I am proud to announce that I have graduated from UVU with a BS in Integrated Studies with Emphasis in Computer Science and Biology! Sure, I have a few loose ends to tie up before they hand over my official degree but not having a high school graduation, yesterday was my first experience and it was an awesome feeling. Now, maybe I'll have more time to post here and talk about the audiobooks I've been reading over the past few months.
Before The Dawn by Nicholas Wade - In my opinion, a caricature of genetic determinism (and I'm not one of those "everything is plastic" people). I really wanted to like this book. I hated it. At some point I will get my thoughts together and elaborate on this.
The Moral Animal by Robert Wright - I loved this one! A great introduction to the field of Evolutionary Psychology. It was written back in '96 but still completely relevant. The reviews on Amazon complained about his philosophy at the end. I thought it was interesting. The conclusions reached by ev psych at first glance may appear to be completely nihilistic, but he pointsout how an evolutionary approach to the study of human nature can lead us to the teachings of Jesus Christ. Christ taught us to love our enemy and to serve non-kin. His teachings are in direction conflict and rebellion to the evolutionary forces that shape our motivations. I also read his "Evolution of God" book. Excellent.
The Red Queen by Matt Ridley - This is a classic. I had only read the first chapter before, I am glad it finally came out in audio so I could read the whole thing. I loved that it deals with human nature but discusses it in terms of biological contingencies that have been in place for billions of years. I really enjoyed the discussion about meiotic drive and how chromosomal shuffling evolved to deal with this issue.
Saturday, April 30, 2011
Friday, February 18, 2011
Snapshot Phylogenetics
Today I presented my Snapshot "Phylogenetics: From GenBank to Trees" project at UCUR at Weber State University. Down load my powerpoint here and learn about automated phylogenetic dataset generation! Now, I am starting on a technical paper for this project.
Thursday, February 10, 2011
Saturday, September 11, 2010
The Grand Design
I just read Stephen Hawking's new book, The Grand Design over the weekend. I was excited to read it but I have to say that I was thoroughly disappointed. I loved The Universe in a Nutshell. I also loved Mlodinow's The Drunkards Walk. This book was supposed to explain M-Theory but it only alluded to it. I can sum up this short book as the following: Anyone who believes in God is stupid, we don't need to invoke God to explain the origin of the universe, I'd love to explain M-theory to you but you are probably a bible believing christian who believes that God literally stopped the sun for Joshua to give him an extra day in battle so you probably wouldn't understand.
My primary interest is in biology and I don't know a lot about physics. I'd love to learn but Hawking's and Mlodinow's condescending attitudes were no help.
Why the attitude? I believe that the answer is simple. Biology has a real scientific answer for the apparent design in nature. As Robert Wright points out in his brilliant book The Evolution of God, Paley was not wrong when he made his argument from design. He noticed that much like a watch has a watchmaker, life must have had a designer. It turns out that he was right. Living organisms, unlike rocks or other minerals were designed and this design may even point to a higher purpose. The designer was natural selection. Natural selection explains the apparent design we see in the natural world.
The world of physics has no equivalent. Hawking and Mlodinow present nothing equivalent to natural selection in their new book. The only way they can explain our universe that is fine tuned for human life, is to appeal to the idea that 10 to the 500th power universes (all unobservable) must somehow exist and we find ourselves in this one because it is the only one in which beings like us could evolve. This is an interesting idea, but it is just an idea. I can't believe that they started the book with "Philosophy is dead" and then, instead of laying out the science, they philosophized about how the universe did not need a creator. Maybe they are right, I don't know. But, their question is not a scientific question but a philosophical one. Natural selection explains the apparent design we see in life on earth. But, from what I got from this book M-Theory does no such thing for the universe itself. It doesn't matter how much Hawking and Mlodinow wish it were otherwise.
My primary interest is in biology and I don't know a lot about physics. I'd love to learn but Hawking's and Mlodinow's condescending attitudes were no help.
Why the attitude? I believe that the answer is simple. Biology has a real scientific answer for the apparent design in nature. As Robert Wright points out in his brilliant book The Evolution of God, Paley was not wrong when he made his argument from design. He noticed that much like a watch has a watchmaker, life must have had a designer. It turns out that he was right. Living organisms, unlike rocks or other minerals were designed and this design may even point to a higher purpose. The designer was natural selection. Natural selection explains the apparent design we see in the natural world.
The world of physics has no equivalent. Hawking and Mlodinow present nothing equivalent to natural selection in their new book. The only way they can explain our universe that is fine tuned for human life, is to appeal to the idea that 10 to the 500th power universes (all unobservable) must somehow exist and we find ourselves in this one because it is the only one in which beings like us could evolve. This is an interesting idea, but it is just an idea. I can't believe that they started the book with "Philosophy is dead" and then, instead of laying out the science, they philosophized about how the universe did not need a creator. Maybe they are right, I don't know. But, their question is not a scientific question but a philosophical one. Natural selection explains the apparent design we see in life on earth. But, from what I got from this book M-Theory does no such thing for the universe itself. It doesn't matter how much Hawking and Mlodinow wish it were otherwise.
Tuesday, August 17, 2010
The spongebob squarepants genome published!
In the Aug 5th issue of nature discusses the recent publication of the A. queenslandica genome. Sponges are among the very simplest multicelluar animals so if we want to ever really understand cancer we need to understand how the first multicellular animals were able to overcome it.
The one thing that stuck out the most to me was that the genome is more complex than many suspected. The sponge has a repertoire of 18000 genes including some distant homologues to genes that code for muscle tissue and neurons in vertebrates. The article quotes Douglas Erwin who claims that this kind of complexity indicates that perhaps sponges descended from more complex animals. Another indication of this is the fact that sponge phylogeny is so poorly resolved and there is even speculation that they may be paraphyletic. Perhaps, they represent the degenerate tips of a tree that is long ago extinct. This is all possible but, I think that such conclusions may be very premature. I think that the kind of complexity we find in the sponge is exactly what we should expect. The genes for the complex neuromuscular system we find in bilaterans today certainly did not come from nowhere. Their predecessors must have evolved in simpler creatures that used them in completely different ways. If this was not the case, then such systems would simply not exist.
This is a common theme in evolution. For example, the genes that comprise the vertebrate eye lurked in our common ancestor with sea squirts filling other functions about the body. Natural selection is not an inventor and it doesn't synthesize new structures out of thin air, it can only tinker with parts that are already at hand. It will be exciting as over the next several years we are able to tease out just exactly what sponges and their relatives used these genes for!
The one thing that stuck out the most to me was that the genome is more complex than many suspected. The sponge has a repertoire of 18000 genes including some distant homologues to genes that code for muscle tissue and neurons in vertebrates. The article quotes Douglas Erwin who claims that this kind of complexity indicates that perhaps sponges descended from more complex animals. Another indication of this is the fact that sponge phylogeny is so poorly resolved and there is even speculation that they may be paraphyletic. Perhaps, they represent the degenerate tips of a tree that is long ago extinct. This is all possible but, I think that such conclusions may be very premature. I think that the kind of complexity we find in the sponge is exactly what we should expect. The genes for the complex neuromuscular system we find in bilaterans today certainly did not come from nowhere. Their predecessors must have evolved in simpler creatures that used them in completely different ways. If this was not the case, then such systems would simply not exist.
This is a common theme in evolution. For example, the genes that comprise the vertebrate eye lurked in our common ancestor with sea squirts filling other functions about the body. Natural selection is not an inventor and it doesn't synthesize new structures out of thin air, it can only tinker with parts that are already at hand. It will be exciting as over the next several years we are able to tease out just exactly what sponges and their relatives used these genes for!
Saturday, June 26, 2010
Phylogenetic dataset workflow literature review
I just got done with my evolution class for the summer semester and for my final project, I wrote a paper reviewing the literature about phylogenetic dataset automation. You can download it here. Enjoy!
Sunday, June 20, 2010
Natural selection
Most natural selection is purifying selection, that is it weeds out harmful random mutations. For the most part, natural selection actually keeps things simple and just maintains what is currently in place. If there are alleles in a population and 1 does not have any fitness advantage over another, then 1 eventually taking over the population can simply be explained by a random evolutionary mechanism such as genetic drift.
Natural selection on the other hand is the only mechanism for adaptive evolutionary change. The complex adaptations we see in nature such as the vertebrate eye for example, represent the accumulation of small changes such that each were more fit than another. There is no mechanism for natural selection to see ahead, each small step had to be beneficial enough on its own to be selected for, there is no perfect archetype being strived for.
Since natural selection can only work with existing variation which must necessarily arise from random variation, it is not possible for any adaptation to simply come out of nowhere. Natural selection tinkers with existing structures to give rise to new ones.
Is there a way to reconcile the fact that in general natural selection tends to be conservative rather than creative with the fact that natural selection is the only known mechanism to generate adaptive structures? I think so. Sean Carroll explained in his book Endless Forms Most Beautiful that over evolutionary time the force of natural selection tends to reduce the number of structures while at the same time increasing their specialization. For example, if a gene is duplicated several times, the resulting redundancy will loosen the constraints of natural selection on these gene sequences. As the conservative force of natural selection pares down this redundancy, new functions will be inevitably carved out from this variation.
In other words, natural selection is not a builder or an inventor. Natural selection is a sculptor.
Natural selection on the other hand is the only mechanism for adaptive evolutionary change. The complex adaptations we see in nature such as the vertebrate eye for example, represent the accumulation of small changes such that each were more fit than another. There is no mechanism for natural selection to see ahead, each small step had to be beneficial enough on its own to be selected for, there is no perfect archetype being strived for.
Since natural selection can only work with existing variation which must necessarily arise from random variation, it is not possible for any adaptation to simply come out of nowhere. Natural selection tinkers with existing structures to give rise to new ones.
Is there a way to reconcile the fact that in general natural selection tends to be conservative rather than creative with the fact that natural selection is the only known mechanism to generate adaptive structures? I think so. Sean Carroll explained in his book Endless Forms Most Beautiful that over evolutionary time the force of natural selection tends to reduce the number of structures while at the same time increasing their specialization. For example, if a gene is duplicated several times, the resulting redundancy will loosen the constraints of natural selection on these gene sequences. As the conservative force of natural selection pares down this redundancy, new functions will be inevitably carved out from this variation.
In other words, natural selection is not a builder or an inventor. Natural selection is a sculptor.
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