Saturday, October 30, 2010

Chapter 8: Hybridization

In this chapter Darwin tackles the issue of reduced hybrid viability, believing that sterility was a by-product of the varied characteristics gained from two different species. To do so he mainly focuses on experiments done on plants and animals and the varied degrees of fertility of hybrids.

In a previous post I discussed wild hybridization and the ability of hybrids to survive in conditions that neither of their parent species thrive in. Many of Darwin's examples are of the intercrossing of closely related species, such as variety of cattle and geese. Darwin believed that the sterility of hybrids was caused by the incompatible crosses of reproductive organs. Today we know that sterility can arise through an incompatible number of chromosomes, a prominent example being mules. Horses and donkeys have different numbers of chromosomes and so the resulting Mule has an unpaired chromosome which leads to difficulty creating a viable embryo.

Darwin made a distinction between hybrids of distinct species and what he called "mongrels" or the offspring of distinct varieties of the same species. This difference leads to a powerful closing statement: "There is no fundamental distinction between species and varieties," (Darwin, 268) based on the observation that mongrels often have increased fertility.

The chapter is difficult to summarize without taking into account modern knowledge of hybridization. Darwin had no direct knowledge of pre and post zygotic barriers, but he did guess at the fact that some reproductive systems in hybrids were non-viable because the parent species were too incompatible.

Chapter 7: Instinct

Despite writing a whole chapter about instinct, Darwin states this right away, "I will not attempt any definition of instinct," (Darwin, 225) because apparently everyone understands what instinct is. If you're unsure, for purposes of this chapter it is inherent knowledge that does not need to be taught (eg, the location of ancestral breeding grounds, how to make a nest, etc).

Darwin muses on the similarities of instinct and habit for a bit, wondering if habits eventually become instinct. This to me seems slightly like the modern concept of the meme, but memes in my opinion cannot be instinctual. Darwin applied the concept of gradual change to the acquisition of instinct as well, and that complex changes don't spring up over one generation.

Darwin also brings up the idea of extra-species altruism, though he doesn't explicitly call it that. "The instinct of each species is good for itself, but has never...been produced for the exclusive good of others," (Darwin 227). Species do benefit other species but it is usually for some sort of gain, whether or not that gain is visible or understood. This again relates back to the theme that there is a great deal of interconnected dependence between different species, which has been repeated throughout Origin.

Instinct hasn't been cracked yet (a brief google search reveals more movies and phones than scholarly discussion) and the nature vs. nurture debate still rages strong. Therefore, Darwin's assertion that instinct is selected for probably isn't off the mark. Many things have a biological basis, even if it's not immediately clear. If animals are born "knowing" something, the simplest explanation is that it's biological. If it is solely biological then selection most certainly applies.  Sociobiology seeks to study the link between genes and behavioral traits.

Darwin gives three examples of natural instinct: cuckoos laying their eggs in other nests to pass off parental investment onto another bird, ants' "slave-making", and bees making honey combs. I get the cuckoo thing, and the bees, but the ants section doesn't really make much sense to me. Admittedly I know nothing about ants apart from what I've seen in A Bugs really, I know nothing. Apparently Formica sanguinea, a type of ant, takes slaves (other species of ants). Even Darwin seemed skeptical of this ant species (to the point of putting a few colonies in his yard to observe), but apparently they take over other species nests rather than building their own (Sonobe, R. Onoyama, K

Thursday, October 14, 2010

Chapter 6: Difficulties on Theory

Here Darwin addresses concerns/confusion concerning his theory of natural selection. In this chapter, Darwin addresses a lack of transitional forms and the so called perfectness of specific structures.

Transitional forms: Darwin recognizes that transitional forms are replaced by successive generations of forms, but questions why there is a lack of fossil evidence (1). There were known fossils in Darwin's time, but not to the extent that there are today. Fossilization is a rare process, and most individuals are destroyed. For instance, there is very little information on chimp evolution due to the fact that so few fossils from that lineage have preserved.

For instance Archaeoptreryx lithographica, an early feathered dinosaur, was not discovered till 1861. Since then, only 7 specimens have been found (2). However, obviously for the species to exist, there had to be much more than 7 individuals.

To address the question of why we don't see transitioning forms today, it's because we don't know what they're transitioning into. Evolution is a very long, slow process.

Darwin inferred from the geological record that Earth in modern times is experiencing a more stable array of climates (of course this is pre-global warming concerns). Therefore, in times of great climate shifts and unstable environments, life may have had to adapt more extremely. Darwin asserts that "continuous conditions" are mainly responsible for the diversity of species populating the world. This means that life is not restricted to one zone, but differs in distribution for select climates (1).

However, it's not just about climate, it's about other species too. The predators, the prey, the whole circle of life bit. Speaking of which, The Lion King (the first movie I ever saw in theaters!) demonstrates a lot of Darwin's ideas. Work with me here, the hyenas move into the lions territory and eat up all the food subjecting the lions to the choice of either finding a new territory or starving to death. Of course in the movie there is option 3, kicking the hyenas out of pride rock in a symbol heavy disney ending, but that's adaption! As a side note, the lioness' fitness was really suffering through that movie. There were only two cubs and then no males for a very long time.

Okay, enough pop culture, back to the book. Darwin brings up the genus Balanus, and that individuals appear as intermediates between the main varieties (1). What exactly is the genus Balanus? Well, it's a type of barnacle. Darwin was a bit of an expert on barnacles so I'm going to trust him on this. He has a multi-volume book about barnacles (he might love them just as much as pigeons, though I don't think that a barnacle can express as much response as a pigeon -- I imagine them to be along the lines of pet rocks, but perhaps less exciting) which I will not be reading. 

Darwin also addresses species that are highly adapted to specific behaviors. His choice example is the bat evolving from a flying squirrel, and a whale evolving from a bear (1). These are very theoretical and very wrong; while bat evolution isn't well documented, whale evolution is and they evolved from large land carnivores (that weren't bears).

Next, Darwin covers so called perfect structures, namely, the eye. We now can trace the mosaic evolution of the eye, but such advances weren't available to Darwin who seems baffled by the perfection. However, he was very certain that all features in species can be explained by gradual change. One argument he uses is that certain organs or features may end up being used, and adapted, for a completely different use than how they were originally selected for (1).

Darwin goes on to discuss vestigial organs (without directly calling them that). He muses that they are leftovers that were useful to an ancestral form, which is true. His other concern is of traits that are assigned importance, but are just by-products of selection. Also, Darwin finally brings up humans, specifically races but doesn't have any explanations for them (1). Which is probably for the best.

Thursday, October 7, 2010

Chapter 5 - Laws of Variation

In this chapter Darwin outlines his views on variation and its causes. Darwin published On the Origin of Species in 1860, in a time when genetic inheritance wasn't well understood. Previously I have mentioned Mendel, however his work did not gain recognition until 1900. One argument constantly made against Darwin is that because he got some details wrong, his whole theory is wrong. Science is a process, old ideas are replaced with new ideas, incorrect information gets corrected. So Darwin didn't understand genetic inheritance, big deal, he was at least able to recognize the fine details of change over time and selection. Sure, evolution is just a theory, but so is gravity. Scientific theories are shown to be true time and time again, can be replicated, and are observed all over. It's not an abstract concept someone just came up with to explain something, it's a repeatedly observed phenomenon. I cannot understand how some people can selectively pick and choose what science they want to believe in. If you don't believe in evolution, what's the point of getting a flu shot every year? A new flu shot attempts to protect patients from the ever evolving strains of flu.

Okay, I'll get off the soap box and onto the chapter. Variation has been a big theme in Origin thus far, so it's fitting that it gets a chapter. Darwin believed that most variation occurred in the womb. Yes, while developmental interruptions or stresses can result in a deformed offspring, these variations are not genetic and thus not heritable. Darwin admits that there is large ignorance concerning the subject. However, Darwin also says that most variation cannot be accounted for by climate and food.

"When a variation is of the slightest use to a being, we cannot tell how much of it to attribute to the accumulative action of natural selection, and how much to the conditions of life," (Darwin, 179). Please Darwin, be more cryptic. This chapter is confusing, and I think part of that is derived from the fact that modern audiences have the benefit of 150 years of the study of evolution. Some of this stuff is just plain wrong and or confusing.

Darwin spends time talking about use and disuse. I could bore you with the details, but it's not how variation arises. Here's the hypothesis: the use of certain traits makes them more prominent and the disuse of other traits causes them to diminish over generations. Observation wise this kind of makes sense, however natural selection acts to select traits that increase reproductive success, not just survival traits. Also, the use of a trait during an individuals lifetime would not make it more prominent in it's offspring. Instead, directional selection can explain the emphasis on certain traits over time.

Darwin recognized that certain structures in the body lead to change in others. Of course, the body must work together in a complementary way to ensure the greatest chances of survival.

There is a section on the variability of secondary sex characteristics (traits associated with sex that are not directly involved in reproduction) and their similarities in placement between closely related species. This idea could be elaborated into the fact that basic body plans are observed throughout nature, but Darwin doesn't take things so far.

Then of course there's a rant about pigeons -- because what would the Origin be without a tangent or two about Darwin's favorite bird? Yes, he knew a lot about breeding them and they did aid in his observations but really, enough with the pigeons! He's essentially hitting on recessive traits appearing, but does not call it this. He believed that the traits get diluted (and uses some questionable math to boot) over generations and believed that both parents needed to have some of this diluted trait for it to appear in offspring. Yes, and no. There are several ways that traits can appear in progeny, I explained recessive traits in my genetics post, and there are also epistatic genes. Anyway, it's not that the trait gets diluted, it just doesn't get expressed because of the other genes dominating it. Genes aren't cumulative. Darwin considered the appearance of such traits to be a throw back to an ancestral trait.

"To admit [to believing in independent creations of species] is, as it seems to me, to reject a real for an unreal, or at least for an unknown, cause. It makes the works of God a mere mocker and deception; I would almost as soon believe with the old and ignorant cosmogonist, that fossil shells had never lived, but had been created in stone so as to mock the shells now living on the sea-shore," (Darwin, 200). Religion is not a subject I choose to tread here on the internet. People are entitled to their beliefs and lack there of as they please. This blog is about Darwin, and I am inferring from the above passage that he may have been able to reconcile the idea of a god with evolution. I personally have not read anything written by him stating his religion. It is, frankly, irrelevant. Religion should not impede scientific observation and theory. Science should not be compromised to religious belief and it is up to scientists to keep their work and spirituality in separate spheres to ensure the greatest quality of research. And that's all I'm going to say about that.

This chapter overall presented several false ideas. Darwin knew there was variation allowing for natural selection, however he had no clue what caused variation. This makes for some confusing reading since he tries to explain variation but then states that his ideas are probably not the main cause of variation.

Saturday, October 2, 2010

Chapter 4: Natural Selection

Finally, we get to natural selection, the big show, the process by which Darwin saw evolution.

"This preservation of favorable variations and the rejection of injurious variations, I call Natural Selection," (Darwin, 144). Well put Darwin. Natural selection can be basically boiled down to the simple concept of traits that allow an individual to survive the best will be passed onto the next generation.

Darwin explains that if there is a sudden change in environment, it's inhabitants must adapt or perish. Also important is the fact that different species have an impact on each other, whether it is a predator/prey relationship or a competition for space or food. This complex relationship seems to have fascinated Darwin as he has mentioned it in previous chapters. "Let it be remembered how powerful the influence of a single introduced tree or mammal has been shown to be," (Darwin, 145). A modern example of this can be seen in invasive species that come to an area and disrupt the local ecology.

Darwin believed that direct changes in climates affected variability, "A change in the conditions of life, by specially acting on the reproductive system, causes or increases variability," (Darwin 145). It is difficult to access the role that the environment plays in variability. Variations are rooted in genetics, but Darwin obviously had no understanding of modern genetics. So yes, while the expression of some genes is determined by factors such as temperature, this is not the case for all genes. Therefore, the directed change of natural selection is acting on existing individuals survival, and not the variations of developing individuals.

"Every selected character is fully exercised by [nature]; and the being is placed under the well-suited conditions of life," (Darwin 146). Darwin cited the example of birds and insects being the same color as their habitat as an example of natural selection. This makes sense: if a bug lives on red leaves, variations of the bug that are red are camouflaged better than variations of another color. Since the other colors would be easier to spot, they would be eaten more and the red ones would be left with more food and access to mates.

Darwin also points out that variations that occur during specific life stages are repeated in offspring. For instance, if a goat is going to grow horns, it will do so at around the same age that it's parents first grew horns. Unknown to Darwin, such developmental features are determined genetically.

Sexual Selection is mentioned in this edition as a process through which selection is determined by mate choice. This is mostly observed in males, as Darwin notes, because they are most often the sex competing for mates. Sexual selection rightly deserves it's own blog post so look for that soon. This sort of selection creates divergence between the sexes (sexual dimorphism) and focuses mostly on contest-competition and displays. Darwin notes examples of deer and birds.

Darwin gives many examples of natural selection in this chapter with animals and plants. However, the evidence he uses is mostly circumstantial and not derived from direct observation. Yet, because evolution is such a long process it is not surprising he could not directly observe many of his theories in action (although he did take 30+ years to publish his ideas, think of how many generations of fruit flies he could have gone through!). As a side note, there was a very interesting study of Galapagos finches, which were regarded as highly inspirational for Darwin, and the effect of climate change on their beaks over many years.

Moving on, Darwin talks briefly about intercrossing (hybridization gets it's own chapter, look forward to that). He also has a tangent about hermaphrodites and their reproductive prospects. Incorrectly, Darwin assumes that no animal species reproduces asexually. Wrong. While sexual reproduction is the norm, there are examples of asexual species and those that can reproduce through parthenogenesis (when an egg develops without fertilization; this has been observed in some fish, reptiles, and insects). I'll let Darwin pass on this one, I don't think he ever encountered any such species in his travels and if he did I doubt he lifted up the legs on each lizard to check it's sex (they'd all be girls)... Basically, what Darwin is saying is that even if a plant or animal can reproduce itself, pairing of animals is essential to create variation and increase diversity.

Darwin explains how different factors impact natural selection, such as isolation and large areas. Darwin's view was that natural selection seeks to fill every niche. Also the layout of the land, and whether or not it is isolated impact natural selection. If no new species are moving into an area, the native species are not challenged and not subject to strong selection due to a change in predators, space or food sources. Darwin favored the idea of species doing better over large areas that they could spread out and populate. Confined, isolated areas stagnate change and create what Darwin referred to as living fossils -- species that have not changed very much over thousands of years because they are so well adapted to their isolated spot and nothing has invaded to force for selection.

Extinction is the next topic Darwin tackles, basically summing it up as varieties that do not do as well become rarer and if they are not selected for over a long enough time, they go extinct. Brilliant insight Darwin. "Consequently, each new variety or species, during the progress of its formation, will generally press hardest on its nearest kindred, and tend to exterminate them," (Darwin 163). Therefore, Darwin believed that extinctions were caused not by extremely different species (with presumable different needs) but rather similar ones competing for the same resources.

The idea of extinction is followed by the important concept of divergence of character. This idea is that as variations become more pronounced, they move towards a category of sub-species, and then fully differentiated species. Darwin never really defines what a species is, which again for purposes of these posts, I am defining as groups that do not/cannot mate with each other and thus do not exchange any genetic material that result in viable offspring. Since Darwin viewed selection as trying to optimize the use of the environment, divergence would allow for the maximization of species in different environments. "As a general rule, the more diversified in structure the descendants from any one species can be rendered, the more places they will be enabled to seize on, and the more their progeny will increase," (Darwin, 170). In this section, Darwin draws an imagined phylogeny tracing many different species back to a common origin. This is one of the most important concepts to be hammered home: species are descendant from common ancestors. The more species diverge, the less related they are to each other.

The importance of this chapter is insurmountable. Darwin ends the chapter quite poetically, "As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications," (Darwin, 177).