Interested in evolution, genetics, statistics, computer science, and their intersection (“bioinformatics”)

Joined October 2019
Excited to announce my first resource publication “Correcting for Bias in Estimates of Watterson’s theta and Tajima's D From Missing Data in Next-Generation Sequencing” out now in Molecular Ecology Resources! Article linked below in short thread 👇
1
4
1
9
1,901
Order of the Sinking Star, the massive puzzle adventure from @Thekla_Inc and @Jonathan_Blow (director of Braid & The Witness) is OUT NOW on Steam, Nintendo Switch 2 and PlayStation 5! 🧩 Get it today: orderofthesinkingstar.com
58
186
54
1,105
1,359,383
Viruses as a whole are referred to here as being a species. I mean species concepts vary but come on…
34
Claus Wilke has a good rebuttal article to Noah’s doomer take: open.substack.com/pub/clausw…
Replying to @Substack
@Noahpinion says the prospect of vibe-coded bioweapons could be the key to persuading the general public to be more concerned about AI risk: "A lot of biologists are skeptical of the idea that even the most superintelligent AI could successfully design a doomsday virus... I urge you not to listen to these biologists." noahpinion.blog/p/two-missin…
1
1
971
Prizes, citations, etc. may have some use in sorting when there’s so much research and they obviously influence who gets jobs but it’s still unfortunate how much some people care about them. The researchers laypeople can name aren’t known for prizes. The work should come first.
I've heard about the litmus test for a great scientist or mathematician (especially from the UK) from Paul Krapivsky: "If a person of perceived eminence wasn't knighted". The titles and prizes create hierarchies of control and influence over you. So, be careful.
1
102
This would be a funny case of pejoration if it became commonplace. Made me think about the fact that genetics was originally the "study of heredity", so one could think "hereditarian" and "geneticist" have the same meaning but to my knowledge they never have.
'Geneticist' is an insult now is it? Insane.
2
85
This is false, scientific consensus refers to majority judgment. E.g. all known bacterial cells have DNA (evidence). The consensus is this is due to common ancestry of all bacteria (judgment). Good sci comm explains the two instead of making assertions as this guy regularly does.
As a scientist, I often see people misunderstand what a “scientific consensus” really means. It’s not a room full of scientists agreeing. It’s years of independent studies all pointing in the same direction. Consensus means consistent evidence, not collective opinion.
1
56
Nick Bailey retweeted
"We all need to attend less to what angers us and far more to our loves. That means not watching CNN or MSNBC or Fox News every night nor scrolling our favorite hate-feeds dunking on those idiots on the other side" - Mering, No Contact, p. 206
"What we see on the left is not merely the inconsistency of the hypocrite but a coherent ideological framework... that justifies discrimination, censorship, and even political violence as moral goods when they are directed at certain sorts of people." - Mering, p. 200
1
3
1
19
4,272
Nick Bailey retweeted
This is well-intentioned but wrong. The vast majority of academics in my field have no social media presence, express zero political views at work, and spend their day trying to understand and cure disease and train others to do so. Their apolitical truth-seeking is not, however, seen as a counter-balance to politicization of academia. It is simply not seen *at all*. The public has no idea who they are, and forms their opinion about academia based on random social media scandals, congressional hearings, or interviews that go viral (usually because the academic being interviews was particularly clueless). The upshot is that it does not take much to change individual perceptions. U Chicago and MIT have shown that people will form strong opinions about which schools are truth seeking based on a handful of symbolic gestures by the president, described in the right language. Better media training and thinking more strategically about visible academic positions would go a long way.
Replying to @Tyler_Menzer
Academics should be aware that their efforts to change public opinion not only failed but backfired, and should now attempt to change public opinion back to believing that they're hunting for truth rather than changing public opinion. Best way to do that is by hunting for truth.
35
41
13
418
66,252
I have a biological update here 😄
1
22
966
Darwin's Origin of Species (1859), Fisher's Genetical Theory of Natural Selection (1930), and Huxley's Modern Synthesis (1942) all do this (screenshots in order). I think Darwin always did it (Gutenberg Project) but Fisher was pushed to for GTNS by a colleague.
Every book has a table of contents, but I’ve only seen two cases where every *chapter* has one. The first is a book on housekeeping, and the second is Churchill’s account of WW2. Go figure.
1
3
563
These companies often document clearly what they mean by their population labels (e.g. spatial and temporal boundaries). “Independent” is relative as all people share a common ancestor and therefore are never totally independent. Also, PCA is sometimes used to make these labels
DNA TESTS The 22-23 & me stuff makes no sense: saying you are 22.7% French, 14% Italian, 7% West Asian, etc. is BS since these categories are not INDEPENDENT. Italians themselves partly West Asian, partly French, etc. This is why we use PCA.
151
Nick Bailey retweeted
postdoc alert 🚨! NIH-funded postdoc in my lab to work on Ancestral Recombination Graphs in space. Please spread the word widely, and please reach out if you're interested! (2-3yr position, start date flexible, pay/benefits good!). details:careers.umich.edu/job_detail…
5
12
1,823
Perhaps a good start on reading would be understanding that “Darwinism” is a vague term comprising multiple ideas (e.g. 5 listed here): darwin200.christs.cam.ac.uk/… and only one (common descent) presents notable problems in the interpretation of Scripture
Replying to @Ligonier
In short, take your time. Do some prayerful reading and research. You might be surprised to find out how weak the case for Darwinism really is.
1
113
Yep and many other high-altitude (even Tibetan specifically) mammals also have mutations in this and EGLN1, such as macaques academic.oup.com/evlett/arti…
Fun fact: snow leopards also have an EPAS1 mutation which helps with living at high altitude. Amazing convergent evolution
5
17
1,426
A little late but how about when Tomoko Ohta DESTROYED adaptationism with FACTS and LOGIC in 1973
In honor of International Women’s Day, name your favorite quote by a woman.
99
I've imaginatively wondered if similar tests could apply to evolutionary DNA/protein LMs. For example, could a model trained on coronavirus genomes/proteomes prior to 2019 predict SARS-CoV-2? @eryney_ok @yun_s_song @pdhsu @ebetica
Demis Hassabis’s “Einstein test” for defining AGI: Train a model on all human knowledge but cut it off at 1911, then see if it can independently discover general relativity (as Einstein did by 1915); if yes, it’s AGI.
2
463
Nick Bailey retweeted
Our work unifies two historically disparate fields: phylogenetics & protein language models (pLMs). Classical phylogenetic models provide a rigorous treatment of time and quantify the effects of mutation & selection, but assume site independence & require aligned sequences. 2/n
2
4
32
3,534
Which AI pro subscription should I get for advanced technical/scientific research?
16%Gemini
34%ChatGPT
40%Claude
10%Grok/other
122 votes • Final results
2
1
6
1,150
I've been trying to put this together and its proving trickier than I thought... lots of publications on these and others, some redundancy, different terms, some qualitative differences...
Has anyone made this for population genetic statistics? This could definitely be done for different homozygosity statistics, heterozygosity, Fst, Gst, Rst, and Qst. Maybe for different measures of nucleotide diversity/divergence and site frequency spectrum tests too.
100