The prestigious science journal Nature recently had an article on the best cities for science. They have some really cool interactive graphs showing scientific productivity of different parts of the world and how many citations each place gets. What struck me was how quickly China grew in terms of volume of publications, but how poorly their articles were cited. Whether that is due to papers being published in primarily Chinese language journals, the papers of being of poor quality, or the scientific community ignoring important papers coming from China for whatever reason is unclear, but I think it shows that other countries have a while to go before achieving scientific dominance.

Typically, DNA is thought to be transcribed into RNA in an exact copy of the DNA minus random errors that occur due to poor fidelity of the polymerase that makes it. However, it's been well known for more than 10 years that RNA can be altered systematically through (still mostly mysterious) mechanisms called RNA editing. This is a well known phenomenon that is pretty much universally believed by all biologists. However, RNA editing was thought to be a mostly rare process that only affected a handful of genes. This group used new technology called deep sequencing that allows for high throughput, quantitative sequencing of millions of RNA molecules at once, and their results suggest that RNA editing isn't as rare as once thought. To be fair, this is an abstract submitted to a conference, so it only has undergone the most minimal editorial (not really peer) review based on a paragraph or so of presented data. This may all be an artifact due to some systematic bias of the sequencing platform. There are probably hundreds of other groups using deep sequencing of RNA, so it will be interesting to see if other groups can replicate this.

That's simply not true. I'll reference you this article which says that between 1997 and 2002, there were around 2700 patients in Canada admitted to the ER for acetaminophen overdose and 69% of them overdosed intentionally. That's about 370 people a year intentionally overdosing themselves with acetaminophen a year. In the US, 26,000 people overdosed on the drug over around 10 years. If the rate of intentional overdose is similar in the US and Canada, that's about 1800 people intentionally overdosing on the drug each year in the US. I personally know at least one person who attempted (and failed) to overdose on the drug. Dying of liver failure is a pretty nasty way to go compared to firearms, but anyone who has worked in any urban ER knows that intentional overdose is pretty common.

The Atlantic magazine just published a really eye-opening article on Steven Hatfill, the FBI's first suspect. It is very clear from the article that the FBI was hell-bent on finding a perpetrator of the crime even in the absence of any solid evidence. It's an interesting and frightening read about how the FBI could completely destroy your job, your friends, your day-to-day life, and your family if they falsely accuse you of a crime.

From reading the projects on the DNA Initiative's website, it seems that they need mitochondrial DNA samples as test samples to develop various forensic techniques.

Cheap: it used to cost millions of dollars to sequence a genome but new technologies are greatly driving down the price. The sequencing guru I mentioned above predicts it will cost about $10,000 some time in the next 10 years Fast: it probably will take a week to sequence. However, the analysis tools are very complicated and will probably take much longer Good: as far as I can tell, this technology is pretty accurate. A good run will sequence every piece of DNA 20 times so sequencing errors tend to get washed out.

So I work in biological sciences, and I have the special privilege of having the guy who sequenced the first cancer genome working down the hall from me (he's also my thesis committee).

There is now technology to sequence entire genomes very quickly using massive parallel sequencing. Ideally, if you were sequencing a tumor from a single person, you would get tissue from the tumor and also from the non-tumor (usually skin) and sequence them at the same time. Then you compare the two to distinguish what is simply variation in each person's genetics and what is acquired by the tumor. In my opinion, that's the best way to do things and probably the most informative because you're looking a tumor in a real person that is subject to all the selective evolutionary pressures that occur in people.

These groups didn't take that approach for reasons unclear to me. Instead, they sequenced cancer cell lines. If you cut out a person's tumor and stick it in a test tube with various growth factors, it will almost certainly die within a week or so. However, you occasionally get some cells that can grow in this situation because they've acquired some mutation that lets them grow in tissue culture. You then expand and passage these cells until they grow rapidly in culture. The problem here is that you're no longer dealing with a normal human tumor; you're selecting for tumor cells that grow in the artificial tissue culture environment. The second problem is that you're not sure what to compare the tumor sequence with. Due to privacy concerns, you almost never know who actually gave the tumor that was made into a cell line (as an aside, look up the HeLa cell line and its sordid history) so you have to compare to the human genome project. The problem here is that there are differences between people and you can't tell whether the "mutation" you see is just a normal variation or actually something in the tumor.

These are the important limitations you have to consider when evaluating these papers.

Now, on to your question. They have 30,000 changes in the DNA compared to their reference "normal" genome. Nearly all of those are in "junk" DNA: as far as we know, they don't code any genes or anything else that regulates genes. Of the ones that are in interesting regions, the vast majority of them are called synonymous mutations which means the DNA is changed but due to the way it is interpreted, the protein that it makes is identical (to use a computer analogy, imagine that an the opcode for JMP was changed from 01 to 02 but both 01 and 02 are translated by the computer as JMP).

Now, a certain number of mutations aren't like that. They either lead to truncated proteins, alter the amino acid sequence of proteins, alter mRNA splicing, etc. There are also other genetic changes such as duplications where the gene sequence is unchanged but may be copied several times to increase the gene dose. These are really the interesting things because they alter protein function or gene dose. From a brief reading, it looks like there are around 100 of these.

Now, it's really difficult to tell whether these mutations are really relevant to cancer progression. Some of them might just happen due to tumors just mutating really fast and not really affect the cancer progression one way or another; they are so called "passenger" mutations that just come along for the ride. You can introduce these mutations into cells in lab to see if they do anything, but the real test is to sequence a bunch of human cancers and see if certain mutations are recurrent. This work is currently underway and will prove very informative about how genetically heterogeneous tumors really are.

So, in short, there are about 100 haystacks. Further sequencing of other tumors will show if these are relevant to cancer in general. In my personal opinion, I think that further sequencing will identify very few common mutations and everyone's cancer will be essentially unique in the mutations it acquires. That will force us to completely rethink how we view cancer on a broader scale as not a single disease but a collection of highly related diseases that need to be treated individually.

I am not a professional in mental health, but I do have some education on this. As others have mentioned, the best thing you could do would be to talk to a professional yourself, especially a professional who has experience with treating people with substance abuse disorders. Unfortunately, it is unlikely you will find a therapist who well-trained in treating other addictions, although they do exist. Often, therapists include friends and family in the therapy, and sometimes, they give therapy to just the friends and family if the person with the problem is unwilling to come.

Unfortunately, there is a lot of really bad advice on this thread. Do not hack his account, disconnect his computer, or any other majorly confrontational thing to take away the source. Do not get a bunch of his friends together and have a movie style intervention. He's addicted to the game; you will just piss him off and he'll never talk to you again and most likely find another way to play. Don't let others tell you that you shouldn't bother helping him because it's too much trouble; the very fact that it got this bad is a testament to how many people decided that it was someone else's problem, and the worst thing that can happen is that your friendship with him dies, and it doesn't seem to be doing so well in its current state anyhow.

Secondly, people only change when they're willing to change, which means that it's ultimately his responsibility, but that does not mean that you can't do anything to help him become more willing. Sit him down and quietly and politely express your concerns but try to engage him in the conversation. Here would be an example script, which I've adapted from the CAGE questions for screening for alcohol abuse:

"John, I've noticed that you've been playing a lot of that game lately, and I'm worried that it's not healthy for you. How do you feel about that game? Do you think that you should play less? Have other people told you that you should play less? Do you ever feel bad or guilty about playing so much?"

From that, you could determine if he's in the pre-contemplative stage (he thinks there's no problem) or the contemplative stage (he realizes there's a problem but isn't sure if he wants to change or doesn't know how). If he's in the contemplating stage, try to get him to verbally state the negative impact of his playing:

"It seems that you recognize that you are playing too much game. Do you think this is hurting your grades? Your social life? Your relationships with your parents? Your ability to date? Do you think cutting down on playing would help you in these areas?"

Once you've gotten him to admit that there are negative impacts of what he's doing, you've done a lot. From there, you should guide him into professional help:

"Well, it relieves me to know that you recognize that you have a problem. I'd just like you to know that as your friend, I'm concerned about you, and if you want help, I can help you get that help (i.e. refer to student health)."

That's really all you have to do. Even if he completely rejects you, you've at least planted some seeds of doubt in his mind. When he reaches rock bottom, those seeds will sprout, and you will have done the best you can as a friend for him.

Best of luck.

I had a professor who argued that the kidney was actually far more important than the brain. Here was his logic. In boxing, the whole point is to beat the living tar out of someone's head, with no regard to how much brain damage you may be causing. However, if you punch someone's kidneys, you've committed a grave offense.

I work in biology, and we use Spotfire DecisionSite to visualize and analyze a lot of our massive genetic data. It's a very powerful program that I barely know how to use. It seems to have packages able to analyze pretty much anything you want, and you can even write your own scripts to help things along.

This post is tremendously over-simplistic to the point of being nothing but Israeli propaganda. Please read the Wikipedia article about the Palestinian exodus to understand what really happened. It is not entirely clear why the majority of the Palestinians left, but there was a lot more going on than the Mufti.