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Yogi Jaeger 💙 @yoginho@spore.social Profile picture
@yoginho
Jul 11, 2019 • 5 tweets • 2 min read • Read on X
Networks & evolution, pt 2: Eric Bapteste. Network thinking to expand our scope of evolutionary explanations. #ISHPSSB19
Eric Bapteste: microbial evolution – complex communities with irreversible metabolic dependencies and widespread lateral gene transfer indicated reticulate patterns of mosaic evolution. #ISHPSSB19
Eric Bapteste: host-microbe interactions also follow reticulate evolutionary patterns. #ISHPSSB19
Tree- and network-based explanations address different questions – genealogical versus systemic perspectives. Trees focus on relatedness, networks on organisation. #ISHPSSB19
What would be a practical approach to inferring interlinked patterns of evolutionary processes? Eric Bapteste suggests comparative analysis of interaction patterns in evolving networks. #ISHPSSB19

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More from @yoginho

Yogi Jaeger 💙 @yoginho@spore.social Profile picture
May 30
@balazskegl @drmichaellevin @ThouArtThat I don't know what @drmichaellevin posted above since he blocked me. But just to make sure: we are *not* part of the same family. And the differences between our philosophies are fundamental, not "minuscule." Neither is @drmichaellevin a revolutionary. Indeed, he is a reactionary.
@balazskegl @drmichaellevin @ThouArtThat I explain why @drmichaellevin's "philosophy" is vacuous, just a PR stunt, here: . TAME is an attempt at disguising that his approach is, in fact, utterly reductionist, the culmination of modernist thinking, not the beginning of a metamodern science.johannesjaeger.eu/blog/why-tame-…
@balazskegl @drmichaellevin @ThouArtThat That's one difference between his work and that of @ThouArtThat and I, who are trying to do serious work, based on solid philosophy, which is aimed at *understanding* the world and our place in it, not to control and manipulate (i.e. engineer) everything.
Read 9 tweets
Yogi Jaeger 💙 @yoginho@spore.social Profile picture
Jan 22
I traveled to Paris to give my philosophy crash course for scientists () to a wonderful group of @lpiparis_ @FIREPhD students, as I do every year.

Contact me if you want to bring this course to your own institute! It's not only fun, but also useful...johannesjaeger.eu/philosophy.html
... allowing you to become a better researcher through philosophy. The course has an interactive, discussion-based format that is based on an online series of lecture which are freely available: .
It helps you reflect on your own scientific practice and world view using a (1) process-based, (2) perspectival-realist, and (3) deliberative approach to the philosophy of science. The course heavily focuses on students' own experiences, practices, and questions.
Read 4 tweets
Yogi Jaeger 💙 @yoginho@spore.social Profile picture
Oct 10, 2023
New blog post just dropped!

"Assembly theory is cool... but doesn't quite do what its inventors say it does."



reviewing this recent Nature paper:



TL:DR: potentially interesting model, wrapped in utterly misleading packaging.johannesjaeger.eu/blog/assembly-…
nature.com/articles/s4158…
"I think assembly theory has lots of merit and potential, but this particular paper frames its argument in a way which is unfortunate and, frankly, more than just a bit misleading. My personal suspicion is that this has two reasons: (1) the authors hyped up their claims ...
... to get the paper published in a glam journal, plus (2) they also overestimate the reach and power of their model in ways which may be detrimental to its proper application and interpretation."
Read 6 tweets
Yogi Jaeger 💙 @yoginho@spore.social Profile picture
Sep 9, 2023
Just received my expected rejection from @elife (after appeal).

The way I was rejected reflects the atrocious attitude of the journal & the whole field of biology towards conceptual work.

It also showcases a lack of intellectual integrity on behalf of the journal editors. 🧵
I submitted the paper knowing full well that @eLife usually restricts its scope to empirical work. The idea was to challenge that restriction, since (in my opinion) biology urgently needs a revival of serious conceptual efforts to prevent the descent of the field into pointless..
@eLife ... construction of large data sets that are increasingly costly to produce but yield diminishing returns in terms of insight and understanding into the workings and organization of living systems. Hence, no surprise when my work was deemed "out of scope." That's fair enough.
Read 21 tweets
Yogi Jaeger 💙 @yoginho@spore.social Profile picture
Jan 19, 2022
The current #COVID19 media coverage around me seems to agree on three things: (1) there is nothing we can do against #omicron, (2) this variant is mild & the wave will be over soon, (3) we're soon going "endemic," to "live with the virus," & back to normality. /1
There seems to be very little push-back against this narrative, which is something that really surprises me. But worse than that: it does *not* bode well for the next pandemic (whether the next #COVID19 variant or something altogether more worrisome). /2
Re (1): we can't do anything & #ZeroCovid was never an option.

Well, we never really tried. Those few countries that did were isolated (either geographically or surrounded by countries who didn't implement any low-incidence measures). /3
Read 23 tweets
Yogi Jaeger 💙 @yoginho@spore.social Profile picture
Feb 19, 2021
Our second paper on dynamical modularity, "Dynamical Modules in Metabolism, Cell and Developmental Biology" by @NickMonk14 & myself is now available as a preprint: osf.io/rydbn via @OSFramework /1
It complements our earlier evolutionary perspective on the subject (osf.io/vfz4t) with its more regulation-based approach and a long list of practical examples that illustrate our novel conceptual framework for the dynamical decomposition of complex systems. /2
Just like our earlier paper, the argument starts with the following observation: modular phenotypic traits imply that the underlying regulatory processes—the epigenotype of the organism—must be dissociable as well. How to decompose them, however, is not a trivial task. /3
Read 16 tweets

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