@albertcardona@mathstodon.xyz
@albertcardona@mathstodon.xyz avatar

albertcardona

@albertcardona@mathstodon.xyz

How does the brain work? Someday, we'll figure it out.
Group Leader, MRC LMB, and Professor, University of Cambridge, UK.
#neuroscience #Drosophila #TrakEM2 #FijiSc #CATMAID #connectomics #connectome #vEM #iNaturalist #entomology
Born at 335 ppm.
Brains, signal processing, software and entomology: there will be bugs.

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gutenberg_org, to books
@gutenberg_org@mastodon.social avatar

in 1757.

English poet Christopher Smart is admitted into St Luke's Hospital for Lunatics in London, beginning his six-year confinement to mental asylums.

A "Commission of Lunacy" was taken out against Smart, and he was admitted to St Luke's Hospital for Lunatics as a "Curable Patient". It is possible that Smart was confined by John Newbery over old debts and a poor relationship between the two.

Books by Christopher Smart at PG:
https://www.gutenberg.org/ebooks/author/31382

albertcardona,
@albertcardona@mathstodon.xyz avatar

@gutenberg_org

There is a Christopher Smart meeting room in Pembroke College, Cambridge, and now I finally made the connection with the poet (I'm slow). As wikipedia says he studied in .

https://en.m.wikipedia.org/wiki/Christopher_Smart#College

lena_r, to random
@lena_r@drosophila.social avatar

I have reviewed grants for ANR (France) and National Sci Centre (Poland), and both offered to pay me. I also reviewed many grants for BBSRC and was never offered any money. I wonder - do the first two pay because I'm a foreign reviewer? Does BBSRC pay foreign reviewers too?

albertcardona,
@albertcardona@mathstodon.xyz avatar

@lena_r

BBSRC doesn’t pay. Eventually they’ll have to or no reviewers will sign up. I mean why would you.

albertcardona, to Cambridge
@albertcardona@mathstodon.xyz avatar

Cambridge University is quite the joyful place. Night climbing:

https://www.cambridge-news.co.uk/news/cambridge-news/secret-society-cambridge-night-climbing-19833077

For prospective students: we have just installed a rock wall inside the bell tower of our new auditorium, with auto-belays. One more good reason to choose Pembroke College.

albertcardona, to Neuroscience
@albertcardona@mathstodon.xyz avatar

Synaptic architecture of a memory engram in the mouse hippocampus
Uytiepo et al. 2024 (Ellisman's lab)

https://www.biorxiv.org/content/10.1101/2024.04.23.590812v1.abstract

futurebird, (edited ) to random
@futurebird@sauropods.win avatar

Java has a interface* called “Set” but the documentation is nebulous & ominous. “may throw an exception” what? does no one even know? There isn’t even a method for intersection & union?! What is the point? I taught my students to use the set object in Python. It was an elegant beautiful experience— Thought we could do it in Java but I think I will just use arraylist, write my own damn methods.

I’m biased, but Java is always more annoying like this. ugh. (*this explains part of my confusion)

albertcardona,
@albertcardona@mathstodon.xyz avatar

@futurebird

In Java, "Set" is an interface. What you are looking for is a "HashSet" https://docs.oracle.com/javase/8/docs/api/java/util/HashSet.html or any other class that implements the interface "Set" like a TreeSet, LinkedHashSet, CopyOnWriteArraySet, EnumSet, and others, such as a Map's key set.

albertcardona, to Neuroscience
@albertcardona@mathstodon.xyz avatar

"Schreckstoff: It takes two to panic", a dispatch by @MarcusStensmyr 2024

"Schreckstoff (fear substance) is an alarm signal released by injured fish that induces a fear response. Its chemical nature has long been debated. A new study finds that zebrafish Schreckstoff is composed of at least three components, two of which elicit the fear response only in combination."

https://www.sciencedirect.com/science/article/pii/S0960982224002513

albertcardona, to random
@albertcardona@mathstodon.xyz avatar

Mason bee, Osmia sp.

Seen this morning at , Cambridge, UK.

albertcardona,
@albertcardona@mathstodon.xyz avatar

I had no idea:

"The nesting habits of many Osmia species lend themselves to easy cultivation, and a number of Osmia species are commercially propagated in different parts of the world to improve pollination in fruit and nut production. Commercial pollinators include O. lignaria, O. bicornis, O. cornuta, O. cornifrons, O. ribifloris, and O. californica. They are used both as an alternative to and as an augmentation for European honey bees. Mason bees used for orchard and other agricultural applications are all readily attracted to nesting holes – reeds, paper tubes, nesting trays, or drilled blocks of wood; in their dormant season, they can be transported as intact nests (tubes, blocks, etc.) or as loose cocoons."

https://en.wikipedia.org/wiki/Mason_bee

pvonhellermannn, to climate
@pvonhellermannn@mastodon.green avatar

#ClimateDiary UK’s Nationwide Won’t Lend to Some Homes Over Flood Risk

“The UK’s second biggest mortgage provider has stopped making loans on some homes at risk of flooding, over fears they may become uninsurable — and therefore, unsellable — over the coming years.”

#ClimateCrisis percolating through everything so much already in the UK, like everywhere else - #Harvest, #Insurance and now also #Mortgages. Surely this will become really significant.

https://www.bloomberg.com/news/articles/2024-04-30/uk-s-nationwide-pulls-mortgage-offers-to-homes-at-flood-risk

albertcardona,
@albertcardona@mathstodon.xyz avatar

@pvonhellermannn

There is a lot of momentum. And the younger generations are well aware of what awaits them and who's fault it is.

jackofalltrades, to climate
@jackofalltrades@mas.to avatar

It's very clear how desperate green tech advocates are to paint the current developments as a win for the climate. But by doing so they only reinforce the status quo.

https://www.euronews.com/green/2024/04/17/wind-energy-saw-record-growth-in-2023-which-countries-installed-the-most

albertcardona,
@albertcardona@mathstodon.xyz avatar

@jackofalltrades

There are a number of larger countries generating a lot of their electricity from wind and solar. The ones listed happen to be dominated by hydro and, in the case of Iceland, geothermal.

For example, the UK routinely generates 20 to 50% of its electricity from wind https://grid.iamkate.co Don't know where the average is this year, but the Office of National Statistics (ONS) of the UK says, for 2020, before the installation of further wind farms: "Wind energy generation accounted for 24% of total electricity generation (including renewables and non-renewables) in 2020" https://www.ons.gov.uk/economy/environmentalaccounts/articles/windenergyintheuk/june2021

The UK didn't make it into the list because it doesn't get to 100% of its electricity from renewables. But the fraction is a large and growing double-digit percent. There's still a fraction from coal (dwindling fast), gas, and nuclear. A number of other countries are in a similar situation: improving fast.

neuralreckoning, to science
@neuralreckoning@neuromatch.social avatar

Suppose you were a funder wanting to design a system to fund science projects that were bottom up rather than top down. How would you do it?

I think you'd want to restrict it to non-faculty to start with, and have some sort of consensus-building rather than competitive approach. Like, maybe you could have an initial round where people proposed ideas, followed by a second round where people indicated who they'd be willing to work with and which aspects of their ideas they'd be willing to drop or modify in order to build consensus. Possibly you might need multiple rounds like this until you iterated on a solution that worked.

Would there by problematic hidden power dynamics in an approach like that? I guess so, there always are. But maybe still better than top down approach?

And is there any chance of finding a funder who would be willing to experiment with such an idea? Or any existing examples of experiments like that? Or more generally, examples of funders taking a non-competitive approach?

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

@neuralreckoning

To non-faculty for sure. My first move would be to expand funding for PhD students: attract many, and with a good salary to bias the choice away from industry.

It's so cheap to support research work that may very well end up saving millions across the board, e.g., software to name just one close to me: https://albert.rierol.net/tell/20160601_Unintended_consequences_of_untimely_research.html

jon, to random
@jon@gruene.social avatar

I’m lost

I’ve just crossed a capital city by train, 3 stops so far*.

Not once been told to mind the gap between the platform and the train.

Not once been warned to not leave behind my luggage.

Not once been warned to not open the doors before the train is at the platform.

Not once been told to label my luggage.

Not once been told to mind the closing doors.

And no one died (as far as I’m aware).

    • I’m now in Belgium having arrived from France earlier
albertcardona,
@albertcardona@mathstodon.xyz avatar

@jon

Recalling here that saying, give the least number of instructions possible, otherwise for every instruction given even just once you will be expected to give it every time or the task won't get done.

albertcardona, to Bloomscrolling
@albertcardona@mathstodon.xyz avatar

A bumblebee of the species Bombus terrestris forages among forget-me-not flowers, light blue and small, and bends them down with her weight when clasping onto one to drink its nectar.

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

From Cambridge with love?

albertcardona,
@albertcardona@mathstodon.xyz avatar

@sciencebase

I have never seen road works done so poorly, ever, anywhere. And it’s not like weather or temperatures are extremes that damage roads, or there’s high tonnage traffic or something. These are residential streets in a country with temperate climate.

alex, to random
@alex@social.alexschroeder.ch avatar

I love our solitary bees. In the late morning hours when it’s still cold they sit at the opening of their tubes, looking out, warming up, trying to find the inner strength to get up and start doing things and I can relate so much.

albertcardona,
@albertcardona@mathstodon.xyz avatar

@alex

Getting out is worth it, though.

Red mason bee, Osmia bicornis http://www.inaturalist.org/observations/209837195

elduvelle, to random
@elduvelle@neuromatch.social avatar

Here are some very interesting suggestions for having a good IT system in your lab (Github, Wiki, website, emails etc.). I’m sure the Mastodon crowd will love these:

https://fraserlab.com/2024/04/22/IT-suggestions-for-new-faculty/

Source: future PI slack, from the

albertcardona,
@albertcardona@mathstodon.xyz avatar

@adredish @elduvelle

A major issue is when to let go of data taking hundreds of terabytes of space, and no one in the lab remembers what exactly it is, and the associated metadata and documentation (a wiki page) was lost some time ago or no longer makes sense. One never has time to go through these.

I do not have a good solution. The solution I'd want is an annual review of data, tied with the 5-year cycle of data servers (that's how long they're expected to last).

jni, to random
@jni@fosstodon.org avatar

Is there a comprehensive archive, with references, of Elsevier's many sins against scientific progress? @albertcardona @brembs The lead authors of a paper I played a small role in want to submit to Cell 🤢 and I would like to dissuade them.

Follow-up Q: I have a vague vibe that, although the entire traditional publishing system needs to die in a fire, NPG are not quite as scummy as Elsie. Is that vibe justified or not really?

albertcardona,
@albertcardona@mathstodon.xyz avatar

@jni @brembs

If given the amount of data out there on (and Springer Nature) the authors remain intent on submitting to their journals, there’s not much you can do. At this point throwing data at such authors doesn’t work anymore. Instead, you could try telling them about Robert Maxwell https://www.theguardian.com/science/2017/jun/27/profitable-business-scientific-publishing-bad-for-science , about how journals don’t have to be expensive to be respectable https://archive.blogs.harvard.edu/pamphlet/2012/03/06/an-efficient-journal/ and drop some shade, with comments like “do you think your grant funder will be happy to see the work published there?”. It’s not like they don’t know – they can’t not know –, it’s that they are still calculating impact towards career advancement as a function of journal impact factor. And sadly, for many institutions, they aren’t wrong.

At least try to get them to send to Science or PNAS, which are meant to be societies for scientists rather than an unapologetically exploitative business.

biorxiv_neursci, to random
@biorxiv_neursci@biologists.social avatar

Mating proximity blinds threat perception. https://www.biorxiv.org/content/10.1101/2024.04.23.590677v1?med=mas

albertcardona,
@albertcardona@mathstodon.xyz avatar

@biorxiv_neursci

“Romantic engagement can bias sensory perception. This 'love blindness' reflects a common behavioral principle across organisms: favoring pursuit of a coveted reward over potential risks.”

“we discover a dopamine-governed filter mechanism in male Drosophila that reduces threat perception as courtship progresses. We show that during early courtship stages, threat-activated visual neurons inhibit central courtship nodes via specific serotonergic neurons. This serotonergic inhibition prompts flies to abort courtship when they see imminent danger. However, as flies advance in the courtship process, the dopaminergic filter system reduces visual threat responses, shifting the balance from survival to mating.”

Cazale Debat et al., 2024, from Carolina Rezaval’s lab.
https://www.biorxiv.org/content/10.1101/2024.04.23.590677v1?med=mas

neuralreckoning, to academia
@neuralreckoning@neuromatch.social avatar

So oral exam at end of PhD. Good idea or just a tradition that doesn't make any sense any more? What are the good things about them? If we didn't do them, how else could we get those good things?

albertcardona,
@albertcardona@mathstodon.xyz avatar

@neuralreckoning @steveroyle @kofanchen @nicolaromano

An additional benefit is that PhD thesis are available online without a paywall.

albertcardona, to Neuroscience
@albertcardona@mathstodon.xyz avatar

How the insect centre for learning and memory, the mushroom body, evolves. By Farnworth et al. 2024, using the example of "the Heliconiini (Nymphalidae), which show extensive variation in mushroom body size over comparatively short phylogenetic timescales, linked to specific changes in foraging ecology, life history and cognition."

Some key findings:

  • number of GABA cells change, concomitant with increase in Kenyon Cell number;
  • number of DANs don't.

"Mosaic evolution of a learning and memory circuit in Heliconiini butterflies"
https://www.biorxiv.org/content/10.1101/2024.04.21.590441v1

25kV, to random
@25kV@mas.to avatar

I've just heard the phrase "carbon terrorist" used in relation to someone who chose to fly domestically rather than take the train. I'm 100% using that

albertcardona,
@albertcardona@mathstodon.xyz avatar

@25kV

My employer when suggesting travelling by train: "we support whatever is cheapest".

Replying to the tune of, did they take into account fuel subsidies and other subsidies into the costs landed on deaf ears – it's all local optimization, despite the money coming from the same place: my employer is the government.

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

The honeybee brain hosts over 600,000 neurons, at a density higher than that of mammalian brains:

"Our estimate of total brain cell number for the European honeybee (Apis mellifera;
≈ 6.13 × 10^5, s = 1.28 × 10^5; ...) was lower than the existing estimate from brain sections ≈ 8.5 × 10^5"

"the highest neuron densities have been found in the smallest respective species examined (smoky shrews in mammals; 2.08 × 10^5 neurons mg^−1 [14] and goldcrests in birds; 4.9 × 10^5 neurons mg^−1 [16]). The Hymenoptera in our sample have on average higher cell densities than vertebrates (5.94 × 10^5 cells mg^−1; n = 30 species)."

Ants, on the other hand ...

"ants stand out from bees and wasps as having particularly small brains by measures of mass and cell number."

From:
"Allometric analysis of brain cell number in Hymenoptera suggests ant brains diverge from general trends", by Godfrey et al. 2021.
https://royalsocietypublishing.org/doi/10.1098/rspb.2021.0199

albertcardona,
@albertcardona@mathstodon.xyz avatar

@futurebird

On fairy wasps, they do include them. This is what they write:

"In the small Hymenoptera, neuron size may be a limiting factor for brain miniaturization, as shown for the smallest insects (the parasitoid wasp Megaphragma [42]), whose larval brains comprise less than 5000 cells, the cell bodies of which are lost during pupation. The brain of the smallest species in our sample (the parasitoid wasps Leptopilina; figure 1) comprised around 30 000 cells (electronic supplementary material, table S1). Similar neuron numbers (2.2 × 105–3.7 × 105 neurons; [43]) have been estimated for fairyflies (Hymenoptera: Mymaridae), which are smaller than the smallest of our samples, suggesting that our cell number estimates may be conservative."

On ants: ants have large antennae and use them for all sorts of tasks, including sensing wind, scent, and mechanoreceptively as if they were hands but also as drums for assessing through vibration the content and properties of what they are touching. Parasitoid wasps ("flying ants", sort of) use their antennae to drum surfaces, a form of active echolocation of caterpillars and larvae inside plant stems or wood. All of these activities need a lot of brain power to process them.

Granted, eyes as 2D surfaces require lots of repeated neurons for contrast and color, and neurons that integrate across them just to process movement in the visual scene. I'd like to see a comparison with the size of antennal lobes and AMMC (antennal mechanosensory and motor center) regions of wasps and ants.

By the way, large brains may be costly for parasitoid wasps for little benefit, say van der Woude et al. 2019 https://academic.oup.com/jeb/article/32/7/694/7326298

albertcardona,
@albertcardona@mathstodon.xyz avatar

@glowl

Regarding nutrient and oxygen flow, would be interesting to compare the brains of a large bee like Xylocopa violacea (violet carpenter bee [1]) with that of a small bat like Craseonycteris thonglongyai (bumblebee bat [2]).

These two species are of about the same size (3-5 cm), yet one is an insect and the other is a mammal. Actually, the bee is larger than the bat! I wonder which one has more neurons.

[1] https://www.inaturalist.org/observations/89535013
[2] By Andaman Kaosung: https://www.inaturalist.org/taxa/41399-Craseonycteris-thonglongyai

Xylocopa violacea on thistle flowers.

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.

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.

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