Sorry to interrupt the fighting, but I had to point this out.
In explaining the scientific illiteracy of the US population, the author of this article talks about the number of Americans who believe in psychic powers, UFOs and astrology. The author then writes:
Seventy-seven percent of those surveyed believe in the theory of global warming, that the planet is being heated by an excess of carbon dioxide in the atmosphere. Of those surveyed, 86 percent said global warming is a serious or "somewhat serious" problem.
This is terribly misleading writing. Unlike the previous three issues, the vast majority of scientific evidence supports the belief that the global temperatures are currently rising, and will continue to do so. While scientists may disagree about how high the temperature is going to rise to, or what factors are most to blame, the fact of global warming accepted by the vast majority of scientists. As written, the article could be read to imply that global warming, like psychic powers, UFOs and astrology, is pseudo-science.
As others have rightfully pointed out, the real question here is economic, and its hard to get economic data on publishing costs.
Mike Rosenzweig was Editor-in-chief of the journal Evolutionary Ecology until he got fed up with his corporate publisher. So he (and his editorial board) left and founded their own journal: Evolutionary Ecology Research. The journal has a variety of progressive policies regarding pricing and ownership. Importantly, he has written a great deal about them- check out this paper (its a.pdf) or others on the site where he breaks down the money issues.
I can argue about definitions, and I guess I will. The problem is that how you define these things is central to the issue of measuring complexity. Until you have some objective measure eof state and environment, I don't see how you can make even a rought estimate...
As Gould has pointed out, the central tendency of life on this planet has always been and always will be bacteria. Animals (let alone humans) are extreme outliers.
Come on, do you really understand biology? Where do you get off saying that we are are "so superior to the roundworm"? I'd like to see you try and self fertilize like roundworms can. Or completely metamorphose like a fly does. The fact is, there is no good measure of "complexity" and "simplicity" at the level of the entire organism. To simply assume that we are more complex than other animals is grounded in nothing more than ego. And finally, like Gould (and many, many others have emphasized) we can only understand developmental complexity by understanding how gene products interact. So even if we are somehow more complex, there is no reason to assume that such complexity would require more genes.
Further, one of the key conditions for the evolution of cooperation (as defined by Axelrod) is that not only do we play repeated games with a group, but we know who we are playing against. In short, how you act towards someone should depend on how they last acted towards you (Tit-for-tat). But in this case, we don't know how other indviduals acted. We just know the sum of how many cooperated and how many did not.
Beyond that, I really know nothing about how game theory scales up beyond two player games (which is what we are talking about here), so I don't know if any of this discussion applies!
What neither group is saying is that they haven't done much of the sequencing of what is commonly assumed to be junk DNA. Most of the work has been done on things like Expressed Sequence Tags (ESTs), which are pieces of DNA that we know contain regions which are expressed (ie transcribed into mRNA).
So how does annotation work? At least at this point, its lots of educated guessing. One of the big areas of bioinformatics research right now is to take DNA sequence and predict where the genes are. There are motifs which are associated with the start of a gene for example. In addittion, non-random use of alternative codons allows a reasearcher to see if punitive genes match exprected freqeuences. (Remember that three nucliotides code for a single amino acid, and while there are multiple combinations that code for a single amino acid, all combinations are not used with equal frequency.)
Once you suspect that something is a gene, figuring out what it does based only on sequence is basicly impossible. If it is quite simmilar to a known gene or genes, we can place it in a family of genes and hypothesize that it shares some function. (Of course, this still needs to be tested.) If it is novel, then we need to do the wet lab experiments to figure out what its function. Eventually, the compuational biologists would like to be able to go from the linear DNA (and hence amino acid) sequence to the three dimensional structure- but we aren't there yet.
As for chunks of "how to grow a tail" and what not, they certinaly exist. But these pseudogenes mutate quite fast once they are no longer being used, so they would be very difficult to reconginze today as any different from their background.
Excellent point. But if you go back and read the Slashdot interview with RMS, you will see that he says that RMS thinks there are many things in the world that are much more cruical than non-free software. But he thinks he can make the most differnece with FSF, so thats where he puts his time.
I heard an intersting interview with Gloria Steinem on the state of feminism at the end of the millienium. She counted as feminism's greatest success that at least in America, most of society believed that women can do everything that men do. (And I'd like to believe that, though I'm not sure I do.) Women are CEOs, governers, and even the Secretary of state. When asked what feminism's biggest upcoming chalange was, she replied that is was convincing people that men can do everything women can do (with the exception of giving birth...) For example, while women are working, just like men, most household chores are still done mostly like women. Though this is hardly a new observation for Feminists (just read _The Second Shift_), it think it is worth repeating.
So where does this fit in with geekdom? In short, the author seems to argue that women can do everything that men can, but they also can do other things which aren't getting done. Now I'm not supposing something simmilar to the second shift, where traditional roles have kept women doing the housework. There really aren't defined gender roles which are specific to hacking (as near as I can tell.) But this article proposes defining such gender roles, and I'm a little uncomfertable with just letting a whole set of things be swept into the "Women's work" catagory, along with everything already being done by men. Like Steinem says, the challange is convincing men that those jobs are crucial, and that they can do them as well.
The Jacob Monad model has been used for years to explain lactose production in simple organisms.
Like I said, since the 1950's. I was simply providing a correct date in response to the above post.
I dont see anything revolutionary in this "advancement" , we have known about it for years.
Well, the MSNBC article leaves it a little vague- I can't comment on the scientifc merit untill I get into lab tommorow and find a copy of Nature. But I think the point is that this is a promoter/repressor system which is easily turned on and off by an experimenter.
and the operon is NOT a set of genes expressed together , rather it is the regulatory and structural genes that regulate production of a certain protein
Were quibiling over scemantics, but I think in actuality, we are both half right. The genetics text infront of me (Griffith's et al., 1996) defines an operon as:
A set of adjacent structural genes whose mRNA is synthesized in one piece, plus the adjacent regulatory signals that affect transcription of the structural genes.
So I think we were both correct. The operon includes the set of genes expressed together (lac Z, Y and A) as well as the regulatory genes involved in that regulation (lac Pand O.)
Yeah, this is exactly the kind of thing I was talking about. There are really only 5 major signalling systems, so this type of problem is quite common. In your case, if you knocked out Sonic hedgehog (Shh), I think you would get something even more extreme than you describe. Shh is involved in the somite-notochord-neural tube signaling, so my guess is that you wouldn't even get the a trunk that was properly patterned, making it difficult for a limb bud to even form. I don't know if this type of experiment is being done, but I'm going to ask someone tommorow!
Sorry that you feel the need to call what I said stupid. I'm really more of an evolutionary biologist though, so that part of your post isn't quite right. Your are right in that the vast majority of living things are and always will be bacteria. The point I was trying to make had nothing to do with people, or any other orgnaism for that matter. I don't think I said anything about numbers of creatures in nature.
My point was that if you classify things as prokaryotes vs eukaroytes, the easiet way to explain eukaroytes is as "basicly everything but bacteria", because for I think that is a good working defenttion for a non-biologist. "Basicly everything but bacteria" is a subset of life which includes plants and animals, amoung other things. If I told non-biologists that eukaroytes have nuclear membranes and prokaroytes don't, that wouldn't help much. If you don't know anything much about biology, would you know if yeast have nuclear membranes? (For those who don't know - obviously not the above poster - they do.) I was simply trying to provide a working defenition so that I could get on with post.
But since you have such a critical eye, I wonder if you have any comments about other ideas in the post. I'd be interested to hear.
Most promoter/repressor sysems, particularly in eukaroytes (that is basicly everything but bacteria) are phenomenally complicated. Lots of very bright people work in this area, but for the most part, we have no idea how the various promoters and repressors of a gene act together to coordinate gene expression at different times. In fact, it was big news about two years ago when a group published a study ilucidating how the various promters and repressors actually worked, and in what combination, to produce certain effects on a specific gene.
With such a complex system, doing basic biology is difficult. For example, if I want to study the role a specific protein plays in the development of an organism, I can mutate it and see what changes. But what if that kills the organism (say, a fruit fly) early in development? I will have no idea if that gene plays a role later in development. But lets say I can engineer a line of flies with this switch acting on the gene I want to study. I can keep that gene on early in development, but shut it off at later times, learning the role of that gene at various points.
I'm not talking about sticking this into people for any reason (I'll let other people continue to bicker about that.) Despite the narrow vision of MSNBC and other popular media reporting on stories like this, I'll bet that the major impact of this advance won't be on any direct human advance, but will be in all the basic research it helps fuel.
The switches(promoters & repressors) are also called operons.
Nope. There called promoters and repressors. In some contexts, they are known as transcription factors. An operon is a set of genes which are expressed together. And the Lac operon was first explored in the 1950s by Jacob and Monod.
I imagine one could patent that primer, which is a small chunk of DNA, but I haven't heard of anyone doing so.
I don't know if anyone has either, but I do know that companies are thinking about this very thing. I have a colaborator at a large US biotech firm. We are actually working on something totally unrelated to their work, but the corporate lawyers have told him that he can't send my a set of primers he designed. He has apparently given them to several people already, and if he gives them to anyone else, he (or his employer) apparently looses some sort of intelectual property rights to them. It turns out I probably won't need them, but this is already something of an issue...
I am not aware of the same phenomenon occuring in any other field.
Another: avian population biology. Most of our knowledge of bird distirbution and population trends in the North American is due to the work of hundreds (or even thousands?) of talented amatures. Many of the censuses which have documented the declines of many bird species have been performed by dedicated bird-watchers. One of the important journals in the field, especially in terms of distribution, North American Birds, is mostly composed of regional resports taken from the observations of legions of bird-watchers.
That said, I think these two fields are in the minority. There may be a few others like them, but they are the exception.
I agree that the QT4 player sucks, but I think that the design team may have learned from some of those mistakes (whitness the slider intead of the wheel in the screenshots.) We won't know what this really all means until we can play with the OS but... (unless you've seen something I haven't.)
Visually, programs that violate this pop up dialogs while the user is working in other programs
I agree. In the new OS, alerts will stick with the program that creates them, rather than jump to the front. (Apple has emphasized this recently- system alerts in oS 8.x don't generaly pop to the front- they are visible in the finder, and a sound lets you know that they are there.)
While I agree with your issue of balance, I completly disagree with manifestness. Why shoudn't things that are functional be decorative as well? Don't get me wrong, I'm not saying that this should get in the way of user interface. What I am saying is that I don't know why the two need to be mutualy exclusive. For example, can't the reason that a part of UI be good at your first chritera be through the second: you are naturally drawn to certain functional objects via their decorative nature?
The idea that people want to see sythetic textures is passé. Would a Ferrari look better if they bolted on some simulated "wood grain" paneling? Better to exploit the natural aesthetic properties of your medium.
Um, on a computer screen, what isn't synthetic? What are the "natural aesthetic properties" of my monitor? Aestheics are, of course, subjective, and Apple's current vision agrees with what I consider to be attractive. It may seem dumb to some, but since most of my time in front of my computer involves looking at the screen, I would like it to be something that is pleasing to look at. For me, themes don't cut it- I find that Apple, more than anyone else, is able to follow Frank Loyd Wright and let form follow function. Themes in *nix always feel bolted on to me- there don't seem like they belong.
I haven't played with any of OSX (I don't know if the developers preview even include Aqua as it was demonstrated.) But my first thought when I saw it on the website was "This is gorgous."
I'm looking forward to playing with OS X to see if it lives up (and I imagine it will.) To me this look doesn't seem artifical or bolted on. It looks like it fits with the way I want to interact with my system. Maybe I can't descrbe it well, but I can feel it when I use my Mac. But thats what makes me a Mac head.
Good lord, we're talking about people who essentially believe in Christianity 1.0. Just because they never upgraded doesn't make 'em evil, it makes them contented users (although God sure did get a lot friendlier in version 2.0, at least in the documentation)
cute analogy- though I think a fork would describe it better. The part of the bible that you are farmiliar with may have not changed since then, but Judiaism has changed a fair bit in the last 2000 years. The foundation may be the same, but tons of new features have been added, and different distributions empahsize differnet things. Orthodoxy keeps almost all of those laws, while Conservative and Reformed movements in the US have changed that empahsis, only incuding the basic install for those who find that suits their need. In addition, many people are merging code. (Note the Jewish Buddist movement, for example.)
The type of sequencing I do (and most everyone else as well) was invented by Fred Sanger in 1971 (for which he won his second Nobel Prize, IIRC.)
Forgive me if I get too simplistic, but I don't know how much molecular biology you know...
The base pairs which form DNA are a purine or a pyrimindine (two differnet types of carbon rings). These base pairs are linked together by phosphate groups. Before these bases are added to the chain, they have a hydroxyl (-OH) group at one end, which is what is used to bridge the gap. What Singer figured out was thatf you instead used a base which was lacking the hydroxyl group, and simply had a hydrogen there, they synthesis reaction could not proceed. So to sequence DNA this way, I run four reactions simultaneously. I take my template, seperate the strands be heating them, add lots of dioxyduclitoides or each kind (the ones with a hydroxyl) and to each reaction, one specific didioxynucletodie (with no hydroxyl group), and a DNA polymerase to synthesize DNA. (Not Taq- its a modified enzyme from a T7 bacteriopahage in my case.) I can then run my four products on a gel, which sorts them by size. I can then just read up the gel- the band furthest down indicates that the first base is whatever that lane corresponds too. I would sketch out an example here, but I need the pre tag.
Anyway, I've simplified alot, but that is the gist, I think. This has nothing to do with PCR- remeber, ir proceeded it by more than 15 years. PCR involves repeated cycles or melting DNA, leting primers aneal, synthesizing DNA, and repeating. In the above process, I do all of that only once...
To make things more complicated, automated sequencing (like that used by all of the genome projects, human or otherwise) uses tecnologies related to PCR, but not identical. Basicly, they use a PCR machine and to run this reaction, and do it mulitiple times. But the key diffeince is in accumulation. The stops in the strands which are synthesized means that there is basicly only a linear increase in the ammount of DNA- PCR is what it is becuase of the exponential increase in template.
The process which the article is talking about (PCR - Polymerase Chain Reaction) is a significant advancement that has allowed the HGP to progress at amazing speed.
To quible about things that don't really matter...
I'm pretty sure that the HGP isn't using PCR based sequencing. Most genome projects use what is known as shotgun sequencing. In short, PCR requires DNA primers- a template (usually of 18-24 base pairs) of known sequence so that Taq (or another DNA polymerase) can begin DNA synthesis. This obviously requires knowledge of the sequence, and so inorder to sequence the genome this way, you have to sequence a little bit, design new primers, and repeat. The extreme delays in the Drosophila genome project have shown why this method doesn't work.
The HGP uses shotgun sequencing, which basicly involves taking DNA, breaking it up into bits, sticking into a cosmid, and growing up a batch of culture (like E. coli) which contains this cosmid, harvesting the cosmid, and sequencing the insert. Then all of these inserts need to be pieced together- the hard part.
Don't get me wrong- PCR is wonderful. I couldn't do my research without it. (Well, I could, but it would be way harder.) But the HGP isn't the be all and end all of biology, and it isn't using PCR.
However, it doesn't seem very useful to the designer of a security product. Any security product needs to be used properly in order to be effective hence most of the social engineering routes on the attack tree are irrelevant to the designer of the software (he cannot control what people do with their passphrases).
I completley dissagree. Part of designing anything involves thinking about not just the object, but how it will be used. While its true that you can't control what users do with passwords, I think that a designer who takes the wetware into account will end up with a more secure product. If the analysis shows that the most likley way for the product to fail is through a human factor, its time to change your notions of how people were interact with the product.
Check out John Martellaro's take on it. John is writing about the Macintosh Web, but his arguments scale quite well, I think. Basicly, he is saying that publishing, whether on the web or in paper, is a business, and web business model has some big problems. If you think its hard for magazines to do good reviews, what do you think a web site with one advertiser on a page is going to do?
drox is right about the problem(s) with your argument. But I think there is a more fundemtntal one. For evolution by natural selection to occur, you need: (its eductation time boys and girls!)
1) Individual variation. 2) A genetic basis for that variation 3) More offspring produced than can survive 4) Non-random survival: the ability to survive and reproduce is effected by those heritable variations.
In this case, you have no evidence that the variation you are speaking of has a genetic basis. And until you can show that it does, I have a hard time believing any of your evolutionary scenarios.
A major question in conservation biology is the minimum size a population can reach and still maintain genetic variablity. As the population size falls, genetic variability is lost. This lack of variation means that the population will be less likley to adapt to future changes, and that by random chance, bad copies of a few genes will be very prevelant in the population. This doesn't bode well for the survival of this population.
There is lots of dissagreement about what this number is, but 50 seems to be a reasonable minimum number of organisms (it might be much higher- more like 500.) There are only 6 animals preserved around the world: an order of magnitude less than what seems to be needed. Even if we could bring back a stock of these animals, would all our efforts be in vain?
Slashdot Mirror
In explaining the scientific illiteracy of the US population, the author of this article talks about the number of Americans who believe in psychic powers, UFOs and astrology. The author then writes:
This is terribly misleading writing. Unlike the previous three issues, the vast majority of scientific evidence supports the belief that the global temperatures are currently rising, and will continue to do so. While scientists may disagree about how high the temperature is going to rise to, or what factors are most to blame, the fact of global warming accepted by the vast majority of scientists. As written, the article could be read to imply that global warming, like psychic powers, UFOs and astrology, is pseudo-science.
Just had to get that cleared up. Carry on....
Mike Rosenzweig was Editor-in-chief of the journal Evolutionary Ecology until he got fed up with his corporate publisher. So he (and his editorial board) left and founded their own journal: Evolutionary Ecology Research. The journal has a variety of progressive policies regarding pricing and ownership. Importantly, he has written a great deal about them- check out this paper (its a .pdf) or others on the site where he breaks down the money issues.
I can argue about definitions, and I guess I will. The problem is that how you define these things is central to the issue of measuring complexity. Until you have some objective measure eof state and environment, I don't see how you can make even a rought estimate...
As Gould has pointed out, the central tendency of life on this planet has always been and always will be bacteria. Animals (let alone humans) are extreme outliers.
Come on, do you really understand biology? Where do you get off saying that we are are "so superior to the roundworm"? I'd like to see you try and self fertilize like roundworms can. Or completely metamorphose like a fly does. The fact is, there is no good measure of "complexity" and "simplicity" at the level of the entire organism. To simply assume that we are more complex than other animals is grounded in nothing more than ego. And finally, like Gould (and many, many others have emphasized) we can only understand developmental complexity by understanding how gene products interact. So even if we are somehow more complex, there is no reason to assume that such complexity would require more genes.
Beyond that, I really know nothing about how game theory scales up beyond two player games (which is what we are talking about here), so I don't know if any of this discussion applies!
So how does annotation work? At least at this point, its lots of educated guessing. One of the big areas of bioinformatics research right now is to take DNA sequence and predict where the genes are. There are motifs which are associated with the start of a gene for example. In addittion, non-random use of alternative codons allows a reasearcher to see if punitive genes match exprected freqeuences. (Remember that three nucliotides code for a single amino acid, and while there are multiple combinations that code for a single amino acid, all combinations are not used with equal frequency.)
Once you suspect that something is a gene, figuring out what it does based only on sequence is basicly impossible. If it is quite simmilar to a known gene or genes, we can place it in a family of genes and hypothesize that it shares some function. (Of course, this still needs to be tested.) If it is novel, then we need to do the wet lab experiments to figure out what its function. Eventually, the compuational biologists would like to be able to go from the linear DNA (and hence amino acid) sequence to the three dimensional structure- but we aren't there yet.
As for chunks of "how to grow a tail" and what not, they certinaly exist. But these pseudogenes mutate quite fast once they are no longer being used, so they would be very difficult to reconginze today as any different from their background.
Excellent point. But if you go back and read the Slashdot interview with RMS, you will see that he says that RMS thinks there are many things in the world that are much more cruical than non-free software. But he thinks he can make the most differnece with FSF, so thats where he puts his time.
So where does this fit in with geekdom? In short, the author seems to argue that women can do everything that men can, but they also can do other things which aren't getting done. Now I'm not supposing something simmilar to the second shift, where traditional roles have kept women doing the housework. There really aren't defined gender roles which are specific to hacking (as near as I can tell.) But this article proposes defining such gender roles, and I'm a little uncomfertable with just letting a whole set of things be swept into the "Women's work" catagory, along with everything already being done by men. Like Steinem says, the challange is convincing men that those jobs are crucial, and that they can do them as well.
Like I said, since the 1950's. I was simply providing a correct date in response to the above post.
I dont see anything revolutionary in this "advancement" , we have known about it for years.
Well, the MSNBC article leaves it a little vague- I can't comment on the scientifc merit untill I get into lab tommorow and find a copy of Nature. But I think the point is that this is a promoter/repressor system which is easily turned on and off by an experimenter.
and the operon is NOT a set of genes expressed together , rather it is the regulatory and structural genes that regulate production of a certain protein
Were quibiling over scemantics, but I think in actuality, we are both half right. The genetics text infront of me (Griffith's et al., 1996) defines an operon as:
So I think we were both correct. The operon includes the set of genes expressed together (lac Z, Y and A) as well as the regulatory genes involved in that regulation (lac Pand O.)Yeah, this is exactly the kind of thing I was talking about. There are really only 5 major signalling systems, so this type of problem is quite common. In your case, if you knocked out Sonic hedgehog (Shh), I think you would get something even more extreme than you describe. Shh is involved in the somite-notochord-neural tube signaling, so my guess is that you wouldn't even get the a trunk that was properly patterned, making it difficult for a limb bud to even form. I don't know if this type of experiment is being done, but I'm going to ask someone tommorow!
My point was that if you classify things as prokaryotes vs eukaroytes, the easiet way to explain eukaroytes is as "basicly everything but bacteria", because for I think that is a good working defenttion for a non-biologist. "Basicly everything but bacteria" is a subset of life which includes plants and animals, amoung other things. If I told non-biologists that eukaroytes have nuclear membranes and prokaroytes don't, that wouldn't help much. If you don't know anything much about biology, would you know if yeast have nuclear membranes? (For those who don't know - obviously not the above poster - they do.) I was simply trying to provide a working defenition so that I could get on with post.
But since you have such a critical eye, I wonder if you have any comments about other ideas in the post. I'd be interested to hear.
With such a complex system, doing basic biology is difficult. For example, if I want to study the role a specific protein plays in the development of an organism, I can mutate it and see what changes. But what if that kills the organism (say, a fruit fly) early in development? I will have no idea if that gene plays a role later in development. But lets say I can engineer a line of flies with this switch acting on the gene I want to study. I can keep that gene on early in development, but shut it off at later times, learning the role of that gene at various points.
I'm not talking about sticking this into people for any reason (I'll let other people continue to bicker about that.) Despite the narrow vision of MSNBC and other popular media reporting on stories like this, I'll bet that the major impact of this advance won't be on any direct human advance, but will be in all the basic research it helps fuel.
Nope. There called promoters and repressors. In some contexts, they are known as transcription factors. An operon is a set of genes which are expressed together. And the Lac operon was first explored in the 1950s by Jacob and Monod.
I don't know if anyone has either, but I do know that companies are thinking about this very thing. I have a colaborator at a large US biotech firm. We are actually working on something totally unrelated to their work, but the corporate lawyers have told him that he can't send my a set of primers he designed. He has apparently given them to several people already, and if he gives them to anyone else, he (or his employer) apparently looses some sort of intelectual property rights to them. It turns out I probably won't need them, but this is already something of an issue...
Another: avian population biology. Most of our knowledge of bird distirbution and population trends in the North American is due to the work of hundreds (or even thousands?) of talented amatures. Many of the censuses which have documented the declines of many bird species have been performed by dedicated bird-watchers. One of the important journals in the field, especially in terms of distribution, North American Birds, is mostly composed of regional resports taken from the observations of legions of bird-watchers.
That said, I think these two fields are in the minority. There may be a few others like them, but they are the exception.
Visually, programs that violate this pop up dialogs while the user is working in other programs
I agree. In the new OS, alerts will stick with the program that creates them, rather than jump to the front. (Apple has emphasized this recently- system alerts in oS 8.x don't generaly pop to the front- they are visible in the finder, and a sound lets you know that they are there.)
While I agree with your issue of balance, I completly disagree with manifestness. Why shoudn't things that are functional be decorative as well? Don't get me wrong, I'm not saying that this should get in the way of user interface. What I am saying is that I don't know why the two need to be mutualy exclusive. For example, can't the reason that a part of UI be good at your first chritera be through the second: you are naturally drawn to certain functional objects via their decorative nature?
Um, on a computer screen, what isn't synthetic? What are the "natural aesthetic properties" of my monitor? Aestheics are, of course, subjective, and Apple's current vision agrees with what I consider to be attractive. It may seem dumb to some, but since most of my time in front of my computer involves looking at the screen, I would like it to be something that is pleasing to look at. For me, themes don't cut it- I find that Apple, more than anyone else, is able to follow Frank Loyd Wright and let form follow function. Themes in *nix always feel bolted on to me- there don't seem like they belong.
I haven't played with any of OSX (I don't know if the developers preview even include Aqua as it was demonstrated.) But my first thought when I saw it on the website was "This is gorgous."
I'm looking forward to playing with OS X to see if it lives up (and I imagine it will.) To me this look doesn't seem artifical or bolted on. It looks like it fits with the way I want to interact with my system. Maybe I can't descrbe it well, but I can feel it when I use my Mac. But thats what makes me a Mac head.
cute analogy- though I think a fork would describe it better. The part of the bible that you are farmiliar with may have not changed since then, but Judiaism has changed a fair bit in the last 2000 years. The foundation may be the same, but tons of new features have been added, and different distributions empahsize differnet things. Orthodoxy keeps almost all of those laws, while Conservative and Reformed movements in the US have changed that empahsis, only incuding the basic install for those who find that suits their need. In addition, many people are merging code. (Note the Jewish Buddist movement, for example.)
The type of sequencing I do (and most everyone else as well) was invented by Fred Sanger in 1971 (for which he won his second Nobel Prize, IIRC.)
Forgive me if I get too simplistic, but I don't know how much molecular biology you know...
The base pairs which form DNA are a purine or a pyrimindine (two differnet types of carbon rings). These base pairs are linked together by phosphate groups. Before these bases are added to the chain, they have a hydroxyl (-OH) group at one end, which is what is used to bridge the gap. What Singer figured out was thatf you instead used a base which was lacking the hydroxyl group, and simply had a hydrogen there, they synthesis reaction could not proceed. So to sequence DNA this way, I run four reactions simultaneously. I take my template, seperate the strands be heating them, add lots of dioxyduclitoides or each kind (the ones with a hydroxyl) and to each reaction, one specific didioxynucletodie (with no hydroxyl group), and a DNA polymerase to synthesize DNA. (Not Taq- its a modified enzyme from a T7 bacteriopahage in my case.) I can then run my four products on a gel, which sorts them by size. I can then just read up the gel- the band furthest down indicates that the first base is whatever that lane corresponds too.
I would sketch out an example here, but I need the pre tag.
Anyway, I've simplified alot, but that is the gist, I think. This has nothing to do with PCR- remeber, ir proceeded it by more than 15 years. PCR involves repeated cycles or melting DNA, leting primers aneal, synthesizing DNA, and repeating. In the above process, I do all of that only once...
To make things more complicated, automated sequencing (like that used by all of the genome projects, human or otherwise) uses tecnologies related to PCR, but not identical. Basicly, they use a PCR machine and to run this reaction, and do it mulitiple times. But the key diffeince is in accumulation. The stops in the strands which are synthesized means that there is basicly only a linear increase in the ammount of DNA- PCR is what it is becuase of the exponential increase in template.
Hope this helps...
To quible about things that don't really matter...
I'm pretty sure that the HGP isn't using PCR based sequencing. Most genome projects use what is known as shotgun sequencing. In short, PCR requires DNA primers- a template (usually of 18-24 base pairs) of known sequence so that Taq (or another DNA polymerase) can begin DNA synthesis. This obviously requires knowledge of the sequence, and so inorder to sequence the genome this way, you have to sequence a little bit, design new primers, and repeat. The extreme delays in the Drosophila genome project have shown why this method doesn't work.
The HGP uses shotgun sequencing, which basicly involves taking DNA, breaking it up into bits, sticking into a cosmid, and growing up a batch of culture (like E. coli) which contains this cosmid, harvesting the cosmid, and sequencing the insert. Then all of these inserts need to be pieced together- the hard part.
Don't get me wrong- PCR is wonderful. I couldn't do my research without it. (Well, I could, but it would be way harder.) But the HGP isn't the be all and end all of biology, and it isn't using PCR.
I completley dissagree. Part of designing anything involves thinking about not just the object, but how it will be used. While its true that you can't control what users do with passwords, I think that a designer who takes the wetware into account will end up with a more secure product. If the analysis shows that the most likley way for the product to fail is through a human factor, its time to change your notions of how people were interact with the product.
Check out John Martellaro's take on it. John is writing about the Macintosh Web, but his arguments scale quite well, I think. Basicly, he is saying that publishing, whether on the web or in paper, is a business, and web business model has some big problems. If you think its hard for magazines to do good reviews, what do you think a web site with one advertiser on a page is going to do?
drox is right about the problem(s) with your argument. But I think there is a more fundemtntal one. For evolution by natural selection to occur, you need: (its eductation time boys and girls!)
1) Individual variation.
2) A genetic basis for that variation
3) More offspring produced than can survive
4) Non-random survival: the ability to survive and reproduce is effected by those heritable variations.
In this case, you have no evidence that the variation you are speaking of has a genetic basis. And until you can show that it does, I have a hard time believing any of your evolutionary scenarios.
There is lots of dissagreement about what this number is, but 50 seems to be a reasonable minimum number of organisms (it might be much higher- more like 500.) There are only 6 animals preserved around the world: an order of magnitude less than what seems to be needed. Even if we could bring back a stock of these animals, would all our efforts be in vain?