Justin's Microbiology Journal
Monday, February 23, 2004
Sorry for the lack of updates. Off to New Zealand/Australia in an hour or two. Back in two weeks. I'm going to try and get a sample of some archaebacteria found in the geothermal springs in New Zealand.
I was able to demo the Motic BA450 without the phase objectives for a day or two, and that confirms I'll get that particular microscope when I get back. Was able to view various protists and several species of algae from my back yard, but without staining or phase contrast, couldn't see much bacterially. The Natto I observed (bacillus subtilis) seemed dead, I'll try again with the phase contrast objectives when I return.
Saturday, February 14, 2004
Found a few new open source publishing resources. OpenMed Central and Genome Biology. Combine that with the MIT open courseware, and you've got access to many of the resources you need to learn bio.
Friday, February 06, 2004
Just got back from working in Sacramento for a friend. Ate nothing but sushi for 2 days straight (he owns several sushi restaurants). Time to get back to work on bio though, my work was all programming.
Changing the mathematical models behind how you think almost always changes your life. It at least changes how you view your surroundings. One book which changed my life was A New Kind of Science by Stephen Wolfram. He has just open sourced the entire book. Please, if you haven't seen his work, I highly recommend it. Two principles changed how I think:
1) Complexity can spontaneously emerge from simple input and simple algorithms.
2) Computational Equivalence means that certain biological, physical, chemical or any other natural process cannot be reduced mathematically to a shortcut equation. The amount of computation that is required to get the answer will remain constant, which means that there are no shortcuts, you simply have to perform the computation to get the answer.
A link to his book is here.
Tuesday, February 03, 2004
What is a billion dollar industry, has major problems with smuggling, and causes Russian mafia types to blow up apartment buildings with 67 people in it? What is now being fought with the very latest in DNA testing? Caviar. The Mercury has the story here.
Man, organic chemistry has changed since I last remember reviewing it. I'm doing the MIT open courseware for OChem. If you want to study along, link is here. Resonance structures, stereochemistry, and conformances of Newman projections is all completely new to me.
One of the reasons I enjoy biology is the "wow" or "aha" value of learning something already extant in nature. There is a cool deep sea fish, the Malacosteid, that uses its own stealth surveillance capabilities to eat other fish. It is bioluminescent in a red wavelength, which most other deep sea fish are blind to (only blue penetrates deep down, so red awareness is not valuable). It, however, can see in red, so it can see its prey illuminated and not alert the prey itself. Interesting read is here.
Got invited to Orkut, spent a considerable part of the day filling out my profile and adding my good friends. Orkut is Google's Friendster counterpart, but is invite only apparently. Heavily weighted towards male and computer science folks, but strangely addictive for browsing, the value of membership has a fungible value, as folks are selling invites on ebay.
Monday, February 02, 2004
Good series on PBS about Genetics called, appropriately, DNA. Last episode was on cancer and Gleevec, one of the new targeted drugs that came about because we started categorizing cancers by their genetic material.
Watched lectures on bacterial injection systems, lysosomal avoidance mechanisms with emphasis on EHEC and EPEC strains. Another bacteria, Listeria Monocytogenes is a tough little bacteria that avoids the lysosome by secreting a protein that dissolves the phagosomal membrane from pinocytosis and swims around in the cytoplasm. It's frequently in the news, check out google news. Avoid soft cheeses if you have a compromised immune system (and always cook your ground beef all the way through to avoid EHEC). Here's another good webpage that shows the various evolutionary tactics that bacteria have developed to enter us, avoid our immune systems, and to replicate.
Going to call both Mikron and Martin Microscopes to order the Motic BA450, see who can deliver the most quickly and at the best price.
