swords and cups

A few nights now waking up at 3 and going over in my mind again and again things said, unsaid, done and undone. Continue to be amazed by the fact that the ex is in a romantic relationship with the man she chose. It still feels surreal and creepy, grotesque and sick, toxic and ugly and just not to be believed. No matter how much work I do during the day on emotion regulation, letting go, prayer and meditation, getting perspective, step work, counseling, medication-- no matter. 3 a.m. is the vulnerable time. I am wide open at 3 a.m. and lack skills to either accept and let go or ward off and defend. My thoughts resound without any borders or control. Any sense of a higher power or recourse to any kind of either rational or emotional relief is obliterated.

Adding to how weird everything seems these days is that there is still no communication from the ex of any kind. People like me fill the silence with the worst imaginings. I don't know why I always have to tell some kind of story when I lack information. I guess it's an impulse as old as dirt. But one practice I am trying is not to tell a story when I don't have any information. To just let blanks stay blank.

In spite of chronic upset, I buckled myself to my blue chair yesterday from 5 am until 4 pm and finally finished the revisions on my dissertation proposal. This work requires a clear mind and a clear mind I do not have. It took quite an effort to repeatedly get back on track and recall what the fuck I was supposedly writing about. Eventually I wrote the new chapter on the molecular phylogeny of the group of cacti that my study species is in and did the bibliography and rewrote the chapter on complementary modeling using species distribution methods and landscape genetics. By the time I finished I didn't really have the energy to proof very much. I just sent it to my advisor. We shall see.

The PhD process was so much more fun and so much easier when I was emotionally stable. The sword realm of science and the cups realm of emotion don't really co-exist comfortably. In particular, I have just found it next to impossible to truly concentrate on technical details for more than about 5 seconds. Check out this description from a methods and materials section of a genome skimming study:

DNA isolation and sequencing — Genomic DNA was isolated using a modified cetyltrimethylammonium bromide (CTAB) protocol ( Doyle and Doyle,
1987 ; Friar, 2005 ). DNA samples were prepared for sequencing by Global Biologics
(Columbia, Missouri, USA) using the following protocol: DNA samples
were quantitated using the Qubit dsDNA HS Assay Kit and Qubit 2.0 Fluorometer
(Life Technologies, Carlsbad, California, USA) and integrity was checked
using the Advanced Analytical Technologies Fragment Analyzer and Genomic
DNA kit (Ames, Iowa, USA); high-molecular-weight DNA (>15 kb) samples
showing no degradation were considered suitable for libraries. A 500–1000-ng
sample of DNA was normalized to 40 μ L in a low-bind 96-well microplate and
sheared to ~300 bp using the Q700 Sonicator (QSonica, Newtown, Connecticut,
USA). The fragmented DNA was blunt-end repaired, 3 ′ adenylated, and ligated
with multiplex compatible adapters using the NEXTfl ex DNA Sequencing Kit
for Illumina (catalog no. 514104; Bioo Scientifi c, Austin, Texas, USA) prior to
being size selected to retain ~200–400-bp fragments with Agencourt AMPure
XP SPRI beads (Beckman Coulter, Brea, California, USA). PCR enrichment
selectively amplified fragments containing DNA with adapters on both ends.
Library validation used the Fragment Analyzer followed by quantitation with
the Qubit dsDNA HS Assay Kit and the qPCR kit for Illumina (Kapa Biosystems,
Wilmington, Massachusetts, USA). Equimolar amounts of each library were
pooled at 10 nM for sequencing. High-throughput sequencing used the Illumina
HiSeq 2000 genetic analysis system (San Diego, California, USA) at the University
of Delaware Sequencing and Genotyping Center for Run 1 (single-end
100-bp reads) and the University of California at Riverside Genomics Core for
Run 2 (single-end 101-bp reads).

Try getting into that while you are grieving the end of a 5 and a half year partnership, have moved twice in one month and have just started on medication for persistent depressive disorder. I dare you. But such was large parts of my life yesterday as I tried to make sense of my own methods and materials section for the genome skimming chapter. Like wrestling a wraith while being assaulted by a banshee.

Fortunately, I have found lab work to be oddly comforting. It's nice and clean in the lab, for one thing. Quiet. You follow the protocol and do the next steps. It's like cooking from a recipe. Order reigns. It's good that I am settling into lab work, since I will be doing DNA extractions on about 120 tissue samples over the next few months.

Anyway, dear reader, the passage of time is not ameliorating my basic misery in any consistent way. Neither are all the work and tools I know how to use. During these passages, we wait and we endure.