[[BTW, I am still waiting for someone to provide me with the number of autocatalytic RNA sequences of length 218 or less. You claim that only a special sequence of 20 nucleotides is needed somewhere along the 218 nucleotide stretch. In which case why didn’t Spiegelman just simply snip out that 20 nucleotide sequence and create a Spiegelman monster of length 20? There is no mention in the literature of a Spiegelman monster of length 20.]]

Probably because he doesn’t know which are crucial and which aren’t. It’s not that easy to tell, you know.

According to Futuyma (1982), they got RNA sequences as short as seven (7) nucleotide residues to replicate.

I agree with you, frankly, that the first replicator doesn’t have to be RNA, even on Earth. But that’s as true for standard theories of abiogenesis as it is for Kaufman’s theory. I wrote a paper about that in the ’80s. It wasn’t peer-reviewed, and so doesn’t count as an authoritative source, but it shows that you can believe in multiple possible early replicators without embracing Kaufman’s theory:

http://members.aol.com/bpl1960/Combo.htm

[[Thus, the probability that the Spiegelman sequence could have been hit on by chance at any time during the earth’s history is 4.5 billion divided by 10^82 or 1 in 10^73. So either we are incredibly lucky to have found the Spiegelman sequence or perhaps there is divine intervention needed. The odds get even worse if we consider that life was already going on earth by at least 3.5 billion years ago and probably even earlier.]]

You are assuming that only one combination out of 10^73 will work. What justification do you have for that assumption?

[[This is another prediction of Kauffman’s theory which is, if we ever find extraterrestrial life on Mars, Europa, Triton, or somewhere else it will not be based on RNA, DNA, or even the 20 or so amino acids making up earthly proteins.]]

I wouldn’t be surprised if the nucleic acids or their equivalent were not the same, but I would be very surprised if no amino acids were involved. We’ve found them in meteorites. There might be a handedness problem (50% of aliens will have dextro- rather than levulo-rotatory amino acids), but I expect every ET out there to use glycine and to be able to drink the stuff. (It’s sweet, I understand.)

O.K. So now you’re questioning the diversity of chemical species on the early earth. I guess only RNA could have existed. BTW, catalysis depends on the molecular shape and binding sites. If chemical species D has the right shape for catalysis of A + B –> C then it will catalyze that reaction. It’s not a conjecture. It’s a well known fact.

BTW, I am still waiting for someone to provide me with the number of autocatalytic RNA sequences of length 218 or less. You claim that only a special sequence of 20 nucleotides is needed somewhere along the 218 nucleotide stretch. In which case why didn’t Spiegelman just simply snip out that 20 nucleotide sequence and create a Spiegelman monster of length 20? There is no mention in the literature of a Spiegelman monster of length 20.

You also claim “RNA has this repeating and failover capacity”. What are you talking about? Are you claiming that repetition of some nucleotide, say UUUUU is a failover mechanism? If so please explain how it works.

That sounds like a lambasting cartoon I did on probability titled “Ask Mr. Ology: Probability.” In it, a rabbit character explains that if you have multiple pairs of pantyhose, the chance of all of them running simultaneously shrinks as you increase the number of pantyhose, until as you near zero probability of all of them running you start to run into the probability that they will spontaneously form a black hole. By the time you are infinitesimally close to a zero intercept for probability of all running, you are virtually certain to form a black hole (intercept 1).

Spurious and unscientific daydreaming, which is what the comic was meant to mock. Oddly enough, that is why your explanation seemed so familiar.

The probability of a molecule catalyzing a reaction is more based on a combination of probabilities of either chemical species existing in the first place – the assemblage becomes less and less likely despite conjecture that two of them will react somehow, as does the probability of being able to obtain the *n* number of pantyhose necessary to risk forming a black hole.

Not really. I think you’re not understanding the point. It’s really hard to explain this stuff without reading the book with all the diagrams but I’ll give it my best shot. There is no specific set of 6,000 molecules that form the autocatalytic set. The number 6,000 to 30,000,000 is so large because the probability that a random molecular species will catalyze a reaction is small. Let’s bump up this probability from something in the range 1 in 6,000 to 1 in 30,000,000 to something quite large, let’s say 0.1 so we can better see what happens.

So 0.1 is the probability that chemical species A catalyzes a chemical reaction X Y chosen at random. That means the probability that A does not catalyze reaction X Y is 0.9.

You add your first chemical species A chosen at random (all of the chemical species are chosen at random, there is no selection of any kind).

You add your second chemical species B.

You add your third chemical species C. Now there is a reaction that A can possibly catalyze, namely B C. The probability that it doesn’t is 0.9.

You add your fourth chemical species D. Now there are 3 reactions that A can catalyze, B C, B D, C D. The probability that A doesn’t catalyze any of them is 0.9^3 which is 0.729.

You add your fifth chemical species E resulting in 6 reactions: BC, BD, BE, CD, CE, DE. Probability that A doesn’t catalyze any of them is 0.9^6 = 0.53.

You add your sixth chemical species F resulting in 10 reactions: BC, BD, BE, BF, CD, CE, CF, DE, DF, EF. Probability that A doesn’t catalyze any of them is 0.9^10 = 0.35.

I think you can see where this is headed. So let’s just list the number of chemical species and the probability the A catalyzes none of them:

7 0.21
8 0.11
9 0.05
10 0.02
11 0.009
12 0.003
and so on.

So by the time you get to just 12 chemical species the chances that A catalyzes none of the other reactions is only 0.3 percent which means the chances that it catalyzes at least one of the reactions is 99.7 percent. The same probabilities apply to all the other chemical species. So by the 12th chemical species it is highly probable that each of the chemical species will catalyze at least one other reaction and an autocatalytic set has been formed. Life has begun.

I hope you can follow the example. At no time was there any “natural selection” of any chemical species. It does not have to be RNA, or DNA, or protein, or anything specific. Life originated spontaneously without any selection being necessary. One organic molecule is as good as another.

Now most critics don’t seem to have a problem with changes in selective pressures over an entire species, and so don’t have a problem with, for example, the peppered moth changing from generally speckled to generally black. But speciation is driven by splitting the population into two groups with no contact between them. Unfortunately, this isn’t illustrated in the video which heads this thread.

Perhaps someone might like to put their minds to creating such a simulation to explain this point better.

Why assume RNA? Because RNA has shown itself, through competition, to be the best example we currently have for a self-replicating molecule capable of complex inheritence and error tolerance. In biology, the leaps often occur when an otherwise sufficient organism has failover ability through repeated sequences: the failover allows the organism to function despite variation. Look at segmented worms, which in earthworms have six segments capable of pumping blood rather than one. One fails, the organism doesn’t die outright: failover capacity. RNA has this repeating and failover capacity: an arbitrary cocktail of 6000+ molecules does not.

So give me the number of RNA sequences of length up to 218 that are autocatalytic. Will all of them still be autocatalytic when you add nucleotides to them? In Kauffman’s theory no RNA is needed at all – the fact that earth life is based on RNA and DNA is a historical accident. It could have been based on some completely different organic molecule. That increases the chances of life arising spontaneously dramatically since no specific organic molecule is needed.

In all likelihood, the hairpin shape probably only takes maybe twenty nucleotides of an “exact” nature – and in that case, they just have to pair up to link properly (one of two rather than one of four). So the probability is more like 2^20 or 10^6.

Seriously, you seem to want to phrase abiogenesis as impossible, which is your right, but it’s not that scientific. You want the conclusion to be that it is impossible, and that Darwinian selection is flawed to being nonfunctional. You’ve already reached your conclusions, so I’m not sure why you want to work backwards to data. That’s like flying into an island city and then demanding a return ticket on the train to the mainland.

The range 6,165 to 34,000,000 is actually a range of 3.7 orders of magnitude. Let’s take the logarithmic average of 460,000 – let’s call it half a million just for simplicity sake. Why is this number so large compared to the autocatalytic RNA examples of Eigen and Spiegelman?

I had to refresh my memory by rereading sections of the book, but the answer appears to be that the number is large because it has to take into account the random chance of assembling an autocatalytic set. There is no hand assembly using an intelligent designer of either human or divine origin. All of this has to come about by random chance.

So essentially the minimum size of an autocatalytic set has to do with the probability that a random molecular species in the set catalyzes one of the reactions. So if we assume that the probability that a given molecular species catalyzes one of the reactions as one in a million, then it will take something close to a million of them to guarantee that each molecular species catalyzes at least one reaction. So as we increase the number of molecular species in the system at a certain point a critical threshold is reached where each molecular species catalyzes at least one reaction. The system turns on and life is born. Kauffman refers to this as a phase transition from non-life to life.

So sure, you can hand tailor RNA systems with far fewer components and make them work, but the chances of them arising naturally on earth is infinitesimal as I showed in my last post.

The great uncertainty in the range of numbers from 6,165 to 34,000,000 has to do with the great uncertainty in the probability that any given chemical species catalyzes another reaction. This depends on so many factors such as molecular shape, composition, and polarity that only approximate figures can be given.

Kauffman has several objections to the RNA world scenario on pages 39 to 43 of his book, but I won’t bore you with them here since I guess most of you consider him to be a crackpot or a pseudoscientist. I don’t know much about the Spiegelman Monster or other such autocatalytic RNA’s produced by others like Manfred Eigen, but from what I can gather this is a specific sequence of nucleotides, is it not? Will any chain of 218 nucleotides be autocatalytic or just this specific sequence?

Assuming that the answer is that it’s only this specific sequence that is autocatalytic, then my problem with it is its biological relevance. It actually seems to fit Behe’s concept of irreducible complexity in that it’s parts have been specifically fitted to its task which implies a designer, which of course there is, namely Spiegelman.

Let’s perform a little calculation to show you what I mean. Consider the Spiegelman monster as some specific sequence of nucleotides of length 218, say AGUUCAAACCC… Now what are the chances that it could have originated randomly during the history of our planet? There are 4 possible nucleotides (A – adenine, G – guanine, C – cytosine, and U – uracil). So the number of possible RNA molecules of length 218 is 4^218 = 10^131. Let’s assume that every cubic micron of the earth’s oceans is used to try a separate RNA sequence of length 218 every microsecond. How long would we expect from the formation of the earth until the Spiegelman sequence is found? Well, a little math here…

Volume of earth’s oceans (from Wikipedia) = 1.3 billion cubic kilometers = 1.3*10^18 cubic meters = 1.3*10^36 cubic microns. So every microsecond there are 1.3*10^36 trials of RNA molecules. That comes out to 1.3*10^42 trials per second or 4*10^49 trials per year. In order to go through all 10^131 possible sequences would take 10^82 years. Thus, the probability that the Spiegelman sequence could have been hit on by chance at any time during the earth’s history is 4.5 billion divided by 10^82 or 1 in 10^73. So either we are incredibly lucky to have found the Spiegelman sequence or perhaps there is divine intervention needed. The odds get even worse if we consider that life was already going on earth by at least 3.5 billion years ago and probably even earlier.

Compare this with Kaufman’s autocatalytic set theory. Kauffman imagines an early earth teaming with all sorts of chemical species. Over time more and more new chemical species are introduced into complex chemical reaction pathways. Eventually the complexity has increased to a point where an autocatalytic set forms among the millions or billions of chemical reactions that are occurring. Kauffman calls this a phase transition and it is as inevitable as the phase transition from ice to water during heating. Thus, the probability that life will form given enough diversity in the chemical species equals one. It does not depend on some specific molecule such as RNA or DNA. Any batch of organic molecules of sufficient diversity will eventually form an autocatalytic set. This is another prediction of Kauffman’s theory which is, if we ever find extraterrestrial life on Mars, Europa, Triton, or somewhere else it will not be based on RNA, DNA, or even the 20 or so amino acids making up earthly proteins.

Another comparison between the Spiegelman monster and the autocatalytic set is as follows. What happens to the Spiegelman monster when you add a nucleotide? Is it still a catalyst? Probably not since its folding properties will have changed. What happens when you add a few chemical species to the autocatalytic set? Assuming that the new chemicals can be catalyzed by existing chemicals in the set or they catalyze other chemical species in the set there is no problem. The set has been increased but it is still autocatalytic.

This is ignoring the fact that they have already built synthetic self-replicating molecules in the lab that, if supplied with the right nutrients, are able to make duplicates of themselves with only handful of molecular species (as little as 3). These could be considered autocatalytic sets in the same way humans are but only contain 3 molecules.

I’m thinking that natural selection started with chemical stability: very stable molecules become rocks or gases. Unstable molecules are in a race to either permanent stability, or relative stability – and replication extends what otherwise is a brief half-life, and enables expansion from an initial event that otherwise would have to suffice.

Probabilities of chemical formation change drastically when enzymes are involved – after all, catalysts by definition alter the energy and concentration threshold of a reaction, which is normally based on high enough collision probability (concentration plus reaction temperature).

[[Great, go and build it. Show it to me when you are ready. You can demo it to me in a petri dish. We’ll even name the species after you: Bacillus bartoni]]

A single strand of nucleic acid isn’t a bacillus. And I think you’ll find that it was already done, repeatedly, in the early 1980s. Google Manfred Eigen.

RNA
H2O
ribose
phosphate ion
adenine
cytosine
thymine
uracil

8 molecules. Water is the solvent, the rest are nutrients, and the ribose can double as a source of energy. 8 << 6,165.”

Great, go and build it. Show it to me when you are ready. You can demo it to me in a petri dish. We’ll even name the species after you: Bacillus bartoni

As I said previously, that number came from the web site I cited which had a range from 6,165 to 34,000,000 so it’s really not such a specific number (a factor of 5,000 between the minimum and the maximum). There is great uncertainty about it. As to how this number was derived I have no idea. I could speculate that it has something to do with protein structure but I really don’t know.

As we speak Craig Venter is engaged in something called the Minimum Genome Project where he seeks to create the world’s smallest free living organism by selectively removing genes. That project should either confirm what Kauffman is saying or utterly refute it. We should know soon whether he runs into a lower limit and whether that lower limit agrees with Kauffman’s predictions or not.

http://money.cnn.com/magazines/fortune/fortune_archive/2004/03/08/363705/index.htm

RNA
H2O
ribose
phosphate ion
adenine
cytosine
thymine
uracil

8 molecules. Water is the solvent, the rest are nutrients, and the ribose can double as a source of energy. 8 << 6,165.

Yes, I am fully aware of the RNA world theory. There is nothing preventing RNA from being part of an autocatalytic set. On our planet it probably was part of the first autocatalytic set. Even if RNA can function as its own enzyme it still must have other chemical species present from which to build a copy of itself. It cannot create atoms from nothing for its new copy of itself. These other chemical species are part of the autocatalytic set.

http://en.wikipedia.org/wiki/Ribozyme

The folded proteins do enzymatic work better, and DNA is better at holding replication – but RNA does both.

RNA is its own enzyme. It’s a one stop shop, a swiss army knife. It’s a self replicating molecule, the basest form of life there is. It can twist and self-replicate using temperature changes alone.

Really, Tom – you should spend some time looking at what we know rather than focusing on the chinks: biology is really really fascinating on its own without making things up.

You need to do a a review of this book some creationist guy at my part-time job keeps telling me about: Creator and the Cosmos (or maybe it’s Creator of the Cosmos, I really can’t remember). I’m a biology guy not an astronomer. I can handle his incessant challenges to Evo but I don’t know squat about cosmology.

Keep up the hard work!

The 6,165 number refers to the number of chemical species for the minimum sized organism under favorable circumstances (I’m not clear myself on what favorable circumstances mean). For the minimal organism if one of the reactions was not necessary or let’s say we had an extra catalyst that was not necessary (e.g., A + B –> C is catalyzed by both Y and Z) then we could drop one of them out (e.g., Z) and we would be down to 6,164 chemical species. So the minimal autocatalytic set would be 6,164 chemical species, not 6,165.

Yes, I understand that. I am asking why 6,1565 is the magic number. You throw this number out there, but you provide us no reason to think that you cannot have a closed autocatalytic set with 6,164, 6,163, or 6 chemicals.

Kauffman’s theory would allow that, in which case the minimum autocatalytic set would have fewer chemical species.

But it doesn’t have fewer chemicals, it has exactly 6,165 chemicals. Not one more or one less. So the hypothesis (it isn’t a theory) obviously does not allow that.

I seriously doubt whether if you put an RNA molecule by itself in a vacuum chamber it could self-replicate since this is a violation of conservation of mass.

How long do you think a human would survive in vacuum chamber? Does that mean humans aren’t alive? How about your average bacteria, how well do you think it would be able to self-replicate in a hard vacuum? Are bacteria not alive?

At the vary least it would require free floating adenine, guanine, cytosine, and uracil molecules to assemble a copy of itself. So that would be 5 molecular species at the very minimum.

Humans need to be provided with considerably more than 5 molecular species. Ignoring the numerous minerals we need, oxygen, water, and the energy-containing molecules that feed us, there are also about a dozen organic vitamins that we must have a constant supply of or all sorts of nasty things will happen. Therefor we are less auto-catalytic than the RNA molecule I mentioned. Under Kaufman’s definition there is no way we can be alive but the molecule I described isn’t.

And what would the little beasty do for energy? It would probably require some sort of metabolism of glucose into other molecules so that would add more molecular species to the mix.

The nucleotide triphosphates it built its clone out of would have provided all the energy such an organism would need. Even in modern organisms the RNA and DNA synthesis pathways get all the energy they need from the bases that those molecules are built out of. There is no reason to think the first organism would not have behaved in the same manner. In modern organisms those molecules are synthesized or obtained from other organisms, but in the very early oceans they (or something similar to them) would likely have been freely available.

“Perhaps you could share why evolution would have to explain this?”

The Irony is, Super-Conductivity Theory May Already HAVE The Answer …

To Account for High-Temperature Super-Conductors, One Kinda-Far-Out Theory Calls for Electrons to Almost Exclusively Exist as Holons and Spinons …

Holons would Carry Only Charge and Spinons Only Spin, Unfortunately this Tends to Lead Right Back to The Boxes-within-Boxes Problem, That The Very Idea of a Point-Particle was Intended to Solve in The First Place!