Rogue Scholar Digest December 6, 2023


This is a summary of the Rogue Scholar blog posts published November 29 - December 5, 2023.


Martin Fenner

Front Matter


December 6, 2023

import requests
import locale
import re
from typing import Optional
import datetime
from IPython.display import Markdown

locale.setlocale(locale.LC_ALL, "en_US")
baseUrl = ""
published_since = "2023-11-29"
published_until = "2023-12-05"
feature_image = 1
include_fields = "title,authors,published_at,summary,blog_name,blog_slug,doi,url,image"
url = (
    + f"posts?&published_since={published_since}&published_until={published_until}&language=en&sort=published_at&order=asc&per_page=50&include_fields={include_fields}"
response = requests.get(url)
result = response.json()

def get_post(post):
    return post["document"]

def format_post(post):
    doi = post.get("doi", None)
    url = f"[{doi}]({doi})\n<br />" if doi else ""
    title = f"[{post['title']}]({doi})" if doi else f"[{post['title']}]({post['url']})"
    published_at = datetime.datetime.utcfromtimestamp(post["published_at"]).strftime(
        "%B %-d, %Y"
    blog = f"[{post['blog_name']}]({post['blog_slug']})"
    author = ", ".join([f"{x['name']}" for x in post.get("authors", None) or []])
    summary = post["summary"]
    return f"### {title}\n{url}Published {published_at} in {blog}<br />{author}<br />{summary}\n"

posts = [get_post(x) for i, x in enumerate(result["hits"])]
posts_as_string = "\n\n".join([format_post(x) for x in posts])

def doi_from_url(url: str) -> Optional[str]:
    """Return a DOI from a URL"""
    match =
    if match is None:
        return None

images = [x["image"] for x in posts if x.get("image", None) is not None]
image = images[feature_image]
markdown = f"![]({image})\n\n"
markdown += posts_as_string

Introducing rOpenSci Mentors - Cohort 2023-2024
Published November 29, 2023 in rOpenSci - open tools for open science
Apoorv Anand, Bruna Wundervald, Eunseop Kim, Emi Tanaka, François Michonneau, Francisco Cardozo, Erle Holgersen, Marie Vendettuoli, Jonathan Keane, Yanina Bellini Saibene
One important aspect of rOpenSci’s mission is to build capacity and promote passionate community members who help the open science and open source software community grow and improve. The rOpenSci Champions Program is a unique opportunity for us to identify, recognize, and reward such individuals and support them in their work to improve their communities and the wider ecosystem.

The Imperative of Reforming Scientific Publishing
Published November 29, 2023 in Upstream
Moumita Koley, Megha Sud
The International Science Council is a non-government organization that brings together 45 international scientific Unions and Associations, over 140 national and regional scientific organizations, including Academies and Research Councils, 60 international Federations and Societies, and Young Academies and Associations. The ISC is charting a path toward the mission to advance human development within sustainable planetary and

ISC23 Project Poster: SCALABLE: Scalable Lattice-Boltzmann Leaps to Exascale
Published November 29, 2023 in JSC Accelerating Devices Lab
Jayesh Badwaik
At the ISC High Performance Conference 2023 a little while ago, we presented a project poster on the SCALABLE project. The work was also presented as a paper at the the Computing Frontiers 2023 conference previously.

It’s 2023 - why are we still not sharing phylogenies?
Published November 29, 2023 in iPhylo
Roderic Page
A quick note to support a recent Twitter thread The article “Diversification of flowering plants in space and time” by Dimitrov et al. describes a genus-level phylogeny for 14,244 flowering plant genera. This is a major achievement, and yet neither the tree nor the data supporting that tree are readily available.

German funder DFG: Why the sudden inconsistency?
Published November 29, 2023 in
Björn Brembs
The DFG is a very progressive and modern funding agency. More than two years ago, the main German science funding agency signed the “Declaration on Research Assessment” DORA.

Resilience: another advantage of openly-licensed content
Published November 30, 2023 in A blog by Ross Mounce
Ross Mounce
As you may have seen in the news, the British Library has been affected by a significant cyberattack. Many of the digital services it provides have gone down and stayed down for many weeks now, whilst investigations take place. I have a lot of sympathy for the BL staff. As has been observed, public services can be a relatively easy target.

Single-segment neck muscles in diplodocids?
Published November 30, 2023 in Sauropod Vertebra Picture of the Week
Matt Wedel
I don’t remember now when I first noticed bifurcated cervical ribs in apatosaurines. I imagine 2016 at the latest, because on our Sauropocalypse that year Mike and I saw examples at both BYU and Dinosaur Journey.

Scholarly societies: like a cat chasing the laser dot
Published December 1, 2023 in
Björn Brembs
You may have seen a neutered version of this post over at the LSE blog. This post below, however, puts the tiger in the tank, as it was enhanced by CatGPT: Maybe scholarly societies have taken “the instruction”follow the money!” a tad too literally?

How many learned societies publish Diamond Open Access journals?
Published December 1, 2023 in A blog by Ross Mounce
Ross Mounce
To seek an answer to the question posed in the title, I sought out reliable data on open access journals. My first port of call was the Directory of Open Access Journals (DOAJ). Although DOAJ certainly isn’t a complete listing of open access journals, as is well documented in ’The OA Diamond Journals Study‘ (2021), it will at least help provide a minimum bound answer to the question.

Bitter Lessons in Chemistry
Published December 1, 2023 in Corin Wagen
Corin Wagen
“And I took the little scroll from the hand of the angel and ate it. It was sweet as honey in my mouth, but when I had eaten it my stomach was made bitter.” –Revelation 10:10 As machine learning becomes more and more important to chemistry, it’s worth reflecting on Richard Sutton’s 2019 blog post about the “bitter lesson.” In

Prediction vs Accommodation: Which is Better and When?
Published December 4, 2023 in Critical Metascience
Mark Rubin
In a recent article published in Synthese, philosopher of science Pekka Syrjänen asks “does a theory become better confirmed if it fits data that was not used in its construction versus if it was specifically designed to fit the data?”

2023 in review: Gigabyte journal coming of age, and more
Published December 4, 2023 in GigaBlog
Hans Zauner
It’s December, the festive season and the end of  year are approaching fast –  and it’s time for our traditional look back on the past 12 months at GigaScience Press . Once more, we are pleased with the view in the rear mirror.  In its 11th year, GigaScience again published exceptional “big data” science (read on for examples). And GigaScience’s

Divide and Conquer: From polar To the Polarverse
Published December 5, 2023 in rOpenSci - open tools for open science
Juan Pablo Ruiz Nicolini
“I’m just a political scientist, standing in front of the R console asking it to help me finish my thesis.” It was 2015, a Political Science master’s student had to process data to hand in his thesis and decided to take the opportunity to learn how to use R. To the long and winding road of the academic requirement was added an extra degree of difficulty: incorporating programming software from scratch, with a somewhat steep learning

INFORMATE: Where Are the Data?
Published December 5, 2023 in Upstream
Ted Habermann, Jamaica Jones, Howard Ratner, Tara Packer
Introduction A recent blog post described a new partnership between Metadata Game Changers and CHORUS aimed at understanding how CHORUS data can help federal agencies, other funders, and other users access and use information from the global research infrastructure to measure this infrastructure and understand connections between research objects.

Yellow Rattle
Published December 5, 2023 in Irish Plants
Jake Dalzell
This is an adapted version of my poster, which is also available as a pdf or png. As with all my work on this site it is CC BY 4.0 (free for use/adaptation as long as I am credited). The Meadow Maker Yellow Rattle ( Rhinanthus minor ) has become well known in restoration ecology and wildlife gardening as a “meadow maker”, which can transform a species-poor patch of grasses into a biodiverse and flower-rich one.

Poster: GEMMERATOR – GEMM Kernel Generator
Published December 5, 2023 in JSC Accelerating Devices Lab
Stepan Nassyr
Poster in institute repository: During the RISC-V Summit Europe 2023 in Barcelona we presented our work generating highly optimized RISC-V and ARM GEMM microkernels for BLIS using a custom software tool. 1 We presented results on the Fujitsu A64FX processor, the in-development RISC-V VEC processor from the EUPILOT project using an

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