Thursday, January 12, 2012

Cry Havoc etc., Part Two

One of the traditional strategies for getting people to assent to things that are dumb is the strategy of the False Dichotomy. It works like this:

1. Formulate a problem in terms of two ‘opposite’ answers (e.g., Faith vs Works; Capitalism vs Communism; XTC vs Adam Ant)

2. Disprove the bejesus out of one answer

3. Wait for your target to embrace the other answer warts and all, hoping they are not imaginative enough to realise there are other options.


For example:

Darth Sophus: “This hairy creature must be an Ewok, or a Wookiee.  While fully grown, it only reaches to mid-thigh, which is very short for a Wookiee. When beaten in games, it does not tear your arms off, which Wookiees have been known to do.  ... [nine pages of argument omitted] ... therefore, this creature must be an Ewok.”

Hairy creature: “Woof! Woof!”

It is usually less obvious than this.





So, I had been writing about Prof Lennox's book 'God's Undertaker' and had gotten up to the anthropic principle. I don't know how likely my two hand-waving explanations-away of the anthropic principle are to be borne out by events. Probably not very. My prejudice against being in a peculiarly unusual universe might just be an irrational prejudice.
But this doesn't mean that the only two possibilities for the origin of the universe are a multiverse or creation by the God of the Judaeo-Christo-Islamic tradition. There are lots of other possibilities, as the orcs are discussing about 70 seconds into this short film.


As I said in Part One, in Chapter 6 Prof Lennox loses me. He makes a very typical Creationist distinction between microevolution and macroevolution and implies, without explicitly saying so, that 'macroevolution' cannot occur by natural means. (Losing me at this point by ignoring all the suggestions that have been made in terms of natural alternatives to simple natural selection on random variation) To me, this supernatural intervention is inconsistent with the behaviour of the Creator(s) postulated in Lennox's discussion of the anthropic principle: a Creator or Creators that would make a universe so exquisitely poised on the values of a few constants to allow life to one day appear would surely allow its progress to unfold according to very unlikely, but natural, events. It does not seem in character for Him/Them to come in with a miracle every time a new genus of beetle is needed. This degree of micromanagement just seems psychologically implausible. And no matter how much Prof Lennox claims it isn't, this is the 'God of the Gaps' pure and simple.

The psychological implausibility of supernatural intervention struck me even more so in Chapter 7, which is about the origin of Life. A universe dependent on one chance in 1040 for the conditions to allow life to exist at all would surely be a universe where the specific conditions for the beginning of life were also incredibly unlikely - happening perhaps just once in the universe, in one pond, or deep in the interior of one comet. But by natural means, not supernatural.

I am confident that the origin of life is a soluble problem. I think its solution is far away, and that it will not be found by working backwards from the incredible complexity of life 'as we know it' - which is no more complex biochemically than the very earliest life we have ever found traces of on our planet.  I don't discount the possibility that life 'as we know it' was intelligently designed - but by creatures inside the universe.


Rather than working backwards, a solution will be found by working forward from physical chemistry. Simultaneously we should be broadening our knowledge of what life is and what raw materials are available for it to get started. Here are some things we should be finding out:

What sort of life exists elsewhere in our solar system? 
If the answer is none, we know we need to keep looking (working forward) for a mechanism by which life could have gotten started on Earth. If we find things that are based different chemistry in different places, we need to look for intelligent designers. If we find things based on broadly similar chemistry (my hunch) we need to look for the cradle of life further away.

What is the maximum lifetime of molecular clouds?
These are the places stars get started. If matter can hang around in them for reasonably long times, in reasonably large lumps, accumulating molecular complexity, and ideally get transferred from one molecular cloud to another, we have a reservoir of time and space for life to get started in.

The sorts of molecules we can observe spectroscopically from molecular clouds in general are not likely to reflect the molecular complexity available, since space is a pretty destructive environment, so we should be investigating the remnants of molecular clouds closer to home by drilling into the middle of comets: What sort of molecules exist in the interior of 'dirty snowballs', relatively safe from ionising radiation? Of course, if there is life there already, the distribution of molecules we find won't help...


 As far as the later chapters go:

I sort of glazed over in the probability chapter. I think this is what most undergraduate students do when people are talking about probability so I don't feel too bad about it. But I have read these kind of 'making a 747 by throwing bits of scrap metal together' arguments before. They are superficially appealing but are just another demonstration of how daunting the task is when you are looking backwards from the very complicated thing. You build up to complexity by walling off bits of the universe so there is a system and a surroundings. Compartmentalisation is the key. More later once I hear what other people think about the second half of the book. P'raps.

The idea of 'information being conserved' doesn't hold in biology. One airborne seed lands on Anak Krakatau. It grows into a plant, and in six months releases ten thousand airborne seeds, all of which are genetically different. Information increases. Sex = Lack of conservation of information.

And, I agree completely with Lennox on Hume and miracles: Hume's 'disproof' is just a classic example of begging the question.

26 comments:

Marco said...

Ok - The thing with ionizing radiation... In known biological systems, these are hugely disruptive to virtually all aspects of cell biology. One thing that I realise it does is that it knocks dna bases away from their dna chains, ionises chemicals which need to be not ionised for any of the metabolism to work - you get the drift, and I get that. However are we not looking at this in terms of the "smartphone" and not the invention of the telegraph when we dismiss this out of hand? We are saying that biology as we know it cannot even survive, let alone thrive in a radiative environment of space. One thing that ionising radiation does *not* seem to do, is change the bases themselves. On Earth, the occasional bit of radiation causing random mutations might be beneficial, but any more than that is just problematic. I want to concentrate just briefly on the "radiation knocks the bases off their parent DNA randomly" part of the knowledge. If we are talking about just the physical chemistry aspect of this, it just randomly changes a strand of polymer, ionising bits, heating bits etc. If the molecule/strand itself is the "inside" of the metabolism energy graph, it is increasing its energy. In terms of what the molecule itself is, it is "mutated". The potential for the molecule to "self catalyse" or be part of a cycle of catalysis has changed. If this were the case, ionising radiation is not the enemy, but a very necessary thing.

Marco said...

The chiral chemistry experiments seem to be right up your alley. You couldn't summarise any important points that have any relevance to the physical chemistry I am thought-experimenting?

Marco said...

Oooh.. Another thing. The NASA discovery mentioned an asteroidal synthesis that in my mind involved liquid solution. Now most small asteroids are more or less clumps of rubble, so if there was anything remotely able to be liquid it would congregate in the gravitational centre of the asteroid, possibly shielded by the rubble? I don't know if this is actually what is the case. The proposed synthesis of NASA troubles me. I think vaporised panspermia bacteria is just as likely an explanation for the observed bases.

Dr Clam said...

I think vaporised panspermia bacteria is just as likely an explanation for the observed bases.

Me too.


I want to concentrate just briefly on the "radiation knocks the bases off their parent DNA randomly" part of the knowledge.

The *parent DNA* or polymer strand is the stuff that is not there in the asteroids: it is the stuff that needs sugar and phosphate and can only exist in the safe warm happy place. So this knowledge is not applicable to any hypothetical reactions of the nucleotides under harsh conditions.

I think DNA was very likely to have first existed as an energy storage entity in short unorganised chains (in some non-DNA based protolife) long before it was harnessed for replication.

Marco said...

Ok. One more stab at the ionizing radiation thing. The whole reason my hunch includes it is that just as if you get beeps when you ring someone on your smartphone you could reasonably think that the reason has something to do with the ancient history back to perhaps telegraph days - the thing with ionizing radiation and mutations gives me the same "I wonder if there is a reason for that in the history of mutations"
Now if we are talking about extremophile bacteria frozen and exposed in outer space, would ionizing radiation have any influence on its genetics? Would a frozen fragment of DNA thrust up with it protected only by a film of icy dust or other frozen fragments only be good for food even if it thrust back into a friendly environment before thawing again? My guess is probably yes to both - However, this freezing - ionization - thawing is the only way to spread from one friendly environment to another distant friendly environment, which is a real requirement for panspermia. I can't help but (still despite your protestations based on actual chemical knowledge) that what works for bacteria is partly due to the fact that it worked somewhat pre-bacteria.

Marco said...

What is the maximum lifetime of molecular clouds?
These are the places stars get started. If matter can hang around in them for reasonably long times, in reasonably large lumps, accumulating molecular complexity, and ideally get transferred from one molecular cloud to another, we have a reservoir of time and space for life to get started in.


This is the kind of thing I'm talking about. The liquid inside of dirty snowballs is the place that I believe autocatalytic (or catalytic cycle) processes are happening, duplicating one or another type of molecule to a number of trillions. When two dirty snowballs collide, this fragments the dirty snowball, including the liquid centre, which separates and freezes into billions of small chunks. The molecules on the small frozen chunks need to be of a type that can survive through the harsh conditions of space by being frozen, and survive re- entry into the core of another snowball. Bacteria (and all living things, in their single-cell stage) have inherited this ability to be frozen and re-thawed. This is the part I'm guessing based on my hunch. Ionizing radiation's effect on a frozen complex polymer of sugars and bases, would be of a nature that would mutate the molecule rather than destroy its ability to be involved in catalytic effects, reactions or to be an energy source for other reactions.

Dr Clam said...

the thing with ionizing radiation and mutations

Ionising radiation causes mutations for the same reason that speeding trucks knock down telephone poles. You don't need to dig any deeper than that.

I am thinking of very large snowballs, where most of the (pre)biomass is never going to be touched by ionising radiation. I guess there is a continuum all the way up to proto-planets where the interior won't even freeze: spreading from one mass to another on the rare occasions when relatively large chunks of one land softly enough on another for something in the interior of the chunk to survive.

Which brings me to a xenobiological suggestion which I was thinking of before and couldn't quite work in: let's dig down, right down, and see what sort of microorganisms are clinging to life in the very deepest bits of the Earth.

Marco said...

Ok. I will leave the ionizing radiation thing for the moment. Believe me, we will get back to it. Let's look at the freezing thing in isolation for a moment. Being that embryos/ sperm and every Imaginable bacteria presumably, can be frozen and rethawed to a functioning, cell, presumably every Special molecule within the cell would also have that ability. I would surmise that chemicals of that nature would be a small subset of known stable compounds of those elements to have that ability(especially in an aqueous solution) clearly, an evolutionary process must be involved, however convoluted, to first build the building blocks. It must somehow involve the weak force for the observed chiral chemistry. There must be some serious process of multiplication of these chemicals by some process, perhaps within an aqueous solution. There must be a significant, repeated spread and mutation to other similar friendly environments. Thus the building blocks that a following process would use, would necessarily be ones that went through a stage of natural selection to explain their(already) complex nature, compared to other stable compounds using the same elements. Do you, or do you not agree that complex molecules could not get to a reasonable concentration without trillions of cycles of natural selection of this nature?

Dr Clam said...

Do you, or do you not agree that complex molecules could not get to a reasonable concentration without trillions of cycles of natural selection of this nature?

I do not agree.

I would not agree here, or there.

I would not agree anywhere.

I would not agree in a box.

I would not agree with a fox.

I would not agree in the rain.

I would not agree unless you sent nanobots to rewire my brain.



1) C + H + O +N + ionising radiation --> simple molecules + complex molecules. Complex molecules are not harder to make than simple molecules: polymers are the evil bugbears of organic chemists.

2) Repeated cycles of freezing and thawing --> separation of molecules on the basis of various chemical and physical properties - i.e., natural chromatography.

Marco said...

Ok. Dr. Clam I am.

First of all when I say complex, it has nothing to do with the length or any other feature in particular. It is the level of "sophistication" a molecule has in being part of an autocatalytic cycle. Basically, it needs a rare sequence of reactions to exist in the first place, but it may catalyse reactions that given certain common environments, causes more of itself to be created.
With number1) ionizing radiation would cause molecules to form or molecules to be torn apart, that wouldn't otherwise do that. Whether the results are simple or complex is irrelevant- it is what they might do different when back in the warm friendly place. I don't understand why you can believe random mutations can be beneficial with long life cycle organisms that are already well adapted, and not for physical chemical "life" in a punctuated molecular cloud.

With 2) that's beneficial right? That would almost certainly happen in the warm happy place of a large comet in an elliptical orbit around a star. I feel without repeated exchange of chemistry, there would be stasis.

Dr Clam said...

Maybe you could start again from the beginning in simple words? You are still using words like 'mutation' and 'selection' that have a meaning in biology but don't have a clear meaning in chemistry.

I don't understand why you can believe random mutations can be beneficial with long life cycle organisms that are already well adapted, and not for physical chemical "life" in a punctuated molecular cloud.

Q. What is the meaning of life?

A. Life (noun): A system which exchanges energy and matter with the surroundings to increase entropy in the surroundings and decrease entropy in itself.


Q. What is the meaning of "life"?

A. Buggered if I know.

Marco said...

In the physical chemical sense, I am defining life as a chemical (molecule)that is part of a catalysis cycle which makes that same chemical persistent. If you were say looking at the analogy of a car being a bacterial cell, I am looking at the evolution of the ball bearing, alloys, rubber, hoses, you get the drift. None of these things exhibit "metabolism" per se, but if you follow the energy graph of their production, it is kind of a metabolism. Therefore mutation is a forced change to one of these molecules, that may or may not reproduce itself or one of the other chemicals in their related cycles. Natural selection is the weeding off of stable chemicals that are unhelpful to the various cycles. Inheritance is the passing on of chemical traits faithfully. If their is a mutation, most traits would still work. There will end up being an ecosystem of molecules that are each part of different cycles of catalysis. They will be way different to the blend of chemicals you would expect if you threw together the elements in just one comet.

Dr Clam said...

I need an example. All I see is chemicals churning around in an unbounded system looking for an energy minimum. What is the thermodynamic driver for a stable 'dynamic' system, as opposed to a pile of inert chemicals?

If you were say looking at the analogy of a car being a bacterial cell, I am looking at the evolution of the ball bearing, alloys, rubber, hoses, you get the drift.

Now, this earns you a good analogy point, because all those thingies - ball bearings, hoses, rubber - evolved in applications not very like cars - carriages, lathes, bicycles, Roman fire engines, Mayan ball games, etc. - going way back in time. What I am saying is:

Car = Every living thing we know about, with very very similar biochemistry.

All these pre-car applications in which ball bearings, etc., evolved = A whole sequence of vanished living things with biochemistry we would look at and go "Whoa!" that probably lived before our solar system formed, given how soon life-as-we-know-it appeared in our solar system.

Marco said...

I think you're going to like where this is going.

Ok. There is one extremely important thermodynamic driver that makes sense to both of us. In a giant Snowball, heavy elements would navigate to the centre (Lead, Uranium, Plutonium radioactive Caesium, take your pick). These elements, as they slowly decay generate heat that keeps the centre of the snowball liquid, no matter what size it is. The outside would necessarily stay solid and act as a kind of "igloo" shielding ionizing radiation that would however have a differential effect the closer you got to the surface. The whole snowball would act as a giant living physical chemistry cell powered by the neucleus at its core. At its core, it would generate all sorts of chiral chemistry due to the "weak force" of the decaying heavy elements. There would be considerable dynamic chemistry going on here. The heavy elements themselves would be catalysing certain reactions. The radiation and particles given off from the core would be powering a whole heap of other reactions, and ionizing radiation from the outside would occasionally melt bits that would work their way closer to the core. Not to mention convective forces creating cycles of chemical reactions. Hey - I would never have really thought of this if you hadn't been so stubborn with the "great big dirty snowball core" theme

Dr Clam said...

At its core, it would generate all sorts of chiral chemistry due to the "weak force" of the decaying heavy elements.

That's like saying, "In the Mediterranean, all sorts of cruise liners would capsize due to houseflies colliding with them." The mismatch of energies involved is just too great.

Okay. So, you are saying there is a whole cascade of chemical reactions occuring (driven by radiation from the core), with a lot of intermediates that can be converted from one to another and maybe (maybe) engage in a catalytic reaction so that the presence of compound X means there will be more compound X. And you are saying that you have a whole bunch of these reactions competing for substrate, right? And since it is not a simple mixture you will have different reactions using different intermediates along the cascade as substrates? So "mutation" is any change in the chemical structure of an autocatalyic species and "selection" is just that if the new species is more efficiently autocatalytic it will take up more of the substrate? So you will end up with a net of reactions that is disippating energy through the *most efficiently autocatalytic* species or mutual groups of species? I think that could work.

"If such a thing could be, it certainly would be." (McElligot's Lemma)

I think your 'chiral' direction is a red fish, though, since one of the first things proto-life is going to do is stockpile resources, and when you start packing compounds together for storage you find that the species of the same chirality pack together more nicely (see Pasteur with his tweezers); my hunch is that all the 'building blocks' of life-as-we-know-it are common compounds that life-as-we-don't-know-it found useful and would have had mechanisms to synthesise and stockpile.

Marco said...

Ok change that bit with chiral chemistry as saying - The weak force would *allow* one chirality pack to dominate as Asimov's donkey analogy went, for the donkey to decide to go in one direction rather than another rather than forever looking at the equidistant food sources.

Marco said...

I'm actually pretty sure all the life-as-we-don't-know-it and life-as-we-know-it use *exclusively* building blocks *AND* resources that can be described as a compound X of your description. I would bet my left arm that if we dug into the core of any comet, we would find the primordial soup of these compound X's near the nuclear core, as well as actual bacteria around the margins of the liquid core. I bet the physical chemist that first published such a theory would get a Nobel prize when the sample return is eventually done. Has anyone ever suggested that comets might have a heavy metal/nuclear core?

Marco said...

Yes is the answer to all of your questions btw.

Marco said...

There is another possibility that the comets themselves are exhibiting metabolism. The comet's tail looks an awful lot like an exhaust system. Pretty handy for getting rid of those volatiles that may have eventually clogged up the cycles of catalysis.

Marco said...

Point the tail in the right direction and you've got a primitive propulsion system ;-)

Marco said...

Maybe in the centre of each modern comet is a giant amoeba controlling the "spaceship". Great idea for a science fiction novel. Pity I don't write fiction.

Marco said...

my hunch is that all the 'building blocks' of life-as-we-know-it are common compounds that life-as-we-don't-know-it found useful and would have had mechanisms to synthesise and stockpile.

I kind of think that DNA is actually the "brains" of life as we don't know it. If the sentient being is in charge of flying the comet, the much slower processing power compared to synapses etc. wouldn't matter so much if you are working out orbit trajectories and which direction to point your exhaust fumes towards to make your next fly-by in umpteen thousand years. Messenger RNA would have started out as a rudimentary nervous system to access the controls. A fine coating of black carbon for insulation/capturing suns energy, but importantly, with viewing holes together with telescopes made from shaping ice into lenses towards the viewing hole. I think they discovered intelligent life on Earth at some point and sent a "messenger" comet to say "Hi" in its language. That didn't work so well, so they sent a comet into a trajectory which approximates the intelligent Earth being's life time. This has appeared to finally pay dividends as a few spaceships were noticed near it during the last fly-by. Communication from comet to comet is via a kind of "smoke signal" from modulating the comet's tail signature.

Dr Clam said...

Okay, I'll play the straight man:

Predictable orbit = thing that is not steered

Tail = points away from sun
whichever way comet is going; not there at all in Oort cloud.

Hot radioactive interior = evidence-free hypothesis

So far as I am concerned all this talk has referred to the pre-biotic universe, which at least in our neighbourhood I presume to have been erased due to colonisation by life-more-or-less-as-we-know-it.

Marco said...

Yes. I am just dreaming, but hear me out. The "steering" bit I got when I read a bit in my research about "non-gravity acceleration" detected in some comets. Of course comets would have to conserve their energy until they really needed to change course. Not all comets are as predictable as Halley's comet. Even slight perturbations at some point in an elliptic orbit can make a big difference to the long term orbit.

I am hypothesising (dreaming) that the tail is a solar powered exhaust system. The Oort cloud would be full of "dormant" comets. Every now and then they are able to be sent on their way to a friendly orbit so they can metabolise again.

Evidence free hypothesis = non-life to life transition happened on Earth. Only evidence of it even happening is that it destroyed the evidence of it happening after it happened.

Hot radioactive interior hypothesis is based on the actual properties of the elements concerned, their relative abundance in the early solar system, and that their extra density would cause them to congregate in the gravitational centre of a great big dirty snowball. They are hardly going to be on the surface, and if the comets don't impact anything large, they are not really going to budge. One has to surmise from circumstantial evidence when it would be impossible to get the evidence (yet)- not invent the simplest theory possible. That is the job of theologians - not scientists. It is only *quantitative* models which need pick the simplest models, not *explanatory* models.

Marco said...

Oh. And I think if life did start in comets, there would be *plenty* of evidence of proto-life also in the comet as well. No matter how advanced the evolution went within a comet, the life would still be swimming in the primordial soup. There is nowhere for it to go, and no neccessity. Just like there is no necessity for bacteria to be extinct just because higher life forms eat them.

Marco said...

Gravitational modelling on surmised heavy element "chunks" impacting a "dirty snow" model of a comet may elucidate whether there is enough evidence.