The Los Alamos Bug

Kannappan writes "'You somehow have to forget everything you know about life', says Steen Rasmussen, a colleague of Norman Packard. Packard and his team are working on creating life artificially, nicknamed The Los Alamos bug (pdf). It will be created out of a molecule called Peptide Nucleic Acid(PNA), with a blend of three different factors crucial to life, viz. containment, heredity and metabolism. The researchers believe that the synthetic lives so created will have an enormous practical value in producing clean fuels, healing injured bodies and acting as tiny diagnosticians roaming our bodies."

Comments

PNA?

[Punboy]

Are there any other lifeforms based on PNA? Why aren't they using DNA?

Do I just need to RTFA?

Re:PNA?

[caenorhabditas]

Normal nucleic acids are composed of sugar, base and phosphate. PNA as described in the article replaces the sugar and phosphate with a peptide (I assume with the R group replaced with the A, T, G or C). The replacement of the sugar-phosphate backbone with a peptide makes the nucleic acid soluble in fat, rather than soluble in water -- the ultimate goal of using PNA rather than DNA or RNA.

And no, I do not believe there are other life forms based on PNA.

Re:PNA?

[JumperCable]

They want to lock in all future life into a proprietary format. With current DNA being patented our only hope left is to create our own truly open source life form.

No word yet on which format Microsoft and Sony intend to back. In related news, Bush is working heavily with Monsanto to ensure that the DMCA is found to be applicable to current life forms. Scientists caught attempting to reverse engineer life should expect to be raided by the FBI by the end of year.

Re:PNA?

[Thomas Miconi]

Run that past me once again in English?

OK. "They're fscking cheating"

They're using PNA because it does fancy stuff "on its own", just because the out of it is soluble in oil, but the inside of it is repelled by oil and prefers water. So it goes up and down according to whether it's "single-stranded" or "two-stranded" (i.e. whether the inside is expopsed or not). You don't need the complex machinery of metabolic reactions which is necessary for "real" life to cut, assemble and move stuff around.

The whole thing is a fraud, at least if TFA from the New Scientist is an accurate description. Never mind that the genome is essentially random bits of PNA that don't code for any chemical machinery. TFA says that it does influence "metabolism" directly, through electromechanical influence. Wow, that leaves a lot of degrees of freedom for evolution to play with, doesn't it ? (Hint: no, it doesn't). I could mention the utter lack of self-regulation (that thing just grows and divides when it's too big, period), removing the essential computational component of life (wonder what Packard's friend Stuart Kauffman would say about that).

The worst part is the thermodynamics. Apparently all the reactions that occur within the bug are "downwards", degrading reactions. The bug doesn't relly "build" anything. The miracle of life lies precisely in its self-constructing aspect: life is able to couple downwards, energy-releasing reactions and upwards, constructive reactions so that the former "feed" the latter. Thus living systems really construct themselves. That "bug" just uses hand-tailored, pre-activated, energy-packed components which are fed to it by the experimenter and degrades them according to a carefully hand-defined pathway. Evolution of the inner processes is utterly impossible because, essentially, there is no real "inner process". It's just like fire - a downwards, energy releasing reaction without any self-regulation. .

If this thing is alive, then so were Sydney Fox' "protocells" from 40 years ago !

That thing is about as relevant to understanding life as Deep Blue was to understanding intelligence - i.e. it gives a good example of what life is not.

Thomas.

Only a matter of time

[FlyByPC]

With our increasing knowledge of the mechanics of life, it's a matter of time until somebody succeeds in creating life from scratch. I don't think it's very controversial these days to say that if we don't already have the power to create life in vitro, we someday will.

For my money, a much more interesting question is, can we create *intelligence* from scratch? Humor aside, I think creating something with recognizable intelligence (not just programming) will be much more difficult -- and have much more profound implications -- than "merely" creating life.

Such experiments should help narrow down the various factors in the Drake Equation. Life, I suspect, is fairly commonplace. I have no idea if intelligence is.

Re:Only a matter of time

[ZachPruckowski]

We are certainly moving towards artificial intelligence. We actually have programs that can write themselves to a limited degree. And so we'll probably have artifical intelligence shortly. But making a new biological species with our level of intelligence sounds tough because of our limited knowledge of the brain.

I'd recommend you read things by Ray Kurzweil on this topic. In particular, "The Singularity" seems relevant. Apparently there is a short collection of essays by him online, but I don't know if it'll have what you're looking for.

Re:Only a matter of time

[MarkRose]

Our brains limit us to only create something less "intelligent" if we were to do it from scratch.

I disagree. If we can determine the origin of intelligence and the mechanisms by which is works, we could improve upon those mechanisms. Also, it depends what kind of intelligence you a measuring. Math-wise, computers are far more intelligent than the average individual at computation. It's quite possible that we could create a device/organism that's better suited to other areas of intelligence.

Re:Only a matter of time

[heinousjay]

Math-wise, computers are far more intelligent than the average individual at computation.

Maybe you don't realize just how much calculus is involved in walking down stairs.

The human brain is a computation engine of more power than people understand. It just doesn't happen at a conscious level, so we're not always aware of it. Our brains operate at a level far above raw computational power, which is really all our machines are good at right now.

Re:Only a matter of time

[ShimmyShimmy]

can we create *intelligence* from scratch?

I think I fundamentally disagree with you in saying that intelligence is hard to create, given life in the first place. At this point in time, science has (almost) undisputedly proved the theory of common descent. I pretty well believe that humans eventually came from single-celled organisms, and so does most of the world.

So assuming that is true, intelligence more or less created itself, through life, by a glorified trial-and-error system. Although it seems surprising at first, if you consider how many many different orananisms there are (were) at any given time, and how many trials (generations) there have been, it becomes much more down to Earth.

Actually I think even 'intelligence' today is still a glorified system of trial and error. Think about solving an elementary algebra problem. What's your first intuition (or was when you were learning)? Isolate the variable, etc? Hell no! Trial and error. It's intuitive and doesn't take much mental 'work'. Example: Mary and Sue have a combined age of 15. Mary is 5 years older than Sue. How old is Mary?

Spit this problem at an average 5th/6th grader and I promise you won't get anything along the lines of x + (x + 5) = 15. You'll just get 3 + 8 = [crossed out], 4 + 9 = [crossed out], 5 + 10 = 15 !! And that's how the problem is solved by a (we'll say) 10 year old.

Now, I know I don't seem to be really getting at anything big, but consider this: the average 10 year old has solved a LOT of 'problems' in his/her lifetime, from how to balance to stand up, how much food to eat so you aren't hungry anymore but don't throw up... I could go on forever, but I will call one example: pouring.

Is it hard to pour water from a pitcher into a cup? I'm pretty sure most of you have figured out how to do this reasonably well by now. To do this problem systematically is EXTREMELY difficult. I'll simplify the problem slightly and boil the problem down to two varibles: The height of water in the cup (we'll say % full), and the tilt on the pitcher (an angle between 0 and 180). There is ABSOLUTELY no simple, one-line algebraic equation to solve this one. You can't simply say, when the cup is 100% full, put the angle to zero. You have to correct for how much water is out of the pitcher already and is about to fall into the cup (a time delay), and also the time it takes to move the pitcher from say, 20 degrees to 0 degrees (more time delay). Even better, the flow of the water within the pitcher depends not only on the angular position (zeroth derivative), and the rate and acceleration (first and second derivatives), but also the "jerk" of the pitcher (third derivative of angular position). Wow. That's hard.

To solve this problem analytically, you would need a lot of math. A LOT. In fact, even more than we know today. Using LaPlace transforms and 3rd order differential equation solvers, this can be done, but even the DE solvers are written in trial-and-error form to some extent. If you've read this far, you're probably asking: What exactly am I getting at?

YOU ALREADY SOLVED THIS PROBLEM! Ever fill up a cup and not spill? Not bad. Basically, your mind (body?) has already found at least some solution to this problem without you knowing it. You have subconciously short-circuited hundreds of PhD's worth of math with a magic black-box of trial and error. Remember when you were a kid? You tilt the pitcher little and tilt it back. Not enough. You do it again. Not enough. You tilt the pitcher until the cup is full. Crap. Spilled it. Note to self: stop before the cup is full.

So there you have it. Our 'intelligence' has solved math problems than most college graduates could do (even with Maple) to save their lives. If it works, do it again, and if it doesn't work, do something different. That's all our 'intelligence' is.

I really don't think this whole 'intelligence' thing is a very novel concept at all.

Re:Only a matter of time

[Shihar]

And the most insidious unintended consequence of our advance in medicine, most people don't appreciate, we have extended our life spans, if you have the money, to the point that we live much longer than we should, we have people living a poor quality of life for decades in their 80's and 90's draining societies resources, and worse we are producing an exploding population. I'm not sure near technology synthesized immortality is such a great thing. There is benefit in the renewal that comes with the old dieing and letting young, fresh people take over.

I think you are looking at life expansion from entirely the wrong perspective. First, life expansion does NOT create a population boom. All of the rich western European nation are in a death cycle right now. Their populations are shrinking. Wealth and the ability to live a long time causes people to simply choose to not have as many children. This is an extremely well documented correlation. The US itself would be in a death cycle like Europe if it wasn't for its influx of immigrants.

Life expansion does not result in a drastically lower standard of living. Being old isn't what makes being old suck. Having your organs fail, your bones become brittle, mental illness, and muscle loss are the reasons why being old is no fun. Fortunately, extending life requires dealing with all of the above. If you have ever watched a National Geographic on a tribe with low life expectancy, you will notice that a 35 year old man looks like an 80 year old American or European. That isn't to suggest that we keep people alive beyond what they would be able to be naturally in the same state, but it isn't right to assume that when people were dying at the age of 40 they were dying looking and feeling like a 40 year old of today.

More importantly, life expansion these days almost entirely revolves around "solving" old age. If someone was to live to be 200 years old, you can bet that they have 'solved' old age and that 200 year old person probably looks about 30. You simply can't extend peoples' lives much longer without curing the natural degradation that your body suffers as you get older.

Finally, I think you drastically overlook the social good that old age offers. In a society where people become older and older, you have people building up vast reservoirs of experience and knowledge. The only social ill old age brings is retirement, and as you see people living longer and healthier lives, you are going to see the retirement age kicked out further. I wouldn't be surprised in a decade or two when life expansion hits its next big surge that our way of thinking about retirement gets radically altered. I wouldn't be surprised if one day the normal mode of 'retirement' is to take a few years off from work every decade or two, but never permanently retire.

Re:Only a matter of time

[gfody]

Singularity Institute for AI

Re:Only a matter of time

[localman]

We are certainly moving towards artificial intelligence. We actually have programs that can write themselves to a limited degree. And so we'll probably have artifical intelligence shortly.

Care to take a bet on that? :)

I don't believe there is anything magical about the brain, and I believe it can be reproduced in a man-made form. But I think it is far far more complex than we yet realize. Even the most advanced neural nets of today are nowheres near the level of complexity of even a rodent brain. And I'm not just talking about the number of neurons. I'm talking about the secondary effects -- the self-organizing nature of the brain, and how different parts, with slightly different layouts are used for vastly different processing tasks. We're still a long ways off. If I had to guess I'd say not within the next 50 years. Perhaps much longer.

And I don't believe that we'll achieve intelligence through direct programming, even through self modifying programs. If you can look at the low level and tell what's happening at the top level (like with a program) then it's far to simple to encode intelligence. Intelligence requires layers of meaning.

Nonetheless, an interesting topic.

Cheers.

Well. that's one way

[inode_buddha]

Well. that's one way to get a life.

Comment removed

[account_deleted]

Comment removed based on user account deletion

Re:Focus on Artificial life

[audacity242]

Lots of seemingly meaningless scientific pursuits have led to things that have had huge impacts on human life.

I seem to recall a silly woman, who specialized in x-ray crystallography, taking a picture of a molecule she wasn't supposed to be wasting her time on. If it weren't for Rosalind Franklin doing that, the discovery of the structure of DNA would have been delayed for god only knows how long.

RNA is thought to be able to do this.

[autopr0n]

Some people think that before DNA evolved, everything was done with RNA. Both hereditary information and the physical catalysts. Like proteins, RNA molecules can fold up into odd shapes and perform catalytic reactions. The only difference is that Protein based system work faster. The Ribosome, which converts RNA into Proteins is actually made from RNA, rather then proteins, and is almost exactly the same in all life.

Re:Focus on Artificial life

[amliebsch]

Seriously... what good the creation of a bug do to humanity?

Imagine a bug that can convert cellulose to alcohol. Or eats dioxins and destroys them. Or generates hydrogen from sun and water. Wouldn't these be somewhat beneficial?

Re:Scientists need to stop playing God!

[Anonymous Coward]

I completly agree. Does GWB even knows that this is happening in a federal lab, using federal taxpayer money?? I have a feeling that we'll soon have a taste of category 6 and higher hurricanes if we continue this way...

I must pray over this.

Not playing God...

[clambake]

Just to remind everyone, it's not playing God if you aren't creating life with pure will power alone...

Re:Not playing God...

[spongman]

I wonder if they'll take the day off when they're done.

Re:Scientists need to stop playing God!

[AbraCadaver]

I'm hoping the parent was trying to be funny (the sasser worm??) but may inflame people who actually think like this, so I'll bite. And yes, this is relevant.

In all the "we are playing god" arguments that I've heard, I ask "where in the Bible/Talmud/Torah/Qur'an does it say 'Ye shall not create life'?". No one can ever give me a direct quote where it says we are forbidden from doing so. So, with that in mind, and given that we are given, the parent would say, from our devine creator, the gifts of intelligence AND curiosity, who is to say that we are not expressly ALLOWED to do this because we were granted the abilities. Now I'm sure I'll get replys that say "well, I'm given the ability to kill or steal, but it doesn't mean that I'm ALLOWED to do so..." and for the asshat that comes up with this argument, I'll counter with: Taking Life or Doing Harm (TM), in that intent, is usually a direct, willful act of agression. Creating, whether it be life, or a painting, or a controversial book, is not intended to be directly harmful in most cases, especially if the intent is to learn, or open a discourse, etc. Sure, some science has yielded results that might be harmful to someone in some circumstance, but I, driving my car to work, might be harmful to someone, in some circumstance, whether it be hitting them or poisoning the air of their great grand children and causing global warming, the seas to melt, and all of us end up doing bad Kevin Costner impersonations. My point is, and this is my own opinion, that the intent of most of the religious texts of the world seem to be "don't be evil bastards." How can creation be evil, when it's A) not intended to be evil, and B) Not even expressly forbidden? (that I know of)

Flame away!

Re:Source of creation, or evolution?

[Vellmont]

While I am not a creationist, I did see the point of their argument - how simple amino acids and organic chemicals were first formed into cells, I have no idea.

I think this is an important question in biology, and I'm sure no biologist would deny it. The problem comes when the creationists merely assume god must have done anything we can't explain. It's the "god in the gaps" argument that's been popular probbably since we first learned to communicate. The problem of course is that science marches on and when you try to find your god in the gaps of science, science eventually closes those gaps. Religion always fights like mad because they've invested much of their belief structure in the argument. The gaps used to be in evolution. Those gaps have closed and now the gaps have moved to the creation of life itself.

The point that people like you were talking to seem to miss is that assuming the existence of a god to explain current lack of scientific understanding of scientific questions has always been a losing proposition. Where religion always fails is when it gets mixed up with scientific questions. Science adapts, and religion tries to cling to dogma. Religion changes too perhaps.. no one is seriously pissed off about heliocentrism anymore, it just takes about 100 times longer.

Re:Sai Dorsai!

[hitmark]

i guess thats where evolution outperforms us. it gives randomness a chance and therefor can discover a better brain by chance.

thing is realy, how to put evolution into effect when creating a microchip or a computer program. and then how to test against parameters so that the program becomes self aware.

ie, the moment we can set down the requirements for selfawareness then we can build something thats selfaware. atleast in theory.

and yes, i have not read the book or whatever it is your refering to. maybe ill have to look it up sometime.

still, i belive one could build a more intelligent "being", that is if one fully understood what it is that make up intelligence. understanding what makes it stronger or faster is simple. understanding intelligence is hard.

but it seems that current research shows that the brain is a neural net in a chemical bath. drop the right amounts of the right chemicals and the neural net pathways are changed or disabled.

so, stacking a bayesian system of values on top of a neural net so that they interact and one should get some interesting results if one pipe the raw data of video and audio into the same setup and let it run for any number of years.

but as of now we dont fully understand how the brain works, and therefor can not yet build a better one. but if we manage to figure out how it works then we should allso be able to design a better one. atleast in theory.

so yes, the monkeys would not be able to build a smarter monkey as they dont have the knowhow about how smartness is designed. but if they understood that then they may well have been able to build a smarter monkey.

thing is tho that to fully understand a brain we may well have to put in into a jar and play around with it while its still "alive". but that flys in the face of medical ethics. maybe its time we have another round of nazi medical research? we may not like what they did, but the results where used to help medical science move forward...