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Comment: Re:Intentionally once for me. (Score 1) 566

by DebateG (#40459411) Attached to: I reach my workplace, primarily/typically, by:
My girlfriend had a similar experience to yours. She was riding her bike down a 4 lane road, 2 lanes going each way around 5 pm. It's not a particularly busy road even during rush hour and it is pretty common to see cyclists on that stretch of road. It was broad daylight. She was staying the right lane, was wearing a reflective vest, and just minding her own business. She rides pretty quickly, so she probably wasn't impeding traffic much more than any other slow moving vehicle. She had ridden down that route many times before with no trouble. A guy drove up behind her. He tried to pull into the left lane to pass her but could not because there was a car there so he pulled back behind her.. Once the left lane cleared, he accelerated, bashed her in the back, knocking her from behind to tumble onto the road. He then drove off into the left lane. Fortunately, a motorist witnessed the entire thing, followed him, recorded his license plate. He realized he was being followed and peeled away onto another road and sped off onto the nearest on ramp. The other witnesses immediately stopped to render aid. She ended up going to the hospital and was treated for minor injuries, but being assaulted at 40 mph by a car is pretty traumatizing. The police ran his placts and found his name and address. They have been completely unresponsive to prosecuting the guy for assault and hit and run, both of which are felonies. She got a lawyer and is suing him, but we haven't heard back as to what became of that. It's not just the motorists that don't care about cyclists. The police also do not think they deserve a right on the road. I'm just happy they chose not to ticket her for obstruction of traffic or something else that they made up to generate revenue.

+ - Network attached storage and backup for dummies

Submitted by DebateG
DebateG (1001165) writes "I am a graduate student in a small research laboratory that recently has been generating large amounts of data. We have been requested to start storing our data in lab instead of a common drive for the entire department, as the department will no longer support the amount of data we have. As such, we are in the marker for network attached storage (NAS). We want to use this drive as a data store where everyone keeps all their data. We also want this drive to be routinely backed up, perhaps to a USB HDD.

Here are the requirements:
1) The setup and maintenance must be performed by people with above average intelligence but not much computing know-how.
2) Because of #1, it should be commercially available. A homebrew setup is unlikely to fly in this environment.
3) The system must support several terabytes of data
4) The system must be backed up routinely. Ideally, we should easily know whether or not the backups really happened.
5) The cost should be less than $1000.

For a small, tech-novice environment that needs both storage and backup, what is a good solution?"

Comment: Re:umm (Score 1) 347

by DebateG (#34860834) Attached to: Nobel Prize Winner Says DNA Performs Quantum Teleportation
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.

Comment: Re:umm (Score 4, Insightful) 347

by DebateG (#34860702) Attached to: Nobel Prize Winner Says DNA Performs Quantum Teleportation
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.

Comment: Re:umm (Score 5, Insightful) 347

by DebateG (#34857870) Attached to: Nobel Prize Winner Says DNA Performs Quantum Teleportation
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.

Comment: But is anyone reading their output? (Score 4, Interesting) 302

by DebateG (#34219054) Attached to: Tide of International Science Moving Against US, EU
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.

Comment: It's called RNA editing, and it's not new (Score 1) 196

by DebateG (#34169882) Attached to: Central Dogma of Genetics May Not Be So Central
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.

Comment: Re:suicide? (Score 1) 164

by DebateG (#31957664) Attached to: Colleague Comes Forward To Defend Anthrax Suspect
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.

Comment: They destroyed Hatfill (Score 4, Informative) 164

by DebateG (#31957458) Attached to: Colleague Comes Forward To Defend Anthrax Suspect
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.
Privacy

+ - Judge Finds NSA Wiretapping Program Illegal

Submitted by
Hugh Pickens
Hugh Pickens writes "The NY Times reports that a federal judge has ruled that the NSA's warrantless surveillance program was illegal, rejecting the Obama administration’s effort to keep one of Bush's most disputed counterterrorism policies shrouded in secrecy. Judge Vaughn R. Walker ruled that the government had violated a 1978 federal statute requiring court approval for domestic surveillance when it intercepted phone calls of Al Haramain, a now-defunct Islamic charity in Oregon, and of two lawyers who were representing it in 2004. Declaring that the plaintiffs had been “subjected to unlawful surveillance,” the judge said that the government was liable to pay them damages. ““Judge Walker is saying that FISA and federal statutes like it are not optional,” says Jon Eisenberg, a lawyer represented Al Haramain. “The president, just like any other citizen of the United States, is bound by the law.” In 2008, Congress overhauled FISA to bring federal statutes into closer alignment with what the Bush administration had been secretly doing legalizing certain aspects of the warrantless surveillance program but the overhauled law still requires the government to obtain a warrant if it is focusing on an individual or entity inside the United States. The surveillance of Al Haramain would still be unlawful today if no court had approved it, current and former Justice Department officials say."
Botnet

+ - Microsoft Fuzzing Botnet Finds 1,800 Office Bugs->

Submitted by CWmike
CWmike (1292728) writes "Microsoft uncovered more than 1,800 bugs in Office 2010 by tapping into the unused computing horsepower of idling PCs, a company security engineer said on Wednesday. Office developers found the bugs by running millions of 'fuzzing' tests, a practice employed by both software developers and security researchers, that searches for flaws by inserting data into file format parsers to see where programs fail by crashing. 'We found and fixed about 1,800 bugs in Office 2010's code," said Tom Gallagher, senior security test lead with Microsoft's Trustworthy Computing group, who last week co-hosted a presentation on Microsoft's fuzzing efforts at the CanSecWest security conference. 'While a large number, it's important to note that that doesn't mean we found 1,800 security issues. We also want to fix things that are not security concerns.'"
Link to Original Source

Comment: Re:Sadly, the article makes no sense (Score 1) 235

by DebateG (#30472688) Attached to: Scientists Crack 'Entire Genetic Code' of Cancer
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.

Comment: Re:Sadly, the article makes no sense (Score 5, Interesting) 235

by DebateG (#30468572) Attached to: Scientists Crack 'Entire Genetic Code' of Cancer

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.

Thus spake the master programmer: "When a program is being tested, it is too late to make design changes." -- Geoffrey James, "The Tao of Programming"

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