Comment author: Manfred 20 May 2011 03:40:51PM *  7 points [-]

Yeah, sure, it sounds fun!

If you're a molecular biology person, I would be interested in an article if there are any good human efforts to design proteins, and what sort of challenges they face and what techniques they use to overcome those challenges. Or even designing whole living systems - we seem to like futurism around here, so "speculative bioengineering" could be fun.

Comment author: virtualAdept 20 May 2011 04:36:26PM 10 points [-]

Oh, your suggestion makes me grin. Systems biology is essentially the theme of my academic career. I will definitely write about those things; the hard part will probably be shutting up about them.

Seeking suggestions: Less Wrong Biology 101

35 virtualAdept 20 May 2011 03:28PM

I’ve been a reader and occasional commenter here for a while now, but previously have not had a solid idea of what I could or wanted to contribute to the community in posting.  In light of recent comments stating an interest in more posts that offer concrete, factual information as well as remembering lukeprog’s call for such things in his Back to the Basics of Rationality post, I am considering a series of condensed posts about biology.  As someone who has spent my formal education on biologically-focused engineering (bioengineering BS, now studying bioinformatics under a chemical engineering department for my PhD) but has always had the bulk of my friends in electrical engineering, computer science, and more traditional chemical engineering, I’ve gotten used to offering such condensed explanations whenever biology works its way into a discussion.  From what I’ve seen on LW thus far, the community educational base leans more in those (non-biology) directions, so I believe this is a niche that could use filling. 

Since biology is a rather broad subject, and you could all go read Wikipedia or a textbook if you wanted a very detailed survey course, my intent is to pick targeted topics that are relevant to current events and scientific developments.  Each post would focus on one such event/Awesome New Study, discussing the biological background and potential implications, including either short explanations or links to the basics needed to understand the subject.  If there are any political ties to the subject, I will withhold my explicit opinions on those aspects unless asked in the comments. 

My questions, then, are the following:

  • Is this something that people here would find interesting/useful in the general sense?  (While I do enjoy talking to myself, doing so on this topic has gotten a bit old, so I really do want to know if no one really thinks this will be helpful.)
  • How long/in-depth would you like?  This question is intended to gauge what my background explanation: background links ratio should be.
  • And most importantly, what are some topics you would like to see discussed?


UPDATE: Having followed the comments so far and done some preliminary outlining, I'm leaning toward a more organized progression of topics that will still tie into current interests and developments, but not be centered on them.  A bit more thought and putting ideas to text indicated that I could group the interest areas into biological categories (molecular, populations, developmental, neuro, etc) fairly easily, which would then allow for a 'foundations' post to introduce each major category, followed by posts that go over What We Know Now, Why We Care, and Where It's Going.  

Comment author: [deleted] 20 May 2011 02:03:30PM 1 point [-]

The books in question are popularisations of many earlier studies, and certainly not 'announcing boldly that it has The Answer'. To quote from the material at http://www.lulu.com/product/paperback/cancer-nutrition-and-survival/243487

"Clinical trials are needed to test such non-toxic therapies. Biological research suggests that cancer is a treatable condition. Although current data is not sufficient to indicate the degree of life extension achievable, many terminal patients might die of other causes, before the cancer kills them. Cancer patients deserve to be offered this opportunity."

In response to comment by [deleted] on I want to save myself
Comment author: virtualAdept 20 May 2011 03:14:51PM *  10 points [-]

I'm trying to think how to frame my response to this. I will essentially never say that something shouldn't be studied (unless the act of studying would cause more harm than good to intelligent test subjects), and I don't know with certainty that vitamin C megadoses would not be helpful. I know a lot of reasons why they probably wouldn't be, but that's all I have.

My major problems with the book itself (from what I can see of it online, and what I've read of the studies on the subject) are:

1) It suggests ('Cancer patients deserve to be offered this opportunity') that some wrong is being done to cancer patients by not chasing this idea farther than it has already been chased. This is both somewhat sensationalist, and revealing that the authors either don't know much about or have chosen to ignore the cognitive environment of cancer research. Cancer researchers would love to find a silver bullet, or even a reasonably effective bronze one. Quite aside from the good it would do for humanity, it would bring them an awful lot of immediate prestige. Existing biases in the field are therefore very much in favor of pursuing avenues of research that might be a bit of a stretch, if there's any hope that it might lead to a breakthrough. This makes blind rejection of potentially useful ideas very uncommon, which strongly downregulates my estimate of the idea's merit.

2) If the authors think that this research has a high potential for payoff, why are they not conducting it themselves, instead of imploring others to do so? There is certainly a much higher personal payoff to be had if it were to actually work, if they were to do it themselves. (I do rather intimately realize that 'doing research onesself' is much simpler said than done, and therefore would accept it as an answer that they are making serious, concerted, and persistent efforts to begin the clinical trials they're calling for.)

In response to comment by [deleted] on I want to save myself
Comment author: Pavitra 20 May 2011 12:49:41PM 4 points [-]

This would be good to know if true. Can we get a second opinion on this, preferably from someone with domain knowledge of medicine?

Comment author: virtualAdept 20 May 2011 01:42:58PM 10 points [-]

I'm a graduate student studying metabolomics, and my lab mate is actually doing her thesis research on cancer metabolism. My knowledge base is strong in the biology involved, and weak in the politics of medical studies and treatment preferences, as I have no direct interface with MDs.

Cancer has no 'silver bullet;' as is generally recognized in medicine nowadays, it is actually a collection of diseases with differing causes, that respond in different ways to various treatments because the mechanisms which promote cancer development, growth, and metastasis differ between forms. There is a consistent cycle in cancer research that pays homage to this fact - someone has good lab results with a new drug, everyone gets excited, and then it's found that its utility is extremely limited (or more often, impossible due to deleterious side effects). This knowledge causes me to have a very low probability estimate for the truth (of the magnitude, at least) of these claims.

Another red flag: If this was such a medical breakthrough, it would be backed up by controlled studies, and it would be a paper in Cell or Nature, not a self-published book announcing boldly that it has The Answer.

If you would like more specific information about cancer, I can either answer questions or send links, later, but at the moment, I need to leave my computer.

Comment author: virtualAdept 19 May 2011 04:43:13PM 2 points [-]

Genetic engineering is simply a tool. A particularly malicious individual with an absurd amount of independent resources, ingenuity, and time on eir hands could use it to make something dangerous - but such a comic book supervillain aspirant could be far more effectively evil simply by making a lot of bombs and using them on densely-populated areas.

In the non-comic book world where we live, genetic engineering is done in a veritable regulatory straightjacket. Development of products for human consumption and/or those that will have contact with non-modified organisms must be exhaustively evaluated for risk potential and its expected benefits justified before the research even gets funded, in most if not all cases.

So, no green goo, and no, you should not be afraid. (Interested in the regulatory practices that keep somewhat bullying-inclined corporations such as Monsanto in check, perhaps, but that has little to do with genetic engineering and much to do with corporate politics and asshattery.)

Comment author: NancyLebovitz 19 May 2011 09:57:45AM 4 points [-]

I'm concerned about allergies-- for example, fish genes being put into tomatoes for cold resistance, though I just found out that it was never commercially produced. Some people can literally die from eating a small amount of fish, and I don't know whether any of the dangerous fish proteins were in the tomatoes.

Even if you're talking about less drastic engineering, moving genes around could make life a lot harder for people who need to know which foods are safe for them.

Comment author: virtualAdept 19 May 2011 04:29:27PM 3 points [-]

Food allergies tend to be a response to one compound, or a very small set of compounds. With respect to using genes from one organism to confer hardiness on another, the chances of conferring the production of a deadly allergen are diminishingly slim, but you'd better believe that if such a thing was to be done, the FDA (or analogous organizations outside the US) would have warnings plastered all over the derivative organism.

The level of justification and background research showing how you're NOT going to destroy the world that is required to even get funding for this sort of thing is.... large.

Comment author: Hul-Gil 14 May 2011 02:01:22AM 0 points [-]

Why programming or other computer science? It is important to be able to know how to use a computer, but beyond that, what's the benefit (unless the student is going to be a professional programmer)? Perhaps it trains the mind in a useful way?

Comment author: virtualAdept 14 May 2011 02:28:39AM 1 point [-]

Exactly that. Being able to think in explicit algorithms is extremely useful for decoding your own thoughts and being able to actually change your mind.

Comment author: virtualAdept 13 May 2011 05:27:56PM *  2 points [-]

Since we're taking students from varied and heterogeneous backgrounds and it's an advanced degree, I'd have a list of required topics, with the students being able to place out of the area of their undergraduate study (if their undergrad major covered one of the topics).

Core areas would include:

  • Probability/statistics

  • Mathematics (at least through basic calc and linear algebra)

  • Computer science (at least basic programming, algorithms, and software architecture)

  • Natural science (chemistry OR biology OR physics)

  • Research experience in a natural science or engineering lab of choice

  • Psychology (emphasis on cognitive biases and memory)

  • Anthropology

  • Philosophy (overview course on historical perspectives)

Also, added seminar courses with mini-units to tie subjects together and place them in context.

Electives would be open-ended, pending an essay to justify their selection.

Anyone have thoughts on whether a business or economics course should be included? I considered that, but I have not taken a formal course in those topics myself, and so don't have a good estimate of their actual utility.

Comment author: virtualAdept 13 May 2011 04:24:23PM 20 points [-]

I've read your conversion story on your blog, and the answers you've posted here so far. The most salient question, to me, has become 'what led you to alter your belief about the existence of a deity,' specifically. Everything I have seen thus far has apparently relied on good feelings when you have participated in services and been around Mormons (and how nice they were/are).

I don't think you could give a less convincing account of why you should believe a god exists than that. The Mormon student I know in the lab is a kind, helpful, delightful person to be around, but so are my Catholic labmate and my atheist friends. If the general Warm Fuzzies you felt are a major part of your reasoning, how do you control for other possible sources of Warm Fuzzies?

If there are other reasons that caused you to believe in a god, those would be what I am reading this thread to hear.

And of course, if I have incorrectly understood the point of your story on your blog, please correct me.

In response to comment by [deleted] on The elephant in the room, AMA
Comment author: calcsam 13 May 2011 03:38:00PM 3 points [-]

This is possibly the best question in the thread. Thank you.

All of my anticipations seem to be driven by stuff. I expect stuff to happen as I, or other people, do, or don't do, things.

When I pray, I expect to feel a greater sense of clarity in my thoughts. I will expect to occasionally feel a great sense of inner peace. This feeling has been described as “A small voice that pierces to the very soul.” “It causes the heart to burn.” “Love, joy, peace, longsuffering, gentleness, meekness.”

As I follow basic Church lifestyle and standards, such as reading the scriptures daily, praying often, attending church and serving therein, avoiding alcohol tobacco, etc, waiting until marriage for sex, and so forth, I expect to develop “Christlike attributes.” I expect to become more patient and loving; I expect to be able to keep clean thoughts and to be humility. I expect to develop related social skills: projecting love through genuine enthusiasm about other people. I expect to be able to maintain a vision of the future motivated by my faith that translates into happiness and an optimistic attitude.

I expect that these things will operate not only in me but in others. I expected that these things would happen to the people I taught in India, for example. I expect to marry another Latter-day Saint; if she continues faithful, I expect these things will similarly help my future wife. I expect that doing these things will help me to have a happy, successful family.

I anticipate that others’ actions not in harmony with these principles will make them less happy in the medium-to-long run (and sometimes the short run). For example, when my fraternity brothers go and watch their porn, I anticipate that they will slowly extinguish their consciences and find difficulty taking joy in the simple, innocent pleasures of life. I anticipate them having greater difficulties having successful relationships and marriages.

I could go on in this vein, but I think that should be enough.

Comment author: virtualAdept 13 May 2011 03:56:06PM 0 points [-]

What has led you to anticipate (for brevity, some of) these things? Including some benefits for you and the predicted detriments for your fraternity brothers.

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