RNA-directed DNA methylation

Functionally interdependent editing and methylation

Editing and methylation at a single site by functionally interdependent activities …cytosine 32 in the anticodon loop of Trypanosoma brucei tRNAThr is methylated to 3-methylcytosine (m3C) as a pre-requisite for C-to-U deamination. Formation of m3C in vitro requires the presence of both the T. brucei m3C methyltransferase TRM140 and the deaminase ADAT2/3. Once formed, m3C is deaminated to 3-methyluridine (m3U) by the same set of enzymes. ADAT2/3 is a highly mutagenic enzyme4, but we also show that when co-expressed with…

Read More

Sal Giardina: apologetics revisited

March 26, 2017 Sal Giardina wrote: “James, I appreciate your responding to my posts but I would prefer that your input would be related to the content of the post.” My reply: If you do not want people to learn how my claims are linked to yours, please tell me that you intend to continue with apologetics rather the concept of energy as information. Apologetics: … the religious discipline of defending or proving the truth of religious doctrines through systematic…

Read More

Wikipedia refutes theistic evolution

RNA-Directed DNA Methylation Besides RNA molecules, a plethora of proteins are involved in the establishment of RdDM, like Argonautes, DNA methyltransferases, chromatin remodelling complexes and the plant-specific Polymerase IV and Polymerase V. All these act in concert to add a methyl-group at the 5′ position of cytosines. In contrast to animals, cytosines at all sequence context (CG, CHG, CHH) may get de novo methylated in plants. There is no such thing as de novo methylation. Methylation is energy-dependent. Virus-driven energy…

Read More

Francis S. Collins refutes theistic evolution

Criticisms of the nutrient-dependent pheromone-controlled evolutionary model Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. — Andrew Jones, BA Editor’s note The 2013 review article by James Vaughn Kohl published in Socioaffective Neuroscience & Psychology and criticized in the above Letter to the Editor was subjected to standard peer review and the revised version was accepted by me after it had…

Read More

George Church refutes theistic evolution (2)

See: George Church refutes theistic evolution George Church may not know that he refuted every aspect of theistic evolution in his presentation on February 8, 2017. Hopefully, someone will tell him how he linked quantum physics from chemistry to biophysically constrained protein folding and all biodiversity, or explain to others how he did that. Here is my explanation of his admissions. I placed the explanation into the context of this poster session submission. Title: Energy as information and constrained endogenous…

Read More

Attacking Young Earth Creationists

‘Residual diversity estimates’ do not correct for sampling bias in palaeodiversity data Abstract excerpt: Evolutionary dynamics such as speciation are inherently a phylogenetic process, and only an explicitly phylogenetic approach will correctly model this process. Reported as: Flawed analysis casts doubt on years of evolutionary research The method assumes that variations in the number of different fossils at any given time are a reflection of how much rock was available. It has been used in more than 150 published research…

Read More

Base pairs, olfaction and RNA thermometers

RNA thermometer controls temperature-dependent virulence factor expression in Vibrio cholerae (2014) Excerpt: The stem-loop can be stabilized by strengthening the base pairing between the fourU element and SD sequence through the substitution of G-C base pairs, and this results in an elevated melting temperature (10). Conclusion: RNA thermometers represent a simple yet elegant mechanism for controlling temperature-dependent gene expression and may be more widespread among pathogenic bacteria that interact with mammalian hosts than is currently known. See also:  MicroRNA Stability…

Read More

Chromatin: The structure of DNA (2)

A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation Excerpt (with my emphasis): Highlights •    A histone H4K20me1-specific live-cell probe, H4K20me1-mintbody, was developed. •    Dynamics and replication timing of Xi were visualized. •    Critical amino acids for the stability and/or folding of the mintbody were revealed. Reported as: Catching histones by the tail: A new probe to track histone modifications in living cells Excerpt: H4K20me1 is most likely associated with the tight packing of a redundant (inactivated) female X…

Read More

Linking RNA structure to function

A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage was reported on September 8, 2016 as: Linking RNA structure and function Excerpt 1) 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. The insult to the intelligence of all serious scientists who have linked energy-dependent changes from angstroms to ecosystems in…

Read More

Non-random pheromone-controlled cell type differentiation

Experience-Dependent Plasticity Drives Individual Differences in Pheromone-Sensing Neurons Aug 17, 2016   •Individual differences in cell types are not random •Sex differences in pheromone-sensing neurons are controlled by experience •Changes in specific cell types are governed via “use it and lose it” plasticity •Targeting plasticity to specific cell types changes animal behavior This was reported as: Long-term exposure to female scents changes courtship behavior in male mice The senior author co-authored Chromatin remodeling inactivates activity genes and regulates neural coding…

Read More