Sunday, September 26, 2010

Natural Selection in the News

An article in the NYTimes last week talks about research with fruit flies that supports the idea of multiple gene frequencies changes over generations leading to change (evolution) and not the idea of big infrequent mutations leading to change. The article termed this "soft sweep" and it makes sense given mutation rates and the chances that a mutation is positive rather than neutral or detrimental to an organism. This is not to say that mutations don't give rise to change (they do), but rather that they do not seem to be the norm.

This research also supports the concept of many genes controlling traits, as opposed to just a single gene for each trait. This is becoming a focal point of disease research. While some diseases may be controlled by a single gene, some diseases are likely subject to control by a whole slew of seemingly unrelated genes. This is why certain disorders may run in families, but have no discernible genetic basis. It makes it very difficult then to access how at risk someone is for a certain disorder, and since environmental factors definitely play a role in gene expression, it could be extremely hard to predict an individuals likelihood for a specific disease.

Friday, September 24, 2010

Chapter 3: Struggle for Existence

Darwin pretty much sums up natural selection in the beginning of the third chapter, "Owing to this struggle for life, any variation, however slight and from whatever cause proceeding, if it be in any degree profitable to an individual of any species, in its infinitely complex relations to other organic beings to external nature, will tend to the preservation of that individual, and will generally be inherited by its offspring. The offspring, also, will thus have a better chance of surviving, for, of the many individuals of any species which are periodically born, but a small number can survive," (Darwin, 132).

Darwin preferred the view of competition between individuals over cooperation in groups as the main drive of evolution, a debate that is still strong today -- how much of a species survival is determined by individual success against group success? Social Darwinism is all about competition, and not really at all about biology at all. However, it is an important distinction to make. Survival of the fittest is Social Darwinism, actual Darwinism is more along the lines of the fittest having the greatest reproductive success. Social Darwinism came about around the time of Darwin's publication, and was quite influential in an already competitive Victorian society. Darwin himself didn't actually espouse the ideas, they were actually started by Herbert Spenser. Social Darwinism was used as a justification for imperialism, exploitation, unchecked capitalism, eugenics, and a slew of other evils (2). The point of this little tangent is that Social Darwinism does not equal Darwinism, at all. I can't tell you how many times I've seen this mistake propagated by the media, specifically network news.

Back to the book, chapter 3 is also kind of short and is all about natural struggle as well as geometric increases in population.

Geometric increase is basically exponential increase, meaning that the population will increase steadily exponentially rather than at a steady linear rate. This accounts for rapid increases in populations. Darwin used the example of elephants, because they live a long time and produce a very small number of progeny. His math leaves a lot to be desired, but he was right in a very basic sense. So Darwin proposed that an elephant lives about 90 years and has 3 calves, and each of those calves grow up to have 3 more. Darwin estimated that after 500 years, there would be something on the order of 15 million elephants stemming from one pair (1). Well, no, actually if we're talking approximately 5 generations, that would be 3^5 elephants, or 243. This is opposed to linear growth in which 5 generations would yield 3x5 or 15 elephants, big difference. Did no one think to check these calculations before publishing; I mean, if Darwin had been right, we'd be up to the empire state building in elephants. Also, not every one of those 3 calves are going to necessarily have three calves because some of them are going to have to be male (or else there will be no elephants). Regardless, geometric growth is how species propagate.

Speaking of those elephants, not all 3 calves will survive to produce calves of their own, thus the struggle for existence. "Hence, as more individuals are produced than can possibly survive, there must in every case be a struggle for existence, either one individual with another of the same species or with the individuals of distinct species, or with the physical conditions of life," (Darwin, 134). Basically, more progeny must be produced because not all of them are going to make it. This also brings up differences in parental investment, species that invest a great deal in their offspring generally have fewer than those who do not beyond birth, but I'll save that for a separate blog post.

Darwin brings up the effect of climate on the struggle for existence, and how particular occurrences such as cold winters or dry summers impact populations short term. Later in the chapter Darwin suggests that certain varieties could mix to produce an individual better suited to a certain environment, and varieties ill-suited to the climate will soon disappear (1). This is basically a primer for natural selection, which is detailed in the next chapter.

He also notes the impact of one species on another. Darwin recognized the relationships between species, and used an example of certain bees associated with specific flowers. Darwin extends this to the bees being impacted by field mice, which are impacted by cats. Therefore, one could muse that a decrease in cats would lead to a decrease in flowers (since the mice would increase and damage the bees in greater number) (1). This co-evolution is widely seen today, and even in ourselves. E. coli is one such example; it has evolved to live in our guts and we depend on it to aid in our digestion.

Darwin leaves us with this small comfort, "When we reflect on this struggle, we may console ourselves with the full belief, that the war of nature is not incessant, that no fear is felt, that death is generally prompt, and that the vigorous, the healthy, and the happy survive and multiply," (Darwin, 143). Doesn't that just leave you feeling warm and fuzzy?


Wednesday, September 22, 2010

Phylogenies

In my search for a modern and illustrative phylogeny, I found this cool poster

I was really hoping to find a phylogeny I had seen in an article last year that showed a really wide array of organisms classified based on their degree of genetic relatedness, however I couldn't find one that fit such a description from a reliable source.


Chapter Two: Variation Under Nature

Darwin begins to define a species by pointing out that each individual of a species has in it, some form of variation. Darwin also goes on to point out that it's more likely that there is one species with, for instance, 3 varieties, rather than 4 distinct species.

This assumption that there are many varieties rather than many distinct species is correct. It is difficult to define what exactly a species is. A generally taught view is that speciation occurs when varieties of a species cannot contribute genetic information to each other, or in other words, two varieties that cannot breed. A few posts back I posted an article that talked about distinct species breeding. One example of this are lions and tigers (two genetically different big cats from different geographical locations, and pretty much universally accepted as separate species) producing "ligers". One note to make is that many hybrid offspring are non-viable, meaning that they are either weak and/or sterile. Liger's don't really count as tigers contributing to the lion gene pool because they cannot be bred.

For purposes of this blog, I'm defining different species as groups of individuals who do not contribute to each others gene pools. Such reproductive isolation can be mechanical, or geographical, and/or pre/post zygotic non-viability.

"And I look at varieties which are in any degree more distinct and permanent, as steps leading to more strongly marked and more permanent varieties; and at these latter, as leading to sub-species, and to species," (Darwin, 126). Darwin defines a species as a variety that is able to flourish in large numbers, and does not assign the rank of species or even sub-species to each and every variant.

"Where many species of a genus have been formed through variation, circumstances have been favorable for variation; and hence we might expect that the circumstances would generally be still favorable to variation. On the other hand, if we look at each species as a special act of creation, there is no apparent reason why more varieties should occur in a group having many species, than in one having few," (Darwin, 129). Basically the processes shaping variation long ago are still shaping variation today, and if creationism was applied to each and every species, there would be no explanation for variation.

It is important to note that the Linnaeus system of classification was widely known during Darwin's time and is still used today. This is a system of classifying organisms based on their relatedness. One major advancement to this system is the use of genetic analysis to see just how closely species are related.

One other observation Darwin made in this chapter was that the dominant genera represented in a region was also apt to have the most variety.

Thankfully, chapter 2 of Origin is much shorter than chapter 1 and pigeon free.

Thursday, September 16, 2010

A brief detour: Genetics

Before I begin detailing Chapter 2 of Origin, I would like to take a brief look at our modern understanding of genetic inheritance. This serves two purposes, a basic grasp of Mendelian principles helps one to understand evolution in light of genetic inheritance, and also I have a genetics exam tomorrow morning (lucky me). The textbook I use for my class is Genetic Essentials: Concepts and Connections by B. A. Pierce, published by Freeman, 2010.

Gregor Mendel (1822-1884) was a little known contemporary of Charles Darwin. His research gained popularity years after his death, and was rediscovered in 1900. Mendel's now famous experiments were done on pea plants. He would take true breeding (homozygous) pea plants that express two different traits (denoted as the P generation) and cross them. The offspring (the F1 generation) would then be genetically heterozygous for whatever trait Mendel was isolating, but would only express the dominant phenotype. The subsequent generation (the F2 generation) derived from crossing the F1 generation would result in a phenotypic ratio of 3:1, meaning 3 plants would express the dominant phenotype to every 1 plant expressing the recessive phenotype.

Hope I haven't lost anyone. These are somewhat confusing terms if you haven't had a biology class in a while.

We receive one set of genetic information from our mother and one from our father. I find the easiest example of this to be sex. Sex is determined by what chromosomes we receive, XX being female, and XY being male. A mother always passes one of her X chromosomes to her offspring. A male will pass on either an X chromosome or a Y chromosome to his offspring. So we can use a Punnet Square to determine the different outcomes for what the offspring may turn out like:

Please excuse the crudeness of my MS paint punnet square. I'm also sure my professor for Sociology of Gender would just love that I used pink for females and blue for males. Anyway, as you can see, the sex ratio is 1:1 for sex.

Mendel was looking at alleles (different forms of the same gene). He focused on the phenotypic (physical) traits of parents and offspring and crossing them to see what happened.

So, the P generation would be YY (heterozygous dominant) and yy (homozygous recessive) for traits. Let's say that YY is yellow and yy is green. The F1 generation would all be Yy (heterozygous) and would all express a yellow color. The F2 generation would be YY, Yy, and yy at a ratio of 1:2:1, with YY and Yy expressing yellow while yy would express green. Mendel found this 3:1 physical expression ratio to hold true across his many experiments. It works as a basic model for predicting the inheritance of unlinked traits.

Punnet squares can also be applied to alleles that don't have complete dominance. An instance of incomplete dominance is when the phenotype of the heterozygous offspring is an intermediate between the two parents (ie a pea plant that is some color between green and yellow); co-dominance is when both phenotypes are expressed (ie a pea plant that is both distinctly yellow and green). In these cases, the F2 generation would have a phenotypic ratio of 1:2:1 (totally yellow, mix, totally green).

Mendel shows that traits that are not expressed can still be carried by heterozygous individuals and may be expressed in the next generation when two carriers reproduce. This ties in with Darwin's instances of animals reverting back to their "aboriginal states".

So how does this play into evolution? Sexual reproduction creates a huge amount of variation. Variation is necessary for natural selection to favor some individuals over others allowing for greater reproductive success and the propagation of the alleles that produce such traits.

Chapter 1: Variation under Domestication

Darwin begins On the Origin of Species with a familiar example, that of domesticated plants and animals, to illustrate the concept of variety. Darwin asserts that variety is product of sexual reproduction, which is correct, and also mentions experiments that suggest that development during the embryonic stages can impact the individual later on (these experiments specifically concentrated on deformities resulting from embryonic trauma). Arguably, this is an early example of nature vs. nurture; Darwin's focus rests on the nature side of this argument. (1)

With domesticated organisms, humans guide the selection process. However, Darwin also points out the sterility of many domesticated plants and animals, as well as their "weak and sickly" nature. He notes that animals taken from the wild have difficulties breeding in captivity, but that animals that have been domesticated breed under quite "unnatural" conditions, such as rabbits in a hutch. (1)

Worldwide domestication of plants and animals began approximately 10,000 to 7,000 years ago, kicking off the first agricultural revolution (2). This allowed for the creation of permanent settlements and stratified societies as well as a population boom (2). Animals that were have been domesticated over thousands of years are dependent on humans for survival, just as humans are equally dependent of them for food (2). The fact that they have been adapted for domestication  means that they will thrive and reproduce under human constraints, whereas animals adapted to the wild have difficulties living and breeding in captivity.

Darwin suggests that traits correspond to use, such as bigger udders in species of cows subject to heavy milking, light wing bones in domesticated fowl that do not need to or are prevented from flying, and drooping ears in livestock that fear no natural predators. (1)

Darwin breaks varieties of similar animals into races. That is to say that there are several races of cows rather than species (1). This terminology leaves a lot to be desired, I prefer to call distinct variants of the same species breeds. To quote Darwin, "I do not believe, as we shall presently see, that all our dogs have descended from any one wild species; but, in the case of some other domestic races, there is presumptive, or even strong, evidence in favor of this view." (pg. 105).

Well, Darwin was wrong about different dogs being from different origins. Dogs have been traced back to the domestication of wolves in the middle east approximately 15,000 years ago. All the variation seen in modern dog breeds is a result of human selection for certain traits (3). However, Darwin was right to think that different domestic breeds were from a common ancestor.

Darwin also cites examples of animals that always have traits that go together as an example of the "mystery" of variation. Darwin had no working knowledge of genes as we do today. However, he was able to recognize some of the basic ideas of inheritance and considered it the rule rather than the exception.

Darwin goes on to talk about pigeons for at least a few pages. Darwin seemed to be quite the pigeon enthusiast and breeder. One thing he did stumble upon was the basic laws of Mendelian inheritance and the reappearance of recessive traits in the F2 generation (that is to say, for those unfamiliar with genetic inheritance patterns, that a recessive trait bred against a dominant trait will not appear in the offspring of that cross, the F1 generation, instead it will appear in the offspring of the F1 generation). Darwin did not do as extensive experiments as Mendel, and historical opinion holds that he was not familiar with Mendel at all. Darwin considered the reappearance of recessive traits to be the individual reverting towards its ancestral form (1). I don't know that this is exactly the clearest explanation; for a while, the importance of gene inheritance and long term evolution was not the focus of science.

If you are reading along with me in Origin, be prepared for just pages upon pages of pigeons. This might be why the book is so unread. Darwin should have written a follow up volume called On the Origin of Pigeons. It might have been longer. 

Once the pigeon saga is wrapped up, Darwin dives into the concept of artificial selection (when humans guide the breeding process of plants and animals to produce specific traits). Artificial selection is historically recorded and is the process through which wild plants and animals are domesticated (1).

Darwin eases his audience into accepting natural selection by giving first the familiar example of artificial selection. If man can do it, why not nature?


Wednesday, September 15, 2010

What's in a species?

Species are often defined as genetically distinct groups that cannot interbreed, but this line is often blurred. Take for instance an article in the NYT from Monday that explores hybridization. While most hybrids do turn out sterile, is it possible that these animal mash-ups are better suited for intermediate environments than their parents? When put into the context of global climate change, are these hybrids a response to environmental pressures?

Well, I don't think necessarily that natural selection is guiding towards cross species mating because most offspring are not viable; the occurrence of these hybrids in the wild is interesting none the less. The evolutionary context is that viable hybrid offspring could be responsible for some modern day species, perhaps even our own. And that is exciting.

Friday, September 10, 2010

Let the Voyage Begin!

It's been almost 151 years since the publication of On the Origin of Species by Charles Darwin. Yet, how many people today can claim that they've actually read this monumentally important work?

I am in the process of reading Origin and, even as someone who studies the processes of evolution every day in class, this is a difficult book to get through. Also, Darwin wasn't exactly right on everything he presented. He didn't have access to the knowledge that we in the 21st century have, such as genetic analysis. However, he still provided great insight into the process of gradual change and introduced evolution into mainstream scientific thought.

So here's the deal: One book, one semester. Each week I hope to post an exploration of a chapter of On the Origin of Species. The edition I am using is the 2nd edition, edited by Joseph Carrol and published by Broadview Texts in 2003. There are 14 chapters, and because this is a project for a class, I have a deadline of 12 weeks.

I have no idea where this project will take me. I hope to give a summary of each chapter, point out what's right, point out what's wrong, and give examples of Darwin's concepts illustrated by modern science. So, for better or worse, let the voyage set sail.