My problem with the fine-tuning argument

[T_aquaticus]

@GJDS

We know enough on the subject (be it chemistry, biochemistry, optical isomers, etc etc) to show that random processes are unrealistic - that is why people have advanced the anthropic and fine turning view.

I think you are going to need to back that up with some actual info, such as the complete list of molecules that can give rise to life, the rate at which they are produced across the whole universe, and how long those molecules have been popping up in our universe. I know of no such information.

@GJDS

At the risk of sounding offensive, you do not know anything on these matters. I have written chemical reaction schemes (as have many chemists) and no reaction for H2/O2 has been random. The complete reaction scheme has been written, and is solve using ordinary differential equations and the Arrhenius rates. We have also detected and measured the relevant species and also the final products with great precision.

How does any of that show that it isn’t random?

Can you predict when each and every molecule will run into each other, and predict what each and every interaction will produce?

@GJDS

I spent some time “attaching” amino acids and tripeptides - the chemistry (experimentally) is complicated and just mixing them gives an unholy mess. This not random - just a mess. Once conditions were defined, we get the desired products - not randomly but clearly, with defined conditions, and quantifiably.

I have personally used a peptide library of over 3,000 randomly assembled peptides. I know they exist because I have used them.

@GJDS

So once again, I state what we do know, and from this show randomness as proposed by some atheists is extremely unlikely. Simply indulging in fantastic what ifs and then saying we do not know is, imo, worse that ideological nonsense.

The hard part is demonstrating that you know these things. It is extremely unlikely that any one person will win the lottery, yet it happens all of the time. Making assertions about probabilities isn’t the same as actually calculating them.

[GJDS]

@T_aquaticus

actual info, such as the complete list of molecules that can give rise to life, the rate at which they are produced across the whole universe, and how long those molecules have been popping up in our universe. I know of no such information.

I am puzzled - you seem to reject what we know and insist on information that is simply stuff of your imagination. By your own reasoning, how do you know there aren’t green fairies in your garden, who can disappear when you try to detect them?

@T_aquaticus

How does any of that show that it isn’t random?

Can you predict when each and every molecule will

Once gain you reject science (both computer simulations and experimental verification) which treats the H2/O2 system as defined (non-random), by looking for other things. If we need to know the mass transport and heat balance for the system, we perform measurements and computer modelling, and we can trace the paths of any particles (if this is required - I am not aware of anyone who would go to so much trouble, but, I guess, we are not all atheists with an ideology).

The point that any reasonable person would accept is this: these systems are known and understood through non-stochastic treatments (not random).

That is the point of this discussion.

I would be surprised if you synthesised with any significant yield 3,000 (or 10) peptides - and I am certain you have not synthesised any peptide using random mixing of reactants.

[T_aquaticus]

@GJDS

I am puzzled - you seem to reject what we know and insist on information that is simply stuff of your imagination.

If you read my post you will see that I am asking you to describe what you know, as in the molecules that you know result in life, the rate at which these molecules are produced, and how long these processes have been going on. This is the type of knowledge you need to know in order to claim that abiogenesis is improbable.

I certainly don’t know what molecules, if any, can give rise to life. I also don’t know of any experiments where they conclusively demonstrated that no molecules can give rise to life. When you claim that you do know the probability of abiogenesis occurring you are laying claim to knowing what these molecules are and how often they are produced.

These are the basic parameters you need to calculate the probability of abiogenesis. You need to know how many winners are possible and how many trials there have been. I don’t see any way around it.

@GJDS

Once gain you reject science (both computer simulations and experimental verification) which treats the H2/O2 system as defined (non-random), by looking for other things. If we need to know the mass transport and heat balance for the system, we perform measurements and computer modelling, and we can trace the paths of any particles (if this is required - I am not aware of anyone who would go to so much trouble, but, I guess, we are not all atheists with an ideology).

You ignored everything I presented.

@GJDS

I would be surprised if you synthesised with any significant yield 3,000 (or 10) peptides - and I am certain you have not synthesised any peptide using random mixing of reactants.

It is a commercially available peptide library, which you can find here. It is a pretty simple approach where they have a tripeptide core that is randomized by adding equimolar ratios of two amino acids for each extension. By doing this you get 8 different peptides per reaction. For example, if you add equimolar ratios of I and K at each of the three steps you get these tripeptide cores:

III
IKI
IIK
IKK
KII
KKI
KIK
KKK

You do this with different combinations over multiple 96 well plates and you end up with over 3,000 different peptides, 8 per well. Add on some fluorescent/quencher tags or whatever else you want and you have a library ready for multiple types of assays.

Here is a paper where they constructed random DNA sequences which they then tested for function in E. coli. This article was even discussed at the Biologos homepage.

Here you can find a paper discussing RNA enzymes that were isolated from random RNA sequences.

[GJDS]

Your mental gymnastics are extraordinary - this is why I get the impression of desperate attempts to maintain a belief system. Nothing you have posted supports random processes for any of your arguments.

Here is a description of a synthesis of a simple dipeptide - nothing random, need optical isomers.:

"It should be easy to envision the concept of the amino protecting group being removed from your dipeptide so that it may attack the free carboxylic terminus of another amino acid. This would in essence create a tripeptide. In the reaction above we see the amino terminus side of valine joining the carboxylic terminus of alanine. This creates the alanylvaline dipeptide. Without protecting groups, the likelihood of generating undesired byproducts increasingly grows. For example, the amino terminus of alanine has an equal probability of attacking the carboxyl terminus of valine, creating the valylalanine dipeptide, if protecting groups are not utilized.

Boc Protection Of Primary Amino Acid:

(the figure of the reaction would not paste - it shows amino acids to dipeptide)

Reference: Latli, Bachir; Hrapchak, Matt; Xu, Yibo; Qui, Fenghe; Krishnamurthy, Dhileepkumar; and Senanayake, Chris. J. Label Compd. Radiopharm 2011, 54, 799-808.
Procedure:
Take a 50 mL vial and charge it with 1.00 g of the amino acid assigned to you by your TA. Dissolve the amino acid in 40.0 mL of methanol, add 2 equivalents of triethylamine, and let the contents of your flask stir for 5 minutes. It would be a good idea to begin heating your sand bath at this time. Assemble a reflux apparatus and turn on your chiller. After 5 minutes has passed, add 1.1 equivalents of Boc2O to your round-bottom flask via a syringe and bring the reaction mixture to reflux. Allow the mixture to stir, uninterrupted for 30 minutes. While your reaction is under reflux, run a TLC on your starting material to find a general solvent system using hexanes and ethyl acetate. Once your solvent system has been determined run TLCs on your reaction mixture to observe starting material transformation. Record these Rf’s
At the end of the 30 minutes remove your reaction flask from heat and allow it to cool slightly. Rotavap off your solvent and then perform an extraction by redissolving your reaction mixture in ~ 20 mL of EtOAc and washing with water (3x). Your desired product will be found in the organic layer. Dry this layer with MgSO4, remove the solids via vacuum filtration, and rotavap down the mother liquor in order to obtain a crude yield.

[GJDS]

It was difficult to paste the portion of a lab manual on peptide synthesis, This second attempt may be successful - this is a portion of the manual and I show this to illustrate my point that random events cannot give significant yields of desired products (we get a mess by just mixing reagents):

[T_aquaticus]

@GJDS

Your mental gymnastics are extraordinary - this is why I get the impression of desperate attempts to maintain a belief system. Nothing you have posted supports random processes for any of your arguments.

Then address what I actually wrote and show that it isn’t random. Can you pick a two hydrogen molecules out of 2 moles of gas and predict which molecule in a mole of oxygen gas it will react with? Can you predict with 100% accuracy what the product of that reaction? If not, then it would appear to be random.

@GJDS

Here is a description of a synthesis of a simple dipeptide - nothing random, need optical isomers.:

Every peptide I have ordered requires HPLC purification to get rid of reactants and unwanted side reactions. Why?

[GJDS]

It is difficult to engage in a significant discussion, although I have tried to make sense of your statements. I re-iterate with established facts of science and leave it there:

1. the H2/O2 reaction is known to the final detail, and any lab can demonstrate the quantitative formation of water in a suitable reactor vessel. The entire reaction scheme is know, it can be demonstrated, reaction rates presented, and measurements made over a large range of conditions - all easily reproduced. If you insist that because gases are reacting, and this is a dynamic process, that needs to be addressed, you are wrong; this is stating the obvious, and is a trivial statement.

I deal with scientific facts and data - your responses to these are not scientific and thus cannot be the subject of a reasonable discussion.

2. I provided a page of a lab manual (which you should read) that shows the step-wise method for the synthesis of dipeptides and tri-peptides. This undergraduate method explains why there are bi-products, how reactions may be guided to favour the desired product, and the relevant chemistry, and steps to purify the product. Your comments indicate to me that you are not familiar with this simple chemistry. Ignorance does not equate with random.

I regret ending this conversation on this note, but frankly I feel embarrassed at having to explain such simple chemistry to you within the context of a science/faith discussion on this site.

[T_aquaticus]

@GJDS

It is difficult to engage in a significant discussion, although I have tried to make sense of your statements.

It is hard to engage in a significant discussion when you refuse to address what I actually write.

@GJDS

I provided a page of a lab manual (which you should read) that shows the step-wise method for the synthesis of dipeptides and tri-peptides. This undergraduate method explains why there are bi-products, how reactions may be guided to favour the desired product, and the relevant chemistry, and steps to purify the product. Your comments indicate to me that you are not familiar with this simple chemistry. Ignorance does not equate with random.

Just the admission that there are unwanted byproducts is all that I need. This is due to the random nature of chemistry.

We could look at the Miller-Urey experiment. There were tons of different products in the reactions they carried out. In fact, reanalysis of the samples from their original experiments demonstrates that all or nearly all of the amino acids found in biology were created in that experiment. This is the type of randomness I am talking about.

@GJDS

I regret ending this conversation on this note, but frankly I feel embarrassed at having to explain such simple chemistry to you within the context of a science/faith discussion on this site.

It is I who apparently needs to explain the basic chemistry to you.

[wkdawson (Wayne Dawson)]

I guess most of the people here have not read Stenger. His final obsession seems to have been to prove with science that God does not exist; sort of an inverse scientific proof of God madness. I could never understand how a man could move to a beautiful place like the Colorado Rockies to prove this and not see the irony in the whole thing. Moreover, it probably takes more sustained effort to believe in God when we see only the most rotten people always being placed in powerful positions where they stomp and the righteous and they never seem to face the judgment day on earth. We really don’t even have to get to science to really doubt God.

I didn’t read this particular book, but I have read another one and I used to be on a skeptic list where Stenger was a member, so I’ve seen some of this before. Somewhat paradoxically, I ended up finding ASA as a result of that involvement (not specifically Stenger, but just in general).

Full disclosure, my area is not cosmology – it is more biophysics and solid state physics. That said, Stenger’s general notion is that the physical constants are mutable, and therefore, there are many universes out there all with different properties where this one just so happens to have “the right stuff” for the emergence of life. The idea is a product of string theory as I vaguely understand it. It presumes that whereas a vacuum (which is not really a vacuum) is there, it has no influence (or limited influence) on the laws of physics in the universes that form in it. I don’t really see why “environment” doesn’t bear any strong influence on the system, it certainly does on more microscales (the size of universes). If the vacuum really creates, why don’t we see other really weird stuff than the predictable virtual particles? Nevertheless, this goes well beyond my area of expertise.

To be fair, they are at least thinking about what a universe/multiverse would be like if material as we understand it were all that make up the universe. It is an effort in creativity, and creativity has helped us to discover concepts like mass, acceleration, relativity, etc. However, unlike mass, relativity, etc., we have scant few ways to really test these concepts; the theory is much further ahead of our means to support it. So you should understand the science part of it as simply a creative playing with ideas. We should accept that ideas will try to conquer these things, and frankly, without that freedom to explore, we blind ourselves. We should want to know as much of the true picture as we can, and if this is so, then it is so. But let’s also be clear, that this is a big if.

I guess if you have made up your mind to be an atheist, then you have to offer something of a creation story. However, in the nihilism frenzy that Victor ensues, I can only come back to that unpleasant question that if the universe simply popped into existence and there is no one to judge us at the end of the age, “why should we be moral?”, other than maybe I feel bad about hurting other people or if I do bad things too often somehow it might catch up with me. At some level, I don’t think ethics is something I should be allowed to pick and chose – certainly not from the vantage point of power. I accept that they may not be immutable, but someone has to be the judge. There is only one that can be that and be fair.

Anyway, Stenger has crossed the river (though maybe not that one from Jordan to Canaan) and now he knows whatever it is that is, or simply has vanished into the great vacuum of oblivion never to be an ephemeral essence of anything again. I still say it is better to look to God, to trust that Jesus somehow really did rise from the dead, and walk in faith that somehow all will be held to account one day. At least then, to see Jesus face to face would make all this walk worth it.

[Vouthon (Colin Cooper)]

“A low probability case is what the multiverse view suggests”

I wouldn’t go so far as to suggest a Bayesian-style approach based upon the low probability of the value of “this or that” constant (i.e. having a seemingly unnatural, very small number), necessarily demands or is suggestive of a multiverse. It most certainly doesn’t and isn’t. I’m often mystified why you think it so.

The multiverse ultimately lives or dies based upon the viability of the string landscape-eternal inflationary model with supersymmetry (as well as evidence of potential bubble collisions) that made it possible to even envisage bubble universes involving divergent constants of nature in the first place. Without the string landscape (and the specific eternal inflation model), inflation would just produce “bubble” universes or “patches” in space-time with the exact same constants, making the multiverse ineligible as a solution to the fine-tuning conundrum.

The inflationary multiverse wasn’t invented as a solution to fine-tuning, it must be remembered. It rather is an idea arising from these other models that was subsequently seized upon as a possible solution to fine-tuning by a number of disgruntled physicists in the hope that the string landscape and SUSY would eventually prove to be true and make the multiverse a viable possibility, scientifically speaking. Unfortunately, it hasn’t played out this way.

The LHC has consistently failed to provide any evidence in favour of SUSY, new particles after the higgs boson, vibrating strings or hidden, curled up dimensions, I should add. Nature seems to be telling us that the string landscape probably doesn’t exist and by extension the multiverse which arises from it.

That’s what you need to be properly indicative of the multiverse; not some low probability value for a constant. Without the string landscape-eternal inflation model, we would have no reason to even imagine that there might be such things as self-contained, causally disconnected patches - or “bubble universes”, to use the seemingly preferred phrase - out there in the infinitude of space, with different constants. It just isn’t conceivable otherwise (well, outside speculative philosophy maybe).

So, if the multiverse is ultimately “discarded” as a scientific theory (and regulated to the realms of speculative philosophy, like God), and if people still use the Bayesian statistical approach to the effect that the values of the constants are deemed to be exceedingly improbable according to any model requiring naturalness, your essentially left with unexplained mystery and no GUT (grand unifying theory), with your best solutions being philosophical notions like “just a mystery”, “God” or “multiverse” which are inherently outside the scope of any testable predictions or hope of being falsifiable.

[wkdawson (Wayne Dawson)]

I think you and GJDS are both hitting around each other’s point.

What GJDS seems to be saying is that there are procedures that you can follow in chemistry that do produce particular products. Chemical engineering is basically a study where you focus on optimizing the yields in large quantity production of some specific chemical. In that sense, there are some things that can be predicted; though the real world is not the laboratory where reagent grade materials can be mixed.

This gets largely to your point. What you seem to be saying is that there is a lot of stuff that cannot be predicted because of many unknowns. For example, in the primordial earth, what was really going on? We can conjecture of course; however, without specifics, this renders the estimates very questionable.

Hugh Ross is basically messing with a version of the Drake equation.

With Carl Sagan, the Drake equation was far too optimistic and we should have already met our “neighbors” a long time ago. … Or maybe Von Daniken (Chariots of the gods) was right all along and aliens built the pyramids and all the other stuff. But I think an easier explanation is that there was nothing else to do, and the Egyptian monarchy paid well enough, so why not go out and build a pyramid. … a little more money for a new gadget toy for the kids.

Ross swings in the other direction rendering life absolutely impossible. Up to now, we have not seen space aliens or genuine reports of flying sauces in the news, and we have not detected any extraterrestrial communication with SETI so far either. Since we have covered quite some bandwidth, that would suggest that the existence of intelligent life on other planets is rather unlikely. (Of course, seeing the world today, maybe that should not be such a big surprise.) So Ross is probably a bit more correct on focusing on the unlikelihood, but I don’t think it really resolves whether life is likely or not.

One interesting thing is that we only have the one system of nucleic acids and amino acids. If there were a vast multitude of different ways life could emerge, why would we not see many alternatives on earth? Maybe they would be very much in the minority, but they actually should be there if this was such a facile process. One interesting thing I have noticed about nucleic acids is that the entropy of the polymer is such that the double helix wind has almost the maximum entropy in the single-stranded DNA/RNA. So forming the double helix is less unfavorable than possibly other materials. It is not a really significant value, but it does lead me to wonder if there are other things we don’t see about these systems.

by Grace we proceed

[heddle (David Heddle)]

@Vouthon

I wouldn’t go so far as to suggest a Bayesian-style approach based upon the low probability of the value of “this or that” constant (i.e. having a seemingly unnatural, very small number), necessarily demands or is suggestive of a multiverse. It most certainly doesn’t and isn’t. I’m often mystified why you think it so.

I don’t think I ever said it demands. One thing that I actually said amounts to this: low probability of the constants is something of a feature of the multiverse, since they essentially call for a random draw. The other point I made is that fine tuning has nothing to do with probability. Anything else I said is just an implication of these two points.

@Vouthon

The inflationary multiverse wasn’t invented as a solution to fine-tuning, it must be remembered.

I must be remembering incorrectly, for I thought it was invented precisely for that reason; to deal with the fine-tuning required to avoid the horizon and flatness problems.

[T_aquaticus]

@wkdawson

This gets largely to your point. What you seem to be saying is that there is a lot of stuff that cannot be predicted because of many unknowns.

What I am saying is that you can’t know with 100% accuracy what the product of any molecular interaction will be, even if you know everything about the conditions. In some conditions you can come close to 100% accuracy, but never quite get there. In other conditions there is an inherent bias towards many different products in about the same amounts.

@wkdawson

One interesting thing is that we only have the one system of nucleic acids and amino acids. If there were a vast multitude of different ways life could emerge, why would we not see many alternatives on earth?

Newly formed life can not compete with life that has already evolved to better fit the environment. This means that you will usually only see the first type of life that emerges. Even now, scientists have to use ultra-pure water in experiments that involve DNA and RNA because life has released copious amounts of RNases and DNases into the environment. These enzymes would quickly destroy any nucleic acid based polymers that were forming out in the environment.

[Vouthon (Colin Cooper)]

I don’t think I ever said it demands. One thing that I actually said amounts to this: low probability of the constants is something of a feature of the multiverse,

Put that way, fair enough!

Probability may feature in the multiverse idea to the extent that the constants in the bubbles are ultimately a result of randomness, rather than an underlying mechanism of physical necessity.

But my point was that this doesn’t make it indicative of there being a multiverse, just because a constant is deemed in the eyes of some to have a low statistical probability.

On its own, cosmic inflation might result in bubble universes if it is “eternal” (rather than chaotic, which is the other viable model and doesn’t lead to a multiverse) but those universes, by themselves in the eternal inflation model, would all have the same constants without the existence of a string landscape.

The multiverse needs cosmic inflation that is eternal and a string landscape, and the string landscape in turn needs supersymmetry or SUSY as I like to call it (in most articulations of string theory).

No SUSY = no string theory = eternal inflation that produces bubble universes all with the same constants… and that’s not even getting to the contested evidence for inflation, since there are a number of prominent theoretical physicists who don’t even believe inflation exists either (whether eternally or chaotically). Get my drift?

What I’m saying to you is that this inflationary-string landscape model is being dealt lethal blows at the moment and appears to be on its last legs. It’s a house of cards. Nobody knows yet what to replace it with but its not producing any testable predictions, after some thirty years of the biggest colliders known to human history smashing particles together at the highest energies our civilization can produce short of a collider the size of the entire solar system and billions upon billions of taxpayer funded dollars/pounds/euros to boot.

The prognosis is not good, therefore, for the “multiverse” even being scientifically possible - so, to look at someone saying, “I believe the value of this constant is improbably small for xyz reasons" and arguing that this logic lends itself to the multiverse, just doesn’t register with me because I doubt whether its even possible anymore to conceive of a multiverse in the first place.

If the multiverse lacks any substantive, testable foundations from the offing, courtesy of lack of evidence for the models that have the multiverse as a consequence and make it possible, or indeed made people start thinking about the idea (namely eternal inflation and the string landscape), then one wouldn’t have any grounds to think that low probability of a constant naturally infers it, would we?

That’s what I’m saying.

As an addendum, a question for you: The value of the cosmological constant can’t be calculated working from first principles. This indicates there may not be a “natural” mechanism to account for why it takes the value that it does. Likewise, quantum physics provides formulas for calculating what the Higgs mass should be, and the Higgs should be very, very heavy. Only its value is actually very, very light with cancellations down to a very fine degree of precision.

This situation undermines and mitigates against the physical necessity “high probability” argument you referred to earlier and which you favour theologically if I read you right (i.e. that the constants are what physics says they must be). “Naturalness” is out as a solution.

An “unnatural” (and to many physicists unsettling) explanation for the Higgs mass or cosmological constant may then be sought, invoking “anthropic” reasoning. Perhaps the Higgs mass isn’t fixed precisely by any underlying theory, but can assume a wide range of values in different regions of the universe - that is, in different bubble universes in a multiverse. It takes the heavy materials-complexity-life permitting value in our universe, simply by chance.

Neat.

So one might next consider this random throw of the dice to explain the fine-tuning anomaly. For that, you need the multiverse, for the probability distribution. But for the multiverse, you need string theory and eternal inflation and SUSY…

And if the probability-multiverse argument is also out, hypothetically, for the reasons I’ve outlined regarding string theory and SUSY…where do we go next?

No natural “physical necessity” explanation; no “anthropic” explanation relying on a probabilistic multiverse.

God is not and can never be a scientific explanation. No supernatural invocation can be, because that ain’t testable. So where do we go from here to solve the fine-tuning problem?

I’m afraid this increasingly looks to be where we are at. A serious impasse.

I must be remembering incorrectly, for I thought it was invented precisely for that reason; to deal with the fine-tuning required to avoid the horizon and flatness problems.

Inflationary theory (one of the two foundations needed for the multiverse concept) was indeed conceived to account for those two fine-tuning problems but not the multiverse itself, which actually emerged from the confluence between eternal inflation and string theory.

You could, I suppose, argue for an indirect genesis leading back to fine-tuning as the original problem, in that respect, but my point still stands: the multiverse itself is independent of fine-tuning or probabilistic speculation, arising as it does as a consequence of inflation and the string landscape. If either of those two theories aren’t true, then you can kiss bye-bye to the multiverse irrespective of how many people think finely-tuned parameters are improbable, because in that eventuality it wouldn’t even be an option to account for a claim of low probability of a constant.

That inflation in turn arose to explain away a fine-tuning is, however, a rather neat irony though isn’t it? Talk about circular!

[wkdawson (Wayne Dawson)]

@T_aquaticus

Newly formed life cannot compete with life that has already evolved to better fit the environment.

Yeah, this is reasonable. By “different”, I was actually talking more like a Monty Python “something completely different”, not using RNA/DNA. I mean, if we are just reduced to RNA/DNA (plus 20 aa proteins and lipids) as the fundamental systems of life, we have already reduced the problem substantially. If there is life on other planets, it would inevitably tend to imply that we should expect to see this same system. The codon tables would then probably be optimized very similarly, and though not a requirement, epiphenomena as it may be, Captain Kirk may even be able to have his weekly space romance. I’m not insisting that it goes that far, but once you narrow the parameter space, it becomes a greater possibility (though surely very small).

Maybe we actually are seeing this in a way. The popular notion has been that the RNA world was first. RNA is really bad at functioning as an enzyme, but is great at functioning as a scaffold. Proteins are really great at functioning as enzymes, but are not particularly good at forming complex scaffolds. I won’t argue that it is impossible to devise some lab experiment where you could get the same sort of structures from proteins as RNA, but it is certainly difficult to do and it is not what nature does. Ditto for enzymatic activity of RNA. So then maybe we are looking at what was once some sort of an “RNA world” and “protein world” that early on joined forces to build ribosomal RNA and RNA polymerase.

Of course, we still have to get even this far with the RNA and proteins. The question that I struggle with is how likely it is for this sort of system (RNA/DNA/protein/lipid) to arise “naturally”. If somehow it is “really easy”, then we should be seeing it everywhere in the universe. Moreover, whether it is “really easy” or “next to impossible”, I find myself questioning whether it serves as a valid argument for or against the existence of God. It is simply what is, and that is all it says. God as creator is an overlay of whatever concept we build out of the science.

[sfmatheson]

@wkdawson

RNA is really bad at functioning as an enzyme, but is great at functioning as a scaffold. Proteins are really great at functioning as enzymes, but are not particularly good at forming complex scaffolds.

Oh heavens, this is all wrong. RNA enzymes are interesting and ubiquitous, and some are essential for life. (Google ‘ribozyme.’) And there are whole ancient families of proteins that do nothing other than serve as scaffolds for the organization of signaling systems. (Google ‘scaffold protein.’) RNA is not well known for “scaffolding,” though I admit I can’t even tell what you mean.

[wkdawson (Wayne Dawson)]

@sfmatheson

Google ‘ribozyme.’

Yes of course. But from any serious reading of the RNA world, we understand that it is not remotely comparable to proteins. There are specialized enzymes – ribosomal RNA being “exhibit A” – but most of the grunt work in the cell is done using proteins.

@sfmatheson

RNA is not well known for “scaffolding,” though I admit I can’t even tell what you mean.

Try thinking about RNA secondary structure and pseudoknots. (Note that “protein secondary structure” and “RNA secondary structure” are two very different animals. RNA ss is globally topological, protein ss is not.) Yes, proteins make barrels and can make jellyroll folds. Proteins can also easily fold with parallel strands too. However, RNA can easily build a hierarchy of multibranch loops and pseudoknots that proteins would be hard pressed to imitate. There are not so many 3k aa proteins out there, but the human genome has plenty of introns that size. RNA is also much larger than proteins, typically. So, as a scaffold (and sometimes an enzyme as in “exhibit A”), fine, but RNA really cannot compete with proteins except for a (comparatively) few special cases.

[sfmatheson]

@wkdawson

Try thinking about RNA secondary structure and pseudoknots.

Those are interesting structural features of RNA that have nothing to do with scaffolding. Can you cite some studies to the contrary? I can’t find any.

@wkdawson

Yes, proteins make barrels and can make jellyroll folds. Proteins can also easily fold with parallel strands too.

What do those have to do with scaffolding? Do you know that there are entire families of proteins that serve as scaffolds for the assembly of signaling complexes, and these families of proteins are called, you know, “scaffold proteins”? You are throwing out structural buzzwords that don’t make your case. Which, by the way, is incorrect.

[wkdawson (Wayne Dawson)]

I am thinking in terms of the machinery. 16S Ribosomal RNA has three major domains that work as units. They are like large lever arms that move the mRNA along. That sounds like a “scaffold”, doesn’t it? … or maybe more correctly, a “lever arm” behaves like a main piece of scaffolding.

If you want to talk about cartilage, fine, you win. but it’s not what I am talking about. This isn’t dictionary stuff, this is work I do for a living.

[sfmatheson]

@wkdawson

They are like large lever arms that move the mRNA along. That sounds like a “scaffold”, doesn’t it?

No, it sounds like… large lever arms.

@wkdawson

If you want to talk about cartilage, fine, you win.

Cartilage? PubMed “scaffold proteins” and you’ll learn a lot about signaling systems that predate cartilage by a billion years give or take. You’ll learn that they are well studied in yeast, which are not well known for their cartilage. So, I’m not sure what it is you are talking about, but molecular biologists know what scaffold proteins are, and they don’t confuse them with cartilage.

http://science.sciencemag.org/content/332/6030/680.long