Thiago Carvalho @cyrilpedia@qoto.org
I've worked on all of science, from B cells to T cells.
https://fellowsherpa.com
Joined Nov 2022
Thiago Carvalho
boosted
“Who serves best doesn’t always understand.”
The Nobel-winning Polish poet Czesław Miłosz on love https://www.themarginalian.org/2018/08/16/czeslaw-milosz-love/
New Yorkers, not great news regarding your Rodent Overlords:
"We evaluated SARS-CoV-2 exposure among 79 rats captured from NYC during the fall of 2021. Our results showed that 13 of the 79 rats (16.5%) tested IgG- or IgM-positive, and partial SARS-CoV-2 genomes were recovered from all 4 rats that were qRT-PCR (reverse transcription-quantitative PCR)-positive."
#COVID #Zoonosis #Covid19 #spillover
cc @n8_upham
"AACR Breast Cancer Research Fellowships provide two-year, $120,000 grants to support postdoctoral and clinical fellows conducting basic, translational, clinical, or epidemiological research focused on breast cancer. Applications are due March 23"
"The other very important advancement in the last 5 years, is the development of single-cell regulatory genomes methods, which allow us to look at enhancer usage at a scale that simply wasn’t possible before. This is allowing us to look upstream of RNA, identifying the regulatory elements that are being dynamically used at different stages of embryogenesis. We can basically follow the regulation of a tissue’s development."
Thiago Carvalho
boosted
Sir David #Attenborough, Knight Grand Cross of the Order of St Michael And St George and close friend of Queen Elizabeth is deemed to be too communist by the legally-bound impartial #BBC controller to be broadcast. #climatebreakdown #Tories #Conservatives #climate https://www.theguardian.com/media/2023/mar/10/david-attenborough-bbc-wild-isles-episode-rightwing-backlash-fears.
Thiago Carvalho
boosted
Shocking
---
RT @JackDAshby
This is heinous. The BBC is censoring not only itself, but David Attenborough, by pulling an episode of its new flagship series on British wildlife as it focuses on UK wildlife declines... in case it upsets right-wing politicans and media. #WildIsles
https://www.theguardian.com/media/2023/mar/10/david-attenborough-bbc-wild-isles-episode-rightwing-backlash-fears
https://twitter.com/JackDAshby/status/1634213555850612736
A very good NY Times piece on the state of the science on mask use - spoiler alert: if used properly, they work.
Thiago Carvalho
boosted
Assistant Professor (tenure-track) @IUPUIBiology
Tenure-track faculty position in the Department of Biology at Indiana University Purdue University Indianapolis (IUPUI).
#ScienceJobs #job
Indianapolis #UnitedStatesUS #Fac...
https://jobrxiv.org/job/indiana-university-purdue-university-indianapolis-27778-assistant-professor-tenure-track/?feed_id=40206
A somewhat related ref that I enjoyed this week was sent to me by Zach Mainen, a perspective on LLMs by Terry Sejnowski
There are a few parts to this - for the first one, how far a descriptive approach will get us in terms of understanding function, I like what Cori Bargmann said in our conversation (which started with an analogy to the Human Genome Project and pathophysiology): understanding the components won't be an explanation, but it will set the boundaries within which the explanation(s) must be found.
In terms of AI, for me the most likely to be useful approach is comparative: to treat it as we would an alien lifeform in questions around the origin of life - but it will not necessarily map directly on to any understanding of the biological brain.
Thiago Carvalho
boosted
@NicoleCRust @MatteoCarandini @Iris @knutson_brain @schoppik @cyrilpedia
As a biologist by training, it seems self-evident that if we are to come up with preventive measures or a cure for e.g., neurodegenerative diseases, we ought to be explicitly studying biological neural networks that suffer from such diseases in the first place.
That is not to say that we aren't going to learn a lot from studies of how artificial networks work and behave. We will. But the cure, for instance, would most likely have to be of the biological kind, and even more likely, an intervention on the immune system, be it vaccination or otherwise–I'm referring to e.g., multiple sclerosis and the Epstein-Barr virus, as there may be many more such cryptic, decade-after-infection effects on the nervous system.
Scribbling about spillovers with my stylish bat-print pen pouch by Madalena
A conversation I had with Marcel LaFlamme @PLOS on #preprints, #peerreview, AI, and, of course, #ReviewCommons has just been posted on the @ReviewCommons site
"As we ask peer review to do more and more things, should we also be looking at new ways to recognize the work of reviewers?
Another way to ask that question is: should outputs other than published articles and big grants count toward research assessment and the development of scientific careers?"
Thiago Carvalho
boosted
On explanations in brain research:
A thread of the same idea comes up again and again in brain research. It's the notion that identifying the biological details (such as the brain areas/circuits or neurotransmitters) associated with some brain function (like seeing or fear or memory) is not a complete explanation of how the brain gives rise to that function (even if you can demonstrate the links are causal). To paraphrase:
Mountcastle: Where is not how https://www.hup.harvard.edu/catalog.php?isbn=9780674661882
Marr: How is not what or why http://mechanism.ucsd.edu/teaching/f18/David_Marr_Vision_A_Computational_Investigation_into_the_Human_Representation_and_Processing_of_Visual_Information.chapter1.pdf
@MatteoCarandini: Links from circuits to behavior are a "bridge too far" https://www.nature.com/articles/nn.3043
Krakauer et al: Describing that is not understanding how https://www.cell.com/neuron/pdf/S0896-6273(16)31040-6.pdf
Poppel: Understanding brain maps does not formulate "what about" the brain gives rise to "what about" behavior https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3498052/
Any other explicit references to add to this list? @Iris, @knutson_brain, Anyone?
Also, I imagine that some form of the opposite idea must also be percolating: the notion that 'algorithmic' descriptions of the type used to build AI will be insufficient to do things like treat brain dysfunction (where we arguably need to know more about the biology to, e.g., create drugs). Any explicit references of that idea? @albertcardona @schoppik, @cyrilpedia, Anyone?
Thiago Carvalho
boosted
What kind of biologist should you be?
I adore this charming - and pretty accurate - chart by @rosemarymosco to help make the decision.
'The consequence is widespread global harm to people's health, wellbeing, and livelihoods—an estimated one in ten people who develop long COVID stop working, resulting in extensive economic losses. In 2021, we called for a coordinated research and health-care agenda to tackle this new medical challenge. However, progress has been excruciatingly slow due to lack of attention and resources.'
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(23)00493-2/fulltext
Thiago Carvalho
boosted
polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies https://doi.org/10.1093/gbe/evad020 #science #evolution #biology #genome #SciComm #evolgen_paper
Disappointing, this one - I was hoping it had some raiding and pillaging in England and getting away origin:
"11. SCOTLAND AND SCOT-FREE
Scot-free is an alteration of shot-free, where shot was a charge or share of a payment. It was a lucky thing to get out of a meal or a night at the tavern shot-free. It later came to mean escaping without injury, and came to be pronounced as scot instead of shot."
Thiago Carvalho
boosted
RT @RoliRoberts
Lucinid clams - #endosymbionts use environmental sulphide for #chemosynthesis. But some #symbiont proteins (sulphide-binding DsrC, metabolism-shunting GAPDH) are found in distant tissues, including haemolymph... how? @jillpeterplan #EESSymbiosis
I've worked on all of science, from B cells to T cells.
https://fellowsherpa.com
Joined Nov 2022
