Monday, December 22, 2008

Winter Break

I just finished a very stressful term that involved applying to grad school, and three tough computer science classes. Now that it is over, I am already getting ready for next term and a whole new set of challenges. This coming term I will be writing up and presenting my undergraduate thesis based on work that I have done on and off since September 2007 under Joe Thornton and Bryan Kolaczkowski. Additionally I will be working on Software Methodology, a demanding Computer Science course that centers around a group programming project. I already have some ideas of what I would like to work on for that course. I am getting interested in Android, Google's new open source mobile phone OS. Developing apps for it seems pretty straight forward. Also once the apps are done, marketing them is as easy as uploading them to the Android marketplace. Although Android doesn't currently reach as broad an audience as the iPhone, I believe that it will eventually overtake the iPhone in the global marketplace. Additionally while the iPhone requires programming in objective C, which I have no experience with, Android is built on Java which I am fairly comfortable with. All in all Android seems a much better investment of my time and energy.

Hope everyone is having a happy holiday season.
-John

Tuesday, September 30, 2008

Eukaryotic cell organelles

In preparation for the biology GRE subject test I need to re-learn (or learn) general biology. My upper division work has been focused on evolution and computational techniques, so I am very rusty on most other biological topics.

Today I went over organelle structure and function in eukaryotes (organisms that have membrane enclosed structures within their cells such as animals, plants, protists, and fungi). As well as containing the chromosomes, the nucleus contains the nucleolus which is the production site for ribosomal subunits. These subunits are then shipped out of the nucleolus, then the nucleus and into the cytoplasm. The ribosomal subunits are destined to either float freely in the cytoplasm where they eventually link up over messenger RNA (mRNA) to make proteins destined for the cytoplasm, or they attach to the walls of the endoplasmic reticulum (ER) where they produce proteins that are destined for a membrane or export out of the cell. It is also interesting to note that the mitochondria and chloroplast produce their own set of robosomes that more closely resembles procharyotic(bacteria, archea, etc) ribosomes.

The destination of proteins is determined by their amino acid sequence, structure, and sometimes post-translational modifications. Proteins that are to be secreted out of the cell have a hydrophobic signal sequence called the signal peptide.

Lysosomes are interesting. They have enzymes inside of them which digest proteins, carbohydrates and nucleic acids. These enzymes function well in an acidic environment where the pH is about 5 (a cell's pH is closer to 7 meaning it is neutral). This fact keeps the overall cell safe because the enzymes aren't able to digest the cell in its higher pH environment. However inside the lysosome, the pH is kept at 5 so that the enzymes are able to do their work. That is a very interesting adaptation.

Peroxisomes are similar and break down fats and harmful chemicals like alcohal. These organelles do so through the production and degredation of peroxide, which if allowed to come in contact with DNA would be very dangerous. Thus the reactions are kept within the peroxisome.

The mitochondria and chloroplast are cool. They have their own DNA, and produce many of their own proteins. They are basically like a small unicellular organism that lives within the cell and produces the energy needed for the cellular function. Biologists theorize that these organelles were once seperate organisms that entered into a symbiotic relationship where they exchanged energy production for protection and a stable environment.

Monday, September 29, 2008

Programming languages

We covered some of the basic programming language types today. The imperative type is the most commonly used one. It is characterized by assignments and statements following a sequential order. C and Java are examples of this. The functional type is less common and includes languages such as scheme, lisp, ML, and Haskell. In its purest form the functional language contains no assignments. The entire program is defined by function definitions, and the invocations of those functions. This idea of a language is called lambda calculus. Logic languages seem pretty interesting. The idea of a logic language is that you define logic relations between variables, and then when you implement the program, you can have it solve for any number of variables. The simple example of this we got in class was say you have a function called append. Rather than defining the function like one would in C where you take in two things and spit out the appended result, in a Logic language like Prolog you have the relational function append that has three things as arguments and the function returns true if the three things satisfy the defined requirement of the first two being subsets of the third. If you pass in a variable you want the function to solve for it will do that for you and spit out all of the solutions. For example ?append([1,2],[3,4],X) would spit out [1,2,3,4]. If you give it ?append(X, [3,4], [1,2,3,4]) it would spit out [1,2]. It seems like logic languages could, in theory, simplify programming.

Artificial Intelligence

This is the first post of what I plan on being many posts about what I learn from day to day in my classes. Yes, this may be a good time to unsubscribe from email updates.

AI is extremely prevalent. More so than I previously thought. When I think of AI I typically think of humanoid robots like Kizmet. Examples that I wouldn't have thought of include the intelligent agents in computer games, wall street trading robots and risk management systems, Google web search, the mars rover... There are tons of examples out there. In fact every computer utalizes concepts that were first thought of in AI research. For example the idea of hard coding expert information into computers was an active area of research in the 80's; today searchable dictionaries, computer diagnostic programs, and online sites like webmd are commonplace.

I am very excited to continue on with this class. I plan on posting a few things that I find the most interesting from each lecture.

Friday, June 27, 2008

Olympic Trials


The Olympic trials event started today. I don't think there have been any races or anything but the fair is going on, and a ton of people are here. I actually live across from one of the corners to Hayward field where the event is occurring so it is very exciting.

My girlfriend and I participated in one of the events that is probably supposed to get visitors to campus to check out the UO. As a result I won this cool "limited edition" medal. For getting a sheet stamped at a few places around campus. Well worth the effort if you ask me.

Summer School

I signed up for a few online classes thinking they would be easy. Unfortunately, although they are easy, they involve a lot of work! Oh well. I am learning about US Politics, International Relations, and English Linguistics.

Saturday, May 10, 2008

Poster on my research & Atheists who make "moral" choices

I am currently making a poster that I will be presenting at an evolution and development conference in Berkeley on the 28th. I am both nervous and excited. It is going to be on work I have done and discussed briefly in this blog for the past year or so. The toughest part will be trying to make the mostly mathematically and computer science based work I am doing interesting to evolutionary biologists. It should be interesting, it is very relevant to that field, I just need to come up with a good way of presenting the data.

Last night I went to a Barack Obama rally here at the University of Oregon. It was a lot of fun and I really hope he gets the presidency. Afterwords I joined some friends from the CIS department for beers, and when they asked me what I was having I informed them that I am one of those weird Atheists who doesn't drink. Really it isn't very weird at all, it is a very logical decision especially given that I have substance abuse issues in my family and showed signs of them myself in high school. That said I had a really good time and didn't feel awkward at all. I usually get very uneasy when telling people that I don't drink because I am afraid they will label me as a religious fanatic of some sort. This time though preceding the "I don't drink" with letting them know I am also an Atheist, really helped take the awkwardness out of the situation for me. I think I will continue to handle social situations involving drinking in this way. 


Wednesday, March 5, 2008

Phylogenetic methods talk

Today I gave a 10 min presentation on phylogenetic methods and evolutionary model selection. So I talked about how evolutionary trees are made from genetic sequence data. I think I nailed it pretty well.

After the talk, this guy asked me if you could use this stuff to predict where evolution will take a species in the future. I told him no, unfortunately to predict that you need to know what the environmental pressures will be, and there is a huge random component as well. I went on to tell him that the really interesting thing that you can do with phylogenetics is, fairly accurately, determine the genetic sequence of the last common ancestor of the species you test. The lab I am working in actually recently did that to help refute one of the main anti-evolution arguments posed by creationists. Creationists say that complex systems such as hormone-hormone receptor interactions are too specific to be explainable by evolution. That argument makes sense since hormone receptors are often very specific to the hormone that they bind. It seems that to explain the evolution of such interactions you would have to literally produce both hormone and receptor in the same lineage and it would have to immediately serve a purpose and rise to fixation. If that were true, it would be nearly impossible to do such a thing evolutionarily.

People in my lab sequenced estrogen receptors and estrogen related receptors from a very wide range of organisms to try and get at a very ancient common ancestral hormone receptor to examine it and see what it was like. They then took the sequence generated from the ancestor and grafted it onto yeast cells so they could examine which hormones it was sensitive to. They found that the ancestral hormone receptor was able to bind a variety of ligands including estrogen, which hadn't evolved yet. That showed that you in fact didn't need to evolve hormone and hormone receptor at the same time, that you could start out with a really unspecific hormone receptor that worked with completely different hormones which was eventually taken advantage of evolutionarily to develop into several different, specific hormone receptor-hormone interactions.

Evolution of Altruism

Today I learned about the evolution of altruism. Darwin admitted that altruistic behavior seemed to go against the idea of evolution. Recently though people came up with the math to show exactly how, even though it has a negative fitness to the individual who practices it, it can actually have an overall positive fitness effect. Here is the formula: rB > C where C is the negative effect to the individual for practicing altruism measured in # of offspring, B is the positive effect of altruism measured in # of extra grandchildren, and r is the proportion of genetic similarity between the altruistic individual and the individual who benefits directly from the altruism. Here is an example: ground squirrels practice altruism by giving warning cries to alert their fellow squirrels about the approach of predators. The squirrel giving the cries puts itself in danger by being an easier target for predation. However more of the offspring will survive if a squirrel does it. So here is the math, say on average a squirrel who has the gene causing it to give warning cries has a shorter life, and on average produces 2 fewer offspring, however the offspring it does produce has higher rates of survival, say 5 of them survive that would have otherwise been eaten. For a given squirrel since half of the DNA comes from mom and half from dad, the r will be equal to 0.5. doing this math we get 2.5> 2 which is true so you would hypothesize that this altruistic behavior would be genetically selected for. This is the same principle that goes into the evolution of extreme altruism as seen in ant colonies. The purest form of altruism is the worker ant who is completely sterile, it has no chance of having offspring. The reason this evolves though is because ants are so inbred that the value for r is extremely high. Any ant in the ant colony shares about 0.8 of its DNA with any other ant so you will hypothesize that any altruistic behavior will be very beneficial to the fitness of the gene that produced that altruistic behavior. Just for a comparison if you compare the entire human population the likelihood that you share genes with any other individual is about 0.0001, which is why we haven't evolved into having classes of drone workers like the ants have.

Tuesday, February 19, 2008

Sympatric Speciation- How to divide a population that is not physically divided.

I will share about sympatric speciation (evolution of one species into two when all populations live together in the same location) and how it ties into the process of evolution as a whole. It is a common misconception that for speciation to occur, populations need to be physically separated from each other. This need not be true, although it is correct that the process must be a result of some form of reproductive isolation there are subtle differences that lead to some methods being viable and others not. First I will define species as two populations that cannot interbreed to produce successful offspring. There are two forms of reproductive isolation, one is prezygotic isolation and the other is postzygotic isolation. Postzygotic reproductive isolation is the phenomena of two populations that are able to breed but always produce offspring that have significantly reduced fitness, and are thus unable to withstand the forces of natural selection over time. Examples of how this would look are: the outcome is lethal to the heterozygote offspring, they could come out sterile, or they may simply have reduced performance in the environment. Postzygotic reproductive isolation can only successfully evolve in populations that are physically separated from each other, this is because if a population is all together, the alleles leading to the reproductive isolation will be selected against because they result in individuals with decreased fitness and thus they will not ever rise to fixation. This is by the same process that two populations that continue to have postzygotic reproductive isolation will never successfully come together again, they are weeded out by natural selection.


Prezygotic reproductive isolation on the other hand is observed when individuals are physically incapable or preferentially driven away from mating outside of their group. These individuals are not selected against by natural selection because they do not end up cross breeding in the first place, thus they do not actually realize problems with heterozygotes having reduced fitness. Examples of this occur when different populations have different mating times so they never end up interbreeding, there may be gamete incompatibilities where the egg of one population rejects the sperm of another, and finally it could be due to the evolved mating preference of the individuals of each population. The fixation of allele frequencies that lead to prezygotic reproductive isolation usually occurs as a result of those alleles leading to an increase in fitness. One example of this in the wild is the stickleback which is a fish found in both lakes and oceans around the world. This fish is currently undergoing speciation due to prezygotic isolation. there are two emerging species of this fish, one typically lives away from the bottom of lakes, and the other is a bottom feeder. I specify that they are emerging species because even though the populations can interbreed, and sometimes do given the right environment, they have already evolved significant differences and inhabit separate niches. The one that lives away from the lakebed has spines and other things that help protect it from predation while the one that lives on the bottom doesn't have spines but does have features that allow it to feed better in that area. When the species are interbred the half-breed that is produced has less fitness than either of the two populations. Thus you can see how the development of mating preference would be advantageous to the survival of each of the sub-populations. It turns out that the probability of spawning between the bottom dwelling sticklebacks and the sticklebacks that live away from the bottom is much lower than within the populations. As a control the two groups were given the chance to breed with populations from separated lakes and it was seen that they do not mind matting with individuals from the other populations as long as they are of the same evolving subtype of stickleback.


From the example of sticklebacks you can see how, when given that the two fish interbreeding results in a half-breed with reduced fitness, you get strong natural selection favoring any genes that cause the two populations of sticklebacks to shy away from interbreeding. Another good example of this may be found on Galapagos island in their finch population. There are several sizes of finch that are each well adapted to feed on a specific type of food when food is scarce. There are finches with large strong beaks that are well suited for the hard nuts that smaller finches cannot crack open. There are finches with long beaks that are well suited for harvesting the seeds from cactus, and there are several others that are equally specialized. As you can imagine, if any two of those finch subtypes bread with each other, you would get offspring that are in between niches and aren’t as well suited to feed on either. Thus this is another example where evolution is being set up to take place. Although all of the finches are still able to breed, natural selection is favoring genes that cause them to not want to breed, because in doing so they reduce the fitness of their offspring. They in fact do exhibit preferential mating, and scientists have noticed that they have evolved different songs. Since birds attract each other for mating with their songs you can see how selection for that trait would end up increasing the birds fitness.


Now that I have described several examples of sympatric speciation known to evolutionary biologists that are currently taking place, I will attempt to concisely list all the steps involved in achieving evolution via sympatric speciation for the purpose of recapping the main points:

  • Populations need to have the opportunity to split into sub niches. For example there needs to be distinct niches that allow for the separating populations to fill them so that they aren’t forced into competition before they have gotten a chance to actually separate out into species.

  • Populations need to have some form of fitness advantage that goes along with developing preferential or physically impossible mating. This could be in the form of a less specialized heterozygote.

  • Populations need to maintain their lack of mating behavior until the process of natural selection has driven them to being fully incapable of cross breeding. At that point you have separate species.


Pre-zygotic reproductive isolation, post-zygotic reproductive isolation, and physical separation all simply set the stage for natural selection. The same process that drives the alleles conferring whatever form of reproductive isolation of two subpopulations to fixation eventually also drives the two populations into separate niches or perhaps direct competition with each other. In the first of the two possible outcomes you will get two similar seeming but distinct species. In the second example you have the potential for one population to wipe the other out, effectively erasing it from ever having existed. It is by this second process eliminating groups and the first pushing populations further and further apart that we do not see a more complete fan of species ranging from the simplest life forms to the most complex. Instead we see species with seemingly profound differences and wonder how they could have ever shared a common ancestor.

Lose Weight and Stay Healthy in as little as 60 seconds a day!

Thats right, you heard it! My revolutionary work out plan will turn around your health in as little as 60 seconds a day. The plan's sound reasoning is based on the "anything is better than nothing" concept. Chances are you do not work out, and you probably feel slightly guilty about it. You have probably tried more exhaustive work out strategies only to find several months down the road that your much needed day of rest quickly flushed all memories of your commitment to health. That is where my plan comes into play. Just do something, anything at all, for as short a period as you desire, every day. Forming habits are hard so I say just give yourself credit for doing anything you can, every day.

On that note I start day one of my work out plan. I did 15 push-up/jump-squat things, it took me about a minute to do and it felt like something I can manage squeezing into my busy college life. Granted I am feeling tired due to not working out in... well, I am not sure really. Anyhow that is all for now.

More later on trading options on the stock market, or perhaps I will write a little about evolution, or maybe even more on statistical model selection applied to evolutionary trees.