#oldposts — Public Fediverse posts

Part three of my three-part introduction is finally up: What can you expect from my blog and what other services will my blog replace?

https://pygospa.codeberg.page/posts/blogging-since-2001-ish/

#introduction #introductions #blogosphere #boycottbigtech #unplugamazon #unplugmeta #unplugtrump #facebook #googleplus #instagram #wordpresscom #goodreads #trakttv #letterboxd #backloggd #discogs #boardgamegeeks #archive #oldposts

Part three of my three-part introduction is finally up: What can you expect from my blog and what other services will my blog replace?

https://pygospa.codeberg.page/posts/blogging-since-2001-ish/

#introduction #introductions #blogosphere #boycottbigtech #unplugamazon #unplugmeta #unplugtrump #facebook #googleplus #instagram #wordpresscom #goodreads #trakttv #letterboxd #backloggd #discogs #boardgamegeeks #archive #oldposts

Part three of my three-part introduction is finally up: What can you expect from my blog and what other services will my blog replace?

https://pygospa.codeberg.page/posts/blogging-since-2001-ish/

#introduction #introductions #blogosphere #boycottbigtech #unplugamazon #unplugmeta #unplugtrump #facebook #googleplus #instagram #wordpresscom #goodreads #trakttv #letterboxd #backloggd #discogs #boardgamegeeks #archive #oldposts

Part three of my three-part introduction is finally up: What can you expect from my blog and what other services will my blog replace?

https://pygospa.codeberg.page/posts/blogging-since-2001-ish/

#introduction #introductions #blogosphere #boycottbigtech #unplugamazon #unplugmeta #unplugtrump #facebook #googleplus #instagram #wordpresscom #goodreads #trakttv #letterboxd #backloggd #discogs #boardgamegeeks #archive #oldposts

Part three of my three-part introduction is finally up: What can you expect from my blog and what other services will my blog replace?

https://pygospa.codeberg.page/posts/blogging-since-2001-ish/

#introduction #introductions #blogosphere #boycottbigtech #unplugamazon #unplugmeta #unplugtrump #facebook #googleplus #instagram #wordpresscom #goodreads #trakttv #letterboxd #backloggd #discogs #boardgamegeeks #archive #oldposts

@deuxcvsix

Aber wenigstens sind wir in Deutschland jetzt wieder noch ein bisschen mehr Mainstream, so EU-weit betrachtet 😉

Ergebnisse der letzten EU-Wahl nach Fraktionen im EP + #BTW25

Bildquelle: What Europe's electorate wants: full speed towards the abyss
https://researchinpeace.blogspot.com/2024/08/what-europes-electorate-wants-full.html
#OldPosts #NotScience

#FightTheFog #AcademicChatter

Rigorous #PeerReview @ PLoS ONE: reject a paper because the editor cannot manage to get (any) reviews in time.

Related #FunFact: as long as reviews are quick, a paper's and the reviewer's reports quality doesn't matter so much. And not only in PLoS ONE.

Related 2017 post:
https://researchinpeace.blogspot.com/2017/09/one-date-that-is-missing-in-many.html
#OldPosts

@chasewnelson

Have one like that, too, on stock. Only funny on the surface. Haunting when one has to deal with it. Intrinsic problem of #evolution: appearances (phenotypes) change over time. The cause of pheno-geno-incongruence is just an expected, not uncommon legacy of how #species originate.

Pics from Monophyletic species 12/2021
https://researchinpeace.blogspot.com/2021/12/monophyletic-species.html
Disclaimer: #LongRead contains #PhyloNetworks
#OldPosts

The real beauty of #democracy is that every people may get the government they truly deserve 😌 #us2024

Two pics from #OldPosts

Visualising U.S. #GunLegislation and mapping politics, economics, and population (Res.I.P. 2018)
https://researchinpeace.blogspot.com/2018/03/visualising-us-gun-legislation-and.html

Part 4: Gehst schaißen! If it is the will of the sovereign, the voters (Res.I.P. 2017)
https://researchinpeace.blogspot.com/2017/12/part-4-gehst-schaien-if-it-is-will-of.html

And in contrast to certain European countries (and SCOTUS), it'll be over in 2, latest 4 years. Na dann, prost. For another 2/4 years.

#Peerreviewed: "We interpret this #paleoclimate as summer dry and winter wet—a climate analogous to modern day warm #Mediterranean climates in the Köppen‐
Geiger climate classification system" https://doi.org/10.1029/2024PA004874

That'd be Csa. Pic: fig. 4, modern analogs 🤨

Well, thanks to #ClimateChange, they all turn Csa eventually: #OldPosts
Wladimir Köppen – a climate-vegetation genius, and what this has to do with wine
https://researchinpeace.blogspot.com/2018/02/wladimir-koppen-climate-vegetation.html

#palaeoclimate #PeerReview #FightTheFog

@russell

Just wondering...has anyone ever tried a network-thinker approach?

Whenever I ran into people getting stuck with unsolvable phylogenies, I showed them there's more than the usual 1-dimensional stick graphs in phylogenetics and "can't" became a "let's" and, ultimately, "done".

Also great to explore only ambiguous signals.

E.g. #OldPosts
Summarizing non-trivial Bayesian tree samples for dating? Just use support consensus networks
https://phylonetworks.blogspot.com/2018/01/summarizing-non-trivial-bayesian-tree.html

@yassie_j

The longevity of #OldPosts is one of the loveliest features of Fedi culture. On twitter, there was not even a notification if someone replied after 24 hours (or was it 48?). The whole system was set up for moving from hype to hype. Here we can let #conversations develop over long periods, re-enforced by #notifications and #hashtags.

Eight months in, I am still stunned by the beauty of the system.

#MastodonCulture

@dezene

Can't help it, sorry.

The Indo-part of Indomalaya was at the time even further away from Malaya but naturally closer to Australia although not really next to it.

Sophisticated top-down reconstructions look nice and make great graphics.

But whether they make sense might require a bit of a palaeo-perspective, too.

And, thanks to Rob Scotese, really everyone can dive into Earth's past.
#OldPosts https://researchinpeace.blogspot.com/2019/04/the-easter-egg-everyone-can-visually.html

@lzvolk @andrewlhipp

If you fancy references, more artwork and prose, some #OldPosts

All solved a decade ago: the asterisk branch in the Fagales phylogeny—https://phylonetworks.blogspot.com/2018/02/all-solved-decade-ago-asterisk-branch.html

The challenging and puzzling ordinary beech – a (hi)story—https://researchinpeace.blogspot.com/2018/04/the-challenging-and-puzzling-ordinary.html

Can we depict the evolution of highly conserved genes, such as the ribosomal RNA genes?—https://phylonetworks.blogspot.com/2019/02/can-we-depict-evolution-of-highly.html

Just a single, easily overlooked tip—https://researchinpeace.blogspot.com/2022/07/just-single-easily-overlooked-tip.html

@erinnacland @academicchatter

In my fields, it usually means pal- or light-reviewed.

But some (especially high-fly) journals have a strict resubmission policy as soon as the paper is not ready to publish to camouflage the actual time-under-review; an example #oldposts
https://researchinpeace.blogspot.com/2017/09/one-date-that-is-missing-in-many.html

And there's a vast grey-zone between predatory and legit publishing, e.g. some Frontiers in... journals are heavily compromised such as ...Genetics and ...Plant Science.

#FightTheFog-Update to https://ecoevo.social/@grimmiges/110101595898174133

Interesting leap in faith: The same clique of authors putting out a preprint claiming all modern-day Fagales genera are younger than 25-20 Ma pop up in the author list of a study just submitted to a high-tier #phylogeny journal indulging in how only the Fagaceae bunch hybridised already in the Eocene (>40 Ma).

Using the fossil record again, but this time without any palaeobotanist in the author list.

PS #OldPosts
https://researchinpeace.blogspot.com/2022/07/just-single-easily-overlooked-tip.html

How shady has Frontiers in... become?

Well, they now sent out #PeerReview invitations to emails they only could have got from dubious sources.

But one has to applaud their AI to make the connection between the occassional customer and the (formerly professional) scientist of the same name.

Related #OldPosts:
Would you like to have your own edited paper collection?—https://researchinpeace.blogspot.com/2019/10/would-you-like-to-have-your-own-edited.html

Aus aktuellem Anlaß, got a paper on Fagus hayatae (#beech) #phylogeography published 2016 in Ecol. Evol. with potentially interesting data, which is nowhere to be found.

Missing here but should be obligatory following each "Conclusion" section: a section on "Data availability". With a link to the phylogenetic matrix, ideally.

#OldPosts D. Morrison and I and why We want to publish our phylogenetic #data – including networks, but where?—https://phylonetworks.blogspot.com/2018/02/we-want-to-publish-our-phylogenetic.html

It was quite lately that I came to appreciate the information in complete plastomes. They can be fascinating (just brooding over those of beeches and maples). Not with respect to #phylogeny, though, but #evolution and #history.

Time for the #OldPosts triple:

Are complete plastome trees always better? Maples, for instance—https://researchinpeace.blogspot.com/2020/07/are-complete-plastome-trees-always.html

#Oaks systematics and complete plastome trees—https://researchinpeace.blogspot.com/2019/10/oaks-systematics-and-complete-plastome.html

Just a single, easily overlooked tip—https://researchinpeace.blogspot.com/2022/07/just-single-easily-overlooked-tip.html

Resistance is *not* futile!

https://fediscience.org/@erinnacland/109682697200496684

In case you haven't yet, one can still join in fighting the Kraken (aka Elsevier)

http://thecostofknowledge.com/

And in case you have forgotten: Remember the "Coalition of Responsible Sharing"?
I found mail! From Elsevier, and in my Junk folder (where it belongs)—https://researchinpeace.blogspot.com/2018/09/i-found-mail-from-elsevier-and-in-my.html

Also: Elsevier's research data "not available/will be made available on request" – what will be your choice?—https://researchinpeace.blogspot.com/2018/05/elseviers-research-data-not.html
#OldPosts

@deuxcvsix
Der Engländer nennt das "pedigree".

2+ #OldPosts dazu
Family trees, pedigrees and hybridization networks—https://phylonetworks.blogspot.com/2012/11/family-trees-pedigrees-and.html
mit Links zu Darwin und Einstein.

Bei uns Barbaren ist Inzucht eher ein Phänomen der moderne:
The first Royal pedigree—https://phylonetworks.blogspot.com/2014/12/the-first-royal-pedigree.html

#FunFact (Haus-)Katzen zeigen keinen Verlust der genetischen Fitness durch Inzucht. Arte hat da eine nette Kurzfilmserie, Folge 3: https://www.arte.tv/de/videos/RC-017243/stubentiger/

And here's the summarising doodle for the final part 3 of my blogpost miniseries Big Data = No Brain? (to be fixed in the hopefully near future)

A cactus tree metaphor for the reticulate #Phylogeny of #Maples

Already online (#OldPosts)
Pt. 1: Complete plastomes vs. 500 nuclear genes
https://researchinpeace.blogspot.com/2022/01/big-data-no-brain-pt-1-complete.html

Pt. 2: Diggin deeper
https://researchinpeace.blogspot.com/2022/10/big-data-no-brain-pt-2-digging-deeper.html

Because these fellas are my constant companions I'm spending my break going through very old posts from another unnamed platform…. 👀
😂😂

#Comedy #Procrastination #AustralianHistory #AustralianPodcast #OldPosts

This week 4 #OldPosts on what #PhyloNetworks have to offer for #Fossil #Phylogenetics in the context of exploratory data analysis (#EDA)

Summarizing non-trivial Bayesian tree samples for dating? Just use support consensus networks—https://phylonetworks.blogspot.com/2018/01/summarizing-non-trivial-bayesian-tree.html

Large morphomatrices – trivial signal—https://phylonetworks.blogspot.com/2020/02/large-morphomatrices-trivial-signal.html

Should we try to infer trees on tree-unlikely matrices?—https://phylonetworks.blogspot.com/2017/07/should-we-try-to-infer-trees-on.html

More non-treelike data forced into trees: a glimpse into the dinosaurs—https://phylonetworks.blogspot.com/2017/08/more-non-treelike-data-forced-into.html

@Thomashegna Given the problems with this group, jumping clades from analysis to analysis, hard to grasp taxonomically, deep rooting and unique, anyone ever thought of doing exploratory data analysis involving networks (data-display and phylogenetic)?

It may be one of the many groups where one simply faces "Hilgendorf's dilemma" #OldPosts on Geneal. World of Phylog. Networks by D. Morrison 2014

The dilemma of evolutionary networks and Darwinian trees—https://phylonetworks.blogspot.com/2014/01/the-dilemma-of-evolutionary-networks.html
#PhyloNetworks

I am back after dealing with some ongoing computer issues with more #oldPosts

Some images of snowy roads of #iceland

Images were edited in #Darktable and posted originally to Mastodon in 2017. Some has been a bit re-re-edited since.

#artWithOpenSource #photography #landscape #landscapePhotography #creativeToots #editbacklog

@dmayhood #Science-#FunFact: most of the papers using the same approach are. It's sort of an industry standard.

Here's what happens if you request the data (that's the usual line: "Data will be provide upon request)–I "entertained" myself poking the windwills a bit.

#OldPosts: Trying to disperse the Impermeable Fog #2: Editors who "entertain" and are not "answerable"
https://researchinpeace.blogspot.com/2018/02/trying-to-disperse-impermeable-fog-2.html

#OldPosts trilogy time (still working on 3rd pt of my maple phylogenomics post). #Phylogenetics, or #Phylogenomics, is not just blackboxes, give your data a closer look using #Phylonetworks. Ex. in my 2019 "Why the emperor has no clothes on" miniseries
#1: The mighty matK—https://phylonetworks.blogspot.com/2019/10/why-emperor-has-no-clothes-on-mighty.html
#2: A thicket of trees—https://phylonetworks.blogspot.com/2019/11/why-emperor-has-no-clothes-on-thicket.html
#3: Conflict or not?—https://phylonetworks.blogspot.com/2019/11/why-emporer-has-no-clothes-on-conflict.html

last #oldPosts took 2 hours to put together because I couldn't find 2 of the images. I need to urgently reorganize my harddrive because this is how things go on every time a portfolio is needed. /o\

More #oldPosts from #Iceland
1 and 3 are images taken from the road. 2 is a composite image of #northernLights I took as snow was rushing in.

These were photographed in Feb 2017 with my phone camera (LGV10), were edited in #Darktable and posted to Mastodon in 2017 as part of #editBacklog

#artWithOpenSource #photography #landscapePhotography #auroraBorealis #creativeToots #photo

in today's #oldPosts something a bit different. Around 2016 I got briefly interested in the idea of drawing sky objects. Cue in a lot of playing around with #krita

first image is an attempt to draw NGC278 from another angle (based on a hubble image)

Other two are completely fictional.

None of these remotely make sense from a science perspective but they were fun to make. :)

#artWithOpenSource #mastoArt #creativeToots

Original NGC 278 image by ESA/Hubble CC-by: https://bit.ly/2oPJTZD

I don't know why it took me a week to realize that #oldPosts is going to take a LOT longer than 1 week. I can't keep posting 5 image posts a day. it is not sustainable especially with the reflection aspect of the whole thing.

@biodatacore Another example: SARS-CoV-2 virus phylogenies, we have now millions of completely sequence genomes, but most of them are bare of any usable signal; the trick is to filter the patterns that can tell us something, and reduced the tips to a representative set.
Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult
https://doi.org/10.1093/molbev/msaa314
Also #OldPosts: https://phylonetworks.blogspot.com/2020/06/how-i-would-realistically-analyze-sars.html
or
https://researchinpeace.blogspot.com/2020/06/inferring-ml-tree-with-12000-or-more.html

@biodatacore That's easy to answer: Whatever you can get or have.
Then you feed it to Phytia, to see if you need more. Or go beyond simple tree-inference.

In Biology, you'll always have too little data. But any data can tell you something re: #phylogenetics, if analysed properly.
5 mutating patterns may be all you need, pending the question and known background. Ex. #OldPosts https://phylonetworks.blogspot.com/2019/02/can-we-depict-evolution-of-highly.html