Slashdot Mirror

I am almost finished with my Bioinformatics Cert from UCSC and the stress of the program is on Molecular Biology and dealing with data from instruments such as microarrays and algorithms that are frequently used like BLAST. The programming languages that appear to be used most are Java and Perl.

A great resource is the National Center for Biotechnology Information's website at http://www.ncbi.nlm.nih.gov/.

It houses genomic/protein data, tools, and pubs related to the field.

The Biomedical Information Science and Technology Initiative, for the National Institutes of Health, says: Today the disciplines of computer science and biology are often too far apart to help one another. A computer-science student often stops studying other sciences after freshman biology or chemistry; a biology student, even one knowledgeable about computers, may not ever have had formal computer-science classes. Biomedical computing needs a better -- and more attractive -- meld of those disciplines. Today computer-science students have little incentive to learn about biomedicine. The barrier is not just the rigorous demands of computer science, it is also the relative rewards: The $50,000 to $80,000 a year that professional programmers earn makes the compensation associated with many research positions in biology laughable. This situation is even more risible when one includes the reality that staff positions on NIH research grants are guaranteed for no longer than the grant award.

This is a problem in every field of scientific computing but it is particularly acute in biology because of the bizarre and heterogeneous data set. Ultimately, the question is whether it is more efficient to teach a computer science student biology or teach programming to a biology student.

People who go into computer science typically do so because of fascination with the tools and techniques, not because they are interested so much in the data. The scientific mindset of the biologist might transfer to computer science much easier than the mindset of the programmer transfer to biology.

The computer has the same fundamental status in biology as the microscope. Computer science in the form of bioinformatics should perhaps be as basic to the study of biology as organic chemistry.

IAB (I'm a bioinformaticist). You're partly correct. Introns (the 'junk' inbetween the exonic regions in DNA and freshly transcribed mRNA) do tend towards non-random sequence. You can use a variety of metrics to make guesses as to where introns and exons begin and end within a gene's coding region based on sequence entropy, on GC/AT frequency, on neural nets or hidden markov models trained on known examples, etc.

These metrics, however, are only useful once one knows something about where a 'gene' starts and ends. The real problem here is that some of the assumptions we've made historically about gene structure has potentially led us astray. Yes, the chromosomes are full of junk DNA but no, it's nothing near random for the most part and is full of 'repetitive' elements (short segments that repeat endlessly, query Genbank for 'ALU Repeat' and see how many sequences you find) that make any sort of pattern matching a tough sell genome-wide. There are also plenty of 'psueudogenes' interspersed throughout the genome, leftovers from a bygone era. It's the question of which of these pseudogenes might actually still BE transcribed that only mRNA expression analysis can provide. Hopkins is definitely on the right track w/ something like SAGE (though it's not exactly high-throughput, hence our man's need for extrapolation to genome-wide numbers).

The paper should be an interesting read to say the least.
-j

"In a study of lifestyles and health of the adult population of some Oxfordshire villages, data were collected upon the usual sleep duration and quality, smoking and drinking habits of 725 men and 759 women. A strong negative association has been found between cigarette smoking and sleep duration on both sexes, and between alcohol consumption and sleep duration in men" [Palmer et. al., 1980, from Ann. Hum. Biol.]

Note that the article also found that people who smoked and drank didnt complain of poor quality sleep etc., suggesting that the negative association was down to the fact that they drank and smoked rather than all smokers being antsy, or whatever.

Link here: abstract.

I.

"Hey, Dr. Bobkowicz. Did you want to talk about that new human-computer interaction experiment now?"
"Actually, yes."
"Hey, why do you have that aluminum bat?"
Blackness. Then sharp pain on my forehead. I awoke to find myself naked and chained to a wall in a room that while it was similarly decorated (plain white walls, no windows, cheap, gray carpet and gray, rubber molding) to the lab, it wasn't a room I recognized. Dr. Bobkowicz returned with another person whose face I couldn't quite recognize. She was carrying a large object in her hands, although my vision was still too blurry to make out what it was.
"Ah, I see you're awake now. Now I would like to talk about that new study. This time, my faithful assisstant, you are the subject."
"I'm the subject? But I didn't sign any consent form for your BDSM fantasy! I -"
"Ah, but I don't need your consent."
"But, the IRB! And what are you holding?"
"This? Oh, it's an electric shrub pruner, which brings us to the first phase of the experiment. I'm going to make you into a cyborg... running Windows XP!"
"What?!? Fuck off, you horrible monster! This body bleeds seven colors!"
By this point my vision was beginning to come back into focus and I really didn't like how she was brandishing that electric pruner, especially since I could now see all of its shiny, metallic, sharp teeth in perfect detail.
"Yes, and I'm going to make some Windows in you so I can take a peek at all those processes occupying your CPU time! Ha ha! You're supposed to laugh at my little joke, flunky."
At this point, her new assisstant, a large, balding 40's-ish man, erupted in forced laughter.
"That's enough, Steve. Now then, first thing's first. You won't be needing that anymore..."
Zzsst! Just like that, my dick was gone.
"You bitch! I needed that to jack off with!"
"Well, no more. Connect the serial port now!"
"Serial port? But that's obsolete technology!"
"Hmmph! Next you'll be trying to tell me that floppy drives are obsolete, too. Install the serial port, Steve."
"No, no! The IRB will make you pay for this, bitch!"
I couldn't bear to watch, so I blacked out.

"Hey, Dr. Bobkowicz. Did you want to talk about that new human-computer interaction experiment now?" "Actually, yes." "Hey, why do you have that aluminum bat?" Blackness. Then sharp pain on my forehead. I awoke to find myself naked and chained to a wall in a room that while it was similarly decorated (plain white walls, no windows, cheap, gray carpet and gray, rubber molding) to the lab, it wasn't a room I recognized. Dr. Bobkowicz returned with another person whose face I couldn't quite recognize. She was carrying a large object in her hands, although my vision was still too blurry to make out what it was. "Ah, I see you're awake now. Now I would like to talk about that new study. This time, my faithful assisstant, you are the subject." "I'm the subject? But I didn't sign any consent form for your BDSM fantasy! I -" "Ah, but I don't need your consent." "But, the IRB! And what are you holding?" "This? Oh, it's an electric shrub pruner, which brings us to the first phase of the experiment. I'm going to make you into a cyborg... running Windows XP!" "What?!? Fuck off, you horrible monster! This body bleeds seven colors!" By this point my vision was beginning to come back into focus and I really didn't like how she was brandishing that electric pruner, especially since I could now see all of its shiny, metallic, sharp teeth in perfect detail. "Yes, and I'm going to make some Windows in you so I can take a peek at all those processes occupying your CPU time! Ha ha! You're supposed to laugh at my little joke, flunky." At this point, her new assisstant, a large, balding 40's-ish man, erupted in forced laughter. "That's enough, Steve. Now then, first thing's first. You won't be needing that anymore..." Zzsst! Just like that, my dick was gone. "You bitch! I needed that to jack off with!" "Well, no more. Connect the serial port now!" "Serial port? But that's obsolete technology!" "Hmmph! Next you'll be trying to tell me that floppy drives are obsolete, too. Install the serial port, Steve." "No, no! The IRB will make you pay for this, bitch!" I couldn't bear to watch, so I blacked out. To be continued...

I wonder if there's a single Java product in existence that isn't slow as molasses AND actually does something useful.

Yes: Image/J and its numerous excellent plugins...

Here's a link to check whatever protein sequence you want against the human genome. Make sure to select "blastp" (for protein sequences) in the pulldown menu. Use the alphabet provided above.. it will find near matches too. Enjoy..

The reason that Amercians with genetically-based diseases survive is due to human ingenuity and compassion, not evolution.

As has been brought up elsewhere in this thread, Homo sapiens out-competed all other hominids on the playing field, and I suspect this is due in no small part to our ingenuity and compassion. However, when we Americans finally do die, 75% of the time it's either caused or largely promoted by a genetic problem. Much like the cave fish with vestigial eyes, though, if perfectly-functioning islets of Langerhans don't figure that prominently in one's relative reproductive success, glitches that prevent them from working properly will be propagated.

Just skimming it, I have two points, one philosophical, one scientific:

- Behe points out that some of Darwin's arguments avoided the question of origins for some biological processes (e.g. eyesight) because the science of the time wasn't equipped to address them. I'd argue things aren't any different now. We're working on a vastly smaller scale and are much better informed, but the issues he tackles are on the far frontiers of structural biology and molecular evolution.

- There are cases where protein motor function exists without being used for real motion. Quite a few articles have been published on the "proton pump" ATPase. This is considered a classical example of a molecular motor, but its function is entirely different from dynein or myosin. This doesn't mean a thing, except that Behe is drawing too many conclusions with his argument of irreducible complexity; it seems very premature to say that the component proteins could not have arisen independently. There are many examples of large conformational changes in proteins, not necessarily having anything to do with locomotion on any scale.

Behe's work is interesting; he raises important questions that are well worth addressing. I think he's a little too eager to declare the issue resolved in favor of molecular design, though. I can't argue that evolution presents a well-formulated answer to these problems, but I don't see any reason why it can't or won't, eventually.

Last thing I heard from developmental biology/biochemistry, they hadn't yet euclidated all of the sub-steps involving thousands of hormones/enzymes/genetic control mechanisms required to turn a tissue into an organ. Sure, we can take some stem cells, hit them with some chemicals and have them start to make kidney cells or neurons or endothelial cells. Convincing these kidney cells to form an organ, however, is a HUGE leap which requires stem cells becoming vascular tissue ( +3 types of cells) and protective sheathing ( +2 types of cells) and accessory nervous/vacular connections ( +2 types of cells). Has anyone made these types of cells? Not that I know about.

Good news is - this type of human-controlled development is possible in C. elegans, a worm. We have sequenced it's entire genome http://www.sanger.ac.uk/Projects/C_elegans/ and more importantly, we know where every single cell in the adult originated from - starting with a 4-cell zygote. PubMed Abstract Link

Maybe in 20 or more years we will have this knowledge for some "higher" animal - Maybe even a vertebrate! Then we can start to understand human organ development.

You are correct that the human genome is "only about" 3 giga basepairs of sequence, but to only store that would be rather egocentric. There are as of Dec 3 2001 some 14396883064 bp in the GenBank, and the amount of sequence information still grows roughly in a exponential manner.

Now, this will not hit the TB line anytime soon. The trouble starts if you are involved in genome sequencing. Then you need to store the raw data for all that sequence. Each some 450 bp of sequence is reconstructed from about 5 - 10 different fairly high reslution gel images (in the ballpark of 150 kBi per image). Also, recall that even short stretches of the sequence can be accompanied with a lot of annotating information, such as names and functions of genes, regualtory elements or pointers to articles explaining the experimental evidence for such. This mutiplies the storage requirement with quite a factor - nothing a neat little linux box with a huge RAID-array cannot handle though. Thats how we handle the sequencing data from Trypanosoma cruzi, by the way.

A selection of possibly relevant books (_Introduction to Genetic Analysis_, Molecular Cell Biology_, etc) can be found at: www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books NSK

Wow! Adult Stem Cells. This isn't new. Adults have always had stem cells AND this has been known. The National Institute of Health has an article [nih.gov] from May 2000 which states,
While stem cells are extraordinarily important in early human development, multipotent stem cells are also found in children and adults.
Again, this is not a new discovery. ~flogger

Guns make suicide easy and private. Most suicides would not happen if the person had to poison themselves, jump to their death, etc. That's why we have such a high suicide rate in the U.S.

This is interesting, because I just read a medline article a couple nights ago I couldn't explain (neither could the researchers) but now it makes sense:


Discordance between facial wrinkling and the presence of basal cell carcinoma

That's right: The more face wrinkles, the less basal cell carcinoma! WTF?

You would think wrinkling would have something to do with the aging rate, which would presuppose ppl to more cancer, but alas, it's not so!

Without the confusing Next Page thing

Background on protein P53

A little more on P53

PubMed Central: an Archive of life science journals

You can get the abstract here for free and demonstrate to yourself that the news article was wrong, and that it was actually in Science, not Nature. Thus endeth my Karma whoring for today. :)

Imagine if you took the 23 human chromosomes, broke them up into a couple of hundred chunks (I forget the exact number) and randomly reassembled them to make the 20 mouse chromosomes. That's what it looks like. So rodent and human chromosomes don't directly map to one another (that site aside) but there are large chunks containing many genes that can be directly compared.

With the mouse genome being sequenced now, that's one of the big things going on -- regions that are similar between the mouse and human sequences are presumably imnportant enough to be conserved over hundreds of millions of years, and therefore give a clue to the location of important features like genes and regulatory elements. That's one of the major pushes in genomics right now.

First, any drug company would buy the data if they had to when developing such a treatment. Celera is selling their data right now and the government data is freely available ( ).

Second, using your example, if they thought that some sequence controlled cancer, but in fact controlled how many balls you have, then this would come out in testing. (Pun inadvertant, but amusing.)

Asperger Syndrome - Asperger Syndrome is a form of Autism, a condition that affects the way a person communicates and relates to others. However people with Asperger Syndrome are usually of average or above average intelligence, (unlike those with Autism). It is sometimes known as 'high functioning Autism'. It causes difficulties in the way a person relates to other people, socializes and forms relationships, amongst other things. (LINK) .

Autism -- a condition characterized by an inability to relate to people. The incidence of the condition is about 2 in every 10,000 live births. Autistic infants do not cuddle and do not like to be picked up. They prefer to be left alone and are intolerant of change in their environment. Autistic children may respond with tantrums to such changes as the rearrangement of furniture or toys. Many autistic children are mute; in others, the development of speech is severely restricted to a repetition of a few words. Physical development is normal. Initially believed to be a consequence of poor parenting, it is now recognized as a neurological disorder. Some autistic children improve spontaneously. Others respond to a specialized plan of treatment. However, less than 25 percent of autistic children get better. Over half of all autistic children require residential placement by the end of adolescence. (LINK) . There is no link between the MMR vaccine and autism. (LINK) .

Selective Mutism -- (formerly called Elective Mutism) is a psychiatric disorder that is characterized by consistent failure to speak in SELECT social settings in which there is an expectation to speak; such as school. (LINK) (warning: sub-par HTML). The crucial diagnostic element is that the child has the ability to both comprehend spoken language and to speak, but fails to do so in select settings. These children will display reasonably appropriate verbal and interactive skills at home in the presence of a few individuals with whom they feel at ease. The term Selective Mutism should separate individuals who demonstrate a selectivity with whom they speak from individuals who speak to no one. A population which should be excluded are immigrants who speak another language, have no history of the disorder, and experience SM for a short period of time. In these cases the mutism is usually transient. (LINK) . The cause or causes of selective mutism is unknown. (LINK) . Selective mutism is sharply different from autism. (LINK) .

If you believe you or a child has a problem, a good place to start is with a medical doctor. Don't rely on the information I provide. I do not vouch for the accuracy of any of this.

Perhaps you are unaware of the many studies which demonstrate that there is a large genetic component to addiction?

Yes, we are all ultimately the masters of our own destiny, and we must take responsability for our actions, but I find your "pull your self up by your own bootstraps" proselytizing somewhat quaint, at best.

Here is a diagram of the ATLAS project's network topology.

Have you actually had to manage a system that works like this? It's a royal pain in the ass.

Yup, I have. In fact, we've managed all of our UNIX systems that way for the last 8 years or so. It's not a pain in the ass at all.. in fact, with the opt_depot scripts we wrote, we support automagic NFS sharing of packages for all Solaris systems in our laboratory. Indidivual system administrators can choose to use a particular package off of their choice of NFS servers, or they can simply copy the package's directory to their local system.

Using symlinks gives you complete location independence.. all you need is a symlink from your PATH directory to the binaries, and a symlink from the canonical package location (e.g., /opt/depot/xemacs-21.5) to the actual location of the package directory, be it local or be it NFS.

There's a group at NLM who is working on tools and standard practices for managing NFS package archives using RPM, and then using the opt_depot scripts to integrate the package archives with each local system automatically.

(eg Tuatara, which is not a reptile; it only looks like one)

(eg Tuatara, which is not a reptile; it only looks like one)

Link
Link
Link
Link
Link
Link
Link

OK, that's enough. You can probably find more yourself. Bottom line: Lots of people would love to believe it works, but despite many years of investigation, the evidence that it works is scant. One would think that if acupuncture was as effective as its proponents claim, the evidence would fall solidly in favor of acupuncture. The fact that it does not ought to tell you something.

Studies like this are fairly artificial since they often simplify the situation and make some questionable basic assumptions. For example, in the late 80s I remember reading a study that proved that a farm which relied on sunlight, the labor of the farmer and his animals and no other external energy input was not self sustainable. Which leads one to wonder, how did we manage to not only survive, but proliferate in the days before fossil fuel?

In any case, the best answer may be a hybrid coal/methanol system as reported in this recent paper. They claim to be able to reduce coal usage by 2.6 million tons and reduce CO2 emmissions by 2.15 million tons while producing 15.4 billion kWh of electricity.

NLM runs some seriously chunky work, too. The National Center for Biotechnology Information (which is part of NLM) is an example of a truly outstanding dynamic web-site based on a really huge database backend. I like to use it as an example of what it's possible to do with a well designed web site. The people at NLM who I've met at meetings seem to be pretty nice, too, and they're helping to do some really worthwhile things, and ISTR that they're looking for workers, too. It would definitely be a good place to look for a government job involving Unix.

Here at NOAA, I know the line office I work in uses Suns and HPs extensively for servers, as well as some VAX and DECAlphas, and we do a lot of cool things with them. We also happen to do a lot of cool things with Windows 2000, but more on the workstation level. I can't really speak for all of NOAA, or the Department of Commerce, of which NOAA is a part, but I'm sure there are plenty of government agencies that use Unix and Linux.

I'm also familiar with several labs at NIH that use Linux almost exclusively. The few exceptions in these labs are things like some SGI and Solaris machines, and a very small number of laptops which dual boot Windows and Linux. If you look, you can find many government job opportunities that require Unix and/or Linux knowledge, and a lot of them are challenging.

I did a project during college at the National Institute of Health and it seemed to me that 90% of the people there used Macs. I know it is proprietary, but I thought I'd mention it since Macs weren't mentioned in the news.

Ben

Although the citizens of the U.S. will probably suffer an unspeakable loss of civil liberties and privacy, we will probably reap many benefits from the medical research that was spurred.

-sting3r

Likewise, there are a lot of evolutionsts who don't know anything about science saying there's a lot of evidence for it.

there are a lot of crazy people who don't know anything about anything saying all kinds of stuff-- for a really good example, click on the link listed as my homepage (which unfortunately isn't really mine). That doesn't mean that you or anyone else should give them a serious audience.

that doesn't change the fact that for the last 300 years, people have been poking around the issue, and that the idea of evolution that is taught in credible universities today is the product of much real-world experimentation. You just can't say the same for creationism, becuase the idea of faith simply rules out the possibility of rational discussion.

http://www.nih.gov/news/pr/sep2001/nhlbi-10.htm

The Times article says, "[This study by European Society of Cardiology in Stockholm] is the first to measure the effect of coffee on arteries."

Oops. The following study by Department of Pharmacology and Therapeutics, Trinity Centre for Health Sciences and Hypertension Clinic, St James's Hospital, Dublin, Ireland, was published last month:
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/quer y_old?uid=11509481&form=6&db=m&Dopt=b

Hypertension 2001 Aug;38(2):227-31
Acute effect of caffeine on arterial stiffness and aortic pressure waveform.
Mahmud A, Feely J
Department of Pharmacology and Therapeutics, Trinity Centre for Health Sciences and Hypertension Clinic, St James's Hospital, Dublin, Ireland.

Caffeine acutely increases blood pressure and peripheral vascular resistance, in part because of sympathetic stimulation. Its effects on large artery properties are largely unknown. In a double-blind crossover study, 7 healthy subjects 26+/-2.6 years of age (mean+/-SEM) were studied for 90 minutes while in the supine position on 2 occasions separated by a week in random order after ingestion of 250 mL caffeinated (150 mg) and decaffeinated (2 mg) coffee. Compared with baseline, arterial stiffness measured by carotid femoral pulse wave velocity increased progressively from 7.2+/-0.41 to 8.0+/-0.6 m/s (P0.05) at 90 minutes after caffeine intake, an effect that may be independent of changes in blood pressure. In addition, arterial wave reflection, measured by applanation tonometry from the aortic pressure waveform, also increased from -5.7+/-7.6% to 5.28%+/-5.6 (P0.01). No such changes were seen with decaffeinated coffee intake. Although the integral of the brachial systolic and diastolic blood pressure values over the 90 minutes was larger (P0.05) after caffeinated than decaffeinated coffee intake, the effect on aortic systolic and diastolic blood pressures was more pronounced (P0.05) than on the brachial artery. These results show a significant effect of caffeine intake on arterial tone and function and suggest that caffeine acutely increases arterial stiffness.

Publication Types:

Clinical trial
Randomized controlled trial
PMID: 11509481, UI: 21400656

-nukebuddy

ImageJ is a Java app that will handle the file without a problem and being in Java it is x-platform. Oh, and the source code is available on the download page.

don't knock ritalin and the other adhd drugs they can help you focus maybe get something done when you have lots of things going on and the bird flies by outside your window and i'm looking out the window and thinking about the bird and the tree and the grass and i get up to go outside and on the way i stop in the kitchen for a snack and my sister has the tv on so i watch that and after a while i start drawing on some paper that is there but i want the green marker and i go to my room to get it and while i am looking for the marker i pick up a book and flip through it and i start reading it in the middle if you only knew how many times i was distracted just writing this you need to look at the rest of the agenda these people have who say oh horrors they have these kids on drugs most are behaviorist bleeding heart kids should feel good about themselves with no background in medicine sorry a bs in psych doesnt cut it or worse yet a degree in journalism or the ones pushing grapefruit pip extract herbal compounds and miracle diets right take your medical information from them i'll sell you a magnet to put on your gas line that makes your car run better you should listen to people who study the brain like dr alan zametkin at nimh instead of the media you could start with this paper if you haven't looked at adhd research you should really take the time to read it i would greatly appreciate it if someone will please mod this out of AC wasteland although probably half the people on here have adhd i ought to just post it under my login confusing to read this no apology i live in this it doesn't bother me not confusing my life looks like a perfectly logical sequence from my point of view but back to the drugs my brain works differently it is no worse to give a kid with adhd ritalin than to give a diabetic kid insulin oh yeah the europeans and chinese are so progressive give the kids one test when they are 12 that determines whether they become worker bees or go on to higher education and you call us drones nice troll though

don't knock ritalin and the other adhd drugs they can help you focus maybe get something done when you have lots of things going on and the bird flies by outside your window and i'm looking out the window and thinking about the bird and the tree and the grass and i get up to go outside and on the way i stop in the kitchen for a snack and my sister has the tv on so i watch that and after a while i start drawing on some paper that is there but i want the green marker and i go to my room to get it and while i am looking for the marker i pick up a book and flip through it and i start reading it in the middle if you only knew how many times i was distracted just writing this you need to look at the rest of the agenda these people have who say oh horrors they have these kids on drugs most are behaviorist bleeding heart kids should feel good about themselves with no background in medicine sorry a bs in psych doesnt cut it or worse yet a degree in journalism or the ones pushing grapefruit pip extract herbal compounds and miracle diets right take your medical information from them i'll sell you a magnet to put on your gas line that makes your car run better you should listen to people who study the brain like dr alan zametkin at nimh instead of the media you could start with this paper if you haven't looked at adhd research you should really take the time to read it i would greatly appreciate it if someone will please mod this out of AC wasteland although probably half the people on here have adhd i ought to just post it under my login confusing to read this no apology i live in this it doesn't bother me not confusing my life looks like a perfectly logical sequence from my point of view but back to the drugs my brain works differently it is no worse to give a kid with adhd ritalin than to give a diabetic kid insulin oh yeah the europeans and chinese are so progressive give the kids one test when they are 12 that determines whether they become worker bees or go on to higher education and you call us drones nice troll though

More information on vibration maschines for use in gaining muscle and bone strength can be found here.

This link shows how the vibration maschine works.

With respect to the story on Discovery: There is a factual error in it. Females do not have lover bone density than males. The volumetric density of male and female vertebrae are identical. However, females have generally smaller bones than males and the force needed to break female bones is therefore smaller than for males. On the other hand the stress (force divided by cross sectional area) needed to break female or male bones are identical. More information can be found here.

The University of Wisconsin provides us with a good example of how the Bayh-Dole Act is implemented. Early work by Dr. Thomson on non-human primates, such as Rhesus monkeys, was federally funded and therefore, the patent obtained on stem cells arising from this work is governed by this Act. In accordance with the law, the invention was disclosed to the NIH, a patent application was filed by the University, through the Wisconsin Alumni Research Foundation (WARF), and WARF licensed the technology to a small company (Geron). Because federal funds were used for this non-human primate work, the government has a non-exclusive, royalty-free right to use the patented cells by or on behalf of the government. This would allow the government laboratories and contractors the right to use the patented cells for further research. In addition, in handling this invention the University must ensure that the goals of the Bayh-Dole Act -- utilization, commercialization, and public availability -- are implemented.

The University of Wisconsin provides us with a good example of how the Bayh-Dole Act is implemented. Early work by Dr. Thomson on non-human primates, such as Rhesus monkeys, was federally funded and therefore, the patent obtained on stem cells arising from this work is governed by this Act. In accordance with the law, the invention was disclosed to the NIH, a patent application was filed by the University, through the Wisconsin Alumni Research Foundation (WARF), and WARF licensed the technology to a small company (Geron). Because federal funds were used for this non-human primate work, the government has a non-exclusive, royalty-free right to use the patented cells by or on behalf of the government. This would allow the government laboratories and contractors the right to use the patented cells for further research. In addition, in handling this invention the University must ensure that the goals of the Bayh-Dole Act -- utilization, commercialization, and public availability -- are implemented.

And I don't see you coming up with a better method for propagating life.

In fact there is a vast human enterprise devoted to correcting and improving on the incompetent design of life. It is called Medical Science.

As for computer scientists, no programmer who wrote a program with the failure rate of child birth would pass his first programming course. Until about 100 years ago, 1 per cent of mothers and over 10 per cent of children died in child birth or soon after. Morton Thiokol Inc. faced an official investigation for a substantially better performance.

they may have had no idea that something sentient would eventually evolve from the whole thing

Maybe they did and maybe they didn't. It's interesting that even with our meagre intelligence you feel the need to cover for them. The main question in your escatogy is whether life has been botched up by malice or incompetence. In either case, they would have flunked any genetic engineering class in the 21st century.

Amen! There isn't a thing in the world stopping "open source" drug development. There are even starting points. The NCI has
data for
~50,000 compounds tested in AIDS and cancer screens. Take the data and go to town. But if you are not willing to do the work and invest the time and resources, don't bitch about the people who do.

The similarity between flagellar and electrical motors is, however, largely illusory. The flagellar motor does not act by using electric current to generate moving magnetic fields; instead it uses the decomposition of ATP to cause changes in the shape of the molecules that, when combined with a sophisticated molecular ratchet, make the protein shaft revolve.

THE PURPLE BOOK "contained the hardware schematics for the IBM PC as well as the code listings for the ROM BIOS," Dave Bradley, one of the machine's 12 original designers, later explained to me. "It contained just about everything you'd want to know if you were going to build a device that would plug into the IBM PC."

In the Purple Book, as Bradley said during the panel, "We told all the PC secrets."

IBM wasn't the first personal computer maker to spill its guts. Apple published the source code for its Apple II. Atari and Commodore also offered similarly extensive documentations. But for Big Blue, a company that built a dynasty on proprietary products, the Purple Book represented a break with tradition as almost as radical as Martin Luther's breach with the Holy Mother Church.

WHY DID IBM SO WILLINGLY bare the soul of its new machine? Bradley again: IBM wanted to "make it as simple as possible to design hardware and software that would work with the PC."

"We wanted the software and hardware industry to participate."

Participate they did. What's more, the Purple Book made the IBM PC easy to copy, and thus, in came the clones. The result: A de facto standard was born, and that standard made way for the widespread deployment and use of PCs. The rest, as they say, is history.

The historical significance is the parallel that exists between the Purple Book of yesterday and the open-source movement of today. The comparison isn't a perfect one. The Purple Book did not constitute a license for use; IBM retained intellectual property rights.

Whatever! The retaining of intellectual property rights is ther whole point. What they did is what everyone else who had attempted to put out a PC would have to do in that era. The subset of technicians working on these technologies was quite small- small enough that a collegial flow of information was necessary even to drum upo interest in one's hardware.

So what IBM was doing was trying to raise itself to a playing field which Apple and Commodore had already delineated; to break into a technological community which was already occupied with other hardwares, it had to disseminate technical information.

There is a parallel today; Geron, the company which licensed the technology to extract stem cells from blastocyst-stage embryos, dissseminated the technology, advice and support to institutions of learning, retains commercial rights to any salable products that come out of these laboratories - or even the precursors of those products.

Then and now, such a technique is to take advantage of an academic desire for learning, or a desire to help the sick, and commercialize its output.

There is really no choice for software developers in the Microsoft world, or for stem cell scientists outside the apron of federal approval, except to sell their first-born breakthroughs to loan sharks.

I've said it before and I'll say it again; capitalist systems cannot sustain innovative energy or scientific responsibility.

That's weird.

On my P100/48Mb linux box, ImageJ, the only Java program I need to run, runs pretty fast. Startup is a bit slower, and it consumes relatively much memory, but once it runs, it runs as fast as a native program. I use the Sun SDK, but I also used Kaffe and the IBM JRE, with comparable results.

Just my personal experience.

http://www.nih.gov/news/stemcell/primer.htm

I suggest people read this before posting because it seems to clear up a lot of the misconceptions readers have, even myself.

psxndc

Here's a good primer on the whole subject:

http://www.nih.gov/news/stemcell/primer.htm

psxndc

PS I will correct myself in saying that cDNA libraries do not deal with stem cells, but I do consider my girlfriend more of an expert than most because she does work in the field and does get cDNA libraries from fetal tissue (though most of it is homologous tissues like pig)