[ExI] Chemical Origins of Life (was Re: Panbiogenesis)

The Avantguardian avantguardian2020 at yahoo.com
Fri Feb 3 16:46:12 UTC 2012

 ----- Original Message -----
> From: Kelly Anderson <kellycoinguy at gmail.com>
> To: The Avantguardian <avantguardian2020 at yahoo.com>; ExI chat list <extropy-chat at lists.extropy.org>
> Cc: 
> Sent: Friday, February 3, 2012 2:53 AM
> Subject: Chemical Origins of Life (was Re: [ExI] Panbiogenesis)
> On Fri, Jan 27, 2012 at 5:29 AM, The Avantguardian
> <avantguardian2020 at yahoo.com> wrote:
>> The biogenesis people say that is because conditions on early earth were 
> different.
>> That is fine. But we can simulate early earth chemically in a lab. We get 
> organics but
>> not life, not yet, *not once*, not after decades of trying.
> This is an extraordinary statement. It's the kind of stuff I read in
> second rate Creationist literature. I expect better of this list.
> Let's dive into the details for a bit. I've been studying this subject
> fairly deeply for about the last two months, so this is pretty fresh.
> I'm not exactly an expert, but I'm trying to learn what I can about
> the chemical origins of life. If I make any mistakes in this posting,
> hopefully they'll get corrected.

How is that simple statement of fact in any way related to Creationist literature? If you find me one credible reference to or evidence of an observed or induced abiogenesis event *anywhere* this geologic eon and I'll ask John Clark to pay you that dollar he's been teasing Damien with all this time.

> First off, simulating RELEVANT environments of the early earth in the
> lab is extraordinarily difficult. Three of the environments in which
> early chemical evolution (pre RNA stuff that must have occurred) is
> hypothesized to have possibly happened are hydrothermal vents at the
> ocean floor,  and/or deep within the crust of the earth assisted by
> minerals and/or inside crystalline structures in clay. (There are
> other hypothesis, but these three give a flavor for how diverse
> current lines of thinking are and how hard it is to follow the
> evidence or reproduce results in the lab.)

There are microbiologists scouring the hydrothermal vents you speak of for extremophiles all the time. Believe me they finding a claymation cell down there would be front page news. Are you suggesting hydrothermal vents are significantly different in pressure, temperature, or chemical composition then as opposed to now? What was *special* about undersea hydrothermal vents then versus now?

> Some simple steps may have occurred in deep space, which is equally
> difficult to simulate in lab conditions. The best vacuum we can
> produce is a thousand times as dense as the typical patch of space in
> a "dense" interstellar cloud. (Only an astronomer would consider a
> vacuum of this quality a "dense" cloud... LOL)

Yes, now the universe doesn't qualify even as a thin gruel. But once it was soup. 

> Just simulating the pressures of the ocean floor or deep within the
> earth's crust in the lab is extraordinarily difficult. Keeping those
> pressures up for a long period of time is impossible. Keeping it up
> for the millions of years that the early earth had to work with (and
> needed) is obviously impractical. Doing so in the presence of the
> right minerals requires knowing what those would be, and we have no
> idea what those might be (if indeed minerals played an important roll
> at all -- but they probably did).

Well we know what minerals are essential to life. Look on a Centrum label for the gist of them. Why would a specific set of minerals then give rise to new life? Why wouldn't those minerals do so now? 

> Many simpler elements of life have been synthesized in the lab, such
> as most amino acids, lipids and simple cellular wall structures that
> are made of lipids, and a few other things have been synthesized in
> enough different ways that there is no doubt the early earth was full
> of these simple chemicals.

Yes. It would have provided a feast for any extra-terrestrial microbe upon landing here.

> There is a great hole in our understanding between these simple
> chemicals and replicative chemical systems with the hereditary memory
> and possibility of mutation that is required to get to life.

It really all boils down to entropy. Life is a self-sustaining biochemical cycle using the free-energy of food to shed entropy into the rest of the universe starting with the food itself. It is a perfectly coordinated dance of thousands upon thousands of molecules each so complex that computers have trouble simulating thir folding as you pointed out.  Here is but a small cross section of the chemistry happening in a whiteblood cell that triggers it to crawl out a capillary at the site of an infection. Note that everything except the very beginning and very end is happening inside the *one cell* and they don't even take you into the inner sanctum of the cell, the nucleus, where all the stuff with DNA happens..


See how the individual dead molecules look like they themselves are alive? Dancing in perfect yet unchoreographed harmony? That's some *serious* negentropy. That's the challenge faced by scientists. It's like putting a bunch of Legos into a cement mixer and expecting the Taj Mahal to come out.

> But it
> seems very highly likely due to the situation on the surface of the
> earth at the time (Hadean Eon -- meteor and comet bombardment, bad for
> life on the surface) that whatever happened happened at very high
> temperatures and pressures. (This seems especially likely since life
> evolved in the first 100,000,000 years after the surface became
> semi-habitable, which was pretty darn fast in those days.) There are
> only a very small number of labs that can simulate these conditions.
> Robert Hazen's (Genesis - The Scientific Quest for Life's Origin)
> telling of his experiments at 2,000 atmospheres and 250 degrees C with
> pyruvate welded into gold capsules the size of a grain of rice are
> harrowing. This is NOT easy stuff to do, even with the most competent
> help in the world and lots of NASA money.

2000 atmospheres is pretty harrowing but we can actually quite easily do 3,000,000 atm in a diamond cell press. Don't think that would help much though. You are welcome to try. Don't think he got any noteworthy results did he? I didn't say it was easy, I said it might be impossible in the modern era, except by nanotech.

> Similarly, we do not have good enough computer simulations to
> determine what might go on chemically in such circumstances that way.
> We can't even fold protein with computers without using supercomputers
> or distributed mesh computing.

Why would computers be able to simulate, at least partially, a modern cell, but not an ancestral "claymation" progenote?

> In addition, we have no equipment capable of sorting out the kinds of
> replicative emergent games that are going on inside of clay. We just
> barely got DNA sequencing machines, and we KNOW that's important.
> There is no equipment that can analyze the crystals in clay at the
> level that would be required to truly follow that line of questioning.

Clay does not reproduce to my knowledge.

> The production of life from chemicals is FAR too large a jump to have
> happened in one jump. There MUST have been an evolutionary system
> prior to RNA to jump start the system. But we have no clear idea of
> what that system might have looked like. Did it involve minerals deep
> in the earth's crust at high temperature and pressure? Who knows? But
> it might have. Or it may have been a small part of an extremely
> complex and unlikely set of circumstances occurring in a number of
> environments.

But if it worked then why doesn't it work now? How come this meneral life doesn't yet exist somewhere? It is highly unlikely that mineral life and normal carbon based life would compete for the same resources or environment so where is it? It just decided to commit suicide because it was inferior or something?

> Am I saying that Panbiogenesis is impossible? No, that's just another
> of a group of interesting theories floating around out there (joke
> intended)...

Well at least you are keeping an open mind about it. After all, Panbiogenesis is more in line with the Copernican Principle than is terrestrial abiogenesis. After all if life is so damn hard to kick start, then it would exaggerate Earth's importance to insist it started here. Furthermore it is bound to piss off the Creationists because the Bible is the main source of the idea that the Earth is somehow special. I am saying, it isn't even the cradle of life.

> Mr. Hazen's book is very interesting. And it points out that we are
> just about as clueless about the chemical origins of life as Newton
> was about Quantum Mechanics. I believe science will eventually figure
> it out.
> However, to criticize the current scientific community for not yet
> producing life in the lab the same way as it came about on the early
> earth plays into the hands of eager creationists and is grossly naive.

It was more an observation than a criticism, but in way a scientist's job is to get criticized. That is part of the peer review process. And believe it or not, I am a certified peer when it comes to microbiology, immunology, and molecular genetics. So let me know if you willing to pay to get your dog cloned. ;-)

> A hydrogen atom is approximately 2.5 x 10^-11 meters (25 pm) in diameter.
> A water molecule is approximately 280 pm across.
> A cell membrane is 10 nm thick
> A clay particle is about 10^-6 m (micrometer) across. (you can see why
> figuring out their crystaline structure is hard)
> A typical Prokaryotic Cell is 250 micrometers across.
> See http://htwins.net/scale/

We can take pretty accurate pictures of nanometer scale protein molecules (1/1000th of a micrometer) using X-ray cystallography, diffraction, NMR, and IR spectroscopy all the time. I seriously doubt any clay crystal could be anywhere near as complex as a protein or DNA.

> The point here is that getting from organic chemicals with less than
> 100 atoms (which is what has been produced in Stanley Miller type
> experiments). Or lipids with a molecular weight around 2000* to
> something with around 1,000,000,000 atoms, which would likely be the
> size of the simplest theoretically functional cell... is an extreme
> jump that requires some kind of emergent, evolutionary process. Or
> God. And I don't think science has had enough time to work on the
> problem to jump immediately to the God hypothesis.

What God hypothesis? Why do you have God on your mind?

> Stating this more carefully... The largest structure we have
> synthesized in the laboratory at this point is a very primitive
> cell-type wall built of lipids. No doubt, there are tens of millions
> of atoms that go into these structures, but they are extremely simple
> compared to a bacteria, and by no means do they approach reproducing
> life forms. They don't even approximate useful cell walls, as there
> are no holes... and even bacteria need to eat and poo.
> We have no mechanism yet to describe the production of proteins
> containing more than a paultry number of amino acids. Amino acids
> don't spontaneously form polymers without a lot of tricky assistance.
> I would be pretty darn impressed if we could show a plausible scenario
> for the spontaneous emergence of just the citric acid cycle.

Ok. Imagine a low entropy universe with a lower fine structure constant. Atoms hold onto their electrons more loosely because of this. Because electrons would easier to move from molecule to molecule, all chemical activation energies would be lower so many reactions that are not now spontaneous would be. The citric acid cycle might have been able to proceed without catalysis, i.e. without enzymes. Likewise polymerases would not have been necessary as every possible polymer would have formed. Lipid bilayers would have been spontaneously forming and wrapping around random mixtures of enzymes and substrates. Then as over the aeons, the fine structure constant grew larger, electrons clung more strongly to their atoms. Only those compartmentalized spaces containing the right mixtures of catalysts, i.e. enzymes would have been able to continue the chemical reactions of life. Those compartments became cells, little time capsules containing information
 patterns that existed in a low entropy universe.

It is just speculation at this point, but it seems plausible to me.  

> In conclusion, it is ridiculous to expect to observe abiogenesis
> directly in the lab. It is many trillions of times more likely that a
> chicken would spontaneously give birth to a dinosaur without
> assistance from Jack Horner!

Ok so lets do the math. Hazen says it took about 100 million years from end of the asteroidal bombardment to first life to show up. Dinosaurs first appeared 230 million years ago. The first bird appeared about 150 million years ago, that means there were about 80 million years between the dinosaur and the bird. So to go from a dinosaur to a bird is slightly more likely than the abiogenesis event Hazen assumed happened here on Earth 3.5 billion years ago. Yet to go from a bird to a dinosaur is a *trillion* times more likely than the same thing happening in a lab? That sounds like Hazen is pulling numbers out of his ass. It doesn't even seem like Hazen's argument is consistent with itself let alone the scientific data. And negative results are still results.    

> Nevertheless, there is enough of a lead to continue to investigate how
> abiogenesis could have occurred terrestrially. Even if you buy into
> panbiogenesis, life had to arise somewhere first, or "God Did It"(TM).

Well it might have happened almost everywhere back when everywhere was pretty small.

> The most interesting concept I've run into during these studies is
> emergence. Totally fascinating stuff that.

Emergence *is* fascinating. Happy discovering.

Stuart LaForge
"When the going gets weird, the weird turn pro."- Hunter S. Thompson 

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