iiinova — where your digital self keeps evolving

Wayne Maddison @waynemaddison.bsky.social · 26/09/2026

The first thing the blue pill would do is to make you think you've taken the red pill.

Reposted by Wayne Maddison

Rodrigo Monjaraz Ruedas @monroderik.bsky.social · 09/09/2026

New Postdoc opportunity to join my lab @nhm.org working with Phylogenomics of Soft Spiders (Fam. Cybaeidae) in collaboration with @mhedin.bsky.social, help me spread the word! workforcenow.adp.com/mascsr/defau...

workforcenow.adp.com

Recruitment

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Wayne Maddison @waynemaddison.bsky.social · 09/09/2026

The Tree of Life web project is back! A phylogenetic view of biodiversity way ahead of its time (ca. 1995!), conceived and led by David Maddison, collaborative & human-curated, widely used in teaching. Defunct technology had doomed it until Travis, Danny, and Andrew revived it. 🥳🎉 🧪 #evolbiol

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Wayne Maddison @waynemaddison.bsky.social · 18/07/2026

An important and beautiful paper on the central role of natural history in ecology and evolutionary biology.

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Reposted by Wayne Maddison

American Naturaliﬆ / ASN 🐌 @asn-amnat.bsky.social · 14/07/2026

Historical Perspective: Sridhar et al. use the backstories of famous scientific papers in Ecology and Evolution to uncover the background roles of natural history that are written out of papers. Available now ahead of print! www.journals.uchicago.edu/doi/10.1086/...

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Wayne Maddison @waynemaddison.bsky.social · 02/07/2026

What is the current maximum capacity of your iPhone battery? (Settings > Battery > Battery Health > Maximum Capacity) 1️⃣ 79% 2️⃣ 80% 3️⃣ 81% 4️⃣ other 📊 Show results

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Wayne Maddison @waynemaddison.bsky.social · 02/07/2026

Am I the only one whose iPhone battery's measured Maximum Capacity has been stuck at 81% for months, even though it seems to be declining? Interesting that Apple judges the batteries to be worthy of warranty/AppleCare replacement when their capacity drops below 80%... 🤔

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Wayne Maddison @waynemaddison.bsky.social · 03/03/2026

Anyone else printing hard copies of their papers, so they can be found in the rubble after the collapse of civilization?

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Wayne Maddison @waynemaddison.bsky.social · 14/02/2026

An old quip: "All stories you read in the newspaper are completely true except those for which you have first-hand information." This has many corollaries, e.g. "All clades are purely diverging, without introgression, except for those for which you have the pertinent data." 🧪 #evolbio

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Wayne Maddison @waynemaddison.bsky.social · 03/11/2025

The end of an era: the Tree of Life Web Project is going dark after 3 decades. Anyone interested in communicating phylogeny online should read David's account of goals, history, and future. @bembidion.bsky.social subulatepalpomere.com/2025/11/02/t...

subulatepalpomere.com

The Passing of the Tree of Life Web Project

The Tree of Life Web Project began its journey almost 40 years ago, and was formally announced in early 1996. It has served thousands of pages of information about the evolutionary tree of life and…

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Wayne Maddison @waynemaddison.bsky.social · 30/10/2025

Have any of you played the ZoL adventure game in Mesquite 4.02? (It's pretty short in its current version.) We'd welcome feedback about it as a game for students learning phylogeny.

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Wayne Maddison @waynemaddison.bsky.social · 29/10/2025

Does Mesquite's phylogenetic adventure game look familiar to anyone? 🧪 #evolbio

Screenshot of Mesquite's log window, saying:
"ZoL: The Great Phylogenetic Adventure!
Level 1

You are standing in an open field.
In front of you, to your surprise, is an organism.
You recognize that it is a Kelp (Ochrophyta).

There is a small mailbox here."

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Wayne Maddison @waynemaddison.bsky.social · 28/10/2025

The scoop: To get to Mesquite's adventure game, type "ZoL" into the log window. You will find yourself in an open field with a mailbox. 📬 (If that does nothing, then you'll need to turn on "Use Log Window for Command" under File>Defaults>.)

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Wayne Maddison @waynemaddison.bsky.social · 28/10/2025

👀 Mesquite's adventure game has been discovered by @josephwb.bsky.social! BTW, for those of you teaching phylogeny of all life or a particular group of organisms, the adventure game is designed for students to test their knowledge of relationships. (Yes, we'll reveal how to access the game!)

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Wayne Maddison @waynemaddison.bsky.social · 25/10/2025

Has anyone taken up the challenge of finding the adventure game in Mesquite? 🔍

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Wayne Maddison @waynemaddison.bsky.social · 25/10/2025

Mesquite 4.02 update released! It fixes a few bugs and adds Codon Alignment and various other improvements. Also, much faster with genomics files with 1000s of loci. www.mesquiteproject.org 🧪 #evolbio @bembidion.bsky.social

Mesquite's two icons, one against a black background, and one against a sun on a sky blue background.

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Reposted by Wayne Maddison

Prof Sam Illingworth @samillingworth.com · 08/09/2025

🌳 Losing touch with nature A new study finds people’s connection to nature has fallen 60% since 1800, risking an 'extinction of experience' without radical change. 🔗 www.theguardian.com/environment/... #SciComm 🧪 #Nature

theguardian.com

Human connection to nature has declined 60% in 200 years, study finds

Prof Miles Richardson says people risk ‘extinction of experience’ in the natural world without new policies

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Wayne Maddison @waynemaddison.bsky.social · 05/09/2025

Confused writing is usually a symptom of confused thinking. As we struggle to clarify writing, we clarify our thoughts. AI writing aids rob us of that struggle, leaving clean-looking text and thoughts still confused for lack of inspection. Writing is not just a product; it is a diagnostic tool.

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Wayne Maddison @waynemaddison.bsky.social · 05/09/2025

The fifth law of thermodynamics is that in a closed system, bureaucracy will always increase over time. There remains the possibility that this is merely a specific instance of the second law, with bureaucracy = entropy.

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Reposted by Wayne Maddison

Steph @observingangel.bsky.social · 06/08/2025

At this juncture in the research pertaining to COVID infection & Long COVID, people really should understand that COVID sets fire to their bodies in a multitude of ways, that death is NOT the only outcome to be concerned about, & that death can still follow COVID infection.

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Reposted by Wayne Maddison

Joey Bernhardt @joeybernhardt.bsky.social · 14/08/2025

Please help us spread the word! Please amplify! We are searching for an associate or full professor (Canada Excellence Research Chair) in Biodiversity Genomics at the University of Guelph! 🐟🌿🦠🐜🐸🐝 Applications are due October 6 2025. careers.uoguelph.ca/job/Guelph-C... #AcademicJobs #EvoBio

careers.uoguelph.ca

Canada Excellence Research Chair in Biodiversity Genomics

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Reposted by Wayne Maddison

Hannah Shelley, MLIS (Maggots, Lycanthropes & Ice Skeletons) @hannahshelley.site · 13/08/2025

Since search is dead, how soon do you think Google Scholar is headed for the Google Graveyard? I'm betting it's soon, and academia is NOT prepared

hannahshelley.neocities.org

Google Scholar Is Doomed

Academia built entire careers on a free Google service with zero guarantees. What could go wrong?

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Reposted by Wayne Maddison

Oregon State University Botany and Plant Pathology @osubpp.bsky.social · 06/08/2025

The Department of Botany and Plant Pathology at Oregon State University is Hiring! We are searching for a Director of the Oregon State University Herbarium and applications are welcomed at the ranks of assistant, associate, or full professor.

Department of Botany and Plant Pathology at Oregon State University is hiring a Directory of the Herbarium

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Reposted by Wayne Maddison

Christopher Dick @chrisdick.bsky.social · 09/07/2025

Herbarium director position opening at Oregon State University ‪@osu-herbarium.bsky.social‬ Great opportunity for herbarium- and field-trained botanists at any rank. bpp.oregonstate.edu/bpp/about/op...

bpp.oregonstate.edu

Open Positions

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Reposted by Wayne Maddison

David Maddison @bembidion.bsky.social · 01/07/2025

A stained-glass piece of mine from a few years ago. #Canada

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Wayne Maddison @waynemaddison.bsky.social · 17/07/2025

Phylogenomics processing of locus-by-locus files with inconsistent taxon names in Mesquite 4, a short video (3 minutes). youtu.be/YdSWQMkW92k (Channel: bit.ly/4eM2SLZ) 🧪 #evolbio @bembidion.bsky.social

youtu.be

Processing of locus-by-locus files with inconsistent taxon names in Mesquite 4

YouTube video by Mesquite ProjectTeam

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Wayne Maddison @waynemaddison.bsky.social · 15/07/2025

Reading and viewing tree files output by different programs in Mesquite 4, a short video (3 minutes). youtu.be/MVk4aira8A8 (Channel: bit.ly/4eM2SLZ) 🧪 #evolbio @bembidion.bsky.social

youtu.be

Reading files with different tree dialects in Mesquite 4

YouTube video by Mesquite ProjectTeam

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Reposted by Wayne Maddison

David Maddison @bembidion.bsky.social · 10/07/2025

A two-minute video showing how to export geographic localities and trees from Mesquite 4 into Google Earth. youtu.be/tdOVmR122ts 🧪 #evolbio

youtu.be

Exporting to Google Earth

YouTube video by Mesquite ProjectTeam

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Reposted by Wayne Maddison

Benoit Nabholz @benoitevol.bsky.social · 10/07/2025

Junior Professor Chair at MNHN Paris : Integrative Taxonomy for Describing Biological Diversity odyssee.enseignementsup-recherche.gouv.fr/procedures/r... filesender.renater.fr?s=download&t...

odyssee.enseignementsup-recherche.gouv.fr

Odyssée

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Wayne Maddison @waynemaddison.bsky.social · 10/07/2025

Update! — Mesquite 4.01 released, fixing a few small and one substantive bug (for details see response post). New: NINJA (for neighbour joining), new merge taxa options, node spots, Google Earth mapping. www.mesquiteproject.org 🧪 #evolbio @bembidion.bsky.social

Two versions of the Mesquite icon. At left is a Mesquite tree leaf against a black background. At right is leaf against a blue sky and sun.

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Wayne Maddison @waynemaddison.bsky.social · 08/07/2025

Naiveté: Hoping people will follow your polite recommendation when defining a standard. When we defined the NEXUS file format in 1997, we considered DATA blocks to be already archaic, and recommended strongly against them. 38 years later, prominent programs still depend on them. 🤦‍ 🧪 #evolbio

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Reposted by Wayne Maddison

David Maddison @bembidion.bsky.social · 28/06/2025

A short video with a Mesquite tip showing how to display chronograms from a BEAST divergence dating analysis. youtu.be/CvxX8GauqLo 🧪 #evolbio @waynemaddison.bsky.social

youtu.be

Displaying Chronograms in Mesquite 4

YouTube video by Mesquite ProjectTeam

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Wayne Maddison @waynemaddison.bsky.social · 28/06/2025

Mesquite 4.0 released! A major update — many new features, small and large (phylogenomics, visualizations, workflow management, &c). Check out the trailer video: www.mesquiteproject.org. Come discuss in our new Google Group (groups.google.com/g/mesquite-project). @bembidion.bsky.social ‬🧪 #evolbio

The two Mesquite logos. At left, a mesquite tree leaf is against a black background. At right, a leaf is against a blue sky and sun.

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Wayne Maddison @waynemaddison.bsky.social · 08/06/2025

Mesquite 4.beta2 released! Much faster reading of files with thousands of matrices. New features since 4.beta include Trace All Changes (known from MacClade) and Import GenBank Numbers. www.mesquiteproject.org & discuss at groups.google.com/g/mesquite-p... ‪@bembidion.bsky.social ‬🧪 #evolbio

Two icons of the Mesquite program, with leaves of the mesquite tree against a black background (first icon) and against the blue sky and sun (second icon).

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Wayne Maddison @waynemaddison.bsky.social · 31/05/2025

As expected, there was more to do than expected.

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Wayne Maddison @waynemaddison.bsky.social · 29/05/2025

Spider taxonomy refreshes my soul. After being distracted by other things for months, I joyfully got back to drawing spider genitalia. Here are this week's drawings. Mostly Habronattus, with one Pellenes. 🧪🐡

Scans of 31 pencil and ink drawings of the male palps and female epigynes of Habronattus and Pellenes jumping spiders.

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Wayne Maddison @waynemaddison.bsky.social · 24/05/2025

If you've programmed anything complex, you've probably suffered nasty bugs that seemed baffling and took many days to solve. Just solved one -- the frequent StackOverflowErrors in Linux graphics in Mesquite. Not our bug, but Java's, but even still, we are left to find the workaround. 🧵

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Wayne Maddison @waynemaddison.bsky.social · 23/05/2025

Mesquite 4 beta released! Many new features, esp. phylogenomic. Check out the trailer and longer video on the home page: www.mesquiteproject.org, and use the download link there to get a copy. Feedback welcome! Ask and discuss on our new Google Group (groups.google.com/g/mesquite-p...).

The Mesquite icon shown, as a Mesquite leaf against a black background, and as a leave against the sun and a blue sky.

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Reposted by Wayne Maddison

McSweeney's @mcsweeneys.net · 11/05/2025

The question isn’t whether people like my daughter have something to offer. It’s whether society is finally ready to stop measuring value with the wrong scale. Autism doesn’t destroy families. Ignorance does. Isolation does. Shame does.

buff.ly

An Open Letter to Robert F. Kennedy Jr., Who Thinks My Daughter is a Tragedy

Dear Mr. RFK Jr., (The “dear” is tradition. Don’t mistake it for affection.) You said autistic children are a burden. That they ruin families. That...

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Wayne Maddison @waynemaddison.bsky.social · 24/03/2025

Why is it that we use as our default length of time for a meeting in the 21st century a unit of time invented a couple thousand years ago?

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Reposted by Wayne Maddison

Aaron Sojourner @aaronsojourner.org · 17/03/2025

Leadership from UC Berkeley. "...we see recent actions going beyond those purposes in ways that threaten core values: academic freedom, freedom of inquiry, & freedom of expression.... we will be steadfast and unrelenting in our efforts to defend those core values."

Like many of you, we are gravely concerned about recent Federal government actions in regard to higher education. While we recognize that the government plays an important role in addressing discrimination and ensuring good stewardship of public resources, we see recent actions going beyond those purposes in ways that threaten core values: academic freedom, freedom of inquiry, and freedom of expression. We do not know what demands the Federal government may make of Berkeley, but do know that we will be steadfast and unrelenting in our efforts to defend those core values. A Berkeley without academic freedom, without freedom of inquiry, without freedom of expression is simply not Berkeley.

We recognize that some of you may find our statement too timid or too bold or deficient in some other way. That’s okay—a key to Berkeley’s excellence is our diversity of opinion and perspective. Robust debate is essential to scholarly advance. The purpose of a university is not to present us with ideas with which we are comfortable. To borrow from Clark Kerr, it is to make us safe for ideas.

We don’t know what will happen. In part because we don’t know what may be demanded of us and in part because we won’t be the only decision makers. But what we do know is that we will stand up for Berkeley’s values and defend them to the very best of our ability. For 157 years, through the education it provides and the research it produces, Berkeley has produced immense economic and societal benefit to its students, California, the nation, and the world; this societal jewel needs to be preserved and defended, and we will toil tirelessly to see that it is.

Fiat Lux.

Rich Lyons

Chancellor

Ben Hermalin

Executive Vice Chancellor & Provost

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Wayne Maddison @waynemaddison.bsky.social · 12/03/2025

If AI invents something, is it unpatentable because it is necessarily based on prior art?

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Reposted by Wayne Maddison

David Noll @david.noll.org · 08/03/2025

Pro-tip for university administrators: when the government illegally cancels your grants, your first response shouldn't be "you kind of have a point."

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