September 15 2008
I gave instructions for the tutorial and most of you are following them well. Use my email for
scheduling appointments or just come and see me after class on Wednesdays. Tutorials contain
critical information so please attend even though they are not mandatory.
Journal Article Critique
The journal article critique is an easy assignment. It is only 2 pages and you already know how
to use the web of science. If you missed the tutorial Michael will go through it in the 2nd tutorial
again. Your critique is of 1 article and will be on the ISI web of science. It is the number 1
index system in the world. Remember the article you choose for the critique should have an
impact actor larger than 1.0. There could be other articles cited by the author and all of this you
can find on the web of science. You want some contradictory views. There is a learning goal and
that is how to find science information. You want to hunt down full length articles. One journal
does not equal the other. There are different opinions on things like global warming for
example. The scientists haven’t sorted out amongst themselves if it is even real or not. This is
an aspect of science. I remember someone who opposed Peter Mitchell. In any day and age of
science there will be critical voices of any view and that will be critiqued and you will have to do
it intelligently based on reading the primary material. You don’t do this by watching TV
because that isn’t scientific information. Most students do a good job and it is easy to get an A
in the assignment.
There is a chance to get good marks with this and the above assignment.
We started to talk about the limits of life to introduce community ecology. It was Charles
Darwin that said ‘nothing in biology makes sense without the concept of evolution’ and I agree
with it. We come back to the timeline of life and the rules/laws that govern the diversity of life
forms and development of ecological communities. Everything is connected. Evolutionary
framework is given to introduce communities in biology, how diverse they are, what can be
There are trenches all through the Atlantic and Pacific oceans and they are 2.1 Km below the
surface. In the 70’s we understood how diverse the biological communities are that are in these
pitch black conditions near the underground smokers. We are 2.1 Km from the surface of the
ocean and the pressure the organisms are exposed to is great. For every 10 metres = 1 full
atmospheric pressure. 100 Kilopascals are in each atmosphere of pressure. We are all adapted to
the atmosphere on earth with slight variations and if you increase the pressure like going deep
into the ocean, no human could survive; you would be crushed to death. These tube worms
would explode long before they would reach the surface and that is why it is hard for biologists
BGYC61H3F.September.15.2008 Lecture 2 1
to study these organisms. We can’t bring them up and preserve them. Some organisms we have
brought them up depressurizing them like we do with divers. Most tube worms won’t survive.
These are packed with bacteria in their body structures, in the billions/ounce, about 285 billion
bacteria for an ounce of tube worm is an average number. It is in the bacteria where the largest
amount of chemical activity happens in the underground volcano environment where life is
contained. Chemosynthesis happens here, unlike photosynthesis, we use electrons from
inorganic sources such as sulphur, hydrogen sulphide, which is important in these underground
communities. Sulphur has an oxidation state of -2 so they give 2 electrons to a chemical or
biosynthetic process. There are other reduced compounds like iron sulphide that contains it as
well. Iron is in oxidation state of +2 so it is ferrous. In essence it can be oxidized and turn into
ferric and electron can be fed into biosynthetic reactions. The light reactions split water and grab
electrons out of the water molecule in photosynthesis. Whether we make amino acids, sugars,
fatty acids, all the building blocks of life as we know it are believed to come about in this way
but in the ocean trenches it is different, electrons come from sulphur. Methane can also be used
but these are prevalent in the oceanic environment.
This is the Pompeii worm which is on record in the Guinness Book. It is an extreme species that
can tolerate extreme conditions. They can easily stand 100 degree C without combusting. They
live under absence of light and very cold conditions. A 2 4 degree Celsius we can have
biochemical activity that doesn’t take a back seat to the kind of reactions that our enzymes go
through. Between 20 25 degree C is where our enzymes are at their peak. Higher than that
the enzyme activity declines and same when it goes lower. The tube worm can do most of these
at the high rates. Many of these organisms are good at acclimatizing to a new condition when it
Two terms you have to keep separate – adaptation (evolutionary term) and acclamation. We are
not adapted to perform under these conditions. As humans we are quite bad at acclimatization
and we require heating and air conditioning. If you raise or drop temperature too much it is
game over. Nobody can survive in Toronto without clothing and shelter. You have heard of a
baby in a car in august with the windows up and the baby won’t survive. If you did this with the
worm it wouldn’t even notice anything was wrong. These ranges are of great interest to
biologists. You see the dogs in the street in august panting and they can’t handle the heat. So
ranges of acclimatization are enormous and we are trying to answer the questions of just how
high they can go. Perhaps when we understand the limits of life there can be life on Mars or
He is a patent lawyer and trained chemist that published some papers. As new information
comes out and gain validity I will discuss it. He says in the ocean trenches chemosynthesis is the
only game in town. He says that in those environments is where life may have in fact originated.
Stanley Miller is the guy who in the 50’s tried to recreate the early primordial atmosphere on
earth and find out what it would have taken to get biological molecules going. He fed electrical
pulses simulating light, he fed in methane and ammonia gas to see if he could find what was in
BGYC61H3F.September.15.2008 Lecture 2 2
the atmosphere early in the life of earth. That lead to the assumption that it was above ground
that life started.
Wachtershauser they say that it isn’t very likely. Stanley Miller, methane and ammonia
together are actually in the primordial atmosphere in very and were in very short supply. There
is no question that he made organic molecules out of these constituents but he used building
blocks of those reactions that didn’t actually happen in the troposphere at that time. We simulate
the Ph (as low at 2.8) that gushes from the smokers and we add the reaction chambers and now
we add the gases that come out and noticed he could make acetic acid molecules. Combining
carbon with sulphur making thiol (compounds where carbon is connected to the SH group). He
made H3C (methyl group) combined with this group making this methyl mercaptan group or
methyl thiol. Once that was formed there was a cascade of reactions and these acids form
compounds with the SH groups. It forms esters between the compounds and the polarization
occurs. Carbon dioxide comes out of the atmosphere and fixes it into organic molecules that can
esterifies with other components that form pioneer cells (organisms). There is more to this
theory. How they would have been closed in cell structures. There is intelligent thought. He
was able to show us it was possible to polymerize carbon after taking it out of the atmosphere
and making something similar to what defines life. He couldn’t show RNA or DNA formation.
The idea that we can have enclosures of biochemical soups in simple cell structures is not new.
Simple lipids can aggravate together as cells and if you have an enclose of molecules that
polymerize and replicate with one another you have definition of a primitive cell. Mio cells are
formed all the time with lipids. Take olive oil and mix it with water and you see bubbles form
and they are called moil cells.
They showed that it wasn’t just acid that they could make out of nothing but they could make
peptides. He went farther than Stanley Miller could in his day. Peptides, not only get
fundamental structure of amino acids but you could string them together in peptide bond form.
Two major contributions are life could have originated in the deep ocean and it is also possible to
form life and you can make amino acids in mixtures of this kind in ocean trenches.
Will that name be on the exam – no. I could ask you questions regarding other things actively
like putting his name into the question.
By default we would assume nothing to occur or if anything occurred it would be at a low rate.
It turns out that in the most unexpected environments you find life. Here is a picture of a
cathedral. He took some samples in the pillars and he found out you could go 2 metres into the
solid limestone and you could fish out bacteria. They were alive; they were not just buried as
corpses. There was no oxygen inside the stone. These organisms live in anoxide environments
and they perform chemosynthesis. There is enough carbon in the limestone. All you have to do
is bring it out of the carbonate. How do you do that? If you had stone or rock made of carbonate
BGYC61H3F.September.15.2008 Lecture 2 3
I gave instructions for the tutorial and most of you are following them well. Use my email for scheduling appointments or just come and see me after class on wednesdays. Tutorials contain critical information so please attend even though they are not mandatory. The journal article critique is an easy assignment. It is only 2 pages and you already know how to use the web of science. If you missed the tutorial michael will go through it in the 2nd tutorial again. Your critique is of 1 article and will be on the isi web of science. It is the number 1 index system in the world. Remember the article you choose for the critique should have an impact actor larger than 1. 0. There could be other articles cited by the author and all of this you can find on the web of science. There is a learning goal and that is how to find science information.