Open Source Biology And Knowledge Distribution

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."

Comments

Re:Acceleration?

[rw2]

But wouldn't you agree that the acceleration of research is greatly increasing? It seems as if the pace of innovation has sped up dramatically.


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. :-)

--
Poliglut

Modern day AI

[rw2]

I don't remember first hand, being only in my 30's, but I've certainly read about the early AI labs and how optimistic they were that we were just around the corner from strong AI being in the labs and then the world.

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.

--
Poliglut

Intellectual Property is a fleeting phenomena

[oxytocin]

IP has not always existed, so it stands to reason that it will not always exist. No more than 100 years of IP and not more than 30-50 years of stronger and stronger economic importance.

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

future fighting

[joq]

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 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), 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 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:Speculation

[rgmoore]

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, 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...

[idgrad]

I find this article just a little too forward thinking and optimistic. I'm a experimental medicine PhD student, and to be honest, I'm pretty sick of hearing all the hype about how knowing the genomic sequence is going to sling shot us into understanding all biological interactions in the next 50 years. Gimmie a break! I really think where we are at this point fits a historical anology:

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

"You Can't Breed With Her, She's Proprietary!"

[LionKimbro]

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...

History v. Microsoft

[milo_Gwalthny]

Interesting article in light of the recent comments by Microsoft's Mundie about innovation. He believed that open-source software stifles innovation. I believe that true innovation is more likely with the quick and open spread of ideas that is typical of modern science.

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?

[tfoss]

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?

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

Not what you're thinking

[update()]

For those who aren't going to read the article, it's not what you expect. (Or what the submitter seems to think.) It has little to do with patent and IP issues and what there is seems misguided to me. The "open-source" hook comes from the idea that between the availability of genomic information, public access to that information and the standardization of techniques, molecular biology and bioengineering is going to become accessible to the home hacker.

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.

Speculation

[nanojath]

A few comments on this story:

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!

Can you recompile the biological kernel?

[Tricolor Paulista]

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?

Only one question.

[famazza]

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!