you shouldn't discount the problem of its analysis.
Well, I'm not exactly discounting, but, (as is being pointed out by multiple people in multiple threads under this story) the spin that's being put out in the BBC article makes it sound like they're claiming to have done a large amount of novel work, and a close read shows that this is unlikely to be the case.
All the sequence was already out there. There are quite a few good gene prediction algorithms publically available, as well as data demonstrating how the accuracy goes up when you take the common subset of their results from a given set of sequences. The algorithms used to predict protein function based on similarity to previously characterized genes are bog-standard in the field.
The issue is, all they've done is re-package a bunch of other people's work -- yes, it's a lot of data, yes, it was probably a bunch of cycles (I see elsewhere that Sun is also involved in this announcement -- go figure!) -- but in the end, it's not that big of a contribution to what we know about the genome.
Well, aside from a s/most of the annotation/all of the annotation/, you're correct.
However, doing the annotation from scratch is rather time-consuming, and not something that can be easily done by Joe (or Jane) Molecular Biologist, because of lack of training and lack of access to the proper tools.
The value of Doubletwist's database is exactly as you've analyzed, but for smaller biotech firms, it's worth it -- because this type of bioinformatics service is quite expensive right now, due to a lack of people who are capable of doing it.
Read the story carefully. 'Gene map' != genome sequence.
What these people have actually done (at least, what's described in the linked BBC story) is to take a load of data that's already been available, and re-analyze it.
Astute observers will note parallels with certain Linux-based IPOs...
As an active weblogger (I'm behind GeneHack), here's my two centavos on the issues that are being raised.
First, the name. It's done, people. We (the people doing the weblogging) call them weblogs. There might be a temporary confusion with web server logs, but that will pass. Soon, people will realize that weblog != web server log.
Second, the point. I weblog (it's a noun! it's a verb!) mostly for myself. I comment on biological issues and anything else I find interesting; the key word being comment. Some weblogs just post pointers to interesting sites; personally I find those less interesting than those that post commentary, either on events or content elsewhere on the web. Additionally, sometimes I'll put an item up on GeneHack so that I remember to look at it again; my archives serve as a log of what I thought was worth saving. On a weblogger-heavy mailing list I frequent, weblogs were described as "bookmarks in time" by Brigitte Eaton, who runs the eatonweb weblog. That's a good capsule summary of what I'm trying to do.
Third, the community issue. I agree that weblogs aren't a good way to generate a community, at least not a large or tightly-knit one. That's not the point. Filtering content is the point; commenting on that content is the point; being active on the web instead of passively grazing is the point. I don't participate in much of the web-based community stuff, like/., for example, because (despite recent innovations) the signal:noise ratio is still way too low. People who email me because of something on GeneHack are much more reasonable to deal with. People who I mail because of items on their weblogs are much more reasonable to deal with. That's much, much more rare on/. and other such sites.
Fourth, and finally, why I read weblogs. The filtering by different people with different tastes and different backgrounds. By checking 10 or 15 sites daily, I'm able to assimilate way more information than I would be able to all on my own, with a good slice of commentary thrown in. After visiting different sites for a short while, I have a fairly good idea of the viewpoints and interests of the authors; I have an idea of how they filter information. Weblogs allow me to get the point of view of smart people in varied fields; more people than I could reasonably meet and interact with in meat space. I find that valuable.
Whew! If you made it to the end of this ramble, congradulations. If you haven't yet, check out some of the sites mentioned in the article. Visit for a few days; find the sites you like. We're a varied lot, and there's something for everyone. If you can't find a site with your point of view, start your own...that's the point.
john.
The coming attention economy
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ShutUp Software
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· Score: 3
'Shutup software' (nice neologism, Jon) is a side effect of the new attention economy. Now so long ago, Wired had a short article about how attention is (or will be shortly) the economic element in shortest supply. (Sorry if that's a crappy summary; I'm not an economist.)
Given that, it seems like 'shutup software' is a natural outgrowth. Anything that lets me use (or appears to let me use) my small amount of attention more efficiently is a Good Thing.
Personally, I'd like to seem some kill|score-filing 'ware that offered some level of randomness. That is, scoring rules that would be applied with some probability, rather that all the time. Anybody know of anything like that?
john.
Genetically modified food
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Gene Leakage
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· Score: 1
People in Europe desperately want these regulations, that's why they are there. Governments couldn't care less. Also, the idea of beef and even milk from hormone-treated cows is absolutely disgusting to the average European; if you mention it at a dinner party, people will stop eating. This is not something protectionist governments made up.
Note also that the Invisible Hand only works if all market participants have full information. However, Monsanto et al. are even against labeling GM foods. Soja is ingredient of virtually every processed food.
I'm still a bit confused, but less so. I would have expected it to work out a bit like this: If a unit of non-GM'd food is selling for X, after the introduction of a GM'd version, selling for, say 0.8X, the original version should be labelled (prominently) as un-GM'd, and then sold for 1.2X. Given this business model (which I freely admit absolutely screws the customer who wants to avoid GM'd food), it's in the best interest of the food provider to be completely up-front about the GM status of their foodstuffs.
If the GM-avoiding portion of the population in Europe is a majority, it seems like that approach would result in some nice profits for somebody...
Of course, I'm talking completely out my @$$ at this point...
john, who needs to quit lurking on this thread and do some work!
Genetically modified food
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Gene Leakage
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· Score: 2
>> 1. There is evidence GM soya causes immune system damage. > Do you have a citation for this? I'm not asking just to be an @$$; I'd actually be interested in seeing the data. This approach scares me. It seems to be very common to require those who are against a particular technology to prove that it is dangerous. It should be up to those wanting to distribute something like this to prove beyond reasonable doubt that it is safe, and not be allowed to release it until they do so, thereby putting the burden of proof on those who will benefit. The minimal field trials that are taking place certainly don't do this. Asking for a citation of a factual statement isn't all that outrageous, is it? The statement wasn't "GM-ed soya might be harmful", it was "GM-ed soya is harmful". A big difference, and all I want is a little bit of proof. Second, proving that something is perfectly harmless over the lifetime of a human animal is a pretty tall order. How do you define harmless?
Additionally, it's sort of a feature of free societies that you can do what you want as long as it's not dangerous to others. So, if you want to stop someone from doing something, then yes, the burden of proof of danger is on you. Otherwise, I could decide that, for example, your computer use is dangerous to me, and demand that you stop it until you prove that it isn't. A silly example? Maybe, but do you see my point?
by playing to ignorant fears, the anti-GM factions are making the situation more dangerous, not less. As a member of the anti-GM faction (I used to not care until I took some time to find out what some of what was going on), I'd like to know which of my fears are ignorant, and how me arguing against GM food makes things more dangerous, as it seems that there are practically no controls currently. The point I was trying to make here was that certain fractions of the anti-GM lobby (from what I can see) are trying to demonize the whole practice of modifying and releasing organisms. It's a rather Luddite-like argument -- "There are things man was not meant to know" -- and I think it's dangerous.
Why? Because you can't put the toothpaste back into the tube, and you can't un-invent something. An overwhelming historical fact about our species is that once we've got the power to do something that's potentially very dangerous and disasterous for all concerned, we're going to do it. Given that, strong pressure aganist the testing of these foods (which I've seen in Europe; don't know about NZ) is just going to drive the testing and development underground. It'll be a lot better for all concerned (potentially all period) if the testing and development happen out in the light of day, in an open process. To continue the analogy in your.sig, to GPL the development, rather than use a closed source propitary model.
I've snipped the rest, you make some good points. I just wanted to clear up the two above.
john.
There's a fallacy at play here. . . .
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Gene Leakage
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· Score: 2
This may be beyond the scope of this forum... Prolly -- but what the hey...
I seem to recall that Mitchondrial DNA had other features? Perhaps reverse twisting, or slightly modified bases (beyond methylation or deamination)? It's circular, like bacterial chromosomes (one of the early indicators that lead to the endosybiotic hypothesis of mitochondrial and *plast origin).
AC- who's having fun tearing up other genetic arguments further down. It is fun to get to be a bio-geek on/., isn't it?
Anything beyond yeast? I can't find references to eukaryotic organisms containing plasmids. ASAIK, only unicellular euks can carry plasmids, and not all of them. You can introduce circular plasmids into metazoans (multicellular organisms) and get gene expression, but they aren't replicated (this is called transient transfection).
People have sucessfully introduced linear DNA molecules into metazoan cells and had it replicate, I believe.
The circularized extrachromosomal DNA of bacteria is called a Plasmid. It can be transferred between species and is unique to prokaryotes. Eukaryotic organisms (plants and animals) don't use these types of genetic elements. Not quite right. Plasmids can and do exist in eukaryotes, such as S. cerevisae (yeast).
john.
Genetically modified food
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Gene Leakage
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· Score: 2
1. There is evidence GM soya causes immune system damage Do you have a citation for this? I'm not asking just to be an @$$; I'd actually be interested in seeing the data.
2. One of the primary goals of the GM food industry is crops you have to buy from them each year. Right now third world farmers do rather better by saving some seeds and replanting them. This is like windows licensing your crops. But, as others have pointed out, this isn't really all that different than hybrids, which are also sterile and give better yield. Why is the Terminator Seed so much more hazardous to Third World crop practice?
3. One of the reasons for such tight current control on GM plants is we don't know enough about genetics yet. We are at the same stage in genetics as the early explosives people were. They knew it could do wonderful things but were never quite sure what was going to happen, and likewise if you got it wrong you made a very big mess. We're considerably further along than that! That's not to say that there aren't reasons for tight controls on release of gene hacked organisms into the environment, but by playing to ignorant fears, the anti-GM factions are making the situation more dangerous, not less.
4. Faced with a removal of their normal target insects and bacteria either move or adapt. If they adapt your genetically modified food is now useless because they've eaten it, and if they move well then you risk destroying another habitat. Also remember the largest target to move onto is Humans. This is a decent point, and one where the above argument (early days of the field) can apply. We currently don't have a good handle on the networked nature of ecosystems, and tampering with seemingly minor variables can cause emergent effects. However, this doesn't mean we shouldn't try to understand, it just means we need to be very careful.
In the UK and most of Europe people tend to prefer their food grown to engineered. We don't allow growth hormone in cattle so our meat tastes a lot better, and most UK supermarkets are talking about ceasing to sell any GM foodstuffs. If people 'prefer' no anti-GM'd food, why are there government regulations to prevent it's sale? I'm fine with the Invisible Hand determining market choice, but there seems to be a bit of a contradiction between your first statement and your second.
john.
There's a fallacy at play here. . . .
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Gene Leakage
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· Score: 2
I thought that the biggest difference between H. sap. DNA and mit. DNA was that H. sap. _had_ DNA and mitochondria had RNA. Again, BUZZ!. Thanks for playing, tho.
Both mitochondria and the cell nucleus of eukaryotes (the organisms that have mitochondria) contain DNA. This serves as a template for the production of RNA. In the mitochondria, the RNA stays put, and is translated into mitochondrial proteins. This process also requires the import of proteins that are encoded in the nucleus.
In the nucleus, some of the RNA stays put, and functions in processes such as mRNA splicing and ribosomal RNA modification. Other RNAs are exported out of the nucleus, into the cytoplasm. There, they either do stuff (for example, the ribosomal RNA directs the production of proteins), or are translated into proteins by the ribosome. Some of those proteins are then imported into the mitochondria (see above).
The only (known) RNA-based organisms are virii. For example, the transmissive form of HIV is a double-stranded RNA retrovirus.
john, more convinced than ever that a basic bio tutorial for geeks needs to be done...
There's a fallacy at play here. . . .
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Gene Leakage
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· Score: 2
It has recently become clear that genes hop from species to species in nature very frequently. You're okay with that statement...
For example we carry fossilised viral DNA in our cellular mitochondria -- they were once free-living virus but have now become so symbiotically linked to other species that their genes are indistinguishable from the "human" genome. But you blow it with this one. We do have integrated retro-viral DNA in our genes. We do have mitochondria, which do have a symbiotic origin (probably). However, they used to be bacteria, not viruses (a big difference!). Additionally, you can easily tell the difference between mitochondrial DNA and H. sap. DNA (assuming you're given a large-ish chunk -- 10 or 20 kilobases), based on differences in nucleotide usage and larger scale gene organization.
Pointless Tech Analogy: It's sorta like the difference between text files across systems. Basically the look the same, but if you look closely (at the line delimiter), you can tell the difference.
john
Hey where did the experts come from
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Gene Leakage
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Suddenly/. is populated with experts in genetic engineering. Actually, I am a rocket scientist^H^H^H^H^H^Hmolecular biologist, although I prefer the term 'gene jockey'
We're creating all kinds of combinations that would just never occur in nature (such as mixing of plant and animal DNA). Sigh. 'Never' is a big word in science. Have you been following any of the sequencing projects? It's looking more and more like horizontal gene transfer (genes moving from one species to another via bacteria or viruses) is a major factor in gene lineages. So, it's quite possible that there's some plant or animal species out there carrying some DNA from the 'other side'.
Who really knows what the effects of introducing radically new gene sequences into the environment will be? Nobody. Anybody who tells you different is trying to sell you something. However, at some point, there's only so much testing that can be done. You've got to 'ship the product', and trust that your tech support can deal with any problems that arise in the field (no pun intended).
This is something that's going to happen sooner or later (i.e., release of a hacked organism into the Big Room with the Blue Sky). All this effort to stop the release is just going to drive it underground. Then, the release will be done illegeally, without the proper controls, and it will go to hell. The best bet for the environmental groups is not to insist on a block to release, but to insist on more and more oversight of the process.
I'm a little disappointed. Based on the book title, I figured I'd get to hear about some nifty thinking about the coming bio revolution.
*BUZT* Thanks for playing.
Look people, genome sequences aren't the answer. Yes, they're necessary; yes, they're useful. However, they no more give you the answers to Life, the Universe and Everything than having a kernel binary gives you the power of a working Linux distro, with all the GNU utilities.
We've still got a long way to go towards figuring out how all that genome information works together to make a critter.
Yes, there have been some applications as far as stiching new genes into existing (usually crop) organisms. However, we haven't yet seen a killer app for biotech. What's it going to be? If I knew, would I be posting to/.?
john., sorry that he couldn't get this up sooner knowing that few will read it now...
That is why the paper on QWERTY published a mere nine years ago by Stan Liebowitz of the University of Texas at Dallas and Stephen Margolis of the University of California, Los Angeles, was called "The Fable of the Keys"
and also:
In 1956 a carefully designed study by the General Services Administration found that QWERTY typists were about as fast as Dvorak typists, or faster.
So, how does this article explain that the people who win the speed-typing contests are always Dvorak typists?
Additionally, the article doesn't say anything about RSI/carpal tunnel -- 'the black lung of hackers' (thanks N. Stephenson for that wonderful imagery!). I was under the impression that Dvorak reduced the damage due to this ailment.
This is as good a place as any: does anyone have any recommendations for a good Open Source typing trainer? I'd like to switch to Dvorak, but I need to retool myself. If there isn't a good one, maybe I'll get a typing instruction book and code one up...anybody interested?
john., off to take some ibuprofen for his aching wrists...
One thing I didn't see in Rob's suggestions: it seems only logical to have some balance between restriction and privledge for moderators. So, given the way the system is (or was), the need to choose between moderation and participation makes sense. Given the way the system is going to be (or is), it seems too restrictive. If everybody (or most everybody) is potentially eligible to moderate, restricting participation as a consequence of moderations seems excessive.
As far as choosing moderators: I think the current system (the Gang of 400) has been working just fine. Don't inadvertently take us backwards by attempting to over-democratize the process -- that way lies chaos!
My personal preference would be for moderators to be choosen by some kind of emergent criteria. That is, for example, a strong positive score on all posted comments. Of course, there needs to be some type of control on this, so people just don't score their friends high to get them to be moderators...hmmm...
From reading initial comments, it seems as if people are getting a little bit more out of this than the average Katz piece. That's good. However, I'm not getting more out of it, because I gave up after the second time I saw a number embedded in the middle of a paragraph.
A public plea to Mr. Katz: You're posting hypertext here. You should take advantage of the things this medium lets you do, like make automagically numbered lists (<ol type="1">), and embed links into your text (for example, why wasn't the book title from ISU Press linked to Amazon.com, or ISU press? Why isn't your email address at the bottom of the article a link?)
Please try to understand: For myself and many others, your facility with this medium has a direct and substantial impact on your credibility. This is directly analogous to how people react to a poorly editted essay in Old Media.
I understand that you're quite busy with family and career, and that picking up HTML might not be a priority. I understand, and I'd like to offer my services. Send me a draft of your forthcoming posts, and I'll mark it up. No charge. I think you've got some interesting things to say, but I (and others) aren't getting to see them, because you're doing the New Media equivalent of printing first drafts on low quality paper, with cheap ink, in a cruddy font, with no copy-editting.
Hmmm..guess I should have a higher caffine level before posting. I wasn't attempting to say that the essay argued that Joe SixPack should go buy a copy of Red Hat (or even Debian), but I think that a reading of it could help to foster understanding between the Morlocks and the Eloi, to use Stephenson's terminology.
It might help some of the Eloi decide to check out what the Morlock life style has to offer, but I don't think (and I wasn't trying to say) that that was the point.
Hold on just a second, while I pick up my brain...Stephenson writes a pretty good stick, eh?
I won't get into why the Stephensen piece was posted in the middle of a slew of Quickies, but I will point that that it's too bad that a lot of potentially interesting discussion about it is mixed with stuff about the RFC poll and the SGI logo.
One point that I haven't yet seen made: IMHO, this piece is potentially as important as 'Cathedral and Bazaar', for not for us. This piece is something that you can show your non-Linux using friends, something to clue them in as to what the hell we're doing, and why it's so important to them, even if they don't recognize it.
Slashdot Mirror
you shouldn't discount the problem of its analysis.
Well, I'm not exactly discounting, but, (as is being pointed out by multiple people in multiple threads under this story) the spin that's being put out in the BBC article makes it sound like they're claiming to have done a large amount of novel work, and a close read shows that this is unlikely to be the case.
All the sequence was already out there. There are quite a few good gene prediction algorithms publically available, as well as data demonstrating how the accuracy goes up when you take the common subset of their results from a given set of sequences. The algorithms used to predict protein function based on similarity to previously characterized genes are bog-standard in the field.
The issue is, all they've done is re-package a bunch of other people's work -- yes, it's a lot of data, yes, it was probably a bunch of cycles (I see elsewhere that Sun is also involved in this announcement -- go figure!) -- but in the end, it's not that big of a contribution to what we know about the genome.
john.
Well, aside from a s/most of the annotation/all of the annotation/, you're correct.
However, doing the annotation from scratch is rather time-consuming, and not something that can be easily done by Joe (or Jane) Molecular Biologist, because of lack of training and lack of access to the proper tools.
The value of Doubletwist's database is exactly as you've analyzed, but for smaller biotech firms, it's worth it -- because this type of bioinformatics service is quite expensive right now, due to a lack of people who are capable of doing it.
john,
trying to fill that gap.
Predicting protein folding is all well and good, but without quite a few other things, like:
it's going to be of limited use.
john.
Read the story carefully. 'Gene map' != genome sequence.
What these people have actually done (at least, what's described in the linked BBC story) is to take a load of data that's already been available, and re-analyze it.
Astute observers will note parallels with certain Linux-based IPOs...
john.
This is a really inaccurate analogy. You can have 'half of cholera', thanks to how recombination works.
Check out a decent genetics textbook; look at the definations for penetrance and expression.
john.
As an active weblogger (I'm behind GeneHack ), here's my two centavos on the issues that are being raised.
First, the name. It's done, people. We (the people doing the weblogging) call them weblogs. There might be a temporary confusion with web server logs, but that will pass. Soon, people will realize that weblog != web server log.
Second, the point. I weblog (it's a noun! it's a verb!) mostly for myself. I comment on biological issues and anything else I find interesting; the key word being comment. Some weblogs just post pointers to interesting sites; personally I find those less interesting than those that post commentary, either on events or content elsewhere on the web. Additionally, sometimes I'll put an item up on GeneHack so that I remember to look at it again; my archives serve as a log of what I thought was worth saving. On a weblogger-heavy mailing list I frequent, weblogs were described as "bookmarks in time" by Brigitte Eaton, who runs the eatonweb weblog . That's a good capsule summary of what I'm trying to do.
Third, the community issue. I agree that weblogs aren't a good way to generate a community, at least not a large or tightly-knit one. That's not the point. Filtering content is the point; commenting on that content is the point; being active on the web instead of passively grazing is the point. I don't participate in much of the web-based community stuff, like /., for example, because (despite recent innovations) the signal:noise ratio is still way too low. People who email me because of something on GeneHack are much more reasonable to deal with. People who I mail because of items on their weblogs are much more reasonable to deal with. That's much, much more rare on /. and other such sites.
Fourth, and finally, why I read weblogs. The filtering by different people with different tastes and different backgrounds. By checking 10 or 15 sites daily, I'm able to assimilate way more information than I would be able to all on my own, with a good slice of commentary thrown in. After visiting different sites for a short while, I have a fairly good idea of the viewpoints and interests of the authors; I have an idea of how they filter information. Weblogs allow me to get the point of view of smart people in varied fields; more people than I could reasonably meet and interact with in meat space. I find that valuable.
Whew! If you made it to the end of this ramble, congradulations. If you haven't yet, check out some of the sites mentioned in the article. Visit for a few days; find the sites you like. We're a varied lot, and there's something for everyone. If you can't find a site with your point of view, start your own...that's the point.
john.
'Shutup software' (nice neologism, Jon) is a side effect of the new attention economy. Now so long ago, Wired had a short article about how attention is (or will be shortly) the economic element in shortest supply. (Sorry if that's a crappy summary; I'm not an economist.)
Given that, it seems like 'shutup software' is a natural outgrowth. Anything that lets me use (or appears to let me use) my small amount of attention more efficiently is a Good Thing.
Personally, I'd like to seem some kill|score-filing 'ware that offered some level of randomness. That is, scoring rules that would be applied with some probability, rather that all the time. Anybody know of anything like that?
john.
People in Europe desperately want these regulations, that's why they are there. Governments couldn't care less. Also, the idea of beef and even milk from hormone-treated cows is absolutely disgusting to the average European; if you mention it at a dinner party, people will stop eating. This is not something protectionist governments made up.
Note also that the Invisible Hand only works if all market participants have full information. However, Monsanto et al. are even against labeling GM foods. Soja is ingredient of virtually every processed food.
I'm still a bit confused, but less so. I would have expected it to work out a bit like this: If a unit of non-GM'd food is selling for X, after the introduction of a GM'd version, selling for, say 0.8X, the original version should be labelled (prominently) as un-GM'd, and then sold for 1.2X. Given this business model (which I freely admit absolutely screws the customer who wants to avoid GM'd food), it's in the best interest of the food provider to be completely up-front about the GM status of their foodstuffs.
If the GM-avoiding portion of the population in Europe is a majority, it seems like that approach would result in some nice profits for somebody...
Of course, I'm talking completely out my @$$ at this point...
john,
who needs to quit lurking on this thread and do some work!
>> 1. There is evidence GM soya causes immune system damage.
> Do you have a citation for this? I'm not asking just to be an @$$; I'd actually be interested in seeing the data.
This approach scares me. It seems to be very common to require those who are against a particular technology to prove that it is dangerous. It should be up to those wanting to distribute something like this to prove beyond reasonable doubt that it is safe, and not be allowed to release it until they do so, thereby putting the burden of proof on those who will benefit. The minimal field trials that are taking place certainly don't do this.
Asking for a citation of a factual statement isn't all that outrageous, is it? The statement wasn't "GM-ed soya might be harmful", it was "GM-ed soya is harmful". A big difference, and all I want is a little bit of proof. Second, proving that something is perfectly harmless over the lifetime of a human animal is a pretty tall order. How do you define harmless?
Additionally, it's sort of a feature of free societies that you can do what you want as long as it's not dangerous to others. So, if you want to stop someone from doing something, then yes, the burden of proof of danger is on you. Otherwise, I could decide that, for example, your computer use is dangerous to me, and demand that you stop it until you prove that it isn't. A silly example? Maybe, but do you see my point?
by playing to ignorant fears, the anti-GM factions are making the situation more dangerous, not less.
As a member of the anti-GM faction (I used to not care until I took some time to find out what some of what was going on), I'd like to know which of my fears are ignorant, and how me arguing against GM food makes things more dangerous, as it seems that there are practically no controls currently.
The point I was trying to make here was that certain fractions of the anti-GM lobby (from what I can see) are trying to demonize the whole practice of modifying and releasing organisms. It's a rather Luddite-like argument -- "There are things man was not meant to know" -- and I think it's dangerous.
Why? Because you can't put the toothpaste back into the tube, and you can't un-invent something. An overwhelming historical fact about our species is that once we've got the power to do something that's potentially very dangerous and disasterous for all concerned, we're going to do it. Given that, strong pressure aganist the testing of these foods (which I've seen in Europe; don't know about NZ) is just going to drive the testing and development underground. It'll be a lot better for all concerned (potentially all period) if the testing and development happen out in the light of day, in an open process. To continue the analogy in your .sig, to GPL the development, rather than use a closed source propitary model.
I've snipped the rest, you make some good points. I just wanted to clear up the two above.
john.
This may be beyond the scope of this forum...
Prolly -- but what the hey...
I seem to recall that Mitchondrial DNA had other features? Perhaps reverse twisting, or slightly modified bases (beyond methylation or deamination)?
It's circular, like bacterial chromosomes (one of the early indicators that lead to the endosybiotic hypothesis of mitochondrial and *plast origin).
AC- who's having fun tearing up other genetic arguments further down. /., isn't it?
It is fun to get to be a bio-geek on
john.
Anything beyond yeast? I can't find references to eukaryotic organisms containing plasmids.
ASAIK, only unicellular euks can carry plasmids, and not all of them. You can introduce circular plasmids into metazoans (multicellular organisms) and get gene expression, but they aren't replicated (this is called transient transfection).
People have sucessfully introduced linear DNA molecules into metazoan cells and had it replicate, I believe.
john.
The circularized extrachromosomal DNA of bacteria is called a Plasmid. It can be transferred between species and is unique to prokaryotes. Eukaryotic organisms (plants and animals) don't use these types of genetic elements.
Not quite right. Plasmids can and do exist in eukaryotes, such as S. cerevisae (yeast).
john.
1. There is evidence GM soya causes immune system damage
Do you have a citation for this? I'm not asking just to be an @$$; I'd actually be interested in seeing the data.
2. One of the primary goals of the GM food industry is crops you have to buy from them each year. Right now third world farmers do rather better by saving some seeds and replanting them. This is like windows licensing your crops.
But, as others have pointed out, this isn't really all that different than hybrids, which are also sterile and give better yield. Why is the Terminator Seed so much more hazardous to Third World crop practice?
3. One of the reasons for such tight current control on GM plants is we don't know enough about genetics yet. We are at the same stage in genetics as the early explosives people were. They knew it could do wonderful things but were never quite sure what was going to happen, and likewise if you got it wrong you made a very big mess.
We're considerably further along than that! That's not to say that there aren't reasons for tight controls on release of gene hacked organisms into the environment, but by playing to ignorant fears, the anti-GM factions are making the situation more dangerous, not less.
4. Faced with a removal of their normal target insects and bacteria either move or adapt. If they adapt your genetically modified food is now useless because they've eaten it, and if they move well then you risk destroying another habitat. Also remember the largest target to move onto is Humans.
This is a decent point, and one where the above argument (early days of the field) can apply. We currently don't have a good handle on the networked nature of ecosystems, and tampering with seemingly minor variables can cause emergent effects. However, this doesn't mean we shouldn't try to understand, it just means we need to be very careful.
In the UK and most of Europe people tend to prefer their food grown to engineered. We don't allow growth hormone in cattle so our meat tastes a lot better, and most UK supermarkets are talking about ceasing to sell any GM foodstuffs.
If people 'prefer' no anti-GM'd food, why are there government regulations to prevent it's sale? I'm fine with the Invisible Hand determining market choice, but there seems to be a bit of a contradiction between your first statement and your second.
john.
I thought that the biggest difference between H. sap. DNA and mit. DNA was that H. sap. _had_ DNA and mitochondria had RNA.
Again, BUZZ!. Thanks for playing, tho.
Both mitochondria and the cell nucleus of eukaryotes (the organisms that have mitochondria) contain DNA. This serves as a template for the production of RNA. In the mitochondria, the RNA stays put, and is translated into mitochondrial proteins. This process also requires the import of proteins that are encoded in the nucleus.
In the nucleus, some of the RNA stays put, and functions in processes such as mRNA splicing and ribosomal RNA modification. Other RNAs are exported out of the nucleus, into the cytoplasm. There, they either do stuff (for example, the ribosomal RNA directs the production of proteins), or are translated into proteins by the ribosome. Some of those proteins are then imported into the mitochondria (see above).
The only (known) RNA-based organisms are virii. For example, the transmissive form of HIV is a double-stranded RNA retrovirus.
john, more convinced than ever that a basic bio tutorial for geeks needs to be done...
It has recently become clear that genes hop from species to species in nature very frequently.
You're okay with that statement...
For example we carry fossilised viral DNA in our cellular mitochondria -- they were once free-living virus but have now become so symbiotically linked to other species that their genes are indistinguishable from the "human" genome.
But you blow it with this one. We do have integrated retro-viral DNA in our genes. We do have mitochondria, which do have a symbiotic origin (probably). However, they used to be bacteria, not viruses (a big difference!). Additionally, you can easily tell the difference between mitochondrial DNA and H. sap. DNA (assuming you're given a large-ish chunk -- 10 or 20 kilobases), based on differences in nucleotide usage and larger scale gene organization.
Pointless Tech Analogy: It's sorta like the difference between text files across systems. Basically the look the same, but if you look closely (at the line delimiter), you can tell the difference.
john
Suddenly /. is populated with experts in genetic engineering.
Actually, I am a rocket scientist^H^H^H^H^H^Hmolecular biologist, although I prefer the term 'gene jockey'
We're creating all kinds of combinations that would just never occur in nature (such as mixing of plant and animal DNA).
Sigh. 'Never' is a big word in science. Have you been following any of the sequencing projects? It's looking more and more like horizontal gene transfer (genes moving from one species to another via bacteria or viruses) is a major factor in gene lineages. So, it's quite possible that there's some plant or animal species out there carrying some DNA from the 'other side'.
Who really knows what the effects of introducing radically new gene sequences into the environment will be?
Nobody. Anybody who tells you different is trying to sell you something. However, at some point, there's only so much testing that can be done. You've got to 'ship the product', and trust that your tech support can deal with any problems that arise in the field (no pun intended).
This is something that's going to happen sooner or later (i.e., release of a hacked organism into the Big Room with the Blue Sky). All this effort to stop the release is just going to drive it underground. Then, the release will be done illegeally, without the proper controls, and it will go to hell. The best bet for the environmental groups is not to insist on a block to release, but to insist on more and more oversight of the process.
john, /.
who's glad to see some bio-stuff on
I'm a little disappointed. Based on the book title, I figured I'd get to hear about some nifty thinking about the coming bio revolution.
*BUZT* Thanks for playing.
Look people, genome sequences aren't the answer. Yes, they're necessary; yes, they're useful. However, they no more give you the answers to Life, the Universe and Everything than having a kernel binary gives you the power of a working Linux distro, with all the GNU utilities.
We've still got a long way to go towards figuring out how all that genome information works together to make a critter.
Yes, there have been some applications as far as stiching new genes into existing (usually crop) organisms. However, we haven't yet seen a killer app for biotech. What's it going to be? If I knew, would I be posting to /.?
john.,
sorry that he couldn't get this up sooner
knowing that few will read it now...
Apparently Rob's alignment only gives him a +1 posting bonus...I don't know why, but I'm a little surprised that it's so low.
(I'm also posting to see what my alignment is...'cuz I'm too lazy to do the math myself.)
john.
From the article:
and also:You did read before posting, yes?
john.
So, how does this article explain that the people who win the speed-typing contests are always Dvorak typists?
Additionally, the article doesn't say anything about RSI/carpal tunnel -- 'the black lung of hackers' (thanks N. Stephenson for that wonderful imagery!). I was under the impression that Dvorak reduced the damage due to this ailment.
This is as good a place as any: does anyone have any recommendations for a good Open Source typing trainer? I'd like to switch to Dvorak, but I need to retool myself. If there isn't a good one, maybe I'll get a typing instruction book and code one up...anybody interested?
john.,
off to take some ibuprofen for his aching wrists...
One thing I didn't see in Rob's suggestions: it seems only logical to have some balance between restriction and privledge for moderators. So, given the way the system is (or was), the need to choose between moderation and participation makes sense. Given the way the system is going to be (or is), it seems too restrictive. If everybody (or most everybody) is potentially eligible to moderate, restricting participation as a consequence of moderations seems excessive.
As far as choosing moderators: I think the current system (the Gang of 400) has been working just fine. Don't inadvertently take us backwards by attempting to over-democratize the process -- that way lies chaos!
My personal preference would be for moderators to be choosen by some kind of emergent criteria. That is, for example, a strong positive score on all posted comments. Of course, there needs to be some type of control on this, so people just don't score their friends high to get them to be moderators...hmmm...
Must think more...
john.
From reading initial comments, it seems as if people are getting a little bit more out of this than the average Katz piece. That's good. However, I'm not getting more out of it, because I gave up after the second time I saw a number embedded in the middle of a paragraph.
A public plea to Mr. Katz: You're posting hypertext here. You should take advantage of the things this medium lets you do, like make automagically numbered lists (<ol type="1">), and embed links into your text (for example, why wasn't the book title from ISU Press linked to Amazon.com, or ISU press? Why isn't your email address at the bottom of the article a link?)
Please try to understand: For myself and many others, your facility with this medium has a direct and substantial impact on your credibility. This is directly analogous to how people react to a poorly editted essay in Old Media.
I understand that you're quite busy with family and career, and that picking up HTML might not be a priority. I understand, and I'd like to offer my services. Send me a draft of your forthcoming posts, and I'll mark it up. No charge. I think you've got some interesting things to say, but I (and others) aren't getting to see them, because you're doing the New Media equivalent of printing first drafts on low quality paper, with cheap ink, in a cruddy font, with no copy-editting.
john.
Hmmm..guess I should have a higher caffine level before posting. I wasn't attempting to say that the essay argued that Joe SixPack should go buy a copy of Red Hat (or even Debian), but I think that a reading of it could help to foster understanding between the Morlocks and the Eloi, to use Stephenson's terminology.
It might help some of the Eloi decide to check out what the Morlock life style has to offer, but I don't think (and I wasn't trying to say) that that was the point.
john.
Hold on just a second, while I pick up my brain...Stephenson writes a pretty good stick, eh?
I won't get into why the Stephensen piece was posted in the middle of a slew of Quickies, but I will point that that it's too bad that a lot of potentially interesting discussion about it is mixed with stuff about the RFC poll and the SGI logo.
One point that I haven't yet seen made: IMHO, this piece is potentially as important as 'Cathedral and Bazaar', for not for us . This piece is something that you can show your non-Linux using friends, something to clue them in as to what the hell we're doing, and why it's so important to them, even if they don't recognize it.
john.
or even phase 2.0.
I think it would be nice if the user info, in addition to tracking posted comments, also tracked submitted and accepted news items/articles.
Just a thought, and I know you prolly don't have time to deal with it now, but I won't remember later, so there ya go.