Wednesday, September 24, 2025

Willow ptarmigan: The #BasicUnits of a #RealisticVirtualEarthForGenetics @WorldUnivAndSch A) #EMBL's 1 protein 3 DNA or RNAs 4 bound ligands https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/7l35 ? B) #JenniferFleming Explore - https://youtube.com/shorts/jY5tJAlr7QY C) @ewanbirney AI model forecasts disease risk - https://youtube.com/shorts/82U65MrKm70 ~ * * * How do genes create an individual organism - for example, C. Elegans - brainstorming and extrapolating? * How do Genes? * Cells? * Molecules? * Atoms? create an individual organism ? * * AND - How best to work w these possible #BasicUnits of #RealisticVirtualEarth #ForGenetics : #EMBL's: 1 unique protein, 3 DNA or RNAs, 4 bound ligands: https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/7l35 toward #ExtremeLongevity (eg 300x #CElegans' lifespan) & even w methylation? & see - https://scott-macleod.blogspot.com/2025/09/willow-ptarmigan.html ~https://x.com/scottmacleod/status/1971402380685214091 Retweeting - The #BasicUnits of a #RealisticVirtualEarthForGenetics @WorldUnivAndSch A) #EMBL's 1 unique protein 3 DNA or RNAs 4 bound ligands https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/7l35 ?

 



The #BasicUnits of a #RealisticVirtualEarthForGenetics @WorldUnivAndSch 
A)
#EMBL's
1 protein
3 DNA or RNAs
4 bound ligands
B)
#JenniferFleming 
Explore -
C)
@ewanbirney 
AI model forecasts disease risk -










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EMBL
European Molecular Biology Laboratory

Jennifer Fleming 
PDBe? proteins etc EMBL  
Explore protein structures with PDBe's new entry pages




Organisms

Homo sapiens

Entry content

1 distinct protein
3 DNA or RNAs
4 bound ligands

from - 







Ewan Birney 
AI model forecasts disease risk over a decade in advance








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AND - 


How best to work w these possible #BasicUnits of #RealisticVirtualEarth #ForGenetics : #EMBL's: 1 unique protein, 3 DNA or RNAs, 4 bound ligands: https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/7l35 toward #ExtremeLongevity (eg 300x #CElegans' lifespan) & even w methylation? & see - https://scott-macleod.blogspot.com/2025/09/willow-ptarmigan.html ~


The #BasicUnits of a #RealisticVirtualEarthForGenetics @WorldUnivAndSch 
A)
#EMBL's
1 unique protein
3 DNA or RNAs
4 bound ligands
B)
#JenniferFleming 
Explore -
C)
@ewanbirney 
AI model forecasts disease risk -



AND


How best to work w these possible #BasicUnits of #RealisticVirtualEarth #ForGenetics : #EMBL's: 1 unique protein, 3 DNA or RNAs, 4 bound ligands: https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/7l35 toward #ExtremeLongevity (eg 300x #CElegans' lifespan) & even w methylation? & see - https://scott-macleod.blogspot.com/2025/09/willow-ptarmigan.html ~

https://x.com/WorldUnivAndSch/status/1971400184187031628

https://x.com/sgkmacleod/status/1971401065431171369







Retweeting -

The #BasicUnits of a #RealisticVirtualEarthForGenetics @WorldUnivAndSch 
A)
#EMBL's
1 unique protein
3 DNA or RNAs
4 bound ligands
B)
#JenniferFleming 
Explore -
C)
@ewanbirney 
AI model forecasts disease risk -

https://x.com/WorldUnivAndSch/status/1970992784258793869



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How best to begin to work with these possible #BasicUnits of a #RealisticVirtualEarthForGenetics @WorldUnivAndSch 
A)
#EMBL's
1 unique protein
3 DNA or RNAs
4 bound ligands
https://wwwdev.ebi.ac.uk/pdbe/entry/pdb/7l35 toward #ExtremeLongevity (eg 300x #CElegans' lifespan) & even w methylation, & see - https://scott-macleod.blogspot.com/2025/09/willow-ptarmigan.html ~

AND by adding these science papers to #TextInTheSideBar to produce #VirtualProteins + therein?

- too.





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- Scott GK MacLeod  
Founder, President, CEO & Professor
CC-4 licensed MIT OCW-centric, Wiki, 
World University & School (WUaS) 
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1) non-profit 501(c)(3) Public Charity 
MIT OCW-centric, 

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 - 





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How do genes create an individual organism - for example, C. Elegans - brainstorming and extrapolating? 



Based on the well-understood developmental processes of the nematode C. elegans, genes create an individual organism through a complex, hierarchical system of molecular regulation, culminating in precise cell lineage and differentiation. The predictable fate of every cell in C. elegans allows for a detailed analysis of how the genetic blueprint is interpreted and executed.
Here is a brainstorming and extrapolation of how genes build an organism like C. elegans:
I. The blueprint: Gene regulatory networks
A single-celled zygote becomes a multicellular organism through cascading gene activation events. The master plan isn't a single set of instructions but rather a vast network of genes that regulate other genes.
1. Maternal-effect genes
The process starts before the sperm and egg even fuse.
  • Initial asymmetry: The mother deposits messenger RNAs and proteins into the egg cell. In C. elegans, a key initial asymmetry is set up by the sperm's entry point, which determines the posterior end of the developing embryo.
  • Transcriptional activation: These maternally inherited molecules activate the first zygotic genes, kickstarting the embryo's own gene expression program.
2. Transcription factors and regulatory modules
These proteins are the master switches of the gene regulatory network.
  • Specification of cell fate: Transcription factors bind to regulatory regions of other genes, either activating or repressing their expression. For instance, GATA transcription factors play crucial roles in specifying the fate of cells that will become the gut and epidermis.
  • Integration of signals: Complex promoters allow a gene's expression to be regulated by multiple transcription factors. This lets a cell's lineage history and local environment influence its fate.
  • Creation of spatial patterns: Gradients of transcription factor expression along the body axis (anterior-posterior, dorsal-ventral) establish the organism's body plan.
II. The execution: Cell-specific fates and interactions
As the embryo develops, gene regulatory networks define the precise role of each cell.
1. The invariant cell lineage
A hallmark of C. elegans development is its predictable and well-documented cell lineage.
  • Asymmetric cell division: After the first cell division, the two daughter cells inherit different sets of molecules from the mother's cytoplasm. This establishes the very first difference between cells.
  • Signaling cascades: Downstream cell divisions are influenced by cell-cell communication. For example, a signaling molecule released by one cell can bind to a receptor on a neighboring cell, altering its transcriptional program and fate.
2. Differentiation into specialized cell types
The final fate of a cell is determined by the specific combination of genes it expresses.
  • Tissue-specific proteins: Genes encode the proteins that give each cell its specialized function and morphology, such as the contractile proteins in muscle cells or the channel proteins in neurons.
  • Behavioral wiring: Genes dictate the formation and connection of the worm's 302 neurons, which collectively form its nervous system and govern its behaviors.
III. The fine-tuning: Post-transcriptional and epigenetic regulation
The path from gene to organism is also controlled by additional layers of regulation.
1. MicroRNAs (miRNAs)
These small RNA molecules regulate gene expression by targeting messenger RNAs for degradation or preventing their translation.
  • Developmental timers: The discovery of the lin-4 and let-7 miRNAs in C. elegans revealed how these molecules function as developmental timers, ensuring that cells progress through their programmed developmental stages at the right time.
  • Gene expression tuning: Other miRNAs act more subtly, buffering against fluctuations in gene expression and providing robustness to the developmental process.
2. Chromatin regulation
Genes are packaged into chromatin, and modifications to this chromatin structure can alter gene expression.
  • Packaging of DNA: The degree of DNA compaction can determine whether certain genes are accessible for transcription.
  • Epigenetic inheritance: Chromatin modifications can be passed down during cell division, "remembering" a cell's history and ensuring its descendants maintain the correct lineage.
IV. Quality control: Programmed cell death
Not every cell that is born is meant to live. The genetic program also includes instructions for cell suicide.
  • Sculpting the organism: In C. elegans, a predictable number of cells (131 in hermaphrodites) die via a process called apoptosis during development. This programmed cell death is essential for the formation of the final adult body plan.
  • Conserved pathway: Genetic analysis in C. elegans first identified the core genes (ced-3, ced-9) that control this process, which has proven to be evolutionarily conserved in humans and other organisms.
V. Extrapolating to higher organisms
The simple, reproducible development of C. elegans reveals fundamental principles that are broadly applicable to more complex organisms, including humans.
  • Modularity and evolution: The underlying gene regulatory networks that specify cell fates are conserved but are arranged and deployed differently to create more complex anatomies. In higher organisms, the networks are larger and more intricate, with greater redundancy, which can buffer against the effects of mutations.
  • Developmental timing: Heterochronic genes, like the let-7 miRNA discovered in C. elegans, have conserved roles in regulating developmental transitions across species, from nematodes to humans.
  • Genetic toolkit: The same basic genetic "tool kit"—transcription factors, miRNAs, signaling pathways—is used in all animals. Differences in how these tools are deployed, along with more complex gene regulation in larger genomes, generate the diversity of life.
  • Stochastic elements: While C. elegans development is highly deterministic, even in genetically identical animals raised in identical conditions, small variations occur. In humans, this randomness, combined with greater genetic variability and environmental influences, creates the subtle differences that make each individual unique



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How do cells create an individual organism - for example, C. Elegans - brainstorming & extrapolating?




Cells create an organism like C. elegans through a predictable process of cell division and differentiation, starting from a single fertilized egg. This single cell undergoes asymmetric division, creating different progenitor cells that divide to produce specific cell types and tissues. Due to C. elegans' transparency and its consistent cell lineage, researchers have mapped its complete cell division and fate, revealing how it develops into a complex, multicellular adult with 959 somatic cells. 
The Foundation of Development
  • A Single Starting Point: The process begins with a single fertilized egg, or zygote. 
  • Asymmetric Cell Division: The very first divisions of this zygote are asymmetric, meaning the two daughter cells produced are not identical. This establishes different "founder cells" that will give rise to specific tissues and organs. 
  • Predictable Cell Lineage: The pattern of cell division and the fate of each descendant cell are highly predictable in C. elegans. 
From Cells to Tissues
  • Cell Division: Cells repeatedly divide to increase the number of cells in the organism. 
  • Cell Differentiation: During these divisions, cells also differentiate, meaning they become specialized to perform specific functions, such as muscle cells, nerve cells, or germ cells. 
  • Tissue and Organ Formation: Descendant cells from the founder cells then form various tissues and organs, such as the vulva for reproduction or the nervous system. 
The C. elegans Model
  • C. elegans is transparent, allowing researchers to easily observe its internal development under a microscope. 
  • Complete Cell Lineage: 
    The entire cell lineage—the complete history of cell divisions and fates from the single-cell stage to the adult—has been meticulously mapped for C. elegans. 
  • Consistent Development: 
    The development of C. elegans is very consistent, with each individual having the same number of somatic cells and the same overall cell arrangement. This makes it an excellent model for studying general metazoan (animal) biology, according to the National Institutes of Health (NIH). 
  • Environmental Response: 
    C. elegans can also respond to its environment, entering a dormant, hardy state called a dauer larva if food is scarce, which then develops into an adult when conditions improve

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How do molecules create an individual organism - for example, C. Elegans - brainstorming & extrapolating?


An organism like the roundworm C. elegans arises from a single cell through a cascade of molecular instructions and processes, moving from the genetic blueprint to the organized, self-assembled structures of a living being. This complex process involves genetic programming, protein synthesis, environmental signaling, and molecular self-assembly that guides the creation of specialized cells, tissues, and organs.
Genetic blueprint and transcription
  • DNA: The foundation is the organism's DNA, which stores all the genetic instructions. Though every cell has the same complete genome, each cell "reads" and expresses only a specific subset of genes relevant to its function.
  • Gene regulation: Regulatory molecules, particularly proteins called transcription factors, determine which genes are turned "on" or "off". This controls the production of different proteins in different cells, a process called differential gene expression.
  • Transcription: When a gene is "on," an enzyme creates a messenger RNA (mRNA) copy of the gene's instructions. This copy is then sent out of the nucleus to the cell's cytoplasm.
Protein synthesis and function
  • Translation: In the cytoplasm, ribosomes—complexes of ribosomal RNA (rRNA) and proteins—translate the mRNA's genetic code into a chain of amino acids.
  • Protein folding: The linear chain of amino acids spontaneously folds into a unique three-dimensional shape. This shape determines the protein's function, enabling it to act as an enzyme, structural component, or signaling molecule.
  • Diversity of function: A specialized cell's identity and function are defined by the specific set of proteins it produces. For example, a muscle cell will produce different proteins than a neuron.
Cellular organization and self-assembly
  • Cellular structures: Proteins and other macromolecules self-assemble into complex structures, forming the building blocks of the cell. Examples include:
    • Lipid membranes: Lipids, with their hydrophilic "heads" and hydrophobic "tails," self-assemble into the cell's membrane and other internal membrane systems, creating a boundary that separates the cell from its environment.
    • Cytoskeleton: Proteins form the cytoskeleton, a dynamic internal scaffolding that gives the cell its shape, allows for movement, and organizes other cellular components.
  • Cell division (Proliferation): Molecular machinery coordinates repeated cell division, or proliferation, to produce many cells from the single fertilized egg. In C. elegans, this process is so predictable that the lineage of every cell has been mapped.
Differentiation and morphogenesis
  • Asymmetric division: Early in C. elegans development, the first cell division is asymmetric, creating two daughter cells with different molecular contents. These differences determine the initial fate of the two cells.
  • Cell-cell signaling: As cells proliferate, they interact with their neighbors, influencing each other's development. Molecules on the cell surface and signaling pathways, like the Notch and Wnt pathways, coordinate these interactions.
  • Morphogen gradients: In some embryos, signaling molecules called morphogens are distributed in concentration gradients. Different concentrations of these molecules activate different genes, causing cells to develop into different structures based on their position.
  • Programmed cell death (Apoptosis): Just as molecular signals direct cells to differentiate, other signals instruct certain cells to undergo programmed death. In C. elegans, this process helps sculpt the final form of the animal.
Extrapolating to higher-order complexity
  • From molecular components to organisms: The principle of molecular self-assembly extends beyond individual cells. Proteins and cells, programmed by the genetic instructions, interact to form complex tissues, which in turn form organs. In C. elegans, this leads to the formation of a nervous system with a precise number of neurons and a simple body plan.
  • Environmental influences: Molecular signals also link the organism to its environment. For example, specific small molecules called ascarosides regulate social behaviors in C. elegans, demonstrating a "chemical language" for inter-organismal communication. Environmental cues can even influence developmental timing, affecting factors like growth and longevity.
  • The origin of complexity: The entire process can be seen as a molecular "program" unfolding, where the components (DNA, RNA, proteins) possess specific properties that cause them to interact in a predictable, self-organizing way. This leads to emergent complexity, with higher-level structures and functions arising from the coordinated actions of simpler molecular parts





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How do atoms create an individual organism - for example, C. Elegans - brainstorming & extrapolating?


To build an organism like
C. elegans from atoms, the process moves through several levels of increasing complexity, driven by physics, chemistry, and genetics. Non-living atoms combine into simple molecules, which self-organize into complex macromolecules, organelles, and ultimately, a living, replicating cell. This initial, single-cell stage is followed by the precise, genetically directed development of the entire multicellular organism.
Stage 1: From atoms to molecules
The process begins with the fundamental components of matter—atoms. The majority of the atoms making up C. elegans, like most living organisms, are carbon (C), hydrogen (H), oxygen (O), nitrogen (N), and phosphorus (P).
  • Bonding through thermodynamics: Atoms, which are not conscious, combine into molecules when it is energetically favorable to do so. This stability is driven by thermodynamic principles.
  • Creating basic molecules: Simple molecules are formed through chemical bonds. For example, hydrogen and oxygen atoms form water (
    image.gif
    ), while carbon and hydrogen atoms form methane (
    image.gif
    ). These form the essential components of a living cell.
Stage 2: From molecules to cells
Within the cellular environment, simple molecules arrange themselves into larger, more complex structures, forming the first unit of life.
  • Macromolecules: The four major classes of macromolecules form the building blocks of the cell:
    • Proteins: Built from chains of amino acid molecules, proteins serve countless functions, such as acting as enzymes to speed up reactions and forming cellular structures.
    • Nucleic acids: DNA and RNA, constructed from nucleotide molecules, carry the genetic blueprint for the organism.
    • Lipids: Made from fatty acids, lipids are a crucial component of the cell membrane and provide energy storage.
    • Carbohydrates: Built from sugar molecules, these provide energy for cellular processes.
  • Organelles: Macromolecules combine into specialized compartments called organelles. For instance, proteins and lipids form the cell membrane, which encloses the cell and its contents. Other organelles, such as mitochondria and the nucleus, are built from specific combinations of macromolecules.
  • The first cell: Once a functional, self-replicating cell is formed, it has crossed the threshold from non-living matter to a living entity. The initial egg cell of C. elegans is a chamber containing all the necessary molecules and instructions (DNA) to begin its development.
Stage 3: From a single cell to a multicellular organism
With the initial cell formed, the process shifts to the controlled, genetically regulated process of development. C. elegans development is particularly well-mapped due to its predictable and transparent nature.
  • Genetic blueprint: The DNA within the nucleus of the fertilized egg cell acts as a blueprint, providing the instructions for the entire organism. All cells of the worm contain this same genetic information, but different genes are expressed in different cells at different times.
  • Cell proliferation: The single-celled egg undergoes repeated cell divisions (mitosis), creating more and more cells.
  • Cell specialization: As cells divide, they begin to differentiate, becoming specialized for specific functions. In C. elegans, the fate of most cells is highly predictable from the beginning, resulting in a mature worm with a precise number of cells (959 somatic cells).
  • Cell-cell interaction: Neighboring cells coordinate their behavior by sending and receiving chemical signals. For example, specific signaling pathways like Notch and Wnt define the different cell types along the worm's axes and create more complex patterns.
  • Apoptosis: Programmed cell death, or apoptosis, is an essential part of development. In C. elegans, a specific number of cells (131) are intentionally eliminated during development, which is a predictable part of its cell lineage.
  • Morphogenesis: Cells move and rearrange to form structured tissues and organs, shaping the body plan of the worm.
  • Growth and maturation: After hatching from the egg, the organism grows and matures through four larval stages, undergoing molts until it reaches adulthood, at which point it can reproduce and begin the cycle again.
Extrapolating the origin of the initial cell
While the development of a multicellular organism from a single cell is well understood, the formation of the first self-replicating cell from non-living atoms is still a subject of scientific research.
  • Prebiotic chemistry: The prevailing hypothesis, known as abiogenesis, suggests that under specific conditions on early Earth, simple inorganic molecules could have reacted to form more complex organic molecules, such as amino acids and nucleotides.
  • Self-organization: Some of these organic molecules could have then spontaneously assembled into more complex structures. For instance, lipids can form small, spherical vesicles (protocells) in water, which can encapsulate other molecules and create a protected, internal environment.
  • Replication: The breakthrough would have been the evolution of a self-replicating molecule, such as RNA, which can both store genetic information and catalyze chemical reactions (like a simple enzyme). A system of such molecules could eventually lead to the more complex and stable DNA-based systems we see today.
The combination of these fundamental physical and chemical principles, coupled with the process of natural selection favoring ever more complex and efficient molecular systems, provides a working hypothesis for how non-living atoms could have given rise to the first living cell, which then contains the genetic instructions to create an entire organism.











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

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

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