Lähdit pois

Joulun ja uuden vuoden aika on monessa perheessä rankkaa. Tuntuu kovin polarisoivalta juhlalta - lisäksi kun itselle ja läheisille on käynyt tapahtumia lähiaikoina, mitkä ovat pistäneet miettimään elämää ja elämistä. Tässä siitä jotain pöytälaatikosta vuoden päätteeksi.

Lähdit pois

Viivana vaimeana kirkonkirjoissa
Tyhjyys tyynenä frontaalilohkossa
Jälkensä jäänteet hautakivessä
Kaiverrettuna kaipuu sydämessä

Jossittelun kaikki mahdolliset jälkiviisaat polut
Tavaan toistamiseen ympyrässä muistojen tomut

Liekkisi kun ei vain ole enää kytemässä täällä
Tuhkaantui pala minuakin ajattomuuden äärellä

Sanovat saapuneen satamaan
Jäähyväisensä jätti kotirantaan
Mielen ja materian maailmaan
Tietoisuuden taakatta tuskattomaan

Olin kanssasi matkakumppanina häviävän hetken
Tovin matkaa kai taitimme elon usvaisen retken

Todellisuuden veistäjän teokseen lopulta kuin loven
Viima vaihtui vieraaksi kautta avaamasi ulko-oven

My only Christmas gift 2018

The only Christmas gift I made/gave this year was an open & ad-free mobile game designed by my older daughter Elea when she was 3; today was the first public release of "Princess Versus Creeps", tested by my 2 and 4 year olds: https://youtu.be/gJG-n7E3Tuw

All assets and source code are openly available at: https://github.com/Syksy/PVC

The dawn of a utopian or a dystopian society for the humankind?

Just in case somebody might've missed it, we possibly just entered a new era of "humankind" just now.

Reports indicate that the Chinese researcher Jiankui He from the Southern University of Science and Technology in Shenzhen China has produced a trial in which two babies, whose embryos have been altered using the CRISPR/Cas9-technology, have possibly been born. The Chinese researcher He has declined to give conclusive confirmation to the trial (probably waiting for an upcoming big scientific conference). Apparently the consensus is that a mother indeed gave birth to twins, in which one of the two babies - thanks to genetic editing - was born immune to the HIV virus due to experiment-driven changes to the CCR5 gene.

While CRISPR, a revolutionary technology, has been around for a while now, this is now the first reported case of actual human beings altered using CRISPR being born that I am aware of. Mostly ethical constraints and/or practicalities have so far prevented such experiments from being conducted - China to a degree might be a wild west of such experimentation, and have previously raised a lot of eye-brows with their rather liberal use of such techniques. Roughly speaking, Western countries have been more conservative in their use of such advances.

Obviously a lot of questions rise, both negative and positive; are we now playing God, and if so, should we? Are we now capable of saving people from otherwise lethal diseases - or, on the other hand, should we be doing that at all and instead let the natural course of things occur? Will us "vanilla" humans eventually vanish, and genetically tailored humans become the standard? Is this the beginning of the dawn of a utopian (i.e. repair fatal traits, ethical enhancement of our species) or dystopian future (e.g. Aldous Huxley's Brave New World and its alpha/beta/.../epsilon-caste humans)? What traits are ethical to alter; IQ? Lethal diseases? Muscularity? Cognitive traits related to e.g. self restraints due to feeling empathy toward fellow human beings (i.e. military utility)?

This is just broad level food for though without going into technical details of whether such experimentation is safe or not and all the specific nuances of how such practices might alter the path for our species. This particular experiment also apparently falls into the grey area of whether or not this is "treatment" or "enhancement", as such technology is not truly available in countries where HIV is rampant. According to researchers working with the particular disease, HIV's not a disease that'd be ideal target for altering a potentially fatal trait in the first wave of such experimentation. 


Some reading (there's already plenty even though the news are a couple days old): 

https://www.technologyreview.com/s/612458/exclusive-chinese-scientists-are-creating-crispr-babies/

http://time.com/5463741/crispr-human-babies/

PhD, 16th of November 2018

Dear all,

10 years ago I started my journey at the University of Turku, or 12 years ago in Aalto University (TKK, Teknillinen Korkeakoulu back then). I stepped into Turku Centre of Biotechnology as a summer intern in 2008 before my Bachelor's, without knowing much of anything, and I was handed over ChIP-seq data and so I became a "data scientist" (without even realizing it). I had no idea what is science (really), how it is done, what people in science are like, and I was frankly quite puzzled. Suddenly my project turned into a Bachelor's thesis at TKK and my first scientific paper, which is still probably my most cited publication. After a series of events I found myself a "PhD student" in 2013.

On Friday we got to celebrate the academic milestone that I now got the right to the title of a PhD after defending my thesis of applying mathematical modeling, statistics, and machine learning in prostate cancer. I hate titles to be frank, but I do value the ever-dripping hourglass of time and events that have come my way. The true meaning of PhD is not so much of the destination (a fancy title and/or "prestige" - I still smell as much of fart and sweat as before obtaining such a title), but rather much more about the journey. I am but a small man, but I dream that some day, somewhere, some patient undergoing a lethal disease will receive better treatment or advice because of something that might've been derived from my work. If there is even one such occurrence, this has been worth it - all else is dust in the wind. This journey is now at an interesting junction thanks to many colleagues (many of whom I am *extremely* happy to also call friends), hard work, mixture of success and failure, a good pinch of curiosity, something of a strange brew of luck and skill, sleepless nights, and special people like Essi without whom this wouldn't have been possible.

I tried to invite as many of you as possible to join me in the celebration, as it has luckily not been a hermit's journey. Thank you to all of you present and also absent, who brought meaning to this task. There were over 80 of you at the defense and over 60 at the Karonkka (the evening party; roughly translates to "Coronation" or "Crowning" in English), but I haven't forgotten the ones who couldn't make it in person.

I don't know where the winds will take me or those that are my companions in life. The following is Robert Frost's poem "The Road Not Taken", which can be (mis)interpreted in many ways. I would say to me it's of the paths we take; looking back questioning our ways and choices, but with a glance to the future acknowledging that whether the road was the better or the worse, it was the path chosen in this gracefully granted sole life that we travel:


"Two roads diverged in a yellow wood,
And sorry I could not travel both
And be one traveler, long I stood
And looked down one as far as I could
To where it bent in the undergrowth;


Then took the other, as just as fair,
And having perhaps the better claim,
Because it was grassy and wanted wear;
Though as for that the passing there
Had worn them really about the same,


And both that morning equally lay
In leaves no step had trodden black.
Oh, I kept the first for another day!
Yet knowing how way leads on to way,
I doubted if I should ever come back.


I shall be telling this with a sigh
Somewhere ages and ages hence:
Two roads diverged in a wood, and I -
I took the one less traveled by,
And that has made all the difference."

Theater (in Finnish): Taru Sormusten Herrasta @ Turun Kaupunginteatteri

(Lord of the Rings @ Turku City Theatre; dialogue in Finnish so hard to follow for non-speakers, albeit if you're die-hard fan you could still follow and enjoy it.)

Taru Sormusten Herrasta @ Turun Kaupunginteatteri oli parhain teatterikokemukseni ikinä tähän mennessä, tosin en ole tällä saralla mikään pro. Älä lue pitemmälle jos haluat välttyä mahdollisilta spoilereilta. Näytelmä oli suomenkielinen, joten kansainväliset kaverit eivät dialogista pääse perille. Arvosana: vahva 4½/5.

Koko trilogia neljään tuntiin (kaksi välitaukoa); lavasteet, akrobatia ja oheistilpehööri ihan Andrew Lloyd Webber -tasoa, mikä on aika kova fiitti ottaen huomioon että kyseessä on kuitenkin Suomen Turku; kyseessä ei ole tosin musikaali. Näytelmä ammensi sekä alkuperäisestä kirjasarjasta (esim. Tom Bombadil mukana) että leffasta s.e. tietyt skenet (esim. Klonkun viimeset otteet Mt. Doomilla sormuksen kanssa ja Gandalf vs. Balrog -standoff) oli ihan yks yhteen ja ne muistu lavasteiden kanssa mieleen elävästi, vaikka en oo vuosikymmeneen nähny trilogiaa. Lisäksi oltiin tehty omia sovitusvalintoja, esim. Gondorin osuutta oli vähennetty huomattavasti (ainoa maininta oli Eowynin lyhyt taisto Minas Tirithissä Nazgul-noitakuningasta vastaan) ja Isildurin kiroama haamukansa puuttui kokonaan. Sinällään kuitenkin kova veto saada abouttiis koko trilogia menemään näppärästi neljään tuntiin. Esim. valtasormuksen "viettelys" saatiin kuvattua oikein hyvin ja osa näyttelijöistä erityisen oivallisia (esim. Klonkku, muitakaan vähättelemättä).

Ainoina semi-nurinan kohteina:
1) Jos ei ole nähnyt leffoja tai lukenut kirjoja, niin tietyt juonenkäänteet etenee aika harppaillen ja "puhtaalta" pöydältä voi olla vaikea ymmärtää mitä tapahtuu (esim. miksi Konkari onkin yhtäkkiä kuningas jne, tietyt muut poliittiset käänteet). Jos ei ymmärrä/muista taustaa, niin osa hahmojen ihmissuhteista jää juonenkäänteiden lisäksi aika pintaraapaisuiksi (esim. Gimli ja Legolas, ja heidän ystävyyden merkitys ottaen huomioon kääpiöiden ja haltioiden pitkä vihanpito taustalla). Eli esim. en ehkä veis tyyliin omia vanhempiani kattomaan, koska eivät tietääkseni ole nähneet leffoja ja kirjatkin ovat varmasti painuneet pitkälti unholaan, jos ovat niitä lukeneet.
2) Ne merkittävät isot taistelukohtaukset mitkä olivat mukana näytelmässä (esim. Minas Tirith, Rautapiha) ovat hyvin vaatimattomia, mutta tän antaa anteeksi kun pistää kontekstiin, että on yritetty improta n. 20 näyttelijän porukalla. Silti jää kaipaamaan "sitä jotakin", mutta toisaalta tässä on "leffa-bias" - siellä isot taistelukohtaukset kun oli 2000-alkupuolen herkkua ja muistaakseni varsin laadukkaita.

Näine pienine kritiikkikohtineen oikein mainio käynti.

Ad Nihilo

So somebody happened to post on /r/nihilism with an idea for a competition of nihilism, with the best poem rewarded with nothing, naturally. Quickly scooped this up from old remains so I'll have to polish it a bit down stream, but I felt confident enough to post it there-in.

Ad Nihilo

A simple moment not so far away
On a seemingly ordinary Monday
Existence promptly ceased to exist
Concept too desensitized to persist

I perceived my self mere electric
Synapses emergent as ego-centric
Wirings not built to last a forever
But to fulfill some temporary fever

History's greatest moments of glory
Deepest pits of whatever is unholy
Melded into an ill-defined convergence
Mundane goals inane just as brilliance

Whenever infinity ends I'll be present
As particles I shall vanish that advent
Quantum memories floating in a void
Lingering residues of us all, destroyed

SOTE eli Suomelle Onnea Tähänastisesta Elosta

SOTE eli Suomelle Onnea Tähänastisesta Elosta

Kaskea savutti pellot täynnä raatavia maaorjia
svensmannit kun kävivät taistoon kohti tsaaria
ei tuntenut viel silloin hakkapeliitta juur maailmaa
mut heräsi sisimmässä koti, uskonto ja isänmaa

Viinaa, tervaa ja saunaa monet heist vannoi
Kiven seitsemän veljestä karjaa kun laukoi
hiihtäen kävi luo joku lääkäri kansantaruja
kulttuuria keräillen tuo kuin idän erämarjoja

Vuosisadan vallankumouksen lähivarjoissa 
Lenin-sedän lempeällä luvalla salaa ajoissa
puskurivyöhykkeen pieni väki vaeltelemaan
onneaan kansakuntana kävi kaitsemaan

Ehdittiin germaanin monarkiaa tänne kaivata
vaan ei dynastiaa päätetty viel tääl kruunata
kun vuodatettiin pitäjän veljistä vuolaasti verta
viel keksittiin häpeäks keskitysleirit nekin kerta

Eikä länsinaapurin neutraalilla mallilla tullut holttia
kun Molotov ja Ribbentrop asettelivat rajatolppia
lumiseen helvettiin helssaamaan Führerkin saapasteli
lie ollut ei pyhimyksiä kumpikaan potero jok taisteli

Aina Petsamon nikkelistä Karjalan kannakseen
sai ikuiseksi majakseen moni mullan kodikseen
rautaesiripun estradilla nousi tuo Kekkoslovakia
pitivät yllä YYA-herran myllykirjeet kovaa lakia

Mutta kun Manu ei hallitusta hajottanutkaan
vahvaa markkaa pohtivat moni silti politiikkaan
laman korkoprosenteista kasvoikin epävakaita
risteillen eleltiin silti vedellen huiviin verovapaita

Helmassaan aikoinaan Järnefelt, Waltari ja Leino
fennomaniaan soi myös Finlandia-hymnin neito
kevyemmin myös myöhemmin Juice ja Gösta
tulkitsivat surumielisten kansalaisten paatosta

Lompsassa vihreätä kultaa ja vientivalttina metalli
muotona jälkimmäisellä lienee kuitenkin musiikki
kasvoi hurmiossa tuo kansa uuteen vuosituhanteen
irkissä janosi nuoret sen taitoa tekstarista Linukseen

Muistetaan tokkiinsa silti viel siis Loordi ja ysiviis
Talvivaarasta ja IT-kuplasta mitä me niistä viis
vaik Noobeleista kapsahti katajaan suur-Nokia
suurin oli kansan suru Torinon Selänteen hopia

Voi anomuksen KELA:an kirjata nykyään netissä
WiFillä jos VR:n pendolino suokin olla myöhässä
reseptit sähköiset olkoot silti aina ajan tasalla
ellei vie Tieto taas projektia kotiin kokemuksella

Tukiloukusta motivaatiota jos sais hakea työhön
monet pohti juoden pitkään yöttömään yöhön
peltipoliisien varjossa rallia eteläänpäin taittui
veljeskansan valuutta kun kans euroiksi vaihtui

Vaihtorahaa pankkikriisistä tuli kuin tonnin setelistä
niin moni jopa perustanee barrikaadien metelistä
näkymätkin suomalaisten kuin PISA:n torni taittui
koulutuslupaus kun Mannerheimintiellä haihtui

Muumien maailmaan tuli ensin aasianmaan tohinaa
sittemmin Syyriasta haastavampaa kansan kohinaa
sulatusuunista leivottiin vastakohtien välistä mutinaa
kuten metropolian postimerkkien nahkaista rotinaa

Varoen kuitenkin kuin Häyhä tulee luovia vaalien alla
vaikka kannatusta tuotetaankin parhaiten makkaralla
täälläpäin talon tapana kuitenkin jotenkin on selvitä
olipa syynä taustalla etanoli, raha tahi herkkä hipiä

Sampoa jauhakaamme mobiilipelibuumin voimalla
vaik siirtoverkkojen omistajat sijaitseekin ulkomailla
muoviämpärijonot kun venyy revontulien loisteessa
samal pahviset vauvakopat kiertelee parrasvaloissa

Varmistaahan meille huomisen wakaa wanha werottaja
kunhan eläkesäästöille ei olis kierosti koittanut noutaja
ikäpyramidi pelottavasti päälleen kun aika salee jo flippaa
finglishiä vuäntäviä ikäpolovet tuimahat suattapi whippaa

Arpa kohtalon tuo tuppaa olemaan sangen arvaamaton
silti sisulla valvoo viitisen miljoonaa alla vähäisen auringon
viipymään jäi tänne tuhansien jäätyneiden järvien äärelle
jotkut perunamaan ja punaisen tuvan unelmien säkeille

Turkasesti toivotellen onnea joka iikalle ja tälle miun maalle pohjoiselle
olkaamme kaikesta huolimatta hyviä toisillemme ja myös huomenelle.

-TDL, itsenäisyyspäivänä 2017

Father's Ashen Letter

Father's Ashen Letter

Died a stillborn past long ago
This spirit of self lingers on
Unable to let grasp of life go
For their tiny steps I fathom

Paper pieces of life around
Words written all scattered
Of love and of care abound
Songs for a world unbattered

These things unable to express
Mornings that do not dawn a sun
Man ought to emotions suppress
Living inside the barrel of a gun

Pushed aside by the long road
Drowned under the anxious yoke
Unshaven worn out face an ode
Ashes under childhood home oak

Words scribbled by a fireplace
Happier days, whispered the wind
Ink smokes as words set ablaze
For my dearest own kin and kind



(Happy birthday, whispers wind
My dear, dear own kin and kind)

Obscurity of Unlikely Facts

In this era of vast flow of information, it has become harder and harder for anybody to keep up with any topic of interest in a comprehensive way. This particularly applies to topics which provoke heated debates and appeals to mankind's intrinsic desire to reinforce their already existing opinions and views.

To this end, I've been playing around with a thought pattern lately which I've now fancily dubbed the law of Obscurity of Unlikely Facts. The purpose of this rather simple "check-list" of a cognitive bias can be applied rather universally, though in fields where it's hard to quantify and to measure a phenomenon in an exact manner it's harder. Simply put the idea behind the whole thing is the saying "Even a Blind Chicken Finds a Kernel of Corn Now and Then". This saying doesn't seem very popular in English, but it's used time to time in Finnish.

The basic idea is, that if we can do the (false) dichomization on whatever topic to be able to say whether a certain fact is TRUE or FALSE, let's say on a political debate, usually people have a set of e.g. 5 main commandments they follow. Suppose a person with an agenda posting the following list (which might be in a narrative format but can be reduced to a list of main hypotheses):

The great Tomato debate thread example:

Arguments by tomato-specialist Foo Bar:
1) Natural tomatoes are always yellow
2) Tomato farmers have gone too far in bringing out unnatural red tomatoes
3) Farmers are backed up by an international tomato X company wanting us to eat addictive (red) tomatoes
4) All tomato farmers are evil
5) Tomato farmers want to make a profit

A pro-red tomato person counters this post in a relevant forum, and pushes in for a counter-attack. He makes a list of the hypotheses and starts collecting counter-material. He then posts the following post (shortened from what you would encounter in real-life):

Counter-post by red-tomatoist Qwerty Asdfg:
"Mr. Bar recently posted a seriously misguided list of curious facts that I feel need to be corrected. He claims that all natural tomatoes are always yellow, but we have discovered many varieties of tomatoes in the wild that are by nature red, as recently published in the International Journal of Tomatoes by Prof. Tomatogic et al. Furthermore, as we encounter these red tomatoes in the wild, it is hilarious to even propose that farmers would be the ones propagating the advance of red tomatoes over yellow ones - majority of tomato subtypes are red, as shown by Prof. Tomatogic. There is zero evidence that e.g. Prof Tomatogic would have any affiliations to company X, and looking at their catalogy at my nearby tomato store I discovered that they do offer a large variety different colours of tomatoes, including yellow ones. Bringing in X in relation to tomato farmers is just ridiculous. This all just shows how misguided Mr. Bar is in his original post; to claim that tomato farmers are evil is just a cherry on the top, and tomato farmers do not want to make a profit - they just aim to produce the healthiest of products and take great pride in their work!"

Now, for starters, both posts by Bar and Asdfg would rub me the wrong way. Both are very extreme and show no signs of lenience towards the opposing view, which in my opinion is the key to detecting a triggered argument which should be taken with a truck-load of salt. But the point of the law of Obscurity of Unlikely Facts is to systematically evaluate Asdfg's counter-arguments, disregarding how ridiculous the original claims may have been.

While Asdfg appeals to reason and even science in his shooting-down of mr. Bar's post, I find above sort of counter-posts questionable. First of all, it addresses every single point from mr. Bar directly in a list-like manner, even if it's narrative. When I see this sort of counter-post, red lights start flashing. To me, it only indicates that Asdfg has first decided that mr. Bar's arguments are to be proven wrong, and then Asdfg has collected the evidence and/or rhetoric arguments to address every single one of them. A statistical basis for the law could probably be found in False Discovery Rate or the lack of corrections for multiple testing, but that's beyond this post.

Now the key point is that when I see somebody go through their opposer's supposed arguments in this non-constructive, list-like systematic way, it makes me question Asdfg's motives - he or she has probably not even tried to understand the original arguments and/or taken the time to consider whether they can be interpreted in a manner that is true.

To summarize the law of Obscurity of Unlikely Facts:
The longer the list of arguments by person A, the more likely that at least one or more of these arguments are true to at least a reasonable extent. In reverse, the longer the list the A's opposer B shoots down systematically, the more likely the person B is biased to just counter A without a proper, through-out and fair inspection. There are multiple factors that affect this (e.g. ad hominem yes/no) or lenience in B's comments, but a systematic list vs. list discussion is very likely to include a degrading amount of cognitive bias and probably ought to be ignored altogether.

If you engage in multiple discussions of sensitive topics, I have found the above simple rule useful in filtering out discussions where the discussion is just not worth my time. Usually they degrade into a kindergarten-level "yes! no! yes! no!" poking spiced with ad hominem, so it's better to move on to a better forum/thread if one really wishes to find out information on the various views to the topic. But above rule can also be used to detect discussions that are a great source of humorous content (Dunning-Kruger effect usually increases in this case as a function of time), in which case one should go grab some popcorn, just sit back, relax and see it unfold in its glorious marvel.

Väsyneen Värssy

Väsyneen Värssy

[Kalevalaisen runomitan mukaan]

Väsy/neenä / virstan / verran
Rämpi / rääsy / roudan / rotua
Mailin / mitan / päähän / päästyä
Olon / aidon / anoa / aikoi
Luoda / lujaks / erheen / elon
Luonne / lumen / lapsen / laihan
Huurteen / huoneen / tumman / talven
Lämmöks / lähteen / muuttaa / muodon

Aurin/gon al' / armoa / ammens
Pimeän / pitkän / taival / taivaan
Kuusten / kuiskeen / mättääl / metsän
Jäätyi / jääkär / matkal / marssin
Tutta/vaks tuo / Tuonen / taimen
Puisen / poven / tuvan / tutuks
Pisti / pitkäks / mullan / maille
Ikui/seen iän / vieraaks / vakaaks

Kasvoi / kukka / lemmen / ladun
Laidun / laineen / vehnän / vinhan
Sikis / sieltä / uusi / uurna
Kuurna / kenen / leivän / leveän
Päivän / päätteeks / leivon / lennon
Siivet / siroet / suojaan / surun
Tuiskeen / tuiman / pohjan / pojan
Mieli / milloin / maata / malttais?

-TDL '17