Open Source Biology And Knowledge Distribution 64
n7lyg writes: "IEEE Spectrum has an opinion piece this month on Open-source Biology and Its Impact on Industry. The article speculates about advancements in biology and biological-based manufacturing and how it is likely impossible for anyone to keep control of the Intellectual Property around genetic engineering. If software was as easy to produce and prevalent as DNA, then it would be similarly impossible to control software as IP."
Re:1970s Speculation (Score:1)
Yes, the infamous statement: 'by the year 2000...'
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"In the land of the brave and the free, we defend our freedom with the GNU GPL."
1970s Speculation (Score:2)
Wonder what happened between the author's definitive speculation and the reality that did not occur?
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"In the land of the brave and the free, we defend our freedom with the GNU GPL."
Re:Not what you're thinking (Score:2)
Actually, all your BASE are belong to us (Score:1)
This future-view brought to you by... (Score:2)
Meanwhile, some [hemp-products.org] biological factories can still get you 10 years in the pen.
Re:Speculation (Score:1)
The evidence of the availablity of home-made DNA sequencing techniques like gel electrophoresis is cited. This is a very dated and limited technology, available as a kit to any high-school biology teacher well over a decade ago. It is an incredible far cry from the kind of DNA analysis on a chip that is in current play in the research sets.
Gel electrophoresis is still in very widespread use in molecular biology. There's a lot of talk about DNA arrays, but they're not much use unless you're just checking to see which known sequences are present. If you're actually creating or checking a novel sequence, or trying to sequence an unknown molecule, then arrays aren't going to help you much. And as far as actual sequencing goes, there are a lot of slab gel machines out there. Sure, there's a move towards capillary machines, but even somewhere like I work (where we've got over 100 ABI 3700s) there's still a place for polyacrylamide gel electrophoresis. I would guess that it's not going to disappear entirely anytime soon - especially for low-throughput tasks.
Re:Not what you're thinking (Score:2)
It quite possibly will, though as you say, there's a lot more involved in biology "hacking" than software.
Molecular biology, at least in the foreseeable future, requires a steady stream of spending on reagents.This is potentially true, though to what extent this slows anybody down depends on exactly what they want to do. After all, exactly the same can be said of homebrewing beer [which, really, IS a "biotechnological" hobby...] Anyway, to be a "real" software hacker requires a steady stream of spending on new hardware and internet access, as well, right? :-)
As patents expire (The core patent on Polymerase Chain Reaction expires somewhere around 2005, as I recall...and a PCR thermocycler is, basically, just a hot-water bath with a timer and a thermostat. Definitely something could at least be approximated usably by a dedicated hobbyist from spare parts...), it will become possible for people to "home brew" (literally) various reagents. I doubt very many people will have a large collection of different fermentation tanks in their garages, but a dedicated "bio-hacker" might get into producing, say, chromomycin, which he can trade with some associates who produce other things.
But coming up with useful projects requires a deep knowledge of the field you're going to work in, far beyond what a coder needs to write a web browser or wedding planning software.Have you noticed how much stuff goes into a web browser these days? :-) But seriously, it again depends on just what one wants to do. There are very complex and difficult projects, and there are very simple ones. Basic procedures for recombinant DNA are fairly simple when working with microbes, and other than the cost of the reagents, as you've mentioned (note to self: look up patent expiration dates on various restriction enzymes...) is pretty cheap to do. Even working with, say, recombinant DNA in plants - I've seen the lengths (and expenses!) computer hackers sometimes go to in building cooling systems for their computers, so I have no trouble picturing some enterprising individual making a home-built "gene-gun".
Even simpler, many of the techniques could be applied to hobby "detection and analysis" problems. Check the microbes growing in your garden, and adjust their populations to optimize the growth of your prize roses, for example. Speaking of which, as one of the "Amateur Scientist" columns in Scientific American mentioned a while back, you can use gel electrophoresis techniques to get a look at the individual dyes that make up the color in those roses, and track it from generation to generation so you know how close you're getting to producing blue ones. Just for sheer twisted amusement, I'd actually like someday to personally do some molecular phylogeny of brewing yeast from around the world...but then again, I'd also like to make neo-trilobites and glow-in-the-dark houseplants someday, so you can judge for yourself how many of my crazy schemes I'll ever actually get to try...(p.s. anybody know any good online information regarding paleoentomology?)
So, to summarize, just as there's a whole range of potentially enjoyable software hacking one can do - from simple throwaway one-shot shell scripts to kernel hacking and web browsers - there's a whole range of biology "hacking" within reach of even "grocery and hardware store"-grade equipment, if one is willing to look beyond human cloning and fluorescent green animals sort of projects that seem to get most of the attention these days...
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Re:Biology in the home (Score:2)
I'm not sure "consumer genetic engineering" is quite the right phrase (can you picture "consumer kernel hacking"?), but I know what you mean, I think.
It's not necessarily as difficult or complex, or even expensive, as you might think. This:
A lab also requires stable environments for the growth of organisms: "artificial wombs" where food is supplied to the growing embryo and the temperature, pH, etc. are kept well-regulated....only applies if you're working with comparatively complex organisms. A wide range of microbes, plants, and a few simple animals can be cultivated with little more effort than sea-monkeys.
The reagents needed for some of the reactions (as someone mentioned in another post) are probably the most limiting thing right now (some biotech equipment is MUCH more expensive, but generally only needed for particular applications - how many hobby biotechnologists would really NEED a mass spectrometer for what they want to do?). The costs and availability of the reagents (such as restriction enzymes, cellulase, DNA polymerase, and so on, depending on what one is trying to do) should improve as time goes on, though.
I would not, though, limit the notion of home biotechnology to "genetic engineering", though that'd be fun for many of us. There are a lot of "biotechnological" activities available that don't need to involve genetic engineering, much of which doesn't require much more sophistication than fermenting your own pickles or yoghurt, or brewing your own beer.
What we would need [...]is some basic education on pH, temperature (yep, ya can't put that embryo in the freezer, Bobby!) etc.This is certainly true, just as some basic education about computers is necessary for software hacking. Fortunately, the information necessary for "biology hacking" is just about as readily available online, in books, and at the local community college as computer information is.
Greater public participation in this kind of hobby would mean less ignorance, and "less ignorance" is something that I think the general public desperately needs (and not only about biology, either...).
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Re:Acceleration? (Score:2)
Well, the genetic material itself is a product of the genetic material, but that doesn't make it simple to understand.
Maybe a scientist will step in here, but it's my understanding the the soup around the genes plays a huge role in how the genes work. This is, again if my non-scientist memory serves me today, why stem cell research is interesting. The soup around the cell hasn't yet told the DNA which genes to use. You have in every cell the needed genes to make any cell, yet a skin cell is different from a liver cell. This is because of the soup allowing certain parts of the sequence to work and masking others. That seems like an important to understand piece to understand, but we are a long way from even understanding the sequence, much less the context.
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Poliglut [poliglut.com]
Re:Acceleration? (Score:4)
Ok, I understand the tools to make tools arguement and the pace of change and all that. But in some ways that makes my point even more appropriate. Despite that effect we still have no strong AI and are still looking at estimates of (at least) yet another decade before we do. You would be correct if you detect in my tone a bit of skeptisism on this yet latest estimate.
Genetics are at least as complicated as the brain and we have essentially no experience with them. That approximation may offend some scientists in the field, and I don't mean for that, but look at were we are. What are there, a couple tests for genetic diseases, a kind of corn that keeps leaking into the mainstream supply and an identity test that couldn't convict OJ?
We had a similar level of cognitive understanding a couple hundred years ago. Certainly Turing understood at least that much more recently. Yet we still stumble.
Couple that with the fact that it isn't 'simply' genetics, but also the surrounding cellular chemistry that makes the genes work that needs to be studied.
There is an awful lot to understand and we don't even come close to having the capability to do so yet.
So, I'm just saying that it's easy to get hyped over this stuff, but be a little cautious about when you promise your deliverables. Ask Minsky why if you still don't believe me.
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Poliglut [poliglut.com]
Modern day AI (Score:5)
They were, obviously, wrong. Today we can't even do speech recognition with sufficient reliability to use it every day, much less get in a car, tell it were we want to go and then read the important news of the day (pre-selected by a Chevy Agent) on the drive.
So too will genetics be. We're at the beginning of an interesting period in research. But for the genetic possiblities to be realized will require something like the kind of AI imagined in the 60's to be available and well understood. There is just that much data available to process.
So, while I'm as excited as the next guy at the possibilities, I'll consider myself lucky indeed if I live to see them realized.
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Poliglut [poliglut.com]
Genetics is not the whole story (Score:2)
While certain spaces are tightly constrained, others are more general. So simple things like eye color have a tightly constrained space (and are likely to be predictable by genetics), complex things like "creativity" will probably prove much more elusive.
(Begin Wild Speculation)
My personal suspicion is that genetics will prove to be a boom industry, and will be good to address certain kinds of cosmetic things, treat/prevent certain kinds of diseases, and so on. Everyone will be beautiful according the the fashion of the time of their birth, and no-one will suffer from ailments like MS or diabetes. But we'll discover that the stuff that we *really* want to change will be out of our reach -- too many variables. So we won't ever be able to have kids who can see in the IR spectrum, have ultra-fast x12 reflexes, or have 300 point IQs. Still, it'll be an interesting world (particularly for that unfortunate generation whose parents thought it was really, really cool for their kids to have a thrid eye).
(End wild speculation)
(See Goodwin's How the Leopard Changed its Spots [princeton.edu] for a good and admittedly controversial intro to the "post-genetic" theory of biology).
bukra fil mish mish
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Monitor the Web, or Track your site!
Biology in the home (Score:2)
I welcome moral discussion of the issue, but I think that I would generally trust the public to work things out more than corporations that really don't care. If everybody has a DNA sequencer, we'll have to invent some rules double-quick. If only companies do, they can sneak stuff by and people might never notice.
However, a well-stocked genetics lab isn't only composed of sequencers, as other posters implicitly assume. A lab also requires stable environments for the growth of organisms: "artificial wombs" where food is supplied to the growing embryo and the temperature, pH, etc. are kept well-regulated.
What we would need before large-scale dissemination of genetic engineering technology is some basic education on pH, temperature (yep, ya can't put that embryo in the freezer, Bobby!) etc. It wouldn't have to be complicated (the machines could handle most of it) but people would need to recognize that spilling lemon juice onto their latest experiment won't work.
I personally am genuinely intrigued by the possibilities presented. Any thoughts on other prerequisites for consumer genetic engineering?
Intellectual Property is a fleeting phenomena (Score:3)
Even the phrase "Intellectual Property" itself is somewhat an oxymoron since property is 'real' (as in real estate) and anything "intellectual" is not real. Like "military intelligence", there is something fishy going on (:>).
The basis of Property is that only one person can possess it at any one time (think of 1 square foot of land that you can stand on, if it helps) whereas the premise of Intellect (ideas) is, like software, it is comparatively costless to replicate as many times as desired.
IP is a useful invention in many regards but just like other constructs that exist outside of natural laws, its time will end as "people" say something like they did about Monarchical rule back a couple hundred years ago (they said, this monarchy thing isn't good for the people, and in 1776 they closed that deal).
Though IP has a very strong value in many business contexts, one way to examine its potential longevity is looking at its "Insurability". IP is not something that is easy to take out insurance on, since it can disappear very quickly and has a strong probability of disappearing. If you take a look at our modern (read 1st) world from the perspective of insurance, you'll see the difference between 1st world and 2nd/3rd is insurance. The notion of the safety that insurance brings is a cornerstone of our economy. Without that safety blanket, IP is sure to be eroded away as open source starts to catch on in all endeavors of the "Intellect", like biology, genomic computation and the of DNA based nanotechnology that can be grown in a bread maker or window box (or even a Windoze Box! :>).
Advertising is another such construct that has not always been around, and one day too will meet its end. ;^>
X
I like this article (Score:2)
Not only are we going to be importing strictly biological solutions to our technology, but I expect we will also be importing biological ideas.
For example, I expect that as nanotech develops, we will find it necessary to create a global "immune system" composed of nanotech dust that recognizes and eliminates non-certified nanotech organisms. I cannot imagine nanotech being safe without such an implementation, just as a person without an immune system cannot survive. It would be too easy for a nanotech organism to develop and begin replication.
There are also an enormous amount of information processing lessons that the brain can teach us. We have local control of some circuits where speed is essential, giving way to higher level(and slower) commands for more complex tasks. Another lesson is to have multiple systems to attempt to handle a problem several different ways simultaneously, and giving control to the best of them for a particular task.
I agree with you on all accounts (Score:2)
However, I can't blame those who make blatantly optimistic prognistications as there are good reasons to do so.
One is personal, it helps to keep your lab motivated if you think the big discoveries are right around the corner.
Another is financial, VC's aren't going to be incredibly eager to give money to a technology that's more than a lifetime from bearing fruit.
This optimism always persists and it does so for very good reasons, IMO.
Re:I agree with you on all accounts (Score:2)
future fighting (Score:3)
Things in that arena are bound to go the route that plagues the technology sector as well regarding patents, I can see it now. Why in the world is there a need to patent [genomic.org] a gene, its not an invention, nor is it one person's creation. The ethics regarding this are scary.
Example, take the company who patented the Breast Cancer Gene (Bionomics [egoli.com.au]), they've been charging scientist exhorbitant fees to allow the scientists wanting to study cures for breast cancer. Sure they should get recognition, maybe even cut a deal with the scientist who discovers the cure, but to halter research over patenting is silly as hell.
Other companies [myriad.com] have taken that same approach towards gene research, which begs questioning by some committee whether its humane for these guys to play with life versus making a quick buck. Anyone here in North America notice how many people are going into Canada for medication as a cause by these companies and their outrageous prices for medicine? Or the Southern Americans crossing into Mexico.
So what's going to happen when "Open Source" biometrics companies start fighting against companies like Human Genome Sciences when they really start monopolizing research, by withholding very important research material? Are we going to suffer because of capitalism...
slightly off topic I know but I see no reasons why the whole area of genomic science shouldn't be "open sourced"
Re:Acceleration? (Score:2)
"I may not have morals, but I have standards."
Mod This Up!!! (Score:2)
I think most
"I may not have morals, but I have standards."
Re:I like this article (Score:2)
"I may not have morals, but I have standards."
sorry it has to be said (Score:1)
Re:Speculation (Score:1)
Re:Speculation (Score:3)
ISTR that the technology needed to manufacture gene chips is actually much simpler than you'd believe. In particular it turned out to be possible to do it using a reprogrammed inkjet printer using the right reagents in place of the standard four colors of ink. The setup cost was still reasonably steep- something like $10,000- but not out of the range of affordability for a dedicated hobbiest. This was a big issue specifically because it brought the technology within the reach of a lot of less well funded labs, rather than just the big boys. Despite the trend of biology toward big science, there's still a lot of great work that can be done on a very tight budget.
And, of course, a lot of the upcoming work in biology is going to be computational rather than experimental. You may not believe it, but it is quite possible to generate publishable results on a home computer. There's even some real suggestion that interesting problems like protein folding are going to be solved not by brute force but by better algorithms. I recently went to the Tolman Medal talk by Bill Goddard [caltech.edu], who claims to be able to narrow the field to about 10-20 possible folds per protein right now and may be able to get it to a single prediction soon. That's using some fairly beefy computing power, but nothing like the LottaFLOPS zillion node clusters that people are discussing building to deal with the folding problem. It's entirely possible that protein folding will be doable with a home computer in a decade.
You've gotta be kidding-50 years..nope-no way... (Score:4)
Discovery of the Rosetta stone in 1799 ( http://www.rosetta.com/RosettaStone.html ) allowed historians/archeoligists to finally understand Egyptian hieroglyphs. Did these historains then understand Egyptian customs, culture and building techniques within the next 50 years? No WAY! Were untrained indivduals, so called hobyists all performing cultural analysis of ancient Egypt? I doubt it. It did, however, launch an era of increased understanding for this lost culture.
We are accelerating in our aquisition of knowledge regarding biological systems, and the genome projects currently underway will no doubt facilitate further acceleration. But knowing the genitic code doesn't mean that everybody is going to be creating transgenic organisms in their garages in 50 years.
Now that we have the genetic code (and remember, it turns out we have FAR fewer genes than we anticipated, 30,000 vs the expected 100,000) the next great leap forward in biology is going to be study of protein protein interactions. How fast will we progress in this regard? To give everyone a yardstick, the gene responsible for cystic fibrosis was identified (without the help of the human genome project) 10 years ago. Are we any closer to a cure for cystic fibrosis? Doesn't look like it (despite the efforts by fantastic researchers in the field). That is one gene, that happens to cause one disease. Its becoming an accepted fact (or at least a paradim) that for many diseases, or biological processes (in the case of biological manufacturing) several genes and therfore proteins interact to produce other products.
A LOT of further study is required in order to understand these interactions, its gonna take a little over 50 years (mabey 100+) for us to understand biology in the manner this author describes. Right now, the following steps need to occur:
1) Linkage of ORFs within the DNA (open reading frames) or full genes (expressed mRNA transcripts) with the proteins they code for. This still needs to be doen for some genes, as the human genome project (as opossed to Celera's efforts-which are "closed source") releyed on sequencing all the DNA as opposed to expressed genes.
2) Study of gene expression and regulation. Much of the DNA sequenced in the human genome project is called "Junk" DNA. In fact, these sequences contain mostifs, called promoter (and in some case suppressor)sequences which regulate the timing of gene expression- in many cases things are produced, or not produced, singnals dampened or aplified based on the timing of gene expression. Much of this work will be performed utilizing "gene chip" technology, for high throughput screening.
3) Study of Protein protein interactions. Much of this work is performed using either immunoprecipitation (mixing together cellular proteins, pulling one your interested in out of solution using immunoprecipitation and seeing what other proteins are stuck to it) and the yeast two-hybrid technique (a very kickass technique for high throughput screening of genomic libraries to identify interacting proteins).
4) Confirmation of function utilizing genetic knockouts, inhibitors or other transgenic model systems.
A lab could easily spend 10 years on performing all of this work on one or two genes of interest, and it would be unlikely they would figure out all the protein-protein interactions. This represents the work of 5 scientists ( a conservative estimate) X 10 years= 50 years of "people" power work per gene. Multiply this by 30,000 (number of human genes identified) =1.5 million years of work. Muliply this by the number of organims you expect to "know" the biology for,(50 is a low estimate) =75 million years of work. Divide this by the number of scientists, and you have the time needed to "understand" all these genes. From my very rough estimation, we'd only need 1.5 million (Very well funded) scientist to complete this work in the next 50 years. Ya right. Don't be expecting a biological version of the replicator for another 100 years at least.
"If we knew what we were doing, it wouldn't be called research, would it?" Albert Einstein
If DNA is Open Source, and Microsoft... oh my... (Score:1)
If DNA is Open Source, and keeping in mind Microsoft's recent anti-Open Source rumblings... What do you predict the fate of "Windows DNA" will be?
On the other hand, it probably doesn't matter-- Windows doesn't have a particularly interesting lineage anyway. Or is this a completely unrelated issue, and I've been caught in the .NET of stupid nomenclature?
Poorly written article (Score:1)
The authors point out that structuring business practices along biological lines can significantly improve the bottom line. The human circulatory system, for instance, is optimized to minimize the work required to pump blood throughout the body. The majority of industrial pumping systems, however, are optimized to minimize the cost of the pipes during construction. This means smaller pipes are used, requiring large pumps that use vastly more energy than necessary.
Similarly, in the human pumping system, the heart has to work too hard when arteriosclerosis reduces the diameter of blood vessels. These vessels then require maintenance in the form of an angioplasty. Industrial pumping systems are designed with built-in arteriolosclerosis, and fixing them requires rebuilding from the ground up. Paying careful attention to several hundred million years of nature's trial-and-error design experience will save human industry considerable energy and resources.
DNA Sequencing Outpaces Moore's Law (Score:1)
Check out the guy's other paper in which he shows that our ability to rapidly sequence DNA is growing at a super-exponential rate, rather than the merely exponential rate of increase of CPU power posited by Moore's Law.
Exponential Improvement in Biological Technologies: A Comparison with Moore's Law [molsci.org]If this keeps up, in a few years you will be able to sequence your own genome in a fraction of a second.
Eponymous Mallard
If it quacks like a duck, it's the Eponymous Mallard
In the future . . . (Score:1)
From the article:
I wouldn't bother bringing a copy along for emergency purposes on my next camping trip.
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Acceleration? (Score:1)
Re:Only one question. (Score:1)
Re:Acceleration? (Score:1)
Genetics are at least as complicated as the brain and we have essentially no experience with them.
No. I can take a complete oposite view of this. Genetics can be as simple as a single gene makes a single protein. I've done it myself, it's called cloning and can have very powerful effects. Also, as you point out later on in your post, there are decades of experience. Even Mendel was learning about the basics of genetics when he bred his little pea plants. That's what you get for using such a broad term.
What are there, a couple tests for genetic diseases, a kind of corn that keeps leaking into the mainstream supply and an identity test that couldn't convict OJ?
ok, 1 apple + 1 orange != 2 apples:
Couple that with the fact that it isn't 'simply' genetics, but also the surrounding cellular chemistry that makes the genes work that needs to be studied.
My friend, the 'surrounding cellular chemistry' is made up of 2 things. The direct product of the genetic material and the environment. The environment is simple.
"just connect this to..."
BZZT.
you lucky guy! (Score:2)
Some of the major problems in peoples genes, ie. genetic diseases are simple 1 gene problems. As such, scientists are successful at treating these diseases which formerly had NO cure today.
Look at cystic fibrosis. It's a genetic disease which causes great discomfort in people and ultimately leads to their death around the age of 20. It's also reasonably common. It's caused by a mutation in only one gene, which leads to a problem in their lung cells.
5 years ago scientist were already getting good results on trials. And in some ways what they were doing is more complicated than genetic engineering, it was gene therapy, where you change the dna of living organisms in vivo.
Plasmid and viral vectors were being experimented with. IIRC one of the viral trials had a 70% success rate in just about curing people.
Yes, in general, it will be on heck of a task to know what everything in our genes really means. Then on top of that there are very complicated interactions. There are illnesses and processes however, which are dependant upon simple interactions and few genes. Those will be understood much more easily and that can have a great impact during your lifetime.
"just connect this to..."
BZZT.
So will "virus" stop being an analogy? (Score:2)
No longer will script-kiddies just be able to wipe you're data, they'll be able to make your hardware literally die. Or turn blue. Or whatever they like. Perhaps the "I Love You" virus of 2020 will actually make your monitor love you. Genetic modification of hardware could certainly make Melissa or Michelangelo more interesting.
And I shudder to think of what will become of the "Killer App".
"You Can't Breed With Her, She's Proprietary!" (Score:3)
First I thought I'd write a comment on what would happen if human genetic manipulation companies decided that in order to protect their intellectual property, they'd have to establish the legal age for breeding up from 18 to 20 (USA statutory rape: 18 years, USA patent duration: 20 years), and I'd include a neat comment about how odd and absurd it would be for people to be considered proprietary.
Then I realized... No, humans have quite a bit of experience with this sort of thing. In fact, people have "protected" their property property by establishing directly whom could breed with whom, frequently with special attention to genetics...
Re:There still needs to be some money. (Score:2)
It is amazing, though, how technically competitive it is considering the amount of money Microsoft spends on their product. I suppose, as a relative newcomer to Free Software, I am still amazed at the quality of the software that is out there. Look at the software we have been given and figure out how much it would cost to buy the equivalent in the Windows world. Operating system, editors, compilers... these aren't trivial pieces of software.
There are two conclusions I could draw:
1) The state of the software world has been so stagnant for so long that these pieces of software are worth nothing and so deserve to be given away for free; or
2) Return on investment is not the only driver of innovation.
Obviously I believe the latter. Some innovation does require a great deal of money, some does not. Einstein and Newton, Picasso and Van Gogh did not require huge amounts of money; today's particle physics and architecture does. I am not sure how to characterize these two types of innovation: is there a fundamental distinction of type between expensive innovation and cheap innovation?
In any case, unless you believe option 1 above, I think you have to agree that a huge amount of innovation has occured with very little monetary investment. Going to SourceForge is the proof.
Re:Rocks or grenades (Score:2)
Maybe we can outline a generic theory of the history of innovation (we'll call it the Milo-Coach theory (g).) Let's take machines as the simplest history to outline.
1) Tools are invented;
2) Tools evolve over thousands of years;
3) Simple machines are invented (using a lazy definition of machines as compound tools );
4) Really complicated machines are designed and built.
I know this is simplistic, but the thing that jumps out at me is that all of these steps involved innovation, but nos. 1 and 3 were not resource intensive, they were thought-intensive while 2 and 4 were probably both. Let me know if you think I'm stretching it (I think we're the only people still reading this thread) on 2. I am assuming it was resource intensive in an opportunity cost sort of way (ie. testing out the new spear might lose you a kill.)
So, can we postulate that innovation is an alternation of revolution and evolution, where evolution is expensive and revolution is cheap? Then, my theory is: revolutions are caused by the availability of resource-cheap evolution, resource-cheap evolution is time-cheap evolution, the end result of revolution is the same as the end-result of much expensive and time-consuming evolution.
OK, it's a bit of a stretch and I can think of a few instances where it does not apply right off the bat, but it *is* only a theory. The application here is that what the article is predicting is the advent of cheaper evolution: the availability of the genome, the availability of much cheaper computing power, and the availability of much cheaper biological experimentation equipment. The theory predicts that these changes will result in revolutionary results in the field.
History v. Microsoft (Score:3)
This article talks about innovation resulting from the spread of info about the genetic 'kernel': the more people who have access to the raw data, the more innovation will result.
"When molecular biologists figure out the kernel of biology, innovation by humans will consist of tweaking the parts to provide new services. Because of the sheer amount of information, it is unlikely that a single corporate entity could maintain a monopoly on the kernel. Eventually, as design tasks increase in number and sophistication, corporations will have to share techniques and this information will inevitably spread widely, reaching all levels of technical ability--the currency of the day will be innovation and design. As with every other technology developed by humans, biological technology will be broadly disseminated."
Beneath this statement is the belief that ownership and innovation are at odds. One of the reasons open-source software is so competitive with products backed by tens of millions of dollars of R&D budgets is that open-source allows everyone on the planet to brainstorm a better way to do things. This is not possible where an 'owner' is attempting to control development.
Thinking about the progress of science and the relative poverty of scientists (compared to Bill Gates that is) also shows that innovation is about more than money, something that doesn't need to be explained to the open-source coders. Maybe somebody should explain that to Mundie.
Re:Acceleration? (Score:3)
Being one of the scientists in the field, I have to both agree & disagree with that. While the assertation that we have essentially no experience with genetics is way off the mark (as is the minimalistic list of uses), the sentiment that our level of understanding is miniscule is right on. Genetics as a discipline is one of the elder biological sciences (remember that wacky monk, mendel?), yet even still we are adsurbly far from having the O'Reilly guide to gene manipulation.
Ya know, one of my big beefs with coverage and speculation about molecular biology/genetics/genomics/proteomics etc etc. is the absolute ignorance of how little we actually know and can do (relative to what is suggested or claimed). We can coax bacteria, yeast & higher organism cell lines to make some small selection of proteins often poorly or incorrectly. We have a complete sequence of the genomes for numerous species, yet the actual interesting side of it (how those genes are regulated, how those genes produce numerous forms of proteins (splicing is very poorly understood), how the proteins interact with each other, and perhaps the most complex problem yet to be asked, how to determine how a protein folds given just its sequence.) is still basically a black box.
Within those 10 years, the genomes of many organisms will be sequenced, providing a parts list for the proteins forming the structural and control elements in those organisms. Biologists, engineers, and physicists are already collaborating on models that will help us understand how those parts work and fit together.
We've got a number of genomes already. Our parts list is equivalent to a spool of wire, a hunk of coal, and a pair of pliers with the task being to build an Athlon. *sigh*
This is not to say we haven't come far, nor to suggest we aren't moving at an ever increasing speed...it's just that we need to keep perspective and realize that so many speculative headlines, especially in this field, are more suited of the weekly world news than any mainstream media.
-Ted
Re:open source biology... (Score:2)
Well, your fingers weave quick minarets; Speak in secret alphabets;
Not what you're thinking (Score:3)
I've seen the speculation before, and it's never seemed too likely to me. For one thing, the costs are different. Once you buy a computer, some O'Reilly books and maybe a compiler, you can code pretty much for free. Molecular biology, at least in the foreseeable future, requires a steady stream of spending on reagents. More importantly, what are people going to do? It's true that the techniques of PCR, DNA cloning and transformation are straightforward. But coming up with useful projects requires a deep knowledge of the field you're going to work in, far beyond what a coder needs to write a web browser or wedding planning software.
The whole thing had a talking-so-far-in-the-future-that-it's-impossible- to-critique quality that characterizes most of the writing about nanotechnology. Sure enough, the article notes "In some ways, this scheme sounds a bit like Eric Drexler's nanotechnological assemblers, except that we already have functional nanotechnology--it's called biology."
I say it's all hot air but I'm eager to see some teenager prove me wrong.
Unsettling MOTD at my ISP.
Re:Only one question. (Score:1)
Uhhh, excuse me. I live in the USA. Creating open source software is fast becoming an obstacle course of intellectual property rights. Want to build a shareware program today? Get a lawyer.
I wonder if 50 years from today, you'll need a lawyer to negotiate a royalty contract before your doctor can legally apply a patentend bio-engineered treatment.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~ the real world is much simpler ~~
Biology GPL (Score:1)
I always distribute 'source' when I distribute my genetic material.
IP (Score:1)
Re:Acceleration? (Score:2)
Hey, they did it on Apollo 13, didn't they?
"...square peg in a round hole..."
-- Chris
Re:Could you imagine... (Score:1)
It's called a nightclub, jackass.
Things Have Changed Greatly Since the Early 70s (Score:1)
True but one of the thing that AI did not have thirty or forty years ago was the advanced neurobiological knowledge that was acquired in the ensuing years. We pretty much understand the function of the retina and the retinal ganglion cells, for example, and we are making great strides in our understanding of such important neural sub-assemblies as the cerebellum and the basal ganglia.
In my opinion, contrary to popular wisdom, AI will not arrive by incremental steps, i.e., we will not see intelligent machines slowly advance to human level. The gap between the two levels is astronomical. However, do not be surprised if a sudden breakthrough in computational neuroscience completely changes the field. If that happens, get ready for an explosion of activity. After that, it won't be a question of "is your computer more advanced than mine?" but "how many robots do you have on your estate?" And if you don't have an income producing estate, you're fucked because the worth of your expertise and labor will be zilch.
Re:Speculation (Score:1)
Speculation (Score:4)
Of course, any statement on what the world is going to be like in 50 years is purest speculation. This story, however, is even pushing that characterization a bit, as it contains several exceptionally questionable assumptions.
Foremost is the idea that people will soon be effortlessly tinkering with genetic modification in their garages in the near future. The evidence of the availablity of home-made DNA sequencing techniques like gel electrophoresis is cited. This is a very dated and limited technology, available as a kit to any high-school biology teacher well over a decade ago. It is an incredible far cry from the kind of DNA analysis on a chip that is in current play in the research sets. The question is, are the powerful corporations who are staking their existence on capitalizing on genetic information going to quietly watch this kind of technology get domesticated, or are they going to fiercely lobby to keep access restricted to the government and corporate level, most likely argument that the dangers of making genetic modification avvailable at the consumer level are simply too great because of the potential for use in terrorism (i.e. biological warfare).
If that's a bit too conspiracy for you, consider the fact that the corporations are far ahead of the curve in the development and posession of these patented technologies. What are they doing with this power? Why, they're deducing functional bits of DNA... and patenting them as fast as they possibly can, usually with some pretty spurious uses attached to justify what is essentially gene-squatting. An Open Source model in genetics is well into the process destroyed by an ignorant, corrupt and complacent government and the fast actions of dozens of greedy corporate giants and hungry start-ups.
This is to say nothing of the incredibly optimistic timeline and assumptions this article makes about how effective "hacking" biology for useful industrial processes is going to be.
My favorite part is the examples given of garage technologies- automobiles and computers. Ah yes... It sure is great living in this capitalistic paradise where cars and computers are being innovated by thousands of inventors using a non-proprietary, open intellectual property model. Think of the horror of living in a world where a handful of corporate monoliths produced the vast majority of vehicles and microprocessors, enforcing proprietary ownership of their technologies through international patent laws!
Re:1970s Speculation (Score:1)
International law happened. With no possibility of profit (seabeds are common property of mankind as regulated by the UN) what incentive was there to develop mining techniques? Simple gee wiz altruism seems to not be cutting it. Aquaculture is now mostly doing things in ponds rather than in the ocean proper - and it is causing its own special environmental problems.
Software (Score:1)
If software was as easy to produce and prevalent as DNA, then it would be similarly impossible to control software as IP
Easy to produce, not necessarily, but prevalent? Quite: Results 1 - 10 of about 49,800,000. Search took 0.17 seconds
Source: Google search for "Software." I rest my case, although it might be pointed out that this many molecules of DNA are present in my pinky :-D
--SAMCould you imagine... (Score:1)
--
George W. Bush
President, United States of America
It's not that simple (Score:2)
I think it's the law, not the amount of information, that prevents centralized control of intellectual property. Or not. In any event, it's what you're allowed to do with it that counts.
Then again, given the hazards of releasing new, untested "services" into the ecosphere, perhaps a little control over the kernel might be a good thing?
Re:So will "virus" stop being an analogy? (Score:1)
-CrackElf
Can you recompile the biological kernel? (Score:4)
Working as I do, a software engineer in a bioinformatics research institute, I can tell you that even at the frontier of research people have no clue as to how some things work, let alone how to change them.
As a computer vision expert, David Marr, said once, "the tools we have for describing nature are very weak." Notice he said describe, not understand or model! For the while, we'd be happy to find that some genes can be used as markers of activity, without knowing the mechanism of that activity at all. IMHO, this fifty-year-forward vision of biotech has some orders of magnitude lacking...
I don't mean it's impossible, it's just the relations involved are much less straightforward than in software. And remember we didn't design it. To find the structure of our own spaghetti code is hard enough, to understand and improve nature's design over millions of years will be an immense task. But the task is ours to tackle!
make DNAImage, anybody?
There still needs to be some money. (Score:1)
One of the reasons open-source software is so competitive with products backed by tens of millions of dollars of R&D budgets...
I'm not seeing many Linux workstations in corporate America. Not on the desks of the average worker, anyhow. Neither the lady at my bank, my accountant or my attorney is using Linux or an open-source software suite. There are a lot of different reasons for that, not the least of which being what we call "network effects", but the end result is that open-source software is only really competitive with big budget products in the server rooms and among /.ers.
Among those whose IQ is merely normal Linux is difficult to pronounce and even harder to install.
While I am a great admirer of the idea of allowing as many people as possible to brainstorm solutions and improve products I also recognize that there are some problems that are going to require some budget to solve. Especially in the area of bio-tech there is going to need to be some capital investment and most capital investment requires a return on that investment.
To some degree obtaining a return on the investment requires some nature of ownership -- we've already seen that you can't count on the stock price sustaining you endlessly if you aren't actually making any profit.
There is no doubt in my mind that there are many brilliant people who could significantly advance the research being done if they had the information to work with. However, while innovation certainly is about more than money, some innovation also requires a great deal of money. The scientists may be personally poor, but many of them have considerable budgets to support their work.
-Coach-
Rocks or grenades (Score:1)
One point that I think is important, though, is the barrier to entry. Anybody with a desktop computer can start creating software. How good the software will be depends upon the tools used and the skills of the person doing the creating. A lot of great software has been created by people with an abundance of pizza and a lot of late nights of bumming code.
In this context, though, we're talking about biology and genomes -- I just don't think we're going to see a lot of guys chugging Pepsi and crunching molecular genetics all night. :) Of course, I could be wrong.
Another big difference between software and genetics is that of gratification. When you create a great piece of software (or even improve an existing piece) you can see it run right away. Give copies to your friends. Post it on your website. I'm not clear that you'll see the same, immediate, tangible results from synthesizing DNA which may take some of the excitement out of such a project for the average hacker.
Anybody can scoop a rock out of the mud. It takes a few more skills and tools to make a hand grenade. :)
-Coach-
Only one question. (Score:3)
Everybody can buy a computer, and start producing open source software. It's cheap, simple, and anyone who can execute a task composed by various commands can program.
And how about biological research? It's not that cheap (at least it's not as cheap as computing). Who's going to spend money with Open Source Biology? Will it worth? Ok, there's always good guys/companies who will spend their money for the Science Evolution, but, will it be as big as Open Source Computing?
The question: Will it work?
Don't worry, I'm upset [to|every]day!
open source biology... (Score:1)
Re:I agree with you on all accounts (Score:2)
That sort of thing, of course, then ends up really hurting investment in the industry, when money goes down the tubes, as it did with AI.
Re:Intellectual Property is a fleeting phenomena (Score:1)
Re:Acceleration? (Score:1)
That's all fair enough to say. However, we have been using genetics for thousands of years, doing selective cross breeding of plants and animals for all kinds of traits.
The surrounding cellular chemistry you speak of really is fun stuff - I suggest taking a developmental biology course if it interests anyone.
And I don't think the problem with convicting OJ was the DNA test - I think it was more likely developmental problems with the jurors...
Re:Poorly written article (Score:1)
Yep, it's just you.
For the record (Score:1)
For the record, as the author of the essay in question, let me point out a few things.
1. Many slashdot readers commented that having the genome isn't the whole game, and this is correct. As I suggest in the essay, real progress in building things out of biology will happen only with the advent of design tools. These design tools will evolve from predictive models, just like in every other field of engineering. The models are being built now, and are probably 5 to 10 years from being useful as design tools. (Humans are, or course, already manipulating genetic systems without models to aid in understanding the process.)
2. The models will be aimed at predicting the behavior of biological systems at the most appropriate resolution. In general, the goal is to build models that quantitatively describe protein-protein interactions and genetic networks, though there are efforts underway to plug metabolism in early on. One difficulty inherent in the process is that the ability measure and model varies significantly depending on the system studied. There are some systems where a single molecule can be identified in a cell, and others where millions of cells are required to get a signal. This directly affects what sorts of models are built and how appropriate they are for the system studied.
For example, there are many models now built on a framework of deterministically solved differential equations. These models are only useful to predict the behavior of deterministic systems. However, many real biological systems involve only a small number of molecules and therefore must be treated stochastically. Yet the experimental tools to provide data at this level of resolution are only just being developed. There is significant progress on both modeling and experimental fronts ongoing.
See, for example: opnsrcbio.molsci.org/alpha/
3. The cost of biological technologies are falling exponentially while the productivity they enable is increasing exponentially. These are independent in the following way: reagents and instruments are becoming cheaper while simultaneously (and independently) becoming more capable through automation and parallelization. The parts for a "state of the art" parallel DNA synthesizer cost only ~$10,000, and both this monetary sum and the assembly cost are well within that expended by computer and car hobbyists. This machine will let you make enough DNA to assemble smallpox from scratch in about a week. Of course, I am not advocating this course of action, but it is worth thinking about. It seems relatively obvious that given the opportunity to tinker, humans will.
More information along these lines is available at: www.molsci.org/~rcarlson/exp_biol_tech.html
4. A general comment about Open Source Biology: Biology is, of course, already very close to open source when you think about how methods are shared. The whole issue of whether the open source software model is useful or appropriate for IP in biology is open. The real question you need to ask yourself is: What happens if there is a Biosoft? Could be good, could be bad -- I don't have the answer. But I suggest we begin considering the question since there are already commercial efforts underway to create proprietary sets of molecules for manipulating biological systems.
5. As far as people's thoughts about whether it will work or not -- it already does. Many pharmaceuticals and industrial enzymes are produced in vats growing bacteria (BACTERIA, not yeast for you home fermentation enthusiasts...). Laundry enzymes are a multi-billion dollar market. Like your snowy slopes? Snowmax is an ice-nucleating protein produced recombinately and used in snowmaking machines world-wide. If memory serves, it ranks first among recombinant proteins by produced weight.
Many labs are inducing plants to produce "biopharmaceuticals". Moreover, there are many projects underway, both commercial and academic, to grow tissues in vats. Artificial bladders have been done and will be tested in humans soon, livers are in progress, and one of the heart projects, headed up by people at MIT, is making very interesting progress. This is difficult work, but not pie in the sky by any means.
Finally, given the audience here, you can help decide how fast this goes and whether it takes place in the open or not. Help figure out the models, help write the code, help write the Bio-GPL (actually the Lesser licence is our favorite model at the moment). Or not.
Your choice.
- Rob