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The "light gun" made me curious.

That's some cool tech, even if the plug is almost as big as the the gun. ;-)

I am 35 and suffer from Asthma. It was caused by allergy (usually is). My spouse is from another state, but suffers from allergy too. Neither my parents nor anyone in the family ever heard of such a thing before. I was recently shocked to find out that a significant part of population suffers from it. According to this it is a 25% population. Check out the mortality rate chart. Note that it accounts statistics only until 1995, but steady growth is evident.

Why our generation, you ask? My theory is that an air-polluting factory near my house had something to do with this. There is a number of things that we have while our parents did not.

I disagree with that. I was always able to tell when poorly made CRTs were on or off by the interference I was getting. The better ones would use better components that would better shield the radiation from being emitted, but I was always able to tell without any other signs.

The problem is that with something like this you're talking about only a very small number of people having problems with it and most people describing it are probably hypochondriacs. In my case it's a fairly well established symptom of tinnitus.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657824/

Well, it has the name of the lead researcher and the journal. I'm pretty sure this is the study: http://www.ncbi.nlm.nih.gov/pubmed/21793784?dopt=Abstract

Do you know any oncologists?

I've gone to lectures, and talked to a lot of them. I've heard that there are dumb oncologists, but I've never met one.

Oncologists are pretty smart. They *already* know the medical literature cold. There aren't that many high-quality clinical studies on a major cancer -- say, breast cancer -- and an oncologist who treats breast cancer will know them all. They may not have *read* them all, because they've heard the results of the studies when they were first reported at medical meetings. But they know them, and they understand the biological mechanisms of cancer as well as anybody knows.

And oncologists *already* use computers in those applications where it's useful. They have electronic medical records in at least the major hospitals. (Some doctors complain that EMRs make it too easy to fill up a medical record with irrelevant information that nobody has time to get through. The old paper records forced doctors to get to the point and concentrate on relevant information.)

PubMed http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed is free and probably the best medical database created for any money.

Oncologists aren't ashamed to search Google when they hit a dead end.

Peter Norvig wrote some great algorithms for Google, and they can do some wonderful things -- translate languages, finish your search request, and other amazing things.

Norvig was lucky. The kind of problems that doctors face haven't fallen to clever algorithms yet.

2 points:

(1) The best way to manage medical information is in a doctor's head. If computers can help, that's great, but don't get overconfident.

(2) You'll never know if a particular computer application works in medicine until somebody does a well-designed randomized controlled trial to find out -- the old scientific method. The results of computers in medicine are mixed. Sometimes it works, sometimes it doesn't. If your life is important, use the scientific method.

The nice thing is that its result is not just spat out of a black box--it gives a pretty accurate confidence measure, and actually links back to the articles that led it to each conclusion.

A question and a comment.

First, how do you know this? It really didn't say how it is going to get an 'accurate confidence measure'? Which leads me to my comment - the completely untested assumption here is that the answer lies in the current literature, if only you could wade through it. That isn't at all clear to me. Much of the 'best' data comes from double blinded placebo controlled studies. The big problem here is that the patients are typically carefully selected for having as few other co morbidities as possible. That's very useful from a research situation but makes the data poorly generalizable to the average patient on the street who has no particular interest in being 'simple' (or rational or compliant). The rest of the medical literature is basically crap. "Expert" opinion which turns out to be wrong as often as not. Observational studies which almost always inflate the efficacy of treatments and can only provide correlation. Much of medicine has really never been studied carefully at all.

Next, if they're using any insurance company's billing data, well you might just as well consult rabbit entrails. In the US the vast majority of that data is entered in an obfuscated, outdated and thoroughly whimsical system called ICD-9 (International Classification of Diseases, version 9). The REST of the world with the possible exception of North Korea is on 10 - a system that is much more useful. But even using one of the more sophisticated medical database systems is still unlikely to give you the detail you need to actually treat someone.

Of course, there is little useful information on how this will work - whether the doc will consult this wonderful oracle or if the insurance company will send you a form letter six months after the patient died saying you should have done something different. If they are going to go through with this,, I hope to hell they are going to carefully monitor it's success (or lack thereof) over time. And do that honestly. My money is that it won't help all that much.

Actually this has been going on for decades, since the early 70s at least, http://www.ncbi.nlm.nih.gov/pubmed/4920342 [nih.gov]. The major problems have been accuracy and having the computing power to process multi TB graphs and vast decision trees. The computer IBM is building is 80 Terra-flops, it wasn't until 98 that a 1 terra flop computer existed.

So because of you we should ban all CFLs? They don't give the vast majority of people "seizures," just you and a small minority of hypersensitive people who really have little scientific backing to their claims.

Now, if by seizure, you meant "fall on the ground, foam at the mouth and bite your tongue" I might be a little more sympathetic. I think your idea of a seizure is more along the lines of a slight discomfort due to the perception of flashing light.

is a relatively slow growing, typically aerotolerant anaerobic gram positive bacterium (rod) that is linked to the skin condition acne... Preliminary research shows healthy pores are only colonized by P. acnes while unhealthy ones universally include the non-pore-resident Staphylococcus epidermidis, amongst other bacterial contaminants. Whether this is a root causality, just opportunistic & a side-effect, or a more complex pathological duality between P. acnes and this particular Staph is not known

So it sounds like bacteria are a necessary part of it.

Homo sapiens has had more impact on biodiversity than any other species. The Great Oxidation Event lasted hundreds of millions of years and, while we have no means of establishing a survey of taxa from that era, it was most likely the result of a very large number of species, and indeed is such a long period of time that many speciation events could readily have occurred. Further, the autotrophs that released the oxygen in the first place had no means of affecting many of the anaerobes that live deep underground—and we do.

Here are your citations for humanity's impact. Suffice it to say that many of them will still be noticeable in a few million years:

• Climate Change, Human Impacts, and the Resilience of Coral Reefs
• Consequences of changing biodiversity
• A continent transformed: Human impact on the natural vegetation of Australia, which went on for something like sixty million years before we screwed it up.
• Tropical forest recovery: legacies of human impact and natural disturbances
• The Future of Biodiversity, the abstract for which starts: "Recent extinction rates are 100 to 1000 times their pre-human levels in well-known, but taxonomically diverse groups from widely different environments. If all species currently deemed "threatened" become extinct in the next century, then future extinction rates will be 10 times recent rates. Some threatened species will survive the century, but many species not now threatened will succumb. Regions rich in species found only within them (endemics) dominate the global patterns of extinction."
• Urbanization, Biodiversity, and Conservation
• Biodiversity inventories, indicator taxa and effects of habitat modification in tropical forest (PDF)

I don't know why you then decided to compare humanity's effect on biodiversity to that of mass extinction events, but let me explain to you why they are completely different.

When an extinction event occurs, there is a single source of pressure that living organisms must accommodate, or at most a couple: the sky is darker, the air is colder, the atmosphere is now filled with water rather than ammonia, et cetera. Humans have not been exerting this kind of pressure at all. We systematically destroy ecosystems, replacing hundreds of species of plants and animals with just one or two (which are, naturally, attuned to depend on us feeding, fertilizing, irrigating, and sheltering them) and we poison the water, air and soil with thousands of chemicals and chemical cocktails (an issue which is now so bad it's affecting us.)

This is too much for evolution to handle. Especially due to chemical poisoning, many of the hardiest species most likely to survive a natural disaster have been snared by exotic and unexpected genetic vulnerabilities. DDT was found to act as a sex hormone in birds, for example, causing males to develop female genitalia. As a South African, I'm sure you're aware that it's still in use, combating Malaria, even though it has been banned in many countries.

We are whittling down biodiversity in ways that the Great Oxygen Catastrophe didn't. It selected one major branch of the tree, the organisms that depended on a reducing atmosphere, and marginalized them, creating room for the healthy and d

Given that senators get older every year, you can rest assured they have never significantly cut funding for aging related research unless it was stem-cell related. For grins, you can do a full-text search for "telomerase" and "aging" in the NIH funded grant database and see how many hits you get. . .

http://projectreporter.nih.gov/reporter.cf

you'll see lots of ideas along the lines you've proposed (not exactly but close). I'm not in the aging field, but I can attest that to the fact that pretty much everyone who took cell biology with me walked out of the aging lecture thinking "why can't we fix this already", so I'm pretty sure others are trying as we speak. The devil is always in the details, of course, and from what little I do know I'm not holding my breath until we get a working gene therapy vector that doesn't give you leukemia as a side effect. . .

For what it's worth, autism isn't the only negative outcome anti-vax folks attribute to vaccination. There may not be much evidence to support most of the claims, but some of them have some meat. For instance, this study found a weak but significant risk of childhood asthma stemming from the Hep B vaccination.

Your maths sucks because it's based on incorrect assumptions, here are some real statistics...

1. Measles is one of the leading causes of death among young children even though a safe and cost-effective vaccine is available.
2. In 2008, there were 164,000 measles deaths globally – nearly 450 deaths every day or 18 deaths every hour.
3. More than 95% of measles deaths occur in low-income countries with weak health infrastructures. [do not take your non-immune kid overseas and make sure he does not come into contact with illegal immigrants]
4. Measles vaccination resulted in a 78% drop in measles deaths between 2000 and 2008 worldwide. [do the maths on that using point 2 above]
5. In 2008, about 83% of the world's children received one dose of measles vaccine by their first birthday through routine health services – up from 72% in 2000.
6. More than 20 million people are affected by measles each year. [combined with point 2 this gives a global figure of ~8 deaths per 1000 cases].
7. The measles vaccine has been in use for over 40 years. It is safe, effective and inexpensive.
Source for the above facts

Furthermore, the first 20 years of licensed measles vaccination in the U.S. prevented an estimated 52 million cases of the disease, 17,400 cases of mental retardation, and 5,200 deaths.....Although it was declared eliminated from the U.S. in 2000, high rates of vaccination and good communication with persons who refuse vaccination are needed to prevent outbreaks and sustain the elimination of measles in the U.S. - WP

Now weigh all that against - Severe side effects of the MMR vaccine:
1. Allergic reaction (less than 1 per million).
2. Long-term seizure, brain damage, or deafness (so rare that the association with the vaccine is questionable).
Source. The same source also gives a figure of 1-2 deaths per 1000 cases in the US. I could not find any credible source claiming a single death from the measles vaccine despite the fact that literally billions of people have received the jab over the last 4 decades.

It is well documented that the measles cures blindness, so I can only congratulate the orchestrators of this anti-vaccine campaign for having the vision to improve America's public health in such a manner.

Apparently, one of the major upsides of sex(from a darwinian, rather than purely recreational, perspective) of the not-intuitively-all-that-sensible arrangement of having to seek out a conspecific, risk sexually transmitted infection, and mate simply in order to reproduce, is the rapid genetic diversification you can achieve by recombining genomes with others. Your asexual organisms have it much easier; but they have to depend on mutation(or, as with some bacteria, quasi-sex genetic exchange mechanisms).

The neat organisms, in my opinion, are the edge cases that can go either way. this piece(sorry about the paywall...) examines snails that can either reproduce sexually or spawn clones asexually. As it turns out, in areas with higher parasite loads, the snails resort to sex at much higher rates in order to keep abreast of the parasite threat, while the less pressured snails go for the rapid and low-risk strategy of asexual cloning.

That's a proposal that I just made here. No self-destruct system was included in the engineered T cells mentioned in the paper. However, it's not an uncommon concept in synthetic biology, and has been included in (for example) numerous iGEM projects. It is a fairly easy pathway to construct and implement.

The minimal mammalian self-destruct mechanism probably consists of a single gene that gets turned on in the presence of a foreign steroid hormone not normally present in the body, but doesn't cause an immune response. Steroid hormones are convenient in that they can pass through cellular membranes without transport, and can directly effect the activation of genes designed to respond to them (although another gene might be required to create an appropriate DNA-binding cofactor; I don't remember my endocrine lectures that well.) This single gene can then direct the cell to produce a protein, such as the peptide described in this paper, which causes T cells to perform self-lysis (to kill themselves, typically for the good of the body.) However, more blunt instruments can be used; directing a cell to very aggressively use up all of its metabolic energy producing something useless is a common mistake often made by inexperienced genetic engineers, and usually causes the cell to die due to resource exhaustion. Thus, adding this foreign hormone would trigger self-destruction of the engineered T cells.

There are other methods, too; one could, for example, make the engineered T cells look like invaders (by introducing an adapter protein that fuses with the original receptor and turns it into a foreign epitope.) The body would then eliminate these T cells just as they originally eliminated the cancerous B cells. This has the advantage of being applicable to the original test patient (since it doesn't require genetic engineering), but requires a lot of tricky pharmaceutical engineering to prevent the adapter drug from getting destroyed before it's bound.

Look at race car drivers- almost no female drivers- yet there is no reason why women should not be as good as men

Except for the well-documented differences in depth perception, which is critical for things like judging when to brake before an upcoming turn.

There is a recent case that shows the opposite. The FDA wanted to revoke the approval for Avastin for use in metastatic breast cancer threapy due to the severe side effects and almost no measurable benefits, not to mention the expense. But some people went hysterical claiming that the FDA is taking away a valuable drug (lot of name calling and mud slinging there) despite that fact that the drug only made you more miserable while the prognosis did not change. http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0000352/ http://www.fda.gov/Drugs/DrugSafety/PostmarketDrugSafetyInformationforPatientsandProviders/ucm193900.htm

Indeed. I really do enjoy my job - all kinds of interesting, challenging stuff - but my manager is one those upward-looking sociopaths who over-promise and have to cut corners to deliver. The "cuts" are in quality and maintainability. It doesn't help that this clueless fuck couldn't handle an abstraction as simple as looping, so he cuts-and-pastes the same block ten times to handle ten different files, instead of using a single loop. Because he doesn't understand these "complex" concepts, he won't accept them in the code -any- of us deliver.

The upshot is that after dealing with this BS for 2+ years, I've now developed a physical condition from the stress: branched retinal vein occlusion. http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0004583/#adam_007330.disease.causes

I have to get stabbed - literally - in the eye every six to eight weeks to see out of my eye. Will this continue for the rest of my life? I don't know - possibly.

If this guy is that unhappy, it may cost him more than his job.

FTA: Both the National Cancer Institute and several pharmaceutical companies declined to pay for the research.

Of course they did. If you cure cancer with one shot, the cash cow of chemo drugs dries up for Big Pharma and the cash cow of donations dries up for the American Cancer Society and other 'non-profit' organization.

Paranoia is not required here. The success rate for grant applications to the National Cancer Institute in 2010 was just 17%. Roughly five out of every six NCI grant applications failed to receive funding. The margin between proposals that receive funding and those which do not is razor thin. Probably the top two-thirds to one-half of NCI proposals contain solid science that is worth doing and ought to be funded. Since the pool of government money is limited, two out of three worthwhile projects won't get funded--mostly through factors that boil down to bad luck.

This treatment is one of many, many, many gene therapy approaches in various stages of development and testing. Most such therapies haven't lived up to their promise, and so it is difficult to get additional funding in this area. I'm thrilled that these guys have managed to hit on the one-in-a-million combination of disease and therapeutic approach that finally (seems to) work, but I'm also not totally surprised that they've had some difficulty acquiring big-money funding.

I'll also note in passing that your conspiracy theory about the American Cancer Society (and other charitable organizations which fund research) is idiotic. Even if we grant the silly assumption that they're just money-grubbing, self-perpetuating bureaucracies interested only in maintaining their own longevity at the expense of cancer patients, this particular treatment is applicable to well under 1% of total cancers and well under 1% of total cancer deaths. Despite falling under a single umbrella name, cancer isn't one disease; it's hundreds of different diseases. This cancer (chronic lymphocytic leukemia) is particularly and specifically vulnerable to the type of therapy used in this study because it is a cancer of the blood (with easily-accessible-to-therapy circulating cells, unlike in any sort of solid tumor), it is relatively slow growing, and the cells involved are a very homogeneous population (easy to specifically target, at least for cancer cells). If I were an evil genius then this is exactly the sort of work I would encourage, because it looks good but will only ultimately help a very small fraction of the population.

I am linked to http://sciencealert.com.au/ and http://www.ncbi.nlm.nih.gov/ which post things to my facebook news feeds occasionally.

Quick calculations:

The body consumes 5-6 mL of oxygen at what I assume is close to STP (1), which comes out 7.14 mg of oxygen. The numbers here (2) indicate the dissolved oxygen content can be fairly high, e.g., "the optimal DO for adult brown trout is 9-12 mg/l." In as much as I assume this would be applied toward diving, dissolved oxygen tends to increase with depth. It does not seem that unreasonable to be able to process a liter of water or less per minute, if not by this mechanism, then by some other. Disposing of CO2 is actually a bigger problem, I think, as it is for the liquid breathing you link to, but I think considerable advantages open up in the context of an artificial apparatus vs. trying to interoperate with a human lung.

(1) "How much oxygen does the human lung consume?" Loer SA, Scheeren TW, Tarnow J., Department of Anesthesiology, Heinrich-Heine-University, Düsseldorf, Germany. http://www.ncbi.nlm.nih.gov/pubmed/9066318
(2) "General Information on Dissolved Oxygen," Sheila Murphy, City of Boulder/USGS Water Quality Monitoring, http://bcn.boulder.co.us/basin/data/NEW/info/DO.html

instantly he gets 500 anonymous comments trying to sell pills, "my political party is better than the other party", troll troll troll.

That reminds me, can I interest you in some tasty fudge? I've heard that it works quite well as a pain reliever for newborn babies, and also for pain relief in sexually active adult males.

Long-term population viability of Fraser River sockeye salmon (Oncorhynchus nerka) is threatened by unusually high levels of mortality as they swim to their spawning areas before they spawn. Functional genomic studies on biopsied gill tissue from tagged wild adults that were tracked through ocean and river environments revealed physiological profiles predictive of successful migration and spawning. We identified a common genomic profile that was correlated with survival in each study. In ocean-tagged fish, a mortality-related genomic signature was associated with a 13.5-fold greater chance of dying en route. In river-tagged fish, the same genomic signature was associated with a 50% increase in mortality before reaching the spawning grounds in one of three stocks tested. At the spawning grounds, the same signature was associated with 3.7-fold greater odds of dying without spawning. Functional analysis raises the possibility that the mortality-related signature reflects a viral infection.

Currently it is extremely difficult to conduct clinical trials for Alzheimer's Disease (AD) treatments since it takes a long time to determine efficacy. An effective AD biomarker such as this blood test could provide much quicker feedback to tell whether and experimental drug is working or not. See for example: The Role of Biomarkers in Clinical Trials for Alzheimer Disease

I think there's one Chinese group that already practises this, the Mosuo. http://www.ncbi.nlm.nih.gov/pubmed/1939297

So you want a real world example. Here's one that actually killed people. People died because of Vioxx. It was a mass poisoning for profit. How come no one went to jail?

Death in drug trial has been described as a "trade secret." On Vioxx, Topol wrote: "Sadly, it is clear that Merck's commercial interest exceeded its concern about the drug's toxicity" (2). More and more concerns are raised by scholars and major journal editors about the type and the quality of published evidence, often biased towards efficacy of new products. The industry, funding over 80% of trials, sets up a research agenda guided more by marketing than by clinical considerations. Smart statistical and epidemiological tactics help obtain the desired results. Budget for marketing is by far greater than for research. Massive advertising to physicians and to the public gets increasingly sophisticated: ghost writing, professional guidelines, targeting of consumer groups and manipulating media for disease mongering. Pervasive lobbying and political ties limit the independence of regulatory bodies.

http://www.ncbi.nlm.nih.gov/pubmed/18982834

I happen to be really pissed about Vioxx because I took it, and there is a history of heart disease in my family. So Merck put my life at risk by withholding negative results. Drug companies pay the bills, and this is the result. If you think this is "cherry picking", I will personally get some Vioxx for you to take. I sure I can find a bunch of other unsafe drugs that are still on the market that you can take as well. Contact me after you take some potentially fatal drug that was put on the market for corporate profit. Until then why don't you shut the fuck up, asshole.

Come now, Note my id... http://www.ncbi.nlm.nih.gov/homologene/105311 FTW or just koinkidink?

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829662/

Those of us that build UV-emitting medical devices know better, and I design lamps from the ground-up.

Because these magnetic particles are less mobile than drugs, there is a good chance they'll tend to stay put and only damage the tumour and local tissue, rather than harming the organism as a whole.

The solution to this is to use guided magnetic targeting. Basically, drugs are encapsulated in a magnetic nanoparticle and injected into the bloodstream relatively close to the cancer site. A magnetic field focusing on the cancer site attracts these particles and the drugs for the most part do not reach non-cancerous parts of the body

http://www.ncbi.nlm.nih.gov/pubmed/15257686

To a homosexual that likes fat, bald FAIL posters pershaps. ... You say a guy's handsome, when you're probably a male yourself

What's the matter, APK... you can't admit when another man is good-looking cause you're afraid you'll get a woody or something? According to this link homophobia is associated with homosexual arousal. http://www.ncbi.nlm.nih.gov/pubmed/8772014 sounds like you're probably a closet fag, APK.

And learn to fucking spell, dickwad. "pershaps"? Not only are you a closet fag but you're apparently an idiot too.

Taxpayer funded research should not be behind pay walls or restricted in any other manner. Exception for information with military applications...mostly.

Can somebody who follows this more closely help me with this?

The National Library of Medicine compiled an internal database of almost every significant medical journal article. With encouragement from Al Gore, they made it free on the Internet as PubMed (on the theory that the public should have free access to the product of tax-funded work). http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed

Either the NLM or another government agency also created a database of articles about chemistry. They also wanted to make it public. However, the American Chemical Society was producing a proprietary database, which it licensed very profitably, which did the same thing, and the free government database would have replaced it. The ACS successfully lobbied the government to prevent the agency from making this database free to the public like PubMed.

Is this correct? Is this the same database?

Really, the only problem with journals now is regarding older material. The NIH is the largest government funding source for biomedical research in this country, and they set a requirement for results to be in open-access or accessible formats for NIH-funded work. This means that new work funded by NIH grants, even if it is published in Nature or other notoriously expensive journals, will have its published results available free of charge.

Of course, academics are aware of the problems getting to other expensive journals and their archives. If you can find someone on the inside sympathetic to your cause, you can probably work something out. I won't name names, but I was able to talk a friend of mine at a large university to let me set up an old Linux system in his lab, that automatically sets up an X-forwarding reverse SSH connection to my own system at home. The result of that of course is I can run an X application on that system - which is inside their network - anytime I want access to journals that they subscribe to.

Certainly other people could make similar arrangements through friends, friends-of-friends, or similar.

Taxpayer funded research should not be behind pay walls or restricted in any other manner

The largest funding source for biomedical research in the US is the National Institutes of Health (NIH). They recently passed a rule requiring NIH-funded work to be published in an accessible manner. This has had some interesting results, as now journals such as Nature and Science have ways to release articles to the public so that they can be in their high-impact journals and accessible freely.

Of course, this only applies to grants that are approved 2010 and onwards; work funded by older grants does not need to worry about this. However, grants that are were issued originally prior to 2010, and are being renewed, do.

In other words, less federally funded work is published behind paywalls now than ever before.

It is already against the law to discriminate based on genetics. You claim that the FCRA is 'violated as a matter of course' - do you have any actual evidence of that?

And before you say 'well just because there is a law against it doesn't mean companies won't do it', why would a law against data mining mean companies won't do it? If you're so paranoid as to believe that people are going to discriminate against you based on genetics, in spite of laws against that, then don't give your genes to anyone, ever, because any one of them could break the relevant laws and use that information against you.

That would be discrimination based on genetics, which is against the law.

... for now. :)

That would be discrimination based on genetics, which is against the law.

'I wonder exactly how far medicine has been set back by this.'

No measurable distance. The summary is rather misleading and the arXiv article isn't exactly clear, either. The previous letter they reference (and co-author) is clearer:

http://www.biotechniques.com/BiotechniquesJournal/2009/December/Letter-to-the-editor-Unexpected-presence-of-mycoplasma-probes-on-human-microarrays/biotechniques-181035.html?service=print

Basically a couple of tiny fragments have been found in the public DNA sequence databases that were misclassified as human, presumably because they were derived from cDNA 'libraries' constructed from cells contaminated with mycoplasma. These sequences are NOT part of the reference human genome sequence. They exist only as small independent files supposedly representing fragments of genes expressed in human cells:

http://www.ncbi.nlm.nih.gov/nuccore/af241217
http://www.ncbi.nlm.nih.gov/nucest/DA466599

but really mapping to mycoplasma sequences. Unfortunately a commercial provider used one of these files in the (semi-automated) design of a microarray. A probe for a sequence like this (one of many thousands on the array) would generally be harmless, since it does not detect a human sequence. Rather embarrasingly, it did appear to give a positive result in some publicly available data sets from researchers who used the array. This suggests that the cells used by these researchers were also contaminated with mycoplasma. So the problem isn't so much an insidious 'in silico' contamination of databases by bug sequences, but rather the actual contamination of cell cultures by mycoplasma, which suggests sloppy lab technique and a lack of routine testing.

'I wonder exactly how far medicine has been set back by this.'

No measurable distance. The summary is rather misleading and the arXiv article isn't exactly clear, either. The previous letter they reference (and co-author) is clearer:

http://www.biotechniques.com/BiotechniquesJournal/2009/December/Letter-to-the-editor-Unexpected-presence-of-mycoplasma-probes-on-human-microarrays/biotechniques-181035.html?service=print

Basically a couple of tiny fragments have been found in the public DNA sequence databases that were misclassified as human, presumably because they were derived from cDNA 'libraries' constructed from cells contaminated with mycoplasma. These sequences are NOT part of the reference human genome sequence. They exist only as small independent files supposedly representing fragments of genes expressed in human cells:

http://www.ncbi.nlm.nih.gov/nuccore/af241217
http://www.ncbi.nlm.nih.gov/nucest/DA466599

but really mapping to mycoplasma sequences. Unfortunately a commercial provider used one of these files in the (semi-automated) design of a microarray. A probe for a sequence like this (one of many thousands on the array) would generally be harmless, since it does not detect a human sequence. Rather embarrasingly, it did appear to give a positive result in some publicly available data sets from researchers who used the array. This suggests that the cells used by these researchers were also contaminated with mycoplasma. So the problem isn't so much an insidious 'in silico' contamination of databases by bug sequences, but rather the actual contamination of cell cultures by mycoplasma, which suggests sloppy lab technique and a lack of routine testing.

And its reported schizophrenia links.

Hmm this isn't really true now is it? For the record, NOBODY knew what the actual final standard for US healthcare would be until Sept 2010 (although the preliminary final ruling was July 2010, but still...). While ICD9 to 10 may have taken ten years, there was no reason to believe it was going to float to the top of the coding systems expected for use until it was written into the federal register last year. And its not like there's a ton of options or anything that could have replaced it, making early adoption risky and potentially pointless or anything.

Interesting where this bacterium was isolated from:
Rhodococcus jostii sp. nov., isolated from a medieval grave.

"The taxonomic position of a bacterial strain isolated from the femur of the remains of Jost Lucembursky, margrave in Moravia, Brno (Czech Republic), was investigated by phenotypic, chemotaxonomic and molecular taxonomic methods..."

Haven't termite gut bacteria been known to digest wood for years?

Maybe. Sort of. Perhaps. I had thought so as well, but a quick Google search indicates that those bugs are not well characterized. Having a single organism with a defined enzyme is obviously an easier system to scale up than the stomach of an insect.

As has been pointed out elsewhere in this thread, if municipalities were really interested in accident reduction, they would increase the length of yellow lights before they installed red light cameras. I won't argue that careless people cause accidents that is self evident, but there is no reason that we should actively increase the chances of putting people in a situation where carelessness leads to an accident.

As for whiplash, you DO in fact get whiplash when hit from behind. A good, properly adjusted (most are not) headrest will decrease the chances of whiplash, but they are not eliminated. In fact, some studies http://www.ncbi.nlm.nih.gov/pubmed/15667814 have shown that firm headrests will INCREASE the chance of whiplash, not decrease it.

But you've entirely sidestepped the point of my original post. A question like "So which is better, a rear-end collision outside the intersection, or a broadside collision inside the intersection?" alone is pointless. You can't consider the question without looking at more data.

okay.
There is this one: http://www.ncbi.nlm.nih.gov/pubmed/10926722
This one : http://www.ncbi.nlm.nih.gov/pubmed/19035449
This second one brings up an important point also mentioned by the_raptor to my previous post... The cancer may have occurred from the exposure to the exciters. Separating both is difficult obviously.

But you also have studies that show no correlation between high-exposure environment and cancer rate, like this one (also mentioned above) :
http://aje.oxfordjournals.org/content/155/9/810.full
or this one :
http://www.ncbi.nlm.nih.gov/pubmed/20570865

which is directly contradicted by this one showing totally opposite conclusions :
http://www.bfs.de/de/elektro/papiere/Stellungnahme_Naila/

So there is no unambiguous word on cancer incidence due to exposition to non-ionizing radiation. In the best case you could say the it is inconclusive. But stating that it is impossible that the exposure of non ionizing radiation, namely radiation at longer wavelength than UV, cannot cause cancer is about as false (or as true) as saying it does cause cancer without a doubt.

okay.
There is this one: http://www.ncbi.nlm.nih.gov/pubmed/10926722
This one : http://www.ncbi.nlm.nih.gov/pubmed/19035449
This second one brings up an important point also mentioned by the_raptor to my previous post... The cancer may have occurred from the exposure to the exciters. Separating both is difficult obviously.

But you also have studies that show no correlation between high-exposure environment and cancer rate, like this one (also mentioned above) :
http://aje.oxfordjournals.org/content/155/9/810.full
or this one :
http://www.ncbi.nlm.nih.gov/pubmed/20570865

which is directly contradicted by this one showing totally opposite conclusions :
http://www.bfs.de/de/elektro/papiere/Stellungnahme_Naila/

So there is no unambiguous word on cancer incidence due to exposition to non-ionizing radiation. In the best case you could say the it is inconclusive. But stating that it is impossible that the exposure of non ionizing radiation, namely radiation at longer wavelength than UV, cannot cause cancer is about as false (or as true) as saying it does cause cancer without a doubt.

okay.
There is this one: http://www.ncbi.nlm.nih.gov/pubmed/10926722
This one : http://www.ncbi.nlm.nih.gov/pubmed/19035449
This second one brings up an important point also mentioned by the_raptor to my previous post... The cancer may have occurred from the exposure to the exciters. Separating both is difficult obviously.

But you also have studies that show no correlation between high-exposure environment and cancer rate, like this one (also mentioned above) :
http://aje.oxfordjournals.org/content/155/9/810.full
or this one :
http://www.ncbi.nlm.nih.gov/pubmed/20570865

which is directly contradicted by this one showing totally opposite conclusions :
http://www.bfs.de/de/elektro/papiere/Stellungnahme_Naila/

So there is no unambiguous word on cancer incidence due to exposition to non-ionizing radiation. In the best case you could say the it is inconclusive. But stating that it is impossible that the exposure of non ionizing radiation, namely radiation at longer wavelength than UV, cannot cause cancer is about as false (or as true) as saying it does cause cancer without a doubt.

Just because it's non-ionizing radiation doesn't mean it can't damage cells, or alter proteins. Otherwise a microwave oven wouldn't be able to cook stuff. Or people wouldn't have to be careful about radar exposure[1].

Damage cells enough and the odds of cancer go up.

The risks are probably not that high (compared to smoking and some toxins). But the phones often operate rather close to heads. And there are measurable effects ) http://jama.ama-assn.org/content/305/8/808.abstract ). So I'd keep my cellphone usage as low as possible. Maybe some people's brains can take it (or might even do better) but others might not fare so well.

[1] http://www.ncbi.nlm.nih.gov/pubmed/10926722

But (unless I missed a memo) we actually don't know what conditions the first life formed in. Although we tend to focus on the ocean environment, it's entirely possible that the first cells formed in some more exotic deep crevise and only later migrated to the surface. In many ways, walking around in the open air makes *us* one of the most exotic extremophiles of the world.

Here is one of the later memos. Yes, the conditions on earth at the beginning of biogenesis (as opposed to the other Genesis) were very, very different that the current environment. We wouldn't like it at all. Many theories of biogenesis use solid phase chemicals (like various clays) as early catalysts and / or structural parts of the earliest life forms.