Wednesday, March 12, 2025

Mammoth Hot Springs (Yellowstone NP, WY): Thanks for the great MIT Harvard #HTGAA https://2025.htgaa.org/ lectures yesterday, Tu 3/11/25, and especially your tour-de-force talk, Professor Chris (Mason), which is here . . . (Dear David (Sun Kong), Chris (Mason), George (Church), Peter (Norvig), and All, ) * Again, and re the text chat - Chris, thanks and excellent: Hypothetically how could humans live to 130 years (so longer than 122 years of age per Jeanne Calment d.1997, I think, at 122 yo) with extreme longevity and aging reversal genetic drug therapies Chris Mason (replying to my question above) - "Reprogramming somatic and stem cells, but LOTS of them" * * Greetings from near Harbin Hot Springs, my physical-digital ethnographic & STEM field site and in seeking to create a #RealisticVirtualHarbin Hot Springs, as well as a #RealisticVirtualEarth emerging with this (and think Google Street View with Time Slider, GMaps, GEarth, and at the GCellView and GMoleculeView levels too and with TensorFlowAI).

 

MIT Harvard 2025 "How to Grow (Almost) Anything" synthetic biology course questions - 

https://worlduniversityandschool.blogspot.com/2025/03/mammoth-hot-springs-yellowstone-np-wy.html

https://scott-macleod.blogspot.com/2025/03/mammoth-hot-springs-yellowstone-np-wy.html . . . 


'HTGAA 2025 || Week 6 |' 


Dear David (Sun Kong), Chris (Mason), George (Church), Peter (Norvig), and All, 

Greetings from near Harbin Hot Springs, my physical-digital ethnographic & STEM field site and in seeking to create a #RealisticVirtualHarbin Hot Springs, as well as a #RealisticVirtualEarth emerging with this (and think Google Street View with Time Slider, GMaps, GEarth, and at the GCellView and GMoleculeView levels too and with TensorFlowAI).

Thanks for the great #HTGAA https://2025.htgaa.org/ lectures yesterday, Tu 3/11/25, and especially your tour-de-force talk, Professor Chris (Mason), which is here - 

Again, and re the text chat - 

Chris, thanks and excellent: Hypothetically how could humans live to 130 years (so longer than 122 years of age per Jeanne Calment d.1997, I think, at 122 yo) with extreme longevity and aging reversal genetic drug therapies


Chris Mason (replying to my question above) - 

"Reprogramming somatic and stem cells, but LOTS of them"



Thanks! … so ‘system-wide’ as George Church has talked about (in contrast to, say, targeting organs, for example)?


Chris Mason (Mar 11, 2025, 1:12 PM)
Might need both

AND further again - 

How could a #RealisticVirtualEarthForLongevity (thinking #GStreetView with #GTimeSlider with #GCellView +)
& with a #RealisticVirtualEarthForAgingReversal & even interoperable with our #AvatarAgentElectronicHealthRecords (#Hastags in #TwitterSphere) help, and as possibly even #HTGAAbiologists code this potentially ? 


As possibly a #GlobalListener's final projects' ideas ... and also as some grand challenges (a process I learned of from MIT and Yale CS alum Jim Spohrer ... and regarding a Universal Translator for all known living languages (7164 by one count) - https://scott-macleod.blogspot.com/2015/03/orchidaceae-wuas-1000-proposed-issip.html (in daily blog) - at MIT OCW-centric wiki World University and School WUaS, of which I'm the founder and head), How could each of the 3 following items in this set of Tweets be kind of grand challenges for Teaching Assistants and related in the 2025 "How to Grow (Almost) Anything" synthetic biology course ...


1 #CircularVectors >#GeneticCircuits per https://2025.htgaa.org/ 2 #CellReplication 3 coding a #RealisticVirtualEarthForGenetics

All in a #RealisticVirtualEarth? 1 #CircularVectors >#GeneticCircuits per https://2025.htgaa.org/ -https://scott-macleod.blogspot.com/2025/03/marble-mountain-wilderness-ca.html 2 #CellReplication in #RealisticVirtualEarthForCells (#GCellView) & 3 coding a #RealisticVirtualEarthForGenetics (eg for #AgingReversal #ExtremeLongevity)?


Retweeting - 

Protocol
Published: 24 February 2025
Circular Vectors as an efficient, fully synthetic, cell-free approach for preparing small circular DNA as a plasmid substitute for guide RNA expression in CRISPR–Cas9 genome editing
Roman Teo Oliynyk & George M. Church 


And 4, how to generate LOTS of stem cells to reprogram "somatic and stem cells," per your observation, Chris (Mason), for aging reversal and extreme longevity genetic drug therapies emerging (FDA approved) ... and potentially with a focus on proving living beyond 122 years of age experimentally (somehow) ... ?

Thanks so much for this opportunity too to join this HTGAA course as a Global Listener especially. 

All the best, thanks, regards, 
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 - 

chm2042@med.cornell.edu

https://directory.weill.cornell.edu/person/profile/chm2042

*

Patrik Artell / Genspace / Lidingö / Sweden / patrikartell@gmail.com

IDR-Quantum Integration Project: Concrete Path to Implementation Strategic Vision: The Shortest Path to Breakthrough
https://docs.google.com/presentation/d/1Cn7qS2M30VH4OYBUGR8EplkHSSAhIZiah1BLQL39PIM/edit?pli=1#slide=id.g2dd0efeeb6c_0_55


*

Lisa - 

Thanks, Lisa - great ! (A #RealisticVirtualEarthForCRISPR (thinking #GStreetView with #GTimeSlider with #GCellView + … so with #MLandAI re #TensorFlowAI))?



* 
Thanks for the information!
@GeorgeChurch & @DavidSunKong, further:
So how best to code for #CellReplication in #RealisticVirtualEarthForCells,  #RealisticVirtualEarthForEvolution, #RealisticVirtualEarthForProteins re #GCellView 'in' #GStreetView w #GTimeSlider #HTGAA?

& re #LifeBegins?:
https://g.co/gemini/share/efeda2f9fa66 -https://ocw.mit.edu/courses/res-7-007-7-06x-cell-biology/ #HTGAAbiologists #HTGAAbios ?


*

As an #HTGAA #GlobalListener, might we add a visionary slide for proposed final project: How to code for a #RealisticVirtualEarthForCells,  (re #RealisticVirtualEarthForEvolution), & especially a #RealisticVirtualEarthForProteins re #GCellView 'in' #GStreetView w #GTimeSlider #HTGAAbios #HTGAAbiologists?




final projects - 

3 aims - 

(example - 'Lincomycin manufacturing and optimization')

1
DNA synthesis in the context of the course 

experimental aims deliverable upon by end of semester

assay and test this 


2
something in the middle ... how would you design the whole pathway 


3
visionary aim 

include re robotics and for production of e.g. of proteins and enzymes 




DNA synthesis is the process of creating DNA molecules, which can be done naturally or artificially. It's a fundamental biological process that's essential for growth, development, and maintenance of living organisms. 
How does DNA synthesis occur?
  • During cell division, DNA is copied so that each new cell has a complete set of genetic instructions. 
  • DNA synthesis occurs during the S phase of the cell cycle. 
  • DNA synthesis follows a semi-conservative model, where each new DNA molecule has one strand from the original and one newly synthesized strand. 
How can DNA synthesis be done artificially? 
  • DNA synthesis can be done artificially using technologies such as Gibson assembly and polymerase cycling assembly.
  • These technologies have become more cost-effective over time, enabling advancements in synthetic biology.
What are the steps of DNA replication? 
  • The initiation of DNA replication occurs in two steps: unwinding a short stretch of the DNA double helix, and then breaking apart the hydrogen bonds between the bases on the DNA strands.


* 
re first presentation

Lincomycin - 

Lincomycin inhibits bacterial protein synthesis by binding to the 23S ribosomal RNA peptidyl transferase loop region, preventing bacterial cell growth and reproduction. 
Here's a more detailed explanation:
  • Mechanism of Action:
    Lincomycin, a lincosamide antibiotic, works by interfering with bacterial protein synthesis, a crucial process for bacterial survival. 
  • Target:
    It specifically binds to the 23S ribosomal RNA (rRNA) within the 50S ribosomal subunit, which is essential for translating genetic information into proteins. 
  • Protein Synthesis Inhibition:
    By binding to this region, lincomycin disrupts the peptidyl transferase loop, a part of the ribosome responsible for forming peptide bonds during protein synthesis. This prevents the ribosome from functioning correctly, halting protein production and ultimately leading to bacterial cell death. 
  • Bacteriostatic Activity:
    Lincomycin is primarily bacteriostatic, meaning it inhibits bacterial growth rather than killing them directly. However, at higher concentrations, it can exhibit bactericidal activity. 
  • Clinical Use:
    Lincomycin is a strong antibiotic and is used to treat severe bacterial infections, particularly those caused by Gram-positive bacteria. 
  • Semi-synthetic derivative:
    Clindamycin, a semi-synthetic derivative of lincomycin, is often preferred for its higher efficacy and broader spectrum of activity. 
  • Lincomycin - an overview | ScienceDirect Topics
    The antibacterial action of lincomycin is the ability of the drug to bind to the 50s ribosomal unit and inhibit protein synthesis.
    ScienceDirect.com
  • Lincocin® lincomycin injection, USP
    Intramuscular administration of a single dose of 600 mg of lincomycin produces average peak serum concentrations of 11.6 mcg/mL at...
    Pfizer
  • Studies of lincosamide formation complete the biosynthetic ...
    Sep 21, 2020 — Lincomycin A is an antibiotic used clinically in the treatment of Gram-positive bacterial infections. ... Lincomycin A...
    PNAS
  • Show all


This is for informational purposes only. For medical advice or diagnosis, consult a professional. Generative AI is experimental.



*


Christopher E Mason

5:14 PM (31 minutes ago)
to me, David, Jim, George, Peter, htgaa2025-TAs@media.mit.edu, htgaa2025-globalTAs@media.mit.edu, Alden, Byron, Donna, Robin

 

Thank you Scott for the nice comments, and thank you David for the ever-amazing course that gets better every year 😊.

 

Cheers,

Chris

 

----------------------------------------------

Christopher E. Mason, Ph.D.

WorldQuant Professor of Genomics and Computational Biomedicine

Department of Physiology and Biophysics

Weill Cornell Medicine

(Dry Lab) 1305 York Ave., 13th floor, Y13-05

(Wet Lab) 413 East 69th St., Belfer Research Bldg., 10th floor, Room 10-60

(Design-BioLab) 1300 York Avenue, 4th Floor, D-407

New York, NY 10021

Director, WQ Initiative for Quantitative Prediction

Affiliate Faculty, New York Genome Center (NYGC)

-----------------------

 

ScienceDirect.com

  • Lincocin® lincomycin injection, USP

Intramuscular administration of a single dose of 600 mg of lincomycin produces average peak serum concentrations of 11.6 mcg/mL at...

Pfizer

  • Studies of lincosamide formation complete the biosynthetic ...

Sep 21, 2020 — Lincomycin A is an antibiotic used clinically in the treatment of Gram-positive bacterial infections. ... Lincomycin A...

PNAS





    * 


    Dear HTGAA 2025,

    I hope you all have been continuing your great work on our protein design challenge and also preparing to share your first final project ideas tomorrow!

    This week we are honored to have joining us former HTGAA TA and now Professor at the Technical University of Denmark, Lisa Riedmayr, and also Professor Christopher Mason from Cornell University!

    Lisa will speak on synthetic biology and genetic medicines, including gene therapy, cell therapy, how to design and construct these medicines including using synthetic promoters.

    Chris will speak about topics including engineering radioprotective tardigrade-human chimeric cells, microbial systems modifications, and epigenome editors to modulate gene expression. His talk is (unambiguously) entitled “A 500-year plan for engineering life on Earth and beyond.” 

    Here is our agenda our agenda for tomorrow, and please note the shif in timing re: lecture and homework review:

    2:05-2:50p ET: Lecture by Lisa
    2:50-3:35p ET: Lecture by Chris
    3:35-3:45p ET: BREAK
    3:45-4:15p ET: Protein Design Homework Review
    4:15-5:00p ET: Final Project Ideas Review


    For registered MIT/Harvard students, please share at least one final project idea to be reviewed in class on 3/11 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.

    For reference, you can view previous final project ideas for Committed Listeners here.

    See you all in class tomorrow!

    Best,
    David

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





    * 



    1 #CircularVectors >#GeneticCircuits per https://2025.htgaa.org/ 2 #CellReplication 3 coding a #RealisticVirtualEarthForGenetics

    All in a #RealisticVirtualEarth? 1 #CircularVectors >#GeneticCircuits per https://2025.htgaa.org/ -https://scott-macleod.blogspot.com/2025/03/marble-mountain-wilderness-ca.html 2 #CellReplication in #RealisticVirtualEarthForCells (#GCellView) & 3 coding a #RealisticVirtualEarthForGenetics (eg for #AgingReversal #ExtremeLongevity)?

    https://x.com/HarbinBook/status/1899960451376857151

    https://x.com/WorldUnivAndSch/status/1899958630000320573

    https://x.com/Q_YogaMacFlower/status/1899959460803805648

    https://x.com/scottmacleod/status/1899959628559245554

    https://x.com/WUaSPress/status/1899960360683397213

    https://x.com/sgkmacleod/status/1899960255821602877

    https://x.com/TheOpenBand/status/1899964062622245133


    Retweeting - 

    Protocol
    Published: 24 February 2025
    Circular Vectors as an efficient, fully synthetic, cell-free approach for preparing small circular DNA as a plasmid substitute for guide RNA expression in CRISPR–Cas9 genome editing
    Roman Teo Oliynyk & George M. Church 





    * *  




    Extinct Mammoth Genes Engineered Into “Woolly Mouse” - George Church Tweet


    Extinct Mammoth Genes Engineered Into “Woolly Mouse”
    Colossal Biosciences has created the world’s first woolly mouse.
    News  
    Published: March 4, 2025 
    | 
    Molly Coddington

    Three editing technologies – RNP-mediated knockout, multiplex precision genome editing and precision homology-directed repair – were used to achieve multiplex editing. A total of eight edits were made simultaneously to modify seven genes.






    * * 

    Thursday, March 13, 2025 


    Dear David (Sun Kong), Chris (Mason), George (Church), Peter (Norvig), and All, 

    Thanks too for your kind words, Chris, and this great 2025 "How to Grow (Almost) Anything" synthetic biology course . . . As a follow up, here are 2 WUaS blog posts with this email thread's contents, and some further questions - 



    In addition - 


    Twitter - How to add #RNPmediatedKnockout #MultiplexPrecisionGenomeEditing & #PrecisionHomologyDirectedRepair >#RVE?

    #MITHarvard 2025 "#HowToGrowAlmostAnything" synthetic biology course 'HTGAA 2025 || Week 6 |' questions -
    https://worlduniversityandschool.blogspot.com/2025/03/mammoth-hot-springs-yellowstone-np-wy.html @WorldUnivAndSch &
    https://scott-macleod.blogspot.com/2025/03/mammoth-hot-springs-yellowstone-np-wy.html How to add #RNPmediatedKnockout #MultiplexPrecisionGenomeEditing & #PrecisionHomologyDirectedRepair >#RVE?




    retweeting a George Church Tweet


    Extinct Mammoth Genes Engineered Into “Woolly Mouse” -

    Extinct Mammoth Genes Engineered Into “Woolly Mouse”
    Colossal Biosciences has created the world’s first woolly mouse.
    News  
    Published: March 4, 2025 
    | 
    Molly Coddington

    "Three editing technologies – RNP-mediated knockout, multiplex precision genome editing and precision homology-directed repair – were used to achieve multiplex editing. A total of eight edits were made simultaneously to modify seven genes."





    AND could some of your laboratories, Chris (Mason), potentially in collaboration with MIT, David (Sun Kong), and Harvard Medical School, George (Church), take on some of these building out a RealisticVirtualEarthForGenetics (thinking #GStreetView with #GTimeSlider with #GCellView +) with the above #RNPmediatedKnockout #MultiplexPrecisionGenomeEditing & #PrecisionHomologyDirectedRepair gene-editing approaches ... and as MIT OCW-centric wiki World University and School seeks to contribute to these Realistic Virtual Earth coding processes with time (potentially LOTs of time with extreme longevity genetic drug therapies emerging, FDA approved)?

    (And see Peter Norvig's INCREDIBLE #ToolifyAIWUaS article mentioning a Realistic Virtual Earth for the first time that I know of other than by WUaS in the PS)

    CHEERS, 
    Scott






    PS



    PPS
    Also 

    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




    Ricky Cordova - TA, I think  

     

    On Mon, Mar 10, 2025, 17:17 David S. Kong <dkong@mit.edu> wrote:

    Dear HTGAA 2025,

     

    I hope you all have been continuing your great work on our protein design challenge and also preparing to share your first final project ideas tomorrow!

     

    This week we are honored to have joining us former HTGAA TA and now Professor at the Technical University of Denmark, Lisa Riedmayr, and also Professor Christopher Mason from Cornell University!

     

    Lisa will speak on synthetic biology and genetic medicines, including gene therapy, cell therapy, how to design and construct these medicines including using synthetic promoters.

     

    Chris will speak about topics including engineering radioprotective tardigrade-human chimeric cells, microbial systems modifications, and epigenome editors to modulate gene expression. His talk is (unambiguously) entitled “A 500-year plan for engineering life on Earth and beyond.” 

     

    Here is our agenda our agenda for tomorrow, and please note the shif in timing re: lecture and homework review:

     

    2:05-2:50p ET: Lecture by Lisa

    2:50-3:35p ET: Lecture by Chris

    3:35-3:45p ET: BREAK

    3:45-4:15p ET: Protein Design Homework Review

    4:15-5:00p ET: Final Project Ideas Review

     

     

    For registered MIT/Harvard students, please share at least one final project idea to be reviewed in class on 3/11 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.

     

    For reference, you can view previous final project ideas for Committed Listeners here.

     

    See you all in class tomorrow!

     

    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 




    * 









    https://yellowstone.net/intro/mammoth-hot-springs/


















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

    ...



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