The computers are not being left *solely* for the purposes of the cluster. The policy of the university admins is to leave them overnight for updates, and anyway the users don't like to turn them off (so they don't have to wait for the computer to boot up in the morning). Therefore we are utilising what sits there idle anyway. Furthermore, anyway you don't take into account the overhead of buying a supercomputer / cluster with 1000+ nodes in the first place -- and we are utilising what has already been payed for (both in terms of money from the university and in terms of energy used / CO2 emission that took to produce the units). Finally, buying a supercomputer / cluster is, due to the necessary bureaucracy involved in expensive investments, a major pain in the ass and also a system-administrative effort.
Of course, this solution cannot replace a proper cluster -- I have already outlined why, and also I agree with you in puncto efficiency. But if you have a bunch of PCs sitting around idle at night, and need calculations -- this may be a cheap and quick solution.
Of course, this solution is not for everyone, but it works quite nice at the university where I'm working. Three departments (chemistry, biology and physics) got together to form a computer administrative unit. Essentially, any workstation at one of these three dpts has the same version of OS (mostly Windows) with the same software installed. And each of these installations includes condor for distributed computing. Effectively, you get something comparable to a 1000+ nodes cluster -- and some of the machines are quite strong!
Scientists and students alike are allowed to use it freely for their computations. There is a batch submission system, and a whole lot of numerical calculations run on these computers during night. There are a few caveats, though:
many biological applications need a large amount of data -- and the moment that you need to transfer gigabytes to each of the nodes (as they do not share storage) the whole thing is no longer reasonable.
you always have to take into account a 1-5% job loss, so if you want e.g. 1000 simulation runs, you should dispatch 1200 runs to be on the safe side. The job loss comes from a) machine being switched off b) machine having all sorts of random troubles (disk full, some weird software interaction) c) some jobs take awfully long to execute, so when 99% of your other jobs are done, you just need to kill the others.
Sometimes you rather launch the job locally and wait two days rather then spend half a day on preparing and testing the batch submission and get the results next morning (my time is more valuable than the CPU time...)
All in all, you get lots of CPU, but low reliability. Which is fine for many applications. Additionally, not only you prevent energy wastage, but you also use the hardware more efficiently (so that the brand new quad core of the dpts secretary actually gets used in a reasonable way).
By the way -- our admins hate it, when Windows computers are being switched off. They run the updates at night, as during the day the users are likely to stop an update that takes to long. I was being bashed for switching off computers during night:-)
j.
I have seen this line of reasoning a few times, and I think it is important to get it straight.
It is perfectly normal that the pricing for services and products is different in different countries. I mean, how retarded do you have to be to think that an item X should cost exactly the same in, say, the country it was produced and the country it has been shipped to after paying tolls?
And especially especially when we are talking about copyrights and international licensing, the matters are complex. Say, I had enough money *and* the juristic possibility to get a special kind of contract in two countries which allows me to play the music for free in these countries... am I obliged to pay -- possibly much more money -- to get the same type of agreement in all other countries in the world?
Nope. Look, I am living in Germany, but I'm not a German citizen. Last.fm is not free in the country of my origin. Discrimination / rascism would have been if they refused to provide me with the same service as German citizens. Or if the Germans living in my country of origin were allowed to listen to last.fm for free, whereas other people would have to pay. That would have been discrimination.
There was a similar discussion in regard to iTunes. iTunes music store is always national -- works only in one country. There are plenty of countries where you cannot buy music from iTunes (even within EU). Are they rascist? Nope. Neither is Walmart, even though there is not a single Walmart in Burkina Faso. Or an online pharmacy shop in London even though it does not ship certain drugs to the U.S. -- legal in London, illegal or not allowed for import in the U.S-
The fact that Internet brings different countries together, and allows you to communicate over juristic and national boundaries doesn't mean that these boundaries do not exist. Don't you forget this.
This is, indeed, an interesting coincidence. "Syf" (sing.) or "syfy" (plur.) in polish means filth, scum, acne and also syphilis: http://en.wiktionary.org/wiki/syf. Makes also an interesting metatextual link to another recent Slashdot submission because of the common saying "syf i malaria" (syphylis and malaria) denoting a complete and utter mess, SNAFU etc.
"Fighting over megapixels" -- for someone who knows basics of photography, this is like fighting over which laptop comes with more preinstalled software tools, or number of features a text editor has. Like, there is *some* point of the discussion up to a certain level, and not much after that, and definitely nowadays this is not the most important factor for a decision which laptop to buy. The "megapixel wars" have ceased a long, long time ago in most of photography-related forums.
Except for professionals, 10MP and more is something like audiophily. And definitely an overkill for a pocket camera, where you are much more likely to hit the resolution boundary of the optical system itself (this is why professional cameras tend to be rather large...). Even 3MP (which was standard years ago) is sufficient for many purposes (given a high quality of the lens).
For photographers, the main fetish was and remains The Lens. A good lens may cost an order of magnitude more than your camera body. In the times of analog film, people often referred to the camera body as "film box", disrespecting its features and extras, compared to the importance of selecting the right lens.
I think the whole "megapixel war" issue started because photography became very popular with digital cameras, however people were not yet aware of the more important points -- and started to project what they knew about image quality (i.e. resolution) to what cameras they buy.
Now the knowledge starts to slowly infiltrate the "casual" photographer community. Having a few cameras, they start to notice other things: quality of the lens, haptics (how the camera "feels" in your hands), stabiliser, reaction time (time between pressing the button and the camera making the photo) etc.
I am a scientist, I did my PhD six or seven years ago, and I am the author of several publications in the fields of molecular biology, molecular evolution and bioinformatics. I have had several collaborations, I used LaTeX and I used Word. Here are a few remarks. Baseline is that there is no real collaborative system out there.
(i) LaTeX
1) It is not true that LaTeX use is limited to CS, Physics and Mathematics. Biologists use it as well, and many journals in the field at least accept LaTeX. Some even prefer it.
2) That said, LaTeX *is not* a collaborative writing tool. It is a typographic system. The fact that it produces nice output is of no relevance when preparing a manuscript that will be converted to whatever system the publisher uses and will look quite different from your version.
3) While it manages a lot of things quite well, collaborative efforts are a pain in the ass. Even if you work together with a savvy scientist, unless the person is an actively working programmer, and uses the same version control system as you do, things like SVN, CVS etc. are not an option. Even though I collaborated with several people who know well how to program, setting up CVS for manuscript creation does not work out. In the end, you revert to writing "%XXX modified by JW3" in your LaTeX source.
(ii) Word
1) most of the experimentally working biologists use Word; some of them use Endnote. Whatever system you intend to use, it must be compatible with people working with Word.
2) the collaborative features of Word are quite well, but not perfect. Versioning can be tough and figures can be a problem. Endnote is not bad for bibliography... assuming that all collaborators use it the same way and have the same databases -- which is unrealistic.
3) manuscripts produced by Word are ugly. Fullstop.
4) if the collaborators use different versions of Word, the result can be a mess.
Some more general remarks.
(i) Bibliography.
The current situation with bibliography is ridiculous, but the fault is at the editorial office side. The authors are supposed to painstakingly follow the bibliography guidelines of the journal, take care of all the interpunction and formatting. True, BibTex or Endnote can take care of most of it, but not all. At the same time, for 99% of the cited sources it would be sufficient to just give the doi (www.doi.com) id or pubmed id or something similar. And it should be the job of the bloody editor to take care of it -- I mean, as an author, not only I don't get any money for my publications, not only I actually have to pay for the additional or color figures or even the publication itself, I also have to (a) pay for the actual research with taxpayers money and (b) do 90% of the editorial job myself! If my English is not acceptable, will it be corrected by the office? No, in most of the cases it will just be rejected by the reviewers.
(ii) What I envision is a fuson between Dropbox (www.getdropbox.com) and some sort of clever versioning system that would allow the people to use their Word or LaTeX or whatever to upload and version files. It would have to take care of figures and bibliography as well. And... THERE IS NO SUCH THING YET OUT THERE.
Please note one more thing: in Windows, if the system asks you to download / update some strange piece of software that you don't recognize, alarm bells go off in your head: what is that? some kind of a trojan, virus or something? All these little things that get to be updated in Linux separately are the equivalent of Windows service pack.
Maybe a short "README for windows users" (one page max!) should be included in the default Desktop installation.
I was able to greatly improve the reactivity of both firefox and opera by moving the cache onto tmpfs systems. Actually, I moved full rc directories (.opera and.mozilla) and just rsync them from time to time.
Caveat - I have a sort of an improvised SSD (using a CF card and an adapter), which is quite slow esp. for concurrent writes. But maybe this is why I noticed it at all. I don't understand why the browsers insist on writing tons of data onto the hard drive when there's plenty of perfectly good memory lying around.
Of course it isn't ignored. It's a whole field of research. And yes, there are plenty of tools, some of them quite old (and most of them requiring maths).
Question whether there was some degree of genetic exchange between Neanderthals and humans have been already asked decades ago -- and most probably, already answered. The answer is based on the sequences that have already been obtained and it is a "no".
Having or not having FOXP2 is not the point. The point is that neanderthals had exactly the same allele, the same sequence of FOXP2 that we humans have. And that small changes to this sequence render humans speechless.
In other words: having a gene for eye pigmentation does not make you blue-eyed. But having a particular version of this gene can. Some people think that this particular version of FOXP2 is necessary for correct speech development.
Yes, it is fascinating, but you have to take into account that FOXP2 is a transcription factor that acts when "collaborating" (dimerising) with other transcription factors (or itself) to regulate a whole range of different genes, which in turn can affect a whole range of physical (phenotypical) features (like speech development). True, people who have a mutation in FOXP2 are normal, but are not able to coordinate the movements required to speak, and this is a quite specific effect. But FOXP2 has definitely other "applications" as well - it is required for correct brain development in general, for example.
This makes any changes (or lack of them) very hard to trace back to specific effects. The fact that neanderthals had the same "version" (allele) of this gene might be an indicator, but then -- it might just be a coincidence. Chimps are just two mutations away.
What complicates the picture even more is the fact that not only the actual sequence of the protein matters -- also the regulatory sites around it (where other transciption factors bind and promote / inhibit the activation of FOXP2). And these tend to be variable even when they work very similarily.
The term "share XX % DNA" is largely incorrect and misleading. In short, if you have mapped 60% of the genome, you can hardly underestimate the significance of this information. I will try to explain why you are on the wrong track.
1) what is usually meant by that is that "XX % of the sequence is identical". This is not always informative, as during evolution, much of the sequence can mutate neutrally without major changes in the phenotype. Two almost identically looking worms (and also quite similar on molecular level), C. elegans and C. briggsae, have a history of 100 million years. Hey, they had more time to accumulate neutral differences than mouse and humans!
Moreover, if one compares these parts of the DNA that code for a protein (and believe me, they are scattered very thin in our genome), this percentage will be very high compared to everything else. The difference between one region of the genome (say, the one they mapped) and another one (say, the one that is still to be sequenced) is very small when compared with the difference between a coding and non-coding region. So whatever you find out about the genetic distance between species based on 60% of the genome is extremely likely to hold also in the case of the whole genome. More! Usually it is sufficient to sequence a few very well known genes (which Paabo and his group did already a decade ago).
Bottom line: we can extrapolate this "XX% DNA in common" from the part that is already sequence, but anyway this is not what one is really after -- because we know it more or less already.
2) when comparing genomes that are far away, one often looks at the genetic composition -- which genes are present in both genomes? Which are absent in one of them? In case of humans and chimps and neanderthals these sets are / will be strikingly similar, but the differences will be enormously informative.
3) Sometimes the phrase "XX % of the genes in common" refers to alleles, that is, slightly different variants of the same gene (think "blue eyes / brown eyes"). This is why we say that we share 50% genes with our mother and 50% of genes with our father. This is also the type of information that one is after.
What I'm saying is that your reasoning is meaningless because founded on a misunderstanding. The website that you were referring to has a subsection titled "Other DNA facts you don't need to know". I couldn't phrase it better, except by adding that the information is potentially harmful.
Please, don't. Don't make the jokes on cloning / restoring the Neanderthal. We all know it'd turn out that some of them actually are among us, possibly taking up even prominent positions in our society. Who'd be surprised if the cloned guy looked exactly like the governor of one of US states?
On a serious note, there are a few scientific issues at stake here.
First let me explain this "positive selection" stuff from the article. When a mutation within a coding region of a gene takes place, it can either be a silent mutation (no change in the resulting proteins) due to the redundancy of the genetic code, or it can change the amino acid sequence of the protein and thereby possibly its function.
Now, mutations happen at random. But depending on what kind of an effect the changes have, they might be wiped out by natural selection. For example, mutations in the "core system", the "kernel" of any living cell -- replication machinery usually are wiped out, because the machinery is so finely tuned that most mutations seriously screw it up. If the changes are largely neutral, the ratio of the mutations that have an effect divided by mutations that are silent (so called dN/dS ratio) is roughly equal to what we would expect based on random model, and we speak of neutral evolution.
On the other hand, environmental pressure, change of times, parasite pressure or many other things can lead to an accelerated rate of evolution -- measured by the fraction nonsynonymous mutations / silent mutations. Thus, one can detect whether a species, gene or genome was subjected to a specific pressure. And if we look at the whole genome, we can tell a lot about what this pressure was. And of course, it works both ways -- we can tell a lot about what the pressure was that shaped us, humans.
* of course, learn more about neanderthals -- who were they, did they mix with humans (current analyses say no, but who knows what one can find in the whole genome). Were they human at all? Did they really talk? What kind of culture did they have?
* by learning about divergence between neanderthals and homo sapiens, answer the fundamental questions of biology -- who are we? what makes us different from animals? What made us spread and neanderthals disappear?
* analysis of genome instead of single genes takes the whole thing up one level.
* tracing back evolution (in general, it is not only about human evolution) -- not by comparing sequences of organisms that live nowadays, but really going back in time. Among others, this will let us test the tools that we routinely use for phylogenetic analysis (that is, tracing back the evolution).
Regards,
j. (who currently works on genome evolution in bacteria)
I did not state that "Darwinism" is an invention of the creationists. I even pointed out that a form of this word (neo-Darwinism) is indeed still used by evolutionary scientists.
However, the word "Darwinism" is eagerly used by creationists, because (i) it allows to make allegations by associations (nazism, communism, Darwinism), and (ii) it suggests that it is valid to critisize Darwin directly -- rather than the Modern Synthesis, which would require much more skill and in depth knowledge.
Nota bene, there are of course ideological links between communism, nazism and Darwinism. Communism did not encourage "Darwinism" (it promoted at times a pseudoscientific ideology called the Lysenkoism, and regular evolutionary biologists were persecuted), but it did not argue the evolution itself. Nazism and certain fashistic ideologies used allegedly "darwinistic" arguments to support numerous crimes. One of the reasons for that is the often misunderstood quote from Wallace -- "survival of the fittest".
Actually, there is a great text by Michael Shermer in the February issue of "Scientific Americans" on two myths on the Modern Synthesis -- if these were busted, it would count for much more than abandoning the term "Darwinism". One myth is what Wallace was trying to avoid -- namely, the term "natural selections" suggests a presence of someone who selects (on purpose), and therefore the idea that evolution is somehow teleological, directed. The second myth was conceived by Wallace himself and his phrase "survival of the fittest" and later by Huxley -- because not survival alone, not strength or perfection in the adaptation to the environment is crucial, but the speed of the propagation of the genes. So not the strongest survive, but those who are more proliferous.
Allow me just a few points. BTW I am an evolutionary biologist. Carl Safina, with all due respect, is not.
First, let's get one thing straight that the author of the article confuses. "Evolution" is the observation that all living things seem to be related, plus the observation of the change of the living world in time. This observations are older than Darwin. "Theory of evolution" is any theory that tries to explain this observation. "Neodarwinism" or "Synthetic Theory of Evolution" is one particular theory that involves the mechanism called "natural selection". Natural selection is a mechanism that can be observed. Darwin's greatness was in linking this mechanism to the rise and change in complexity of all living things, and in the ability to foresee the consequences that only recently started being fully understood.
1) "Equating evolution with Charles Darwin ignores 150 years of discoveries"
First, nowadays formally we use the terms "neodarwinism" or "synthetic theory of evolution". "Darwinism" is most often used in certain popular (non-scientific) texts, and also by creationists.
2) "Using phrases like Darwinian selection or Darwinian evolution implies there must be another kind of evolution at work, a process that can be described with another adjective."
Well, of course, as any of my students would immediately ask "what about lamarckian evolution?" (an alternative explanation for the process of evolution, largely rejected or falsified by observations)
3) "And isms (capitalism, Catholicism, racism) are not science."
Yeah, right, like electromagnetism, empiricism or autism.
4) "What Darwin had to say about evolution basically begins and ends right there."
If this only was so simple. Darwin, as I mentioned before, not only proposed natural selection as an important mechanism of evolution, but also was able to point out the consequences, ranging from kin selection to the role of sexual reproduction.
5) Do you really believe that creationists would less fiercely attack a "synthetic theory of evolution"? The problem is much, much deeper than just an association or a given name.
Yes, I heard that comment a few times -- never from people who have at least a single scientific publication, at least one scientific collaboration. In other words, with exception to some fields of science or particular environments (like CS where people often know these tools anyway), you do not know what you are talking about.
I mean, I *do* use SVN and LaTeX+BibTeX, but I collaborate with people who do not and will not use these tools.
With all these different solutions, overloaded with features, one could think whatever you need, you will find it.
What I would love to see is a collaborative system for creating scientific papers: with bibliography management, figure and table management, conversion from and to word (and LaTeX?), some sort of equation editing...
Just a few quotes:
Obviously not having experience with a vector-based illustrator was Erin's downfall in this task - but, then, how many people have used one?
don't understand why GIMP doesn't just layout its windows like photoshop does. It wouldn't lose usability, surely, and it would help the transition of first-time-users immensely.
I'd love to see a welcome screen for the first time you open up your desktop, with little videos explaining a few key concepts to how Linux and Ubuntu work. Maybe it could ask "What do you want to do?" and then explain how they could do this.
Come on. Is he serious? What does that thing do on slashdot? Slow news day, eh?
j.
P.S. It should be "Where do you want to go today" and not "What do you want to do"
Hey, that is such an exceptional story -- a distribution that aims at user friendliness and fails to achieve it. I have never seen anything like that before!;-)
"Its primary goals are to be easy to use and user-friendly (...) Upon booting the Granular live CD ISO with the default settings my test PC, which uses an old ATI Rage 128 video card, the system froze at the loading screen. A quick reboot and selection of safe VESA settings solved this problem with no fuss."
Come on. Am I the only one to think that the above is funny?
Slashdot Mirror
The computers are not being left *solely* for the purposes of the cluster. The policy of the university admins is to leave them overnight for updates, and anyway the users don't like to turn them off (so they don't have to wait for the computer to boot up in the morning). Therefore we are utilising what sits there idle anyway. Furthermore, anyway you don't take into account the overhead of buying a supercomputer / cluster with 1000+ nodes in the first place -- and we are utilising what has already been payed for (both in terms of money from the university and in terms of energy used / CO2 emission that took to produce the units). Finally, buying a supercomputer / cluster is, due to the necessary bureaucracy involved in expensive investments, a major pain in the ass and also a system-administrative effort.
Of course, this solution cannot replace a proper cluster -- I have already outlined why, and also I agree with you in puncto efficiency. But if you have a bunch of PCs sitting around idle at night, and need calculations -- this may be a cheap and quick solution.
j.
Scientists and students alike are allowed to use it freely for their computations. There is a batch submission system, and a whole lot of numerical calculations run on these computers during night. There are a few caveats, though:
All in all, you get lots of CPU, but low reliability. Which is fine for many applications. Additionally, not only you prevent energy wastage, but you also use the hardware more efficiently (so that the brand new quad core of the dpts secretary actually gets used in a reasonable way). :-)
By the way -- our admins hate it, when Windows computers are being switched off. They run the updates at night, as during the day the users are likely to stop an update that takes to long. I was being bashed for switching off computers during night
j.
I have seen this line of reasoning a few times, and I think it is important to get it straight.
It is perfectly normal that the pricing for services and products is different in different countries. I mean, how retarded do you have to be to think that an item X should cost exactly the same in, say, the country it was produced and the country it has been shipped to after paying tolls?
And especially especially when we are talking about copyrights and international licensing, the matters are complex. Say, I had enough money *and* the juristic possibility to get a special kind of contract in two countries which allows me to play the music for free in these countries... am I obliged to pay -- possibly much more money -- to get the same type of agreement in all other countries in the world?
Nope. Look, I am living in Germany, but I'm not a German citizen. Last.fm is not free in the country of my origin. Discrimination / rascism would have been if they refused to provide me with the same service as German citizens. Or if the Germans living in my country of origin were allowed to listen to last.fm for free, whereas other people would have to pay. That would have been discrimination.
There was a similar discussion in regard to iTunes. iTunes music store is always national -- works only in one country. There are plenty of countries where you cannot buy music from iTunes (even within EU). Are they rascist? Nope. Neither is Walmart, even though there is not a single Walmart in Burkina Faso. Or an online pharmacy shop in London even though it does not ship certain drugs to the U.S. -- legal in London, illegal or not allowed for import in the U.S-
The fact that Internet brings different countries together, and allows you to communicate over juristic and national boundaries doesn't mean that these boundaries do not exist. Don't you forget this.
j.
This is, indeed, an interesting coincidence. "Syf" (sing.) or "syfy" (plur.) in polish means filth, scum, acne and also syphilis: http://en.wiktionary.org/wiki/syf. Makes also an interesting metatextual link to another recent Slashdot submission because of the common saying "syf i malaria" (syphylis and malaria) denoting a complete and utter mess, SNAFU etc.
j.
"Fighting over megapixels" -- for someone who knows basics of photography, this is like fighting over which laptop comes with more preinstalled software tools, or number of features a text editor has. Like, there is *some* point of the discussion up to a certain level, and not much after that, and definitely nowadays this is not the most important factor for a decision which laptop to buy. The "megapixel wars" have ceased a long, long time ago in most of photography-related forums.
Except for professionals, 10MP and more is something like audiophily. And definitely an overkill for a pocket camera, where you are much more likely to hit the resolution boundary of the optical system itself (this is why professional cameras tend to be rather large...). Even 3MP (which was standard years ago) is sufficient for many purposes (given a high quality of the lens).
For photographers, the main fetish was and remains The Lens. A good lens may cost an order of magnitude more than your camera body. In the times of analog film, people often referred to the camera body as "film box", disrespecting its features and extras, compared to the importance of selecting the right lens.
I think the whole "megapixel war" issue started because photography became very popular with digital cameras, however people were not yet aware of the more important points -- and started to project what they knew about image quality (i.e. resolution) to what cameras they buy.
Now the knowledge starts to slowly infiltrate the "casual" photographer community. Having a few cameras, they start to notice other things: quality of the lens, haptics (how the camera "feels" in your hands), stabiliser, reaction time (time between pressing the button and the camera making the photo) etc.
j.
They also accept LaTeX.
j.
I am a scientist, I did my PhD six or seven years ago, and I am the author of several publications in the fields of molecular biology, molecular evolution and bioinformatics. I have had several collaborations, I used LaTeX and I used Word. Here are a few remarks. Baseline is that there is no real collaborative system out there.
(i) LaTeX
1) It is not true that LaTeX use is limited to CS, Physics and Mathematics. Biologists use it as well, and many journals in the field at least accept LaTeX. Some even prefer it.
2) That said, LaTeX *is not* a collaborative writing tool. It is a typographic system. The fact that it produces nice output is of no relevance when preparing a manuscript that will be converted to whatever system the publisher uses and will look quite different from your version.
3) While it manages a lot of things quite well, collaborative efforts are a pain in the ass. Even if you work together with a savvy scientist, unless the person is an actively working programmer, and uses the same version control system as you do, things like SVN, CVS etc. are not an option. Even though I collaborated with several people who know well how to program, setting up CVS for manuscript creation does not work out. In the end, you revert to writing "%XXX modified by JW3" in your LaTeX source.
(ii) Word
1) most of the experimentally working biologists use Word; some of them use Endnote. Whatever system you intend to use, it must be compatible with people working with Word.
2) the collaborative features of Word are quite well, but not perfect. Versioning can be tough and figures can be a problem. Endnote is not bad for bibliography... assuming that all collaborators use it the same way and have the same databases -- which is unrealistic.
3) manuscripts produced by Word are ugly. Fullstop.
4) if the collaborators use different versions of Word, the result can be a mess.
Some more general remarks.
(i) Bibliography.
The current situation with bibliography is ridiculous, but the fault is at the editorial office side. The authors are supposed to painstakingly follow the bibliography guidelines of the journal, take care of all the interpunction and formatting. True, BibTex or Endnote can take care of most of it, but not all. At the same time, for 99% of the cited sources it would be sufficient to just give the doi (www.doi.com) id or pubmed id or something similar. And it should be the job of the bloody editor to take care of it -- I mean, as an author, not only I don't get any money for my publications, not only I actually have to pay for the additional or color figures or even the publication itself, I also have to (a) pay for the actual research with taxpayers money and (b) do 90% of the editorial job myself! If my English is not acceptable, will it be corrected by the office? No, in most of the cases it will just be rejected by the reviewers.
(ii) What I envision is a fuson between Dropbox (www.getdropbox.com) and some sort of clever versioning system that would allow the people to use their Word or LaTeX or whatever to upload and version files. It would have to take care of figures and bibliography as well. And... THERE IS NO SUCH THING YET OUT THERE.
j.
Funny. I have never heard about the Streisand Effect until someone mentioned it on Slashdot :-)
j.
Here is a HOWTO:
http://linuxgazette.net/151/weiner.html
j.
Please note one more thing: in Windows, if the system asks you to download / update some strange piece of software that you don't recognize, alarm bells go off in your head: what is that? some kind of a trojan, virus or something? All these little things that get to be updated in Linux separately are the equivalent of Windows service pack.
Maybe a short "README for windows users" (one page max!) should be included in the default Desktop installation.
j.
Don't forget Are you sure you want to install this program? [Y]es [N]o [F]uck yeah j.
This will go unnoticed, but what the heck.
I was able to greatly improve the reactivity of both firefox and opera by moving the cache onto tmpfs systems. Actually, I moved full rc directories (.opera and .mozilla) and just rsync them from time to time.
Caveat - I have a sort of an improvised SSD (using a CF card and an adapter), which is quite slow esp. for concurrent writes. But maybe this is why I noticed it at all. I don't understand why the browsers insist on writing tons of data onto the hard drive when there's plenty of perfectly good memory lying around.
Cheers,
j.
We already know that this is not the case.
Of course it isn't ignored. It's a whole field of research. And yes, there are plenty of tools, some of them quite old (and most of them requiring maths).
Question whether there was some degree of genetic exchange between Neanderthals and humans have been already asked decades ago -- and most probably, already answered. The answer is based on the sequences that have already been obtained and it is a "no".
j.
Having or not having FOXP2 is not the point. The point is that neanderthals had exactly the same allele, the same sequence of FOXP2 that we humans have. And that small changes to this sequence render humans speechless.
In other words: having a gene for eye pigmentation does not make you blue-eyed. But having a particular version of this gene can. Some people think that this particular version of FOXP2 is necessary for correct speech development.
j.
Yes, it is fascinating, but you have to take into account that FOXP2 is a transcription factor that acts when "collaborating" (dimerising) with other transcription factors (or itself) to regulate a whole range of different genes, which in turn can affect a whole range of physical (phenotypical) features (like speech development). True, people who have a mutation in FOXP2 are normal, but are not able to coordinate the movements required to speak, and this is a quite specific effect. But FOXP2 has definitely other "applications" as well - it is required for correct brain development in general, for example.
This makes any changes (or lack of them) very hard to trace back to specific effects. The fact that neanderthals had the same "version" (allele) of this gene might be an indicator, but then -- it might just be a coincidence. Chimps are just two mutations away.
What complicates the picture even more is the fact that not only the actual sequence of the protein matters -- also the regulatory sites around it (where other transciption factors bind and promote / inhibit the activation of FOXP2). And these tend to be variable even when they work very similarily.
j.
The term "share XX % DNA" is largely incorrect and misleading. In short, if you have mapped 60% of the genome, you can hardly underestimate the significance of this information. I will try to explain why you are on the wrong track.
1) what is usually meant by that is that "XX % of the sequence is identical". This is not always informative, as during evolution, much of the sequence can mutate neutrally without major changes in the phenotype. Two almost identically looking worms (and also quite similar on molecular level), C. elegans and C. briggsae, have a history of 100 million years. Hey, they had more time to accumulate neutral differences than mouse and humans!
Moreover, if one compares these parts of the DNA that code for a protein (and believe me, they are scattered very thin in our genome), this percentage will be very high compared to everything else. The difference between one region of the genome (say, the one they mapped) and another one (say, the one that is still to be sequenced) is very small when compared with the difference between a coding and non-coding region. So whatever you find out about the genetic distance between species based on 60% of the genome is extremely likely to hold also in the case of the whole genome. More! Usually it is sufficient to sequence a few very well known genes (which Paabo and his group did already a decade ago).
Bottom line: we can extrapolate this "XX% DNA in common" from the part that is already sequence, but anyway this is not what one is really after -- because we know it more or less already.
2) when comparing genomes that are far away, one often looks at the genetic composition -- which genes are present in both genomes? Which are absent in one of them? In case of humans and chimps and neanderthals these sets are / will be strikingly similar, but the differences will be enormously informative.
3) Sometimes the phrase "XX % of the genes in common" refers to alleles, that is, slightly different variants of the same gene (think "blue eyes / brown eyes"). This is why we say that we share 50% genes with our mother and 50% of genes with our father. This is also the type of information that one is after.
What I'm saying is that your reasoning is meaningless because founded on a misunderstanding. The website that you were referring to has a subsection titled "Other DNA facts you don't need to know". I couldn't phrase it better, except by adding that the information is potentially harmful.
j.
On a serious note, there are a few scientific issues at stake here.
First let me explain this "positive selection" stuff from the article. When a mutation within a coding region of a gene takes place, it can either be a silent mutation (no change in the resulting proteins) due to the redundancy of the genetic code, or it can change the amino acid sequence of the protein and thereby possibly its function.
Now, mutations happen at random. But depending on what kind of an effect the changes have, they might be wiped out by natural selection. For example, mutations in the "core system", the "kernel" of any living cell -- replication machinery usually are wiped out, because the machinery is so finely tuned that most mutations seriously screw it up. If the changes are largely neutral, the ratio of the mutations that have an effect divided by mutations that are silent (so called dN/dS ratio) is roughly equal to what we would expect based on random model, and we speak of neutral evolution.
On the other hand, environmental pressure, change of times, parasite pressure or many other things can lead to an accelerated rate of evolution -- measured by the fraction nonsynonymous mutations / silent mutations. Thus, one can detect whether a species, gene or genome was subjected to a specific pressure. And if we look at the whole genome, we can tell a lot about what this pressure was. And of course, it works both ways -- we can tell a lot about what the pressure was that shaped us, humans.
* of course, learn more about neanderthals -- who were they, did they mix with humans (current analyses say no, but who knows what one can find in the whole genome). Were they human at all? Did they really talk? What kind of culture did they have?
* by learning about divergence between neanderthals and homo sapiens, answer the fundamental questions of biology -- who are we? what makes us different from animals? What made us spread and neanderthals disappear?
* analysis of genome instead of single genes takes the whole thing up one level.
* tracing back evolution (in general, it is not only about human evolution) -- not by comparing sequences of organisms that live nowadays, but really going back in time. Among others, this will let us test the tools that we routinely use for phylogenetic analysis (that is, tracing back the evolution).
Regards,
j. (who currently works on genome evolution in bacteria)
I did not state that "Darwinism" is an invention of the creationists. I even pointed out that a form of this word (neo-Darwinism) is indeed still used by evolutionary scientists.
However, the word "Darwinism" is eagerly used by creationists, because (i) it allows to make allegations by associations (nazism, communism, Darwinism), and (ii) it suggests that it is valid to critisize Darwin directly -- rather than the Modern Synthesis, which would require much more skill and in depth knowledge.
Nota bene, there are of course ideological links between communism, nazism and Darwinism. Communism did not encourage "Darwinism" (it promoted at times a pseudoscientific ideology called the Lysenkoism, and regular evolutionary biologists were persecuted), but it did not argue the evolution itself. Nazism and certain fashistic ideologies used allegedly "darwinistic" arguments to support numerous crimes. One of the reasons for that is the often misunderstood quote from Wallace -- "survival of the fittest".
Actually, there is a great text by Michael Shermer in the February issue of "Scientific Americans" on two myths on the Modern Synthesis -- if these were busted, it would count for much more than abandoning the term "Darwinism". One myth is what Wallace was trying to avoid -- namely, the term "natural selections" suggests a presence of someone who selects (on purpose), and therefore the idea that evolution is somehow teleological, directed. The second myth was conceived by Wallace himself and his phrase "survival of the fittest" and later by Huxley -- because not survival alone, not strength or perfection in the adaptation to the environment is crucial, but the speed of the propagation of the genes. So not the strongest survive, but those who are more proliferous.
j.
Allow me just a few points. BTW I am an evolutionary biologist. Carl Safina, with all due respect, is not.
First, let's get one thing straight that the author of the article confuses. "Evolution" is the observation that all living things seem to be related, plus the observation of the change of the living world in time. This observations are older than Darwin. "Theory of evolution" is any theory that tries to explain this observation. "Neodarwinism" or "Synthetic Theory of Evolution" is one particular theory that involves the mechanism called "natural selection". Natural selection is a mechanism that can be observed. Darwin's greatness was in linking this mechanism to the rise and change in complexity of all living things, and in the ability to foresee the consequences that only recently started being fully understood.
1) "Equating evolution with Charles Darwin ignores 150 years of discoveries"
First, nowadays formally we use the terms "neodarwinism" or "synthetic theory of evolution". "Darwinism" is most often used in certain popular (non-scientific) texts, and also by creationists.
2) "Using phrases like Darwinian selection or Darwinian evolution implies there must be another kind of evolution at work, a process that can be described with another adjective."
Well, of course, as any of my students would immediately ask "what about lamarckian evolution?" (an alternative explanation for the process of evolution, largely rejected or falsified by observations)
3) "And isms (capitalism, Catholicism, racism) are not science."
Yeah, right, like electromagnetism, empiricism or autism.
4) "What Darwin had to say about evolution basically begins and ends right there."
If this only was so simple. Darwin, as I mentioned before, not only proposed natural selection as an important mechanism of evolution, but also was able to point out the consequences, ranging from kin selection to the role of sexual reproduction.
5) Do you really believe that creationists would less fiercely attack a "synthetic theory of evolution"? The problem is much, much deeper than just an association or a given name.
Cheers,
j.
Yes, I heard that comment a few times -- never from people who have at least a single scientific publication, at least one scientific collaboration. In other words, with exception to some fields of science or particular environments (like CS where people often know these tools anyway), you do not know what you are talking about.
I mean, I *do* use SVN and LaTeX+BibTeX, but I collaborate with people who do not and will not use these tools.
j.
Speaking of liver...
With all these different solutions, overloaded with features, one could think whatever you need, you will find it.
What I would love to see is a collaborative system for creating scientific papers: with bibliography management, figure and table management, conversion from and to word (and LaTeX?), some sort of equation editing...
Can anyone suggest something?
j.
Come on. Is he serious? What does that thing do on slashdot? Slow news day, eh?
j.
P.S. It should be "Where do you want to go today" and not "What do you want to do"
Hey, that is such an exceptional story -- a distribution that aims at user friendliness and fails to achieve it. I have never seen anything like that before! ;-)
January
"Its primary goals are to be easy to use and user-friendly (...) Upon booting the Granular live CD ISO with the default settings my test PC, which uses an old ATI Rage 128 video card, the system froze at the loading screen. A quick reboot and selection of safe VESA settings solved this problem with no fuss."
Come on. Am I the only one to think that the above is funny?
January