Just a Log

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Just a log by zzalpha

Well, it's basically just a log.

I like to log things. Thoughts, what I did, what I didn't and what I'd like to do.
Often this devolves into whining; but it makes for some entertaining reading much later.

[2018-08-21 Tue] :

  • Exporting org to html allows for the exclusion of some tags, by specifying:
    #+EXCLUDE_TAGS: <tags to be excluded> and
    #+EXPORT_EXCLUDE_TAGS: <tags to be excluded
    • it works with both of them on.
  • Have decided on a monolithic file, as opposed to several files being assembled together and then made to play nice.
  • protocol: tag personal notes at the very outset, write them under a separate heading.
    • I did not particularly enjoy rearranging to accommodate some of the personal tags.
    • of course, the tagging is just a bonus. Writing is the real priority.
    • Besides this whole discussion is moot if I decide to keep everything private/undisclosed.
  • [X] Date stamps in human readable format.
    • found some code online. included in this source file (locally applied and evaluated)
  • Quite tired of fiddling around with org-mode and agenda and capture
    • right now I am reluctant to tweak the config files too much.
    • would like to use it substantially so that I can find opportunities to learn more.
  • used rsync to transfer files to remote host:
    • rsync -v -P --progress -e ssh /path/to/local/file <user>@<remote>:/path/to/remote/file
      • -v : verbose
      • -P : partial; enable partial downloads (ie downloads resumed from when last interrupted)
      • --progress : displays progress bar
      • -e ssh: rsync by itself is unencrypted. use ssh.
    • rsync -v -P --progress -e ssh <user>@<remote>:/path/to/remote/file /path/to/local/file
      to transfer from remote to local.
      • to try/check: how to transfer entire directories (uses the -r recursive flag)
      • differences between paths to files having a trailing / and not. (trailing / implies contents of the directory and not the directory itself)
    • A: use -a aka archive option. It preserves attributes and other things. (but does it produce an archive?)
    • [ ] create a clean folder containing files to be synced with remote.
      • [ ] segregate other production junk to folders for individual webpages.
    • [ ] document/maintain the purposes of these elisp snippets, preferably with source URLS.

Further fiddling:

  • cronjobs are a battle for another day.
    • what would happen if cron runs while pages are being edited?
  • org-capture to append to this file.
    • appending under the right time-stamp?
    • appending at the right level.
    • not going to work on adding entries retroactively.
  • gh-pages: can these be hosted on github/gitlab pages?
    • they do offer "static hosting" after all.
      • github seems to insist on Jekyll.
      • here I am, feeling guilty about rich text.
        • it all started with gopher. fml.
      • gitlab has emacs- and org- publishing templates.
        • where's the fun in that?
    • could consider Dropbox.
  • done hosted on gitlab. need a better URL/title.
    • phlogiston
    • it wasn't fun.
    • gitlab's commits take ages.
    • to leverage/automate pushing to gitlab, I will have to learn git
      • that's for another day far, far away.
  • rsync a list of files.
    • meta: rsync or rsync. develop a uniform system for programs and CLI.
    • how does rsync handle symbolic links?
      • very poorly. "No such file or directory"
    • how about nonsymbolic links aka hard-links?
      • hard-links appear to preserve the contents as they are synced.
      • I am confused how this works across systems.
      • rsync can deal with a pair of hard-links ONLY if both of them are part of the set of files being transferred.
      • do I need the -h option then?
        • not unless I intend to send a pair of hard-linked files and need them to be linked remotely too.
        • so, no.
  • proposed solution:
    • a folder with files that are hard-links of rendered pages, synced with public_html
    • when a page is edited and re-rendered, hard-links ensure that the changes to these files are reflected.

DONE rsync implemented!

  • each webpage is in its own folder; the rendered html, txt and pdf files can stew along with it.
  • a pristine folder reflecting remote public_html with hard-links to the rendered html files of these webpages.
  • render → test html locally → run rsyncpublished!
  • [X] ← Now to test if these changes are actually applied downstream.

[2018-08-22 Wed] [2/2] :

DONE reviewing edits

  • I'm editing a massive, monolithic file.
  • with emacs.
  • there are non zero odds that I delete something by accident. (modal editing pitfall)
  • review before committing!
    • M-x diff-buffer-with-file applies diff to the current buffer. nifty.

DONE closing minibuffer

  • find quicker shortcuts to close minibuffers.
  • currently using SPC w w followed by SPC w d. Too long.
  • use toggle-maximise-buffer:
    • SPC w m brings the main buffer back to focus.
    • the other buffers are not really gone, SPC w m brings it back.

want to learn:

  • valgrind and cachegrind.
  • the science and algorithms behind caching.
  • persistence in caching for very frequenlty accessed memory locations, even when there is a deluge other random reads.

[2018-08-24 Fri] :

  • I'm sick. Can I do something today?

[2018-08-25 Sat]:


  • should I increase page width? why do I like the text jammed into less than half the page?

watson:   biology

  • I was sick last night and I couldn't sleep; so decided to resume Watson's Molecular Biology of the Gene.
  • 100 pages in and it is still heavily dealing with chemical and thermodynamic considerations.
  • I don't really understand free energy, but for now I am going to think of it as the net measure of spontaneity/feasibility of a reaction taking the bond energies (enthalpy) and the change in entropy (increase/decrease in disorder) into consideration. \(\Delta G=\Delta H-T\Delta S\)
    • The more negative \(\Delta G\), the more spontaneous/feasible the reaction.
    • fwiw, (from my understanding) this feasibility has little to do with the rate of the reaction.
  • A long biosynthesis pathway may have one or more reactions that have a slightly positive \(\Delta G\). However, this is fine as long as the net change in free energy of the whole pathway is negative.
    • this was baffling at first, but a nice example cleared up some of it.
    • Nucleic acid synthesis has a slightly positive \(\Delta G\), ~0.5 \(kcal/mol\).
    • Nucleic acid synthesis occurs (roughly as): the addition of an NTP (nucleotide triphosphate) to the existing nucleic acid strand; the nucleotide is added and pyrophosphate is released (pyrophosphate is a pair of linked phosphate groups).
    • Pyrophosphate is broken down by an enzyme pyrophosphatase; with an accompanying \(\Delta G\) of ~7 \(kcal/mol\).
    • This drop in free energy more than compensates for the slightly positive \(\Delta G\) of attaching a nucleotide to the nucleic acid.
    • moral: reactions do not occur in isolation, feasibility/spontaneity of a reaction also takes into consideration the accompanying reactions.
    • bonus: this sort of explains why triphosphates are more useful than diphosphates; the release of phosphate groups is not accompanied by a significant release of free energy. The biosynthesis would be reversible, especially if phosphate were to accumulate in the cell.
  • TODO a topological study of the structure of DNA   reading papers
    • linking numbers of covalently closed, circular DNA.
    • twist and writhe of supercoiled DNA; the relation between these and linking numbers.
    • negative and positively supercoiled DNA; and how thermophiles use positive superhelical density as a store of free energy to prevent denaturing at higher temperatures.
    • resources that I unearthed:
      • Dorothy Buck, Erica Flapan (eds) – Applications of Knot Theory
      • Darcy, Sumners – Applications of Topology to DNA

[2018-08-26 Sun]:


  • I spent an entire dream worrying over my choice to type content in a heading as opposed to a list. inane does not imply lack of stress.
  • Another one involved having to answer "What do you want in life?" … in writing, using org-mode. involved a lot of editing. perhaps there was a time constraint as well. if I wasn't clear above: more inane, less stress please.
  • The third one of the day, equally exhausting and unpleasant. I'm not going to document these anymore.


  • have been thumbing through Baez's pages tagged biology.
  • it is both inspirational and depressing at once.
    • I am trying to learn these things to quench a personal curiosity and for intellectual satisfaction.
    • my efforts are decidedly not rigorous.
      • I don't really pause to think/investigate de novo.
      • does that reflect a degenerate approach to learning, or is it an attitude to biology?
      • neither are my credentials or my career on the line: nor is there an authority to enforce standards.
      • my apporach is that of a dilettante, an amateur.
    • working in a vacuum is not easy.
    • working in any form at all is better than the alternative: to wallow in the dark in self-inflicted limbo.
    • placing anything that I deign to do in the context of where I stand re: goals, ambitions and the real world is an instant downer.
      • "hey I really like this" → "maybe I could do this" → " … "
      • I think this explains the observed paradox of dropping every project just as I get really excited about it.
    • I do not have any solutions, merely obervations.
    • I am not ready to make/take compromises yet.
  • all that said, I would like to read his archives both thematically and systematically.
  • dutifully added to project stack @ lazarus

words, made-up and real:   wordsmith

  • mortenila aka m-probability (:
  • bechameleon
  • iguanahedron
  • polygondwanaland
  • ansatz – the initial estimate used to start off a calculation
  • bikeshedding – wasting thought and planning on trivialities ("building the bikeshed when planning a nuclear power plant")

DONE dnf update except texlive.

I had to update ~6000 packages today; installed texlive-full last week. (although, I did read that texlive gets updated just once a year.)
solution: sudo dnf update --exclude=texlive*

[2018-08-27 Mon]:

pedagogy of watson:

how does one learn something that is as fact-based as biology? I cannot come at it from first principles; the truth is gleaned from experimental data. The best I am able to do is slowly imbibe the various cases that are presented in the book, to have a surface-level understanding of how things function in general. I should look to other sources for investigative/modelled learning – like petrinets and operads and such.

For now, this casual fact-stream is easily followed (perhaps with a lot of attrition), and I can claim to be active with watson.

watson   biology

it is remarkable how scientists working in these fields have made progress, not from first principles, but from chemistry – which, in my opinion, is a very chaotic science.

[2018-08-28 Tue]:

TODO create music pages

  • export music out of spotify
  • import that massive list on Keep.
    • maybe it would be better to use discogs or rateyourmusic or last.fm?
    • something needs to be done.

  • alsamixer and its insistence on ESC being the button to quit. I need to find a different frontend, maybe one for PulseAudio.

[2018-08-29 Wed]:

  • updated lazarus:
    • degrading pointersOnC and prometheus to inactive.
    • set up footnotes to each explaining why they are in limbo, and what could be done to salvage them.
    • set up a separate section for passive projects such as lazarus, emacs/org.
    • geeklog replaced by htmlpublish (done) and gopherpublish (todo)

word:   wordsmith

  • antiphon – a hymn sung in response.
  • moiety – half
  • thelonious (adjectified nouns are trivially easy to come up with, but this one is special – it brings a non-existent adjective to mind first)

watson:   watson

  • DNA → RNA → proteins is a crescendo in chaos. Proteins are absolute mayhem.
  • architectural proteins – that bind to DNA not through residue:base-pair interactions, but by an 'indirect readout' of how DNA bends from the double-helix norm; sometimes even stabilizing the bends in the process.
  • protein linguistics. bio linguistics. I'm excited.
  • redundancy in the biological code; and redundancies in the chemical aspects of the biological process.
  • how would one design an artificial protein?
    • finding a protein whose structure activates/is activated by a specific ligand/sequence; and no other: specificity (– parallels to regular expressions!)
  • catalysts affect the rate of the reaction, not its feasibility.

And I finished Ch6: The Structure of Proteins!
I haven't taken any notes in these last two structural chapters. I am unsure if the urge to do revisit and do that is a mortenila roadblock or something genuine. I think I'll go for the run-through.

  • magnification of single point mutations in DNA to RNA and proteins – can this be modelled/predicted?

Oh man. I know what I want. MIT Foundations of Computational and Systems Biology

oh no:

that meta(un)stable island at the top of a U-bend.

[2018-08-30 Thu]:

These dates are out of whack. Most of what I did today is actually in yesterday's log; because it was initiated yesterday. Diurnal lag.

watson   watson

  • Biology as computation:

    thinking of biological processes as computation. I could try to write a program that predicts what would happen when I try to hybridize an oligonucleotide with one mismatch with a piece of DNA (site directed mutagenesis); I could attempt to simulate what the effects of a single point mutation have on the final translated protein (say). But on the other hand, I could just run these precise experiments and know the consequence – or if run massively parallely, know the consequences, probabilistically.

    it seems to be an irreversible computation with real-world side effects.
    this is a great train of thought.

    (this feels Wolfram-esque, when applied to the universe)

  • Techniques of Molecular Biology

    this is the new chapter, and it's the most … technical one. the previous ones came from an axiomatic standpoint; while this is a reminder that to the actual chap in the lab, it's not a double helix he's really dealing with, but a miniscule trace compound in a substrate. the tyranny of scale and chemistry.

    exercises in inference. it's amazing how much knowledge we have sequentially amassed. they did not "build a better camera" and then image all the details.

    it's fascinating. I'd like to read a book on the progress of these techniques/ the story of these inferences, starting from miasma.

  • a hitch and a hunch …

    applying a metric to DNA – introns (portions of the gene that are not translated to proteins) – exons (parts of the gene that are expressed) – a map of the sequence with this metric applied – under the assumption that proximity indicates related functional behaviour (upto an extent) – imagine a tangled string this way …

    and/or a sufficiently large protein straddles the two zones.

    • now done with this chapter on Techniques of Molecular Biology.
    • it was not an easy read, and I did little more than a perfunctory skim.
    • I think it would be a good idea to revisit the 3 chapters in this section.
      • I would also like to revisit (again, for an overview) the technical chapter – just so I have an idea of the tools that exist to probe.
    • will this be a barrier to progress?
      • if so, I am willing to abandon it.

word up:   wordsmith

  • aliquot – a divisor/fraction of something.
  • a murmuration (of starlings)
  • in vivo (vivo: life), in vitro (vitro: vitreous, glass)

[2018-09-01 Sat]:

  • cleaned room with a broom and a mop, after ages.
  • fought off (in vain) the ant nest under my mattress.
  • did little yesterday.
  • the "redo these last four chapters" is a roadblock to continuing.
  • tempus fugit
  • I had a dream worthy of Curb Your Enthusiasm today. In fact, it shines a whole new(?) light on its etymology …

hikikomor, I

  • it is now 10 days since I stepped out of the house.
    • should I maintain a counter for this sort of thing?
    • it would have to be in the context of mental status/health.
    • I cannot see a possible scenario where I have to go out anywhere in the near future.
    • I used to meet A once a fortnight; but I am going to revise that to 3 months.
      • so … November.
    • I might go out for that rare meal outside.
  • a related mental health indicator could be time of last conversation.
    • what counts as a conversation?
      • any interaction that feels meaningful and fuels social "sustenance".
      • if I restricted it to spoken word, the current rate is once in 10 days (I think).
      • increasing the volume/frequency of IM conversations reduces the need for spoken word.
      • emails! also count as very good longform conversation; though by their long and asyncronous nature, are much more infrequent. they are satisfying to receive, and frustrating to respond (procrastination, single-threading a slew of topics, editing nightmare)
    • I haven't blocked people on IMs in a while – probably because my despair is less immediate.
      • blocking people and /etc/hosts/ is a quick actionable step that forces other pursuits (at least until the next nap).
      • am also more ashamed of my blocking days now – they were a form of signalling.
      • have also been using externalities to stay on line – "X has an issue/event coming up, perhaps I should stick around to support him"
      • I do have a regular desire to go AWOL: it is also quickly subsumed by a quick nap/ change in mood.
    • haven't been deleting chat logs in some time.
      • this old practice was first initiated to stop re-reading old chat logs back in 2013.
      • the oldest chat now is from [2018-07-18 Wed]; which leaves me 46 days.
        • which is unprecedented in the last two years.
      • I think I'd like to create a github-commit-history like chart … in emacs, if it's not a pain.
        • doing it for the emacs. srsly.
          • yeah I am doing this to avoid watson. fite me.
        • there's an org-habit, which runs on an org-agenda.
        • which is overkill. let's go de novo.

DONE hollerith

Have cooked up hollerith which serves as a log of how social I have been. It's described in full glory at: hollerith:logging social behaviour.

  • half of it looks like a punch-card (hence the name) – it logs with which people I have had conversations.
  • the other half measures the volume of interactions (using the number of messages exchanged).
    • there's a nice ascii! bar graph showing the variation in this volume across a month.
  • utility?
    • it appears I have been far more gregarious than I thought.
    • but this comes at the heels of a highly isolated down phase; which was not documented at all.
    • there might be some insights on when/why I feel alone and uneasy. (immediately after a high volume interaction?) (after a lull of a few days?) (after high productivity/excitement)?
  • future directions:
    • log carbon based interactions, rare as they may be.
    • initiation: who initiates conversations
    • couple it with moods … to see more patterns.
    • maybe I'll capture the next downphase.

and… published! (:

[2018-09-02 Sun]:

quickfixes [2/2]

  • [X] timestamps when exported are a faded white … I need to make them bolder.
    • hang on … I fixed this somewhere; I just haven't bothered to apply it everywhere.
  • [X] update index.html to reflect the newcomer.

  • it would be super easy to maintain hollerith if I logged everyday.
  • what are the odds of me being disciplined enough to do that?
  • is watson dying?
  • the internet is unbelievably slow. it's only the 2nd of the month; this is further evidence that the monthly cycle starts somewhere in the middle of the month.
  • should import the txti.es pages sometime.

watson:   watson

  • started writing.
  • finding it tedious.
  • there are a tonne of details, and everything seems important.
  • I'll give it a readthrough instead.

words:   wordsmith

  • loess
  • scissile
  • in tedia res
    • quite proud of this one
    • I'm going to use it.

[2018-09-03 Mon]:

in tedia res

  • the internet connection is just terrible. it looks like I need to restart the router everytime a page is fully loaded!
  • have been having strange, but not unpleasant dreams. I was about to have quesadillas and shakes with a girl who was third-wheeled by the same pair as I was. it was a kung pao quesadilla (I've never had either of these things). did not get to taste it, woke up disappointed and hungry. had a biscuit instead.
  • updated and fixed some stuff on hollerith
  • she came in my dream, but as an incompatible nucleotide.
  • the ants have invaded my keyboard. RIP
  • the return keycap is busted. RIP
  • RIP my mood.
  • remap CAPS to RET?
    • yes. it is weird though.
  • SPC is going to be the next to fall, I know it.
  • who cares anymore.
    • it's not like I am doing even anything remotely useful here.
  • also, it's good to know: CTRL J and CTRL M act as carriage return and line feed.
    • although they work in subtly different ways.
    • both emacs and TTY terminals respect these bindings.
  • I ought to use a to initiate edit mode in emacs/vim.
  • CTRL J/K works to navigate suggestions in spacemacs.
  • couple of rubberbands and a lot of curse-words later, the RET key is "fixed" [1/1]
    • but it's extremely ugly.
    • and slightly sticky.
    • but it doesn't pop out, which is the temptation I forget to resist.
    • I should stick to using Caps Lock.
    • [X] Maybe Disable the key using ~/.Xmodmap?
  • went out for dinner, alone.
  • bought my first cigarette.
    • am I incentivizing going out?

watson   watson

  • did a quick readthrough of the chapters on structures of DNA/RNA/proteins. I think I understand this stuff, but I don't know the specifics off the cuff.
  • the chapter on techniques still remains.
    • a lost cause. everything is so similar, familiar, and yet so confusing!
    • will revisit if I ever need it, or find a better resource online.

[2018-09-04 Tue]

in tedia res

  • [X] if I can remap the BackSpace key to the left hemisphere of the keyboard …
    • done. xmodmap -e 'keycode 94 = BackSpace'
    • it is transient though, I want to see how useful it is to have all control keys on one part of the keyboard, an obvious advantage being that my right hand can be tethered to the HJKL keys.
    • the key that is being mapped to is the one I had never layed eyes on before, right next to LShift.
    • it is nice having Caps Lock tied to RET; however, I still accidentally hit TAB when aiming for Caps Lock.
    • have disabled BackSpace temporarily to see if the new binding is viable/to get used to it.
      • xmodmap -e 'keycode 22 = NoSymbol'
    • I frequently mishit Z while going for the new BackSpace. A lot of importance is now being placed on the left pinkie.
  • can you read my mind
  • it feel like summer … indeed.

watson   watson

  • have started the new chapter.

the smoking gun

smoked two more cigarettes today. it's a strange paradigm: I don't care about the consequences of smoking because I am not interested in incentivizing what's in my self-interest, but I also care enough to enjoy/relish some small pleasures …
is there a paradox lurking somewhere?

[2018-09-05 Wed]

word up:

  • isopycnic – meaning same density.
  • compote – stewed fruit (etymologically same as compost)
  • distal – distant, further away (as opposed to proximal) (anatomy/biology?)

watson   watson

  • satellite DNA, so called because it appeared as a separate layer, close to the bulk DNA upon centrifugation: these were repeated short sequences, hence their AT/CG ratio was different from that of the bulk DNA (explains the separate layer)
  • these cell division stage names are the worst. why would you have M-phase and metaphase?
  • remember, the DNA duplication stuff has already happened before they talk about S-phase, etc. In particular, meiosis starts with having a diploid cell, with one chromosome from each parent. (why do they have one chromosome from each parent? there's a lot about … genetics I don't understand.)
  • linear DNA can be supercoiled.
    • as expected, the book suddenly talks about the supercoiling of linear DNA
    • which doesn't make much sense because the whole point of twist and writhe and supercoiling in cccDNA was that they are constrained topologically.
    • how can linear DNA be supercoiled?
    • well, think in terms of the two ends of the DNA being tethered. so the coiling cannot be simply undone by moving the tails around.
    • and why is thinking in terms of tethered tails valid?
    • DNA/chromosomes can be really long, and it may be helpful to think in terms of shorter stretches in between being tethered.
      • also structures called nuclear scaffolds that make the DNA much more rigid.
  • the "Nucleosome Linking Number Paradox"! (in the context of cccDNA):
    • addition of a nucleosome reduces linking number by ~1.2 (measured)
    • a nucleosome involves the DNA wrapping 1.65 times around the nucleosome, so that increases the writhe by 1.65; expected linking number decrease is -1.65
    • -1.2 is not equal to -1.65. Whaddup!
    • turns out, the DNA winding slightly decreases from the usual 10.5 bp/turn to 10.2 bp/turn, and that explains this discrepancy!
      • but how?
  • I really want to do a writeup on these topological aspects. (there's not much I have learned about wobble bases yet)
    • also, Hoogsteen base pairs and triplex DNA sounds fun.
  • if I think about it, it all feels like a massive scam.
  • I finished the chapter: Genome Structure, Chromatin and the Nucleosome.
    • I understood most of it.
    • I am not elated though.
    • I feel like I didn't learn/absorb much.
    • I am also very, very tired and feel crabby.
    • so all is well, yeah? :\
  • buzzwords: translational frameshift, algebraic biology, molecular set theory, "On a non-trivial application of Algebraic Topology to Molecular Biology", topological RNA structures, non-helical models of DNA structures.
    • (needed to close the browser)

in tedia res

  • no.
  • in part it feels terrible because it's all for a futile cause – not that overwhelming futility about the universe in general, but something more specific, and much more personal.
  • purveyor of sour grapes and dour regret
  • why am I even indulging in this pursuit?
    • because it's a dead end, and I'm afraid if I set my sights on something I actually want to do, I will fail yet again.
      • the one thing I dearly want is to go back to math.
      • that is the one thing I have repeatedly failed at.
  • I need to sleep.
  • strange dreams:
    • one was an elaborate ruse to run a dual-lingual pun on Wuthering Heights.
    • I appear to be depressed and I message/am messaged by a truly distant acquaintance – who compares me to Snowden and tries to prop me up.
      • like in real life, in dreams too I can't read a long message when I receive it – I try to defer the pleasure/anxiety.
  • I had the chance to go through an old phone today.
    • it was from a different time.
    • everyone in it was different; I can even see the germs of transition.
    • it's sobering.
    • and I am responsible for some of it; I affected people negatively enough to push them to where they are today.

[2018-09-06 Thu]


  • installed LineageOS on a Samsung Galaxy Note 2 – a 6 year old phone.
  • it involved installing adb on the system, and heimdall-suite, an opesource replacement for odin the firmware flashing tool for Samsung.
  • once that was done, it was extremely easy: adb push twrp-recovery-blah.img /sdcard/ pushed twrp to the phone, heimdall flash --RECOVERY twrp-recovery-blah.img --no-reboot flashed recovery.
  • flashing LineageOS, openGapps and SuperSU was a breeze from within TWRP.
  • this stuff was well documented on the LineageOS website; the Note 2 being a supported device.
  • near vanilla AOSP is such a delight over Samsung bloatware.
  • it's mostly smooth except for some stuttering when scrolling – no idea even how to google for this, or where the problem could be.
  • battery lasts ~2 hours though, but this being the old era of smartphones, can pick up a replacement battery myself.
  • I am tempted to flash LineageOS on the Redmi too – I need to backup and stuff first.
    • need to unlock bootloader, which involves registering with Mi.
    • might not do it anytime soon, so I'll add it to the stack.

org-mode … for bookmarks?

  • I need a solid way to handle bookmarks – across devices, and across browsers (oh no).
  • and it should involve org-mode, because … org-mode?
  • re:cross-platform, there's orgzly on android.
    • is it even relevant? I don't know, but I should try to set up sync with it.
  • deferred to a fairer day.


  • I don't even have anything I want to sync, but I want to install this.
  • aka finding solutions to problems you don't have.
  • have installed, and set up a sync on the phone and the system.
  • not put to use though.


  • maven – an expert. (from Hebrew mebhin, "one who understands")

in tedia res:

  • truncheons, sticks in the mud, and the march of progress.
  • but in the end, it's all in the past

DONE mido (Redmi unlocking/flashing)

  • after a lot of shenanigans with creating a Xiaomi account
  • and pulling out the sole Windows system I have
  • installing the Mi drivers
  • it tells me that I have to wait for 72 hours before unlocking.
  • 72 hours.
  • this is the single worst OEM I have experienced.

[2018-09-07 Fri]


  • starting the new chapter on Replication of DNA. this should be good!

[2018-09-08 Sat]

wordup   wordsmith

  • trifecta: a triple (originates from correctly guessing the first three spots while betting on horses) (tri + perfecta)
  • peregrine. what a lovely word. I wish it had a non-avian usage.
  • lanyard
  • crespice
  • Urschleim – primordial soup (Ger. ur + slime)

in tedia res

  • all is violent, all is bright
  • Spare Ohs – Andrew Bird
  • Irene – Rodrigo Amarante

watson   watson

  • Okazaki fragments and the difference between leading and lagging strand syntheses.
  • topoisomerases working upstream and relieving positive supercoiling as the DNA helicase/replication fork moves.
  • how sliding clamps improve the processivity of DNA polymerase
  • AAA+ proteins that help install the sliding clamps (among other things)
    • AAA: ATPases associated with various activities.
  • the trombone model of coordinating DNA replication
  • the replisome

[2018-09-09 Sun]

watson   watson

  • chromosome end are called telomeres.
  • mismatches between leading and lagging strand syntheses (ie the inability to generate DNA in the absence of an RNA primer) leads to a portion of the end of the lagging strand being unreplicated.
    • (this applies to linear chromosomes)
  • so after every cell duplication, a portion of the telomere is lost.
  • there are two ways in which cells deal with this:
    • use a protein that acts as a primer-template instead of RNA (used by some bacteria)
    • telomerase: an enzyme that extends the telomere sequence in a manner similar to DNA polymerase, except it reverse transcribes from a specific (exogenous) RNA sequence.
    • telomere shortening is linked to senescence and refusal to duplicate (Hayflick limit)
    • cancer cells are "immortal": they produce and use telomerase.
    • telomerase inhibition is a promising anti-cancer strategy.
  • damn, this stuff is good. it is explained in painfully low detail in this book, which reminds me that this is a beginner's book; despite how sophisticated I feel upon reading it.
  • also, how is the Hayflick limit bypassed at the birth of an organism?
    • (reading the wiki mentions how the proof for the previous model – all cells are immortal – may have been flawed due to presence of pluripotent/stem cells in the mixture)
    • is The Immortal Life of Henrietta Lacks related to this?
      • it is! (immortal cancer cells harvested from a single cell of an unsuspecting woman; 20 tonnes of her cell HeLa have been manufactured so far)
  • I just realized: the genetic code probably does not refer to it from a programmable code perspective – it makes much more sense from a code-breaking sense.
    • how can you systematically approach it as a coding/engineering problem?
  • done with this chapter. I'm impressed with myself. I have seen some stuff, I don't think I have learned anything substantial.
    • "ain't no thang that can't be a spectator sport" – me, 2018.
    • the spectator. that's going to be my new persona.

in tedia res

  • the dumbest thing you can do to a website is to add an unmoderated comments section.
    • and yet the ensuing dumpster fire is extremely entertaining.
  • I'm starting to think I lack ambition.
    • I do have desire, though.
  • yesterday, I played some chords and sang made-up lyrics along. was interesting.
    • I could do something more well defined.
  • Seu Jorge.
    • haven't heard any Bowie, but this Portuguese version is fantastic: Life Aquatic: Studio Sessions with Seu Jorge
    • the magic of good music.
  • started listening to Unknown Pleasures by Joy Division.
    • for some reason the opener Disorder reminds me of Interpol's Untitled.
    • I should really check out more Interpol. Untitled seems to have been the outlier though.
  • there is certainly some form of pleasure I derive in solitary pursuit of things I like. there is a different kind of pleasure that arises from pursuits that are shared with others, and a third … sense is tickled when vetted and validated by an abstract society.
    • have failed the last one; the first two are still in play.
    • what's the point of anything, anyway?
  • there is a word for what I'm going for these days. autodidact.
    • except, I can't take things seriously; commitment lurks in the context of an endgoal, which is shrouded in questions about the future.
    • I am resolute on avoiding that question at all costs.
  • why panic?
    • fear of not knowing.
    • fear of having to start all over.
    • in fact, it's a justified horror. I have to start all over.
    • there's very little I know.
  • but why panic at all?
  • but there are some unalienable things I think.
    • I don't know what they are for me though.

[2018-09-10 Mon]

ex communicado

  • some mornings I wake up, feeling up to the prospect of reinitiating contact with someone in my life.
  • I feel guilty that I haven't been in touch – mostly because of my spurning them down. I was in a poor place then.
  • it is very easy to keep the status quo and keep silent.
  • I also know that given a few hours to let these feelings of affinity and initiative subside, I will be very glad and thankful that I did nothing foolish like ping them.
  • I don't want to feel/sound desperate.
  • I am afraid it will be/feel different; which is obvious, but I'm not looking forward to seeing proof of it.
  • maybe I am not their friend anymore, which is a real possibility. I try to avoid knowing the truth of that fact.
  • I am definitely on the road to not being their friend; each passing day of silence establishes that.
  • I also know that when I feel asocial and depressed, I am going to want to revert to the status quo of not being in contact with most people.

these are my crosses to bear.
I can bear them in abject silence.
while sometimes I stumble under their burden
I am mostly fine
lumbering on, alone.
the past is a young desert,
with ships on the bed
drying in the sun
and aqueducts that lead to nowhere
all is abject, but
if I squint hard enough
I can hear the faintest trickle of blue
and see the gentle lapping of the sea.

  • and now that I have written this, I am back to the usual.
  • there is great pretence afoot.

wordup   wordsmith

  • foundling – a child that has been abandoned by its parents (as opposed to runaways/orphans)
  • majuscule – like miniscule, but on the larger side.

per se lingua

  • Gerald Murnane strikes me as the a who lived his life, fully, in his own microcosm.
  • I wonder if I have felt as strongly drawn to a culture or a language.
    • was definitely into the Scots because of Kidnapped.
    • have held a minor foray into Latin (Lingua Latina per se Illustrata)
    • the Icelandic language and its geography have interested me. haven't done anything about it.
    • dying languages evoke very strong interest and melancholy in me – the idea of the death of a culture and it being irretrievable.
      • it's highly eclectic and with not so great resources for the casually interested. also doubt the existence of literature as an end reward (which would make it less of an academic venture)
    • Tengwar/Quenya: aiya Earendil elenion ancalima.
      • I think I subliminally resist conlangs, for some reason.
    • briefly considered French to read the Tohoku papers.
    • Mongolian and Armenian, but that's just for their script.
    • ancient Greek. or even katharevousa. for the etymological itch. thalassa, thalassa the wine dark sea
    • I have never had any sort of inclination to learn an Indian language. I'm not very fond of this subcontinent.
    • have recently considered Portuguese/Spanish to explore South American literature. Borges, Aira, Marquez and such.
  • so, in summary, lots of sporadic desire, very little sustained ambition.
  • there's also the question of whether I want to learn the spoken word.

the partially exhumed life

  • is there a notion of a life that is worth living?
    • is an irrelevant life worth living?
    • what would a 'no' imply?
      • that I should strive to be more relevant?
      • or that nothing I do really matters?
  • I don't have many strong obligations to do something or be somebody.
  • I wanted to be a scientist as a kid and solve fundamental mysteries.
    • as an adoloscent, I wanted to be a mathematician and chip away at pure math.
    • I relished the prospect of being particularly useless to humanity, a la Hardy.
    • my young-adult dream has been shot down, repeatedly, by me.
  • when I read about/learn about people who dedicate their lives to effecting change and improvement,
    • I feel shame.
    • and yet I feel no inclination to
    • am I living a life that is not worth living?
    • how do people find meaning in their lives?
  • perhaps the question is of a life that is not worth living, and the answers are weaker.


  • it has been three days since I tried unlocking the bootloader on my phone.
  • time to wipe and try to flash my perfectly functional phone! (yay)
  • if this goes south, I'm calling it now!

in tedia res

  • I am listening to A Mineral Love by Bibio and was surprised it wasn't as dark as I recalled it.
  • turns out I was conflating Bibio with Baths …

[2018-09-11 Tue]

DONE mido:

  • unlocked the bootloader easily enough.
  • installed TWRP. flashed LineageOS-15.1, openGappsnano.
  • was tempted to use microG instead of openGapps; but the benefits of having an easy access to certain services and features outweighed FOSS purity considerations.
  • wanted to root it, but neither Magisk nor SuperSU worked.
    • TWRP refused to mount /data upon reboot.
    • installed, wiped, reinstalled everything several times.
  • was unable to resolve this bug;
  • decided to flash a different recovery instead: RedWolf, and things work as they should.
  • haven't flashed SuperSU/Magisk yet … the phone is rooted though, I can grant, control and restrict root access using Privacy Guard.
  • disabled Google Assistant in Trebuchet (the launcher)
  • have refrained from installing old apps en masse.
  • there'a a built in Dark Mode in LineageOS-15, which is awesome, and precludes the need for fixes like Substratum.
  • had some trouble getting Signal to authenticate. also, signal was previously on the old number. RIP
  • Trebuchet's app drawer is now a generic unsorted jumble, and I can't find a way to install the old version.
  • the adrenaline has been flushed, it's a boring phone again.


  • [ ] set up syncthing
  • [X] transfer music
  • [ ] install magisk? :\

in tedia res

  • lots of thoughts from ancient personal history.
  • I think I get what's happening here: the gaps are being filled, slowly.
    • this is an excruciating development.
  • have a slight premonition that watson is dead in the water.
    • why?
    • 30% through. by established tradition, I should be ceasing soon.
    • it was a very casual read; I don't think I know anything of substance.
    • I'm starting to feel I'm on the downslide.
      • about time.
      • or I'm sleep deprived.
  • I need to distract myself from these retrospectives.

[2018-09-13 Thu]

in tedia res

  • I guess I didn't really do anything yesterday.
  • I was dragged into a group chat yesterday.
    • haven't been in one since 2014, I think.
    • the dynamic is different – like a three-body problem.
    • how do I handle this on hollerith?
      • right now, I'm just adding it to the
  • had a depressing dream last night; was a truant, but lived next door, and watched my parents' marriage deteriorate.
    • I prefer boring dreams that I do not remember.
  • there's an OEIS movie!
    • the first 1000 plots, set to the music of a certain other plot.
  • looks like today will be the day I step out socially, again. that'll be 20 days.
  • I am a motivational leech.
    • or to be charitable, a symbiont.
    • when someone I know makes a foray into something, I latch onto that, and try to learn
    • for a fleeting while at least.
    • on the other hand, sometimes, wih some people, and with some topics, the opposite effect occurs: I am intimidated and avoid anything to do with the venture.
  • anyway, had a creative idea where sometimes, the thoughts of people in company get scrambled. maybe write a script with this idea.
    • it's never happening, and I can tell 3 minutes from conception.
  • I should continue with watson. another day, another chapter.
    • I am currently in the chapter "The Repair and Mutability of DNA", which is all about those error correction mechanisms.
    • probably won't resume today, I hope I do, tomorrow.
  • I miss


  • I think it is far more dangerous to have a file open in emacs in the command mode than in the insert mode.
    • pressing dd unintentionally (the binding is common to both qutebrowser and emacs) results in a line being lost and not knowing about it in command mode, and detectable junk in insert mode.
    • the winner is clear.
    • the only problem is that it is disturbing to leave a file in insert mode.
    • the natural way to save a file involves exiting insert mode; closing a file without saving leads to unincorporated edits.
      • TODO: find out how emacs manages unsaved edits. it seems to be more complicated than a .swp file.
    • a solution might be to close the emacs window (S-Q)
    • another solution might be to keep emacs in its own workspace.
      • (usually keep it on workspace 1, along with the browser)
      • workspace 2 is now where the emacs at.

wordup   wordsmith

  • symbiont: an organism that is existing in symbiosis with another. (I like the -bont derivative)
    • endosymbiont

[2018-09-14 Fri]

in tedia res

  • stepped out to meet and have lunch with A.
  • he brought me an ukulele from Bali (:
    • it has a really cool etching of an owl on its front.
    • it's a rather strange instrument: the middle two strings are the thickest, and the tuning is GCEA.
    • it sounds good when played open, but feels out of tune when chords are played.
    • probably the strings – new strings take some getting accustomed to.
    • it might be the fret spacings, which would make it a lost cause. but I doubt this is the case: these things are a standard measurement.
    • while the fretting is chromatic, it seems a bad idea to use this for anything less cheery than the usual stuff.
    • that makes it the 7th instrument I have owned (6 stringed and a clarinet)
      • I did have a toy piano and a blue harmonica as a child (not counting them)
      • I have fooled around with a pair of congas, flutes, J's banjo and that pot like contraption A owns.
        • (it's called an udu)
      • I started out wanting to learn the bagpipes, and now I have a ukulele.
        • story of my life -\(`')_/-
      • I once saw a Stradivarius at close quarters with V.
    • it's 10 years since I first picked up an instrument.
      • one of the few things that has been intensely personal and out of the purview of how good/bad I really am.
      • I've had my good days when I've been in pocket.
      • H encouraged me a lot.
  • this phantom panic when sounds in the music you hear are similar to the doorbell/ringtone …


  • found a solution to a problem posed by A: prepend multiple lines with content from the clipboard.
  • solution:
    • use the usual visual-mode – shift I – insert text – escape
    • pasting text in insert mode: C-R followed by "; finish with a return.
    • make sure that the copied text does not contain a newline – yy pulls the newline along.
  • feels great!

wordup   wordsmith

  • shatner's bassoon: from Brass Eye. "part of the brain that deals with time perception" :D
  • Fata Morgana

[2018-09-15 Sat]

in tedia res

  • so yesterday, I was in contact with a total of 9 people. that's going to be the record for a while.
    • partly due to the opening of another group chat.
  • had a dream last night (forget the details), but I woke up in the middle to document the name vimp for vim based ASCII editing, a la gimp. I discern fine wordplay even in my dreams.
  • installed lmms. I will probably never use it.
  • supercollider. programmed music composition/generation. maybe someday.
  • this game/music development platform called TIC-80 (not to be confused with the game TIS-100)
    • downloaded.
    • installed.
    • tempted to make a foray.
    • should I learn lua?
      • downloaded a book called Programming in Lua
  • need a break from the uke – have been using it for mindless fingerpicking while reading something else.
    • I think tuning at high pitches is a hit and miss.
    • GCEA may not be the best tuning for my style of playing.
    • have tried other ad hoc stuff, some of them were good for a tune or so, none versatile for several.
    • the middle two strings are the thickest – this needs to be leveraged in picking/designing any tuning.
      • having the outer strings an octave lower sounds terrible.
      • does it have a truss rod?
      • look at other alternate tunings.
  • played the guitar for a bit.
    • I remember this guitar sounding disappointing when I first bought it.
    • it sounds fine now. either it has tempered well, or I have grown more tolerant/fond of it.
    • the electronics is shot (the tone pots)
    • but the strings have been holding up for ~4 years! which is remarkable!
  • should I declare watson as dead?
  • discussed the prospect of a custom display for funcoid with A.
    • I am quite fond of the idea.
    • in general, it reflects my attitude/desire to build universes outside the purview of the real world out there.
    • there seem to be a lot of cool ancient consoles out there: VT220, minitel etc.
    • I wish I could … (well, that's for the next section)

the partially exhumed life

  • haven't talked too much today.
    • feel frustration re: where I am; precipitated by my recent indulgence in carbon-based socializing.
    • joshed around a bit re: holding a job with A. regret that.
    • I also had to change the password to KUnet yesterday. it brought me down hard.
  • am pondering over where exactly I got derailed
    • being too ambitious?
    • being too naive?
    • was I lazy?
    • am I dumb?
    • have I been an impostor?
  • who cares?
  • it's all over in reality.
    • it will never be over in my head.
  • what about watson?
    • what about that exercise in futile defiance/defiant futility?
    • what about it?
  • can you even be defiant without an exit strategy/hope?

wordup   wordsmith

  • slovenly: immoral woman, rascal, knave. do you have the same geographical question as I do?
  • mangione

[2018-09-16 Sun]

in tedia res

  • had a strange dream (aren't all memorable dreams strange?) where I was talking about isotopes with magic numbers and called Au as an example.
    • the victims of my "scientific" lecture were a friend and his dad.
    • of course, Au is not even stable from a nuclear sense; and the astute dad asks me if I was not conflating chemical nobility with nuclear stability.
    • I clarified that I was wrong after waking up.
  • Cavalo songs sound less magical on the album than acoustic/live
  • what do I do today? possibilities, in order of preference:
    • I stay in all day.
    • [X] I go out for dinner and a smoke.
    • I go out for dinner.
    • A invites me over, and I decline, citing "ill health"
    • A invites me over, I go, I have a smoke as a reward on the way home.
    • A invites me over, I go, I abstain from a smoke.
  • "I identify as a geothermal vent." – me, 2018.
  • shared a long rant with R on the Aryan Migration/Invasion Theory.
    • it's a dumpsterfire topic, of absolutely no relevance to the future. it is an ideological blackhole.
    • I don't care. nobody ought to care.
    • there are far more interesting, useful and less controversial questions that need to be resolved.

word   wordsmith

  • je ne sais quoi – an indescribable or indefinable feeling that distinguishes from other cases that are superficially similar.
    • almost but not quite, entirely like
  • situs inversus – a benign medical condition where all the internal organs are flipped about the central axis (heart on the right etc.)
    • situs solitus – the normal positions of organs in the body.
  • budgerigar – good cockatoo. (I'm learning the spelling for the first time. always thought it rhymed with briar)
  • confrere – colleague.

[2018-09-17 Mon]

wordup   wordsmith

  • milquetoast – a timid, meek and unassertive person (from a character from a comic)
  • ataraxia – calmness, impassivity (from ancient stoic language)
    • ataractic

in tedia res

  • and the E string broke. two days after I make a remark on its remarkable resilience. RIP
    • "things die, and people fall apart."
  • want to get into mapmaking.
  • I also want to start reading something.
    • sebald is in my sights. perhaps something other than The Rings of Saturn?
  • I operate like a hypoglycemic when it comes to motivation.
  • "A hero has fallen."
  • I am a very theoretical friend.
    • well, what do I mean by that?
    • I am now a well defined trope people reach out to.
    • an atavism, the occasional throwback, the fixed point from the past
    • people think they haven't changed after getting hitched, but they are mistaken.
      • when talking to me, they revert to an old mode.
      • which ceases when the conversation ends.
    • not a rant, just some observations.
  • self-sufficiency is where it's at.
  • Wintergatan on !yt. by all that is blessed.

[2018-09-18 Tue]

wordup   wordsmith

  • triptych: a three panel painting.
  • caboodle: the whole lot, shebang.

in tedia res:

  • nothing really happened today.
  • music:
    • Mark Farina – Mushroom Jazz series.
    • Madlib – Yesterday's New Quintet series.
  • futility and utility
  • haven't felt like doing anything, really.
  • changed wallpaper.

[2018-09-19 Wed]

in tedia res

  • some days, it's sheer poa alpina.
  • the thought of shutting down labradoc, hollerith has crossed my mind.
    • thoroughly useless ventures.
  • music: The Beta Band
    • Who's gonna shape the corners, of my mind today?
    • What's in those dusty rooms I fear for in every way?
  • music: Depeche Mode.

Author: zzalpha

Created: 2018-09-19 Wed 12:23