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Dr. Bortrum

 

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09/04/2001

Ice, Life and Hydrogen Bonds

Sometimes I envy those who work in fields where they have the
luxury of postulating all kinds of theories that will never be
proved right or wrong. One example is the view held by some
that there are other universes than our own, each with their own
Big Bang. I can accept that. After all, it''s hard enough to try to
understand one Big Bang, so what''s a few more? However,
David Deutsch in England has proposed that we live in a
"multiverse", a slew of universes in which each of us has twins,
each leading a completely different life. The September 2001
issue of Discover magazine has an article about Deutsch
describing him as one of the world''s leading theoretical
physicists. I''m no theoretical physicist but I find his theory hard
to swallow. But I''m pretty sure no one will ever prove him
wrong (or right!).

Another field where confirming a theory is pretty problematical
is the origins-of-life field. All kinds of theories have been
proposed as to how the first life appeared on earth. I doubt the
answer will be known in my lifetime, but it''s nice to see that
experiments are being done that support at least the feasibility of
certain suggested origins. What do we know? We know the
earth formed 4.5 billion years ago and that, amazingly, fossils of
tiny organisms have been found in rocks more than 3.5 billion
years old. Initially, the earth was hot and was bombarded with
so many asteroids and other space junk, that life would have
been unthinkable for a half billion years or so. Yet, within a few
hundred million years after that, cyanobacteria (the type
associated with pond slime) were thriving.

Something had to be present to permit these bacteria to form -
organic compounds. Without simple organics to start with, we
couldn''t have had the more complex amino acids and proteins
that form DNA and everything else composing a living thing.
How did the organics form? You need carbon, oxygen,
hydrogen and nitrogen for sure. In 1953, Stanley Miller, a
graduate student of Nobelist Harold Urey at the University of
Chicago, put methane, ammonia, and other gases in a flask with
some water and simulated lightning with electric sparks. He
figured this mixture was something like what would have been
present in the atmosphere 4 billion years ago. Sure enough, the
water turned brownish; amino acids and other organic molecules
were formed. I remember the sensation the experiment caused in
the media of the 1950s. Some commentators would have had
you believe that the creation of life in the laboratory was just
around the corner.

Problem solved? Not quite. These amino acids and other
compounds somehow had to come together to link up and stay
linked up in order for something approaching a living thing to be
formed and survive. Conditions on earth were still not conducive
to life, at least out in the open. Although Miller''s experiment
showed that organic compounds might have formed on earth,
many have felt that the source was comets from outer space
crashing into the earth. The questions then become could the
organics have formed in space and could they then survive the
trip to earth intact?

The answer to the first question is a resounding yes. Studies of
the spectra of cold gas clouds in outer space over the past decade
show that space is indeed loaded with many different organic
compounds and with lots of water. The particles of dust and
condensed gases in the cold molecular clouds of space also
contain frost rich in water ice. If particles like these come
together in a comet that plows into the earth, we''ve got the water
and the organics to put us in the life business.

So, we know the organics are out there. The second question is
could they survive the trip to earth over the thousands or millions
of years it takes the comet to get here? The August 2001 issue of
Scientific American has an article by David Blake and Peter
Jenniskens of NASA Ames Research Center that provides an
answer. The article''s title is "The Ice of Life" and shows how
that frosty water ice could have nurtured formation of the
organics and then cradled them on the long journey to earth.

To understand the article we need to know a little about water.
We know that water, with just two atoms of hydrogen and one of
oxygen, is about as simple a molecule as you can get, right?
Wrong! Water is an amazingly complex substance and it''s this
complexity that makes it such an interesting and important part
of our world. My well-worn 1945 edition of Linus Pauling''s
"Nature of the Chemical Bond" has some pertinent information.
For one thing, water''s structure is not H-O-H, with the atoms and
the bonds (-) all in line. Instead, the hydrogen atoms, and the
bonds are closer to being at right angles (actually 105 degrees) to
each other. This makes the structure sort of like an arrowhead,
with the oxygen at the point. Pauling also makes the point that
there''s some positive charge on the hydrogens and some negative
charge on the oxygen.

I know this doesn''t sound very exciting but these charges also
give rise to something hugely important. That negative charge
on the oxygen attracts a positively charged hydrogen from
another neighboring water molecule. The result is a weak bond
between that oxygen and the neighboring hydrogen, which is
strongly bonded to its own oxygen atom. This "hydrogen bond"
between its own oxygen and the oxygen in the neighboring water
molecule may not excite you either. But consider this. Pauling
shows that, without those hydrogen bonds, water would freeze at
minus 100 degrees Centigrade and boil at minus 80 degrees
Centigrade, not plus 100 C! You''d be dried up as a mummy!
Those hydrogen bonds are responsible for life as we know it.

Pauling also mentions that in certain forms of ice, because of the
weakness of these hydrogen bonds, at very low temperatures the
water molecules can rearrange themselves almost as though the
ice were liquid. And that''s the key point in the article by Blake
and Jenniskens of the NASA Ames Research Center.

The ordinary ice that we take out of the freezer and add to our
drinks is "hexagonal" ice. Its crystal structure consists of the
water molecules arranged in hexagons as in a beehive, an open
but rigid structure that rejects impurities or organic compounds.
Freeze tissues containing water and ice forms and tears the tissue
apart. Part of the problem is that when you freeze water, the ice
is less dense than liquid water and the water expands as it
freezes. That''s also why ice floats in your drink. In this
hexagonal ice, the hydrogen bonds are also locked up as part of
the crystal structure.

But there are other forms of ice. Ten years before Pauling''s book
appeared, researchers were slowly depositing water vapor on a
surface in vacuum. Instead of hexagonal structure, they found
the ice had no discernible structure! We call stuff like this
without any long-range order "amorphous". You''re quite
familiar with amorphous stuff, that windowpane or the glass you
drink from, for example. Glass is an amorphous form of silica,
which can also be quite crystalline in the form of quartz.

Today, researchers know that out in space where it really gets
cold and where the dust particles may only be a hundred
thousandth of an inch thick, the water ice on these particles is
mostly amorphous. So, if these teensy particles have also
trapped gases like methane and ammonia, we have the
ingredients for making organic compounds. But hey, it''s cold out
there and this is ice, not liquid water! But Pauling said that
hydrogen bonds could form and rearrange in some forms of ice at
low temperatures.

This is just the opening we need. It''s been found that ultraviolet
radiation out in space can stimulate the hydrogen bond
wanderings. That rearrangement of hydrogen bonds allows the
other stuff trapped in the ice or at the surface to also mix a bit
and react. It''s very cold, near Absolute Zero, and the reactions
will be very slow. We''re not in a hurry though - we have tens or
hundreds of thousands of years to form these compounds before
the particles get caught up and condense into a comet and then
head for the earth.

The NASA Ames workers have deposited thin films of water on
a surface in vacuum in an electron microscope at very low
temperatures. They then followed what happens as the resulting
amorphous ice heats up. Their results translate to the following
scenario. At the extremely low temperatures near Absolute Zero,
ultraviolet radiation causes the ice to flow like water and organic
molecules are formed. As the ice heats up, the hydrogen bonds
break and re-form. This allows the organic molecules to get
together to form more complex compounds.

Now a surprising discovery - as the temperature goes higher the
ice begins to crystallize into a "cubic" form of ice. This could be
murder for the compounds but, the surprise, about two thirds of
the ice remains amorphous. So, if we have a comet with all these
compounds mixed in with the ice, as the comet approaches the
sun and earth and heats up, the compounds are still OK. Finally,
as the comet comes speeding down to hit the earth, it heats up to
the point where the ice becomes hexagonal ice and expels the
compounds. However, by this time the comet is near or on the
earth and the compounds are scattered around into the oceans,
available to form more exotic compounds. So, whether the
organics were made on earth or came from space, or both, we''ve
got the necessary ingredients for life. Next week, the next step.

Meanwhile, I can''t end without congratulating Brian Trumbore
on the best round of his life last week. I was witness to this
historic event. Brian was dropping putts in the cup from all over
the greens. I won''t reveal his score, except to note it was a mere
22 strokes lower than mine. Only a week before, I had taken
him by a stroke on the front nine of the same course! (No
comment on the second nine.)

Allen F. Bortrum



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-09/04/2001-      
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Dr. Bortrum

09/04/2001

Ice, Life and Hydrogen Bonds

Sometimes I envy those who work in fields where they have the
luxury of postulating all kinds of theories that will never be
proved right or wrong. One example is the view held by some
that there are other universes than our own, each with their own
Big Bang. I can accept that. After all, it''s hard enough to try to
understand one Big Bang, so what''s a few more? However,
David Deutsch in England has proposed that we live in a
"multiverse", a slew of universes in which each of us has twins,
each leading a completely different life. The September 2001
issue of Discover magazine has an article about Deutsch
describing him as one of the world''s leading theoretical
physicists. I''m no theoretical physicist but I find his theory hard
to swallow. But I''m pretty sure no one will ever prove him
wrong (or right!).

Another field where confirming a theory is pretty problematical
is the origins-of-life field. All kinds of theories have been
proposed as to how the first life appeared on earth. I doubt the
answer will be known in my lifetime, but it''s nice to see that
experiments are being done that support at least the feasibility of
certain suggested origins. What do we know? We know the
earth formed 4.5 billion years ago and that, amazingly, fossils of
tiny organisms have been found in rocks more than 3.5 billion
years old. Initially, the earth was hot and was bombarded with
so many asteroids and other space junk, that life would have
been unthinkable for a half billion years or so. Yet, within a few
hundred million years after that, cyanobacteria (the type
associated with pond slime) were thriving.

Something had to be present to permit these bacteria to form -
organic compounds. Without simple organics to start with, we
couldn''t have had the more complex amino acids and proteins
that form DNA and everything else composing a living thing.
How did the organics form? You need carbon, oxygen,
hydrogen and nitrogen for sure. In 1953, Stanley Miller, a
graduate student of Nobelist Harold Urey at the University of
Chicago, put methane, ammonia, and other gases in a flask with
some water and simulated lightning with electric sparks. He
figured this mixture was something like what would have been
present in the atmosphere 4 billion years ago. Sure enough, the
water turned brownish; amino acids and other organic molecules
were formed. I remember the sensation the experiment caused in
the media of the 1950s. Some commentators would have had
you believe that the creation of life in the laboratory was just
around the corner.

Problem solved? Not quite. These amino acids and other
compounds somehow had to come together to link up and stay
linked up in order for something approaching a living thing to be
formed and survive. Conditions on earth were still not conducive
to life, at least out in the open. Although Miller''s experiment
showed that organic compounds might have formed on earth,
many have felt that the source was comets from outer space
crashing into the earth. The questions then become could the
organics have formed in space and could they then survive the
trip to earth intact?

The answer to the first question is a resounding yes. Studies of
the spectra of cold gas clouds in outer space over the past decade
show that space is indeed loaded with many different organic
compounds and with lots of water. The particles of dust and
condensed gases in the cold molecular clouds of space also
contain frost rich in water ice. If particles like these come
together in a comet that plows into the earth, we''ve got the water
and the organics to put us in the life business.

So, we know the organics are out there. The second question is
could they survive the trip to earth over the thousands or millions
of years it takes the comet to get here? The August 2001 issue of
Scientific American has an article by David Blake and Peter
Jenniskens of NASA Ames Research Center that provides an
answer. The article''s title is "The Ice of Life" and shows how
that frosty water ice could have nurtured formation of the
organics and then cradled them on the long journey to earth.

To understand the article we need to know a little about water.
We know that water, with just two atoms of hydrogen and one of
oxygen, is about as simple a molecule as you can get, right?
Wrong! Water is an amazingly complex substance and it''s this
complexity that makes it such an interesting and important part
of our world. My well-worn 1945 edition of Linus Pauling''s
"Nature of the Chemical Bond" has some pertinent information.
For one thing, water''s structure is not H-O-H, with the atoms and
the bonds (-) all in line. Instead, the hydrogen atoms, and the
bonds are closer to being at right angles (actually 105 degrees) to
each other. This makes the structure sort of like an arrowhead,
with the oxygen at the point. Pauling also makes the point that
there''s some positive charge on the hydrogens and some negative
charge on the oxygen.

I know this doesn''t sound very exciting but these charges also
give rise to something hugely important. That negative charge
on the oxygen attracts a positively charged hydrogen from
another neighboring water molecule. The result is a weak bond
between that oxygen and the neighboring hydrogen, which is
strongly bonded to its own oxygen atom. This "hydrogen bond"
between its own oxygen and the oxygen in the neighboring water
molecule may not excite you either. But consider this. Pauling
shows that, without those hydrogen bonds, water would freeze at
minus 100 degrees Centigrade and boil at minus 80 degrees
Centigrade, not plus 100 C! You''d be dried up as a mummy!
Those hydrogen bonds are responsible for life as we know it.

Pauling also mentions that in certain forms of ice, because of the
weakness of these hydrogen bonds, at very low temperatures the
water molecules can rearrange themselves almost as though the
ice were liquid. And that''s the key point in the article by Blake
and Jenniskens of the NASA Ames Research Center.

The ordinary ice that we take out of the freezer and add to our
drinks is "hexagonal" ice. Its crystal structure consists of the
water molecules arranged in hexagons as in a beehive, an open
but rigid structure that rejects impurities or organic compounds.
Freeze tissues containing water and ice forms and tears the tissue
apart. Part of the problem is that when you freeze water, the ice
is less dense than liquid water and the water expands as it
freezes. That''s also why ice floats in your drink. In this
hexagonal ice, the hydrogen bonds are also locked up as part of
the crystal structure.

But there are other forms of ice. Ten years before Pauling''s book
appeared, researchers were slowly depositing water vapor on a
surface in vacuum. Instead of hexagonal structure, they found
the ice had no discernible structure! We call stuff like this
without any long-range order "amorphous". You''re quite
familiar with amorphous stuff, that windowpane or the glass you
drink from, for example. Glass is an amorphous form of silica,
which can also be quite crystalline in the form of quartz.

Today, researchers know that out in space where it really gets
cold and where the dust particles may only be a hundred
thousandth of an inch thick, the water ice on these particles is
mostly amorphous. So, if these teensy particles have also
trapped gases like methane and ammonia, we have the
ingredients for making organic compounds. But hey, it''s cold out
there and this is ice, not liquid water! But Pauling said that
hydrogen bonds could form and rearrange in some forms of ice at
low temperatures.

This is just the opening we need. It''s been found that ultraviolet
radiation out in space can stimulate the hydrogen bond
wanderings. That rearrangement of hydrogen bonds allows the
other stuff trapped in the ice or at the surface to also mix a bit
and react. It''s very cold, near Absolute Zero, and the reactions
will be very slow. We''re not in a hurry though - we have tens or
hundreds of thousands of years to form these compounds before
the particles get caught up and condense into a comet and then
head for the earth.

The NASA Ames workers have deposited thin films of water on
a surface in vacuum in an electron microscope at very low
temperatures. They then followed what happens as the resulting
amorphous ice heats up. Their results translate to the following
scenario. At the extremely low temperatures near Absolute Zero,
ultraviolet radiation causes the ice to flow like water and organic
molecules are formed. As the ice heats up, the hydrogen bonds
break and re-form. This allows the organic molecules to get
together to form more complex compounds.

Now a surprising discovery - as the temperature goes higher the
ice begins to crystallize into a "cubic" form of ice. This could be
murder for the compounds but, the surprise, about two thirds of
the ice remains amorphous. So, if we have a comet with all these
compounds mixed in with the ice, as the comet approaches the
sun and earth and heats up, the compounds are still OK. Finally,
as the comet comes speeding down to hit the earth, it heats up to
the point where the ice becomes hexagonal ice and expels the
compounds. However, by this time the comet is near or on the
earth and the compounds are scattered around into the oceans,
available to form more exotic compounds. So, whether the
organics were made on earth or came from space, or both, we''ve
got the necessary ingredients for life. Next week, the next step.

Meanwhile, I can''t end without congratulating Brian Trumbore
on the best round of his life last week. I was witness to this
historic event. Brian was dropping putts in the cup from all over
the greens. I won''t reveal his score, except to note it was a mere
22 strokes lower than mine. Only a week before, I had taken
him by a stroke on the front nine of the same course! (No
comment on the second nine.)

Allen F. Bortrum