In California a year or three ago one of the major grocery store chains was slapped with a class action lawsuit and lost, IIRC. They were just ringing items up slightly wrong, like collard greens as the more expensive kale (happened to me. Twice. I don't shop at that chain anymore) or $.99 instead of $.79 for misc. food in a can, small stuff, stuff you probably don't notice 99% of the time. Spread it out across a year, they could screw customers out of maybe $100 each. Multiply that by however many people you've got buying groceries at your stores and that's a lot of "revenue."
This is so much less nasty than the old way--a number of years ago I had to get my upper GI (mouth to small intestine) checked out and had a more old-fashioned proceedure done. That is, the camera was on a cable about as big around as standard coax cable. The cable was coated with novocane and shoved up my left nostril and down my throat, through the stomach and into the small intestine, about 25 feet worth in all. It was an especially unpleasant experience, but at least the cable didn't have to go the other way...
It also involved choking down about two quarts of a barium sulfate "milkshake," which was extremely dense. After the proceedure was over I was initially confused why the doctor asked how long it would take for me to get home from the hospital. It was much clearer to me why when I got home and made a dash for the can. Extremely dense, that milkshake was!
The lab that I work in has engineered a variant of green fluorescent protein (GFP) that is pH sensitive (I had nothing to do with the project, mind you). It responds to pH by varying the ratio of green to blue fluorescence, but the blue state is fairly dim. This means that it is difficult to tell the pH as cells have natural autofluorescence in the blue and to a lesser extent in the green ranges of the visible spectrum, making it difficult to pick out the fluorescence from the pH-sensing GFP. So making a pHish isn't feasible, yet.
That's their PR department talking. On their science page we get this little bit of information: "So far, the researchers have succeeded in isolating two types of gene promoters in the zebra fish -- an estrogen-inducible promoter and a stress-responsive promoter. These promoters have been used to drive the fluorescent colour genes in transgenic zebrafish. Such fluorescent-coloured transgenic fish will be able to respond to the presence of chemicals like oestrogen through the estrogenic promoter and heavy metals and toxins through the stress-responsive promoter. The fish will immediately display the colour depending on the type of environment the colour has been specified for." So the organism has to be in an environment that produces a stimulus inducing the production of red fluorescent protein*, ie either estrogen or something that hits the stress-response promoter. Otherwise the zebrafish has its natural color (which is pretty anyway--I have some in my aquarium). The red fluorescent zebrafish that the company is offering for sale are always expressing the red fluorescent protein, which means that it is under the control of a different promoter and not useful as a pollution (or estrogen) detector in any way. Which means that these guys intentionally produced a GM novelty that is useless for science.
* The red fluorescent protein is almost certainly DsRed aka drFP583, isolated from Discosoma sp. red, a sea anemonie. There are only 45 or 46 genes out there that have been cloned that are members of the GFP (green fluorescent protein) family, ie proteins having the same 3D fold and sequence similarity. Of these 46, only 3 or 4 are red with DsRed being the most commonly used in molecular biology. Most are green, one yellow, at least one cyan, and some others while brilliantly colored are nonfluorescent.
There's a reason for the quotation marks. The researchers did obtain a movie of sorts, in that they repeated their basic experiment to get different timepoints in the melting process. However the frames making up the movie are electron powder diffraction (EPD) images. What you get is basically a pattern of rings centered like a bullseye, and the spacings between the different rings can tell you information about the material like how the atoms are configured. Put in the time component from several images and you can get (in this instance) a "movie" of aluminum melting.
I tried to find a free EPD image, but the closest thing I found was xray powder diffraction, with fake color--what you get from a diffraction image is greyscale. Anyway, it's a similar experiment, except the material is bombarded with xrays instead of electrons.
But seriously, food science is still science. The happiest research chemist I ever met was the guy who develops new flavors of gummy bears. However, it's still at best highly questionable that any real research is done by Japanese (or whoever) whaling.
I've never heard of the show until today, but it sounds cool. I'm especially interesting in the tree cannon, since my roommate made a sort of tree missile using six or seven sticks of dynamite and a ~60 ft doug fir (ahh...to be young and stupid in rural Montana), and I've heard of Survival Research Lab's Pitching Machine which chucks 6 ft long 2x4's up to 800 feet, but a tree cannon sounds like something different. Unfortunately a brief googling didn't seem to turn up anything.
The six genes specifying the utilization of L-fucose as a carbon and energy source are known as the "fuc" genes. Among them is L-fuculose kinase, also known as "fucK." The abstract of the paper where the genes were cloned (and I think named) can be found on PubMed.
Many more young people than you might think have cancer, and it's typically not due to HIV. I've had the unfortunate experience of visiting my 20-something brother in the cancer ward (he got better, thankfully) and there was a surprisingly large fraction of people there who had cancer and were 30 or younger. At a page at the CDC, I found in the Summary Health Statistics for U.S. Adults, 1999, table 5 (don't download--8 MB!) that the percent of cancer among adults age 18-44 is a whopping 1.9%, far more than at that age who have HIV. For comparison, the other age brackets: 45-64 7.9%, 65-74 17.4%, 75+ 22%. That's for cancer of some kind, but some kinds of cancer strike primarily at specific age groups. My brother's Hodgkin's disease, a lymphoma, typically strikes men in their mid to late twenties. Leukemia also frequently strikes the young, for example the incidence of Acute Lymphocytic Leukemia (ALL) is 10 times greater for the 1-4 years old bracket than the for those in their early 20's. The point being cancer's not just for the very old, or rather that some cancers aren't.
Robert Park's a University of Maryland Physics professor (emeritus? on leave?), Director of Public Information, Washington Office of the American Physical Society and writer of the American Physical Society's weekly What's New column, and is the author of "Voodoo Science: The Road From Foolishness to Fraud." You can download his CV here , and it will basically tell you he's a scientific somebody.
Most of this is correct, except that cellulose is actually a polymer made up of glucose. More specifically, cellulose is beta(1,4)-linked glucose. This online lecture has a picture of cellulose both as a linear chain and as how linear chains can form a more complex sheets (not pictured: the sheets can then stack). We can't use cellulose because we don't have cellulase, a series of enzymes that can hydrolyze the chain. It's been a while, but I think it pops off glucose pairs, not monomers but I could be mistaken.
All comments about the Stryker aside, maybe the Army's trying to learn something from the Navy. I'd like to think that leaving the cruiser USS Yorktown dead in the water for 2 1/2 hours due to a divide by zero error would motivate a switch from microsoft to something more robust. I'd also like to think asses of the dimbulbs in charge are still smarting from the cornholing courtmartial they received, but they probably got promoted instead.
2003 saw the first scientifically reported incidence of a whale flatulence. A picture and writeup can be found here. Warning: the picture caption is bound to induce fits of giggles in young children...or people like me who still find poop jokes funny.
Pity you couldn't get that article; it was really a fun read with a truly massive bibliography. If you were taught that the Miller-Urey experiment was proof of evolution, then your organic chemistry teacher was either wrong or you misunderstood. At any rate, this is the only example I have ever heard of. Still, the challenge remains: find me a textbook which claims that Miller-Urey is proof of evolution.
"Indeed physics and chemistry are deterministic - they go where the Gibb's free energy dictate they go. Which is why polypeptides don't spontaneously form."
So if you know this, then why make a comment you know to be false, ie chemistry being non-deterministic? Besides, polypeptides do spontaneously form under certain conditions. There is nothing special about an organism or the enzymes and ribozymes it uses to make this happen. It's all still the same chemistry. On a closely related note, I just found this really neat article by Stuart Kauffman (okay, it's just an editorial blurb in Nature on the actual article, Nature vol 382 pg 525-528 (1996) sadly not available online or I'd link it) on a 32-amino acid polypeptide that can autocatalyse its own synthesis by accelerating the condensation of 15- and 17-amino acid fragments in solution. I wonder what's been found in the six years since that was published?
"Aside from chlorophyll, where does adding sunlight produce anything but decay?"
There is nothing special or unique about chlorophyll. You add light or energy of some kind to a system, you (may) get some change. For light, you may get degradation of a compound if it has a photolabile group, you may get isomerization about a chemical bond, or fluorescence, or a change of phase, or drive some anabolic reaction. Photochemistry's a hopping field of study: just google "light polymerization" for one example that's especially topical. I myself had no idea that there was so much out there, commercial light polymerizers and all!
"I have read far more on the topic than the abstract you mention, it's just typical of the work in the field (probably why you selected that one)."
Yet you've also been trying to use a number of old creationist chestnuts which suggests either the abiogenesis material you've read is badly out of date or is written solely by creationists. Spend an afternoon on the talkorigins abiogenesis pages--what have you got to lose?
"You seem to understand fundamentals of chemistry - work out the equilibrium constant of a moderate sized protein in an aqueous solution, given the energy of peptide bonds for a selection of amino acids. Figure it out to 150 or 200 proteins in the peptide. I could give you the answer but working it out yourself you may learn something significant. "
Well, I would like to think that I haven't wasted the last decade I've spent studying biochemistry and chemistry. But far from informative and speaking of creationist chestnuts, I suspect what you're asking me to do is one of the classics. You want me to sit down and calculate the odds of a peptide forming--a specific length, a specific sequence, from a pool of amino acids, at random. In the abiogenesis link that I provided in my first post in this thread is ample description of why this argument is fallacious, right up at the top under the heading "Problems with the creationists' "it's so improbable" calculations."" You can't miss it--they even talk about the same 32-mer autocatalytic protein that I found just by googling around, and the page links to more examples of similar autocatalytic proteins! Wow. SunY looks really interesting.
" I brought up Miller-Urey because that discredited experiment is still taught so widely that many folks here cite it as proof, since it's what they were taught was proof of evolution. It's nice to talk with someone who is beyond that."
Miller-Urey is in textbooks, but it is not used as "proof" of evolution and never has been. Neither have I ever seen anyone here attempt to use it as "proof" of evolution. The experiment shows that it is possible for a very simple system resembling conditions found on a prebiotic earth to generate relatively complex molecules. This is how it has been treated in all of my old undergrad biology and biochemistry textbooks and I challenge you to find a recent textbook that does treat the Miller-Urey experiment as "proof" of evolution.
"That article at the Royal Society (at least from its abstract, the article is not freely available for a couple of years it looks like)"
I don't think my university has a site license, but I may be wrong. Try this link--it is to a.pdf of the article directly--warning it is fairly large.
"The key point that is never addressed in any papers I'm aware of is that in order to get to an accurately reproducing cell where natural selection could take over and exert an effect on reproduction..."
This is due to a misunderstanding on your part. Natural selection could act on something as simple as an imperfect self-replicating system that is subject to some environmental pressure to provide something for selection. A cell is not explicitly required.
"Yet simple probstat will show you that any non-deterministic reaction or process will tend toward the mean, toward increasing entropy."
Except that physics and chemistry are not random, they are deterministic. If I spark a mix of hydrogen and oxygen, we all know that we'll get water. A good work on self-ordering chemistry that is also topical to the issue of the orgin of life is "The Origins of Order: Self-Organization and Selection in Evolution" by Stuart A. Kauffman. Second, entropy can of course be overcome by adding additional energy to the system; this is how a freezer works.
"Until the RNA stage, there is no possible high-fidelity reproduction mechanism."
This is not true. Google "Cairns-Smith" or "Kauffman" with "self-replication" or read the talkorigins page I linked in my previous post and some of the references therein.
"And in the early earth (by current theories) there was not a superabuncdance of O2, hence there was not a strong ozone layer, and there was a lot of hard UV around. That alone would tend to break up any long chain molecules, if the temperature and other reactants didn't get in the way."
High levels of molecular oxygen in an atmosphere is thought to be indicative of life, and as such would not be present in any quantity on a prebiotic earth. Geologic evidence supports the notion that the earth started off with a reducing or at least non-oxidizing atmosphere, as the first evidence of an oxidizing atmosphere (such as iron oxide deposits) occur in rock no younger than about 2.5 billion years old. However, ozone is not the only compound that can block UV. For example, water is a good UV blocker, and the abstract of the paper I linked makes it clear that the author's view is that life arose in or around hydothermal vents, which is to say underwater (the first ocean is believed to have condensed ~4.4Gya). From the abstract: "The universal ancestor we infer was not a free-living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occured. The first free-living cells are suggested to have been eubacterial and archaebacterial chemoautotrophs that emerged more than 3.8 Gyr ago from the inorganic confines." Which is to say that the authors vie
I've read articles by Behe and Dembski and was not favorably impressed. Behe and Dembski are not taken seriously by the scientific community for that matter either. For example, read Nature's review of Behe's "Darwin's Black Box" (Nature 1996, Volume 383, pages 227-228, available pay-only from them, but freely available here). Another review that is available online is from the National Center for Science Education--the premier science education body in the USA. Naturally, both it and Nature (and, well, science in general) are firmly in the evolutionists' camp. You've probably heard it before, but why not give talkorigins a try? They have their own pages on Behe and Dembski as well.
Depending on how recent the source and who you talk to, Coelacanth is a name belonging to either a genus or a family, not just one species. There are ~125 species identified from fossils alone, which are used as index fossils; this is not a problem since they are morphologically distinct from each other and the modern coelacanth species.
Abiogenesis has moved on in the 50 years since Miller-Urey. Might I suggest reading a recent article: "On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells," it can be found here, just click journals, then Vol 358, January, then pg 59, freely available in.pdf or.svg format. I'd give the link there directly, but the Royal Society doesn't do that for some reason. Anyway, the article and the references contained therein might get one up to speed. A more tractable account of modern abiogenesis research is available on talkorigins' own website as well.
Actually, $1500 per article isn't all that bad. Not too long ago I got a paper published. It cost $350 per figure, plus a charge for the first 10 pages (that I now forget) and then an additional charge for pages past the first ten. The total cost of publication for the lab for my paper was well over $2000.
I did some more looking around the Nobel website while responding to some posts and found this gem in the Statues of the Nobel Foundation: " 10.
No appeals may be made against the decision of a prize-awarding body with regard to the award of a prize.
Proposals received for the award of a prize, and investigations and opinions concerning the award of a prize, may not be divulged. Should divergent opinions have been expressed in connection with the decision of a prize-awarding body concerning the award of a prize, this may not be included in the record or otherwise divulged.
A prize-awarding body may, however, after due consideration in each individual case, permit access to material which formed the basis for the evaluation and decision concerning a prize, for purposes of research in intellectual history. Such permission may not, however, be granted until at least 50 years have elapsed after the date on which the decision in question was made."
So in 50 years Damadian and his supporters might be able to find out exactly what criteria the prize committee used to award the Physiology or Medicine prize to Lauterbur and Mansfield but not to Damadian, but they'll never be able to appeal that decision.
"Q. Has X been nominated as a candidate for the Nobel Prize? Where do I find a list of Nobel Prize nominees?
A. According to the Statutes of the Nobel Foundation, nominators must not make public the names of the nominees nor inform nominees privately of the proposals. Even invitations to propose names are confidential. Proposals received for the award of a prize, and investigations and opinions concerning the award of a prize may not be divulged. The names of the nominees are classified as confidential information for at least fifty years."
Damadian might have had an idea of whether or not he was up for one through a scientific rumor mill, but it is clear by the rules governing the awarding of a Nobel prize that he does not now know and will not know for another 50 years 100% for certain whether or not he was nominated.
Awarding of a Nobel, as another poster has already mentioned, is not necessarily awarded to the first person who came up with an idea--a Nobel and being credited with being first are simply not the same. My beefs with Damadian are that he falsely claims that MRI wouldn't exist without him, indeed Lauterbur's 1973 paper doesn't even mention Damadian's work and even Damadian's supporters must conceed that the idea of MRI was conceived independently by Damadian and Lauterbur. Also it isn't up to Damadian whether or not he gets the Nobel for his work on MRI, it is solely up to the committee that awards the Nobel. While there is precedence for awarding the Nobel to persons who have greatly advanced the field and at the same time not granting the Nobel to the first person to publish on it, there is no precedence for someone getting added to a prize after it has already been awarded. While I have sympathy for Damadian and find his being left off the prize questionable, I think his actions since then are inappropriate and a waste of time.
No, all it means is that he wasn't among the honorees, and seeing the action he is taking he wants the prize very, very much. Nothing more can be drawn from this. Someone in the running for the prize might hear rumors that they've been nominated for the Nobel, but they never actually know until it's been awarded...or they find out 50 years later when the names of the nominees are revealed. But most people are long dead by then so it's a moot point.
From the first link: "In an interview Friday, Damadian said that without his work 'MRI wouldn't exist.'"
This is just not so. While Mozart's music would not have been made without Mozart, we're talking about a scientific discovery that's just waiting for somebody to pick up on. You can replace one scientist for another and the advance of human knowledge will continue. It may be slightly faster or slower, require more or less people and/or resources, but it will continue--and I say that as a someone who currently does science for a living. This claim is shameless grandstanding on Damadian's part. It's baseless as well--Lauterbur's first paper on MRI doesn't even site Damadian, and it's unlikely that Lauterbur (and the reviewers for Nature) were unaware of Damadian's paper in Science, especially given the small size of the field at the time. Besides, it isn't up to Damadian or whoever he gets to write to the Nobel committee because it is solely up to that committee who gets the prize. I don't think anyone has ever been added to a prize after the fact anyway.
I'm niether a physiologist nor and oncologist, but as a tumor gets larger doesn't the interior tend to have restricted blood flow and as a result less nutrient/oxygen access and then die off? Perhaps the EPR technique requires a certain minimum size.
Old long boring lecture and math...boy that brought back an old memory of mine. I was taking my last calculus class at Iowa State University and had this absolutely ancient prof. I was curious and looked him up on the faculty website, and he had been at ISU since the mid-1940's (I took his class in 1997). He was the sllllooooowwwwwwwwweeeeessssstttttttttttt lecturer I have ever heard of, even when they make fun of them on TV or in the movies. When he'd work his way down to the bottom of the blackboard, he'd draw a vertical line and then start at again at the top and over to the left. Only it took soo long that people would make the "falling bomb" whistle and "boom" noises as he slowly drew the line. A friend of mine took the same class a year later and recorded a lecture one day. When we put the VCR on fast forward he was moving at normal speed.
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In California a year or three ago one of the major grocery store chains was slapped with a class action lawsuit and lost, IIRC. They were just ringing items up slightly wrong, like collard greens as the more expensive kale (happened to me. Twice. I don't shop at that chain anymore) or $.99 instead of $.79 for misc. food in a can, small stuff, stuff you probably don't notice 99% of the time. Spread it out across a year, they could screw customers out of maybe $100 each. Multiply that by however many people you've got buying groceries at your stores and that's a lot of "revenue."
This is so much less nasty than the old way--a number of years ago I had to get my upper GI (mouth to small intestine) checked out and had a more old-fashioned proceedure done. That is, the camera was on a cable about as big around as standard coax cable. The cable was coated with novocane and shoved up my left nostril and down my throat, through the stomach and into the small intestine, about 25 feet worth in all. It was an especially unpleasant experience, but at least the cable didn't have to go the other way...
It also involved choking down about two quarts of a barium sulfate "milkshake," which was extremely dense. After the proceedure was over I was initially confused why the doctor asked how long it would take for me to get home from the hospital. It was much clearer to me why when I got home and made a dash for the can. Extremely dense, that milkshake was!
The lab that I work in has engineered a variant of green fluorescent protein (GFP) that is pH sensitive (I had nothing to do with the project, mind you). It responds to pH by varying the ratio of green to blue fluorescence, but the blue state is fairly dim. This means that it is difficult to tell the pH as cells have natural autofluorescence in the blue and to a lesser extent in the green ranges of the visible spectrum, making it difficult to pick out the fluorescence from the pH-sensing GFP. So making a pHish isn't feasible, yet.
That's their PR department talking. On their science page we get this little bit of information: "So far, the researchers have succeeded in isolating two types of gene promoters in the zebra fish -- an estrogen-inducible promoter and a stress-responsive promoter. These promoters have been used to drive the fluorescent colour genes in transgenic zebrafish. Such fluorescent-coloured transgenic fish will be able to respond to the presence of chemicals like oestrogen through the estrogenic promoter and heavy metals and toxins through the stress-responsive promoter. The fish will immediately display the colour depending on the type of environment the colour has been specified for." So the organism has to be in an environment that produces a stimulus inducing the production of red fluorescent protein*, ie either estrogen or something that hits the stress-response promoter. Otherwise the zebrafish has its natural color (which is pretty anyway--I have some in my aquarium). The red fluorescent zebrafish that the company is offering for sale are always expressing the red fluorescent protein, which means that it is under the control of a different promoter and not useful as a pollution (or estrogen) detector in any way. Which means that these guys intentionally produced a GM novelty that is useless for science.
* The red fluorescent protein is almost certainly DsRed aka drFP583, isolated from Discosoma sp. red, a sea anemonie. There are only 45 or 46 genes out there that have been cloned that are members of the GFP (green fluorescent protein) family, ie proteins having the same 3D fold and sequence similarity. Of these 46, only 3 or 4 are red with DsRed being the most commonly used in molecular biology. Most are green, one yellow, at least one cyan, and some others while brilliantly colored are nonfluorescent.
There's a reason for the quotation marks. The researchers did obtain a movie of sorts, in that they repeated their basic experiment to get different timepoints in the melting process. However the frames making up the movie are electron powder diffraction (EPD) images. What you get is basically a pattern of rings centered like a bullseye, and the spacings between the different rings can tell you information about the material like how the atoms are configured. Put in the time component from several images and you can get (in this instance) a "movie" of aluminum melting.
I tried to find a free EPD image, but the closest thing I found was xray powder diffraction, with fake color--what you get from a diffraction image is greyscale. Anyway, it's a similar experiment, except the material is bombarded with xrays instead of electrons.
Expected follow-up: "Japanese food scientists announce newly discovered whale is tasty."
But seriously, food science is still science. The happiest research chemist I ever met was the guy who develops new flavors of gummy bears. However, it's still at best highly questionable that any real research is done by Japanese (or whoever) whaling.
I've never heard of the show until today, but it sounds cool. I'm especially interesting in the tree cannon, since my roommate made a sort of tree missile using six or seven sticks of dynamite and a ~60 ft doug fir (ahh...to be young and stupid in rural Montana), and I've heard of Survival Research Lab's Pitching Machine which chucks 6 ft long 2x4's up to 800 feet, but a tree cannon sounds like something different. Unfortunately a brief googling didn't seem to turn up anything.
The six genes specifying the utilization of L-fucose as a carbon and energy source are known as the "fuc" genes. Among them is L-fuculose kinase, also known as "fucK." The abstract of the paper where the genes were cloned (and I think named) can be found on PubMed.
Many more young people than you might think have cancer, and it's typically not due to HIV. I've had the unfortunate experience of visiting my 20-something brother in the cancer ward (he got better, thankfully) and there was a surprisingly large fraction of people there who had cancer and were 30 or younger. At a page at the CDC, I found in the Summary Health Statistics for U.S. Adults, 1999, table 5 (don't download--8 MB!) that the percent of cancer among adults age 18-44 is a whopping 1.9%, far more than at that age who have HIV. For comparison, the other age brackets: 45-64 7.9%, 65-74 17.4%, 75+ 22%. That's for cancer of some kind, but some kinds of cancer strike primarily at specific age groups. My brother's Hodgkin's disease, a lymphoma, typically strikes men in their mid to late twenties. Leukemia also frequently strikes the young, for example the incidence of Acute Lymphocytic Leukemia (ALL) is 10 times greater for the 1-4 years old bracket than the for those in their early 20's. The point being cancer's not just for the very old, or rather that some cancers aren't.
Robert Park's a University of Maryland Physics professor (emeritus? on leave?), Director of Public Information, Washington Office of the American Physical Society and writer of the American Physical Society's weekly What's New column, and is the author of "Voodoo Science: The Road From Foolishness to Fraud." You can download his CV here , and it will basically tell you he's a scientific somebody.
Most of this is correct, except that cellulose is actually a polymer made up of glucose. More specifically, cellulose is beta(1,4)-linked glucose. This online lecture has a picture of cellulose both as a linear chain and as how linear chains can form a more complex sheets (not pictured: the sheets can then stack). We can't use cellulose because we don't have cellulase, a series of enzymes that can hydrolyze the chain. It's been a while, but I think it pops off glucose pairs, not monomers but I could be mistaken.
All comments about the Stryker aside, maybe the Army's trying to learn something from the Navy. I'd like to think that leaving the cruiser USS Yorktown dead in the water for 2 1/2 hours due to a divide by zero error would motivate a switch from microsoft to something more robust. I'd also like to think asses of the dimbulbs in charge are still smarting from the cornholing courtmartial they received, but they probably got promoted instead.
2003 saw the first scientifically reported incidence of a whale flatulence. A picture and writeup can be found here. Warning: the picture caption is bound to induce fits of giggles in young children...or people like me who still find poop jokes funny.
Pity you couldn't get that article; it was really a fun read with a truly massive bibliography. If you were taught that the Miller-Urey experiment was proof of evolution, then your organic chemistry teacher was either wrong or you misunderstood. At any rate, this is the only example I have ever heard of. Still, the challenge remains: find me a textbook which claims that Miller-Urey is proof of evolution.
"Indeed physics and chemistry are deterministic - they go where the Gibb's free energy dictate they go. Which is why polypeptides don't spontaneously form."
So if you know this, then why make a comment you know to be false, ie chemistry being non-deterministic? Besides, polypeptides do spontaneously form under certain conditions. There is nothing special about an organism or the enzymes and ribozymes it uses to make this happen. It's all still the same chemistry. On a closely related note, I just found this really neat article by Stuart Kauffman (okay, it's just an editorial blurb in Nature on the actual article, Nature vol 382 pg 525-528 (1996) sadly not available online or I'd link it) on a 32-amino acid polypeptide that can autocatalyse its own synthesis by accelerating the condensation of 15- and 17-amino acid fragments in solution. I wonder what's been found in the six years since that was published?
"Aside from chlorophyll, where does adding sunlight produce anything but decay?"
There is nothing special or unique about chlorophyll. You add light or energy of some kind to a system, you (may) get some change. For light, you may get degradation of a compound if it has a photolabile group, you may get isomerization about a chemical bond, or fluorescence, or a change of phase, or drive some anabolic reaction. Photochemistry's a hopping field of study: just google "light polymerization" for one example that's especially topical. I myself had no idea that there was so much out there, commercial light polymerizers and all!
"I have read far more on the topic than the abstract you mention, it's just typical of the work in the field (probably why you selected that one)."
Yet you've also been trying to use a number of old creationist chestnuts which suggests either the abiogenesis material you've read is badly out of date or is written solely by creationists. Spend an afternoon on the talkorigins abiogenesis pages--what have you got to lose?
"You seem to understand fundamentals of chemistry - work out the equilibrium constant of a moderate sized protein in an aqueous solution, given the energy of peptide bonds for a selection of amino acids. Figure it out to 150 or 200 proteins in the peptide. I could give you the answer but working it out yourself you may learn something significant. "
Well, I would like to think that I haven't wasted the last decade I've spent studying biochemistry and chemistry. But far from informative and speaking of creationist chestnuts, I suspect what you're asking me to do is one of the classics. You want me to sit down and calculate the odds of a peptide forming--a specific length, a specific sequence, from a pool of amino acids, at random. In the abiogenesis link that I provided in my first post in this thread is ample description of why this argument is fallacious, right up at the top under the heading "Problems with the creationists' "it's so improbable" calculations."" You can't miss it--they even talk about the same 32-mer autocatalytic protein that I found just by googling around, and the page links to more examples of similar autocatalytic proteins! Wow. SunY looks really interesting.
" I brought up Miller-Urey because that discredited experiment is still taught so widely that many folks here cite it as proof, since it's what they were taught was proof of evolution. It's nice to talk with someone who is beyond that."
.pdf of the article directly--warning it is fairly large.
Miller-Urey is in textbooks, but it is not used as "proof" of evolution and never has been. Neither have I ever seen anyone here attempt to use it as "proof" of evolution. The experiment shows that it is possible for a very simple system resembling conditions found on a prebiotic earth to generate relatively complex molecules. This is how it has been treated in all of my old undergrad biology and biochemistry textbooks and I challenge you to find a recent textbook that does treat the Miller-Urey experiment as "proof" of evolution.
"That article at the Royal Society (at least from its abstract, the article is not freely available for a couple of years it looks like)"
I don't think my university has a site license, but I may be wrong. Try this link--it is to a
"The key point that is never addressed in any papers I'm aware of is that in order to get to an accurately reproducing cell where natural selection could take over and exert an effect on reproduction..."
This is due to a misunderstanding on your part. Natural selection could act on something as simple as an imperfect self-replicating system that is subject to some environmental pressure to provide something for selection. A cell is not explicitly required.
"Yet simple probstat will show you that any non-deterministic reaction or process will tend toward the mean, toward increasing entropy."
Except that physics and chemistry are not random, they are deterministic. If I spark a mix of hydrogen and oxygen, we all know that we'll get water. A good work on self-ordering chemistry that is also topical to the issue of the orgin of life is "The Origins of Order: Self-Organization and Selection in Evolution" by Stuart A. Kauffman. Second, entropy can of course be overcome by adding additional energy to the system; this is how a freezer works.
"Until the RNA stage, there is no possible high-fidelity reproduction mechanism."
This is not true. Google "Cairns-Smith" or "Kauffman" with "self-replication" or read the talkorigins page I linked in my previous post and some of the references therein.
"And in the early earth (by current theories) there was not a superabuncdance of O2, hence there was not a strong ozone layer, and there was a lot of hard UV around. That alone would tend to break up any long chain molecules, if the temperature and other reactants didn't get in the way."
High levels of molecular oxygen in an atmosphere is thought to be indicative of life, and as such would not be present in any quantity on a prebiotic earth. Geologic evidence supports the notion that the earth started off with a reducing or at least non-oxidizing atmosphere, as the first evidence of an oxidizing atmosphere (such as iron oxide deposits) occur in rock no younger than about 2.5 billion years old. However, ozone is not the only compound that can block UV. For example, water is a good UV blocker, and the abstract of the paper I linked makes it clear that the author's view is that life arose in or around hydothermal vents, which is to say underwater (the first ocean is believed to have condensed ~4.4Gya). From the abstract: "The universal ancestor we infer was not a free-living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occured. The first free-living cells are suggested to have been eubacterial and archaebacterial chemoautotrophs that emerged more than 3.8 Gyr ago from the inorganic confines." Which is to say that the authors vie
I've read articles by Behe and Dembski and was not favorably impressed. Behe and Dembski are not taken seriously by the scientific community for that matter either. For example, read Nature's review of Behe's "Darwin's Black Box" (Nature 1996, Volume 383, pages 227-228, available pay-only from them, but freely available here). Another review that is available online is from the National Center for Science Education--the premier science education body in the USA. Naturally, both it and Nature (and, well, science in general) are firmly in the evolutionists' camp. You've probably heard it before, but why not give talkorigins a try? They have their own pages on Behe and Dembski as well.
Wikipedia
.pdf or .svg format. I'd give the link there directly, but the Royal Society doesn't do that for some reason. Anyway, the article and the references contained therein might get one up to speed. A more tractable account of modern abiogenesis research is available on talkorigins' own website as well.
talkorigins (one of many)
geology.about.com
Depending on how recent the source and who you talk to, Coelacanth is a name belonging to either a genus or a family, not just one species. There are ~125 species identified from fossils alone, which are used as index fossils; this is not a problem since they are morphologically distinct from each other and the modern coelacanth species.
Abiogenesis has moved on in the 50 years since Miller-Urey. Might I suggest reading a recent article: "On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells," it can be found here, just click journals, then Vol 358, January, then pg 59, freely available in
Actually, $1500 per article isn't all that bad. Not too long ago I got a paper published. It cost $350 per figure, plus a charge for the first 10 pages (that I now forget) and then an additional charge for pages past the first ten. The total cost of publication for the lab for my paper was well over $2000.
I did some more looking around the Nobel website while responding to some posts and found this gem in the Statues of the Nobel Foundation:
" 10. No appeals may be made against the decision of a prize-awarding body with regard to the award of a prize.
Proposals received for the award of a prize, and investigations and opinions concerning the award of a prize, may not be divulged. Should divergent opinions have been expressed in connection with the decision of a prize-awarding body concerning the award of a prize, this may not be included in the record or otherwise divulged.
A prize-awarding body may, however, after due consideration in each individual case, permit access to material which formed the basis for the evaluation and decision concerning a prize, for purposes of research in intellectual history. Such permission may not, however, be granted until at least 50 years have elapsed after the date on which the decision in question was made."
So in 50 years Damadian and his supporters might be able to find out exactly what criteria the prize committee used to award the Physiology or Medicine prize to Lauterbur and Mansfield but not to Damadian, but they'll never be able to appeal that decision.
From the Nobel wesite
"Q. Has X been nominated as a candidate for the Nobel Prize? Where do I find a list of Nobel Prize nominees?
A. According to the Statutes of the Nobel Foundation, nominators must not make public the names of the nominees nor inform nominees privately of the proposals. Even invitations to propose names are confidential. Proposals received for the award of a prize, and investigations and opinions concerning the award of a prize may not be divulged. The names of the nominees are classified as confidential information for at least fifty years."
Damadian might have had an idea of whether or not he was up for one through a scientific rumor mill, but it is clear by the rules governing the awarding of a Nobel prize that he does not now know and will not know for another 50 years 100% for certain whether or not he was nominated.
Awarding of a Nobel, as another poster has already mentioned, is not necessarily awarded to the first person who came up with an idea--a Nobel and being credited with being first are simply not the same. My beefs with Damadian are that he falsely claims that MRI wouldn't exist without him, indeed Lauterbur's 1973 paper doesn't even mention Damadian's work and even Damadian's supporters must conceed that the idea of MRI was conceived independently by Damadian and Lauterbur. Also it isn't up to Damadian whether or not he gets the Nobel for his work on MRI, it is solely up to the committee that awards the Nobel. While there is precedence for awarding the Nobel to persons who have greatly advanced the field and at the same time not granting the Nobel to the first person to publish on it, there is no precedence for someone getting added to a prize after it has already been awarded. While I have sympathy for Damadian and find his being left off the prize questionable, I think his actions since then are inappropriate and a waste of time.
No, all it means is that he wasn't among the honorees, and seeing the action he is taking he wants the prize very, very much. Nothing more can be drawn from this. Someone in the running for the prize might hear rumors that they've been nominated for the Nobel, but they never actually know until it's been awarded...or they find out 50 years later when the names of the nominees are revealed. But most people are long dead by then so it's a moot point.
From the first link: "In an interview Friday, Damadian said that without his work 'MRI wouldn't exist.'"
This is just not so. While Mozart's music would not have been made without Mozart, we're talking about a scientific discovery that's just waiting for somebody to pick up on. You can replace one scientist for another and the advance of human knowledge will continue. It may be slightly faster or slower, require more or less people and/or resources, but it will continue--and I say that as a someone who currently does science for a living. This claim is shameless grandstanding on Damadian's part. It's baseless as well--Lauterbur's first paper on MRI doesn't even site Damadian, and it's unlikely that Lauterbur (and the reviewers for Nature) were unaware of Damadian's paper in Science, especially given the small size of the field at the time. Besides, it isn't up to Damadian or whoever he gets to write to the Nobel committee because it is solely up to that committee who gets the prize. I don't think anyone has ever been added to a prize after the fact anyway.
I'm niether a physiologist nor and oncologist, but as a tumor gets larger doesn't the interior tend to have restricted blood flow and as a result less nutrient/oxygen access and then die off? Perhaps the EPR technique requires a certain minimum size.
Old long boring lecture and math...boy that brought back an old memory of mine. I was taking my last calculus class at Iowa State University and had this absolutely ancient prof. I was curious and looked him up on the faculty website, and he had been at ISU since the mid-1940's (I took his class in 1997). He was the sllllooooowwwwwwwwweeeeessssstttttttttttt lecturer I have ever heard of, even when they make fun of them on TV or in the movies. When he'd work his way down to the bottom of the blackboard, he'd draw a vertical line and then start at again at the top and over to the left. Only it took soo long that people would make the "falling bomb" whistle and "boom" noises as he slowly drew the line. A friend of mine took the same class a year later and recorded a lecture one day. When we put the VCR on fast forward he was moving at normal speed.