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User: John+Newman

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  1. Re:Dear FSF on iPad Is a "Huge Step Backward" · · Score: 1

    To my surprise, one of the most important functions I wanted in a book reader was not there -- I could not import my own documents.

    There are a few apps for that. I like MobileStudio. It lets you upload arbitrary files to the iPhone/Pod via FTP, and can view PDFs, Word and iWork docs (among others). I use it for viewing PDFs of scientific papers on the go, works awesome.

  2. Re:Free sppech? on Supreme Court Rolls Back Corporate Campaign Spending Limits · · Score: 3, Interesting

    You cannot tax a corporation. Increased tax burdens just trickle down to reduced wages for low level employees and increased prices. I'm not sure why that is so hard for people to get.

    You cannot tax me. Increased tax burdens just trickle down to less disposable income to spend on cars and cable tv and smaller tips for low level employees like delivery boys and waitstaff. I'm not sure why that is so hard for corporations to get.

  3. Re:The extrapolation for lung cancer is badly flaw on Scientists Crack 'Entire Genetic Code' of Cancer · · Score: 1

    That's a pack a day for 47 years, which is admittedly within the bounds of possibility, but still an awful lot of smoking.

    Never worked in a VA hospital, eh? :) You measure smoking history in "pack-years" (actually packs/day * years). 47 is pretty unremarkable. It's not until you hit triple digits that it seems extraordinary.

  4. Re:Mandating vaccines... on Mandatory H1N1 Vaccine For NY Health Workers Suspended · · Score: 2, Informative

    Most reports are that swine flu has been mild compared to the typical in most individuals. This includes reports that some exposed have never developed any symptom. The reported numbers for swine flu rely on the presumption of swine flu rather than the regular seasonal flu, not actual tests. That is, died so must have been swine flu.

    What evidence there is suggests that children and the elderly should have priority for vaccination (greater potential benefit for the same risk). Healthy adults should be at the end of the list.

    Fucking shit, could you cram any more potently concentrated misinformation into a single post?

    The swine flu is *usually* a mild flu, just like the regular seasonal flu. But it *is* killing healthy young people, which the regular flu does not. It's landing them in the hospital, and then killing them after prolonged ICU courses. The mortality rate for pregnant women hospitalized with novel H1N1 infections is about 50% based on case series from several hospitals, including my own.

    There is no "presumption" here. Novel H1N1 is tested via PCR of nasal swabs or sputum samples, and/or at autopsy on lung tissue. Every suspicious hospitalized case in California (at least) is tested like this. For certain, every death in the hospital is definitively tested. There is no "presumption". Novel H1N1, followed by bacterial superinfection, is what is killing these healthy young people. Just like in 1918.

    The formal CDC recommendations are that *young* people be first in line for the vaccine. OK, pregnant women, infants and the immunocompromised are first, but of the general public, young people are next. For once, the elderly can safely wait, since most have partial immunity from the 1957 pandemic H1N1, and the most severe cases of novel H1N1 are in young people, not old (where it's acting much like the seasonal flu).

    Seriously, read the CDC recommendations on who should get the vaccine. In fact, the CDC has an unbelievable website on novel H1N1 with the best real data available on rates, outcomes, and recommendations.

    Read a few of the emerging case reports, like the these 68 young people in Oceania who were in the ICU on heart-lung machines, of whom 1/3 died. Or the 10 young ICU cases from Michigan back in the spring.

    This is serious stuff, and healthy young people (especially pregnant) are at risk. If you want relative risk, then know that the swine flu has already, beyond any doubt, killed more young healthy Americans than the number who got Guillain-Barre from the 1976 vaccine, and the flu season hasn't even started yet. Get the vaccine.

  5. Re:Any systems depend on a pulse on Artificial Heart Recipient Has No Pulse · · Score: 1

    How about vein or arteries stiffening? I can imagine that having a pulse might help these vessels keep certain elasticity and fight stiffening.

    Sure, but being too stiff only matters in that it's harder for the vessel to accommodate the pressure increase of systole. The result then is that the peak BP is transmitted directly to the organs, instead of being dampened by the elastic vessels. If there is no systole, I'm not sure it would matter if your vessels became as stiff as lead pipes.

    I wonder if the lack of elasticity would make them more likely or less likely to form atherosclerotic plaques - the "narrowing" of the arteries that goes with the "hardening" part and causes pain and damage to the organs those narrowed vessels feed. On the other hand it's probably academic to wonder what the effects would be 20 years down the line. Bridge to heart transplant is still the goal. I don't think we even did artificial hearts anymore (until this new one) because the benefit was so minimal. LVADs more or less replaced them, but are explicitly a bridge to transplant only.

  6. Re:Poor Title on F-22 Raptor Cancelled · · Score: 1

    non-stealthy F-35s

    Is that the variant where you take a stealthy F-35 and strap it to a barn door?

  7. Re:The Patents at Issue on Breast Cancer Gene Lawsuit Argues Patents Invalid · · Score: 1

    The DNA in question must be "isolated". The DNA is not "isolated" when it is naturally occurring. Nobody is claiming your DNA that you were born with. Only an isolated DNA product.

    Ah, thank you for clarifying that. Then I would be in the clear, of course, to isolate and clone BRCA1 from my own germline DNA and then develop a diagnostic test of my own. Because, by your interpretation, Myraid could only own the rights to their specific isolate of BRCA1. The current law, however, appears to extend that right to *any* isolate of BRCA1, even one created by completely independent technique from my very own DNA, as well as any application of any isolate of BRCA1 for genetic testing. How this is functionally different from owning the rights to the gene itself escapes me.

    What complicates this specific case, as I'm sure you know, is that Myraid did not discover the identity nor the importance of the BRCA1 gene, nor did they develop any unique techniques for isolating it. Nor was it their idea to develop a diagnostic test for the gene (seriously? How could anyone think this wasn't a goal of the scientific community from the beginning?). They were the first to create an isolate, likely by a matter of days, by completely obvious and open techniques, and they were the first to file a patent.

  8. Re:I don't understand it. on Breast Cancer Gene Lawsuit Argues Patents Invalid · · Score: 5, Informative

    it's just that without Myriad, *no one* would know that having the BRCA1 gene was a precursor to breast cancer.

    Are you ^!&%! kidding? Are people so bamboozled by the FUD of pharmaceutical companies that anyone who doesn't know the truth assumes that the big, nice company must have sunk a ton of time and money into finding this gene from scratch, and without them the gene would never have been found? The truth is very, very different, and this is why Myriad is so hated in the scientific community.

    BRCA1 was discovered by Mary-Claire King, now a geneticist at the University of Washington, following over a decade of government-funded basic science work that started when she was a graduate student and then junior faculty at UC Berkeley. Back then genetics was hard work - not hard like today, *really* hard. When she started no one really believed that one could even find a gene for a trait that wasn't expressed 100%, it just seemed too complicated to pick one mutation out of a huge haystack when you had to allow for some people having the bad mutation yet having a normal phenotype. Remember this is before the human genome project, before automated sequencing; she even started before PCR. Just pinning the candidate gene down to one small region of one chromosome took over a decade of work by dozens of people.

    As the process came towards fruition, they first narrowed the field to a small part of chromosome 17 (paper), then made a laborious map of the region of interest (paper), and then together with a group at the NIH, they identified the actual single gene we now know as BRCA1, sequenced it, and spelled out the mutations in it that caused breast cancer in the affected families (paper1, paper2). Notice that all of this was done completely in the public eye, with all of her lab's results published immediately so as to help other researchers advance the field with her. It was good science.

    But wait, where's Myriad genetics so far? What's left to do? Didn't we already "discover" BRCA1? How could anyone patent it now? All good questions. The next thing to do was to make a copy of this gene, by itself, in a test tube. This would be preliminary work for all sorts of biochemical analysis. The act of copying a gene off of a chromosome onto a separate loop of DNA in a test tube is called "cloning". Cloning is still pretty hard even today, especially for long genes like BRCA1. It can take months, especially since you usually need to copy it in bits and then glue those bits together.

    What Myriad understood, and perhaps Dr. King did not, is that a cloned gene (that loop in a test tube) is patentable because it's considered "artificial", even if it's a perfect copy of a natural sequence of DNA. Myriad jumped in at this point, threw their whole company into cloning the gene and then patenting it, and did it before Dr. King or anyone else realized they were in a race. Ironically, Dr. King's lab had probably already cloned it in pieces (usually a prerequisite to sequencing) but hadn't made a complete intact copy yet, and certainly hadn't filed any patents. Myriad did none of the prior work on BRCA1. They did not come up with the idea of hereditary breast cancer. They did not do the laborious work of mapping where BRCA1 might be. They did not pinpoint the gene that was BRCA1. They did not sequence

  9. Re:Misleading or Deceptive Conduct on Merck Created Phony Peer-Review Medical Journal · · Score: 1

    What you link to is the real "Journal of Bone and Joint Surgery", which *is* a very reputable, genuinely peer-reviewed, and very old journal for actual orthopedists. Definitely not to be confused with the Merck fake.

  10. Re:Credit on A New Kind of Science Collaboration · · Score: 3, Insightful

    hat's exactly the sort of thing this new openness initiative is trying to prevent. Currently, while your paper is waiting in the publication queue, your data is at risk for being used without credit. If you confront the other person, it turns into a he-said, she-said dispute, as neither side has the evidence needed to prove plagiarism, rather than independent discovery. With an initiative like this, you can get your data and experimental procedure out there earlier in the process, making it much clearer that you were the first to discover or research in the area that you're working on.
    This sounds like a good way to get hosed out of any credit for developing an interesting idea. The way the process works now in biology is that you first have the flash of an unexpected result or an interesting insight. You then spend weeks to months hashing out the significance of this new idea and planning experiments to flesh it out. Those experiments then take months to years to complete. Somewhere in the middle of those months to years, you realize that the idea will work out, and that completing the line of inquiry will land you in a prominent journal or propel your career. You then spend further months to years actually getting the first chunk of data into a journal. (This for a successful idea - of course, the idea can fail at any juncture.)

    Today, your risk of being scooped is mostly towards the end of this process, after the idea has cleared most doubt and after the experiments are sufficiently advanced for you to begin presenting the data at conferences and submitting it to journals. You can build up a two-three year head start in blood, sweat and tears (i.e. painfully worked out protocols and accumulated materials) that make it difficult for all but the largest labs to catch up, should they so desire.

    In this transparent world, your idea would be out there from day #1. At the latest, from the first experiments. At that point you have no lead and no investment, and *anyone* can swoop in and develop your idea faster than you can. When it comes down to a race, he with the most postdocs wins, and that's not you. Sure, you can try to take credit for the flash of insight. But who is the community (and the tenure board) going to reward - the guy who claimed to think of it first (maybe everyone else had already thought of it, but deemed it too trivial to comment on...) or the guy who does the actual work to *prove* it? Under the current model you have few good recourses for complaint, but under this model you'll never have standing to complain in the first place.

    The traditional model of lab-secret research is the worst possible model except all others that have been proposed. It's the only way for the "little guy with a big idea" to make way in the world without bringing research to a grinding halt with something like patents [shudder].
  11. Two things... on What is the First Day in a University Lab Like? · · Score: 1

    Two things to guide your experience:

    1. Summer undergrads almost never get anything of substance accomplished in a molecular biology lab. I started working in labs at age 16, and the first time I started to feel even modestly productive was after two years of grad school. The first time I even generated any data at all worth publishing was after a year-long (~1000 hr) senior project. A summer is just too short. You're there to learn the techniques, to gain some experience in how to design an experiment and how it fits into a bigger picture, and to muddle through your experiments as best you can. The techniques are complex, the science is complex, and you haven't been exposed to any of it before. Also understand that many of the more "interesting" experiments have time-frames of months, rather than weeks, anyway, so you'll likely be doing either simpler work or self-contained chunks of more complex work. But if you learn these "simple" tasks well and can perform them reliably, you can be a genuine asset to the lab. It takes about ten years to train an independent scientist, and this is your Year 0. But that's OK. Everyone else in the lab knows this, too. Be nice, be inquisitive and curious, and do your best to be helpful.

    2. Be especially nice to the technicians (aka research assistants) and the staff scientists (the post-postdocs). Odds are they've been around longer than the itinerant postdocs and grad students, and they know how everything works and where everything is. They'll be happy to teach you if for no other reason than to make sure you don't mess anything up, as they would be the ones who have to fix it afterwards. :) Unlike postdocs and grad students, this is their job, and they're not desperately trying to scrape together enough data to graduate or (worse) to establish an independent career. They will usually have more time and patience to teach the bright young undergrad the ropes. Treat them with the utmost respect, and they will be your best mentors.

    And remember to have fun!

  12. Re:sooo..... on NBC to Create Programs Centered on Sponsors · · Score: 1

    That was the first thing that came to my mind, too. Like this is a new thing - Viper, anyone?

  13. Re:Cue TMNTs on Alligator Blood May Be Source of New Antibiotics · · Score: 3, Informative

    Really? I thought that once you had them in a warm environment, alcohol would help increase circulation and even out body temperature. Or perhaps it will cause a sudden rush to the heart of cold blood that was near the skin. I've not got any training in cold weather rescue, so excuse my ignorance.
    Alcohol is a mild vasodilator, so it would reverse your body's major defense against cold, restricting blood flow to the extremities/surface and keeping a pool of warm blood in the core. Even after the person is in a warm environment, vasodilation is dangerous because the extremities/skin are cold, the blood there is cold, and suddenly moving a bunch of warm core blood through the cold extremities and back will lower the core temperature further. The teaching is that this could kill a patient by pushing their core temperature down suddenly, past the critical value. When resuscitating a severely hypothermic patient, you always warm from the inside out, and you never give vasodilators.
  14. Re:Truly Awful! on Scientists Discover Gene For Ruthlessness · · Score: 1

    I know, seriously. Stop sending your rich folk and government officials here for treatment, will 'ya?, they're tying up our beds.
    Why is it that so few people can hold in their minds simultaneously the non-exclusive thoughts that our health care system is the best in the world for those few who can have all that money can buy, and not the best for everyone else?
  15. Re:god damn it on Daily Caffeine Protects Your Brain · · Score: 1

    Perhaps then Alzheimer's is caused by cholesterol damage? You know, if it walks like a duck and quacks like a duck, then... what was I about to say?
    It might. At least, high cholesterol is associated with a higher risk for Alzheimer's. And statins, which alter cholesterol metabolism, are protective against Alzheimer's. There's some very interesting science about why that is, having to do with the makeup of the lipid particles in the cell membrane in which the Alzheimer's Precursor Protein lives. Quack quack.
    http://www.ncbi.nlm.nih.gov/pubmed/18288926
    http://www.ncbi.nlm.nih.gov/pubmed/17986151
  16. Re:Just what we need on US Cyber Command Wants Greater Attack Mentality · · Score: 1

    In the past 10 years the US has initiated 2 military actions against foreign powers.
    To be perfectly fair, over the past 10 years has any sovereign nation initiated more?
  17. Re:Losing my faith in politics on The Man Who Guards Clinton's Wikipedia Entry · · Score: 1

    John McCain wants us to stay in Iraq for 100 more years.
    Typical of the left. Lying about their opponent and declaring them the "enemy". HERE is a video of what he said.
    The full context is even more damning, IMO, because if taken at face value it shows that McCain has no idea whatsoever what is actually happening in Iraq. It looks better for him if you take the "left's" perspective.

    Iraq has absolutely nothing in common with our presence in Europe, Japan or Korea, except that there are American soldiers there. Landstuhl has far more in common with Ft. Lewis than it does with Camp Victory, and has since 1945. No US soldier ever died of hostile fire during the Germany or Japan occupations. Iraq is an old-fashioned military occupation of a hostile populace, and there are maybe two examples in the twentieth century of that temporarily working out well for the occupier, set against dozens of examples of abject failure - whether that failure was admitted after one year or twenty. I think McCain is a reasonably bright and forward guy, so I just can't believe that he really thinks Iraq is just like Germany, or will very soon be.

    Much more likely he's determined to fight to the end to finally defeat those Communists in the North, whether it takes 50 years or 100. Unfortunately, the similarities there are all too real, including the fact that this occupation failed long before we realized it.
  18. Re:Almost 7 Billion People... on The Uncertain Future of Global Population Numbers · · Score: 1

    After all, look how well colonization worked out for the Greeks in the long term. They are a major economic and military superpower still, aren't they?
    Thanks to their spread, they did manage to make themselves the major economic, cultural and military power in the Eastern Mediterranean and Near East for almost 2000 years (c. 480 BC to 1453 AD). Not too shabby for the inhabitants of a tiny peninsula of barely-fertile rock. In the long term, of course, we are all dead.
  19. Re:This doesn't address the issue. on US House Rejects Telecom Amnesty · · Score: 1

    It's easy to say that, but it's like asking a well-behaved child to disobey their parents' bad commands, or a soldier to disobey his commanding officer's illegal orders. In both situations the 'right' thing to do, the thing that -shouldn't- get you in trouble, is to disobey. But everyone -knows- what'll actually happen is that you take the full brunt of the anger if you disobey, and you are -very- likely to come out unscathed if you obey.
    Which is exactly what happened. One telecom company did stand up to the NSA in early 2001: Qwest. And both the company and its former CEO may have paid a price for their insolence. One can only hope they will ultimately be rewarded once the lawsuits against their competitors start making headway.
  20. Re:Speak really slowly for me... on Democrats Propose Commission To Investigate Spying · · Score: 1

    In just one generation after that their children were solidly middle class, and now my generation is all college educated with good jobs. The government lifting people up isn't the answer - giving people opportunities to lift themselves up is.
    So these colleges you all went to - I assume you all paid full fare at private schools? No federal loans or work-study, either. (No wonder your family was dirt-poor if you paid cash for all that! Wow.) Didn't take any classes in subjects supported largely by federal grants. Too bad - we need more people in the sciences. Drove on private roads to get there. Must have been private schooled from kindergarten. No public tax-supported schools for you all, or your kids. And you all must be such devoted children, supporting your parents and grandparents without any help from Social Security or Medicare. Do you send the checks back or just shred them? Just how much do you pay on your employee insurance plan for your 79 year-old grandfather? In the event, I'm sure you'd never dream of seeking care for them at that famous cancer center that is largely supported by federal money. Heck, none of you have probably ever seen a doctor at all, seeing as how they were all supported by federal money at some point in their training.

    For all that, I heartily salute you and your up-from-the-bootstraps generation. I cannot even begin to fathom how difficult it must have been to do all this without the slightest help from the government.
  21. Re:A pile of hoopla on Mega-Cash Prizes and Revolutionary Science · · Score: 2, Insightful

    Now if we only had grant funding..
    Exactly. The standard NIH R01 investigator grant, which supports most successful mid-career biomedical scientists, pays around $100-250,000 per year for four years, renewable with reasonable progress. This is enough to support the investigator (at an academic's salary), lab space (universities generally take 50% of the top), and anywhere from 1-4 employees, depending on the location (yes, grad students and postdocs make that little money). These are the grants that get science done in the US. No scientist in their right mind would choose a chance at a multi-million dollar prize over an R01. What we need aren't risky one-off million-dollar prizes, it's more of these secure, renewable million-dollar-over-several-years grants. Unfortunately, as often commented today, R01 funding is falling rapidly as the NIH budget is frozen, costs continue to inflate, and the NIH has reasonably focused on preserving its seed corn - young investigator and training grants.
  22. Re:Actually speed does kill on 70% of P2P Users Would Stop if Warned by ISP · · Score: 1

    Also, about the "speed doesn't kill" quote... would rather be in a accident going 70 or going 90? Think that extra 20 is not going to make a difference? You want to take that risk with your life? Imagine a head-on at 70, 70+70=140. Now at 90, 90+90=180.... hmmm... both are bad, but I'd rather take my chances with 140.
    Indeed. KE = 1/2*mv^2...
    140^2 = bad.
    180^2 = dead...along with the person you hit.
  23. Re:Obscurantism on Getting The Public To Listen To Good Science · · Score: 1

    Simply put, I don't want to be on cyclosporine for the rest of my life. Oh, that is quite a downside. That's what cloned stem cells will (eventually) be for. They, and whatever they are differentiated into, are of your own body and genome so there should be no rejection.
  24. Re:Jaded Medical Student, at your service! on The Obesity Epidemic — Is Medicine Scientific? · · Score: 1

    If a doctor could give the exact same pill to two completely different people and get the exact same result, that would be science. If a physicist could aim two photons at a slit and hit the exact same spot on the far wall each time, that would be science.
  25. Re:Hypocrisy on First New Nuclear Plant in US in 30 years · · Score: 1

    The answer? Yes. Sure as heck it would be a war crime, because the bombs by your definition did not bring the war to a close and did not save more lives than they cost.

    Now -- if the Germans dropped the bombs and won, that'd be a lot better than a full-scale invasion of America, wouldn't it?
    So two bombs would have been a war crime, but a hundred bombs would have just been war. I like the symmetry, at least: One man shot to death is a murder, but a thousand men shot to death is a battle. But what about a thousand bombs? What if the bombs killed more people than would have died in an invasion? Morality by balance sheet?

    FWIW, I don't personally agree with the premise that the nuclear bombings of Japan were substantively different from the non-nuclear fire-bombings, and trying to reason out the morality of that leads one down a very twisted and confused path.