For what very little it's worth, Tibet at various times over the last ~1500 years has been a part of China, semi-autonomous, tributary, separate sovereign nation(s), been invaded by Mongols, Gurkhas, Chinese, British, been a major regional power, and has successfully invaded China. Where's the cutoff point in looking at history to decided whether Tibet is independent or instead is as much of a part of China as Manchuria (or at least Xinjiang or maybe even Tiawan) is? Or to what extent does the history matter?
Great. This probably limits my chance of being able to eat whale, unless maybe I go to Japan where they've been conducting whale research for years. Then I can add my data point for the "Just how tasty is whale?" study.
Or maybe Norway; I think they are collaborating on the work.
No, it's not exactly clear. Being a little cynical, it might be a researcher who wanted to do something weird (build a snailbot to see if it could be done) then PT Barnumed it to get some funding. Not meant to be insulting or to say this is how it really is, just that sometimes people do get funding this way. I know of a guy who gets craploads of money from the US Navy to develop underwater adhesives when all he really is interested in is how mussels stick to rocks so tightly. Does good work too, just kinda off on a tangent to what he's getting the money for.
Then there's also the National Aerospace Plane (NASP) going back to the Reagan years. This site has some more information on it. I wish I could remember more specifics, but hasn't there recently been an announcement that the US was going to test munitions in 2006 or 2007 that when in actual production are to be launched from orbit? Given the clear military interest (and spending) on the NASP, perhaps it became a black project and never was actually cancelled. Or maybe I should hunker down in my backyard bombshelter with my aluminum foil hat.
I had a good laugh at your comment on Grenada, because a friend of mine's uncle was there. He said he was one of the guys who came in on cargo planes to secure the airport. It came down from on high that his ranger unit was ordered to roar out of said cargo plane on freakin' motorcycles at the same moment the ramp touched down--to be more dramatic, not for any tactical reason. Reasoning just out of the movies and typical of Reagan. Anyway, he broke his ankle when another biker smacked into him leading to a four or five motorcycle pile-up. Secured the airfield without any real difficulty, well past the motorcycle pile-up anyway. Hell Grenada was secured without any real difficulty; we had 19 KIA while they had about 40, everybody cheered when they saw an american soldier. Didn't find shit for weapons either, not that the people of Grenada were really interested in picking up a gun for communism anyway. You can read a little about it here, although they've got him listed as breaking his leg, not his ankle.
I disagree. It just has to function at some minimally acceptable level the first time. Life is inherently squishy and flexible, there really is no "right" answer. Take an enzyme, for example. It might be 300 amino acids in length, but the number of amino acids that are explicity required for catalysis or proper folding is a tiny fraction of that number. An enzyme I've worked on has two main isoforms, sequence identity within an isoform is about 50%, between isoforms drops down to 10%. They all have comparable levels of activity. Then you can add to it some of life's error checking/avoiding. For example, if you look at the genetic code, of course you've got three bases A, T, C, or G in a row making up a codon, for 64 possible codons but only 20 standard amino acids. Except for the amino acids methionine and tryptophan, each amino acid can be encoded by at least two different codons. The redundancy isn't higgily-piggily either, alanine is encoded by GCA, GCC, GCG, and GCT--the last position is variable instead of just randomly varying across all three positions. Further, similar amino acids are often encoded by codons that are similar. For alanine, if we change for example the first position we can get either serine, proline, or threonine. These amino acids are not entirely unlike alanine and depending on location within the protein the difference may be negligible. Similarly, if we change the first position of the alanine codon, we can get valine, aspartic acid, glutamic acid, and glycine. While aspartic acid and glutamic acid are unlike alanine, valine and glycine are similar. Still, that's a layer of protection in the event of a screw up. If only computers were 1% as robust as life, then the appearance of the Blue Screen of Death (TM) would be so rare that it would warrant an article in the friggin newspaper instead of an almost daily occurance for those of us cursed with Windows 98 boxes.
I think I'd also add to that list that law (or at least lawyers) start with a conclusion-guilt or innocence-and look for evidence that can be construed to support this conclusion and ways to undermine evidence against the conclusion. Science ideally works nearly 180 degrees the other way. Start with hypothesis, run experiments to test hypothesis, if evidence doesn't support hypothesis, consider throwing out hypothesis. This is why lawyers tend to make piss-poor scientists and vice versa.
Also there's the phrase "beyond a reasonable doubt." Remember the OJ Simpson trial? I interviewed for grad school at the university that one of the DNA experts was at. When he was asked something to the effect of "Could it be possible that it wasn't OJ's DNA found at the crime scene even though that sample and his DNA matched" the guy answered that yes, it was possible that it wasn't OJ's DNA. While this is factually correct, the odds were estimated at 1 in 4 billion or something and clearly falls within "beyond a reasonable doubt." Or the DNA expert was just a lunkhead--that university didn't impress me much.
Heh. Reminds me of an accident that occured in a lab a friend of mine worked in a few years back. An undergraduate was pulling a 5-liter bottle of methanol off the (top!!) shelf of the reagent cabinet, slipped, and dumped the whole bottle on her head. A grad student ran back to his desk and pulled out a fifth of vodka from a drawer, handed it to the undergrad and yelled "DRINK!" then got to his car and drove her to the emergency room. Luckily she had just recently turned 21. Was back at work the next week, too.
I just skimmed the article late this evening (early this morning? Whatever.). Anyway, it looked like what they'd done was to attach a single-stranded DNA sequence at one end to a slide, the other end is attached to a 1-micrometer diameter bead. Charge repulsion between the bead and the slide stretches the DNA strand, keeping it under tension. DNA with various sequences then can be introduced into the system, if they match the opposite strand of the fixed DNA strand well, then it will hybridize forming a double stranded DNA. Double stranded DNA forms a double helix structure which is more "fixed" structure than single stranded DNA, which can range from nearly linear to a random coil depending in part in the amount of tension its under and the sequence. Regardless, if there is a hit then the distance between the bead and the slide will change as the DNA is hybridized into a double strand, forming the double helix that we've all seen in biology textbooks. One problem is that multiple different DNA strands can hybridize nearly as tightly as an exact match, for example if we have the sequence 5' ACTGACTGACTG 3' then 5' CAGTCAGTCAGT 3' will bing to it, but so will 5' CAGTCAATCAGT 3', which differs by only one position. I hope I did that right, it's late, but anyway you can still get hybridization of DNA molecules that are only very similar but are not quite identical. This study used DNA strands 10's of nucleotides long so being off by one or even a couple of positions will still result in tight binding, although this can be tweaked a bit by messing with the DNA concentration; lower concentrations will favor more exact matches in general. But still, cool idea.
Or anything about sequence specificity. For example, can they make a probe bind only the sequence ATGCTGACCTT, or can they make a probe specific for only AxxCTGxCCTT? The concentration is important too--the higher the concentration of particles the easier (generally) it will be for something similar to bind and make a false positive.
Still, the ability to bind and report the binding of a single molecule of DNA of a (presumably) highly specific sequence is quite the accomplishment.
Yes, the protein is edible. I don't have the reference handy, but a study was done recently where they fed GFP (green fluorescent protein; the proteins used to make this fish red and green are members of the GFP family) to rats. A fraction of the GFP made it through didestion, resulting in green shit. Literally.
"And this is not the situation that occurred, it is only your misunderstanding of the lead-up to parsons paper"
No, apparently I have not made myself clear. What I am refering to (and mentioned previously in passing) is the ample evidence from many different fields (geology, archaeology, paleontology, linguistics...) that provide evidence that humanity is ancient, a point Parsons also makes: "Using our empirical rate to calibrate the mtDNA molecular clock would result in an age of the mtDNA MRCA of only ~6,500 y.a., clearly incompatible with the known age of modern humans. Even acknowledging that the MRCA of mtDNA may be younger than the MRCA of modern humans, it remains implausible to explain the known geographic distribution of mtDNA sequence variation by human migration that occurred only in the last ~6,500 years." Science by its very nature is conservative, so we look at the possibilities primarily by order of plausibility. To consider a date of ~6,500 years is true, we must first investigate all other more plausible explanations first, explanations that I mentioned way back in my first post which the creationists, now six years after the publication of Parson's paper, have yet to consider.
"There were NO experiments done to observe the behaviour of the D-Loop prior to Parsons paper."
This is false. Parsons cites another study conducted along similar lines to his own (Howell, N. et al (1996) Am. J. Hum. Genet. 59, 501-509); he also cites phylogenic studies looking at the same issue. It is interesting that the creationists chose not to cite either the phylogenetic studies or the similar, earlier study (Howell, 1996).
"The dozens of experiments you speak of were ALL conducted as follows: Human and Chimp mtDNA D-Loops are differ by X, and chimps and humans diverge Y years ago, thus the mutation rate of the D-Loop is X/Y."
see the first point and below. And secondly, not all studies were done on humans and chimps, or necessarily between different species.
"The FIRST experiment to measure the D-Loop's actual rate gave a rate 20 times higher than X/Y."
Again, false. It looks like that rate is being revised downwards as well--see Gibbons, A. (1998) Science 279, 28-29: " Several teams of evolutionists promptly went back to their labs to count mtDNA mutations in families of known pedigree. So far, Stoneking's team has sequenced segments of the control region in closely related families on the Atlantic island of Tristan da Cunha, where pedigrees trace back to five female founders in the early 19th century. But neither that study nor one of 33 Swedish families has found a higher mutation rate. 'After we read Howell's study, we looked in vain for mutations in our families,' says geneticist Ulf Gyllensten of Uppsala University in Sweden, whose results are in press in Nature Genetics. More work is under way in Polynesia, Israel, and Europe." Gibbons also mentions that a five-fold higher rate than anticipated is found when all the available data at that time was pooled from multiple studies. Both statemenst the creationists again chose not to mention when citing the article.
"Based on this, scientists proposed that in spite of the fact the D-Loop appears neutral by every known test, we must assume neither X nor Y can be adjusted to fit the experimentally observed rate."
This is incorrect. The D-loop, as mentioned by Parsons: "While the CR [control region of the D-loop] is certainly under less selectional constraint than coding genes, the region has crucial regulatory functions and internal sub-regions display quite different levels of variation both within and between species. Some portions of the CR are thus not as free to evolve as others and it is quite plausible that selectional constraint, while clearly present, need not be absolute between one generation and the next. In this light, it is interesting to note that the observed substitution of the nucleotide at position 234 occurs w
My roomate and I grew a watermellon in our backyard last summer. It was the size of a golfball. Then the slugs ate it--since one slug stayed out in the middle of the yard until midmorning and risked being eaten by the crows it must have been darn tasty. Stupid slugs.
I'd really like to thank you for that link to the ICR. Several months back I was arguing the exact same issue and I was wondering where exactly the source was from. Now whenever I need to present clear-cut examples of "scientific" creationist fraud I've got another excellent example. The ICR can't even read a table correctly: the "dates" that they give for the lava samples aren't dates at all, but instead refer to how far an individual sample was from the expected concentration of Ar-40. The ICR also fails to mention that some samples had lower levels of Ar-40 than expected. The true irony is that rather than this article (Dalrymple) undermining the validity of radiometric dating, it is clearly supporting.
But don't take my word for it. Read the paper yourself: G.B. Dalrymple, "40Ar/36Ar Analyses of Historic Lava Flows," Earth and Planetary Science Letters, 6 (1969): pp. 47-55. It'll be available at (or at least through interlibrary loan) any university.
"The multiple lines of inquiry you refer to are ALL based on the assumption of chimp/human common ancestry. From a creationist stance, rejecting the predictions on that assumption in favor of the observed data is not unreasonable. The fact that the method main stream science had accepted as valid suddenly matches the bible nicely is interesting to creationists. Scientifically, they aught to do some work to confirm the validity of the method before making any claims about a method they had formerly rejected. But aside from that, on the surface this seems to be better evidence for creationism than common descent. And the data was all obtained by main stream science, using accepted main stream methods"
If we wish to test a hypothesis and expect X, and set up dozens of different experiments with different points of view based on different underlying assumptions and experimental methods, when all but one produces X, does that allow some group to proclaim Y? No. A much more reasonable approach would be to go back to that one experiment and try to find out why it doesn't match the others--whether or not you believe X or Y. This is exactly the case we have with mitochondrial eve. We went back to this dating method using the D-loop, and found that this loop does not behave as expected. It does not matter if we assume a 5 million year last common ancestor with a chimpanze or not. If we expanded the last common human-chimp ancestor to a 1-10 million year range the study would have still produced discrepancies between the D-loop and the rest of the mtDNA. If a creationist still wishes to argue that we're still making assumptions even though when we look at the fossil record we've expanded our range to a ridiculous point, then we no longer are arguing about our mtDNA dating technique but instead are arguing about paleontology and geology (and physics if they start questioning some of the radiometric dating techniques). This is well beyond the scope of the paper I referenced and again shows the difference between main-stream science and "scientific" creationists.
It depends. Both Science and Nature are not exactly what you'd call popular journals, so unless you actually do science for a living they'll probably be too technical (or at least too dry). Another reason not to get either journal is the fact that the articles are extremely terse, imagine having the work of five people over the course of two years compressed down into three pages. Both Science and Nature do have about 20-30 pages or so of broader interest bits in their "News and Views" sections and the like. Another point to consider is that some public libraries have a subscription to Science and Nature, failing that you may be able to obtain photocopies of articles through an interlibrary loan program--not sure if the public libraries do this, though. If you're still interested, Science is probably the more rounded of the two; Nature as the name implies is more biologically oriented. Size wise, the two journals are about 150 pages--again due to article compression.
And almost every time some article is posted that has something to do with evolution the "scientific" creationists come out of the woodwork. You'd think a technology and science website like/. wouldn't have so many or that they'd be so voiciferous...unfortunately you'd also be wrong.
"Mitochondrial Eve has been shown in secular literature (ever heard of the magazine "Science") to have lived ~6000 years ago. Evidence of the flood here."
What's going on?! I used the exact same message (below) already once this week for the exact same argument. Fortunately somebody else already took care of the rest of your message so I don't have to.
One nit to pick. Going back to the original "Research News" article in Science (vol 279 issue 5347 pg 28-29), we see that instead of this being evidence for a ~6000 year old mitochondrial eve, we have to reconsider some of our beliefs about mitochondrial DNA (mtDNA), or more specifically a region of mtDNA called the D-loop, which comprises only 7% of mtDNA and which most mtDNA studies have used. One of the biggies is that most mtDNA studies use "so-called "noncoding" sequences of the control region of mtDNA, which do not code for gene products and therefore are thought to be free from natural selection." to quote the article. Another is to check and see if we are instead hitting "hotspots," regions with above-average mutation rates; hotspots will have more back- and parallel-mutations which will cloud the picture. A third is that the mutation rate may vary over time. A fourth is to investigate the issue of heteroplasmy--having multiple mtDNA sequences, even though for a given region there should be only one. For a while it was thought to be rare, now 10-20% of the population could be heteroplasmic. All of these issues would need to be addressed by the creationists before it could be considered evidence of a ~6,000 year old mitochondrial eve rather than a problem with the underlying assumptions of the technique. Indeed, with the advancement of our ability to manipulate and sequence DNA, we no longer have to utilize only 7% of the mtDNA--we can sequence the whole thing--all 16,000 or so base pairs of it. A recent study published in Nature (vol 408 pg 708-713, Dec. 2000) using mtDNA--all of it--found that the D-loop (used in most mtDNA studies) does not have a constant mutation rate. The study goes on to show (again using the whole mtDNA sequence) that the date of "mitochondrial eve" is about 170,000 years ago. A more reader-friendly report by the author of the Nature paper can be found here.
Say, you ever get a chance to actually read that Dalrymple article you so badly mangled? Here's a refresher. Just go up the thread.
"But don't make out as though there isn't a similar tendency on the other side of the fence. Rejecting the observed mutation rate because it is too high(evolutionists) is every bit as bad as rejecting a predicted rate because it is too low(creationists)."
Is it? I think the actions of main-stream science and "scientific" creationism bear witness to the vast difference between the two. We used this dating technique for a while, and then it was discovered that the mutation rate of the D-loop that we were using was ~20 fold higher than what we expected. What happened? The creationists trumpeted it as evidence for their "model," completely ignoring other possibilities and were extremely happy with their one piece of data that they believed supported their religious view, however out of line with all other information that one bit of data might be. Main-stream scientists scratched their heads and wondered why this one bit of evidence was now so far out of line with their expectations based on information from multiple of lines of inquiry. Main-stream science looked, and in 2000 a plausible explanation and a correction for the MTeve date was published. The investigation of mtDNA, as you mentioned, still continues. As a result of the information learned, our methods may have to be slightly modified; mainly it looks like a study using the D-loop must be relegated to recent events, whole mtDNA for old events. What happened with the creationists? They stopped thinking about the issue when they could construe it to look in their favor. Worse, since it has become clear that the 6000 year old date is based on a faulty study, they failed to correct themselves. The "scientific" creationists betray themselves by their actions.
"On a related note, mitochondrial DNA seems to indicate that our common mother (mitochondrial eve) existed ~6000 years ago, less than the 70,000 years proposed here."
One nit to pick. Going back to the original "Research News" article in Science (vol 279 issue 5347 pg 28-29), we see that instead of this being evidence for a ~6000 year old mitochondrial eve, we have to reconsider some of our beliefs about mitochondrial DNA (mtDNA), or more specifically a region of mtDNA called the D-loop, which comprises only 7% of mtDNA and which most mtDNA studies have used. One of the biggies is that most mtDNA studies use "so-called "noncoding" sequences of the control region of mtDNA, which do not code for gene products and therefore are thought to be free from natural selection." to quote the article. Another is to check and see if we are instead hitting "hotspots," regions with above-average mutation rates; hotspots will have more back- and parallel-mutations which will cloud the picture. A third is that the mutation rate may vary over time. A fourth is to investigate the issue of heteroplasmy--having multiple mtDNA sequences, even though for a given region there should be only one. For a while it was thought to be rare, now 10-20% of the population could be heteroplasmic. All of these issues would need to be addressed by the creationists before it could be considered evidence of a ~6,000 year old mitochondrial eve rather than a problem with the underlying assumptions of the technique. Indeed, with the advancement of our ability to manipulate and sequence DNA, we no longer have to utilize only 7% of the mtDNA--we can sequence the whole thing--all 16,000 or so base pairs of it. A recent study published in Nature (vol 408 pg 708-713, Dec. 2000) using mtDNA--all of it--found that the D-loop (used in most mtDNA studies) does not have a constant mutation rate. The study goes on to show (again using the whole mtDNA sequence) that the date of "mitochondrial eve" is about 170,000 years ago. A more reader-friendly report by the author of the Nature paper can be found here.
A lot of it is open source; unfortunately a lot of it also epitomizes what's wrong with non-commercial software. You might have just one small group, one lab, or even just one guy who's little baby that program is. For what I've used, the majority of the open source software and freeware runs on unix, not windows, although there is a growing commitment to linux and windows that will become dominant in the next couple of years. Most of it runs. Sort of. If you're willing to fight with it. The only thing worse than the user interface is the manual, if one exists at all (although exceptions exist, such as Deep View Swiss PDB Viewer). While I'd agree that many biologists have poor computer skills, that's rapidly changing as more and more the problem is data interpretation as opposed to data acquisition. There are many subdisciplins where a good percentage of the biologists also possess some ability for computer programming (or at least script writing) just becuase that's the only way to force the software to work. I'd also agree that a CD package with documentation on a popular set of programs would be great, but that's complicated by the fact that the geneticists don't do biochemistry who don't do cell biology etc. That and getting a bunch of scientists together on something like this is like herding cats.
Might I suggest none, at least for the first year? Seriously. You don't need a computer or any gadget past a pen(cil) and paper to take notes in class and all campuses have computers adequate for typing up your papers and whatever rudimentary graphing or programming or spreadsheet needs will be for your freshman year and for some majors for all of college. Also, you won't have ready access to computer games or Slashdot while you're in your dorm or apartment eating doritos and consuming, well, whatever. I don't know about the rest of you, but the first year or three I spent way too much time playing games on the computer until I deleted them all, right down to solitare.
The actual Nature article is "Computational design of receptor and sensor proteins with novel functions," in the May 23, 2003 issue (Vol 423 No 6936 pp101-205). It is important to note that they are not making fully functional enzymes yet, but have accomplished the rather daunting task of designing/directing the evolution of a given protein binding substrate A and making it bind a new, completely different substrate B. Their wild-type substrate interacts with 12-18 residues, so multiply that by your 20 standard amino acids across these interacting residues and you have a crapload of sequences to deal with (10^15 to 10^23; I'll take their word for it). I thought the statement "Designer proteins such as this can be developed for bioremediation of weapons dump sites (TNT) and sensitive sensors of drugs/contaminants that can easily be grown in bacteria." was kind of cute as when you search Pubmed with "TNT reductase" you get back a number of articles on bacterial enzymes that allow them to munch TNT. A few years back I got to work on a project to solve the structures of enzymes that pop NO2 groups off of TNT and related compounds; the bacteria that these proteins were subcloned out of were found in the heavily contaminated soil of a former World War 2 munitions plant. Pretty cool what evolution can do when you add a new component to the environment of some organism.
When I was younger, I was a total science/technology/computers/etc. nut (ie, fellow nerdling). As I've grown older and now spend most of my day working either at a computer or at the bench in the lab at work I'm less likely to futz around with chemicals at home or mess around on my computer. Why would I want to do those things when I spend 50-70 hours a week doing something similar at work? Instead I've started reading more and more history (especially ancient), philosophy, humor, and nonfiction. Not so much popscience--too many errors in areas I'm familiar with to be enjoyable anymore. I've also taken up backpacking, hunting, and woodworking. Although that last one remains linked to work--my roomate and I swipe pallets from work and recycle the lumber into bookcases and tables and such. I'd love to take up metalworking or auto repair but the community college courses are too spendy for this poor grad student.
I know I'm not alone in my nontechnical or at least nonHIGHtechnical pursuits; U. Oregon grad students seem to enjoy a lot more outdoorsy hobbies than I would have ever imagined "nerds" doing. It's not just here: I've got a friend working at Microsoft and he says he rarely uses his home computer anymore and says its similar with a number of his coworkers--they'd rather grab a pack and go camping.
Besides just needing a balance between technology and simplicity hobbies are pretty good ways at meeting people you wouldn't normally encounter. Especially women. Think about this: which is sexier, the nerd who is a wizard programmer and their hobbies include programming and playing computer games or the nerd who's a wizard programmer and spends their weekends restoring a 54 Ford pickup or hiking or making pottery?
Bioremediation is groovy.
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Salt From Plants
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· Score: 2, Interesting
There's lots of cool stuff going on right now with bioremediation. My roomate's looking for a postdoc position and one of the labs he was looking at was using bacteria to gather up heavy metals. It was pretty slick: the bacteria were engineered to express proteins designed to bind metal ions on their cell surfaces. They'd eventually have so much metal bound that they would begin to fall to the bottom of your sludge pond or whatever your body of contaminated water was in and they could be harvested. For at least one metal (Mercury? Cadmium? Gonna hafta ask him.) it was looking like the settled-out engineered bacterium-laden sludge from a contaminated site was more enriched in the metal than mined ore!
This should help out a bit with cabin fever. I've lived in some cold places (upper Midwest) but damn. I imagine their problems with depression and suicide increase dramatically in the winter, so now they've got something to do. Now that I think about it, they already had one thing to do so I wonder how much the birth rate will decrease about 9 months after winter, now that they've got high-speed internet access (and pr0n).
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For what very little it's worth, Tibet at various times over the last ~1500 years has been a part of China, semi-autonomous, tributary, separate sovereign nation(s), been invaded by Mongols, Gurkhas, Chinese, British, been a major regional power, and has successfully invaded China. Where's the cutoff point in looking at history to decided whether Tibet is independent or instead is as much of a part of China as Manchuria (or at least Xinjiang or maybe even Tiawan) is? Or to what extent does the history matter?
Great. This probably limits my chance of being able to eat whale, unless maybe I go to Japan where they've been conducting whale research for years. Then I can add my data point for the "Just how tasty is whale?" study.
Or maybe Norway; I think they are collaborating on the work.
No, it's not exactly clear. Being a little cynical, it might be a researcher who wanted to do something weird (build a snailbot to see if it could be done) then PT Barnumed it to get some funding. Not meant to be insulting or to say this is how it really is, just that sometimes people do get funding this way. I know of a guy who gets craploads of money from the US Navy to develop underwater adhesives when all he really is interested in is how mussels stick to rocks so tightly. Does good work too, just kinda off on a tangent to what he's getting the money for.
Then there's also the National Aerospace Plane (NASP) going back to the Reagan years. This site has some more information on it. I wish I could remember more specifics, but hasn't there recently been an announcement that the US was going to test munitions in 2006 or 2007 that when in actual production are to be launched from orbit? Given the clear military interest (and spending) on the NASP, perhaps it became a black project and never was actually cancelled. Or maybe I should hunker down in my backyard bombshelter with my aluminum foil hat.
I had a good laugh at your comment on Grenada, because a friend of mine's uncle was there. He said he was one of the guys who came in on cargo planes to secure the airport. It came down from on high that his ranger unit was ordered to roar out of said cargo plane on freakin' motorcycles at the same moment the ramp touched down--to be more dramatic, not for any tactical reason. Reasoning just out of the movies and typical of Reagan. Anyway, he broke his ankle when another biker smacked into him leading to a four or five motorcycle pile-up. Secured the airfield without any real difficulty, well past the motorcycle pile-up anyway. Hell Grenada was secured without any real difficulty; we had 19 KIA while they had about 40, everybody cheered when they saw an american soldier. Didn't find shit for weapons either, not that the people of Grenada were really interested in picking up a gun for communism anyway. You can read a little about it here, although they've got him listed as breaking his leg, not his ankle.
I disagree. It just has to function at some minimally acceptable level the first time. Life is inherently squishy and flexible, there really is no "right" answer. Take an enzyme, for example. It might be 300 amino acids in length, but the number of amino acids that are explicity required for catalysis or proper folding is a tiny fraction of that number. An enzyme I've worked on has two main isoforms, sequence identity within an isoform is about 50%, between isoforms drops down to 10%. They all have comparable levels of activity. Then you can add to it some of life's error checking/avoiding. For example, if you look at the genetic code, of course you've got three bases A, T, C, or G in a row making up a codon, for 64 possible codons but only 20 standard amino acids. Except for the amino acids methionine and tryptophan, each amino acid can be encoded by at least two different codons. The redundancy isn't higgily-piggily either, alanine is encoded by GCA, GCC, GCG, and GCT--the last position is variable instead of just randomly varying across all three positions. Further, similar amino acids are often encoded by codons that are similar. For alanine, if we change for example the first position we can get either serine, proline, or threonine. These amino acids are not entirely unlike alanine and depending on location within the protein the difference may be negligible. Similarly, if we change the first position of the alanine codon, we can get valine, aspartic acid, glutamic acid, and glycine. While aspartic acid and glutamic acid are unlike alanine, valine and glycine are similar. Still, that's a layer of protection in the event of a screw up. If only computers were 1% as robust as life, then the appearance of the Blue Screen of Death (TM) would be so rare that it would warrant an article in the friggin newspaper instead of an almost daily occurance for those of us cursed with Windows 98 boxes.
I think I'd also add to that list that law (or at least lawyers) start with a conclusion-guilt or innocence-and look for evidence that can be construed to support this conclusion and ways to undermine evidence against the conclusion. Science ideally works nearly 180 degrees the other way. Start with hypothesis, run experiments to test hypothesis, if evidence doesn't support hypothesis, consider throwing out hypothesis. This is why lawyers tend to make piss-poor scientists and vice versa.
Also there's the phrase "beyond a reasonable doubt." Remember the OJ Simpson trial? I interviewed for grad school at the university that one of the DNA experts was at. When he was asked something to the effect of "Could it be possible that it wasn't OJ's DNA found at the crime scene even though that sample and his DNA matched" the guy answered that yes, it was possible that it wasn't OJ's DNA. While this is factually correct, the odds were estimated at 1 in 4 billion or something and clearly falls within "beyond a reasonable doubt." Or the DNA expert was just a lunkhead--that university didn't impress me much.
Heh. Reminds me of an accident that occured in a lab a friend of mine worked in a few years back. An undergraduate was pulling a 5-liter bottle of methanol off the (top!!) shelf of the reagent cabinet, slipped, and dumped the whole bottle on her head. A grad student ran back to his desk and pulled out a fifth of vodka from a drawer, handed it to the undergrad and yelled "DRINK!" then got to his car and drove her to the emergency room. Luckily she had just recently turned 21. Was back at work the next week, too.
I just skimmed the article late this evening (early this morning? Whatever.). Anyway, it looked like what they'd done was to attach a single-stranded DNA sequence at one end to a slide, the other end is attached to a 1-micrometer diameter bead. Charge repulsion between the bead and the slide stretches the DNA strand, keeping it under tension. DNA with various sequences then can be introduced into the system, if they match the opposite strand of the fixed DNA strand well, then it will hybridize forming a double stranded DNA. Double stranded DNA forms a double helix structure which is more "fixed" structure than single stranded DNA, which can range from nearly linear to a random coil depending in part in the amount of tension its under and the sequence. Regardless, if there is a hit then the distance between the bead and the slide will change as the DNA is hybridized into a double strand, forming the double helix that we've all seen in biology textbooks. One problem is that multiple different DNA strands can hybridize nearly as tightly as an exact match, for example if we have the sequence 5' ACTGACTGACTG 3' then 5' CAGTCAGTCAGT 3' will bing to it, but so will 5' CAGTCAATCAGT 3', which differs by only one position. I hope I did that right, it's late, but anyway you can still get hybridization of DNA molecules that are only very similar but are not quite identical. This study used DNA strands 10's of nucleotides long so being off by one or even a couple of positions will still result in tight binding, although this can be tweaked a bit by messing with the DNA concentration; lower concentrations will favor more exact matches in general. But still, cool idea.
Or anything about sequence specificity. For example, can they make a probe bind only the sequence ATGCTGACCTT, or can they make a probe specific for only AxxCTGxCCTT? The concentration is important too--the higher the concentration of particles the easier (generally) it will be for something similar to bind and make a false positive.
Still, the ability to bind and report the binding of a single molecule of DNA of a (presumably) highly specific sequence is quite the accomplishment.
Yes, the protein is edible. I don't have the reference handy, but a study was done recently where they fed GFP (green fluorescent protein; the proteins used to make this fish red and green are members of the GFP family) to rats. A fraction of the GFP made it through didestion, resulting in green shit. Literally.
"And this is not the situation that occurred, it is only your misunderstanding of the lead-up to parsons paper"
No, apparently I have not made myself clear. What I am refering to (and mentioned previously in passing) is the ample evidence from many different fields (geology, archaeology, paleontology, linguistics...) that provide evidence that humanity is ancient, a point Parsons also makes: "Using our empirical rate to calibrate the mtDNA molecular clock would result in an age of the mtDNA MRCA of only ~6,500 y.a., clearly incompatible with the known age of modern humans. Even acknowledging that the MRCA of mtDNA may be younger than the MRCA of modern humans, it remains implausible to explain the known geographic distribution of mtDNA sequence variation by human migration that occurred only in the last ~6,500 years." Science by its very nature is conservative, so we look at the possibilities primarily by order of plausibility. To consider a date of ~6,500 years is true, we must first investigate all other more plausible explanations first, explanations that I mentioned way back in my first post which the creationists, now six years after the publication of Parson's paper, have yet to consider.
"There were NO experiments done to observe the behaviour of the D-Loop prior to Parsons paper."
This is false. Parsons cites another study conducted along similar lines to his own (Howell, N. et al (1996) Am. J. Hum. Genet. 59, 501-509); he also cites phylogenic studies looking at the same issue. It is interesting that the creationists chose not to cite either the phylogenetic studies or the similar, earlier study (Howell, 1996).
"The dozens of experiments you speak of were ALL conducted as follows: Human and Chimp mtDNA D-Loops are differ by X, and chimps and humans diverge Y years ago, thus the mutation rate of the D-Loop is X/Y."
see the first point and below. And secondly, not all studies were done on humans and chimps, or necessarily between different species.
"The FIRST experiment to measure the D-Loop's actual rate gave a rate 20 times higher than X/Y."
Again, false. It looks like that rate is being revised downwards as well--see Gibbons, A. (1998) Science 279, 28-29: " Several teams of evolutionists promptly went back to their labs to count mtDNA mutations in families of known pedigree. So far, Stoneking's team has sequenced segments of the control region in closely related families on the Atlantic island of Tristan da Cunha, where pedigrees trace back to five female founders in the early 19th century. But neither that study nor one of 33 Swedish families has found a higher mutation rate. 'After we read Howell's study, we looked in vain for mutations in our families,' says geneticist Ulf Gyllensten of Uppsala University in Sweden, whose results are in press in Nature Genetics. More work is under way in Polynesia, Israel, and Europe." Gibbons also mentions that a five-fold higher rate than anticipated is found when all the available data at that time was pooled from multiple studies. Both statemenst the creationists again chose not to mention when citing the article.
"Based on this, scientists proposed that in spite of the fact the D-Loop appears neutral by every known test, we must assume neither X nor Y can be adjusted to fit the experimentally observed rate."
This is incorrect. The D-loop, as mentioned by Parsons: "While the CR [control region of the D-loop] is certainly under less selectional constraint than coding genes, the region has crucial regulatory functions and internal sub-regions display quite different levels of variation both within and between species. Some portions of the CR are thus not as free to evolve as others and it is quite plausible that selectional constraint, while clearly present, need not be absolute between one generation and the next. In this light, it is interesting to note that the observed substitution of the nucleotide at position 234 occurs w
My roomate and I grew a watermellon in our backyard last summer. It was the size of a golfball. Then the slugs ate it--since one slug stayed out in the middle of the yard until midmorning and risked being eaten by the crows it must have been darn tasty. Stupid slugs.
So, um, take THAT!
I'd really like to thank you for that link to the ICR. Several months back I was arguing the exact same issue and I was wondering where exactly the source was from. Now whenever I need to present clear-cut examples of "scientific" creationist fraud I've got another excellent example. The ICR can't even read a table correctly: the "dates" that they give for the lava samples aren't dates at all, but instead refer to how far an individual sample was from the expected concentration of Ar-40. The ICR also fails to mention that some samples had lower levels of Ar-40 than expected. The true irony is that rather than this article (Dalrymple) undermining the validity of radiometric dating, it is clearly supporting.
But don't take my word for it. Read the paper yourself: G.B. Dalrymple, "40Ar/36Ar Analyses of Historic Lava Flows," Earth and Planetary Science Letters, 6 (1969): pp. 47-55. It'll be available at (or at least through interlibrary loan) any university.
"The multiple lines of inquiry you refer to are ALL based on the assumption of chimp/human common ancestry. From a creationist stance, rejecting the predictions on that assumption in favor of the observed data is not unreasonable. The fact that the method main stream science had accepted as valid suddenly matches the bible nicely is interesting to creationists. Scientifically, they aught to do some work to confirm the validity of the method before making any claims about a method they had formerly rejected. But aside from that, on the surface this seems to be better evidence for creationism than common descent. And the data was all obtained by main stream science, using accepted main stream methods"
If we wish to test a hypothesis and expect X, and set up dozens of different experiments with different points of view based on different underlying assumptions and experimental methods, when all but one produces X, does that allow some group to proclaim Y? No. A much more reasonable approach would be to go back to that one experiment and try to find out why it doesn't match the others--whether or not you believe X or Y. This is exactly the case we have with mitochondrial eve. We went back to this dating method using the D-loop, and found that this loop does not behave as expected. It does not matter if we assume a 5 million year last common ancestor with a chimpanze or not. If we expanded the last common human-chimp ancestor to a 1-10 million year range the study would have still produced discrepancies between the D-loop and the rest of the mtDNA. If a creationist still wishes to argue that we're still making assumptions even though when we look at the fossil record we've expanded our range to a ridiculous point, then we no longer are arguing about our mtDNA dating technique but instead are arguing about paleontology and geology (and physics if they start questioning some of the radiometric dating techniques). This is well beyond the scope of the paper I referenced and again shows the difference between main-stream science and "scientific" creationists.
It depends. Both Science and Nature are not exactly what you'd call popular journals, so unless you actually do science for a living they'll probably be too technical (or at least too dry). Another reason not to get either journal is the fact that the articles are extremely terse, imagine having the work of five people over the course of two years compressed down into three pages. Both Science and Nature do have about 20-30 pages or so of broader interest bits in their "News and Views" sections and the like. Another point to consider is that some public libraries have a subscription to Science and Nature, failing that you may be able to obtain photocopies of articles through an interlibrary loan program--not sure if the public libraries do this, though. If you're still interested, Science is probably the more rounded of the two; Nature as the name implies is more biologically oriented. Size wise, the two journals are about 150 pages--again due to article compression.
/. wouldn't have so many or that they'd be so voiciferous...unfortunately you'd also be wrong.
And almost every time some article is posted that has something to do with evolution the "scientific" creationists come out of the woodwork. You'd think a technology and science website like
"Mitochondrial Eve has been shown in secular literature (ever heard of the magazine "Science") to have lived ~6000 years ago. Evidence of the flood here."
.
What's going on?! I used the exact same message (below) already once this week for the exact same argument. Fortunately somebody else already took care of the rest of your message so I don't have to.
One nit to pick. Going back to the original "Research News" article in Science (vol 279 issue 5347 pg 28-29), we see that instead of this being evidence for a ~6000 year old mitochondrial eve, we have to reconsider some of our beliefs about mitochondrial DNA (mtDNA), or more specifically a region of mtDNA called the D-loop, which comprises only 7% of mtDNA and which most mtDNA studies have used. One of the biggies is that most mtDNA studies use "so-called "noncoding" sequences of the control region of mtDNA, which do not code for gene products and therefore are thought to be free from natural selection." to quote the article. Another is to check and see if we are instead hitting "hotspots," regions with above-average mutation rates; hotspots will have more back- and parallel-mutations which will cloud the picture. A third is that the mutation rate may vary over time. A fourth is to investigate the issue of heteroplasmy--having multiple mtDNA sequences, even though for a given region there should be only one. For a while it was thought to be rare, now 10-20% of the population could be heteroplasmic. All of these issues would need to be addressed by the creationists before it could be considered evidence of a ~6,000 year old mitochondrial eve rather than a problem with the underlying assumptions of the technique. Indeed, with the advancement of our ability to manipulate and sequence DNA, we no longer have to utilize only 7% of the mtDNA--we can sequence the whole thing--all 16,000 or so base pairs of it. A recent study published in Nature (vol 408 pg 708-713, Dec. 2000) using mtDNA--all of it--found that the D-loop (used in most mtDNA studies) does not have a constant mutation rate. The study goes on to show (again using the whole mtDNA sequence) that the date of "mitochondrial eve" is about 170,000 years ago. A more reader-friendly report by the author of the Nature paper can be found here
Say, you ever get a chance to actually read that Dalrymple article you so badly mangled? Here's a refresher. Just go up the thread.
"But don't make out as though there isn't a similar tendency on the other side of the fence. Rejecting the observed mutation rate because it is too high(evolutionists) is every bit as bad as rejecting a predicted rate because it is too low(creationists)."
Is it? I think the actions of main-stream science and "scientific" creationism bear witness to the vast difference between the two. We used this dating technique for a while, and then it was discovered that the mutation rate of the D-loop that we were using was ~20 fold higher than what we expected. What happened? The creationists trumpeted it as evidence for their "model," completely ignoring other possibilities and were extremely happy with their one piece of data that they believed supported their religious view, however out of line with all other information that one bit of data might be. Main-stream scientists scratched their heads and wondered why this one bit of evidence was now so far out of line with their expectations based on information from multiple of lines of inquiry. Main-stream science looked, and in 2000 a plausible explanation and a correction for the MTeve date was published. The investigation of mtDNA, as you mentioned, still continues. As a result of the information learned, our methods may have to be slightly modified; mainly it looks like a study using the D-loop must be relegated to recent events, whole mtDNA for old events. What happened with the creationists? They stopped thinking about the issue when they could construe it to look in their favor. Worse, since it has become clear that the 6000 year old date is based on a faulty study, they failed to correct themselves. The "scientific" creationists betray themselves by their actions.
"On a related note, mitochondrial DNA seems to indicate that our common mother (mitochondrial eve) existed ~6000 years ago, less than the 70,000 years proposed here."
One nit to pick. Going back to the original "Research News" article in Science (vol 279 issue 5347 pg 28-29), we see that instead of this being evidence for a ~6000 year old mitochondrial eve, we have to reconsider some of our beliefs about mitochondrial DNA (mtDNA), or more specifically a region of mtDNA called the D-loop, which comprises only 7% of mtDNA and which most mtDNA studies have used. One of the biggies is that most mtDNA studies use "so-called "noncoding" sequences of the control region of mtDNA, which do not code for gene products and therefore are thought to be free from natural selection." to quote the article. Another is to check and see if we are instead hitting "hotspots," regions with above-average mutation rates; hotspots will have more back- and parallel-mutations which will cloud the picture. A third is that the mutation rate may vary over time. A fourth is to investigate the issue of heteroplasmy--having multiple mtDNA sequences, even though for a given region there should be only one. For a while it was thought to be rare, now 10-20% of the population could be heteroplasmic. All of these issues would need to be addressed by the creationists before it could be considered evidence of a ~6,000 year old mitochondrial eve rather than a problem with the underlying assumptions of the technique. Indeed, with the advancement of our ability to manipulate and sequence DNA, we no longer have to utilize only 7% of the mtDNA--we can sequence the whole thing--all 16,000 or so base pairs of it. A recent study published in Nature (vol 408 pg 708-713, Dec. 2000) using mtDNA--all of it--found that the D-loop (used in most mtDNA studies) does not have a constant mutation rate. The study goes on to show (again using the whole mtDNA sequence) that the date of "mitochondrial eve" is about 170,000 years ago. A more reader-friendly report by the author of the Nature paper can be found here.
A lot of it is open source; unfortunately a lot of it also epitomizes what's wrong with non-commercial software. You might have just one small group, one lab, or even just one guy who's little baby that program is. For what I've used, the majority of the open source software and freeware runs on unix, not windows, although there is a growing commitment to linux and windows that will become dominant in the next couple of years. Most of it runs. Sort of. If you're willing to fight with it. The only thing worse than the user interface is the manual, if one exists at all (although exceptions exist, such as Deep View Swiss PDB Viewer). While I'd agree that many biologists have poor computer skills, that's rapidly changing as more and more the problem is data interpretation as opposed to data acquisition. There are many subdisciplins where a good percentage of the biologists also possess some ability for computer programming (or at least script writing) just becuase that's the only way to force the software to work. I'd also agree that a CD package with documentation on a popular set of programs would be great, but that's complicated by the fact that the geneticists don't do biochemistry who don't do cell biology etc. That and getting a bunch of scientists together on something like this is like herding cats.
Might I suggest none, at least for the first year? Seriously. You don't need a computer or any gadget past a pen(cil) and paper to take notes in class and all campuses have computers adequate for typing up your papers and whatever rudimentary graphing or programming or spreadsheet needs will be for your freshman year and for some majors for all of college. Also, you won't have ready access to computer games or Slashdot while you're in your dorm or apartment eating doritos and consuming, well, whatever. I don't know about the rest of you, but the first year or three I spent way too much time playing games on the computer until I deleted them all, right down to solitare.
The actual Nature article is "Computational design of receptor and sensor proteins with novel functions," in the May 23, 2003 issue (Vol 423 No 6936 pp101-205). It is important to note that they are not making fully functional enzymes yet, but have accomplished the rather daunting task of designing/directing the evolution of a given protein binding substrate A and making it bind a new, completely different substrate B. Their wild-type substrate interacts with 12-18 residues, so multiply that by your 20 standard amino acids across these interacting residues and you have a crapload of sequences to deal with (10^15 to 10^23; I'll take their word for it). I thought the statement "Designer proteins such as this can be developed for bioremediation of weapons dump sites (TNT) and sensitive sensors of drugs/contaminants that can easily be grown in bacteria." was kind of cute as when you search Pubmed with "TNT reductase" you get back a number of articles on bacterial enzymes that allow them to munch TNT. A few years back I got to work on a project to solve the structures of enzymes that pop NO2 groups off of TNT and related compounds; the bacteria that these proteins were subcloned out of were found in the heavily contaminated soil of a former World War 2 munitions plant. Pretty cool what evolution can do when you add a new component to the environment of some organism.
When I was younger, I was a total science/technology/computers/etc. nut (ie, fellow nerdling). As I've grown older and now spend most of my day working either at a computer or at the bench in the lab at work I'm less likely to futz around with chemicals at home or mess around on my computer. Why would I want to do those things when I spend 50-70 hours a week doing something similar at work? Instead I've started reading more and more history (especially ancient), philosophy, humor, and nonfiction. Not so much popscience--too many errors in areas I'm familiar with to be enjoyable anymore. I've also taken up backpacking, hunting, and woodworking. Although that last one remains linked to work--my roomate and I swipe pallets from work and recycle the lumber into bookcases and tables and such. I'd love to take up metalworking or auto repair but the community college courses are too spendy for this poor grad student.
I know I'm not alone in my nontechnical or at least nonHIGHtechnical pursuits; U. Oregon grad students seem to enjoy a lot more outdoorsy hobbies than I would have ever imagined "nerds" doing. It's not just here: I've got a friend working at Microsoft and he says he rarely uses his home computer anymore and says its similar with a number of his coworkers--they'd rather grab a pack and go camping.
Besides just needing a balance between technology and simplicity hobbies are pretty good ways at meeting people you wouldn't normally encounter. Especially women. Think about this: which is sexier, the nerd who is a wizard programmer and their hobbies include programming and playing computer games or the nerd who's a wizard programmer and spends their weekends restoring a 54 Ford pickup or hiking or making pottery?
There's lots of cool stuff going on right now with bioremediation. My roomate's looking for a postdoc position and one of the labs he was looking at was using bacteria to gather up heavy metals. It was pretty slick: the bacteria were engineered to express proteins designed to bind metal ions on their cell surfaces. They'd eventually have so much metal bound that they would begin to fall to the bottom of your sludge pond or whatever your body of contaminated water was in and they could be harvested. For at least one metal (Mercury? Cadmium? Gonna hafta ask him.) it was looking like the settled-out engineered bacterium-laden sludge from a contaminated site was more enriched in the metal than mined ore!
This should help out a bit with cabin fever. I've lived in some cold places (upper Midwest) but damn. I imagine their problems with depression and suicide increase dramatically in the winter, so now they've got something to do. Now that I think about it, they already had one thing to do so I wonder how much the birth rate will decrease about 9 months after winter, now that they've got high-speed internet access (and pr0n).