lncRNAs control cell differentiation

lncRNAs control cell differentiation - Mutations don't result in evolution


Excerpt: "Several years ago, biologists discovered a new type of genetic material known as long noncoding RNA. This RNA does not code for proteins and is copied from sections of the genome once believed to be “junk DNA.”

Since then, scientists have found evidence that long noncoding RNA, or lncRNA, plays roles in many cellular processes, including guiding cell fate during embryonic development. However, it has been unknown exactly how lncRNA exerts this influence.

Inspired by historical work showing that structure plays a role in the function of other classes of RNA such as transfer RNA, MIT biologists have now deciphered the structure of one type of lncRNA and used that information to figure out how it interacts with a cellular protein to control the development of heart muscle cells. This is one of first studies to link the structure of lncRNAs to their function.

“Emerging data points to fundamental roles for many of these molecules in development and disease, so we believe that determining the structure of lncRNAs is critical for understanding how they function,” says Laurie Boyer, the Irwin and Helen Sizer Career Development Associate Professor of Biology and Biological Engineering at MIT and the senior author of the study, which appears in the journal Molecular Cell on Sept. 8.

Learning more about how lncRNAs control cell differentiation could offer a new approach to developing drugs for patients whose hearts have been damaged by cardiovascular disease, aging, or cancer.

In the new study, the researchers decided to investigate which regions of the 600-nucleotide RNA molecule are crucial to its function. “We knew Braveheart was critical for heart muscle cell development, but we didn’t know the detailed molecular mechanism of how this lncRNA functioned, so we hypothesized that determining its structure could reveal new clues,” Xue says.

To determine Braveheart’s structure, the researchers used a technique called chemical probing, in which they treated the RNA molecule with a chemical reagent that modifies exposed RNA nucleotides. By analyzing which nucleotides bind to this reagent, the researchers can identify single-stranded regions, double-stranded helices, loops, and other structures.

This analysis revealed that Braveheart has several distinct structural regions, or motifs. The researchers then tested which of these motifs were most important to the molecule’s function. To their surprise, they found that removing 11 nucleotides, composing a loop that represents just 2 percent of the entire molecule, halted normal heart cell development.

The researchers then searched for proteins that the Braveheart loop might interact with to control heart cell development. In a screen of about 10,000 proteins, they discovered that a transcription factor protein called cellular nucleic acid binding protein (CNBP) binds strongly to this region. Previous studies have shown that mutations in CNBP can lead to heart defects in mice and humans.

Further studies revealed that CNBP acts as a potential roadblock for cardiac development, and that Braveheart releases this repressor, allowing cells to become heart muscle.

“This is one of the first studies to relate lncRNA structure to function,” says John Rinn, a professor of stem cell and regenerative biology at Harvard University, who was not involved in the research.
Long non coding RNA molecule - a complex structure built from passive DNA.

“It is critical that we move toward understanding the specific functional domains and their structural elements if we are going to get lncRNAs up to speed with proteins, where we already know how certain parts play certain roles. In fact, you can predict what a protein does nowadays because of the wealth of structure-to-function relationships known for proteins,” Rinn says.

Building a fingerprint

Scientists have not yet identified a human counterpart to the mouse Braveheart lncRNA, in part because human and mouse lncRNA sequences are poorly conserved, even though protein-coding genes of the two species are usually very similar. However, now that the researchers know the structure of the mouse Braveheart lncRNA, they plan to analyze human lncRNA molecules to identify similar structures, which would suggest that they have similar functions.

“We’re taking this motif and we’re using it to build a fingerprint so we can potentially find motifs that resemble that lncRNA across species,” Boyer says. “We also hope to extend this work to identify the modes of action of a catalog of motifs so that we can better predict lncRNAs with important functions.”
The researchers also plan to apply what they have learned about lncRNA toward engineering new therapeutics. “We fully expect that unraveling lncRNA structure-to-function relationships will open up exciting new therapeutic modalities in the near future,” Boyer says."

My comment: Can you see the obvious contradiction in this article? These crucial RNA molecules don't tolerate mutations. Mutating only 2% of lncRNA:s nucleotides results in abnormal heart cell development. Researchers admit that lncRNAs have a very important role in cellular differentiation. This is because they are in response of establishing epigenetic information layers for the developing cell. Especially this means histone epigenetic markers. 'LncRNAs are poorly conserved', as evolutionists say. This means there are huge differences in them between different species. Human/Chimp lncRNAs are very different. Evolutionists claim that human lncRNAs have rapidly evolved. However, mutations in these crucial RNA-molecules are associated with serious diseases. That's why we have nothing to do with apes. The theory of evolution is the most serious heresy of our time. Don't be deceived.


Insane Probability of Evolution

Evolution is not mathematically possible


Excerpt: "Let us assume the "first living cell" had 300 gene complexes, with an average length of 3,000 nucleotides (or nucleotide pairs).  Human gene complexes are far more complicated, and longer, than the gene complexes of the "first living cell" (if such a cell ever existed).

Now let us assume the probability of a random permutation of 3,000 nucleotides, being able to create a gene complex for the "first living cell," was 10‑5.  This number is ridiculously generous to the theory of evolution (i.e. the real probability is much, much less than that).

Thus, we have a probability that an RNA or DNA strand for the "first living cell" would have a viable permutation of nucleotides is: 10(‑5x300) which is equal to 10‑1,500.  The "‑5" is the probability of a single new gene complex forming from a randomly generated permutation of 3,000 nucleotides; and the 300 is the number of gene complexes which must be made.
Using the above example, 50 of the 300 gene complexes would be used to create one protein structure.

But even the above probability of 10‑1,500 ignores a lot of things, such as the viability of different combinations of proteins (remember, proteins must fit together, thus just having a bunch of proteins doesn't help at all, they must be a "set" of proteins which have very specific shapes and have specific amino acids in just the right places), but we will use the above numbers.

Remember, 10‑100 is an impossible probability.  A probability of 10‑500 is an insane probability because it is 10400 times smaller than an impossible probability.

Now we are talking about a number which is 101,000 times smaller than an insane probability (i.e. 10(1,500‑500) equals 101,000)."

My comment: Have a blessed Easter!


G protein-coupled receptors act as little computing devices

G protein-coupled receptors act as little computing devices decoding complex information


Excerpt: "Scientists at the National Institute on Drug Abuse (NIDA) Intramural Research Program (IRP) have uncovered evidence that shows a more complex and elaborate role for the body's hard-working G protein-coupled receptors (GPCRs) than previously thought, suggesting a conceptual advance in the fields of biochemistry and pharmacology. With more than 800 members in the human genome, GPCRs are the largest family of proteins involved in decoding signals as they come into the cell and then adapt the cell's function in response. NIDA is part of the National Institutes of Health.

Manipulating how cells respond to signals is key to developing new medications. Although pharmacologists have studied GPCRs for many years, there is still a debate on how they operate—are they isolated units that randomly collide with each other or are they deliberately coupled together to receive signals? The NIDA scientists conclude that GPCRs form part of very elaborate pre-coupled macromolecular complexes. Simply put, they act as little computing devices that optimally gather and process information coming into the cell, allowing the cells to adapt and change their function.

"These findings represent many years of complex and highly nuanced science, following the trail as chemical signals travel through the body at the cellular level," said NIDA Director Nora D. Volkow, M.D. "This remarkable discovery will open new avenues for medication development for addiction, pain and other conditions, offering more precise targets with fewer side effects."

"The specific macromolecular complex investigated in this study has therapeutic implications not only for addiction, but also for Parkinson's disease and schizophrenia," said Dr. Sergi Ferré, who led the team of scientists. "Discovering that these protein interact with other signals in preformed complexes gives us more precise targets for medication development."

To unravel the complex journey of the body's GPCRs, scientists used biophysical tools, including fluorescent biosensors; biochemical tools, such as cell signaling in neuronal cultures; as well as computational models."

My comment: Diet, climate, stress factors, social interactions, physical activity, toxicants and other inputs generate signals that travel from cell to cell throughout the body. Signals are typically transmitted by non coding RNA molecules, such as microRNAs. G protein-coupled receptors DECODE these important signals so that cellular mechanisms can alter the way DNA is read into transcription. This decoding contributes to histone markers, DNA methylation profiles and RNA epigenetics.

Changes in organisms are based on these Intelligent mechanisms, not random errors. There's no mechanism for evolution. Don't get lost.


DNA methylation plays key role in stem cell differentiation

DNA methylation plays key role in stem cell differentiation


Excerpt: "Northwestern Medicine scientists have discovered how the process of DNA methylation regulates the development of spinal cord motor neurons, according to a study published in the journal Cell Stem Cell.

DNA methylation, an epigenetic mechanism that determines whether or not a gene is expressed, guides stem cells as they transform from blank slates into specialized cells, according to Evangelos Kiskinis, Ph.D., assistant professor of Neurology in the Division of Neuromuscular Disease and senior author of the study.

Motor neurons are highly specialized neuronal cells that connect the central nervous system to muscle and degenerate in amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease.

"If you look at DNA methylation patterns in ALS patients, they are all over the place," said Kiskinis, who is also a professor of Physiology. "Is it a driver of disease, or is it just a byproduct? Our study provides us with a platform to address these intriguing questions."

The investigators used a variety of cutting-edge technologies—including single cell RNA-Sequencing and a methylation-focused adaption of CRISPR-Cas9 gene editing, known as epigenetic editing—to create a series of stem cells that each lacked different enzymes that trigger DNA methylation.

After analyzing the stem cells along with the differentiating neural progenitors and the motor neuron populations, Alberto Ortega, Ph.D., senior postdoctoral fellow in Kiskinis' laboratory and lead author on the study, concluded that the enzyme DNMT3A triggered DNA methylation, which in turn repressed or counterintuitively activated the key transcription factors that controlled differentiation of stem cells into spinal cord motor neurons.

"DNA methylation governs gene expression potential and hence cell identity," Kiskinis said. "As stem cells transition from early progenitors to committed progenitors to developed neurons, DNA methylation allows for the induction or suppression of key transcription factors. In turn, those transcription factors govern cell type function and specificity."
"Our study nicely shows the importance of epigenetics on controlling different steps of the development of the human central nervous system by tuning the expression levels of transcription factors," Ortega added.

In addition, the scientists found irregular DNA methylation patterns could have downstream consequences related to the function of these neurons, according to Kiskinis.

"It seems if you don't set your DNA methylation patterns correctly, there's a cascade of irregular gene expression that results in defective cells," Kiskinis said. "This is intriguing, because people usually think about methylation in the context of cell differentiation—the role in developed neurons is largely overlooked."
Further investigation could shed light on spinal cord diseases, as patients with ALS have irregular patterns of methylation, according to Kiskinis. In addition, patients with ALS exhibit a high rate of genetic variants associated with the DMNT3A enzyme—another puzzling link."

My comment: DNA methylation patterns that are necessary for cellular differentiation are regulated by non-coding RNA molecules, such as microRNAs, piRNAs, siRNAs and lncRNAs. The DNA has no control over cellular differentiation. Irregular patterns of methylation are linked to genetic variants i.e. genetic degradation. This is once again a clear evidence that aberrant methylation patterns result in genetic degradation. That's why there's no mechanism for evolution. Don't be deceived.


The obvious link between epigenetic factors and genetic mutations

Due to rapid genetic degradation scientists try to repair human DNA


Excerpt: "The new editors allow researchers to rewrite all four bases that store information in DNA and RNA. Those four bases are adenine (A) which pairs with thymine (T) (or uracil (U) in RNA), and guanine (G) pairs with cytosine (C). Mutations that change C-G base pairs to T-A pairs happen 100 to 500 times every day in human cells. Most of those mutations are probably benign, but some may alter a protein’s structure and function, or interfere with gene activity, leading to disease. About half of the 32,000 mutations associated with human genetic diseases are this type of C-G to T-A change, says Liu, a Howard Hughes Medical Institute investigator at Harvard University. Until now, there was little anyone could do about it, he says."


Excerpt: "Single‐gene and genome sequencing studies have identified base substitution mutations as a causative mechanism in human genetic diseases and cancer. These mutations do not occur randomly but are often enriched at specific DNA (deoxyribonucleic acid) sequences. The genome of most human cells contains about 50 million 5‐methylcytosine bases, the majority of them occurring at the CpG dinucleotide sequence. Methylated CpG dinucleotides are the targets of many of the mutations, mostly transition mutations (C→T or G→A), found in genetic disorders and in malignant tumours. The mechanisms that increase mutations at CpG sites include spontaneous deamination of 5‐methylcytosine and preferential interaction of such sequences with physical or chemical carcinogens. As a consequence of enhanced mutagenesis at methylated CpGs, the CpG frequency in mammalian genomes has been strongly depleted over evolutionary time."

Key Concepts

  • Methylated CpG sequences are preferentially mutated.
  • Deamination of 5‐methylcytosine leads to transition mutations at CpGs.
  • Exogenous carcinogens target methylated CpGs.
  • CpG mutations are frequent in genetic diseases and cancer.
  • DNA repair may be affected by methylation of CpG sequences.

My comment: Deamination of 5-methylcytosine is often caused by oxidative stress (keywords: deamination oxidative stress). Oxidative stress is typically result of weak nutrition (or overnutrition), lack of exercise, mental stress, bad life habits (alcohol consumption or smoking) etc.

This is why DNA sequences (also called genes) are driven by lifestyle. Any change in organisms is based on epigenetic regulation of existing biological information or gradual but inevitable corruption of information. That's why there's no mechanism for evolution. Don't get lost.


The DNA gene is dead

More reasons why DNA doesn't determine traits


  • Now it's clear that a single length of DNA can be transcribed in multiple ways to produce many different RNAs, some coding for proteins and others constituting regulatory RNAs.
  • By starting and stopping in different places, the transcription machinery can generate a regulatory RNA from a length of DNA that overlaps a protein-coding gene.
  • The same sequences are being used for multiple functions. That introduces complications into the evolution of the genome, which had until recently been assumed to act through single DNA mutations affecting single genes.
  • Moreover, the code for another regulatory RNA might run in the opposite direction on the facing strand of DNA.
  • More fundamentally, it muddies scientists' conception of just what constitutes a gene. In the established definition, a gene is a discrete region of DNA that produces a single, identifiable protein in a cell. But the functioning of a protein often depends on a host of RNAs that control its activity. If a stretch of DNA known to be a protein-coding gene also produces regulatory RNAs essential for several other genes, is it somehow a part of all those other genes as well?
  • Multiple and overlapping genes can occupy a single strip of DNA that also produces several functional RNAs that don't encode proteins.
  • To make things even messier, the genetic code for a protein can be scattered far and wide around the genome. The ENCODE project revealed that about 90 percent of protein-coding genes possessed previously unknown coding fragments that were located far from the main gene, sometimes on other chromosomes.
  • Offering a radical new conception of the genome, Gingeras proposes shifting the focus away from protein-coding genes. Instead, he suggests that the fundamental units of the genome could be defined as functional RNA transcripts.

My comment: The cell uses the DNA for building different RNA-products. It's likely that the cell is able to choose appropriate strands of the DNA and build essential RNA transcripts for different purposes. Overlapping, embedded  and opposite-directional DNA strands tell us about very complex, designed mechanisms the cell uses for building RNA-products. After realising this complexity and the way the DNA is used, we should also understand that

- The DNA is not your destiny
- Genetic determinism is a serious heresy
- The DNA doesn't dictate traits of organisms
- The DNA has no control over cellular processes
- Mutations never lead to evolution but gradual degradation of the genome
- It's a waste of money to buy a DNA test. Those tests tell you about genetic markers left by epigenetic mechanisms and genetic errors. (http://www.els.net/WileyCDA/ElsArticle/refId-a0006159.html)


The theory of evolution is full of chicken-egg dilemmas

The most inconvenient chicken-egg dilemmas of the theory of evolution

Evolutionists' belief in their theory is so strong that they are blind to see the impossibility of their theory. Here's the most serious chicken-egg dilemmas.

RNA Pol-ii
1. RNA polymerase is an enzyme that is a complex molecular machine and is intended to synthesize RNA from either DNA or RNA. The RNA polymerase is composed of a number of complex proteins. But proteins can't be produced without the RNA polymerase. Where did it come from?

2. DNA repair mechanisms need several complex enzymes. If life originated in the primordial soup, the sun's UV rays, background radiation, etc. would have destroyed the first assumed DNA molecules just in hours without a functioning repair mechanism. Just DNA is not enough to build proteins because the cell also needs epigenetic information structures for protein production and thousands of other fully functional mechanisms and machines. Where did the DNA repair mechanisms come from?

3. A unicellular organism can not evolve into multi-cellularity because the necessary information needed for cell differentiation is given from parents to offspring. For example, a growing flatworm C Elegans (1031 cells) needs accurate information for its cellular differentiation and specialization.  It gets that information only from its predecessor by using non coding RNA molecules (lncRNAs and miRNAs). Where did the predecessor come from?

4. Bacterial life span varies from a few minutes to a maximum of weeks (bacteria are able to stay in a dormancy even for years but then they have stopped all functionality). They have to be replicated so that the population survives and continues to exist. How did the first assumed bacterium develop a super complex replication machinery just in a few hours or weeks?

5. An RNA thermometer is a temperature-sensitive non-coding RNA molecule which transmits information from outside world for the cell and helps it regulate gene expression. RNA-thermometers are widely used by bacteria and plants. It is coded from DNA by RNA-polymerase and modified by several complex mechanisms. The RNA thermometer is read by cellular reading machineries. Which evolved first, the sensor, the signal routing mechanism or the reading mechanism? There are hundreds of different receptors in living organisms responding to nutrients, climate, stressors, light, chemicals etc.

There are no observed answers to these chicken-egg problems. But they are very important issues and people should demand evolutionary biologists to give relevant answers (based on scientific evidence) for these problems.


Astronaut experiences rapid genetic alterations after epigenetic adaptation - Genetic degradation

Astronaut experiences rapid genetic alterations after epigenetic adaptation - Genetic degradation


Excerpt: "Scott and Mark Kelly are identical twin brothers — at least, they were until Scott spent a year living in space.

When Scott Kelly returned to Earth after a 340-day voyage aboard the International Space Station (ISS) two years ago, he was 2 inches taller than he'd been when he left. His body mass had decreased, his gut bacteria were completely different, and — according to preliminary findings from NASA researchers — his genetic code had changed significantly. (Interestingly, Scott Kelly has since shrunk back down to his initial prespaceflight height.)

A new NASA statement suggests the physical and mental stresses of Scott Kelly's year in orbit may have activated hundreds of "space genes" that altered the astronaut's immune system, bone formation, eyesight and other bodily processes. While most of these genetic changes reverted to normal following Scott Kelly's return to Earth, about 7 percent of the astronaut's genetic code remained alteredand it may stay that way permanently.

The changes are "thought to be from the stresses of space travel, which can cause changes in a cell’s biological pathways," the NASA statement said. "Such actions can trigger the assembly of new molecules, like a fat or protein, cellular degradation, and can turn genes on and off, which change cellular function."

Two Brothers

Scott spent nearly a year aboard the ISS as part of a unique NASA project called the Twins Study, which aims to reveal the long-term effects of space travel on the human body and mind. In March 2015, he flew up to the ISS to begin what would become the single longest space mission any astronaut has ever accomplished. Most astronauts stay aboard the ISS for six months at a time. Scott Kelly stayed in orbit for 340 days.

Meanwhile, Scott Kelly's identical twin brother, Mark (a retired astronaut, himself), remained on Earth as a control subject. The Kelly brothers are the only twin astronauts in history, NASA said. Because identical twins are born with identical DNA — the genetic code that tells cells when and how to work — the Kellys made ideal subjects for before-and-after comparison.

Researchers tested both Kelly brothers before, during and after Scott's year in space to map specific changes in the astronauts' physical and mental health. Most of Scott's physical changes — including his 2-inch height gain — proved to be temporary responses to the low-gravity, low-oxygen environment of space, NASA said.

However, genes involved in bone formation, oxygen deprivation, immune system responses and DNA repair remained transformed after Scott Kelly's return to Earth, NASA reported. The reason behind this could involve a complicated reaction to an unusual type of stress: the stress of space.

"Oftentimes, when the body encounters something foreign, an immune response is activated," Christopher Mason, a Twins Study researcher and an associate professor at Weill Cornell Medical College, told Business Insider. "The body thinks there’s a reason to defend itself. We know there are aspects of being in space that are not a pleasant experience, and this is the molecular manifestation of the body responding to that stress."

Understanding why and how these "space genes" activate will be crucial to planning longer manned space missions. The way NASA sees it, Scott Kelly's year in space is a significant "stepping stone to a three-year mission to Mars."

More than 200 researchers in 30 states are helping to analyze the Kelly brothers' various test results, looking for space-induced changes in Scott Kelly's cognition, metabolism, microbiome and many other physiological processes. NASA will publish the comprehensive findings of these tests in a single study later this year."

My comment: Life is not driven by gene sequences. Genes are driven by lifestyle. Scott Kelly experienced epigenetic alterations due to loss of gravity, stress factors, low contribution to bacterial environment etc. Modification on his epigenome triggered genetic alterations. Not 7% but a few hundreds of SNP and CNV mutations. After he came back to the Earth, his epigenome recovered but genetic alterations didn't. This is how organisms experience changes in nature. Environmental factors, such as diet type, stressors, climate, sensory stimuli, toxicants etc. contribute to organisms' epigenome through several types of receptors and RNA-mediated signaling mechanisms.

About 7 % of Scott Kelly's DNA expression profiles remained altered. Seems that he didn't evolve. Seems that there were no stable phenotypic alterations.

Any change in organisms is based on epigenetic regulation of existing biological information OR gradual but inevitable disappearance of information. That's why there's no mechanism for evolution.


Reasons why DNA doesn't determine traits

Multiple different information layers in the cell respond to environmental signals

1.  DNA sections (sequences) are never used directly by cellular mechanisms. Parts of the DNA are always read into a template RNA strand (transcription) before further processing. The template RNA is then modified by several complex mechanisms, such as alternative splicing machinery. The mature RNA-product is regulated by several epigenetic factors and mechanisms before final protein production. 

2. DNA genes need to be told at what level they are activated or silenced. This is regulated by several mechanisms and factors, such as chromatin structure and folding (3D genome). Histone epigenetic markers affect strongly the folding and shape of chromatin. Chromatin structure is organized by complex motor protein called condensin. It is able to form loops so that certain parts of the DNA can be in flanking state regulating the activity of transcription

3. Histone code is a biological database. Histones are structural proteins of chromosomes. Histones pack and order DNA into structures known as nucleosomes so that it fits within a cell’s nucleus. Each nucleosome contains two subunits, both made of histones H2A, H2B, H3 and H4 – known as core histones – with the linker histone H1 acting as a stabilizer. Many chemical modifications can be found in the tails of the histones. These include, but are not limited to acetylation, mono-, di-, or tri-methylation and ubiquitination, and can occur in different amino acids in the tails of the different histones.  
Any real histone code has the potential to be massively complex; each of the four standard histones can be simultaneously modified at multiple different sites with multiple different modifications. To give an idea of this complexity, histone H3 contains nineteen lysines known to be methylated—each can be un-, mono-, di- or tri-methylated. If modifications are independent, this allows a potential 419 or 280 billion different lysine methylation patterns, far more than the maximum number of histones in a human genome (6.4 Gb / ~150 bp = ~44 million histones if they are very tightly packed). And this does not include lysine acetylation (known for H3 at nine residues), arginine methylation (known for H3 at three residues) or threonine/serine/tyrosine phosphorylation (known for H3 at eight residues), not to mention modifications of other histones. (https://en.wikipedia.org/wiki/Histone_code)

Histone markers are regulated and maintained by long non coding RNA-molecules that have a crucial role in development of embryonic cells. Histone markers affect strongly traits of organisms. For example skull morphogenesis is regulated by histone deacetylases. Fur, coat and pigment colors are also regulated by histone markers. And thousands of other traits...

4. DNA methylation is involved in the regulation of several cellular processes such as chromatin stability, imprinting, X chromosome inactivation and carcinogenesis. It strongly affects alternative splicing and RNA polymerases. Methylation stabilizes the genome and disrupted or aberrant methylation patterns are often the reason for genetic errors.

5. Non coding RNA molecules are transcribed from the DNA by very complex mechanisms called RNA polymerases I and II. They are not direct copies of the DNA because of complex modifications. Their job is to transmit epigenetic markers (over 140 different types) for the DNA, histones and other RNA:s. In this way cells are able to get information from surrounding environment. RNA-molecules are often packed into transporters called extracellular vesicles.

6. Transcription factors are proteins produced by previous mechanisms 1.-5.

The cellular information can be categorized as follows:

A. DNA - 
a passive digital information layer, a library for production of RNAs.
B. DNA methylation - analog information layer, meta-data
C. Chromatin structure and folding - analog information

D. Histone markers - a digital database  CONVERTED to chromatin folding (A/D converter)
E. Epigenetic markers of RNA - both digital, analog and meta-data
F. Transcription factors - meta-data

All living organisms receive signals from surrounding environment. This means diet types, climate, stress factors, sensory stimuli, toxicants etc. Any change in organisms is due to epigenetic regulation of existing biological information or gradual but inevitable disappearance of information. That's why there's no mechanism for evolution. Don't get lost.


Three different evolutionary trees - The theory of evolution is pseudoscientific storytelling

Three different evolutionary trees - The theory of evolution is pseudoscientific storytelling

DNA does not determine traits of organisms. You can explore why your skin cell is completely different from the liver cell although both have exactly the same DNA. As you understand the mechanisms of cell differentiation, you realize that there is no mechanism for evolution. 

The actual regulatory functions of the cell are mediated by both non-coding and coding RNA molecules, most notably lncRNAs and microRNAs. MicroRNA molecules have several vital regulatory functions, such as protein production and intercellular communication. Various miRNA transcripts are known in the human genome of more than 5500. Evolutionary theory can be debunked by the fact that the comparison of microRNA transcripts between the organisms produces a completely different evolutionary tree of life than the traditional Darwinian fossil based tree:

If we compare long non-coding RNA molecules, that are in response of setting epigenetic markers in place during the embryonic development (for example sperm lncrnas, supplied by thousands of different extracellular vesicles), we again get a completely different evolutionary tree: human and chimpanzee genomes are less than 30 percent consistent. The similarity of human and pig lncRNA transcripts is significantly higher, i.e., 57%. 

Evolutionary theory is therefore the most serious heresy of our time. There is no known mechanism for evolution and there is no scientific evidence for it. Any change in organisms is based on epigenetic regulation of existing biological information or gradual but inevitable corruption of information. Life only arises from life and life itself is the best proof of Creation and Intelligent Design. Do not get lost, good people.


The presence and role of spermatozoal RNAs contribution to development is now appreciated

The presence and role of spermatozoal RNAs contribution to development is now appreciated


Excerpt from abstract: "Having been debated for many years, the presence and role of spermatozoal RNAs is resolving, and their contribution to development is now appreciated. Data from different species continues to show that sperm contain a complex suite of coding and non-coding RNAs that play a role in an individual's life course. Mature sperm RNAs provide a retrospective of spermatogenesis, with their presence and abundance reflecting sperm maturation, fertility potential, and the paternal contribution to the developmental path the offspring may follow.

Sperm RNAs delivered upon fertilization provide some to the initial contacts with the oocyte, directly confronting the maternal with the paternal contribution as a prelude to genome consolidation. Following syngamy, early embryo development may in part be modulated by paternal RNAs that can include epidydimal passengers. This provides a direct path to relay an experience and then initialize a paternal response to the environment to the oocyte and beyond. Their epigenetic impact is likely felt prior to embryonic genome activation when the population of sperm delivered transcripts markedly changes. Here, we review the insights gained from sperm RNAs over the years, the subtypes, and the caveats of the RNAs described. We discuss the role of sperm RNAs in fertilization and embryo development, and their possible mechanism(s) influencing the offspring's phenotype. Approaches to meet the future challenges as the study of sperm RNAs continues, will include, among others, elucidating the potential mechanisms underlying how paternal allostatic load, the constant adaptation of health to external conditions, may be relayed by sperm RNAs to affect a child's health."

My comment: Traits are determined by non-coding RNAs during reproduction. They are in response of transmitting essential epigenetic information especially for histone markers and DNA methylation profiles. DNA of embryonic cells doesn't determine traits.


One genotype can produce a diversity of phenotypes - Epigenetics

One genotype can produce a diversity of phenotypes - DNA doesn't determine traits


Excerpt: "Dog cloners, and increasingly the general public, understand that clones are not always physical matches of the original. One genotype can produce a diversity of phenotypes, the outward physical appearance. After all, the first cloned cat named Carbon Copy (CC) looked nothing like the original, highlighted veterinarian Sophia Yin in an interview with geneticist Leslie Lyons: “The cool thing about CC is that it shows that even though two animals are genetically identical, they may not look or act identical. A clone is never actually identical because there are so many different environmental factors that come into play.”
And perhaps of most importance to pet owners, pet cloning companies increasingly admit that clones do not match the original pet’s personality. “The new puppies and kittens will be the same sex as the donor, but just as it is in nature, may have slight phenotypic differences 
(My comment: Sometimes the differences can be significant), such as different markings due to natural epigenetic factors,” reports Viagen Pets FAQ. “The environment does interact with genetics to impact many traits such as personality and behavior.”"

My comment: These two cats are genetically identical but they have different epigenomes. DNA genes don't determine traits of organisms. Please remember that the DNA is the same in every stage of metamorphosis of butterflies, for example.
The DNA is just passive information library that cells use for building RNA products. Epigenome means different types of epigenetic information layers and regulatory factors needed for cellular differentiation. These are DNA methylation, histone epigenetic markers, non-coding RNA molecules, regulatory proteins and over 140 different types of epigenetic markers of RNA. Organisms experience variation and adaptation due to changed diet types, climate, stress factors, sensory stimuli etc. Adaptation never leads to evolution because alterations in epigenetic information layers result in gradual but inevitable degradation or recombination of existing biological information. This can be observed as genetic mutations, loss of genes and chromosomes and negative consequences within organisms, such as pathogenic bacteria and viruses, parasites etc. The theory of evolution is the most serious heresy of our time.


Long and sad (expensive) story about pseudoscientific ApoA-I Milano mutation

ApoA-I Milano mutation is nothing more but a genetic leftover


Excerpt: "Here’s a brief summary. The name refers to a mutated form of the Apo-A1 lipoprotein, first identified by researchers at the University of Milan, when a patient presented from a village in northern Italy (Limone sul Garda). This person had blood chemistry that could only be described as alarming: very low HDL and elevated triglycerides. One would normally think that someone with that profile was at great cardiovascular risk, but the patient showed no signs of atherosclerosis or any other problem of the sort. It turned out that the patient had a mutated form of lipoprotein A-1, a major constituent of HDL particles. It’s a single amino acid replacement – arginine for cysteine at position 173 of the protein. Careful work with blood testing of all the residents and genealogy established that all the people with this mutation (just over 3% of the village, so maybe three dozen people in all) descend from a single person, Giovanni Pomarelli, who was born with it in the 1700s. Further study of the population in Limone showed that the mutation did seem to have an unexpected cardioprotective effect – how else to explain the unfavorable blood profiles with the lack of the usual problems?

Well, good. What we have here is one of nature’s random shots that tells us something very interesting about cardiology and human lipid handling. A great deal of work has gone into trying to figure out what it is about the mutation that makes it different – as far as I know, current thought is that it’s both the loss of the arginine and the addition of the cysteine contribute. But the next step was to try to figure out how to turn these insights into a therapy for the large number of people in this world who are not descendants of Giovanni Pomarelli. As is so often the case, that was where things started to get really tricky. Gain-of-function mutations like this are rare, and they present a real problem for drug development. Put simply, we’re a lot better at messing things up. We can make inhibitors and antagonists, ligands that block interactions and so on, so if you have a beneficial loss-of-function mutation, we can often come up with some way to mimic that. Might be a small molecule, might be a big ol’ antibody, but one way or another, we can often take some good cracks at blocking whatever needs to be blocked.
But a mutant protein that’s actually working better poses a problem. How do you recapitulate that with a small molecule? In this case, it’s hard to see a way to do it – the only thing that seems workable is to find a way to get that new protein into a patient. Out-and-out gene therapy in mice, using a viral vector, looks impressive: forcing the mice to make the new protein that way, along with a low-cholesterol diet, led to “rapid and significant regression” of atherosclerosis, but gene therapy in humans is still in its early days, and no one is going to line up to be the first for this one. To go even further, eventually we’re going to have the nerve (and the knowledge that lets us get that nerve!) to mutate the human germ line itself, and for all I know, everyone a hundred years from now will be born with something like this mutant lipoprotein. But we’re definitely not there yet. So the brute-force approach, which is available right now, is to just give the mutant protein itself as an injection, let it circulate around in the blood and do its thing as if the body were producing it. That gives you a mixed situation that’s not found in nature – a handful of people have only Apo-A1-Milano, the rest of us have none – but it seems plausible.

And it certainly seemed plausible in animal models, that’s for sure. Infusion in both mice and rabbits seemed to reduce atheroma lesions in their blood vessels. Safety trials were done in humans with recombinant protein, and in 2003, a study funded by Esperion Therapeutics was published. Patients got five weekly treatments, and the results were positive – but were they positive enough? Esperion couldn’t produce enough of the protein for a longer trial, as I understand it, and what they saw was an increase in atheroma volume in the control group (+0.14%) and a decrease in the treatment group (-1.06%). That certainly seemed real, but you would have to have more to declare victory: a longer trial in more patients, long enough to determine real cardiovascular outcomes. Esperion could not deliver that, but they were bought up by Pfizer (for an impressive $1.25 billion dollars) around the time that work was published, and Pfizer can deliver that sort of big, expensive effort.

That did not work out. Not even a little bit. Five years later, the whole thing was a wipeout – Pfizer spun out what was left of Esperion and sold Apo-A1 Milano to The Medicines Company for $10 million, a whacking loss of greater than 99% on that deal. The Medicines Company are turnaround specialists – their thing is to buy what they feel are undervalued drug programs from larger companies and try to get them to market in some form. They’re smaller, so they don’t need multibillion dollar payouts to be successful (although I’m sure that they wouldn’t be averse).

Cerenis Therapeutics also took up the challenge. They’re a French company founded by a former research head at Esperion, and they went into the clinic with their own variation on Apo-A1 Milano HDL, but reported disappointing results. “Disappointing” is hardly even the right word: no change at all in atheroma volume between treatment groups and controls. Instead of a dose/response, they got what looks like random noise, a complete bomb. That first link has some interesting comments from cardiologists about these results – they were reluctant to think that this whole approach was in trouble, but kept holding out for better trials.

Meanwhile, the Medicines Company trial got underway, but back in August came some disquieting news. An independent committee was examining the data, and the optimistic case said that they might find a strong enough response to stop the trial early. But they recommended that it continue as planned. And now a later look at the numbers have led the company to completely stop development. That leaves the whole Apo-A1 Milano story in disarray; to the best of my knowledge, no one is is working on it, and after these results, you’d have to have a pretty compelling reason to get back in."

My comment: The DNA is not your destiny. Genetic determinism is a serious heresy, such as the theory of evolution. Life is not driven by DNA genes. Genes are driven by lifestyle.


Bioproduction faces 'evolutionary' mechanisms - LOSS OF PRODUCTION

Rapid and large-scale mutations are detrimental to bioproduction


Excerpt:"The transition towards sustainable biobased chemical production is important for green growth, but productivity and yield of engineered cells frequently decrease in large industry-scale fermentation. This barrier to commercialization of more bioprocesses is largely ascribed to the physical inefficacies of large cubic-meter steel tanks.

Bioengineers have long debated whether it was realistic for evolution to eliminate production of engineered production cells during the relatively short time courses of large industrial-scale production.

According to a new study published in Nature Communications, the role of evolution has been underestimated in limiting bioprocesses.

“Using a new ultra-deep DNA-sequencing approach, we found that evolution constrains bioproduction. We can use this insight to redesign our cell factories to produce more efficiently at industrial large-scale,” says Morten Sommer, Professor and Scientific Director of the Bacterial Synthetic Biology section at the Novo Nordisk Foundation Center for Biosustainability, DTU.

Detrimental evolution underestimated

The study from the Novo Nordisk Foundation Center for Biosustainability suggests that the mechanisms of evolution are constraining the scale-up by a variety of mutations wider and faster than previously expected.

"Using a new ultra-deep DNA-sequencing approach, we found that evolution constrains bioproduction. We can use this insight to redesign our cell factories to produce more efficiently at industrial large-scale"
Findings indicate that evolution is a more important threat to scale-up, and it cannot be ruled out that it limits the efficiency of commercialized large-scale fermentation.

Evolution of non-productive cell subpopulations leads to loss of production in our case studies. The speed of evolution depends on the biochemical product, but it can definitely happen within industrial time-scales. This makes it difficult to scale-up biobased processes,” says Peter Rugbjerg, Postdoc at the Novo Nordisk Foundation Center for Biosustainability.

Nevertheless, by using ultra-deep sequencing of thousands of different cells, it is now possible to score the different error modes of scale-up and design against evolution earlier.

The researchers are now validating their bioinformatics approach and testing how widespread the problem is in actual industry by collaborating with fermentation companies.

Early evolution determined the long-term fate at scale

Results hint that engineered production genes in chemical producing bacteria were mainly mutated by non-expected disruptions and genetic rearrangements, rather than the slower, classical point mutations known as single nucleotide polymorphisms (SNPs). The mutations make the nonproducing cells more fit in the competition for nutrients of a fermentation tank.

We discovered that a wide diversity of genetic disruptions turned producing cells into nonproducing when we deep-sequenced thousands of production organisms over time. Cells have many build-in ways to remove unneeded genes, and it turned out the most important are overlooked in standard analysis tools,” says Peter Rugbjerg, Postdoc at the Novo Nordisk Foundation Center for Biosustainability.

The evolutionary mutants that eventually led to complete loss of production could be detected very early at frequencies below 0.1 %, which may permit future identification of failing fermentations earlier.

Residing at ultra-low frequency when grown in the laboratory, the mutants played no negative role on production in shake flasks and were traditionally difficult to detect. However, the advantage of lost production means these early mutations had already determined the magnitude of production decline that happens as the process is scaled up to industrial growth durations.

“Based on these findings I would encourage companies running industrial scale fermentations to deploy deep sequencing of the fermentation populations to assess the extent of detrimental evolution,” says Morten Sommer."

My comment: Intensive competition of nutrients results in adaptation but with a heavy cost of biological information. This is not evolution but devolution. These real life observations reveal the actual consequences of ecological adaptation. Gene loss, information loss, loss of functions etc. This same phenomenon is happening all over nature. The theory of evolution is the most serious heresy of our time. Don't get lost.