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…)

Here are some definitions of Natural Selection I found on the web for your review:

• The differential survival and reproduction of organisms with genetic characteristics that enable them to better utilize environmental resources [source]
• Natural selection is the process in which some organisms live and reproduce and others die before reproducing. Some life forms survive and reproduce because they are better suited to environmental pressures, ensuring that their genes are perpetuated in the gene pool. [source]
• Process by which the genotypes in a population that are best adapted to the environment increase in frequency relative to less well-adapted genotypes over a number of generations. source
• The concept developed by Charles Darwin that genes which produce characteristics that are more favorable in a particular environment will be more abundant in the next generation. [source]
• the differential survival and/or reproduction of individuals within a population based on hereditary characteristics. [source]
• The process by which new species evolve when influenced by selective pressure (Martin et al, 2000). Natural selection occurs when the natural factors of environmental resistance tend to eliminate those members of a population that are least well adapted to cope and thus, in effect, select those best adapted for survival and reproduction (Nebel et al, 1998). [source]
• central thesis of the biologist Charles Darwin which suggests that within every population of living organisms there are random variations which have different survival value. Those which aid survival (or enhance reproductive capacity) are ‘selected’ by being genetically transmitted to succeeding generations. [source]

There are things I don’t like about most of these definitions. A definition may focus on environmental conditions and thus ignore many very important other things such as developmental processes and mating. Definitions may focus on the individual’s survival, etc., which works, but we may want to speak of traits as well as individuals. Some definitions use active verbs such as “ensuring that their genes are perpetuated in the gene pool.” This may not be linguistically wrong but it incorporates teleological concepts, which don’t need our help in creeping into our thinking (especially in the formal definition of a natural force!). There is often a direct link to Charles Darwin. This is good because it is true that this is his concept. However, a modern definition of Natural Selection needs to be Neo-Darwinian. So specifically referring in the definition to Darwin without more attention to the historical development is inadequate. Referring to Darwin’s concept as a concept about genes is jarringly wrong.

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As a whole these definitions are not terrible, but they are mostly flawed for one reason or another. The definition I want to lay out here will have specific reference to the same process these definitions are about. However, there is also one very large problem with many of these definitions that is a bit more subtle than most but that is, to me, critical, that relates to the object of study. It is probably best to not assume a one-to-one correspondence between the process of Natural Selection that we are going to describe here and the concept of “adaptation.” Ultimately, I would like to say that “adaptation” is the noun and “Natural Selection” is the verb in a key evolutionary process. But having said that, a useful and precise definition of Natural Selection may have to leave out processes that are nonetheless related to adaptations, both in terms of understanding the historical aspects of an adaptation and the functional aspects, but that do not fall under the process “Natural Selection” as it is best defined.

An adaptation may reach its particular form through the process of Natural Selection, but there are aspects to that form that have to do with, for instance, abiotic realities. You cannot have adaptations that involve swimming without bodies of water, for example. Our definition does not say “Oh, and there must be air, and water, and trees to climb in.”

I actually want to provide TWO different (linguistically) but identical (functional) definitions of natural selection. The first is the coolest one, the simplest one, the one that makes you think. The second is a better pedagogical tool and serves better as the basis for adaptationist analysis of biological systems. The second also links better to certain historical aspects of the development of the concept.

The first definition is conceptually related to the following definition of evolution:

Change in allele frequency over time.

Which is something of an oversimplification, but an allowable one. And in this context we can define Natural Selection as:

Nonrandom elimination of alleles.

I believe that this was suggested by Ernst Mayr.

This is a cool definition because it is short, sweet, and correct. Note the very important asymmetry that this definition implies. There is no non-random generation of novel alleles. Only elimination. This jibes with selection as a creative force, but neutral processes as providing the raw material. Neutral processes lay down the sediments that become the marble, Natural Selection is the sculptor. The adaptation is the sculpture.

The second definition, and the one I really want to get to, involves the so called “three necessary and sufficient conditions” and it goes something like this:

1. Variation in a trait
2. Heritability of the trait
3. Differential fitness conferred by the trait.

Just as important as these elements is the theoretical and logical framework in which they are placed. They are the THREE NECESSARY and SUFFICIENT conditions. Let’s parse that out more.

Three … That there are three is obviously because all important things happen in threes, sevens, or tens, for unknown cosmic reasons. Be that as it may, I want to point out that “three” implies “three different” things. If two of them could have been combined, then we would have only two. But there are three.

What this implies is the following: If there is a trait that varies, then it meets the first criterion. But “No,” you say, “what about hair color? If I see a bunch of people with different color hair, and I KNOW they dyed their hair to get that way, this is not trait related to selection. So it does not meet the first criterion.”

But you would be wrong. Remember, there are THREE DIFFERENT criteria. The first one is variation. If you see a bunch of dogs and they have different coats because they went to a very creative groomer, or a bunch of students standing around the cafeteria with blue, red, unnaturally black, and vivid yellow hair because they all went to Target and got dye and colored their hair, then in both cases you have met the first criterion because there is variation. By saying “these traits are not inherited” you have skipped ahead and cheated.

The second criterion is usually stated as “heritability” and that is a small problem, because the term “heritability” has a specific meaning in biostats that falls apart for our present use. It is the measured variance in the genotype divided by the measured variance in the phenotype, squared. (Thus indicating something like the proportion of measured phenotypic variance that is accountable by genetic variation.) What is meant in our definition, however, is this: Is the variation in the trait conferred by genes? The dyed hair and the clipped poodle do not meat this criterion.

The third criterion is often stated as “Differential Reproductive Success” and that is simply wrong. The correct term is “Differential fitness” and it has to be differential fitness that is conferred by the trait. Why fitness instead of Reproductive Success (RS)? That is an important matter, and I will not discuss it here. For now, let’s just go with it.

OK, back to the theoretical context: Necessary.

Why are these three necessary? By necessary it is meant that ALL of them have to be true or it is not Natural Selection. This is fairly obvious. If you are missing any one of these three then what you are observing may be an interesting phenomenon but it is not Natural Selection. This also speaks to the need to be Neo-Darwinian. Darwin was aware of inheritance, but lacking an understanding of the mechanism, the necessary requirement of “heritability” (remember, shorthand for “the trait is passed on by genes”), any Darwinian definition (and I’ve avoided using his specific words here) is not good enough.

I had said at the beginning that the ordering of the three conditions is important. This is because they interact with each other in order. Here is how.

First, you need a trait that shows variation. Second you need to show that that trait is heritable, AND that the inheritance pattern relates to that variation. Third you need to show that the variation that is heritable maps on to differential fitness. So there is a strong logic to the order, that is embedded in the functional meaning of Natural Selection and any test criteria that are set up to investigate possible cases of it.

So the ordering works both for the understanding of the concept (pedagogy) and the investigation of the phenomenon.

Sufficient. That is a really important part of the context for this definition. If these three conditions are true, then Natural Selection IS happening. There is no alternative. The force of Natural Selection is activated when these three conditions are met, no matter what.

Does this mean that the selective force will have an effect? It depends. Natural Selection is a force, but there are other forces, including other instances of Natural Selection that may be operative in a particular organism. Gravity is a force but a fly can still walk on the ceiling. The gravity is still acting on the fly, but so is another force (adhesion) that keeps it up there.

This is an important point that bears emphasis. When the Three N&S Conditions of N.S. are working, Natural Selection happens. Period. The absence of an EFFECT is due to countervailing forces (including chance, because within it’s operation there are still stochastic effect).

I believe it is incorrect and counterproductive to make “Sexual Selection” distinct from and parallel to “Natural Selection.” Darwin was puzzled by apparent inconsistencies, especially along the lines of exaggerated traits mostly in males, and came up with Sexual Selection as a process to explain this. Fine. But I think it is best to think of both Sexual and Artificial Selection as subsets of Natural Selection.

The term “Selection” by itself is often used interchangeably with “Darwinian Selection,” but often (usually?) as not really meaning the same thing as Natural Selection. Natural Selection works between generations on reproducing organisms and their genomes. Darwinian Selection, or selection in general can work on other things, like prospective students trying to get into law school, or neurons during culling, etc.

This has been an enhanced repost from a very long time ago. You might imagine that I’m about to write a post on Falsehoods related to Natural Selection, and needed this post nearby. You’d be right!

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Other posts of interest:

• How to get rid of spiders in your house
• Why is your poop green?
• How many cells are there in the human body?
• Is there really a plot hole in Harry Potter Goblet of Fire?
• How long is a human generation?
• Is blog ever really blue?
• How to not get caught plagiarizing
• The origin of the domestic chicken
• What are the three necessary and sufficient conditions of Natural Selection?
• How do I get rid of foot fungus?
• Which is better, Tap Water or Bottled Water?
• Has Global Warming stopped?

Also of interest: In Search of Sungudogo: A novel of adventure and mystery, which is also an alternative history of the Skeptics Movement.

Several parallel discussions inspire me to write this post partly in the hope that you will chime in.

The chance of life elsewhere in the universe just went to near zero. Or did it?

I was just hanging around minding my own business the other day when someone said to me, “you know, every single one of the five thousand or so exoplanet holding stars found to date have the gas giants in the inner, Goldilocks zone, and the smaller Earth-like planets are too far out to have life. So, the chance of life on other planets is way lower. Zero, basically.”

So, that was depressing.

Then, I went to the opening of the Bell Museum, and watched the planetarium show. After the show, I asked one of the people running the show, a somewhat snotty graduate student from the U, about this news. He got even snottier and told me that was ridiculous, that there are plenty of systems with Earth-like planets in the Goldilocks zone. I asked him how many. Plenty. I asked him if the number was double digit percentage or single digit percentage. He said may be single, but that was enough. I told him I had heard zero, which is not many. He said that was wrong.

Just a few minutes later, on visiting the rest of the newly opened museum, the penny dropped.

It turns out one of the major faculty members at the U in astronomy is one of the planet hunters, and a huge portion of the overall universe level exhibitry in the museum is devoted to showing this one guy’s work and talking about exoplanets and stuff. That must have been his student. Clearly, I had stepped in a pile of something.

My question is, a pile of what, exactly? Is there really recent research that suggests that the Earth’s solar system is unique among a sample of 5,000 or so? Or not? Or what?

The origin of life vs evolution

A long time ago, maybe 20 years now, some evolution-believing but sympathetic to religion people decided to say that the origin of life is not really in the purview of biology, and therefore should not be addressed in textbooks, high school courses, etc. You can think whatever you want about the origin of life, but it has nothing to do with evolution.

I’ve written about this. See:

“We can know nothing about the origin of life”
Is the origin of life different from evolution?

More recently, I find myself repeatedly being dragged into Twitter arguments between people saying that the origin of life is separate from evolution, vs. not.

The reason to say that they are separate is to allow religious people to have their god of the gaps, in this case, the ultimate gap. The pre-life gap.

The conception involves a very serious misconception about what the word “evolution” or the term “evolutionary biology” refer to. Most people misunderstand this.

I’ll give you an example. I was at a conference many years ago at the original Bell (not the one that just opened) and a well meaning but not well informed science teacher said to a room full of science teachers, “Evolution is simple. It is simple to teach. All evolution is…” then he proceeded to lay out the three Necessary and Sufficient conditions for Natural Selection.

Unfortunately, that is not what evolution is, and even more dramatically, it is not what evolutionary biology is about.

Evolution is the change over time in organisms, no matter how that happens.

Evolution is the idea of common ancestry and differentiation of lineages form common ancestors.

Evolution is increase of diversification over time, speciation, and extinction.

So that is three or four, maybe five things, depending on how you count them, that evolution is, and none of them need involve natural selection.

Oh, and natural selection is also part of evolution.

The point is this: If you think evolution is only this one thing, and define it very narrowly, then it is easy to figure that the origin of life is not part of evolution. But evolutionary biology is really the study of life in general, and all of it, in the context of evolutionary theory, and evolutionary theory involves everything from how molecules selectively interact (in primordial soup and in cells and other places) to how genes mutate, to how populations randomly drift genetically apart, or interact genetically, to how coeval lineages of organisms affect each other’s evolution (co-evolution), to how life and non life interact, to how natural selection creatively shapes life.

Evolution and evolutionary biology are two terms that refer to a thing and the study of a thing that is whopping big and complicated and wonderful and amazing and confusing and only barley understood.

To say that the origin of this thing is somehow separate is idiotic.

But to underscore the stupidity of this idea further, allow yourself to consider the following idea as possibly true.

Life evolved more than once.

Even more amazing an idea, and a very interesting hypothesis that we hope one day to test:

Under certain conditions, which are not uncommon in the universe, life almost inevitably arises, just as under certain conditions, a crystal is likely to form, rain is likely to fall, or a fire is likely to ignite. Life, in other words, happens.

If that is true, then the multiple origins of many life systems is clearly of no small interest to evolutionary biologists, and is very much part of “evolution.”

Which brings me to my third thought.

Life evolved independently on Mars, Earth’s Moon, Earth, and who knows where else. Or not.

There is a study just out published in Astrobiology, by Dirk Schulze-Makuch, that addresses part of this. I’ve asked for a copy of the paper, and if I get it, I’ll tell you about it. Without the paper, all I have is the breathless press release, and I’m not going to report on that.

But I can tell you that the basic idea seems to be that there is vague isotopic evidence of past life on the Earth’s Moon, and reconstructions of the Moon’s history suggest that at some point after its formation, and another time later when it was very volcanic, there would have been pools of water, an atmosphere, and some degree of protection from radiation, so life could have been there.

I’m of the belief that life is not that hard to get started. Why do I think that? Because it isn’t that hard to maintain it. Bacteria, especially, survive and do well under a wide range of conditions. A very simple virus can exploit cellular machinery pretty easily. Even though conditions on the early Earth were probably pretty tough, bacteria seem to have arisen early and held on — or perhaps re-started? — for a very long time. This is little more than a gut feeling, but it seems to me that life starting up isn’t that unlikely of an event, given the right conditions.

The reason we don’t see life originating again and again on our planet now may be because the startup does poorly in aerobic conditions. It may be because any molecules that start to form up in a way that leads to life are inevitably tasty food for existing life. Hell, there may be life almost starting up all the time in some places, and then being guzzled up by bacteria of some sort. And there are people looking for that sort of thing so maybe we’ll find that eventually.

Here’s my question on this. Which is harder to see happening, harder to believe, harder to accept, given what we know, and what we like to guess, about life?

1) Life started once, say, on Mars, and that’s it. Just that one time. Life found later on the Moon or on Earth came from Mars by a large rock hitting life-bearing mars, spreading rocks across the inner solar system, and some of those rocks eventually landed on the Moon and Earth, burning to a crisp in the atmosphere but somehow the bacteria on the rocks survive.

or

2) Life starts up easily and did so on Mars, the Moon, and Earth. For the first two, conditions for life were transient and have ended. For the Earth, conditions for life are a bit longer lived, and will end later.

Yes, yes, this all assumes there was life on Mars or the Moon, and we simply do not know that to be true at this time. This argument only matters if we pretend it was true, or at least possible. So this is speculation.

How has Darwin’s theory of Natural Selection fared over the last 150 years, and what needs to be done to bring this theoretical approach to bear as we increasingly examine complex systems, including human society?

Pagel discusses both the controversial nature of and the sheer simplicity of Darwin’s Natural Selection, very briefly summarizes the range of applications that has been made of it, then focuses on the core questions “which cut across the hundreds of specific topics of evolutionary investigation.” Pagel will not conclude, as was recently suggested by the New York Times, that Darwin needs to die (or Darwinism at least) for us to get on with our work in applying evolutionary theory. Quite the contrary, in fact.

The core areas Pagel addresses are: Descent with Modification, Variation, Speciation and Adaptation. These concepts are interwoven with questions about the nature of tinkering and perfection and Gouldian contingency. Since Pagel’s Insight is itself a well adapted summary of a huge set of questions, it would be absurd for me to summarize it for you here. Just get it and read it. But I will make a few comments on selected items.

Pagel, because he just can’t stop himself from doing this sort of thing, compiled and analyzed a huge data set. This consisted of papers “that include the term ‘natural selection’ in their title, abstract or keywords, recorded separately for subject areas as identified by the ISI Web of Knowledge. Data are derived from a search on ‘natural selection’ in November 2008, yielding 14,232 hits over all years.”

From this he produces a graph that shows several interesting things. For instance, there is a huge range of subject areas in which Natural Selection appears non-trivially. Genetics and Heritability and Evolutionary biology unsurprisingly top the list. Psychology, Nutrition, and Pathology are modestly represented. Meteorology sports several hundred papers with the term. The lowest number is found in Chemistry.

Alarming and disturbing, not to mention annoying, is the fact that the lower-ranked subject areas include most of the medical subjects. This underscores my long time assertion that medical research pays an insufficient level of attention to Evolutionary Theory.

Pagel is a wanton adaptationist. In a paper some years ago, he articulated a position on adaptation that I have slightly modified and named after him, which I call Pagel’s Wager. Pagel’s Wager is this: If you observe a heritable system in nature, bet it is an adaptation. You’ll usually win the bet. More importantly, the cost of betting against a heritable system being an adaptation is very high. You miss getting to work on (or at least think about) something interesting.

In the paper under consideration, Pagel summarizes his current thinking on this:

Which view is correct? Not everything is an adaptation: human blood just happens to be red, and human chins might be relics of the way the human jaw develops. But the weight of evidence suggests that it is probably wise not to bet against natural selection. The struggle for existence means that traits have to pay their way. The traits observed now probably improve an animal’s chances of surviving and propagating, and those traits that do not will tend to be lost. For example, fish that have adapted to life in dark underwater caves lose the ability to see.

I have also defined another biological guideline called Pagel’s Rule. He does not address this concept in the Nature Insight piece, but I’m inclined to give it to you anyway:

“In considering two or more adaptationist explanations for a given trait, where all else is equal, determine which is the most insidious or evil. That is likely to be the correct explanation.”

Regarding contingency, Pagel makes an interesting comment (referring to a paper in the same issue of Nature). As you will already be aware, the “contingency” concept, championed by Stephen Jay Gould, is that if you play the ‘tape of evolution’ again and again, you will get quite different results each time. Pagel mentions what might be Gould’s favorite example of this phenomenon: If the whopping big object that hit the earth about 65 million years ago missed, the evolution of mammals would have been a very different story, and it is likely that not even Stephen Jay Gould himself would have evolved. (Well, SJG did not put it exactly that way ….). Pagel reviews some of the evidence testing this idea and concludes that “Contingency does not seem to be the pervasive force that Gould suspected.” And he’s got a point.

Pagel crams a LOT more into this small paper, including commentary on human evolution and human language, co-evolution, and speciation. I’ll leave you with this bit on Darwin and diversification:

The size and details of monophyletic groups illustrate an important feature of life. Rather than designing each species from scratch, as an engineer might, evolution is conservative, using the same designs over and over. Darwin recognized, as the comparative anatomist Geoffroy Saint-Hilaire had before, that the hands of moles, horses, porpoises and bats all used the same bones.

Please find the paper, read it, and enjoy it. Link and references below.

Since I’m sitting at a computer that automatically puts me through to Nature, I am not absolutely certain, but I think you can access the article here.

Mark Pagel (2009). Natural selection 150 years on Nature, 457 (7231), 808-811 DOI: 10.1038/nature07889

reposted

In the vicinity of Rio Tercero…

Hearing … of the remains of one of the old giants, which a man told me he had seen on the banks of the Parana, I procured a canoe, and proceeded to the place. Two groups of immense bones projected in bold relief from the perpendicular cliff [but] I could only bring away small fragments of one of the great molar-teeth … sufficient to show that the remains belonged to a species of Mastodon. The men who took me in the canoe, said they had long known of them, and had often wondered how they had got there: the necessity of a theory being felt, they came to the conclusion, that … the mastodon formerly was a burrowing animal!

In remote St. Fe …

A tooth which I discovered … interested me much, for I at once perceived that it had belonged to a horse. Feeling much surprise at this, I carefully examined its geological position, and was compelled to come to the conclusion, that a horse, which cannot … be distinguished from the existing species, lived as a contemporary with the various great monsters that formerly inhabited South America. Mr. Owen and myself, at the College of Surgeons, compared this tooth with a fragment of another, probably belonging to the Toxodon, which was embedded at the distance only of a few yards in the same earthy mass. No sensible difference in their state of decay could be perceived; they were both tender, and partially stained red. … Certainly it is a marvellous event in the history of animals, that a native kind should have disappeared to be succeeded in after ages by the countless herds introduced with the Spanish colonist! But our surprise should be modified when it is already known, that the remains of the Mastodon angustidens (the tooth formerly alluded to as embedded near that of the horse, probably belonged to this species) have been found both in South America, and in the southern parts of Europe.

Weighty considerations of the distribution of extinct and extant fauna lead Darwin to the neighborhood of modern geological concepts.

Very few species of living quadrupeds, which are altogether terrestrial in their habits, are common to the two continents, and these few are chiefly confined to the extreme frozen regions of the north. The separation, therefore, of the Asiatic and American zoological provinces appears formerly to have been less perfect than at present. The remains of the elephant and of the ox have been found on the banks of the Anadir (long. 175° E.), on the extreme part of Siberia, nearest the American coast: and the former remains, according to Chamisso, are common in the peninsula of Kamtschatka. On the opposite shores, likewise, of the narrow strait which divides these two great continents, we know, from the discoveries of Kotzebue and Beechey, that the remains of both animals occur abundantly: and as Dr. Buckland has shown they are associated with the bones of the horse, the teeth of which animal in Europe, according to Cuvier, accompany by thousands the remains of the pachydermata of the later periods. With these facts, we may safely look at this quarter, as the line of communication (now interrupted by the steady progress of geological change) by which the elephant, the ox, and the horse, entered America, and peopled its wide extent.

Now, here we have Darwin on the verge of understanding the rise of the Panama Land bridge (or something like that) based on the biogeography. The above passage, the following passage, and other material is very frustrating. If Darwin was not such a geological gradualist he could have advanced geology to the 1950s with a single fell swoop of reasoning!!!!

The occurrence of the fossil horse and of Mastodon angustidens in South America, is a much more remarkable circumstance than that of the animals mentioned above in the northern half of the continent; for if we divide America, not by the Isthmus of Panama, but by the southern part of Mexico, .. where the great table-land presents an obstacle to the migration of species, … we shall then have two zoological provinces strongly contrasted with each other. Some few species alone have passed the barrier, and may be considered as wanderers, such as the puma, opossum, kinkajou, and peccari. The mammalogy of South America is characterized by possessing several species of the genera of llama, …, tapir, peccari, opossum, anteater, sloth, and armadillo. If North America had possessed species of these genera proper to it, the distinction of the two provinces could not have been drawn; but the presence of a few wanderers scarcely affects the case. North America, on the other hand, is characterized by its numerous rodents, and by four genera of solid horned ruminants, of which section the southern half does not possess a single species.

Just so you know, South and North America were separated, and had largely independent mammalian evolution (and migration), until very recently, about five million years ago, when the isthmus of Panama was raised.

Darwin is seeing the very time-deep echo of this event, masked by subsequent migration of North American mammals in to South America, and clouded by the more pressing (to him) question of Old World and New World relationships.

It is interesting that the monkey’s (appearing in both the old world and new world tropics) don’t freak him out. They freak me out.

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Struthio Rhea

I will now give an account of … the Struthio Rhea, or South American ostrich. This bird is well known to abound over the plains of Northern Patagonia, and the united provinces of La Plata. It has not crossed the Cordillera; but I have seen it within the first range of mountains on the Uspallata plain…. The ordinary habits of the ostrich are familiar to every one. They feed on vegetable matter; such as roots and grass; but at Bahia Blanca, I have repeatedly seen three or four come down at low water to the extensive mud-banks which are then dry, for the sake, as the Gauchos say, of catching small fish. Although the ostrich in its habits is so shy, wary, and solitary, and although so fleet in its pace, it falls a prey, without much difficulty, to the Indian or Gaucho armed with the bolas. When several horsemen appear in a semicircle, it becomes confounded, and does not know which way to escape. They generally prefer running against the wind; yet at the first start they expand their wings, and like a vessel make all sail. On one fine hot day I saw several ostriches enter a bed of tall rushes, where they squatted concealed, till quite closely approached. It is not generally known that ostriches readily take to the water. Mr. King informs me that at the Bay of San Blas, and at Port Valdes in Patagonia, he saw these birds swimming several times from island to island. …When swimming, very little of their bodies appear above water, and their necks are extended a little forward: their progress is slow. On two occasions, I saw some ostriches swimming across the Santa

The following passage is thought by some Darwin scholars to reflect one of Darwin’s most significant “aha” moments, leading to his understanding of evolutionary processes. The bird described here is known as the Avestruz Petise, and was named by the ornithologist Gould as Rhea darwinii. However,since the bird was earlier named (based on reports, not specimens) Pterocnemia pennata (the Lesser rhea), Darwin’s name does not survive today in the annals of taxonomy.

Read the passage then I’ll note its presumed significance.

…I repeatedly heard the Gauchos talking of a very rare bird which they called Avestruz Petise. They described it as being less than the common ostrich (which is there abundant), but with a very close general resemblance. … The few inhabitants who had seen both kinds, affirmed they could distinguish them apart from a long distance. … This species occurs most rarely on the plains bordering the Rio Negro; but about a degree and a half further south they are tolerably abundant. …They are said to prefer the plains near the sea. When at Port Desire, in Patagonia (lat. 48°), Mr. Martens shot an ostrich; and I looked at it, forgetting at the moment, in the most unaccountable manner, the whole subject of the Petises, and thought it was a two-third grown one of the common sort. The bird was cooked and eaten before my memory returned. Fortunately the head, neck, legs, wings, many of the larger feathers, and a large part of the skin, had been preserved. From these a very nearly perfect specimen has been put together, and is now exhibited in the museum of the Zoological Society. Mr. Gould, who in describing this new species did me the honour of calling it after my name, states, that besides the smaller size and different colour of the plumage, the beak is of considerably less proportional dimensions than in the common Rhea …

Eventually, Darwin made note of the fact that over time, distinct but similar species seemed to differ by grades (such as in size) in the fossil record, as and the same pattern could be seen across geographical space. In his notebooks, he was to eventually note that the variation across space and time seemed to be two ways of looking at the same pattern of change. He made the link between biographical variation in the Rhea and the finches on the Galapagos and similar variation seen in the fossil fauna such as discussed here, along the South American Atlantic coast.

In a note book dated to “1836 and after” (late in the voyage), Darwin wrote a passage that has been the focus of a great deal of attention. In it, he demonstrates his waffling about the nature of species. He frames his introspection in terms of “creation” and at the same time struggles with the evidence from biogeography, which suggests that closely related species would have a common ancestor. He also addresses extinction. Darwin is essentially asking “… where are the transitional forms?”

Remember, this is his notebook writing … it is very much stream of consciousness, conflicting, and hard to understand. I’ll provide you with the entire relevant passage unedited except for the removal of some geologizing. It is painful and wonderful at the same time:

Speculate on neutral ground for 2 Ostriches: bigger one encroaches on smaller;–change not progressive; produced at one blow, if one species altered. …

Should urge that extinct Llama owed its death not to change of circumstances; reversed argument, knowing it to be a desert. Tempted to believe animals created for definite time:–not extinguished by change of circumstances.

The same kind of relation that common ostrich bears to Petisse–[S. Darwinii] and difft. kinds of extinct Guanaco to recent. In former case position, in latter time (or changes consequent on lapse), being the relation, as in first cases distinct species inosculate [To pass into; to join or unite so as to become continuous; to blend] so must we believe ancient ones [did] not gradual change or degeneration from circumstances, if one species does change into another it must be per saltum–or species may perish. This representation of species important, each its own limit and represented. Chiloe creeper; Fournarius, Callandria. Inosculation alone shows not gradation.

an animal in two (gemmiparous by nature or by accident) we see an individual divided either at one moment or through lapse of ages. Therefore we are not so much surprised at seeing Zoophite producing distinct animals, still partly united, & egg which becomes quite separate. Considering all individuals of all species as each one individual divided by different methods, associated life only adds one other method where the division is not perfect.

Dogs, Cats, Horses, Cattle, Goat, Asses, have all run wild and bred, no doubt with perfect success. Showing how creation does not bear upon solely adaptation of animals. Extinction in same manner may not depend. There is no more wonder in extinction of species than of individual.

When we see Avestruz [the Petisse or smaller Ostrich, Struthio Darwinii] two species certainly different, not insensible change; yet one is urged to look to common parent? Why should two of the most closely allied species occur in same country? In botany instances diametrically opposite have been instanced–

Of this passage, Nora Barlow (in her publication on these notebooks) wrote, in 1945:

We can see the mill at work, grinding out hypotheses. … In biological fields the throes of question and doubt, of comparison of masses of facts, of discardings and reviewing, were still to continue for 23 years before the Theory of Evolution as we know it, found expression.

Well said, Nora.

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Bahia Blanca is a port at the northern end of Patagonia. Chapter V of The Voyage begins:

THE Beagle arrived on the 24th of August, and a week afterwards sailed for the Plata. With Captain Fitzroy’s consent I was left behind, to travel by land to Buenos Ayres.

I tried Googling that … using “get directions.” Google maps was unable to compute a route. In fact, Google Maps has no roads whatsoever in Argentina. But, I was able to make a map showing the two locations, to give you an idea of what this must have been like. Darwin walked (well, there were horses) between these two points:

And along the way, he found some fossils. Here are brief excerpts describing some of his finds. As you read through this (it’s long, but I’ve tried to edit it down as much as possible) keep in mind the following things: Evidence for evolution, climate change, large scale global synthesis, connections between observations and theory. It is all here. This is Darwin coming to an understanding of the Big Picture of Evolution.

At Punta Alta, a low cliff, about twenty feet high, exposes a mass of [sediment] containing numerous recent shells. We may believe a similar accumulation would now take place … where tides and waves were opposed. In the gravel a considerable number of bones were embedded. … the following list may give some idea of their nature: 1st, a tolerably perfect head of a megatherium, and a fragment and teeth of two others; 2d, an animal of the order Edentata, as large as a pony, and with great scratching claws; 3d and 4th, two great Edentata related to the megatherium, and both fully as large as an ox or horse; 5th, another equally large animal, closely allied or perhaps identical with the Toxodon …, which had very flat grinding teeth, somewhat resembling those of a rodent; 6th, a large piece of the tesselated covering like that of the armadillo, but of gigantic size; 7th, a tusk which in its prismatic form, and in the disposition of the enamel, closely resembles that of the African boar; it is probable that it belonged to the same animal with the singular flat grinders. Lastly, a tooth in the same state of decay with the others: … but the part that is perfect, resembles in every respect the tooth of the common horse.* … the space in which they were collected could not have exceeded one hundred and fifty yards square. It is a remarkable circumstance that so many different species should be found together; and it proves how numerous in kind the ancient inhabitants of this country must have been.

… in another cliff of red earth, I found several fragments of bones. Among them were the teeth of a rodent, much narrower, but even larger than those of the Hydrochærus capybara; the animal which has been mentioned as exceeding in dimensions every existing member of its order. There was also part of the head of a Ctenomys; the species being different from the Tucutuco, but with a close general resemblance.

The remains … were associated … with shells of existing species. … similar to the species now living in the same bay: it is also very remarkable, that not only the species, but the proportional numbers of each kind, are nearly the same [as the modern fauna] … If I had not collected living specimens from the same bay, some of the fossils would have been thought extinct … We may feel certain that the bones have not been washed out of an older formation, and embedded in a more recent one, because the remains of one of the Edentata were lying in their proper relative position (and partly so in a second case) …

…

From the shells being littoral species … we may feel absolutely certain that the remains were embedded in a shallow sea, not far from the coast. From the position of the skeleton being undisturbed, and likewise from the fact that full-grown serpulæ were attached to some of the bones, we know that the mass could not have been accumulated on the beach itself. …

From the general structure of the coast of this part of South America, we are compelled to believe, that the changes of [elevation] have … of late … been in one direction, and … very gradual. If, then, we look back to the period when these quadrupeds lived, the land probably stood at a level, less elevated only by a few fathoms than at present. Therefore, its general configuration since that epoch cannot have been greatly modified; …

The surrounding country, as may have been gathered from this journal, is of a very desert character. … Here, then, is an apparent difficulty: we have the strongest evidence that there has occurred no great physical change to modify the features of the country, yet in former days, numerous large animals were supported on the plains now covered by a thin and scanty vegetation.

That large animals require a luxuriant vegetation, has been a general assumption, which has passed from one work to another. I do not hesitate, however, to say that it is completely false; and that it has vitiated the reasoning of geologists, on some points of great interest in the ancient history of the world. The prejudice has probably been derived from India, and the Indian islands, where troops of elephants, noble forests, and impenetrable jungles, are associated together in every account. If, on the other hand, we refer to any work of travels through the southern parts of Africa, we shall find allusions in almost every page either to the desert character of the country, or to the numbers of large animals inhabiting it. The same thing is rendered evident by the many sketches which have been published of various parts of the interior. When the Beagle was at Cape Town, I rode a few leagues into the country, which at least was sufficient to render that which I had read more fully intelligible.

Well, you don’t really want to hit at Gaucho … they hit back rather hard….

The Gauchos are the cowboys of the so-called Southern Cone and Pampas. The Gauchos are a Latin American version the horse mounted pastoralists that emerge wherever four things are found together: Grasslands, horses, people and cattle. Like all horse-mounted pastoralists, they have been known to have certain cultural tendencies or traits. These include being incredibly good horse riders. It includes a disdain for any sort of locomotion that does not involve a horse. The Gauchos are held in high esteem as a symbol of trustworthiness and strength, this symbol commonly exploited in regional politics in Argentina and Brazil, or by sports teams (in a mascot-like fashion), even in North America.

The Gauchos are beings with four hooved-legs and two heads because a Gaucho is nothing without his horse. Most wars in the region required Gaucho calvary.

Darwin spent a fair amount of time among the Gauchos, and both Darwin and Fitzroy wrote quite a bit about them.

Darwin mentions the Gauchos as part of the calvary in play during junta’s more or less ongoing in Monte Video, in his July and August entries in one of his notebooks. In Baia Blanca, traveling (and getting lost) in a small boat, he gives us a flavor in this entry of September 7th, 1832, of the Gaucho as an exotic entity from the perspective of an English gentleman:

In the evening we arrived at the creek … — There were several of the wild Gaucho cavalry waiting to see us land; they formed by far the most savage picturesque group I ever beheld. — I should have fancied myself in the middle of Turkey by their dresses. — Round their waists they had bright coloured shawls forming a petticoat, beneath which were fringed drawers. Their boots were very singular, they are made from the … hide of the hock joint of horses hind legs, so that it is a tube with a bend in it; this they put on fresh, & thus drying on their legs is never again removed. — The spurs are enormous, the rowels being from one to two inches long. — They all wore the Poncho, which is large shawl with a hole in the middle for the head. — Thus equipped with sabres & short muskets they were mounted on powerful horses. — The men themselves were far more remarkable than their dresses; the greater number were half Spaniard & Indian — some of each pure blood & some black. — The Indians, whilst gnawing bones of beef, looked, as they are, half recalled wild beasts. — No painter ever imagined so wild a set of expressions. …

On October 8th, Darwin notes in the same journal:

The Captain had bought from the Gaucho soldiers a large Puma or South American lion, & this morning it was killed for its skin. — These animals are common in the Pampas, I have frequently seen their … footsteps in my walks: it is said they will not attack a man; though they evidently are quite strong enough. — The Gauchos secured this one; by first throwing the balls & entangling its front legs, they then lassoed or noosed him, when by riding round a bush & throwing other lasso’s, he was soon lashed firm and secure.
The “Balls” he refers to is the boleadoras … a triplet of stone, wood, or metal spheres wrapped in leather and fastened to each other by ropes or thongs, swung over the head and thrown as a very effective hunting tool. You bind up and whack (with the three rocks) whatever you are going after.

In August 1833, Darwin arranged a trip inland with Gaucho guides in the vicinity of Rio Negro. His track across land to Buenos Ayres was considered dangerous unless the travel party was well guarded. He traveled with Gauchos and local Indians, and made many observations not only of the landscape but also of local custom.

Shortly after passing the first spring we came in sight of the famous tree, which the Indians reverence as a God itself, or as the altar of Walleechu. — It is situated on a high part of the plain & hence is a landmark visible at a great distance. — As soon as a tribe of Indians come in sight they offer their adorations by loud shouts. — The tree itself is low & much branched & thorny, just above the root its apparent diameter is 3 feet. It stands by itself without any neighbour, & was indeed the first tree we met with; afterwards there were others of the same sort, but not common.

Being winter the tree had no leaves, but in their place were countless threads by which various offerings had been suspended. Cigars, bread, meat, pieces of cloth &c &c. — poor people only pulled a thread out of their ponchos. — The Indians both pour spirit & mattee into a hole & likewise smoke upwards, thinking thus to afford all possible gratification to Walleechu. — To complete the scene the tree was surrounded by the bleached bones of horses slaughtered as sacrifices. All Indians of every age & sex make their offerings, they then think that their horses will not tire & that they shall be prosperous. — In the time of peace the Gauchos who told me this had been witnesses of the scene; they used to wait till the Indians passed on & then steal from Walleechu their offerings. The Gauchos think that the Indians consider the tree itself as a God; but it seems far more probable that it is an altar.

Apparently the Gaucho shared the almost universal belief among cattle pastoralists that “All cattle are mine…”

About two leagues beyond this very curious tree & 11 from the town we halted for the night: at this instant an unfortunate cow was spied by the lynx-eyed Gauchos. Off we set in chase & in a few minutes she was dragged in by the Lazo & slaughtered.

And despite what might be thought of as “civilized disdain” for these people, Darwin also showed an empathy for the Gaucho way of life…

— We here had the four necessaries for …life “en el campo”,-pasture for the horses, — water (only a muddy puddle) — meat — & fire wood. The Gauchos were in high spirits at finding all these luxuries, & we soon set to work at the poor cow. — This was the first night which I passed under the open sky with the gear of the Recado for a bed. There is high enjoyment in the independence of the Gaucho life, to be able at any moment to pull up your horse and say here we will pass the night. The death-like stillness of the plain, the dogs keeping watch, the gipsy group of Gauchos making their beds around the fire, has left in my mind a strongly marked picture of this first night, which will not soon be forgotten.

The above references are all from one of Darwin’s notebooks. In his more formal writing for publication, we find more eloquent descriptions.

…their appearance is very striking; they are generally tall and handsome, but with a proud and dissolute expression of countenance. They frequently wear their moustaches, and long black hair curling down their backs. With their brightly-coloured garments, great spurs clanking about their heels, and knives stuck as daggers (and often so used) at their waists, they look a very different race of men from what might be expected from their name of Gauchos, or simple countrymen. Their politeness is excessive : they never drink their spirits without expecting you to taste it; but whilst making their exceedingly graceful bow, they seem quite as ready, if occasion offered, to cut our throat.

The Gaucho, when he is going to use the lazo, keeps a small coil in his bridle hand, and in the other holds the running noose, which is made very large, generally having a diameter of about eight feet. This he whirls round his head, and by the dexterous movement of his wrist keeps the noose open; then, throwing it, he causes it to fall on any particular spot he chooses. … The bolas, or balls, are of two kinds: the simplest, which is chiefly used for catching ostriches, consists of two round stones, covered with leather, and united by a thin plaited thong, about eight feet long. The other kind differs only, in having three balls united by the thongs to a common centre. The Gaucho holds the smallest of the three in his hand, and whirls the other two round and round his head; then, taking aim, sends them like chain shot revolving through the air. The balls no sooner strike any object, than, winding round it, they cross each other, and become firmly hitched. The size and weight of the balls varies, according to the purpose for which they are made: when of stone, although not so large as a big apple, yet they are sent with such force as sometimes to break the leg even of a horse. I have seen the balls made of wood, and as large as a turnip, for the sake of catching these animals without injuring them. The balls are sometimes made of iron, and these can be hurled to the greatest distance. The main difficulty in using either lazo or bolas, is to ride so well, as to be able at full speed, and while suddenly turning about, to whirl them so steadily round the head, as to take aim: on foot any person would soon learn the art. One day, as I was amusing myself by galloping and whirling the balls round my head, by accident the free one struck a bush; and its revolving motion being thus destroyed, it immediately fell to the ground, and like magic caught one hind leg of my horse; the other ball was then jerked out of my hand, and the horse fairly secured. Luckily he was an old practised animal, and knew what it meant; otherwise he would probably have kicked till he had thrown himself down. The Gauchos roared with laughter; they cried they had seen every sort of animal caught, but had never before seen a man caught by himself.

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Years later, according to this story, Sebastian Cabot came to this area and discovered an unusually large native who appears to have been a European cabin boy in that early ill-fated shore party, saved and brought up by the natives. He was brought back to Europe, and later returned to La Plata where he was never seen again.

There are multiple versions of this story, but it is similar to dozens of cases of trans-Atlantic culture contact of one kind or another. One of the more famous of these stories is related in Darwin’s Voyage, and we’ll get to that later.

As the Beagle passed farther south, the (relatively) cosmopolitan nature of the coastal communities gave way to a much more frontier-like setting, becoming increasingly stranger and increasingly dangerous (at least in perception) to the traveling Europeans. The coastline also became increasingly unknown, and since the Beagle’s primary mission was to map this coast line, Darwin spent a lot of time in this area (two years, approximately). This meant that he did not need to chose between biologizing, geologizing, or getting to know the locals. He did all three in abundance.

I staid ten weeks at Maldonado [Near Montevideo], in which time a nearly perfect collection of the animals, birds, and reptiles, was procured. Before making any observations respecting them, I will give an account of a little excursion I made as far as the river Polanco, which is about seventy miles distant, in a northerly direction. I may mention, as a proof how cheap every thing is in this country, that I paid only two dollars a day, or eight shillings, for two men, together with a troop of about a dozen riding-horses. My companions were well armed with pistols and sabres; a precaution which I thought rather unnecessary; but the first piece of news we heard was, that, the day before, a traveller from Monte Video had been found dead on the road, with his throat cut. This happened close to a cross, the record of a former murder.

I am especially fond of the following passage, but it requires some explanation (as does my fondness for it).

Euro-Americans are kind of stupid when it comes to certain things, one being how to assess the “intelligence” or abilities of other people. The way it works with many Euro-Americans is this: You have a way of doing things, and know it is good and right. You also have a body of knowledge and know that it is appropriate and proper. Now, everyone else who does not share your behavior and body of knowledge must, therefore, be lesser in a number of ways. Of lesser intelligence, of lesser education, of lesser ability, etc.

(See this example)

This is of course a very ethnocentric, cultural-centric and ego-centric viewpoint. What many Euro-Americans do not know are the following two things: 1) Not everyone else, in other cultures, views the world this way; and 2) A thoughtful examination of these ways of acting and knowing will reveal that they are not the only or best ways.

Having said this, it is important to realize that when someone from “The West” arrives in some other part of the world, there will often be a conflict in knowledge or ability in many areas where the European is the one who knows the cool things or has the cool stuff. Or the reverse. This conflict is what drives some people to explore other parts of the world, to understand these differences and enjoy them. I spent a fair amount of time living in the Central African rain forest doing just this, trying to understand the ways of life of people who were good at, and knew about, totally different things than myself.

Many of my fondest memories of those experiences center on these conflicts. Like the time that four Efe (Pygmy) men asked me to borrow a blanket. It was night, very cold, and we had no shelter. All I had to give them was a folded up sheet that I had taken from the store room at the research camp 12 kilometers away. This was a sheet I had not folded or put away … it was just sitting there on the shelf.

It turned out that this was a very thin cotton king-size sheet. If an Efe person (remember, they are very small people) has a piece of cloth of their own, it will be a maximum size of about 1.2 meters by 1 meter in size, but usually this would be cut into three pieces to be shared. This king size sheet was way, way bigger, but it did not look as big when it was still folded up.

So, I handed the folded sheet to one of these guys. He unfolded it once, then again, and at this point it is about the size of one of their own cloths. Then he unfolded it again. And again. And it was now huge. At this point, they are laughing at the absurdity of how large this sheet is. Of course, they totally get the size difference between “us and them” (although we all forgot this difference far more often than we cognized it). They thought of me as absurdly large. Whenever I would encounter some object of theirs that was really really small (like a house or a “chair”) I would be struck by the size differences of the people and their artifacts, and the same in reverse happened. One (or maybe two) more unfoldings, and this sheet was large enough to cover two of their houses. They did not stop laughing for a very long time. They are probably still laughing.

Similarly, this: A central part of my research involved mapping everything in, so I had mapping tools. Meanwhile, the Efe already knew where most things were … they were familiar with the geography of their neighborhood. But of course, I wanted to know the limits and extent of their knowledge. What was their mental map like, and how did it differ from an “objective” map, made with my mapping tools. As a result, I was often asking them where things were, but with the guys I was working with most of the time, I also showed them how my mapping tools (including a compass) worked. After a year and a half or a bit less, I was able to navigate myself around their territories as well as they could, and in some cases, when we were all lost, it was me, and not them, finding the way to a known point, using my trusty compass.

With that in mind, let’s see what Darwin wrote…

On the first night we slept at a retired little country-house; and there I soon found out, that I possessed two or three articles, especially a pocket compass, which created unbounded astonishment. In every house I was asked to show the compass, and by its aid, together with a map, to point out the direction of various places. It excited the liveliest admiration that I, a perfect stranger, should know the road (for direction and road are synonymous in this open country) to places where I had never been. At one house a young woman, who was ill in bed, sent to entreat me to come and show her the compass. If their surprise was great, mine was greater, to find such ignorance among people who possessed their thousands of cattle, and “estancias” of great extent. It can only be accounted for by the circumstance that this retired part of the country is seldom visited by foreigners. I was asked whether the earth or sun moved; whether it was hotter or colder to the north; where Spain was, and many other such questions. The greater number of the inhabitants had an indistinct idea that England, London, and North America, were different names for the same place; but the better informed well knew that London and North America were separate countries close together, and that England was a large town in London! I carried with me some promethean matches, which I ignited by biting; it was thought so wonderful that a man should strike fire with his teeth, that it was usual to collect the whole family to see it: I was once offered a dollar for a single one. Washing my face in the morning, caused much speculation at the village of Las Minas; a superior tradesman closely cross-questioned me about so singular a practice; and likewise why on board we wore our beards; for he had heard from my guide that we did so. He eyed me with much suspicion; perhaps he had heard of ablutions in the Mahomedan religion, and knowing me to be a heretick, probably he came to the conclusion that all hereticks were Turks. It is the general custom in this country to ask for a night’s lodging at the first convenient house. The astonishment at the compass, and my other feats in jugglery, was to a certain degree advantageous, as with that, and the long stories my guides told of my breaking stones, knowing venemous from harmless snakes, collecting insects, &c., I repaid them for their hospitality. I am writing as if I had been among the inhabitants of central Africa: Banda Oriental would not be flattered by the comparison; but such were my feelings at the time.

See also:

Verdesio, Gustavo. (2001) Forgotten Conquests: Rereading New World History from the Margins. Temple University Press.

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.There 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:Click 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

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