Alternative splicing of pre-mRNA

Energy is information. Objections over ruled. You're fired!

Objection: In the law of the United States of America, an objection is a formal protest raised in court during a trial to disallow a witness’s testimony or other evidence which would be in violation of the rules of evidence or other procedural law.
Americanism (ideology) links the laws of United States of America to God’s “Laws of Biology.”  Pseudoscientists violated the rules of evidence that link Darwin’s “conditions of life” from God’s “Laws of Biology” to all nutrient energy-dependent biophysically constrained pheromone-controlled biodiversity on Earth.
Laws of biology: why so few? (2010)

…every biological decision is optimal in a given environmental context. However, due to complex nature of biological organization it is difficult to think of a universal law or a theory in biology connecting all the levels, from atoms to ecosystems.

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

  1. In Section One, the focus is on links between atoms and ecosystems via amino acid substitutions. In Section Two, the focus is on examples of links across a continuum of nutrient-dependent, pheromone-controlled, epigenetically-effected, receptor-mediated ecological adaptations via amino acid substitutions and changes in the microRNA/messenger RNA balance.
  2. Nutrient-dependent pheromone-controlled ecological adaptations exemplify how sensing nutrients and secreting the metabolites of nutrients accomplishes different tasks. Efficient circuits enable the functional flexibility that is required in ever-changing ecologies that cause species diversity. Biophysical constraints on ecological adaptations are exemplified in physical proof which suggests that Kohl’s Laws of Biology (Kohl’s Laws) represent what Darwin called ‘conditions of life.’

Natural selection for nutrient energy-dependent codon optimality is exemplified in species from archaea to humans. See for example: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (2015)

The bias between codons or amino acids, and mRNA expression levels has been previously recognized across species and is thought to result from selection for efficient, accurate translation, and folding of highly expressed genes (Ikemura, 1982; Akashi, 1994; Akashi & Gojobori, 2002; Drummond & Wilke, 2008; Kudla et al, 2009; Novoa & Ribas de Pouplana, 2012). The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

That perspective on sequence changes between paralogs in evolution and human disease placed endogenous RNA interference into the context of Intelligent Design after Darwin and all other serious scientists had linked it from sunlight to all biodiversity on Earth via their observations and experimental evidence of biologically-based cause and effect.
See for example: Nutrient-dependent/pheromone-controlled adaptive evolution: a model

…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’.

See for comparison: Membrane Patterns Carry Ontogenetic Information that is Specified Independently of DNA
Reported as: Peer-Reviewed Paper: Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms

Wells recognizes that various well-established processes like alternative splicing and RNA editing often determine the amino acid sequence of proteins.

Like all pseudoscientists before him, Wells failed to recognize the most important fact of all. That fact was expressed in the context of the fact that gene expression is energy-dependent in DEPENDENCE OF RNA SYNTHESIS IN ISOLATED THYMUS NUCLEI ON GLYCOLYSIS, OXIDATIVE CARBOHYDRATE CATABOLISM AND A TYPE OF “OXIDATIVE PHOSPHORYLATION”(1964)

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

The pseudoscientists that failed to acknowledge that fact are among the losers that were placed into the following perspective:
Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge.Kalevi Kull (2016)
The losers can now be recognized in the context of the failure to provide the free delivery of God’s “billion dollar baby” to  healthcare practitioners. Simply put, many healthcare professionals were not told how to link energy from endogenous RNA interference (RNAi) to healthy longevity in all living genera. They were not told that natural selection for energy-dependent codon optimality and endogenous RNAi have always linked angstroms to ecosystems in all living genera via RNA-mediated amino acid substitutions in supercoiled DNA. Why didn’t all medical practitioners learn that supercoiled DNA protects all organized genomes from virus-driven energy theft and genomic entropy.
See for examples of what was missing:
Get Well in the RNAi Way-RNAi, A Billion Dollar Baby in Therapy

RNAi has targeted exogenous genes in models of viral infection…

RNA-triggered gene silencing (1999)
RNA-Guided Human Genome Engineering (2015)

Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

Alnylam Pharmaceuticals: RNAi Failure Could Catch Monsanto Investors Off Guard ? (2016)

The other technology besides CRISPR gene editing, which is the subject of this post is called RNAi technology. See link in references below as to the differences between CRISPR & RNAi technologies.

…something went horribly wrong, they don’t really know what it was other than it failed, caused death of some patients and so they discontinued the experimental drug. This has an uncanny similarity to and is reminiscent of the Tryptophan disaster – GM Potato & Árpád Pusztai affair & the GM pea causes allergic reactions to name a few.

“Deep inside its labs, Monsanto is learning how to modify crops by spraying them with RNA rather than tinkering with their genes”

Spraying crops with RNA causes RNA interference in the same way that the CRISPR/Cas9 technology replaced virus-altered RNA interference via use of other viruses that caused the innate immune response to link amino acid substitutions to DNA repair if the missing amino acids were again made available. It is like fighting fire with fire, which sometimes works to extinguish the life of one fire that is out of control but does not prevent other fires from emerging and destroying other properties, or the same property at a later date. The ominous prophecies from the Holy Bible now loom larger if, like all other prophecies, they are correct. Those who survive the next viral apocalypse seem likely to live long enough to die a fiery death that clearly will be linked to the sun’s biological energy from the protection of supercoiled DNA that once helped to ensure our healthy longevity.

See for comparison:  A Christian Worldview & Mental Health (2011)

Christian concern for the whole person includes both mind and body, so this volume encourages readers to think about theoretical and spiritual issues within Christian mental health care. Views are collected from various disciplines such as ethics, psychology, theology, counseling, and psychiatry. In its consideration of a Seventh-day Adventist spiritual identity in mental health theory and practice, this text will prove very valuable to mental health education.

The Christian worldview links what organisms eat to natural selection for energy-dependent codon optimality and healthy longevity, which links supercoiled DNA from the physiology of reproduction to all morphological and behavioral diversity in species from microbes to humans. The Christian worldview has typically been one in which peaceful coexistence is the desired goal. That goal is based on what is known about energy-dependent symbiosis and homeostasis in species from microbes to humans. The atheistic worldview is shared by proponents of Intelligent Design and others who are biologically uninformed. They seem to think that Darwin replaced the Laws of Biology, when what he repeated asserted was that “conditions of life” come first. Only pseudoscientists have continued to link mutations from natural selection to the evolution of one species from another across millions of years.
The pseudoscientists have organized a “March for Science” in an attempt to keep forcing their pseudoscientific nonsense on the biologically uninformed masses in the United States of American who were taught that they could break any of God’s Laws that they chose to break, after the Laws were broken by those who chose to believe in, and to teach, their ridiculous theories to several generations of children that grew up to become liberals.
But wait, here are a few more claims that can be placed into the context of the Laws of Biology, but not into the context of mutation-driven evolution.
Worm gene could be key to developing obesity treatment
Nutrient energy-dependent changes in the microRNA/messenger RNA link endogenous RNA interference to biophysically constrained biodiversity in nematodes that is exemplified in differences between C. elegans and P. pacificus, a predatory nematode with teeth. The physiology of reproduction is controlled by pheromones in all living genera and the pheromones link microRNAs from supercoiled DNA to chromosomal inheritance in different species.
See also from 2013: Extracellular Regulation

During Caenorhabditis elegans development, the hermaphrodite-specific neurons (HSNs) migrate and then extend axons toward their functional targets. Posttranslational modification of heparan sulfate proteoglycans are important for HSN development, and so Pedersen et al. (p. 1404) tested the effect of disrupting or reducing chondroitin and heparan sulfate synthesis during C. elegans development. The results suggest that proteoglycan biosynthesis is tightly regulated by a microRNA pathway to shape the cell surface glycosylation architecture required to direct neuronal migration.

Females More Prone to Disease Due to Key Immunological Difference
This means the sex difference in cell types can be linked to the advent of sexual reproduction in yeasts via the conserved molecular mechanisms we detailed in the molecular epigenetics section of our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior
See for comparison: Today on Darwin Day, Trey the Explainer Sends a Gift. He Power Owns Dr. Ben Carson! (Video)
The “Explainer” dismisses facts about energy-dependent endogenous RNA interference and pretends that the variants in the fossil record support the ridiculous theories of neo-Darwinian theorists. There is no way to explain his ignorance, or why he flaunts it.
See also: Team develops tool that maps functional areas of the genome to better understand disease

…sections of DNA called “enhancers” dictate where and when the gene information is read out.

Energy as information dictates gene expression in the context of established links from chirality to autophagy in species from microbes to humans.

See: Light Could Propel Nanorobots on a “Fantastic Voyage” Through the Human Body

“Light is a more effective option to communicate between the microscopic world and the macroscopic world,” said Tang.

All pathology is caused by virus-driven energy theft. The barrage of misinformation you are being subjected to is increasing each day.

See:How evolution alters biological invasions
also reported as:

Superspreader phages transfer drug resistance
Lucky for us, bacteriophages infect bacteria, not humans. That doesn’t mean they don’t have profound effects on us, however. A new report in the journal mBio from researchers at the University of Miami and the National Cancer Institute describes “superspreader” bacteriophages that promote DNA transfer from one bacterium to another – and some of this DNA codes for antibiotic resistance genes.

Does life have a purpose?


Behavior (4): All responses are RNA-mediated in birds

Bird Genomes Abound

Scientists complete the largest-ever comparative genomic study of birds.

By Ruth Williams | December 11, 2014

Excerpt: “The results of this effort provide not only the most precise genetic history of birds to date, but also reveal why avian genomes tend to be small compared to those of other vertebrates: because they have lost a lot of genes and have far fewer repeat sequences. Furthermore, the data show that, compared with mammals, both the nucleotide sequences and the order of genes tend to be more conserved—perhaps because of the smaller number of repeat sequences, which would reduce the possibility of homologous recombination events.”

See also: 3-D maps of folded genome: Catalog of 10,000 loops reveals new form of genetic regulation
Excerpt: “More and more, we’re realizing that folding is regulation,” said study co-first author Suhas Rao, a researcher at Baylor’s Center for Genome Architecture and a 2012 graduate of Harvard College. “When you see genes turn on or off, what lies behind that is a change in folding. It’s a different way of thinking about how cells work.”
See also: Slight alterations in microRNA sequences hold more information than previously thought
Excerpt 1): “We know now that miRNAs are regulators of protein-coding and also of non-protein-coding RNA transcripts and that they regulate the abundance of the affected transcripts, the miRNA “targets,” in a sequence-dependent manner. What makes miRNAs so important is their involvement in fundamental processes such as development and homeostasis. Not surprisingly, miRNAs and their dysregulation have also being linked to many human conditions, diseases, and syndromes.”
Excerpt 2): Dr. Rigoutsos states that “one can reasonably assume that analogous observations likely hold true for other cell types as well.” sex and individual population differences
My comment: Sven Bocklandt occupied one of the 2 rooms linked to the same dormitory shower facility with me when were attending the 1995 conference International Behavioral Development Symposium: Biological Basis of Sexual Orientation and Sex-typical Behavior where I presented my model as a poster session. That conference presentation led to publication of From Fertilization to Adult Sexual Behavior and to my award-winning journal publication concurrently published as a book chapter in the Handbook of the Evolution of Human Sexuality (authors copy here): The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences.
Abstract:  The across-species genetic conservation of intercellular and extracellular chemical communication enables unicellular and multicellular organisms to functionally distinguish between self and non-self. Non-self olfactory/pheromonal input from the social environment elicits a vertebrate neuroendocrine response. The organization and activation of this neuroendocrine response modulates the concurrent maturation of the mammalian neuroendocrine system, the reproductive system, and the central nervous system during the development of sexual preferences that may be expressed in sexual behavior. Psycho-physiological mechanisms for the development of these sexual preferences include focus on unconscious affects that are detailed in reciprocal cause and effect relationships. Olfactory/pheromonal conditioning elicits neuroendocrine effects accompanied by unconscious affects on the development of sexual preferences. Integrating these unconscious affects extends to humans a developmental model of behavior that includes the development of male sexual preferences for other males.
See also: Foreword: Sexual Development—Nature’s Substrate for Nurture’s Influence by Milton Diamond, who is first author of our 1996 Review: From Fertilization to Adult Sexual Behavior
If you were a geneticist at UCLA who finally realized after nearly two decades that the first behavioral response is RNA-mediated not DNA-determined, what would you tell other serious scientists about your inability to accept that fact. Would you say nothing but then ask  Is There a Role for Epigenetics? in the Basis of Human Sexual Orientation.
See also: Fetal Brain Gene Expression Patterns Differ By Sex  (2003)
Excerpt 1) “These gene expression differences are found before genital hormone manufacture could possibly begin to play a role in influencing sexual development of the brain.”
My comment: That means the differences are RNA-mediated.
Excerpt 2) “It rebuts 30 years of scientific dogma that the hormones, estrogen and testosterone, alone were responsible for differences between the male and female brain.”
My comment: In our 1996 review, we rebutted the decades of scientific dogma by reporting on the molecular epigenetics of RNA-mediated sex differences in cell types that were obviously nutrient-dependent, but not so obviously pheromone-controlled.
Now that is obvious that RNA-mediated nutrient-dependent pheromone-controlled cell type differentiation occurs via amino acid substitutions that stabilize protein folding in species from microbes to man, Vilain and others like him should simply claim their incredible ignorance of biologically-based cause and effect or offer an alternative explanation of how an evolutionary event altered DNA that was naturally selected and led to the biodiversity of cell type differences in all cells of all individuals of all species.
Instead, we see evidence of the head-in-the-sand attitude of researchers who would rather not examine the biological basis of RNA-mediated events and instead keep looking for clues to RNA-mediated disorders and diseases.
Excerpt: “Fascinating as it may be to understand the biological basis of sexual orientation, however, not everyone is convinced it’s a necessary line of investigation. “Should we test this? Is it important for us to know?” asked McCarthy. “Homosexuality is not a disease, it’s part of natural human variation. I’m not sure there’s a good reason to delve this deeply into it. I think we’ve reached the point that we have enough evidence that there’s a biological basis for sexual orientation.” It would be more helpful to people to get a better handle on the epigenetics of cancer or mental illness, she added.”
Peg’s statement is a clear indicator of what Lewis Thomas reported in his article and book chapter: A Fear of Pheromones, but also in On Smell as cited in The Scent of Eros: Mysteries of Odor in Human Sexuality
In 2010, Peg interrupted a conversation between me and Barry Komisaruk, who had linked GnRH secretion via LH to behavior in 1990, reported in Love as sensory stimulation: physiological consequences of its deprivation and expression. I had hoped to discuss with Barry the significance of the the Rolland and Moenter poster, which led from their 2011 publication Regulation of gonadotropin-releasing hormone neurons by glucose to publication of Reproductive neuroendocrine dysfunction in polycystic ovary syndrome: insight from animal models.
Update: It would be interesting to compare liver gene expression patterns in homosexuals to heterosexuals to see if liver gene expression differs from male and female expression patterns in homosexuals.
I agree. For example: The microbial digestion of nutrients is linked from ecological variation in nutrients and their metabolism to species-specific pheromones in mice and humans. The de novo Creation of odor receptor genes called TAARs synergistacally links differences in nutrient uptake of choline to its metabolism in the liver (Patel et al., 2014) and to RNA-mediated invents linked to sex differences in cell types that respond to pheromones via the same neuronal system in mice and humans (the GnRH neuronal system).