Coronavirus Genetics:They Added The Radioactive Marks Then Treated Them As The Virus

Assumed conclusions became premises for what followed

This post was published by Jon Fleetwood. Support him by subscribing at Substack and following at Instagram / X / Facebook.

The coronavirus genetic story that eventually became part of the machinery used for pandemic determinations had to begin somewhere.

  • Before reference genomes.
  • Before PCR targets.
  • Before variants.
  • Before genomic surveillance.
  • Before software could compare a new sequence against thousands of sequences already classified as “coronavirus.”

There had to be a first body of accepted coronavirus genetic information.

Trace that information backward, and its observational foundation is startlingly modest.

Researchers were not directly observing the physical entity the resulting sequence purported to represent and reading genetic letters from it.

They were looking at marks produced by radioactive material deliberately added to their sequencing experiments.

From those marks, scientists accepted a chain of invisible (literally not directly observed) molecular events sufficiently large to conclude that they “knew” specific nucleotide identities, at specific positions, along genetic sequences of specific lengths, attributed to coronavirus.

  • Those conclusions became sequences.
  • Those sequences became prior information.
  • Prior information could then enter subsequent experiments.
  • And the resulting sequences could become still more prior information.

That is where the government-curated closed loop begins.

And this problem is not unique to coronavirus: every purported viral sequence space is ultimately a closed loop built on inference, because its foundational sequences enter through interpretations of experimental signals rather than direct observation of an intact physical virus and its genetic sequence, while later sequences are built, classified, or interpreted using genetic information whose ancestry leads back to those earlier inferences.

Which raises questions:

  • How much are we being asked to believe about the purported genetic reality of viruses that was never directly observed, but inferred from experimental signals?

  • How were those foundational inferences independently validated without assuming the same molecular story used to interpret the signals?

  • When did inferred nucleotide identities and positions become treated simply as “the viral sequence”?

  • If those inferred sequences became references and prior information for later sequencing, how much subsequent “confirmation” is genuinely independent?

  • Can a self-referential sequence system validate the physical reality it claims its sequences represent from within that same system?

  • Where is the independent physical anchor outside the sequence universe that breaks the loop?

  • What would actually falsify the foundational viral sequence interpretation rather than simply produce another sequence, variant, mutation, or classification within the same framework?

  • How did an inference-dependent genetic system ultimately acquire the authority to help determine cases, variants, outbreaks, and pandemics in the physical world?

The Primary Source Says Exactly What They Actually Read

Go back to Allan Maxam and Walter Gilbert’s foundational 1977 sequencing paper.

They wrote:

“DNA can be sequenced by a chemical procedure that breaks a terminally labeled DNA molecule partially at each repetition of a base.”

Then:

“The lengths of the labeled fragments then identify the positions of that base.”

And finally:

“the DNA sequence can be read from the pattern of radioactive bands.”

That is their description, not mine.

Read it again in physical terms.

  • The material is “terminally labeled.”
  • The resulting fragments are “labeled fragments.”
  • Their lengths supposedly “identify the positions” of bases.

And what researchers ultimately see is a:

“pattern of radioactive bands.”

The sequence is what they claim can be “read from” those bands.

That distinction is enormous.

Because the radioactive material responsible for making the products detectable was not something scientists saw announcing the presence of a genetic sequence.

Researchers supplied the radioactive label.

The thing producing the detectable signal was therefore already in the experiment because they had put it there.

And from the pattern subsequently produced by that added reporter, they asked the reader to accept an extraordinary amount about a molecular world that was not itself visible in those marks.

Look at What the Marks Don’t Tell You

A radioactive mark does not say:

  • I am DNA.
  • I am 37 nucleotides long.
  • I terminate at position 37.
  • position 37 contains G.
  • the mark immediately above me represents position 38.
  • all these marks represent different-length pieces sharing one molecular endpoint.
  • these pieces represent one continuous genetic sequence.

And it certainly does not say:

  • I came from coronavirus.

What does the researcher actually have?

At the readout stage, a mark at a location.

Now watch what has to be accepted before that mark becomes:

“G at position 37.”

First, Believe the Label Story

You must accept that the radioactive label scientists introduced became associated with the intended material.

You must accept that it was associated at the intended molecular endpoint.

You must accept that the material carrying it was the molecular species the researchers said it was.

None of those propositions is printed in the radioactive mark.

The mark does not contain a photograph of its molecular history.

You are accepting that history because the experimental methodology says that is what happened.

Then Believe the Chemistry Story

Maxam and Gilbert describe different chemical reactions intended to preferentially cleave at different nucleotide categories.

So now you must accept that those reactions behaved sufficiently as expected in the particular material being analyzed.

You must accept the claimed nucleotide preferences.

You must accept that the intended molecular cleavage occurred.

You must accept that the labeled product subsequently producing the mark was produced through that intended mechanism.

Again, you do not see any of that in the mark.

The mark does not contain: GUANINE.

It is a mark.

The identity G comes only after accepting the molecular explanation for why that particular reaction produced that particular signal.

Then Believe the Length Story

Now the products are run through a polyacrylamide gel.

Maxam and Gilbert say they are:

“resolved by size”

and that:

“The lengths of the labeled fragments then identify the positions of that base.”

But the photographic film does not print:

36 nucleotides

beside one mark and:

37 nucleotides

beside another.

It gives spatial positions.

You must accept that migration through the gel corresponds sufficiently to relative fragment length.

Now:

where the mark appears

has become:

how long the supposed fragment is.

But even that still does not give you nucleotide position.

Then Believe the Position Story

This is the part that is easy to hide inside the word “sequencing.”

Different molecular lengths are not automatically consecutive positions along one genetic chain.

Suppose you have three products interpreted as:

  • short
  • slightly longer
  • slightly longer again.

Why should those mean:

  • position 35
  • position 36
  • position 37?

They can only mean that if you accept another invisible molecular proposition:

the relevant fragments form the intended nested family sharing a common endpoint.

If they do, then progressively longer fragments can be interpreted as terminating progressively farther along representations of one underlying sequence.

Now:

migration location

has become:

fragment length

which has become:

nucleotide position.

But look at what the marks themselves show.

  • They don’t show the common endpoint.
  • They don’t show a nested family.
  • They don’t show one underlying chain.
  • They don’t display nucleotide coordinates.

All of that has to be accepted before a location on a piece of film becomes position 37.

Then Believe the Letter Story

Now combine the two interpretive systems.

The vertical position of the mark is interpreted through migration and fragment length to establish a purported nucleotide position.

The reaction in which the mark occurs is interpreted through the chemical-specificity model to establish a purported nucleotide identity.

And suddenly:

dark mark here

becomes:

G at position 37.

Think about the transformation.

The experiment did not visibly show G.

It did not visibly show 37.

It showed a mark produced through an experimental system containing radioactive material the researchers themselves had introduced.

To believe G, you have to accept the labeling, chemistry, specificity, and cleavage story.

To believe 37, you have to accept the electrophoresis, fragment-length, common-endpoint, nested-fragment, and positional story.

That is how much invisible molecular meaning has already been packed into one letter at one position.

And we haven’t even gotten to coronavirus yet.

Now Believe the Coronavirus Story

Even if you grant every preceding inference, you have reached something like:

G at position 37 of the sequence represented by the material subjected to this experiment.

Nothing about the radioactive mark itself establishes:

G at position 37 of coronavirus genetics.

For that, another chain must be accepted.

  • The material subjected to sequencing has to be what researchers say it is.
  • The material classified as cloned DNA has to contain the intended inserted material.
  • That material has to correspond to what researchers call cDNA.
  • That supposed cDNA has to faithfully correspond to material they classify as RNA.
  • And that RNA has to be properly attributable to the biological preparation researchers classify as coronavirus.

Only after that entire chain is accepted does:

radioactive mark

become:

“coronavirus nucleotide G at position 37.”

Look at what has been compressed into a single character.

  • G requires one chain of inference.
  • 37 requires another.
  • sequence requires those positions to belong together.
  • coronavirus requires another provenance chain entirely.

And the finished genetic string displays none of that uncertainty or inferential scaffolding.

It simply prints: G.

Then This Entered Coronavirus Genetics

This is not merely an objection one could hypothetically make about an old sequencing technology.

In 1984, M.E.G. Boursnell, T.D.K. Brown, and M.M. Binns published Sequence of the Membrane Protein Gene From Avian Coronavirus IBV.

Their abstract says:

“cDNA clones prepared from genomic RNA of coronavirus IBV have been sequenced.”

And:

“A sequence of 1224 bases is presented”

The paper used both chemical and enzymatic sequencing methods; it should not be described as Maxam-Gilbert-only.

But the crucial historical transformation remains.

What eventually enters the coronavirus literature is no longer a set of experimental marks.

It is:

  • 1,224 bases.
  • Exact letters.
  • Exact order.
  • An informational object attributed to coronavirus.

Another 1984 paper by Boursnell and Brown reported that:

“770 bases have been determined”

from what the researchers classified as genomic cDNA clones of IBV.

Again, the operative word is: determined.

The reader sees the finished determination.

The enormous ladder underneath it disappears.

Now the Inferences Can Be Joined Together

The sequence story does not stop with individual determinations.

Separate stretches can be compared.

Matching portions can be interpreted as overlaps.

Now:

inferred sequence A

plus

inferred sequence B

plus

an inferred overlap

becomes:

one longer sequence.

And something remarkable happens.

The larger sequence acquires an exact length even though that larger informational object was not itself the original direct sequencing readout.

Individual letters acquire exact coordinates inside it.

Previously separate determinations become one continuous genetic representation.

The inferred world is getting larger.

Then the Story Begins Referring Back to Itself

This is the pivotal transition.

Once accepted coronavirus sequences exist, researchers possess prior coronavirus sequence information.

In 1985, Binns and colleagues reported work on what they identified as the IBV spike gene.

Their abstract states:

“RNA sequences encoding the surface projection (spike) of the coronavirus infectious bronchitis virus, strain Beaudette, have been cloned into pBR322 using cDNA primed with a specific oligonucleotide.”

Their paper explicitly cites the group’s preceding 1984 coronavirus sequencing work.

This is where the informational architecture changes.

At first:

experiment

? signal

? sequence determination.

But once sequence information exists, specifically chosen nucleotide reagents can enter subsequent experiments.

Now the direction can become:

accepted sequence information

? sequence-specific experimental design

? new experimental material

? new signals

? new sequence determination.

The conclusion has become part of the next experiment’s premise.

That does not mean the earlier sequence mechanically dictates every unknown nucleotide subsequently called.

It means something more fundamental:

the coronavirus sequence world has begun feeding information back into the procedures used to expand the coronavirus sequence world.

And the Earlier Sequences Become the Larger Sequence

By 1987, Boursnell and colleagues announced completion of what they classified as the IBV coronavirus genome.

Their own description is striking:

“The complete sequence has been obtained from 17 overlapping cDNA clones”

And:

“Approximately 8 kilobases at the 3? end of this sequence have already been published.”

The modern IBV reference record still cites those earlier 1984 and 1985 sequence papers in its provenance.

So the first pieces didn’t disappear.

They became part of an expanding coronavirus sequence record.

The architecture now looks like this:

marks from an added reporter

? interpreted nucleotide identities

? interpreted nucleotide positions

? local purported coronavirus sequences

? overlapping sequence representations

? established coronavirus sequence information

? sequence-informed experiments

? additional sequence determinations

? larger coronavirus sequences

? reference sequences

? still more sequence-dependent work.

This Is the Closed Loop

Strip away four decades of technical terminology and look at the information flow.

Researchers begin without an established coronavirus sequence universe.

They introduce a radioactive reporter.

They observe marks produced by that reporter.

They accept an enormous invisible molecular explanation for what those marks supposedly mean.

The marks become nucleotide identities and positions.

Those determinations become purported coronavirus sequences.

Those sequences become accepted coronavirus information.

Accepted coronavirus information becomes usable in subsequent sequence-specific experiments.

Those experiments produce additional signals.

Those signals produce additional sequence determinations.

Those sequences expand the existing coronavirus information space.

And the expanded information space becomes prior knowledge for what follows.

The conclusion becomes a premise.

Then the next conclusion becomes another premise.

Then another.

The sequence universe increasingly corroborates, organizes, and extends itself from within.

From Marks to Pandemic-Era Genetics

Decades later, the instruments changed completely.

SARS-CoV-2 sequencing was not performed by reading Maxam-Gilbert autoradiographs.

That distinction is important.

But by then, coronavirus genetics was no longer starting from nothing.

It had become an immense informational realm containing reference sequences, presumed gene boundaries, nucleotide coordinates, conserved regions, sequence comparisons, primers, probes, alignments, phylogenies, and classifications.

During COVID-19, sequence-dependent systems became operationally consequential.

  • PCR assays depended on predetermined sequence targets.
  • Genomic surveillance compared reported sequences against existing references.
  • Mutations were defined relative to established coordinates.
  • Lineages were inferred from sequence relationships.

And genetic laboratory determinations became part of the evidence infrastructure through which authorities identified and tracked what they classified as SARS-CoV-2.

The WHO’s own international reporting framework illustrates how consequential laboratory classification can become: for novel influenza with pandemic potential, it says a laboratory-confirmed infection must be reported even when “Evidence of illness is not required.”

That does not mean the 1970s radioactive bands themselves “caused” a later pandemic declaration.

The point is deeper.

The sequence universe had become capable of supplying operational facts about purported viruses without returning to direct observation of the physical entity at every step.

Go Back Outside the Loop

This is the question the finished sequence system makes remarkably easy to forget.

Suppose a new sequence resembles an established coronavirus sequence.

That is evidence inside sequence space.

Suppose reads align to a coronavirus reference.

That is a relationship inside sequence space.

Suppose PCR primers designed from coronavirus sequence information generate the signal the assay’s interpretation rules classify as positive.

Again, sequence-derived information has structured the interrogation.

Suppose another purported genome clusters with existing coronavirus sequences.

That establishes another relationship within the sequence universe.

None of those relationships, simply by multiplying, changes the epistemic character of the system’s entrance point.

So go backward.

Before the reference:

What justified the sequence?

Before the sequence:

What justified the letters?

Before the letters:

What justified their positions?

Before the positions:

What was actually observed?

Eventually you reach the uncomfortable answer supplied by the sequencing pioneers themselves:

“the pattern of radioactive bands.”

And the radioactive material producing those detectable patterns?

The researchers had deliberately put it into the experiment themselves.

Bottom Line

The closed-loop, self-referential coronavirus genetic story that eventually became part of the machinery used for pandemic determinations did not begin with direct observation of the physical entity its sequences purport to represent.

At the foundational sequencing layer, the observational endpoint was vastly smaller:

marks produced by radioactive material researchers intentionally added to their experiments themselves.

To turn those marks into even one purported coronavirus nucleotide at one exact position, you are being asked to accept that

  • the label attached correctly;
  • the intended molecular material was present;
  • the chemistry behaved correctly;
  • the nucleotide preferences held;
  • cleavage occurred as proposed;
  • the resulting products were the intended products;
  • migration represented molecular length;
  • the fragments formed the intended nested family;
  • they shared the required endpoint;
  • their lengths therefore represented successive positions;
  • and their reaction patterns therefore established particular nucleotide identities.

Then you must accept that those calls belong to one continuous underlying sequence.

Then that separately determined sequences overlap as proposed.

Then that the laboratory transformations connecting the sequenced material backward to what researchers called RNA behaved faithfully.

Then that the material ultimately represents the genetics of the entity called coronavirus.

Only after carrying that enormous stack of propositions does:

a mark produced by an added radioactive reporter

become:

“G at position 37 of a coronavirus genetic sequence.”

Then something even more consequential happens.

That inferred sequence becomes established information.

  • Established information can structure subsequent experiments.
  • Those experiments generate more signals.
  • Those signals generate more sequences.
  • Those sequences become larger references.
  • And those references provide the informational world in which later coronavirus sequences can be detected, compared, classified, and interpreted.

So follow the system all the way backward:

pandemic-era genetic determinations

?

reference-based coronavirus genetics

?

larger coronavirus sequences

?

overlapping earlier sequence determinations

?

called nucleotide strings

?

inferred nucleotide identities and positions

?

interpreted fragment lengths

?

marks on film

?

radioactive material researchers deliberately put into the experiment.

That is the epistemic entrance point.

The marks were observed.

The vast purported physical coronavirus genetic reality subsequently made to stand behind them was not contained in those marks.

It had to be inferred.

Then the inferences became sequences.

And the sequences became premises for the story that followed.

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