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09/14/2005

Fishing for Birds

We’ve talked before about animals exhibiting behaviors once
been thought to be exclusively human. For example, the famed
African grey parrot Alex not only has an extensive vocabulary
and the ability to distinguish colors and numbers of objects but
also may toy with visitors or new researchers by deliberately
giving wrong answers to their questions. We’ve also talked
about crows or ravens that have learned to deceive their more
aggressive colleagues by pretending to eat at a source that has no
food, then switching to the real food location. You may have
seen mention of these latter birds in an article in the August 4
New York Times Sunday Magazine section.

In the same vein, Michael Noonan, professor of animal behavior
at Canisius College in New York State, has stirred up the animal
behavior community with his studies of orcas, killer whales,
housed in Marineland in Ontario, Canada. When on Marco
Island in Florida, I like to watch the pelicans and gulls follow the
fishing boats to the docks, where the birds wait for the fishermen
to clean their catch and toss the remains back into the water.
Well, one of the whales in Ontario decided to capitalize on the
gull’s taste for fish in order to add variety to its own diet.

Noonan noticed that this particular orca would swallow a fish but
then spit out the regurgitated fish onto the surface of the water.
The orca then sank below the surface, waiting for a gull to take
the bait. The orca then proceeded to gulp down the unwary gull.
According to an article on the Canisius Web site, Noonan found
that, within a couple of months, a younger orca had observed his
older brother’s ploy and began engaging in the same gull-baiting
behavior. Eventually, all the orcas in that Canadian Marineland
were enjoying gulls as a side dish. One or more of the group was
a mother orca, a case in which the parent learns from its offspring.

Obviously, this “cultural learning”, in which a behavior is
transmitted to and adopted by others in a community, is not only
the province of us humans. Although I enjoy finding examples
that show we aren’t as different from animals as we may think,
it’s clear that we are unique in many respects. What is it that
really does separate us from our fellow animals? With the recent
sequencing of our human DNA, scientists are trying to find the
particular genes or sequences in our DNA that place us in a
special category. As an aside, I found an interesting point about
DNA in Bill Bryson’s book “A Short History of Nearly
Everything”. He points out that no molecule is alive and that
DNA is, in the words of geneticist Richard Lewontin, “among
the most nonreactive, chemically inert molecules in the living
world.” It is this very “unalive”, unreactive nature of DNA that
gives us life and allows the DNA to be sustained and transmitted
largely unchanged from generation to generation.

Which brings us to poor Clint. Clint died last year of heart
failure at the tender age of 24 and I doubt that any of us read or
heard of his passing. However, Clint’s legacy is one that may be
long remembered in the annals of science. Clint, a resident of
the Yerkes National Primate Research Center in Atlanta, was the
chimpanzee whose blood was used in an international effort to
decode the chimpanzee genome. The work was performed by
the Chimpanzee Sequencing and Analysis Consortium, a group
of 67 researchers in the U.S., Israel, Italy, Germany and Spain.
According to an article by Alvin Powell on the Harvard
University Web site, the effort was led by Eric Lander of the
Broad Institute (a joint Harvard/MIT collaboration), Richard
Wilson of the Washington University School of Medicine in St.
Louis and Robert Waterson of the University of Washington,
Seattle. It’s clear that teamwork is the name of the game in the
DNA sequencing field!

The relatively complete sequencing of Clint’s DNA was
announced last month and papers were published in Nature and
online by Science. According to Francis Collins, director of the
National Human Genome Research Institute, quoted in an AP
dispatch by Malcolm Ritter, “It’s a huge deal. We now have the
instruction book of our closest relative.” What’s the big deal?
With the DNA “instruction books” of the human and the
chimpanzee in hand, we’re closer to answering the question,
“What makes us human?” Remember that DNA is like a ladder
with rungs, the rungs being so-called “base pairs”. The bases are
4 chemicals that we can abbreviate as the letters A, C, T and G;
A only pairs with T and C with G. Thus, the “rungs” are A-T
and C-G pairs. If we know all the letters on one side of the
ladder, we know the letters on the other side.

So, how do we differ from the chimp? All we have to do, it
would seem, is lay down the A, G, C, T “letters” in each DNA
ladder side by side and see where they differ. It’s not that
simple. There are some 3 billion rungs (base pairs) that form the
rungs in the DNA “ladders” in each of the chimp and human
DNAs. That’s a lot of rungs! What have they found so far?
Among those 3 billion base pairs, there are 40 million places that
differ in the chimp and human DNAs. Of the 40 million, 35
million are cases where the base pairs differ and 5 million are
sites where a portion of the code has been added or deleted. To
put the findings in perspective, the differences between chimps
and humans are about 10 times greater than the differences
between individual humans. There are also 50 genes that we
humans have that the chimpanzee does not.

After chimps and humans branched off from a common ancestor
some 6 million years ago, both species have evolved, becoming
different from that ancestor and from each other. One of the
areas the researchers are focusing on is to compare regions in
DNA in which genes are changing at different rates in humans
and chimps compared to other mammals. The hope is that the
sources of various diseases and immune responses in humans and
chimps can be traced. We know that chimps and humans have
different responses to HIV/AIDS, for example. Indeed, the
researchers have found that the most rapidly changing genes in
humans, chimps and other mammals are in areas related to
immune responses to diseases.

Unfortunately, it isn’t enough to determine which of the “letters”
in the chimp and human DNAs differ. The complexity of the
problem is noted in an article by Edwin McConkey and Ajit
Varki in the September 2 issue of Science. They write, “Can we
now provide a DNA-based answer to the fascinating and
fundamental question, ‘What makes us human?’ Not at all!”
They go on to say that it isn’t enough to see which genes are
different. We have to know the function of each gene, what
protein or proteins it orders be made (the gene is “expressed”),
when and at what stage in the life of the chimp or human this
happens and also the effects of environments on the DNA.
There’s a lot more work to be done!

The same issue of Science contains an editorial and articles that
bemoan the possibility that we have most of the chimpanzee’s
DNA figured out but that we are in danger of the chimpanzee
itself becoming extinct. Unless poaching, the eating of so-called
“bush meat” and loss of habitat due to logging and clearing are
addressed, gorillas, chimpanzees and orangutans could be gone
within a generation. We owe our closest relatives better than
that.

Allen F. Bortrum



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-09/14/2005-      
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Dr. Bortrum

09/14/2005

Fishing for Birds

We’ve talked before about animals exhibiting behaviors once
been thought to be exclusively human. For example, the famed
African grey parrot Alex not only has an extensive vocabulary
and the ability to distinguish colors and numbers of objects but
also may toy with visitors or new researchers by deliberately
giving wrong answers to their questions. We’ve also talked
about crows or ravens that have learned to deceive their more
aggressive colleagues by pretending to eat at a source that has no
food, then switching to the real food location. You may have
seen mention of these latter birds in an article in the August 4
New York Times Sunday Magazine section.

In the same vein, Michael Noonan, professor of animal behavior
at Canisius College in New York State, has stirred up the animal
behavior community with his studies of orcas, killer whales,
housed in Marineland in Ontario, Canada. When on Marco
Island in Florida, I like to watch the pelicans and gulls follow the
fishing boats to the docks, where the birds wait for the fishermen
to clean their catch and toss the remains back into the water.
Well, one of the whales in Ontario decided to capitalize on the
gull’s taste for fish in order to add variety to its own diet.

Noonan noticed that this particular orca would swallow a fish but
then spit out the regurgitated fish onto the surface of the water.
The orca then sank below the surface, waiting for a gull to take
the bait. The orca then proceeded to gulp down the unwary gull.
According to an article on the Canisius Web site, Noonan found
that, within a couple of months, a younger orca had observed his
older brother’s ploy and began engaging in the same gull-baiting
behavior. Eventually, all the orcas in that Canadian Marineland
were enjoying gulls as a side dish. One or more of the group was
a mother orca, a case in which the parent learns from its offspring.

Obviously, this “cultural learning”, in which a behavior is
transmitted to and adopted by others in a community, is not only
the province of us humans. Although I enjoy finding examples
that show we aren’t as different from animals as we may think,
it’s clear that we are unique in many respects. What is it that
really does separate us from our fellow animals? With the recent
sequencing of our human DNA, scientists are trying to find the
particular genes or sequences in our DNA that place us in a
special category. As an aside, I found an interesting point about
DNA in Bill Bryson’s book “A Short History of Nearly
Everything”. He points out that no molecule is alive and that
DNA is, in the words of geneticist Richard Lewontin, “among
the most nonreactive, chemically inert molecules in the living
world.” It is this very “unalive”, unreactive nature of DNA that
gives us life and allows the DNA to be sustained and transmitted
largely unchanged from generation to generation.

Which brings us to poor Clint. Clint died last year of heart
failure at the tender age of 24 and I doubt that any of us read or
heard of his passing. However, Clint’s legacy is one that may be
long remembered in the annals of science. Clint, a resident of
the Yerkes National Primate Research Center in Atlanta, was the
chimpanzee whose blood was used in an international effort to
decode the chimpanzee genome. The work was performed by
the Chimpanzee Sequencing and Analysis Consortium, a group
of 67 researchers in the U.S., Israel, Italy, Germany and Spain.
According to an article by Alvin Powell on the Harvard
University Web site, the effort was led by Eric Lander of the
Broad Institute (a joint Harvard/MIT collaboration), Richard
Wilson of the Washington University School of Medicine in St.
Louis and Robert Waterson of the University of Washington,
Seattle. It’s clear that teamwork is the name of the game in the
DNA sequencing field!

The relatively complete sequencing of Clint’s DNA was
announced last month and papers were published in Nature and
online by Science. According to Francis Collins, director of the
National Human Genome Research Institute, quoted in an AP
dispatch by Malcolm Ritter, “It’s a huge deal. We now have the
instruction book of our closest relative.” What’s the big deal?
With the DNA “instruction books” of the human and the
chimpanzee in hand, we’re closer to answering the question,
“What makes us human?” Remember that DNA is like a ladder
with rungs, the rungs being so-called “base pairs”. The bases are
4 chemicals that we can abbreviate as the letters A, C, T and G;
A only pairs with T and C with G. Thus, the “rungs” are A-T
and C-G pairs. If we know all the letters on one side of the
ladder, we know the letters on the other side.

So, how do we differ from the chimp? All we have to do, it
would seem, is lay down the A, G, C, T “letters” in each DNA
ladder side by side and see where they differ. It’s not that
simple. There are some 3 billion rungs (base pairs) that form the
rungs in the DNA “ladders” in each of the chimp and human
DNAs. That’s a lot of rungs! What have they found so far?
Among those 3 billion base pairs, there are 40 million places that
differ in the chimp and human DNAs. Of the 40 million, 35
million are cases where the base pairs differ and 5 million are
sites where a portion of the code has been added or deleted. To
put the findings in perspective, the differences between chimps
and humans are about 10 times greater than the differences
between individual humans. There are also 50 genes that we
humans have that the chimpanzee does not.

After chimps and humans branched off from a common ancestor
some 6 million years ago, both species have evolved, becoming
different from that ancestor and from each other. One of the
areas the researchers are focusing on is to compare regions in
DNA in which genes are changing at different rates in humans
and chimps compared to other mammals. The hope is that the
sources of various diseases and immune responses in humans and
chimps can be traced. We know that chimps and humans have
different responses to HIV/AIDS, for example. Indeed, the
researchers have found that the most rapidly changing genes in
humans, chimps and other mammals are in areas related to
immune responses to diseases.

Unfortunately, it isn’t enough to determine which of the “letters”
in the chimp and human DNAs differ. The complexity of the
problem is noted in an article by Edwin McConkey and Ajit
Varki in the September 2 issue of Science. They write, “Can we
now provide a DNA-based answer to the fascinating and
fundamental question, ‘What makes us human?’ Not at all!”
They go on to say that it isn’t enough to see which genes are
different. We have to know the function of each gene, what
protein or proteins it orders be made (the gene is “expressed”),
when and at what stage in the life of the chimp or human this
happens and also the effects of environments on the DNA.
There’s a lot more work to be done!

The same issue of Science contains an editorial and articles that
bemoan the possibility that we have most of the chimpanzee’s
DNA figured out but that we are in danger of the chimpanzee
itself becoming extinct. Unless poaching, the eating of so-called
“bush meat” and loss of habitat due to logging and clearing are
addressed, gorillas, chimpanzees and orangutans could be gone
within a generation. We owe our closest relatives better than
that.

Allen F. Bortrum