Triple Helix — Designing a New Molecule of Life 152
Anti-Globalism sends in this quote from Scientific American about attempts to synthesize molecules that function as well or better than the natural building blocks of life:
"A molecule that some researchers study in pursuit of this vision is peptide nucleic acid (PNA), which mimics the information-storing features of DNA and RNA but is built on a proteinlike backbone that is simpler and sturdier than their sugar-phosphate backbones. ... Many studies have demonstrated PNA's suitability for modifying gene expression, mostly in molecular test-tube experiments and in cell cultures. Studies in animals have begun, as has research on ways to transform PNA into drugs that can readily enter a person's cells from the bloodstream. ... Some scientists have suggested that PNAs or a very similar molecule may have formed the basis of an early kind of life at a time before proteins, DNA and RNA had evolved. Perhaps rather than creating novel life, artificial-life researchers will be re-creating our earliest ancestors."
Sounds like razors (Score:5, Funny)
Soon we will have the "quatro helix DNA" and then 5 helixes and so on.
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That pretty much sums it up.
Attempts to create novel "life forms" using this rather than DNA are not coming any time soon. We can't even make life forms de novo using the established DNA codons.
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I'd say that's because the easiest way to make RNA based life forms is to start with something simpler and work your way up - RNA does not an organism make, it needs an established cell to back it up.
The article suggests that this may be something closer to the first self-replicating molecules to emerge from the primordial soup. In order to have DNA or proteins evolve, you need some sort of proto-DNA or proto-protein like this that is more complex, but a self-contained unit capable of autonomous replication
Re:Sounds like CPU cores (Score:1)
First we had dual core, then some went for three and now the quad-core is the norm.
Re:Sounds like razors (Score:5, Funny)
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I for one am going multicored, with 6 hypothreaded DNA/RNA/PNA/ZNA quad strands.
That'll show 'em.
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Soon we will have the "quatro helix DNA" and then 5 helixes and so on.
That's nothing- I heard AMD are doing their own research with 8 helixes!
Er. (Score:2, Insightful)
If PNA functions "as well or better", then what exactly was the reason that RNA and DNA evolved in the first place?
Re:Er. (Score:5, Insightful)
Don't make the mistake of anthropomorphizing evolution. There is no committee that considers all possible solutions and states "This is the best one". Evolution is a case of what happens happens and what doesn't die out is what's left and so considered successful.
It is entirely possible that there are much more efficient ways for life to exist or function, but are different than the way life happened to happen here on earth. Or it could be that life DID happen that way but the methodology was not optimal for the environment at the time so the DNA/RNA based forms outlived them.
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Who anthropomorphised evolution? If PNA had existed earlier, then clearly it did not function "as well as or better than" RNA or DNA, and now it's gone. Did woolly mammoths function better than elephants? Did neanderthals function better than homo sapiens sapiens?
I might be nitpicking the blurb, but whatever.
Re:Er. (Score:5, Informative)
That said, I agree that it seems unlikely that such a fundamental shift as switching from PNA to DNA/RNA seems unlikely to have fluked itself into existence unless there's some tradeoff in, eg, efficiency of producing the molecules, or the difference is really pretty minor after all.
Re:Er. (Score:4, Insightful)
How is "evolutionary progress" not "progress"? This is the only measuring stick I've used. If PNA had indeed existed before DNA or RNA (as the article seems to suggest), and was snuffed out, then clearly it didn't function better than RNA/DNA when it came to surviving in a particular environment, or evolving. What is the "functionality" of an organism if not survival and procreation?
Re:Er. (Score:5, Insightful)
in a particular environment, or evolving
This is the exact point i'm trying to make that you seem to be missing. Survival in a particular environment does not mean a life form is best at surviving in any environment. If there was a long enough period where the stimuli and environmental pressures involved made RNA/DNA based life the most efficient, then there would be none of the alternative life forms remaining when the pressures change.
Just because a species goes extinct does not mean that that species was not "fit for survival" at all. It simply means that the species was not fit for survival given the pressures and stimuli of the time they went extinct.
The only measuring stick that matters to evolution is procreation, you're right about that. The part people forget is everything else that happens is just rolls of the dice with no specific desired outcome. If it helps the species survive the current pressures, the trait remains. If not, it either dies out or falls recessive within the species gene pool.
Re:Er. (Score:5, Insightful)
If it helps the species survive the current pressures, the trait remains.
Oops! You mean, "If it doesn't hurt the species' survival under the current pressures, the trait remains."
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In other words, sometimes you just need some good luck, like with starting a business.
Makes sense to me.
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I completely agree that evolution doesn't mean 'progress' or things getting 'better'. Nevertheless, there unarguably has been a trend in the direction of more COMPLEX life forms over the entire period of evolution of life on earth. Not saying that More Complex means Better. However, More Complex generally suggests More Sophisticated, which, in the popular imagination at least, is perceived as 'better'.
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But my point is that talking about the absolut 'functionality' of an organism isn't really productive or meaningful, at least not in terms of natural selection. Evolution by natural selection is a pretty good optimization technique in isolation, but an ecosystem is immensely complex, every element changing all the time (including not just climate, but every other species in proximity and even just incidentals of geography and configuration).
Natural selection is like a hill-climbing algorithm on the
But was it ever there? (Score:3, Insightful)
The big if in your statement is "If PND had existed" perhaps it never expressed in any species and so was never around to compete.
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From the article (in fact, it's right there in the summary):
Some scientists have suggested that PNAs or a very similar molecule may have formed the basis of an early kind of life at a time before proteins, DNA and RNA had evolved. Perhaps rather than creating novel life, artificial-life researchers will be re-creating our earliest ancestors.
Re:But was it ever there? (Score:5, Insightful)
I can conceive of a situation where such a molecule might actually be selected against. If the molecule were "too" stable and inhibited molecular evolution, it's quite possible that early life with essentially a "broken" system like RNA, which made events like transcription errors and insertions more likely, then it's quite possible that RNA could have won out over the technically "better" molecule simply out-evolving it.
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This could happen right now -- the AIDS virus has crappy reproductive fidelity. Reverse transcriptase does a lousy job of transcribing RNA to DNA so the offspring have lots of mistakes. It has a very much higher rate of mutation, as a result, than DNA transcription enzymes. So what you see is that DNA-based lifeforms evolve very slowly, and AIDS evolves very rapidly. If it managed to kill off all us humans you could (if you weren't dead) make the case that RNA is "better than" DNA because we all died.
Th
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If it managed to kill off all us humans you could (if you weren't dead) make the case that RNA is "better than" DNA because we all died.
A virus that kills the host is a poor virus. The ideal is to multiply and spread. A dead body can't make new virus particles, and it can't move around and spread the virus.
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Depends on the virus. There's some interesting research done on this. If the host is the target system for the virus (as in the AIDS virus) it wants the host to live as long as possible, with as little incapacitation as possible, to spread as widely as possible. This is also the route seen with colds and influenza. If the host is just a stepping stone along the viral pathway, it doesn't care, and sometimes will even benefit from the host being as sick as possible for as long as possible, as seen in eg y
Fixation (Score:1)
The choice between left- and right- handed amino acids was one such decision that was fixed by the system freezing into using one handedness over the other.
A slight difference in the proportion of DNA:PNA could have been amplified by feedback until only one survived.
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Evolution isnt a thinking thing capable of measuring... anything. Its a process that just happens. "It" doesnt care if a species succeeds or fails.... and lots of different species have failed horribly. If evolution was really some sort of progressive force, than less species would die out, as it goes right now, many more species have failed than succeeded.
And terms such as "better" doesnt really do much good. Cockroaches will probably outlive humans. Are they "better" or more "evolved" than human beings? T
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Wow. Its really been a long time since I've seen someone be so completely wrong on the internet. You really must be one of these scientiffic materialists that missed the boat.
Its encoded right into the whole idea of natural selection that the "fittest survive". Or rather that when selection pressures act on a specific biological group, the members of that group which are most able to survive the selection pressure, continue on to reproduce. Of course the trick is that a good set of DNA gets better and bette
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> don't apply human rationality to evolutionary processes
Mwaha, thanks to the theory of manifolds we can declare human thought to be a space and form the conclusions we make to be invariant of said space. Thusly [sic] we can anthropomorphize anything and make valid conclusions based on the difference.
Yes, I've been reading Wikipedia. [Citation needed] Can you tell?
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All the species on earth are consistently co-evolving (in genetic and/or cultural dimensions) in such a way that comparing modern homo sapien to neanderthal in terms of 'better' or 'progress' or 'improvement' does lose its meaning. I think it's pretty safe to say that complexity of organisms tends t
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you did when you were wondering how PNA could have existed if it wasnt the "best".
Do not forget that time frame is everything. just because PNA didnt survive does not mean that it was less efficient period full stop end of story. All it means is that it may have been less efficient for the pressures of that period in time
We like to think of ourselves as "advanced" creatures. Think how well OUR genes would have done if we had arisen in say...the middle of an Ice age.
No trees, no tools, no sticks, tiger food.
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So, to say that PNA functions "as well as or better than" DNA or RNA, full stop, end of story, is nonsense. Thanks. Exactly what I was driving at.
Technically, our genes did arise during an ice age, which started 2.6 million years ago and is still ongoing. We survived the last glacial period perfectly fine, as well; plenty of species did not. In fact, I would say that homo sapiens sapiens is very well equipped to survive glacial periods, and to claim that there would be no sticks around is silly.
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Re:Er. (Score:5, Interesting)
PNA might function better than DNA/RNA, but its cost (resources, time to create) is higher and couldn't be afforded by the first organisms.
By your logic humans who wouldn't survive a nuclear war are less efficient than roaches that would survive it.
Just, roaches will never start a nuclear war in the first place.
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Absolutely. Roaches are awesome, and may very well beat us at life. On the other hand, roaches will never get off this rock without hitch-hiking, whereas we might. The game isn't over yet.
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Which is better (from a selfish point of view)?
If your goal is to get off this rock quick, why wait until you've evolved and amassed enough science and tech to go into space (tanking the economy in the process) when you can just hitch a ride?
Earth-born bacteria that hitchhiked along with Mars rovers Spirit and Opportunity possibly are now living on Mars. We (humans) are not.
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which proves their superiority *bah da bum!*
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It is entirely possible that there are much more efficient ways for life to exist or function, but are different than the way life happened to happen here on earth. Or it could be that life DID happen that way but the methodology was not optimal for the environment at the time so the DNA/RNA based forms outlived them.
Or that it simply hasn't come to that point in our evolution. Why assume that the human genome is at its peak?
Re:Er. (Score:5, Insightful)
Where did I assume that? What i'm saying is there IS no way to define a peak, since its variable dependant on the time frame and environmental pressures as to what is considered "optimal".
Also (Score:2, Insightful)
So what's 'better' about PNR? Well, what immediately springs to mind is that it'd be similar to amino acids. And for life, amino acids and proteins are necessary. PNR could be considered 'more primitive' in the sense that it'd be more minimal - it could reuse a lot of the chemical pathways that would need to exist for amino acids.
What's 'worse' about it? I don'
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was not optimal for the environment at the time
Into account, that is already taken
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For all intents and purposes evolution has done this. The DNA on your chromosomes are PACKED with proteins running all along the major groove of the DNA, just like in this "triple-helix".
The difference here is that this version is simple and pure - a continuous protein helix intertwined within the DNA's double helix. In your own body the protein component consists of smaller parts that are highly dynamic, constantly jumping on and off.
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So why not dump a whole lot of this newfangled triple helix stuff in the environment and wait a few billion years? Let's see who's the winner then! Will it be DNA or PNA? SMS your prediction to 999-HELIX and win a spaceship!
PNA Too stable? (Score:5, Interesting)
Perhaps PNA is too stable, so that life forms based on it couldn't evolve through mutations quickly enough to adapt to changes.
Re:PNA Too stable? (Score:5, Insightful)
An excellent point; possibly the same reason why we're stuck with bodies which break down far too quickly -- an immortal organism simply wouldn't evolve.
Re:PNA Too stable? (Score:5, Funny)
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"Who wants to live forever?"
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Freddy Mercury?
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Nwabudike Morgan?
(but even 500 years would be nice)
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> If you're immortal, but you have lots of offspring who spread out (so they don't compete for resources with the immortal parents), and mutations happen at mitosis, you could have an immortal, evolving species.
Not really. We humans also have mutations at mitosis. Mutations in your body: most of the time nothing bad happens, sometimes the cell dies, sometimes cancer happens, and only very rarely do you grow an extra organ that makes beer come out of your nipples.
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The problem isn't just mutation but also crossover events and other more common ways to "mix and match" genetics, a more stable backbone would decrease the chance of that happening.
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Perhaps in the post-apocalyptic radioactive earth, when the rate of mutation will skyrocket, PNA, or another stable genetic molecule, will emerge as the dominant genetic molecule.
Of course, it would first emerge in bacteria, but perhaps over millions of ye
Re:Er. (Score:5, Insightful)
Possibly because evolution requires a molecule that is not too stable.
I'm just speculating here... the basis of evolution is random changes in DNA which result in a phenotype which may confer an advantage to one individual over another. If you have an absolutely error-proof system of DNA replication, you effectively limit evolution. But you don't want too many changes at one time, which would actually be detrimental. The ideal balance is somewhere in between... and it may be that a DNA double-helix with a sugar backbone is the ideal molecule for allowing just the right frequency of random changes for evolution to progress.
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Re:Er. (Score:5, Insightful)
"A synthetic molecule called peptide nucleic acid (PNA) combines the information-storage properties of DNA with the chemical stability of a proteinlike backbone."
I see two possible reasons PNA was not selected.
First, as others have said, it's stable. Evolution requires a bit of mutation to move forward. Out of a billion mistakes, maybe 1(or less) will cause an organism to be more 'fit.' So, you have a balancing act between errors and fitness, where too many errors reduce an organisms fitness and two few reduce it's adaptability.
Second, the protien backbone is possibly biologically expensive. There are many who believe advances in human intellegence is linked very closely with the availability of massive amounts of protein provided by cooking our food. So, the availability and neccesity of protein could be limiting factors in evolution. So any process which provides the same function with significantly less biological cost, even if slightly inferior in other ways, may be selected.
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Assuming the protein = intelligence theory to be true, then wouldn't a child raised in a vegan household have a lower intelligence than a child who grew up on, say, a ranch, where red meat was the primary food source?
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Except there are plenty of vegan foods that contain protein.
Here's the first google result for searching "vegan protein":
http://www.vrg.org/nutrition/protein.htm [vrg.org]
Also, IANAV, but I did know that meat was not the only source of protein.
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DNA's relative malabillity
eg its vulnerablities to mutations caused by external situations
was what made it that evolutionary and easier to work with
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I disagree, we already have PNA - protein + DNA. The protein component is just more complex than a simple helix running parallel to the DNA, instead it functions to regulate the DNA.
http://bioweb.wku.edu/courses/biol566/Images/NucleosomeF09-30A.JPG [wku.edu]
Good (Score:2, Interesting)
Re:Good (Score:5, Funny)
Yeah sugar-phosphate is just too scary. Lets create life based on stuff we aren't made of like lead and mercury.
Triple helix... finally (Score:3, Funny)
This will be how science finally gets us to 6-asses. I am pre-ordering my 6-assed monkey right now.
But will this really be an improvement? I don't even want to think about how many razor blades will be needed to shave all those asses. They'll probably have to come out with a 12-bladed disposable razor or something...
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Binding Affinity (Score:5, Informative)
IIRC, PNA had one outstanding feature: It binds to a complementary DNA strand much stronger than DNA itself (due in part to the lack of repulsion in the protein backbone. DNA's phosphate backbone is negatively charged).
Sadly, this means that two stands of PNA will bind extremely strongly to each other, and the forces required to unpair (part of the replication process) them would require different, "stronger" enzymes - so no chance of cell division, and no chance of life. (Still sounds cool though!)
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I don't have much of a biology background but what you say makes sense. If the chemical bonds are stronger in PNA then you have to have other higher energy state free radicals floating about to break them apart which would likely be ractive with other chemical structures in cells that are not reactive chemically with the enzymes that unzip DNA. You might have a more stable "code of life" with PNA but It might not lend itself to the complexities of a eukarotic cell.
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I think it would be better for making immortal beings. Except they can't heal themselves.
See: a life-based computer that is like a brain.
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I am not a bio-engineer and I'm only partially good at skydiving analogies, but I had wondered how plans for using bio-computers would function. I get how they have been using cells with inputs to control things experimentally, but if you want to use biology based memory storage there must be some way to control what is being stored. Again, might be talking out of an orifice, but wouldn't something like this lead to methods of storing bits?
Even if you could only store 256Kb per cell, that's still a lot of i
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Queue prediction of Google moving into biotech.
I just hope that Bio-Google won't turn into grey goo-gle.
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http://www.biogoogle.com/search?q=life+the+universe+and+everything [biogoogle.com]
Results 1-10 of 1.7E39 strands of PNA (1.41912E17 seconds)
Tip: Search BioGoogle in Vogonic
42 [wikipedia.org] ...
Re:Binding Affinity (Score:4, Interesting)
That is, do DNA-based cells exposed to PNA stop being able to reproduce themselves? (DNA unzips, PNA wiggles in and binds, everything shuts down)
Re:Binding Affinity (Score:4, Informative)
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Wasn't this part of a movie plot? (Score:2, Funny)
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Re:Wasn't this part of a movie plot? (Score:5, Insightful)
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God bless science.
Does It Self Correct (Score:2)
As all science-accepting persons knew, when you accept Evolution by Natural Selection as the means of development of intelligent life, it up until now has required some faith because of the impression of 500,000 monkeys pounding away on typewriters, writing:
"To be or not to be, that is the ka;lija;kja"
As believers in the accumulation of complexity, we knew we were missing something. Recently, that missing piece became apparent in a behavior of certain cancers that would attack a human and then, almost mirac
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rifers trilogy? (Score:2)
kinda reminds me of the writings from this guy:
http://en.wikipedia.org/wiki/Peter_watts [wikipedia.org]
Threshold protocol activated (Score:3, Funny)
Way better than fast food? (Score:1, Funny)
So they're using Wendy's Hamburgers for this? Sounds delicious
what could possible go wrong (Score:2, Interesting)
This deserves a "whatcouldpossiblygowrong" tag. They will end up developing some horrible new superbug that will kill us all or create some other horrible disease, or mess something up. When dealing with these sorts of things there are unintended consequences and the results can be disasterous. Manipulating genetics is far too dangerous in my opinion, especially since organisms self reproduce. We could end up contaminating our food supply or unleashing mutants that invade the world. It has already been show
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5th Element? (Score:1)
Species 8472 called (Score:1)
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I, for one, welcome our new fluidic space-dwelling overlords [memory-alpha.org]!
Poor choice of naming (Score:2)
Don't worry ... (Score:2)
Can't see the forest for the trees (Score:2)
DNA's greatest advantage is its LACK of stability, which allows it to mutate and create all the diversity we have on the planet now. OK engineering a more stable form of genetic material may be cool, but that wouldn't necessarily make it a better/more successful life form. In fact, quite the opposite.
as always (Score:2)
Counterargument (Score:2)
Have you watched any "reality TV?"
Cheers,
Dave