K Barrett wrote:
Nothing makes you feel older than finding out everyting you were taught
isn't true anymore.

It's even worse when it's your job. Research that required three years
of late nights in the lab when I was a grad student now takes about 15
minutes on the computer. Many of the techniques that I learned are
completely obsolete, and it has been less than ten years since I
defended my dissertation.

Nick

I saw a TV show on my new 60" HD TV about a census of marine micro organisms
that is currently underway.

They are using cutting edge genetic sequencing tools to count new micro
organisms in sea water. They collect the water, strain it through ever
finer filters to collect a gooey glob of micro organisms and then they
extract their DNA by slicing it into tiny nucleotide bits, then they
replicate these bits, then they REASSEMBLE them back into complete
genomes....and out of this gene puree and reassembly process comes something
a computer program can use to count the number of unique organisms that were
in the sea water sample BEFORE they were chopped to bits.

One of the remarkable things they have discovered, other than the Amazing
and unpredictably large number of new species at the microscopic level are
lots of gene groups with interesting mutations on gene groups which they
already know are used by these organisms to do things like turn light into
energy, break down oily carbon compounds, enhance immunity to cold, etc.

It is just scary what bags of genes called 'humans' can infer about
themselves based on what is literally a sampling of their gene pool.



wrote in message
oups.com...
K Barrett wrote:
Nothing makes you feel older than finding out everyting you were taught
isn't true anymore.

It's even worse when it's your job. Research that required three years
of late nights in the lab when I was a grad student now takes about 15
minutes on the computer. Many of the techniques that I learned are
completely obsolete, and it has been less than ten years since I
defended my dissertation.

Nick

Was that on the Sorceror II? J Craig Ventner's effort? He was the fellow
that beat the government's Human Genome Project to sequence the human
genome. He also was one of the folks I was thinking about when I asked my
question. A few years ago he was on 'Science Friday' (NPR) talking about
how he scoops up plankton, sequences the DNA, and has found over 800 genes
that deal with handling light. Again, I wondered 'how does he know?' Plus,
he's got one hell of a web page:
http://www.sorcerer2expedition.org/v.../HTML/main.htm

Jealousy overwhelms me.

K Barrett

"al" wrote in message news:i_x2h.5189$Z66.2452@trnddc07...
I saw a TV show on my new 60" HD TV about a census of marine micro
organisms that is currently underway.

They are using cutting edge genetic sequencing tools to count new micro
organisms in sea water. They collect the water, strain it through ever
finer filters to collect a gooey glob of micro organisms and then they
extract their DNA by slicing it into tiny nucleotide bits, then they
replicate these bits, then they REASSEMBLE them back into complete
genomes....and out of this gene puree and reassembly process comes
something a computer program can use to count the number of unique
organisms that were in the sea water sample BEFORE they were chopped to
bits.

One of the remarkable things they have discovered, other than the Amazing
and unpredictably large number of new species at the microscopic level
are lots of gene groups with interesting mutations on gene groups which
they already know are used by these organisms to do things like turn light
into energy, break down oily carbon compounds, enhance immunity to cold,
etc.

It is just scary what bags of genes called 'humans' can infer about
themselves based on what is literally a sampling of their gene pool.



wrote in message
oups.com...
K Barrett wrote:
Nothing makes you feel older than finding out everyting you were taught
isn't true anymore.

It's even worse when it's your job. Research that required three years
of late nights in the lab when I was a grad student now takes about 15
minutes on the computer. Many of the techniques that I learned are
completely obsolete, and it has been less than ten years since I
defended my dissertation.

Nick

Yes, the Sorcerer II expedition. Very VERY Amazing.

"K Barrett" wrote in message
. ..
Was that on the Sorceror II? J Craig Ventner's effort? He was the fellow
that beat the government's Human Genome Project to sequence the human
genome. He also was one of the folks I was thinking about when I asked my
question. A few years ago he was on 'Science Friday' (NPR) talking about
how he scoops up plankton, sequences the DNA, and has found over 800 genes
that deal with handling light. Again, I wondered 'how does he know?'
Plus, he's got one hell of a web page:
http://www.sorcerer2expedition.org/v.../HTML/main.htm

Jealousy overwhelms me.

K Barrett

Another thing was - I'm vaguely recalling this - that a lot of DNA in the
human genome is from viruses that have attached to it in the dim past,
raising the question(s) how do they know and what then is human?

I don't mean to beat this to death, because Nick and Rob have already
answered, but boy. If you wanted to start writing thrillers with conspiracy
theories you wouldnt have to go much further than a DNA lab.

K Barrett

"al" wrote in message news:i_x2h.5189$Z66.2452@trnddc07...
I saw a TV show on my new 60" HD TV about a census of marine micro
organisms that is currently underway.

They are using cutting edge genetic sequencing tools to count new micro
organisms in sea water. They collect the water, strain it through ever
finer filters to collect a gooey glob of micro organisms and then they
extract their DNA by slicing it into tiny nucleotide bits, then they
replicate these bits, then they REASSEMBLE them back into complete
genomes....and out of this gene puree and reassembly process comes
something a computer program can use to count the number of unique
organisms that were in the sea water sample BEFORE they were chopped to
bits.

One of the remarkable things they have discovered, other than the Amazing
and unpredictably large number of new species at the microscopic level
are lots of gene groups with interesting mutations on gene groups which
they already know are used by these organisms to do things like turn light
into energy, break down oily carbon compounds, enhance immunity to cold,
etc.

It is just scary what bags of genes called 'humans' can infer about
themselves based on what is literally a sampling of their gene pool.



wrote in message
oups.com...
K Barrett wrote:
Nothing makes you feel older than finding out everyting you were taught
isn't true anymore.

It's even worse when it's your job. Research that required three years
of late nights in the lab when I was a grad student now takes about 15
minutes on the computer. Many of the techniques that I learned are
completely obsolete, and it has been less than ten years since I
defended my dissertation.

Nick

K Barrett wrote:
Another thing was - I'm vaguely recalling this - that a lot of DNA in the
human genome is from viruses that have attached to it in the dim past,
raising the question(s) how do they know and what then is human?

In many cases, old viral sequence has features that scream "virus"
(long terminal repeats, etc) or can be identified by homology to
current, active viruses. But sometimes, it's not obvious that there is
a bright line dividing "human" and "virus." Viruses can pick up human
sequences. The reverse can also happen: sometimes, the evolutionary
history of a human gene includes insertion of viral elements. For
instance, the salivary amylase gene appears to have been generated when
a retroviral sequence inserted into the promoter region of an ancestral
pancreatic amylase gene. The retroviral sequence is what causes the
amylase gene to be expressed in salivary glands. So, in this case, the
sequence of a virus has become human.

Thanks again! This is great. Like having my own little continuing
education class.

Science really has exploded since I was in school. Recently I googled
Robert J. Griesbach USDA in order to read if he had any papers published on
microfungus (a question from a different thread here and more orchid
related) and came up with a list of abstracts for his papers, someof which
dealt with color (blue) in phalaenopsis. One google search on terms led to
another and another and I came away impressed at how some very minute
research leads to greater knowledge.

Anyway,

Thanks again for filling me in. I appreciate it.

K Barrett
wrote in message
oups.com...
K Barrett wrote:
Another thing was - I'm vaguely recalling this - that a lot of DNA in the
human genome is from viruses that have attached to it in the dim past,
raising the question(s) how do they know and what then is human?

In many cases, old viral sequence has features that scream "virus"
(long terminal repeats, etc) or can be identified by homology to
current, active viruses. But sometimes, it's not obvious that there is
a bright line dividing "human" and "virus." Viruses can pick up human
sequences. The reverse can also happen: sometimes, the evolutionary
history of a human gene includes insertion of viral elements. For
instance, the salivary amylase gene appears to have been generated when
a retroviral sequence inserted into the promoter region of an ancestral
pancreatic amylase gene. The retroviral sequence is what causes the
amylase gene to be expressed in salivary glands. So, in this case, the
sequence of a virus has become human.

K Barrett wrote:
Another thing was - I'm vaguely recalling this - that a lot of DNA in the
human genome is from viruses that have attached to it in the dim past....


Yes, I remember reading about this several years ago. In the years that
have passed since then, I have often wondered what I would look like and
what I would feel like if there was a way to magically get rid of all
the useless crap in my DNA and leave only the pure me.

Steve

al wrote:

...............They collect the water, strain it through ever
finer filters to collect a gooey glob of micro organisms and then they
extract their DNA by slicing it into tiny nucleotide bits, then they
replicate these bits, then they REASSEMBLE them back into complete
genomes....and out of this gene puree and reassembly process comes something
a computer program can use to count the number of unique organisms that were
in the sea water sample BEFORE they were chopped to bits.

One of the remarkable things they have discovered, other than the Amazing
and unpredictably large number of new species.........................

Well no wonder! It sounds to me like they are MAKING new species.

Steve

It does sound very counter intuitive doesn't it? At it's core is the idea
that the base pairs of the DNA ladder must reassemble a certain way and
that, with mathematical probability, when very long base pair segments from
different stands overlap with each other they can be assumed to part of the
same species. The scientists, their lap equipment, and their computers are
doing what your own RNA does; putting back together after replication what
belonged together in the first place. However, they *are* doing it with
more than one species genes at a time. The mind does not boggle quite as
much when you think of it this way....


"Steve" wrote in message
...
al wrote:

...............They collect the water, strain it through ever finer
filters to collect a gooey glob of micro organisms and then they extract
their DNA by slicing it into tiny nucleotide bits, then they replicate
these bits, then they REASSEMBLE them back into complete genomes....and
out of this gene puree and reassembly process comes something a computer
program can use to count the number of unique organisms that were in the
sea water sample BEFORE they were chopped to bits.

One of the remarkable things they have discovered, other than the Amazing
and unpredictably large number of new species.........................

Well no wonder! It sounds to me like they are MAKING new species.

Steve