Tuesday, February 19, 2013

Six impossible things before breakfast

Occam's razor is involved in the following assertions being protected from the burden of proof:

1) Random mutations and natural selection is necessary and sufficient to explain the origin of species from other species.

2) Abiogenesis occurred on Earth

3) Abiogenesis requires the conditions of a Planet (We don't know how abiogenesis happens, we haven't demonstrated it happening, so how can we presume what it needs?)

4) Pre-life is more fragile than life

5) pre life has been extincted by life because life is superior ( we don't yet know what came before life and see 2 through 4 we have no gnosis of where that might be, so we cannot possibly know the results of the two coexisting)

6) pre life has an x need for mass flux/energy flux/reproduction.....  We do not know of the process, so we certainly cannot know quantitatively of the need for any particular feature of the process.

Sunday, February 17, 2013

Definition of Marcomony

Marcomony is the replacement of parsimony in science, where the burden of proof would normally be shifted away from a solution deemed as "simpler", by simply *not* shifting the burden of proof.

Thus competing hypotheses given the same evidence are on essentially a level playing field. A multitude of makhO's disposable razors rather than Okham' s individual razor.

I have listed in my head every case I could think of where parsimony is used in science, and I cannot think of a single one (yet), where I believe parsimony has benefitted science.

I believe models *must* necessarily be simpler than reality - eg Newtonian mechanics doesn't take into account relativistic effects. It is not true that the simplest solution is the most likely to be true. The point of simpler models is to fit better into our (perhaps prejudiced) world view, and to be able to be explained to a lay or more naive public.

Saturday, February 16, 2013

Show me the metabolism, marconomics, part 3

"Kauffman is chiefly concerned with reproduction as the defining feature of life. He makes only a superficial discussion of metabolism that does not consider its central thermodynamic requirements. But ultimately, metabolism is what is most important."

This reminded me of an "alien life" forum that was discussing, among other things, how we would recognise life as we don't know it. There was a consensus that at a minimum, reproduction AND metabolism would need to be observed. However, when we are talking about abiogenesis, the conundrum is more about how they have to simultaneously come about. Meaningful reproduction is impossible without metabolism to generate the work energy that reproduces something. Metabolism is pretty useless if the system that metabolises is a one off that cannot be reproduced faithfully and it's important features "locked away" for future use. The blueprint of "the system" doesn't need metabolism to exist, it needs metabolism to perform work and reproduce.

"Without petrol, the most splendidly engineered automobile will just sit there. Without a plausible metabolism, the most elegant net of autocatalytic reactions is an empty exercise in symbol manipulation."

Why can't a car be considered a living thing for the purpose of this exercise? For that matter why can't a primitive stone axe head? They perform work and can be reproduced. The system graph and energy transfers is what is important in defining what metabolism and reproduction is, not our experience of how extremely complex things that we have studied intimately perform these same system graph characteristics. Thus things like, "mass flux", "high energy flux", "vesicles", "Proto-metabolism" etc. are not particular requirements when talking about the "system" before life as we know it. The energy graph is important for when metabolism is occurring, and that the system is locked away with reproducible features when the energy/reactants source is depleted. Thus if an axe head lies in the ground undisturbed for millions of years, it would be easy to reproduce. If it was being constantly bombarded by energy flux, ie. people using it, it would just wear away until it was no longer useful. Thus, an extremely encapsulated system, with persistent, naturally reproducible features is more relevant than looking at the amount of energy flux a motorcar needs to keep going, and applying it to the needs of an axe head.

"(1) Through a long and complicated process of prebiotic development containing all the most interesting parts of the story of the origin of life.

(2) As a system created by someone or something.

I don’t intend this as an argument in favour of intelligent design [see definition 1], still less of Intelligent Design [see definition 2]. Ockham’s razor suggests we should stick with explanation (1) unless we should find some very compelling evidence for (2). At any rate, the essential requirements of the pre-biotic processes leading to life based on the chemistry we know are going to be the same as the requirements of pre-biotic processes leading to life based on different chemistry."

Ockham s razor is a lie perpetrated by scientists to make out they have gnosis when they have none. Anyway, have you considered dust cloud life? Or plasma physics life?

We don't know that life that could create chemical life is based on chemistry. We have no gnosis on the requirements of life that may have generated biochemical life through an evolutionary prebiotic process of design. All we have is human experience of design as an evolutionary process with intelligent input. The intelligence is not enough to design something complicated from scratch, and thus the sequence of precedents from transistor to computer may be accessible to historians a million years into the future. Equally, whether intelligently designed or not, we should have confidence in the possibility of precedent biological life "designs" for us to discover.

"What I am arguing is that both the ‘RNA world’ and the ‘Protein world’ are historically late phenomena, and that the critical events for the origin of life lie much deeper."

I absolutely agree with this.

"There is no reason to expect that living systems today preserve the same chemistry of the first living systems. "

I absolutely *disagree* with this. Evolution and evolutionary design processes build on what is known to work. No point changing from silicon to something else.

Thursday, February 14, 2013

Show me the Metabolism, Marcomony Part 2.

"What are the requirements a catalytic system of complex polymers (CSCP) must have in order to be relevant to the origin of life?
The CSCP must be secured from the overwhelming tendency of matter and energy to become more randomly distributed in the universe. "

Already here we can see the erosive characteristics of parsimony in action starting to create poisoned fruit. Having rejected Kauffman's model of the origin of life based on CSCP due to not being able to demonstrate metabolism or how it would self generate, it becomes the assumed system for the rest of the post. I would change it to thus: The CSCP or whatever other system relevant to the start of life, must be secured...

In fact when I read it, I had automatically added that to the sentence because a CSCP has a vanishingly small chance of being a descriptive model of what actually hapened. Thus, I agreed with the sentence with a proviso that it does not validate CSCP in any way as a transitionary proto life form.

Thus Marcomony would dictate that we look this as a systems problem rather than as a CSCP problem.

The minimum requirement from a systems perspective is that energy finds its way in, and that the inside can be made less random by making the outside more random. Although that does require at least some "food" or reactants matter to get in and some "waste" or products matter to get out, the minimalist in me is saying that the in could be mainly light, and the out mainly heat, as something non-living that could exist in nature.

Thus a CSCP may or may not be something that comes between non-life and life, or may have been skipped for something that could actually happen, rather than being a wish myth.

When I saw the diagram, I got all excited. When I read about specific chemistry, I got all confused. Not because I didn't understand, but because I was thinking purely in abstract terms of the following.

Condition 1: An Edge.
Condition 2:A Proto-metabolism.
Condition 3: A Selectively Permeable Edge.
Condition 4: A Complexifiable Proto-Metabolism.

Systems we have designed ourselves with a great deal of effort.

 in all this, all it had proved to me that CSCP to do all this is impossible in terms of all the pieces that are required to just come together for no reason.

This is why, about this time last year, I had decided that a comet could provide the required edge to the system, and a catalytic species X would be the resultant more complex, less random thing being generated within the comet(s). The comet surface makes a natural, non-living edge.

Of course, we will have opportunities to see what is in comets now, as an indication of what may have been happening 4 billion years ago.

Show Me the Metabolism, Marcomony! Part one

This is in response to History of life posts by my arch nemesis Herr Fellows of Parsimony fame.

"My thesis is that the network of catalytic polymers and substrates that Kauffman postulates as an initial self-organising complex system which can give rise to more lifelike systems is so inordinately complex and unlikely that it in no way addresses the crucial problem of the origin of life."

Completely agree. I would even extend that to say that it is probably impossible.

"Any chemist would ask: 'What is driving this cycle of reactions? Where is the energy coming from? What is preventing this system from dissipating?'
There is no such thing as 'Order for Free'. That is the Law. If you want order at point A, you need to dump your disorder at points not-A. Should anyone claim there is such a thing as 'Order for Free', let them be unto you even as the homeopaths and the creationists."
Absolutely. It is a very contrived system that is required, and a plausible natural mechanism is required that would probably  generate it (Not *possibly* generate it - it needs a contrived repeatable mechanism that we would think hah! that just could work if I could repeat the conditions precisely)
Metabolism is the key. My thought is that any systems which generates copies of something is showing metabolism anyway. You can see energy being burned in the suns in the sky and emanating from the hot cores of planets and dumped randomly into the rest of the universe. There are not just a few planets and suns - They have imperfect copies of themselves all over the universe. It is a loose use of metabolism and reproduction, but the universe is full of things that make their outside more random and are reproduced somehow.

Thursday, February 07, 2013

Food Nazi's gone nuts

I did some research on my own diet and possible deficiencies and I decided that I probably was a little deficient in Selenium. Selenium is required in trace amounts, especially to help remove heavy metals, such as mercury from the body. It is also toxic in larger, non-natural quantities. Knowing I was on the low side, and wanting to get my selenium from natural sources. The best natural source of Selenium is Brasil nuts. But there is a twist, as I found out that un-shelled brasil nuts come from a part of South America that has a very high soil Selenium content, and thus unshelled nuts that you can buy are up to 10 times higher in Selenium than than shelled nuts. I figured I could buy nuts in shell on the Internet. Ironically, I bought some from a parrot food and toy specialist.