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.
Wednesday, June 16, 2010
Endosymbiosis
According to the endosymbiotic theory the first eukaryote was formed by the merger of 2 prokaryotes. But how did this happen? The traditional idea was that a primitive eukaryote engulfed the ancestor of our mitochondria since eukaryotes are known for phagocytosis, the abilty to engulf other cells. However, this is probably not how it happened because the ability to engulf other cells requires energy. It is now known that all eukaryotes either have mitochondria or have lost them at some point. Nick Lane contends in his book Power, Sex, Suicide that this links the origin of eukaryotes with the acquisition of mitochondria. So, before the host cell acquired mitochondria, it wasn't going around engulfing other cells. Lane suggests that perhaps these two ancient prokaryotes started out their symbiotic relationship by living in close proximity and progressed over time to one cell living inside the other.
Genetic studies suggest that the host cell was most likely a methanogen archea. These cells are anaerobic meaning they survive on sulpher and stay away from oxygen. This seems unlikely because if this were true, why did eukaryotes appear just as oxygen levels were rising? As Lane points out, more oxygen means more sulphates because oxygen reacts with sulpher from volcanoes to produce sulphates. But, as we all know, most eukaryotes thrive in the presence of oxygen. Besides, what would use would a methenogen have for mitochondria which are useless without oxygen? Lane believes that the most likely answer is that the ancestor of mitochondria had a diverse genetic toolkit. Perhaps, it had the genes for utilizing hydrogen and oxygen. Once it started supplying the hydrogen for the methanogen, it would no longer be dependent on deep sea vents and could venture off into oxygenated environments. This primitive eukaryote would have had to adapt to the oxygenated environment before the mitochondria ancestor living inside it lost its oxygen utilizing genes through disuse.
This chain of events is just one way eukaryotes could have evolved. The lesson here is that there were enough contingencies that the ascent beyond bacteria only happened once on earth in the billions of years that bacteria have populated the earth. We are truly lucky to have made it through this bottleneck. The biggest gulf in all of life is the divide between prokaryotes and eukaryotes. This gulf is much vaster than even the chasm between no life and life. We have more in common with a humble yeast cell than it does with a bacterium.
Mitochondria are the powerhouses, of the cell and without them, complex life may not even be possible. Bacteria have been around for billions of years yet, they are eternally bacteria. There are many disadvantages to maintaining mitochondria. Their genes evolve about 20 times faster than nuclear genes as they are more susceptible to mutation. Also, the genetic machinery must be maintained in each of the hundreds of mitochondria in each cell. Over time, in difference lineages, genes have migrated from the mitochondria to the nucleus. But, there is not even 1 example of a eukaryote losing all of its mitochondrial genes, therefore there must be a huge advantage to these genetic outposts. Lane argues that local control of energy production is absolutely essential. If mitochondria didn't have their own genomes, they would not be able to individually regulate energy production. Regulating hundreds of mitochondria from the nucleus would be extremely complex and it may not even be possible for such a mechanism to evolve.
Endosymbiotic theory is a beautiful illustration of the fact that the way nature solves problems aren’t always the most straightforward but reflect phylogenetic contingencies inherent to particular lineages. The merger of 2 simple prokaryotes, despite some of the disadvantages may have been the only way for complex life to evolve on earth. According to Lane, it is also why we are most likely alone in a universe full of bacteria.
Genetic studies suggest that the host cell was most likely a methanogen archea. These cells are anaerobic meaning they survive on sulpher and stay away from oxygen. This seems unlikely because if this were true, why did eukaryotes appear just as oxygen levels were rising? As Lane points out, more oxygen means more sulphates because oxygen reacts with sulpher from volcanoes to produce sulphates. But, as we all know, most eukaryotes thrive in the presence of oxygen. Besides, what would use would a methenogen have for mitochondria which are useless without oxygen? Lane believes that the most likely answer is that the ancestor of mitochondria had a diverse genetic toolkit. Perhaps, it had the genes for utilizing hydrogen and oxygen. Once it started supplying the hydrogen for the methanogen, it would no longer be dependent on deep sea vents and could venture off into oxygenated environments. This primitive eukaryote would have had to adapt to the oxygenated environment before the mitochondria ancestor living inside it lost its oxygen utilizing genes through disuse.
This chain of events is just one way eukaryotes could have evolved. The lesson here is that there were enough contingencies that the ascent beyond bacteria only happened once on earth in the billions of years that bacteria have populated the earth. We are truly lucky to have made it through this bottleneck. The biggest gulf in all of life is the divide between prokaryotes and eukaryotes. This gulf is much vaster than even the chasm between no life and life. We have more in common with a humble yeast cell than it does with a bacterium.
Mitochondria are the powerhouses, of the cell and without them, complex life may not even be possible. Bacteria have been around for billions of years yet, they are eternally bacteria. There are many disadvantages to maintaining mitochondria. Their genes evolve about 20 times faster than nuclear genes as they are more susceptible to mutation. Also, the genetic machinery must be maintained in each of the hundreds of mitochondria in each cell. Over time, in difference lineages, genes have migrated from the mitochondria to the nucleus. But, there is not even 1 example of a eukaryote losing all of its mitochondrial genes, therefore there must be a huge advantage to these genetic outposts. Lane argues that local control of energy production is absolutely essential. If mitochondria didn't have their own genomes, they would not be able to individually regulate energy production. Regulating hundreds of mitochondria from the nucleus would be extremely complex and it may not even be possible for such a mechanism to evolve.
Endosymbiotic theory is a beautiful illustration of the fact that the way nature solves problems aren’t always the most straightforward but reflect phylogenetic contingencies inherent to particular lineages. The merger of 2 simple prokaryotes, despite some of the disadvantages may have been the only way for complex life to evolve on earth. According to Lane, it is also why we are most likely alone in a universe full of bacteria.
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