Wednesday, February 01, 2012

I have lost faith in scientists

Having read the book "God's Undertaker", and the book "Amino Acids and the assymetry of life", I have come to the conclusion that a huge chunk of science is "eating fruit from the poisonous tree" in the sense that working assumptions are being used routinely that have a heap of experimental evidence going against them (as opposed to the legal metaphor where evidence is gathered illegaly). Alternatively, they place false doubts on experimental evidence because the simple mathematical models they put on them don't match with those experimental results.

For instance, one would be confused for thinking that the thousands of experiments done on the origin of life on Earth have demonstrated the plausibility of life originating on Earth. Nothing of the sort has happened. ALL the experiments start with the assumption that life started here, and they concentrate on one particular tiny aspect that has to happen a particular way for life to have started here, and the proof that it happened comes DIRECTLY from the assumption - ie. we are here so it must have happened.

With chirality, almost all carbonaceous meteorites have demonstrated chirality with their organic molecules. This has been used to prove that similar Earthly chiral molecules have non-life origin, rather than the quite different *Similar Earthly chiral molecules are as much linked to life as those from Carbonaceous Chondrite Asteroids*. There is no evidence for or against living matter having been in asteroids other than this chirality evidence, which wouldn't rule it out, but retain the possibility. Racemic organics would have ruled it out.

The explanation of how the meteoric  (and Earthly petroleum) organics had become chiral is based on mathematical models of carbon molecules under high pressure. It is not based on experimental evidence. It is a classic case of believing the simplified model over testing out a typical experimental observation to back up a possible working model.

A similar thing with the model of how Comet organics became chiral.

22 comments:

Chris Fellows said...

1) We never asked you to have faith in us. Not if we were me. We said: here is the process, here is the data, here is what we think provisionally based on the data so far, learn 2 think n00b and stop taking peope on faith.

2) Don't despair. Iterating towards truth is a process that never ends. It makes sense to look 'under the streetlight' for the keys you lost on the other side of the road, if there is no way to get to the other side of the road. You might not find your keys but you might find a nice shiny rock, or a hairpin, or...

I predict that about the time Anthropogenic Global Warming is finally shuffled off to the hall of shame with Lysenkoism and the Tuskegee Experiment, we will have incontrovertible evidence of panspermia. Then all this stuff will be re-examined, just as all the evidence for continental drift was re-examined and made 'obvious' once the mid-ocean ridges were discovered. Maybe we'll live so long... no thanks to the rebel colonists nerfing their space exploration programme about the time we were born :(

Marco said...

Hmm.. The process. I like your concept of the process (starting with first you guess).

This is the process that is happening as I see it. First, get indoctrinated through high school and University into all the assumptions and rules and structure of your chosen science. Then you choose to research something that peers that are studying the same science thing is worth studying (after all, they are the ones to review it). You are then free to make your guesses, even challenging pet theories of your colleagues/professors. But under NO circumstances are you allowed to EVER challenge ANY of those underlying assumptions that you learnt through undergraduate studies. I am mainly stressing the obvious ones that I've mentioned over and over for biology, which makes studies, that for instance, Klaus Rohde is doing appear completely meaningless to me as science. However, these chirality things I've read up a lot now and I'm a little bit horrified in the disconnect between experiments and models. Experiments which I've perceived give the exact source for *LEFT* chirality in amino acids is disrespected because the theory cannot explain the connection between the source of chirality and the chemical outcome (the forces should be too tiny to make a difference). Meanwhile, in experiments with the consensus proximal cause of chirality in comets, I perceived a failure for the experiment to demonstrate it, but because the theoretical basis explained it better than the other, it is regarded as the sole candidate.

Marco said...

http://www.gasresources.net/OpticalAcitivity.htm


Perhaps for reason of its historical provenance in fermented wine, the phenomenon of optical activity in fluids was for some time believed to have some intrinsic connection with biological processes or materials.  Such error persisted until the phenomenon of optical activity was observed in material, some believed previously to be uniquely of biotic origin, extracted from the interiors of meteorites.

Is this all they've got? Would they find an abiotic process for the surface of comets?

Chris Fellows said...

If you don't stop talking about 'they' I will have to get you a tinfoil hat.

Experiments which I've perceived give the exact source for *LEFT* chirality in amino acids is disrespected because the theory cannot explain the connection between the source of chirality and the chemical outcome (the forces should be too tiny to make a difference).

What experiments are these?

Marco said...

Bonner et al (1976) left handed longitudinal polarized electrons vs unnatural right handed polarized electrons from a linear accelerator.

Marco said...

Asymmetric radiolysis by polarized electrons. Section 5.2 page 83 of the book I'm reading. Experiments seemed to indicate natural spin polarized electrons favour the L enantiomeric found in life. Anti natural spin polarized electrons favour the opposite chirality.

Section 5.3 explains the Vester-Ulbricht process, which breaks it down to the individual processes thought to occur, and would elucidate a theoretical framework to explain Why it would work. This V-U process still appears to evade experimental verification.

I am not sure why the experiments in 5.2 should not be enough to demonstrate an expectation that autocatalytic reactions in the presence of beta decay would always produce an enhancement effect biased towards L enantiomers of amino acids.

Chris Fellows said...

One swallow does not a summer make.

I will say this again: Mobile phone metaphor.

You are a slave to parsimony in trying to explain the immense differences in chirality dsitribution we see in terms of teensy weensy energy differences. There is simpler, less parsimonious explanation.

Remember Pasteur and his tweezers? If you want to pack the individual molecules of a racemic mixture together into an ordered lattice, there is an energy difference that is significant on our ambient temperature between packing identical molecules and packing the two handednesses together.

Hypothesis: Long ago an achiral proto-organism wanted to store something (might not have been amino acids)as a reserve of carbon, or nitrogen, or whatever. In order to avoid bad osmotic effects, it did this by polymerising the somethings together, like nowadays we make starch or glycogen or glutenin. This polymerisation will produce something that can be packed most effectively if it is all of the same isomer. All you need is *one* proto-enzyme that preferentially polymerises (contingently, randomly, independent of beta decay) a particular isomer, and Le Chatelier's principle will do the rest for you.

Marco said...

Your answer explains WHY proto life should choose one chirality over another, but not HOW it chose left over right, or at what stage it did. I see it as impossible that an achiral proto-life can exist. However, if we stick to the axioms we can agree upon - when you have our autocatalytic species model, of course autocatalytic processes at any rate magnify small enantiomeric excesses, even if they happened randomly. I think it chose left more often than it chose right for whatever reason - I believe only forces that violate parity could have been party to this, directly or indirectly. Whether on Earth or in Comets, the radiolysis experiments indicate a definitive preference in that direction. Certainly no radiolysis experiments indicated the opposite preference, although obviously understanding why some experiments showed results and heaps came up blank, especially when breaking the problem down makes it difficult to prove anything.

I agree you only need one thing that shows a chiral preference. If there is one type of beta decay in the presence of particular environment of autocatalytic species that shows a preference - this will carry through once these more chiral species propagate to other environments.

Marco said...

Pasteur could tell left from right. The weak force can tell left from right. Things that are already chiral can tell left from right. An achiral proto-life cannot tell left from right. It has to pick randomly (like engineers picked randomly that electric currents flow from positive to negative), and if it contrasts with the opposite decision when environments combine, it is back to square one each time.

Chris Fellows said...

I see it as impossible that an achiral proto-life can exist.

Then I will mock you a second time. Why, for the love of God, do you see such a thing as impossible? What motivation do you have for believing such a wacky thing that leads you to grasp at stupid thermodynamically ridiculous straw(man) mechanisms? All the evidence you have been talking about suggests to me that extraterrestrial chirality is biotic in origin.

Your answer explains WHY proto life should choose one chirality over another, but not HOW it chose left over right, or at what stage it did.

It doesn't need to. What part of (contingently, randomly) don't you understand? Proto-life is not doing anything else with chiral molecules but collecting them and stapling them together. It does not need any particular complex mechanism for this. There may have been left-collecting proto-life, right-collecting proto-life, and indiscriminate proto life: left-collecting won out in the great struggle for existence and left heaps of chiral compounds lying around for future generations to find. It is not a profound mystery related to deep symmetry-breaking in subatomic woo-woo land: it is just a contingent historical fact. IMHO.

Chris Fellows said...

P.S. Just because I have not made a long reply to your counterarguments about mass and energy fluxes into comets does not mean I am convinced.

Marco said...

I see it as impossible that an achiral proto-life can exist.

Then I will mock you a second time. Why, for the love of God, do you see such a thing as impossible? What motivation do you have for believing such a wacky thing that leads you to grasp at stupid thermodynamically ridiculous straw(man) mechanisms? All the evidence you have been talking about suggests to me that extraterrestrial chirality is biotic in origin.

Like I said, it is an axiom that we disagree upon, and doesn't really change the argument about extraterrestrial chirality. I think it (extraterrestrial chirality) is a combination of biotic and prebiotic matter that is coexisting. I disagree with the axiom that biotic systems removed all traces of pre-biotic systems.

It doesn't need to. What part of (contingently, randomly) don't you understand?

I guess that's the point - I don't believe any coherent proto-life can lock away what it has "learnt" through contingent, random processes. It's like in Star Wars - The dark side of the force is more powerful, but it cannot distinguish between good and evil, and thus is destined to destroy itself, while the light side of the force... well. Its not really why I think that, but I do buy into the "no information for free" bit to some extent (Wickramasinghe, Lennox). The weak force is not an intelligent input per se - it can only give meaning to one bit of information at a time, but I guess that what I am saying is, is that you are one of them :-) If you can believe in random processes leading to real information, then you can probably believe in perpetual motion machines. The weak force is a naturalistic way to get determinism back into the equation without requiring intelligent input. Spin charged electrons from beta decay is the only experimental success where determinism has gone in the required direction.

Chris Fellows said...

Where does my mechanism create information?

Chris Fellows said...

Like I said, it is an axiom that we disagree upon

Cop-out factor: 10/10. It's like you believing that all bicycles are orange, and when I point out that there is no fundamental reason for bicycles to be orange, you just say 'Oh well, it's an axiom we disagree about'.

Marco said...

Working backwards, The impossibility of achiral proto-life is based on the observation that all the interesting things that happen within a living cell require homochirality to function. Working forwards, from the model of autocatalytic species in the types of reactions we are talking about, it is in the nature of these autocatalytic reactions to amplify enantiomeric excesses, even if as you say, the original excess is from random chance. Thus before you get to something more like proto life (an RNA world is a plausible analogy) chiral molecules and processes would be a lot more common than racemic or achiral ones. Am I missing something here?

As far as Your belief that biotic processes destroyed evidence of prebiotic processes goes, there is absolutely no reason to believe that. The only reason would be if you knew for 100% sure where it started, say Earth, and noticed no evidence. Humans live comfortably with and rely on primitive biota, and there is no reason why life and proto life wouldn't have the same relationship in the environment where they evolved.

Marco said...

Any mechanism that can be called proto-life must necessarily have an information capacity. It may be hard to get our head around because essentially, they are not much more than "lucky chemicals". However, to be better survivors, their action must depend on the changing circumstances in some way, and whether that means they follow a different chain of reactions if the temperature is lower, or whatever, this information is imparted and made meaningful as part of the catalytic cycles.

Chris Fellows said...

all the interesting things that happen within a living cell require homochirality to function.

You have a pretty hardcore definition of 'interesting' that is very unlike my own.

Am I missing something here?

Yes, you seem to be suggesting mysterious autocatalytic reactions occurring outside of proto-life are important. My model is for how an enantiomeric excess could be achieved without any autocatalysis whatsoever. Contra Kauffman, I believe these nets of autocatalytic reactions cannot possibly have existed outside of proto-life: they are things only a little less unlikely than angels with golden tablets.

As far as Your belief that biotic processes destroyed evidence of prebiotic processes goes, there is absolutely no reason to believe that.

I am thinking their is absolutely no reason to go on arguing with you. By definition, proto-life is less efficient than life-life. It is competing for the same chemical and energy resources. The analogy of archaebacteria 'hanging on' in extreme environments is not valid since the archaebacteria and us are on a level playing field on the scale I am looking at: we are both slightly different A380s, while protolife is wood and fabric biplanes.

I don't know why you liked my metabolism posts, you seem to have totally ignored everything in them - and your own valuable observations on rejecting parsimony. I have no idea where you are coming from in insisting on an abiotic origin for the observed enantiomeric excess to the extent that it would cause you to 'lose faith' in me :(

Marco said...

Ok. Regarding Kauffman - I do not believe his ideas on autocatalytic cycles are fruits of the poisonous tree in the sense that they don't necessarily presume where they need to happen - if they can happen, they should be able to happen wherever the conditions are right. The glaring problem with his ideas, which you demonstrated ably in your metabolism posts, is that without a concurrent explanation for how a system could demonstrate metabolism, it is an excercise in wishful thinking. However, I think that you are locked into thinking that the barrier between inside and outside has to be some kind of membrane within the liquid warm happy place with competing proto life within the same happy place. My solution is that the metabolism is like the sort of thing a chemist does with his experiments - apply energy and remove undesired byproducts. The "membrane" is the flask that you are doing experiments in. The whole of the autocatalytic cycle reactions just has to happen inside a naturally occuring vessel which has the tendency to let energy in and unwanted heat and byproducts out. We did go over this, and you came to the conclusion that it "might" work. I am going aginst what Lennox says in the sense that it is not the intelligent input of the chemist that is important, but that the net of reactions involves metabolism.

Marco said...

I don't really think it is worth arguing about the origin of extraterrestrial chiral molecules. You and I both think that the most likely explanation is that they are from living things. Our argument goes deeper than that to the nature of prebiotic life, and whether there will be evidence for that as well, amongst asteroids, comets and other planets.

I want an alternative model for "physical chemistry" life to the one I have proposed.

All the difficult bits - warm happy place, energy source, suitable reactants, metabolism, proto-natural-selection, are not just plausible, but even an expectation for me in my mind, with my comet model. None of your objections make sense to me, and you haven't really come up with an alternative possibility, especially for the metabolism.

Marco said...

I think I've got to separate what is my "pet theory on the origin of life" with the various disposable razors associated with it. It is not so much parsinomy leading me to agree with the "RNA world" and "autocatalytic cycles" as described by various people, including Richard Dawkins, but as a way to fulfill the requirement of proto-life "locking away" its extra complexity over non-life by propogating and building on it - a proto-evolution, if you like. Your explanation that it is very different to life, fragile and less efficient doesn't convince me at all. In the environment that it "proto-evolves" it should be quite successful and efficient.

I find your assertion that archaebacteria and Humans are the same under the hood is only valid to a point. It is like saying that a computer hardwired for a flight simulator is the same as one hardwired with solitaire. The hardware is the same, but the software counts for some things. I also believe that no matter how extinct a predecessor might be, everything leaves evidence of some kind of their previous presence. On Earth, evidence remains in the genetic code. I think on environments where proto-life existed, we would be able to eventually find telltale chemical signatures, once we can interpret them and connect them with descendents (archaebacteria).

Chris Fellows said...

I think I am going to have to make a long power point with lots of animated gifs. I just seem to be apocalyptically bad at communicated what I mean. You may feel the same! ;)

Marco said...

You go ahead and do that. I have meant to post some comet photos to bolster my feeble case for them being living things. I have pretty much decided that the black stuff on comets is crude oil. It will prove to be chiral in nature, and I postulate that it is being generated from within the comet by pseudo-biological synthesis. This will be very similar to the stuff that has been found in meteorites, except that the only way that it would have avoided being processed by earthly biology was if it ended up compressed under pressure and cold in a much larger parent body before it ended up on Earth.