Thursday, January 22, 2009

Tonya's Comments on the Introduction and Chapters I-II

My turn :)

p5) As many more individuals of each species are born than can possibly survive, there is frequently a recurring struggle for existence

This idea of a struggle for existence can mean many things. For instance, it can be an aggressive struggle such as when a food supply diminishes, or it can be a passive struggle (e.g. individuals being killed off by a deadly virus).

Natural selection almost inevitably causes much Extinction of the less improved forms...

Does he really have to use the term 'less improved'? Yes, I agree in a certain context they are less improved because they went extinct in a certain situation, but perhaps if the situation would be different then they would be the improved form.

I'm not really liking the subchapter headings posted at the top of each chapter and not above the paragraphs associated with each topic. I guess I am supposed to guess which paragraph goes with each topic (not that it is hard, it is just annoying).

p7) [individuals of the same variety or sub-variety of older cultivated plants and animals] generally differ much more from each other than do individuals of any one species or variety in a state of nature.

What?! Maybe I am not understanding this correctly but this cannot be true, can it?

Darwin thinks it is absurd that some people thing that every race which breeds true has had a wild prototype (p19) :)
Darwin also believes it is always best to study some special group (p20). Yay beetles!

p26) it is difficult, perhaps impossible, to bring forward one case of the hybrid offspring of two animals clearly distinct being themselves perfectly fertile.

Can anyone please explain this sentence to me?????

p36) Interesting tidbit: the barbarians of Tierra del Fuego would rather eat their old women over their dogs in dismal times. Hmm.

p40) We know nothing about the origin or history of any of our domestic breeds.

Awe Darwin, if only you knew how far we have come.

p42) Facility in preventing crosses is an important element of success in the formation of new races

Prezygotic and postzygotic mating barriers!

Interesting tidbit #2: cats are valued by women and children, not by men.

p52) I was very impressed with Darwins understanding of incipient species and that not all must attain the rank of species but there are a multitude of situations that can occur.

Here, Darwin describes a species as: a set of individuals closely resembling each other

p54) What does he mean when he states "plants low in the scale of organization". This is an odd way of writing about a plant with uncomplicated morphology, if that's what he even means.

p56) ...where many species of a genus have been formed, on an average many are still forming...

Is this an active area of modern research? Very interesting!

p57) large genera the amount of difference between the species is often exceedingly small.

Yes, (with my very limited experience) I would agree with this statement as this is true in Nicrophorus (Silphidae: Coleoptera) which has many species; however, the opposite is not true because in Brychius (Haliplidae: Coleoptera), there are only three species and they are really hard to tell apart.

Wednesday, January 21, 2009

Introduction and Chapters I-II notations

Some of a host of random notations and questions I had while reading through the first ~60 pages of OTOOS

p3) Naturalists continually refer to external conditions ... as the only possible cause of variation

Is this statement true? Did no one before Darwin publish an explanation for variation that relied on factors intrinsic to organisms?

p6) Furthermore, I am convinced that Natural Selection has been the main but not exclusive means of modification.

From the get-go, Darwin is making it clear that he thinks NS works in concert with other natural phenomena to modify the species of the world. It takes a while to get out of him what he thinks these other natural phenomena are but eventually he talks about them.

p8) But I am strongly inclined to suspect that the most frequent cause of variability may be attributed to the male and female reproductive elements having been affected prior to the act of conception.

Okay, in Chapter I he starts laying down the framework for how he thinks variability in organisms occurs. The problem is that ...this is massively generalistic and begs big questions. The (to use the modern terminology) gametes are affected? By what? By ...the organism's thoughts? By actions of the environment? By use and disuse? The answer here can't be NS because that's not going to affect reproductive elements, NS is only acting on whole organisms, not parts of them.

p11) Nevertheless some slight amount of change may, I think, be attributed to the direct action of the conditions of life -- as, in some cases, increased size from amount of food ...

So the conditions of life cause variation in organisms. Is this limited to that one individual in its life or is this something that becomes inheritable, e.g., an acquired characteristic? I'd say it's not but then a few sentences later...

The great and inherited development of the udders in cows and goats in countries where they are habitually milked ... is another instance of the effect of use. Not a single domestic animal can be named which has not in some country drooping ears; and the view suggested by some authors, that the drooping is due to the disuse of the muscles of the ear ... seems probable.

This is the beginning of a book full of comments that show that Darwin did not have a scientific problem with acquired characteristics; he just didn't think that they alone explained variation. If promoting acquired characteristics makes one a Lamarckist than Darwin is being a Lamarckist in OTOOS. (and I use the term Lamarckist in its general sorta pop-sci understanding of the term. Even wikipedia tells me that's too simplistic but ...just go with it)

p20-29 I won't quote but basically Darwin gives a great litany of well thought-out reasons why domesticated pigeons, even though they show amazing amounts of variation, must be descended from one ancestral species. It's weird reading this in a book full of Darwin deferring to popular opinion at the time that domesticated dogs must have descended from several ancestral species.

p32-42 Darwin is doing the best job he can at explaining out artificial selection as the driving force behind variation in domesticated species. And it's a great job: he establishes that breeders are picking up tiny, minute differences in their animals. He establishes that not all of these animals breed. He makes it certain to explain that breeders don't aim to make a new variety of, say, dog. No one sat down and decided to make a Dalmatian. But breeders picking small changes in generation after generation will eventually produce a new breed of dog. Artificial selection may be intelligently-driven but it does not have directionality, since breeders can't control what the next generation of bred organism will look like. Or, more to the point, breeders can't create novel features, they can merely select for them.

All Darwin has to do now is replace the word "artificial" with "natural" and "breeders" with "nature" and he can convince the reader that NS occurs.

p43) No one supposes that all the individuals of the same species are cast in the very same mould.

This became part of discussion today because the Mayr introduction to this OTOOS publication mentions how Darwin took species away from typological understanding into a population-level understanding. There was a lot said today about this and ...a lot more can easily be said about it. I don't have much to add.

p46) I am inclined to suspect that we see in these polymorphic genera variations in points of structure which are of no service or disservice to the species, and which consequently have not been seized on and rendered definite by natural selection.

Later in the text Darwin will come back to this with his commentary on how one should make phylogenetic trees (although, of course, he doesn't use that terminology.) But, when I read this, I fail to see how Kimuran neutral theory (or at least the first assertation of it) is in anyway contradictory to natural selection. DNA and RNA aren't organismal structures (they literally build strucutres) but if they're not under selection than they can be as neutral as they want to be.

Chapter II is generally a long discussion on how the "What is a species?" discussion will never have any definite winner. To cut to the chase...

p52) From these remarks it will be seen that I look at the term species, as one arbitrarily given for the sake of convenience to a set of individuals closely resembling each other, and that it does not essentially differ from the term variety, which is given to less distinct and more fluctuating forms.

In our modern biological world we could probably argue that species have definite molecular markers and that we could use those to define a "species", but even in that case there might be more unsampled populations out there which actually show a marker that is 'partway' between one defined species and another.

Embracing Darwin's worldview partially means embracing the idea that species are abstracts. In a Darwinian world, species barriers "break down" as we take modern-day populations of organisms and expose them to the fourth dimension. In so doing we see that somewhere the species we are tracing back in time start off as a 'variety' of another species, and that species the same, and so on and so on etc.

four-dimensional populations of organisms that are all more re n

Further thoughts on the Introduction and Chapters I-II

First, apologies to Shari, I only did a so-so job of keeping my mouth shut in class today. I will try to do better at keeping mum in future. Despite that, I do think we had a good discussion which raised a lot of issues that are well worth thinking about. A few further thoughts, in no particular order:

1. Darwin begins his introduction by emphasizing that he's not going off half-cocked--he's thought long and hard about the species problem and isn't being hasty. Clearly, Darwin was concerned with the reception he was going to get.

2. I find it both impressive and amusing that Darwin considered this book an abstract, far too short to include the many facts he'd collected to support his hypothesis. One can easily understand his reasons (see #1), but one can also be glad that he had an editor who recognized that at some point additional facts stop adding weight to the argument and instead end up obscuring it.

3. Interesting, in light of modern arguments about whether some version of creationism can/should be taught in science classes, to see "special creation" treated as a testable scientific hypothesis (and rejected not so much because the facts disprove it, but because of its failure to explain phenomena that Darwin's theory explains). Many scientists today would argue that creationism is not a scientific hypothesis at all, so that it doesn't make sense to talk about evaluating it as such. My own view is that creationism could be (and has been) pitched in both ways. For instance, if a creationist says that the world was created by God to appear as if evolution by natural selection had occurred (e.g., God created fossils in order to fool paleontologists), then that's not really scientific since the "hypothesis" is defined as "whatever's consistent with any conceivable evidence."

3a. There's a connection between #3 and long-standing philosophical issues of evidence and confirmation. Is it always bad for a theory to be consistent with the evidence "by definition"? What if a theory is developed in order to explain certain known facts, as Darwin's theory was? To what extent (if any) do those same facts count as evidence in support of the theory? After all, if the theory was developed in order to explain known facts, it couldn't possibly be inconsistent with those facts, so isn't the theory guaranteed to be "supported" by what's currently known? Put this way, it sounds like previously-known facts shouldn't count as evidence in favor of a theory. But there are many, many cases--The Origin being one example--in which known facts have been interpreted as supporting a theory that was developed to explain them. What justifies this? Is it that Darwin's theory can explain a wide variety of apparently-disparate facts, thereby "unifying" them? Does "unification" count as evidence in favor of a theory? Think of the common phrase "That explains a lot"...

4. Darwin is clearly worried that he can't offer a mechanistic theory of variation and inheritance. But does he really need one? This gets back to the issue of how to establish the domain of a scientific theory--how does one decide exactly what phenomena a given theory should explain/predict/unify? Why couldn't Darwin have said, without apology, "Organisms vary, and offspring tend to (but don't necessarily) exhibit the same variations as their parents. My theory shows how natural selection, acting on heritable variation, can give rise to new species. My theory is silent on where variation comes from in the first place, and why it is inherited. For my purposes, I will simply assume the brute empirical fact of heritable variation, which will hopefully be explained in future by some obscure monk." After all, every scientific theory takes for granted something that is explained by some other theory. For instance, the Modern Synthesis of Darwinian selection with Mendelian genetics takes for granted the underlying molecular and developmental mechanisms that drive transmission and development, and simply deals with the consequences of those mechanisms. At most, it seems to me that Darwin could've just said something about the features that any theory of variation would have to have in order to allow evolution by natural selection to occur (e.g., blending inheritance won't work, because all variation would be quickly eliminated, leaving none for selection to work on).

Darwin's theory of pangenesis

For reference, below is a quote from the 2nd ed. of Darwin's Variation (v. 2, 457), summarizing his theory of pangenesis:

"It is universally admitted that the cells or units of the body increase by self-division or proliferation, retaining the same nature, and that they ultimately become converted into the various tissues and substances of the body. But besides this means of increase I assume that the unites throw off minute granules which are dispersed throughout the whole system; that these, when supplied with proper nutriment, multiply by self-division, and are ultimately developed into units like those from which they were originally derived. These granules may be called gemmules. They are collected from all parts of the system to constitute the sexual elements, and their development in the next generation forms a new being; but they are likewise capable of transmission in a dormant state to future generations and may then be developed. Their development depends on their union with other partially developed or nascent cells which precede them in the regular course of growth...Gemmules are supposed to be thrown off by every unit, not only during the adult state, but during each stage of development of every organism; but not necessarily during the continued existence of the same unit. Lastly, I assume that the gemmules in their dormant state have a mutual affinity for each other, leading to their aggregation into buds or into the sexual elements. Hence, it is not the reproductive organs or buds which generate new organisms, but the units of which each individual is composed. These assumptions constitute the provisional hypothesis, which I have called Pangenesis."

When reading the Origin, keep in mind that Darwin developed his theory of pangenesis many years after he first developed and published the idea of evolution by natural selection.

Galton conducted blood transfusion experiments to test whether gemmules were carried in the blood. Galton and Darwin corresponded extensively about the design of these experiments and their results. Darwin was clearly reluctant to believe the negative results, and ended up criticizing the experiments in a letter to Nature after the results were published. That Darwin would criticize after the fact experiments that he heartily approved of before they were conducted is widely viewed as a rare instance of Darwin closing his mind to relevant data (and acting like a bit of a jerk).

Also, keep in mind that Mendel himself didn't actually propose an underlying mechanism to explain the statistical patterns of inheritance he observed. The aim of Darwin's theory of pangenesis was to serve as a concrete mechanism that would explain both transmission (inheritance) and development. To our modern eyes, Mendel's data cry out for an explanation in terms of genes on chromosomes--the mechanistic explanation almost seems to jump out of the data themselves. But that's not how things would've appeared to Darwin, had he been aware of Mendel's data. It's hard to say exactly how knowledge of Mendel's work might have affected Darwin's thinking.