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Molecular Robot Mimics Life's Protein-Builder

Soulskill posted about a year and a half ago | from the robots-are-taking-everybody's-jobs dept.

Biotech 53

ananyo writes "The ribosome, the molecular machine that translates our genetic code to build the body's proteins, is a mechanical marvel. Now, chemists have invented a nanomachine that can achieve a similar feat. The artificial system is not about to displace nature's ribosome, a complex of proteins and RNA. It is much simpler, and only about about one-tenth of the size — and, it is achingly slow, destroys the code it reads and can produce only very short chunks of protein, known as peptides. It does, however, show that some of the tactics of biology's molecular machines can be adopted to make useful chemicals. The device relies on a rotaxane — a large molecular ring threaded onto another molecule that acts as an axle (abstract). The axle is lined with three amino acids, and a chain of three more amino acids hangs from the outer edge of the ring. Heating the device prompts the ring to move along the axle, adding amino acids one-by-one to the chain attached to the ring."

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53 comments

I preferred the BBC's slightly ambiguous headline (4, Informative)

wonkey_monkey (2592601) | about a year and a half ago | (#42559895)

Re:I preferred the BBC's slightly ambiguous headli (4, Funny)

Dexter Herbivore (1322345) | about a year and a half ago | (#42560071)

Bringing the word 'apes' into any discussion about the development of life is sure to aggravate certain groups.

Re:I preferred the BBC's slightly ambiguous headli (5, Insightful)

bmo (77928) | about a year and a half ago | (#42560235)

>Bringing the word 'apes' into any discussion about the development of life is sure to aggravate certain groups.

Good. Let them be mad. Let them rail against reality.

It's high time we stopped walking on eggs about this issue. There is this fallacy that each person's opinion about the universe is just as valid as another's. As if we have to be polite about them like we have to be polite about the pictures of their kids.

No. No we don't.

If you believe the universe was created in 4004 BC at 9am, you are a nut. There are no qualifiers to go with that. Not "you might be a nut" or "some people would disagree with you." No. You're a full-blown nutcase.

And yes, we are apes. Big naked apes. Deal with it.

--
BMO

Re:I preferred the BBC's slightly ambiguous headli (4, Funny)

durrr (1316311) | about a year and a half ago | (#42560333)

I disagree.

We are actually big clothed apes.

Re:I preferred the BBC's slightly ambiguous headli (1)

BadMrMojo (767184) | about a year and a half ago | (#42560581)

I disagree.

We are actually big clothed apes.

Speak for yourself.

Re:I preferred the BBC's slightly ambiguous headli (2)

Anonymous Coward | about a year and a half ago | (#42560587)

It's high time we stopped walking on eggs about this issue. There is this fallacy that each person's opinion about the universe is just as valid as another's.

That is now the reason I, and at least some others I know, walk on eggshells with such issues. One reason is to not drag other stuff into that crapstorm, as it doesn't help much to turn every biology topic, or even many non-biology topics, into the same tired old argument that has little to do with the particular subject at hand. The people who get into such arguments, especially when unprompted or off-topic, are not the type that are going to change their mind any time soon or find an epiphany in an internet argument. If anything in my experience, they just dig in more.

The other, is to try to take the "high road" with such things, as there are plenty of people who will take any little thing they can to turn around and use against you in such arguments. Will being polite stop them? Nope, but it sometimes slows them down, or makes them resort to more extreme non sequitur arguments that are more obviously BS to less rabid people who stand a chance of seeing the other side. Unfortunately, there are a few people who respond positively to a "that is fucking stupid" response instead of something politer. But in my experience, far more people respond to that as a confirmation that they were right to begin with.

If you don't care about teaching such people, you can ignore the second one. But the first reason still probably applies, why frustrate people on both sides for no gain, and fill comments with crap to wade through to find on-topic stuff? (Unless in the mood for trolling...)

Re:I preferred the BBC's slightly ambiguous headli (2)

bmo (77928) | about a year and a half ago | (#42560815)

>If you don't care about teaching such people, you can ignore the second one.

I've tried to teach people. I've had a discussion on here that exemplified what happens.

I took someone at his word that he was serious about being a Young Earth Creationist, that he had a valid opinion, and that maybe I could convince him otherwise by appealing to his belief that God is All Powerful, and that, really, the literal biblical Creationism bullcrap is merely a limit by Man on what God can do, because "who the heck are you to say that God didn't use the Big Bang and Evolution to create Man?"

I could get him right up to the edge of knowledge, that the idea of biblical literal creationism is a human fable constructed by savages who didn't even know that the Earth revolves around the Sun. And if you're God, isn't it far more elegant to create something that operates on its own instead of having to meddle with it every second?

You get them right up to that point, and then they repeat something they were told when they were 5 years old.

Maybe it's time that people who buy into that were finally told that believing that stuff is like still believing in the Easter Bunny and Santa Claus.

--
BMO

Re:I preferred the BBC's slightly ambiguous headli (0)

Anonymous Coward | about a year and a half ago | (#42561225)

The point wasn't that being polite is a guaranteed success, as in fact it has a pretty dismal absolute success rate on such topics. The point was that, on average, it has a better relative success rate than being too aggressive. Occasionally you can get it to work, especially if you know some one pretty well as a friend, and know a kick in the bum helps them move forward from time to time. Otherwise, instead of just repeating something they were told when they were 5, they will wallow in it.

Re:I preferred the BBC's slightly ambiguous headli (1)

Anonymous Coward | about a year and a half ago | (#42560639)

We usually reserve the word "nuts" for people why have views outside the norm in their community.
For most of the creationists, their foolish views are absolutely inline with the local norms. These folks haven't gone off the rails on their own, they've been dragged along by a know-nothing movement that is rampant in America.

Re:I preferred the BBC's slightly ambiguous headli (1)

Anonymous Coward | about a year and a half ago | (#42560655)

If you believe the universe was created in 4004 BC at 9am, you are a nut.

Equally nutty is anyone who states that they know for a fact that the universe is millions and billions of years old. Anything you think are "facts" regarding these events are just observations and conclusions of puny little human brains. "But we have scientific proof!", you say. Only as far as our understanding of things, only as far as our puny little human brains can comprehend.

I think big-bang creation of the universe is less likely than the FSM (blessed be his holiness) creating everything. Who are you to say that your conclusions are more valid than mine? And why do you care about my personal beliefs anyway?

Re:I preferred the BBC's slightly ambiguous headli (2)

bmo (77928) | about a year and a half ago | (#42561045)

Then why create models of anything ever?

The scientific method works because the universe is consistent and not arbitrary. That you can create models and test them against reality. It's far better than Aristotle's gedankeneperiments on how things "should" work instead of investigating the reality.

  For example, we know that light has a speed and that it's pretty consistent throughout the universe and that the physics concerning light tells us how far away things are. If a photon has been travelling 4.6 billion years to get to us, the universe is *at least* that old because it had to originate somewhere.

There is the Young Earth Creationist assumption that God created the entire universe including "old" photons in flight all at once, merely to fool Man (and that fossils are the same thing, to test one's faith). This is inelegant, and basically says that God is a capricious asshole.

And you say that both the scientific and religious opinions deserve equal weight because "hurr durr, we don't know anything"

Then why were we given brains to witness the universe? Because God set us all up to fail?

Such a being doesn't deserve worship. Satan is more respectable in that regard.

--
BMO

Re:I preferred the BBC's slightly ambiguous headli (1)

Ambvai (1106941) | about a year and a half ago | (#42561575)

I've played with this as a thought exercise, and my favorite result is that the entire universe, along with given rules, etc. started from a single random seed and propagated out following those rules at high speed. Then, some 4000 years ago, God sat down and started the actual interesting part of things.

Alternatively, for the Sim[X], Dwarf Fortress, etc. players among us, the first few billion years were in the loading screen and the last few thousand years have been a part of active gameplay.

Not that I actually believe this, but it's a neater explanation than a lot of the other answers I've gotten.

Re:I preferred the BBC's slightly ambiguous headli (2)

HiThere (15173) | about a year and a half ago | (#42562335)

While I "sort of" agree with you conclusions, I totally disagree with your certainty.

1) You can't prove the universe is logically consistent. That's an assumption.
2) You can't prove that the universe wasn't created one nano-second ago, with all evidence in situ.
3) You can't prove that this isn't a computer simulation.
4) ...this list has gone on as long as I have patience, but it can be extended ad lib.

Note that no valid estimate of the probability of any of the above is even possible. Where they are consistent is that it is plausible to act AS IF the universe were durable and logically consistent, and that the "facts" that you remember as having been learned are accurate. But this is exactly what a young earth creationist is doing. I may believe that his beliefs aren't useful, and that many of the "facts" that he learned are wrong, but there is no evidence. In fact, IIRC, Bayesian theory predicts that in such cases there is no possible evidence that will convert him to your point of view. You *might* be convinced of his point of view by a personal appearance from some god or other, but you'd be likely to talk yourself into beleiving that it had been a hallucination. I.e., it's also doubtful that any evidence would convert you to his point of view.

Re:I preferred the BBC's slightly ambiguous headli (1)

bmo (77928) | about a year and a half ago | (#42563979)

You're seriously arguing for Last Thursdayism? Really?

--
BMO

Re:I preferred the BBC's slightly ambiguous headli (1)

HiThere (15173) | about a year and a half ago | (#42569525)

Actually, I am. But only as a part of an ensemble of other theories. So if "Last Thursdayism" recommends a course of action that the perponderance of the ensemble recommend against, I don't perform the action.

Well, in a theoretic sense, that's what I'm arguing in favor of. As a computational short cut I use the model recommended by the Standard Model. But that doesn't imply certainty, what it implies that that most of the models recommend the same course of action as the Standard Model in most circumstances. Think of it as the Heisenberg interpretation of Quantum Mechanics applied to cosmogony.

And when I think about it, that approach is rather wierd because when I think of Quantum Mechanics, etc. I prefer the EWG Multi-World interpretation. Perhaps it's because there's no rigorous framework for cosmogony. It's hard to validate the Multi-World intepretation unless you have a mathematical framework to validate it against, but it's easy to say "There's no basis for choosing". Of course the actual Heisenberg analogy would say "There can't be a basis for choosing", but I don't think that's totally clear. OTOH, since one of the possibilities in the hat is that the universe isn't logically consistent, ...

Re:I preferred the BBC's slightly ambiguous headli (1)

bmo (77928) | about a year and a half ago | (#42569803)

But that is merely arguing for hypotheses that are untestable.

Science doesn't revolve around the untestable. We leave that to metaphysics and religion. Stuff we can't test, even mathematically, we can't do anything with, and testable things have gotten us where we are today in terms of scientific and technological advancement. Aristotle's penchant for thought experiments, trying to bend the Universe to how it *ought* to be, as opposed to how it *is* by direct or even indirect observation, held back scientific, technical, and philosophical advancement for a long time, until various members of the medieval Church started challenging it (I am currently reading "Before Galileo" by John Freely, a pretty good read).

Using untestable ideas (Last Thursdayism, a parody) that rely on recursive untestable hypotheses gets you nowhere, except a headache, religion, or madness (like TimeCube). As Carl Sagan illustrated in his book "The Demon Haunted World," I could attest that there is a dragon in my garage, and each objection I could nullify by making a untestable statement, like "he's invisible" and "no, paint won't stick" and "spreading powder on the floor won't detect his footprints since he floats" ad infinitum and ad nauseam. If i kept defending the invisible dragon to the bitter end, not letting you know that I was putting you on, you would find that I was quite mad.

--
BMO

Re:I preferred the BBC's slightly ambiguous headli (1)

HiThere (15173) | about a year and a half ago | (#42576317)

To rule out an idea because you can't test it is an indefeasible bias in favor of your current ideas, which also can't be tested WRT the differences in assumptions of the other "untestable" ideas.

One may argue that a certains set of ideas is more pragmatically useful than other ideas that are consistent with the observations, but that's not the same as arguing that they are true. We may be living in a computer simulation. It may be such a limited simulation that you are the only real entity. These can be consistent with all observations. Pragmatically, they aren't useful, because they don't allow one to make predictions of unobserved phenomena (without additional assumptions as the the nature of the simulation, etc.). But there's no valid reason to say they aren't true.

Note that this is analogous to arguing whether the standard model of physics or string theory is correct. We can't validly choose between them, because they both can be made to make predictions consistent with all existing observations. And BOTH have large amounts of "gosh numbers" that are required to have particular values not because of any underlying theory, but only to match observations.

When making practical predictions, I usually use Newton's physics, even though I know that it is "false", because it's close enough to being right. So being practically useful isn't proof of truth. NASA also uses Newton's physics for obital calculations, so it's quite close to being correct.

But when one is trying to determine truth, one needs to work with the ensemble of all ideas consistent with current observations....and then add a large helping of uncertainty.

Re:I preferred the BBC's slightly ambiguous headli (1)

bmo (77928) | about a year and a half ago | (#42578571)

To rule out an idea because you can't test it is an indefeasible bias in favor of your current ideas

You're using that word wrongly....

But when one is trying to determine truth, one needs to work with the ensemble of all ideas consistent with current observations....and then add a large helping of uncertainty.

OK, so I'm being trolled.

Bye.

--
BMO

Re:I preferred the BBC's slightly ambiguous headli (1)

Anonymous Coward | about a year and a half ago | (#42561473)

Anything you think are "facts" regarding these events are just observations and conclusions of puny little human brains.

That is true of all facts, opinions and thoughts, and not just regarding those particular events. And yet, despite many people acknowledging the fallibility of human thought, they are able to move on and live practical lives applying those fallible facts.

Re:I preferred the BBC's slightly ambiguous headli (1)

wonkey_monkey (2592601) | about a year and a half ago | (#42560675)

If you believe the universe was created in 4004 BC at 9am, you are a nut. There are no qualifiers to go with that. Not "you might be a nut" or "some people would disagree with you." No. You're a full-blown nutcase.

What if you're brought up on a desert island and that's all you've ever been told? And you have no facilities or education to determine otherwise?

Not that I don't see your point. I'm just a hopeless pedant and feel it necessary to point out that there are qualifiers to go with that, and there are plenty of shades of grey from my example up to a well-educated but close-minded Christian fundamentalist.

Re:I preferred the BBC's slightly ambiguous headli (0)

Anonymous Coward | about a year and a half ago | (#42560825)

Yea, 50 of them, and none of which are appreciated by Christian fundamentalists.

Re:I preferred the BBC's slightly ambiguous headli (0)

Anonymous Coward | about a year and a half ago | (#42562089)

Congratulations. You've just discovered what Republicans and Democrats discovered long ago: being polite means people might change their minds. Better to galvanize everyone into their respective positions by being total assholes and calling them "nuts" for having beliefs different from yours.

Re:I preferred the BBC's slightly ambiguous headli (2)

bmo (77928) | about a year and a half ago | (#42562837)

People who take extreme positions like the world being 6000 years old deserve to be ridiculed. We laugh at the Flat Earth Society, why do we not laugh at these people who also have a warped world view that flies against reality, a reality that has been further against this "the world began in 4004 BC as calculated by a monk in the dark ages" since the Renaissance.

But to top this off, they have political power. The Flat Earth Society has no political power, because any FES candidate running for office would be questioned about his ability to work for his constituents by operating on some sort of actual logic. But we give a break to those who believe in the calculations of a medieval monk. (funny how the people who claim YEC claim to be biblical literalists, when there is nothing in the bible, actually, that spells out actual age of the Earth even when calculating the begats - the begats must use WAGs for ages and such).

There are opinions that recognize some sort of reality, and there are the ones who, when looked at briefly rationally, one must believe the people who hold such a belief are insane. At least the Democrats and Republicans, even the most extreme on either side have philosophies that are based at least somewhat on the observation of human behaviour. Creationists? The shoehorns for their worldviews are made of Adamantium.

--
BMO

Re:I preferred the BBC's slightly ambiguous headli (1)

citizenr (871508) | about a year and a half ago | (#42560373)

Bringing the word 'apes' into any discussion about the development of life is sure to aggravate certain groups.

http://www.youtube.com/watch?v=zCdBZHBs0y0 [youtube.com]

Re:I preferred the BBC's slightly ambiguous headli (1)

Anonymous Coward | about a year and a half ago | (#42561635)

yeah, but we're talking about microscopic robot apes here.. how cute is that?

Re:I preferred the BBC's slightly ambiguous headli (-1, Offtopic)

nuhasifa (2813723) | about a year and a half ago | (#42561675)

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Cool ... (1)

gstoddart (321705) | about a year and a half ago | (#42559897)

Bring on the booster spice. ;-)

Re:Cool ... (1)

Sparticus789 (2625955) | about a year and a half ago | (#42559939)

He who controls the spice, controls the formation of protein!

Re:Cool ... (0)

Anonymous Coward | about a year and a half ago | (#42560001)

All hail Rosy Palmer and her 5 sisters!

Re:Cool ... (4, Informative)

gstoddart (321705) | about a year and a half ago | (#42560075)

Think Larry Niven [wikipedia.org] , not Frank Herbert

Re:Cool ... (1)

HiThere (15173) | about a year and a half ago | (#42563643)

IIRC, the term is boosterspice, one word.

Apple to file infringement lawsuit in... (0)

Anonymous Coward | about a year and a half ago | (#42559949)

3... 2... 1...

I welcome (0)

Anonymous Coward | about a year and a half ago | (#42560011)

our future robot overlords.

Hubris and Nemesis (-1)

m.shenhav (948505) | about a year and a half ago | (#42560027)

As we have seen with Climate, Ecology, the Economy, the Human Body and a bunch of other Complex Systems - this is a potential Pandora's Box. Messing around with Complex Systems that have evolved over time scales several orders of magnitude greater than our ideas about them have can produce Lethal Black Swans [wikipedia.org] . Disturbing Ancient Non-Linear systems is a recipe for disaster.

Re:Hubris and Nemesis (1)

Samantha Wright (1324923) | about a year and a half ago | (#42560165)

Personally, I would be much more concerned about the effects of indoctrinating our youths with 1-sided Linear Time in place of the 4-sided Truth, but the hospital's firewall considers timecube.com a hate site, so you'll have to settle with a big fat "no" instead of full-force trolling.

Re:Hubris and Nemesis (0)

Anonymous Coward | about a year and a half ago | (#42560301)

the hospital's firewall considers timecube.com a hate site

Well, I can't speak for everybody, but I know I hate it.

Re:Hubris and Nemesis (2)

ColdWetDog (752185) | about a year and a half ago | (#42560353)

You could try some random page on Fox News. Such a page would make about the same amount of sense. You would miss HTML code that only a Geocities site could love, but you can't have everything.

Re:Hubris and Nemesis (1)

jiriw (444695) | about a year and a half ago | (#42560329)

Disturbing Ancient Non-Linear systems is a recipe for disaster.

What are you blabbering about? They're not disturbing an ancient system, they are making an entirely new one. That the end-result, a small string of amino acids, is about the same, is the only thing it has in common with the ribosome. Humans already make custom proteins on a massive scale... in yeast tanks with genetically modified yeast, for example. And that works a lot faster than this little Rotaxane thingie.

From TFA:

The ribosome, the molecular machine that translates our genetic code to build the body’s proteins, is a mechanical marvel. Now, chemists have invented a nanomachine that can achieve a similar feat.

That doesn't sound like they are making a Frankenstein's monster, protein by protein, now... does it? Please read the article(s) first before you sprout any nonsense. There are genetic engineering processes commonly used today which are definitely much more dangerous than a piece of molecular Meccano, stringing a small peptide (sorry if I make it sound simple, it's still an enormous achievement to get something like this working and I'm not a biochemist so I'll have to treat the parts that go beyond my knowledge with proper awe ;) )

Re:Hubris and Nemesis (0)

Anonymous Coward | about a year and a half ago | (#42562895)

It's not biochemistry and it's an otherwise-uselss proof-of-concept.

Re:Hubris and Nemesis (1)

m.shenhav (948505) | about a year and a half ago | (#42567433)

I was not referring to the technology as used on its own. This technology becomes most interesting when its self replicating (or part of a self replicating system) and place in a natural system, like a human body or an ecosystem. Sure you can say this has safe applications, but the road this technology is going to on the whole is into large scale intervention in very old complex systems, and that road is what concerns me.

Re:Hubris and Nemesis (0)

Anonymous Coward | about a year and a half ago | (#42560695)

I've been messing around with this non-linear circuit all week, and haven't been able to get anything exciting out of it, let alone a disaster. I once hooked the power supply up backwards, but didn't get any noise or magic smoke, just non-visible damage to a 10 cent component. If only I had some linear system to create some excitement around here, like a Tesla coil. So far, I've discovered disturbing non-linear systems is a recipe for boredom (unless you are a mathematician, then it may be a recipe for a lot of excitement... just remember, if excitement lasts for 3.9 hours, you are ok, but for 4.0 hours, you should see a doctor, as that system is not as linear as it looks).

How long? (1)

steelfood (895457) | about a year and a half ago | (#42560341)

People like Sergey Brin are working on putting IC's into the human body, but this is the real future of melding man and machine.

How long before we as a race are more machine than man?

Re:How long? (2)

AaronLS (1804210) | about a year and a half ago | (#42560601)

Not disagreeing, but I imagine people won't perceive these things as machines. It will be such a gradual adoption. Not many people think of glasses, hearing aids, hip implants, pace makers, etc. as being robot/machine like. Since people generally won't widely use anything until it is comfortable and offers more benefits than hindrances, these products will tend towards designs that are less noticeable. We probably will move towards being cyborgs, but no one will call it that, except for the rare introspective persons who says "Hey, you reallize that we are like cyborgs now.", and everyone will be like "Yeh, I guess so" and then go about their day. It'll be very much like the tricorders in StarTrek that you think "Wow will we ever have something like that?", but today now that we all have handheld computers, no one really makes a big deal about it accept for the occasional reflection someone does.

Re:How long? (0)

Anonymous Coward | about a year and a half ago | (#42560705)

We're already machines. Don't let the meat fool you, a machine can be developed out of things other than metal.

familiar! (1)

Anonymous Coward | about a year and a half ago | (#42560501)

OMG lol!! That animated video of this nano-machine working totally reminds me of myself when I'm drunk. I walk around trying to see how many beer cans I can stack on my head until they fall off!! I'm a macro-scale version of this thing!!

Re:familiar! (0)

Anonymous Coward | about a year and a half ago | (#42564437)

Yes, for intelligently designed nanotech, the thing seems almost drunkenly stupid. Of course, as they say about evolution, the wonder is that it works at all.

I dub thee (4, Funny)

Culture20 (968837) | about a year and a half ago | (#42560771)

Robosome.

Re:I dub thee (0)

Anonymous Coward | about a year and a half ago | (#42561767)

Robosome, what are your Prime Directives?

Re:I dub thee (2)

thygate (1590197) | about a year and a half ago | (#42562485)

He's no different from the rest of you organisms, shooting DNA at each other to make babies. I find it offensive.

Funny Comments And All... (0)

Anonymous Coward | about a year and a half ago | (#42562853)

...but isn't this a rather important step for nanotechology? I admit I am not as knowledgable about the current state of nano-tech as I would like to be, but this sounds rather encouraging!

Obviously doesn't belong on /. (0)

Anonymous Coward | about a year and a half ago | (#42562919)

Seeing as nobody here has anything intelligent to say about this, it doesn't belong on slashdot.
Chiming in as a synthetic/computational organic chemist:

Neat idea, no practical functionality presented. Nice bench work.

Do the words "Grey Goo" ring any bells? (2)

mmell (832646) | about a year and a half ago | (#42562931)

Just askin', 'cuz this looks like step one . . . hooray for progress!

A work in progress (1)

HHealthy (2803519) | about a year and a half ago | (#42577583)

It certainly seems like at this point due to its low transcripting speed it is of limited usability . But as with most innovations the main creative step has been taken already. Moreover modifing the sidechains of amioacids or alterations alike in this molecular ensemble may lead to batch of discrete function protein builders which is much more interesting as it offers diversity wih respect to ribosomes. For funding, research and peer finding please refer to the non-profit Aging Portfolio.
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