Triple Helix — Designing a New Molecule of Life

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."

Comments

Er.

[Futile Rhetoric]

If PNA functions "as well or better", then what exactly was the reason that RNA and DNA evolved in the first place?

Re:Er.

[Adambomb]

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.

Re:Er.

[dfm3]

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.

Re:Er.

[Futile Rhetoric]

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.

[Adambomb]

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.

[Adambomb]

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".

Re:Er.

[BytePusher]

"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.

Re:Er.

[Kagura]

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."

Re:Er.

[Golddess]

Not quite true. It could be that it doesn't hurt it, but doesn't help it either, in which case there are no pressures for or against that trait, so it may or may not remain.

Re:Binding Affinity

[DarkOx]

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.

Re:PNA Too stable?

[Futile Rhetoric]

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.

Also

[MoellerPlesset2]

There's no such thing as a universal 'better'. What's better has all to do with circumstances, environment - It's the driving force of evolution.
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't know. One likely reason that comes to mind is that it may not be stable enough for long chains, and hence, more complex life. That's the case for RNA. And the RNA-to-DNA transition in nature wasn't an easy one for sure: It's an very energy-demanding reaction that requires radical-formation. (in fact, chemists didn't even think radical reactions occured in biological systems until a decade or two ago)

But was it ever there?

[pentalive]

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.

Re:But was it ever there?

[MightyMartian]

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.

Re:But was it ever there?

[smellsofbikes]

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.

There's a balance point for information stored genetically. If you store a lot of information, you can handle more situations, but reproduce more slowly because your cells take longer to divide. If you pare down your genetics to the bare minimum you are very specialized and do extremely well in precisely one environment, and get outcompeted in any other. Likewise, if you have high-fidelity genetic reproduction, a group of animals with that ancestry will continue to do very well in a fixed environment, but if the environment is changing a lot, lower-fidelity genetic reproduction allows for faster adaption at the cost of individual success, because the vast majority of mutations will be detrimental or deadly to the individuals. But as a group, they'll do better. That's what the AIDS virus does: as a group, they evade our immune system, even though individually they die in large numbers.

Re:Wasn't this part of a movie plot?

[game kid]

They want to make a redheaded punk-haired girl, so it's a noble cause. ;)

Re:PNA Too stable?

[matt4077]

Unlikely... Given the hoops the cell jumps through to keep DNA somewhat stable, it would have to be quite a few orders of magnitude more stable to be below the current rate of mutations that survive the different repair mechanisms.