Dude, you owe me some money. Just go to any large biology lab and take a look at the post-docs! Most of them will be beaten down "push overs" and I am sure they will use any computer program that their PI provides for them. As for what they think of the journals, I think almost all scientists are in agreement on that one.
Just because they found this gene expressed in the prefrontal cortex of humans and chimps doesn't mean that it has anything to do with the development of it. This is a problem the evolutionary-development people have all the time: expression does not equal causation. Just because we have a different flavor of this gene in our PFC doesnt mean that it actually does something. If they really wanted to demonstrate this they would have to create a trasgenic chimp when the human gene had been inserted in place of its own...I am not aware of anyone capable of doing such an experiment currently. Besides, why do you think it is in Genome Watch or whatever journal instead of Nature or Science?
While I agree with your premise that coporate America is not interested in science unless it postively affects the bottom line, I don't agree with your argument that it leads to our grad students and post-docs getting outcompeted by "happy and eager" scientists from elsewhere. Having interacted with biologists from several European countries and elsewhere, I still beleive the US is still the best place to do science when it comes to funding. I find that most foreign scientists are happy to live and work in the US, due to the resources available(despite the current regime). During my time as a grad student I did not pay a dime in tution and also recieved enough stipend money to live comfortably. This was not so 30 years ago when most grad students in the US had to pay their way through school. I challenge you to name a country where the basic science funding opportunities are better.
The problem with the "publish first and review later" model that quite a few people are putting forth is that this would make it impossible to sort through the sheer amount of information available. You have to do a ton of reading just to "stay current" with the literature and that is only what has been peer-reviewed and published. Imagine doing all of this reading and then having to keep in mind that it has not been reviewed and it could have been totally fabricated (I don't believe a lot of published reports anyways but that is a different debate) Like most scientists, I have been on both sides of the process, reviewing papers and publishing in Nature. It is a grueling process and what is does is serve to sort out the important findings from the spurious and the mundane. I do think that journals charge an exorbitant amount of money for access and I think it is funny that they make the authors pay publication costs. On the other hand we do need to have elite journals so that we do not spend all of our time reading articles rather than doing research! If you insist on open access you can always publish in PloS or in some hybrid form of PNAS. They are well respected and have decent impact ratings.
I am a developmental biologist (hence the name), so I study how a single cell (the zygote) eventually becomes an organism with a multitiude of different tissue types and organs. I would study and eventually fix the embryos in formaldehyde before they very far. Most of the time the embryos I studied were externally fertillized (fish, frog), so we could just put adults together and collect the embryos after they mated. The only viviparous animal I have studied is mouse, and I really disliked having to kill the moms to get the embryos.
I have done research using the embryos of frogs, fish, and unfortunately mice. In all cases and at every instituion I recieved training on how to properly treat the animals. The animals were always treated with the utmost care (we need healthy and happy animals to do experiments) and any time an animal needed to be sacrificed it was anesthetized (CO2 or tricane). There are not really any ethical issues in my view, but I really disliked having to sacrifice pregnant mice to get their embryos.
Amid all of the chaos of today's world (our lovely wars in the middle east etc.), this is the most depressing story I have read all week. A scientist was forced out of a field that he has dedicated a significant portion of his life to by some self-important zealots(at least he has tenure already). I find it ironic that the people on the far left of the polictical spectrum perpetrating these acts are achieving the goals of the far right (halting the progress of science). Perhaps I am just biased because I have done animal research myself...
I am a fourth year graduate student getting my PhD in Cell Biology at a top univeristy in the US and the situation is not as bleak as people make it out to be. Granted, there are way too many post-docs for the amount of tenure-track faculty positions that become available every year, but most of the folks I have worked with have landed decent jobs at good schools(stanford, georgetown, UT austin). In our program there are NO foreign graduate students, but there are a fair amount of foreign post-docs. It is always going to be that way as long as the US continues to be the world leader in funding. I believe that the solution to our problem is to grant fewer to PhDs-thats right. Restrict the number of people getting their doctorate and eliminate the glut of people stuck doing multiple post-docs just to land a position at nowhereville state university. The pool of talented scientists is always going to remain constant-you cannot train someone to have scientific insight. If people really love the science they do they will stay the course-unfortunately this course now involves doing almost 10 years of post-graduate work before you can even apply for a faculty position.
While this might sound like a good idea to some of the techies out there, this is a nightmare for traditional fans. When I go to see the Giants at Pac Bell I want to see a Ball Game in the most beautiful ballpark in the US, not read my e-mail and surf. Now there are going to be a whole bunch of yuppies on their cell phones and laptops working during the game. I might just have to inadvertantly spill my beer to get them to stop working.
Re:If you're interested in the author....
on
Everything and More
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· Score: 1
He has an BA from Amherst in lit and an MFA from University of Arizona. He has also been given one of the Macarthur Genius awards. I think his interest in math comes from the fact that his father is/was a professor of mathmatics at the University of Illinois. Currently he is teaching at Pomona College..Basically, he is a god in post-modern literature-read Infinite Jest if you want proof.
I am a huge DFW fan so you might consider my opinion to be slightly biased...
Everything and more was a fantastic read even though I had to spend about half to the time going back to certain points in the text to understand his explainations and abreviations. Basically, it is a 300+ page essay on why Cantor's work on set theory was so important in the grand scheme of mathmatics and the way we percieve math. I only took the requisite 2 years of calculus in high school/college and I was able to understand all of DFW's main technical points. Despite the fact that the main topic is logic and math, DFW's unique style of writing shines through. If you enjoy Everything and More, try reading Infinite Jest-it is the Gravity's Rainbow of our generation.
The problem isn't really with the Telemeres per se, as the telomere knockout mice don't show a shortened life span in the 1st generation. The problem with cloning from ES cells is that the imprinted genes are all misregulated (here for the details http://www.sciencemag.org/cgi/content/full/293/552 7/95)
Basically, imprinting is the process by which the parents can pass down traits to their progeny through modification of the DNA itself without changing the actual sequence. This mode of inheritance is deemed epigenetic. We know very little about how epigenetic modifications happen or exactly how they control gene expression. Aside from all of the moral blather, this fact alone should keep us from even thinking about cloning humans.
Not so informed...
We are not 50-75 years away from getting cells to change their DNA as you state. Researchers have been able to change the DNA sequence of mammalian ES cells by homologous recombination since the mid-eighties when the first "knock-out" mouse was made. Now people do it routinely and eloquently. The key dinstinction is that we cannot alter the DNA content of somatic cells in vivio very easily. Some groups have had limited success using viruses as vectors to introduce wild type versions of genes in the place of mutated copies, but this only works as long as the infected cells live and until the host's immune system responds to the virus. This was the case for chloride ion channel that is mutated in cystic fibrosis. It is rare that a single mutation in one gene is responsible for a given disease, most diseases like cancer are caused by multiple mutations. The next key breakthrough will be how these multiple lesions can be fixed in all of the afflicted cells in vivo.
You have a good point about the fact that we know very, very little about how all viruses function, but that is only a consequence of the fact that only a few have been beat to death by researchers. Take the lambda phage for example, is their anything we don't know about it? Where did that get us? To address your folding problem, we don't need to know the structure of every single protein in this minimal organism they want to create; we just need to know their FUNCTION. Granted whoever figures out the folding problem is going to be my hero, but I don't think that it will benefit manking more. This kind of rhetoric makes you sound like a structural biologist.
Are you high? When are you going to use a gram of a restriction enzyme? A unit of restriction enzyme costs about $.10(check the NEB catalogue www.neb.com) and you would use about five units to digest one microgram of DNA to completion(overkill). Anyone can afford restriction endonucleases. Learn your basic molecular before you start spouting off about it. (I suggest a dose of Maniatas)
Sorry Pal, but you're gonna get it. Single traits can be traced back to single genes, see just about every mouse knock out paper that has been done to date(yes, yes I know about background specific effects). Granted genes do work together to pattern extremely complex structures such as the brain; however, single genes have been demonstrated to be necessary for very specific structures and/or functions. This is the whole point of this Anthropologist's ramblings. A single mutation in the regulatory region of this gene could be responsible for "creativity". This single mutation is a lot easier to explain from an evolutionary standpoint then your gene network theory. Did every single gene in your imaginary network obtain a mutation at the same instant? It just doesn't make evolutionary sense. It is true that that there are many methods of genetic control and regulation that we just have no clue about, but that doesn't mean we should toss logic out the door. Non-biologists (anthropologists especially) should just keep quiet at this point
This is an interesting paper, but I have no idea why it made it into the mainstream press. The concept of using comparative genomics to identify ORFs is not novel; however, the results of using this tecnique on the mouse a human genomes are interesting. Now that we have the genomes of all of these organisms(mouse, human, fly, worm, fish coming soon) the largest obstacle is just sorting out the genes from all of the crap dna accumulated over the years. These researchers found a large group of genes that hadn't been previously identified by conventional methods designed for analyzing just one genome. They consequently confirmed their data by isolating the RNA from these genes by RT-PCR showing that they were at least transcribed. The highlight of the paper is the apparent lack of conservation beween the mammalian genomes and the fish(I think that they used fugu)as two-thirds of their "new" genes don't have homologues in the fish. Why this paper was in the news-I have no idea. Besides, the article was in PNAS!
I agree that the creation of a National Science Library is necessity. Unless you are under the aegis of a large university or sucessful professor, your access to scientific journals is severely limited. When I look up papers online I spend half the time chasing down a password for whatever journal its in. If you want to read anything published before 93 you are in an even deeper quagmire, as you pretty much have to have the hard copy on hand. The only journal that I know of that has made all of its issues available without charge online is PNAS(back to like 1903). If only scinece and nature could follow suit.
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Dude, you owe me some money. Just go to any large biology lab and take a look at the post-docs! Most of them will be beaten down "push overs" and I am sure they will use any computer program that their PI provides for them. As for what they think of the journals, I think almost all scientists are in agreement on that one.
Just because they found this gene expressed in the prefrontal cortex of humans and chimps doesn't mean that it has anything to do with the development of it. This is a problem the evolutionary-development people have all the time: expression does not equal causation. Just because we have a different flavor of this gene in our PFC doesnt mean that it actually does something. If they really wanted to demonstrate this they would have to create a trasgenic chimp when the human gene had been inserted in place of its own...I am not aware of anyone capable of doing such an experiment currently. Besides, why do you think it is in Genome Watch or whatever journal instead of Nature or Science?
While I agree with your premise that coporate America is not interested in science unless it postively affects the bottom line, I don't agree with your argument that it leads to our grad students and post-docs getting outcompeted by "happy and eager" scientists from elsewhere. Having interacted with biologists from several European countries and elsewhere, I still beleive the US is still the best place to do science when it comes to funding. I find that most foreign scientists are happy to live and work in the US, due to the resources available(despite the current regime). During my time as a grad student I did not pay a dime in tution and also recieved enough stipend money to live comfortably. This was not so 30 years ago when most grad students in the US had to pay their way through school. I challenge you to name a country where the basic science funding opportunities are better.
The problem with the "publish first and review later" model that quite a few people are putting forth is that this would make it impossible to sort through the sheer amount of information available. You have to do a ton of reading just to "stay current" with the literature and that is only what has been peer-reviewed and published. Imagine doing all of this reading and then having to keep in mind that it has not been reviewed and it could have been totally fabricated (I don't believe a lot of published reports anyways but that is a different debate) Like most scientists, I have been on both sides of the process, reviewing papers and publishing in Nature. It is a grueling process and what is does is serve to sort out the important findings from the spurious and the mundane. I do think that journals charge an exorbitant amount of money for access and I think it is funny that they make the authors pay publication costs. On the other hand we do need to have elite journals so that we do not spend all of our time reading articles rather than doing research! If you insist on open access you can always publish in PloS or in some hybrid form of PNAS. They are well respected and have decent impact ratings.
I am a developmental biologist (hence the name), so I study how a single cell (the zygote) eventually becomes an organism with a multitiude of different tissue types and organs. I would study and eventually fix the embryos in formaldehyde before they very far. Most of the time the embryos I studied were externally fertillized (fish, frog), so we could just put adults together and collect the embryos after they mated. The only viviparous animal I have studied is mouse, and I really disliked having to kill the moms to get the embryos.
I have done research using the embryos of frogs, fish, and unfortunately mice. In all cases and at every instituion I recieved training on how to properly treat the animals. The animals were always treated with the utmost care (we need healthy and happy animals to do experiments) and any time an animal needed to be sacrificed it was anesthetized (CO2 or tricane). There are not really any ethical issues in my view, but I really disliked having to sacrifice pregnant mice to get their embryos.
Amid all of the chaos of today's world (our lovely wars in the middle east etc.), this is the most depressing story I have read all week. A scientist was forced out of a field that he has dedicated a significant portion of his life to by some self-important zealots(at least he has tenure already). I find it ironic that the people on the far left of the polictical spectrum perpetrating these acts are achieving the goals of the far right (halting the progress of science). Perhaps I am just biased because I have done animal research myself...
I am a fourth year graduate student getting my PhD in Cell Biology at a top univeristy in the US and the situation is not as bleak as people make it out to be. Granted, there are way too many post-docs for the amount of tenure-track faculty positions that become available every year, but most of the folks I have worked with have landed decent jobs at good schools(stanford, georgetown, UT austin). In our program there are NO foreign graduate students, but there are a fair amount of foreign post-docs. It is always going to be that way as long as the US continues to be the world leader in funding. I believe that the solution to our problem is to grant fewer to PhDs-thats right. Restrict the number of people getting their doctorate and eliminate the glut of people stuck doing multiple post-docs just to land a position at nowhereville state university. The pool of talented scientists is always going to remain constant-you cannot train someone to have scientific insight. If people really love the science they do they will stay the course-unfortunately this course now involves doing almost 10 years of post-graduate work before you can even apply for a faculty position.
While this might sound like a good idea to some of the techies out there, this is a nightmare for traditional fans. When I go to see the Giants at Pac Bell I want to see a Ball Game in the most beautiful ballpark in the US, not read my e-mail and surf. Now there are going to be a whole bunch of yuppies on their cell phones and laptops working during the game. I might just have to inadvertantly spill my beer to get them to stop working.
Amen
He has an BA from Amherst in lit and an MFA from University of Arizona. He has also been given one of the Macarthur Genius awards. I think his interest in math comes from the fact that his father is/was a professor of mathmatics at the University of Illinois. Currently he is teaching at Pomona College..Basically, he is a god in post-modern literature-read Infinite Jest if you want proof.
I am a huge DFW fan so you might consider my opinion to be slightly biased... Everything and more was a fantastic read even though I had to spend about half to the time going back to certain points in the text to understand his explainations and abreviations. Basically, it is a 300+ page essay on why Cantor's work on set theory was so important in the grand scheme of mathmatics and the way we percieve math. I only took the requisite 2 years of calculus in high school/college and I was able to understand all of DFW's main technical points. Despite the fact that the main topic is logic and math, DFW's unique style of writing shines through. If you enjoy Everything and More, try reading Infinite Jest-it is the Gravity's Rainbow of our generation.
The problem isn't really with the Telemeres per se, as the telomere knockout mice don't show a shortened life span in the 1st generation. The problem with cloning from ES cells is that the imprinted genes are all misregulated (here for the details http://www.sciencemag.org/cgi/content/full/293/552 7/95)
Basically, imprinting is the process by which the parents can pass down traits to their progeny through modification of the DNA itself without changing the actual sequence. This mode of inheritance is deemed epigenetic. We know very little about how epigenetic modifications happen or exactly how they control gene expression. Aside from all of the moral blather, this fact alone should keep us from even thinking about cloning humans.
Not so informed... We are not 50-75 years away from getting cells to change their DNA as you state. Researchers have been able to change the DNA sequence of mammalian ES cells by homologous recombination since the mid-eighties when the first "knock-out" mouse was made. Now people do it routinely and eloquently. The key dinstinction is that we cannot alter the DNA content of somatic cells in vivio very easily. Some groups have had limited success using viruses as vectors to introduce wild type versions of genes in the place of mutated copies, but this only works as long as the infected cells live and until the host's immune system responds to the virus. This was the case for chloride ion channel that is mutated in cystic fibrosis. It is rare that a single mutation in one gene is responsible for a given disease, most diseases like cancer are caused by multiple mutations. The next key breakthrough will be how these multiple lesions can be fixed in all of the afflicted cells in vivo.
You have a good point about the fact that we know very, very little about how all viruses function, but that is only a consequence of the fact that only a few have been beat to death by researchers. Take the lambda phage for example, is their anything we don't know about it? Where did that get us? To address your folding problem, we don't need to know the structure of every single protein in this minimal organism they want to create; we just need to know their FUNCTION. Granted whoever figures out the folding problem is going to be my hero, but I don't think that it will benefit manking more. This kind of rhetoric makes you sound like a structural biologist.
Are you high? When are you going to use a gram of a restriction enzyme? A unit of restriction enzyme costs about $.10(check the NEB catalogue www.neb.com) and you would use about five units to digest one microgram of DNA to completion(overkill). Anyone can afford restriction endonucleases. Learn your basic molecular before you start spouting off about it. (I suggest a dose of Maniatas)
Sorry Pal, but you're gonna get it. Single traits can be traced back to single genes, see just about every mouse knock out paper that has been done to date(yes, yes I know about background specific effects). Granted genes do work together to pattern extremely complex structures such as the brain; however, single genes have been demonstrated to be necessary for very specific structures and/or functions. This is the whole point of this Anthropologist's ramblings. A single mutation in the regulatory region of this gene could be responsible for "creativity". This single mutation is a lot easier to explain from an evolutionary standpoint then your gene network theory. Did every single gene in your imaginary network obtain a mutation at the same instant? It just doesn't make evolutionary sense. It is true that that there are many methods of genetic control and regulation that we just have no clue about, but that doesn't mean we should toss logic out the door. Non-biologists (anthropologists especially) should just keep quiet at this point
This is an interesting paper, but I have no idea why it made it into the mainstream press. The concept of using comparative genomics to identify ORFs is not novel; however, the results of using this tecnique on the mouse a human genomes are interesting. Now that we have the genomes of all of these organisms(mouse, human, fly, worm, fish coming soon) the largest obstacle is just sorting out the genes from all of the crap dna accumulated over the years. These researchers found a large group of genes that hadn't been previously identified by conventional methods designed for analyzing just one genome. They consequently confirmed their data by isolating the RNA from these genes by RT-PCR showing that they were at least transcribed. The highlight of the paper is the apparent lack of conservation beween the mammalian genomes and the fish(I think that they used fugu)as two-thirds of their "new" genes don't have homologues in the fish. Why this paper was in the news-I have no idea. Besides, the article was in PNAS!
I agree that the creation of a National Science Library is necessity. Unless you are under the aegis of a large university or sucessful professor, your access to scientific journals is severely limited. When I look up papers online I spend half the time chasing down a password for whatever journal its in. If you want to read anything published before 93 you are in an even deeper quagmire, as you pretty much have to have the hard copy on hand. The only journal that I know of that has made all of its issues available without charge online is PNAS(back to like 1903). If only scinece and nature could follow suit.