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  1. Re:Penny-Arcade Sounds Off on Troika Games Closes · · Score: 1

    Hm. Are they sure they aren't talking about Peter Molyneux? Black and White, Dungeon Keeper, etc are nice examples of this.

    Is he still coasting on past success? Or do the first 5 hours (and damn good reviews based on only those first 5 hours) keep him afloat?

  2. Re:Martian Life... on Microbes Alive After Being Frozen for 32,000 Years · · Score: 1

    Please mod parent up, for Illserve gets the idea of self/non-self. Wouldn't it be strange if the human immune system had to 'know' about everything we could possibly ever come in contact with?

  3. As an amature coffee roaster on Popcorn-Popper -> Coffee Roaster Mod · · Score: 2, Informative

    I always went by sound of the beans (first and second crack), and look. I have something similar to an air popper, an IRoast

    I find that for each batch of beans, the ambient conditions, exactly how much I put into the roaster, and any number of random factors contribute to how well the roast comes out. No matter how much control I have over the interior of the roaster (and my roaster lets me set up to 3 different temperature points to achieve during the roast), I always wind up programming the last stage of roast to go longer than I need to. I do this because the roasts are easier to measure by eye/ear for 'doneness'. I can guestimate approximately when it will be done by time, but it never seems to come out the same.

    I wonder if all the TC's, etc, really get you a better roast, or if it's just cool to say "Look what I did!"

  4. Re:I can you like to argue a fact on U.S. Denies Patent on Part-Human Hybrid · · Score: 1

    First off (and now you're really sounding like an asshole) I work in acedemia. At Harvard, if you'd like to be precise. I don't do any money-raising public relations bullshit.

    I don't need to, my PI raises plenty of grant money through the NIH.

    So get off your fucking high horse, you're embarrasing yourself.

    DB SNP: Guess what the FIRST hit on google is for "dbsnp"? Oh shit, it's DB SNP! You are one lazy ass motherfucker.

    A gene:
    "the DNA sequence necessary and sufficient to express the complete complement of functional products derived from a unit of transcription"

    Yes, people have been attaching a number of different meanings to it, and it's a word in transition. The one I use above is a pretty damn common one.

    For something that is abstract, algorithms are more than able to predict where they occur in the genome. There's also available splice sites, etc.

  5. Re:I like to say ignore the fools on U.S. Denies Patent on Part-Human Hybrid · · Score: 1

    I can you like to argue a fact until someone refutes it, then hide behind your own ignorance.

    Way to go!

    For your information, dbSNP is a database of human variation. If you went there, you could look up exactly how different we are from chimps - which was the original conversation.

    And, for your information, I'm a biologist/bioinformaticist. So I may have a slight idea of what I'm talking about - just like you might know more than I do about Psychology. Though, your understanding of the scientific method may be lacking...

  6. Re:in all fairness on Web-Only Album Wins Grammy · · Score: 1

    Whoa, nice musical choices. Of course, you didn't pick anyone who's gotten there starts in the last 5 (10, 15?) years.

    Granted, that gives them time to master their instruments, as you put it...but it's nice to stay on the boat and keep listening to new music.

    Try out some Death Cab for Cutie, or Enon, or kick it with Mogwai and The Ex-Models. None of those bands is a big recycled band either. And some of them haven't been around for 20 years.

    No offense to anyone, but if your musical tastes and aquisitions stop when you're in college, it's like you died. I think (in my not so humble opinion) that it's well worth keeping up with new music comming out - you just have to be massively selective, to avoid the crap.

  7. Re:Wow - you had me at "US denies patent". on U.S. Denies Patent on Part-Human Hybrid · · Score: 1

    You know, you can quote the differences between chimps and humans at the base-by-base level of accuracy by doing chimp-human alignments. And we *can* know (not perfectly, but pretty close) how similar humans and chimps are.

    I use chimp-human differences to predict which allele is the ancestral one when I look at SNP data.

    If you look at say...dbSNP, you'll find downloadable tables of all the differences between humans and chimps. It will not find every difference because of regions of low sequence quality, but it comes close enough.

    I wonder if you work in the field, or just like to say "Ignore the fools"...

  8. Re:how long until on Identifying World's Species With Genetic Bar Codes · · Score: 3, Interesting

    Well, you may want to look up Admixture mapping to start. We don't really have species, but we have people from various backrounds with differing genetics that cluster by location due to population movements, bottlenecks, and migration.

    Or: Yeah, you can tell the difference between say...chinese and japanese people by looking at the frequency of various single nucleotide polymorphisms.

  9. Re:I have never heard of a technology more.. on Identifying World's Species With Genetic Bar Codes · · Score: 1

    I'm pretty sure they aren't sequencing the whole organism. Just a few spot checks.

    Sequencing is still pretty expensive - up for a few dollars a read (where a read is 500-1000 bp), and you've got to do a whole genome (say...3 billion bp for humans.) We're talking millions of dollars, minimum, plus LOTS of work for people to assemble all of that data (I have friends over in the finishing group at the Broad Center for Genome Research - I work in the medical and population genetics part of the Broad...)

    It just ain't that easy, yet...but the technology is improving much faster than computers are, so maybe in 10-20 years we'll be able to do that.

  10. Re:The hard part is... on Identifying World's Species With Genetic Bar Codes · · Score: 1

    If you had some sequence to the left and right to prime off of that was constant over many organisms, I'd say that was an extremely highly conserved, and thus very important (and interesting) region.

    You aren't amplifying more than 500 or so bp (what's the reasonable limit on sequencing now? Is it up to a KB yet?), and finding two very highly conserved sequences with sufficent variation would be...interesting.

    I'd love to see how they pick regions to sequence for this...

  11. Re:SUPPLY AND DEMAND on BitTorrent Community After SuprNova Shutdown · · Score: 1

    Laser Fart. Best show ever.

    Or, I know what I get for free. You be the judge.

  12. Re:full text on BitTorrent Community After SuprNova Shutdown · · Score: 1

    We draw the line at letting the person who first came up with the idea have some period of exclusivity where they can take advantage of all their hard work to make some level of profit.

    After that time is over, the idea should go in the public domain.

    That was the original intent of copywrite, patents, etc. However, while patents have kept more a more reasonable timeframe, copywrite is out of freakin' control.

    If copywrite was limited to say - 20 years? That would be enough to make plenty of profit, and your kids would get the works for free. The fact that copywrite still exists on things produced in the early part of the last century is the problem.

  13. Re:Drop that crack pipe! on Gosling Claims Huge Security Hole in .NET · · Score: 1

    How 'bout if most of the bioinformatics tools written over at MIT's Broad Institute were all written in java. I've got a lot of 'number crunching apps' running right now.

    Some of them are even running on our compute cluster...yummy.

  14. Re:Difference on Cellphone Drivers Drive Like Drunks · · Score: 1

    I think what you're getting at is that you need to stratify the data into two groups: people who talk on the cell phone, and people that don't. Then, look at the trends in both groups.

    After that, see if there's a statistical signifigance between the cell phone users change over time the the non-cell phone users.

    The grandparent's hypothesis is confounded by the fact that the populations were not stratefied.

    -Jim
    "Population Genetics Statistics is my bag. Sorta."

  15. Re:Not applicable on Hitchhiker's Guide to the Galaxy Screening Reviews · · Score: 1

    Perhaps if this is looked of as a 'performance' of the work (and the radio and book as similar performances of the underlying idea), then it makes sense.

    I often love to see bands who perform their songs differently then the studio recording. You get to see different aspects of the song, derive new meaning, or just enjoy a change of pace. I doubt someone in the audience is going to yell "You're playing it wrong!" when a band plays a song differently.

    Of course, I'm not quite sure how often mass-market crap throws variation into their performances. Perhaps we want fast-food style entertainment (it's the same everywhere, every time), and we're gluttons for consistency...

  16. Re:The IDE Issue... on Java Application Development on Linux · · Score: 1

    Jbuilder has all the stuff you mention as well. Not to mention that both have built in support for CVS, remote debugging (and debugging into an app server is HANDY), support for jsp and JSF, etc.

    They are both really good at what they do. They both have lots of plugins.

    I got JBuilder on an acedemic license for $400. I've used eclipse as well. I found Jbuilder easier to use, but you may find eclipse easier.

    I'd say: try both, see what you like and if it's worth the cash for JBuilder. If you're on a budget, then eclipse is a heck of a lot nicer than any text editor out there...

  17. Re:Learn it all for yourself. It's part of growing on What You'll Wish You'd Known · · Score: 1

    I don't have a master's degree. Whoops. Just ten years in the field.

    I must not be doing the research I thought I was. I guess if I get that first author in nature in the next few months, I may feel a little better about my inability to advance the field.

  18. Re:Learn it all for yourself. It's part of growing on What You'll Wish You'd Known · · Score: 2, Interesting

    As someone who's been in the sceince field for about 10 years now...

    I think science is a really interesting mix of formal training and being 'self taught'. You gain the basis of learning from school, but that generally doesn't cover the scope of what you'll be researching once you're out of school.

    I know that my formal education mearly gave me the vocabulary and the beginnings of the methodologies neccesary to work in the field. After getting past the basics, you tend to learn by teaching yourself - reading papers, doing research, discourse with other scientists.

    Perhaps this is what seperates the people who work at some level of what is essentially a lab tech (think: the hands) from the people that move on to being an investigator or manager (the brains.) Everyone gets the basics, but only certain people are driven enough to spend the rest of their lives extending their knowledge.

  19. Re:You people are fucking idiots on Patents and Open Source Biotech · · Score: 1

    Dear Dickcheese,

    As someone who works as a visiting scientist in the genomics lab at the Broad Institute (think: MIT) and at harvard labs (my primary job), I can tell you something: Basic research is doing much of the research that provides first round targets for drugs.

    We're the ones who do genetic studies, and find associations between mutation and phenotype. Drug companies can use these associations to target their drug development pathways.

    They aren't all small molecule shotgun methods, you know?

    Wait, maybe you don't.

    But I must say, I find the word 'dickcheese' amusing.

  20. Re:This "paper" is a mess on P2P Manifesto:Peer To Peer Study/Project · · Score: 1


    Finally, "the tragedy of the commons" is in various ways a bad analogy for the situation. The commons is a finite, grassy area which the industry of raising sheep was based. Without an owner or owners to divide up the commons and control it, each sheep owner was only as interested in, and had as much control in, keeping their own sheep fed. The tragedy of the commons doesn't decry how innovation doesn't occur. It decries how without ownership production of the norm disappears. But, clearly artworks already created do not disappear. You're crying out about the loss of *new* works of art, be them in the same genres that exist or new genres that do not exist yet.


    The tragedy of the commons is that everyone wants to take music, movies, and other entertainment content for free. But once there's no incentive to create them, the commons will be destroyed (overgrazed, if you will), and there will be nothing left to take.

    I'm sorry. Art takes time and money to create. I know and have worked with amature film makers, am friends with 2 groups of community theater people, hang out with tons of semi-professional musicians.

    They all need money to excel at their work. If you want them to work for little to no money, then they will not have the time to produce many, if any works. As it is, most of them count themselves LUCKY if they are able to break even on any given project.

    Break even does not mean they had a million dollar cocaine party. They work full time jobs, and breaking even pays for materials, software licenses, etc. Their salaries for working on their projects are effectively $0.

    How many people do you spend time with who are in the creative fields? What have you been publishing? How much did it cost for you to do your last theater production?

    Are you an idealist, or are you an active participant in the field?

  21. Re:Simple solution ... on Patents and Open Source Biotech · · Score: 1

    I think people have no idea of how much some of these processes cost, and what "high throughput" biology is all about.

    Take the Hapmap project. They're aiming for 5,000,000 variants x 300 people. At a low price of say...$0.05 cents each, that's low low price of $75,000,000. The good thing is that the technology costs are going down, so they'll probably finish the whole project for closer to $50M. That doesn't count all the human labor costs, just the reagents.

    What's cool is that this is essentially an open-source biology project. All the data is published on the hapmap website, free for anyone to use. The money *does* have to come from somewhere, though.

    -Jim

    (P.S. Look for those 500K variants on a chip this year. Cool stuff is comming. We'll have whole-genome on a chip scans soon - arguably this year depending on what you consider adequate coverage for a population.)

  22. What am I missing here? on Patents and Open Source Biotech · · Score: 5, Interesting

    Here's an article quite:
    BIOS will soon launch an open-source platform that promises to free up rights to patented DNA sequences and the methods needed to manipulate biological material.

    I thought you can't patent DNA sequences, only processes on sequences. Gene patents without specific purposes were thrown out years ago, weren't they?

    I understand why methods are being patented. They are costly to develop. They aren't obvious. Without patents, I'm not sure what the desire is to invent a new method to cheaply assay something.

    My work uses data very similar to sequence data (genotype data), and the data gathering process has become a commodity over the last few years. Everyone's developed their own machines, methodologies, and patents. You can sign up with any of these guys, and essentially the bottom line is: cents / data point. You weight that in against the size of the batches you're planning on doing over the next number of years, the reliability and service provided by the company's platform, and go.

    These companies would not be innovating newer, cheaper solutions if I could just take those solutions back to the lab and they didn't earn a penny for their effort. As it is, these companies are working on slim margins, and not many of the startups are successful.

    In the past, before these companies came out with their turnkey solutions, we'd have to roll our own. And that means detection systems, possibly robots, databases, protocols for chemical processes, etc.

    When I worked in the lab, we did one of these, based on a paper that was published in 1999. Even standing on the back of another researcher, it took us 18 months to have a working assay system that was 'production ready' for JUST OUR LAB (granted, it's the MIT genome center, and we're a big-ass lab.) Just about the time we finished, the first decent turn key solution came out...and it was cheaper and easier than what we'd developed.

    I love what I do for a living. It's a good time, and interesting work. Would I do it for free, if I had to work a normal job?

    No way. This job alone takes huge amounts of time, outside research, etc to excel. If I wasn't compensated for my hard work, I'd have no time to *do* that hard work.

    (given all that, we're working on open-sourcing chunks of our source code, to at least give something back to the community - but source code is the least of our assets.)

  23. Re:P2P is Awesome on P2P Manifesto:Peer To Peer Study/Project · · Score: 1

    I can't decide. Is the parent post satire, or plagurism?

    And, could I steal someone's ideas, and just modifiy a few words with find-replace over a P2P network?

  24. Re:This "paper" is a mess on P2P Manifesto:Peer To Peer Study/Project · · Score: 1

    So, basically, in order for people to get their free music, we need to give up some art forms (movies), switch back to very small distributions (you can come see my play, performing in my city for a few months, instead of renting the DVD), and we will not have any more of the 'extravagant' works we used to have.

    Oh, and regarding the musicians who can only make music off their performances: You're aware that there are people (individuals, mostly) who compose multi-part, extremely layered music, and just DON'T TOUR. Let's write to them, and tell them to fuck off, because they can't make a cent, doing what they do best.

    I applaud your desire to squash creativity, and limit artists creativity to what they could pull off 500 years ago. Oh, but while you're making that comparison to 500 years ago, ignore all the changes in technology of the last 500 years.

    Personally, I want to see artists skip the middle man, and distribute their own works. That way, they don't need to sell a million copies of a CD. They can charge more 'reasonable' rates - say a buck or 3, and sell 50,000-100,000 cd's. THat'll cover their costs, and provide some standard of living. Do they want to tour? Great, hook 'em up with some more cash.

    I still don't know what people could do to preserve other art forms that have been invented in the last 500 years. Oh well, fuck the artist. Maybe they can perform that new movie "The tragedy of the commons."

  25. Re:This "paper" is a mess on P2P Manifesto:Peer To Peer Study/Project · · Score: 1

    If you tell me that I can only be creative for my own enjoyment, and can't make money off it, then I'll tell you this: Nobody is going to create music, movies, etc anymore.

    There will be nothing left for you to enjoy, because people will not have any incentive to produce works and distribute them.

    If you're ok with that, great. But don't expect the same quality of movies, music, etc to be released. These things take time and money to create.

    And no, I'm not talking about Hollywood trash, I'm talking about indie music, movies, etc. Where am I going to 'perform' my movie (which is some people's justification for music)?

    If you want everything for free, you can have it...but there'll be nothing created you want.