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Originally Posted by Uncle Erik /img/forum/go_quote.gif
Congrats! I remember when you made the move so you could finish your degree, and I'm very happy to hear that you've made it!
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Thanks a lot Uncle Erik. It's very exciting.
I'm happy to know that I've made it too. There was a *cough* BIG *cough* hiccup that occurred back in November which made this seem like it might not happen, but I can't talk about it until after my defense. But it is a good story
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| Any plans for after the test? Remember that drunken posting can get you in trouble with The Powers That Be. |
There is a bar on campus literally about 100 feet away from the exam room. I plan to go to the bar and start drinking beer for several hours.
Before I start to enjoy the beer too much, I'm going to call my wife, my parents, her parents, and my friends to share with them. And then I'm going to drink some more beer! I don't think I'll be able to drink too much, because I expect I'll have to do some work to my thesis to incorporate last minute changes required by the examination committee on Friday and Saturday - but it'll be a fun night anyway!
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Originally Posted by intoflatlines /img/forum/go_quote.gif
Congratulations! I can only dream.. I am in my fourth year of undergrad (transferring schools messed up my credits) so I have one year left. It seems like an eternity, but I can't even imagine going to grad school! I just want to be done.
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I know that feeling... LOL I'm feeling it right now. I can't wait to be done. I also can't wait to tell everyone my nightmare story.
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Originally Posted by smrtby123 /img/forum/go_quote.gif
Wow I am always inspired when I see another person rise to the level of PhD. Your commitment to the furthering of human knowledge is commendable. What did you do your PhD/Thesis work on?
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Thanks a lot, I appreciate the kind words. I hope I'm furthering human knowledge, cause I'm certainly not fattening my wallet.
Most (sane) people who do Ph.D's (at least in the sciences) will do all three to five of their research chapters on related topics. Chapter 2 is on something called mutational meltdown - which falls into the realm of theoretical population genetics and conservation genetics. Basically it revolves around the question: How small can a population get before it is very certain to go to extinction due to genetic factors?
Chapter 3 is about something called compensatory mutations. Genetic mutations generally fall into three categories: those that are good, those that are bad, and those that don't really do anything. Compensatory mutations represent a class of mutations that don't fall into any of the above categories. They tend to be good to have, if you already have a different (and often specific) bad mutation somewhere else in your genome- but if you don't have that bad mutation, then they are bad themselves. Compensatory mutations are implicated heavily in antibiotic resistance and antiretroviral therapy failure in HIV. If you're a bacteria, it's a good idea to have a gene that gives you resistance to antibiotics you are encountering in your environment, because it means you don't die- but if you don't have any antibiotics in your environment, than that gene means either you're doing something you don't need to do- or you're doing something in a non-optimal way - e.g. they are costly. The problem with antibiotic resistance isn't so much with the resistance genes themselves, but rather with secondary mutations - compensatory mutations - which allow the bacteria to maintain it's antibiotic resistance even in the antibiotic free environment- e.g. it mitigates the costs of maintaining antibiotic resistance in the antibiotic free environment. There is a similar story with HIV-1, but it's more complicated. Anyway, compensatory mutations are also important for conservation genetics- because they can allow small populations (that have accumulated large numbers of bad mutations) to become healthy again much more quickly than would be expected without compensatory mutations. We took microscopic worms called Caenorhabditis elegans, and knocked genes out of them (made them sick)- and then maintained them for 100 generations and ascertained whether or not they were able to become healthy again after 100 generations. The answer was yes. Since the deleted genes were still deleted at the end of the experiment, this must be due to mutations that occurred elsewhere to fix the damage caused by the knocked out gene.
The forth chapter is also about compensatory mutations, but it's a mathematical / statistical treatment of compensatory mutations. We ask the question: How many compensatory mutations exist for every bad (deleterious) mutation? The answer, averaged over many viruses, bacteria, and some eukaryotes, is 11.84. That's a lot bigger than anyone expected it to be. As much as 30% of all deleterious (bad) mutations will have no compensatory mutations, but almost 40% of compensatory mutations will have greater than 20 possible compensatory mutations.
The fifth chapter was about studying compensatory mutations within genes. Do these compensatory (fixer) mutations exist close to the deleterious (bad) mutations within the genes they are contained within, or are they scattered at random? Do they exist in clumps in some regions of the gene, above and beyond any clumping around the site of the deleterious mutation? And, do compensatory mutations tend to occur close to the site of the deleterious mutation in the three dimensional structure of the protein? The answer to all three questions above is: yes. This was basically a statistical study using software that I wrote. It was fun, and is sort of the jumping off point for my postdoc work.
The sixth chapter of my thesis was about the evolution of cooperation. Why do things help each other out, instead of screwing each other over? The classic example of this is something like the Prisoner's Dilemma- although there have been many studies of the evolution of cooperation. One of the things most of these studies have in common is that they typically are a-mechanistic. I wanted to build a mathematical model based on a simple mechanism- sharing. If I have a lot of stuff, and you don't have any- I could give you some of my stuff and it wouldn't cost me very much, but you'd benefit a lot. For example, if I had dozens of headphones, including a lot of high end Stax, and maybe the baby-O, I might be inclined to give away to my friends some of my lesser headphones. There is a classic example of this in vampire bats. Vampire bats need to consume a blood meal every 72 hours- if they don't, they die. So if one vampire bat has not successfully fed after 48-72 hours, but another vampire bat has just successfully consumed a blood meal, the second bat will give the first bat some of it's blood. The second bat will still be able to to go at least another 48 hours without eating, but it gives the first bat more time to successfully feed. This is a pretty easy mechanism to understand, so we modeled it to try and understand why it isn't more common.
Turns out it's uncommon because the necessary conditions for sharing to be met are very restrictive.
And now I've given up on most of that, and I'm working in a biochemistry lab- because I wanted to do something new and different.
Cheers all, and thanks for the interest,
Brad
