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Tim Howes

@timhowes.bsky.social

computational biologist and data scientist San Francisco Bay Area biology, evolution, statistics, open source software

4 Posts441 Follower 939 Folgt

Ellen Leffler @ellenleffler.bsky.social · 2mo ago

Job opening: I'm looking for a lab tech primarily supporting ongoing projects and running computational analyses for the lab. Apply here and reach out with questions! utah.peopleadmin.com/postings/205...

Nicole 🪲@fossilforager.bsky.social · 4mo ago

Baleen whales!!! 🐋

Dr. Solomon David @solomonrdavid.bsky.social · 4mo ago

Please enjoy baby Alligator Gars feeding on brine shrimp (Artemia), set to a Bluey instrumental 🙂 🐟🧪gars are planktivorous at this stage (20 mm, 12 days post-hatch), but will soon switch to eating insects and fish! They’re also already breathing air!

Jocelyn Anderson Photography @jocelynanderson.bsky.social · 4mo ago

A pair of Sandhill Crane colts play while staying warm and cozy under their mom's wings.

Jocelyn Anderson Photography @jocelynanderson.bsky.social · 4mo ago

This Sandhill Crane colt still has the whitish egg tooth on the tip of the beak. They use this pointy bit to help break free from their egg shell. The egg tooth is temporary and will fall off within two weeks. Photo is heavily cropped.

Katie O'Reilly @drkatfish.bsky.social · 5mo ago

You don't only have to look up to be in awe of the moon(fish)! www.kpbs.org/news/2015/05...

First In Fish: 'Fully Warm-Blooded' Moonfish Prowls The Deep Seas

"It's hard to stay warm when you're surrounded by cold water but the opah has figured it out," a NOAA Fisheries biologist says.

kpbs.org

Stephen Wild @stephenjwild.bsky.social · 5mo ago

Time for this again

A meme with two panels. In panel 1 the woman looks disgusted. In panel 2 intrigued.

Text, panel 1: fake data.

Text, panel 2: silicon sample

Opinion Today@opiniontoday.bsky.social · 5mo ago

It’s Called Silicon Sampling, and It’s Going to Ruin Public Opinion Polling: Pure fictions are on the brink of being treated as scientific and political knowledge. (@leifw.bsky.social and @beenwrekt.bsky.social, The New York Times-unlocked) www.nytimes.com/2026/04/06/o...

でんか @k-hermit.com · 8mo ago

This bobtail squid burrowing into the sand is already adorable, but please watch till the very end! It sticks out its little arms and earnestly sprinkles sand over itself 🦑𓂃◌𓈒𓐍

Daryll Marie @daryllmarie.bsky.social · 10mo ago

And one more, there was an iguana party on Key West this morning 🦎🌿

An iguana’s upper body photographed up close. Behind it, a blurred second iguana can be seen

Nicole 🪲@fossilforager.bsky.social · 12mo ago

gartastic

An illustration of two alligator gar on a teal background. The fish have a long alligator-like snout and are covered in armored scales. The fish are greenish-brown and have some speckled darker spots and markings on their fins and back.

でんか @k-hermit.com · 12mo ago

Thiago Carvalho @cyrilpedia.bsky.social · 12mo ago

'We hypothesized that cDC suppression in PDAC may further impair tumor immunity. We found that low tissue expression of Flt3L partially underlies cDC deficits. Treatment with systemic Flt3L & CD40 agonists restored cDC number & function in murine models & clinical trial samples from PDAC patients'

Combined Flt3L and CD40 agonism restores dendritic cell–driven T cell immunity in pancreatic cancer

Flt3L and CD40 agonism enhance dendritic cell immunosurveillance in human and murine pancreatic cancer and engage type I immunity.

science.org

Julia M. Rohrer @dingdingpeng.the100.ci · last yr.

Ever stared at a table of regression coefficients & wondered what you're doing with your life? Very excited to share this gentle introduction to another way of making sense of statistical models (w @vincentab.bsky.social) Preprint: doi.org/10.31234/osf... Website: j-rohrer.github.io/marginal-psy...

Models as Prediction Machines: How to Convert Confusing Coefficients into Clear Quantities

Abstract
Psychological researchers usually make sense of regression models by interpreting coefficient estimates directly. This works well enough for simple linear models, but is more challenging for more complex models with, for example, categorical variables, interactions, non-linearities, and hierarchical structures. Here, we introduce an alternative approach to making sense of statistical models. The central idea is to abstract away from the mechanics of estimation, and to treat models as “counterfactual prediction machines,” which are subsequently queried to estimate quantities and conduct tests that matter substantively. This workflow is model-agnostic; it can be applied in a consistent fashion to draw causal or descriptive inference from a wide range of models. We illustrate how to implement this workflow with the marginaleffects package, which supports over 100 different classes of models in R and Python, and present two worked examples. These examples show how the workflow can be applied across designs (e.g., observational study, randomized experiment) to answer different research questions (e.g., associations, causal effects, effect heterogeneity) while facing various challenges (e.g., controlling for confounders in a flexible manner, modelling ordinal outcomes, and interpreting non-linear models).

Figure illustrating model predictions. On the X-axis the predictor, annual gross income in Euro. On the Y-axis the outcome, predicted life satisfaction. A solid line marks the curve of predictions on which individual data points are marked as model-implied outcomes at incomes of interest. Comparing two such predictions gives us a comparison. We can also fit a tangent to the line of predictions, which illustrates the slope at any given point of the curve.

A figure illustrating various ways to include age as a predictor in a model. On the x-axis age (predictor), on the y-axis the outcome (model-implied importance of friends, including confidence intervals).

Illustrated are
1. age as a categorical predictor, resultings in the predictions bouncing around a lot with wide confidence intervals
2. age as a linear predictor, which forces a straight line through the data points that has a very tight confidence band and
3. age splines, which lies somewhere in between as it smoothly follows the data but has more uncertainty than the straight line.

__Alex Monahan__@a13x.bsky.social · last yr.

DuckDB may have an adorable mascot, but this is serious DB tech! As a larger-than-memory system, data durability is critical!

v@avi.im · last yr.

I went through DuckDB's WAL, and it does everything I was asking for in my blog post: 1. Per record checksum 2. Explicit error on checksum failure 3. Configurable behavior 4. Partial recovery 5. Safe truncation of the WAL only when WAL contents are checkpointed

The Conversation U.S.@us.theconversation.com · last yr.

Where first graders watch educational media, before the impact of eliminating federal funds: * PBS - 45% * Nickelodeon - 14% * YouTube - 9% (from a 2025 study by child development researchers)

PBS accounts for nearly half of first graders’ most frequently watched educational TV and video programs

PBS KIDS produces popular age-appropriate programs. It also has a website and multiple apps with games and activities.

buff.ly

Julia Silge @juliasilge.com · last yr.

I'm excited to speak this afternoon at #useR2025 on outgrowing your laptop with #Positron for #rstats users! You can check out my slides at juliasilge.github.io/useR-2025/

Galaxy brain meme format outlining options for working with data: CSV file, parquet & duckdb, databases, and remote SSH sessions

Robert Boessenecker, Dr. of Whaleontology ™️@coastalpaleo.bsky.social · last yr.

A couple of giant green anemones (Anthopleura xanthogrammica) in a Santa Cruz #tidepool, dwarfing a field of their smaller relative, aggregating anemones (Anthopleura elegantissima). 🦑🦀 #norcal

Two giant green anemones in a tidepool: they are large and circular with an olive green stalk and bright lime green tentacles fading to a more khaki color.

David Shiffman, Ph.D. 🦈@whysharksmatter.bsky.social · last yr.

Glow-in-the-dark marsupial shows off its luminous fur — July’s best science images

The month’s sharpest science shots, selected by Nature’s photo team.

nature.com

Gary Shteyngart @shteyngart.bsky.social · last yr.

Had a great time on @KQED Forum. www.kqed.org/forum/201010...

In Gary Shteyngart’s “Vera, or Faith,” A Child Navigates Family, American Dystopia | KQED

We talk to writer Gary Shteyngart about the future and families.

kqed.org

Eiko Fried @eikofried.bsky.social · last yr.

Psychologists & related fields: what is a big methods question that you believe remains somewhat unanswered & that you'd love to see adressed? There may be an opportunity for a large-scale meta-science project with many teams trying to figure out a question. Any thoughts welcome! #psychscisky

Daniel Bolnick @danielbolnick.bsky.social · last yr.

Many attendees arrived by the Lady Rose Ferry on Sunday, sailing three and a half hours down the Alberni inlet fiord. Here’s the ferry arriving at Bamfield…

Max kuhn @topepo.bsky.social · last yr.

Positron is definitely visually more than RStudio, and this is a helpful overview.

Posit@posit.co · last yr.

Take a quick tour of Positron, Posit's next-generation data science IDE, built by the creators of RStudio. Read the blog to learn more: posit.co/blog/a-quick...

A screenshot of the Positron interface, labeled with its components: "Activity bar," "Primary side bar," "Editor," "Secondary side bar," and "Panel." The text "A quick tour of Positron" is on the left.

Vincent Arel-Bundock @vincentab.bsky.social · last yr.

"My First R Package" Next week I’ll be giving a hands-on workshop on #RStats We'll start from scratch and build our very own 📦 Re-use go-to functions, boost reproducibility, and share code with colleagues. I always a blast teaching this and am excited to meet the new group! tinyurl.com/mv2hrd8n

Julia M. Rohrer @dingdingpeng.the100.ci · last yr.

At this point, I might as well -- Here's an infographic showing different ways to include age as a predictor. The top shows two extremes, just as a plain old numerical predictor (imposes linear trajectory) vs. categorical predictor (imposes nothing whatsoever). And then three solutions in between!

Infographic illustrating different ways to model age.
First panel shows two "extreme" cases; including age as a linear numerical predictor (df = 1) or including age as a categorical predictor (df = number of years of age minus 1).
Second panel shows an intermediate solution in which age is categorized into broader bins (df = number of categories minus 1, here 5 - 1 = 4).
Third panel shows an intermediate solution in which age is included with a polynomial (df = degrees of freedom of the polynomial, here 4).
Fourth panel shows an intermediate solution in which age is modeled with the help of splines (df = degrees of freedom of the splines, here 4).

Andrew Mercer@awmercer.bsky.social · last yr.

Maybe use the same number of bins as you have knots in the spline? That’d make it easier to compare the two.

Nicole 🪲@fossilforager.bsky.social · last yr.

A lil tribute to the kelp forests along the California coast 🌊✨

An illustration featuring a leopard shark, bat ray, and the California state marine fish: the garibaldi. They are swimming next to giant kelp and illustrated on a vibrant blue background.

Nicole 🪲@fossilforager.bsky.social · last yr.

I just think sea slugs are neat 💕

A graphic-style illustration of 3 sea slugs (known as nudibranchs). Dark blue bold rounded text below the slugs reads “Nudibranch Admirer”. The slugs are vibrantly colored with hues of blue, yellow, orange, and purple and are illustrated on a saturated light blue background.

nina matsumoto 🌸@spacecoyote.com · last yr.

sometimes Louie will babble nonsense that vaguely sounds like @bobservo.bsky.social

David Shiffman, Ph.D. 🦈@whysharksmatter.bsky.social · last yr.

Anglerfish ancestors once roamed the seafloor. Here's how we know : Short Wave : NPR

Think anglerfish are weird? Wait until you hear how they evolved : Short Wave

There are over 200 species of deep-sea anglerfish; some are long and thin, some are squat and round, some have fins that they use to "walk" along the sea floor, and others have huge eyes set far back…

npr.org

Rosemary Mosco @rosemarymosco.com · last yr.

All proceeds from my @topa.to store in June go to the Institute for Bird Populations, @instbirdpop.bsky.social! Times are tough for nonprofits, and monitoring bird populations is more important than ever. Show your support with a tasteful print or tasteless mug. topatoco.com/collections/...

The super-talented artist and author Rosemary Mosco is donating proceeds from her shop in the month of June to IPB! There's an image of a poster of female North American birds, a yellow warbler tshirt, and a mug that says Mornings Can Kiss My Cloaca.

Jocelyn Anderson Photography @jocelynanderson.bsky.social · last yr.

A male Baltimore Oriole flying towards his next tree top to perch and sing his clear and sweet song.