This is surprisingly like the first step you'd take if you were about to start hacking the firmware on an embedded board: before you change bits, you upload a known good firmware to prove your programming process is working correctly.
But the next steps looks more like software on a computer: You'll have to fix all those compilation-errors on first run, then look out for bugs in the software. Finally, when you ship the software, people use it and report other bugs. And since you can't update running processes at the current moment, you need to terminate and replace it.
So that the assembled genome would be recognizable as synthetic, four of the ordered DNA sequences contained strings of bases that, in code, spell out an e-mail address, the names of many of the people involved in the project, and a few famous quotations.
Yep! There is some error-checking built into dna-replication. The protein that does the replication is called DNA Polymerase. From its wikipedia article:
Error correction is a property of some, but not all, DNA polymerases. This process corrects mistakes in newly-synthesized DNA. When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA. The 3'-5' exonuclease activity of the enzyme allows the incorrect base pair to be excised (this activity is known as proofreading). Following base excision, the polymerase can re-insert the correct base and replication can continue.
Gripe: "artificial life" already has a somewhat lengthy history of usage, referring to emulating biological activity or traits in software or hardware. It's often shortened to just alife or a-life.
It's related to genetic algorithms, genetic programming, and the like.
It would be nice if the using-real-chemicals-and-alive-stuff hacking were called "synthetic life", or something to distinguish it from existing terminology.
That use maybe should have been "simulated life" all along, so as to be more exact. This is a living organism that is artificially made, "artificial life" applies to it just as much as the other subject. Though the more specific terms that capture the way in which their somethings are artificial are good too.
'This is a living organism that is artificially made, "artificial life" applies to it just as much as the other subject.'
Maybe. But if you end up with a living organism, then that it's not artificial life; it's life (albeit artificially manufactured) . Whereas the software stuff is never anything but artificial.
Long run I'd expect anything that's alive to be called life, regardless of the process that lead to it.
Are we sure that the CS term predates the biological term? I mean, we might not have really succeeded in creating (biological) artificial life in the 1950's, but someone was almost certainly trying.
In all seriousness, the dangers brought up in the article can only come from a person lacking significant knowledge of bacteria.
Unimaginable numbers of bacteria permeate every part of the world, including miles within the earth, deep sea volcanic vents, radioactive waste, the rain drops falling on our heads, and us, up our noses, in our skin pores, our guts, etc.
Those simple bacteria evolve at staggering rates, and swap genes like DJ Danger Mouse mixing tracks.
Any new synthetic, or extraterrestrial, or magical, life form would have to compete. And unless you believe in magic it is unlikely to out-compete in a pre-existing niche.
The grey goo danger often thrown at nano-tech, is possible only if we violate one or more of the basic laws of thermodynamics.
And when it comes to antibiotic resistant bacteria, well we are already doing a great job of breeding those within ourselves.
But if you grew a barrel full of MRSA and then poured it down your toilet, the SA wold quickly lose its metabolically expensive MR. Because there is no Methicillin in the sewer, the resistance to Methicillin is a disadvantage. And the only way the Staphylococcus aureus could survive is if it dumped this feature.
But luckily you're probably taking antibiotics so you are a niche where MRSA can out-compete and thrive.
> And unless you believe in magic it is unlikely to out-compete in a pre-existing niche.
Cars are faster than land animals. Planes are faster than birds. Not being constrained by needing to have come from slow gradual iteration might open some possibilities, some terrifying. Biology doesn't produce the wheel.
To consider this as a possibility is not to believe in magic.
> Cars are faster than land animals. Planes are faster than birds.
There's no comparison.
I'm sitting here looking out the window at my car, and there are caterpillars out there that are moving faster than it. Not only that, but that caterpillar can refuel itself. And it'll turn itself into new ones next year. In the meantime, my car will sit and rust.
Really, it's the height of hubris to think that we can engineer something that works as well as what untold generations has evolved.
(And I'll apologize for the tangent, but this is also the fatal conceit of those who believe that any central authority can manage our economy any better than the market can on its own.)
"Really, it's the height of hubris to think that we can engineer something that works as well as what untold generations has evolved."
Why? Technological progress through logical deduction is patently more efficient than evolution through natural selection. Modern technology has already far surpassed the capabilities of natural organisms in a number of areas, all within a geologically minute timespan.
Just because a caterpillar can self-replicate, doesn't make it better than a car in every single respect, otherwise we'd be riding caterpillars to work. In terms of self-replication and regeneration, nature has us beat (for now). But if you want to send packets of information halfway around the globe, there is no biological process that comes anywhere close to our technological capability.
"(And I'll apologize for the tangent, but this is also the fatal conceit of those who believe that any central authority can manage our economy any better than the market can on its own.)"
But it can, or at least, a market with regulatory oversight is more efficient than a completely unregulated market place.
Natural environments and unregulated markets suffer from very similar problems. They don't magically gravitate toward the most efficient solution; very often they'll do incredibly stupid things that would leave an intelligent observer scratching their head.
However, natural selection does produce very robust ecosystems, which is why life has flourished for millions of years, and why caterpillars will outlast your car.
Logically, the best approach is to combine natural selection with intelligent oversight. Left to its own devices, an unregulated market has a tendency to fall into traps which benefits an individual or subgroup for a short time, but disadvantages the market in the long run. The Prisoner's Dilemma, the Tragedy of the Commons and the Market of Lemons are all common effects that can be circumvented by intelligent regulators, but would cause great damage to any market left to its own devices.
I think quoting oil drillers is not really opportune at the moment if you want to give an example of how the damage from technology is going to be 'limited'.
See there's thing thing called an apple and this other thing called an orange.
And there's this discussion about artificial and natural micro organisms competing in the same niche. Like using light energy to capture CO2 for example.
"Why? Technological progress through logical deduction is patently more efficient than evolution through natural selection. Modern technology has already far surpassed the capabilities of natural organisms in a number of areas, all within a geologically minute timespan."
There's a lot of hubris packed up into that statement. I really don't think you're considering the whole effort, the economy, the resources, the externalities that are involved in all those things that "surpass" natural organisms. The real place we've surpassed natural organisms is in many ways in global organization. Those things that we consider faster, stronger, better etc. than natural organisms are not self-standing things, but things that require our care and attention and vast amounts of energy, resources and infrastructure in upkeep.
And it's far from clear to me that logical deduction is more efficient than evolution. Evolution can certainly result in silly designs, that's for sure (the retina's layering, vas deferens' route, etc.); but evolution also has an appetite for complexity and resilience far exceeding anything the human mind can grasp today, aided or not.
"I really don't think you're considering the whole effort, the economy, the resources, the externalities that are involved in all those things that "surpass" natural organisms."
No, I have, and that's precisely the point. Our technology doesn't exist in a vacuum; it's an integral part of our civilisation. Machines do require an enormous amount of resources to back them, but so what? It's the end result that matters.
Many cells in nature also require relatively vast resources to be of use. For example, a mammal sperm cell requires billions of cells and massive amounts of resources to be of use. Take the sperm cell out of the body, and it will die far quicker than your car will rust.
"And it's far from clear to me that logical deduction is more efficient than evolution. Evolution can certainly result in silly designs, that's for sure (the retina's layering, vas deferens' route, etc.); but evolution also has an appetite for complexity and resilience far exceeding anything the human mind can grasp today, aided or not."
Yes, but it has had a few billion years head start, whilst the scientific method is only a few hundred years old.
From a computer science perspective, evolution and science both involve accumulating information and processing this information to produce useful designs. The pace of change, therefore, is dictated by how fast information can be gathered, and how much processing power can be applied to it.
Bacteria are particularly successful in this area. They are continuously passing around information and testing new designs. There is no intelligence involved in this process, but they make up for it through sheer numbers. Bacteria are, essentially, an unimaginably vast distributed computing network, continuously sifting through information and applying genetic algorithms to it.
We have a far smaller computing network, made up of our own neurons and our manufactured microchips. However, despite being trillions of times smaller, our networks are vastly more efficient. If they weren't, then death rates from bacterial infection would remain constant, yet they've been falling globally, and in developed countries, dying of a bacterial infection is today extremely rare.
Is there a man-made process that can restore oxygen from carbon dioxide more effectively than photosynthesis? It also has to be reasonably cheap though ...
I think considering the possibility that removing gradual iteration as a constraint, or considering the big picture, could lead to improvements of some natural designs, true or not, is unlikely to be fatal!
I don't see how anyone would just dismiss this point a priori. Both of those things seem, intuitively, to be fundamental constraints in evolution. Human biology plus technology leads to us out-competing every other similarly sized animal in any land niche we choose. The question is whether bacteria biology plus human ingenuity could have any similar advantages over biology alone. If you trust your snap judgment without extremely careful consideration, I just hope you're not in charge of the relevant policy decisions!
> Really, it's the height of hubris to think that we can engineer something that works as well as what untold generations has evolved.
Even if true, it's irrelevant because nature's definition of "works" isn't always mine.
It isn't yours either.
For example, you're not using caterpillars or other "nature" for transportation so either you're stupid or you don't believe that caterpillars are superior to your car for certain purposes. (Caterpillars are cheaper, so you didn't choose the car for its price/performance either.)
I think there's a risk that you're underestimating the scale required to make those things work. Not only are cars and their engines pretty big, but they need a huge amount of infrastructure for their construction (think about where that all that metal came from, never mind everything else), maintenance, feeding (the whole oil economy), roads, signals, piloting, etc.
Cars are faster than land animals. Planes are faster than birds.
Fuel, jet fuel.
Biology doesn't produce the wheel.
Tumble weeds? Insects which curl up into a wheel to quickly roll away from danger? Can a car drive up stairs?
Indeed if we genetically engineered a large animal to run on gasoline AND provided it with an ample supply of gasoline, it would move faster than anything else... as long as it had gasoline.
If we engineered a bacterium to eat oil and/or gasoline and dispersed in the gulf.... already there, eating oil, consuming the oxygen in the water in the process.
If we added it to an oil well... already there, lots of bacteria deep within the earth, eating everything from metal to methane. Probably not consuming the world's oil reserve only for lack of oxygen or any other oxidizer.
...some possibilities, some terrifying.
Ebola, HIV, the flu de jour all quite terrifying, all 100% natural.
And unlike you, they don't care. They will keep evolving and trying to kill you as fast and as hard as they can, every minute of every day.
> Ebola, HIV, the flu de jour all quite terrifying, all 100% natural.
If you can't imagine anything more terrifying than those, it is a failure of imagination. See Jared Diamond's point about how when humans and large animals coevolved gradually in Africa, the animals could gradually adapt, whereas when fully evolved homo sapiens were introduced in the rest of the world 40,000 years ago, almost all the megafauna were killed off almost immediately.
> They will keep evolving and trying to kill you as fast and as hard as they can,
Thankfully, this is wrong. Diseases that kill you quickly are at a severe disadvantage.
I can easily imagine an HIV that's as easy to transmit as the common cold.
Franky we got lucky with HIV, it could have been something like that and we along with cheetahs and a few other species don't have much genetic diversity within the species and are thus susceptible to extinction via disease.
This is why I want the biotech pedal to the metal. Because in my opinion the probably of us accidental creating something horrific are far less then something horrific being created quite naturally. Like in some shared living space with humans and domestic animals, it could happen in any given moment and spread quickly around the world. We don't need labs to die of something horrible.
> Indeed if we genetically engineered a large animal to run on gasoline AND provided it with an ample supply of gasoline, it would move faster than anything else... as long as it had gasoline.
Do you think gasoline is magic? Gasoline has almost exactly the same energy content as fat. Tons of animals have access to fat.
This is a good point. At the same time, bacteria have been mutating for much longer than birds or land animals, and they iterate generationally at an unbelievable speed compared to their multi-cellular cousins.
The risks should be taken seriously, even the seemingly far-fetched ones, but need to be viewed in the context of an already cut-throat competitive landscape. IMHO, the bigger risk is intentionally designing malicious life forms (bio-weapons) more so than than beneficial ones getting out of hand.
It doesn't only bother me practically. Yes I did consider the fact that they'd have to compete, though I didn't consider the fact that they evolve all the time anyway, that's a good point. BUT, especially if they're talking about something as drastic as eating up a significant amount of carbon in the air, it will change the ecosystem. It'll pose the same danger as moving animals across continents.
But really it bothers me in a different way. I'll say morally, for a severe lack of better term. Maybe existentially. It doesn't sit right with me that we'll be living amongst creatures created in a lab, and that there's no way to differentiate them. I don't believe in God, but I like that we exist within a certain biological framework, it just feels like part of our identity. That the players are allowed to change the rules bothers me.
Your dog is genetically engineered. Your tomato. Your children. And I don't mean in the lab, but the usual way, by using your intelligence to choose suitable stock and then breeding until you get what you want. The shortcut in the lab is just faster and cheaper, not different in any basic or ethical way.
But that old-time genetic engineering still plays by the rules of nature, so to speak. Grafting branches between trees is pushing it a little. Splicing genes, not to mention synthesizing them from scratch, I think is pretty clearly of a different nature.
Golden delicious apples were a sport. Any really new feature in evolution is. The advantage of doing it in the lab is, its lots safer. You know what you're getting - just what you wanted. Not all the other random accidental changes you couldn't measure. Grandma's better tomato could actually make you sick - she had no idea what she was doing and no control over the process.
It has the potential to be different in the way that building a 747 is different than breeding a bird to be able to carry people across the Pacific Ocean. Either may be possible, but it's different.
I don't understand, you will never create a 747 with bird genes. In fact, they can do nothing with this technology that could not have been done by infinite monkeys with gene-splicing equipment. The only difference I see is the speed.
Bacteria will often take up DNA from their environment, and this ability, called "competence" is widely used in molecular biology. In this case, they treated the cells with a chemical called polyethylene glycol, which increases the efficiency by which the cells can pick up the DNA molecules. The procedure for transplanting genomes was described by the same group in a paper in 2007. It is possible to use a small needle ("DNA microinjection") to inject DNA into cells; one can also use an electric field to disrupt the cell membrane and force DNA into a cell, which is called electroporation. In this case though, the PEG transformation was sufficient (and because these artificial chromosomes were so large, they might not survive being shot through a needle or zapped with electricity too well).
The initial pieces of DNA (oligonucleotides) are synthesized chemically - the components are added to a reaction one at a time, and the reaction is controlled so that at each step, only one base gets added. There is a lot of chemistry optimization and QC to be able to make relatively long fragments accurately. They ordered the building block pieces (1080 bases long) from a company called Blue Heron, which specializes in putting together long DNA molecules.
The sequences were designed to be partially overlapping, so that the complementary sequences could fit together. Overlapping pieces of DNA can be combined by a process called homologous recombination. There is existing machinery in the yeast cells that they used to join together such complementary sequences. The molecules were assembled hierarchically, so they first made 10kb fragments, then put 10 x 10kb together to make 100kb fragments, and then finally put the 10 100kb fragments together. The overlapping sequences at the ends determined which fragments will stick together.
So if the DNA pieces overlapped did that overlapping base pairs somehow get removed when the pieces were joined? Otherwise I'd think the next final DNA sequence would look a lot different from what they were intending to copy.
PEG is the abbreviation for PolyEthylene Glycol. Just a chemical they add that makes the transformation work more efficiently.
DNA, as you probably know, is a double-stranded molecule, and the strands have complementary sequences. When the overlapping pieces are joined, one strand of one molecule overlaps with its complement on the other piece, and vice versa - the pieces aren't just joined end-to-end.
This is a nice step for technology and a really huge deal for human culture and religion.
A certain Someone said once "Let the earth put forth vegetation, plants yielding seed, and fruit trees bearing fruit in which is their seed, each according to its kind, upon the earth."
That certain Someone later said: "Behold, man has become like one of us..."
You say they "just copied the genome" like that's easy to do. This is a landmark because they synthesized the entire genome using nothing but the sequence stored in a computer, much more difficult than replicating a pre-existing piece of DNA.
It's fairly likely that every life-form that currently exists in this planet has a common ancestor that self-assembled billions of years ago. Your genetic code is the result of a huge amount of cycles of copies (and mutations) of that common ancestor's DNA.
The life form that Venter created is separate from that lineage - its genetic code was synthesized from basic building blocks, not copied from an ancestor (at least in a biochemical sense; the information content was indeed copied, but that's another hurdle).
Whether or not this makes it "artificial life" depends on your definition of "life", and there's a surprising amount of controversy there.
I think it's pretty accurate. There was only information to begin with, and now there is life. It happens that information was gained from a pre-existing cell, but this new cell has nothing to do with the cell it's derived from, it's made completely by the work of humans. That has never happened before.
Edit: However, I know what you mean about it not being 100% artificial, as in completely designed by humans: Maybe "synthetic life" is better?
Further edit: More than using a pre-existing genome, what makes it not completely artificial is that they had to put their DNA into another cell, basically cloning using synthesized DNA rather than natural DNA.
I don't know about that, to date genetic engineering consisted of taking DNA from one organism, isolating a desired trait from another organism and using a gun or splicer to "inject" that code into preexisting DNA. These guys scaffold the DNA from the basic building blocks. There is a huge difference. Personally to me they are both artificial life as neither occurred via random selection, it is just one used a current organisms DNA as the building block, while the other used the bare elements to put together all of the DNA. The value of the second approach is that you don't get all of the junk that comes with harvested DNA you only get what you specify.
Consider natural and artificial vanilla flavoring; it's more technical usage than misleading.
(Natural vanilla is harvested from beans, resulting in vanillin, etc. Artificial vanilla is synthesized from e.g., bacteria, and in specific cases molecular synthesis.)
More than that: an OS is millions of lines of code. The hardware is a hundred thousand. But cells! They have orders of magnitude more wiring than all the bits of DNA put into them. I liken it to a vast machine that can create either 1) a man or 2) a mouse. The dna programs the switch: man or mouse. Pretty trivial in comparison.
You're probably getting negged because you appear to be disparaging the accomplishment. But yeah, they did copy over an existing dna structure, they didn't create one from scratch.
However, the scientists did (according to the arstechnica article, posted above) have to remove a section of the DNA (something to do with the bacterium cutting DNA originating in yeast into small pieces... sigh, wish I understood this sort of thing). So they did actually make modifications to the genome, I think...
To be disappointed that they used existing DNA to do this is uninformed. We are so far away from synthesizing a completely novel form of life from scratch. This step is needed before we ever get close to designing our own cell — it's the leap from using hand tools to CNC.
I agree that disappointment in this accomplishment is crazy, it's an amazing feat
That said, people can sometimes go batty and start thinking something was achieved when it wasn't. I think it's reasonable to clarify that this isn't a full realization of "artificial life" just yet (though it clearly is a partial realization, as the scientists did alter the genome (also, apparantly they removed potentially disease-inducing strands of DNA, according to the NYTimes). The poster who got negged expressed this distinction in a fairly dismissive fashion that appeared to disparage the achievement. But you should be able to point out (diplomatically, one would hope)that a monumental achievement isn't an even more monumental achievement without being accused of minimizing the achievement itself!
That comment can safely be ignored. It makes lots of vague accusations about Venter, and one concrete accusation - that Venter is responsible for patents on genes involved in breast cancer. That accusation is wrong: it's a reference to the BRCA patent by Myriad genetics, which has nothing to do with Venter.
