Tuesday, November 15, 2011

Project Update

The work on Origin of Species presented on this site was done as a term project for a class during the fall of 2010. For the fall of 2011, this project has been extended as an independent study. The work is still in progress but more information will be available in January 2012 concerning how the updated version will be distributed.

One of the most surprising things to come out of this project was the continued readership after the Origin chapter summaries were finished. The site still generates approximately 100 page views per month from a variety of IP addresses around the world. The entire motivation behind this project was to present an accessible, and neutral look at Darwin's works for the general public. I think that by virtue of the summaries still being read by unique visitors from a variety of countries that this accessibility and presentation goal has been a success.

Thank you for your readership, and I hope to share the in depth and improved Darwin project with you in the beginning of 2012.

Sunday, January 30, 2011

The Politics of Education

Something that gets a fair amount of attention, but is by no means new, is the controversy surrounding the teaching of evolution in schools. It points the overall feeling toward evolution that the United States holds. I have taken entire classes where the curriculum is dedicated to analyzing the rift between science and religion. The most important thing that I've gathered from observing and learning is that evolution will not be taken seriously unless teachers are behind it and it is presented as a law of nature, not a hypothesis. 

I received a public school education and I was taught about evolution. I don't really recall there being much issue and there was never town wide dissent and arguments around teaching. I don't remember ever discussing the topic of evolution at church. However, I was also in high school when the intelligent design movement really received nationwide attention in 2005 in Kitzmiller v Dover Area School District. At this time I was no longer in biology class so I don't know what my teachers reactions were or if it was even discussed. 

In defense of intelligent design, it is a good way of reconciling religion and evolution, however it is by no means science. I have attended a lecture by one of it's lead proponents, Dr. Michael Behe, and watched several specials and documentaries in which the above mentioned court case and the "teach the controversy" movement have been analyzed. Behe's arguments rely on proof by an absence of evidence, which is not how science operates. 

In my opinion, science and religion can't be compared because they are fundamentally different in the way they analyze the world. In religion, "truth" is set out and mandated; there are guidelines. People seek religion to give answers, and they can't really be rewritten, only interpreted through a new view point or sect. In science, "truth" is what has yet to be disproved. Something that has been held for years must be abandoned in light of new evidence. Yet people are constantly being forced to choose between evolution and creation as if they are opposing viewpoints in an argument. Creation is a religious origin explanation, based on faith. Evolution is a scientific theory concerning long term change, based on study and observation. It's not going to be quick or easy to make them compatible especially since evolution does not give an origin of life. 

Evolution is not about the origin of life. It is about the process of change that species undergo over time in response to various selective pressures. Creation is about the origin of life, but fundamentally denies the ability of species to change. 

The problem lies in people wanting an explanation for how and why we're here. Evolution can tell us that it's because our ancestors adapted to bipedal locomotion and enriched our diets allowing for the brain to get bigger and more complex. But it cannot tell us what led to the first single celled organism (I'm hopeful that someday science will be able to figure that one out). Therefore, I suppose that when it is contrasted against religion, it is somewhat unsatisfying in it's ability to provide answers. 

I really don't like to involve myself in a debate between religion and science because I don't think they should be debated in the first place. However, because I live in the United States, this debate deeply affects how funding is allocated to the types of things I study. This debate taints the perception of my field, the study of human evolution, and how people react to me when they find out what I study. This debate leads to preachers on my campus, harassing me on my way to class telling everyone that those who believe in evolution are going to hell. 

The US needs better biology education because by propagating this so called controversy we are only further fueling this "argument". The theory of evolution needs to be given it's credit as a scientific theory on the same level as the theory of gravity, not a theory as in some lofty idea that may or may not be true. 

Sunday, December 5, 2010

Arsenic Bacteria

Well I guess my science education hasn't been as good as I thought; last Thursday it was reviled that a bacteria had been evolved in a lab that swaps arsenic for phosphorus. The media is hailing the as rewriting the building blocks of life as we know it. I feel like I should have learned how essential the building blocks of life are, unless it turns out they're not really that essential.

First off, on Wednesday morning I read that NASA was going to have a press release about alien life. So I was hoping for so news from deep space, not from earth. This bacteria not extraterrestrial at all!

The building blocks of life are considered to be oxygen, carbon, hydrogen, nitrogen, sulfur, and phosphorus. My question lies with anaerobic organisms. What role does oxygen play for them? Bacteria have been discovered that use arsenic instead of oxygen (though this is a very different process than replacing phosphorus with arsenic; phosphorus is a key component in the structure of DNA). So is oxygen considered a building block for anaerobic organisms? My intro-level biology course has me believing it isn't. Also, a google search of oxygen and anaerobic bacteria turns up mostly results of anaerobic bacteria not needing oxygen at all (but little is mentioned on if and how oxygen in any of its forms plays a role in their structure).

To anaerobes, oxygen gas can be lethal. However, oxygen is also a key part of water (H20),  and anaerobic organisms can live in it. The bacteria were originally found in a lake before being artificially introduced into a phosphorus free environment and forced to die or survive on arsenic. The individual bacteria grew larger, and more hollow. I find the increase in size unsurprising, since arsenic has a larger radius than phosphorus.

Let's consult our periodic tables. Phosphorus and arsenic are Group V elements (as is nitrogen), so they are similar in structure, but arsenic is bigger than nitrogen or phosphorus. Interestingly all the building blocks are non-metals while arsenic is a metalloid, that's about the most interesting thing that I've gathered from this.

Come on NASA, this is not alien life. This is some bacteria artificially induced into using arsenic. Bring me some silicon based lifeforms and then we'll talk.

We are too narrow in our idea of what life can be. Research in the past has been aimed at looking for environments similar to earth (hence looking for those building blocks) on other planets. But should we really be expecting extraterrestrial life to have evolved along the same path that life here has? Sure, all Earth life is built on DNA, but that isn't the universal code it's portrayed as (it's not even totally consistent in all discovered life). Can we expand our imaginations beyond looking for DNA based organisms? If our origin of life turns out to be earth based, the chances of other planets having an identical path of evolution is infinitely small. With research like this we're already showing that life isn't as strictly controlled as once believed. Will we even recognize extraterrestrial life if/when we find it? My expectation is that on the minute chance that any alien life is ever discovered in my lifetime (and I'm giving myself at about 60 more years) that it won't look like anything we know or could have imagined possible on earth.

Thursday, December 2, 2010

Sexual Selection and Parental Investment

The concepts presented are from discussions in two anthropology courses: Bio-Cultural Evolution taught by Dr. J. Kurland in Spring 2009 and The Evolution of Human Mating taught by Dr. D. Puts in Spring 2010, both at the Pennsylvania State University.

Parental investment in animals is the degree of care that a parent puts into it's offspring. For some species this may be carrying young to term, sitting on eggs, rearing young to adulthood, etc. Generally, the females of a species has a higher parental investment than males. In many species, males only contribute their sperm, which is low in parental investment. Sperm is practically an unlimited resource, whereas in some species eggs are limited, and energy costly to produce because they are such large cells.

Species with low parental investment generally create more progeny than those with high parental investment. When parental investment is different between the sexes, the sex that invests more is known as the slow sex (because they must go longer between matings due to their investment). Again, because females tend to invest more they are usually the slow sex. Due to the energy and time costs of their parental investment, the slower sex is the choosier sex; if the degree of parental investment is going to be high, the choosy sex will want to find the best genetic mate. Therefore, members of the fast sex must compete to mate with the slow sex.

This is where sexual selection comes in. The slow sex selects for good or attractive traits and mates with those in the fast sex that carry such traits. Sexual selection is the source for many sexually dimorphic traits between males and females. One popular example is the peacock's tail. A peacock has an iconic, but detrimental tail. The theory is that peahens favored bright and long tail feathers and eventually through runaway sexual selection the peacock's tail as we know it today was evolved. While the tail is certainly beautiful, it can land a peacock in a deal of trouble with predators making them easy to spot and catch. However, the catch is that while the individual is in danger, he is more likely to mate with a female because of the tail. It increases his Darwinian fitness while decreasing his individual survival.

The peacock's tail is also fitting for the "sexy-sons" hypothesis. In this hypothesis, it is thought that female selection results in male offspring with the attractive trait, and female offspring attracted to the trait. Thus the trait and it's attraction is preserved in successive generation guaranteeing the male offspring to have a good chance at mating.

Sexually dimorphic traits can be very costly to males, be it investing energy into developing the traits or the dangers that accompany them (ie. predators). However, despite the costs to the individual, it increases fitness which is what life is all about (in some opinions). This the core idea behind Richard Dawkins' book The Selfish Gene. Admittedly I have not finished the book but from my understanding it's about genes sometimes sacrificing the individual (through the means of altruism) in order to propagate themselves in the gene pool. Obviously I don't think Dawkins is suggesting that genes literally have hopes and dreams but rather that it is evolutionary adaptive for individuals of a species to cooperate (especially closely related individuals) to ensure survival of species (and genotypes). In a University of Portland commencement speech, Paul Hawken remarked, "We are here because the dream of every cell is to become two cells."

Wednesday, December 1, 2010

Chapter 14: Recapitulation and Conclusion

Well here we are at Darwin's closing statements, summarizing and reasserting the theory that he has so beautifully explained over the course of On the Origin of Species. When I started this project, it was an effort to save people from reading the book while still being able to understand its core tenants and science. However, it truly is a book that everyone (at least those with an interest in evolution and biology) should read. While some parts were daunting and drawn out, it really is a magnificently written scientific theory. Darwin spent a large portion of his life mulling over his observations, and perfecting them to the best of his ability. This is his life's work and legacy and it's really brilliant when you consider what was known and widely believed at the time.

If you are going to read nothing else, read chapter 14.

Darwin restates the concepts of variations withing species, and the struggle for existence. Darwin notes quite strongly that no matter how complex or perfect a trait or species may seem, it must have arisen through gradual modification. He also recovers geographical isolation, hybrids, sexual selection, geometric increases in population.

Darwin promotes the concept of use and disuse again. This theory is pseudo-Lamarckian and not really supported by evidence. In the absence of selective pressure, traits cannot appear or disappear. I suspect that Darwin considered use a selective pressure but the genetic basis of a trait and phenotypic expression would not be altered by use or disuse.

In closing, Darwin was confident that future research would support and expand his theory; his prediction was completely right. Today evolution is a main tenant of biological science and is fundamental in understanding life.

"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved," (Darwin, 398).

Chapter 13: Mutual Affinities of Organic Beings: Morphology: Embryology: Rudimentary Organs

We're nearing on the homestretch with chapter 13, there's only one chapter after this one and it's basically a summary of Darwin's theory.

So here we go: Darwin begins by analyzing the shortcomings of the classification system, while it can show relationships, they are not very informative when it comes to inheritance and descent. Darwin was especially concerned with similarity in body plans and symmetry, as well as non-specialized traits and their impact on showing classification groups. He was also a proponent of discovering the genealogy of closely allied species and using that to classify them. However, in Darwin's time, it was difficult to discern genealogy without the knowledge and technology of DNA analysis.

Darwin explores the concept of convergent evolution, in which different species come to have the same adaptation but not from common ancestry but rather similar modifications. Darwin does not call it convergent evolution, but the concept of bats and birds having wings for the same use and not because they share a recent ancestor was recognized at the time by Lamarck's classification system. One example he gives that whales and fish have similar exteriors because they're adapted to the same surroundings but they themselves are not closely related.

On morphology, Darwin asserts that crucial parts such as limbs are reworked from an original template rather than completely thrown out and grown anew (ie: the fin of a whale is a modified leg from a former terrestrial ancestor). Darwin saw the analogous body plans of many different species as proof of common ancestry rather than a creator.

Darwin also talks about embryology and the similarity of early embryos of related species as well as how embryos are adapted just as well as adult forms for the conditions surrounding them. Darwin uses the example of a pigeon, shocker, to measure differences in juvenile and adult pigeons of different breeds to show their similarities at the juvenile stages. Darwin went off popular theory that embryos resemble ancient species. While they are simple and basically laid out I don't know that I agree with that exact assessment.

Darwin also covers vestigial traits, which he refers to as rudimentary organs and cites instances of underdevelopment in some individuals and fully functioning individuals. Vestigial organs are somewhat controversial today, because for some examples it is possible that the function is currently unknown. However, in most cases it is found that vestigial organs were useful in an ancestor and have now been replaced or rendered useless but are retained. 

And finally, I thought this quote was pretty funny out of context, "For the male is a mere sack, which lives fora  short time and is destitute of mouth, stomach, or other organ of importance, except for reproduction," (Darwin 369). He was referring to male larvae becoming "complemental males".

Tuesday, November 30, 2010

Chapters 11 and 12: Geographical Distribution and Geographical Distribution continued

Darwin spends two chapters on geographical distribution, rather than just making one forty page chapter on the subject. Without the knowledge of plate tectonics as mentioned in the last post, Darwin didn't really have a scientific context fro the similarities of species that he was seeing in distant lands other than they must have originated from a common ancestor and by one set of means or another managed to migrate to present locales. It was known based on the geological record that the sea level had changed over Earth's history, but the concept that the continents had undergone massive shifts wasn't widely accepted until the mid 20th century.

Darwin suspected that wide spread species began to divide in to variants specialized to a specific location and climate, thus branching into distinct species.  Therefore, all similarities between species could be accounted for by inheritance and similarities were products of selection. This fits with his theories and he strongly believed that all variants despite their present day location, had stemmed from a common ancestor. Placed into the context of modern understanding, this is possible, but at the time, Darwin faced a difficult task of explaining how such widespread migration across land and sea could have happened. However, despite this difficulty he reasoned that to reject the idea of migration and to accept separate acts of creation would be to accept miracles over his entire theory.

Darwin covers Charles Lyell's (the father of geology) concept of means of dispersal. This idea is that migration has been greatly affected by climate change which corresponds to sea level changes. According to this theory, continents and islands were once connected to each other by land bridges that are now covered by ocean. This is true of some land masses (Eurasia and North America were connected by a land bridge that allowed for human migration some 10,000 years ago) but this theory is limited to the idea that the continents don't move. Darwin question Lyell's assertion that all islands were once connected to mainland, and rightly so, since many have been formed by underwater volcanoes.

Darwin believed that plants were better at dispersing themselves than mammals, citing plants that are found around the world and that no continent shares a common mammal (at least one known at the time). Darwin even details his own personal experiments at seeing how well different seeds and other plant material handled sea-water travel to support the idea that seeds could float from the mainland to an island. Other means include seeds on floating driftwood birds transporting seeds by ingesting the fruits of plants, and then fly to islands to deposit them. Darwin even went so far as to investigating bird droppings on his property for evidence of seeds (hardy seeds were unsurprisingly better preserved than soft ones). Darwin also proposed transport via iceberg during glacial periods.

The concept of climate change is explored further while Darwin analyzes the impact of the ice age on different species in Europe and how it forced adaptation or migration south for many species. Darwin also alludes to the concept of the Bering Strait, "We can further understand the singular fact remarked on by several observers, that the productions of Europe and America during the later tertiary stages were most closely related to each other than they are at the present time; for during these warmer periods the northern parts of the Old and New Worlds will have been almost continuously united by land, serving as a bridge, since rendered impassable by cold, for the inter-migration of their inhabitants," (Darwin, 325). It's very striking that in the 1800's (and even earlier) modern concepts were already being predicted and hypothesized thus laying the ground work for modern science.

Above was chapter 11, detailing acts of creation against dispersal from a common source, with attention to plants. Chapter 12 concerns fresh water species and islands.

Specifically with fresh water fish, Darwin inferred that those isolated in Europe would not find their way to North America due to the distance. However, similar species within closer proximity could have been dispersed through changes in water level such as flooding. Again, Darwin repeats the idea of birds transporting plant matter.

For islands, which Darwin had an intimate working knowledge from his travels on the H.M.S Beagle, Darwin proposed that species found in such isolated areas stemmed from relatives on the mainland. Certain species are more able to get to far islands than others, for example birds and bats are able to travel a greater distance than terrestrial mammals.

Finally, Darwin speaks of his Galapagos studies. Namely, he discusses the variations observed on different islands, mentioning specifically birds and plants and that differences between them and mainland species have been generated through selection.