"It has been determined" that infected dairy herd serology can be disclosed | Hacker News Reader

"It has been determined" that infected dairy herd serology can be disclosed

hogvet51.substack.com

61 pointsctoth39 comments

> In a Breitbart article, USDA Secretary Brooke Rollins blithely assures us that increased biosecurity supported by the Trump Administration will negate the need for vaccines. I have to wonder how that’s going to work out for poultry flocks next to dairy (or feedlot) H5N1 B3.13 or D1.1 outbreaks, especially when she is also taking cattle vaccines off the table in the same conversation? I’ll give Secretary Rollins credit for one thing - she definitely does not hide her intentions in 3rd person language anonymity! She will own these comments!

That'll be something to keep in mind.

"negate the need for vaccines" i guess we should start to buy only imported powdered milk as US milk won't be safe for human consumption anymore. what is wrong with these people, go be corrupt and steal government money but leave this shit alone.

I hear raw milk is good for you.

I hear that too. But I also hear of the occasional death when the unpasteurized milk has a pathogen in it. It's rolling the dice.

You just have to boil it first ;)

> what is wrong with these people

Brain worms, eating road kill, the usual.

you couldn't write a joke with this but here we are. fiction could never predict this reality, its too stupid to be believable.

A few weeks back a friend hit was traveling in a co-worker's car on a freezing cold day and hit a deer and called us. The next day my wife was driving that direction, picked it up and hauled it back to a friend's place where they cut it up. It's in our fridge right now.

Worth noting that Rollins is the same USDA Secretary who advocated for Americans to keep chickens in their yards to counter rising egg prices. Besides that not making financial sense, it also creates even more vectors for H5N1 to spread.

The fact that indicators of decision-making have to be indirect, speaks to the risk environment of public health officials. Post Fauci, it's huge.

Is this problem also a function of both devolution of power to states and the environment post animal activism? Or just the "don't ask don't tell" of US policy these days? A bunch of laws got passed about revealing inner truths of animal husbandry in the wake of activist filming in chicken houses and piggeries.

We depend on the massive herds of food animals. We depend on clear information sharing about their health. They aren't just tasty beef and cheese, they are disease vectors and storage grounds of infection. This information policy nightmare isn't good.

> Post Fauci, it's huge.

How is Anthony Fauci related to this? He headed the NIAID, not the USDA.

Are you really going to try to say that the absurd levels of bile, vitriol, and threats that he received for doing his job during a pandemic has zero knock-on effect for other public health officials?

Woah, I'm not sure how you got that from my comment. It was a genuine question since OP made it seem as if Dr. Fauci had played some role in the USDA's handling of the H5N1 epidemic. In fact I was concerned OP was trying to pin yet another conspiracy on him.

I remember in 2020 how a career public servant, colleague to those in USDA, was contradicted by the president because it made the administration's COVID response look bad.

Recently, the US president has decided he doesn't want to protect his public servant's lives anymore https://apnews.com/article/fauci-trump-security-detail-4b2e3...

As others note, its the public health aspect of being a voice for science and reason, against the political backlash and death threats. I did not mean to imply USDA and NIAD related, except in needing public health policy people making decisions and statements in the public eye.

On a related note, "Trump ends Fauci’s security detail and says he’d feel no responsibility if harm befell him": https://apnews.com/article/fauci-trump-security-detail-4b2e3...

> “You can’t have a security detail for the rest of your life because you worked for government,” Trump said.

Coming from the guy who will have security detail for the rest of his life because he worked for the government. Truly comical time to be alive

This isn't my field but I always feel it's disingenuous to show PCR results without telling me how many cycles of PCR you did. PCR is effectively a magnifying glass and you're obscuring the level of magnification you used to get a detection. It doesn't seem, on it's own, to ever be a useful piece of information.

For a diagnostic application, the cycle count doesn't really matter. Either the DNA your primers are targeting is present or it is not. That's why they talk about a "positive" or "negative" PCR test -- the presence or absense of the viral DNA is a binary.

For diagnostic use like this, the standard is 30±10 cycles, but it doesn't really matter if it's ten or a hundred, since all you're really doing is verifying the presence of the target genome.

Is a robust citation each available for each of those related claims?

I'm not looking for dogmatic assertions, I mean the fundamental and reproducible papers proving those claims.

Because those are all in direct opposition with the parent. And two views of an issue will not be resolved by each claiming opposite dogma.

Hopefully someone can present the evidence. A textbook citation is not enough. Are there really controlled experiments showing these things? Or is it mostly theoretical? Is it time to ask what we know--are these "facts we have been taught", or have we looked into the scientific validity of the proofs with the criticality of a practicing scientist?

I think that very solid citations here would actually go a long way to inform the parent, but I doubt that anything short of that would do so.

I do not have the time or the inclination to perform a comprehensive literature review for the benefit of a web forum. The body of work in this area is massive, well understood, and public. You can replicate results in any university microbiology course. Thousands of students do these things every day. You can even construct your own PCR setup from a cd rom drive and parts and do it at home. Reagents and primers are available on the open market.

If, given all that, the difference between acceptance and rejection is some links in a forum post, there wasn't really any interest in the truth to start with.

> is present or it is not.

Yes. And don't you use a /threshold/ mechanism to detect presence? Or you have tests so sensitive that a /single/ molecule or equivalent will deliver a reliably positive signal? I mean if it's that good why are you even doing PCR amplification in the first place?

> the standard is 30±10 cycles

The difference between 2^30 and 2^40 is massive.

Yes, if the DNA target is present, it will be replicated. If it is not, it will not. The point is to see whether that happens (positive result) or not (negative result). If, after PCR, there is a shitload of viral DNA in your assay, you know the virus was present in the sample. You compare assays between pre and post PCR samples to determine this.

The difference between a shitload and a bigger shitload reflects cycle count but not the nature of the result.

PCR is a basic tool. It amplifies, much like your car stereo. If you can hear music when tuning in an AM station, you don’t question the automatic gain correction the stereo is doing internally. PCR is the same way. If the target is present, it is detectable. If it isn’t then it isn’t. There are so many variables at play that the number of cycles isn’t very meaningful.

Kary Mullis, inventor of PCR does not agree with your analogy.

He also

* believed in astrology

* denied Avogadro’s number (???)

* practiced telepathy

* didn’t believe in HIV causing AIDs

* didn’t believe in climate change

* didn’t believe in the ozone hole

While he certainly had incredible intelligence, clearly him believing something isn’t a hugely convincing reasoning.

disclaimer: i am a person who believes in Avogadro’s number and not astrology. truly an intellectual outcast and rebel

he didn't deny avogadro's number so much as say that its definition was somewhat arbitrary.

IIRC he made the comment before the modern redefinition of SI units. See https://en.wikipedia.org/wiki/2019_revision_of_the_SI#Mass_a... for more details about the ongoing issues associated with absolute numeric counts of elements and their association with mass.

this is useful context, thanks. would edit my prior comment but it is no longer editable. after some more research it seems his comments on the matter were reasonable

Can you expand on this? What does he not agree with?

Is sample contamination more impactful (likely to lead to a false positive) at 100 or 200 cycles than at 20? I remember some distrust of high PCR cycle counts during COVID but I never quite understood the fear.

If there is contamination with the target sequence then it will be found by the PCR analysis. I don’t know the practical limits of sensitivity but theoretically it can detect a single occurrence of the target sequence.

With enough cycles, dead virus you're successfully fighting off can be detected. It doesn't need contamination. For what it was used for, those were false positives that inflated the counts.

You run PCR for cycles. You run it for 32 cycles? You've got a 4 billion times multiplication of the input signal. You see the problem? "Detectable" isn't a single ended specification with "PCR." You really do need to disclose how many cycles you ran.

Similarly there's ionizing radiation in your home. Right now. Flowing through you. If it's not above the background it's not interesting or material. So just saying "we found radiation" is equally meaningless unless you tell me that level in relation to something.

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