Science journalists or paid propagandists? (4)

By: James V. Kohl | Published on: January 19, 2017

Prognostic value of the MicroRNA-29 family in multiple human cancers: A meta-analysis and systematic review  

….low expression of miR-29 is associated with aggressiveness and poor prognosis of malignant neoplasms. More importantly, miR-29 might serve as a key biomarker for predicting the recurrence and progression of human cancers.

Feeding on the Unseen: Ingestion and Assimilation of Bacteriophages by Brachionus plicatilis (Rotifera)
ATP Production Increases with Addition of Varying Concentrations of Vespa Amino Acid Mixture (VAAM)
I found nothing else in other Society for Integrative & Comparative Biology (SICB) 2017 conference abstracts that appears to link either energy-dependent RNA-mediated amino acid substitutions to healthy longevity or that appears to link virus-driven energy theft to all pathology.
It is disappointing to see the ongoing lack of integration. For comparison, Dobzhansky (1964) Biology, molecular and organismic. It may still be the best representation of how worthless the SICB conference or any other conference that fails to integrate the information known to serious scientists can be.
He claimed:

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

The SICB members may profit themselves by acquiring funds for research that fails to integrate what is known to all serious scientists, but Dobzhansky (1964) also noted:

Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule.

In 1973, Dobzhansky wrote:

Cytochrome C is an enzyme that plays an important role in the metabolism of aerobic cells. It is found in the most diverse organisms, from man to molds.  E. Margoliash, W. M. Fitch, and others have compared the amino acid sequences in cytochrome C in different branches of the living world. Most significant similarities as well as differences have been brought to light. The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids. Fitch and Margoliash prefer to express their findings in what are called “minimal mutational distances.” It has been mentioned above that different amino acids are coded by different triplets of nucleotides in DNA of the genes; this code is now known.

Forty three years later we have a track record that clearly shows SICB researchers may selfishly proceed with funding attempts that lead nowhere.
See for example these links from past SICB conferences to abstracts that mentioned the term ‘microRNA’
2010 Where’s the Glass? Biomarkers, Molecular Clocks and microRNAs suggest a 200 Million Year Missing Precambrian Fossil Record of Siliceous Sponge Spicules
2011 Molecular paleobiological insights into the origin of the Brachiopoda
2012 No abstracts found (At the Society for Neuroscience conference in 2012, I learned about the importance of microRNAs.)
2013 MicroRNA regulation of alternative phenotypic development of the annual killifish, Austrofundulus limnaeus
2014 Establishing RNAi in Ciona intestinalis to determine gene function during peripheral nervous system development
2014 Epigenetic regulation of alternative developmental trajectories in an annual killifish
2015 MicroRNAs and comparative genomics in arthropod endocrinology and reproduction
The 2015 presentation of 2015 MicroRNAs and comparative genomics in arthropod endocrinology and reproduction was reported in: All in the (bigger) family

Juvenile hormone is thought to be specific to insects, whereas methyl farnesoate is inactive in that group. But researchers have learned that production of both hormones depends on the same rate-limiting enzymes. And Jerome Hui of the Chinese University of Hong Kong found that in both insects and crustaceans, the same set of micro RNAs control expression of the genes for those enzymes.

My comment to Science published at 2:54 pm on 1/29/15
See: The phylogenetic utility and functional constraint of microRNA flanking sequences by senior author Jerome Hui
This was reported as: ‘Junk DNA’ Used To Sort Species

They first compared non-coding sequences between human, chimpanzee, gorilla, orangutan, and macaque, and successfully recovered the evolutionary history of human and our close relative, showing that chimpanzees share the closest common ancestor with human, followed by gorilla, orangutan, and then macaque being the more distant relatives. They have also successfully used this new method to reveal the relationships of other animals, such as the insects and nematodes.

Re: “…chimpanzees share the closest common ancestor with human, followed by gorilla”
See again: Nothing in Biology Makes Any Sense Except in the Light of Evolution

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla (p. 127).

After they linked microRNA flanking sequences to what Dobzhansky reported in the context of nutrient energy-dependent RNA-mediated amino acid substitutions, I thought it would be clear that changes in the microRNA/messenger RNA balance are the link from ecological variation to ecological adaptation in all living genera. Indeed, that is what more than 57,000 published works on microRNAs suggests.
See: microRNA and ask what has happened with the information people has been presenting at the SICB meetings during the past two years
2016 MicroRNA regulation of an insect diapause
2017 Extreme Vertebrate Anoxia Tolerance and Small RNA Expression
Simply put, most of the SICB 2017 presenters ignored everything known to all serious scientists about energy-dependent RNA-mediated biophysically constrained protein folding chemistry.
See instead:
Ultraviolet filters in stomatopod crustaceans: diversity, ecology and evolution (2015)

The surprising localization of these filters in the crystalline cones was revealed by the fluorescent properties of three of the filter types found in rows 3–6, which emit blue, cyan or green light when stimulated with strong UV illumination. These filters are composed of mycosporine-like amino acids (MAAs), compounds commonly associated with photoprotection in marine organisms (Carreto and Carignan, 2011; Shick and Dunlap, 2002). In eukaryotes, MAAs are typically acquired through their diet (Hylander and Jephson, 2010; Newman et al., 2000) and subsequently modified for use as photoprotectants or, in the case of stomatopods, as optical filters.

Can invertebrates see the e-vector of polarization as a separate modality of light? (2016)

In honey bees, the twisted retinulae of the regular ommatidia (ventral to the DRA) abolish PS of the long UV photoreceptors (Labhart, 1980; Wehner et al., 1975). But the short, proximal UV receptor R9 is little affected by the twist and remains polarization-sensitive. Neighboring ommatidia twist in opposite directions, producing two e-vector tuning types of R9. Together with the long, polarization-insensitive UV receptors, they could theoretically form a 3D system, in which one analyzer channel, represented by the polarization-insensitive long UV receptors, measures light intensity (for details, see Wehner et al., 1975).

The unusual eyes of Xenos peckii (Strepsiptera: Xenidae) have green- and UV-sensitive photoreceptors

To contrast our mRNA sequences against other opsins, we utilized the blastx algorithm to predict the amino acid sequences of the opsins. Amino acid sequences of 50 known additional opsins from GenBank (Table S1) were aligned using the Clustal W algorithm (Saitou and Nei, 1987). This alignment was subjected to a neighbor-joining algorithm to perform a phylogenetic analysis as implemented in MEGA v. 6.06 (Tamura et al., 2007).

Saitou and Nei (1987) used a mathematical model to reconstruct phylogenetic trees. That fact bastardized the works of all serious scientists who have linked energy-dependent changes from angstroms to ecosystems in all living genera via what is known about the biophysically constrained physiology of energy-dependent reproduction. In that context, see these other SICB 2017 presentations and try to find any explanatory power that might be accepted by a serious scientist.
Exercising when sick: The role of pathogens on animal activity
You Make Me Sick: Energetic Signals Regulating Seasonal Sickness Responses
Transcriptional Response to West Nile Virus Infection in Zebra Finches
No evidence of a role for wild songbirds or rodents in spreading avian influenza virus across an agricultural landscape
Applying Metagenomic Sequencing to Search for the Cause of an Elusive Avian Disease: Avian Keratin Disorder in Black-capped Chickadees
Home Is Where the Gut Is: Variation Among Mosquito Species and Their Endosymbionts Across Different Habitats
Microbiome engineering effects developmental plasticity, physiological performance, and disease resistance in larval amphibians
Dicistrovirus infections in honey bees (Apis mellifera): establishment of an infection model
Drivers of Community Structure and Implications for Diversity-Disease Relationships
Sing Out Loud: A Signaler’s Perspective on Condition Dependence
Rheological behavior of insect hemolymph on macro-, micro-, and nano-scales
The 2013 Chikungunya Viral Outbreak in Grenada: A Phylogenetic Analysis of Introduction and Spread
Seroprevalence of antibodies against Mycoplasma gallisepticum and Avipoxvirus in nine species of birds with differential access to feeders
Host movement ecology and feeding behavior influence how resource provisioning affects parasitism for wildlife
Transcriptional Response to West Nile Virus Infection in Zebra Finches

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