Please Learn Math - Conspiracies - Conspiracy Theories & Facts

Please Learn Math

posted 2 years ago by GnarlyToad 2 years ago by GnarlyToad +5 / -10

I continually see memes quoting statistics that claim to show the ineffectiveness of vaccines.

Anybody with even middle school level math competency should be able to see through the misrepresentation of these statistics.

A recent example stated that 85.7% of deaths over a particular week in Scotland were vaccinated people. The conclusion drawn was that the vaccines don't work because the vast majority of people dying were vaccinated.

What was left out in the post was that 94% of Scotland has received at least 1 dose and 74% has received 3 doses. That leaves only less than 6% of the population unvaxxed accounting for 12% of the deaths. This data suggests (suggests, doesn't prove anything), just the opposite of the conclusion drawn.

Misuse of statistics makes people look either stupid or dishonest. If you see something posted like this, you should immediately question your source. Anybody passing off this kind of stuff isn't vetting their sources or their numbers either through actual intent to mislead or sheer stupidity. Either way, the source cannot be trusted. Trusting such a source is just allowing yourself to be duped (which makes you a dupe) or a liar yourself.

Hold yourself to higher standards of integrity, please, everybody. It doesn't help anybody to lie about facts or pass on lies about facts.

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– GnarlyToad [S] 0 points 2 years ago +1 / -1

Here is what you said:

You introduced the concept of variants which I never acknowledged as a valid construct.

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– KiloRomeo 1 point 2 years ago +1 / -0

Yes. That doesn't mean I don't it's possible just that I don't believe their covid variants.

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– GnarlyToad [S] 0 points 2 years ago +1 / -1

What's not to believe about them? Viruses mutate so of course there are variants.

Here's a study:

Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia.

On what basis do you gainsay this study?

All of this is just, what? Fake?

Nextstrain

All you do is naysay science then claim you aren't a science denier. The science here is overwhelming. You have to be a fool to deny it.

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– KiloRomeo 1 point 2 years ago +1 / -0

Like I said before: I acknowledge that virus mutate. I don't acknowledge all the canonical variants of covid as meaningful pushy because I don't trust their sequencing techniques. Can you validate that their methods are better than a dice roll?

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– GnarlyToad [S] 0 points 2 years ago +1 / -1

I am not an expert in sequencing techniques. Are you? Here's the thing: scientists publish studies in scientific journals that are peer reviewed. So if their sequencing techniques are flawed, they get called out. It's not a perfect system, but when there are experts reviewing sequencing techniques I'm going to trust them much more than someone on the internet who, for no stated reason, doesn't trust their sequencing techniques. I'd love to see you walk into a lab and say, "I don't trust your sequencing techniques." It's laughable.

You tell me: what's wrong with their sequencing techniques? They lay it all out there for anyone to replicate. Your experts could publish a study demonstrating that the sequencing techniques do not work.

Here is a description in that last study I cited:

SARS-CoV-2 positive samples were randomly selected and tested with primers targeting the E gene, which has been previously demonstrated in our reports to be the most sensitive target [10,11].

Is this a step in sequencing that you do not agree with? Why or why not?

Samples with Ct value [less than or equal to] 28 were chosen for further analyses.

What criticism of this step do you have?

Total nucleic acids were extracted from 500 [mu]L UTM-medium on the QIAsymphony SP using the QIAsymphony DSP Virus/Pathogen Midi Kit (Qiagen), following manufacturer's instructions.

Can you pinpoint for me what is wrong with this sequencing step?

High resolution melting was used for the qualitative detection of p.N501Y and p.E484K mutations in the SARS-CoV-2 genome.

How about these steps?

Briefly, extracted RNA was used as a template for the VirSNiP SARS B1351 assay on the LightCycler ® 480 Real-Time PCR System (Roche Diagnostics). Positive and negative control (NTC) were included in all experiments.

4 [mu]L Roche master mix, 0.5 [mu]L reagent mix (containing primers and probes), 5.5 [mu]L PCR-grade water and 10 [mu]L of template were mixed to a total volume of 20 [mu]L. Amplification was performed following manufacturer's instruction.

After normalization and temperature shift determination, the different melting curves were generated.

p.E484K is associated with a shift from 52°C to 57°C while p.N501Y is associated with a shift from 60°C to 65°C. LightCycler® 480 Software was used to analyze all data.

Samples were randomly selected from the 1508 specimens that underwent HRM screening. 479 barcoded libraries were prepared using the Ion AmpliSeq SARS-CoV-2 Research Panel (Thermo Fisher Scientific) and the Ion AmpliSeq Library Kit Plus (Thermo Fisher Scientific), following manufacturer's protocol.

The panel consists of 237 amplicons that allows for the sequencing of 99% of the SARS-CoV-2 reference genome (NC_045512.2), covering from position 43 to position 29,842. All the reactions were performed in a Veriti[TM]Dx 96-Well Thermal Cycler (Applied Biosystems[TM]). Libraries were quantified with the Qubit dsDNA HS Assay kit (Life Technologies) and then diluted to 30 pM. Libraries were loaded into the Ion Chef[TM] Instrument (Thermo Fisher Scientific) for template enrichment and chip loading. Sequencing was performed with the Ion S5 GeneStudio Sequencer using the Ion 510 & Ion 520 & Ion 530 Kit-Chef and the Ion 530[TM] chip-kit (all Thermo Fisher Scientific).

After alignment, the following plugins were run on the Torrent Suite[TM] Server (Thermo Fisher Scientific): the SARS_CoV_2_variant caller, the SARS_CoV_2_CoverageAnalysis, the SARS_CoV_2_annotateSnpEff and the generateConsensus. Sequences kept for further investigations were the ones possessing a mean depth of coverage [greater than or equal to] 500 and a percentage of gaps [less than or equal to] 20% of the entire sequence. For variant calling, variants with a genotype quality (GQ) score [greater than or equal to] 30, a coverage (FDP) [greater than or equal to] 500 and a minimum alternate allele frequency of 70% (AF [greater than or equal to] 70%) were kept for further investigations.

Clade and lineages of 479 specimens were defined with the Nextclade v2.29.1 web application (https://clades.nextstrain.org/), the GISAID CoVsurver mutation App (https://www.gisaid.org/epiflu-applications/covsurver-mutations-app/), the pangolin web app developed by the Centre for Genomic Pathogen Surveillance-version v.3.1.11 - (https://pangolin.cog-uk.io/) and the Ultrafast Sample placement on Existing tRee (UShER) web tool by UCSC (https://hgwdev-angie.gi.ucsc.edu/cgi-bin/hgPhyloPlace). SNPs and INDELs frequencies were evaluated in the CovidMiner data portal (https://covid-miner.ifo.gov.it/app/home) and in the GISAID database (https://www.gisaid.org/).

FASTA sequences have been uploaded in the GISAID database. S2 Table enlists Accession IDs and virus names.

FASTA sequences were aligned with ClustalW. The Maximum Likelihood (Tamura-Nei method) method was used to generate a phylogenetic tree of the 479 sequences. Alignment and tree were computed with Molecular Evolutionary Genetics Analysis (MEGA) v.11.

What part(s) do you determine are flawed and untrustworthy? Do you have some suggestions to improve their sequencing methods?

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