Rogue Scholar Digest January 17, 2024


This is a summary of the Rogue Scholar blog posts published January 10 - January 16, 2024.


Martin Fenner

Front Matter


January 17, 2024

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 = "2024-01-10"
published_until = "2024-01-16"
feature_image = 4
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

Evolutionary Biology goes Asia: the 3rd AsiaEvo Conference
Published January 10, 2024 in GigaBlog
Chris Hunter
The group photo of most of the participants at AsiaEvo 2023. In the beginning GigaScience was at the first AsiaEvo conference, which took place in Shenzhen, China in 2019.

The Papermill Alarm
Published January 10, 2024 in Stories by Adam Day on Medium
Adam Day
There’s this phrase used by some technologists: ‘epistemic security’. Epistemic security has to do with things like the spreading of misinformation on social media. I.e. if we spend enough time on social media reading unreliable information, how does that influence us? That’s a matter of epistemic security. Epistemic security is interesting because if you start a conversation about epistemic security at a party, they don’t invite you back.

Every Rogue Scholar blog post now also available in JATS XML format
Published January 10, 2024 in Front Matter
Martin Fenner
On Monday the Rogue Scholar science blog archive added support for exporting the blog posts in various formats: markdown, ePub, and PDF. Today I am adding another export format: JATS XML, the standard format for scholarly articles. JATS is again automatically generated with the Pandoc universal document converter, with some initial tweaks of the Rogue Scholar metadata.

Type I Error Rates are Not Usually Inflated
Published January 11, 2024 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 article, I offer an alternative view.

The speed (or lack thereof) of science
Published January 11, 2024 in
Björn Brembs
It was my freshman year, 1991. I was enthusiastic to finally be learning about biology, after being forced to waste a year in the German army’s compulsory service at the time. Little did I know that it was the same year a research paper was published that would guide the direction of my career to this day, more than 30 years later. Many of the links in this post will go to old web pages I created while learning about this research.

rOpenSci 2023 Code of Conduct Transparency Report
Published January 12, 2024 in rOpenSci - open tools for open science
Yanina Bellini Saibene, Mark Padgham, Kara Woo
The rOpenSci community is supported by our Code of Conduct with a clear description of unacceptable behaviors,instructions on how to make a report, and information on how reports are handled. We, the Code of Conduct Committee,are responsible for receiving, investigating, deciding, enforcing and reporting on all reports of potentialviolations of our Code.

DIY API with Make and {plumber}
Published January 12, 2024 in Andrew Heiss’s blog
Andrew Heiss
Complete tutorial and code See the full tutorial here. You can also see the tutorial’s code here and the code for the final API here.

Opportunism, helpfulness, disappointment, persistence: the genesis of the Brachiosaurus rib paper
Published January 12, 2024 in Sauropod Vertebra Picture of the Week
Mike Taylor
Just a quick post about the genesis of the Brachiosaurus rib paper (Taylor and Wedel 2023) that I wrote about at the very end of last year. Although this is in some respects a minor paper, I’m fond of it because it fell into place so quickly and easily.

Scholarly journals vs Scholarly Blogs.
Published January 12, 2024 in Henry Rzepa’s Blog
Henry Rzepa
First, a very brief history of scholarly publishing, starting in 1665[1] when scientific journals started to be published by learned societies. This model continued until the 1950s, when commercial publishers such as Pergamon Press started with their USP (unique selling point) of rapid time to publication of ~3 months,[2] compared to typical times for many learned society publishers of 2 years or longer.

Improved PDF-formatted Rogue Scholar blog posts
Published January 12, 2024 in Front Matter
Martin Fenner
On Monday the Rogue Scholar science blog archive launched the export of blog posts in PDF and other formats. Over the last few days I have been busy improving the PDF output, and today I am releasing a new version, available for all the more than 13K science blog posts archived by Rogue Scholar. The PDF is generated using the open source Pandoc universal document converter in combination with the Weasyprint library.

A Decade of FAIR – what happens next? Q&A on FAIR workflows with the Netherlands X-omics Initiative
Published January 13, 2024 in GigaBlog
Scott Edmunds
Marking the 10 th anniversary of the formulation of the FAIR principles, we have one of our GigaBlog Q&A’s with Peter-Bram ’t Hoen, Alain van Gool, Anna Niehues and Casper de Visser from the Netherlands X-omics Initiative and Radboud University Medical Center in Nijmegen, authors of a new paper on publishing FAIR workflows.

R-universe now builds MacOS ARM64 binaries for use on Apple Silicon (aka M1/M2/M3) systems
Published January 14, 2024 in rOpenSci - open tools for open science
Jeroen Ooms
Abstract / TLDR R-universe now provides MacOS arm64 binaries for all R packages.

On Rheumatoid Arthritis and the Things Most People Don’t Know About It
Published January 14, 2024 in Martin Paul Eve
Martin Paul Eve
I have suffered from rheumatoid arthritis (RA) for almost twenty years now, which is almost half my life. If I had known back at the start of my diagnosis what I know now, I do not know for sure that things would be very different, but there was a heck of a lot I did not know. How complex is this disease and the things it does? This complex: “Rheumatoid arthritis” sounds like the sort of disease that old people get that isn’t very serious.

Scopus: caught-out and shirking responsibility
Published January 14, 2024 in A blog by Ross Mounce
Ross Mounce
In December last year, it was widely publicized e.g. in Science magazine [1], that Scopus has been instrumental in legitimizing publication scams whereby authors pay to bypass real scholarly peer review and have their work published on a website that looks like a real scholarly journal but is in fact not a proper journal, merely an impersonation of one.

How to Update a Translation with Babeldown
Published January 16, 2024 in rOpenSci - open tools for open science
Maëlle Salmon
As part of rOpenSci’s multilingual publishing project 1 , we have been developing the babeldown R package, for translating Markdown-based content using the DeepL API.

Starting at
Published January 16, 2024 in Chris Hartgerink
Chris Hartgerink
In October, I shared I started to look for a regular job — last week, I started as a senior software engineer for until end of 2025. In this role, I will be contributing to digital public goods using data for social impact.

Need for Consistent and Uniform Guidelines Regarding the Use and Disclosure of AI-generated Scholarly Content
Published January 16, 2024 in Upstream
Uttkarsha Bhosale, Gayatri Phadke, Anupama Kapadia
As we witness the ever-evolving landscape of technology, we realize that artificial intelligence (AI) is not just a buzzword anymore; it’s a reality that is already leading to transformation in how scholarly research is published and disseminated.

Improving Rogue Scholar metadata conversions
Published January 16, 2024 in Front Matter
Martin Fenner
Last week the Rogue Scholar science blog archive added export of blog post content in various formats (Markdown, ePub, PDF, JATS XML). This week Rogue Scholar is improving the existing metadata export, and adding metadata export in JSON-LD format.

30 Years of Citcom, Ellipsis and Underworld
Published January 16, 2024 in Underworld Geodynamics Community
Louis Moresi
CITCOM is a geodynamics modelling code based on the finite element method that is designed for planetary evolution modelling where large spatial variations and strong non-linearities occur in the material properties.

How has The Carpentries made an impact (on me)
Published January 16, 2024 in Jabberwocky Ecology
Ethan White
What impact did The Carpentries have on me? As a learner, it taught me most of my essential day-to-day computational tools. As an Instructor, it changed how I teach, allowing me to reach more students including those that need help the most. As an organiser, it taught me skills that are essential to collaborating and to managing teams. As a creator, it taught me how to hand off the work to the next leg in the never-ending relay race.

Understanding Misinformation and Science in Societal Debates

Published January 16, 2024 in Leiden Madtrics
Leiden Madtrics
In a new research project, we explore the interaction between misinformation and science on social media during COVID-19. This is part of the new research line on the role of science in societal debates of our Focal Area Engagement & Inclusion. The past years have shown that science can play an important role in societal debates. Science was clearly pivotal in the development of COVID-19 vaccines.

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