Tuesday, March 18, 2025

Galápagos tortoises: MIT Harvard "How to Grow (Almost) Anything" synthetic biology courses - HTGAA 2025 Week 7 || Genetic Circuits | * Brainstorming, and regarding developing with synthetic biology a pharmaceutical genes' drug therapy to help people live beyond 122 years old (so regarding aging reversal AND extreme longevity / healthspan genetic drug therapies emerging), and with a muscle wasting reversal AND a higher, faster, stronger, more supple athletics' genetic component, per 2 student presentations just now, how best to begin to formulate these genetic drug discovery question? * * * Unlock the Power of AI with NotebookLM: Introductory Session by GEG Ahmedabad

 


MIT Harvard "How to Grow (Almost) Anything" synthetic biology courses - HTGAA 2025 Week 7 || Genetic Circuits |

*

Brainstorming, and regarding developing with synthetic biology a pharmaceutical genes' drug therapy to help people live beyond 122 years old (so regarding aging reversal AND extreme longevity / healthspan genetic drug therapies emerging), and with a muscle wasting reversal AND a higher, faster, stronger, more supple athletics' genetic component, per 2 student presentations just now,  how best to begin to formulate these genetic drug discovery question?


Dear Professors' David (Sun Kong), George (Church), HTGAA, Peter (Norvig), and All, 

Greetings, and thanks for another excellent 2025 How to Grow (Almost) Anything synthetic biology class today, Tu 3/18/25. Brainstorming, and regarding developing with synthetic biology a pharmaceutical genes' drug therapy to help people live beyond 122 years old (so regarding aging reversal AND extreme longevity / healthspan genetic drug therapies emerging), and with a muscle wasting reversal AND a higher, faster, stronger, more supple athletics' genetic component, per 2 student presentations just now,  how best to begin to formulate these genetic drug discovery question?

Slides 10 & 13 - 

Healthspan research projects (and team?) 

As a HTGAA Global Listener, and brainstorming, I was very appreciative of Alex Tran's slide 10  for "Engineering a Viral Cure for Lactose Intolerance" as an example for developing an approach (poster?) for developing a slide for developing with synthetic biology a pharmaceutical genes' drug therapy to help people live beyond 122 years old:

Alex Tran

And I was very appreciative of Yolanda Xie's healthspan focus with her slide 13: "Dose-response relationship of transient alterations in telomerase expression" 
Yolanda Xie 

The beginnings of a  possible team for this ?

And Cale Harrison at Pfizer UK, and a Cornell alumnus, might we further explore doing this with Pfizer UK somehow, and regarding your role there, Cale? 

And how to do this also in developing a #RealisticVirtualEarthForGeneticCircuits, #RealisticVirtualEarthForGenetics, and in 1 iterating #RealisticVirtualEarth (and see too Peter Norvig's INCREDIBLE #ToolifyAIWUaS article mentioning for the first time outside of MIT OCW-centric wiki World University and School WUaS a #RealisticVirtualEarth for STEM 

And re this
"Perturb-FISH" Tweet from Chris Mason who gave a tour-de-force talk in HTGAA last week -
https://x.com/mason_lab/status/1900164225294622720 ... ie 

... and thinking Google Street View with time slider, GMaps, GEarth, GCellView, GMoleculeView with TensorFlowAI ... and where little Pegman could become our #AvatarAgentElectronicHealthRecords regarding genetic drug therapies and even editing and adding genes especially)?

Suggestions, Professors David Sun Kong, George Church, Peter Norvig, All? 

Greetings! How are you? How many Global Listeners are there in HTGAA 2025? 

Scott Gordon MacLeod, Canyon, 94516, SF Bay Area, US

Also asked in text chat about - 
#FilmTo3D apps (in microscopy especially) and #FilmToNDimensional apps could bring these questions to biology with computing with genetic circuits - in completely new ways (light sheet microscopy + ?) ... and into a #RealisticVirtualEarth #ForGeneticCircuits ?

Thanks, best regards, thanks for the incredible 2025 HTGAA course,
Scott
Scott GK MacLeod

- 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





Notes - 

1



2
Gibson assembly - 

Gibson Assembly is a molecular cloning method that joins DNA fragments in a single, isothermal reaction, allowing for seamless assembly of multiple fragments without the need for restriction enzymes or specific sites. 
Here's a more detailed explanation:
  • How it works:
    Gibson Assembly relies on three enzymes: a 5' exonuclease, a DNA polymerase, and a DNA ligase. 
    • The exonuclease chews back the 5' ends of DNA fragments, creating single-stranded overhangs. 
    • These overhangs then anneal to complementary sequences on other fragments, forming a joined structure. 
    • The polymerase fills in any gaps, and the ligase seals the nicks, creating a fully assembled, seamless DNA molecule. 
  • Advantages:
    • No restriction enzyme sites needed: Gibson Assembly bypasses the need for specific restriction enzyme sites, making it more versatile. 
    • Seamless cloning: It creates a seamless join between fragments, avoiding any cloning scars. 
    • One-step reaction: The entire assembly process occurs in a single tube, isothermal reaction. 
    • Multiple fragment assembly: It can efficiently assemble multiple DNA fragments into a single construct. 
  • Applications:
    • Synthetic Biology: Gibson Assembly is widely used in synthetic biology to assemble large DNA constructs, such as genetic pathways, for various applications. 
    • Cloning: It's a powerful tool for cloning DNA fragments into plasmids, bacterial artificial chromosomes (BACs), and other vectors. 
  • Key Features:
    • Isothermal: The reaction occurs at a constant temperature (typically 50°C). 
    • Overlapping ends: DNA fragments are designed with overlapping ends that facilitate annealing and assembly. 
    • Developed by: Daniel Gibson and colleagues at the J. Craig Venter Institute
 


2
Neuromorphic computing - 

The term “neuromorphic” was coined by Carver Mead in the late 'eighties to refer to artificial neural systems whose architecture and design principles are based on those of biological nervous systems (Mead, 1990). SiN circuits represent therefore one of the main building blocks for implementing neuromorphic systems

https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2011.00073/full#:~:text=The%20term%20%E2%80%9Cneuromorphic%E2%80%9D%20was%20coined,blocks%20for%20implementing%20neuromorphic%20systems.



3 

BioBricks™ is a standard for interchangable parts, developed with a view to building biological systems in living cells. The picture to the left shows BioBrick™ part BBa_B0034 within a plasmid. The part is flanked by a standard BioBrick™ prefix (P) and suffix (S).

https://parts.igem.org/Help:An_Introduction_to_BioBricks#:~:text=BioBricks%E2%84%A2%20is%20a%20standard,)%20and%20suffix%20(S).



4
KEGG and Reactome are pathway databases as natural genetic circuits?

While both KEGG and Reactome are valuable pathway databases, they do not represent natural genetic circuits in the way that a biological system's genetic code does. They are curated databases that compile and organize information about known pathways and reactions, rather than being direct representations of the genetic code. 
Here's a more detailed explanation:
  • KEGG:
    • KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases that focuses on genomes, biological pathways, diseases, drugs, and chemical substances. 
    • The KEGG PATHWAY database contains manually drawn reference pathway maps and organism-specific maps generated by matching KO assignments in the genome with reference maps. 
    • KEGG aims to provide a resource for understanding high-level functions and utilities of biological systems from molecular-level information. 
    • KEGG is used for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics, and other omics studies. 
    • KEGG is a curated database, meaning that the information is compiled and organized by experts, rather than being a direct representation of the underlying genetic code. 
  • Reactome:
    • Reactome is a free, open-source database and website of human biological pathways built from connected biological reactions or pathway steps. 
    • Reactome encompasses all biological events, including binding, phosphorylation, transport, and classical biochemical events. 
    • Reactome is an all-inclusive resource of human pathways for basic research, genome analysis, pathway modeling, systems biology, and education. 
    • Like KEGG, Reactome is a curated database, meaning that the information is compiled and organized by experts, rather than being a direct representation of the underlying genetic code. 
  • Natural Genetic Circuits:
    • Natural genetic circuits refer to the actual biological pathways and regulatory networks encoded within an organism's DNA. 
    • These circuits involve genes, proteins, and their interactions, which control cellular processes and development. 
    • KEGG and Reactome provide a framework for understanding these circuits, but they are not a direct representation of the genetic code itself. 
In summary: KEGG and Reactome are valuable tools for understanding biological pathways, but they are not the same as natural genetic circuits. They are curated databases that compile and organize information about known pathways, while natural genetic circuits are the actual biological pathways and regulatory networks encoded within an organism's DNA

5 
And again - 

Great new #AItools for a #RealisticVirtualEarthForProteins in #RealisticVirtualEarth #ForEverything
What if we could stand inside #AlphaProteo in a #NDimensional #WUaSMultimediaBarn to #WikiBuildCode it out further like in the #HarbinWarmPool @HarbinBook ?









Retweeting - 

Google DeepMind
@GoogleDeepMind

We’re presenting AlphaProteo: an AI system for designing novel proteins that bind more successfully to target molecules. 🧬

It could help scientists better understand how biological systems function, save time in research, advance drug design and more. 🧵 dpmd.ai/3XuMqbX




6


7 

Greetings #HTGAAbios #HTGAAbiologists #HTGAA fr #MITOCW-centric @WorldUnivAndSch & in growing a #RealiisticVirtualEarthForSyntheticBiology #RealisticVirtualEarthForGenetics in #RealisticVirtualEarth & #RealisticVirtualHarbin & #AgingReversal & #ExtremeLongevity #GeneTherapies ~

https://x.com/Q_YogaMacFlower/status/1889391367325098296

https://x.com/WorldUnivAndSch/status/1889391208340004930

https://x.com/scottmacleod/status/1889391284261102037

https://x.com/HarbinBook/status/1889391962719130003

https://x.com/sgkmacleod/status/1889391654450446421

https://x.com/WUaSPress/status/1889391885153935765

--


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 



* 


Dear HTGAA 2025,


I hope you all enjoyed a great experience in lab building your first DNA constructs via Gibson Assembly. I’m looking forward to seeing the results of your transformations!

This week we are honored to have joining us Professor Ron Weiss, Director of the MIT Synthetic Biology Center. Ron’s talk is entitled “Mammalian Synthetic Biology Foundations, Applications, and Neuromorphic Computing”. Ron will overview fundamentals of genetic circuits and how they can be utilized to program cells for a host of applications from cancer immunotherapy to programmable organoids and neuromorphic computing. Ron will be joined by Biological Engineering doctoral student Evan Holbrook, who will speak about “Online weight adjustments of intracellular neural networks.”

Our agenda is as follows:

E15-341

2:05-3:20p ET: Homework Review & Final Project Feedback
3:20-3:30p ET: BREAK
3:30-5:00p ET: Ron and Evan lecture


As a reminder, for MIT/Harvard students, please share at least one final project idea via the link here.

For Committed Listeners, please share at least one final project idea to be reviewed during your node meeting time next week via the link here.

See you all in class tomorrow!

Best,
David

——————

Professor Weiss is one of the pioneers of synthetic biology. He has been engaged in synthetic biology research since 1996 when he was a graduate student at MIT and where he helped set up a wet-lab in the Electrical Engineering and Computer Science Department. After completion of his PhD, Weiss joined the faculty at Princeton University, and recently returned to MIT to take on a tenured faculty position in the Department of Biological Engineering and the Department of Electrical Engineering and Computer Science.

Evan Holbrook a second year Biological Engineering PhD student studying how to build tunable intracellular neural networks in human cells. His main project is using genome editing to change the weights of intracellular neural networks. This approach will allow engineered cells to intelligently modify their own genomes to achieve any behavior.


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




* * *  


Dear Vishal, All, 


Thanks for this NotebookLM invitation to the "Unlock the Power of AI with NotebookLM: Introductory Session by GEG Ahmedabad" talk this Saturday at 4:30 am Pacific Time (California), Ithink. I won't be able to make it, but would be interested in seeing a video recording if it's possible (I also received a curious GEG Ahmedabad email yesterday saying something about being 'denied' ... so I won't register for this). 

I did however come into conversation with it in yesterday's MIT OCW-centric wiki World Univ & Sch WUaS News and Q&A in agenda item 3 at about the 9:15 minute marker (and especially regarding welcoming Rosary School, Rajkot, India - https://www.rosaryschoolrajkot.org/admission - high school students and graduates to matriculate at #GrowWithGoogleWUaS MIT OCW-centric wiki World Univ & Sch WUaS for free online WUaS degrees from home, for example, Bachelor and AA/AS undergraduate degrees ... potentially with courses in English and Hindi, as well as with time for other areas and secondary high schools + in India  all 22 scheduled languages in India) - 


Will seek to use NotebookLM for note taking in a MIT / Harvard How to Grow Almost Anything synthetic biology course with George Church I'm in -  https://2025.htgaa.org/ - beginning momentarily. I just added this - https://2025.htgaa.org/ - to https://notebooklm.google.com/ ... and asked "What is a Gibson assembly?" ... and it said javascript needs to be enabled. More later. 

Thanks for the heads' up about NotebookLM! :)

Best regards, Namaste, thanks, 
Scott


Notes - 

Unlock the Power of AI with NotebookLM: Introductory Session by GEG Ahmedabad

https://x.com/GEGAhmedabad/status/1901198070068502919

https://www.linkedin.com/posts/geg-ahmedabad_dear-learners-and-innovators-geg-ahmedabad-activity-7306960688541757440--Tuc


GEG Ahmedabad
@GEGAhmedabad
Join us for an insightful session on
@NotebookLM
 by
@DrVishalVaria
 on 22.03.25 5pm IST.
Register:
https://forms.gle/VJGq92ywiZYskK3D9

@GegProgram
 
@GoogleForEdu
 
@GEGAgraIndia
 
@GEGPune
 
@GEGDelhiNCR
 
@GoogleIndia
 
@GlobalGEG
 
@GegSurat



https://x.com/GEGAhmedabad/status/1901198070068502919



AND 

Researching with AI: Unlocking the Power of Google’s NotebookLM

https://youtu.be/mKsbjZLGPfw 


What does Google NotebookLM do?
AI Overview
Google NotebookLM is an AI-powered collaborator that helps you organize your ideas and enhance productivity by allowing you to upload documents and then read, take notes, and collaborate with the AI to refine and organize your thoughts





Google NotebookLM is an AI-powered collaborator that helps you organize your ideas and enhance productivity by allowing you to upload documents and then read, take notes, and collaborate with the AI to refine and organize your thoughts. 
Here's a more detailed breakdown of what NotebookLM does:
  • AI-Powered Collaboration:
    NotebookLM acts as an AI assistant that helps you understand complex information by becoming an "instant expert" in the documents you upload. 
  • Document Upload and Analysis:
    You can upload your documents, and NotebookLM will analyze them, allowing you to read, take notes, and collaborate with the AI to refine and organize your ideas. 
  • Enhanced Note-Taking and Organization:
    NotebookLM helps with streamlining your note-taking process, offering features like effortless summarization, topic extraction, and cross-referencing. 
  • Productivity Focus:
    While other AI tools focus on general conversation and task completion, NotebookLM is designed to enhance productivity in note-taking and writing tasks. 
  • Features:
    NotebookLM's features include streamlined organization, effortless summarization and topic extraction, enhanced note-taking, cross-referencing, idea synthesis, custom study guides, FAQ generation, timelines for historical context, and briefing document creation. 
  • Privacy and Data Protection:
    Google emphasizes that they value your privacy and do not use your personal data to train NotebookLM 



* 

Dr. Vishal Varia

5:48 PM (2 hours ago)
to me
Thanks Scott,

For inviting Rosary School students. I will check the courses and opportunities and inform you.

I don't know what "denied" email you received. Let me know more for this as i haven't emailed any such knowingly from my side.

Also, I will be doing the needful for recording.

Regards,
Vishal


* 

Dear Learners and Innovators,

GEG Ahmedabad is thrilled to invite you to an insightful introductory session on Google's revolutionary AI tool, NotebookLM. Join us to explore how this powerful platform can transform your research, learning, and content creation processes.

What is NotebookLM?
NotebookLM is an AI-powered workspace that helps you understand, summarize, and synthesize information from your documents. It acts as your personal AI assistant, enabling you to extract key insights, generate summaries, and even create content based on your uploaded sources.

Join us for a comprehensive introduction covering:

  • Introduction to NotebookLM: Understand the core functionalities and benefits of this cutting-edge tool.
  • Demo of NotebookLM: Witness a live demonstration showcasing its practical applications.
  • Case Studies: Explore real-world examples of how NotebookLM is being used across various fields.
  • Practical Use Cases: Learn how to leverage NotebookLM for research, podcast creation, enhanced learning, and much more.
Session Details:
  • Date: 22nd March 2025 (Saturday)
  • Time: 5:00 PM to 6:00 PM IST
  • Platform: Google Meet

Expert Speaker: Dr. Vishal Varia, Google Champion, Certified Trainer, Innovator, and Leader of GEG Ahmedabad.

Dr. Vishal Varia brings a wealth of experience and expertise in Google technologies and AI. He will guide you through the intricacies of NotebookLM and demonstrate its potential to enhance your productivity and creativity.

Registration:
To register for this free session, please fill out this form: https://forms.gle/VJGq92ywiZYskK3D9

The Google Meet link will be shared with registered participants on the day of the event.
Don't miss this opportunity to discover how NotebookLM can revolutionize your workflow. We look forward to seeing you there!
Sincerely,
Dr. Vishal Varia
Leader, GEG Ahmedabad
PS: Attendance Certificates will be issued to those who attend, perform the task and submit the feedback form. The session will be in English Language to enable international attendees to join and understand. However, Q & A will be answered in English, Hindi or Gujarati as the case may be.


Session45_NotebookLM.jpg

--


Dr. Vishal Varia
GFE Certified Innovator
GFE Certified Trainer
LinkedIn: Dr. Vishal Varia | Wakelet: Dr. Vishal Varia
Member - GEG Pune, GlobalGEG
Leader - GEG Ahmedabad, Global GEG 
FB Group: GEG Pune | GEG Ahmedabad
YouTube: GEG Pune | GEG Ahmedabad



* 

HI Vishal, All,

Thanks for your email too. I think MIT OCW-centric #GrowWithGoogleWUaS World University and School  WUaS may need to come into conversation with you and GEG India regarding developing online courses toward free WUaS degrees from home - for students in India, and in all 22 scheduled languages. 

You'll find the 'denied' message in the PS below, and while I hit reply all, I don't think this included the email address for GEG Ahmedabad. .

I also registered for the session after all, and look forward to the recording.

How best to develop MIT OCW-centric (https://ocw.mit.edu/ and https://csfirst.withgoogle.com/s/en/home) #GrowWithGoogleWUaS World University and School WUaS free degrees online from home for students in India in all 22 scheduled languages, but first in English and Hindi, and especially for the Rosary School Rajkot to begin?

Regards, 
Scott 


AND 
Agenda item 3 



PS

Your message in GEG Ahmedabad was denied

Inbox

Google Groups noreply@groups.google.com

Sun, Mar 16, 9:01 PM (2 days ago)
to me
Unfortunately, your recent post to the GEG Ahmedabad group was rejected by a group owner or manager.
Possible reasons your post was rejected include:
  • Your post was more relevant to a different group or conversation.
  • Your post did not conform to the posting guidelines of this group.
  • Your post needs more information.
More information about moderation tools is available at the Google Groups Help Center.

Google Groups allows you to create and participate in online forums and email-based groups with a rich community experience. You can also use your Group to share documents, pictures, calendars, invitations, and other resources. Learn more.


PPS

--


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 




* 







https://upload.wikimedia.org/wikipedia/commons/thumb/c/c7/A_giant_tortoise_%286063988953%29.jpg/1600px-A_giant_tortoise_%286063988953%29.jpg?20180313095645
















https://en.wikipedia.org/wiki/Gal%C3%A1pagos_tortoise

https://commons.wikimedia.org/wiki/Category:Chelonoidis_niger

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