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Startup Offers Pre-Built Biological Parts

kdawson posted about 5 years ago | from the we-can-assemble-it-for-you-wholesale dept.

Biotech 71

TechReviewAl writes "A new startup called Ginkgo BioWorks hopes to make synthetic-biology simpler than ever by assembling biological parts, such as strings of specific genes, for industry and academic scientists. While companies already exist to synthesize pieces of DNA, Ginkgo assembles synthesized pieces of DNA to create functional genetic pathways. (Assembling specific genes into long pieces of DNA is much cheaper than synthesizing that long piece from scratch.) Company cofounder Tom Knight, also a research scientist at MIT, says: 'I'm interested in transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things.'"

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First-post question recycling! (1, Interesting)

Empiric (675968) | about 5 years ago | (#29653929)

So, to reprise a previous question, in an improved form...

If we synthesize a living organism in totality, does Common Descent become untrue?

If so, how will we know when Common Descent became no longer true?

Re:First-post question recycling! (1)

Adolf Hitroll (562418) | about 5 years ago | (#29653939)

It will be common copyrighted and be damn sure that the monsanfucktards are all wet about this...

Time to grab a rifle and shoot them at sight. Don't give them a chance, and while you're at it, off the congressmen and anyone wearing a shirt in wall street.

Well, nuke them from orbit, it's the only way to be sure.

Re:First-post question recycling! (1)

masshuu (1260516) | about 5 years ago | (#29654511)

i'm sorry, but your violating my copyright on DNA gene vG10.974.4485.011 revision 76.
Under the licence that i released that DNA sequence, it STATED that any use of it in a living being, that living being must pay a royalty of $5,000 a month or be terminated within 3 days.

gah, brings a new meaning to copyrighting life

Re:First-post question recycling! (0)

Anonymous Coward | about 5 years ago | (#29654585)

No it's not in an improved form, you've been asking this question on Slashdot for weeks and have been given perfectly valid answers that you simply ignore, so kindly fuck off, IDiot.

P.S. No the world wasn't created 6000 years ago, no god isn't real and no ID isn't the process of creation you ignorant religious retard. No you wont go to heaven when you die, you'll just rot in the ground. Sooner, rather than later hopefully.

Re:First-post question recycling! (1)

Empiric (675968) | about 5 years ago | (#29654753)

Um, no, I haven't been asking this question for weeks.

I have not the slightest idea what you mean by "ignoring" the answers. I found such answers as I received interesting, as I expressed. The answers I saw indicated a continuum of opinion--if simple genetic manipulation, no, if complete synthesis, perhaps. Now I'm inquiring on more views on that "perhaps", because that type of edge-case is where it's philosophically and scientifically interesting. I'm sorry you feel so defensive about what to me is an interesting question of science, apart from your ad hominem fantasies and clear defensiveness regarding why I'm asking. Same basic reason we have Slashdot marking "offtopic" something that is clearly and directly on-topic, as a matter of simple fact. Slashdot, though, has clearly devolved from years past. C'est la vie.

As for the last part, well, you're just incoherently babbling. In short, I don't believe the world is 6000 years old, and as for being "ignorant" or a "retard", well, I and Mensa know otherwise as clear fact.

See ya later!

Re:First-post question recycling! (1)

Anonymous Coward | about 5 years ago | (#29655091)

"Now I'm inquiring on more views on that "perhaps", because that type of edge-case is where it's philosophically and scientifically interesting. I'm sorry you feel so defensive about what to me is an interesting question of science, apart from your ad hominem fantasies and clear defensiveness regarding why I'm asking."

Yes, you enquire initially, then you just put words into people's mouths to draw your own conclusions, or simply resort to insulting people when they do not agree with your intelligent design viewpoint, or simply try and link answers to ID where there is no link:

http://slashdot.org/comments.pl?sid=977815&cid=25172863 [slashdot.org]

http://slashdot.org/comments.pl?sid=1389277&cid=29610603 [slashdot.org]

http://slashdot.org/comments.pl?sid=1389277&cid=29610215 [slashdot.org]

"As for the last part, well, you're just incoherently babbling. In short, I don't believe the world is 6000 years old"

It's called sarcasm, although not entirely of course, because you do indeed believe in ID and other such unscientific fiction.

"I and Mensa know otherwise as clear fact."

No, because Mensa don't let stupid people in. You're blatantly a stupid person. Even if by some miracle you did have a high enough IQ to be a member of Mensa, it apparently has no bearing on your ability for logical and rational thought which you fail at quite miserably. Having an IQ of 200 is little use if the rest of your brain couldn't make any use of said IQ whatsoever.

Again, fuck off with your IDiocy. Would you believe the Lord of the Rings story was a real set of events if you'd been preached it since childhood too? Do you still believe in Santa and the Easter bunny also?

Re:First-post question recycling! (1)

Empiric (675968) | about 5 years ago | (#29655313)

So, if I had a sympathetic view toward ID, at any time, I am not entitled, somehow, to ask a purely scientific question?

Is it significant, from a purely scientific standpoint, if in 10 years Common Descent will no longer be true? YES.

Would it be useful and necessary, purely scientifically, to specify when that point occurred, that is, to have clear criteria on such questions as "what is 'descent'" and related scientific and definitional questions? YES.

Others actually contributed to these questions. I credited them as doing so, and/or responded with further constructive analytical narrowing. You are simply an AC troll, so afraid of simple questions you reflexively associate IN YOU OWN MIND to your fear, you need to reflexively and fallaciously "connect" the question to ID and jump into a spastic series of ad hominems. Really, this set of inferences and your motivations is crystal-clear. If you haven't noticed it's obvious, just letting you know.

I'm asking a question regarding science. I get to do that, here. Even if I previously advocated ID. Even if I currently advocate ID. Even if I was wrong on some historical post. Even if I was wrong on all of them.

And yes, I am a Mensa member. I'm sure, par for the course, you'll expect me to take your assertion of reality over what I directly know to be reality. If it makes you feel better, though, I never could compete well in the occasional Trivial Pursuit game at the meetings.

Re:First-post question recycling! (1)

radtea (464814) | about 5 years ago | (#29655777)

So, if I had a sympathetic view toward ID, at any time, I am not entitled, somehow, to ask a purely scientific question?

You're perfectly entitled to do so, and when you come up with one please ask it.

Is it significant, from a purely scientific standpoint, if in 10 years Common Descent will no longer be true? YES.

Nope. What currently active research questions depend on the truth or falsity of common descent? For example, most scientists currently believe that there are other life systems in the universe, so on that basis we're pretty sure common descent is false today: there are living organisms on a planet in the life zone of some other star that do not have common ancestry with us.

So what? The falsity of common descent due to life on other planets has exactly zero impact on scientific questions of interest regarding life on Earth. Likewise, the possible falsity of common descent at some hypothetical time in the future has exactly zero impact on scientific questions about life in the past.

If we were to find that common descent was false in the past it would be of scientific interest, because it would allow us to study a situation where evolution by variation and natural selection occurred involving two independent life systems. This seems to me quite probable: that abiogensis occurred multiple times and we are the descendents of the particular system that got the monopoly. Particular means of genetic encoding do form "natural monopolies" that will tend toward the total domination of one at the expense of all others. Unfortunately, if it happened, it did so too early to leave any meaningful evidence.

Your question as stated has no scientific interest, and yet for some reason you keep asserting that it does. As only someone who has no understanding of the actual role common descent plays in the scientific investigation of the orgins of the diversity of life would think that, it is no suprise that the people here responding to you have infered that you have no understanding of the role common descent plays in the scientific investigation of the origins of the diversity of life. That is, you are behaving exactly like a typical creationist/IDtroll, and are being treated accordingly.

Re:First-post question recycling! (0)

Anonymous Coward | about 5 years ago | (#29656043)

"So, if I had a sympathetic view toward ID, at any time, I am not entitled, somehow, to ask a purely scientific question?"

You're entitled to do what you want, just don't start crying when people like me get fed up of you trying to link it to purely non-scientific crap in a weak attempt to try and do away with your blatant insecurity in your own beliefs.

"Is it significant, from a purely scientific standpoint, if in 10 years Common Descent will no longer be true? YES.

Would it be useful and necessary, purely scientifically, to specify when that point occurred, that is, to have clear criteria on such questions as "what is 'descent'" and related scientific and definitional questions? YES."

It's also scientifically significant if a giant goat monster spawns from an egg at the bottom of the ocean and decides to wander round the world raping every guinea pig it finds.

Sorry, what was your point exactly again?

"I'm asking a question regarding science. I get to do that, here. Even if I previously advocated ID. Even if I currently advocate ID. Even if I was wrong on some historical post. Even if I was wrong on all of them."

Yes, you do. I also get to call you an annoying ignorant cock when you ignore the answer and falsely link scientific questions and answers to the unscientific turd in which you believe.

"And yes, I am a Mensa member. I'm sure, par for the course, you'll expect me to take your assertion of reality over what I directly know to be reality"

No, you're welcome to keep living what you "know" to be reality. Just don't keep pestering the rest of us with it.

No one cares if you just tell us outright you believe in ID, when people start to hate you is when you start a conversation on the premise of being scientific and eventually turn it round to be entirely unscientific, insulting and twisting the words of anyone who points this out or disagrees with that.

Re:First-post question recycling! (1, Insightful)

Anonymous Coward | about 5 years ago | (#29659909)

That even has the same freshman philosophy major Everett and Copenhagen QM garbage when it gets answers it doesn't like. It seems to somehow think that if we were to create, in some unspecified fashion, an organism that this would violate common descent; therefore humans and chimpanzees don't have a common ancestor, therefore evolution is wrong, therefore Jesus. A particularly bizarre ID troll and as impervious to logic and evidence as any of them.

Re:First-post question recycling! (1)

Gerafix (1028986) | about 5 years ago | (#29660057)

Haha, what? If we managed to synthesize a completely new organism then any offspring it would have would be descended from those first organisms. Simple concept.

Re:First-post question recycling! (1)

jfengel (409917) | about 5 years ago | (#29661183)

If we synthesize a living organism in totality, does Common Descent become untrue?

Common descent will have been true, which is the important part. It's a fundamental part of evolutionary history, crucial to understanding what has gone before.

There's no reason that this planet couldn't have had several parallel threads of common descent. It would have made evolutionary history harder to unravel, adding more noise to a signal that turned out to be pretty clear once we found it.

It means that future biologists will find the state of evolution on this planet harder to untangle, but that's their problem, not ours. The idea of common descent has already given rise to much more intricate and useful understandings of evolutionary history (e.g. through molecular biology).

I'm ready to place my order (5, Funny)

Anonymous Coward | about 5 years ago | (#29653931)

5' 5", 110lbs, female, further details can be found in attached magazine. Do you give volume discounts?

Re:I'm ready to place my order (1)

MichaelSmith (789609) | about 5 years ago | (#29653953)

5' 5", 110lbs, female, further details can be found in attached magazine. Do you give volume discounts?

Should the mood code be rotary adjustable?

Re:I'm ready to place my order (1)

someone1234 (830754) | about 5 years ago | (#29654153)

Buy five with hardwired moods (since it is a volume discount). Probably less prone to faults.

Re:I'm ready to place my order (4, Funny)

SlashWombat (1227578) | about 5 years ago | (#29654483)

By "volume discounts" I hope you don't mean if she turns out to be 250lbs, you don't have to pay as much?

Re:I'm ready to place my order (1)

MichaelSmith (789609) | about 5 years ago | (#29654529)

By "volume discounts" I hope you don't mean if she turns out to be 250lbs, you don't have to pay as much?

No, weight has to be 110.

(not enough Neil Young fans here apparently).

Re:I'm ready to place my order (2, Funny)

Sique (173459) | about 5 years ago | (#29654227)

Which volume do you want to be discounted?

Hey wow (1)

QuantumG (50515) | about 5 years ago | (#29653933)

Seems that ordinary people may soon be able to do synthetic biology. No wet lab required.

I could imagine getting into that. Design a few "circuits", send away for them to be built, unpack the slides and.. expose em to ultraviolet light and see if they turn yellow, I guess.

Re:Hey wow (1)

religious freak (1005821) | about 5 years ago | (#29654053)

Yeah, then your average idiot [slashdot.org] could then order away the correct parts for a virus, either knowing or not knowing what he was doing, and end up really screwing things up. This type of stuff will be difficult, if not impossible to control. I'm not optimistic.

Re:Hey wow (2, Interesting)

foobsr (693224) | about 5 years ago | (#29654163)

I'm not optimistic.

But it is mandatory to be because this is progress. </sarcasm>

CC.

Re:Hey wow (2, Insightful)

QuantumG (50515) | about 5 years ago | (#29654825)

An average idiot like you perhaps? Did ya know that DNA does not a virus make? Of course not. Basically what you're suggesting is that "oh no, someone might be able to download the plans for a nuclear weapon of the internets!!"

Re:Hey wow (2, Interesting)

J.Y.Kelly (828209) | about 5 years ago | (#29655117)

Did ya know that DNA does not a virus make?

Are you sure about that [virology.ws] ...?

Re:Hey wow (1)

religious freak (1005821) | about 5 years ago | (#29658601)

Franky yes, an average idiot like me. And unless you've got a PhD in bio, an average idiot like you too.

If you're not worried, you're not paying attention... if you're interested in this stuff, I'd suggest you watch this: http://fora.tv/2008/11/17/Drew_Endy_and_Jim_Thomas_Debate_Synthetic_Biology [fora.tv]

It really is an excellent discussion of all of the salient issues pertaining to synthetic biology. It's not going to make your hair curl or keep you amazingly excited like the mostly terrible edutainment stuff we have today, but it will discuss the facts in detail with two distinct points of view.

(I guess my post could be seen as trollish if you didn't click on the link to the profile I linked to - he's a GNAA idiot that forgot to hit the anonymous button when posting his stupid nonsense, and also a 27-year old IT geek)

Does this mean... cyborgs? (1)

Capsy (1644737) | about 5 years ago | (#29653947)

Are they saying they can "program" the human genetic code and create an improved species? Or that they can grow body parts? Because either way, cybernetics is sure to follow in this field footsteps.

Re:Does this mean... cyborgs? (3, Interesting)

Rand310 (264407) | about 5 years ago | (#29654057)

Apparently they've streamlined a technique whereby the biological mishmash of understanding is standardized into 'code-like' organization. So instead everyone looking up how to make their own gene of their liking, knowing everything about the whole process from the DNA, to the organism to output, you instead just plug in what you want.

In biology there are known 'promoters' (that say "Start"), terminators ("END"), with the gene in the middle, and a number of other little addons and 'features'. Currently in the lab I have to paste these together on my own, from different sources, using different techniques on each. I have to bring each piece into my local standard before I can put them all together. Because it is MUCH easier to change a few bases, or add/delete, than it is to synthesize de novo entire strands of DNA, there exists a need to have modular, standardized 'code' that can easily be swapped from one project to another. These guys make that easy, I guess. When your goal is not just to change/alter a gene, but to set up a few altered/new/engineered genes (or even an entire pathway) at once, this could save a lot of headache.

Re:Does this mean... cyborgs? (5, Interesting)

Rand310 (264407) | about 5 years ago | (#29654081)

Oh, and by the way, if there are any ambitious young coders who want to revolutionize bioengineering, all you have to do is write some decent software which can objectively navigate the complicated but exceedingly logical rules of basic cloning. Someone who could write a program with a nice GUI where you just dragged around genes along a plasmid backbone, told it what organism you're to be working in, and have it spit out the plasmid one should use, the oligos & primers needed to be ordered, along with the enzymes to be used could enable a lot of time to be saved in the lab and make a lot of synthetic biology MUCH more accessible. It's a simple kind of code. Great fun for the programming mind. But the current software is god-awful, and exceedingly limited.

Re:Does this mean... cyborgs? (2, Insightful)

Matrix14 (135171) | about 5 years ago | (#29654125)

Mostly to satisfy my own curiosity, is this written up somewhere outside of the academic literature? Or, if not, any pointers to a good place to start reading?

Re:Does this mean... cyborgs? (1)

lazybratsche (947030) | about 5 years ago | (#29656117)

Part of the problem in my experience is that there isn't a single, reliable cloning manual out there that provides start-to-finish logical guidance. Most people do their projects in an ad-hoc sort of way. If I have a particular cloning project, my resources are (in order) my PI, my labmates, the NEB catalog, and whatever I can google up.

You'll probably want a decent background in molecular biology -- equivalent to one or two intermediate college courses, or whatever you can self-learn from the right textbooks. Molecular Biology of the Cell is one of the better textbooks out there. There are some relevant manuals on cloning out there, but mostly they're concerned with the gory details on what biologists do at their bench. One is written by Maniatis. It doesn't really present a unified, logical approach, but is really just a collection of protocols and recipes for accomplishing individual steps, without providing much guidance for a whole project. Still, if you have access to a university library, it's probably in the reference section, and it has a lot of good information covering the basic theory of all sorts of techniques. Another good resource is the New England Biolabs website -- they sell reagents and kits for subcloning, and their technical references are excellent. So good, in fact, that their catalog was passed around one of my undergrad lab classes as a supplemental textbook of sorts.

The big challenge for you is to put all of that crap together -- distilling the accumulated lab superstition and hodge-podge of tools into a flowchart of decisions that outputs useful cloning advice.

Unfortunately, most such attempts are written by biologists with a bit of coding background... and end up being the crappy sorts of projects that I could do myself, if I wanted to put the time in. The better computer scientists making their way into biology are all going into bioinformatics, which involves big sexy problems like analyzing and comparing whole genomes. The routine concerns of everyday biologists haven't attracted the right talent.

Re:Does this mean... cyborgs? (1)

Matrix14 (135171) | about 5 years ago | (#29728759)

Awesome, thanks!

Re:Does this mean... cyborgs? (1)

Rand310 (264407) | about 5 years ago | (#29663961)

NEB catalog & technical reference for actual enzyme data and a few conceptual tips at the end: http://www.neb.com/nebecomm/neb_mail_form.asp

Molecular Cloning for actual protocols: http://molecularcloning.com/

Molecular Biology of the Cell for conceptual background: http://www.garlandscience.com/textbooks/0815332181.asp

agreed! (3, Interesting)

mauthbaux (652274) | about 5 years ago | (#29654283)

First, I agree completely. I can't tell you how much time a program like that would save.

I'd just like to add in a quick feature request. It would be very nice if it could take the .ab1 files from sequenced clones and quickly align and compare them to the theoretical construct, and then indicate what needed to be done differently. For example, "your inserts are forming concatemers: adjust their concentration relative to the vector during the ligation step, or treat them with CAP (alkaline phosphatase)." or "this particular sequence has internal cut sites: use this restriction endonuclease instead."

The software that I'm using now does allow you to figure out situations like the above, but all it does is alignments; Analyzing the reasons why something didn't work out takes guesswork, and the comparisons prettymuch have to be done manually. For the concatomers example, I'd have to back to my original insert sequence, make a text document of the DNA sequence, import multiple copies into the program, reverse a couple of them (sense/anti-sense), and then manually align the second and third copies. It's very time consuming when it really shouldn't be.

Re:Does this mean... cyborgs? (3, Interesting)

interkin3tic (1469267) | about 5 years ago | (#29654297)

+1. It blows my mind how terrible the software is. Bioedit has some powerful tools in it, but finding out whether or not it has a tool you haven't used before, and then figuring out how to use it often takes hours. But it's really the little things that it does to you when you are worn down from trying to make it do new things that really goes above and beyond, to that realm of "Oh my god, whoever made this was an evil genius."

For instance if you tell it to line the similar parts of two sequences it asks you if you want to save the statistics. Then while you're annoyed with that, it resizes the window to almost fullscreen. You go to close it, and it closes the window behind it, usually the page for the genomic sequence.

I would generalize it to any young coder should consider bio-related software. For instance imaging software for microscopy is also terrible in my experience. Imaris is useful for pulling together multiple microscope images over time to make a 3d movie. Importing multiple files to stitch together, the version we have invariably puts what should be the last frame as the second frame. I'm told the more current version fixes that, but as far as I can tell the solution is that the new version doesn't even attempt to put the movies together.

Consider getting Tom Hall to publish the source (1)

tlambert (566799) | about 5 years ago | (#29654775)

Consider getting Tom Hall to publish the source

Otherwise no BioEdit fixes unless Tom can get around to them.

-- Terry

ImageJ (0)

Anonymous Coward | about 5 years ago | (#29657745)

ImageJ [nih.gov] - free and Open Source, and consequently plugins to do pretty much everything you can think of (or if not, roll your own) (see here [uhnresearch.ca] for a good bundle).

Re:Does this mean... cyborgs? (0)

Anonymous Coward | about 5 years ago | (#29654563)

Darwin won't survive the science of the 21st century.

Re:Does this mean... cyborgs? (0)

Anonymous Coward | about 5 years ago | (#29654961)

Darwin has been dead for some time. What are you trying to say?

Almost there (1)

gringer (252588) | about 5 years ago | (#29654865)

I began my course in genetics with essentially this programming goal in mind (making bad biological software better). Now I've got enough genetic theory under my belt to have a crack at something like this (although my practice is mostly low-level clinical biochemistry). Just a few more months...

Re:Does this mean... cyborgs? (1)

shic (309152) | about 5 years ago | (#29655497)

I consider myself comfortable with software - and I'm fascinated by the prospect of synthetic DNA. A glitch is that I don't have a degree-level background in either chemistry or biology - and this makes it very hard for me to appreciate what sort of things are viable. I would definitely like to know more about this field...

Can you recommend a text-book that explains the relevant biochemistry for this from-the-ground-up?

Re:Does this mean... cyborgs? (1)

Rand310 (264407) | about 5 years ago | (#29663971)

see my post above.

Re:Does this mean... cyborgs? (1)

LabRat007 (765435) | about 5 years ago | (#29656029)



I'm a little lost here. In my lab we already engineer discrete parts like promoters, terminators, resistance makers and individual genes all by their lonesome into plasmids that we use as starter material. Then we cut and paste with restriction enzyme and T4 ligase to make our "composite material" or BioBrick as they would call it. How is this product better? Its only 235 dollars per 50 reactions according to the NEB website...maybe their way saves a dollar or two when you buy the kit....

But the current software is god-awful, and exceedingly limited.

I know its a bit off topic but I'm curious. What software do you use? I primarily use Sequencer and Clone Manager myself. Occasionally Vector NTI. They get the job done but there is certainly room for improvement.

Re:Does this mean... cyborgs? (1)

mhajicek (1582795) | about 5 years ago | (#29663449)

So what you're saying is that they have a rudimentary DNA compiler with documentation?

"Augments" (1)

plasmacutter (901737) | about 5 years ago | (#29654333)

Are they saying they can "program" the human genetic code and create an improved species?

This is not cybernetics, it's eugenics (not the obviously unethical "extermination" eugenics but the more deviously unethical establishment of a 'genetic elite').

In star trek they're called "augments", in gundam seed they're called "coordinators", but im sure in practice it will be called "oops!, we accidentally gave you gills!"

Re:"Augments" (1)

Capsy (1644737) | about 5 years ago | (#29654527)

Gills could be useful...

Really though, this could be deemed unethical. But then again, societies advance based on unethical things. For instance, the Nazis provided a lot of medical knowledge because of unethical research. Not saying it was right, but we would be behind the power curve.

Re:"Augments" (1)

DirePickle (796986) | about 5 years ago | (#29656791)

Lie down on table. I take lungs now, gills come next week.

Building blocks (4, Funny)

cjfs (1253208) | about 5 years ago | (#29653949)

The key innovation of the BioBrick assembly standard is that a biological engineer can assemble any two BioBrick parts, and the resulting composite object is itself a BioBrick part that can be combined with any other BioBrick parts.

Sounds great in theory. In reality, you'll always be missing one of those stupid little yellow bricks and they won't sell them individually.

Oh Great (1, Funny)

Anonymous Coward | about 5 years ago | (#29654025)

So instead of "enlarge your penis" emails we will get "get a larger penis" emails.

Re:Oh Great (0)

Anonymous Coward | about 5 years ago | (#29654611)

...or "get an extra penis" emails.

Male pornstars will have two extra, one next to the original and another in one armpit.

Obligatory reference: (3, Funny)

shacky003 (1595307) | about 5 years ago | (#29654065)

Do the founders wear bras on their heads?

Re:Obligatory reference: (1)

Scroatzilla (672804) | about 5 years ago | (#29659357)

Of course. It's ceremonial.

Wake Up Little Susie (0)

DynaSoar (714234) | about 5 years ago | (#29654091)

"I'm interested in transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things.'"

Boy is this guy in for a wake up. No matter how well you replicate a strand, you can't replicate the environment without violating the exclusion principle -- the two can't be in the same place. And with different environments comes different expressions. It says he's a "research scientist". I'm betting the field isn't biology.

Re:Wake Up Little Susie (1)

FlyingGuy (989135) | about 5 years ago | (#29654215)

Obigitory - "didn't look very hard before spouting off did ya."

You might want to give a read here. [wikipedia.org]

Ohhh and maybe here [unizar.es] too.

Or here. [biobricks.org]

These two guys are formidable minds, so ya just might want to think before you blast your mouth off.

Re:Wake Up Little Susie (0, Troll)

DNS-and-BIND (461968) | about 5 years ago | (#29654303)

Yeah...they could never possibly be wrong. We should never question them, because they're better than us. Even to test their theories smacks of iconoclasm and heresy. It is well and good that the Inquisition ensures that we don't think for ourselves and instead rely on the reputation of academics.

Re:Wake Up Little Susie (1)

DynaSoar (714234) | about 5 years ago | (#29663877)

Obigitory - "didn't look very hard before spouting off did ya."

You might want to give a read here. [wikipedia.org]

Ohhh and maybe here [unizar.es] too.

Or here. [biobricks.org]

These two guys are formidable minds, so ya just might want to think before you blast your mouth off.

Ah. Appeal to authority, the refuge of the science fanboi.

I know Harold Morowitz from our visits to the Santa Fe Institute and from George Mason (my daughter studies there). I quote him here regularly, especially his "Energy Flow In Biology". I've also quoted his story about being the first to try to sell fairy shrimp. It was a miserable failure. If he can tell you he can be wrong, so can I.

I don't know Knight, but I was right -- he's an engineer, not a biologist. And it was his statements I took issue with. Identical strands do not necessarily produce the same result. They are sensitive to environment to an extraordinary degree. An example is the different amounts of coverage and symmetry of coat colors in dogs due to the minute differences in pH from being between litter mates vs. being at the end of the line while in the womb.

If I were the sort to repay appeal to authority with the same, I'd have made a bigger deal about "our" trips to Santa Fe (not he and I together, but more than one each) as well as a few other salient points. But I don't, because I've had some object lessons on that. Such as:

Basil Hiley also has an exceptional mind. He was the physics partner of David Bohm. He'd come to Karl Pribram's lab to work on an update to the latter's book that provided evidence that Gabor's maths describing holography, specifically having to do with 'logons', could be used to describe the interaction of the dynamic electrical fields around neural dendrites, and their possible communication without direct connections. Basil needed to access his email. We had Macs with Netscape in the lab. He wasn't familiar with them and asked me to configure things for him. I did so. He thanked me and added "I could never have done it. I'm just a mathematical physicist." And he was serious.

In any case, I was right, and the non-biologist Knight overstated. I wouldn't have expected many to believe it, and my having been modded down by those who didn't understand what I was talking about bears that out. Why they don't just give us a '-1 Wrong' mod to use, I don't know -- people use other mod keys for that anyway.

In another case I was wrong. I asked Karl and Basil (and Mari Jibu and Kunio Yasue) why they didn't use tensor calculus to describe the fields. Basil finally said it could work but would take more effort than using Gabor's functions. But it took the mathematical physicist an hour of thinking about it before answering. So consider carefully that while you might be able to provide reference to work by parties not present, you can never be sure in a forum such as this when you'll run across someone who'd feel quite comfortable in their company for some obvious reasons. Then you can kiss my exceptional mind. And same for the guy below who also got modded down for daring to make the point that one should question authority, especially when it's presented by someone other than that authority. Kiss his too.

Re:Wake Up Little Susie (1)

FlyingGuy (989135) | about 5 years ago | (#29664569)

I replied do to your overwhelming bombast.

And you might be correct that the process might not work.

And since you have zero cred ( at least as far as I can tell ) in the field, and Knight does ( hence my references ), coupled with the fact that the guy was accepted to MIT at the age of 14, his accomplishments are massive, he studied biology under a guy who is a very well respected professor in the field, I am thinking that I would not make the flat out assertion that he is dead wrong on pretty much ANY subject.

I suppose Knight could get a pHD in the subject(s) of biochemistry, genetics, and cellular biology if he felt it was a requirement, but since he is a principal investigator at CSAIL I think he might just be on the right track, BUT you could be correct.

Re:Wake Up Little Susie (1)

FlyingGuy (989135) | about 5 years ago | (#29664613)

I didn't think your response was a troll at all since most of the "modding" that gets done around here is done by fanbois.

And just for your edification, I am not any kind of a fanboi, but long ago I did learn not to make absolute statements regarding someones research as it is unwise.

Good (1)

OrangeCatholic (1495411) | about 5 years ago | (#29654097)

TFA:

I'm interested in transitioning biology from being sort of a craft....to an engineering discipline with standardized methods...

Good! Geneticists would benefit from getting smarter. Anybody taken a look at Monsanto's work? I don't think "train wreck" quite captures the epic fail quality they've managed to achieve.

God Chmod! (1)

Tumbleweed (3706) | about 5 years ago | (#29654099)

I want my monkey-man!

Plasmids kinda do this already. (2, Interesting)

mauthbaux (652274) | about 5 years ago | (#29654197)

'I'm interested in transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things.'"

To some extent, this is already done with common bacterial strains, and the plasmid vectors we already use. Most of the plasmids we use in the industry have specific sets of features such as multiple cloning sites, inducible repressors, ORIs, antibiotic resistance sites etc... You need a plasmid that has a kanamycin resistance gene, high copy number, will add a His tag to your product, and lacks cut sites for a particular restriction enzyme? It's likely in the catalogues already. And if what you're trying to assemble is already in the catalogues, it's a target that may not be worth pursing anyway, since you're unlikely to get a publication or a patent off of it.

The approach he seems to be pushing here seems to be analogous to buying a car piece by piece rather than as a pre-assembled package. The difference is that while average joe has no idea how to fabricate a synchro for his transmission, your average molecular biologist is already quite adept at designing primers and cloning fragments out of a cDNA library. The hard part for the scientists is then characterizing, validating and optimizing the expression of their target; and then later demonstrating the functionality of the product. To continue the analogy, it would be showing that the car ran, was reliable, and was safe for the passengers. Having readily available gene circuits (the famous lac operon for instance) may help with the planning and initial development, but it really won't speed up the bulk of the work we do.

I'll readily admit that many of the expression/knockout constructs are somewhat ad hoc in nature, but interoperability isn't typically a concern. The thing is that evolution is a pretty laissez faire system where "duct tape and bailing wire" construction is more often the rule than the exception. Nature cares about what works, not about what conforms to standards (codon-amino acid translation being the biggest exception that comes to mind). As a result, expression systems have to be tailored to the organism that they'll be expressed in. For instance, bacteria cannot express functional mammalian genes unless the introns are removed from the sequence first. Sufficiently large yeast proteins will cause an immune reaction because the glycosylation patterns are recognized as foreign. Many genes won't be expressed very well at all unless the regulatory elements in the flanking sequences are also included. Once you start looking at things like inducible expression and tissue-specific expression, things get even more complicated, and more varied between species. In short, it's complicated, and the idea of instituting standards to achieve interoperability between expression systems is pretty much a pipe dream.

In short, I have my doubts about the plausibility of this plan, and I'll be mighty impressed if he pulls it off.

Re:Plasmids kinda do this already. (3, Informative)

QuantumG (50515) | about 5 years ago | (#29655329)

Wow. Retarded reply gets modded up to the highest post.. I'd be surprised, but hey, it's a non-IT article on Slashdot.

How would you feel if I told you that teenagers have been using biobricks to do some of this "pipe dream" stuff for about 10 years now. That there's an annual international competition to showcase what they come up with and that has been running since 2003? That biobricks are a standard part of genetic engineering of microbes for industrial use? That basically everything you said was so horrendously outdated and ignorant that you sound like someone talking about the impossibility of heavier than air flight in 1913.

I know things have been bad around here for a long time and we've all come to just accept it, but would it be too much to ask that the moderation system undergo a little bit of review? I'm gunna ask the Taco.

Re:Plasmids kinda do this already. (0)

Anonymous Coward | about 5 years ago | (#29659083)

The thing is, I don't see any significant problems with mauthbaux's post. Points were that cross-species interoperability is tricky, that vectors already exist which accomplish much of what this system allows, and that a system like this is unlikely to save much time in the long run due to concerns with validation of the product. Your rebuttal fails to adress any of these points (instead reverting to name calling).
 
For a hobbyist, this system may be a good way to start out; but none of the genetics or molecular biology classes I've taken have ever talked about doing it this way; (indeed, I hadn't heard of this system at all until this article). For industrial and research use; the point still stands that if you're getting it from a catalogue, you're not very likely to get a patent or a publication out of it; since both require something novel. As for being "standard part of genetic engineering of microbes for industrial use," perhaps it is for prokaryotic expression systems. My experience has mostly been with CHO, HEK, and various murine carcinoma expression lines, which only transiently express plasmids anyway.
 
You sound like the newbie gamer who just built his own system, and is now trying to lecture a mainframe administrator on how he's ignorant and horendously outdated in regard to computer systems.
 
captcha:apprise

Old news. (2, Informative)

Hurricane78 (562437) | about 5 years ago | (#29654269)

It's called "bio bricks", and it's old news.

I read about before 2006.

brrr... (2, Interesting)

arcite (661011) | about 5 years ago | (#29654411)

You not come here! Illegal!

I just do eyes. Just - just eyes. Just genetic design. Just eyes!

Good luck (1, Insightful)

Anonymous Coward | about 5 years ago | (#29654413)

"...transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things."

Like Software Engineering, then. Good luck with that. -j

Bioshock IRL? (0)

Anonymous Coward | about 5 years ago | (#29654593)

Bioshock IRL?

I want a pony! (1)

jipn4 (1367823) | about 5 years ago | (#29656059)

I'm interested in transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things.

Well, that's nice. I want a pony, too. But that's not how biology works.

In fact, it's not even how engineering works anymore.

A century ago, people built big things from small numbers of standardized parts. People could buy devices, take them apart, repair them, modify them, etc. These days, many mass produced products are built around custom-designed and custom-manufactured parts, from specially moulded cases to custom integrated circuits.

Building things from standardized parts really only works if performance and efficiency are secondary; they rarely are in biology.

Re:I want a pony! (1)

Rand310 (264407) | about 5 years ago | (#29664023)

At the moment, biology is where engineering was a century ago. We NEED standardized parts. We have lots of ground that we could cover very quickly if we didn't have to reinvent the wheel each time we wish to make a small machine.

We now know there are all these different parts. We want to put them together into small mini-machines with anywhere from 2 to 10 parts working together or so. But each one has to be taken from different sources, put together in a completely arbitrary and new manner in order to see where they interact. It would be so useful to take these well-known and established pieces and be able to swap them around to build small machines in a timely manner. We're no where near the current engineering concept of customization.

And some journalist (1)

AniVisual (1373773) | about 5 years ago | (#29657881)

... will notice again how biohazardous materials can be built from these parts and everybody will start panicking at the new tech.

Awesome (1)

chmxjc (1574677) | about 5 years ago | (#29662737)

The next millionaires?

Mini Moggies (1)

aurizon (122550) | about 5 years ago | (#29666247)

I have a strange desire to have a bunch of 3 inch long cats, as smart as regular cats, smaller brain cells, I guess, all optimized to breed true and live long and prosper. Why? I have this desire to have about 100 of them as pets and be a catherd.
Can you imagine sitting down with 100 of them all over you, little tiny whiskers, higher frequency purrs. Have to keep them in, I guess, or they would take over

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