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User: VoidEngineer

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Comments · 501

  1. Re:+4? Are the moderators mad? on Smart Mobs · · Score: 2

    Fair enough. I concede the argument.

  2. Aromatic Compounds on DARPA Has $3.2M to Sniff You Out · · Score: 4, Informative

    So, odors are generally caused by 'aromatic molecules'. The nose, actually, is a molecular shape sensing device. Knowing what a terrorist smells like is central to knowing what kind of compounds and chemicals they've been working with. Somebody who smells acidic, dusty, and metallic is doing very different kind of work than somebody who smells of of wood/bark, musty, or moldy. The first person may be working with metals and acid etching things, whereas the second person may be a mycologist, and growing fungus. Between the two, the former is more likely to be making a bomb; the later bioweapons.

  3. Re:Bioengineering on Bioinformatics in The Economist · · Score: 1

    Oh, I think that 128bit would be a good platform, as well as any other multiple of 64, especially 256bit computing. Although, due to chunking, I would not attempt to do serious genetics work on a 32bit computer.

    And please don't think that I'm trying to give the last word on this subject. I'm merely trying to point an optimal method for number crunching. There are certainly many optimal algorithms. I suspect that each algorithm will ultimately produce different results, so it's important to consider methods to be used before going out and spending alot of time and money coding a project.

    And, as you said, 128bit could do the task. 64bit chips are more available on the open market at the present time. Now, a 256bit processor, with an 8bit coprocessor, could do some amazing work in a number of applications which need to compute matrices.

    I'm not trying to say that what I've suggested is the last word on this subject. Far from it. A great book on the subject is:

    Genetic Algorithms + Data Structures = Evolution Programs. Zbigniew Michalewicz. 1996

  4. Re:64 combinations != 64 bit on Bioinformatics in The Economist · · Score: 1

    Ummm. That's exactly my reasoning. 26bit computing is perfect for analyzing language, but only as it is written in the Roman Alphabet. Other alphabets, such as Cyrillic, would need other platforms.

    And exactly my point that they are both related to molecular biology. But seriously... James Watson and crew, who theorized the double helix structure of nucleic acids back in the 50s, were part of a growing trend of molecular biologists who were investigating stereoscopic visualization of chiral molecules. And you are correct that visualization techniques and databases don't necessarily have anything to do with each other. Genetics, however, encodes what is fundamentally a chiral molecule and is therefore fundamentally encoding stereoscopic data. So, there is a connection, exactly at the molecular biology level.

  5. Re:Bioengineering on Bioinformatics in The Economist · · Score: 1

    Ah, just what I need: another sarcastic anonymous coward.

    Sorry for sharing knowledge. I'll keep my mouth shut and write closed source code in the future.

  6. Re:Spielberg Over the Hill? on Taken? · · Score: 1

    I bet he looks at demographics data alot, and that a lot of his story telling is based on Neilson ratings and so forth. A story which a Nerd finds interesting is different than a story which a Non-Nerd finds interesting.

    Well, at least he's not playing 'in-crowd' and is giving new actors chances to work with folks who've been in the industry for awhile.

    But yeah, his credits will be rolling before long.

  7. Re:Bioengineering on Bioinformatics in The Economist · · Score: 1

    Nah. I'm not exactly 'lost'. I did live in the hometown of Gregor Mendel for a year during high school, where I studied mendelian genetics (Received a scholarship, via the 1994 congressional information act, and went with the Youth For Understand program). I also studied genetics at the University of Chicago's Department of Ecology and Evolution. Anyhow, I happen to know alot about genetics, actually... to the point that I'm making comments based on 'insider information' much like many people make 'inside jokes' which don't make sense to other people.

    I would suggest the new mod: "Inside Info"

  8. Re:Bioengineering on Bioinformatics in The Economist · · Score: 1

    Thank you. =)

    I agree that the problem can be implemented with a 23bit model. I believe that model is valid in many cases. However, I see the 64 bit model as being more accurate and representative of the underlying mathematics of genetics. Moreover, one can do the calculations with a 64bit model, and utilize a 23bit model as a check... if the 64bit model runs correctly, the results should be reducible to a 23bit explanation, and can be checked via another algorithm.

    Also, I believe that the 64bit model can model a bunch of stuff that the 23bit model leaves out, including mutations, loops, reverses, and so forth. (i.e. aaa.aaa.CCC.ggg.ggg.ttt.ttt becomes aaa.aaC.CCg.ggg.ggt.ttt.ttX) I forget what that's called, but you get the idea. Deletion! Ah. Deletion, mutation, etc.

    Anyhow, the 64bit model is really slick mathematically, and one can do really crazy cool masking and information analysis on the matrices which are formed.

  9. Re:Bioengineering on Bioinformatics in The Economist · · Score: 1

    What, so you can represent each possible codon as a single bit? Last I checked, you can represent 64 values with a measly six bits. (2^6 = 64).

    That's fine, but the point is that one can make sort of a 'virtual gene' or 'genetic codon probability template', which happens to be optimized for a 64 bit computer, utilizing genetic algorithms. I agree with you that you can represent 64 values with six bits, which isn't exactly what I was refering to. The idea is to map each possible codon onto a bit of the packet which is going to analyzed by the processor. Probably, one will want to create a big-Indian or little-Indian (endian, whatever) ordering scheme.

    For example:
    AAA = 10000000000000000000000000000000000000000000000000 00000000000000
    AAC = 01000000000000000000000000000000000000000000000000 00000000000000
    AAG = 00100000000000000000000000000000000000000000000000 00000000000000
    AAT = 00010000000000000000000000000000000000000000000000 00000000000000
    etc.
    and so forth. Therefore,
    11110000000000000000000000000000000000000000000000 00000000000000


    would equal ( Protein | AAA, AAC, AAG, AAT).

    Great for optimizing a mainframe for crunching through a combinatorial space of codons, searching for proteins.

  10. Viewpoints on Bioinformatics in The Economist · · Score: 5, Interesting

    Hmmm. Seems like it would be easier to say that everything which has been done in computer science has 'been done', whereas everything that hasn't been done in computer science, 'hasn't'.

    Seriously, though, you may be mis-categorizing your subjects. Look at computers as computational entities, rather than disk drives, monitors, and so forth. In that case, an optical computer or a biocomputer operates on many of the same systems priciple as a 'digital computer', and there is therefore much to be done in the field of computer science.

    Absolutely. Optical computing is getting some great advances in Holographic Video at the MIT Spatial Imaging Group. And chemical computing is advancing nicely in Carbohydrate Chips at the University of Chicago.

    For my money, I'd bet on optical video cubes, 3D television, and biochips in the future... which are all applications of computer technology. Remember, 'computer' use to refer to the job title of a person.

    For my money, I think that the future has got SnowCrash, Cryptonomicon, Neuromancer, Count Zero, Mona Lisa Overdrive, and Johnny Mnemonic written all over it (and maybe a bit of Jurassic Park.

  11. Bioengineering on Bioinformatics in The Economist · · Score: 0

    Hmmm... I had a bunch of bioengineering classes at college. It's really interesting because if you understand the mathematical basis of the genomic codon, you will know that there are 64 different combinations of 'A', 'C', 'G', 'T' in a three letter sequence, aka 'codon'. (4^3=64).

    Hence, 64 bit computing is an ideal platform for crunching though genomic data. Hence the development over the past decade of advanced stereoscopic visualization techniques (aka virtual reality), because of nucleic acids are chiral molecules, of a complex sort. Hence the development of genomic databases, which run on unix/linux operating systems and can parse terrabyte and pettabyte storage area networks.

  12. Re:Opportunity Cost on Yet Another Call for Linux Standardization · · Score: 2, Interesting

    I hear what you are saying, but instead of looking at the glass as half empty, look at it half full. In 12 years, linux has managed to gain a couple of percentage points of the desktop market. Holy cow! That's major! That's amazing! Think about BeOs, NextStep, OS2, and Amiga. Hell, even Irix, Solaris, and AIX have been loosing ground in the desktop market.

    I understand what you are driving at, as things currently stand. My thinking is that a half dozen advertising gurus could take linux, repackage it, and make a marketable desktop operating system that could replace Windows, if they could find a better user interface metaphore than 'Windows'. But, let's face it, 'Windows' is a pretty damn good metaphore for operating a computer. If that marketing and advertising team could think up of a better metaphore than 'java' or 'windows', they would stand a chance of reinventing the market. By and large, this kind of thinking is very rare, and the notable exceptions have been Windows, Apple, Sun, Macromedia, and so forth... (notice the metaphorical marketing that is inherent in these companies' logos?).

    Hmmm... will need to think about this some more.

  13. Pimp OS on Naked Objects Version 1.0 Released · · Score: 2, Funny

    Yep, I can see the slashdot headline now: "Pimp OS uses Naked Objects foundation"...

    Hmmm, I'm looking at the screenshot which is posted on the article, and I'm a little amused...

    Customer?
    Communication?
    ChildBenefitScheme?!?!
    Case?
    Payment?
    Officer?

    I mean, I can understand that a PimpOS or a SlutOS would want to be object oriented and all. But isn't keeping a record of all your activities going to get you into trouble in most places?

    I suppose that the developers are located in Nevada or Amsterdam or someplace.

  14. Comments on Scientists Don't Read the Papers They Cite · · Score: 1

    Agreed. Science is full of huge problems. The fact of the matter is that science at the major research universities is often a vicious, unplesant experience. People argue, debate, name call, and stereotype, much like on Slashdot and anywhere else.

    The big difference with science, in my opinion, is that there are protocols for conducting behavior, which allows people to argue, debate, name call, and stereotype without it leading to all out hostility (usually).

  15. Reference Materials on Scientists Don't Read the Papers They Cite · · Score: 1

    Some interesting books on the topic:

    Hull, David. Science as a Process.
    Kuhn, Thomas. The Structure of Scientific Revolutions.
    Knuth, Donald. The Art of Programming.

  16. Re:Ineffectual Propriety on Lessig Spins Copyright Law · · Score: 1

    How different is that to patenting the human genome? How different is that to pharmaceutical companies going into the jungle, finding out about the plants the indigenous people use, and then patenting the active ingredients in the plants and then charging the poor bloody Indians for doing as their ancestors have done since year dot?

    I agree that it's not much different. From the patent law perspective, I believe that a lot of it has to do with processes, and the difficulty of creating complex systems. For instance: monkeys at keyboards. What is the chance that they write any work of Shakespeare? Pretty low. Similar analogies go for genetics, as I understand it. A person can't patent a 'frog', in the same way that a person can't patent 'gravity' or 'electricity' or 'magnatism'. But you can patent a 'frog slime remover & distiller' (which could have genomic and pharmaceutical uses), or a 'dinosaur replication system', which are similar to the concept of patenting a 'plane', or a 'submarine', or an 'automobile.' I could be wrong, as I don't have any patents, but I've been studing the process for about 5 years now.

    It goes like this:
    If you don't measure it, you can't control it.
    If you can't control it, you can't improve it.


    Have you ever thought about patenting things yourself? You seem to have a good concept of the motivation behind patenting a process or concept. Your points nicely suggest a 'Jurassic Park' thought analogy.

    People will play the system - they'll do what you measure, especially if their pay depends on it.
    If you measure the wrong thing, you will get the wrong thing.


    Seems like you've already been in this business before. Great insights. If I had mod points, I would have modded you up. I'm always trying to measure things, and you have mentioned a very serious problem to the inventive mind... namely, how to value the thing being measured. Metametrics? Metrics of metrics... Hmmm...

    In the UK (and I think the rest of EU), patent law is more sensible; you cannot patent a discovery (as distict from an invention) and you can't - shock - patent something that previously existed.

    Yeah, well I never claimed that the US was sensible. I mean, how can you take the US seriously, when the US Code has more lines of code than Windows. My thinking is that overpopulation is getting the best of us, and the rest of the world.

    I advise you all to sink a few pints, get laid, and type the letter "E" a lot. Do it now, before someone decides to patent beer, genitalia, and the alphabet.

    Agreed.

  17. Re:+4? Are the moderators mad? on Smart Mobs · · Score: 1

    When did I admit that I had 'no idea'? And when did I even bring up 'N^N'? Read the article again, and explain to me when I introduced 'N^N'.

    Anonymous Coward introduced the term 'N^N' in the posting 'Rubbish!'. I think that this whole N^N thing may be off topic. It's like calculating a standard deviation, when the topic was discussing how to calculate an average. Kudos to other folks for being able to calculate N^N, and to point out that I was wrong in the fact that N^N increases faster than N!. My claim, however, was that N! increases faster than f(x^N) where x is a static number. That is, my claim was that factorial functions increase faster than exponential functions.

    Part of the problem is that there are too many capital N's in this discussion. Let me differentiate the problem, and be more concise. Please substitute M! for N! from here on in this discussion.

    Premise 1: Please select a static number, and refer to this number as 'x'.

    Premise 2: The range of these functions is within the range of real numbers |R, and extends to infinity.

    Premise 3: The method of incrementing M and N is in accordance to interger counting.

    Claim 1: M! will increase at a slower rate than f(x^N) while M
    if/for (m = 0; m < n; m++) RATE { m! < f(x^n) }

    Claim 2: M! will increase at the same rate as (f(x^N) while M = N.
    if/for (m = n; m = n; m++) RATE { m! = f(x^n) }

    Claim 3: M! will increase at a faster rate than (f(x^N) while M > N.
    if/for (m = n+1; m < infinity; m++) RATE { m! > f(x^n) }

    Claim 4: Because the range of numbers extends to infinity, M! will eventually outpace the f(x^N), for any static number x.

    Reread the article, and then go study thermodynamics, quantum theory, and nonlinear dynamics at the University of Chicago. You will then understand how these topics relate to networks and group theory. Remember that analysts describe stocks in the market as 'hot' or 'cold'. Moreover, Black and Scholes Options Pricing model is based on a modified thermodynamics model. And frankly, network routers with fiber optic backbones propogate information across the internet according to laws and formula derived from areas such as quantum group theory and network theory. They are, after all, using fiber optics, and optics is a domain of quantum field theory. Reeds Law is one such application of quantum networking and information theory.

    I never brought up 'N^N'. Anonymous Coward did, and it was off topic.

  18. Response to Question on Act On Total Information Awareness · · Score: 1

    Hmmm... Well, I've worked with similar systems in Chicago. Used to work in climate controlled server room which 'monitored' a 10,000 user network.

    The truth of the matter is that the watchers are typically bored to death with what they are doing, and automate the process, because 99% of human activities are actually rather benign and boring. Interesting note: something like 50% of internet traffic at major universities is pornography related... (Hold on to this though for a moment).

    The question is: when the abuses grow to the point where a lot of people do disagree with them, will those people have the power to change what they see wrong?

    Interesting question. OK, my guess is that it will have a lot to do with whether or not the abuses affect the people's ability to access sex, drugs, and rock and roll. If pornography, pharmaceuticals, and napster aren't affected, then the TIA will probably be able to function pretty close as it is designed.

  19. Re:Please shut up you stupid fag on Smart Mobs · · Score: 1

    Suit yourself.

    And I dare you to not use vulgarities while doing so. I bet you can't.

  20. Re:Robotic Bulldozers on 30 Years Since Last Man on the Moon · · Score: 1

    I totally agree with this article.

    But, I have to wonder... What would happen if we sent a robotic bulldozer to the moon, paved a street, and put up a 'for sale' sign? Think that the commercial sector would go for it? People are clammoring for space tourism, and I bet that there are some crazy folks out there that might just through money at a public utilities company on the moon, if somebody were to design it.

    Of course, there is the X-Prize Competition which is trying to do exactly what you mentioned: come up with a more efficient launch vehicle.

  21. Re:The Space Shuttle on 30 Years Since Last Man on the Moon · · Score: 1

    That assumes that the long term space travelers have some type of interest and desire to land (walk) in a gravitational field (on land). Who says that the long-term space astronauts of the future will care if their bones are made of glass?

  22. Re:know thou math on Human-Computer Interfaces From 2003 to 2012 · · Score: 1

    Unless thou hast renormalized thy constants and thy variables, in which case a probability of 1 means whatever thou hast defined it to mean within your operating paradigm.

    Absolutes are only as absolute as people believe them to be.

  23. Re:Media Labs on Human-Computer Interfaces From 2003 to 2012 · · Score: 1

    I give it 30 to 1 odds on holographic video and three dimensional television within the next 30 years. For more information on holographic video, check out this Spatial Imaging Lab

    I'd also give 2 to 1 odds on voice recognition within the next 10 years. Heck, 5 to 1 odds that the voice recognition in Windows Longhorn actually is functional enough to unplug the keyboard and dictate all your commands.

    20 to 1 odds for grid networking infrastructure within the next 20 years.

  24. Re:Rubbish! on Smart Mobs · · Score: 1

    d00d. how can anyone accept anything else you've said after a smack down such as getting N^N vs N! wrong?

    Perhaps they can't. Although I hope that I never post something such as 'd00d'. Moreover, I happen to be able to learn from my mistakes and am able to get back up after a smack down. Also, I'm not an Anonymous Coward and I keep track of my comments and mistakes. The end result is that I become more educated and wise with each mistake I make and 'smack down' which I receive. Trust me, I've been 'smacked down' more times than you have, and by better people than you.

    As far as getting N^N vs N! wrong, I don't typically work in combinatorics or in factorials. I typically work with vector mathematics, such as eigenfunctions and matrices.

  25. Mess that one up on Human-Computer Interfaces From 2003 to 2012 · · Score: 1

    Well, I messed that post up. The computing cluster link may have been offtopic, anyhow, so I'll leave it out. But, you should visit MIT's media lab site, anyhow....

    And, of course, there is the Washington States Human Interface Technology Laboratory. HIT Marks, heh...