User:Jeff Zahir/Notebook/0001

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6/24/2016

Biochemistry requires the widest foundation knowledge of any hobby I've ever pursued: Biology, Chemistry, O-Chem, Genetics, physics, Math, Computer Science, Electronics, Specialized tools and instruments, Experiment design...and that's before you've decided what species to work with!

Clearly I'm not going to have time (I'm in my 60's) to learn all that, but I will try to learn enough, and do enough, to keep my interest going. This is my hobby, not my livelihood and I have no ambitions to make money from what I do. I'm basically the equivalent of an old-guy excitedly presenting my project at an elementary school science fair.

A couple of classes in bio simply isn't going to cut it. I've logged ~30 hours (so far) reading and watching YouTube lectures from MIT and Berkley on organic chemistry refreshers, recombinant DNA and cell biology to get up to speed on the basics. I figure that with another 500 hours or so, I should be ready to do some basic lab work. I've worked in this field, but I don't really know it.

7/30/2016

I've just finished my first read of Alberts et.al. "Molecular Biology of the Cell" and thankfully most of it was review. Some of the protocols and methods at the end will be very helpful and I'd like to go through the problems book as well.

There are also several on-line labs on this site that would be a great introduction to the labs and protocols I'll be using. I've logged close to 100 hours of study time on this project and a few thousand dollars so far so this is now officially my hobby.

8/4/2016

  • Started a subscription to Science magazine. I'm looking for a literature club but until I find one, I'll be creating presentation materials and summaries for presentation later.
  • Started a Coursera class on Bioinformatics. I really don't have more than an hour a day to give to it so I don't expect much to come of it but committing the time I have is important to keeping my momentum alive.

8/8/2016

An excellent biohacking academy presentation by Maureen Muldavin was live streamed from Oakland tonight. Titled: "In Silico Plasmid Design" it introduced tools like Snap Gene viewer and looking up plasmids on Adgene. Cheesh! Pricey little fellers aren't they?

8/16/2016

Another Biohacker Academy from Oakland called "Experimental Design". It gave a good introduction to differential screening and making sure you think through all the ways you could get false positives and negatives.

8/18/2016

I just finished the introductory module to the Johns Hopkins Coursera course on Genomic Data Science. It occurs to me that I may actually have something to offer this discipline. I'm a professional statistician and I've been using Python and R for about 10 years. That doesn't mean I'm any good at it (although some have said I am) but it does mean I won't be learning everything from scratch.

9/4/2016

Just completed (didn't do the problem sets on this one) another of the coursera classes on bioinformatics. This one focused on Bioconductor in r. I had to go through the videos twice in order to check the code I copied from the instructor. The r code was pretty standard but it's still a bit theoretical. Having an actual application that requires effort to derive non-trivial solutions will be the only way I can really know this program.

There seems to be one repository/standard for each sequencer manufacturer, species and university. It sort of reminds me of the balkanization of the internet in the early '90s and connectors in the '70s. Eventually it'll work itself out but early adopters get bragging rights for overcoming these obstacles. I need a motive to dive deep into one of these in order to get familiar with any of them.

10/4/2016

I've been slogging through "Genetics and Molecular Biology" by Robert Schleif for about two months now. This is really too advanced a read for my level but it's the only free book I've found that gives a clear understanding at a molecular level of what's behind the experiments I can do at home.

Another gem I'm reading is "Bioinformatics for Dummies". I got the idea from The Biol 368 [[1]] class from Loyola Marymount on this site that used it. It doesn't just show you what to do, it provides the motivation for why you might want to do it. I'm getting close to the 500 hours I estimated I needed before I could actually start some bench work. Time to break open the shrink wrap on all those new supplies I've bought :-)

11/5/2016

THE WALL.

I've come to a crossroads in this hobby that gives me pause.

  • I can continue to develop my lab space to be fully functional which will cost me money and time building things. I enjoy building things so this would be rewarding.
  • I can divert my attention to bioinformatics and start building the tools, experience and results in this area of "experimentation". There's a DIY group here trying to sequence the Pacific Salmon genome that would provide focus, help and guidance on this. This is the one area that I actually have any existing knowledge to apply which could leverage learning with meaningful results.
  • I can divert attention to learning the basics. This would cost $250 for a single text book and a commitment to reading this and working through the problem sets. I could send my write-ups to any number of people who have demonstrated a willingness to help me learn this material. I enjoy learning and the easy strokes I get from memorizing trivia. This would also allow me to approach "labs" with calm confidence.

I could do all three but with the 12 hours a week I have to devote to this, I think I'd become bored and leave the hobby.

12/1/2016

THE DOOR.

It seems senseless to me to pipette into a buffer if I have no idea why. I've read about it (or "skimmed" more accurately) in quite a few of the books I've read but I've never rolled up my shirt sleeves and done the work (a common problem with autodidacts). I have now practiced calculating ΔpH on half a dozen weak acid base interactions and I think I have a pretty firm grasp of it. Without calculations behind my recipes and without knowing what each component was doing in the recipe I was always a bit tenuous about my bench work. Now it feels like I did when I first mastered Ohm's law in electronics or my first book of etudes on the violin. Each equipped me to take the next step.

I still don't fully understand how these equilibria interact with the equilibria or stasis of biological elements let alone living metabolic pathways. It looks like most of the standard protocols we use in biochem were created by brute force experiments and the science explaining why came as an afterthought (i.e. Biochem. is as much a technology as it is a science). I'm sure I'll run into many more "walls" as I get into these complexities but I'm excited that I've chosen this "door".

This legislative session has my back to the wall so I'm having to dedicate more time to work than hobby. That makes me value and enjoy my lab time even more.

1/28/2017

I've been reading my text ("Biochemistry" 8th ed. by Berg, Tymoczko, Gatto and Stryter) for two months now and I just started the third chapter. I could perceive this as a glacial pace but by leaving a few days between reads and allowing myself to hear lectures from the YouTube collection "Fundamentals of Biochemistry" multiple times, I feel more confident that I'm actually learning the materials to an applied level. It would be all too easy for me to re-conjure the feelings of anxiety I used to get in college when studying difficult material, but not being on the clock makes this so much more fun. So far I've drawn up 25 pages of notes and illustrations in a notebook that I can be proud of once I've completed the book. I've made some flash cards of Amino Acids so I can memorize a few things during my breaks at work.

3/1/2017

I originally had no intention of pursuing this as anything but a hobby but I now have a position with the Washington State Department of Health working with epidemiologists studying vaccinations. I'm not sure where this is going to take me, but what I've learned so far has already helped me understand my colleagues discussions of their work. I don't know if everyone who studies biology becomes as hooked as I have or as rewarded but I certainly hope so.

5/9/2017

I've now started studying immunology in earnest. Strange how difficult I thought O-chem was only to have it eclipsed by Bio. Now immunology towers over them all as the most complicated set of things to learn and memorize I've ever approached. Until now, the connection of all of this to human pathology has been missing and its actually grounding my understanding in a different way than the prior subjects. My Janeway's text does a good job of supplying pretty pictures with each concept but its hard to take book notes. I've got to find a short-hand for these concepts that will adequately describe all the subtleties of these pathways.

Notes

  • This portion of the notebook documents progress in building the technical knowledge necessary for this hobby.


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