a_j_millar - Network

Single field tree at the foot of Cademuir, in Manor #ScottishBorders. Its challenges are clearer close to...#ThickTrunkTuesday #Trees...

Single field tree at the foot of Cademuir, in Manor #ScottishBorders.

Its challenges are clearer close to...

#ThickTrunkTuesday #Trees #CellsRegeneration

#ElonMusk #RoyalSociety #USPolIn his response to Geoffrey Hinton on X, "That said, what specific actions require correction? I will...

#ElonMusk #RoyalSociety #USPol

In his response to Geoffrey Hinton on X, "That said, what specific actions require correction? I will make mistakes, but endeavor to fix them fast."

What does the evidence show on the pace of global heating and the causal role of burning fossil fuels?

Does the US public data and funded science come back online "fast"?

➡️ https://climate.copernicus.eu/copernicus-2024-first-year-exceed-15degc-above-pre-industrial-level

The palette of heartwood and brown rot, revealed after #StormEowyn. #RBGEdinburgh #ThickTrunkTuesday #Fungi #Trees

The palette of heartwood and brown rot, revealed after #StormEowyn.

#RBGEdinburgh #ThickTrunkTuesday #Fungi #Trees

📢 BOOM! 🤯 AI build-a-genome 🤖🧬 . Larger than LLMs. And it's all (claimed to be) Open."Genome modeling and design...

📢 BOOM! 🤯
AI build-a-genome 🤖🧬 . Larger than LLMs. And it's all (claimed to be) Open.

"Genome modeling and design across all domains of life with Evo 2"

The design function for Synthetic Genomics? which already has (some) build capability. HT Uriel Urquiza.

➡️ https://arcinstitute.org/manuscripts/Evo2

#SyntheticBiology #BioEngineering #genome #AiResearch

8/8 📚🔗 All the #OpenData, scripts etc are on FAIRDOMHub.org, with a copy on Zenodo.➡️ ...

8/8 📚🔗 All the #OpenData, scripts etc are on FAIRDOMHub.org, with a copy on Zenodo.

➡️ https://fairdomhub.org/investigations/570

Let us know if it’s useful to you!

6. 7/8 🌐📚 Future prospects: there was so little biochemical data for our specific proteins, we had to rely on genome-wide data (PBMs)....

6. 7/8 🌐📚 Future prospects: there was so little biochemical data for our specific proteins, we had to rely on genome-wide data (PBMs). We could then estimate Kd for ANY sequence. That means, also for sequence variants.

Our earlier Framework Model v2 (FMv2) and FM-Life models link the clock right up, through plant metabolism, growth, development and physiology, to seed-to-seed adaptation in real weather.

Anyone who assembles these parts gets to predict how an Arabidopsis genome sequence variant will be adapted to climatic conditions. With a full causal chain. The mechanisms of evolutionary adaptation.👀 #GoForIt

Sure it’s simplified and there’s much to validate but it’s there. DNA-binding Kd is just where we started, there’s more known biochemistry to add.

#Evolution #LifeCycle #QuantitativeBiology #Arabidopsis

5. 6/8 📈🔍 Technical: we first estimated protein levels based on absolute RNA levels per cell, from earlier work with Mark Stitt, then...

5. 6/8 📈🔍 Technical: we first estimated protein levels based on absolute RNA levels per cell, from earlier work with Mark Stitt, then used NanoLUC reporter protein fusions to test those protein levels in vivo. For several proteins, this simple approach matched the data, indicating that RNA regulation really is critical.

The calibrated NanoLUC assays should be broadly useful for testing bulk protein levels, so get up close and quantitative with your plant cells! Here’s the protocol:

➡️ https://doi.org/10.17504/protocols.io.4r3l29n4jv1y/v1

5/8 🔬🧩 The simulated Kd values for the Evening Complex binding overlapped with the empirical data on its DNA-binding protein LUX ✅...

5/8 🔬🧩 The simulated Kd values for the Evening Complex binding overlapped with the empirical data on its DNA-binding protein LUX ✅

Simulated CCA1/LHY bound much less tightly than its measured Kd. Likely, the plant regulates these proteins in ways we haven’t modelled: future research directions!

We point to lots specific hypotheses, data and knowledge gaps, see Dataset EV1. We’re not pursuing any of them.

#MicDrop #GoForIt #PlantGenetics #MolecularBiology

3/8 🧬📊 For the first time (or do update us), we've modelled dynamic, plant gene circuits with absolute units for both RNA and...

3/8 🧬📊 For the first time (or do update us), we've modelled dynamic, plant gene circuits with absolute units for both RNA and protein copies per cell.

You can compare our mathematical models directly to your biochemical data. Over time, both approaches should benefit! #SystemsBiology

4/8 🤖🧪 Those absolute units mean that we can predict the DNA-binding dissociation constants (Kd) of our clock transcription factors in vivo, for example.

After some tricky calibration, we estimated comparable Kd values in vitro from our earlier data and the literature, extending the method to any promoter sequence (more on this later).

So, did they match?

#Bioinformatics #GeneExpression

2/8 Historical🔖 . I had worked to identify the genes in the plant circadian clock since 1988. My group published the first mathematical...

2/8 Historical🔖 . I had worked to identify the genes in the plant circadian clock since 1988. My group published the first mathematical model of how these genes build the plant circadian clock 20 years ago!

One of our papers was in the first volume of Molecular Systems Biology, the very same journal that has just published my last paper on these models.

A shout out to their editors, including founding editor Thomas Lemberger @tlemberger 🙏
@MolSystBiol

1/8 🌱🔬 Exciting developments in biology!Our research investigates the 24-hour, biological clock in plants, now using absolute protein...

1/8 🌱🔬 Exciting developments in biology!

Our research investigates the 24-hour, biological clock in plants, now using absolute protein quantification thanks to Uriel Urquiza’s hard work with me, Karen Halliday and Nacho Molina.

It points to some simple conclusions, some unknown regulatory mechanisms and the promise of a whole new level of understanding. 🧵

➡️ https://doi.org/10.1038/s44320-025-00086-5

Edited to add the Synopsis image.

#Plantsci #Circadian #OpenData

#ElonMusk #RoyalSocietyI hope that the Royal Society reforms its processes fundamentally, so that it is fit for more of the challenges to...

#ElonMusk #RoyalSociety

I hope that the Royal Society reforms its processes fundamentally, so that it is fit for more of the challenges to science. Not just those that we have recognised for years like disinformation, but what the evidence shows is an unprecedented mid-century of climate and nature crises, with existential threats to societies. We need science and scientists to be part of the solution, not collateral damage.

3/3
Ends.

Refers to https://fediscience.org/@A_J_Millar/113990769863860215

#ElonMusk #RoyalSocietyProfessor Bishop's resignation blog detailed how Elon Musk has recently promoted disinformation on science and...

#ElonMusk #RoyalSociety

Professor Bishop's resignation blog detailed how Elon Musk has recently promoted disinformation on science and attacked evidence-based policies, science advice and personally attacked a public scientist, Dr. Anthony Fauci. He now does so as the owner of a major media platform.

Those actions are not compatible with the conduct required of a Fellow, and I do not want a Fellowship that can include such actions. They undermine the purpose of the Royal Society. In an era of fake news, they are not a blip, they are part of a much broader pattern, yet the Royal Society's leadership has not found a way to handle even this extreme case.

2/3

#ElonMusk #RoyalSocietyProfessor Andrew Millar's statement on resigning from Fellowship of the Royal Society on 12 Feb 2025, thread...

#ElonMusk #RoyalSociety

Professor Andrew Millar's statement on resigning from Fellowship of the Royal Society on 12 Feb 2025, thread 1/3...

Fellowship of the Royal Society is a substantial honour. You are selected by distinguished scientists in a process that involves your peers around the world. I was in awe when I met the other Fellows who were elected with me in 2012.

The Society and its Fellows champion science, supporting new research, using the consensus evidence to inform policy-making, and more. I saw how important that role can be, when I was one of the Chief Scientific Advisers in the Scottish Government.

#ElonMusk #RoyalSocietyI have resigned my Fellowship of the Royal Society, due to their Council's inability to take proportionate action...

#ElonMusk #RoyalSociety

I have resigned my Fellowship of the Royal Society, due to their Council's inability to take proportionate action on Elon Musk's current promotion of disinformation and attacks on evidence-based policies and science advice, as detailed by Professor Bishop @deevybee .

➡️ https://deevybee.blogspot.com/2024/11/why-i-have-resigned-from-royal-society.html

The Society and its Fellows champion science, both generating and using evidence. Hold to that strategy! I hope their leadership finds a better way through the tactics.

Link to longer statement added 13 Feb:
➡️ https://fediscience.org/@A_J_Millar/113996095951623704

Iron is an important plant nutrient, usually acquired through the roots 👨‍🏫 📖 but perhaps also by other routes, at least in this...

Iron is an important plant nutrient, usually acquired through the roots 👨‍🏫 📖

but perhaps also by other routes,
at least in this #HungryTree 👀🌳.

#Trees #ThickTrunkTuesday

... shattered chaos! The trunk failed so low into the roots that the falling splinters levered up a divot of soil and undergrowth, which...

... shattered chaos! The trunk failed so low into the roots that the falling splinters levered up a divot of soil and undergrowth, which it's now wearing like a wig.

This sycamore sported a bold dog's-leg limb with more growth than the original trunk, next an old path in its valley in #Edinburgh....

This sycamore sported a bold dog's-leg limb with more growth than the original trunk, next an old path in its valley in #Edinburgh. Until Storm #Eowyn last month caused ... 👇 🧵

#ThickTrunkTuesday #Trees

Big Beech in the Borders#ThickTrunkTuesday #Trees #Scotland

Big Beech in the Borders

#ThickTrunkTuesday #Trees #Scotland

#ThickTrunkTuesday Blah photo on a dark day, any tips genuinely appreciated, but 👀 Biology. Near-catastrophic damage up the trunk and...

#ThickTrunkTuesday
Blah photo on a dark day, any tips genuinely appreciated, but 👀 Biology.

Near-catastrophic damage up the trunk and branches (fire below? tear-out?), now zipping back together from the top 💪🌳 .

#Trees #PlantSci #CellsRegeneration