Claire Wyman’s thesis

On this page, you will find Claire’s PhD thesis along with some of her recommendations from the paper and a backstory of her time as a PhD student at UC Berkeley. The text below was written by Claire to accompany her thesis. 


Here the guide to the ancient texts of a UC Berkeley PhD thesis


When I was a graduate student (“all we had was Earth, Air, Fire and Water.  None of it pure!” Last line from a MolBi follies skit about kits and outsourced experimental work)


A scanned copy of my thesis is available for you to read here. I recommend these highlights:

Acknowledgements, p. 9 of pdf = good review of my Berkeley days experiences.

Abstract, p. 6-7 of pdf = what it is all about.  If I must say so myself well written, throughout the whole text you will not find wasted words or throw away phrases like:  “it was shown…” or “next we did…”.

Inserted quotes, p. 8, 17, 174, 185 of pdf = food for thought to nourish us on the journey.

Methods, p. 45 of pdf = protocol for fun only, received comments from only 1 of 3 faculty readers who was not happy but let it slide.

Figure 3.2, p. 66-67 of pdf = “nuclear events in Tetrahymena conjugation” or: kinky mating among single cells.


Here some explanation of other antiquated features:


Word processing was still relatively new and not available to all.  Many wrote their thesis on a typewriter (look it up for guide to this primitive text producing machine).  This meant there was a possibility that pages had different margins and perhaps this could interfere with reading all the text once bound.  So, the final and most terrifying step for a finished PhD was to submit the “to-be-bound” pages to the library “margin lady”.  If disapproved the whole thing had to be reprinted and re-evaluated.  Thankfully computer word processors and printers largely solved this problem, as long as you followed the instructions.  The margin lady still had her job to do.

And the format, binding etc?  what’s going on there.  Officially a student had to produce one hard copy of the thesis on “archival” quality paper (read 100% cotton, acid free and VERY expensive).  This copy, along with any other on inferior paper, were bound by the library in the form you find here.  Usually, 5-10 copies were printed for self, advisor, lab, mom and dad and significant others.  The text was only printed on one side of the paper to maximize cost and tree or cotton plant destruction.  Otherwise, I don’t know why except that type written on both sides usually severely smudged the first side.


The order of items and their format was prescribed (abstract, acknowledgements, toc, etc etc exactly in this order for all theses).  Figures were at the end of the chapters. Color was not possible to print on the page.  Those who needed color had to paste in actual photographs (all archival quality paste and photos).  Look like some figures were drawn by hand. Well yes, they were with the help of very advanced graphic tools like rulers, fine pens and Letraset (look it up for a history lesson).  Computer programs could produce some graphs but not much else.  Check out particularly the, at that time, honestly, state of the art sequence alignment and analysis figures! (ex. p. 144, 146 in pdf).  Some of my fellow grad students were writing code that eventually morphed into FASTn and FASTa (look it up for a genomics history lesson), so at the time it did not get better than this.


I basically got a PhD for sequencing >10Kbp of tetrahymena DNA.  This (cloning, sub-cloning, and sequencing both strands) took a year of more-or-less non-stop work (at one point I had been to the lab all but 2 days in an 8-month period- life was still good, I did live in Berkeley CA), so that I could finish experiments before my advisor moved her lab to another city. This would all be done now by WAY more efficient methods by commercial companies, but not then.  All of this was radiolabeled DNA, chain termination sequencing reactions run on meter long X mm thick denaturing acrylamide gels.  We all washed these glass plates, cleaned them, assembled the glass plate sandwich and poured our own gels, carefully loaded small volumes with special thin/flat pipette tips into wells defined by shark tooth combs (look it up for fun).  The gels were extracted by a delicate process of peeling the plates apart (and hoping the gel stuck to one plate and did not tear), adhering the gel to large sheets of filter paper and drying.  The dried gel was exposed to x-ray film and revealed sequence eventually read/typed in manually.  At least we had computers to type the sequence information, store and analyze.  When I was a graduate student, if you walked into a lab and observed one person running a ruler over a large x-ray film and reciting ACTG in apparently random order and another person typing in this dictation, YOU DID NOT TALK to them, you did not even ask if it was OK to talk to them.  To make sure the read/typed sequence was correct this of course had to be repeated.  Now magically DNA to be sequenced is sent off in the post and results return by e-mail in a week or so.  The times they have changed.


Hope you enjoyed the read.

If you are wondering, the path from PhD to where I am now was more direct and can be found in my CV.


Keep up enjoying your own journey and follow it where it takes you.  May not necessarily be where you thought you were going.