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09/21/1999

Microorgasms, Microorganisms and Microscopes

Tropical storm Floyd treated yours truly gently compared to his
horrible treatment of places like Bound Brook, a town I drive
through most weeks to play golf. My main problem was to stem
the small flow of water in our basement. More inconvenient has
been the fact that we are among the million inhabitants of New
Jersey having who must boil our water to eliminate various types
of vile microorganisms. As a result, I was in the supermarket
trying to locate bottled water and was proud that I stooped to
peer under a lower shelf of the completely emptied shelves
devoted to H2O and located in the shadows about 10 remaining
one-gallon jugs of Deer Park water. A tall, husky gentleman
watched me and wondered why the run on water, saying that
Summit wasn''t involved in the warnings. I informed him to the
contrary, having checked it out on our water company''s Web site.
Taking his fair share of the jugs, he then thanked me profusely,
saying I may have saved his life! It turns out that a couple years
ago he had leukemia and a weakened immune system made him
quite vulnerable to infection.

This incident and its relationship to microorganisms was quite
fitting in view of what I said last week would be a topic for this
week''s column. Many years ago at Bell Labs I was again
peering, this time through my microscope, when one of our
assistants walked over and in all seriousness asked if I were
looking at microorgasms. Keeping a straight face, I replied that
no, I was actually looking at niobium selenide fibers. This
fellow had no scientific background but in retrospect I feel that
inadvertently he had asked a question of profound significance. I
am not aware that anyone has pursued the question as to what
level of development in the evolutionary chain (that Kansas
Board of Education notwithstanding) did the orgasmic process
arise? Do microorganisms experience microorgasms? How
would we know one way or the other? I suspect that when, in
1674, Leeuwenhoek peered through his microscope and
discovered microorganisms, he must have felt an intellectual
orgasm at such a momentous discovery. At a higher
evolutionary level, those male spiders that get eaten by their mate
during or after lovemaking surely must have some sort of strong
incentive to even consider approaching a given female! There
obviously is a whole field of research open for exploration. I''ll
check out whether I may have missed work in this field and will
report any findings in a later column.

Were I really searching for microorgasms through my Bell Labs
microscope, I would have had not only the limitations of rather
low magnifying power but also the "depth of field" would be
quite small. That is, in general, ordinary microscopes with glass
lenses tend to focus at a very limited range of depth at higher and
higher magnifications. You have the same effect when you take
a clasp picture with your camera and the background becomes
fuzzy. While this may not be a problem for many biological
studies, it does limit the ability to observe three-dimensional
objects with an optical microscope.

A fairly recent kind of optical microscope called a "confocal"
microscope provides a clever way around this limitation. By
marrying a computer to the optical microscope, the focus of the
microscope is raised or lowered in a series of steps and just the
view in focus in each step is recorded. These images are then
processed and reconstructed in the computer to give a three
dimensional image. It''s sort of like medical scanners such as the
CATSCAN or some MRI techniques that take pictures of slices
of your anatomy. I have never seen a confocal microscope
myself but they are now fairly common.

Another type of microscope with which I am quite familiar is the
Scanning Electron Microscope or SEM. I imagine the cost of the
thousands of SEM Polaroid photos I took during my career at
Bell Labs must have been several tens of thousands of dollars.
You have seen SEM pictures of all kinds of things, insects being
a popular subject in media articles and advertisements. Dust
mites in particular seem to be a favorite subject, making one
queasy about going to bed at night with all those ugly creatures
feasting on your dead skin! The SEM is based on the use of a
beam of electrons instead of a beam of light and gives beautiful
three-dimensional pictures with a large depth of focus. A feature
of most SEMs is that the sample has to be electrically conductive
to avoid "charging" of the sample, which leads to fuzziness or
blotting out of the charged areas of the sample. This means that
an insect, for example, must be coated with a film of conducting
material such as gold or aluminum. So when you see those dust
mites, they''re might be gold plated dust mites! Today, there are
SEMs, rather expensive ones, that do not require this coating.
Another disadvantage of most SEM models is that the sample
can only be studied under a high vacuum. "Environmental"
SEMs now permit the examination of samples that can be moist
and can be examined under slightly humid conditions.

Typically, SEMs are limited in magnification to showing features
that are hundreds or thousands of atoms in size at the highest
power magnification. Another type of scanning microscope is
the scanning tunneling microscope, or STM. Gerd Binnig and
Heinrich Rohrer at the IBM Research Lab in Zurich, Switzerland
invented the STM and received the 1986 Nobel Prize for their
effort. What they did was to refine an earlier instrument called a
topografiner invented by Russell Young of the National Bureau
of Standards (now the National institute of Standards and
Technology or NIST). In the topografiner, a voltage was applied
to a very fine tip, in essence a needle, and the tip was scanned
over and extremely close to the surface of a metal. When the tip
is close enough to the surface, a current flows across the gap
between the tip and the surface. This is called a "tunneling"
current and I think we discussed a little about such a current in an
earlier column.

In a typical STM, our "needle" or pointed piece of a metal or
other material is mounted on the end of a cantilever, sort of like a
diving board with a needle mounted on the under side of the
diving end. Hopefully, there are a few of you out there who
might also liken it to a phonograph needle tracking the grooves
in one of those ancient long-playing vinyl records. However, in
the STM, as in the topografiner, the tip of the needle does not
touch the surface but comes very close to it. How close?
Approximately 10 Angstroms, or one nanometer. For those
unfamiliar with such terms, a nanometer is one ten millionth of a
centimeter and there are 2.54 centimeters in an inch. In other
words, controlling that separation between tip and surface is one
helluva job! To control vibrations at this level is a major task in
mechanical design, which is where the IBM workers made their
crucial contribution.

Now, in one mode of operation, combining electronic circuitry
and the ingenious mechanical design, the point is scanned across
the sample while keeping the tunneling current constant. This
means that the height of the point above the surface has to be
adjusted up or down as scanning proceeds. The difference in
height can be measured by shining a laser light beam onto the
cantilever at an angle and measuring its deflection on a detector.
Recording these height readings allows the construction of a
topographical map of the surface. What happens if the tip is
treated so that at only a single atom protrudes at its end? The
hills and valleys of this topographical map correspond to
individual atoms. This truly remarkable ability to detect
individual atoms is what led to the Nobel Prize for the IBM
workers.

You may have read articles predicting that in the future there will
be microfactories making very tiny circuits or machines. While
I''m somewhat skeptical that many of the predictions are pretty
far out, the STM has been used to move and deposit individual
atoms on a surface. Workers at IBM, for example, spelled out
IBM in individual atoms using this technique and have made
what they call "quantum corrals" by positioning 48 iron atoms in
a circle on a copper surface. I gather that they showed that an
electron could be contained just like a cow inside this corral.
There are also other examples of demonstrations of the feasibility
of making electronic devices on the atomic scale which have led
to predictions that enormous computing power might be
available on thumbnail size chips.

Another type of scanning microscope is the atomic force
microscope or AFM. In an AFM no voltage is applied to the fine
point mounted on the cantilever. There are three modes of
typical operation. In the "contact" mode, the simplest to
understand, the point is dragged (scanned) across the surface and
is in actual physical contact. This is certainly a direct approach
and is most sensitive but there is the possibility of damage to
either the tip or the surface. In the "non-contact" mode the point
is held above the surface and the force of attraction is measured
during scanning across the surface. A third method is the
"tapping" mode, akin to blind person tapping his cane. Again,
under the right conditions, a topographical map can yield hills
and valleys corresponding to individual atoms.

In essence, the AFM "feels" the atoms as the point is dragged
along. There is a force known as the Van der Waals force that
results in the tip being attracted to the surface up to a very small
separation between tip and surface. As the tip moves even closer
this force turns into repulsion. By knowing how "springy" our
diving board or cantilever is this force can be calculated and the
various modes of operation can be controlled. The applications
of the AFM are exploding in that it has now been applied to look
at specimens ranging from living neurons to liquids to genes.

There are now many other versions of these scanning
microscopes involving magnetic fields, electrochemical actions
such as electroplating, etc. In all of them the atoms aren''t
actually "seen" but are certainly capable of being monitored
individually and with suitable computer processing, pictures of
the atomic structure of the surface can be derived. Actually, for
many applications there is no need to identify individual atoms;
in fact, doing so could result in a "not seeing the forest for the
trees" effect. For such applications, then tips can be less sharp
and I would imagine the electronics could be less demanding and
expensive. By modifying the tips by coating them with different
materials such as biologically active compounds, wondrous
things are in the process of being achieved and I hope to report
on some of these in detail later.

Back to Floyd. One of my golfing buddies just called a few
minutes ago and mentioned that he had seen on TV a picture of
the bridge I normally use to cross the river in Bound Brook. He
said there was debris on the bridge, implying the water had risen
some 30 feet! Unbelievable!

Allen F. Bortrum

[Editor: Re the above bridge, I noticed some unidentified barrels
that had washed up on it, reportedly filled with toxic chemicals
from a local American Cyanimid plant. But we won''t tell
Bortrum because then he''ll worry too much when he crosses that
bridge in the future].



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-09/21/1999-      
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Dr. Bortrum

09/21/1999

Microorgasms, Microorganisms and Microscopes

Tropical storm Floyd treated yours truly gently compared to his
horrible treatment of places like Bound Brook, a town I drive
through most weeks to play golf. My main problem was to stem
the small flow of water in our basement. More inconvenient has
been the fact that we are among the million inhabitants of New
Jersey having who must boil our water to eliminate various types
of vile microorganisms. As a result, I was in the supermarket
trying to locate bottled water and was proud that I stooped to
peer under a lower shelf of the completely emptied shelves
devoted to H2O and located in the shadows about 10 remaining
one-gallon jugs of Deer Park water. A tall, husky gentleman
watched me and wondered why the run on water, saying that
Summit wasn''t involved in the warnings. I informed him to the
contrary, having checked it out on our water company''s Web site.
Taking his fair share of the jugs, he then thanked me profusely,
saying I may have saved his life! It turns out that a couple years
ago he had leukemia and a weakened immune system made him
quite vulnerable to infection.

This incident and its relationship to microorganisms was quite
fitting in view of what I said last week would be a topic for this
week''s column. Many years ago at Bell Labs I was again
peering, this time through my microscope, when one of our
assistants walked over and in all seriousness asked if I were
looking at microorgasms. Keeping a straight face, I replied that
no, I was actually looking at niobium selenide fibers. This
fellow had no scientific background but in retrospect I feel that
inadvertently he had asked a question of profound significance. I
am not aware that anyone has pursued the question as to what
level of development in the evolutionary chain (that Kansas
Board of Education notwithstanding) did the orgasmic process
arise? Do microorganisms experience microorgasms? How
would we know one way or the other? I suspect that when, in
1674, Leeuwenhoek peered through his microscope and
discovered microorganisms, he must have felt an intellectual
orgasm at such a momentous discovery. At a higher
evolutionary level, those male spiders that get eaten by their mate
during or after lovemaking surely must have some sort of strong
incentive to even consider approaching a given female! There
obviously is a whole field of research open for exploration. I''ll
check out whether I may have missed work in this field and will
report any findings in a later column.

Were I really searching for microorgasms through my Bell Labs
microscope, I would have had not only the limitations of rather
low magnifying power but also the "depth of field" would be
quite small. That is, in general, ordinary microscopes with glass
lenses tend to focus at a very limited range of depth at higher and
higher magnifications. You have the same effect when you take
a clasp picture with your camera and the background becomes
fuzzy. While this may not be a problem for many biological
studies, it does limit the ability to observe three-dimensional
objects with an optical microscope.

A fairly recent kind of optical microscope called a "confocal"
microscope provides a clever way around this limitation. By
marrying a computer to the optical microscope, the focus of the
microscope is raised or lowered in a series of steps and just the
view in focus in each step is recorded. These images are then
processed and reconstructed in the computer to give a three
dimensional image. It''s sort of like medical scanners such as the
CATSCAN or some MRI techniques that take pictures of slices
of your anatomy. I have never seen a confocal microscope
myself but they are now fairly common.

Another type of microscope with which I am quite familiar is the
Scanning Electron Microscope or SEM. I imagine the cost of the
thousands of SEM Polaroid photos I took during my career at
Bell Labs must have been several tens of thousands of dollars.
You have seen SEM pictures of all kinds of things, insects being
a popular subject in media articles and advertisements. Dust
mites in particular seem to be a favorite subject, making one
queasy about going to bed at night with all those ugly creatures
feasting on your dead skin! The SEM is based on the use of a
beam of electrons instead of a beam of light and gives beautiful
three-dimensional pictures with a large depth of focus. A feature
of most SEMs is that the sample has to be electrically conductive
to avoid "charging" of the sample, which leads to fuzziness or
blotting out of the charged areas of the sample. This means that
an insect, for example, must be coated with a film of conducting
material such as gold or aluminum. So when you see those dust
mites, they''re might be gold plated dust mites! Today, there are
SEMs, rather expensive ones, that do not require this coating.
Another disadvantage of most SEM models is that the sample
can only be studied under a high vacuum. "Environmental"
SEMs now permit the examination of samples that can be moist
and can be examined under slightly humid conditions.

Typically, SEMs are limited in magnification to showing features
that are hundreds or thousands of atoms in size at the highest
power magnification. Another type of scanning microscope is
the scanning tunneling microscope, or STM. Gerd Binnig and
Heinrich Rohrer at the IBM Research Lab in Zurich, Switzerland
invented the STM and received the 1986 Nobel Prize for their
effort. What they did was to refine an earlier instrument called a
topografiner invented by Russell Young of the National Bureau
of Standards (now the National institute of Standards and
Technology or NIST). In the topografiner, a voltage was applied
to a very fine tip, in essence a needle, and the tip was scanned
over and extremely close to the surface of a metal. When the tip
is close enough to the surface, a current flows across the gap
between the tip and the surface. This is called a "tunneling"
current and I think we discussed a little about such a current in an
earlier column.

In a typical STM, our "needle" or pointed piece of a metal or
other material is mounted on the end of a cantilever, sort of like a
diving board with a needle mounted on the under side of the
diving end. Hopefully, there are a few of you out there who
might also liken it to a phonograph needle tracking the grooves
in one of those ancient long-playing vinyl records. However, in
the STM, as in the topografiner, the tip of the needle does not
touch the surface but comes very close to it. How close?
Approximately 10 Angstroms, or one nanometer. For those
unfamiliar with such terms, a nanometer is one ten millionth of a
centimeter and there are 2.54 centimeters in an inch. In other
words, controlling that separation between tip and surface is one
helluva job! To control vibrations at this level is a major task in
mechanical design, which is where the IBM workers made their
crucial contribution.

Now, in one mode of operation, combining electronic circuitry
and the ingenious mechanical design, the point is scanned across
the sample while keeping the tunneling current constant. This
means that the height of the point above the surface has to be
adjusted up or down as scanning proceeds. The difference in
height can be measured by shining a laser light beam onto the
cantilever at an angle and measuring its deflection on a detector.
Recording these height readings allows the construction of a
topographical map of the surface. What happens if the tip is
treated so that at only a single atom protrudes at its end? The
hills and valleys of this topographical map correspond to
individual atoms. This truly remarkable ability to detect
individual atoms is what led to the Nobel Prize for the IBM
workers.

You may have read articles predicting that in the future there will
be microfactories making very tiny circuits or machines. While
I''m somewhat skeptical that many of the predictions are pretty
far out, the STM has been used to move and deposit individual
atoms on a surface. Workers at IBM, for example, spelled out
IBM in individual atoms using this technique and have made
what they call "quantum corrals" by positioning 48 iron atoms in
a circle on a copper surface. I gather that they showed that an
electron could be contained just like a cow inside this corral.
There are also other examples of demonstrations of the feasibility
of making electronic devices on the atomic scale which have led
to predictions that enormous computing power might be
available on thumbnail size chips.

Another type of scanning microscope is the atomic force
microscope or AFM. In an AFM no voltage is applied to the fine
point mounted on the cantilever. There are three modes of
typical operation. In the "contact" mode, the simplest to
understand, the point is dragged (scanned) across the surface and
is in actual physical contact. This is certainly a direct approach
and is most sensitive but there is the possibility of damage to
either the tip or the surface. In the "non-contact" mode the point
is held above the surface and the force of attraction is measured
during scanning across the surface. A third method is the
"tapping" mode, akin to blind person tapping his cane. Again,
under the right conditions, a topographical map can yield hills
and valleys corresponding to individual atoms.

In essence, the AFM "feels" the atoms as the point is dragged
along. There is a force known as the Van der Waals force that
results in the tip being attracted to the surface up to a very small
separation between tip and surface. As the tip moves even closer
this force turns into repulsion. By knowing how "springy" our
diving board or cantilever is this force can be calculated and the
various modes of operation can be controlled. The applications
of the AFM are exploding in that it has now been applied to look
at specimens ranging from living neurons to liquids to genes.

There are now many other versions of these scanning
microscopes involving magnetic fields, electrochemical actions
such as electroplating, etc. In all of them the atoms aren''t
actually "seen" but are certainly capable of being monitored
individually and with suitable computer processing, pictures of
the atomic structure of the surface can be derived. Actually, for
many applications there is no need to identify individual atoms;
in fact, doing so could result in a "not seeing the forest for the
trees" effect. For such applications, then tips can be less sharp
and I would imagine the electronics could be less demanding and
expensive. By modifying the tips by coating them with different
materials such as biologically active compounds, wondrous
things are in the process of being achieved and I hope to report
on some of these in detail later.

Back to Floyd. One of my golfing buddies just called a few
minutes ago and mentioned that he had seen on TV a picture of
the bridge I normally use to cross the river in Bound Brook. He
said there was debris on the bridge, implying the water had risen
some 30 feet! Unbelievable!

Allen F. Bortrum

[Editor: Re the above bridge, I noticed some unidentified barrels
that had washed up on it, reportedly filled with toxic chemicals
from a local American Cyanimid plant. But we won''t tell
Bortrum because then he''ll worry too much when he crosses that
bridge in the future].