nothing "top tier" ever gets announced. Something becomes top tier because it proofs itself to be top tier.
Counter-example: PLoS Biology was announced as Top Tier, and became so. They made the journal attractive by the editorial board they recruited. This is what the backers of this new journal will do: between Max Planck, HHMI and Wellcome they can get any of the top biomedical researchers in the world lend their names to this journal.
Dreadful as it sounds,/. is closer to the optimal form of online journal than most online journals, which seem to be trying to emulate the limitations of paper journals as closely as possible. Given that everything is published (made public) in arxiv.org anyway,
Life scientists and medical researchers rarely, if ever, publish in arxiv.org (or have even heard of it), exactly because it is not peer-reviewed. This journal is for life science and biomedical research.
It is a fact that Israel is the new apartheid S. Africa with shades of Nazi Germany thrown in (like when the Israeli Jews got caught harvesting organs from Palestinian prisoners for Jewish transplantees-- Israel admitted to it, and "apologized", as if that makes it OK).
You may want to curb your blood-libel tall-tales a bit to make your antisemitism less obvious,
"What's actually going on is that Israel is forcing foreign scientists wanting to visit the Palestinian territories to travel through Israel, and then saying "oh, we made you come here, why don't you also give some lectures for free". Imagine the US used military force to keep international planes from landing in Canada and then asked foreign scientists diverted through the US to also give free talks in the US; it would be quite outrageous."
It would also be outrageous is Israel is doing it, which it isn't. I would ask you to find citations for that ever happening. And what is this about "Israel paying"? When a scientist is invited to speak at an academic institution the institution is paying. There is zero government involvement. There is also no involvement from other institutes, unless they are pooling resources for an event (say, a conference).
" 'No side trips' is a common condition for invited talks".
I am an associate professor and I have been invited to give hundreds of talks, at institutes and companies in the US and in many other countries. I have never heard of this "Common Condition".
At most I ask my paying hosts for accurate dates, telling them I will be travelling more. I have never encountered any kind of objection to that, nor a request to share the primary travel venue. Of course, I do not ask for extra travel or Room & Board for the "side" travels.
"Apparently, Israel isn't interested in that."
Again what is "Israel" the university of Tel Aviv? The University of Haifa (which, BTW, in which the majority of students are Palestinians)? The Israeli Immigration authorities? The Mossad? El-Al?
Actually, it does not refute anything. HGT has been known to exist for a long time in all of life's kingdoms, and has no impact on the Theory of Evolution. It is yet another genetic variety generating mechanism, on top of sex. The authors provide a very plausible mechanism to explain how the gene got fixed in the population.
BTW, if you don't believe in evolution, how can you on the one hand accept their inference of HGT which is based on evolutionary considerations (sequence similarity and homology), but on the other hand claim that the conclusion from that inference is that evolution is wrong. that's like saying that You calculate the area of a circle using Pi=3.14, and then claim that Pi=3.5. Doesn't make sense.
"Philosophers, incidentally, say a great deal about what is absolutely necessary for science, and it is always, so far as one can see, rather naive, and probably wrong. For example, some philosopher or other said it is fundamental to the scientific effort that if an experiment is performed in, say, Stockholm, and then the same experiment is done in, say, Quito, the same results must occur. That is quite false. It is not necessary that science do that; it may be a fact of experience, but it is not necessary. For example, if one of the experiments is to look out at the sky and see the aurora borealis in Stockholm, you do not see it in Quito; that is a different phenomenon. 'But,' you say, 'that is something that has to do with the outside; can you close yourself up in a box in Stockholm and pull down the shade and get any difference?' Surely. If we take a pendulum on a universal joint, and pull it out and let go, then the pendulum will swing almost in a plane, but not quite. Slowly the plane keeps changing in Stockholm, but not in Quito. The blinds are down too. The fact that this happened does not bring on the destruction of science. What is the fundamental hypothesis of science, the fundamental philosophy? We stated it in the first chapter: the sole test of the validity of any idea is the experiment."
-- (Lecture 2, Basic Physics, from the Feynman Lectures on Physics)
While this is extremely interesting, we need a link to the actual journal article, or to some source material, not just a link to a blog. Without that we can only assume this is an attempt to turf slashdot to drive traffic to your blog and generate ad revenues.
1) The blog has no ads
2) The links to the original article are in the end of the post
3) How do you expect to understand an article in a scientific journal, when your reading skills are so obviously lacking as to not notice (1) and (2)
The National Institutes of Health annual budget: $29 billion. That money funds most of the university biomedical research in the US
http://www.nih.gov/about/budget.htm
Current NIH funded projects include among other things the human genome, the human microbiome, almost all cancer research in the US, obesity, diabetes, communicable diseases..
The National Science Foundation has an extramural grant budget of $6 billion.
The Department of Energy has an extramural research grant budget of $24 billion Among other things they fund alternative energy research, genomic research,
You might say the US federal government should be funding more, but you cannot say it is not funding anything at all.
The space race and the Manhattan project were both driven by wars: WWII and the Cold War. Maybe that is what it takes for a government to fund major research: fear of losing power and primacy to an opponent.
Indeed, and this is an understatement. I've been told that the reason dogs can track you by smell is not so much that your OWN cells produce a unique smell, it's more that they're actually smelling your unique bacterial garden growing on your body. Which is also why they need fairly fresh clothing or scent, it changes over time. Another interesting tidbit I was told in microbiology class: every time you made out with someone, you probably picked up new SPECIES of bacteria in your mouth. Of course, he was talking to a classroom of college students, maybe that's not true for dating in a senior center.
Note that I'm not saying that I myself have so much as wiki'd this information. But if this is new knowledge, I've been massively lied to.
True. But the thought was that every human would have a core microbime, at least in the gut. Even if there were variances between people, and within the same person over time. But it appears to be that there is no set of core species.
Also, you're talking about skin, somewhat different story given that there is a lot less symbiotic and interlinked metabolic activity going on there, so a lot less need of "social engineering" of bacteria.
But I would think you could get a person's DNA from a stool sample (although I wouldn't want to.) Your body sheds a very large number of intestinal cells every day. There's more bacteria, but there's still billions of your own cells, many with your DNA still intact.
Yes, in this case you could use human-specific primers to amplify only the shedded human intestinal cells that are in the feces.
Common knowledge you can find in most microbiology or immunology textbooks.
Quite the opposite. What you would find in most textbooks is the assumption that there is a core human gut microbiome common to whole human populations. The Nature article refutes this. There are millions of $ being put into sequencing the human core gut microbes, but apparently there are no core gut microbes, and this human microbiome sequencing strategy needs rethinking.
Actually, no, the "science" in junkdna.com, is, well, junk. Also, junk DNA was for the past 20 years a tongue-in-cheek misnomer. It was basically known that we don't know what those regions do,although it was well agreed that some portion of them was functional.
Can someone explain what genome sequencing actually does? Does it "simply" give you a complete description of the base pairs of someone's DNA?
Yes. Actually, even less than that. "Shotgun" sequencing give you a collection of random seqeunces of base pairs, ~1,000 BP long. You need quite a few of those to reassmeble the human genome, computationally.
Or is it a little more complicated than that, telling you where the individual genes begin and end? What information can you derive when you know the sequence of all the base pairs?
To determine that, you need to perfomr a computational analysis on the assembled (see above) genome. Gene prediction algorithms are relatively relaible, although there is room for improvement and error reduction.
You can derive a lot of information, depending on how sophisticated the algorithms that your use are, and how much of an error margin you allow yourself: the beginning and end of genes, region that control gene transcription (that's copying DNA to RNA) and gene translation (that's RNA to protein), alternative splicing (differnt transcripts of the same gene). Once you have your translated protein sequences, you can do a lot more with that: predict their 3D atomic structure, look for similar proteins in other organisms, discover rates of evolution, detect hidden viruses in the genome, locate disease causing mutations....
Note to flash guy: you're an ass and a publicity hound.
(1) Your game has a URL tag on it, so it's impossible for fuddrucker's to represent it as their own.
Yet they did. Nota bene: not everyone is as sophisticated as a/.r. Most people do not realize that a different URL tag means someone else created it. And they cannibalized it for their own gain
(2) Fuddrucker's accounted for only a small portion of total hits, and yet you're complaining about the bandwidth usage?
His bandwidth, it's his to complain about. Fuddruckers should pay him for that portion. Or at least ask nicely.
(3) Despite the evidence that the link was not particularly stressful nor malicious in any way, you went way out of your way to do something incredibly malicious back.
Plagiarism and stealing bandwidth. They could have asked nicely AND did a better job of giving credit.
Plagiarism for profit purposes is greedy, shows undue pride, obviously Fuddrucker's web designer was envious of the Flash programmer's skill, but too slothful to acquire or implement them. Four deadly sins right there.
Slashdot Mirror
If you look at the figures, you'll see that the IEA-evidenced annotations outperform the curated ones.
This is no science journalism. It's the site of the International Society of Biocuration. which has about 1500 members to date. http://colleagues.biocurator.org/affiliations it's too bad that you are ignorant of the field: http://www.ploscollections.org/article/browseIssue.action?issue=info%3Adoi%2F10.1371%2Fissue.pcol.v03.i05
You must not be reading th etop journals in the field: http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020142
http://biocurator.org/what.shtml
nothing "top tier" ever gets announced. Something becomes top tier because it proofs itself to be top tier.
Counter-example: PLoS Biology was announced as Top Tier, and became so. They made the journal attractive by the editorial board they recruited. This is what the backers of this new journal will do: between Max Planck, HHMI and Wellcome they can get any of the top biomedical researchers in the world lend their names to this journal.
Dreadful as it sounds, /. is closer to the optimal form of online journal than most online journals, which seem to be trying to emulate the limitations of paper journals as closely as possible. Given that everything is published (made public) in arxiv.org anyway,
Life scientists and medical researchers rarely, if ever, publish in arxiv.org (or have even heard of it), exactly because it is not peer-reviewed. This journal is for life science and biomedical research.
This would be primarily an experimental biology journal. So not exactly feasible to reproduce experiments within the reviewing time/budget.
You may want to curb your blood-libel tall-tales a bit to make your antisemitism less obvious,
"What's actually going on is that Israel is forcing foreign scientists wanting to visit the Palestinian territories to travel through Israel, and then saying "oh, we made you come here, why don't you also give some lectures for free". Imagine the US used military force to keep international planes from landing in Canada and then asked foreign scientists diverted through the US to also give free talks in the US; it would be quite outrageous."
It would also be outrageous is Israel is doing it, which it isn't. I would ask you to find citations for that ever happening. And what is this about "Israel paying"? When a scientist is invited to speak at an academic institution the institution is paying. There is zero government involvement. There is also no involvement from other institutes, unless they are pooling resources for an event (say, a conference).
" 'No side trips' is a common condition for invited talks".
I am an associate professor and I have been invited to give hundreds of talks, at institutes and companies in the US and in many other countries. I have never heard of this "Common Condition".
At most I ask my paying hosts for accurate dates, telling them I will be travelling more. I have never encountered any kind of objection to that, nor a request to share the primary travel venue. Of course, I do not ask for extra travel or Room & Board for the "side" travels.
"Apparently, Israel isn't interested in that."
Again what is "Israel" the university of Tel Aviv? The University of Haifa (which, BTW, in which the majority of students are Palestinians)? The Israeli Immigration authorities? The Mossad? El-Al?
Actually, it does not refute anything. HGT has been known to exist for a long time in all of life's kingdoms, and has no impact on the Theory of Evolution. It is yet another genetic variety generating mechanism, on top of sex. The authors provide a very plausible mechanism to explain how the gene got fixed in the population. BTW, if you don't believe in evolution, how can you on the one hand accept their inference of HGT which is based on evolutionary considerations (sequence similarity and homology), but on the other hand claim that the conclusion from that inference is that evolution is wrong. that's like saying that You calculate the area of a circle using Pi=3.14, and then claim that Pi=3.5. Doesn't make sense.
"Philosophers, incidentally, say a great deal about what is absolutely necessary for science, and it is always, so far as one can see, rather naive, and probably wrong. For example, some philosopher or other said it is fundamental to the scientific effort that if an experiment is performed in, say, Stockholm, and then the same experiment is done in, say, Quito, the same results must occur. That is quite false. It is not necessary that science do that; it may be a fact of experience, but it is not necessary. For example, if one of the experiments is to look out at the sky and see the aurora borealis in Stockholm, you do not see it in Quito; that is a different phenomenon. 'But,' you say, 'that is something that has to do with the outside; can you close yourself up in a box in Stockholm and pull down the shade and get any difference?' Surely. If we take a pendulum on a universal joint, and pull it out and let go, then the pendulum will swing almost in a plane, but not quite. Slowly the plane keeps changing in Stockholm, but not in Quito. The blinds are down too. The fact that this happened does not bring on the destruction of science. What is the fundamental hypothesis of science, the fundamental philosophy? We stated it in the first chapter: the sole test of the validity of any idea is the experiment." -- (Lecture 2, Basic Physics, from the Feynman Lectures on Physics)
While this is extremely interesting, we need a link to the actual journal article, or to some source material, not just a link to a blog. Without that we can only assume this is an attempt to turf slashdot to drive traffic to your blog and generate ad revenues.
1) The blog has no ads 2) The links to the original article are in the end of the post 3) How do you expect to understand an article in a scientific journal, when your reading skills are so obviously lacking as to not notice (1) and (2)
The National Institutes of Health annual budget: $29 billion. That money funds most of the university biomedical research in the US http://www.nih.gov/about/budget.htm Current NIH funded projects include among other things the human genome, the human microbiome, almost all cancer research in the US, obesity, diabetes, communicable diseases.. The National Science Foundation has an extramural grant budget of $6 billion. The Department of Energy has an extramural research grant budget of $24 billion Among other things they fund alternative energy research, genomic research, You might say the US federal government should be funding more, but you cannot say it is not funding anything at all. The space race and the Manhattan project were both driven by wars: WWII and the Cold War. Maybe that is what it takes for a government to fund major research: fear of losing power and primacy to an opponent.
Quite an accepted term, really. The first google page provides you with two journals having biomedicine in their titles, from Wiley and Elsevier.
Indeed, and this is an understatement. I've been told that the reason dogs can track you by smell is not so much that your OWN cells produce a unique smell, it's more that they're actually smelling your unique bacterial garden growing on your body. Which is also why they need fairly fresh clothing or scent, it changes over time. Another interesting tidbit I was told in microbiology class: every time you made out with someone, you probably picked up new SPECIES of bacteria in your mouth. Of course, he was talking to a classroom of college students, maybe that's not true for dating in a senior center.
Note that I'm not saying that I myself have so much as wiki'd this information. But if this is new knowledge, I've been massively lied to.
True. But the thought was that every human would have a core microbime, at least in the gut. Even if there were variances between people, and within the same person over time. But it appears to be that there is no set of core species. Also, you're talking about skin, somewhat different story given that there is a lot less symbiotic and interlinked metabolic activity going on there, so a lot less need of "social engineering" of bacteria.
Every man is an island
and obviously, the summary was written in the 40s, before feminist criticism of language became familiar to the mainstream.
Obviously, you did not recognize the John Donne reference.
But I would think you could get a person's DNA from a stool sample (although I wouldn't want to.) Your body sheds a very large number of intestinal cells every day. There's more bacteria, but there's still billions of your own cells, many with your DNA still intact.
Yes, in this case you could use human-specific primers to amplify only the shedded human intestinal cells that are in the feces.
Yeah, but can they land it in the Hudson?
Common knowledge you can find in most microbiology or immunology textbooks.
Quite the opposite. What you would find in most textbooks is the assumption that there is a core human gut microbiome common to whole human populations. The Nature article refutes this. There are millions of $ being put into sequencing the human core gut microbes, but apparently there are no core gut microbes, and this human microbiome sequencing strategy needs rethinking.
So, is it possible to uniquely identify someone say by their shit?
No, because the composition of your shit changes over time. RTFA. You are an island, but with a huge population migration turnover rate.
Actually, no, the "science" in junkdna.com, is, well, junk. Also, junk DNA was for the past 20 years a tongue-in-cheek misnomer. It was basically known that we don't know what those regions do,although it was well agreed that some portion of them was functional.
Can someone explain what genome sequencing actually does? Does it "simply" give you a complete description of the base pairs of someone's DNA? Yes. Actually, even less than that. "Shotgun" sequencing give you a collection of random seqeunces of base pairs, ~1,000 BP long. You need quite a few of those to reassmeble the human genome, computationally. Or is it a little more complicated than that, telling you where the individual genes begin and end? What information can you derive when you know the sequence of all the base pairs? To determine that, you need to perfomr a computational analysis on the assembled (see above) genome. Gene prediction algorithms are relatively relaible, although there is room for improvement and error reduction. You can derive a lot of information, depending on how sophisticated the algorithms that your use are, and how much of an error margin you allow yourself: the beginning and end of genes, region that control gene transcription (that's copying DNA to RNA) and gene translation (that's RNA to protein), alternative splicing (differnt transcripts of the same gene). Once you have your translated protein sequences, you can do a lot more with that: predict their 3D atomic structure, look for similar proteins in other organisms, discover rates of evolution, detect hidden viruses in the genome, locate disease causing mutations....
yet this tiny band was blowing up warships and taking out hundreds of Merkavas
"Tiny band": estimated 3,000 regulars + 10,000 reserves. Not exactly "tiny" by Middle Eastern standards
"hundreds of merkava tanks": 14
"blowing up warships": one ship was damaged and towed for repairs. Hardly blown up, definitely not in the plural
I must congratulate you on managing to compress so many lies into a singe sentence....
more like 99....
(1) Your game has a URL tag on it, so it's impossible for fuddrucker's to represent it as their own.
Yet they did. Nota bene: not everyone is as sophisticated as a /.r. Most people do not realize that a different URL tag means someone else created it. And they cannibalized it for their own gain
(2) Fuddrucker's accounted for only a small portion of total hits, and yet you're complaining about the bandwidth usage?
His bandwidth, it's his to complain about. Fuddruckers should pay him for that portion. Or at least ask nicely.
(3) Despite the evidence that the link was not particularly stressful nor malicious in any way, you went way out of your way to do something incredibly malicious back.
Plagiarism and stealing bandwidth. They could have asked nicely AND did a better job of giving credit.
Plagiarism for profit purposes is greedy, shows undue pride, obviously Fuddrucker's web designer was envious of the Flash programmer's skill, but too slothful to acquire or implement them. Four deadly sins right there.