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Comments · 69

  1. Re:I'm amazed on Woman Admits Sending $400K To Nigerian Scammer · · Score: 4, Interesting

    ...because we don't live in a world of 99 uniform dumbasses and 1 genius. We live in a world with lots of dumbasses and lots of very smart people, with most folks somewhere in the middle. It's a normal distribution so, yes, 50% are below the mean.

  2. Re:I have always held that we controlled evolution on Scientists Discover Proteins Controlling Evolution · · Score: 1

    Yes, the environment can certainly lead to changes in gene expression patterns. And yes, sometimes some of these can be heritable. Note that it's *not* a mutation in the DNA code itself, but a modification to the packaging proteins that DNA is bound to. This doesn't change the gene sequences but can control how strongly the gene is expressed (and possibly which form of a given gene is expressed), if at all. This can happen through several mechanisms that I'll admit I don't know a huge amount about: acetylation of histones, DNA methylation, etc. There's a well-written layman's introdution in this New Scientist article if you're interested.

    However, I've never heard of these "epigenetic" changes affecting big, morphological features which tend to be *strongly* conserved:

    If you raise 5 generations of mice in total darkness, at least one offspring will be born blind in the newest generation.

    My first reaction is pretty strong septicism, so if you can point me to a reputable source for that, I'd be fascinated to read it.

    If you're saying that environmental stresses directly lead to actual controlled and heritable changes in the DNA sequence, I'm even more skeptical and would really love to see a source.

  3. Re:Monetization on German Doctor Cures an HIV Patient With a Bone Marrow Transplant · · Score: 1

    Well spotted, thanks for pointing out my mistakes.

    Behold the power of peer review!

  4. Re:You know one kind of method for one kind of ill on German Doctor Cures an HIV Patient With a Bone Marrow Transplant · · Score: 3, Informative

    The drug is Granulocyte Macrophage Colony Stimulating Factor (GM-CSF) if anyone wants to look it up. It's just a growth hormone that you have produced in your body naturally. They just give you a *lot* of it, causing your stem cells to start dividing. Some stay in your bone marrow, the excess cells move out into the bloodstream, from which they can be painlessly extracted.

    I know someone who's had cells extracted that way, and she described it like Marrow (very apt name!) does. The hormone treatment made her feel like she had a cold coming for about a week, and the extraction procedure (required about 2 hours sitting in a comfy chair) was just "really boring".

    If you sign up to be a bone marrow donor (you should if you can! Brits check out the Anthony Nolan Trust), that's what you're signing up to do: feel like you have a mild cold, be bored for two hours and hopefully save someone's life.

    Very rarely (more common in people 50+) the drug doesn't work well and they do ask if they ca take your cells directly from the bone. I know a woman who had this done too. She stayed in hospital for 2 days after, rested in bed for another 2 days and was back in work after a week. It wasn't great fun, but it healed up perfectly and painlessly after a few weeks. She said it was definately worth it to try saving someone's life.

  5. Re:Like to see this replicated on German Doctor Cures an HIV Patient With a Bone Marrow Transplant · · Score: 1

    Beats me. I'm just a software engineer. Maybe SlashBugs can help you out there.

    Based on my activity in this thread so far, I'm actually slightly more likely to start ranting at people. I really must stop that...

    Anyway:

    How large of a sample of people do you need to do a genome comparison and locate the gene that provides the immunity?

    In this specific case, I think it's known to be CCR5. I don't know the story in detail, but I think they identified the HIV receptors and then started looking at the gene, so they alrady knew what they were looking for. In general though, this is hugely variable between diseases. In something like Downs' Syndrome and a few kinds of cancer, the difference is very easy to spot because it's a huge genetic change. Downs' sufferers have a whole extra chromosome and, IIRC, there's a type of leukemia that's characterised by an arm of one chromosome translocating onto another choromosome. These are both very obvious, so you have a high signal:noise ratio.

    Most genetic disesases and heritible vulnerabilities to disease are much more complex, so the analysis is looking for an unknown pattern of small changes in the whole genome. As an example, I know someone who's looking at genome information from healthy people and a specific subset of breast cancer patients. She's doing statistical analyses of all the information she has, trying to find and significant pattern that'll tell her who's particularly predisposed to the condition. Here the signal:noise ratio is much lower because she's looking for changes that are probably much smaller, maybe mutations in just one or two genes. She has genetic information from a few hundred cancer patients and is finding it difficult to see any statistical significance. Bigger programs, as run by people like the WHO, get samples from tens or hundreds of thousands of people (depending on the disease), which obviously increases the statistical power of the study.

    That was a bit of a tangent from your question, but I think this stuff is cool :D.

    Can gene therapy be utilized here?

    In principle, yes. Lacking the CCR5 gene doesn't seem to have big side-effects, although may increase your risk of getting West Nile Virus (unfortunate, but not as bad as AIDS). There are several fairly easy techniques to stop cells from making CCR5 or to block its activity in the lab, so it's very tempting to try thm in patients. However, delivering these techniques to a person without unacceptable side-effects is still tricky. A few clinical trials have shown promise (the X-SCID trial that cured a few immuno-suppressed "bubble boys" but later gave two of them leukemia; the cystic fibrosis trail that cured the patients completely but only for about four weeks... etc.), but there isn't really much ready to be used used in the clinic yet.

  6. Re:Like to see this replicated on German Doctor Cures an HIV Patient With a Bone Marrow Transplant · · Score: 5, Informative

    If it makes you feel better, I'm at the end of a PhD in the field. So I know more about HIV and AIDS than most of the population and, indeed, am one of the "phoney researchers" who generates the same data that I am, apparrantly, ignoring.

    Tell us - what's your Ph.D. in?

    Try getting your science from reputable schools or journals rather than mass-market paperbacks.

  7. Re:Like to see this replicated on German Doctor Cures an HIV Patient With a Bone Marrow Transplant · · Score: 3, Informative

    Depends how you choose to express the siRNA.

    Plasmids are generally pretty safe, if you pick one with decent copy-number control. Something like Epstein Barr virus' dormant plasmid would be pretty good, as it automatically keeps itself to just a few copies of itself per cell and constantly expresses a couple of RNA molecules. Just remove the viral genes and throw your shRNA in there under the same promoter... should work like a charm.

    There are also some viruses that always integrate into a specific, safe part of the genome. Adeno-associated virus, for example, always slots itself into the same site (somewhere on chromosome 19 IIRC?) and lies dormant. It has a tiny capacity for payload genes so is often ignored, but if you just want to express a few shRNAs it's be ideal.

    But yes, the radiation will still be a bitch. I've seen several patients going through it, who all agree that the treatment is better than the disease, but only just.

  8. Re:Like to see this replicated on German Doctor Cures an HIV Patient With a Bone Marrow Transplant · · Score: 5, Insightful

    Malaria kills far more people per year than AIDS, and seems likely to keep that up for the forseeable future.

    I assume that you don't have the sickle-cell anemia that gives partial protection against the malarial parasite?

    OK then, I've got the bolt-cutters ready. Call my secretary and make an appointment for your sterilisation.

  9. Re:Monetization on German Doctor Cures an HIV Patient With a Bone Marrow Transplant · · Score: 5, Informative

    Making money off of a disease which is very much kept in the vague, unclear, opaque situation is evil.
    Where is the reproducible proof that HIV exists?
    Where is the reproducible proof that HIV causes AIDS?

    Go to the (American-run but internationally funded and popular) National Centre for Biotechnology Information here: http://www.ncbi.nlm.nih.gov/sites/entrez ...and type "HIV" into the search box. You'll get just under 192,000 peer-reviewd articles from groups all over the world, funded by various governments, public and private companies, charities and rich donors. Anything from HIV genome sequences and molecular sctructures through molecular biology, disease progression, transmission studies, all the way to local- regional- and global epidemiological studies. The evidence is pretty damn strong and well understood from the atomic level up to the global level.

    Altenatively, click on the "Reviews" tab and it'll give you a mere 24,000 articles assessing, collating and criticising the others. Have fun!

    True for HIV, True for HPV.
    True for whatever.

    When you've finsihsed the HIV evidence, feel free to look up the 15,000 HPV articles (or just 12,600 if you restrict your seach to "HPV AND cancer"). The HPV thing is actually very easy: most viruses carry genes evolved to push cells into their growth phase, because that forces the cells to release and synthesise resources that the virus must hijack to replicate. HPV-associated cancer happens when the viral gene gets incorporated into the cell's DNA (rare, but through well-established mechanisms) and get permanently switched on, making the cell grow and divide constantly. Any biology undergrad could tell you that if you asked. It's more common in the cervix simply because it's out of sight, and doesn't get noticed until it's really big and nasty. (Which is why all sexually actve women should be screened: catch it within the first 5 years and the cure rate is better than 98%. It's an easy cure if you *find* it)

    THINK first. Do your research.

    My undergraduate degree is in virology and I've just finished a PhD looking at how viruses interact with cancer and parts of the immune system. I've done plenty of thinking, and a hell of a lot o research. Now it's time for *you* to think, and for *you* to do some fucking research.

    You're no better than the creatioists who say that evolution's impossible but have never botheres to get a fcuking clue how it actually works.

  10. Re:Like to see this replicated on German Doctor Cures an HIV Patient With a Bone Marrow Transplant · · Score: 5, Informative

    Background for non-biologists: HIV typically gains entry to cells by binding two molecules on the healthy cell surface. These are CXCR4 and CCR5. About 1% of white males (other genders/races vary slightly) don't have CCR5; they seem completely healthy and their cells are highly resistant to HIV infection. So blocking the activity of CCR5 seems like an easy way to stop viral infection with no exprected side effects. Tricky to do, but probably worth the effort.

    Anyway, the answer is "yes", sort of. Several antibodies and small peptides are in trials to block the CCR5 receptor; some are showing promise in animal trials.

    The most famous is Maraviroc, a small molecule that binds CCR5 and stops is from binding HIV. It's sold by Pfizer and currently in use as an anti-HIV drug.

    Another interesting possibility is gene therapy. Another group has recently made CD4 T cells (one of the cell types that HIV infects) express a small molecule to block their own CCR5 receptors, which works very well. I haven't seen a paper on it, but you should also be able to use similar techniques to completely shut down CCR5 production (using virus- or plasmid-borne shRNA, for example).

    Finally, another group has managed to make rabbits produce antibodies against CCR5 receptors (Vaccine
    Volume 26, Issue 45, 23 October 2008, Pages 5752-5759). Those antibodies are able to bind to CCR5 and completely block HIV infection, which is great. Stimulating an immune response against the patient's own immune cells sound a bit dodgey to me, but my immunology isn't great: maybe there's a well-established way around this problem that I just don't know about.

  11. Re:I like violent music... on Video Games Linked To Child Aggression · · Score: 2, Funny

    >Violet is ok, it's that ultra-violet music you want to keep away from your eyes and skin.

    All things in moderation. Micheal Jackson would have benefited from some exposure to ultra-violet music.

  12. Re:I think that the Turing test is too simple on New Contestants On the Turing Test · · Score: 1

    If the turing test is really that simple, where are all the winning programs?

    Chess is a system in which, for any given board position, there's an optimum move. Even if you lack the resources to calculate the ideal, you're still limited to a small number of pieces which can move in a small number of ways.

    Compare this to the complexity of Go, which lacks a really good AI. With the freedom to put a piece on any free spot, the system becomes much more difficult to predict.

    Now thnk about a human conversation. Subliterate 'net trolls nonwithstanding, you can reasonably expect a real person to have something coherent, grammatical(ish) and informed on a huge range of subjects. They can ask insightful questions of you and show creativity wnd maybe even humour when responding to your questions. And that's without involving emotional responses to the conversation.

    I'm not saying that the Turing test is a good indicator of sentience or conciousness (largely because I can't define those clearly enough to judge). I /am/ saying that a human-like conversation that's allowed to range freely over a range of topics would be incredibly difficult to acheive. (You'd also need a careful smattering of typos for full authenticity)

    Anyway, how do you know for sure that I'm not a stimulus-response box? You have no information at all about my internal state and, as I'm posting on slashdot, you do have reason to think I'm not fully human :).

  13. Re:Fast forward? on TiVo Wins Appeal On Patents For Pause, Ffwd, Rwd · · Score: 2, Funny

    As everyone has already said, this is a hardware patent.

    TiVo found a way to fit a flux capacitor inside their boxes.

  14. Is Micro-SD the right choice? on SanDisk, Music Publishers Push DRM-free SlotMusic Format · · Score: 5, Insightful

    Am I thinking about the same micro-SD as everyone else? Smaller than my little finger nail?

    It's small enough to get lost in your pocket, sucked up by a vacuum cleaner or whatever. They're also fiddly to handle: can you imagine picking through your album collection with a pair of tweezers, squinting at the 3mm x 5mm labels to find the one you're after?

    It seems a bizzarre choice for a portable music medium. If they're not intended for carrying around but supposed to be used only once, to get the music onto your player/computer, why not just sell the download?

  15. No expectation of privacy in a public space on 10 Percent of Colleges Check Applicants' Social Profiles · · Score: 2, Insightful

    ..including the internet.

    Arguably the universities should restrict themselves to the application documents and interviews, in the spirit of fair play.

    However, these kids have created publicly viewable profiles for themselves and chosen to leave the privacy settings off so anyone with a net connection can view them. They've then loaded up these profiles with photos and information that make them look bad, and still decided to leave it all open to public view.

    There's no way someone who's done all this could possibly complain that someone has invaded their privacy. They've undoubtedly tried to find all the online information about their prospective colleges and professors; it's a two-way street.

  16. Re:Have you even looked? on YouTube Bans Gun and Knife Videos In the UK · · Score: 1

    >You are the one who is calling bullshit, so you have the obligation of demonstrating bullshit.

    Really, really no.

    You said "This contraversial statement is true".
    Dynasoar asked "Do you have any evidence?"

    You made a controversial claim, it's up to you to support it. ...or should we just assume that everything we read is true until we find evidence to the contrary?

  17. Re:Boycott Vibrant in-frame popups on Google Reverses "Absurd" Mozilla Code Ban · · Score: 2, Insightful

    They are "paying" us to look at the ads, by giving us otherwise free services or content.

    If what a website has to offer is worthless to you, don't visit it and you won't add to their revenue by seeing the ads.

  18. Re:PCR? With what primers? on Rover Exiting Crater To Continue Martian Marathon · · Score: 3, Informative

    Use random primers, just like you do for reverse transcription when you want to pick up all the RNA sequences in your sample. The reaction's efficiency would take a hit, but if all they want to do is detect DNA (or maybe even sequence a few very short sections) it could probably be made to work.

    A bigger problem is the enzyme used in the PCR. IANABiochemist, but I'd expect the PCR to only work if the Martian bugs hava genomes based on double-stranded DNA chemically very similar to ours.

    There are plenty of stable nucleotides that could work as components of DNA but, for some reason, aren't used in Earth's life. Ditto chirality: Using the same constituent atoms, one can build almost identical but left- or right-"handed" versions of molecules. For some reason -- probably just chance -- Earth's life is based on "lefthanded" molecules, meaning that we can't produce or consume right-handed molecules. For example, if we synthesise right-handed sugars (easy for a chemist to do, but expensive), they have the same chemical composition, melting point etc, but the structure is such that our enzymes can't use it as a source of energy. Heck, even the sequence of any DNA scooped into the chamber will be important, as if influences the reaction conditions you need for the PCR to work.

    If there is life on Mars, this test would only be able to detect it if Martian life is spookily similar to our own. Which would, I'll admit, be even more exciting than just "life on Mars" because it would hint toward evidence of Panspermia or possibly some sort of fundamental rules about what life is able to look like.

  19. Re:Stop Complaining on BBC's Open Player Claims Not Followed Through · · Score: 1

    I think the license fee system here works fairly well (my own problems with the colection agency's administrative fuckups nonwithstanding). 1) is subjective of course, but for the most part I'm happy with the service. For the £149/year they provide 4 TV channels (with regional variants), 6 radio stations, a great news website and the iPlayer service, all without adverts. A lot of their programming is bought from external production companies, but they commission and make plenty of their content in-house. Historically they've been good at introducing new talent because their semi-independence from ratings means they can afford occasional risks. Better yet, all of that is totally free from adverts. I think it's a pretty sweet deal. 2) Possibly. For the content you could get it seems fair to me; think of it more like a package of TV and radio channels with a news service and it seems reasonable. Of course, for people who never or seldom watch the BBC's output, they're forced to pay for services they don't use. It's the same dilemma as any socialised system. 3) Recourse from what? We have three other terrestrial analogue TV broadcasters, many more on terrestrial digital (also free), a paid-for satellite service, a free satellite service and two cable TV companies. There's plenty of competition.