Slashdot Mirror

In spite of Microsoft claims to the contrary, open source is helping to cure cancer.

Sagres Discovery (my employer) takes advantage of naturally occuring retroviruses in mice to identify genes that cause cancer. This isn't novel technology (in fact its been around for nearly 20 years), but Sagres has turned it into a high throughput saturation screen with robotics,open source bioinformatics tools, and clustered Linux computing.

The Bioinformatics Open Souce Conference conference was held in Endmonton, Canada last week. In one of many projects moving towards open source standards and information, the National Cancer Institute announced caBIO, an open API for accessing NCI's comprehensive cancer databases.

Could you please provide a reference for these vectors, as I searched PubMed for "recombinant retrovirus tet GFP SIN" and found nothing (I also tried using "tat" instead of "tet" with the same result :). I really am curious about this.

"Their LTRs (control centers) lack promoters and enhancers, they lack Psi packaging signals for the viral RNA to be packaged, and (once integrated into the cell's genome) lack all lentiviral/retroviral structural genes (gag, pol, env, rev, tat, etcetera) which make a virus a virus."

You indicate that the recombinant is integrated into the cellular genome, and lacks the necessary structural/regulatory coding sequences "once integrated into the cell's genome." From that statement, I take it that the viral vector contains at least the gag, pol, and env coding sequences along with the GFP marker transgene. Or are the retroviral proteins provided in trans in producing the infectious vector? Also, if the vectors "lack promoters and enhancers", how is the GFP (or any other transgene) expressed? Perhaps you meant that the vectors lack the promoters/enhancers associated with the wild-type virus?

"If in the event that this vector infects a cell already infected by a real pathogenic lentivirus (ie HIV-1)where the structural genes already are (in trans) it STILL wouldn't generate further vector virions because the viral vector provirus lacks LTRs to transcribe the viral RNA, and even if it somehow was transcribed it couldn't be packed into the protein particle as it lacks the RNA secondary structure element known as the psi signal. So no "new hybrid cell/virus that carries the deadly portion and the reproduction capability". No way of that happening that I can think of."

Though I don't know the details of the vector(s) you are using, I don't see how something lacking at least some LTR sequences is still a lentiviral/retroviral vector. How does a construct become described as a retroviral vector let alone become a provirus, in the accepted meaning of those terms, without LTR sequences? In short, it doesn't. So there must be some LTR sequences present.

As to "No way of that happening ..." in the event of a wild-type provirus (of the same type) already present in the cell providing biological functionality in trans, such that a "new hybrid cell/virus that carries the deadly portion and the reproduction capability" would be formed, I can certainly envision the mechanism for how that can happen, even without the psi signal being present in the incorporated vector.

Hint: Think of the retroviral replication mechanism, the fact that retroviruses are double-stranded RNA viruses, the fidelity of the replication and reverse transcription process, and the availability of all necessary processing and packaging functionalities available in trans from the wild-type provirus.

Please, if you would, provide one or more PubMed references as to this/these vectors (not the older stuff that I already know about :-)

Just to correct on minor misstatement on my part. The genetic defect in question does not necessarily cause anxiety disorders, it simply makes one prone to them. Usually external events trigger them. Afterwards they sort of feed on themselves. I can point you to a great deal of literature on the subject if you'd like to refrain from making ignorant comments about it in the future.

Here are some places where you can begin to educate yourself.

Go to the source man! I generally refuse to make any comment on any scientific study until I've read the publication. Those of you submitting stories on a new biomedical science publication, please remember to at least point to the PubMed abstract of the paper. For those of you wanting to comment on the study, please read it, before doing so. If any of you can provide free access to the paper, please post it here! Thanks.

Go to the source man! I generally refuse to make any comment on any scientific study until I've read the publication. Those of you submitting stories on a new biomedical science publication, please remember to at least point to the PubMed abstract of the paper. For those of you wanting to comment on the study, please read it, before doing so. If any of you can provide free access to the paper, please post it here! Thanks.

Not according to a study done by the U.S. Department of Health and Human Services (PDF format). Scientific Evidence on Condom [ In ]Effectiveness for Sexually Transmitted Disease (STD) Prevention

The important facts are that there is NO proof that condoms provide any protection from gonorrhea, chlamydia, trichomoniasis, chancroid, syphilis, genital herpes, or human papillomavirus. Here's a simple chart with important details. 10,000 physicians agree. Read more.

Condoms protect against HIV/AIDS only 85% of the time.

In contrast, abstinence has a 100% success rate in preventing every STD that exists. It works every time it's applied! (I no more need a "study" to prove this figure than I need a "study" to prove that unplugging my CAT 5 cable/phone line prevents my computer from acquiring viruses via the Internet.) Abstinence is totally free and available to all, regardless of socio-economic status.

Abstinence is "self denial" in the same way that seat belts, traffic lights, guard rails, and stop signs are forms of self denial. They are there to give you guidance; they exist to benefit you, not to oppress you. If you "liberate" yourself from wisdom and sage advice, you are running full speed over a cliff. Your pride tells you that you are being suppressed and limited from things that are good. In reality, you are being liberated from destructive acts so that you will be free to live to your full potential with prosperity and sound mind and body.

IWAMB (I was a molecular biologist, until I discovered programming paid better, at least before the last round of layoffs...)

This news should not be surprising. The technology to synthesize multiple large genes has been around for years; and it has been known that the pieces could be combined in a host cell to yield whole, infectious virions. The novel thing here is that somebody has combined the two technologies, creating the polio genes synthetically before putting them into a host.

Two older articles describing the combination of cloned viral genes in vivo to make infectious virus are:
This article showed that the bovine herpesvirus genome could be cloned into a bacterial vector, maintained indefinitely, then reintroduced into cow cells to produce active virions.
This article showed that infectious rabies virus could be produced by putting cloned rabies genes into a suitable host.

Nowdays, if you have a gene sequence, you can synthesize it in pieces and assemble it (with modifications, if you choose) with PCR quite easily. You don't need any source material from the original organism. I synthesized a small gene from scratch myself, once, back when I was an underpaid M.S. in a biotech company.

Of course, I never tried this with a whole FREAKIN' POLIO VIRUS!!!!! WTF!!!! Didn't these guys ever read "The Stand"?!

-dexter ("Don't Fear the Reaper", my ass) riley

IWAMB (I was a molecular biologist, until I discovered programming paid better, at least before the last round of layoffs...)

This news should not be surprising. The technology to synthesize multiple large genes has been around for years; and it has been known that the pieces could be combined in a host cell to yield whole, infectious virions. The novel thing here is that somebody has combined the two technologies, creating the polio genes synthetically before putting them into a host.

Two older articles describing the combination of cloned viral genes in vivo to make infectious virus are:
This article showed that the bovine herpesvirus genome could be cloned into a bacterial vector, maintained indefinitely, then reintroduced into cow cells to produce active virions.
This article showed that infectious rabies virus could be produced by putting cloned rabies genes into a suitable host.

Nowdays, if you have a gene sequence, you can synthesize it in pieces and assemble it (with modifications, if you choose) with PCR quite easily. You don't need any source material from the original organism. I synthesized a small gene from scratch myself, once, back when I was an underpaid M.S. in a biotech company.

Of course, I never tried this with a whole FREAKIN' POLIO VIRUS!!!!! WTF!!!! Didn't these guys ever read "The Stand"?!

-dexter ("Don't Fear the Reaper", my ass) riley

The funny thing, the sequence for smallpox has been available for quite some time at NCBI (National Center for Biotechnology Information, as are the sequences for at least 2000 viruses and phages (per my last count).

I'm all for public knowledge of such sequences if they lead to productive research in the areas of disease control. However, with the current technology of being able to construct viruses from sequence data, it might be prudent to restrict such data to only respectable research centers.

One of the more prominent deaths from virally-mediate gene therapy was Jesse Gelsinger. You are probably thinking of him. That page is pretty comprehensive in terms of describing why he died, and the metabolic defect that they were trying to correct.

The clinical trial that he was taking part in was immediately halted, and there was some soul-searching in the scientific community for a while. But a quick search on gene therapy indicates that it's still quite an active area of research (look here, sort by date).

A while ago, gene therapy was discussed on Slashdot. I found a couple of good articles on the future and hazards of using viruses to deliver corrective DNA to diseased tissue. Follow the link to them from my Web site, unless you're the copyright police! Hope they are helpful.

Expression of Mouse Interleukin-4 by a Recombinant Ectromelia Virus Suppresses Cytolytic Lymphocyte Responses and Overcomes Genetic Resistance to Mousepox

Oh shit.

What if, say, a virus could be designed to destroy cancer cells?

Spore survival in space

There are two from hundreds of links from PubMed on NASA research.

Spore survival in space

There are two from hundreds of links from PubMed on NASA research.

Spore survival in space

There are two from hundreds of links from PubMed on NASA research.

You maintain your right not to reproduce by maintaining your responsibility to keep your pants up. It's an issue of self-control. To women: don't get drunk and go to wild parties where sexual predators are waiting to impregnate you at your most vulnerable moment. Sexual intercourse sets in motion the process of reproduction. (duh) You choose not to reproduce by choosing not to fornicate. When you choose to have sex, you are choosing to be a mother for the rest of your life -- to carry out the responsibilities, duties, and sacrifices of motherhood and possibly grandmotherhood. You may or may not conceive, but you are fully aware that the likelihood exists.

Condoms don't work all the time, and only stop about 98% of sexually transmitted diseases

98%? Where do you get that figure?

That's not a good enough reason to demonize contraceptives

I got your reason to demonize right here! It's a study done by the U.S. Department of Health and Human Services (PDF format). Scientific Evidence on Condom [ In ]Effectiveness for Sexually Transmitted Disease (STD) Prevention

The important facts are that there is no proof that condoms provide any protection from gonorrhea, chlamydia, trichomoniasis, chancroid, syphilis, genital herpes, or human papillomavirus. Here's a simple chart with important details. 10,000 physicians agree. Read more.

Condoms protect against HIV/AIDS only 85% of the time. If you knew that you had 15% chance of winning the lottery, wouldn't you enter every time? If you have 15% chance of dying, why do you play the game? It's funny how optimism is oblivious to statistics.

Another problem is that researchers can go months, even years on wrong information, and theories. If these were published, yes theres a possibility they could be discounted, but they could be perpetuated, with lots of wrong data all over the place.

How is this different from any other science. I mean, in physics, there's lots of papers out there that will eventually be shown to be wrong. That's how science is supposed to work.

It's a shame that biology has become so profitable. Hoarding data and discoveries is not how science advances. The history of chemsitry and physics are ample illustrations of that fact.

PubMed

Comma, duh.

A diet high in saturated fat can raise your LDL, which can get damaged; this doesn't make you fat, however.

The important thing to remember is that it isn't what calories, but how many.

The Atkins diet induces a state called Ketosis (as in Ketone) where the products of fat breakdown (for energy) accumulate and cannot be used to make more energy; these products act as apetite suppressants and help people diet. A breakdown product of sugars (it happens to be called pyruvate) allows you to metabolise these ketones. So, if you eat fat but no sugar, the fat can't be burned for as many calories and produces compounds that help suppress your appetite.

This may not have beneficial effects on your health. My Dad (who is a nutritionist) is extremely leary of it - not because it won't make you lose weight (it will,) but because it may not have overall beneficial effects on your health.

The thing that demonstrably has a beneficial effect is EXERCISE.

In the case of Type II diabetes, which is muchw worse to get than heart disease, even very mild interventions (150 minutes of activity per week, slight reduction in Caloric intake) cut the risk of getting diabetes by 58%.

That's not a great big shock for doctors, but it is for the weight-loss industry, which is trying to convince you that you have to be thin to be healthy. You do not; if you're obese, your health benefits from being thinner, but even a (relatively, very slight) drop in weight can be of great benefit.

• Your body fat doesn't just sit there. It makes estrogen-like hormones. Even in guys. The more of these you have circulating, the more likely your prostate (or your breasts--yes, males too) will develop a tumor.
• It correlates with colon cancer. Cause unknown.
• Fat-soluble anything gets stored in your fat. If you have lots of fat, any fat-soluble poisons (natural or man-made) that you consume have a place to stay. Less fat, less room for stored fat-soluble molecules.

Okay, I'll agree the summary of the article is rather fitting and somewhat funny, but the rest of Restil's comments are in very bad taste.

In case no one noticed, the guy is mentally ill. He has serious problems, and they are not his fault. He didn't chose to "drive himself into depression" or any such thing. Manic depression (aka bipolar disorder) is one the most clearly nuerochemically linked and genetically linked mental illnesses there is. It's hardly his fault that some of his nuerotransmitters receptors are functioning incorrectly. Unlike simple (unipolar) depression, manic depression can't be solved by talk therapy alone, it is a physical illness of the brain that must be controlled with medication.

Yes, he's paranoid. Yes, he seems unable to hold a job. Yes, he has suicidal epsiodes. Is this his fault? No! He has a disease that literally makes his mind unable to function the way a normal person's does. Join the rest of us in the 21st century and quit blaming the patient for something beyond his control.

In the mean time, moderators, why am I reading this distasteful junk at Score:4?

For more info on bipolar disorder, see here, here, or here.

I've been to many of their events and know people there: the EFF isn't rolling in money- quite the opposite. It really is a non-profit, and money is their limiting factor: more money = more cases they could take. Far fewer people donate than you'd think, including people who have directly benefited from their work (if you're at a US internet security or encryption company that hasn't donated, try to change that!). They try to be at or ahead of the curve on tech issues, and this means that its harder to get the grandparent sympathy donation(2). And their main donation source- us, the techie crowd- just hasn't been doing to well lately. Unfortunately the number of cases the EFF should fight doesn't go down in an economic downturn, its probably the opposite: Congress is chumming for dollars with Disney / MPAA more than ever.

(1) in the economics sense

(2) If the EFF was a medical nonprofit, they wouldn't be the ones with the big-eyed sick children, they'd be the ones worrying about prions 20 years ago. Harder to explain, but often more important.

What happens when science reaches the point where we can have the biological equivalent of CNC mills?

We would call them ribosomes. :)

What are the ethical issues involved?

Currently, the best source for stem cells is a human embryo. But using human material, such as aborted fetuses, in research is a contensious issue because it can be construed as the sacrifice of human life for scientific progress.

source

Even if much of the potential of adult stem cells is realised, there are circumstances where they are unlikely to be useful.... The isolation and growth of adult stem cells have to date proved very difficult. Stem cells generally represent a very small proportion of cells in adult tissues. Unambiguous identification is difficult as their presence in a tissue or mixture of cells is generally inferred from a research observation rather than indicated by any specific biochemical marker which might aid their purification... Current understanding of the potential of adult stem cells for redifferentiation is still very limited. Although many studies suggest that such processes occur, there is often a degree of ambiguity... In their natural location in the body adult stem cells do not exhibit great potential for differentiation into new cell types but have evolved to give rise only to specific cell lineages.

House of Lords report

While adult stem cells hold real promise, there are some significant limitations to what we may or may not be able to accomplish with them. First of all, stem cells from adults have not been isolated for all tissues of the body. Although many different kinds of multipotent stem cells have been identified, adult stem cells for all cell and tissue types have not yet been found in the adult human. For example, we have not located adult cardiac stem cells or adult pancreatic islet stem cells in humans. Secondly, adult stem cells are often present in only minute quantities, are difficult to isolate and purify, and their numbers may decrease with age. For example, brain cells from adults that may be neuronal stem cells have only been obtained by removing a portion of the brain of epileptics, not a trivial procedure.

Stem Cells: A Primer

"This shows us that the genetic code, and therefore, evolution is much more plastic than people might have thought."

"I think this work will cause researchers to start looking at genetic sequences that they might have thought at first were simply aberrations," he said. "Instead, they might signal discoveries like ours."

Or maybe people already know that. It's already well established that different organisms use different translation tables when synthesizing proteins. The NCBI lists 17 such tables in their section on gene transltation. Heck, the human nucleus and mitochondria use different translatation tables! Is it really such a surprise that those differences might occasionally include an additional amino acid?

"This shows us that the genetic code, and therefore, evolution is much more plastic than people might have thought."

"I think this work will cause researchers to start looking at genetic sequences that they might have thought at first were simply aberrations," he said. "Instead, they might signal discoveries like ours."

Or maybe people already know that. It's already well established that different organisms use different translation tables when synthesizing proteins. The NCBI lists 17 such tables in their section on gene transltation. Heck, the human nucleus and mitochondria use different translatation tables! Is it really such a surprise that those differences might occasionally include an additional amino acid?

omfg you flaming faggot queerballs. would you like me to stick a brick inside your anus?

A query on Pubmed returns 491 results. It seems that at least some scientists regard Halitosis as a medical term/phenomenon.

The LONGER the material is radioactive the LESS harmfull the radiation from the material is.

Yup. For instance, Uranium 238 has a half-life of about 4 billion years, which means that a given quantity of U-238 is safer than the same quantity of just about any other radioactive isotope.

The problem with PU isn't the radioactivity it has, it is the fact that it is a heavy metal which is very toxic much like lead. With soemthing that stays "hot" for a 100,000 years the toxicity of the material is what your concerned about not the radiation.

This part is incorrect. Pu is indeed a heavy metal, but it is almost completely insoluble in water (with a concentration expressed in parts per million). Another heavy metal is Bi (bismuth), the active ingredient in Pepto-Bismol. If Bi were water-soluble, Pepto-Bismol would be a deadly poison, as it is immediately right of Pb (lead) and two rows down from As (arsenic). (Bi also has the interesting distinction of being the heaviest element with at least one stable isotope.) In addition, Pu-239 (both the most common and the most stable Pu isotope) has a half-life on the order of 20,000 years, making it a rather "warm" isotope. To get a medically significant amount of Pu into your bloodstream by ingestion in a single incident, you would need to swallow a significant fraction of a kilogram of the metal, which would be more than enough to blast your intestinal epithelial cells with a strong alpha burst. The 100,000 year figure in the article takes into account (a) secondary radioactivity induced by the waste in the surrounding materials, and (b) the composition of the waste. Fission waste is a blend of many radioactive isotopes of widely varying half-lives: some "hot", some "warm", and some "cool".

If the U.S. bureaucracy would stop sheep-bleating and pull its collective head out of its ass and pay attention to ongoing fission research, they would find out that the Yucca Mountain project is totally unnecessary because the time it takes for fission waste to cool could be dramatically cut by re-"burning" the waste mixed in with fresh fuel, allowing the "warm" waste to become "hot", thus reducing the danger to a span of a mere century or two at most. They would also start the gears turning on building plants based on the fuel-pellet design operating in Europe, where an overheat of the (liquid metal) coolant causes the fission reaction to spontaneously stop without human intervention and without risk of hydrogen explosions, eliminating the most prominent dangers of traditional fission reactors.

Unfortunately, they're opposed to the former because it's the same process used to turn U-238 into Pu-239 in the first place, making it a "security risk" (Waste recycling is a security risk, but multiple tons of highly radioactive waste stored at a well-known location for 100,000 years isn't?), and they're opposed to the latter because the voting public is anti-nuclear-anything. (Better ban smoke detectors next, they use Americium created in fission reactors!)

Sigh

The behavior of receptors (the actual membrane proteins that do something when neurotransmitters bind to them) themselves is actually quite straightforward and easy to quantify in a large percentage of cases. The big problems come afterwards. One of them is understanding how the input from the receptors is added up into an output in terms of firing. If you have access to a university library, you could get a copy of a review article here. However, firing is NOT binary or remotely computer-like in any way. The whole idea that there are useful brain-computer analogies to be drawn is entirely misguided and has poisoned the way too many people think about brain function. Firing is not necessarily a discrete event because there are multiple types of firing (burst spikes vs. normal spikes, etc.). Also, the temporal PATTERN of spikes matters and influences how later information is processed both pre and post-synaptically. And how a neuron processes the spatiotemporal pattern of inputs it gets from the thousands of other neurons it's connected to is not understood. It's extremely complex, and unfortunately not the kind of thing you can just read a web page and pick up. A good low-level neuroscience textbook is Kandel & Schwartz's _Essentials of Neural Science_, but if you have a strong quantitative background and are serious about understanding these things, you might want to check out Koch's _Biophysics of Computation_ (which sticks mostly to computation in single cells as opposed to networks of them) or Dayan and Abbott's _Theoretical Neuroscience_.

Since these viruses infect bacteria and not eukaryotic cells, you can more specifically refer to them as bacteriophages. But while I see your point regarding knee-jerk reactions to terms like "cloning" and "viruses," at the same time, people have been using viruses for non-malignant purposes for quite a long time already, specifically for the purpose of immunization. The first scientific demonstration of this was way back in 1796 (with the use of the cowpox virus to immunize people against smallpox.) Immunization has gotten so commonplace that I don't think that too many people worry about having to be purposefully infected by a live attenuated virus like measles or mumps or rubella in order to go to school or work at a hospital. While there will definitely be some phobic people out there, I think that the utilization of viruses has become so relatively mundane that it won't be as big a deal as with cloning or even the theory of evolution.

And also, I'd like to add that the idea that cancer can be caused by just a single mutation caused by a single hit (yes, that's called 'the single hit hypothesis') is not very popular anymore. Most people agree there has to be some acumulation of damage before things go bad enough to produce cancer. That would explain why your risk of getting cancer increases as you get older, for instance. Have look here for some concepts.

Maybe now he'll volunteer for immediate contribution to the visible human project. Hey, it's only fair.

You can't lose the space because slashcode adds it on purpose to prevent you from posting long unbroken strings of characters and widening the page. If you must include a link, then do it as html source:

<a href="http://goatse.cx">Important Information&lt/a>

So your link would be: like this

Second, I can not recall a specific name for this condition. I shall try and explain what happens the best I can. The right side of my brain, usually associated with artistic thought, dominantly handles my sences. Basically, I sence things like I am left handed. I am not left handed however, the left side of my brain is the dominant controler of my moter skills making me right handed. This causes problems because I do not sence things the same way most people do, I may find some obsure meaning from a situation where just about everyone else picks up on the logical meaning right away. On the other side of the coin, when I try to express myself, I have trouble expressing the parts of my ideas that "paint the picture." For the record now, up until this point I have been writing for about 25 minutes. As stated in the previous post, I can overcome some of this by concentrating harder. But, it has a tendancy to burn me out quicker mentally.

In addition, although not disabilities, I have Dysthymic Disorder [basically long term (~10 years) mild depression] and Avoidant Personality Disorder (I do not like being with groups of people, but am not hostile towards them.) These are my souvenirs from America's wonderful public educational system.

Thanks for taking an interest.

40 minutes

Not only that, but the gene at fault is actually the gamma subunit of the interleukin-2 RECEPTOR whose gene lies on the X chromosome. The interleukin-2 gene is located on chromosome 4.

The entire human genome is available for free searches thanks to the NIH and your hard-earned tax dollars. Have fun searching for your favorite genes using the NCBI's Map Viewer.

More pedestrian information on SCID can be found here.

Not only that, but the gene at fault is actually the gamma subunit of the interleukin-2 RECEPTOR whose gene lies on the X chromosome. The interleukin-2 gene is located on chromosome 4.

The entire human genome is available for free searches thanks to the NIH and your hard-earned tax dollars. Have fun searching for your favorite genes using the NCBI's Map Viewer.

More pedestrian information on SCID can be found here.

That's just one of the problems with gene therapy.

The other major problem is that we still don't know enough about how viruses (or other vectors for gene insertion) interact with biological systems to ensure efficacy, or safety either. Several gene therapy clinical trials involving viral vectors have been abandoned, simply because the body responded (normally) to the presence of virus in the body.

You may be interested in looking through these articles on gene therapy from Real Scientific Journals; at the risk of pissing off the copyright police, I've linked to two good, readable review articles on the topic at my web site. I hope these can dispel some of the myths about GT.

• Crack Cocaine
• Heroin
• PCP
• Methamphetamines

• Crack Cocaine
• Heroin
• PCP
• Methamphetamines

• Crack Cocaine
• Heroin
• PCP
• Methamphetamines

• Crack Cocaine
• Heroin
• PCP
• Methamphetamines

Here's an update -- I used BLADE-ENC to simply encode a publicly available sequence from yeast from NCBI as FASTA into an mp3 formatted file Can I copyright it now?

There have also been directives to fund bioterrorism defense grants as a direct result of 9/11 and the anthrax attack.

Lately I have been diagnosed with Reynaud's Disease (or phenomenon). Basically cold weather causes the blood vessels in my hand to spasm or constrict, making some of my fingers white or numb.

The causes seem fairly murky, but stress or emotion can be a factor and I have seen pages alledge that working with vibrating tools can be a factor. I wonder if computer use/gameplay can cause this kind of condition in the fingers. Anyone else have experience with this?

L

As an audiologist I have to be pedantic and note that bone conducted sound does not give you the same cues for locating the sound (i.e. no head shadow). So saying you can hear it in steroe is a little misleading. While you can add additional streams of sound, you will loose lots of timing and amplitude cues (no head shadow, and bone conducts sound faster than air) you use to locate where a sound is coming from . The "speaker" however sounds pretty neat, and a $40 bone oscillator is even cooler (typically in the $100's). I wonder if the frequency response goes up to the ultrasonic range. If you really want to hear some weird stuff, you can actually hear frequecies by bone conduction that your cannot hear by air conduction (over 24 kHz). (Science and Lancet) There is a company in Tucson doing some cool stuff with this to make hearing aids and tinnitus maskers.

As an audiologist I have to be pedantic and note that bone conducted sound does not give you the same cues for locating the sound (i.e. no head shadow). So saying you can hear it in steroe is a little misleading. While you can add additional streams of sound, you will loose lots of timing and amplitude cues (no head shadow, and bone conducts sound faster than air) you use to locate where a sound is coming from . The "speaker" however sounds pretty neat, and a $40 bone oscillator is even cooler (typically in the $100's). I wonder if the frequency response goes up to the ultrasonic range. If you really want to hear some weird stuff, you can actually hear frequecies by bone conduction that your cannot hear by air conduction (over 24 kHz). (Science and Lancet) There is a company in Tucson doing some cool stuff with this to make hearing aids and tinnitus maskers.

I found these points interesting:

Novartis was one of the companies which successfully lobbied for the European convention allowing companies to patent genes

New global trade rules have also allowed big corporations to patent crop varieties and, in effect, the genes of plants, animals and human beings.

Even without going into ethical debates, gene patenting is notoriously dubious. The standards that these companies apply to patenting genes is very poor at best. My patent law is not up to scratch, so i would be happy if someone could point me in the right direction on this. However, my genetic knowledge is rather good ;-)

Essentially, companies (such as novartis) cast a very wide net when patenting genes. Alot of the time, they dont actually do anything particularly pro-active when attempting to discover them. They essentially take a pool of all genes expressed in a certain tissue ("mRNA") and randomly sequence these genes. And then slap a patent on them. This is quite clearly discovery. Furthermore, it is cheap, non-directional, quick and easy.

Originally, companies like novartis argued that cloning genes would take a strategy of e.g. specifically identifying genes causing a disease. This takes alot more effort and money, and is more likely to have medical significance. Therefore it is easier to argue that patenting is to some degree fair.

However, the first strategy is quite clearly against patenting law (even the stretched definition for gene patenting). For example, I often see "patents" for DNA sequences of the gene MYB (which I know quite well ;-), despite the fact that it was originally identified in 1986. If this isnt prior art, I do not know what is.

This is a result of the essentially random, "wide-net" strategy the companies are utilising. Even worse, it is trivial to check (using a homology search) whether there is "prior art" on a gene or not. But the companies do not do this.

BUT I COULD. And may well do. I have been thinking about comparing the database of patented DNA sequences against those in the public domain (It will take some time to set up, which i dont have right now, and significant computer resources, which i dont have right now - help anyone? reply to this as above email wrong ;-) . It will show huge proportion of "patented" sequences have prior art.

But who would I go to with these results? Could the companies be held responsible? If, so what would be the result?

Can, will, and has. Lest you forget, the Constitution of the United States was written on the presumption that there's no such thing as a theoretical government ability-- and with good reason.

If fingerprints were put in such a card, I'd want some safeguards put in place so that identities would be protected during police proceedings such as you mentioned. Still, the technology side isn't necessarily evil -- why is it so wrong if your fingerprint identifies you as being at the scene of a crime? An eye-witness could do that as well. Maybe we should eliminate eye-witnesses as a matter of course to protect privacy?

Now who's succumbing to logical fallacies? What "safeguards" could you possibly put into place here? If data is available via the card, it's available. It's not like the card can ask if you're a police officer or a street vendor. And obviously nobody has a problem with your thumbprint identifying you at the scene of a crime. The problem is when my thumbprint identifies me as buying a stack of pr0n and a bottle of lube. Not that anyone would care, you rejoin... unless of course you have some public standing, or aspire to some public standing, or maybe they just don't like you much.

Why should I, as a health non-AIDS getter be punished for living a healthy lifestyle? Smokers often have to pay higher insurance premiums because they're a greater risk. Why is AIDS any different?

Because, in this age of enlightenment, whether or not you are insured can determine whether you live or die. Smoking is a risk factor you initiate yourself; AIDS not necessarily so. This is true for most diseases. You would sentence someone to death-- when medicine could keep them alive-- because it's "not fair" that they don't have to pay extra for their insurance because of their higher "risk"? That's a sad commentary on your character, man.

As to the genetic identification, I have high hopes that by the time that we get sophisticated to easily sequence everyone's DNA, we'll also have good methods for fixing problems in our DNA.

Oh. Well, okay then. If you're pretty sure we'll all be able to turn into perfectly healthy supermen by the time someone figures out what genes determine disposition to Alzheimer's... Oh, wait.

But right now, things are worse. Those bozos at my bank give people access to my bank accounts if they can recite my social security number and mother's maiden name! It's all about raising the bar, and putting my secret information encrypted with my PIN on a hard-to-compromise smart card would be a step in the right direction.

I have a friend who was robbed in just such a manner. Guy walked into a bank, claimed to be him, and withdrew a couple thousand dollars. I'd like to point out a few things: (1) he got his money back pretty rapidly, (2) the bank was after the guy like you wouldn't believe, (3) the bank already had a photo of my friend on file... they could have just used it, and (4) this is the only occurrance of this type of which I am aware among everyone I know. This is not the sort of story that makes me particularly inclined to centralize a great deal of personal information, or even submit to a compulsory, incontrovertible identification scheme.

Furthermore, what's the point of encryption if everyone has the key? And this is not a small system; anyone who wants the key will, eventually, have it.

True fact. The gene that is linked to Sickle-Cell Anemia only causes it under unlikely mutations. If you are a carrier of this gene however, it provides a degree of protection against Malaria. Therefore it is found most often in malarial reigions of the world.

The issue is, If we wipe out a disease such as sickle cell from the worlds population then those people who live in malarial reigons will be far more at risk possibly causing large-scale epidemics.

Healthy babies are good but not if preventing one disease causes an outbreak of another possibly worse one. We have to be careful about our assumption that we *know* what will happen. This is what all the nonfiction opponents of genetic engineering are really on about. We simply *dont* know what all of our genes do or how they behave in specific combinations and under specific conditions. There are just so many possibilities that total prediction and total control is not possible.

Gattaca was less about genetic engineering as ego and fear. It showed a socity so wrapped in its own genetic confidence and so afraid of its own diseases that babies with a 10% chance of heart disease were treated as if they were already dead. The assumption that say the likely appearence of a gene coding for melanin in the skin meant that you were permanantly incapable of any significant task no matter how smart you actually were.