Lightnews — Scholar-powered news

Reposted by Alex Crits-Christoph

Johannes Cairns @jcairns.bsky.social · 11h

Massive undertaking with @teppo-h.bsky.social and others out. We studied 4 years (!!!) of synthetic 23 microbial species community evolution with/without antibiotic. Resistance mutations occurring over years led to stepwise restructuring and ultimately recovery of undisturbed community composition.

Teppo Hiltunen @teppo-h.bsky.social · 11h

Evolution induced state shifts in a long-term microbial community experiment www.biorxiv.org/content/10.1...

Evolution induced state shifts in a long-term microbial community experiment

Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian evoluti...

www.biorxiv.org

7 11

Reposted by Alex Crits-Christoph

Sheryl Gay Stolberg @sherylnyt.bsky.social · 14h

BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice:

760 7.7K 14K

Reposted by Alex Crits-Christoph

Jeremy Faust, MD @jeremyfaust.bsky.social · 12h

We have breaking news in Inside Medicine.

We had heard rumors of RIFs to CDC.

But this is the first visual confirmation that it has occurred tonight, and at high levels in the agency.

Here is what we know...and then some well-sourced rumors (but rumors, nonetheless, not confirmed) 🧵...

8 160 270

Alex Crits-Christoph @acritschristoph.bsky.social · 19h

Because when some audiences hear "Make the proof" they do not hear "Make up the proof" because they don't have the (correct) prior intuition that everything he does is a scam.

So when a comment *assumes* someone hears "make up", it misses the mark with the audience most important to reach

1 2

Alex Crits-Christoph @acritschristoph.bsky.social · 19h

HOWEVER, we also know his process is going to be irrevocably flawed and politically motivated, and so in practice everything he does we should assume is in fact going to be "making up the proof".

Imo it can be good to push back on short viral gotchas like this bc they can hurt with some audiences.

1 1

Alex Crits-Christoph @acritschristoph.bsky.social · 19h

Yeah "make the proof" vs "make up the proof" is key.

RFK isn't consciously saying he's going to make up evidence here, he pretty clearly genuinely believes he's searching for confirmatory truth and means as much. It's silly to think he meant "We're gonna make up data to fit our beliefs", he didn't!

1 1

Reposted by Alex Crits-Christoph

Kevin Zollman @kevinzollman.com · 1d

A reoccurring frustration for philosophers of science: Many scientists know how to do science like people know how to ride a bike. When they reflect on the practice of science, they repeat platitudes about how science works. Those platitudes are often wrong, sometimes even about their own field

D. J. Hicks @danhicks.bsky.social · 1d

*sighs in philosopher of science*

Looking for confirmatory evidence is an entirely normal part of science. The primary problem here is the eugenics and the fascism, not the lies to children about "the scientific method."

One Bluesky account is quoting another. Inner post has a video of RFK Jr., some person I don't recognize (Tylenol and autism guy, maybe?), Marco Rubio (I think), and Trump. Post text: "RFK Jr on Tylenol and autism: 'It is not proof. We're doing the studies to make the proof."

Outer post text: "We're doing studies to prove it (* not how studies work)"

2 10 51

Reposted by Alex Crits-Christoph

D. J. Hicks @danhicks.bsky.social · 1d

The "gold standard science" stuff plays on the same oversimplified picture of science, and that's part of the reason scientists have had such weak-ass responses to it

Kevin Zollman @kevinzollman.com · 1d

It's not that I think RFK is going to do good science on this topic. I think it's important to criticize it for the right reasons.

I think perpetuating the children's version of the scientific method leads to scientific skepticism.

2 2 11

Reposted by Alex Crits-Christoph

Emmanuele Severi @emmseveri.bsky.social · 1d

www.science.org/doi/10.1126/...

#microsky #microbiome

DGRs FTW

Targeted protein evolution in the gut microbiome by diversity-generating retroelements

Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, su...

www.science.org

7 16

Reposted by Alex Crits-Christoph

Rachel M. Wheatley @rachelmwheatley.bsky.social · 1d

Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈

The Lancet Microbe @lancetmicrobe.bsky.social · 2d

New research article

Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA

2 25 58

Reposted by Alex Crits-Christoph

Noah Fierer @noahfierer.bsky.social · 1d

New paper out demonstrating how we can use strain-level analyses of soil metagenomes to investigate the biogeographical patterns exhibited by a dominant group of soil bacteria (Bradyrhizobium)
academic.oup.com/ismej/advanc...

Validate User

academic.oup.com

2 4 6

Alex Crits-Christoph @acritschristoph.bsky.social · 1d

well limited by 300 chars, but the full claim would be "Statistically significant increase in organisms A and B, which are more likely than the average member to encode for genes X and Y. Therefore these genes and the phenotype they can be inferred to likely confer may play a role in the difference"

Alex Crits-Christoph @acritschristoph.bsky.social · 1d

(Well actually, the genes quite literally are changing in abundance along with the organisms, but this is a metaphorical argument that it's better to frame gene function in the context of the organisms that encode them instead of in isolation)

1

Alex Crits-Christoph @acritschristoph.bsky.social · 1d

I dislike that much more typical framing of functional questions in metagenomes, because (with some rare exceptions), metabolic genes are not increasing or decreasing in abundance in a study

Organisms with these genes are, not the genes themselves.
But the genes may explain why the organisms are!

1

Alex Crits-Christoph @acritschristoph.bsky.social · 1d

What I really like about your approach here and EnrichM is that the question is framed like: "We saw these differently abundant organisms, can we statistically identify which genes may explain that" instead of the very typical metagenomic "gene go up, gene go down".

It's also how we did it here:

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms - Nature Microbiology

Using metagenomics and proteomics on Mediterranean grassland soil samples resulted in the recovery of 793 metagenome-assembled genomes and provided insights into microbial activity in this environment, and how this changes with soil depth and exposure to extended rainfall.

www.nature.com

1 1

Alex Crits-Christoph @acritschristoph.bsky.social · 1d

So that [and similar arguments] is why it's best to report this like "increases in organisms A and B, which encode genes X and Y" and not necessarily claim changes in metabolic fluxes or products

I do think it's then reasonable to suggest how this may impact phenotype, while making caveats clear

1

Reposted by Alex Crits-Christoph

Filip Husnik @filiphusnik.bsky.social · 1d

Pretty excited to share our new preprint!
Non-photosynthetic Plastid Replacement by a Primary Plastid in the Making
www.biorxiv.org/content/10.1...

40 77

Alex Crits-Christoph @acritschristoph.bsky.social · 1d

I think it heightens preexisting tradeoffs between efficiency (at least in the short term) and pedagogy. Consequentially, academia will have harder decisions on how to prioritize long-term student learning vs immediate scientific efficiency.

But despite the gloom, I'm optimistic, students are smart

1

Reposted by Alex Crits-Christoph

Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 1d

My HPLC was definitely overlooked

www.nature.com/articles/d41...

Prizes must recognize machine contributions to discovery

The future of science will be written by humans and machines together. Awards should reflect that reality.

www.nature.com

20 57 300

Reposted by Alex Crits-Christoph

Craig MacLean @craigmaclean.bsky.social · 2d

New pre-print www.biorxiv.org/content/10.1...
Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social!
#phagesky#microsky

Trade-offs between phage resistance and conjugative ability shape the ecological and evolutionary response of a multidrug resistance plasmid to plasmid-dependent phage

Phage therapy is a promising alternative to antibiotics to treat multidrug resistant infections. Plasmid dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill ...

www.biorxiv.org

1 28 50

Reposted by Alex Crits-Christoph

Keith Smith @drkeithsmith.bsky.social · 1d

How can we tell what's inside an #exoplanet? @timlichtenberg.bsky.social et al review how a planet's atmosphere interacts with its interior. Atmospheric observations can distinguish between lava worlds, water worlds, temperate surfaces or supercritical interiors. ☄️
www.science.org/doi/10.1126/...

1 14 55

Reposted by Alex Crits-Christoph

gostin.bsky.social @gostin.bsky.social · 1d

RFK has mounted a full assault on @CDCgov-- slashing funding & staff, & and turned the agency into a political tool that can no longer be fully trusted on public health recommendations, especially vaccines.

Out today in JAMA Health Forum

Peter Lurie CSPI

jamanetwork.com/journals/jam...

Assault on the Centers for Disease Control and Prevention—Budget Cuts, Political Control, and the Erosion of Trust

This JAMA Forum discusses measures the Trump administration has taken against the US Centers for Disease Control and Prevention that include budget cuts and program eliminations, workforce reductions ...

jamanetwork.com

3 4

Reposted by Alex Crits-Christoph

Ákos T Kovács @evolvedbiofilm.bsky.social · 2d

Glad to share a collaboration with Yicen Lin's group at Kunming University of Science and Technology published in ISME Journal

Synergistic biodegradation of polyethylene by experimentally evolved bacterial biofilms
academic.oup.com/ismej/advanc...

#MicrobiomeEcology at #LeidenBiology

1 7 8

Reposted by Alex Crits-Christoph

Carl Zimmer @carlzimmer.com · 2d

Today my @nytimes.com colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link: nyti.ms/3IWXbiE

nyti.ms

140 1.8K 4.6K

Alex Crits-Christoph @acritschristoph.bsky.social · 2d

and the nice thing about climate change is, every bit counts! Unless we're playing "Oh but will talking about ERW distract people from the obviously most important thing which is getting rid of fossil fuels" game, which is kinda true but also kind of paternalistic IMO

2