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12/12/2007

Travelers - Animal and Cosmic

In my November 9 issue of Science, I found three articles that
provide follow-up material on subjects I wrote about in past
columns. These articles related to the decoding of the genome of
drug-resistant strains of tuberculosis, to the origin of cosmic rays
and to the subject of last week’s column, the “inner compass”
that provides guidance to birds, fish and other animals in their
travels.

MRSA and drug-resistant TB are two medical problems of great
concern these days. Researchers at the Broad Institute and
Harvard School of Public Health have sequenced most of the
genome of an extensively drug-resistant TB strain as part of an
international effort to decode the genomes of various drug-
resistant and drug-sensitive TB bacteria. The Broad-Harvard
team finds that there are roughly 30 or so mutations in the drug-
resistant TB genome compared to the genome of old fashioned
TB that is treatable with drugs. This relatively small number of
mutations holds out the hope that it should be a less daunting
task to identify those mutations that confer drug resistance and
come up with a drug or drugs to treat drug-resistant TB. Of
course, this will involve developing new diagnostic tools and
drug R&D is not a speedy process. We’re talking years here but
at least it should be feasible.

Turning to cosmic rays, which enter the Earth’s atmosphere from
all directions, there’s been an ongoing quest for decades to find
the source. Of particular interest have been the really high-
energy cosmic rays, which really aren’t “rays” as we think of
them, but are particles. If you’re sitting with a cosmic ray
detector waiting to catch a super high-energy cosmic ray, you’d
better have a lot of patience – or a slew of detectors that cover a
lot of area. Here we’re talking cosmic rays that have the energy
equivalent to a good size hailstone. This may not impress you
but chances are this cosmic ray is actually just a single proton, a
hydrogen atom without its electron. Physicists talk about cosmic
rays having energies expressed in terms of electron-volts (eV).
At the low end, at only a hundred billion eV or so, a few of these
particles strike an area of a square centimeter in the Earth’s
atmosphere every second.

On the other hand, at the super high-energy end, at a hundred
billion billion eV (that’s 1 followed by 20 zeroes!), there may be
only one particle hitting a square kilometer in a century or more!
That’s a long time to wait. Enter the Pierre Auger Southern
Observatory in western Argentina. The observatory consists of
1600 surface detectors spread out over an area roughly the size of
Rhode Island (3,000 square kilometers). The observatory has
been in operation since 2004 and has recorded a million cosmic
ray events in that time. Of the million, only 80 have had energies
over 40 billion billion eV, the super high-energy particles of
interest. The Pierre Auger Collaboration of several hundred
authors (!) from 89 different institutions worldwide report their
results in an article titled “Correlation of the Highest-Energy
Cosmic Rays with Nearby Extragalactic Objects”.

Well, their definition of “nearby” may seem a stretch – the
nearby objects are roughly 250 million light-years away; that’s
over a billion trillion miles! For these super high-energy
particles to have made their way over such vast distances without
losing energy is remarkable and the new data and analysis of
older results now indicate the likely source to be what are known
as “active galactic nuclei” (AGN). An AGN is a galaxy that has
a black hole that is busy gobbling up gas and stars and ejecting
vast plumes of plasma into the space between galaxies. If AGNs
are indeed the source, these cosmic “hailstones” have had a
remarkable journey indeed!

Finally, last week we talked about migrating songbirds and their
having some kind of inner compass to guide them on their way.
In that column, I didn’t mention what that inner compass might
consist of. However, I do recall discussing on at least one
occasion the view that birds and fish depend on tiny magnetite
crystals in their beaks or noses to determine their position with
respect to the earth’s magnetic field. An early proponent of the
magnetite compass was Michael Walker who, with Joseph
Kirschvink of the California Institute of Technology, published a
paper in Science in 1984 reporting the discovery of magnetite-
like crystals in tuna.

Later, in 1997 and 2000, Walker and other colleagues published
papers in Nature reporting the discovery of strings of magnetite
crystals in the noses of rainbow trout. However, at about the
same time a compound called cryptochrome was found in the
eyes of all sorts of animals ranging from fruit flies to mice. The
interesting thing about cryptochrome is that when light strikes it
there are two intermediate states formed and the relative amounts
of the two intermediates depends on the orientation of the animal
with respect to the surrounding magnetic field.

The finding of cryptochrome has led to the suggestion that
information about the amounts of these two intermediate states is
transmitted to the brain from the eyes via the optic nerves. This
in turn has led to the postulate that birds can actually “see” the
magnetic field of the earth by turning their heads one way or the
other. If true, how the magnetic field information would register
in the brain is up in the air. Walker is quoted as saying the idea
of evolution coming up with two organs for sensing the magnetic
field is absurd. The cryptochrome camp includes John Phillips at
Virginia Polytechnic Institute and Henrik Mouritsen at the
University of Oldenburg in Germany. They maintain the
evidence favoring the involvement of cryptochrome in sensing a
magnetic field is just as good as the evidence for magnetite.

Mouritsen and Phillips hope to settle the question by
experimenting with mice in which the cryptochrome has been
genetically engineered out of the picture. What the experiments
will be wasn’t mentioned but I imagine one experiment will be to
compare the performance of normal mice with the performance
of knockout mice in mazes.

Whatever the results, I would expect that in another year or so
we’ll know a lot more definitely how animals find their way,
sometimes over thousands of miles. Meanwhile, as far as our
own species is concerned, we males will probably continue to be
chastised by our wives or significant others for being stubborn
and not asking directions.

Allen F. Bortrum



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-12/12/2007-      
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Dr. Bortrum

12/12/2007

Travelers - Animal and Cosmic

In my November 9 issue of Science, I found three articles that
provide follow-up material on subjects I wrote about in past
columns. These articles related to the decoding of the genome of
drug-resistant strains of tuberculosis, to the origin of cosmic rays
and to the subject of last week’s column, the “inner compass”
that provides guidance to birds, fish and other animals in their
travels.

MRSA and drug-resistant TB are two medical problems of great
concern these days. Researchers at the Broad Institute and
Harvard School of Public Health have sequenced most of the
genome of an extensively drug-resistant TB strain as part of an
international effort to decode the genomes of various drug-
resistant and drug-sensitive TB bacteria. The Broad-Harvard
team finds that there are roughly 30 or so mutations in the drug-
resistant TB genome compared to the genome of old fashioned
TB that is treatable with drugs. This relatively small number of
mutations holds out the hope that it should be a less daunting
task to identify those mutations that confer drug resistance and
come up with a drug or drugs to treat drug-resistant TB. Of
course, this will involve developing new diagnostic tools and
drug R&D is not a speedy process. We’re talking years here but
at least it should be feasible.

Turning to cosmic rays, which enter the Earth’s atmosphere from
all directions, there’s been an ongoing quest for decades to find
the source. Of particular interest have been the really high-
energy cosmic rays, which really aren’t “rays” as we think of
them, but are particles. If you’re sitting with a cosmic ray
detector waiting to catch a super high-energy cosmic ray, you’d
better have a lot of patience – or a slew of detectors that cover a
lot of area. Here we’re talking cosmic rays that have the energy
equivalent to a good size hailstone. This may not impress you
but chances are this cosmic ray is actually just a single proton, a
hydrogen atom without its electron. Physicists talk about cosmic
rays having energies expressed in terms of electron-volts (eV).
At the low end, at only a hundred billion eV or so, a few of these
particles strike an area of a square centimeter in the Earth’s
atmosphere every second.

On the other hand, at the super high-energy end, at a hundred
billion billion eV (that’s 1 followed by 20 zeroes!), there may be
only one particle hitting a square kilometer in a century or more!
That’s a long time to wait. Enter the Pierre Auger Southern
Observatory in western Argentina. The observatory consists of
1600 surface detectors spread out over an area roughly the size of
Rhode Island (3,000 square kilometers). The observatory has
been in operation since 2004 and has recorded a million cosmic
ray events in that time. Of the million, only 80 have had energies
over 40 billion billion eV, the super high-energy particles of
interest. The Pierre Auger Collaboration of several hundred
authors (!) from 89 different institutions worldwide report their
results in an article titled “Correlation of the Highest-Energy
Cosmic Rays with Nearby Extragalactic Objects”.

Well, their definition of “nearby” may seem a stretch – the
nearby objects are roughly 250 million light-years away; that’s
over a billion trillion miles! For these super high-energy
particles to have made their way over such vast distances without
losing energy is remarkable and the new data and analysis of
older results now indicate the likely source to be what are known
as “active galactic nuclei” (AGN). An AGN is a galaxy that has
a black hole that is busy gobbling up gas and stars and ejecting
vast plumes of plasma into the space between galaxies. If AGNs
are indeed the source, these cosmic “hailstones” have had a
remarkable journey indeed!

Finally, last week we talked about migrating songbirds and their
having some kind of inner compass to guide them on their way.
In that column, I didn’t mention what that inner compass might
consist of. However, I do recall discussing on at least one
occasion the view that birds and fish depend on tiny magnetite
crystals in their beaks or noses to determine their position with
respect to the earth’s magnetic field. An early proponent of the
magnetite compass was Michael Walker who, with Joseph
Kirschvink of the California Institute of Technology, published a
paper in Science in 1984 reporting the discovery of magnetite-
like crystals in tuna.

Later, in 1997 and 2000, Walker and other colleagues published
papers in Nature reporting the discovery of strings of magnetite
crystals in the noses of rainbow trout. However, at about the
same time a compound called cryptochrome was found in the
eyes of all sorts of animals ranging from fruit flies to mice. The
interesting thing about cryptochrome is that when light strikes it
there are two intermediate states formed and the relative amounts
of the two intermediates depends on the orientation of the animal
with respect to the surrounding magnetic field.

The finding of cryptochrome has led to the suggestion that
information about the amounts of these two intermediate states is
transmitted to the brain from the eyes via the optic nerves. This
in turn has led to the postulate that birds can actually “see” the
magnetic field of the earth by turning their heads one way or the
other. If true, how the magnetic field information would register
in the brain is up in the air. Walker is quoted as saying the idea
of evolution coming up with two organs for sensing the magnetic
field is absurd. The cryptochrome camp includes John Phillips at
Virginia Polytechnic Institute and Henrik Mouritsen at the
University of Oldenburg in Germany. They maintain the
evidence favoring the involvement of cryptochrome in sensing a
magnetic field is just as good as the evidence for magnetite.

Mouritsen and Phillips hope to settle the question by
experimenting with mice in which the cryptochrome has been
genetically engineered out of the picture. What the experiments
will be wasn’t mentioned but I imagine one experiment will be to
compare the performance of normal mice with the performance
of knockout mice in mazes.

Whatever the results, I would expect that in another year or so
we’ll know a lot more definitely how animals find their way,
sometimes over thousands of miles. Meanwhile, as far as our
own species is concerned, we males will probably continue to be
chastised by our wives or significant others for being stubborn
and not asking directions.

Allen F. Bortrum