his work on the anatomy of the soil nematode Caenorhabditis elegans. C. elegans is a simple roundworm that has only ~1000 somatic cells, of which ~300 are neurons. It was originally chosen as a modern model organism to study behavior, beacause of the simplicity of its nervous system. In the worm research community, Sir John is most reknowed for his serial electron micrograph reconstruction of all of the synaptic connections of all 302 neurons of the worm. Thus it is mostly due to his work that C. elegans is the ONLY organism in which scientists know the entire anatomy (that is, the wiring diagram) of the nervous system.
On a related note, at a recent C. elegans seminar I attended, the speaker made mention of Sir John, saying (to paraphrase) "Only Sulston is interested in these long boring projects, like serial EM reconstructions and the human genome project". Said in jest, of course:)
kids in school don't need more computer hardware/software. They need more teachers and better teachers. Computer software is becoming easier and easier to use (even Linux), it doesn't take a whole lot of time to learn how to use a word processor and spreadsheet or do a google search these days. It's much more important to teach kids to read, write, and do math. If Microsoft, or anyone else for that matter, is really concerned about education in this country they should divert their efforts towards hiring top notch teachers, attracting them and keeping them with competitive salaries and benefits. Current teacher salaries are a joke, no wonder public education sucks. Offer starting salaries of 50-60k/year with full health and retirement, and hire M.S. degree level people.
I once obtained RNA secondary prediction software from Washington University. Before we could obtain it, we had to sign waivers that we would not re-distribute it outside of our own research university. Once we got the software though, it came in source form. So AFAIK the source for academic software developed for life sciences is probably available upon request, you just can't redistribute it at will. As for publications, the alogrithms for predicting the RNA secondary structures were published, but not the code itself. Hope this is informative.
technical differences between clones and twins
on
First Cloned Human Embryo
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· Score: 4, Interesting
1. in vitro vs. in vivo fertilization. There are so-called maternal effects, such as placental-embryonic interactions, that have profound but as-yet not completely understood effects on embryonic development. an in vitro fertilized embryonic clone will be no different genetically from a clone, but there are epigenetic effects that must be considered. This is not to mention materal effect genes, where a gene that acts embryonically is provided from the mother's, rather than the zygote's, genome.
2. genetic imprinting. Fertilized zygotes have DNA contributions from two parents, whilst cloned embryos only from one parent. DNA is often covalently modified (e.g., methylation) in a process called imprinting, where the modified allele is silenced. Modifying these silenced alleles often has deleterious consequences.
3. Telomere length. Chromosomal ends are maintained by special DNA structures called telomeres. The lengths of telomeres are often different between different cell types, and usually reflects the state of differentiation of the cells. Telomeres are known to affect life span and this is probably one of the main reasons why cloned animals have poor life spans.
There are just some factors that I can think of off-hand, I'm sure there are many others. Just because organisms have identical DNA sequences do not mean that they will develop identically, even if you do not take environmental effects into consideration.
Don't get me wrong, I am all for cloning and stem cell research, but it is prudent to think through ethical concerns before plunging ahead.
yup yup, the strips are good for initial screening, but they are also give lots of false positives, and have shelf lives. They are similar to pregnancy test kits. Basically, they are crude ELISA assays.
I also agree with you on the distinction between efficiency and sensitivity. Not having seen any data though, I hesitate to draw conclusions on the sensitivity of the bead assay.
Re:desktop not what you think it means
on
Desktop Biodetectors
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· Score: 3, Interesting
FYI I do work with DNA, I am a postdoc at Harvard Med School. The fact of the matter is, antibodies are a bitch to work with. Unless you make a hybridoma you can't mass produce antibodies, and even if you do have a good antibody the best you can do is an ELISA assay. There is no way that ELISA is more sensitive than PCR. This bead technology is likely to be more sensitive than PCR, faster than PCR, or both. It's also not that hard to extract DNA, usually a simple organic extraction gives you a good enough sample to work with.
Re:Resistance drops by a factor of about 1 million
on
Desktop Biodetectors
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· Score: 2
The detector is not detecting the organism, it is detecting its DNA. The basic idea is as follows: suppose you have a nasal swab that you suspect has anthrax in it. You extract DNA from the swab, and chemically tag the DNA with gold. In your detector, you have a piece of cloned anthrax DNA that consists of sequence unique to Bacillus anthracis, also chemically tagged with gold. The cloned DNA in the detector can be thought of as half of a capacitor; without the other half, current cannot flow and thus you have strong resistance. If there is anthrax DNA in the swab sample, it hybridizes to the detector DNA via Watson-Crick base-pairing. Because this hybridization is DNA sequence-dependent, only DNAs with identical sequences will hybridize to each other (this is an oversimplification but suffices for this discussion). When the gold-tagged sample DNA binds to the detector DNA, this completes a circuit and resistance drops dramatically. On the other hand, if no anthrax DNA is present in your nasal swab sample, then nothing hybridizes to the detector, and no current flows through the circuit. Even if there is DNA from other bacterial and/or viral species, there won't be anthrax-specific sequences and therefore those DNAs will not hybridize to the detector.
desktop not what you think it means
on
Desktop Biodetectors
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· Score: 3, Informative
The term "desktop" as used in the eetimes article probably does not mean what your typical computer geek thinks it means, as evidenced by the many posts so far. It's not a consumer device that sits on top of an home/office desk of the overly paranoid. Rather, it probably means that the device is sufficiently bulky as to make it not portable, and therefore must sit on a workbench in a lab. While such a device is useful for testing labs, its utility is somewhat less because it can't be used in the field.
That said, this is really cool technology. It's potentially much faster than the standard tests today, either polymerase chain reaction (PCR) or spore cultures (which is the *only* way to 100% reliably test for anthrax but is also the most time consuming protocol). Aside from testing for microbial agents, it sounds like the technology may have applications in high-throughput gene analysis.
Personally I tend to agree with you. Unfortunately, most (non-geek) people often dislike digital images. I bought a digital camera before my daughter was born, for the purpose of uploading pictures to a website so that all the relatives, grandparents, etc. could see new baby pictures immediately. But all they wanted were printouts. To paraphrase my mom, "I don't want to have to boot up the computer every time I want to show my friends a picture of my granddaughter!" The only thing that digital has going for me now, insofar as baby pictures for the grandparents goes, is that I can see what the pictures will look like before they are printed, and therefore decide which ones I want to print in the first place. Which is what these guys are probably trying to sell, I guess.
hmm, why is this modded as flamebait? the comments sound reaonable to me...
getting back on topic, someone's.sig file says something to the effect of "the only intuitive interface is a nipple". ease of use, for most people, seems to be a function of familiarity than anything else.
Speaking as someone who has almost used Macs exclusively for 10 years for work purposes (communications, graphics, and word processing in an academic lab), I would argue that macs aren't necessarily easy to use; rather, they are easy to learn to use. to me, one of the UI concepts of MacOS that I find most inconvenient is the assumption that I *want* to use the mouse for everything. for instance, there is no easy way to access contexual menus in MacOS except with the mouse, unlike the Alt-keystroke under windows. Personally I find it much easier to work faster in windows because many functions in contextual menus can be accessed by keystrokes. I found that its less stressful on my hands when I don't have to go back and forth from keyboard to mouse all the time.
Then again, some of my co-workers who are staunch Apple protagonists claim that the contextual menus at the top of the screen that require a mouse to access is precisely what allows them to work faster. I believe that MacOs is easy to learn, but "ease-of-use" is probably pretty objective.
In theory it's possible, but it would be extremely difficult. When sperm fertilizes an oocyte, the position of sperm entry plays a critical role in embryonic development; that is, the position of sperm entry defines the polarity of the embryo.
Further, the oocyte is, for the most part, transcriptionally inactive. Many genes that function during embryogenesis are expressed maternally; the mRNA is expressed and stored but not translated during oogenesis until the gene products are needed later. To use a computer analogy, these maternal-effect genes are loaded into memory when the oocyte was still not yet an oocyte, and cached for later use after fertilization. A stem cell would lack such "cached" genes.
This is not to say it couldn't be done, but a developing organism is much more than just dividing stem cells.
the contamination refers to mouse retroviral contamination, not contamination by mouse genes, per se.
audiophiles are some of the silliest people I know
on
Insanely Audiophile
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· Score: 2
I know this one guy who has like this insanely expensive stereo system, but the only CD he owns is the Dolby Digital test CD, that has cannons firing in 5 channel surround sound.
If I had the money, I'd rather spend it on software (i.e., music CD's) rather than hardware. I consider my 600 dollar shelf system extravagant:)
Of course, HP's printers are still shipping with Windows-only drivers... and Windows-only configuration tools... and described as "Linux-compatible" in their advertisements
shoot, if a printer is networkable and speaks postscript, are the tools for printer configuration that ship with linux not good enough already? Not trying to be a troll, just an honest question.
Eukaryotic genes are arranged in an exon-intron structure. Exons are segments of DNA that actually code for amino acids; introns are segments of junk DNA that don't code for amino acids. If I use letters to indicate exons, and numbers to indicate introns, a typical gene looks something like this:
A1B2C3D4E5F
Cells use a mechanism called alternative splicing to generate different proteins from within the same gene. So to use the example gene above, the cell can make ABCDEF, ACDEF, ABDEF, ABC, AEF, etc.
Further, the same protein expressed in a different context can have different functions. For instance, protein A, when present together with proteins B and C, may have a different function than when proteins D and F are present as well.
The label "supernatural" has been proven time and again to simply indicate something that's not completely understood.
FYI I read PNAS all the time. Sure there are plenty of good research articles in there, some which have been published by our lab, but there are junk articles too. Short of me spending some time on Medline to pick out a specific article, let's just say the research university that I work at has about a dozen Academy members, some who are Nobel laureates, who are faculty members. While I respect them all for their contributions to science, it is also true that I personally know of cases where other non-member faculty members have used their personal relationship with those members to push papers into PNAS that either (a) would not get published elsewhere, or (2) would have been late to press and competing labs may gave gotten out their papers first. Its a "you scratch my back I'll scratch yours" situation.
Non-peer review is certainly not the solution to the over-proliferation of papers in science; I don't know what the answer is. Nonetheless, the peer-review process is fundamentally flawed if research grants are awarded on a purely productivity basis.
the problem with peer review is that, by and large, science is an "old boys school". Regardless of what academics will have you be believe, getting your data published in a good journal, especially if your results are novel and/or contraversial, is more influenced by who you know than what you've done. The worst possible example of this is in the journal The Proceedings of the National Academy of Sciences. In principle, for a reasercher to be elected to the Academy is an extreme honor and often it is seen as a launching pad to the Nobel Prize. As such, PNAS allows publication of reearch papers from their members sans the standard peer review process. However, in recent years when productivity and competition for grant money has become the most cut-throat, PNAS has become a dumping ground for results that could not have been published elsewhere, or for results that are so provocotive that submission to standard peer-review journals would run the risk of getting similar results published by your competitors first in other journals. Not only this, PNAS has also been used as favors for members to non-members who have trouble getting published elsewhere.
PNAS is the extreme example. Other journals, although theoretically peer-reviewed as well, have essentially the same problem: even if your results suck (but don't suck too bad), if you're buddies with the chief editor then you can get published most of the time.
I dunno, I think you're painting a bleaker picture than needed. A lot of commercials on AM sports radio is for local businesses, and listeners of internet radio are probably mostly people who are outside the normal broadcast area.I don't think there would be much effect in terms of the local radio stations.
look at it this way, it's probably aimed primarily at people who are located outside of the broadcast area of the team they are interested in, e.g., NY Yankee fans living in California. Satellite TV season sports packages easily cost upwards of 100 dollars per season, if not more. People living within the broadcast market will just watch Tv/listen to the radio. Even if I were on a business trip and wanted to catch the action of the latest home team's game, 9 bucks is quite reasonable even for a one time fee, heck that's about how much it costs for a couple of pr0n flicks in a hotel pay-per-view. As far as commercials go, in baseball it's not even an issue considering they have commercial breaks anyway between innings. It's a pity it won't be free anymore but servers and bandwidth cost money. I think 9 bucks is a pretty reasonable price.
The annoyance at someone writing in all caps is imho a diversion from the real issue, which is the fact that someone's copyrighted material is alledgedly being pirated and the owner of said material is royally pissed off. Who cares if he is writing in caps? not every is savvy about the so-called and largely self-imposed net ettiqutte. I happen to think he has a valid point, and if in fact he and his lawyer are able to prove that the accused have pirated his works, they should push to have them proscecuted to the extent of the law. If you want to get free reading material of the net goto the Gutenburg project. I also have very little sympathy for Napster users who are sharing copyrighted music; if you want to share music, share free (as in beer and sometimes in speech) music. The record companies should go after individuals and sue them instead of Napster.
let me first say that I think KDE is great and personally I like it much better than GNOME. However, the one thing that is really inconvenient is that KDE packages are huge and monolithic, not necessarily in terms of byte-size but in terms of functionality. For instance, if I want to update Konqueror only, I have to update the entire kde-base (I think, it may be another kde-* package) package. GNOME I think also has the same problem on a slightly smaller scale. I'd love to be able to be able to update specific apps or libraries without having to download the entire package; the ideal installer would then detect dependencies and prompt for additional downloads as needed.
that people give away their fair use rights doesn't bother me all THAT much. what really pisses me of is some people who have these kickass home entertainment systems, but have no taste in movies; who needs to watch Howard the Duck in 5 channel surround sound anyway? It's like the people who have these really nice, expensive stereo systems and the only CD they own is the Dolby decoder test CD with the cannon-firing sounds. Why, back in my day we used mono cassette players plugged into 5 dollar computer speakers, and WE LIKED IT!
Slashdot Mirror
On a related note, at a recent C. elegans seminar I attended, the speaker made mention of Sir John, saying (to paraphrase) "Only Sulston is interested in these long boring projects, like serial EM reconstructions and the human genome project". Said in jest, of course :)
kids in school don't need more computer hardware/software. They need more teachers and better teachers. Computer software is becoming easier and easier to use (even Linux), it doesn't take a whole lot of time to learn how to use a word processor and spreadsheet or do a google search these days. It's much more important to teach kids to read, write, and do math. If Microsoft, or anyone else for that matter, is really concerned about education in this country they should divert their efforts towards hiring top notch teachers, attracting them and keeping them with competitive salaries and benefits. Current teacher salaries are a joke, no wonder public education sucks. Offer starting salaries of 50-60k/year with full health and retirement, and hire M.S. degree level people.
I once obtained RNA secondary prediction software from Washington University. Before we could obtain it, we had to sign waivers that we would not re-distribute it outside of our own research university. Once we got the software though, it came in source form. So AFAIK the source for academic software developed for life sciences is probably available upon request, you just can't redistribute it at will. As for publications, the alogrithms for predicting the RNA secondary structures were published, but not the code itself. Hope this is informative.
2. genetic imprinting. Fertilized zygotes have DNA contributions from two parents, whilst cloned embryos only from one parent. DNA is often covalently modified (e.g., methylation) in a process called imprinting, where the modified allele is silenced. Modifying these silenced alleles often has deleterious consequences.
3. Telomere length. Chromosomal ends are maintained by special DNA structures called telomeres. The lengths of telomeres are often different between different cell types, and usually reflects the state of differentiation of the cells. Telomeres are known to affect life span and this is probably one of the main reasons why cloned animals have poor life spans.
There are just some factors that I can think of off-hand, I'm sure there are many others. Just because organisms have identical DNA sequences do not mean that they will develop identically, even if you do not take environmental effects into consideration.
Don't get me wrong, I am all for cloning and stem cell research, but it is prudent to think through ethical concerns before plunging ahead.
I also agree with you on the distinction between efficiency and sensitivity. Not having seen any data though, I hesitate to draw conclusions on the sensitivity of the bead assay.
FYI I do work with DNA, I am a postdoc at Harvard Med School. The fact of the matter is, antibodies are a bitch to work with. Unless you make a hybridoma you can't mass produce antibodies, and even if you do have a good antibody the best you can do is an ELISA assay. There is no way that ELISA is more sensitive than PCR. This bead technology is likely to be more sensitive than PCR, faster than PCR, or both. It's also not that hard to extract DNA, usually a simple organic extraction gives you a good enough sample to work with.
The detector is not detecting the organism, it is detecting its DNA. The basic idea is as follows: suppose you have a nasal swab that you suspect has anthrax in it. You extract DNA from the swab, and chemically tag the DNA with gold. In your detector, you have a piece of cloned anthrax DNA that consists of sequence unique to Bacillus anthracis, also chemically tagged with gold. The cloned DNA in the detector can be thought of as half of a capacitor; without the other half, current cannot flow and thus you have strong resistance. If there is anthrax DNA in the swab sample, it hybridizes to the detector DNA via Watson-Crick base-pairing. Because this hybridization is DNA sequence-dependent, only DNAs with identical sequences will hybridize to each other (this is an oversimplification but suffices for this discussion). When the gold-tagged sample DNA binds to the detector DNA, this completes a circuit and resistance drops dramatically. On the other hand, if no anthrax DNA is present in your nasal swab sample, then nothing hybridizes to the detector, and no current flows through the circuit. Even if there is DNA from other bacterial and/or viral species, there won't be anthrax-specific sequences and therefore those DNAs will not hybridize to the detector.
That said, this is really cool technology. It's potentially much faster than the standard tests today, either polymerase chain reaction (PCR) or spore cultures (which is the *only* way to 100% reliably test for anthrax but is also the most time consuming protocol). Aside from testing for microbial agents, it sounds like the technology may have applications in high-throughput gene analysis.
Personally I tend to agree with you. Unfortunately, most (non-geek) people often dislike digital images. I bought a digital camera before my daughter was born, for the purpose of uploading pictures to a website so that all the relatives, grandparents, etc. could see new baby pictures immediately. But all they wanted were printouts. To paraphrase my mom, "I don't want to have to boot up the computer every time I want to show my friends a picture of my granddaughter!" The only thing that digital has going for me now, insofar as baby pictures for the grandparents goes, is that I can see what the pictures will look like before they are printed, and therefore decide which ones I want to print in the first place. Which is what these guys are probably trying to sell, I guess.
getting back on topic, someone's .sig file says something to the effect of "the only intuitive interface is a nipple". ease of use, for most people, seems to be a function of familiarity than anything else.
Speaking as someone who has almost used Macs exclusively for 10 years for work purposes (communications, graphics, and word processing in an academic lab), I would argue that macs aren't necessarily easy to use; rather, they are easy to learn to use. to me, one of the UI concepts of MacOS that I find most inconvenient is the assumption that I *want* to use the mouse for everything. for instance, there is no easy way to access contexual menus in MacOS except with the mouse, unlike the Alt-keystroke under windows. Personally I find it much easier to work faster in windows because many functions in contextual menus can be accessed by keystrokes. I found that its less stressful on my hands when I don't have to go back and forth from keyboard to mouse all the time.
Then again, some of my co-workers who are staunch Apple protagonists claim that the contextual menus at the top of the screen that require a mouse to access is precisely what allows them to work faster. I believe that MacOs is easy to learn, but "ease-of-use" is probably pretty objective.
Further, the oocyte is, for the most part, transcriptionally inactive. Many genes that function during embryogenesis are expressed maternally; the mRNA is expressed and stored but not translated during oogenesis until the gene products are needed later. To use a computer analogy, these maternal-effect genes are loaded into memory when the oocyte was still not yet an oocyte, and cached for later use after fertilization. A stem cell would lack such "cached" genes.
This is not to say it couldn't be done, but a developing organism is much more than just dividing stem cells.
the contamination refers to mouse retroviral contamination, not contamination by mouse genes, per se.
If I had the money, I'd rather spend it on software (i.e., music CD's) rather than hardware. I consider my 600 dollar shelf system extravagant :)
shoot, if a printer is networkable and speaks postscript, are the tools for printer configuration that ship with linux not good enough already? Not trying to be a troll, just an honest question.
fucking the plumber wouldn't change mitochondrial DNA, which is inherited only maternally.
connected to and controlled by linux. Now *that* would be cool. set a cron job to 'cat toast /dev/toaster' every morning at breakfast. :)
A1B2C3D4E5F
Cells use a mechanism called alternative splicing to generate different proteins from within the same gene. So to use the example gene above, the cell can make ABCDEF, ACDEF, ABDEF, ABC, AEF, etc.
Further, the same protein expressed in a different context can have different functions. For instance, protein A, when present together with proteins B and C, may have a different function than when proteins D and F are present as well.
The label "supernatural" has been proven time and again to simply indicate something that's not completely understood.
Non-peer review is certainly not the solution to the over-proliferation of papers in science; I don't know what the answer is. Nonetheless, the peer-review process is fundamentally flawed if research grants are awarded on a purely productivity basis.
PNAS is the extreme example. Other journals, although theoretically peer-reviewed as well, have essentially the same problem: even if your results suck (but don't suck too bad), if you're buddies with the chief editor then you can get published most of the time.
Joe Cartoon rocks. The website that brought you the web's first killer app: blowing up a gerbil in a microwave (among other gerbil-genocidal humor).
I dunno, I think you're painting a bleaker picture than needed. A lot of commercials on AM sports radio is for local businesses, and listeners of internet radio are probably mostly people who are outside the normal broadcast area.I don't think there would be much effect in terms of the local radio stations.
look at it this way, it's probably aimed primarily at people who are located outside of the broadcast area of the team they are interested in, e.g., NY Yankee fans living in California. Satellite TV season sports packages easily cost upwards of 100 dollars per season, if not more. People living within the broadcast market will just watch Tv/listen to the radio. Even if I were on a business trip and wanted to catch the action of the latest home team's game, 9 bucks is quite reasonable even for a one time fee, heck that's about how much it costs for a couple of pr0n flicks in a hotel pay-per-view. As far as commercials go, in baseball it's not even an issue considering they have commercial breaks anyway between innings. It's a pity it won't be free anymore but servers and bandwidth cost money. I think 9 bucks is a pretty reasonable price.
The annoyance at someone writing in all caps is imho a diversion from the real issue, which is the fact that someone's copyrighted material is alledgedly being pirated and the owner of said material is royally pissed off. Who cares if he is writing in caps? not every is savvy about the so-called and largely self-imposed net ettiqutte. I happen to think he has a valid point, and if in fact he and his lawyer are able to prove that the accused have pirated his works, they should push to have them proscecuted to the extent of the law. If you want to get free reading material of the net goto the Gutenburg project. I also have very little sympathy for Napster users who are sharing copyrighted music; if you want to share music, share free (as in beer and sometimes in speech) music. The record companies should go after individuals and sue them instead of Napster.
let me first say that I think KDE is great and personally I like it much better than GNOME. However, the one thing that is really inconvenient is that KDE packages are huge and monolithic, not necessarily in terms of byte-size but in terms of functionality. For instance, if I want to update Konqueror only, I have to update the entire kde-base (I think, it may be another kde-* package) package. GNOME I think also has the same problem on a slightly smaller scale. I'd love to be able to be able to update specific apps or libraries without having to download the entire package; the ideal installer would then detect dependencies and prompt for additional downloads as needed.
that people give away their fair use rights doesn't bother me all THAT much. what really pisses me of is some people who have these kickass home entertainment systems, but have no taste in movies; who needs to watch Howard the Duck in 5 channel surround sound anyway? It's like the people who have these really nice, expensive stereo systems and the only CD they own is the Dolby decoder test CD with the cannon-firing sounds. Why, back in my day we used mono cassette players plugged into 5 dollar computer speakers, and WE LIKED IT!