Bottom-up biology
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A special issue of Nature extends examples of human idiocy touted by biologically uninformed theorists to claims about: Bottom-up biology
How is that a multitude of different molecules within a lipid envelope all come together to carry out the basic functions required to sustain organisms? Conventionally, biologists have worked from the top down to dissect how components in cells interact in their natural environment. But now technical advances are allowing researchers to take a different tack: using engineering principles to reconstruct biological processes from the bottom up. This special issue explores the potential and possible limits of bottom-up cell biology.
The special issue obfuscates the fact that the creation of energy must be linked from top-down causation to energy-dependent bottom-up cause and effect.
Focus on the benefits of building life’s systems from scratch (11/7/18)
Top down involves a decomposition process. So although a researcher can make a career out of unpicking the workings of a cellular machine such as a ribosome or mitochondrion, the starting point for such projects has always been the role of these structures in existing cells. The work is directed by the context in which it originated and into which it will fold back once complete.
No serious scientist starts with the role of these structures in existing cells. Serious scientists link energy as information from the physiology of reproduction to biophysically constrained cell type differentiation via feedback loops.
How biologists are creating life-like cells from scratch (11/7/18)
Almost anything life-like requires cellular energy, usually in the form of ATP. And although this can be added from the outside to feed a synthetic system, many biologists working on bottom-up approaches argue that a true synthetic cell should have its own power plant, something similar to an animal cell’s mitochondrion or a plant’s chloroplast, both of which make ATP.
Cytosis for ages 10+ starts with ATP and links the creation of energy to the creation of RNA and all biodiversity via claims from 1964.
Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”
The synthesis of RNA in isolated thymus nuclei is ATP dependent.
Which biological systems should be engineered? (11/6/18)
Engineering a ‘minimal chassis’ that is capable of sustained gene expression and functional homeostasis would be an invaluable starting point for building synthetic cells that produce proteins, form tissues and remain viable for months to years. This would require detailed understanding and incorporation of metabolic pathways, trafficking systems and nuclear import and export — an admittedly tall order.
Order Subatomic and Cytosis
Learn what others ages 10+ have learned about metabolic pathways, trafficking systems and nuclear import and export.
Cell parts to complex processes, from the bottom up (11/6/18)
…changes in the size and shape of encapsulated compartments — manipulations that are easy in microfabricated systems, but not in living cells — have revealed roles for these parameters in controlling the oscillatory behaviour of proteins involved in cell division2 and the sizes of organelles3.
The oscillatory behavior of proteins is energy-dependent and it has been linked from olfaction to the physiology of reproduction and all biophysically constrained biodiversity in: Olfaction Warps Visual Time Perception
Cellular stretch reveals superelastic powers (10/31/18)
Latorre and colleagues’ work has revealed a more complex relationship between cell size and the forces that cells experience than was previously appreciated. Future studies should attempt to unravel the mechanisms that enable cells to enter a state of superelasticity and to recover from high levels of deformation. Now that we know cell shape is not an appropriate proxy for assessing cellular tension, it will be crucial to develop ways to accurately monitor tension levels in tissues, so as to better understand the factors that influence tissue shape.
Cellular stretch must be viewed in the context of energy-dependent supercoiled DNA and the virus-driven degradation of messenger RNA that links negative supercoiling to mutations and all pathology.
Active superelasticity in three-dimensional epithelia of controlled shape
Fundamental biological processes are carried out by curved epithelial sheets that enclose a pressurized lumen. How these sheets develop and withstand three-dimensional deformations has remained unclear. Here we combine measurements of epithelial tension and shape with theoretical modelling to show that epithelial sheets are active superelastic materials
See: MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination (2013)
Reported as MicroRNA
The researchers discovered that there was an intermediate function, which is termed a “ternary,” or three-way switch. This function relates to the fact that ZEB has the ability to turn itself on due to a positive feedback system. This allows a cell to keep intermediate levels of all four proteins required for the switch. Ben-Jacob notes that the hybrid, or partially on-off state, also supports cancer metastasis by enabling collective cell migration and by imparting stem-cell properties that help migrating cancer cells evade the immune system and anticancer therapies.
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RNA methylation, behavior, and disease
6 MIN READ
0
Modelling life scientifically: RNA-mediated events
12 MIN READ
0
Energy-dependent RNA methylation (8)
4 MIN READ
0
Energy-dependent RNA methylation (6)
9 MIN READ
0
Energy-dependent RNA methylation (2)
5 MIN READ
0
Thermotolerance and longevity (2)
3 MIN READ
0
Virus-driven energy theft: definition?
5 MIN READ
0
Energy-dependent biodiversity (4)
4 MIN READ
0
Energy-dependent biodiversity
5 MIN READ
0
Energy-dependent creation and entropy
4 MIN READ
0
RNA-mediated physics, chemistry, and molecular epigenetics (4)
5 MIN READ
0
RNA-mediated physics, chemistry, and molecular epigenetics (3)
5 MIN READ
0
RNA-mediated physics, chemistry, and molecular epigenetics
9 MIN READ
0
Half truths support theories without facts
4 MIN READ
0
Confusing effects and affects of visual input
2 MIN READ
0
Ignore the evidence: Rachel Feltman
5 MIN READ
0
Jay R. Feierman: twenty years of antagonism
5 MIN READ
0
Energy dependent RNA-mediated immunity (5)
4 MIN READ
0
Energy dependent RNA-mediated immunity (3)
8 MIN READ
0
Energy dependent RNA-mediated immunity (2)
10 MIN READ
0
Energy-dependent RNA-mediated immunity (1)
10 MIN READ
0
RNA-mediated DNA modifications
5 MIN READ
0
Science vs semantics
4 MIN READ
0
Soil bacteria, bulls, cows, microRNAs, and mammary glands
3 MIN READ
0
Hybrids: making microbes and Democrats into monkey’s uncles?
11 MIN READ
0
Bacteria see the light and they adapt
7 MIN READ
0
The Light and Darkness of “Evolution 2.0”
11 MIN READ
0
Will modern human populations adapt to the Zika virus?
5 MIN READ
0
Models of scientific literacy
3 MIN READ
0
The radical pair mechanism of ecological speciation
3 MIN READ
0
Hydrogen-Atom Transfer in DNA Base Pairs (4)
4 MIN READ
0
Blood test links atoms to ecosystems
2 MIN READ
0
Another failed rescue attempt
5 MIN READ
0
Juvenile hormone links atoms to ecosystems
3 MIN READ
0
Teleophobes vs teleophiles: a recent history
2 MIN READ
0
Ecological genomics: teleophobes respond (too late)
10 MIN READ
0
Genes, orchid odors, and pheromones from blonds
5 MIN READ
0
Finding peace and π in the light of H bond energy
5 MIN READ
0
Perry Marshall: too much information for atheist PZ Myers
3 MIN READ
0
Epigenetic (re)programming of behavior
4 MIN READ
0
Assumptions prove ignorance
5 MIN READ
0
NORAD: air defense and defense against genomic entropy
7 MIN READ
0
Did Dobzhansky see the UV light of creation?
10 MIN READ
0
Manufacturing fossil “evidence”
4 MIN READ
0
RNA-mediated theory killers (3)
7 MIN READ
0
RNA-mediated regulatory mechanisms link microbes to humans (3)
5 MIN READ
0
Essential pseudoscientific concepts of atheism
3 MIN READ
0
A two-faced protein enables RNA-mediated DNA repair (4)
6 MIN READ
0
A two-faced protein enables RNA-mediated DNA repair
2 MIN READ
0
Plasma created by sunlight and RNA–mediated epigenetic heredity
2 MIN READ
0
Stress-perturbed mitochondrial dysfunction
4 MIN READ
0
Theorists can’t understand biology
6 MIN READ
0
Sensationalizing no new mechanism
2 MIN READ
0
Fossils vs cell types and the brain
3 MIN READ
0
Designing, engineering, and protecting biodiversity
3 MIN READ
0
The virome, microbiome, replisome and supercoiled DNA
2 MIN READ
0
Skip the politics; embrace the facts
5 MIN READ
0
Controled Stem Cell Expansion
3 MIN READ
0
Human pheromone deniers: What’s next?
5 MIN READ
0
700 million years of evolution?
5 MIN READ
0
RNA-mediated retrotransposon-mediated biodiversity
3 MIN READ
0
Mystery machine vs model (2)
2 MIN READ
0
Energy and evolution: another opinion?
2 MIN READ
0
Supercoiled DNA constrains virus-driven genomic entropy
2 MIN READ
0
Let there be anti-entropic light (2)
4 MIN READ
0
Foundamentals of theory
4 MIN READ
0
Microbes to humans 2015 Nobel Prize
2 MIN READ
0
Is mainstream science in “Science” pseudoscience?
5 MIN READ
0
Mechanisms of stress: from genes to cancer
9 MIN READ
0
Viruses come alive: Tree of life pseudoscience
6 MIN READ
0
Theorists have not seen the light
4 MIN READ
0
A Darwinian pediatrician and expected life span
2 MIN READ
0
A 5-10K comparison of design principles to evolution
3 MIN READ
0
Alternative pre-mRNA splicing and ecological adaptation
7 MIN READ
0
Exosomes and the RNA-mediated future of medicine
5 MIN READ
0
From fertilization to RNA-mediated events and back
2 MIN READ
0
Phytochemical link from the sun to cell types
2 MIN READ
0
“New” quantum biology. Pirating the old
3 MIN READ
0
Cell types, SNVs, CNVs, and chromosomes
3 MIN READ
0
A “new” code enables ecological adaptation
4 MIN READ
0
Anti-entropic containment of energy: symbiosis 1.0
5 MIN READ
0
The “great filter” is an epigenetic trap
4 MIN READ
0
Information and communication (2)
6 MIN READ
0
Unraveling evolutionary pseudoscience
2 MIN READ
0
From “Blood Music” to Evolution 2.0
5 MIN READ
0
Ecology replaces the extended evolutionary synthesis
4 MIN READ
0
The stability of organized genomes (3)
3 MIN READ
0
Viruses, amino acids, and somatic cell types (2)
5 MIN READ
0
Viruses, amino acids, and somatic cell types
4 MIN READ
0
Big Bang Cosmology vs Reality
< 1 MIN READ
0
Hematopoiesis and practopoiesis
4 MIN READ
0
Koonin: viruses killed neo-Darwinism
3 MIN READ
0
RNA-mediated morphological AND behavioral phenotypes
2 MIN READ
0
Becoming biologically informed (3)
3 MIN READ
0
Easy editing: Reinventing our RNA world
3 MIN READ
0
Riding the wrong direction
3 MIN READ
0
Decreased phenotypic variation: Faith in Facts
7 MIN READ
1
RNA-mediated gene duplication, fixation, and ecological adaptation
6 MIN READ
0
MicroRNA controlled growth and brain development
7 MIN READ
0
“New” epigenetic mechanism for lifelong learning?
3 MIN READ
0
Protein folding and Google page rank
2 MIN READ
0
Olfactory perception of genetic information
2 MIN READ
2
Nutrient stress-induced RNA-mediated pathology
< 1 MIN READ
0
RNA-mediated development (2)
< 1 MIN READ
0
Creating and maintaining the human virome
2 MIN READ
0
Ignoring top-down causation
2 MIN READ
0
Alternative splicings: epigenetics meets pharmacogenomics
4 MIN READ
0
Epigenetic regulation of aging by glycine and GnRH
5 MIN READ
0
Pattern recognition: biogeochemical structure and function
5 MIN READ
0
Viruses and the human-like microbiome
3 MIN READ
0
Informing the biologically uninformed
< 1 MIN READ
0
One amino acid substitution, genes, and brain activity
3 MIN READ
0
Gene expression, immortality, and cancer
6 MIN READ
0
A lighting requirement for life
11 MIN READ
3
Scientists lose. A sci-fi author gains credibility
2 MIN READ
0
Computing via phosphorylation and fixation
3 MIN READ
0
Virus-driven cancer treatment and prevention
2 MIN READ
0
A special issue on nutritional epigenetics
5 MIN READ
0
Retinoic acid + one receptor regulate the genome
3 MIN READ
0
Epigenetics: microRNAs effect an integrative pathway
4 MIN READ
0
Tissue type variation and expression of genes
< 1 MIN READ
0
Chance mutations — not natural selection
5 MIN READ
0
How to find a “holy grail” under your nose
3 MIN READ
0
Physics, chemistry, light, and life
2 MIN READ
0
An epigenetic mark links algae, worms, and flies
2 MIN READ
0
Thermodynamics and protein folding landscapes
2 MIN READ
0
RNA-mediated silencing of a chromosome
3 MIN READ
0
Pathology constrains X-linked evolution
2 MIN READ
0
Feedback loops link insects to human brains
2 MIN READ
0
DNA Methylation and organized genomes (2)
10 MIN READ
0
DNA Methylation and organized genomes
7 MIN READ
0
Amino acid-dependent cell type differentiation
8 MIN READ
0
Origin of life and cancer (1,2,3)
2 MIN READ
0
MicroRNAs and invasive phenotypes
< 1 MIN READ
0
Silencing genes and serious scientists
3 MIN READ
0
The miRNA/mRNA balance: a suboptimal strategy?
2 MIN READ
0
Deeply ingrained thoughts
< 1 MIN READ
0
Too many targets for theories
3 MIN READ
0
Methylation maintains cell type differences
3 MIN READ
0
Creating nothing but a theory
4 MIN READ
0
Viruses and ecologically adapted animals
2 MIN READ
0
Quantum correlations/pseudoscience
3 MIN READ
0
Anti-entropic solar energy
5 MIN READ
0
Luis P. Villarreal tells it like it is
3 MIN READ
0
RNA-directed gene choice
5 MIN READ
0
Two types of microRNA are not double agents
2 MIN READ
0
Epigenetics Skeptism
5 MIN READ
0
Is DNA-directed transcription RNA-mediated?
2 MIN READ
0
RNA directed DNA methylation and cell types
4 MIN READ
0
Rejecting what is known about viral microRNAs and nutrient-dependent microRNAs
2 MIN READ
0
Reverse phosphorylation
7 MIN READ
0
RNA-mediated “repurposing” is nutrient-dependent and pheromone-controlled
3 MIN READ
0
RNA-mediated "repurposing" is nutrient-dependent and pheromone-controlled
3 MIN READ
0
From 3-D to epigenetically-effected 4-D genome make-up
5 MIN READ
0
Let there be anti-entropic light (1)
11 MIN READ
0
Nutritional epigenetics, exercise, and immune system integrity
4 MIN READ
0
What if Darwin was not still dead?
2 MIN READ
0
How fast can evolutionary theory be changed?
5 MIN READ
0
Biological energy and a microbiome model of a light-driven time machine
3 MIN READ
0
Sneaking up from behind (2)
3 MIN READ
0
An epigenetic trap (the sequel)
10 MIN READ
0
All of "like kind" in the (bigger) family
6 MIN READ
1
Environment epigenetically shapes the immune system
3 MIN READ
0
Beneficial microbes kill beneficial mutations
4 MIN READ
0
Constrained evolution is ecological adaptation
5 MIN READ
0
Unconstrained evolutionary innovability
4 MIN READ
0
Mutagenesis: Replacing facts with theories
5 MIN READ
0
Amino acid homeostasis for a Happy New Year!
6 MIN READ
0
From Hydra to humans vs a Lakatosian research program
4 MIN READ
0
Unified nutritional and molecular mechanisms
9 MIN READ
0
Chemical ecology and RNA-mediated control of DNA loops
< 1 MIN READ
0
Jumping back: Science or Pseudoscience? (2)
2 MIN READ
0
Jumping back: Science or Pseudoscience?
6 MIN READ
0
Glycine and GnRH: Am I being pedantic?
4 MIN READ
0
Extensive molecular evidence vs ridiculous theories
2 MIN READ
0
Dual genomes: exposing the evolution industry
5 MIN READ
0
Sackler Colloquium: Effects or AFFECTS on Behavior
2 MIN READ
0
Thermodynamic constraints and ecological adaptations sans evolution
6 MIN READ
0
Ecological adaptations reported as evolution in insects and mammals
4 MIN READ
0
Biologists puzzled by evolved RNAs and decaying DNA
6 MIN READ
0
SNPs and millions of small variations in the human genome
3 MIN READ
0
Making sense of quotes scattered across disciplines
2 MIN READ
0
Complex behaviors of cell types in cancer
6 MIN READ
0
We need pattern recognition, not a prologue
6 MIN READ
0
Sexual differentiation of cell types in plants
2 MIN READ
0
In theory, or supported by experimental evidence?
5 MIN READ
0
It’s cell type differention, not cell fate determination (2)
3 MIN READ
0
No excuses: Creation and the meaning of organismal complexity
7 MIN READ
0
No understanding of biodiversity
2 MIN READ
0
Behavioral ecology: please continue to believe in our fantasies
3 MIN READ
0
2014 and 2004 Nobel Prize in Medicine
3 MIN READ
0
RNA-mediated genetic engineering (Part 2)
3 MIN READ
0
RNA-mediated events are not a matter of faith
2 MIN READ
0
Color vision refutes the evolutionary dogma of gene duplication
4 MIN READ
0
Unassailable evidence vs assumptions
4 MIN READ
0
Forces of "Nature" limit dissemination of information
4 MIN READ
0
Metabolism, fixation, health or neurodegerative disorder
2 MIN READ
0
Physics, Chemistry, and Molecular biology (PCMb)
2 MIN READ
0
Physics denied; pseudoscientific nonsense accepted
2 MIN READ
0
RNA-directed DNA methylation and RNA-mediated events
5 MIN READ
1
Mathematical model: microRNA and epigenetic regulation
2 MIN READ
0
Quantum physics meets Evolutionary Psychology News
2 MIN READ
0
A molecular visualizer of worthwhile molecular biology
2 MIN READ
0
RNA-mediated species diversification from microbes to primates
3 MIN READ
0
Insect homology and diversity attributed to mutations
2 MIN READ
0
The quantum biology of consciousness
3 MIN READ
0
Genes and Race: Human History?
2 MIN READ
0
Don't tell the Creationists
2 MIN READ
0
Social experiences epigenetically effect gene networks
2 MIN READ
0
Functional coding variants are not mutations
2 MIN READ
0
Understanding the role of mutations and evolution
4 MIN READ
0
Hormones effect sensitivity to androsterone
2 MIN READ
0
Music to our ears and song in birds: a common sense approach
2 MIN READ
0
The challenges of a Darwinian approach to anything
3 MIN READ
0
How Species Diversify
2 MIN READ
0
The same neural mechanisms are at work in worms and humans
2 MIN READ
0
Evolutionarily innovative DNA mistakes?
< 1 MIN READ
0
Epigenetic effects on the evolution of behavior
2 MIN READ
0
Human pheromones and the definition of life
2 MIN READ
0
Human pheromones and inner conflict about evolution (1102 words)
4 MIN READ
0
Human pheromones and the visual appeal of other people (Part Three)
2 MIN READ
0
Human pheromones and the visual appeal of other people (Part Two)
2 MIN READ
0
Adam’s rib: Pheromones and the adaptive evolution of human sexuality
2 MIN READ
0
A fallacious leap? Ancestral and derived traits
3 MIN READ
0
Modeling odor processing in microbes, mice, and mankind
2 MIN READ
0
Human Pheromones in Socioaffective Neuroscience & Psychology
2 MIN READ
0
The biology of behavior: Seeing more clearly
< 1 MIN READ
0
Do Pheromones Play a Role in Our Sex Lives: Scientific American
< 1 MIN READ
0
Docosahexaenoic acid and autism: praying for hope, or preying on hope
< 1 MIN READ
0
Timing is key in the proper wiring of the brain: study
2 MIN READ
0
Progress in brain research (e.g., starting over)
< 1 MIN READ
0
Avian recognition of human faces
< 1 MIN READ
0
A lesser role for olfaction and pheromones in humans?
1 MIN READ
0
Pheromones and sexual behavior in birds
< 1 MIN READ
0
