...the more we look, the more we find ancient viruses hiding inside our genomes, as well as those of other creatures.
— Neil Shubin, The Wall Street Journal, 14-15 Mar 2020.
Replies to Cosmic Ancestry, 2020
somatic RNA ...passed on to embryos | from James Powers | 16 May 2020...Thanks for the posting on the transport of RNA to germ lines in your What’s New 12 May 2020. Here is the cited preceding companion paper that I had saved in my "Weird Biology Class 1" file [link below]. I wonder what Charles Darwin would think? The RNA paper continues to confirm my belief that epigenetic teleology is indeed a part of New Biology and supersedes Neo-Darwin evolution. What could be a better Science Fiction story about how I could use an RNA brain booster to determine the genotype and phenotype of my child – just by thinking?
By the way, the more that I think about star formation, the more I believe that we are missing a major building block of the universe. Stars are impossible with our (or my) current knowledge of astrophysics. This is reminiscent when Lord Kelvin calculated the age of the sun by calculating how much energy that the sun generated by the combustion of coal. He had no idea about nuclear fusion and the strong nuclear force. I believe that modern science is laboring under a similar condition of ignorance.
Stay safe! ...Jim Powers | Napa, CA
Somatic RNA can be passed on to embryos: the referenced What'sNEW article.
Additional thoughts re Italian data.... | from Reg Gorczynski | 24 Apr 2020Coronavirus has been detected on particles of air pollution by scientists investigating whether this could enable it to be carried over longer distances and increase the number of people infected. The work is preliminary and it is not yet known if the virus remains viable on pollution particles and in sufficient quantity to cause disease.
The Italian scientists used standard techniques to collect outdoor air pollution samples at one urban and one industrial site in Bergamo province and identified a gene highly specific to Covid-19 in multiple samples. The detection was confirmed by blind testing at an independent laboratory. Leonardo Setti at the University of Bologna in Italy, who led the work [https://www.medrxiv.org/content/10.1101/2020.04.15.20065995v1], said it was important to investigate if the virus could be carried more widely by air pollution. "I am a scientist and I am worried when I don't know," he said. "If we know, we can find a solution. But if we don't know, we can only suffer the consequences."
Two other research groups have suggested air pollution particles [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151372/] could help coronavirus travel further in the air [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7156797/]. A statistical analysis [https://www.medrxiv.org/content/10.1101/2020.04.11.20061713v1] by Setti's team suggests higher levels of particle pollution could explain higher rates of infection in parts of northern Italy before a lockdown was imposed, an idea supported by another preliminary analysis
[https://www.medrxiv.org/content/10.1101/2020.04.06.20055657v1]. The region is one of the most polluted in Europe.
Chandra Wickramasinghe re: Airborne transmission | Ted Steele re: sequence testing
Reg Gorczynski re: widespread exposure | Brig Klyce re: mutations | 17-19 Apr 2020
Wickramasinghe: ...we have to take account of the KD spread data and the mid latitude jet stream that fits the 30-60 degree latitude belt, but goes from west to east. It could go through a whole circuit without deposition to the ground so the temporal connections may be dealt with that way?
Steele: ...I have no problem with swabbing the environment for viral RNA and protein- I am sure that can be done. At present the focus is on detecting the RNA sequence in infected subjects - I have no problem with that either (in every infection cycle "empty" virions get released- e.g. those without a genome). The assay as I think I understand it is usually set up to "dissolve away the protein" or to release the RNA so the RT -PCR assay can get going. This is the same as releasing genomic DNA from cells in sequencing assays of all sorts..
The RNA sequence is crucial as that indicates the source and the stage of infection in a person-to-person chain (because in every infection a healthy person will attempt to cripple the replicating virus by introducing APOBEC/ADAR deaminase-mediated mutations (broadly C-to-U and A-to-I(G)) on either the top (+) or bottom (-) strand of the double stranded replicating form (RF) of the virus. We can tell from the sequence motif which APOBECs (C-sites) are active- there are two A-site ADARs (1/2) and their motifs are hard two separate (both are WA, where W = A or U).
What happened in central China Nov -Dec 2019? The behaviour of the Chinese government is all we can go on. They quarantined almost all of central China on about Jan 14 and shuffled 500-700 people in a lock down. They then had spray teams in protected suites out dousing roads, machinery etc - graphic movies on our evening news TV. That says logically they had some idea of the extent of the environmental viral contamination (whether they assayed viral protein, or viral RNA). I think the Chinese government knew by then that the contamination was immense in their vital industrial heartland – and if they sampled vegetation as well as wild and domestic animals they would have found the virus RNA signature everywhere, I think at high dose. Wuhan itself from all the rumours of deaths was hit with a high dose. I high dose of this common cold virus, can kill a lot of people. At lower doses less so, and then the elderly co-morbid are clearly at risk (people in their 70s like me with asthma). I think New York City from all reports we see got a very high dose- and everything points to a Wuhan scenario in that city. But all the numbers are suspect- COVID-19 positivity will be very high in New York City- so everyone who dies there is likely to be positive for COVID-19. Same in Lombardy region of Italy that displayed all the same signs of a high dose in-fall (and this will apply to Spain, and Tehran/Qom). The extend of antibody positivity for COVID-19 coat proteins will be a very important epidemiological number, as Reg keeps pointing out. That should have been instituted very early in the peace....
Gorzinski: ...In a startling finding, new Stanford research reveals between 48,000 and 81,000 people in Santa Clara County alone may already have been infected by the coronavirus by early April — that's 50 to 85 times more than the number of official cases at that date. The estimate comes from a first-in-the-nation community study of newly available antibody tests that suggest how widespread the invisible — and perhaps benign — companion has been in the Bay Area's hardest-hit county. Not only do the numbers show how the U.S.'s severe shortage of testing led to a profound undercount of COVID-19 cases, they indicate the virus is far less deadly than believed. Just how much of an undercount? Stanford's low-end estimate of Santa Clara County cases is nearly double the confirmed total — 28,000 — for the entire state of California. The study estimated 2.5% to 4.2% of residents here carry antibodies to the pathogen, a marker of past infection that suggests it may be safe for them to go back to work and school. "The most important implication is that the number of infections is much greater than the reported number of cases," concludes the research paper, published Friday morning in the online journal medRxiv.
Santa Clara County, home to Stanford University and 1.9 million residents, was one of the first hot spots for the coronavirus in the country. As of Friday, it officially had recorded 1,833 cases and 69 deaths related to coronavirus. The new Stanford study comes at a time when health experts and elected officials look to immunity as one way to blunt the impact of the pandemic. It is not yet known if antibodies prevent future infection. If so, antibody protection could offer people a safe route out of strict "sheltering." The research also implies that the death rate is far lower than believed. At the time of research, 39 county residents had died — a fatality rate, based on estimated infections, of only 0.12 to 0.2%. California's assumed death rate, based only on confirmed cases, is 3%. The study also showed how Santa Clara County's hospitals appeared to have dodged the long-feared surge of patients: Unlike New York, Santa Clara County's hospitals have yet to be overwhelmed. Fewer than 600 people are being treated for the virus at hospitals throughout the Bay Area. The Stanford study, led by Dr. Eran Bendavid, an infectious disease specialist and professor of medicine with Stanford Health Policy, shows whether someone has been infected by the virus in the past. They recruited participants by placing targeted advertisements aimed at Santa Clara County on Facebook. They used Facebook because it allows for targeting by zip code and sociodemographic characteristics. In contrast, COVID-19 virus testing only tests people with significant symptoms. It does not measure the true number of people who have been infected by the virus, many of whom have no symptoms or very mild symptoms. Several other teams worldwide also have started testing population samples. Like Stanford, they've found that there's a large underestimate of infections. Reports from the town of Robbio, Italy, where the entire population was tested, suggest at least 10% rate of infections. A survey in the western Germany municipality of Gangelt, highly affected by illness, found a 14% positive rate.
Klyce: ...Here is a cropped screengrab from a figure linked from [ "Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States," by J.R. Fauver, M. E. Petrone, E. B. Hodcroft et al., doi:10.1016/j.cell.2020.04.021, 11 Mar 2020]. If "mutations" means single-nucleotide mutations, then, all of these sequences are 99.967% identical?
our message re: Coronavirus | with Ted Steele | 26 Mar 2020
from Graham Steele: ...you guys need to provide me - if we want the media to follow and report this potential alternative narrative - with a 'one page' brief that outlines in layman's terms;
from Chandra Wickramasinghe: This is my response on the trot...
from Reg Gorczynski: I support that response Chandra....I am really concerned that everyone's response to this "social distancing" having any effect on curtailment on incidence will be presumed to reflect a validity to the prior hypothesis (person-to-person spread). It is importantly also what we would predict if you lock people up and have zero exposure to a community environment with foamite spread (after infall of virus from the stratosphere...but no-one except us has proffered that explanation!) Also the key issue (scientifically) is that there is data supporting the latter hypothesis which the former cannot, and it also offers an approach to preemptive testing for newer infections (atmospheric origin). ...Reg
hemolithin protein isolated from a meteorite | James Powers | 07 Mar 2020
...By the way, the article on the hemolithin protein isolated from a meteorite is interesting. Unfortunately, the described protein is composed of only glycine amino acids. Glycine has no chirality. If the amino acid was alanine, for example, we could determine if the protein was due to a chemical process or a biological origin. If it has equal numbers of left-handed and right handed amino acids, then this would indicate a chemical process. If the protein was a result of biology, then there would be a predominance of left- or right-handed amino acids. Keep on. ...Jim Powers | Napa, CA
Brig Klyce – Good work! ...You are aware that amino acids racemize over time, probably faster if agitated, as by radiation in space.
Powers – Amino acids will racemize in time. However amino acids in proteins cannot racemize without destroying the protein.
Klyce – ...Wasn't there also alanine in this one? Was its chirality noted?Powers – I took a closer look at this paper. They did find Alanine in some of the peptide fragments. The peptides are listed in the table. However, they did not account for this in the structure. They did not mention alanine in the discussion or conclusions. I looked at the structure again. The hydroxy of hydroxyglycine in the structure is not bound to the amine nitrogen, which is how commercial Hydroxyglycine is described. The hydroxy is bound to the alpha-Carbon in the chain. I don't know what to make of all this. Mass spec cannot determine chirality.
Corona virus and cosmic life | facebook chat with Greg Irwin | 29 Feb 2020
Greg Irwin – Does the original concentration in Wuhan work with that hypothesis? ( 27 Feb 2020)
Brig Klyce – Wuhan is right there, yes. But also noteworthy -- a meteor fell Oct 11 North of Wuhan. It would have penetrated deep into the atmosphere (see https://vixra.org/pdf/2002.0118v1.pdf). Entirely possible that the meteor and cometary dust that landed higher were all fragments of the same comet and therefore encountered at the same time. [On second thought, this makes sense only if the meteor arrived after the dust had reached the jetstream.]
Irwin – ...My doubts regarding panspermic explanations are founded where they've always been. Let me paste in two excerpts from the article.
"The support for the alternative view that life is a cosmic phenomenon stems mainly from the fact that the information content of life at a genetic and molecular level is super-astronomical; and this needs at least an astronomical or cosmological setting."
And: "The panorama of life on Earth is the result of the assembly of such bacterial and viral genes that has come to be assembled like pieces of a gigantic jig-saw puzzle over some 4.2 billion years."
How is complexity developing (from scratch) over 4.2 billion years incredible ("super-astronomical"), while that complexity developing over 13.8 billion years — and shipped around the cosmos for further assembly — is credible? You know I don't see that one.
Klyce – I don't either. I thought you knew that. I will email you a paper, "Some Things Are Simply Given". I can't put it online yet, because it's to be published in a forthcoming book. Basically, I think life must have always existed (and so the standard big bang needs tweaking.) Then I run into the coalition of Darwinists and creationists, both of whom love the standard, one-time-only big bang.
Irwin – Do send it to me. I knew that Wickramasinghe and Hoyle remained skeptical about the big bang. I know that you struggled for years against just-so stories being used to fill gaps in science, but 'life must have always existed' sounds like a just-so capitulation. Where will you look for such life? Or for its seepage or transmission from that place or non-place to our cosmos?
I don't think Darwinists love the big bang; they have had to struggle to adapt to it as a given (as Christians have had to adapt (or fail to adapt) to Darwinism). It is those very Darwinian difficulties that set you out toward Panspermia, I believe.
Creationists of the inerrantist and young earth mindset can't go for the big bang either. We creationists who are more agnostic about God's how do find ourselves buoyed by the discovery that matter is not eternal — but that, as it were, came to us; we did not seek it or expect it any more than the rest of the world did. The big bang was delivered to us (all) in about 1965 as surely as the evolution of our species was in 1859.
Klyce – Dude -- you are undoubtedly my best correspondent for this (loosely specified) issue. Comments to consider with the paper --
I think the creationists want to show that science is inconsistent for relying on material causes, because these don't work for the origin of life and evolution. I agree they don't work. But if life always existed they don't have to work. That way, science can remain fully consistent. And creationists have [everyone has] to give up only the standard, one-time-only/in-the-finite-past big bang. Can't creationists see that life from eternity is a miracle!