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

[Kelly Anderson]

On Fri, Feb 3, 2012 at 9:46 AM, The Avantguardian
<avantguardian2020 at yahoo.com> wrote:
>
>  ----- 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?

Creationists are always saying that the emergence of life was so
immensely complex that it could not have possibly happened without
God's hand. The panbiogenesis argument feeds these fanatics with
quotes from scientists about how improbable the emergence of life is.

Your statements about our ability to create the right conditions in
the lab are vastly overstated, and the kind of thing that the
creationist crowd would just eat up. Don't be surprised if you are
quoted in creationist literature someday with statements like that.
When making statements about life's origins, you always have to think
in terms of two things, 1) What would this sound like out of context,
and 2) How could this be misconstrued by a malicious creationist to
make a plausible argument to the great unwashed masses.

> 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.

Not going to happen. We can assume that the same STEPS that took place
in the prebiotic earth are taking place now, all the time, on earth.
However, since there is bacterial life everywhere now, the results of
these steps get eaten as food by the bacteria before scientists can
put the pieces together, or before life can reemerge spontaneously.

Just the efforts required to get a few deep earth cells from deep
mines in South Africa are harrowing. We just don't have the equipment
to figure out what's going on in the deep rocky earth. People are
always saying that the oceans are the great unknown domain... and
while that is true... long after we've figured out everything in the
ocean, we still will have a long way to go in understanding the
biological processes taking place in the deep crust of the earth.

>> 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.

I saw a nat geo video just yesterday where one of these guys was
saying how difficult it was to visit the hydrothermal vents, and how
the original find near the Galapogos was only then being visited for
the second time, after 30 plus years. So NO, we do not scour these
vents ALL THE TIME... we have no idea of the cycles of life that take
place around vents. We just have a couple of snapshots, and the guy
was saying, if you only saw trees in the winter, you would think trees
didn't have leaves. Well, apparently, that is the level of
understanding this guy thinks we have about the life cycles around
vents.

Extremophiles are already cellular forms of life. We're talking about
prebiotic semi-living systems.

>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?

Of course not. Don't be silly.

>What was *special* about undersea hydrothermal vents then versus now?

Now, they are covered with extremophiles, worms, crabs, etc. that eat
the evidence. That's what's different 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.

Yup, long long ago.

>> 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?

Ok, you aren't thinking along the lines I am. Think more of chemical
reactions that might take place on the surface of subterranean
crystalline structures. Those minerals could have acted as catalysts
for early prebiotic reactions. That's Hazen's hypothesis, and it is
just a guess at this point... but he has some interesting experimental
evidence that more interesting things happen to organic molecules when
there is a crystalline substructure that can support more regular
growth of molecules. Think of the minerals as scaffolding that can be
used to build up complex organic structures that could not form just
floating around in water. It is a very interesting hypothesis.

>> 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.

You are correct about that. LOL. Just don't get stuck on just one
theory. We don't know enough to pick a winning theory at this point.
Panbiogenesis is one theory among many. And it is too early to say
that we even have the right theory in our bag of hypothesis at this
point. This is bleeding edge science. Anybody who thinks they have all
the answers at this point is sadly mistaken.

Take Stanley Miller, for example... him and his students have been
able to attract most of the NASA research money for abiogenesis
research up to about a decade ago because they were the first to build
amino acids, and their idea of the ocean of prebiotic soup has been
the prevailing hypothesis for decades WITHOUT ANY REAL PROOF that is
what happened. We NOW know that amino acids are formed in dozens of
ways. Easily. Everywhere. If we get stuck on any hypothesis to that
degree, it slow science down.

This area is really different than most of science today because it is
so young, and has learned so little about the subject matter. Working
on prebiotic life today is like being Galileo or Newton. We're just
barely getting started, and it is truly VERY exciting because it is
such an unknown.

>> 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.

Doesn't everything? :-)

> 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.

Now you're sounding like you want to be quoted by creationists
again... just a little. :-) But I get your point.

>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..
>
> http://www.studiodaily.com/main/technique/tprojects/6850.html

There was a TED speaker who noted about this animation that it was
highly unrealistic. It's too slow, it doesn't get across the idea that
being inside of a cell is a bit like being in a shooting gallery. But
it is all likely to be explained through emergent prebiotic chemistry
someday. We will NEVER be able to disprove panbiogenesis. We'll never
be able to prove it either, though if we find similar life out there
somewhere, it will be evidence... however you'll have to prove now
that it didn't come from earth... reverse panbiogenesis... :-)

>
>
> 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.

Now you ARE sounding like a creationist. Emergence will eventually
show how all this could have happened. It may or may not have happened
here first, but even if it happened somewhere else first, it had to
happen first somewhere, right? So we should try and figure that 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.

Not me. I'm no experimental scientist!

> Don't think he got any noteworthy results did he?

As a matter of fact, he has gotten noteworthy results. He's gotten
enough results to attract serious NASA money, even though the Stanley
Millerites fought against it at first.

> I didn't say it was easy, I said it might be impossible in the
>modern era, except by nanotech.

I'm not sure what nanotech has to do with high temperatures and
pressure... Maybe I missed your point.

>> 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?

Computers can only simulate simplistic models of modern cells. We
can't simulate a cell at the atomic level.. see protein folding...
You're being defensive now.

>> 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.

Ah, now here you are uninformed. This is cool stuff. James Ferris of
Rensselaur Polytechnic Institute induced clays to act as scaffolds in
the formation of RNA. John Desmond Bernal, Jack Szostak, Gustaf
Arrhenius, Leslie Orgel and many others have done fascinating work in
this area.

The basic idea is this...

Clay forms microscopic structures (see Graham Cairns-Smith 1988) that
are sheet like, and layered. These can form in one of three directions
that look a little like the surface of a silicon wafer... when wet
clay gets on top of one of these layers, it's directions align with
the clay underneath.. providing a rudimentary form of reproduction
when they subsequently separate. "In two-dimensional crystal genes,
information would be held as a pattern on one face of the crystal",
Graham says. It's a wild hypothesis, but so is panbiogenesis... but if
the right clay pattern could evolve, then it could provide the surface
to catalyze the creation of complex RNA sequences.

>> 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?

It does. But all the intermediates get eaten. We now have worms
burrowing through all the clay in the world that might otherwise play
these games.

>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?

It is slow. It is sensitive. In the energetic processes of life, from
worms to microorganisms, there is no chance for it to do it's thing
now a days. And in the lab, we don't have hundreds of millions of
years to see what might happen.

>> 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.

Of course I am. I never said it was ridiculous. However, to the normal
man on the street, it sounds ridiculous. Picture a normal guy being
approached by two Jehovah's Witnesses and being asked, "Do you think
Occam's razor would say that it is more likely that life came drifting
in from outer space, or that God Did It?" What's the answer going to
be? Well, for a large majority of people, he God hypothesis sounds
more rational. We have been trained by society norms to make fun of
people like Dennis Kucinich.

http://www.youtube.com/watch?v=gSRWRbuMqyc

Just remember that extraordinary claims require extraordinary
evidence. To the guy on the street, panbiogenesis initally sounds like
Dennis Kucinich. Do you really want to feed that? That gives the
Witnesses the fuel they need to say, "See, science is more crazy than
religion!"

> 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.

And if we can prove it scientifically, then it would be a great step
forward. Aside from that, we don't know that life is so damn hard to
kick start. That is also a hypothesis. It may be relatively easy,
given 100,000,000 years. :-)

Remember, we all believe in evolution here, and you can't easily prove
that in a lab either.

>> 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. ;-)

No thanks on the cloned dog. Though the pet dinosaur evolved from a
chicken sounds kinda fun. (See last month's Wired Magazine)

Scientist's job is to be criticized by other scientists, until the
argument is over and a THEORY emerges, HOWEVER, this particular aspect
of science (abiogenesis and evolution) has very important
sociological, religious and political ramifications! We can't go
spouting off about panbiogenesis and then complain when a born again
christian or Mormon gets elected president and laws against
transhumanist interests get passed. We bring it on ourselves when we
espouse ideas that are viewed as so far out of the mainstream.

>> 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.

No, but they present their own challenges in imaging. We're getting
better at this stuff all the time. But it is hard to get research
money to study the evolutionary crystal structures of clay. That's the
kind of $1000 toilet seat story that ends up on the second page of the
Wall Street Journal as a waste of the public's money. Again, it's very
political in this area of science, and you can't lose sight of that.

>> 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?

Because it was my conversations with the Jehovah's Witnesses that led
me to dive into this stuff more deeply. I realized I did not know
enough to counter their arguments against abiogenesis, so I felt the
need to go and educate myself. In other words, their creationist bull
shit (the form of the argument, more than the argument itself) pissed
me off and made me want to study more.

>> 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.

I don't think I'm interested in speculating on the evolution of life
in alternative universes. You change the universal constants like
that, and you probably go messing up other stuff.

> 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.

Sure, I'm good with math... as long as you don't start throwing up
equations... LOL

>Hazen says it took about 100 million years from end of the asteroidal bombardment
>to first life to show up.

Yes. Though there is the possibility of a few extra tens of millions
of years underground for things to have gotten started before coming
top side. But that is a minor point.

>Dinosaurs first appeared 230 million years ago.

Following you so far.

> 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?

Actually, I said going from a bird back to a dinosaur... atavistic
de-evolution is more likely than abiogenesis. I'll stick with that.

>That sounds like Hazen is pulling numbers out of his ass.

Sorry, that number came out of MY ass, not his! Let's be very clear
about the anal genealogy of this particular number. :-)

> It doesn't even seem like Hazen's argument is consistent with
> itself let alone the scientific data. And negative results are still results.

Look. Once you get the DNA rolling, changing one animal into another
is relatively simple, just change the genes. The initial abiotic
evolution of life from chemistry was likely VERY complex, involving a
number of intermediate processes... Or maybe it was simple. Nobody
knows.

>> 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.

I'm not sure how the universe being small and hot makes the evolution
of life more probable... but maybe.

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

Oh yeah. And Hazen is the best I've found so far at explaining
emergence. I really want to go into a quiet room and think deeply
about emergence. I think there is something there that is awaiting a
genius like Benoit Mandelbrot or Charles Darwin to make it completely
obvious to the rest of us. I think there is a collective moment of
"DUH!" in our future on this subject. I think some day, many of us
will be thinking along the lines of T.H. Huxley when we think of
emergence...

My reflection when I first made myself master of the central idea of
the Origin was, "How extremely stupid not to have thought of that." -
Thomas Henry Huxley

-Kelly