Yogi Jaeger 💙 @yoginho@spore.social Profile picture
Jun 5, 2020 16 tweets 7 min read Read on X
A little thread on the causal role of genes in complex regulatory systems, the subject of my recent paper in #BioEssays with philosopher James DiFrisco.

This is part of a collection of papers initiated by @drmichaellevin.

👇🏻
@drmichaellevin Our paper introduces different views on causality to biologists. Physical notions based on law-like regularity of phenomena, or transfer of matter & energy are not really suitable in biology, where general laws are rare & the transfer of information often more important. /1
@drmichaellevin Instead, we use a notion of causality, (introduced by philosopher David Lewis) which is based on counterfactual conditionals, e.g. "if A would not have happened, B would not have happened, therefore A is a cause of B.” /2
@drmichaellevin A particularly useful counterfactual concept of causality for biology is developed in James Woodward’s interventionist account (“Making Things Happen”, OUP, 2003).

oxfordscholarship.com/view/10.1093/0… /3
@drmichaellevin On Woodward's account, A is a cause of B, if — when I intervene in a particular way on A — B will change. The methodology of classical genetics is obviously conforming very closely such an account: it treats genes as actual difference-makers, e.g. philsci-archive.pitt.edu/3833. /4
@drmichaellevin The special role of genes in biology has often been defended based on their causal specificity, i.e. their mapping to their effects in a fine-grained & well-defined way. /5
@drmichaellevin In our paper, we examine if such a privileged role for genes is still warranted in the context of complex regulatory dynamics. The answer is a clear no. /6
@drmichaellevin Feedback regulation & the multi-level nature of biological regulatory systems renders the causal effects of genes unstable, because they become heavily dependent on history & context. /7
@drmichaellevin Furthermore, individual genes often have no effect at all in redundant & robust regulatory systems, implying that they may not be proportional (at the right level of explanation) for such cases. /8
@drmichaellevin Finally, genetic effect are often no longer specific either in the context of complex regulation. Thus, genetic causation is unstable, no longer proportional, and unspecific at the systems-level. /9
@drmichaellevin To understand the causal structure of regulatory systems, we need to intervene on them at the systems level. This is only possible with properly formulated & validated dynamical systems models. /10
@drmichaellevin We show that inter-level causation through regulatory constraints also conforms to Woodward’s interventionist view of causation. To gain a causal view of a regulatory system, we do *not* need to reduce it to the molecular level. In fact, we need not to reduce it! /11
@drmichaellevin This account of genetic causation in complex regulatory systems shows that “bottoming out” at the genetic or molecular level is the wrong strategy if we are to understand causal effects on systems-level dynamics. /12
@drmichaellevin We propose that an alternative approach, based on Woodwardian interventions on constraints affecting the default dynamics of underlying processes, is more suitable to study the dynamics of regulatory systems. /13
@drmichaellevin I explain our analysis & our proposed approach in this lecture in my #BeyondNetworks course: . /14
@drmichaellevin Last but not least, I highly recommend James Woodward’s 2010 paper on “Causation in Biology” for definitions of causal stability, proportionality, and specificity: philpapers.org/rec/WOOCIB. /15

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More from @yoginho

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
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
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
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
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
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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