It is very hard. For most experiments, you're not trying to detect a few molecules of DNA. You can set up your detection sensitivity so that a tiny bit of contamination won't be detected. For something like this, were you are trying to detect very small amounts of DNA, it becomes much, much harder. Firstly, you use very purified reagents. All the reagents need to be aliquoted individually in a location physically separate from where the DNA is. This is typically done in a specialized clean hood that can be sterilized with UV radiation. The reagents are combined in a similar hood and then transferred to where the tube with the DNA is. All of this needs to be done using gloves that are changed frequently. Next, you have to be very careful about what pipettes you use. The pipettes from each step need to be thoroughly cleaned, possibly DNAse treated to remove DNA. Again, each part of the experiment should use different sets of pipettes. To ensure that things are not contaminated, you have to use various controls such as leaving out the polymerase, dNTPs, etc. I'm sure if you got some other biologists together, they could brainstorm about a dozen precautions. It's not impossible to do, but it can be hard. I personally have lost months of research time because I accidentally contaminated something. Replacing all my reagents to clean ones did nothing, so I figured it was my pipettes, but the problem didn't go away when I thoroughly cleaned them. Eventually, I switched to using different sets of pipettes for each step, and the problem resolved. You may say that I'm not a careful scientist, but while talking to people to resolve my problem, pretty much everyone said they've experienced something similar. None of use proposed and published any crazy theory to justify it.

Yeah, they did the proper controls on the DNA generation of frequency. I think that could, within the confines of current science, be a reasonable claim. They did not do those same controls on the transmissible assembly of DNA through these water nanostructures. That claim is the one I think is unbelievable. If I were writing this paper, I would make it explicit that these controls were performed for both experiments. The fact that they did not do this leads me to conclude they were trying to trick the reader into assuming they did.

I take back my assertion that this is a hoax. Apparently, this Nobel Prize laureate has a history of producing very tenuous science on this topic. I think he's actually serious, which is pretty sad.

I am a biologist by trade, and I can say that this paper is very, very poorly done. If it was submitted to any major journal in the field, the peer reviewers would tear it to shreds. Here is the big experiment: 1) Take DNA and place it in tube #1 diluted around 1 million fold 2) Separate it from tube #2 containing all the building blocks of DNA, but not properly assembled 3) In between tube #1 and tube #2 is a special piece of metal 4) Subject the entire thing to low frequency magnetic field 5) There is an induction of the DNA to emit oscillatory radiation 6) DNA replicate magically appears in tube #2 from the building blocks I can buy the assertion that DNA at certain dilution transmits some strange radiation. It's step 5 to 6 that I think is complete and utter garbage. They don't do the proper controls for step 4 to 5. What happens when no DNA is present in tube #1? What happens when there is no inducing field? What happens when the building blocks are present in tube #2? They clearly know that this is an issue because they do the exact controls from steps 4 to 5. The "synthesis" of new DNA can easily be explained by one explanation: contamination. DNA sequencing techniques are sensitive enough to detect one or two copies of that sequence. If any of their reagents, tools, or lab members got even a single molecule of DNA on them and transferred it to tube #2, they would see that result. This is a basic fact that pretty much all molecular biologist learns (usually the hard way, by accidentally contaminating something of importance). To give the authors the benefit of the doubt, I'll go ahead and say they have successfully duped Slashdot with a hoax spoofing the claims of homeopathy.

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.