pretty obvious.

(Just in case it is not: Imagine measuring the mass of several elephants. The variation can be represented by the standard deviation, range, or whatever you like, among your measurements. It is such and such. Now do the same thing with a bunch of mice. Again, you have some measure of variation. Now do it for the mice and elephants combined. Here, the variation will be larger than for either. This is not the same as if you want to compare variation or patterns of variation between mice and elephants. Do do that, you need to scale the variation, say by using the coefficient of variation. In this case, combining the coefficients of variation might show less variation when combined than for either group simply because of sample size effects. But what I’m talking about here is total variation. Mice are tiny, elephants are huge, so their total size variation runs Continue reading Of skinks and monkeys