Thoughts on the Existence of the Universe

[Fickle]

Baruch

So there are times that reductionism works ... like with uncomplicated things like salt crystals.  But there are times when reductionism doesn't work ... like with highly complicated things like humans.  If you misapply your method, you will conclude that humans are the same as salt crystals.

We can have very few parts but many options. There are more ways to arrange a deck of 52 cards than there atoms on the Earth. Now we may not have very many basic particles however we have an infinite number of possible field variations relative to each part because the fields linking them are a gradient.

Thus we might come to the conclusion that almost anything may become more than the sum of it's parts. It is not reducing everything to it's basic parts but realizing the pattern of how the parts relate to one another...information.

[trdsf]

The primary thrust of my argument is to point out that anthropomorphism infects YOUR argument.  Dawkins coined the term Selfish Gene, not me.

And he was very careful to point out the sense in which he meant 'selfish', and it is not in terms of any active will on the part of the gene -- the word 'selfish' is meant as a metaphor, a mental shorthand to grasp that the "desire for survival" (it's difficult to avoid anthropomorphizing because the metaphors are quite useful) on the part of the gene is without any particular regard for the organism that carries it.  Clearly the gene has no actual 'desires' or any ability to express 'selfishness' any more than a single cog in a pocket watch can wish you a good morning.

And anyway it makes for a much catcher title than "The Survival-Optimized Gene Complex".

An excerpt from my previous post:

The atoms in any living organism are in a higher state of energy and lower state of entropy than they would be as constituent atoms.  This places them in an unstable state far from equilibrium.  From a chemical/thermodynamic perspective, they should just die and decompose versus taking energy from the environment to maintain their low state of entorpy (we all will eventually succumb to entropy.)  While it is true that energy from the sun (or thermal vents) could provide the energy for some initial chemical reactions, it is unreasonable to conclude that they would just continue indefinitely without some force to drive them.   Most reactions involve a compromise between lowering energy and increasing entropy.  Something that increases energy and lowers entropy must have an external driving force.

I might be willing to grant that the collection of atoms that makes up a living organism is in a low state of entropy, but the individual atoms are not particularly.

And there is an external driving force: fundamentally, everything on this planet is solar powered.  Even carnivores, because the herbivores which they eat, eat plants which use sunlight to power chemical reactions that allow them to store energy.  That's what a plant in the food chain is: a solar battery converting sunlight into food for an herbivore or omnivore.  You just ate a salad?  You just ate a bowl of sunlight made into a form that you can digest.

Planet Earth is emphatically not a closed system.  If it were, we wouldn't be here.  And that's the fundamental error in your assertion here: you're talking about individual systems as if they were closed systems.  Individual humans are not thermodynamically closed.  The entire planet isn't thermodynamically closed.  Stephen Hawking in A Brief History of Time calculated that the decrease in entropy involved in memorizing that book is far more than offset by the increase in entropy involved in the simple release of body heat while memorizing it.  So the appeal to entropy here is not relevant.

At some point in the history of life on earth, a self-ordering, autocatalytic chemical system had to develop characteristics to which selfishness could be attributed.  The driving energy and/or the chemicals needed for reaction would have had to exhaust themselves at some point in a process that took millions of years.  At that point those pre-biotic replicator molecules should have simply ceased to exist.  Instead those autocatalytic chemicals must have had to manipulate the environment in order to extract energy in an act of self-preservation. 

While the will to live/self-preservation can be rationalized in a sentient being, it can’t be explained in a simple organism or the replicator molecules you describe.

It is accepted as a tenet of evolution that self preservation is the default mode for all living organisms.  While I accept that, I am asking HOW that came to be.  I can understand it in a sentient being, but not in a molecule.  Natural abiogenesis dictates actual anthropomorphism of a replicator/pre-biotic molecule.  Since I equate that with an inanimate object like the Statue of Liberty actually singing and dancing, I think it is reasonable to consider the supernatural as an explanation.

This is a profound misunderstanding of the process of abiogenesis.

All that happened was that a molecule capable of self-reproduction accidentally arose out of the uncounted billions of billions of billions of relatively random chemical reactions going on in the pre-biotic water of Earth, powered by a combination of solar radiation, locally produced heat (volcanic or otherwise), the odd bolt of lightning.

That the molecule copied itself has nothing to do with "self preservation" or the "will to live".  It copied itself because it could copy itself.  Because that was the chemical function of that molecule.  Absolutely zero intelligence or will was required for the process.

Do you think sugar dissolves in hot tea because it wants the tea to be sweet?  It dissolves in tea only because it is soluble in water.  That's all.

You're the one insisting on anthropomorphizing here.  Self-preservation and will have nothing to do with evolution.  Think of all the insects that die pretty much as soon as they lay their eggs -- a single mayfly breaks your theory.

All abiogenesis is, is the random appearance of one molecule that can self-replicate.

Since it is made from its local chemistry, it's clear that it should be surrounded by the same sorts of molecules from which it was assembled (it'd be pretty hard to put together a molecule based on hafnium in a soup of miscellaneous carbon-based molecules), and from which more copies can be made, and it does so only because that's what a self-replicating molecule does.

The first one was certainly slow and inefficient, and probably not completely accurate, but it was the only game in town, so it would have come to be the dominant molecule in its area.  Along the way, copying errors would have been made.  Some would have broken the molecular machine, and not reproduced.  Others would have been better copiers, either faster or more accurate or maybe even both, and they would have come to dominate.  Ultraviolet radiation, which was in tremendous supply in the pre-oxygen atmosphere that lacked an ozone layer, would have broken up some molecules, changed others, and added further mutations to the mix.

And these random chemical experiments are taking place in their uncounted billions per cubic centimeter of water (there are something on the order of 10²² molecules per cm³) over hundreds of millions of square kilometers of surface water to a depth of a few meters over hundreds of millions of years.  I expect it happened multiple times, but only the best replicator survived and the oceans were eventually chemically predated (as in predators, not as in calendars) to the point where the concentration of free hydrocarbons was too low for a reasonable chance of another replicator arising new -- the really useful molecules would have been 'consumed' by the existing replicators.

After that, it was pure evolution: random interactions over vast stretches of time.

When you're talking numbers like that, I have to believe that abiogenesis becomes inevitable just as a matter of pure statistics.  The numbers are too huge for it to not happen -- if it were a one in a billion chance, it would have happened instantly billions of times.  That's the kind of scale we're talking about here.

Now, why can't we nail down the specifics?  Because we're talking about one molecule about 3.7 billion years ago.  Because we don't have a spare planet to watch for a couple hundred million years, and even if we did, we can't monitor every cubic centimeter of water continually.

[Baruch]

Many authors complain that the publisher chooses the title of the book, for marketing.

I really liked you exposition trdsf.  Self-replication implies catalysis, and a cell is a very advanced catalytic system.  Also the "purpose" of a particular sub-system might have been different in the pre-Cambrian, but later adapted to new uses.  And for that reason, I think that we cannot know in detail, what purpose a given DNA strand served back then, only that most of the DNA is "junked" today, not useful today, but held in reserve for future needs.  So to really understand, one has to know the full history, past and future.  Just knowing the present context of a gene is useful, but not enough.

[sdelsolray]

As others have mentioned, anthropomorphism infects your arguments.  Consider removing it.

The primary thrust of my argument is to point out that anthropomorphism infects YOUR argument.  Dawkins coined the term Selfish Gene, not me. 
...

I have made no argument in this thread, yet.

You project with a side salads of, "Hey look over there", and denial.  Lame.

I was going to take things one at a time, but that didn't work, so I'll string two things together in the interests of efficiency.

You use anthropomorphism to support an argument from incredulity.

I changed my mind.  Three things.  The two above plus you don't seem to understand the difference among open, closed and isolated entropic systems.  Perhaps you know the difference but are ignoring it.  That would certainly be more devious, adventurous and entertaining.

[Baruch]

open = heat/energy/info is able to go thru the boundary in both directions
closed = heat/energy/info is not able to go thru the boundary ... because it is insulating
isolated = heat/energy/info is not able to go thru the boundary ... because of distance

Please enlighten us ;-)

[trdsf]

Many authors complain that the publisher chooses the title of the book, for marketing.

I really liked you exposition trdsf.  Self-replication implies catalysis, and a cell is a very advanced catalytic system.  Also the "purpose" of a particular sub-system might have been different in the pre-Cambrian, but later adapted to new uses.  And for that reason, I think that we cannot know in detail, what purpose a given DNA strand served back then, only that most of the DNA is "junked" today, not useful today, but held in reserve for future needs.  So to really understand, one has to know the full history, past and future.  Just knowing the present context of a gene is useful, but not enough.

And it's hard to even call it 'junk' DNA since under the right circumstances, those genes can still be activated.  Chickens can be given their dinosaur ancestors' teeth and tail, for instance.  One wonders what ancient traits might still be in our DNA, though I'm not sure what parts and structures we might want to have back...

[u196533]

Let’s agree on some basic chemistry/thermodynamics to get us on the same page.  Otherwise, we’ll waste time in violent agreement on irrelevant tangents. This might be remedial for some of you, but bear with me.

The 2nd Law of Thermo applies to all systems, not just closed ones.  Yes, it is true that an open system can absorb energy in order to lower it’s entropy. However that new energy is still distributed as much as possible within the system as dictated by the 2nd Law.   The Krebs cycle that cells use to create ATP is an example of entropy within an open system.  (It can be debated as to whether entropy can be defined as disorder.  While I think that it can, I will stick with the classic, therefore irrefutable, definition associated with heat/energy transfer.)

There is also a drive to lower energy, and most reactions are a compromise between lowering energy and increasing entropy.  Chemist use the Gibbs Free energy equation to determine whether a reaction will occur spontaneously based on its increase (or decrease) in entropy combined with its increase (or decrease) in enthalpy (internal system energy).  For example a crystal can form spontaneously when it’s loss in entropy is offset by the reduction in energy that occurs when it crystallizes.
 
A system will not spontaneously lower it’s entropy AND increase it’s energy.  That can occur, but work must be done by an outside force to make that happen.  The result is a not a stable system since it is far from equilibrium.  That system will eventually lose it’s energy and/or increase it’s entropy in a move toward equilibrium.

The atoms that comprise a living system are far from equilibrium since they are collectively in a lower state of entropy and a higher state of energy than they would be as constituents.  That is why things decompose when they die.  Living things maintain their low entropy by consuming energy (food).  However, that contradicts the normal drive to lower energy and move toward equilibrium. 
Only living things exhibit this behavior.  This can be explained for some things like a baby in the womb.  It is being force fed nutrients and supplied energy.  It can be explained in sentient beings by self-preservation.  We eat because we don’t want to succumb to entropy and die.   

However, this can’t be explained in the simple chemical systems described in the origin of life narrative.  It is conceivable that the perfect environment of driving energy and chemicals existed for a period of time to allow the first replicator molecules to incubate.  (I think it is unreasonable to claim that a stable environment existed on earth for hundreds, let alone millions, of years, but I won’t argue that point.)   However at some point in the evolution from replicator to early life those replicator molecules and/or primitive life forms HAD to have manipulated the environment to extract energy and/or obtain food.  How could a chemical system exhibit self- preservation and seek out energy versus just ceasing and moving toward equilibrium like an inorganic system would do?  This is equivalent to a candle opening a window as it runs out of oxygen or a hurricane abruptly changing direction to avoid land and find more warm water.

The first one was certainly slow and inefficient, and probably not completely accurate, but it was the only game in town, so it would have come to be the dominant molecule in its area.  Along the way, copying errors would have been made.  Some would have broken the molecular machine, and not reproduced.  Others would have been better copiers, either faster or more accurate or maybe even both, and they would have come to dominate.  Ultraviolet radiation, which was in tremendous supply in the pre-oxygen atmosphere that lacked an ozone layer, would have broken up some molecules, changed others, and added further mutations to the mix.
While this was not part of my original argument, I have to respond to these outdated ideas.  Please look into the latest research on replicator molecules.  To say that replicator molecules are not common is an understatement.  The assumption that a replicator molecule could mutate during reproduction and the resulting mutant would also be a replicator molecule is absurd.  That idea may have been fine back in the 1970’s, but the last 30 years of cellular and micro-biology have disproven that idea. 

[Baruch]

And it's hard to even call it 'junk' DNA since under the right circumstances, those genes can still be activated.  Chickens can be given their dinosaur ancestors' teeth and tail, for instance.  One wonders what ancient traits might still be in our DNA, though I'm not sure what parts and structures we might want to have back...

Monkey tails, definitely tails .. at least for politicians ;-)

Activating junk DNA is another example of Jurassic Park insanity though.  I envisage giant meat eating chickens.

[PopeyesPappy]

Please look into the latest research on replicator molecules.

That's good advice. I suggest you try it.

The assumption that a replicator molecule could mutate during reproduction and the resulting mutant would also be a replicator molecule is absurd.

Sorry but no. Recent research on varients of the R18 ligase ribozyme proves that mutations to the original sequence can result in improved polymerization. tC19Z could only polymerize up to 95 nucleotides. That's about 50% of it's length. Just four mutations later tC9Y can polymerize up to 206 nucleotides. That's 102% of it's length.

The bar chart depicts various improvements to the class I ligase ribozyme5 that can perform a single ligation reaction compared with its approximately 118-nucleotide length. Variants of this ribozyme type were selected in vitro to perform multiple ligation reactions in search of processive polymerization. These included the E278-19 ribozyme3 that can perform three successive ligation reactions, the R18 ribozyme that can polymerize 14 nucleotides2, the B6.61 ribozyme that can polymerize 20 nucleotides4, and the tC19Z ribozyme, that can polymerize up to 95 nucleotides6. The latest development tC9Y, can polymerize up to 206 nucleotides8, thereby finally exceeding its own length (202 nucleotides). Compared with tC19Z, this record-setting ribozyme has three cold-derived mutations (blue circles) in addition to one 'general up' mutation (red circle). The per-position error rates of most of these polymerases falls in the 0.1â€"1% range, putting them near the minimum level needed to sustain biological information in the long run.

[u196533]

The Recent research on variants of the R18 ligase ribozyme might contradict my last statement, and I probably stand corrected.  However, I have to wonder if this is a self replicating molecule or a catalyst. (Interesting stuff though.) Either way this was a tangent that I should not have brought up since it detracts from my primary argument.

[u196533]

That ligase ribosome is not a replicator molecule; it is a simple catalyst.  When the energy that drives the polymerization or the reactants are consumed, does the polymerization cease?  Or does this molecule seek additional reactants and/or energy?

[PopeyesPappy]

As far as I know no one claimed the R18 family is self replicating. In fact it is considered a dead end, but the research is one of the early attempts to create self replicating RNA. I brought it up because it is a clear cut example from the field of study in question that shows mutations can improve the ability to perform multiple ligation reactions. But if you get right down to it your claim that, "The assumption that a replicator molecule could mutate during reproduction and the resulting mutant would also be a replicator molecule is absurd" is absurd. If your claim were true then the only progeny that would be able to reproduce would be an exact clone of its parent, and we know that is false.

[widdershins]

Lol, this started as a thread to give a tired old argument about how the universe requires a maker, who does not require a maker because REASONS, but then SCIENCE HAPPENED!  Only here can a thread go from borderline retarded to "What they fuck are you guys saying?  Is that even English???  The words...sooo big....they hurt!"

[u196533]

In fact it is considered a dead end, but the research is one of the early attempts to create self replicating RNA. I brought it up because it is a clear cut example from the field of study in question that shows mutations can improve the ability to perform multiple ligation reactions
No, it is not an example of self replication.  The replicator molecule would have to replicate WITHOUT a catalyst (auto-catalytic).  The is an example of a catalyst that could string together amino acids.  Then it mutated into another catalyst that could string a few more amino acids than the original.  The best minds in chemistry and molecular biology have been at this for over a century, and that's the best you can do?

"The assumption that a replicator molecule could mutate during reproduction and the resulting mutant would also be a replicator molecule is absurd" is absurd. If your claim were true then the only progeny that would be able to reproduce would be an exact clone of its parent, and we know that is false.

DNA is a complex molecule that has a mind boggling process for replicating.  Errors can be made that substitute amino acids (etc. guanine for an adenine) or other errors that lead to mutation.  It does not follow that a much smaller less complex molecule that simply replicates itself would also produce a replicator.  Decades of research have yet to show that.  The research tends to show the opposite.
Your argument is a classic example of circular logic:
Natural abiogenesis occurred. 
Therefore since DNA/RNA is too complex to be the original, a replicator molecule was the ancestor that evolved into DNA.
DNA mutates into something that replicates.
Since abiogeneis is true, the replicator molecule must have mutated into something that replicates.

[u196533]

Only here can a thread go from borderline retarded to "What they fuck are you guys saying?  Is that even English???  The words...sooo big....they hurt!"

Allow me to re-state my argument in more common terms (hopefully without losing too much technical accuracy):
Chemical reactions have 2 primary drives.  1.  They want to lose energy.  (Things burn readily because that allows them to give off energy.) 2.  They want to disperse/distribute their energy as much as possible.  (Batteries discharge until the electrons are equally distributed among the cells.  Heat moves from hot to cold surfaces until everything is at the same temperature. Etc.)
Most reactions are a compromise between these 2 drives.  They will increase one to decrease the other and vice versa.  However, a system will not take on energy AND consolidate its energy spontaneously.  That requires an outside force to do work to make that occur.  When it does occur, the system is in an unstable state, and will revert back (lose energy and/or disperse the energy) at its first opportunity.
Living things exist in this unstable state.  If you look at any life form as a bag of chemicals, you will conclude that it will decompose.  (It ultimately does when it dies.)  We eat things (consume energy) to maintain this unstable state.  However, living things are the only things that seek to take on energy to maintain an unstable state.  What drives us to do that when a non-living thing would just cease or decompose?
The only natural explanation is self-preservation.  If you apply it to the origin of life from non-life, that means that at some point, a simple chemical system HAD to have searched for food and avoided “unfriendly” chemicals that would cause it to decompose.  (There was no cell membrane to cocoon it, and these molecules are reactive and unstable.) 

Yes.  I suppose this is an argument from incredulity, but that does not invalidate it.  I would sooner believe that 2 penguins walked from Antarctica to get on Noah’s ark. 

I don’t care what someone else believes provided they aren’t an asshole.  If you choose to believe this, then I suggest that you do some research on the large laundry list of hurdles associated with the origin of life from non-life.  (Creating proteins from amino acids, proteins break down in water, homo-chirality, preventing unwanted reactions without a cell membrane, creation of a cell membrane, etc. etc.)  Then consider that most of those reactions are not favorable from a chemical/thermodynamic perspective.  (The result is a system in an unstable state.)  If you dig into it and still believe that it is reasonable, that’s fine.   At least you will be able to justify your belief.  However, don’t just read some book written 40 years ago before we knew anything about molecular biology and swallow it hook, line and sinker.  That is not the hallmark of a critical thinker.