So then why was he showing you how to work a pager? (yes, apparently I was a lawyer in another life.)
That's okay, I'm accustomed to OCD-levels of indignant demands for detail --- I work in scientific programming.:-)
He was demonstrating how a pager worked (by phoning his own pager with my cell phone, entering the phone number after the beep, etc.), presumably so that the next time he wandered away for a few hours I could leave angry digits on his pager display.
As to why, I wish I knew. Personally, I would have rather spent those fifteen minutes back in the room with my wife to help with her pelvis-shattering contractions. It would have been nice if the doctor could also.:-P
I cannot follow your story. If you paged the doctor, why was he showing you how to work a pager? And how do you know that it rang only once?
Sorry, wasn't being very clear. What I heard upon phoning the pager number was a ring followed by a beep. There was no indication (such as, say, a recorded message) that I was supposed to enter a phone number (followed by the hash sign).
Not a particularly interesting story, perhaps, but on topic and true:-)
I had not realized that I've never actually had to call someone's pager before until my wife went into labor at three in the morning and I had to call the ob-gyn. The pager rang once and then beep! Silence. I'm confused, rattled, sleep deprived; I leave a message (words that will never find human ears) and phone the hospital. Get the switchboard operator to track the guy down.
While my wife's in labor, the ob-gyn actually has the whatsit to pull me aside and spend a solid fifteen minutes showing me how to work a pager.:-/
Incidentally, most of the physicians I work with have iPhones.
Steve Palumbi did this back in the mid-90's for whale and dolphin products being sold in commercial markets in Korea and Japan (Baker and Palumbi 1994 Science 265: 1538; Baker et al. 1995 Molecular Ecology 5:671). Essentially they went around the fish stalls taking samples and amplifying and sequencing them in their hotel room. From the latter article abstract:
This 'spot check' revealed a surprising variety of species for sale, including minke, fin and humpback whales and one or two species of dolphins sold as 'kujira' or whale. In the Korean survey, DNA amplifications were conducted by two of us (C.S.B. and F.C.) working with independent equipment and reagents. The two sets of DNA amplifications were returned to our respective laboratories and sequenced independently for cross-validation. Among the total of 17 species-specific sequences we found a dolphin, a beaked whale, 13 Northern Hemisphere minke whales (representing at least seven distinct individuals) and two whales which are closely related to the recognized sei and Bryde's whales but could not be identified as either using available type sequences. We suggest that these two specimens represent a currently unrecognized species or subspecies of Bryde's whale, possibly the so-called 'small-form' reported from the tropical waters of the Indo-Pacific.
Until these guys went out and actually did the sequencing, no one knew for sure how much illegal whaling activity was going on.
I work in AIDS research. The conflicts that are emerging in the field of malaria research are very similar to what we are experiencing in our field, which in both cases is a consequence of the severe funding bottleneck for biological sciences. The Gates Foundation has been an extremely important source of funding for basic science as well as providing resources for prevention and outreach in areas of the world suffering from the heaviest burden of these diseases. Unfortunately, the current funding philosophy seems to be to reward a massive sum of cash to a very select subset of scientists in the field.
This has created some unfortunate divisions in our field. If you can access the article, see:
http://www.nature.com/nm/journal/v13/n5/abs/nm0507-515.html
(I've also been able to Google for excerpts from the article.)
Basically, both the Gates Foundation and the NIH have pumped massive funding into a single research consortium, leaving many other labs scavenging for funding to sustain their clinical research. Throw in some questionable data-sharing practices and lack of scientific collaboration by the consortium, and you'll obviously create a lot of resentment.
It seems unusual to me that most of the rest of the genome displays much genetic diversity and yet the conservation of this particular region is interpreted as evidence of a population bottleneck. Strong selection at this site seems more consistent with this data than a past extinction, which should cause an overall paucity of sequence variation.
I can't find the article on PNAS so I can't figure out if the article is just reporting the results inaccurately. Does anyone have a link?
It's heartening to see HIV research being conducted in primate systems. Very little is understood about naturally-occuring resistence to HIV.
First of all, it is incorrect to think of the process of adaptation as approaching a static optimum (or "pinnacle"). The optimum changes with the environment; over geological scales of time, there can be novel demands imposed on the human species. This could take the form of microbial plague or global climatic change, for example.
Second, it is important to note that most other species are also at, or very close to meeting the current demands of the environment. The house fly is at its pinnacle of evolution to the same extent that one could make the statement of human evolution.
Finally, natural selection is part of, but not the entirety of, evolutionary change. Mutation and drift also constitute evolution. Thus, human evolution can never cease, regardless of whatever comforts technology may provide. Indeed, our own technology arguably presents another selective pressure on our species. The human enviroment is not necessarily natural.
It's worth noting that Dinococcus' DNA repair mechanism exists because life in a dessicated environment (e.g. dry soil) causes breaks in the DNA strand. Because of genetic redundancy mediated through possessing three copies of its genome, Dinococcus can reanneal its genome using intact segments from multiple strands. Thus, Dinococcus has not adapted to conditions of high levels of radiation as its tolerance of radiation might suggest.
It seems short-sighted to me for the Chinese government to be blocking various North American news sites while allowing unfettered access to a Web simply saturated with the visual viscera of our culture. Look at Beijing and Tokyo. The uniform of the next revolution, IMHO, is bleached hair, skater pants and Nikes. Punk DIY is just starting to grow under the glass towers of corporate Hong Kong. Let 'em keep the Times.
If I want the gene sequence to a well-characterised species (i.e. one for which there are molecular genetic studies), I can perform a search through the genome database at The National Center for Biotechnology Information and download the base pair sequence for free, in addition to any other sequences that it is evolutionarily related to.
Needless to say, this is a great benefit to biological work.
Given that all of these sequences were obtained by researchers at various universities and institutes, using equipment that is funded by their own grants, why is it that a company with similar equipment needs the sort of reimbursement we are discussing here?
Moreover, if genome sequence information from Joe Public is used in fruitful biomedical research, will he be reimbursed? The historical record suggests not. HeLa cells, for example, were obtained from a female cancer patient whose name is immortalised in the abbreviation "HeLa". They are a ubiquitous "study organism" in molecular genetic laboratories. But I have yet to hear of recompensation for her estate.
Of all the genes that are going to be characterised in our genome, we share a large proportion (I apologise for not having an exact figure here) with most other organisms including the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli. These latter genetic systems have been extremely well-characterised by extensive resesarch over the past decade or so. Thus, I suspect that to a large degree, much of what we will find in our genome will not come as any surprise.
What we have come to realise from what information is available is that most of the genetic variation that makes us biochemically, morphologically, and perhaps behaviourally different from one another is in the developmental regulation of these common genes. What is the more exciting aspect of the genome sequence is not each and every gene itself but the small sequences associated with, and perhaps even the spatial distribution of, these genes.
So the exciting discoveries will most probably not be in finding "the gene" for making one tall, but rather how patterns of developmental regulation -- in the varying spatial and temporal expression of a common pool of genes -- create variants in height.
This will require not a few, but rather thousands of genome sequences! I am waiting with bated breath for the technological advances in computing and mechanical power that will allow me to point a tricorder at each individual specimen and obtain a complete characterisation of its genome, contrasted with its phenotype (physical appearance). What's exciting is that this is in a sense already possible, with DNA chips that can measure the varying levels of transcription of each gene.
I have to concur with Ridley about one comment: This is a very exciting time to be in biology.
The article forgot to mention how useful this satellite imaging service is to ecological research. Quite understandable, really, since we tend to get slotted into the queue far below other "Big Money" science. There are many projects at our department, however, for which satellite-quality information of large-scale geographic patterns is very useful: for example, mapping out habitat (vegetation) availability and clinal variation of temperature, etc.
In fact, a good friend of mine in the Serengeti is using a different satellite technology (GIS -- sorry, but I forget what the acronym translates to) to study the foraging and dispersal behaviour of lions. The take home message is that this is REALLY useful stuff and that there are a lot of us that can't wait for more of those birds to go up.
When they specify the detection of a 1-metre square area, does this mean that a lawn chair would show up as a big honking off-white 1m2 pixel?
There's an interesting statement in the article regarding the sensory experience in raves and Ecstasy as "training for the Internet and virtual reality." Whereas training has usually been used to refer to media education as a preparation for new media -- insulating ourselves and being aware of extensions to our nervous system -- here it seems that ravers are preparing to become passive to the medium.
At some party I've mostly forgotten (no, it wasn't THAT good) I overheard a woman describing her trip to an unspecified region of Africa and encountering some natives. She showed them the cover of a magazine with a person's face on it; taking the magazine, they turned it over and around in puzzlement as if they did not understand what it was they should be seeing. This woman went on to make fairly derisive comments about these people but I suspect that their only shortcoming was not being trained to recognize the print and flat surface of the image on that magazine as a person's face.
Is it the case that younger generations increasingly exposed to drugs and raves can better appreciate virtual reality or the Internet?
"I've yet to read a theory explaining evolution which I feel has a substantial chance of being substantially correct." - Either you are referring to a subfield of evolution or you are simply not well-read on my discipline. What is your definition of evolution? I define it as "genetic change over time". I suspect however that you mean to use "evolution" to refer to macroevolutionary change, or speciation.
First of all, I want to make clear that there is a substantial body of theoretical work in evolutionary biology describing the generation and maintenance of genetic variation, game theory for the evolution of optimal behaviours, formation of secondary sexual characteres (e.g. plumage) by selection, the response to selection on multiple characters generated by a common set of genes...
So I hope that I have made my case that we are far from not having a "good theory of how evolution occurs"!
Now, speciation is a question that does have many unresolved matters. Some candidate theories include founder-flush theory, allopatric speciation, and resource competition and niche differentiation. Which of these are you familiar with?
I'm curious. What evolutionary theory fails to explain observed phenomena, predicts future phenomena and is not empirically testable? With the exception of amateur theories, there is a robust body of evolutionary theory that we continue to study and empirically verify in biology.
If a theory is presented in a journal that fails to explain empirical data and does not provide a means of verification, it does not succeed as a theory insofar as no one cares to study it. As a theoretical evolutionary biologist, I can tell you that we are very careful about meeting these criteria.
So the take home message is that those "theories" you may be referring to are ones that we don't take seriously, but that evolutionary theory as a discipline is quite vital!
Although the mutations of DNA are a molecular phenomenon and thus must be bound by whatever rules govern quantum mechanics, it does not follow that DNA can "sample multiple mutations simultaneously." A gene is with few exceptions required to be trascribed and, if the active gene product is not the mRNA transcript, translated into a protein. Only then is the mutation expressed via interactions with other proteins in biochemical and regulatory pathways. It is highly unlikely that DNA is "aware" that one mutation is more advantageous than another, especially within changing genomic contexts and environments! Such a conclusion is the frequent and unfortunate consequence of the phrase "X evolved to do Y", that effectively anthropomorphizes X into a living, thinking being. (I say anthropomorphise because human characteristics are often bestowed upon X as well!) It should be clear that the article contains a collection of facts from physics and then mis-applied into statements about biology. I don't seek to disagree that quantum mechanics may have very useful applications to computation and fundamental physics, but it is another ballgame altogether in evolutionary biology! I wish these chuckle-headed comments on my chosen discipline would please stop. It's very annoying when religious people shout in my face waving a pamphlet about the refutation of an entire body of science by two or three unrelated facts stuck together.
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So then why was he showing you how to work a pager? (yes, apparently I was a lawyer in another life.)
That's okay, I'm accustomed to OCD-levels of indignant demands for detail --- I work in scientific programming. :-)
He was demonstrating how a pager worked (by phoning his own pager with my cell phone, entering the phone number after the beep, etc.), presumably so that the next time he wandered away for a few hours I could leave angry digits on his pager display.
As to why, I wish I knew. Personally, I would have rather spent those fifteen minutes back in the room with my wife to help with her pelvis-shattering contractions. It would have been nice if the doctor could also. :-P
I cannot follow your story. If you paged the doctor, why was he showing you how to work a pager? And how do you know that it rang only once?
Sorry, wasn't being very clear. What I heard upon phoning the pager number was a ring followed by a beep. There was no indication (such as, say, a recorded message) that I was supposed to enter a phone number (followed by the hash sign).
Not a particularly interesting story, perhaps, but on topic and true :-)
I had not realized that I've never actually had to call someone's pager before until my wife went into labor at three in the morning and I had to call the ob-gyn. The pager rang once and then beep! Silence. I'm confused, rattled, sleep deprived; I leave a message (words that will never find human ears) and phone the hospital. Get the switchboard operator to track the guy down.
While my wife's in labor, the ob-gyn actually has the whatsit to pull me aside and spend a solid fifteen minutes showing me how to work a pager. :-/
Incidentally, most of the physicians I work with have iPhones.
Steve Palumbi did this back in the mid-90's for whale and dolphin products being sold in commercial markets in Korea and Japan (Baker and Palumbi 1994 Science 265: 1538; Baker et al. 1995 Molecular Ecology 5:671). Essentially they went around the fish stalls taking samples and amplifying and sequencing them in their hotel room. From the latter article abstract:
This 'spot check' revealed a surprising variety of species for sale, including minke, fin and humpback whales and one or two species of dolphins sold as 'kujira' or whale. In the Korean survey, DNA amplifications were conducted by two of us (C.S.B. and F.C.) working with independent equipment and reagents. The two sets of DNA amplifications were returned to our respective laboratories and sequenced independently for cross-validation. Among the total of 17 species-specific sequences we found a dolphin, a beaked whale, 13 Northern Hemisphere minke whales (representing at least seven distinct individuals) and two whales which are closely related to the recognized sei and Bryde's whales but could not be identified as either using available type sequences. We suggest that these two specimens represent a currently unrecognized species or subspecies of Bryde's whale, possibly the so-called 'small-form' reported from the tropical waters of the Indo-Pacific.
Until these guys went out and actually did the sequencing, no one knew for sure how much illegal whaling activity was going on.
I work in AIDS research. The conflicts that are emerging in the field of malaria research are very similar to what we are experiencing in our field, which in both cases is a consequence of the severe funding bottleneck for biological sciences. The Gates Foundation has been an extremely important source of funding for basic science as well as providing resources for prevention and outreach in areas of the world suffering from the heaviest burden of these diseases. Unfortunately, the current funding philosophy seems to be to reward a massive sum of cash to a very select subset of scientists in the field. This has created some unfortunate divisions in our field. If you can access the article, see: http://www.nature.com/nm/journal/v13/n5/abs/nm0507-515.html (I've also been able to Google for excerpts from the article.) Basically, both the Gates Foundation and the NIH have pumped massive funding into a single research consortium, leaving many other labs scavenging for funding to sustain their clinical research. Throw in some questionable data-sharing practices and lack of scientific collaboration by the consortium, and you'll obviously create a lot of resentment.
It seems unusual to me that most of the rest of the genome displays much genetic diversity and yet the conservation of this particular region is interpreted as evidence of a population bottleneck. Strong selection at this site seems more consistent with this data than a past extinction, which should cause an overall paucity of sequence variation.
I can't find the article on PNAS so I can't figure out if the article is just reporting the results inaccurately. Does anyone have a link?
It's heartening to see HIV research being conducted in primate systems. Very little is understood about naturally-occuring resistence to HIV.
First of all, it is incorrect to think of the process of adaptation as approaching a static optimum (or "pinnacle"). The optimum changes with the environment; over geological scales of time, there can be novel demands imposed on the human species. This could take the form of microbial plague or global climatic change, for example.
Second, it is important to note that most other species are also at, or very close to meeting the current demands of the environment. The house fly is at its pinnacle of evolution to the same extent that one could make the statement of human evolution.
Finally, natural selection is part of, but not the entirety of, evolutionary change. Mutation and drift also constitute evolution. Thus, human evolution can never cease, regardless of whatever comforts technology may provide. Indeed, our own technology arguably presents another selective pressure on our species. The human enviroment is not necessarily natural.
It's worth noting that Dinococcus' DNA repair mechanism exists because life in a dessicated environment (e.g. dry soil) causes breaks in the DNA strand. Because of genetic redundancy mediated through possessing three copies of its genome, Dinococcus can reanneal its genome using intact segments from multiple strands. Thus, Dinococcus has not adapted to conditions of high levels of radiation as its tolerance of radiation might suggest.
It seems short-sighted to me for the Chinese government to be blocking various North American news sites while allowing unfettered access to a Web simply saturated with the visual viscera of our culture. Look at Beijing and Tokyo. The uniform of the next revolution, IMHO, is bleached hair, skater pants and Nikes. Punk DIY is just starting to grow under the glass towers of corporate Hong Kong. Let 'em keep the Times.
If I want the gene sequence to a well-characterised species (i.e. one for which there are molecular genetic studies), I can perform a search through the genome database at The National Center for Biotechnology Information and download the base pair sequence for free, in addition to any other sequences that it is evolutionarily related to.
Needless to say, this is a great benefit to biological work.
Given that all of these sequences were obtained by researchers at various universities and institutes, using equipment that is funded by their own grants, why is it that a company with similar equipment needs the sort of reimbursement we are discussing here?
Moreover, if genome sequence information from Joe Public is used in fruitful biomedical research, will he be reimbursed? The historical record suggests not. HeLa cells, for example, were obtained from a female cancer patient whose name is immortalised in the abbreviation "HeLa". They are a ubiquitous "study organism" in molecular genetic laboratories. But I have yet to hear of recompensation for her estate.
Of all the genes that are going to be characterised in our genome, we share a large proportion (I apologise for not having an exact figure here) with most other organisms including the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli. These latter genetic systems have been extremely well-characterised by extensive resesarch over the past decade or so. Thus, I suspect that to a large degree, much of what we will find in our genome will not come as any surprise.
What we have come to realise from what information is available is that most of the genetic variation that makes us biochemically, morphologically, and perhaps behaviourally different from one another is in the developmental regulation of these common genes. What is the more exciting aspect of the genome sequence is not each and every gene itself but the small sequences associated with, and perhaps even the spatial distribution of, these genes.
So the exciting discoveries will most probably not be in finding "the gene" for making one tall, but rather how patterns of developmental regulation -- in the varying spatial and temporal expression of a common pool of genes -- create variants in height.
This will require not a few, but rather thousands of genome sequences! I am waiting with bated breath for the technological advances in computing and mechanical power that will allow me to point a tricorder at each individual specimen and obtain a complete characterisation of its genome, contrasted with its phenotype (physical appearance). What's exciting is that this is in a sense already possible, with DNA chips that can measure the varying levels of transcription of each gene.
I have to concur with Ridley about one comment: This is a very exciting time to be in biology.
The article forgot to mention how useful this satellite imaging service is to ecological research. Quite understandable, really, since we tend to get slotted into the queue far below other "Big Money" science. There are many projects at our department, however, for which satellite-quality information of large-scale geographic patterns is very useful: for example, mapping out habitat (vegetation) availability and clinal variation of temperature, etc.
In fact, a good friend of mine in the Serengeti is using a different satellite technology (GIS -- sorry, but I forget what the acronym translates to) to study the foraging and dispersal behaviour of lions. The take home message is that this is REALLY useful stuff and that there are a lot of us that can't wait for more of those birds to go up.
When they specify the detection of a 1-metre square area, does this mean that a lawn chair would show up as a big honking off-white 1m2 pixel?
There's an interesting statement in the article regarding the sensory experience in raves and Ecstasy as "training for the Internet and virtual reality." Whereas training has usually been used to refer to media education as a preparation for new media -- insulating ourselves and being aware of extensions to our nervous system -- here it seems that ravers are preparing to become passive to the medium.
At some party I've mostly forgotten (no, it wasn't THAT good) I overheard a woman describing her trip to an unspecified region of Africa and encountering some natives. She showed them the cover of a magazine with a person's face on it; taking the magazine, they turned it over and around in puzzlement as if they did not understand what it was they should be seeing. This woman went on to make fairly derisive comments about these people but I suspect that their only shortcoming was not being trained to recognize the print and flat surface of the image on that magazine as a person's face.
Is it the case that younger generations increasingly exposed to drugs and raves can better appreciate virtual reality or the Internet?
"I've yet to read a theory explaining evolution which I feel has a substantial chance of being substantially correct."
- Either you are referring to a subfield of evolution or you are simply not well-read on my discipline. What is your definition of evolution? I define it as "genetic change over time". I suspect however that you mean to use "evolution" to refer to macroevolutionary change, or speciation.
First of all, I want to make clear that there is a substantial body of theoretical work in evolutionary biology describing the generation and maintenance of genetic variation, game theory for the evolution of optimal behaviours, formation of secondary sexual characteres (e.g. plumage) by selection, the response to selection on multiple characters generated by a common set of genes...
So I hope that I have made my case that we are far from not having a "good theory of how evolution occurs"!
Now, speciation is a question that does have many unresolved matters. Some candidate theories include founder-flush theory, allopatric speciation, and resource competition and niche differentiation. Which of these are you familiar with?
I'm curious. What evolutionary theory fails to explain observed phenomena, predicts future phenomena and is not empirically testable? With the exception of amateur theories, there is a robust body of evolutionary theory that we continue to study and empirically verify in biology.
If a theory is presented in a journal that fails to explain empirical data and does not provide a means of verification, it does not succeed as a theory insofar as no one cares to study it. As a theoretical evolutionary biologist, I can tell you that we are very careful about meeting these criteria.
So the take home message is that those "theories" you may be referring to are ones that we don't take seriously, but that evolutionary theory as a discipline is quite vital!
Although the mutations of DNA are a molecular phenomenon and thus must be bound by whatever rules govern quantum mechanics, it does not follow that DNA can "sample multiple mutations simultaneously." A gene is with few exceptions required to be trascribed and, if the active gene product is not the mRNA transcript, translated into a protein. Only then is the mutation expressed via interactions with other proteins in biochemical and regulatory pathways. It is highly unlikely that DNA is "aware" that one mutation is more advantageous than another, especially within changing genomic contexts and environments! Such a conclusion is the frequent and unfortunate consequence of the phrase "X evolved to do Y", that effectively anthropomorphizes X into a living, thinking being. (I say anthropomorphise because human characteristics are often bestowed upon X as well!) It should be clear that the article contains a collection of facts from physics and then mis-applied into statements about biology. I don't seek to disagree that quantum mechanics may have very useful applications to computation and fundamental physics, but it is another ballgame altogether in evolutionary biology! I wish these chuckle-headed comments on my chosen discipline would please stop. It's very annoying when religious people shout in my face waving a pamphlet about the refutation of an entire body of science by two or three unrelated facts stuck together.