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03/13/2003

Spines and Other Biominerals

I’m looking out at the five-foot mound of snow that covers a fair
portion of our backyard. It makes me want to be back walking
the beach at Marco Island in spite of the possibility of an
encounter with an alligator (see last week’s column). Sea
urchins, with their sharp spines, were another hazard that kept
me from testing the waters of the Gulf. In the February 21 2003
issue of Science, I found a scanning electron microscope (SEM)
photo of a sea urchin spine. The photo was in an article titled “A
Bright Bio-Inspired Future” by Trevor Douglas, a chemist at
Montana State University in Bozeman.

I have a fondness for Bozeman dating back to an overnight stay
there which may have saved my marriage after three horrendous,
thunderstormy nights with my family in a tent in Yellowstone. I
may have mentioned before that, on the morning of our
departure, my wife threatened to take a plane home after finding
me unable to fold the wet tent into an appropriate shape to stuff
into the carrier on top of our car. (I’ve never been good at
wrapping and folding things.) The clean, dry, pleasant motel in
Bozeman that night put us all in a better mood and we’ve never
been in a tent again!

But I digress. Back to Trevor Douglas. He and virologist Mark
Young made a splash in the media several years ago when they
claimed to have carried out experiments using the world’s
smallest test tubes. This was accomplished using the “husks” of
viruses as the test tubes. A virus is essentially a strand of DNA
or RNA in a “box” made of protein. Take out the DNA or RNA
and you have left a tiny box or husk. The Bozeman workers
found that the pores in the viral husks would open or close,
depending on the pH of certain solutions. With the pores open,
they could trap the salts or other reactants inside the cage and
grow crystals that conform to the shape of the cage. Viruses are
very uniform and there are all kinds and shapes. Their work
demonstrated the opportunity to make large numbers of identical
tiny objects/crystals of different shapes. A visit to the Montana
State Web site shows they’re now investigating these viral husks
as switches. They are either open or closed and conceivably
could have some application in a biocomputer, should such a
concept come to pass.

But I digress again. The purpose of Douglas’ article in Science
was to provide a perspective on the work reported in another
article in that issue by workers at my old stomping grounds, Bell
Labs. I was actually led to this article by an item given to me by
Brian Trumbore from the March 10 Business Week titled “Bell
Labs: Catching up to the Clam”. The item credits the Bell Labs
workers with having succeeded in mimicking the process by
which mollusks build up their shells. Their paper is titled
“Direct Fabrication of Large Micropatterned Single Crystals”.
Having spent half my career at Bell Labs growing or studying
single crystals, I was used to fairly large uniformly solid crystals
or thin single crystal layers for light emitting diodes.

However, Joanna Aizenberg and her colleagues at Bell Labs are
growing single crystals that resemble nothing like what I’ve been
accustomed to. I was shocked to look at Douglas’ SEM photo of
the sea urchin spine, loaded with pores and empty spaces in the
structure, and find that it was a single crystal of calcite, a
crystalline form of the compound calcium carbonate. The Bell
Labs paper includes an SEM photo of part of the skeleton of
another sea creature, the brittlestar. The photo shows an array of
little microlenses, each about 2 thousandths of an inch in
diameter. Each lens is connected to its neighboring lenses by
bridges of calcite. As with the sea urchin spine, this leaves lots
of pores and open space in the structure and again, the whole
array is one single crystal of calcite.

How does nature accomplish this feat of “biomineralization” in
which a single orderly arrangement of atoms is maintained
throughout a highly porous structure of inorganic calcite? It
turns out that these inorganic biominerals contain small but
significant amounts of organic molecules in the structure.
Offhand, it should be even harder to maintain an orderly
arrangement of atoms with interloping organic molecules to
disrupt the structure in a brittlestar or sea urchin spine. However,
these organic compounds are actually the key to forming the
single crystal in the first place.

My understanding of the process is that a mix of certain organic
compounds (porphyrins are an example) forms a patterned array.
However, the mix of different molecules presents a disorderly
surface to the solution (seawater, I presume) from which the
calcium carbonate is deposited. This disorderly surface
discourages crystallization and induces the formation of layers of
amorphous calcium carbonate (ACC). Remember that an
amorphous material has no long-range crystal structure (compare
amorphous glass with crystalline quartz).

On the other hand, other organic molecules (alkanethiols for
example) can form what’s known as a SAM, a self-assembled
monolayer. A SAM contains a bunch of lined up molecules that
present a very orderly surface to the solution and promotes the
growth of crystalline calcium carbonate (calcite). An amorphous
material is thermodynamically unstable and wants to become a
more stable crystalline material. A SAM gooses this process
along.

Aizenberg and her coworkers cheated a bit by using a process
known as photolithography, employed in silicon chip
manufacture, to form patterned arrays of tiny posts on a glass
substrate, regularly spaced. After coating the array of posts with
a thin layer of gold or silver, they used an atomic force
microscope tip to lay down a nano-size SAM. The rest of the
array was covered with a “disorderly” mix of organic
compounds. They then simply placed the array in a calcium
chloride solution, put it in a desiccator containing powdered
ammonium carbonate and waited.

Within a half hour a layer of amorphous calcium carbonate had
formed. Within an hour the nano-SAM had begun its job of
initiating the crystallization of the amorphous material. The
crystallization proceeded to spread throughout the layer until a
region of about a millimeter in size had converted to single
crystal calcite. The result was a patterned array much like the
brittlestar.

In other experiments, they found that the porous microstructure
also served as “microsumps” that removed water during the
crystallization. Also, by adding dyes, they showed that
impurities may also be removed along with the water. The
patterning and the resulting porous structure are also thought to
help in relieving stresses that arise during the formation of the
crystalline calcite. When you have a transformation from
amorphous to crystalline, or even from one crystalline form to
another, there can be a substantial change in volume. In a
normal single crystal, this can lead to cracking of the crystal. In
a micro- or nano-size porous structure, the stresses don’t get a
chance to build up to the point of cracking. Such cracking
wouldn’t make for a happy clam or an effective sea urchin spine!

I’m certainly no expert on the growth of biominerals like clam
shells, but it seems to me that this paper makes a strong case for
Nature’s preference for patterned porous structures. For me, it’s
nice to see that Bell Labs is still engaged in high quality
fundamental studies, especially after its episode of scientific
fraud last year and the horrendous financial troubles of Lucent
Technologies. An item in the paper this week celebrated the
issuance of Bell Labs’ 30,000th patent. I hope there are many
more to come.

Allen F. Bortrum



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Dr. Bortrum

03/13/2003

Spines and Other Biominerals

I’m looking out at the five-foot mound of snow that covers a fair
portion of our backyard. It makes me want to be back walking
the beach at Marco Island in spite of the possibility of an
encounter with an alligator (see last week’s column). Sea
urchins, with their sharp spines, were another hazard that kept
me from testing the waters of the Gulf. In the February 21 2003
issue of Science, I found a scanning electron microscope (SEM)
photo of a sea urchin spine. The photo was in an article titled “A
Bright Bio-Inspired Future” by Trevor Douglas, a chemist at
Montana State University in Bozeman.

I have a fondness for Bozeman dating back to an overnight stay
there which may have saved my marriage after three horrendous,
thunderstormy nights with my family in a tent in Yellowstone. I
may have mentioned before that, on the morning of our
departure, my wife threatened to take a plane home after finding
me unable to fold the wet tent into an appropriate shape to stuff
into the carrier on top of our car. (I’ve never been good at
wrapping and folding things.) The clean, dry, pleasant motel in
Bozeman that night put us all in a better mood and we’ve never
been in a tent again!

But I digress. Back to Trevor Douglas. He and virologist Mark
Young made a splash in the media several years ago when they
claimed to have carried out experiments using the world’s
smallest test tubes. This was accomplished using the “husks” of
viruses as the test tubes. A virus is essentially a strand of DNA
or RNA in a “box” made of protein. Take out the DNA or RNA
and you have left a tiny box or husk. The Bozeman workers
found that the pores in the viral husks would open or close,
depending on the pH of certain solutions. With the pores open,
they could trap the salts or other reactants inside the cage and
grow crystals that conform to the shape of the cage. Viruses are
very uniform and there are all kinds and shapes. Their work
demonstrated the opportunity to make large numbers of identical
tiny objects/crystals of different shapes. A visit to the Montana
State Web site shows they’re now investigating these viral husks
as switches. They are either open or closed and conceivably
could have some application in a biocomputer, should such a
concept come to pass.

But I digress again. The purpose of Douglas’ article in Science
was to provide a perspective on the work reported in another
article in that issue by workers at my old stomping grounds, Bell
Labs. I was actually led to this article by an item given to me by
Brian Trumbore from the March 10 Business Week titled “Bell
Labs: Catching up to the Clam”. The item credits the Bell Labs
workers with having succeeded in mimicking the process by
which mollusks build up their shells. Their paper is titled
“Direct Fabrication of Large Micropatterned Single Crystals”.
Having spent half my career at Bell Labs growing or studying
single crystals, I was used to fairly large uniformly solid crystals
or thin single crystal layers for light emitting diodes.

However, Joanna Aizenberg and her colleagues at Bell Labs are
growing single crystals that resemble nothing like what I’ve been
accustomed to. I was shocked to look at Douglas’ SEM photo of
the sea urchin spine, loaded with pores and empty spaces in the
structure, and find that it was a single crystal of calcite, a
crystalline form of the compound calcium carbonate. The Bell
Labs paper includes an SEM photo of part of the skeleton of
another sea creature, the brittlestar. The photo shows an array of
little microlenses, each about 2 thousandths of an inch in
diameter. Each lens is connected to its neighboring lenses by
bridges of calcite. As with the sea urchin spine, this leaves lots
of pores and open space in the structure and again, the whole
array is one single crystal of calcite.

How does nature accomplish this feat of “biomineralization” in
which a single orderly arrangement of atoms is maintained
throughout a highly porous structure of inorganic calcite? It
turns out that these inorganic biominerals contain small but
significant amounts of organic molecules in the structure.
Offhand, it should be even harder to maintain an orderly
arrangement of atoms with interloping organic molecules to
disrupt the structure in a brittlestar or sea urchin spine. However,
these organic compounds are actually the key to forming the
single crystal in the first place.

My understanding of the process is that a mix of certain organic
compounds (porphyrins are an example) forms a patterned array.
However, the mix of different molecules presents a disorderly
surface to the solution (seawater, I presume) from which the
calcium carbonate is deposited. This disorderly surface
discourages crystallization and induces the formation of layers of
amorphous calcium carbonate (ACC). Remember that an
amorphous material has no long-range crystal structure (compare
amorphous glass with crystalline quartz).

On the other hand, other organic molecules (alkanethiols for
example) can form what’s known as a SAM, a self-assembled
monolayer. A SAM contains a bunch of lined up molecules that
present a very orderly surface to the solution and promotes the
growth of crystalline calcium carbonate (calcite). An amorphous
material is thermodynamically unstable and wants to become a
more stable crystalline material. A SAM gooses this process
along.

Aizenberg and her coworkers cheated a bit by using a process
known as photolithography, employed in silicon chip
manufacture, to form patterned arrays of tiny posts on a glass
substrate, regularly spaced. After coating the array of posts with
a thin layer of gold or silver, they used an atomic force
microscope tip to lay down a nano-size SAM. The rest of the
array was covered with a “disorderly” mix of organic
compounds. They then simply placed the array in a calcium
chloride solution, put it in a desiccator containing powdered
ammonium carbonate and waited.

Within a half hour a layer of amorphous calcium carbonate had
formed. Within an hour the nano-SAM had begun its job of
initiating the crystallization of the amorphous material. The
crystallization proceeded to spread throughout the layer until a
region of about a millimeter in size had converted to single
crystal calcite. The result was a patterned array much like the
brittlestar.

In other experiments, they found that the porous microstructure
also served as “microsumps” that removed water during the
crystallization. Also, by adding dyes, they showed that
impurities may also be removed along with the water. The
patterning and the resulting porous structure are also thought to
help in relieving stresses that arise during the formation of the
crystalline calcite. When you have a transformation from
amorphous to crystalline, or even from one crystalline form to
another, there can be a substantial change in volume. In a
normal single crystal, this can lead to cracking of the crystal. In
a micro- or nano-size porous structure, the stresses don’t get a
chance to build up to the point of cracking. Such cracking
wouldn’t make for a happy clam or an effective sea urchin spine!

I’m certainly no expert on the growth of biominerals like clam
shells, but it seems to me that this paper makes a strong case for
Nature’s preference for patterned porous structures. For me, it’s
nice to see that Bell Labs is still engaged in high quality
fundamental studies, especially after its episode of scientific
fraud last year and the horrendous financial troubles of Lucent
Technologies. An item in the paper this week celebrated the
issuance of Bell Labs’ 30,000th patent. I hope there are many
more to come.

Allen F. Bortrum