Will Shoemaker

@shoestrapped

Microbial life scientist applying principles from physics CNRS Chaire de Professeur Junior @ Genoscope 🇫🇷 Grilli lab alumni @ ICTP 🇺🇳/🇮🇹 Lennon lab PhD @ IUB 🇺🇸

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Will Shoemaker@shoestrapped· Jul 9

Great to see this important study published. For some time I've pointed to the preprint version when students ask about co-evolution between humans and their microbiota. "Limited codiversification of the gut microbiota within humans"

Will Shoemaker@shoestrapped· Jul 7

Cool new work on the quantification of species interactions over time, led by former labmate Javier Aguilar journals.aps.org/prxlife/abst...

FIG. 1. Sketch of the experimental protocol to measure interactions with pulse experiments. The axes represent the experiment duration (t),
the population density of the perturbed species (bottom, depicted as a sheep; xj in the text), and the population density of the target species (top,
depicted as a goat; xi in the text). The per-capita growth rates are measured in the curves of the top (g(E)
i ), while perturbations are introduced
in the species of the bottom. Each element of the interaction matrix is calculated as the difference between the growth rates of the perturbed
and baseline trajectories.

FIG. 2. Temporal variability of interaction measures. (a) Top: Temporal evolution of yeast (Y), galactose (G), and ethanol (E) densities
in the baseline trajectories. Bottom: Temporal evolution of interactions induced by yeast perturbations. (b)(i) Galactose dynamics in the
baseline trajectory—initially ethanol-free—and in the perturbed trajectory, which includes ethanol from the start (dotted and solid lines,
respectively). (b)(ii) Similar to pane (b)(i) but showing ethanol evolution. (b)(iii) Yeast population dynamics with and without the initial
presence of ethanol. (b)(iv) Evolution of the interaction measure ME→Y . (c) Temporal evolution of inferred interactions among grasshoppers:
Melanoplus femur-rubrum (M), Spharagemon collare (S), and Phoetaliotes nebrascensis (P). Details of the parameters and model used to
generate (a) and (b) are given in Sec. VB.

FIG. 5. Temporal dependence disentangles direct and indirect interactions. (a) Sketch illustrating the hallmarks of direct and indirect
interactions. In the limit t → 0, direct interactions approach a finite value (M(0)
i,j ), while indirect interactions vanish proportionally to M(1)
i,j t.
(b) Interaction measures for short experiment durations in a multispecies consumer-resource model. The interactions MC→C tend to zero,
while MR→C converge to a positive value as t → 0. (c) Interaction measures between consumers at various discrete experiment durations
(dots); data are fitted with a parabolic function (solid line), and extrapolation to t = 0 correctly recovers the interaction limit (M(0)
C→C = 0).
Synthetic datasets and parameter choices are available in Sec. VB

FIG. 8. Effect of noise in interaction measures. (a) Self-interaction measures in a dataset generated with a noisy process [Eq. (21)].
(b) Top: Trajectory of a consumer and a resource with small white-noise perturbations. Bottom: Effect of small noise on interaction
estimates in a consumer-resource model from a single realization. The dashed line in (b) indicates the interaction measure in the absence
of noise. (c) Absolute difference between the average interaction computed using Eq. (23) and the interaction measured without noise,
Er(M¯ ) =|M¯ − M
|. As expected, statistical errors decrease as the number of realizations, N, increases. Synthetic datasets and parameter
choices are available in Sec. VB.

Will Shoemaker@shoestrapped· May 23

Will Shoemaker@shoestrapped· May 12

Adding Maaløe's bacterial physiology school

Will Shoemaker@shoestrapped· Apr 25

Sounds familiar. From Richard Rhodes’ “The Making of the Atomic Bomb”

Will Shoemaker@shoestrapped· Mar 29

Acquired 💯

Will Shoemaker@shoestrapped· Mar 26

Had a great time talking microbial macroecology with the folks at JHU, with the bonus of learning some new physiology + biological physics. Thanks to Will Ludington for being a gracious host and Frank Liu for the action shot!

Will Shoemaker@shoestrapped· Mar 13

Heading to Denver for the APS Global Physics Summit. Feel free to reach out if you’d like to grab a coffee/drink. I’ll be presenting Wednesday @ 12:12

Will Shoemaker@shoestrapped· Mar 8

A personal honor to have the work of myself and my collaborators covered in Il Piccolo, the Trieste newspaper that published James Joyce when he lived here.

Will Shoemaker@shoestrapped· Feb 15

How it feels when someone appreciates your paper.

Will Shoemaker@shoestrapped· Jan 28

Happy to share my solo-authored Perspective "An Interpretation, Survey, and Outlook of Microbial Macroecology"! Making time these last few months to take stock of the patterns us microbial ecologists examine + models we invoke has been invaluable. Feedback welcome! ecoevorxiv.org/repository/v...

Will Shoemaker@shoestrapped· Jan 24

RIP Michael Parenti. Your voice will be missed.

Will Shoemaker@shoestrapped· Jan 17

How to tell you're in for a good read

Will Shoemaker@shoestrapped· Jan 9

"You’ll notice that Gurowski is so angry here at the dotard (Winfield) Scott that he uses the worst insult any European military commentator can think of: He compares him to the Austrians." Original article on wayback web.archive.org/web/20140427... New article in "They Should Have Been Hanged"

Will Shoemaker@shoestrapped· Jan 9

Talked with a friend last week about Adam Gurowski, a Pole Hegel-trained organizer of the November uprising against the Tsar, who later worked as a translator for the Union. In his diary he saw the CSA for what it was, more so than most northerners. Some quotes below from John Dolan's updated piece

Will Shoemaker@shoestrapped· Dec 16

Ended up adding some amaro Montenegro, might make another for Xmas

Will Shoemaker@shoestrapped· Dec 8

New version! Additional support for our original characterization of fluctuations around steady-state abundance (sojourn trajectories) + sojourn times reflect temporal dynamics to a greater extent than other common macroeco measures (residence and return times) www.biorxiv.org/content/10.1...

Will Shoemaker@shoestrapped· Dec 6

Thinking back to undergrad, mandatory physics courses were 100% disconnected from biology. This gap (IMO) impedes the quantitative training of bio students. So papers like Zim et al that connect microbial physiology to electric circuits have great pedagogical value journals.aps.org/prxlife/abst...

Will Shoemaker@shoestrapped· Nov 11

Open call for proposals for ICTP's Physics Without Frontiers, which "works to teach, train, and inspire physics and mathematics university students worldwide, with focus on countries in the Global South, to help build the next generation of scientists." Due December 15 www.ictp.it/home/physics...

Will Shoemaker@shoestrapped· Oct 24

Heading back to Trieste after a fine week at the University of Maribor visiting the lab of Dr. Maja Rupnik, expertly organized by PhD candidate Urša Miklavčič. Plenty of microbial macroecology, sporulation, and žlikrofi 🇸🇮

Will Shoemaker@shoestrapped· Sep 4

Rarefaction curves of richness as a function of # paintings! A good pedagogical example of the many ways one can sample biodiversity.

Will Shoemaker@shoestrapped· Aug 25

Abandon linkedin

Will Shoemaker@shoestrapped· Aug 11

Way behind on this, but I had a great time last month at "ECO²STAT 2025: Decoding Complexity in Ecology and Economics" in Cagliari, Sardinia. Excellent talks (in a deconsecrated church!) and local food. Thanks to the organizers for all the effort they put in. www.agile-group.org/eco2stat2025/

Will Shoemaker@shoestrapped· Jul 18

Will Shoemaker@shoestrapped· Jul 2

However, the CV of community members can vary, leading us to ask how this parameter should relate to the sojourn time. From the SLM we predict that ASVs with larger CVs (larger sigma) should have larger average sojourn times. A prediction that again holds both in data & analytic prediction.

Will Shoemaker@shoestrapped· Jul 2

Together, these observations predict that the deviation *within a sojourn period* should be invariant with respect to sojourn time, which holds in the empirical data. Alternatively stated, we are able to parameterize a general scaling relationship specifically for the human gut microbiome

Will Shoemaker@shoestrapped· Jul 2

2nd: The relationship between sojourn time & the *area* under the trajectory. The lack of a relationship is consistent with growth timescale being << typical sojourn time. The area did have a clear relationship with a function of the CV, which was well-explained by a prediction obtained from the SLM

Will Shoemaker@shoestrapped· Jul 2

1st we calculated the # of days between when a community member left and subsequently returned to its steady-state abundance, known as the sojourn time. The distribution of sojourn times could not be explained by the known stationary-distribution, requiring a non-trivial dependence on growth rate

Will Shoemaker@shoestrapped· Jun 11

Think it’s time for a reread in light of ongoing NSF + NIH defunding

Will Shoemaker@shoestrapped· Jun 7

Some summer reads