Rogue Scholar Digest December 13, 2023


This is a summary of the Rogue Scholar blog posts published December 6 - December 12, 2023.


Martin Fenner

Front Matter


December 13, 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 = "2023-12-06"
published_until = "2023-12-12"
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

Stochastic parrots, cap and gown edition
Published December 6, 2023 in Chris von Csefalvay
Chris von Csefalvay
It’s not every day that you find out you have climbed the exalted heights of another discipline. My work is pretty interdisciplinary, but it shocked me, too, that I’m apparently holding forth on neoliberalism and the epistemic question in African universities (archive link): Figure 1: Apparently, I’m commenting on neoliberalism in African universities.

Google’s Search Generative Experience (SGE) is now available in 120+ countres. What you need to know
Published December 7, 2023 in Aaron Tay’s Musings about librarianship
Aaron Tay
Note: This is a lightly edited piece of something I wrote for my institution What is Google’s Search Generative Experience (SGE)? In past ResearchRadar pieces, we have discussed about how search engines both general (e.g. Bing Chat, Perplexity) and academic (e.g Elicit, Scite Assistant, Scopus (upcoming)) are integrating search with generative AI (via Large Language Models) using techniques like RAG (Retrieval Augmented

A trip down memory lane: An online departmental connection map from 1989.
Published December 7, 2023 in Henry Rzepa’s Blog
Henry Rzepa
In 2023, we very much take for granted that everyone and pretty much everything is online. But it was not always so and when I came across an old plan indicating how the chemistry department at Imperial College was connected in 1989, I was struck by how much has happened in the 34 years since. Nowadays all the infrastructures needed are effectively “built in” to the building when it is constructed and few are even aware of them.

Documentation, documentation, documentation
Published December 7, 2023 in Front Matter
Martin Fenner
Writing software is more than writing code – good documentation is one essential aspect. A lot of the tools and libraries that make writing documentation easier use markdown as a file format, combined with metadata in yaml format and optionally some additional functionality, e.g. mdx – which combines markdown with jsx for JSX-based projects such as React.

Make-or-buy decisions in research and research software
Published December 7, 2023 in Daniel S. Katz’s blog
Daniel S. Katz
Make-or-buy decisions are common in business and research. They often involve an analysis of the pros and cons of creating something (e.g., a physical item, software, a service) vs. acquiring it from someone else.

How sauropods increased the size of ventral neck muscles
Published December 8, 2023 in Sauropod Vertebra Picture of the Week
Mike Taylor
Last time I promised you exciting news about sauropod neck-muscle mass. Let none say that I do not fulfil covenents. And, as usual, when talking about sauropod neck muscle mass, I’m going to start by talking about bird legs. Look at this flamingo: Ridiculous, right? Those legs are like matchsticks. How can they possibly work.

Brief thoughts on qualitative and quantitative projects
Published December 10, 2023 in Sauropod Vertebra Picture of the Week
Mike Taylor
Back in the first post about our recent paper on bifurcated cervical ribs in apatosaurines, I noted: I’m fond of this one because it’s pleasingly low-tech and traditional.

The journey from Journal “ESI” to FAIR data objects: An eighteen year old (continuing) experiment.
Published December 10, 2023 in Henry Rzepa’s Blog
Henry Rzepa
Around 1996, journals started publishing what became known as “ESI” or electronic supporting information, alongside the articles themselves, as a mechanism for exposing the data associated with the research being reported and exploiting some of the new opportunities offered by the World Wide Web. From the outset, such ESI was expressed as a paginated Acrobat file, with the Web being merely a convenient document delivery mechanism.

Type I Error Rates are Not Usually Inflated
Published December 10, 2023 in Critical Metascience
Mark Rubin
The inflation of Type I error rates is thought to be one of the causes of the replication crisis. Questionable research practices such as p-hacking are thought to inflate Type I error rates above their nominal level, leading to unexpectedly high levels of false positives in the literature and, consequently, unexpectedly low replication rates. In this new article, I offer an alternative view.

No Synths! Use of AI in scientific publications
Published December 10, 2023 in quantixed
Stephen Royle
Bands have been known to declare “No Synths!” on their albums. This statement was a badge of pride indicating that the artists hadn’t used any modern trickery in their recordings. Today, the growing use of artificial intelligence (AI) and large language models (LLMs) in science has created a similar scenario. Advocates argue that these tools improve every aspect of science, including the publication process.

How to create separate bibliographies in a Quarto document
Published December 11, 2023 in Andrew Heiss’s blog
Andrew Heiss
tl;dr If you want to skip the explanation and justification for why you might want separate bibliographies, you can skip down to the example section, or just go see some example files at GitHub. Why use separate bibliographies? In academic articles, it’s common to have a supplemental appendix with extra tables, figures, robustness checks, additional math, proofs, and other details.

Archiving individual science blog posts
Published December 11, 2023 in Front Matter
Martin Fenner
Sometimes we want to preserve a blog post to read or reuse later. There are generic tools for that purpose, including read-it-later apps such as Instapaper or Pocket. For scholarly blog posts, the right place can also be a reference manager, which stores the content and the metadata, especially if a DOI was registered for each blog post. Reference managers can store full-text documents and typically use PDF as the file format.

What I learned from getting bodied by a robot.
Published December 12, 2023 in Chris von Csefalvay
Chris von Csefalvay
Say you’re busing tables and you’re trying to pass someone in a wheelchair. What do you do? Do you say “excuse me” and wait for them to move? Do you say “excuse me” and then try to pass them? Do you just try to pass them? Do you say nothing and just try to pass them? All of these are, actually, pretty legitimate answers. Now, say you’re a robot.

VU Amsterdam supports ResearchEquals
Published December 12, 2023 in Liberate Science
Chris Hartgerink
VU Amsterdam is now a supporting member of ResearchEquals, sustaining and governing the development of modular publishing. VU Amsterdam joins as the third institutional supporter, alongside Tilburg University and KU Leuven. VU Amsterdam supports new research initiatives through their VU Open Access Innovation Fund. They support open, free and fair publishing alternatives set up by and for researchers.

FAIR Data Digest #23
Published December 12, 2023 in FAIR Data Digest
Sven Lieber
Open data of 16.2 million Dutch vehicles that can be used to enrich Wikidata

SC23 WHPC Workshop Paper: OpenGPT-X – Novel Architecture Exploration
Published December 12, 2023 in JSC Accelerating Devices Lab
Chelsea John
The Supercomputing Conference 2023 took place in Denver, Colorado, from November 12th to 17th. For the Women in HPC workshop, we submitted a paper, which focused on benchmarking different accelerators for AI. The paper was accepted and I was invited to hold a lightning talk to show the work, spun off our OpenGPT-X project.

Abschied von Jenny Delasalle: „What will survive of us is love“
Published December 12, 2023 in Open Access Blog Berlin
Maxi Kindling
– English below –Die Nachricht, dass Jenny Delasalle am vergangenen Freitag, den 8. Dezember 2023, nach schwerer Krankheit verstorben ist, haben wir mit großer Betroffenheit gelesen. Für die Open Access Community in Berlin und weit darüber hinaus ist ihr Tod ein großer Verlust.

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