Field of Science

Blogging the Origin: Chapter I: Variation Under Domestication

This has been a long time coming and Darwin's birthday and the anniversary of the publication of On the Origin of Species have come and gone. Despite all the other things I'm trying to do, I've missed posting and am taking steps to rectify that issue. Nevertheless, I read Chapter I Variation Under Domestication awhile ago and made a few notes.

First, let me start out by saying this is one of the hardest chapters to get through (so far, Im not done, but this chapter was excruciating at times). Compared to the elegance of some of his later prose, I wonder if this chapter was cobbled together at the last minute or if Darwin himself didn't care about the issues and simply wanted to get the information down.

If I could, I would go back in time and drop about 400 periods on Darwin's desk for him to use just for this chapter! Consider this sentence:
 All such changes of structure, whether extremely slight or strongly marked, which appear amongst many individuals living together, may be considered as the indefinite effects of the conditions of life on each individual organism, in nearly the same manner as the chill affects different men in an indefinite manner, according to their state of body or constitution, causing coughs or colds, rheumatism, or inflammation of various organs.
67 words. 8 commas. 1 period.  or this one
As a single bud out of the many thousands, produced year after year on the same tree under uniform conditions, has been known suddenly to assume a new character; and as buds on distinct trees, growing under different conditions, have sometimes yielded nearly the same variety—for instance, buds on peach-trees producing nectarines, and buds on common roses producing moss-roses—we clearly see that the nature of the conditions is of subordinate importance in comparison with the nature of the organism in determining each particular form of variation;—perhaps of not more importance than the nature of the spark, by which a mass of combustible matter is ignited, has in determining the nature of the flames.
113 words. 8 commas. 3 clause-related dashes. 2 semi-colons. 1 period.

I tell my students that if they can not read one of their own sentences without taking a breath, it's too long.

OK, enough with the bitching and moaning.

For me, the point of this chapter is to make it clear that variation exists. All squirrels are not the same, even those squirrels in my own backyard are not the same. We have to remember that the argument Darwin is making has not been made before. Evolution by natural selection as a concept did not exist. Darwin has a game plan to convince the reader of the 'truth' of his idea. Step 1 requires that organisms of the same species have variations. In this chapter he is using the domesticated animals and plants that numerous people (at least literate people) would be familiar with. A much greater percentage of the population had direct ties to agriculture then, compared to now. Also the wealthy, who tended to be the most educated, were often involved in various breeding programs for dogs, horses, roses, etc. Darwin was starting with an issue virtually everyone would be comfortable with. He is trying to convince his readers that organisms within a species vary, which is a concept everyone essentially knew and was familiar. The goal is to convince the bulldog dog breeder that the variations they observe are akin to the variations the rose horticulturalist sees which are akin to the variation the sheep farmer sees, etc. Basically all things vary from one another.

Here are some assorted thoughts....

1. Here's a shout out to any creationists who wanted a quote to use inappropriately. Within the very first paragraph, Darwin is wrong. He establishes that various domesticated species shown more variation than  natural species. Compare breeds of dogs with wolves or domesticated roses with wild roses. This appears to be true and I think it is. It's the conclusion I find faulty:
And if we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment, we are driven to conclude that this great variability is due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent species had been exposed under nature. (emphasis mine)
I argue that the natural species have to cope with so many diverse conditions that there is selection for a vast array of traits that are not necessary in the domesticated species. It's the lack of uniformity in nature which eliminates wolves that are hairless or weigh 200 pounds. Chihuahua sized wolves would have a difficult time taking down an elk (though they might do ok against rabbits). There are so many pressures on natural species that are removed on domesticated species that Darwin has it backwards here.

2. Darwin then makes an extremely important point.
No case is on record of a variable organism ceasing to vary under cultivation. Our oldest cultivated plants, such as wheat, still yield new varieties: our oldest, domesticated animals are still capable of rapid improvement or modification.
Variation continues even under prolonged domestication! From a genetic standpoint (Darwin didn't have access to this information), we'ld conclude that there are still extensive heterozygosities within the organism and that variants continue to arise (hmm, I wonder where those come from...). Regardless, this observation is key for later points he will make and I suggest you underline or highlight this passage in the book.

3. In the next section 'Effects of Habit and of the Use or Disuse of Parts; Correlated Variation; Inheritance', I think Darwin starts off by trying to incorporate ideas of Lamarck. He starts with three examples of Use or Disuse which is inherited.
I find in the (1) domestic duck that the bones of the wing weigh less and the bones of the leg more, in proportion to the whole skeleton, than do the same bones in the wild-duck; and this change may be safely attributed to the domestic duck flying much less, and walking more, than its wild parents. The great and inherited development of the (2) udders in cows and goats in countries where they are habitually milked, in comparison with these organs in other countries, is probably another instance of the effects of use. (3) Not one of our domestic animals can be named which has not in some country drooping ears; and the view which has been suggested that the drooping is due to disuse of the muscles of the ear, from the animals being seldom much alarmed, seems probable. (emphasis mine)
I find the ideas of use or disuse here problematic. Example 1, I think is basically sound; Examples 2 and 3, I think are wrong. It's not the use of the udder or the disuse of the ear muscles that made one big and the other droop. It's that the best milk producers, which had bigger udders, were not used for veal. The disuse of ear muscles did not lead to drooping, well it did, but the point is that people kept those cute flop earred bunnies from being eaten by foxes. In the case of ducks, stronger legs were beneficial and wings that allowed flight cost a lot to make and led to stress from having to be frequently clipped. My issue is with the cause-effect conclusion being made, not with the premise of variation and selection being alluded to.

4. Darwin envisions X-linked chromosomal traits without knowing it.
The laws governing inheritance are for the most part unknown. No one can say why the same peculiarity in different individuals of the same species, or in different species, is sometimes inherited and sometimes not so; why the child often reverts in certain characters to its grandfather or grandmother or more remote ancestor; why a peculiarity is often transmitted from one sex to both sexes, or to one sex alone, more commonly but not exclusively to the like sex. It is a fact of some importance to us, that peculiarities appearing in the males of our domestic breeds are often transmitted, either exclusively or in a much greater degree, to the males alone. (emphasis mine)
  5. In the next section 'Character of Domestic Varieties; Difficulty of Distinguishing between Varieties and Species; Origin of Domestic Varieties from One or More Species' Darwin makes what I think is the first argument that there is inherent variation in natural species.
I cannot doubt that if other animals and plants, equal in number to our domesticated productions, and belonging to equally diverse classes and countries, were taken from a state of nature, and could be made to breed for an equal number of generations under domestication, they would on an average vary as largely as the parent species of our existing domesticated productions have varied.
6. Dog breeds disorient even Darwin.
I have, after a laborious collection of all known facts, come to the conclusion that several wild species of Canidæ have been tamed, and that their blood, in some cases mingled together, flows in the veins of our domestic breeds.
Sorry all domesticated dogs descended from the gray wolf (or the gray wolf at the time). Even though the breeds show such profound morphological differences. He repeats this mistaken claim a couple of paragraphs later. (Not judging here, I have the advantage of molecular genetics and an additional 150 years of research and this book.)

7. Darwin hits on some early genetics without knowing it.
The offspring from the first cross between two pure breeds is tolerably and sometimes (as I have found with pigeons) quite uniform in character, and everything seems simple enough; but when these mongrels are crossed one with another for several generations, hardly two of them are alike and then the difficulty of the task becomes manifest.
If one organism that has a lot of homozygosity (2 alleles of a gene that are the same: AA, BB, CC instead of Aa Bb Cc for three distinct genes) is bred to another organisms that has a lot of homozygosity that is different from the first (aa, bb, cc), then the progeny will all be Aa Bb Cc, because they each get one allele from each parent. When we cross an Aa Bb Cc progeny to another Aa Bb Cc progeny we can get all kinds of offspring (AA Bb Cc or Aa BB cc or Aa bB CC or etc). From just this example with three genes, there are 27 different possible genotypes, of which I showed three genotypes.

8. Finally in the section 'Unconscious Selection' there are some interesting points.
On the view here given of the important part which selection by man has played, it becomes at once obvious, how it is that our domestic races show adaptation in their structure or in their habits to man’s wants or fancies. We can, I think, further understand the frequently abnormal characters of our domestic races, and likewise their differences being so great in external characters, and relatively so slight in internal parts or organs. Man can hardly select, or only with much difficulty, any deviation of structure excepting such as is externally visible; and indeed he rarely cares for what is internal. He can never act by selection, excepting on variations which are first given to him in some slight degree by nature. No man would ever try to make a fantail till he saw a pigeon with a tail developed in some slight degree in an unusual manner, or a pouter till he saw a pigeon with a crop of somewhat unusual size; and the more abnormal or unusual any character was when it first appeared, the more likely it would be to catch his attention. But to use such an expression as trying to make a fantail, is, I have no doubt, in most cases, utterly incorrect. The man who first selected a pigeon with a slightly larger tail, never dreamed what the descendants of that pigeon would become through long-continued, partly unconscious and partly methodical, selection. Perhaps the parent-bird of all fantails had only fourteen tail-feathers somewhat expanded, like the present Java fantail, or like individuals of other and distinct breeds, in which as many as seventeen tail-feathers have been counted. Perhaps the first pouter-pigeon did not inflate its crop much more than the turbit now does the upper part of its œsophagus,—a habit which is disregarded by all fanciers, as it is not one of the points of the breed. (emphasis mine)
I would like to point out that the prose has become more elegant and the passion and conviction Darwin has is palpable.

He dabbles in psychology.
Nor let it be thought that some great deviation of structure would be necessary to catch the fancier’s eye: he perceives extremely small differences, and it is in human nature to value any novelty, however slight, in one’s own possession.
Then comes a critical point:
These views appear to explain what has sometimes been noticed—namely, that we know hardly anything about the origin or history of any of our domestic breeds. But, in fact, a breed, like a dialect of a language, can hardly be said to have a distinct origin. man preserves and breeds from an individual with some slight deviation of structure, or takes more care than usual in matching his best animals, and thus improves them, and the improved animals slowly spread in the immediate neighbourhood.
And this conveys some of the awesome power that molecular genetics gives us. We know all dog breeds came from the parent species. We know broccoli, kale, and cabbage are descendants from the same progenitor. But Darwin didn't have genetics, DNA sequencing, or even knowledge that DNA carried the genetic code!

9. In the last section 'Circumstances Favourable to Man’s Power of Selection' we touch on some population genetics.
But probably the most important element is that the animal or plant should be so highly valued by man, that the closest attention is paid to even the slightest deviations in its qualities or structure.
and I would submit that those highly valued animals or plants are propagated at high numbers and those deviations are rapidly bred to increase the population size as fast as possible.

Finally, Darwin ends the chapter on a note Monsanto would find amusing.
With plants which are temporarily propagated by cuttings, buds, &c., the importance of crossing is immense; for the cultivator may here disregard the extreme variability both of hybrids and of mongrels, and the sterility of hybrids; but plants not propagated by seed are of little importance to us, for their endurance is only temporary. (emphasis mine)
So there are my overall thoughts and a bunch of tidbits of personal interest. What stood out to you?  

Fordham's review of state science standards

As a number of people have already pointed out, the Fordham Institute has released its 'The State of State Science Standards 2012'. This is of particular interest to me as I played a small role in developing the life sciences standards for Minnesota. I was disappointed to see that Minnesota only earned a C, and appalled that this is worse than the B the previous standards earned (more on that in another post if at all).
Can we really trust an evaluation that uses this color scheme?
Based on my experience as an course instructor, about this time I should be bouncing with delight because with so many D's and F's, the evaluators have to grade on a curve. What? there's no curve? That's not fair, Professor Lightweight curves. You know, my parents taxes pay your salary so you better fix my grade. I mean I worked really hard on these standards.... 

Anyway, I wanted to look at this in a little more detail to see if I could glean any insights. The short answer is I couldn't, but if you want to read a bit more feel free.

The reviewers broke down their evaluation into the following categories: Content & Rigor and Clarity & Specificity. Content & Rigor was further broken down into the sub-categories: Scientific Inquiry & Methodology, Physical Sciences, Physics, Chemistry, Earth & Space Science, and Life Sciences. As I played a role in the life sciences standards, I immediately  looked to see how Minnesota did....6/7! Not too shabby, if you ask me. Indeed the overall sense was that 'The treatment of life science and earth and space science is excellent'. YAY us. They noted that the 'flow and logic are such as to convey an understanding of the concepts rather than coming across as a list of topics to check off.' They also noted that the 'life science content is presented quite minimally'. This latter point reads like a negative, but I do not necessarily agree that a minimalistic approach is bad. By focusing on concepts and not specific content, we allow a teacher to deliver the material in a way they are most comfortable with. A teacher with a passion for gardening can deliver the genetics material using botanical examples, another with interests in infectious disease can use pathogenic bacteria. If the reviewers want to ding us for that, fine, I can live with it. Other aspects of the standards do seem to be problematic and I wonder if the reviewers were already annoyed when they evaluated the life science standards.

I was disappointed that the reviewers did not praise the evolution standards, because I spent considerable effort convincing my colleagues on the committee that evolutionary theory is a central and unifying concept in the life sciences that deserves being supported (ie let's stop using change over time and use the more concise term evolution). Of course, the reviewers did not attend a year+ of meetings and discussions so I'll excuse the slight.

The map released with the review (shown above) shows the overall ratings. However, I hypothesized that this review could be used to get a sense of how politics and cultural forces affect science standards. If this hypothesis is correct, then I predicted the life science scores would be most valuable (I don't see laws being discussed regarding the speed of light or the periodic table). So I mapped the life science scores and decided to use a color scheme that wasn't so shitty as the one the Fordham Institute used.
Purple is 7 and Grey is 0 (7 is high)
While I can pick and choose specific states and say 'AHA!' (like Oklahoma for instance), the data is not compelling. Kansas, not a beacon of life science education, earned a 7. There is really no correlation with political leanings or cultural issues that explain the spectrum of color. So my hypothesis is not correct, and I still learned something.

I also mapped Scientific Inquiry and Methodology to see what kind of results I'ld get.
How does Texas get a 7 when McLeroy was in charge?!?!
This is even worse, there's really no good distribution of scores. I don't think we can learn much from this either.

So what's going on? Well you have to realize every state is developing their standards using different ground rules. When we worked on our standards, we used the NAEP document as well as the revised standards of Massachusetts and Virginia (I think), both of which received a 9/10 overall score. However, there were rules (aka laws) that had to be followed. For instance in Minnesota, it was legislatively mandated that the science standards include reference to local indigenous peoples and their contributions to science. This was noted in the review 'Though a minor issue, the standards are occasionally marred by an inappropriate focus on local beliefs.' Every state does this process differently and this means that the standards documents are not being written the same way, they have slightly different goals, different authors (we were fortunate to have a plethora of K-12 teachers, a few scientists, and science related business people on our committee), and have different processes of approval.

What that means is that each standards document is a quite independent venture and there is not necessarily any connection between these documents in the different states. Thus, I find the review and evaluations to be sound as a mechanism to evaluate the strength of state science standards based on a clear criterion. However, I also find that a standards document does not necessarily predict learning outcome, teacher effectiveness, or reflect the state of science education in a particular state. While nationalizing the standards would set a bar, a standard if you will, I do not believe it is feasible in our current political and cultural climate.