I think rsync pretty much provides all you need in one tiny command-line to get data from A to B.
But if you want to increase your resilience against failing network connectivity, and make sure you don't delete anything that hasn't been properly copied to your server, I suggest you take a look at datamover: http://www.cisd.ethz.ch/software/Data_Mover
Essentially, it's a daemon written in Java that monitors an outgoing directory. Everythings that is written in there gets safely copied over to a central storage drive. Behind the scenes, they use rsync to do the copying, but it's wrapped in tons of features that improve the reliability of the moving process, like a quiet period before a file gets moved (good for applications that write their output incrementally and sporadically into files), multiple retries on network time-outs, high-water marks, data transformation (e.g. compression) during the move process, etc. It also is very anal about sending you emails for anything that could possibly be a data integrity problem.
We rely on it to store the raw data from scientific experiments. With the proper configuration, your holiday pictures should be just fine.
Thanks to the TPA (Travel Promotion Act), there's really No Problem(TM). In addition to all the border troubles, simply charge the poor guy visiting another $10, which can then be spent on promoting tourism.
What a brilliant idea: An entrance fee to the US... just like a theme park.
I'm in a quite similar situtation, and perhaps I can provide a few hints from what we're currently doing.
I'm working for a relatively well-known institute in academia (biotech field), with a group that among other research projects, also provides web-based services to the research community. Funding is partially tied to the operation of the services, so there is actually enough pressure to make sure that they work and work correctly at all times.
Still, until about a year ago, development was very ad-hoc, in a mix of languages, and with many "islands of knowledge", where some parts of the system were only known to one post-doc, and other parts could only be fixed by the group head (who, as they are, was usually busy with many other things...). After some hard times and near-misses, we started looking around for ways to improve our development.
I was quite attracted by the ideas of Agile, and I believe that they're a good fit to the kind of processes you find in science, as well as in software engineering. We initially had a professional Scrum coach come in and talk with us about software development practices, and then decided to apply Scrum to our processes.
It's now a bit more than 1 year since then, we're still using Scrum with a few adaptations to fit the academic environment (we're also using Scrum for projects that are really science and research, not software development). In a recent secret poll among the team, Scrum got high marks for making the team more productive, and for creating an environment where code and knowledge is shared. People are happy with the structure that Scrum provides, and we always know where the project stands. Incidentally, we also write better software faster.
But we're still improving the way we work. The transition is slow and painful, and we're only slowly adopting things such as test-driven development, automated builds and pair programming. In my experience, there's a lot of resistance against these "newfangled" methods in the academic culture, especially that of people who weren't trained as software engineers, but rather as physicists, chemists, biologists, but now find themselves producing software.
Some hints on what I've found useful in re-shaping our work environment:
- You can't change the whole structure in one day. Get permission to run a small, isolated project in "the new way", and use this to demonstrate the advantages. Remember, there are many metrics for success: Code quality, timely delivery, not having single points (persons) of failure, as well as team velocity and personal satisfaction. Try to make a case from this small project (and gain experience while doing so), and then grow it out slowly.
- I would not advise to do some clever "breaking the build, and thus showing everybody how fragile the system is" exercise. This may not be seen as constructive.
- Instead, provide convincing evidence by example that your way is more productive and more certain. Bugs that are fixed stay fixed, and don't creep in later again. Timelines are better kept. That sort of thing...
- If you can get someone in to talk about the current best thinking in software development, do so (someone else mentioned this already). It's good to hear an outside opinion, and to understand that these practices are not theoretical but used by large companies world-wide.
Maybe I can provide some insight, as a close colleague at work died last year in a tragic outdoor accident.
Basically, what it boiled down to was as follows: The family/next of kin have right to access all of the deceased person's personal files, emails, etc. Company property is exempt of course - for IP reasons. The system administrators should release a copy of the person's email mailboxes, and all other relevant files to the next-of-kin, after examining that no business-relevant data goes out.
They will not and should not release anything to you, you're (iirc) not related.
I am sure there's a procedure in place at Gmail, etc. to deal with such a situation, as this is not the first time something like this happens.
The more important question is: does the family really want the information? That's an ethical and moral question, and only they can answer that for themselves. So, if they ask you to hack the root account, it's OK for you to do so, but keep all you see private to the family and yourself, and don't force any information on family members who don't want to know. Let them decide.
Disclaimer: I'm not in the US, and assume you are - so the legal implementation may vary.
"Kudelski will lose their case", states the man who pirated their chip cards
Image legend: Christopher Tarnovsky: "Why would I have published these codes on the net for free? I am not stupid, and I never had the intention of taking that risk."
Main text: PAID ACCESS SYSTEMS. A key witness in the court case opposing the Swiss group against the media giant News Corporation was passing by in Amsterdam, attending a conference on computer piracy. We met him.
François Pilet, Amsterdam Saturday, March 29 2008
The audience is glued to the lips of Christopher Tarnovsky. In front of a podium of hackers and security specialists - with an average age of 25 - the self-taught electronics specialist revealed the techniques that allow him to break open chip cards that block access to pay TV chains in the whole world.
The scene takes place in the Mövenpick hotel in Amsterdam, where the European edition of the Black Hat conference was held Thursday and Friday last week. This is one of the prime professional meetings dedicated to computer piracy. Among the twenty or so speakers invited to this big get-together, Christoper Tarnovsky talked for more than one and a half hour in the "Lausanne" room - a sign of destiny (Tr. note: Lausanne is a Swiss city close to the headquarters of the Kudelski Group).
Employed by NDS
The 39 year old American is accused of having been recruited in 1999 by the Israeli company NDS, a competitor of Kudelski, to break the security codes of Canal+ (French Pay TV) and publish them on the Internet, and to have repeated the operation, to the detriment of the Swiss group and its clients. The publication of these codes allowed hundreds of thousands of savvy users to access encrypted TV channels without paying the subscription fees.
The American satellite TV company Echostar also uses Kudelski cards to protect their content. They confirmed having lost hundreds of millions of US dollars due to these pirate activities and demand one billion US$ of damages from NDS, a subsidiary of the media group News Corp.
This April, Christopher Tarnovsky will take the witness stand in a California court in defense of NDS, his employer for ten years following 1997. According to him, Kudelski and Echostar have wholly invented the conspiracy they claim having been victim of in order to mask the weakness of their encryption.
In his eyes, the case against NDS is nothing short of an extortion attempt. "Sure, I've broken the cards of Kudelski", he annoyedly states. "I was paid by NDS to do it. This is an activity that all companies in the trade do. But why would I have published these codes on the Net for free? I am not stupid, and I never had the intention of taking that risk."
Having become an awkward asset, Tarnowsky is no longer employed by the group since a year. He started his own company, Flylogic, through which he offers his know-how to electronics manufacturers, to test the resistance of new products to pirate attacks before they are launched.
Christoper Tarnovsky details the general weakness of systems based on certain chips designed by a handful of companies like Motorola and Infinenon (sic), systems used in products as divers as garage door remotes, car alarm systems and TV decoders.
"Unbreakable? That's wrong!"
"The manufacturers of semiconductors claim that their chips are unbreakable. The companies integrating them into their products trust the specifications they obtain. They believe that their secrets will be well kept. That is wrong, of course." He showed pictures of his laboratory, set up with second-hand equipment worth a couple of thousand dollars. The centerpiece is a powerful Zeiss microscope to access the heart of the chip, where the precious codes are hidden. Successive layers of silicone are peeled away, using acids and lasers.
The engineer then explains how he takes over control of the card by short-circuiting one by one its protections with long microscopic needles. It takes a few minutes fo
OK, perhaps the open-source context is wrong for the data source, but please tell me how describing MythTV (to name the PVR solution I'm most familiar with) as open source is teeth-grindingly wrong?
If I remember the news items correctly, the toll collect system was actually designed to comply with a certain set of privacy standards. The traffic cameras only save information for about every tenth vehicle passing by. That is still enough to eventually find (and fine) those who don't pay the traffic charge, but still isn't systematically collecting information about the whereabouts (and thus trajectory) of every vehicle. I thought at that time that this was thoughtful. It is my feeling, however, that the German Minister of the Interior Schäuble would like to see a firmware upgrade to these cameras rather today than tomorrow, so that they can save all the information, and make tracking of vehicles possible. So I agree, registrations are harmless, if done right, but they lead us one good step further on the slippery slope.
* Not everybody has access to the services TiVo provides (they're not operating world-wide, and alternatives at least around here (in Switzerland) are nowhere near $5/mo, but are bundled with digital TV)
* Some people prefer an open-source alternative, not only to the PVR itself, but also for the data source
* Screen scraping works. Sort of. Sometimes. As soon as your scraper gets popular, the web site will change its layout to foil scraping attempts, and you can start new. It's an arms race, unfortunately, and there's no real way out of it. The networks and content providers jealously guard their data, and only license it to redistributors.
* Schedules Direct is such a licensing partner. Instead of distributing the data in proprietary format, they use standard XML. That is good.
and, most important of all:
* If you had read TFA (or even the freaking post), they're aiming to drop the price. For now, they have no idea how popular their service will be, but want to make sure they don't create a financial sinkhole. The folks behind this are from the MythTV and XMLTV community, and I'd be surprised if they see this as a get rich quick scheme. They're too realistic for that.
Try this one then: PubMed reference... The real article seems to be published in Nature Neuroscience.
Personally, I wouldn't call New Scientist a garbage journal by the way, its aim isn't to be a strict scientific journal, but rather to bring news about science to the reasonably well educated masses. A bit like Nature was before they split off into many many subjournals.
Here's a manual translation of the article. It may not be very elegant; I didn't have much time...
Soviet space shuttle: Curious discovery at the persian gulf
While shooting footage for the formula 1 race in Bahrain, a TV crew from Düsseldorf by chance stumbled over a rumour about a russian space shuttle, said to be located since some time in that region, without anybody taking an interest in it. A little while later, the Germans were standing in front of a relic of the soviet space shuttle program of the eighties: A vehicle strongly resembling the US shuttles. It may be a prototype version of the space shuttle "Buran" ("Snowstorm".
With this shuttle project, at times employing up to 30'000 people, the soviets wanted to catch up with the americans in manned space flight. But the project was not under a good sign. Already at its inception in the late seventies it was clear that the Soviet union actually had no use for a re-usable space craft. "Buran", the name of the sole soviet shuttle ever to make it into space, was a pure prestige project - and an extremely expensive one at that.
November 15 1988, after more than ten years of development, Buran took off for the first and last orbital flight, without crew. This flight ended according to plan after two orbits of the earth. One year later, the iron curtain came down - and with it, the major part of funding for soviet space exploration.
[CAPTION]: TV producer Maier in the cockpit of the shuttle: Relic from the soviet union
While the "Buran" shuttle was able to carry more payload than US shuttles and could be controlled remotely, neither its on-board computer nor its life support system ever worked satisfactory. The space ship was decomissioned, and was destroyed in May 2002, when the ceiling of a hangar in the Baikonur space center crashed. A second shuttle named "Ptitchka" ("Little bird"), which was completed in 1990, was never used: The program was stopped officially in 1993.
Besides the two soviet shuttles that were ready to fly, there were said to be three more, unfinished, shuttles, and a series of test versions. Today, one is being used as a restaurant in Moscow, another was sold by Russia to Sydney as an exhibition piece for the 2000 olympic games. "Ptitchka" is said to be in Baikonur still.
It is not clear which model was found at the persian gulf by the TV crew from Düsseldorf. Nobody knows, how this museum piece ended up there. According to TV producer Chris Maier, this could be the model once located in Sydney. This notion is supported by the fact that the shuttle supposedly performed 25 atmospheric test flights. Various reports claim that the Russians delivered the aerodynamic test plane "Buran OK-GLI" to Australia, which was used to test the automatic landing system of the space shuttles. For this reason, the shuttle was the only test variant equipped with engines.
"We need to get confirmation on which version this is", concedes Maier. However, the shuttle has already attracted a potential buyer: According to Volker Hartmann, a member of the TV crew, German enterpreneur Kai Niedermeier, who is doing business in the gulf states, wants to do a world tour with the space shuttle - and auction parts of its hull on the internet.
You are completely right. "Unlimit" is always within some limits, as every company who actually pays something to a provider upstream to offer this service would be on the slippery slope to extinction , if they wouldn't care how much you use the "unlimited" service.
Unlimited is a marketing ploy, nothing more and nothing less.
Point in case, a DSL provider in Germany offers a no-transfer-limit DSL account. I have just read that they regularly (every month or so) identify those users who pull more than 20GB per month, and send them a polite letter, offering them 100 Euros (100-something US$), if they terminate their account at once. Moreover, they can keep the DSL router and other hardware they got for free when signing up. Basically, they're saying, we don't want you, here's some cash if you leave right away (and sign a statement that you won't re-apply for their service if you keep up your downloading habits).
Actually, it's not that complicated once you're used to the process... Or put differently, if you take enough care to explain it in plain and simple terms to the soccer moms, they'll realize it's not much more complicated than loggin into AIM (taking a wild guess here --- I'm not using AIM) which I'm confident they can manage.
As the person who originally posted the story, I am living in Switzerland, so I can maybe provide a little insight into the mechanics of the system.
It's been a while since my nice bank has switched from the TAN system to the calculator/login device + chip card, but if I remember it right, it's not only the TAN that authenticates you, it's your user name (or more precisely, your account number - after all, we're in Switzerland, the home of number accounts) and a password of your own choice, plus the current TAN, used only once. This seems to me to be a pretty good system, as you prove your identity by:
knowing your account number
knowing your personal, secret password
knowing the current, one-time-pad TAN
With the login device I am using now, you need to:
know your account number
posess the chip card
unlock the chip card with a PIN of your choosing (and 3 bad tries block the card forever)
read a challenge off the login screen, and type it into the login device
post back the response the login device generates
Knowledge of any one of these is useless, you need to know all of them, so I think the system is pretty secure. Frankly, I was slightly mystified to read that US banks rely on only one token of authentification... I would have imagined systems similar to the ones I described are commonplace. Seems I was wrong.
Disclaimer first: I am not an astronomist, but at least, I am a german native speaker...
SPIEGEL ONLINE EXKLUSIVE
"Opportunity" finds proof for martian floods by Thorsten Dambeck
The mars rover "Opportunity" managed to find proof that once upon a time, there was flowing water on mars. As SPIEGEL ONLINE heard from sources within NASA, the US space agency will make this discovery public tonight.
[caption]Water trace: Light stones close to Oppotunity's landing spot (NASA/JPL)[/caption]
"I am flabbergasted, I am astonished", said Steve Squyres, scientific head of the rover mission, in face of the pictures from the second mars vehicle "Opportunity". No other landing zone is similar to the broad plain Meridiani Planum, where Spirit's sister probe landed. The scientist was especially taken in by the light rock formation that appeared in front of the rover's camera eyes, peering out of the dark martian sand.
After thorough mineralogical and chemical analysis of the rocks in the past few weeks, it seems clear now that Squyres spontaneous excitement was justified. As SPIEGEL ONLINE found out from sources within the US space administration, the rock formation is sedimental stone which was definitely built up in a stagnant body of water.
First suspicion hardened
The "smoking gun", the irrefutable proof for the existence of past floods on mars, is said to be a sulphate compound that was found in the rocks, and which can only come into existence in the presence of water. NASA will present these results tonight, Tuesday, at 8 PM german time on a press conference in Washington.
Already the first close-up pictures of the formation fed the suspicion of planetologists, that the rock formation may have been built by sedimentation, by the process of deposition. The single strata were clearly visible on the high-resolution snapshots from Opportunity's panoramic camera. An important contribution to the discovery can be assumed to have been made by the Mossbauer-Spectrometer "Mimos II" , built by the physicist Gostar Klingelhofer from Mainz, which is responsible for the mineralogical analysis of ferrous martian rocks.
Breakthrough with german instruments
Already on the 9th of February, German members of the rover research team reported surprising results from their APXS ("Alpha Particle X-Ray Spectrometer") instrument. According to these reports, analyses of a light rock named "Robert E." using the spectrometer found substantially higher levels of zinc and sulphur than in all previously investigated mars rocks. "This indicates that the rock is a hardened, salt-containing sediment, and not of volcanic origin", said a member of the Max-Planck Institute for Chemistry, where the APXS spectrometer was built.
But even if non-volcanic processes are being favored more and more: Until last week, NASA scientists emphasized that various formation mechanisms -- including variants without the influence of liquid water -- are possible. Now, it seems, liquid water made the race.
With this, the US-rover would have confirmed from the ground what the european probe "Mars Express" already discovered from orbit: End of January, ESA scientists interpreted the breath-taking pictures of the red planet as clear evidence that once upon a time, rivers and seas existed on mars.
What you're describing is not de novo drug design, but rather tinkering, which indeed happens regularly in the drug development process.
The whole zoo of phenethylamine derivates comes from a process of optimization. That part of "drug design" is in fact very common in drug development (not only in psychoactive drugs, but drugs in the common sense of therapeutic substance).
The initial, biologically active, substance usually has some beneficial properties (i.e. it is active), but some undesired properties, such as causing side effects (not specific enough), or having low activity (low bioavailability [basically, it isn't taken up well in the blood stream, or isn't taken up properly by the target organ]). In these cases, medical chemists start playing around with side-groups of the molecule, trying to enhance the desired pharmacological, pharmacokinetic and pharmacodynamic properties. The way I understand it, this process is half science, half art.
What I was referring to when I talked about rationally designed drugs is more than just tinkering. It's saying "We have this disease that's caused by an overactivity of protein XYZ. Let's have a look at protein XYZ and design a completely new compound that will bind to it and dampen that activity", for instance. This is what maybe one day will be possible, but not yet.
To come back to your example, as far as I know, there's no way even within the phenethylamines to look at the structure of two members of this class, and just by looking at the structure predicting what exact effects each of them will have. It's more a kind of trial-and-error process, hardly rational drug design.
Soon we will design drugs, rather than find drugs.
I hope that we will one day indeed design rather than blindly search. We're centainly on the road to it. But then again, I heard the same line about designed drugs coming soon when I started studying biology, and that was, hmm, about 10 years ago.
To be fair, rational design has made some big steps forward, but the number of drugs and drug candidates that were designed completely in silico is really small. Likewise, the combinatorial chemistry approach is useful, but hasn't kept up with the big promises that hyped this approach maybe 5 years ago. But I may be biased there, the idea of blindly throwing together molecules and then letting a high-throughput assay sort out what works and what doesn't has always rubbed me as somewhat contrary to the ideal of science. It's a bit like simply bringing in more and faster monkeys to get that shakespeare play written.
Combinatorial chemistry and rational drug design can still learn a lot from nature, and in fact the two can be combined. It is impossible (and will stay so even in the future) to examine all possible chemical structures for a desired activity. For instance, there are 10^62 different molecules of a molecular weight below 500, a typical cutoff for drug molecules. If you would synthesize one molecule of each, you'd make a ball of mass that covers the whole solar system. (quoting from a recent seminar by Prof. H. Waldmann).
We can't explore the whole chemical diversity, but we may not need to. If you compare a random molecule library to one based on substructures occurring in nature, you'll find that the "natural" library has much higher hit rates than the random one. In a way, nature has worked for us as a filter, selectively enriching substructures that are meaningful in the context of proteins and receptors. Proteins are largely composed of conserved folds, therefore the structures that bind to them are likely to have conserved structures as well. Considering the more creative solutions nature uses to overcome extreme problems will enrich this library of natural structures, and thus be beneficial to rational drug design.
I believe that exploring extremophiles can give us great advances in anything from biomaterials to new drug leads. Put in the most simplest way, by looking at extremophiles, we are asking nature to show us its more uncommon solutions to problems. In these extreme environments, organisms have evolved some fairly impressive tricks just to stay alive (try staying alive in a hot water spring a somewhat over 80C for any length of time, and you'll see what I mean).
The input we get from extremophiles is valuable, because it is tried and proven to work. I see the benefit, however, more in a gain of knowledge than in actually harvesting these creatures. Such a responsible exploration can lead to new interesting molecules without killing off species. Hopefully there's enough financial interest in learning from an extremophile versus harvesting the extremophile organism, since finding/growing/hunting extremophiles tends to be expensive, and if the molecule can be made synthetically or using bacterial/eukaryotic expression systems, this should prove economically more interesting.
If I remember corrently, the original patent for the use of thermostable Thermophilus aquaticus DNA polymerase belongs to Roche. Before I posted this comment, I checked in espacenet for any patents by Invitrogen regarding "thermostable" or "thermophilus" or "aquaticus". I couldn't find any hits.
You are right, however, there are a number of patents regarding Taq polymerase, but they actually patent a method using this enzyme, or a laboratory-made mutation of this enzyme, mostly with the goal of improving fidelity of DNA replication. That is in accordance with established copyright laws (afaik -- ianal), they didn't simply patent something they found, but a method that uses it.
If you are a researcher at a non-commercial institution, you are if I'm correctly informed, exempt from certain patent laws, and I heard of people who have their own expression vectors for Taq polymerase, and use it to produce polymerase for their lab's use.
Also, no biotech company would go to the point of "harvesting" the polymerase from Thermophilus aquaticus, when you can have your friendly E.coli make the same protein in a much easier way.
I these kind of grammatical constructions very popular with german-language lawyers, who that especially contracts or licensing agreements a lot of clarity through the use of this technique, gain, believe, are, believe.
I believe what you're referring to must be Schachtelsatze, or "nested sentences", which indeed is a (quite obsolete) rhetorical style in german. It's not used much, and if it is, it's generally in literature. Probably 95% of its useage is simply to show off, I'd assume.
It works basically more or less like this: you start a sentence, and at some word, where you'd like to add additional information about it, you start a subclause. In that one, you can do the same again. Effectively, you're embedding sentences within sentences. Since in German, the verb often comes at the end, once you're through, you must clean up by adding all the verbs at the end. So it's a bit like pushing and popping indeed.
An artificial, exaggerated example was taken from here:
german: Schon immer mal wollte ich einen Satz, der zwar grammatikalisch richtig gebildet, jedoch durch die Anfugung von Nebensatzen, die durch ein Komma, welches das Verb bzw. das Hilfsverb, das dieserart jeweils erst nach dem Schachtelsatz, der eigentlich den Zusammenhang, der ebenfalls im Nebensatz, der kurz vor dem Verb, welches das Satzende, das das Verb bzw. das Hilfsverb, das durch das bereits genannte Komma, das ja die Nebensatze, die eingeschachtelt worden sind, abschachtelt, ineinander verschachtelt wurde, endlich bringt, wieder entschachtelt, verschachtelt worden ist, erklart wird, erklaren sollte, genannt wird, somit einschachtelt, getrennt werden, verschachtelt wird, ist, formulieren.
english, (almost) german word order: I always wanted a sentence, which however gramatically corrently formed, but through the addition of subclauses, that are with a comma, which the verb or the auxiliary verb, which in this way each time only after the nested clause, that actually the context, that also in the subclause, that shortly before the verb, which the end of sentence, which the verb or the auxiliary verb, which through the previously mentioned comma, which now the the subclauses, which have been nested, nests in, has been nested in each other, finally mentions, de-nests again, has been nested in, is explained, should explain, is mentioned, therefore nests in, are separated, is nested in, is, to formulate.
english, understandable (sort-of): I always wanted to formulate a sentence, that is formed gramatically correct, but that is nested in through the addition of subclauses. These subclauses are separated by a comma, which nests in the verb or auxiliary verb, which then gets only mentioned after the nested clause. The nested clause should explain the context, which also is explained in the subclause that has been nested in shortly before the verb, which de-nests (the sentence) again before the end of the sentence. The subclause thus relates to the verb or auxiliary verb. The verb nests sentences through the use of a comma, which marks the nesting of the subclauses that were nested in.
Hope that helps or at least doesn't confuse more than before...
I couldn't agree more with you. There has been a lot of pressure lately on universities to generate revenue by building up patent portfolios, which can be sold to companies. I have seen this fact also being used as an argument to hinder collaboration (especially by people with lots of influences).
One anecdote (I can't name names, but I know the persons involved) is a highly cited researcher, who maintains an immense output of publications/year by forcing others that want to build on his previous work to collaborate with joint senior authorship.
This despite the fact that publication in most journals requires you to sign a paragraph stating that you will provide the materials used in the work to qualified researchers asking you for it. This persons excuse was that the work was done in collaboration with a company (of which the person, incidentally, is CEO), and thus they cannot be sent to any other lab.
I very much subscribe to the notion of credit where credit is due, but joint authorship for several members of that persons group for providing basic materials seems a bit overboard.
Since when has 'restricting the spread of advanced XYZ knowledge' ever worked? Sure, the RIAA/MPAA would love to contain the spreading of the dangerous knowledge that you can use file sharing programs, and microsoft would love to keep all the advances knowledge about how to build an OS secret. After all, knowing how an OS works could arguably lead to damages and lives lost, like hacking into a power grid (yes, I am becoming a bit melodramatic, I'll stop now, I promise).
My point is: It's a bad idea to restrict the spread of knowledge, since we simply can't. Good textbooks about biology will teach you a fair bit about molecular biology, and lab techniques. All this can be used for good or for bad purposes, as with (almost) all technology. So how do you wish to contain this knowledge? Prohibit anyone from teaching biology? Or perhaps teach biology only in the US, thus protecting the homeland? (oops I am bitter again...)
In that vein, do you think that amending the GPL would help in containing information? Bad people who are planning to kill usually don't worry too much about breaking the terms of a license. And as for the Ebola genome, it's here, courtesy of the NIH. And it is there, publicly available, since some people are actually wanting to study it to find a remedy, and fortunately, they are not all employed by the USAMRIID or DoD but are all over the world.
True, bioinformatics is indeed a fantastic open-source playground, due to NIH and other agencies generous granting, as well as the fact that most bix'ers I know are avid open source supporters.
In the wet lab, the situation is different, though, and I believe that's what Dr. Jefferson has set his sights on, correct me if I am wrong, though.
Re:Unintended Consequences: Less New Medicine
on
The Opening of Biotech
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· Score: 3, Insightful
I think I do see your point, but I guess a distinction can be made between tools, i.e. methods, reagents, protocols (and to some extent labware) that are necessary for basic science and the drug development process. In the end, cheap access to basic biotech techniques may be beneficial for big pharma, as well, cutting down research costs.
There are some things on the market in biotech where the distributor (typically the company didn't invent it, they bought the rights from a university) are more or less monopolizing a technique, with the help of patents and license agreements. And the price that you pay at university for this stuff is - while it's expensive - nothing to the price big pharma has to spend for the same thing. I am not talking about hi-tech equipment, but for instance a method + all the reagents to create stably transfected cell lines (that is, a cell that expresses a newly inserted gene). Sure, the work of the person who built up the system needs to be acknowledged, but the price for this kit is just a phantasy price.
In the end, I think, big pharma wouldn't suffer all that much, and neither would drug development
How unproductive. No wonder cancer hasn't been cured yet, if this is the sort of "me, me, me" squabbling that goes on in science.
Understandable though, assuming that this credit leads to further funding for the said scientists.
Yes, you are right... collaborating instead of competing for sure could lead to more interesting research, faster breakthroughs and a good community spirit among scientists. But in biology (that's the only discipline I can really talk about), this is pretty much a thing of the past, since grants, funding, positions in academia as well as in industry are to a large extent a direct function of how many papers you have published, and in what journals you published them. Only the best and brightest (something like 20-30 articles at age 35, and a handful of them in excellent journals) will get a shot at a group leader position.
This system has its merits, but one corollary is that you're not actually selecting the best and brightest, but perhaps the best-connected and those who can "sell" their work better than others. Another corollary, which is more damaging in the long run perhaps, is that nobody shares his data unless his authorship is acknowledged and under lock and seal. Conferences have become boring. I hear that 10-15 years ago, people would come to conferences and share the freshest, most exciting data from their lab. Nowadays, nobody gives a talk or shows a poster at a conference where the data isn't already published (i.e. you most likely read it already), or at least accepted for publication (i.e. you maybe read the e-pub ahead of print).
It's sad, and it's - exactly as you stipulate - due to all the rewards being tied to your publication record. Publish or perish, as they say.
Slashdot Mirror
I think rsync pretty much provides all you need in one tiny command-line to get data from A to B.
But if you want to increase your resilience against failing network connectivity, and make sure you don't delete anything that hasn't been properly copied to your server, I suggest you take a look at datamover: http://www.cisd.ethz.ch/software/Data_Mover
Essentially, it's a daemon written in Java that monitors an outgoing directory. Everythings that is written in there gets safely copied over to a central storage drive. Behind the scenes, they use rsync to do the copying, but it's wrapped in tons of features that improve the reliability of the moving process, like a quiet period before a file gets moved (good for applications that write their output incrementally and sporadically into files), multiple retries on network time-outs, high-water marks, data transformation (e.g. compression) during the move process, etc. It also is very anal about sending you emails for anything that could possibly be a data integrity problem.
We rely on it to store the raw data from scientific experiments. With the proper configuration, your holiday pictures should be just fine.
Thanks to the TPA (Travel Promotion Act), there's really No Problem(TM). In addition to all the border troubles, simply charge the poor guy visiting another $10, which can then be spent on promoting tourism.
What a brilliant idea: An entrance fee to the US... just like a theme park.
I'm in a quite similar situtation, and perhaps I can provide a few hints from what we're currently doing.
I'm working for a relatively well-known institute in academia (biotech field), with a group that among other research projects, also provides web-based services to the research community. Funding is partially tied to the operation of the services, so there is actually enough pressure to make sure that they work and work correctly at all times.
Still, until about a year ago, development was very ad-hoc, in a mix of languages, and with many "islands of knowledge", where some parts of the system were only known to one post-doc, and other parts could only be fixed by the group head (who, as they are, was usually busy with many other things...). After some hard times and near-misses, we started looking around for ways to improve our development.
I was quite attracted by the ideas of Agile, and I believe that they're a good fit to the kind of processes you find in science, as well as in software engineering. We initially had a professional Scrum coach come in and talk with us about software development practices, and then decided to apply Scrum to our processes.
It's now a bit more than 1 year since then, we're still using Scrum with a few adaptations to fit the academic environment (we're also using Scrum for projects that are really science and research, not software development). In a recent secret poll among the team, Scrum got high marks for making the team more productive, and for creating an environment where code and knowledge is shared. People are happy with the structure that Scrum provides, and we always know where the project stands. Incidentally, we also write better software faster.
But we're still improving the way we work. The transition is slow and painful, and we're only slowly adopting things such as test-driven development, automated builds and pair programming. In my experience, there's a lot of resistance against these "newfangled" methods in the academic culture, especially that of people who weren't trained as software engineers, but rather as physicists, chemists, biologists, but now find themselves producing software.
Some hints on what I've found useful in re-shaping our work environment:
- You can't change the whole structure in one day. Get permission to run a small, isolated project in "the new way", and use this to demonstrate the advantages. Remember, there are many metrics for success: Code quality, timely delivery, not having single points (persons) of failure, as well as team velocity and personal satisfaction. Try to make a case from this small project (and gain experience while doing so), and then grow it out slowly.
- I would not advise to do some clever "breaking the build, and thus showing everybody how fragile the system is" exercise. This may not be seen as constructive.
- Instead, provide convincing evidence by example that your way is more productive and more certain. Bugs that are fixed stay fixed, and don't creep in later again. Timelines are better kept. That sort of thing...
- If you can get someone in to talk about the current best thinking in software development, do so (someone else mentioned this already). It's good to hear an outside opinion, and to understand that these practices are not theoretical but used by large companies world-wide.
- I found Joel Spolsky's 12-point assessment very useful to find out where your organization stands: http://www.joelonsoftware.com/articles/fog0000000043.html ... These are also good points to whisper into management's ears.
Maybe I can provide some insight, as a close colleague at work died last year in a tragic outdoor accident.
Basically, what it boiled down to was as follows: The family/next of kin have right to access all of the deceased person's personal files, emails, etc. Company property is exempt of course - for IP reasons. The system administrators should release a copy of the person's email mailboxes, and all other relevant files to the next-of-kin, after examining that no business-relevant data goes out.
They will not and should not release anything to you, you're (iirc) not related.
I am sure there's a procedure in place at Gmail, etc. to deal with such a situation, as this is not the first time something like this happens.
The more important question is: does the family really want the information? That's an ethical and moral question, and only they can answer that for themselves. So, if they ask you to hack the root account, it's OK for you to do so, but keep all you see private to the family and yourself, and don't force any information on family members who don't want to know. Let them decide.
Disclaimer: I'm not in the US, and assume you are - so the legal implementation may vary.
"Kudelski will lose their case", states the man who pirated their chip cards
Image legend:
Christopher Tarnovsky: "Why would I have published these codes on the net for free? I am not stupid, and I never had the intention of taking that risk."
Main text:
PAID ACCESS SYSTEMS. A key witness in the court case opposing the Swiss group against the media giant News Corporation was passing by in Amsterdam, attending a conference on computer piracy. We met him.
François Pilet, Amsterdam
Saturday, March 29 2008
The audience is glued to the lips of Christopher Tarnovsky. In front of a podium of hackers and security specialists - with an average age of 25 - the self-taught electronics specialist revealed the techniques that allow him to break open chip cards that block access to pay TV chains in the whole world.
The scene takes place in the Mövenpick hotel in Amsterdam, where the European edition of the Black Hat conference was held Thursday and Friday last week. This is one of the prime professional meetings dedicated to computer piracy. Among the twenty or so speakers invited to this big get-together, Christoper Tarnovsky talked for more than one and a half hour in the "Lausanne" room - a sign of destiny (Tr. note: Lausanne is a Swiss city close to the headquarters of the Kudelski Group).
Employed by NDS
The 39 year old American is accused of having been recruited in 1999 by the Israeli company NDS, a competitor of Kudelski, to break the security codes of Canal+ (French Pay TV) and publish them on the Internet, and to have repeated the operation, to the detriment of the Swiss group and its clients. The publication of these codes allowed hundreds of thousands of savvy users to access encrypted TV channels without paying the subscription fees.
The American satellite TV company Echostar also uses Kudelski cards to protect their content. They confirmed having lost hundreds of millions of US dollars due to these pirate activities and demand one billion US$ of damages from NDS, a subsidiary of the media group News Corp.
This April, Christopher Tarnovsky will take the witness stand in a California court in defense of NDS, his employer for ten years following 1997. According to him, Kudelski and Echostar have wholly invented the conspiracy they claim having been victim of in order to mask the weakness of their encryption.
In his eyes, the case against NDS is nothing short of an extortion attempt. "Sure, I've broken the cards of Kudelski", he annoyedly states. "I was paid by NDS to do it. This is an activity that all companies in the trade do. But why would I have published these codes on the Net for free? I am not stupid, and I never had the intention of taking that risk."
Having become an awkward asset, Tarnowsky is no longer employed by the group since a year. He started his own company, Flylogic, through which he offers his know-how to electronics manufacturers, to test the resistance of new products to pirate attacks before they are launched.
Christoper Tarnovsky details the general weakness of systems based on certain chips designed by a handful of companies like Motorola and Infinenon (sic), systems used in products as divers as garage door remotes, car alarm systems and TV decoders.
"Unbreakable? That's wrong!"
"The manufacturers of semiconductors claim that their chips are unbreakable. The companies integrating them into their products trust the specifications they obtain. They believe that their secrets will be well kept. That is wrong, of course."
He showed pictures of his laboratory, set up with second-hand equipment worth a couple of thousand dollars. The centerpiece is a powerful Zeiss microscope to access the heart of the chip, where the precious codes are hidden. Successive layers of silicone are peeled away, using acids and lasers.
The engineer then explains how he takes over control of the card by short-circuiting one by one its protections with long microscopic needles. It takes a few minutes fo
OK, perhaps the open-source context is wrong for the data source, but please tell me how describing MythTV (to name the PVR solution I'm most familiar with) as open source is teeth-grindingly wrong?
If I remember the news items correctly, the toll collect system was actually designed to comply with a certain set of privacy standards. The traffic cameras only save information for about every tenth vehicle passing by. That is still enough to eventually find (and fine) those who don't pay the traffic charge, but still isn't systematically collecting information about the whereabouts (and thus trajectory) of every vehicle. I thought at that time that this was thoughtful.
It is my feeling, however, that the German Minister of the Interior Schäuble would like to see a firmware upgrade to these cameras rather today than tomorrow, so that they can save all the information, and make tracking of vehicles possible.
So I agree, registrations are harmless, if done right, but they lead us one good step further on the slippery slope.
That's right, it's what you pay for your TiVo.
But:
* Not everybody has access to the services TiVo provides (they're not operating world-wide, and alternatives at least around here (in Switzerland) are nowhere near $5/mo, but are bundled with digital TV)
* Some people prefer an open-source alternative, not only to the PVR itself, but also for the data source
* Screen scraping works. Sort of. Sometimes. As soon as your scraper gets popular, the web site will change its layout to foil scraping attempts, and you can start new. It's an arms race, unfortunately, and there's no real way out of it. The networks and content providers jealously guard their data, and only license it to redistributors.
* Schedules Direct is such a licensing partner. Instead of distributing the data in proprietary format, they use standard XML. That is good.
and, most important of all:
* If you had read TFA (or even the freaking post), they're aiming to drop the price. For now, they have no idea how popular their service will be, but want to make sure they don't create a financial sinkhole. The folks behind this are from the MythTV and XMLTV community, and I'd be surprised if they see this as a get rich quick scheme. They're too realistic for that.
Try this one then: ... The real article seems to be published in Nature Neuroscience.
PubMed reference
Personally, I wouldn't call New Scientist a garbage journal by the way, its aim isn't to be a strict scientific journal, but rather to bring news about science to the reasonably well educated masses. A bit like Nature was before they split off into many many subjournals.
Here's a manual translation of the article. It may not be very elegant; I didn't have much time ...
Soviet space shuttle: Curious discovery at the persian gulf
While shooting footage for the formula 1 race in Bahrain, a TV crew from Düsseldorf by chance stumbled over a rumour about a russian space shuttle, said to be located since some time in that region, without anybody taking an interest in it. A little while later, the Germans were standing in front of a relic of the soviet space shuttle program of the eighties: A vehicle strongly resembling the US shuttles. It may be a prototype version of the space shuttle "Buran" ("Snowstorm".
With this shuttle project, at times employing up to 30'000 people, the soviets wanted to catch up with the americans in manned space flight. But the project was not under a good sign. Already at its inception in the late seventies it was clear that the Soviet union actually had no use for a re-usable space craft. "Buran", the name of the sole soviet shuttle ever to make it into space, was a pure prestige project - and an extremely expensive one at that.
November 15 1988, after more than ten years of development, Buran took off for the first and last orbital flight, without crew. This flight ended according to plan after two orbits of the earth. One year later, the iron curtain came down - and with it, the major part of funding for soviet space exploration.
[CAPTION]: TV producer Maier in the cockpit of the shuttle: Relic from the soviet union
While the "Buran" shuttle was able to carry more payload than US shuttles and could be controlled remotely, neither its on-board computer nor its life support system ever worked satisfactory. The space ship was decomissioned, and was destroyed in May 2002, when the ceiling of a hangar in the Baikonur space center crashed. A second shuttle named "Ptitchka" ("Little bird"), which was completed in 1990, was never used: The program was stopped officially in 1993.
Besides the two soviet shuttles that were ready to fly, there were said to be three more, unfinished, shuttles, and a series of test versions. Today, one is being used as a restaurant in Moscow, another was sold by Russia to Sydney as an exhibition piece for the 2000 olympic games. "Ptitchka" is said to be in Baikonur still.
It is not clear which model was found at the persian gulf by the TV crew from Düsseldorf. Nobody knows, how this museum piece ended up there. According to TV producer Chris Maier, this could be the model once located in Sydney. This notion is supported by the fact that the shuttle supposedly performed 25 atmospheric test flights. Various reports claim that the Russians delivered the aerodynamic test plane "Buran OK-GLI" to Australia, which was used to test the automatic landing system of the space shuttles. For this reason, the shuttle was the only test variant equipped with engines.
"We need to get confirmation on which version this is", concedes Maier. However, the shuttle has already attracted a potential buyer: According to Volker Hartmann, a member of the TV crew, German enterpreneur Kai Niedermeier, who is doing business in the gulf states, wants to do a world tour with the space shuttle - and auction parts of its hull on the internet.
You are completely right. "Unlimit" is always within some limits, as every company who actually pays something to a provider upstream to offer this service would be on the slippery slope to extinction , if they wouldn't care how much you use the "unlimited" service.
Unlimited is a marketing ploy, nothing more and nothing less.
Point in case, a DSL provider in Germany offers a no-transfer-limit DSL account. I have just read that they regularly (every month or so) identify those users who pull more than 20GB per month, and send them a polite letter, offering them 100 Euros (100-something US$), if they terminate their account at once. Moreover, they can keep the DSL router and other hardware they got for free when signing up. Basically, they're saying, we don't want you, here's some cash if you leave right away (and sign a statement that you won't re-apply for their service if you keep up your downloading habits).
Actually, it's not that complicated once you're used to the process... Or put differently, if you take enough care to explain it in plain and simple terms to the soccer moms, they'll realize it's not much more complicated than loggin into AIM (taking a wild guess here --- I'm not using AIM) which I'm confident they can manage.
It's been a while since my nice bank has switched from the TAN system to the calculator/login device + chip card, but if I remember it right, it's not only the TAN that authenticates you, it's your user name (or more precisely, your account number - after all, we're in Switzerland, the home of number accounts) and a password of your own choice, plus the current TAN, used only once. This seems to me to be a pretty good system, as you prove your identity by:
With the login device I am using now, you need to:
Knowledge of any one of these is useless, you need to know all of them, so I think the system is pretty secure. Frankly, I was slightly mystified to read that US banks rely on only one token of authentification
Disclaimer first: I am not an astronomist, but at least, I am a german native speaker...
SPIEGEL ONLINE EXKLUSIVE
"Opportunity" finds proof for martian floods
by Thorsten Dambeck
The mars rover "Opportunity" managed to find proof that once upon a time, there was flowing water on mars. As SPIEGEL ONLINE heard from sources within NASA, the US space agency will make this discovery public tonight.
[caption]Water trace: Light stones close to Oppotunity's landing spot (NASA/JPL)[/caption]
"I am flabbergasted, I am astonished", said Steve Squyres, scientific head of the rover mission, in face of the pictures from the second mars vehicle "Opportunity". No other landing zone is similar to the broad plain Meridiani Planum, where Spirit's sister probe landed. The scientist was especially taken in by the light rock formation that appeared in front of the rover's camera eyes, peering out of the dark martian sand.
After thorough mineralogical and chemical analysis of the rocks in the past few weeks, it seems clear now that Squyres spontaneous excitement was justified. As SPIEGEL ONLINE found out from sources within the US space administration, the rock formation is sedimental stone which was definitely built up in a stagnant body of water.
First suspicion hardened
The "smoking gun", the irrefutable proof for the existence of past floods on mars, is said to be a sulphate compound that was found in the rocks, and which can only come into existence in the presence of water. NASA will present these results tonight, Tuesday, at 8 PM german time on a press conference in Washington.
Already the first close-up pictures of the formation fed the suspicion of planetologists, that the rock formation may have been built by sedimentation, by the process of deposition. The single strata were clearly visible on the high-resolution snapshots from Opportunity's panoramic camera. An important contribution to the discovery can be assumed to have been made by the Mossbauer-Spectrometer "Mimos II" , built by the physicist Gostar Klingelhofer from Mainz, which is responsible for the mineralogical analysis of ferrous martian rocks.
Breakthrough with german instruments
Already on the 9th of February, German members of the rover research team reported surprising results from their APXS ("Alpha Particle X-Ray Spectrometer") instrument. According to these reports, analyses of a light rock named "Robert E." using the spectrometer found substantially higher levels of zinc and sulphur than in all previously investigated mars rocks. "This indicates that the rock is a hardened, salt-containing sediment, and not of volcanic origin", said a member of the Max-Planck Institute for Chemistry, where the APXS spectrometer was built.
But even if non-volcanic processes are being favored more and more: Until last week, NASA scientists emphasized that various formation mechanisms -- including variants without the influence of liquid water -- are possible. Now, it seems, liquid water made the race.
With this, the US-rover would have confirmed from the ground what the european probe "Mars Express" already discovered from orbit: End of January, ESA scientists interpreted the breath-taking pictures of the red planet as clear evidence that once upon a time, rivers and seas existed on mars.
What you're describing is not de novo drug design, but rather tinkering, which indeed happens regularly in the drug development process.
The whole zoo of phenethylamine derivates comes from a process of optimization. That part of "drug design" is in fact very common in drug development (not only in psychoactive drugs, but drugs in the common sense of therapeutic substance).
The initial, biologically active, substance usually has some beneficial properties (i.e. it is active), but some undesired properties, such as causing side effects (not specific enough), or having low activity (low bioavailability [basically, it isn't taken up well in the blood stream, or isn't taken up properly by the target organ]). In these cases, medical chemists start playing around with side-groups of the molecule, trying to enhance the desired pharmacological, pharmacokinetic and pharmacodynamic properties. The way I understand it, this process is half science, half art.
What I was referring to when I talked about rationally designed drugs is more than just tinkering. It's saying "We have this disease that's caused by an overactivity of protein XYZ. Let's have a look at protein XYZ and design a completely new compound that will bind to it and dampen that activity", for instance. This is what maybe one day will be possible, but not yet.
To come back to your example, as far as I know, there's no way even within the phenethylamines to look at the structure of two members of this class, and just by looking at the structure predicting what exact effects each of them will have. It's more a kind of trial-and-error process, hardly rational drug design.
Soon we will design drugs, rather than find drugs.
I hope that we will one day indeed design rather than blindly search. We're centainly on the road to it. But then again, I heard the same line about designed drugs coming soon when I started studying biology, and that was, hmm, about 10 years ago.
To be fair, rational design has made some big steps forward, but the number of drugs and drug candidates that were designed completely in silico is really small. Likewise, the combinatorial chemistry approach is useful, but hasn't kept up with the big promises that hyped this approach maybe 5 years ago. But I may be biased there, the idea of blindly throwing together molecules and then letting a high-throughput assay sort out what works and what doesn't has always rubbed me as somewhat contrary to the ideal of science. It's a bit like simply bringing in more and faster monkeys to get that shakespeare play written.
Combinatorial chemistry and rational drug design can still learn a lot from nature, and in fact the two can be combined. It is impossible (and will stay so even in the future) to examine all possible chemical structures for a desired activity. For instance, there are 10^62 different molecules of a molecular weight below 500, a typical cutoff for drug molecules. If you would synthesize one molecule of each, you'd make a ball of mass that covers the whole solar system. (quoting from a recent seminar by Prof. H. Waldmann).
We can't explore the whole chemical diversity, but we may not need to. If you compare a random molecule library to one based on substructures occurring in nature, you'll find that the "natural" library has much higher hit rates than the random one. In a way, nature has worked for us as a filter, selectively enriching substructures that are meaningful in the context of proteins and receptors. Proteins are largely composed of conserved folds, therefore the structures that bind to them are likely to have conserved structures as well. Considering the more creative solutions nature uses to overcome extreme problems will enrich this library of natural structures, and thus be beneficial to rational drug design.
That is an excellent point.
I believe that exploring extremophiles can give us great advances in anything from biomaterials to new drug leads. Put in the most simplest way, by looking at extremophiles, we are asking nature to show us its more uncommon solutions to problems. In these extreme environments, organisms have evolved some fairly impressive tricks just to stay alive (try staying alive in a hot water spring a somewhat over 80C for any length of time, and you'll see what I mean).
The input we get from extremophiles is valuable, because it is tried and proven to work. I see the benefit, however, more in a gain of knowledge than in actually harvesting these creatures. Such a responsible exploration can lead to new interesting molecules without killing off species. Hopefully there's enough financial interest in learning from an extremophile versus harvesting the extremophile organism, since finding/growing/hunting extremophiles tends to be expensive, and if the molecule can be made synthetically or using bacterial/eukaryotic expression systems, this should prove economically more interesting.
If I remember corrently, the original patent for the use of thermostable Thermophilus aquaticus DNA polymerase belongs to Roche. Before I posted this comment, I checked in espacenet for any patents by Invitrogen regarding "thermostable" or "thermophilus" or "aquaticus". I couldn't find any hits.
You are right, however, there are a number of patents regarding Taq polymerase, but they actually patent a method using this enzyme, or a laboratory-made mutation of this enzyme, mostly with the goal of improving fidelity of DNA replication. That is in accordance with established copyright laws (afaik -- ianal), they didn't simply patent something they found, but a method that uses it.
If you are a researcher at a non-commercial institution, you are if I'm correctly informed, exempt from certain patent laws, and I heard of people who have their own expression vectors for Taq polymerase, and use it to produce polymerase for their lab's use.
Also, no biotech company would go to the point of "harvesting" the polymerase from Thermophilus aquaticus, when you can have your friendly E.coli make the same protein in a much easier way.
I these kind of grammatical constructions very popular with german-language lawyers, who that especially contracts or licensing agreements a lot of clarity through the use of this technique, gain, believe, are, believe.
I believe what you're referring to must be Schachtelsatze, or "nested sentences", which indeed is a (quite obsolete) rhetorical style in german.
It's not used much, and if it is, it's generally in literature. Probably 95% of its useage is simply to show off, I'd assume.
It works basically more or less like this: you start a sentence, and at some word, where you'd like to add additional information about it, you start a subclause. In that one, you can do the same again. Effectively, you're embedding sentences within sentences. Since in German, the verb often comes at the end, once you're through, you must clean up by adding all the verbs at the end. So it's a bit like pushing and popping indeed.
An artificial, exaggerated example was taken from here:
german:
Schon immer mal wollte ich einen Satz, der zwar grammatikalisch richtig gebildet, jedoch durch die Anfugung von Nebensatzen, die durch ein Komma, welches das Verb bzw. das Hilfsverb, das dieserart jeweils erst nach dem Schachtelsatz, der eigentlich den Zusammenhang, der ebenfalls im Nebensatz, der kurz vor dem Verb, welches das Satzende, das das Verb bzw. das Hilfsverb, das durch das bereits genannte Komma, das ja die Nebensatze, die eingeschachtelt worden sind, abschachtelt, ineinander verschachtelt wurde, endlich bringt, wieder entschachtelt, verschachtelt worden ist, erklart wird, erklaren sollte, genannt wird, somit einschachtelt, getrennt werden, verschachtelt wird, ist, formulieren.
english, (almost) german word order:
I always wanted a sentence, which however gramatically corrently formed, but through the addition of subclauses, that are with a comma, which the verb or the auxiliary verb, which in this way each time only after the nested clause, that actually the context, that also in the subclause, that shortly before the verb, which the end of sentence, which the verb or the auxiliary verb, which through the previously mentioned comma, which now the the subclauses, which have been nested, nests in, has been nested in each other, finally mentions, de-nests again, has been nested in, is explained, should explain, is mentioned, therefore nests in, are separated, is nested in, is, to formulate.
english, understandable (sort-of):
I always wanted to formulate a sentence, that is formed gramatically correct, but that is nested in through the addition of subclauses. These subclauses are separated by a comma, which nests in the verb or auxiliary verb, which then gets only mentioned after the nested clause. The nested clause should explain the context, which also is explained in the subclause that has been nested in shortly before the verb, which de-nests (the sentence) again before the end of the sentence. The subclause thus relates to the verb or auxiliary verb.
The verb nests sentences through the use of a comma, which marks the nesting of the subclauses that were nested in.
Hope that helps or at least doesn't confuse more than before...
I couldn't agree more with you.
There has been a lot of pressure lately on universities to generate revenue by building up patent portfolios, which can be sold to companies. I have seen this fact also being used as an argument to hinder collaboration (especially by people with lots of influences).
One anecdote (I can't name names, but I know the persons involved) is a highly cited researcher, who maintains an immense output of publications/year by forcing others that want to build on his previous work to collaborate with joint senior authorship.
This despite the fact that publication in most journals requires you to sign a paragraph stating that you will provide the materials used in the work to qualified researchers asking you for it. This persons excuse was that the work was done in collaboration with a company (of which the person, incidentally, is CEO), and thus they cannot be sent to any other lab.
I very much subscribe to the notion of credit where credit is due, but joint authorship for several members of that persons group for providing basic materials seems a bit overboard.
Since when has 'restricting the spread of advanced XYZ knowledge' ever worked? Sure, the RIAA/MPAA would love to contain the spreading of the dangerous knowledge that you can use file sharing programs, and microsoft would love to keep all the advances knowledge about how to build an OS secret. After all, knowing how an OS works could arguably lead to damages and lives lost, like hacking into a power grid (yes, I am becoming a bit melodramatic, I'll stop now, I promise).
My point is: It's a bad idea to restrict the spread of knowledge, since we simply can't. Good textbooks about biology will teach you a fair bit about molecular biology, and lab techniques. All this can be used for good or for bad purposes, as with (almost) all technology. So how do you wish to contain this knowledge? Prohibit anyone from teaching biology? Or perhaps teach biology only in the US, thus protecting the homeland? (oops I am bitter again...)
In that vein, do you think that amending the GPL would help in containing information? Bad people who are planning to kill usually don't worry too much about breaking the terms of a license. And as for the Ebola genome, it's here, courtesy of the NIH. And it is there, publicly available, since some people are actually wanting to study it to find a remedy, and fortunately, they are not all employed by the USAMRIID or DoD but are all over the world.
True, bioinformatics is indeed a fantastic open-source playground, due to NIH and other agencies generous granting, as well as the fact that most bix'ers I know are avid open source supporters.
In the wet lab, the situation is different, though, and I believe that's what Dr. Jefferson has set his sights on, correct me if I am wrong, though.
I think I do see your point, but I guess a distinction can be made between tools, i.e. methods, reagents, protocols (and to some extent labware) that are necessary for basic science and the drug development process. In the end, cheap access to basic biotech techniques may be beneficial for big pharma, as well, cutting down research costs.
There are some things on the market in biotech where the distributor (typically the company didn't invent it, they bought the rights from a university) are more or less monopolizing a technique, with the help of patents and license agreements. And the price that you pay at university for this stuff is - while it's expensive - nothing to the price big pharma has to spend for the same thing. I am not talking about hi-tech equipment, but for instance a method + all the reagents to create stably transfected cell lines (that is, a cell that expresses a newly inserted gene). Sure, the work of the person who built up the system needs to be acknowledged, but the price for this kit is just a phantasy price.
In the end, I think, big pharma wouldn't suffer all that much, and neither would drug development
How unproductive. No wonder cancer hasn't been cured yet, if this is the sort of "me, me, me" squabbling that goes on in science.
... collaborating instead of competing for sure could lead to more interesting research, faster breakthroughs and a good community spirit among scientists. But in biology (that's the only discipline I can really talk about), this is pretty much a thing of the past, since grants, funding, positions in academia as well as in industry are to a large extent a direct function of how many papers you have published, and in what journals you published them. Only the best and brightest (something like 20-30 articles at age 35, and a handful of them in excellent journals) will get a shot at a group leader position.
Understandable though, assuming that this credit leads to further funding for the said scientists.
Yes, you are right
This system has its merits, but one corollary is that you're not actually selecting the best and brightest, but perhaps the best-connected and those who can "sell" their work better than others. Another corollary, which is more damaging in the long run perhaps, is that nobody shares his data unless his authorship is acknowledged and under lock and seal. Conferences have become boring. I hear that 10-15 years ago, people would come to conferences and share the freshest, most exciting data from their lab. Nowadays, nobody gives a talk or shows a poster at a conference where the data isn't already published (i.e. you most likely read it already), or at least accepted for publication (i.e. you maybe read the e-pub ahead of print).
It's sad, and it's - exactly as you stipulate - due to all the rewards being tied to your publication record. Publish or perish, as they say.