Wednesday, May 14, 2025

Port Orford Cedar (Chamaecyparis lawsoniana): How best to grow a #RealisticVirtualEarthForSyntheticBiology w "#AlphaFold3 predicts the structure & interactions of all of life’s molecules' w #BenchlingForRandD https://www.benchling.com/ for #AgingReversalGenetic & #ExtremeLongevityGenetic #drugTherapies? * AlphaFold 3 predicts the structure and interactions of all of life’s molecules & Benchling: Cloud-based platform for biotech R&D * * * * May 16, 2025 HTGAA 2025 || THANK YOU! | from David Sun Kong * In 1st group picture - I'm in the 1st column, 7 pictures down, holding virtual Harbin Hot Springs' gatehouse in Google Street View on smartphone AND a World University and School sticker ... In 2nd group picture - I Scott MacLeod am in the 3rd column, 4 pictures down not holding any object ... Am watching and listening now to the MIT, Harvard and Committed Listener student presentations I didn't or wasn't able to see and hear ... as a Global Listener in the MIT and Harvard HTGAA 2025 synthetic biology course. Thanks much to its faculty!


How best to grow a #RealisticVirtualEarthForSyntheticBiology w "#AlphaFold3 predicts the structure & interactions of all of life’s molecules' w #BenchlingForRandD https://www.benchling.com/ for #AgingReversalGenetic &  #ExtremeLongevityGenetic #drugTherapies? 


AlphaFold 3 predicts the structure and interactions of all of life’s molecules &  Benchling: Cloud-based platform for biotech R&D 


How best to grow a #RealisticVirtualEarthForSyntheticBiology w "#AlphaFold3 predicts the structure & interactions of all of life’s molecules'
https://blog.google/technology/ai/google-deepmind-isomorphic-alphafold-3-ai-model/#future-cell-biology w #BenchlingForRandD
https://www.benchling.com/ for #AgingReversalGenetic & #ExtremeLongevityGenetic #drugTherapies?

Benchling image - 





Googles ALPHAFOLD-3 Just Changed EVERYTHING! (AlphaFold 3 Explained)


AND

The Benchling R&D Cloud

AND 

As an example or place in an emerging realistic virtual earth - 

in 

Friday, May 9, 2025





*
AlphaFold 3 predicts the structure and interactions of all of life’s molecules 


*
In @WorldUnivAndSch dev. a #RealisticVirtualEarthForAgingReversal w #AlphaFold3server "#AlphaFold3 predicts the structure and interactions of all of life’s molecules"



Languages WUaS - 







Retweeting -

The first stage of the Neurona Therapeutics clinical trial is supported by CIRM.

Investigational therapies that receive RMAT designation are eligible to receive expedited development review and planning guidance from the @US_FDA.









*
How best to interoperate "impact of modifying genes and proteins? 🧬" w a #RealisticVirtualEarthForGenes #RealisticVirtualEarthForProteins
@WorldUnivAndSch #WUaSunivs 
https://www.toolify. ai/ai-news/revolutionizing-education-with-machine-learning-and-ai-2574306 
-#ToolifyAIWUaS w https://blog. google/technology/ai/google-deepmind-isomorphic-alphafold-3-ai-model/#future-cell-biology think #GstreetView w #TimeSlider #GAtomView ?
https://twitter. com/scottmacleod/status/1796502507575025975 

https://twitter. com/WorldUnivAndSch/status/1796502696910012679 

https://twitter. com/TheOpenBand/status/1796503322985460072 

https://twitter. com/sgkmacleod/status/1796503237778141566 

https://twitter. com/HarbinBook/status/1796503144375230473 

https://twitter. com/WUaSPress/status/1796502812538650981 



Retweeting - 

What is the impact of modifying genes and proteins? 🧬

We're developing the #opensource Perturbation Catalogue to answer this, integrating harmonised and curated gene, variant, and expression data

Are you a postdoc or full stack dev? Help us build this!

https://twitter. com/OpenTargets/status/1796148051146313846. ... to https://wiki.worlduniversityandschool. org/wiki/Virtual_Worlds and https://wiki.worlduniversityandschool. org/wiki/Aging_Reversal_Genetics and https://wiki.worlduniversityandschool. org/wiki/Open_Access_Resources (from https://wiki.worlduniversityandschool. org/wiki/Subjects)



*

Retweeting - 

What is the impact of modifying genes and proteins? 🧬

We're developing the #opensource Perturbation Catalogue to answer this, integrating harmonised and curated gene, variant, and expression data

Are you a postdoc or full stack dev? Help us build this!







A #RealisticVirtualEarthFor #AgingReversalMachine too? Thnx #PeterNorvig for #ToolifyAI WOW! article: 
"#RevolutionizingEducation w #MachineLearning & AI" : @WorldUnivAndSch #WUaSunivs 



*

A #RealisticVirtualEarthFor #AgingReversalMachine too? Thnx #PeterNorvig for #ToolifyAI WOW! article: 
"#RevolutionizingEducation w #MachineLearning & AI" : @WorldUnivAndSch #WUaSunivs 











*


WOW: "#AlphaFold3 takes us beyond proteins to a broad spectrum of biomolecules. This leap could unlock more transformative science" - to accelerate #WUaSDrugDesign & #WUaSgenomics research"-Steps to #RealisticVirtualEarthFor #ForProteins #ForPharmaceuticals #AgingReversalMachine?







Retweeting - 

1.8M+ researchers have used @GoogleDeepMind’s AlphaFold protein predictions in their work on vaccine development, cancer treatment + more. AlphaFold 3 is the latest breakthrough, predicting the structures + interactions of all of life’s molecules with unprecedented accuracy. We’re sharing access to these capabilities through AlphaFold Server to enable other scientific discoveries. blog.google/technology/ai/




*
AlphaFold 3 predicts the structure and interactions of all of life’s molecules
May 08, 2024


Introducing AlphaFold 3, a new AI model developed by Google DeepMind and Isomorphic Labs. By accurately predicting the structure of proteins, DNA, RNA, ligands and more, and how they interact, we hope it will transform our understanding of the biological world and drug discovery.



G
Google DeepMind AlphaFold team
I
Isomorphic Labs


AND 

In what ways @HankGreelyLSJU @johncumbers All could #AlphaFold3 be emerging #CSvocabulary to also predict #GeneExpression  -https://blog.google/technology/ai/google-deepmind-isomorphic-alphafold-3-ai-model/#future-cell-biology & in building a #RealisticVirtualEarthForGenetics >https://www.toolify.ai/ai-news/revolutionizing-education-with-machine-learning-and-ai-2574306 eg in #GStreetView w #TimeSlider #GCellView #GAtomView ?








Retweeting - 

Another indication of the complexity of gene expression, in this case in regard to splicing. My sense in this (very interesting) paper is that we still lack the vocabulary to talk about the organizational and spatiotemporal processes here. #HowLifeWorks 





* * *  



Aryan Choudhary at IIT Delhi India ... 


Aryan, Great! What about storing DNA as data AND GOING both ways Data < > DNA … so digital < > physical, and actual < > virtual … and potentially, brainstorming-wise in a #RealsiticVirtualEarth (and think GStreetView with TimeSlider and TensorFlowAI + especially)?


Aryan -

Regarding your slide 270, and ‘Future Vision’ - in storing Data in DNA - and aging reversal and extreme longevity for example - going both ways would allow for genetic information developments on both sides of the Physical-Digital … and over time re the Google Street View with G time slider, TensorFlowAI and brainstorming at the GMoleculeView level and GeneView levels … and potentially with the Python language to begin.



Aryan, It’s kind of a goal at MIT OCW-centric wiki World University and School WUaS and in / with a Physical-Digital #RealisticVirtualEarth #ForSyntheticBiology too (#Twitter) … and for the co-constitutionality of going both ways … (thinking GStreetView with TimeSlider #GCellView #GgeneView #GMoleculeView TensorFlow AI and potentially for aging reversal and extreme longevity genetic drug therapies emerging … and with Python language as integral … What’s your email if … sgkmacleod@worlduniversityandschool.org is mine … Namaste, Scott)




Google search: 

encoding data as dna

Encoding data into DNA involves converting digital information (like text, images, or audio) into a sequence of nucleotides (A, T, C, and G) within a DNA molecule. This process, sometimes called DNA data storage, leverages DNA's high storage density and long-term stability. The encoded DNA sequence can then be stored and retrieved, allowing for the recovery of the original digital data







AND 

Anandita (in Indonesia), Did you by chance use Benchling? (And if you  could, how would you integrate this with AlphaFold3Server … and for the HBB protein and re machine learning prediction … per your slide 307 - https://docs.google.com/presentation/d/1g2tAjWA_NHVcTpy3ETmHhmhopl8xNbkn0cO5kXeI1eU/edit?slide=id.g3546bfed8e0_62_0#slide=id.g3546bfed8e0_62_0 ) Thanks so much! Yogically, Scott (Scott GK MacLeod - at MIT OCW-centric wiki World Univ & Sch planned in all 200 countries, and main languages - and especially for Indonesia WUaS - sgkmacleod@worlduniversityandschool.org)





AND

@Aprajita Shukla, Manipal, India 

Great visionary project @Aprajita Shukla, Manipal,India  ! Could such ink somehow be engineered to grow or develop through time?





On Mon, May 12, 2025 at 12:30 AM David S. Kong <dkong@mit.edu> wrote:
Dear HTGAA 2025,

It’s hard to believe, but the semester is almost at its conclusion—this week we have our HTGAA 2025 FINAL PRESENTATIONS, featuring all of our MIT and Harvard students and global Committed Listeners!

We have some 13 hours of student final presentations this year, featuring an incredible diversity of projects. I couldn’t be more excited for the students to showcase their creative work from the semester!

It is an honor to invite all of our HTGAA faculty, teaching assistant instructors, and alumni to join our student presentations! We would love to see you in person Tuesday or via zoom (Tuesday and/or Wednesday).

Our presentation schedule for the week is as follows:

///
Tuesday May 13 | E14-341 (for those joining in person)

2:05pm-5:00pm ET: MIT & Harvard student final project presentations!



///
Wednesday May 14 (ALL VIRTUAL)

9:00am-7:00pm ET: Global Committed Listener final project presentations!


///

For MIT & Harvard students: A reminder that grades are due to MIT on Thursday, so you must complete all of your documentation by Wednesday at 11:59pm ET. This includes documentation for every weekly homework, lab, and for your final projects.

For Committed Listeners: A reminder that your completed documentation for all weekly homework, labs, and your final projects are due May 28th at 11:59pm ET!

Thanks so much everyone and excited to see you on Tuesday and Wednesday!

Best,
David

--------------
David Sun Kong, Ph.D.
Director
Community Biotechnology Initiative
MIT Media Lab




--


Society, Information Technology, and the Global University (2025, forthcoming) 

- Scott GK MacLeod  
Founder, President, CEO & Professor
CC-4 licensed MIT OCW-centric, Wiki, 
World University & School (WUaS) 
- USPS US Post Office, General Delivery, Canyon, CA 94516 


1) non-profit 501(c)(3) Public Charity 
MIT OCW-centric, 
 World University and School - http://worlduniversityandschool.org  

2) for profit general stock company WUaS Corporation in CA - http://worlduniversityandschool.org/AcademicPress.html

(m) 412 478 0116 - sgkmacleod@gmail.com 


World Univ & Sch Innovation Research -  scottmacleod.com 






* * * * 


Tue May 27, 2025



May 16, 2025

HTGAA 2025 || THANK YOU! |

Inbox

David S. Kong

May 16, 2025, 2:46 PM (11 days ago)
to David


Dear HTGAA 2025,


Thanks so much to each and everyone of you for a spectacular end to the semester! For those that were unable to join, it was an epic two days of final project presentations, with MIT & Harvard students presenting for more than 3 hours and our global Committed Listeners presenting for nearly 10 hours! 😱🤯And at least a few of us were there to witness all 13 hrs+ of HTGAA brilliance. Thanks to all for your endurance and perseverance!

It was truly an awe-inspiring set of presentations. I am so grateful to each and every student for all of your hard work, creativity, and passion. You give me so much hope for the world!

And none of this would be possible without the dedication and excellence of all of our HTGAA faculty, teaching assistants, and biology department collaborators—thanks to each of you from the bottom of my heart for all of your contributions! And special thanks and deep gratitude to our HTGAA 2025 sponsors, Twist Biosciences, Thermo Fisher Scientific, Opentrons, and Waters Corporation. Our work simply would not be possible without you!

I leave you with links to the presentations below and some photographs. I invite you to watch, or at least scan through the student presentations when you have a little time, to be inspired and to appreciate the wonderful work of our students: 


Global Committed Listener slides:

For all Committed Listeners, please also complete this course survey! You can express your interest to join our teaching team and to continue research with us as well :) 


Of course, our work together is not over, and as was shared at the end of our global session, this is merely ’the end of the beginning.’ HTGAA has been a magical journey this year, but we are only getting started. Onwards and I am grateful to be on this adventure with you all!

Sincerely,
David

PS, here are two social media posts about the course as well!





--------------
David Sun Kong, Ph.D.
Director
Community Biotechnology Initiative
MIT Media Lab



--------------
David Sun Kong, Ph.D.
Director
Community Biotechnology Initiative
MIT Media Lab




https://docs.google.com/presentation/d/1g2tAjWA_NHVcTpy3ETmHhmhopl8xNbkn0cO5kXeI1eU/edit?usp=sharing



In 1st group picture - 

I'm in the

1st column, 7 pictures down, holding virtual Harbin Hot Springs' gatehouse in Google Street View on smartphone AND a World University and School sticker ...


In 2nd group picture - 

I Scott MacLeod am in the 

3rd column, 4 pictures down not holding any object  ... 


Am watching and listening now to the MIT, Harvard and Committed Listener student presentations I didn't or wasn't able to see and hear ... as a Global Listener in the MIT and Harvard HTGAA 2025 synthetic biology course. Thanks much to its faculty!



* * 


presentations by #MITHarvardRegisteredStudents: DAUNTING OPPORTUNITIES to grow a #RealisticVirtualEarth #ForSyntheticBiology . . .  

In reviewing the final #MITHarvard #HTGAA2025 presentations by #MITHarvardRegisteredStudents: DAUNTING OPPORTUNITIES to grow a #RealisticVirtualEarth #ForSyntheticBiology & w "#AlphaFold3 predicts the structure & interactions of all of life’s molecules" https://scott-macleod.blogspot.com/2025/05/port-orford-cedar-chamaecyparis.html ~


https://x.com/WorldUnivAndSch/status/1928161248882868257

https://x.com/WUaSPress/status/1928163521847521576

https://x.com/HarbinBook/status/1928165520110391724

https://x.com/sgkmacleod/status/1928162706294722783

https://x.com/scottmacleod/status/1928164592594866597

https://x.com/Q_YogaMacFlower/status/1928162038976561281

https://x.com/TheOpenBand/status/1928164130973683847



Retweeting -

David Sun Kong, Ph.D.
@davidsunkong
I’m thrilled to announce that the application for the 2025 edition of our
@medialab
 and global synthetic biology course, “How to Grow (Almost) Anything” is now open! Application link in thread 👇

https://x.com/davidsunkong/status/1876687155604631779





 





https://upload.wikimedia.org/wikipedia/commons/thumb/3/32/Lawson%27s_Cypress%2C_Six_Rivers_National_Forest%2C_Klamath%2C_California_1.jpg/960px-Lawson%27s_Cypress%2C_Six_Rivers_National_Forest%2C_Klamath%2C_California_1.jpg



























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

https://species.wikimedia.org/wiki/Chamaecyparis_lawsoniana


...


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