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foaylward, to random
@foaylward@genomic.social avatar

Giant viral signatures on the Greenland ice sheet

https://doi.org/10.1186/s40168-024-01796-y

foaylward, to Pubtips
@foaylward@genomic.social avatar

‘We need to slow down scientific publishing’

'We focus on metrics to evaluate a scientist’s career: how many articles they have published, how many times they were cited, what was the impact factor of all these articles. '

https://english.elpais.com/science-tech/2024-04-26/elisabeth-bik-expert-in-scientific-integrity-we-need-to-slow-down-scientific-publishing.html

elduvelle,
@elduvelle@neuromatch.social avatar

@foaylward @ElisabethBik cool article!

foaylward, to evolution
@foaylward@genomic.social avatar

Happy to share the latest manuscript from our lab, in which we propose that eukaryotes evolved from a genomic chimera of Asgard archaea and giant viruses.

https://www.biorxiv.org/content/10.1101/2024.04.22.590592v1

This is a controversial topic, but we believe we have strong evidence to suggest a critical viral role in eukaryogenesis.

foaylward,
@foaylward@genomic.social avatar

As bizarre as this all sounds, I believe we have strong phylogenetic evidence supporting this model. Importantly, this model has also been proposed before by Phil Bell based on first principles or eukaryotic organization and similarities between the nucleus and virus factories formed by viruses during infection

https://doi.org/10.3389/fmicb.2022.858064

albertcardona,
@albertcardona@mathstodon.xyz avatar

@foaylward

How cool is that. Been looking for a paper I read 15 or 20 years ago proposing a viral theory of DNA origin, whereby an inserted DNA virus on an RNA genome would then replicate the whole bacterial genome as DNA, and the bacterium became dependent on that insertion from then on. Will read yours and Phil Bell’s to see if I can find a reference to it.

foaylward, to science
@foaylward@genomic.social avatar

Just saw that #OpenAccess publication charges at some Nature publishing group journals are >$12,000 (!!!)

This is just getting crazy - APCs have really gone off the rails. These fees can't possibly be sustainable in the long term...

#APCs #OpenScience #science

jonny,
@jonny@neuromatch.social avatar

@foaylward
They're sustainable for as long as we suckers continue to pay them

foaylward, to random
@foaylward@genomic.social avatar

"one study of people’s shoes found that 95% had faecal bacteria on the bottom and a third contain E coli. He says people are walking on dog droppings all the time and not realising."

https://www.theguardian.com/lifeandstyle/2024/feb/10/the-joy-of-socks-why-were-all-taking-our-shoes-off-now-to-fight-those-germs?CMP=Share_AndroidApp_Other

foaylward, to science
@foaylward@genomic.social avatar

Counting citations hasn't been a reliable measure of scientific impact for a while, especially on platforms like Google Scholar that compile info from random documents. Hyper-authorship, predatory journals, etc have all contributed to the problem.

This preprint just drives home how important it is to measure scientific impact more carefully and without reliance on automated metrics

Google Scholar is manipulatable

https://arxiv.org/abs/2402.04607

MarkHanson,

@elduvelle @foaylward yeah, chiming in, in many countries researchers are incentivized or outright pressured to publish in "high impact" or other box-ticking-exercise journals, and they receive bonuses, salary raises, or positions based on their CV and what is on it.

That's not to say that's good, but it is the reality that ~half the world experiences? And these conversations from Western perspectives often discount that as "bad," but lack appreciation for what drives it despite it being "bad."

elduvelle,
@elduvelle@neuromatch.social avatar

@MarkHanson so.. what drives it? Why would a university or government reward their researchers for publishing “impactful” science, whatever that means? Why don’t they instead encourage them to publish good science?

@foaylward

foaylward, to Microbiology
@foaylward@genomic.social avatar

Cool paper looking at biomass degradation in leaf cutter ant fungus gardens:

Mapping microhabitats of lignocellulose decomposition by a microbial consortium

https://www.nature.com/articles/s41589-023-01536-7

foaylward, to Microbiology
@foaylward@genomic.social avatar

What's the brand of your most reliable -80 freezer?

I need a new one - recommendations welcome!

#MolecularBiology #Microbiology

foaylward, to bioinformatics
@foaylward@genomic.social avatar

Gotta check these out!

Robust, scalable, and informative clustering for diverse biological networks

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03062-0

foaylward, to academia
@foaylward@genomic.social avatar

The number of predatory conferences seems to be ballooning. I get several SPAM emails every week for invitations to meetings that cost >$1500 to attend. These are not in my area of study.

When I check the website, the meetings look legit, and have a long list of (apparently real) invited speakers.

I guess it has just become very profitable to run conferences and charge outlandish registration fees? Even if the meetings are real, I can't imagine they are particularly good.

#academia

foaylward,
@foaylward@genomic.social avatar

The latest ones that invited me to speak were the International Drug Discovery Science Technology meeting in Osaka, and the Plant Science and Molecular Biology World Congress in Barcelona.

Has anyone every been to any of these? I have never heard of them, but the websites look legit.

albertcardona, (edited )
@albertcardona@mathstodon.xyz avatar

@foaylward

Charitably one could think these conferences might be a way for academics to go on a trip on grant money. But I have never met anyone who mentioned going to any such "world congress" obviously balloney conferences.

The flip side is that just like some journals are cashing in "special issues", conference series have sprouted like mushrooms and are largely self-serving, now detached from the communities that hatched them.

foaylward, to Microbiology
@foaylward@genomic.social avatar

Happy to share our latest paper, in which we examined the timing at which different microbial groups colonized the ocean!

The first author (Carolina Martinez) is starting her lab at UC Santa Barbara in 2024 and is looking to recruit postdocs and PhD students, so if this looks interesting to you, please reach out to her!

A timeline of bacterial and archaeal diversification in the ocean

https://elifesciences.org/articles/88268

foaylward, to evolution
@foaylward@genomic.social avatar
foaylward, to random
@foaylward@genomic.social avatar

Latest predatory publishing scam: Not just spamming my inbox ~5 times a week with special issue invites, but now spamming me with emails claiming I have registered to submit to the special issues...

foaylward, to random
@foaylward@genomic.social avatar

For the academics out there, so you have a #slack account in your lab, and is it useful?

I've had one for years and it's been quite handy for code sharing and just general lab communication. But it might be hard for me to maintain due to policies at my University.

timreadmicro,

@foaylward We have a lab and its a roaring success. It has become an essential communication tool, especially channels created for different projects and interests within the lab and for communicating new publications, talks, software etc

elduvelle,
@elduvelle@neuromatch.social avatar

@foaylward I find it amazingly useful!

foaylward, to random
@foaylward@genomic.social avatar

The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian

https://www.science.org/doi/full/10.1126/sciadv.adh5138

"Our findings redefine the lower limit of eukaryotic gene expression noise and uncover molecular requirements for achieving ultralow noise, which is expected to be important for vital cellular functions."

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