Showing posts with label nano world. Show all posts
Showing posts with label nano world. Show all posts

Sunday, March 3, 2024

This I Believe, Classical

THIS I BELIEVE, CLASSICAL*

Richard Allen Hart, PhD, 15  Dec  2023

This I Believe    Cultural Evolution    Factual Links    Related Topics    Outlines

Who, what, where is God? Our current situation is the result of four stages: the Creation, the single cell, biological evolution, and cultural evolution. It is a changing mix of all four.

Evolution is not continuing as it has; with short term reserves (glucose and fat, cash and savings, education and research), optimizing one action until the environment is exhausted.

For the first time in a history of over 4 billion years life is making conscious predictions and is directing evolution. Preparing for the future is more important than recreating the past. 
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The potential for life is being found throughout the universe. The basic stuff making up genes is now found to be self-assembling. With a large enough brain mass, consciousness appears.

Brains produce and sort spontaneous ideas. Creative brains ask questions. Questions demand answers: real and imaginary. Love (caring) and charity. God and hope. Friends and enemies. 

The environment allows and limits biological (material) and political (immaterial) cycles. The “educated” can entertain an idea without needing to own it and needing to destroy all others (the natural brute-force animal-level of thinking and acting that life is now surpassing).

What is appropriate, changes with time. This applies to English moths and to cultural customs. The dark moths hiding on tree bark became lighter when burning coal was banned in England. 

The 2,000-year-old core teachings of Jesus remain as cultural customs adjust to industrial and political developments. They provide a common need including honesty and sincerity.

Grandma anticipated living with Jesus as she now does. The changes from small country to mega-church fascinated her. The Cooperative Baptist splitting from the Southern Baptist and back distressed her. Important things are strongly tied to our childhood and our schooling.

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Humans act on their beliefs. Each task and level of organization requires its own application of basic rules in three flavors: Guess (immediate), believe (individual), and know (factual). 

Beliefs are polarized toward the past (religions and politics), knowing the facts, toward the future. The “educated” see little conflict in new revelations of the continuing creation. Strongly held beliefs are real to the believer. This is a continuous source of highly resistant conflict.

The history of human nature shows that church and state can be independent or any combination. Their environments may serve different purposes best when separated. Both require well “educated”, active, learners to balance highly trained and skilled participants.

A belief in God and a belief in the United States of America Constitution are both made of the same stuff that is of little consequence until acted upon; made real. Jesus placed mankind on a positive path acceptable to a patient God. The Constitution and Bible both place humans above animals. The time has come to create the needed environment. 

This I Believe   Cultural Evolution    Factual Links     Related Topics

         *Addendum

Having worked two months on "the best" citations to ground this "one page essay" in reality I have convinced myself it is an endless task. Each month a new unexpected event occurs that challenges rationalizations based on what is known at the time. I find this work is just a first attempt to solve a problem of how evolution works above the basic biological level.

I am aware of three ways bureaucracies "solve" a complex problem: 1. Make a policy statement with or without money and keep it at a distance (Don't get involved.).

2. The seminar in which persons, at all administrative levels, who are actually involved on a daily basis are invited to present their experience. It is fun to watch these people interact when all are treated as equally important in providing needed information. No one person knows all. 

The air quality in the New Science Building degenerated when maintenance was "out sourced" causing severe eye irritation. We found the floor cleaner is sold by the strength of its odor, that has little to do with cleaning power. The Business Office buys by the odor! Buy an odorless, less expensive, and more effective cleaner.

3. Define the problem accurately. My best example is being seated near a man who only took million dollar contracts. There was no charge if the process of defining the problem solved the problem, which happened most of the time. His comment on the occasion, an International meeting in Honolulu to feed the poor was, "This banquet setting is not the way to do this." 

The problem we are facing, now that the Nano World has been revealed, is how to become successful in the third level of existence: abiotic, biological, and cultural. The failure of the direct application of biological rules to the nano world and world history indicate the same mismatch for the cultural world. It took two world wars to create a single currency (the Euro).  

So today, 24 Feb 2024, I am sorting what I have in hand to post on the Internet. I need to add more comments as I can no longer remember what is in each citation. Out of sight, out of mind. Browse the find column on the right side of videos for a wealth of related insights. 

God in the bio-nano-world is a far more wondrous concept than ever imagined in the past 4,000 years. We can now "see" everything. I learn as I write and then search for verification.

This page is a condensation of three one-page attempts to explain the world I have lived in the past 93 years. At times it becomes key words that unfold into endless stories when searched after logging into Wikipedia or Googling: Google Wikipedia.

The nano world is young and growing. A lot has changed since I last taught classical genetics 30 years ago: Automated equipment to duplicate and sequence genes. Finding genes shared by every living organism and saved functionally and non-functionally in human chromosomes. Engineering better and even new genes which renews the discussion of god and ethics.

Evolution with Hypertext

 

I have limited serious attempts to communicate with others to one page. It all started with a two-year leave with the US EPA, Denver, CO, 1978-1980. If a topic goes longer than that you either do not understand what you are doing or you're lying, in research and government work.

 

Several times, in the past dozen years, I have started to write something about the world that I have lived in. Each time my world has expanded by the time I finished the paper. This time a single page can be made as meaningful as a reader wishes when I use hypertext links to automated updates.


                     This I Believe   Cultural Evolution    Factual Links     Related Topics

           

  Preview of Epilogue (at end of Related Topics)


Biological evolution follows two basic rules: (8 Mar 2024)
1. A space (environment) niche.
2. A self reproducing entity (with variation, with errors). 

Cultural evolution adds two more:
3. Spiritual-and-religious (S/R). Unverifiable individual beliefs.
4. Science. Verifiable and verified group beliefs. 


When these mix well (no harm) there is peace and prosperity.

Factual Internet Links to Cultural Evolution

                                             Factual Internet Links to Cultural Evolution                                                                                             

    Introduction to God's Million Year Secret Nano World

Nanotechnology & NanoMedicine | Andrew Hessel | Exponential Medicine 2015, 25min. https://www.youtube.com/watch?v=IDQBd9cVZAc Self-assembling, number, and size.

A Biobot (How Nano Robots Will Change Medicine Forever | NanoSyrinx, 33 min, 2023)

Harvard (BioVisions) Inner Life of the Cell with Music  https://www.youtube.com/watch?v=Nnpl4mE-pX0&t=20s3 min, 2022, with titles. With narration: https://www.youtube.com/watch?=dp6qRNNGPj412 min, 2022. With neither: https://www.youtube.com/watch?v=wJyUtbn0O5Y3 min, 2012. 


Your Body's Molecular Machineshttps://www.youtube.com/watch?v=X_tYrnv_o6A6 min, 2018. 
motor protein changes ATP chemical energy to work. https://en.wikipedia.org/wiki/Kinesin. Also
https://www.youtube.com/watch?v=9RUHJhskW00, Ron Vale (UCSF, HHMI) 1: Molecular Motor Proteins, 35 min, 2017, super good

Log into Wikipedia to fully open Google Wikipedia listed items and scan the find list on right side.

WEHImovies (The Walter and Eliza Hall Institute of Medical Research) in Australia. Pick from 76 videos.

https://www.ibiology.org/explore/ U UTAH. Pick from 689 video talks nicely sorted by topic.


How these Animations were Made

https://www.youtube.com/watch?v=7Hk9jct2ozY, DNA animation (2002-2014) by Drew Berry and Etsuko Uno wehi.tv, 7 min, 2019, very good.  Size and time (speed).

Molecular animation – Tech Talk by Drew Berry wehi.tv (2022). https://www.youtube.com/watch?v=qbyzEiBvbXw, 37 min, 2022. Browning movement and ATP.

Animations of unseeable biology | Drew Berry | TEDYouTube·TED·Jan 12, 2012, 9 min.


https://www.reddit.com/r/blender/comments/qltqd4/atp_synthase_using_pdb_files/, 2022, endless loop. Draw ATP synthase using pdb files with Blender free software. Do it yourself!


Newer DNA Sequencing

How does the Oxford Nanopore Work? https://www.youtube.com/watch?v=CGWZvHIi3i0, 2 min, 2016, super good video of the artificial cell wall pore, and motor protein. 

Bioengenineered cell membrane natural sized nanopores that transport a single strand of RNA or DNA through an electric field that detects each nucleotide in a DNA strand in about ten minutes. No dyes needed. how nanopore sequencing works2 min, 2019, very good.


How does nanopore DNA sequencing work? https://nanoporetech.com/applications/dna-nanopore-sequencing2 min, 2024 company edition, super good.


BestDx Academy https://www.youtube.com/watch?v=FYEWrUVJ2as, same as above.

https://www.youtube.com/@HMCH-bt2ue catalog of how a dozen work, 2024, up to date.


The history of third generation DNA sequencing using bionanoengineered nanopores to correct errors and omissions in first and second (next) generation DNA sequencing methods.

https://www.youtube.com/watch?v=7XLhHul5Nc4, 29 min, 2024, very good.


Genome Sequencing for Pathogen Discovery - Joseph DeRisi (UCSF, HHMI), https://www.youtube.com/watch?v=2LPfWuKBN_o, 26 min, 2018. Sequencing millions of fragments at a time by one photo with each addition of a nucleotide and using a computer to sort out overlapping sequences including the details of a complete study. Very good.
       
Old DNA Agar Gel and Packed Columns Sequencing Systems Still in Use

Bringing the cost of sequencing down from millions of dollars over years to less than a thousand dollars in a few hours resulted from the co-evolution of nucleotide detection and software to sort and match billons of DNA fragments. 

https://www.youtube.com/watch?v=mI0Fo9kaWqo Next Generation Sequencing 1: Overview - Eric Chow (UCSF), 30 min, 2018, very good. Three leading tool makers at that time (dated).

https://www.youtube.com/watch?v=2yI_SoOWFMU DNA Damage Response, 4 min, 2018, a breast cancer cure. DNA is damaged thousands of times a day

http://www.google.com/search?q= DNA polymerase DNA replication png, 3 min, 2015, 3D film. This polymerase produces new DNA strands and repairs DNA damage.


"Epigenetics refers to mechanisms of gene expression regulation that do not involve changes to the underlying DNA sequence."  https://www.youtube.com/watch?v=IAu44BkOaSs Introduction to Epigenetics - Learn.OmicsLogic.com, 13 min, 2019, a checklist as genes are expressed?
Basic Primer in Epigenetics https://www.youtube.com/watch?v=WgERHur3FMQ, 6 min, 2022


Fossil pseudogene genes still in our DNA! The Genes We Lost Along the Way: //www.youtube.com/watch?v=6Vc2bM2aQsw, 13 min, 2021 (PBS Eons) Ancient DNA in humans.
Virus additions to the human genome form and protect the placenta, fetus, and new born. https://www.bbc.com/future/article/20230519-the-viruses-that-helped-to-make-you-human#, 20 May 2023


A recent unintended loss of genes that cause disease is cultural. Vulnerability of the industrialized microbiota, https://www.science.org/doi/10.1126/science.aaw9255?ijkey=85b792f52f40cbd08c3a832b46ae81fe87a17909&keytype2=tf_ipsecsha

And even smaller genetic particles are being found. Viroid-like colonists of human microbiomes,  https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1


Mitochondrial DNA. https://www.youtube.com/watch?v=vnw76pfiteQ&t=557s, 31 min, 2020, 

Jared Rutter (U. Utah, HHMI) 1: Mitochondria: The Mysterious Cellular Parasite. Circular genes.


How reading DNA has world wide implications for the practice of medicine and research finance.

"Mitochondrial DNA variation in Human Origins and Disease", https://www.youtube.com/watch?v=zOU6ptM8Y94, Case University, 58 min, 2017. At 40 min the variations in Human Origins derived from female mitochondria.

A Mitochondrial Etiology of Common Complex Disease https://www.youtube.com/watch?v=1aCHrHwm_AI, 59 min, 2018. At 5 min anatomical and Mendelian (nuclear chromosomal). At 7 min bioentergentic dysfunction (female mitochondrial).


What is life and how does it work? - with Philip Ball, https://www.youtube.com/watch?v=tw54LmxR21A, 52 min, 2024. At 0:00 min, double-helix; at 3:26, DNA sequence; at 6;53 genome; 7:58 central dogma; 9:33 readout; 13:10 non-coding; 15:05 noncoding RNA; 17:00 splicing RNA; 21:00 disordered proteins; 22:00 gene regulation; 25:30 humans; 30:30 intestines; 32:50 fingers; 35:27 causal emergence; 38:20 cognitive processing; 39:30 agency; 47:10 forms.  


                                                       Current Research 2024


Australia rock. https://youtu.be/0NdpJ1Ukp5k?list=PLTiv_XWHnOZpmajNtq8AtBItVDYadNR5q 

3 min, 2020. First life on earth 2 - 3 billion years ago. NASA seeing is believing. Microbial mat.


Where to find ancient life now on our world? white smoker deep sea vents, temperature and pressure but not electomagnetic*

https://www.youtube.com/watch?v=cX4zzFWx9mA&list=PLTiv_XWHnOZpmajNtq8AtBItVDYadNR5q&index=1, 2 min, 2021


Where to find life other than on our world? https://www.youtube.com/watch?v=kz9VhCQbPAk&list=PLTiv_XWHnOZpmajNtq8AtBItVDYadNR5q&index=3, 4 min, 2015


Bioelectric Fields at the Beginnings of Life, https://pubmed.ncbi.nlm.nih.gov/36636557/, abstract, 2022. Proposed cell electromagnetic skeleton.


                       This I Believe   Cultural Evolution    Factual Links     Related Topics

Educational Research 1980-1990

1.) Ice is _____ dense than water.  A) more  B) less  C) same  D) varies  E) do not know (cannot use the question to report what I know with the confidence that it will be useful in further learning). [Ice is not more dense because it is hard. It floats!]

This question was included on successive multiple-choice biweekly tests until the top response was "do not know" rather than wrong.  The question separated two groups of students. It then tested nothing. Students taking the general study class for credit marked correctly. The rest increasingly marketed, do not know.  I could never develop a presentation that changed this. Tradition overpowers education.

It took a test that encouraged the development of meaningful learning; to score for knowledge and judgment. Student scores and item difficulty were combined in my first attempts at training a computer to tutor, write tests, score, and post grades for classes in large lecture halls. 

The goal of cultural evolution research is to learn enough to promote cultural evolution beyond the basic biological-power-makes-right, to oaths and rules that are held sacred peacefully.