Plenty of Room at the Bottom

Environmental selection is natural selection (2)

I believe that if you put enough biologically uniformed theorists in the same room, they will invent more theories to support the pseudoscientific nonsense they have touted in the past. See for example:

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk

Acknowledgments

The synthesis presented here is a product of the American Association for the Advancement of Science’s 2017 annual meeting, as the ideas came together in the session entitled “Beringia and the Dispersal of Modern Humans to the Americas.”
 

Every aspect of every level of biophysically constrained food energy-dependent biologically-based cause and effect is placed back into the context of a ridiculous theory of human migration and evolution. The theory accurately attests to the link from one food energy-dependent base pair change to biodiversity in human populations via fixation of one amino acid substitution. But then, something goes horribly wrong.

The theory requires the fixation of the amino acid substitution to automagically occur in the context of the sun’s anti-entropic virucidal energy. The theory fails to mention the fact that the physiology of pheromone-controlled reproduction and the microRNA-mediated creation of all cell types in all living genera is required.

See for comparison: Anything published since the time I learned about the importance of microRNAs during the 2012 Society for Neuroscience annual meeting in New Orleans, LA.

From 2000/10/15 to 2012/10/15 microRNA Items: 1 to 20 of 19910

From 2012/10/15 to 2018/04/26 microRNA Items: 1 to 20 of 53458

The number of biologically informed serious scientists who have linked the energy-dependent creation of microRNAs to biophysically constrained viral latency and all biodiversity via the pheromone-controlled physiology of reproduction in bacteria continues to rapidly increase.

This begs the question: When will biologically uninformed science idiots stop attending meetings that facilitate their attempts to invent more ridiculous theories?

For God and Country

Faith in evolution: Paleontology as a molecular science

Keeping the faith

For the last 20 years, Mary Schweitzer, a paleontologist at North Carolina State University in Raleigh, has amassed a wealth of evidence that she’s isolated protein fragments from dinosaurs as much as 80 million years old. That bucks the conventional wisdom among paleontologists who argue that proteins, which are made of chains of amino acids, can’t survive more than 1 million years or so. So far, no group other than Schweitzer and her collaborators has managed to replicate the findings. She contends that’s because others don’t follow her methods. If Schweitzer is right and outside researchers eventually do confirm her findings, it could transform dinosaur paleontology into a molecular science. That, in turn, could help researchers answer long-standing questions, such as whether dinosaurs were warm- or cold-blooded, and work out the dinosaur family tree.

The evidence does not show that the protein fragments are from dinosaurs as much as 80 million years old. No experimental evidence of biophysically constrained biologically-based cause and effect suggests that is possible. But she is keeping her faith in evolution despite the fact the nothing but mathematical models support that pseudoscientific nonsense.
See for comparison: Paths of the Trinity: Being-in-Relationship as Theology, an Answer to Zen Buddhism
In the comments, Jay Kimooyoung wrote:

As people get more informed of the range of interpretive tools that have been avalialbe across different times and different cultures, with their commonality and distinctions, both apparent and real, hopefully they will interact with the world more freely, and then collectively enter into a more ‘enlightend’ stage in the next chapter of our history.

The 2017 Nobel Laureates in Chemistry shared their prize for linking energy-dependent changes from electrons to ecosystems in all living genera via the cryo-EM technology that enables observation at the level of changes in atoms and hydrogen-atom transfer in DNA base pairs in solution. Virus-driven theft of quantized energy occurs at that level of examination, which is how the degradation of messenger RNA is linked to all pathology. If you are not willing to “inform yourself” or to believe serious scientists, do not wait for anyone to “…enter into a more ‘enlightend’ stage in the next chapter of our history.”
Energy is information. The virus driven energy theft that links the degradation of messenger RNA to all pathology is proof that the number of biologically uninformed science idiots who claim to be scientists is greater than the number of serious scientists. The number of self-serving theologians is of secondary concern.
Jay Kimooyoung

New discoveries are made through numerous attempted experiements. Such attempts require huge investment of energy and accumulated information. In the development of science, they are as much the integral part as pigeonhalling confirmed data. Attempted memes are the background soil for the progress in science.

And more so is with the situation of theology. What ultimately validates is not correspondence according to objectified criteria. It is the extent of sincere dedication that serves to carry the weight of life. In that sense, every theology contains element of self-service. Concern could be a matter of degree rather.

To my horror, “Answers in Genesis” just published Celebrate Your Inner Virus — a reversal of their long-standing theological perspective that links the “Curse” from the virus-driven degradation of messenger RNA to all pathology.

It is important that we understand the design present in viruses because God made them

See for comparison: Did God Make Pathogenic Viruses?

Pathogenesis is evidence of something gone wrong, a mutation or the accidental movement of genes, and not evidence of a system deliberately designed to cause human disease and suffering.

My life’s works have served to refute all the pseudoscientific nonsense touted by neo-Darwinists and “Big Bang” cosmologists. “Answers in Genesis” now appears to be supporting them.
See for comparison: https://www.youtube.com/watch?v=HaKf2VuOyl0&feature=youtu.be Video interview about the death of Robin Williams Quantum Souls Published on 10 May 2017
https://www.youtube.com/watch?v=OIkbH9dcAkw&feature=youtu.be Superbugs, Bacteriophages and Phage Therapy: An Interview with James Kohl Published on 17 May 2017
https://www.youtube.com/watch?v=iTvT0p9Q5TY Food Energy-Dependent Cell Type Differentiation Refutes Theory of Evolution
https://www.youtube.com/watch?v=wfPy5QDJp7w&feature=youtu.be How to Treat Cancer as a Disorder of Energy Transfer
https://www.youtube.com/watch?v=s7_fQ2fS5UY&feature=youtu.be Charles Darwin Taught Conditions of Life, Not Mutations
https://www.youtube.com/watch?v=HCQI7fMi8ts Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 1
https://www.youtube.com/watch?v=ObHVOdi99Rw Quantized Energy Links Olfaction from Angstroms to Ecosystems Part 2
See also: Base-pair opening dynamics of the microRNA precursor pri-miR156a affect temperature-responsive flowering in Arabidopsis

Based on these results, we propose that fine-tuning of the base-pair stability at the cleavage site is essential for efficient processing of pri-miR156a at a low temperature and for reduced flowering sensitivity to ambient temperature changes.

All the co-authors are from South Korea and so is Jay Kimooyoung.
I ride for God and country with the American Legion Riders. See for comparison: Energy as information and constrained endogenous RNA interference

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection.

This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes

Re: The viral hecatomb
In his 2010 publication “The Great Pheromone Myth“, Richard L. Doty challenged all accurate representations of the top-down energy-dependent creation of RNA and biophysically constrained pheromone-controlled biodiversity.
On 5/16/17, he published: Olfactory dysfunction in neurodegenerative diseases: is there a common pathological substrate?

…antibodies or other evidence of viral infection have been found to be higher in the autopsied brains of people with neurodegenerative diseases with the most smell loss (figure 2), relative to the brains of healthy controls. Whether a close relationship exists between smell dysfunction and antibodies or other indicators of viral involvement is unknown.

The close relationship that exists between smell dysfunction indicators of viral involvement has been exquisitely detailed in my life’s history of published works and presentations. All of them link what is now known about the virus-driven degradation of messenger RNA from mutations to all pathology in species from microbes to humans.
See: Viral MicroRNAs, Host MicroRNAs Regulating Viruses, and Bacterial MicroRNA-Like RNAs

Currently, only a limited number of miRNA and miRNA-like RNAs have been found in bacteria and viruses, a number that is sure to increase rapidly in the future. The interactions of these small noncoding RNAs in such primitive species have wide-reaching effects, from increasing viral and bacterial proliferation, better responses to stress, increased virulence, to manipulation of host immune responses to provide a more ideal environment for these pathogens to thrive. Here, we explore those roles to obtain a better grasp of just how complicated disease truly is.

See also: Deep-Sea Viruses Destroy Archaea
See also: High potential for temperate viruses to drive carbon cycling in chemoautotrophy-dominated shallow-water hydrothermal vents

…inducible provirus-host interactions occurring in these systems can profoundly influence the functioning of the microbial food web and the efficiency in the energy transfer to the higher trophic levels.

Summary: The virus-driven theft of quantized energy prevents the efficient transfer of energy that is required to link the physiology of pheromone-controlled reproduction to all biodiversity on Earth. Instead, the virus-driven degradation of messenger RNA has been linked to all pathology.
Remember, anytime a pseudoscientist like Richard L. Doty claims that mammalian pheromones and/or human pheromones do not exist, that pseudoscientist is trying to cover up a history of ignorance. The history of ignorance has caused the unnecessary suffering and premature death of millions of people during the past two decades. Pseudoscientists have placed their faith in evolution and in the nonsense touted by people like Doty, who never learned to link the metabolism of food energy to pheromones or linked species-specific pheromones from the physiology of reproduction to biophysically constrained viral latency and all biodiversity.
See for comparison: “Cytosis

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

See also: Subatomic

Subatomic introduces a unique variation on deck building with a highly accurate chemistry theme, with the ultimate goal of building Elements to score points, but allowing many varying types of strategies.

Lethal virus kills 5 billion people?

Entertaining yourself to death

Summary: Food energy is required for the creation of enzymes that metabolize the food, which links the metabolism to the pheromone-controlled physiology of reproduction in species from microbes to humans via alternative splicings of pre-mRNAs, which are now called microRNAs in more than 65,000 published works. The horrid tradjedy of of yet another preventable death by suicide extends those works to preventing the cause of death of those killed by Stephen Paddock.
Vegas gunman transferred $100K, set up cameras at hotel room
Excerpts with my emphasis:

Lombardo said he is “absolutely” confident authorities will find out what set off Paddock, a 64-year-old high-stakes gambler and retired accountant who killed himself….

…speculated that there was “some sort of major trigger in his life — a great loss, a breakup, or maybe he just found out he has a terminal disease.”

…a “psychological autopsy” may be necessary to try to establish the motive. If the suicide didn’t destroy Paddock’s brain, experts may even find a neurological disorder or malformation

He said there could be a genetic component to the slaughter…

“The genetics load the gun, personality and psychology aim it, and experiences pull the trigger, typically,” Clemente said.

He later worked for a defense contractor.

“No affiliation, no religion, no politics. He never cared about any of that…

Two former facebook friends are among those who claim that “nobody cares” that I have detailed the facts about the virus-driven cause of death for Stephen Paddock and his victims. When will others learn why there was no obvious motive to his madness?
The excerpts above clearly indicate that virus-driven epigenetic drift led to the deadly constraint-breaking mutations via everything known to serious scientists about epitranscriptomics and biophysically constrained viral latency.
Simply put, like most people, Stephen Paddock failed to protect himself from the virus-driven degradation of messenger RNA that serious scientists have linked to all pathology in all living genera. Psychiatrist/antagonist Jay R. Feierman put that fact into the context of this post to the “Evolutionary Psychology” Yahoo Group.

168958 Origin and Evolution of RNA-Dependent RNA Polymerase OPEN ACCESS

I find this article interesting because of the “object of study.” We are used to thinking about evolution at hierarchical levels above that of protein enzymes. Yet, protein enzymes are “structural design features” and follow the same principles of evolution by natural selection as structural design features at higher hierarchical levels, such as certain kinds of behaviors and even species. Compared to other kinds of evolution, protein enzyme evolution is very conservative in that it does not change much through phylogeny. We essentially have the same enzymes for metabolizing glucose as do bacteria and other single cell animals.

The death of Stephen Paddock and his victims can now be attributed to medical professionals, like Jay R. Feierman, and anyone else who claims: “We are used to thinking about evolution at hierarchical levels above that of protein enzymes.”
The creation of protein enzymes requires an energy source. That fact refutes every aspect of the pseudoscientific nonsense touted by biologically uninformed science idiots. [An idiot is someone with no professional expertise: A biologically uninformed science idiot is someone like Feierman, who has professional expertise but no common sense.] Feierman linked to this article: Origin and Evolution of RNA-Dependent RNA Polymerase (with my emphasis)

With the emergence of a variant with properties of reverse transcriptase, and subsequently a DNA polymerase, a fundamental step occurred to originate the first genomes based in DNA, being the bridge to move from a RNA/Protein World to a DNA/RNA/Protein World (Gilbert, 1986; Müller, 2006). When DNA molecules emerged, by variation, other classes of polymerases appeared. With the complexification of the biological system, functions such as replication, repair, and recombination emerged, very high error rates were selected against, and the new variants arose to work in specific processes.

My summary: The authors eliminate the energy-dependent creation of enzymes (1) reverse transcriptase and (2) a DNA polymerase. In the second act of their tragic comedy routine, they eliminate the biophysical constraints that link the physiology of pheromone-controlled reproduction from natural selection for energy-dependent codon optimality to the creation of enzymes and food energy-dependent RNA-mediated DNA repair via feedback loops.
See: Feedback loops link odor and pheromone signaling with reproduction
The feedback loops link the sense of smell in bacteria from the physiology of their pheromone-controlled reproduction to our visual perception of energy and mass in the context of the space-time continuum.
See: Olfaction Warps Visual Time Perception

The behavioral gain produced by a congruent relative to an incongruent odor is accompanied by elevated neural oscillatory power around the object’s flicker frequency in the right temporal region ~150-300 ms after object onset, and is not mediated by visual awareness. In parallel, odors bias the subjective duration of visual objects without affecting one’s temporal sensitivity. These findings point to a neuronal network in the right temporal cortex that executes flexible temporal filtering of upstream visual inputs based on olfactory information. Moreover, they collectively indicate that the very process of sensory integration at the stage of object processing twists time perception, hence casting new insights into the neural timing of multisensory events.

Virus-driven degradation of messenger RNA links alterations in the timing of multisensory events to the suicide of Stephen Paddock and to the unnecessary suffering and premature death of his victims. That fact was placed into the context of Feierman’s thinly veiled attack on the practice of Precision Medicine.
See: Energy as information and constrained endogenous RNA interference, which was presented during the Labroots: Precision Medicine Virtual Conference February 22-23. 2017
Description:

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection. This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes

Stephen Paddock killed 59 people and more than 500 people were injured. On 10/4/17, there were only 637 views of my 7 minute-long presentation. With release of the cell biology game “Cytosis,” which is scheduled to be available later this month, everyone who is not dead yet will be able to learn how to protect themselves from the cause of death by suicide: viruses. The virus-driven degradation of messenger RNA will also be the cause of death for people who have not learned the difference between energy-dependent healthy longevity and the virus-driven energy theft that will kill them either directly or indirectly.

A board game taking place inside a human cell! Players compete to build enzymes, hormones and receptors and fend off attacking Viruses!

See also this comment to the human-ethology Yahoo group (reproduced below)

See for comparison: Transcription factor clusters regulate genes in eukaryotic cells

Attempts continue to link epigenetic drift and epitranscriptomics to RNA-mediated cell type differentiation outside the context of natural selection for energy-dependent codon optimality and the biophysically constrained pheromone-controlled physiology of reproduction. All past attempts have failed.

The reason for those attempts and the reason all past attempts have failed may require more clarification from people like Jay R. Feierman. Others realize that the enzymes linked from metabolism to survival of all species did not create themselves and did not evolve, which means that no species evolved via natural selection for beneficial mutations. Pseudoscientists have been left behind with their hypothetical scenarios.’

See for example: Origin and Evolution of RNA-Dependent RNA Polymerase

“Based in the present results, we suggest a hypothetical scenario where initially a ribozyme with polymerase activity could have enhanced its activity by the binding of a simple cofactor, as magnesium (Shechner et al., 2009; Horning and Joyce, 2017), thus, exerting the functions of replication of some information stored on RNA molecules (Kim and Higgs, 2016; Tagami et al., 2017).”

See for comparison: Lipid Encapsulation of Self Replicating Ribozymes

“Despite their challenges, ribozymes have made an interesting niche for themselves in the field of abiogenesis. The evolution of a successful RNA polymerase ribozyme is a lofty goal. While its discovery would not be the be-all and end-all of abiogenesis research, it would represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered.”

I have discussed the claims about abiogenesis and ribozymes in the context of “…a system of heredity and evolution through natural selection…” with scientists who have repeatedly assured me that the claims are nothing more than examples of what Richard Feynman placed into the context of “human idiocy.” Food energy is required for the creation of enzymes that metabolize the food, which links the metabolism to the pheromone-controlled physiology of reproduction in species from microbes to humans via alternative splicings of pre-mRNAs, which are now called microRNAs in more than 65,000 published works.

See for example: miRNA as viral transcription tuners in HPV-mediated cervical carcinogenesis

Discovery of microRNAs (miRs) in recent years and differential expression of a set of specific miRs in HPV infection and cervical lesions indicate that among various regulatory mechanisms, role of these differentially expressed miRs in the post-transcriptional control is pivotal.

When will people like Feierman and Jones begin to examine the extant literature that links energy-dependent biophysically constrained biologically-based cause and effect as detailed in the molecular epigenetics section of our 1996 review:
From Fertilization to Adult Sexual Behavior
How many more people will needlessly suffer and/or die prematurely due to the ignorance and arrogance of biologically uninformed science idiots?

diseases-disorders

The Aquatic Ape / Waterside Ape divergence

See also: The Aquatic Ape: New evidence? (9/8/16)
Walt Patrick 

Now that I’m semi-retired…. My major focus is the development of village-scale energy sovereignty.
I believe that sustainable community stands on an interlocking foundation of effective and sustainable energy systems, and I’m working to develop ways that a community can meet its energy needs without having to rely on multi-national energy corporations.

My comment: Thanks to Walt for introducing me to Elaine Morgan’s work. He loaned me his copy of “The Aquatic Ape” in 1982. Thanks to Janissa Wilson for introducing me to Walt Patrick. Thirty-four years have passed, and I remember their friendship and their influence as if it was only yesterday.
See (from yesterday and earlier today):
The Waterside Ape — Sir David Attenborough considers whether new evidence will help a once widely ridiculed theory of human origins move towards to mainstream acceptance.
My comment: He takes a giant step forward in an obvious attempt to keep biologically uninformed theorists from being subjected to ridicule because they missed the paradigm shift.
He then takes small steps backwards to put the “The Aquatic Ape” back into the context of ridiculous theories, which he uses to link his divergence from claims in the “The Aquatic Ape.” He needs an evolutionary theory to evolve one theory into a new theory that becomes “The Waterside Ape.” Otherwise, he gets credit for nothing more than finally acknowledging what serious scientists have known for several decades.
The reports on the efforts of the serious scientists are exemplary. So is the attempt to put them all into the context of evolutionary theory at a time when energy-dependent changes have been linked from angstroms to ecosystems in all living genera in the context of energy as information.
See also:  A Chat with Information Scientist Pedro Marijuán
I’ve commented twice on this article, which is  on Suzan Mazur’s blog site, and both comments were promptly removed.
See for comparison: Kalevi Kull: Censorship & Royal Society Evo Event
My Jul 31, 2016 11:51am comment has not yet been removed:

James Kohl Founder at RNA-mediated.com

This response may not, at first, appear to be directed against the claims you have supported with your series of interviews. But watch closely as they squirm under the weight of experimental evidence that collectively refutes their ridiculous theories and philosophy.

The Origin of The Extended Evolutionary Synthesis: An Interview with Massimo Pigliucci

Moving forward:

Claims linked to the Extended Evolutionary Synthesis have since run out of “wiggle room”. Listen to: The Waterside Ape, which closes the case on how the nutrient-energy-dependent pheromone-controlled physiology of reproduction links ecological variation to ecological adaptation via RNA methylation and RNA-mediated amino acid substitutions in supercoiled DNA, which differentiates all cell types in all living genera.

part 1
part 2
Ongoing attempts have failed to place everything known about biophysically constrained RNA-mediated protein folding chemistry and epigenetic effects on supercoiled DNA into the context of evolution. The attempts will continue to fail until researchers and theorists stop trying to make what is known fit into their theories about millions of years of evolution. No experimental evidence of biologically-based cause and effect links what is known about energy-dependent changes from angstroms to ecosystems in all living genera.
See also: Elaine Morgan is a tenacious proponent of the aquatic ape hypothesis: the idea that humans evolved from primate ancestors who dwelt in watery habitats. Hear her spirited defense of the idea — and her theory on why mainstream science doesn’t take it seriously.

See for comparison: Study Links RNA Alterations to Stomach Cancer  September 14, 2016

Written By: Xuan Pham Science Writer, PhD LabRoots

Description: I am a human geneticist, passionate about telling stories to make science more engaging and approachable.

For comparison: I am a medical laboratory scientist who has followed the literature on biologically-based cause and effect since 1982.

The historical perspective on the current literature clearly states this:

For several years it has been apparent that an ecological approach is imperative for all studies in population genetics, including those pertaining to man. It also offers a potentially useful point of view to the physical anthropologist, the ethnologist, and the archeologist, and it should provide an important integrative bridge between the various fields of anthropology. — Blood, Bulbs, and Bunodonts: On Evolutionary Ecology and the Diets of Ardipithecus, Australopithecus, and Early Homo

See also: Unravelling the genetic mystery behind mitochondrial disease

Excerpt:
Mitochondrial disease is an illness that robs its sufferers of energy, and damages muscles and major organs like the brain and heart. About one in 5000 babies – or one Australian baby born each week – are born with a severe form of the disease, which can often lead to an early death.

My comment: Virus-driven energy theft of quantised energy is the cause of all pathology. That fact is not a genetic mystery. It is fact known to all serious scientists who understand why Church et al., (2015) applied for this patent RNA-Guided Human Genome Engineering.

Viruses steal the energy that all cell types require for cell-type differentiation, which links ecological variation to ecological adaptation and healthy longevity in the absence of excess nutrient-stress and/or excess social stress. Stress-linked pathology is manifested when changes in hydrogen-atom transfer in DNA base pairs in solution facilitate codon usage in codon usage that enables their proliferation and prevent cell type differentiation.

The energy stolen by viruses is quantised energy:

See: A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution

My comment: This is not a quantum theory of neural cell signalling throughout evolution. It exemplifies what is know to serious scientists about the obvious links from ecological variation to ecological adaptation, which is nutrient-energy-dependent and pheromone-controlled in species from microbes to humans.

See also: Two fatty acyl reductases involved in moth pheromone biosynthesis 7/18/16

Studies over the last two decades have pinpointed that the epigenetic effect of pheromone-driven adaptive evolution is one of the major factors driving the successful diversification of Lepidopteran insects10. In moths, a few substitutions in critical amino acids in the key pheromone biosynthetic enzymes are sufficient to create a novel pheromone component11,12.

See also: Role of olfaction in Octopus vulgaris reproduction 1/1/15

Future work on O. vulgaris olfaction must also consider how animals acquire the odours detected by the olfactory organ and what kind of odour the olfactory organ perceives. The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000).

Kohl (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model is also cited in Two fatty acyl reductases involved in moth pheromone biosynthesis.

In my 2013 review, I concluded:

the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

The criticisms of my 2013 review may be of interest in the criticisms of Elaine Morgan’s works, since there is still no other model that links ecological variation to ecological adaptation.

In his Criticisms of the nutrient-dependent pheromone-controlled evolutionary model, Andrew Jones wrote:

James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. It was a mistake to let such a sloppy review through to be published.

Andrew Jones did not offer any other model for comparison. He seemed to think that he could support his criticisms via his claim in his thesis:

Despite their challenges, ribozymes have made an interesting niche for themselves in the field of abiogenesis. The evolution of a successful RNA polymerase ribozyme is a lofty goal. While its discovery would not be the be-all and end-all of abiogenesis research, it would represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered.

The current state of college education in the United States of American and perhaps elsewhere is reflected in the thesis by Andrew Jones as a continuation of the pseudoscientific nonsense that is used to support hypothesis-free science with claims that a system of heredity and evolution through natural selection may exist outside the context of any model that links energy-dependent changes from angstroms to ecosystems in all living genera.

See this invited review of nutritional epigenetics, for example: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems 4/10/14

Abstract:

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.

In 2004, Elaine Morgan suggested it might be another 10 years before her concept of ecological adaptation gained more acceptance. If not for students like Andrew Jones, acceptance of historical works that link angstroms to ecosystems in all living genera via experimental evidence of biologically-based cause and effect would already be accepted. Until the experimental evidence is accepted and the theories are declared by all serious scientists to be ridiculous, you and your loved ones will suffer and die from virus-driven pathology. Why aren’t you already as sick of that as I am after 40 years experience as a medical laboratory scientist?

 

rp_levels-of-organization.jpg

The Aquatic Ape: New evidence?

The Waterside Ape

In 1960, the eminent Oxford marine biologist Sir Alister Hardy proposed a revolutionary idea: that our human ancestors had not started their existence on the wide savannahs of Africa, but had become accustomed to living alongside water – swimming and diving in the shallows, collecting the abundant food, and learning to use language and fashion tools. Hardy asserted that this adaptation to living at the waterside –whether by rivers and pools or by the ocean – would also account for a whole range of peculiarities about the human form, including the layers of fat beneath the skin, the relative lack of body hair, the development of language and speech, and what he called our “runaway brains”.

Perhaps surprisingly, it was a screenwriter rather than a scientist, Elaine Morgan, who took up Hardy’s theory and, for over 40 years, progressively refined the evidence for the idea. Most mainstream paleo-anthropologists ridiculed and rejected the Hardy-Morgan thesis for decades, but some influential scientists asked for the proposal to be approached with an open mind.

Sir David Attenborough first considered the controversial theory on Radio 4 in 2004, and in this new two-part series, he brings listeners up-to-date with the story and the evidence put forward since then – for both the hypothesis and also for its continuing detractors. Back in 2004, Sir David asked Elaine Morgan how long it would take for the aquatic adaptation theory to become a mainstream account of human origins. She answered: “I’ll give it ten years.” As the programme reviews the new evidence, has she been proved right?

Presenter/Sir David Attenborough, Producer/Richard Collins for Pier Productions

Re: As we review the new evidence, has she been proved right?

My comment: No experimental evidence of biologically-based cause and effect ever suggested that Elaine Morgan was wrong.  She accurately predicted that 2014 would be the year in which she was proved right. As far as I know, she was predictably right.
See this 2014 invited review of nutritional epigenetics (and energy-dependent RNA-mediated cell type differentiation):

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

The invited review was requested by guest editors for a special issue of “Nutrients.” The reason for the request was clear.
In Nutrient-dependent/pheromone-controlled adaptive evolution: a model (2013), I concluded:

…the largest contributor to the development of our personal preferences may be the unconscious epigenetic effects of food odors and pheromones on hormones that organize and activate behavior. If so, the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.

My 2014 invited review was returned without review. No factual representations of epigenesis and epistasis have been offered for comparison to the ridiculous claims of theorists. For example:
In Mutation-Driven Evolution, which was published on the same day as my 2013 review, Masatoshi Nei concluded:

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements.

In my model, and in the context of Elaine Morgan’s claims, viral latency is biophysically constrained by the nutrient energy-dependent physiology of reproduction in all living genera.
See also: Epigenetics and Genetics of Viral Latency

… viral latency is responsible for life-long pathogenesis and mortality risk…

For brief reviews of Elaine Morgan’s claims, see:

I do not believe any experimental evidence of energy-dependent biologically-based cause and effect suggests that we evolved from any other species. I suspect that Sir David Attenborough will not be the first to consider my model in the context of his review of Darwinian and/or neo-Darwinian theories. There is too much known to serious scientists about energy-dependent RNA-mediated cell type differentiation to reach any other conclusion than the one reached by Paul M. Lieberman in Epigenetics and Genetics of Viral Latency.
I reiterate:

… viral latency is responsible for life-long pathogenesis and mortality risk…

See for comparison:

See also:

The idea that Elaine Morgan can be proved right without proving that Darwian and neo-Darwinian theories are overwhelmingly wrong is an idea that should have been considered during the past 40 years. Instead, consideration of the claims made by theorists have left theorists with nothing more than their ridiculous theories.
See for comparison: Structural diversity of supercoiled DNA, Glucose Tightly Controls Morphological and Functional Properties of Astrocytes,
Tight DNA packaging protects against ‘jumping genes,’ potential cellular destruction Thanks to Teresa Binstock for bringing this article about supercoiled DNA to my attention.
“Tight DNA packaging” and “tightly coiled DNA” are terms used to obfuscate the facts about supercoiled DNA that have already linked viral latency to all pathology.
Supercoiled DNA protects the organized genomes of all living genera from virus-driven entropy. That fact has been the focus of my efforts here and at RNA-mediated.com
Why is Teresa Binstock — co-author of our 1996 Hormones and Behavior review — the only one who seems to be following the literature on RNA-mediated cell type differentiation?

See also: Systematic chemical screening identifies potential antimalarials with new mechanism of action

When Schreiber’s team looked for compounds that met both criteria – displaying a novel mechanism of action and activity during all three disease stages – a series of compounds stood out. All of them acted on the same target, phenylalanyl-tRNA synthetase, a complex enzyme that contributes to protein synthesis. When they tested the compounds in mice, it eradicated the malaria parasites during all three stages of the disease.

Cause and effective treatment are RNA-mediated via links from metabolic networks to genetic networks across species.
rp_levels-of-organization.jpg

Virus-driven downsizing of the human brain (2)

The effects of virus-driven energy theft on brain development in mammals typically occur more rapidly during gestation and early prenatal development. That’s why the connection from biophysically constrained RNA-mediated amino acid substitutions and protein folding chemistry during life history transitions has been largely ignored.

Persistent Structural Plasticity Optimizes Sensory Information Processing in the Olfactory Bulb

Excerpt:
…coordinated structural plasticity is consistent with stable, yet flexible, decorrelated sensory representations. Together, our study reveals that persistent, coordinated synaptic structural plasticity between interneurons and principal neurons is a major mode of functional plasticity in the OB.
My comment: “Decorrelated” sensory representations link food odors and pheromones from the epigenetically-effected RNA-mediated innate immune system to supercoiled DNA in the context of everything known about how angstroms and ecosystems are linked via energy-dependent feedback loops to all biodiversity. Healthy longevity exemplifies the links to biodiversity that are eliminated by virus-driven energy theft.

Decorrelation links ecological variation to ecological adaptation via biologically-based cause and effect.

Reported as: The relentless dynamism of the adult brain

Excerpt:

 “We expected to see the synapses gradually stabilizing, as happens during brain development. But astonishingly, these synapses proved to be highly dynamic throughout the life of the new neurons. Also, these dynamics were reflected in the principal neurons, their primary synaptic partner,” explained first author, Kurt Sailor, from the Institut Pasteur.

The experience dependent de novo creation of olfactory receptor genes links ecological variation from RNA-mediated amino acid substitutions to the physiology of reproduction and cell type stability in all cell types of all vertebrates and invertebrates via biophysically constrained protein folding chemistry. That fact eliminates the claims of all neo-Darwinian theorists and big bang cosmologists from any further consideration whatsoever in the context of biologically-based cause and effect.

Alternative splicing of pre-mRNA

Energy-dependent RNA methylation (3)

I wrote: Stop trying to claim anything about energy-dependent cause and effect on any other site including your own. You betrayed my trust in you. I do not take that lightly.

On 6/4/16, Tomi Aalto replied:

“You don’t own the knowledge.”

My comment: Researchers own nothing without patents based on the knowledge. They do not own the knowledge that leads others to learn more about what has been accurately portrayed in the context of biophysically constrained biologically-based cause and effect.
Tomi Aalto is correct. Any biologically uninformed layperson or scientist who makes a living by stealing the knowledge from others can do that without fear of litigation. That’s why misrepresentations about what is known have led to delayed understanding about the role of energy and virus-driven energy theft in RNA-mediated cell type differentiation.
Simplistic theories about mutations and evolution have prevailed.
For comparison, the systems complexity of energy-dependent RNA-mediated cell type differentiation and virus-driven energy theft linked to all pathology is overwhelming.
See: Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression
Excerpt:

…specific tRNAs can form ‘‘inducible’’ pathways with their direct target transcripts, which are enriched for their cognate codons.  Such target transcripts can become stabilized in the context of their favored tRNA content or can be more effectively translated—ultimately yielding greater protein output.

My comment: The stability of the target transcripts is energy-dependent and controlled by the physiology of reproduction, which links metabolic networks to genetic networks via RNA-mediated amino acid substitutions and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy. That is the fact that people like Tomi Aalto want to portray as if they came to their conclusions based on their “raw insight.” It is a fact that people like Sean Ovis want to portray as if it did not refute the pseudoscientific nonsense of neo-Darwinian evolution.
The fact was reported as: Researchers uncover how “silent” genetic changes drive cancer
Excerpt:

[It] challenges previous assumptions about how tRNAs function and suggests that tRNAs can modulate gene expression, according to the researchers. Tavazoie points out that “it is remarkable that within a single cell type, synonymous changes in genetic sequence can dramatically affect the levels of specific proteins, their transcripts, and the way a cell behaves.”

My comment: They have indirectly linked energy-dependent RNA methylation to what they place into the context of “…the way a cell behaves.” This makes it appear that cancer cells are nothing more than cells that behave badly. The cause of their “bad behavior” is not addressed for comparison to the behavior of differentiated cells that contribute to the energy-dependent healthy longevity of species from microbes to humans.
See also:  Small Non-coding RNAs Associated with Viral Infectious Diseases of Veterinary Importance: Potential Clinical Applications
Excerpt:

The emerging correlation between miRNA expression and disease pathogenesis and outcomes suggests the potential use of miRNAs as biomarkers. In the first report that described the role of a miRNA as a diagnostic and prognostic marker in humans, Takamizawa et al. demonstrated that in patients with lung cancer, lower let-7 levels predicted a significantly worse prognosis after potentially curative resection (6).

My comment: I continue to wonder why virus-driven energy theft is not considered in the context of nutrient-dependent pheromone-controlled biodiversity, which links the morphological and behavioral phenotypes of microbes from insects to primates.
See for comparison: Subcaste-specific evolution of head size in the ant genus Pheidole
Excerpt:

A recent study of global Pheidole demonstrated that body size variation was similar in Old and New World species, and that Pheidole communities repeatedly evolve similar size distributions despite inhabiting a range of biomes (Economo et al., 2015). These results also imply strong constraints on body size evolution. Future work at community scales is still needed to determine whether Pheidole species assemblages show divergence in morphology with respect to diet partitioning (e.g. to escape competition).

My comment: Biophysically constrained energy-dependent ecological adaptations link differences in ants to differences in primates. They also link virus-driven energy theft to the Dutch famine.
See also: The potato disease that changed the world

“We found four basic gene sequences in P. andina that are a close match to the variant that caused the famine in the 1840s. Our analyses also show that P. andina and the historical variant of P. infestans split into two distinct groups before the modern Mexican varieties developed,” says Martin.
In layman’s terms, this means that the disease may have originated in the Andes earlier than variants of the disease evolved in Mexico.
Does that give us a definitive blueprint? No, not really, but it does cast doubt on the idea that Mexico is the site where the disease originated. It also confirms that the evolutionary history of blight is very complex. We need to know more.
And although Martin recently completed his time in Copenhagen, he is continuing his research on blight.
NTNU has awarded Martin a tenure-track position as part of the Onsager Fellowship Programme, which recruits young, outstanding researchers to strengthen the university.

My comment: The strength of many universities is based on pseudoscientific nonsense like he will be touting because he does not know that de novo gene creation is energy-dependent and that virus-driven energy theft caused the potato blight.
See also: The Virus that Destroyed the Dutch Economy
Excerpt:

…there was a reason, and it was called the Tulip Breaking Virus, or mosaic virus. It was transmitted either by contact with the bulb of an infected tulip or by different species of aphids. It changes pigmentation by affecting the distribution of anthocyanin, a pigment that can appear different colors depending on the pH of its area.

My comment: The inability of most mainstream scientists to link Rosalind Franklin’s works with the tobacco mosaic virus to her questions about the representations of a static DNA double helix should by now have been attacked with experimental evidence that links energy-dependent changes from angstroms to ecosystems. The Zechiedrich lab may need to stop poking fun at others and tell them to stop touting pseudoscientific nonsense about mutations and evolution. It seems likely that anyone who is currently combating evolution to fight disease may need to help attack the neo-Darwinian theorists.


Unless all serious scientists attack, there may be no end to the pseudoscientific nonsense touted by evolutionary theorists.
See for example: New faculty member investigates how genes are born and proliferate
Excerpt:

“It has recently become clear that new genes can arise from DNA that previously did not code for protein, and that each species has a set of genes that is uniquely its own,” says Dr. Zhao, who is currently a postdoc at the University of California, Davis. “I am interested in examining how these genes originate, spread, and contribute to the adaptation of populations to their environment.”

My comment: Quantized energy as information is linked from the epigenetic landscape to the physical landscape of newly created genes by two epigenetic traps that link supercoiled DNA to protection of all organized genomes from virus-driven energy theft in the context of the energy-dependent physiology of reproduction.
See: Positive feedback loops and epigenetic traps and other blog posts for facts about epigenetic traps
See also: Drosophila’s New Genes January 23, 2014
My comment:

The de novo creation of genes has previously been reported to be the “holy grail” of evolutionary biology. If that is true, what’s reported here exemplifies the fact that the “holy grail” involves only the direct olfactory/pheromonal link from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man.

See, for example, our 1996 Hormones and Behavior review article: From Fertilization to Adult Sexual Behavior (e.g., the section on molecular epigenetics where TB wrote): “Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans…”

The alternative splicings are obviously nutrient-dependent and they lead to 1) de novo gene creation and 2) chromosomal rearrangements, which are exemplified in sex diffferences at the advent of sexual differentiation in the cell types of yeasts that sexually reproduce. The physiology of reproduction is controlled by the metabolism of nutrients to pheromones in species from microbes to man. That means de novo creation of genes probably occurs via conserved molecular mechanisms in all species (see: Organizational and activational effects of hormones on insect behavior).

Alternatively, mutation-driven evolution can be substituted for the nutrient-dependent pheromone-controlled ecological adaptations that enable species divergence. Theorists need only explain how natural selection for mutations occurs so that their theory can be compared to a model of ecological variation and natural selection of food.

The model incorporates what is required for the Creation of new genes that enable organismal complexity via ecological, social, neurogenic, and socio-cognitive niche construction. What’s required is food and nutrient-dependent pheromone-controlled reproduction. See for example:  Nutrient-dependent/pheromone-controlled adaptive evolution: a model
 
See also: Are We Eating Our Way to Prostate Cancer—A Hypothesis Based on the Evolution, Bioaccumulation, and Interspecific Transfer of miR-150

Excerpt:

 9. Conclusions
This is a hypothesis-driven manuscript, so we have had our limitations in terms of finding desired published literature. We, however, think that there is a possibility of moving towards the identification of a non-invasive diagnostic biomarker for PCa and/or aggressive PCa by quantifying circulating miR-150. The core idea of miR-150 being bioaccumulated and interspecifically transferred is also vital for the identification of a possible therapeutic biomarker for PCa, as we believe that we are what we eat.

The senior author, Lynnette Ferguson was one of the two guest editors for a special issue of “Nutrients.” After I published: Nutrient-dependent/pheromone-controlled adaptive evolution: a model Justin M. O’Sullivan and Lynnette Ferguson asked me to submit an invited review of nutritional epigenetics.
See also the logical extension of this model to: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Abstract excerpt:

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

My comment: My invited review was returned without review by Justin M. O’Sullivan and Lynnette Ferguson, which explains why Ferguson’s group claims “This is a hypothesis-driven manuscript, so we have had our limitations in terms of finding desired published literature.”
My review of nutrient energy-dependent RNA mediated cell type differentiation had been published, I might have moved forward with the obvious link from virus-driven energy theft to all pathology, which I have since established in a series of poster presentations. Justin M. O’Sullivan and Lynnette Ferguson are only two of the academically untalented and biologically uninformed researchers I have encountered whose despicable behaviors are common. They have no choice but to use the ideas and works of others in attempt to make gains without making the effort that is required to integrate the information across disciplines.
See for comparison: Vast Complexity of Immune Micro RNA Signals Jon Lieff has been following in my footsteps since the time I commented on this representation of:  Alternative RNA Splicing in Evolution
I wrote:

In our 1996 Hormones and Behavior review, we wrote:”Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans.”

http://www.hawaii.edu/PCSS/bib…
The alternative splicings are nutrient-dependent and appear to be enabled by the experience-dependent de novo creation of olfactory receptor genes, which enable additional receptor-mediated nutrient uptake and the metabolism of nutrients to species-specific blends of pheromones that control reproduction in species from microbes to man.
Your focus on the importance of pre-mRNA and alternative splicing is exemplary, especially in the context of neuronal plasticity.
C. elegans is the model organism of neurogenic niche construction that links nutrient-dependent ecological and pheromone-controlled social niche construction to socio-cognitive niche construction in vertebrates and invertebrates. See for review:
http://www.socioaffectiveneuro…
What you are helping to detail is self-assembly with evidence of olfactory/pheromonal self-organization that is currently missing from evolutionary theory, which attributes speciation to mutation-initiated natural selection even though there is no experimental evidence for that (as I mentioned elsewhere).

Excerpt:

…while scientists used to think the RNA was just a ‘middleman’, they’ve realised over the past few decades that it does so much more than that – it can control which proteins are produced in the cell.

My comment: Who taught serious scientists to think that RNA was just a ‘middleman’? Do you know any serious scientist who ever believed that? What they are claiming is that evolutionary theorists were taught to believe in pseudoscientific nonsense about energy-dependent RNA methylation and protein folding biochemistry during thermodynamic cycles of protein biosynthesis and degradation that link metabolic networks to genetic networks in all living genera.

Scientists May Have Found the Key to Curing Autism, Cancer and HIV

Excerpt: They have previously used this tool to remove HIV from human immune cells and shut down HIV replication permanently, according to a study published in Nature in March.

Precision medicine can widen cancer care options: studies (Update)

Excerpt: “Mutation in the HER2 gene favors the growth of cancer cells.”

My comment: Virus-driven energy theft causes all mutations.

De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity
Abstract excerpt:

The ability to design extensive hydrogen-bond networks with atomic accuracy enables the programming of protein interaction specificity for a broad range of synthetic biology applications; more generally, our results demonstrate that, even with the tremendous diversity observed in nature, there are fundamentally new modes of interaction to be discovered in proteins.

My comment: The ability to link energy-dependent changes hydrogen-atom transfer in DNA base pairs in solution from microRNA flanking sequences to adhesion proteins and supercoiled DNA that protects all organized genomes from virus-driven energy theft and all pathology may never become known. Experimental evidence of biophysically constrained biologically-based cause and effect is not something that most neo-Darwinian theorists have considered.  Instead, they report findings that are reported in the science news, like this:
Tibetans inherited high-altitude gene from ancient human (7/2/14)
New Scientist, April 23, 2016 High Altitude Survival
Excerpt:

Perhaps the most dramatic evidence of modern benefits from ancient DNA is seen in the Tibetans. Emilia Huerta-Sanchez at the University of California in Merced and her colleagues found that about 8 per cent of Tibetans carry a particular piece of Denisovan DNA. Most bits of Denisovan DNA are not present in more than 0.2 per cent of East Asians, so geneticists suspected the ancient DNA must have given its Tibetan owners significant advantages.
The stretch of ancient DNA overlaps with the EPAS1 gene, the Denisovan version of which seems to help people survive the low-oxygen conditions at high elevations. It’s possible that Denisovans were adapted to life at altitude and passed that trait to humans. “But we’ll never know because we cannot take physiological measurements of Denisovans,” says Huerta-Sanchez.

My comment: This news was portrayed by the biologically uniformed David Klousie, in the following context.

A high priority of our aquatic ancestors was to hold their breath longer, those that were able to function in low-oxygen conditions for longer times had a higher probability of providing more food for their children, by being able to access food that was deeper which required holding their breath longer. Seems reasonable to entertain the idea that Denisovans spent a lot of time in the water.

My comment: I am convinced that until RNA methylation is linked to behavior, no one will be forced to admit that their theories have become more ridiculous on almost a daily basis.  I look forward to publication of the article that will link RNA methylation to behavior, but wonder how much more nonsense I can tolerate until the end of this month.

Alternative splicing of pre-mRNA

Secular humanism and ecoterrorism

Noncoding RNAs Not So Noncoding

Excerpt:

“Were there going to be dozens of [micropeptides]? Were there going to be hundreds, like there are hundreds of microRNAs?” says Ingolia. “We just didn’t know.”

See also: Number of microRNAs in Human Genome Skyrockets
Excerpt:

“…researchers from Thomas Jefferson University in Philadelphia have released data that adds another 3,707 novel miRNA sequences to the human genome, in addition to the 1,900 sequences previously described. The results from this study were published recently in PNAS through an article entitled “Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs”.”

My question: If you think there are hundreds of microRNAs when there are thousands of them, you may be less likely to ask where tissue-specific microRNAs come from. But, if you do ask where they come from, you might also ask how they get to specific tissues that require energy-dependent maintenance and/or RNA-mediated DNA repair. That is a question that all serious scientists should be able to answer. The answer, for example, can be placed into the context of Christ’s work on heterochronic parabiosis.  See Christ et al., (2014) The Pharmacology of Regenerative Medicine.
Regenerative medicine links the National MicroRNAome Initiative from metabolic networks to genetic networks in the context of the Precision Medicine Initiative via nutrient-dependent RNA-mediated amino acid substitutions.

See also: Mitochondrial Ultrastructure and Glucose Signaling Pathways Attributed to the Kv1.3 Ion Channel

This article is part of the Research Topic Brain nutrient sensing in the control of energy balance: new insights and perspectives

The article links energy-dependent changes in microRNA flanking sequences from the innate immune system to supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy in the context of the physiology of reproduction and fixation of nutrient-dependent RNA-mediated amino acid substitutions.

Other articles in the Research Topic will undoubtedly link changes in the microRNA/messenger RNA balance from energy-dependent changes in angstroms to energy-dependent changes in ecosystems via what is already known about supercoiled DNA. For example, more than 50, 500 indexed PubMed articles provide details about how energy-dependent microRNAs are linked to healthy longevity and how virus-driven energy theft links mutations to all pathology.

See:MicroRNA

See for example: Cross Talk between Cancer and Mesenchymal Stem Cells through Extracellular Vesicles Carrying Nucleic Acids
Conclusion:

…EVs derived from both MSCs and tumor cells display common ncRNAs; however, the functions they exhibit may be diverse depending on the cellular environment. Since ncRNAs interact with numerous molecular partners, their function is complex and depends on the cellular context. The response to EVs not only depends on their ncRNA/protein content but also on the metabolic pathways activated in recipient cells as well as their specific function. The same EVs, for instance, may trigger opposite actions in normal and tumor cells (22). Pandolfi and co-workers (164) have suggested that there is a RNA language that uses miRNAs response elements in different transcripts as “letters.” These diverse sets of miRNAs may form diverse “words,” thus performing different molecular and cellular functions. This hypothesis may, therefore, explain the different functions carried out by the same miRNAs in different contexts on tumor development. Taking into account that EV transport is bidirectional and that tumor cells can change the content of MSC-EVs and vice versa (160, 161), it is possible that the individual ncRNA display different and even opposite functions in vivo.

My comment: Serious scientists have passed the tipping point that conclusively links energy-dependent microRNAs to healthy longevity and virus-driven energy theft to mutations and all pathology via what is known about RNA-directed DNA methylation and biophysically-contrained protein folding chemistry.

See also: Structural diversity of supercoiled DNA

Excerpt:

Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.

See what the biologically uninformed secular humanist and ecoterroist Sean Ovis does with everything known to serious scientists about the modulation of DNA metabolic processes:

Virus Driven Energy Theft

Conclusion:

If you are a creation scientist, you can take comfort in the fact that as you get older, the control of these viral fragments is considerably weakened, and eventually one or more of these jumping genes will be let loose in your body to wreak havoc on your DNA. When that happens, you can thank God, because they will have brought you closer to him.

See what Jimmy Carter did about his cancer, for comparison: Jimmy Carter announces he is cancer-free

Excerpt:

Carter announced in August that doctors had told him that four spots of cancer had spread to his brain. He said his fate “is in the hands of God, whom I worship.”

My comment: A clear difference between ecoterrorists and a former president of the United States has emerged. Are the selfish ecoterrorists a threat to national security?

The ecoterrorists do not want others to learn about virus-driven energy theft in the context of the Precision Medicine Initiative or the National MicroRNAome Initiative.

They are hate-mongers who want you to believe that nothing can help you and nothing can save you from the suffering and death that they have brought to you via their ignorance and belief in nothing.

For comparison see the studies that are being published on energy-dependent RNA methylation.   Don’t be surprised by what’s coming from serious scientists who know how cell type differentiation occurs.

For example: Mechanism and biological role of Dnmt2 in Nucleic Acid Methylation

Abstract:

A group of homologous nucleic acid modification enzymes called Dnmt2, Trdmt1, Pmt1, DnmA, and Ehmet in different model organisms catalyze the transfer of a methyl group from the cofactor S-adenosyl-methionine (SAM) to the carbon-5 of cytosine residues. Originally considered as DNA MTases, these enzymes were shown to be tRNA methyltransferases about a decade ago. Between the presumed involvement in DNA modification-related epigenetics, and the recent foray into the RNA modification field, significant progress has characterized Dnmt2-related research. Here, we review this progress in its diverse facets including molecular evolution, structural biology, biochemistry, chemical biology, cell biology and epigenetics.

My comment: Frank Lyko is a co-author. He is also the co-author of Epigenetic Regulation by Heritable RNA

Excerpt: 

RNA-mediated inheritance could provide an attractive mechanism that allows a rapid adaptation to changing environmental conditions without affecting the genetic makeup of an organism.

My comment: We will continue to see that neo-Darwinian theorists are left with no fall-back position. No experimental evidence of biologically-based cause and effect has ever linked mutations from natural selection to evolution. Now, what is known about RNA methylation will be added to what is known about RNA-directed DNA methylation, and there will be no place for theorists to hide. They will be embarrassed and asked to leave — anywhere they are found.

Physics

Creating gravity, nucleic acids, receptors, and supercoiled DNA (2)

See also: Creating gravity, nucleic acids, receptors, and supercoiled DNA

Scientists make first direct detection of gravitational waves

Excerpt:

Almost 100 years ago today, Albert Einstein predicted the existence of gravitational waves — ripples in the fabric of space-time that are set off by extremely violent, cosmic cataclysms in the early universe. With his knowledge of the universe and the technology available in 1916, Einstein assumed that such ripples would be “vanishingly small” and nearly impossible to detect.

My comment: Kudos to Greg Bear for indirectly linking gravitational waves and the speed of light on contact with water to the nutrient-dependent pheromone-controlled structure of supercoiled DNA in species from microbes to humans, which prevents virus-driven genomic entropy in all living genera. He started to do that in 1985 and finished in less that 20 years.

See: The Darwin Code by Greg Bear
The gravitational waves can now be linked from energy-dependent hydrogen-atom transfer in DNA base pairs in solution to cell type differentiation in all genera via what is currently known about biophysically constrained RNA-mediated protein folding chemistry and supercoiled DNA. Olfaction links the gravitational waves to vibrations in supercoiled DNA. If no food odors are linked from the vibrations to the de novo creation of receptors that allow nutrients into the cells, the nutrient-dependent innate immune systems of cells and organisms is compromised.Viruses take advantage of compromised immune systems and they proliferate by stealing more energy from cells. Without the nutrient-dependent microRNAs that enable DNA repair, viruses proliferate and viral microRNAs prevent the nutrient energy-dependent supercoiling of DNA that prevents the virus-driven entropy, which is linked to all pathology.
See for instance: Molecular Vibration-Sensing Component in Human Olfaction
Excerpt: These results are consistent with a vibrational component in human olfaction.
Reported as:  ‘Quantum smell’ idea gains ground
See also: Terahertz underdamped vibrational motion governs protein-ligand binding in solution
Excerpt:

It seems likely that proteins have evolved such underdamped vibrational motions by providing an interaction site which is pre-organized44 in order to arrive at the optimal degree of damping for efficient biochemical reactivity and function.

Reported as: Proteins ‘ring like bells’: Quantum mechanics and biochemical reactions
Excerpt:

…quantum mechanics and coherent ringing might be at the basis of all biochemical reactions

My comment: The gravitational waves were not linked from quantum mechanics to classical physics, which means the physicists missed a link to the basis for all biochemical reactions via the de novo creation of olfactory receptor genes. De novo gene creation is the holy grail of biologically-based cause and effect.  The failure to link the gravitational waves to the creation of genes exemplifies the failure of physicists to link meaningful discoveries from chemistry to the conserved molecular mechanisms of biologically-based cause and effect.The discovery of gravitational waves may be the physicists most meaningful event in the past 100 years, but it is meaningless to chemists or to biologists, or to anyone who is interested in Combating Evolution to Fight Disease. Physicists make only vague inferences about the “nature” of the universe. Today’s reports on the discovery of gravitational waves attest to the amount of nonsense that can be heralded as if simulations, “real” simulations, and inferences might lead to something that would benefit anyone or anything on Earth. Can you find any benefit in these reports?

‘We can hear the universe’: Scientists detect gravitational waves, predicted by Einstein (LA Times)

“…these waves are the soundtrack of the cosmos.””Some physicists said this is as big a deal as the 2012 discovery of the subatomic Higgs boson, sometimes called the “God particle.” Some said this is bigger.””Sensitivity is crucial because the stretching and squeezing of space-time by these gravitational waves is incredibly tiny. Essentially, LIGO detects waves that stretch and squeeze the entire Milky Way galaxy “by the width of your thumb,” Hanna said.”
In Milestone, Scientists Detect Gravitational Waves As Black Holes Collide (NPR) Teukolsky says the discovery shows just how extraordinary the natural world can be. “The universe is stranger than any kind of fiction we could imagine,” he says. “I mean, it’s preposterous.”
Observation of Gravitational Waves from a binary black hole merger How did LIGO make the first detection of gravitational waves from a binary black hole merger? What did we learn? Read the science summary of our paper…
My comment:I do not intend to make “light” of this discovery, which cost billions of dollars and theoretically helped to confirm theoretical predictions that were made more than 100 years ago.However, if you read the paper, I think you will see that it avoids any claims that might link their computer simulations and inferences to refutations of neo-Darwinian nonsense, which means that millions to billions more research dollars may be spent to develop ridiculous theories that support the big bang cosmology industry and the evolution industry.Those theories have already been placed into the context of the importance of understanding Dobzhansky’s “light of evolution.” It is the light (and gravity) on Earth that supports femtosecond chemical reactions. The chemical reactions link quantum physics to quantum consciousness via the RNA-mediated amino acid substitutions that stabilize organized genomes in the context of the nutrient-dependent physiology of reproduction in all living genera. For comparison, see this report.
Observation of Gravitational Waves from a binary black hole merger
Alongside this substantial progress in the indirect observation of black holes, there have been dramatic improvements in our theoretical understanding of these bizarre objects
My comment: This theoretical understanding can be placed into the context of Schodinger’s claims in “What is Life?” This link opens the pdf.
Excerpt:

Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight)

My comment: Unless the claims about gravitational waves are placed into the context of “negative entropy,” serious scientists are left with an attempt to ensure more government funding for research that might also support theories, while failing to acknowledge Schrodinger’s facts or the facts that Darwin integrated into his claims about the “conditions of life.” For contrast, see this report:

The first measurement of a black hole merger and what it means” What Made the Gravitational Waves? Once we have identified a gravitational wave in the data (more details here and here) supercomputers around the world start buzzing to determine what created the signal that we detect. We do this by trying out millions of combinations of different numbers (parameters) that describe a gravitational wave signal. The parameters that describe you might be height, age, hair and eye color, etc. The gravitational wave signal from GW150914 came from two dense objects spiraling in to one another and merging.”

My question(s): Who made the two dense objects and when were they made? How are the parameters that describe us linked to the gravitational wave signal?Here is my summary of all the reports I have seen on gravitational waves.

Biology to a Physicist

Should I keep looking at more reports?

They did not link their finding from atoms to ecosystems. I had hoped that someone would ask a question to elicit an answer that links their finding to what is known about molecular epigenetics.

Gravitational waves detected 100 years after Einstein’s prediction (Science Daily)

My comment: A reporter for the Christian Science Monitor asked about the source of the information. The presenters answered in terms of simulations, “real simulations” and inferences — after some individual claims about “nature” and the billions of years that it took for the gravitational waves to reach earth.Is the billions of years an estimate based on simulations, “real simulations” and inferences?

Gravitational waves discovery ‘is monumental,’ physicist says These waves radiate from their sources at the speed of light, stretching and squeezing the very fabric of space-time with predictable cadences. The achievement “is monumental,” says Lawrence Krauss, a theoretical physicist and cosmologist at Arizona State University in Tempe. There are very few times in the history of astronomy where new windows open, and this is one of them, he says, adding, “This will be the astronomy of the 21st century.”Beyond expectations for astrophysical discoveries, gravitational waves may also hold the potential to reveal important clues about the nature of gravity itself.This has been a nagging thorn in the side of theoretical physicists working an another Big Idea – that the four basic forces of nature are low-energy remnants of what was a single force during the earliest fractions of a second after the big bang. These forces are gravity, electromagnetism, the strong force binding particles in the nuclei of atoms, and the weak force governing radioactive decay.Physicists have been able to show through quantum theory that three of the four forces have a common ancestor. Gravity remains the stubborn holdout.Through the direct study of gravitational waves, “we potentially can learn about the nature of gravity” in ways that might point to a quantum theory of gravity, speculates Dr. Krauss at Arizona State University.

My comment: During the live newscast, Dr. Weiss mentioned that “a miracle of sorts” links the equations from 1915 to their inferences. I’m not sure what he thinks is a miracle. I think it is a miracle that people like Lawrence Krauss and Neil de Grasse Tyson are willing to discuss how nothing became everything known to serious scientists about the links from atoms to ecosystems.

See: The Existence of Nothing 2013

My comment: The people who presented their findings on gravitational waves said good-bye to all newscast watchers at (11:41). They continued with questions off-line a few minutes after Dr. Weiss mentioned the “miracle of sorts” that links their discovery to the equations from 1915 based on computer simulations, “real” computer simulations and inferences.Hopefully, we will learn more about what the Russians and Japanese and perhaps even the Chinese think about this “miracle of sorts” and the presentation of the findings funded by the National Science Foundation.

Scientists glimpse Einstein’s gravitational waves (Update)
Wobbling like jelly“The waveform that we can calculate based on Einstein’s theory of 1916 matches exactly what we observed in 2015,” Shoemaker told AFP.
“We can now listen to the universe rather than just look at it,” said professor B S Sathyaprakash of Cardiff University. “This window turns on the soundtrack for the universe.”
Indirect proof of gravitational waves was found in 1974 through the study of a pulsar and a neutron star. Scientists Russell Hulse and Joseph Taylor won the Nobel Prize for physics for that work in 1993.

My comment: Somehow I knew someone would report the discovery of gravitational waves instead of just the ability to detect them. I did not think this would come from “Nature.”

Discovering gravitational waves

For comparison: Findings from the 2015 Nobel Prize winner in Physics, Chemistry, and Medicine link atoms to ecosystems via feedback loops and biologically-based cause and effect reported, with co-authors, by one of the two 2004 Nobel Laureates in Medicine.
See for example: A novel multigene family may encode odorant receptors: a molecular basis for odor recognition
See also: Feedback loops link odor and pheromone signaling with reproduction

My comment: Reproduction is important to the survival of all species on Earth. For comparison, see yet another report on the gravitational wave discovery.

Cosmic breakthrough: Physicists detect gravitational waves from violent black-hole merger (Washington Post: February 11 at 6:41 PM)

Until now, astronomy has been almost exclusively a visual enterprise: Scientists have relied on light, visible and otherwise, to observe the cosmos. But now gravitational waves can be used as well.Since they pass through matter without interacting with it, gravitational waves would come to Earth carrying undistorted information about their origin. They could also improve methods for estimating the distances to other galaxies.A black-hole collision sounds like a dramatic event, but it’s not really the big news for the physicists. The headline is that LIGO finally worked. Success in detecting gravitational waves is a win for Big Science and for the institutions that backed the project.
My comment: The “Big Science” of biophysically constrained RNA-mediated protein folding chemistry and the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to humans has lost another round to the theorists.
See for example, the report by Rachel Feltman: What Do We Actually Know About Pheromones?
What qualifies a science journalist to report on biologically-based cause and effect and dismiss what is known to serious scientist before moving on to tout the pseudoscientific nonsense of theoretical physics as if it was more important? Feltman interviewed me and two human pheromone-deniers, who appear to know nothing about the nutrient-dependent pheromone-controlled physiology of reproduction in any species.
See my comments on her science journalism.
Now this: En’Cas’ing The Stress: Engineering a Human Cell Line Knockout of Heat Shock Response Genes

Excerpt:

The Heat Shock Response (HSR) is an evolutionarily conserved response to high temperatures and other stresses that controls adaptive proteostasis, and is primarily regulated by the factor, Heat shock transcription factor 1 (HSF1).

See also: From Toxins to Culture: How Environment Shapes the Infant Brain

Description: Prenatal and perinatal environmental factors, from toxins to maternal care and culture, profoundly influence the brains of infants, sometimes resulting in lifelong pathologies. The effects of these factors have only recently been rigorously assessed in humans, and the mechanisms by which they affect the brain are only beginning to be understood. This symposium discusses recently established links between autism and vehicular air pollution in both the developed and developing world; and how the microbiome, a target for infections and nutrition-related pathologies, directly affects the developing brain and can contribute to development of autism. The session also discusses how maternal inputs and cultures modify the impact of the physical environment on the brain, and how epigenetic mechanisms mediate the long-term impacts of prenatal and perinatal factors. These findings have broad implications for policies to preserve the health of children and adults around the world.

Speakers:
Beate Ritz, UCLA
Air Pollution Impacts Fetal Development and Increases Autism RiskElaine Y. Hsiao, University of California, Los Angeles (UCLA)
The Role of Gut Microbiomes in Neurodevelopmental DisordersBruce McEwen, Rockefeller University
Mother-Infant Interactions Influence Both Cognitive and Physical DevelopmentMoshe Szyf, McGill University

Excerpt:

Dr Szyf will present evidence that the “social environment” early in life can alter DNA methylation, the basis for the emerging field of “social epigenetics”. By highlighting the impact that external factors and the social environment can have on gene expression, he will provide a mechanistic basis for the long term effects of early childhood experience.

My comment:  All big wins for biomedical science link metabolic networks to genetic networks in the context of model organisms that link atoms to ecosystems in all living genera by what is already known to serious scientists about supercoiled DNA.Energy-dependent changes in base pairs link atoms to ecosystems via hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA. The supercoiled DNA links RNA-mediated amino acid substitutions to what is known about the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding chemistry. The chemistry is linked to supercoiled DNA during thermodynamic cycles of protein biosynthesis and degradation, which is perturbed by viruses. Virus-driven energy theft is linked to all pathology on Earth.If you were a researcher whose work was supported by the big bang cosmology industry or by the evolution industry, would you reveal the fact that all theories about biologically-based cause and effect are missing the most important link from atoms to ecosystems if they do not include what is known to serious scientists about virus-perturbed protein folding?

rp_levels-of-organization.jpg

Nutrient-dependent RNA-mediated cause and effect

Could the food we eat affect our genes? Study in yeast suggests this may be the case

(2016)

Excerpt: “Cellular metabolism plays a far more dynamic role in the cells than we previously thought,” explains Dr Ralser. “Nearly all of a cell’s genes are influenced by changes to the nutrients they have access to. In fact, in many cases the effects were so strong, that changing a cell’s metabolic profile could make some of its genes behave in a completely different manner.
“The classical view is that genes control how nutrients are broken down into important molecules, but we’ve shown that the opposite is true, too: how the nutrients break down affects how our genes behave.”

My comment: Nutrient-dependent metabolic networks are linked to genetic networks. The epigenetic effect of nutrients is linked to hormones that affect the behavior of all vertebrates and invertebrates via conserved molecular mechanisms that link microbes to humans.

From Fertilization to Adult Sexual Behavior

(1996)

Excerpt:

In this regard it seems important to emphasize that chemosensory communication is ubiquitous throughout life among species from single celled yeasts to primates, including humans (see for review Kohl and Francoeur, 1995). Chemical stimuli, odors, including pheromones, are essential components of reproductive sexual behavior in most, if not all, species. Pheromonal communication has been seen to elicit physiological and behavioral changes that benefit both male and female individuals and, in humans, these olfactory sensations seem to exert their influence whether or not an individual is conscious of odor detection.
Evolutionary conservation, both of pheromonal communication and its importance to behavior, is indicated by the involvement of a key mammalian reproductive hormone. For instance, a yeast pheromone, the alpha-mating factor, is very similar in structure to mammalian gonadotropic releasing hormone (GnRH). When injected into rats, this chemical binds to pituitary GnRH receptors and brings about the release of LH. Loumaye, Thorner, and Catt (1982) note: “GnRH and the yeast alpha-mating factor appear to represent a highly conserved effector system which includes the peptide ligand, the cell-surface receptor, and the physiological regulation of reproductive function” (p. 1325).

See also:
Non‐enzymatic glycolysis and pentose phosphate pathway‐like reactions in a plausible Archean ocean
Regulation of ribosomal DNA amplification by the TOR pathway
Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway
Other Publications from Ralser (Ralser’s group 2005- 2015)
My comment: It has been 20 years since we linked what organisms eat and the pheromones they produce to chemosensory communication throughout life among species from single celled yeasts to primates via a highly conserved RNA-mediated effector system which includes the peptide ligand, the cell-surface receptor, and the physiological regulation of reproductive function.
It has been 10 years since Nobel Laureate, Linda Buck co-authored Feedback loops link odor and pheromone signaling with reproduction (2005)
Obviously, something has gone horribly wrong. The metabolic background is a global player in Saccharomyces gene expression epistasis was published and reported in the context of a question. Could the food we eat affect our genes?
Everything known to serious scientists about biophysically constrained RNA-mediated protein folding chemistry and cell type differentiation links nutrient-dependent amino acid substitutions to the stability of supercoiled DNA in the organized genomes of all living genera.  How could anyone not know that the supercoiled DNA links metabolic networks and genetic networks to epistasis. Why would anyone ask “Could the food we eat affect our genes?” Why would anyone suddenly claim that a “Study in yeast suggests this may be the case.”
What experimental evidence of biologically-based cause and effect suggested that a case could be made for any other links from atoms to ecosystems?