This comment was removed from a “tree of life” discussion site by the “site staff.” In the context of anonymous “peer” review, the comment was removed for the following reason: PSEUDOSCIENCE, with an added threat that my account might be suspended in case of regular violations of the guidelines that led the “site staff” to remove this comment.

Young earth creationists addressed the “Tree of life” nonsense in: “Evolutionary Predictions Fail the Reality Test.”

Excerpt:

Evolutionary developmental biologist Sean Carroll describes the implications of the stunning details:

When the sequence of these homeoboxes were examined in detail, the similarities among species were astounding. Over the 60 amino acids of the homeodomain, some mice and frog proteins were identical to the fly sequences at up to 59 out of 60 positions. In Dobzhansky’s (1973) claim, a single amino acid substitution differentiates cell types of chimpanzees and humans from gorillas. One “Tree” expert claims:

…this first tree of life is also important in revealing what we don’t know…

Compared to the creationists, these tree experts appear to know nothing about RNA-mediated amino acid substitutions and cell type differentiation.

My summary: Comments that someone considers to include pseudoscience auto-magically include non-mainstream theories. No matter how ridiculous the mainstream theories have become in the light of experimental evidence that links top-down causation to biologically-based cause and effect, non-mainstream facts are dismissed.

That explains why “Pseudoscientific beliefs are widespread, even among state school science teachers and newspaper reporters.[5]”

My comment: Every aspect of the ‘Tree of life’ for 2.3 million species released nonsense is probably considered by serious scientists to be based on pseudoscience.

Excerpt 1) 

A first draft of the “tree of life” for the roughly 2.3 million named species of animals, plants, fungi and microbes—from platypuses to puffballs—has been released.

My comment: Serious scientists now use genome wide sequencing to differentiate species that pseudoscientists simply names.

Excerpt 2)

The initial draft is based on nearly 500 smaller trees from previously published studies.

My comment: The previously published studies probably did not include contributions from serious scientists who perform genome wide sequencing to differentiate species.

Excerpt 3)

As a result, the relationships depicted in some parts of the tree, such as the branches representing the pea and sunflower families, don’t always agree with expert opinion.
Other parts of the tree, particularly insects and microbes, remain elusive.
My comment: The opinions of experts are based on genome wide sequencing that differentiate species from microbes to humans. Experts do not exclude insects and microbes.

Excerpt 4 with my emphasis)

“As important as showing what we do know about relationships, this first tree of life is also important in revealing what we don’t know,” said co-author Douglas Soltis of the University of Florida.

My comment: The “Tree of Life” researchers appear to know nothing about nutrient-dependent RNA-mediated gene duplication and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species via their physiology of reproduction. What’s missing from this first “tree of life” is everything currently known to serious scientists about physics, chemistry, and the conserved molecular mechanisms of biophysically constrained protein folding. What’s missing reveals that fact that they know nothing about viruses and cell type differentiation.

See for comparison:

Researchers discover contenders in molecular arms race of major plant disease

Excerpt: Researchers have discovered how a tiny viral protein enables the infection of a complex plant, and the finding could lead to understanding viral diseases in other plants, animals and humans.

My comment: Understanding the role that viruses play in perturbed protein folding links viral microRNAs to all pathology, which has typically been prevented by nutrient-dependent microRNAs.

See: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

Excerpt:

In summary, the spectrum of protein-coding variation is considerably different today compared to what existed as recently as 200 to 400 generations ago. Of the putatively deleterious protein-coding SNVs, 86.4% arose in the last 5,000 to 10,000 years, and they are enriched for mutations of large effect (Supplementary Fig. 14) as selection has not had sufficient time to purge them from the population.

See also: The palaeolithic diet and the unprovable links to our past

Excerpt:

…genetics play a pretty minor role in determining the specifics of our diet. Our physical and cultural environment mostly determines what we eat. Textbook examples include genes associated with lactose tolerance, starch digestion, alcohol metabolism, detoxification of plant food compounds and the metabolism of protein and carbohydrates: all mutations associated with a change in diet.

My comment: That claim was linked to this claim in Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

Excerpt:

Of the putatively deleterious protein-coding SNVs, 86.4% arose in the last 5,000 to 10,000 years, and they are enriched for mutations of large effect (Supplementary Fig. 14) as selection has not had sufficient time to purge them from the population.

My comment: The claim that selection has not had sufficient time to purge the mutations from the population was placed into the context of beneficial mutations via this report: The palaeolithic diet and the unprovable links to our past.

Excerpt:

Textbook examples include genes associated with lactose tolerance, starch digestion, alcohol metabolism, detoxification of plant food compounds and the metabolism of protein and carbohydrates: all mutations associated with a change in diet.

My comment: Theorists have not yet realized that they can not link virus perturbed protein folding to our past via mutations, natural selection, or evolution. Changes in diet must be linked from our past to ~5-10K years of ecological variation and ecological adaptations via biophysically constrained nutrient-dependent RNA-mediated protein folding and the amino acid substitutions that differentiate all cell types in all individuals of all living genera.

On August 21st, the research team led by Prof. Yigong Shi from School of Life Sciences, Tsinghua University in China published two side-by-side research articles in Science, reporting the long-sought-after structure of a yeast spliceosome at 3.6 angstrom resolution determined by single particle cryo-electron microscopy (cryo-EM), and the molecular mechanism of pre-messenger RNA splicing. Until now, decades of genetic and biochemical experiments have identified almost all proteins in spliceosome and uncovered some functions. Yet, the structure remained a mystery for a long time. The works, primarily performed by Dr. Chuangye Yan, and Ph.D students Jing Hang and Ruixue Wan under Prof. Yigong Shi’s supervision, settled this Holy Grail question and established the structural basis for the related area. This work was supported by funds from the Ministry of Science and Technology and the National Natural Science Foundation of China.

My comment: Re: the settled “Holy Grail” question:

Excerpt 1)

The involved proteins and RNAs assemble into and dissociate from spliceosome in a strict order during splicing, endowing extreme dynamics and flexibility of the spliceosome. These features guarantee the accomplishment of the complex splicing reaction, but at the same time tangling the structural investigations of spliceosome.

Excerpt 2)

…[this] group provided the first structural insight into the molecular mechanism for pre-mRNA splicing: the spliceosome is in essence a protein-directed ribozyme, with the protein components essential for the delivery of critical RNA molecules into close proximity of one another at the right time for the splicing reaction (shown in Figure 2).

Summary of their findings: Linking physics to chemistry and the conserved molecular mechanism of cell type differentiation via alternative splicings of pre-mRNA and the nutrient-dependent de novo creation of olfactory receptor genes is not an easy task. Nevertheless, the links from atoms to ecosystems were predicted by co-author Teresa Binstock in our 1996 review of RNA-mediated cell type differentiation.

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 (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

My comment: Attempts to move forward from our accurate representations of biologically-based cause and effect have been stalled by evolutionary theorists for nearly 2 decades. The theorists seem to want mutations to be the cause of cell type differentiation via natural selection and evolution. It has not been possible to convince them to not put natural selection for anything except food in the primary position that must be considered in the context of Darwin’s “conditions of life.”

Darwin’s conditions of life are linked across generations by RNA-mediated DNA mechanisms.

See also:

Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH

New Research Surfaces Spelling Bad News For Tylenol: It Doesn’t Just Kill Pain…

My comment: The effect on glucose is readily linked to affects on behavior via metabolic networks and genetic networks in all living genera.

 

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