@foaylward@genomic.social
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foaylward

@foaylward@genomic.social

Associate professor at #VirginiaTech. Interested in viral diversity and the tree of life. Also posts pictures of flowers and cats.
#virology #microbiology #evolution #genomics #bioinformatics

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foaylward, to random
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Giant viral signatures on the Greenland ice sheet

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

foaylward, to Pubtips
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‘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

foaylward, to evolution
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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,
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Over the last decade, strong evidence has accumulated that Asgard archaea are the closest cellular relatives of eukaryotes, but it has remained unclear why some eukaryotic genes, such as multi-subunit RNA polymerase and some DNA polymerase subunits, do not show clear affinity to archaea (i.e. they support a 3-domain tree). We propose that these 3D genes were acquired from viruses, and that eukaryotes are therefore a archaeal-virus chimera.

foaylward,
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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

foaylward, to science
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Just saw that 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...

elduvelle, to academia
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Is it common that US universities don’t pay their faculty for 3 months every year? What’s up with that 🤔

foaylward,
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@elduvelle yes - 9 month salaries are common. Summer salary can be budgeted in grants, etc.

foaylward, to random
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"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
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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

foaylward,
@foaylward@genomic.social avatar

@elduvelle excellent point! In many cases it is not needed or desirable.

But even when trying to self evaluate, I often ask what discoveries would have the broadest relevance, and what lines of inquiry could lead to the most drastic developments. But that is a much more nuanced discussion of impact that can't be captured by metrics.

foaylward,
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@elduvelle And on a more practical note, many scientists are forced to report metrics of impact. For example I had to report the number of papers I published and the number of citations I received in my faculty annual report.
So if we are going to do that we should at least be aware of what biases these metrics have.

foaylward, to Microbiology
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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
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What's the brand of your most reliable -80 freezer?

I need a new one - recommendations welcome!

foaylward, to bioinformatics
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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
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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.

foaylward,
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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.

elduvelle, to random
@elduvelle@neuromatch.social avatar

What do people use nowadays as ? (Does the concept even still exist?)

It’s to keep track of relevant of interest as my main source used to be… Twitter and ResearchGate, which I’ll both be leaving before 2024

foaylward,
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@jonny @elduvelle I always wondered why the enhanced PDF readers were so prevalent even though they are super clunky and take forever to load.

foaylward, to Microbiology
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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
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Postdoctoral Fellow in Phylogenomics/Bioinformatics

https://jobrxiv.org/job/uc-santa-barbara-27778-postdoctoral-fellow-in-phylogenomics-bioinformatics/

foaylward, to random
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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 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.

foaylward,
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@PhilippBayer maybe I'll have to move over to that or another alternative. I might be able to keep a free slack version but the 90 day window is a pain.

foaylward,
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@elduvelle @PhilippBayer yeah code could be shared but it would need to be backed up somewhere else pretty quickly.

foaylward,
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@elduvelle @PhilippBayer the free version is essentially just a place for lab announcements, sharing papers for the journal club the next day, etc. Still useful, but certainly limited.

foaylward, to random
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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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