As
a researching scientist your job is to answer questions that no one
else in the world knows the answer to.
Often these questions are not easily answered, or chances are someone
would have already answered it.
Therefore, another major component of a researcher’s job is to continually
develop new ideas for how to find these answers. This can take place through advances in
technology or pure ingenuity of the creative mind. This takes time. The scientist must integrate known
information on the topic by making links between many seemingly separate pieces
of information, resulting in one continuous mesh of knowledge. Once this is complete, the ideas blossom. Everyone has their own way of learning. Personally, I learn information much more
thoroughly by writing about it because this forces me to integrate the
information in my mind so that I can smoothly re-tell the story while adding my
own elements and ideas. That is what you
will find below. You won’t see the
learning process – just the final product.
I hope that my ideas, opinions and ways of presenting the information will
twist the topic of interest into something new and interesting to anyone
reading.
My
interests (what you can expect me to write about):
All
of my interests in Biology stem from the desire to understand the process of
evolution: how does it work and what is it capable of? (Read: Nothing in Biology
Makes Sense except in the Light of Evolution,
by Theodosius Dobzhansky, The American Biology Teacher, Vol. 35, No. 3, 1973, pp.
125-129.) Although I am presenting my interests as separate topics, further posts of mine will show how they all interconnect.
1)
Composition of the genome: Noncoding DNA and regulatory mechanisms
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| Nature Vol. 441 2006 "What is a Gene?" |
Scientists
are continually making new discoveries that fundamentally change their view of
how a cell works. The most profound
example of this is the realization that an extremely low percentage of the
human genome actually encodes genes. In
fact, distantly related species have many of the same genes. What then is responsible for the drastic
phenotypic differences we see between different organisms? The answer seems to be in their regulatory
processes! The fact that such a
fundamental fact of life was so recently discovered shows that the way we
have been going about the study of cellular function has been incredibly
inefficient. This revelation about
genome composition was a result of increased efficiency of genome
sequencing. Further advances in systems
biology are likely to reveal even more groundbreaking fundamental
discoveries.
2)
The cellular role of reactive oxygen species (ROS), both in modern biodiversity
and throughout evolution of life on earth
One of the most
interesting adaptations leading to the evolution of complex multicellular life
is the ability to breathe and metabolize oxygen. Along with
the evolutionary advantage of energy production that is 18 times more efficient
than glycolysis, another major energy-generating pathway, comes the disadvantage of reactive oxygen species (ROS) as byproducts of metabolism.
This is a disadvantage because ROS are capable of damaging all major components
of the cell, resulting in contribution to the aging process and various
diseases as shown in both common model organisms and humans. Since the
evolution of metazoans 0.5 billion years ago, ROS have become part of various
beneficial cellular functions as well (cell signaling, immune response). I am
interested in the biodiversity of the cellular role of ROS - in other words, how diverse are the adaptations that organisms have evolved to handle both endogenous and exogenous sources of ROS? Further: who is most well-adapted, what is the cellular mechanism behind this extreme adaptation and can we use this information to improve the health of humans? Evolution is something that occurs over an inconceivable amount of time and its likely capability to "out think" us should not be overlooked.
3) Systems biology
A professor for a graduate course in genetics assigned us to read a story that used a metaphor to compare geneticists to biochemists, with a bias towards geneticists as being the more clever scientists (“The Salvation of Doug” by William T. Sullivan). In the story the two scientists (one a geneticist and one a biochemist) decided to try and figure out how a car was built, however they could not get into the building themselves to watch the manufacturing process. The geneticist’s approach was to remove one of the workers from the manufacturing process, and examine the resulting functional changes in the car in the absence of that person (making a mutation and observing the resulting phenotype). The biochemist’s approach was to isolate separate parts of the car and see how they work together, to figure out each part’s distinct function (protein isolation). Although this type of approach may be an accurate metaphor for the reductionist approach often taken in biochemistry, I have an idea for a different metaphor to represent those biochemists that use the tools of systems biology. The systems biologist would observe the workers without them knowing. The only way to do this would be to take snapshot pictures of the process in action by stopping the manufacturing process at different points in time. These snapshots could then be compiled to derive the story of how the building of the car occurs. The geneticist has no knowledge of how the workers put together the car and the first biochemist is on a wild goose-chase (you can’t study one small piece of the puzzle and expect to learn much about what the big picture looks like). However, the systems biologist sees everything involved in the process (workers and what components of the car they’re interacting with) and from the sequence of photographs can formulate a detailed, informed and testable hypothesis of how it occurs. Therefore, systems biology is a field with unique advantages that can hold its own ground among the many areas of biological research.
Although systems biology isn’t always able to answer function-related questions, its advantages should not be underestimated:
1) It gives the scientist the big-picture view of the cell - the more techniques you use (i.e. proteomics, transcriptomics, etc.) the less likely it is that you’re missing or “not seeing” something (like turning a 2D picture into a 3D picture)
2) Because of the wealth of information it provides, it is hypothesis-generating – in other words, it tells you precisely where to look to answer your question.
3) It gives a quantitative nature to biology.
With continued progress on effective experimental set-up and data analysis techniques, the ability to extract valuable information by systems biology is improving. A recent example of this kind of progress is Buescher et al. in a March 2012 issue of Science.
4) Deep-sea hydrothermal vent ecosystems: Exploration in an effort to understand the limits of biodiversity on earth
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| Photo credit to Woods Hole Oceanographic Institution |
The way in which life began on earth, followed by over 3 billion years of evolution has resulted in a wide variety of life forms. The most extreme of this biodiversity can be found in extreme environments such as hydrothermal vents. Hydrothermal vent ecosystems are one of the few on earth where the primary source of energy is geothermal rather than solar. This is reflected in the fact that the primary producers of this ecosystem are chemoautotrophic microbes rather than photosynthetic organisms. A defining characteristic of this ecosystem is that symbiosis with chemoautotrophic microbes is a way of life among metazoans, with an estimated 96% of the biomass in a symbiotic relationship. Chemoautotrophs derive their energy from hydrothermal vent fluids, which are high in temperature, reduced, anoxic, and contain high concentrations of dissolved metals and trace elements. Although the conditions found at hydrothermal vents are not traditionally considered habitable for life, life not only thrives there - it is hypothesized to have begun there. The mechanisms by which organisms are able to survive are still being uncovered by scientists, and are extending the limit for the kind of biodiversity known to exist on earth.
