Life origins problem

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Paranoid__Android
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Life origins problem

Postby Paranoid__Android » Wed Jan 25, 2012 5:14 pm UTC

I know this topic has been discussed before but this is a differnet angle on it that is concerning me. I was reading an article about RNA and how strands have been fabricated that can duplicate other RNA molucules, thus giving credability to the hypothesis that life originated from RNA moluclues (maybe forming in undersea vents, primeval soup ect.).
However the RNA molucule fabricated was 198 bases long. So for this to form randomly 198 bases would have to randomly assemble themselves in the right order.
Now this molucule wont even replicate itself, I'm assuming that one that could hypothetically do this would need to be longer and not shorter.

Now this is my resoning, please correct me if you think an estimate is wrong or my maths is faulty.
For 198 bases to randomly assemble (by randomly adding a base to the end of a chain) from an abundant supply of the 4 constituent bases you'd have a (1/4)^198 = 1 / 6.2x10^120 chance of getting the correct outcome. (is this right?)

Now say on earth we have a site that has an abundance of those 4 bases per every square dm 10cmx10cm (this sounds high to me, but I guess in areas where there are good conditions [such as an undersea vent] would have a much higher concentration) and each one adds a base to whatever chain it is working on every tenth of a second. Leading to 4 x pi x radius of earth^2 == 4 x pi x 6400 000 0dm^2= 5.14x10^16 possible sites.

Molecular life is said to have formed within ~500 million years of the crust solidifying and oceans forming on earth. 500 million years is 1.55 x 10^16 seconds which leads to 1.55x10^17 attempts at a suitable RNA strand at every site.
This means that over the 500 million years there are 1.55x10^17 x 5.14x10^16 = 7.97 x 10^33 trials to get the right combination. This falls FAR FAR short of the 6.2x10^-120 chance of getting the right result.

Surely these probabilities mean life forming through this method or other similar methods is pretty much statistically impossible.
Does this mean life must have come from outer space?

Edit: surface area of a sphere is not 4pi x r :/
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Re: Life origins problem

Postby LaserGuy » Wed Jan 25, 2012 5:47 pm UTC

Paranoid__Android wrote:Now this is my resoning, please correct me if you think an estimate is wrong or my maths is faulty.
For 198 bases to randomly assemble (by randomly adding a base to the end of a chain) from an abundant supply of the 4 constituent bases you'd have a (1/4)^198 = 1 / 6.2x10^120 chance of getting the correct outcome. (is this right?)


There is no reason to believe that there is only one combination that is correct. DNA strands can have very substantial differences and still be able to replicate just fine, so it is likely that there are many possible combinations of bases that all produce a replicating molecule. There is also no reason to believe that there are only four bases that actually work--indeed, we know this is not the case. RNA and DNA only have 3 bases in common, but RNA uses uracil whereas DNA uses thymine for the fourth. It seems plausible that there was a period where five bases were used in order to transition from one to the other. Finally, we don't know for certain that 198 bases is the minimum required number. It's just one we've found that works.

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Re: Life origins problem

Postby thoughtfully » Wed Jan 25, 2012 6:02 pm UTC

Your analysis is also subject to the same problems as the Drake equation, which tries to estimate the abundance of intelligent life in the galaxy. It depends on a number of parameters that are simply impossible to determine to useful precision. Pulling plausible values out of various dark orifices can result in plausible results that vary by many, many orders of magnitude, and is little better than speculation.
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Re: Life origins problem

Postby Paranoid__Android » Wed Jan 25, 2012 6:21 pm UTC

Thanks for the correction on the number of bases.

There will only be a finite number of ways to construct an RNA molucule that will self replicate (which is below a reasonable number of bases). say there were ~10 000 different ways of constructing a self replicating RNA molucule. This would mean the probability of getting any one of them randomly is the probablility of getting one of them randomly, multiplied by the number of differnet ways. in this case 10 000. This is a big number but it still leaves the probablility well below the amount of trials that are being done. It would only reduce the probability by four orders of magnitude.

And you are right in saying that 198 isn't a theoretical minimum but surely the process of self replication is fairly complicated and so a strand would have to be quite long to complete that process. even if a way was found that was somehow only 100 bases long it would still produce a probability of (1/3)100 = 1.94 x 10^-48 which is still many orders of magnitude below what I predicted.


@thoughtfully
The drake equation has 7 diffenrent variables, I've only guessed at the number of sites and the rate at which a molucule is added to the chain. The first one is a guess, but I think it's a guess in favor of the current theorys, and I'm sure a genticist could give me a better approximation to the second one. Even if I were many orders of magnitude out in my predictions, the probability of a random correct assembly is still so many more orders of magnitude more unlikely, if that makes sense.
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Re: Life origins problem

Postby LaserGuy » Wed Jan 25, 2012 6:47 pm UTC

Paranoid__Android wrote:Thanks for the correction on the number of bases.

There will only be a finite number of ways to construct an RNA molucule that will self replicate (which is below a reasonable number of bases). say there were ~10 000 different ways of constructing a self replicating RNA molucule. This would mean the probability of getting any one of them randomly is the probablility of getting one of them randomly, multiplied by the number of differnet ways. in this case 10 000. This is a big number but it still leaves the probablility well below the amount of trials that are being done.

And you are right in saying that 198 isn't a theoretical minimum but surely the process of self replication is fairly complicated and so a strand would have to be quite long to complete that process. even if a way was found that was somehow only 100 bases long it would still produce a probability of (1/3)100 = 1.94 x 10^-48 which is still many orders of magnitude below what I predicted.


Sure, but you're just picking 10000 out of thin air. If we say that, I don't know, 1 billionth of a billionth of the combinations work, then using your same calculation, we end up with life happening spontaneously pretty much all the time, everywhere on Earth. What you choose for this number has an absolutely massive impact on how your calculation falls out, and we have virtually zero information on it.

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Re: Life origins problem

Postby Gigano » Wed Jan 25, 2012 6:55 pm UTC

Your calculations are likely to be worthless because you make the fatal and unsupported assumption that RNA molecules assemble 'randomly'. They don't, period. Because RNA is single stranded it can, much like a protein, fold in on itself. Ribosomes do this for instance: they are basically folded RNA with some proteins. And because single stranded RNA is inherently unstable, there is a natural tendency for stable folded RNA structures to survive for longer periods of time. Some sequences of RNA allow for a more stable macro-structure than other sequences, much the same goes for proteins.

In case you are wondering how mRNA in living organisms today is able to remain stable enough to allow for translation: mRNA has several key structures countering instability such as a poly-adenine tail (which attracts stabilising proteins) and a 5'-cap.
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Re: Life origins problem

Postby LaserGuy » Wed Jan 25, 2012 7:03 pm UTC

I think I'm going to add this because I think it summarizes the problem nicely. Spoiled a section of this article for brevity.

Spoiler:
So let's play the creationist game and look at forming a peptide by random addition of amino acids. This certainly is not the way peptides formed on the early Earth, but it will be instructive.

I will use as an example the "self-replicating" peptide from the Ghadiri group mentioned above [7]. I could use other examples, such as the hexanucleotide self-replicator [10], the SunY self-replicator [24] or the RNA polymerase described by the Eckland group [12], but for historical continuity with creationist claims a small peptide is ideal. This peptide is 32 amino acids long with a sequence of RMKQLEEKVYELLSKVACLEYEVARLKKVGE and is an enzyme, a peptide ligase that makes a copy of itself from two 16 amino acid long subunits. It is also of a size and composition that is ideally suited to be formed by abiotic peptide synthesis. The fact that it is a self replicator is an added irony.

[...]

The probability of generating this in successive random trials is (1/20)^32 or 1 chance in 4.29 x 10^40. This is much, much more probable than the 1 in 2.04 x 10^390 of the standard creationist "generating carboxypeptidase by chance" scenario, but still seems absurdly low.

[...]

1 chance in 4.29 x 10^40 is still orgulously, gobsmackingly unlikely; it's hard to cope with this number. Even with the argument above (you could get it on your very first trial) most people would say "surely it would still take more time than the Earth existed to make this replicator by random methods". Not really; in the above examples we were examining sequential trials, as if there was only one protein/DNA/proto-replicator being assembled per trial. In fact there would be billions of simultaneous trials as the billions of building block molecules interacted in the oceans, or on the thousands of kilometers of shorelines that could provide catalytic surfaces or templates [2,15].

[...]

So, if on our prebiotic earth we have a billion peptides growing simultaneously, that reduces the time taken to generate our replicator significantly.

Okay, you are looking at that number again, 1 chance in 4.29 x 10^40, that's a big number, and although a billion starting molecules is a lot of molecules, could we ever get enough molecules to randomly assemble our first replicator in under half a billion years?

Yes, one kilogram of the amino acid arginine has 2.85 x 10^24 molecules in it (that's well over a billion billion); a tonne of arginine has 2.85 x 10^27 molecules. If you took a semi-trailer load of each amino acid and dumped it into a medium size lake, you would have enough molecules to generate our particular replicator in a few tens of years, given that you can make 55 amino acid long proteins in 1 to 2 weeks [14,16].

So how does this shape up with the prebiotic Earth? On the early Earth it is likely that the ocean had a volume of 1 x 10^24 litres. Given an amino acid concentration of 1 x 10-6 M (a moderately dilute soup, see Chyba and Sagan 1992 [23]), then there are roughly 1 x 10^50 potential starting chains, so that a fair number of efficent peptide ligases (about 1 x 10^31) could be produced in a under a year, let alone a million years. The synthesis of primitive self-replicators could happen relatively rapidly, even given a probability of 1 chance in 4.29 x 10^40 (and remember, our replicator could be synthesized on the very first trial).

Assume that it takes a week to generate a sequence [14,16]. Then the Ghadiri ligase could be generated in one week, and any cytochrome C sequence could be generated in a bit over a million years (along with about half of all possible 101 peptide sequences, a large proportion of which will be functional proteins of some sort).

Although I have used the Ghadiri ligase as an example, as I mentioned above the same calculations can be performed for the SunY self replicator, or the Ekland RNA polymerase. I leave this as an exercise for the reader, but the general conclusion (you can make scads of the things in a short time) is the same for these oligonucleotides.



tl;dr: If you dumped a truckload of raw materials into a medium-sized lake, you could expect to form a replicator, purely by chance, within a couple of years.

[edit]Fixed some carrots.

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Re: Life origins problem

Postby Paranoid__Android » Wed Jan 25, 2012 7:14 pm UTC

LaserGuy wrote:Sure, but you're just picking 10000 out of thin air. If we say that, I don't know, 1 billionth of a billionth of the combinations work, then using your same calculation, we end up with life happening spontaneously pretty much all the time, everywhere on Earth. What you choose for this number has an absolutely massive impact on how your calculation falls out, and we have virtually zero information on it.


Surely consideing geneticists have been working on this for decades and haven't thought up a single RNA strand that can self replicate, with the advantage of reverse engineering, there cant be that many ways of doing it.

@Gigano
Surely even if an RNA structure survives for longer, the next base that gets added to it is still a random one. Even if you had stable bases knocking around, they wouldn't have the code to self replicate. Maybe my calculations are wrong but I'm not convinced it's a worthless line of thinking.

Edit: ninjad
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Re: Life origins problem

Postby mfb » Wed Jan 25, 2012 7:28 pm UTC

Paranoid__Android wrote:
LaserGuy wrote:Sure, but you're just picking 10000 out of thin air. If we say that, I don't know, 1 billionth of a billionth of the combinations work, then using your same calculation, we end up with life happening spontaneously pretty much all the time, everywhere on Earth. What you choose for this number has an absolutely massive impact on how your calculation falls out, and we have virtually zero information on it.


Surely consideing geneticists have been working on this for decades and haven't thought up a single RNA strand that can self replicate, with the advantage of reverse engineering, there cant be that many ways of doing it.

They did not have the sterile medium-sized lake (nor the possibility to analyze the complete lake afterwards), or the possibility to perform 10^whatever tests in the lab. Even if there are 10^20 self-replicating RNA parts: If they are in 10^50 possible strings, you have a hard time to find one of these. And they are not randomly located in the space of possible combinations - they tend to clump around a few "good" strings, where the exchange of some bases does not break the functionality.

The numbers are just made up, of course.

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Re: Life origins problem

Postby Gigano » Wed Jan 25, 2012 8:02 pm UTC

Paranoid__Android wrote:Surely even if an RNA structure survives for longer, the next base that gets added to it is still a random one. Even if you had stable bases knocking around, they wouldn't have the code to self replicate. Maybe my calculations are wrong but I'm not convinced it's a worthless line of thinking.


That is assuming bases are even added to the RNA sequence, which does not have to be necessarily. If they add little to nothing to the stability of the total structure they may last, if not then they don't last. Natural selection on a biochemical level.

It becomes a whole different story when the stability of the RNA molecules becomes less and less important, but rather the complementary DNA sequence that it mimics (i.e. protein coding) becomes the essential role for RNA. Then you get a selection for RNA sequences that are complementary to the codons on tRNAs bound to particular amino acids to form subsequent peptides. But that is an entirely different story.

Also, you are (I think) forgetting that RNA (and DNA) are their own code for self-replication. All you need is the complementary nucleotide for each of the bases (adenine & uracil, guanine & cyotsine). For this annealing to occur all you need is a low enough temperature to allow the formation of hydrogen bonds and a ligation reaction to join the basepairs of the new strand to each other at the 3' and 5' ends. Though single strandedness is often cited as one of the three major differences between RNA and DNA*, double stranded RNA does exist. It is found in most cells and even solely encompasses the genome of viruses. Increase the temperature and you will melt the double stranded into two complementary strands.

Though thinking about the origins of RNA being the 'first' self-replicator is worthwhile, spending time on 'random assembly calculations' is not worth your time, especially when it comes to biology where everything is a little bit less exact than in the other sciences.

Finally, you seem to imply that the stability of RNA relies on the bases themselves. This is not quite true, rather the stability depends upon the overall structure and phosphate bonds in-between riboses. Nucleotides are quite stable, linking them up into a chain isn't really, unless you make them for example into a double helix.

*The major three difference between RNA and DNA are:
1) RNA has ribose instead deoxyribose
2) RNA has uracil instead of thymine
3) RNA is single stranded
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Re: Life origins problem

Postby thoughtfully » Wed Jan 25, 2012 8:15 pm UTC

Another factor is that random processes often aren't. It can be helpful to model them as random, but whether or not that works depends on the particulars. Some factors might be shorter chains of bases being more stable than long ones, and interactions among chains (or between chains and other environmental factors) that might break up some participants more favorably than others.
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Re: Life origins problem

Postby Izawwlgood » Wed Jan 25, 2012 8:20 pm UTC

SciAm had an article a while back how different abiotic substrates could contribute to the favorable formation of different portions of life precursors. My guess is base addition isn't random due to abiotic processes alone, let alone the formation of microenvironments from eventual vesicle formation (and hell, from other 'stuff').
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Re: Life origins problem

Postby Paranoid__Android » Wed Jan 25, 2012 8:32 pm UTC

I can't really discount these points, they all seem fair and scientific. I stand corrected.

Yes, one kilogram of the amino acid arginine has 2.85 x 10^24 molecules in it (that's well over a billion billion); a tonne of arginine has 2.85 x 10^27 molecules. If you took a semi-trailer load of each amino acid and dumped it into a medium size lake, you would have enough molecules to generate our particular replicator in a few tens of years, given that you can make 55 amino acid long proteins in 1 to 2 weeks

I think it would be an interesting test to the theory to get a swimming pool of raw materials (not bother with the lake to increace the concentration), and see if after a few years or so there are any self replicating chains. It wouldn't be too hard to find them either as once you get one it would start an irriversable chain reaction of replications.
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Re: Life origins problem

Postby drash » Wed Jan 25, 2012 8:56 pm UTC

I ran in to a more formal treatment of this problem a little while ago, called Eigen's Paradox: http://en.wikipedia.org/wiki/Error_thre ... 7s_Paradox Good job catching it quasi-independently!

If we imagine an RNA world in which there are chains of some fifty nucleotides, we can arrive at a functional system. The RNA will replicate itself by base-pairings, folding in to more or less predictable patterns based on the arbtrary sequence; selection will favor certain molecular phenotypes based on pH or something, and off we go to an exciting world of RNA as an information-carrier.

But, these molecules cannot exceed a certain length, because they use only the simplest of reproductive methods. If there's a 1% chance of a given base pair mismatching, there's a good chance of fidelity in short chains, and almost none once you exceed three digits. Modern biology has a way around this, of course- enzymes, which are themselves many thousands of base pars long. In other words, the self-replicating capacities of RNA aren't enough to jump-start the system to the level of coded enzymatic reaction.

So, obviously, JEEEESUUUUSSSS. Or possibly just energetically unfavored proteins/adhesion to mineral surfaces.

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Re: Life origins problem

Postby Gigano » Wed Jan 25, 2012 8:59 pm UTC

Paranoid__Android wrote:I think it would be an interesting test to the theory to get a swimming pool of raw materials (not bother with the lake to increace the concentration), and see if after a few years or so there are any self replicating chains. It wouldn't be too hard to find them either as once you get one it would start an irriversable chain reaction of replications.


I think this already being done on very small scales, but a larger experiment also attracts my attention. It would be very hard though to prevent contamination with the outside world. Also the results in the pool offer no guarantee that what happens in there is able to happen in actual nature.
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Re: Life origins problem

Postby Angua » Wed Jan 25, 2012 10:19 pm UTC

Just one thing - you don't necessarily need the RNA to be self-replicating, it can be enough for it to make more RNA (and not necessarily make the same thing each time) which would be enough to speed up the process until you get RNA that is able to take on other roles.

edit: I've got a headache so can't be bothered to go through my notes from last year on the different theories of how life started. The RNA world is definitely in vogue at the moment though. Maybe tomorrow, if I remember/have time.
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Re: Life origins problem

Postby Scyrus » Wed Jan 25, 2012 10:27 pm UTC

Gigano wrote:I think this already being done on very small scales, but a larger experiment also attracts my attention. It would be very hard though to prevent contamination with the outside world. Also the results in the pool offer no guarantee that what happens in there is able to happen in actual nature.


Perhaps we can isolate the pool to avoid contamination?

Maybe we can even expand this experiment, why not mimic the most probable scenario for abiogenesis?
Like so:

Spoiler:
Image
Goals of:
Exp 1: Abiogenesis. Exp 2: Replicating RNA


This image is extremely inaccurate, but you get the point.
Experiment 1 would take a ridiculous amount of time to even show results, but how long would Experiment 2 take*?
*Assuming it was set up by a competent person knowledgeable in the field instead of a crackpot

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Re: Life origins problem

Postby yurell » Wed Jan 25, 2012 10:42 pm UTC

I found this interesting piece on youtube:

http://www.youtube.com/watch?v=U6QYDdgP9eg

Warning, though, I'm not a biochemist, or even an organic chemist, so I can't vet the vid as it were.
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Re: Life origins problem

Postby Gigano » Wed Jan 25, 2012 10:54 pm UTC

@Scyrus

I understand your idea on isolation, but maybe I should have been clearer. Your design, assuming it's feasible, will certainly prevent contamination during the experiment. But what about before, during the set-up? You will still need to construct the pool, inject chemicals and whatnot, all without any outside contaminant entering the system via construction workers or their suits & materials. With proper supervision and design a solution may be offered.
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Re: Life origins problem

Postby Scyrus » Wed Jan 25, 2012 11:13 pm UTC

Gigano wrote:@Scyrus

I understand your idea on isolation, but maybe I should have been clearer. Your design, assuming it's feasible, will certainly prevent contamination during the experiment. But what about before, during the set-up? You will still need to construct the pool, inject chemicals and whatnot, all without any outside contaminant entering the system via construction workers or their suits & materials. With proper supervision and design a solution may be offered.



No, I understood what you meant. I forgot to mention that the setup would be as sterile as possibly conceivable.
Construct a factory specifically for making highly sensitive and/or sterilized equipment. For example, build a box-like building that has absolutely no air vents and so forth. Build a series of airlock chambers that will serve as entrance and only contact between the inside and the outside of the factory. Use strong pumps to create a vacuum inside the entirety of the complex. And then, workers have to go inside with their own oxygen supply and could only work for a certain number of time before they would have to return for more oxygen. They would wear a suit completely covered so that they themselves couldn't contaminate the experiments and or equipment with microbes.

This factory would allow for the least possible contamination I can think of at the top of my head, perhaps one of you can work upon it to create something more useful.

I made another image to help explain:
Spoiler:
Image
You may ask: Whats the obsession with the vacuum? Its to prevent the flow of heat and or particles that are exotic to our controlled experiment, allowing for greater control over environmental conditions.


EDIT: This...vacuum lab idea may seem kind of pointless to some of you, but I can imagine it being useful for performing experiments that are highly sensitive to external forces.
Also, the lightsources within the structure would have to be regulated (angled? dimmed?) so they wouldn't interfere much in the experiments. You can create sterile environments for experiments or carry them in the vacuum lab right there.
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Re: Life origins problem

Postby Yakk » Wed Jan 25, 2012 11:16 pm UTC

Life is pervasive. Making a large swimming pool full of raw life food-stuff and completely excluding all life is going to be hard.

You'll want to build a amino-acid factory inside, seal the entire place, heat it up until no life could survive (note: this includes really primitive life, like prions), then manufacture the massive amount of amino acids in the pool and see what happens. Any leak in the containment will ruin the experiment, as will anything surviving the initial sterilization.

Oh, and we need to keep the environment relatively "nice" while still keeping it sealed (temperature, acidity, etc), as a sealed environment can quite often go off the rails.

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Note that what you describe above doesn't work. They tried to do this with interstellar space craft. The result was selecting for some microbes that could survive their sterilization procedures. Stick those microbes into a vat of nearly ideal life food, and guess what would happen?
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Re: Life origins problem

Postby Scyrus » Wed Jan 25, 2012 11:21 pm UTC

Well then, create sterilization procedures that are radical to the extreme. Eradicate all known possible forms of life and then build the vacuum lab thing.

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Re: Life origins problem

Postby yurell » Wed Jan 25, 2012 11:51 pm UTC

It is really hard.
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Re: Life origins problem

Postby Paranoid__Android » Wed Jan 25, 2012 11:58 pm UTC

An easier way around might be to split the experiment up into say 500 small containers. if any one gets contaminated it wont ruin the rest.
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Re: Life origins problem

Postby gmalivuk » Thu Jan 26, 2012 4:14 am UTC

Paranoid__Android wrote:
LaserGuy wrote:If we say that, I don't know, 1 billionth of a billionth of the combinations work, then using your same calculation, we end up with life happening spontaneously pretty much all the time, everywhere on Earth. What you choose for this number has an absolutely massive impact on how your calculation falls out, and we have virtually zero information on it.
Surely consideing geneticists have been working on this for decades and haven't thought up a single RNA strand that can self replicate, with the advantage of reverse engineering, there cant be that many ways of doing it.
Relatively speaking, sure. A billionth of a billionth isn't very many, after all.

But have we tried a billion billion different strands in those few decades? Because if not, why should we expect to have stumbled across one of that tiny fraction that work?
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Re: Life origins problem

Postby Ulc » Thu Jan 26, 2012 9:30 am UTC

Scyrus wrote:Well then, create sterilization procedures that are radical to the extreme. Eradicate all known possible forms of life and then build the vacuum lab thing.


I take it you have never worked in a lab where keeping things sterile is important? We're talking massive amounts of each of the 20 amino acids alone, together with a large amount of minerals and small compounds (I saw the term "truck load"!), manufacturing this is hard by itself, manufacturing it without getting contaminated by bacteria is pretty much impossible.

And you can't really sterilize it, since all methods of sterilization is invasive, and might introduce reactions and/or breakdown by itself. But lets say that you find a way to do this. Then you're faced with the problem of the swimming pool, it has to be built and then sterilized, and that's actually hard by itself, Basically you'd have to highly pressure the area, then boil the swimming pool for several hours to produce enough superheated steam to sterilize the rest of the closed environment, then cool it down again.

After these two factors you get into the problem of dumping the raw materials in. You can't use trucks. You can't bring it in by hand, and you most certainly have to sterilize everything (see invasive) before it goes in. The most likely approach would probably be to put this "impossible to manufacture" raw materials in small plastic bags (sterilized before use) of about 2 kg, then wash the plastic bags really well before going in with them (in sterilizing agents), then carrying it in by hand in a space suit. And hoping to god that going in and out 100k times doesn't see a single failure of sterilization

Yes, we can manufacture mostly sterile things (but keep in mind that even things like syrings are a "good enough" approach), but what is being proposed here involves a necessity of completely failure free sterilization, since you'd be dumping whatever got through into a vat of more or less ideal nutrients and leaving it for several tens of years.

The most common lab approach to sterilization is "good enough - lets throw some antibiotics into it as well", for good reasons too, keeping life out your experiments are a bit like kids out of the cookie jar - in the long run, utterly futile.

Edit: Something I forgot to mention:

Another problem with contamination is that the bacteria might not survive. This might seem like the ideal thing, but it really isn't. Because if it dies, the cell membrane breaks down, which leads to a lot of long chain RNA's being released into the mix, quite possible acting as a template for new RNA's, even if it isn't able to self-replicate.

Which leads to quality control. You need to know whether the above has happened, meaning you have to know if bacteria got in. So you have to scan several tons for material for single bacteria, something we can't do at the moment, and something that there's no reason to believe we'll ever be able to do. And even if we could, it's an extra step, meaning extra risk of contamination.
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Re: Life origins problem

Postby PM 2Ring » Thu Jan 26, 2012 12:34 pm UTC

Scyrus wrote:Well then, create sterilization procedures that are radical to the extreme. Eradicate all known possible forms of life and then build the vacuum lab thing.

Do it on the Moon.

:)

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Re: Life origins problem

Postby Fire Brns » Thu Jan 26, 2012 4:13 pm UTC

Assuming the initial assumtion with statistics: "it is statistically impossible for this process to occur".
(I am not going to considered the original modifications at this moment)

a)
statistical chance for life to form = x
planets required for (x≈1)=y; y=1/x
y-1≈z

z is the number of planets that failed to create life.

b)
Not every trial according to the math needed to occur for the RNA to form; It could have happened on the 2nd try or the 30th.
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Re: Life origins problem

Postby Izawwlgood » Thu Jan 26, 2012 4:19 pm UTC

PM 2Ring wrote:
Scyrus wrote:Well then, create sterilization procedures that are radical to the extreme. Eradicate all known possible forms of life and then build the vacuum lab thing.

Do it on the Moon.

:)

And select for every organism that can survive the trip. Well done!
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Re: Life origins problem

Postby Scyrus » Thu Jan 26, 2012 5:44 pm UTC

Forget human workers and oxygen, make the lab a closed system, with a handful of remotely controlled robots and a big quantity of all needed elements inside. Destroy all possible life within the lab. Take control of said robots and create everything needed to make the experiment, including making the nucleotides manually. :D

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Re: Life origins problem

Postby gmalivuk » Thu Jan 26, 2012 5:49 pm UTC

So the robots themselves are also made in hard vacuum by other robots? And those other robots: same thing again?
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Re: Life origins problem

Postby Scyrus » Thu Jan 26, 2012 5:51 pm UTC

Yes, its robots all the way down :)

But I reckon at some point nothing would survive such a hard process

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Re: Life origins problem

Postby Izawwlgood » Thu Jan 26, 2012 5:58 pm UTC

Scyrus wrote:Destroy all possible life within the lab.

What part of this is so difficult for you to understand; the above quoted part is not as easy as waving a wand over your stuff and chanting 'Destructo Viva!'
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Re: Life origins problem

Postby Scyrus » Thu Jan 26, 2012 6:15 pm UTC

Not easy? It's near impossible. You're taking it too seriously. Surely there must be a way for such an experiment to be possible, though, even if it's not by repeated sterilization processes. What would be more efficient than current methods? If this experiment were conceived, would it not bring useful knowledge about the early steps in the origin of life? I'm merely bouncing ideas, even if they're not great. I believe bouncing ideas with other people gets you to achieve new thoughts.

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Re: Life origins problem

Postby Izawwlgood » Thu Jan 26, 2012 6:29 pm UTC

Scyrus wrote:You're taking it too seriously.

The practical limitations of this experiment have been pointed out already. Saying 'sterilize it harder' isn't really an idea.

And the Miller Urey experiment already showed some of this. Trying to compute or create early RNA precursors would be neat, but would probably require more than what we're capable of. I think it'd be most interesting to, instead of allowing it to form randomly, setting up a screen of small RNA molecules, and seeing if any exhibit self-replicating or otherwise interesting properties. Sort of a reverse screen, instead of a forward screen. You could even start with known primitive replicators and go from there.

In fact, I wager it's already been done.
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Re: Life origins problem

Postby Scyrus » Thu Jan 26, 2012 6:39 pm UTC

And then study those that exhibit the replicating mechanism? But then you might miss many other combinations that would also potentially have the ability to replicate.
If we take the earlier goal of discovering the finite number of arrangements that allow for replication we could perform the original poster's calculations with much more accuracy and determine the probability of life having formed wherever.

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Re: Life origins problem

Postby Izawwlgood » Thu Jan 26, 2012 6:53 pm UTC

Doing the randomized experiment bigger doesn't solve that problem though, as it only selects for the easiest forming self replicator.

Out of curiosity, why do you think 'finding all the possible self replicators' is somehow more useful or interesting than 'demonstrating self replicators can spontaneously generate'?
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Re: Life origins problem

Postby Scyrus » Thu Jan 26, 2012 8:10 pm UTC

Finding just one self replicator by having them spontaneously generate already demonstrates their ability to spontaneously generate, so the hypothetical experiment I attempted earlier was capable of doing both, they aren't mutually exclusive.

As for it's importance, having all of them would give a greater degree of accuracy to any calculations involving the probability of life forming on Earth, which was initially the original topic. I was merely attempting to give a possible way of refining those same calculations so that, maybe, in the future, one could use the answers they provide to arrive at new conclusions, for example, if the probability of life forming on Earth were extremely small EVEN taking into account the time span, it could suggest an external factor, perhaps, or if it were ridiculously high it would bring the question as to whether similar life forms have developed on other Earth-like planets, and IF not, why?
Sure, its an extremely far fetched way of arriving at any useful conclusions, but it was my attempt at doing so by staying on topic. I apologize if it was extremely indirect and unorthodox.

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Re: Life origins problem

Postby Yakk » Thu Jan 26, 2012 8:14 pm UTC

So such a project (perfect sterilization of a huge clean room containing lots of biological building blocks), at our current level of technology, seems to be in the LHC level range. Theoretical physics has brought us the nuclear bomb and GPS. Maybe after WW3, where the winner uses bio weapons to defeat the enemy, theoretical biology will have as much cache, and it can demand huge projects like "the ultimate clean room" to find out how life started out, much as physics can ask for huge sums to figure out details on how the universe started out.
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Re: Life origins problem

Postby Izawwlgood » Thu Jan 26, 2012 8:16 pm UTC

Scyrus wrote:Finding just one self replicator by having them spontaneously generate already demonstrates their ability to spontaneously generate, so the hypothetical experiment I attempted earlier was capable of doing both, they aren't mutually exclusive.

Right, this is why I'm saying they should do a reverse screen. We know that RNA can spontaneously generate; throw a bunch of nucleotides in a vat in the right conditions, and they'll form chains. What remains to be demonstrated (I bet it's been worked on extensively actually) is what the smallest self-replicating chain is, and to what extent components of it are redundant. By showing that any given sequence is self-replicating, and has x% redundancy, you can calculate the probability of it's random formation. You don't need sterile swimming pools to do this.

Furthermore, the reason doing this experiment at Olympic scales is somewhat pointless, is processing. So you end up with a vat of randomized RNA oligomers, and a disproportionate chunk of them are the same, because that sequence is self-replicating. Yippie. You've just identified a self-replicating sequence. You have not identified ALL the potential sequences, merely the first to generate. By increasing the size of the experiment, all you do is increase the likelihood that the simplest self-replicator will generate; you do NOT increase the likelihood of finding new/novel/unique self-replicators, nor do you identify any other potential characteristics of those that do.

Which is, again, why doing a reverse screen is better than a forward screen.
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