Covid-19 vaccines and treatments: we must have raw data, now • Hacker News Board

Re: Covid-19 vaccines and treatments: we must have raw data, now

#221

Post by guywhocodes » Fri, Jan 21, 2022, 5:15 AM UTC

rsfern wrote: post #208

guywhocodes wrote: post #187

Earlier quoted context omitted.

But we have a similar noise in COVID death and injury as we have incentivized hospitals to register everything and everyone as COVID related. And I believe we all know just about any PCR test can be made positive if you use enough cycles. Sorry but I can't distrust VAERS and then trust the COVID injection complication data added by the same people but now with financial incentives.

You shouldn’t distrust VAERS per se, but it’s purpose is not risk assessment. It’s purpose is surfacing rare side effects for further study. You don’t have to trust the drug co’s for that, we also have vaccine safety datalink system; so far the only notable side effect of the mRNA vaccines has been the myocarditis in younger people. https://pubmed.ncbi.nlm.nih.gov/34477809/ Also your point about PCR testing is not ac…

> Also your point about PCR testing is not accurate.

Source on that? Because all graphs I've seen show impossible to miss fluorescence around 35 cycles and up.

AFAICT VSD only does specific research at their own behest and currently don't have a section on COVID-19 vaccines.

Btw your link is dead.

I had pericarditis and some immediate reaction, my cardiologist thinks it was partially intravenously applied. Looking at the data on severe reactions from where I live I've been able to obviously tell that CDC must have used incredible criteria for their numbers. At least initially, I stopped caring when it eventually became clear to me that we do not really want to know how many are harmed.

And from the perspective of everyone involved I understand it, I too want this to be over, I too want this to be a safe magic bullet. But seems to me somewhere between 1:1000-10000 have significant heart issues from the Pfizer vaccine, but when we were rolling it out the numbers were claimed to be 1 in 230M.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#222

Post by guywhocodes » Fri, Jan 21, 2022, 5:24 AM UTC

leppr wrote: post #205

nsainsbury wrote: post #82

Earlier quoted context omitted.

Actually, I would argue we don't have good data from the use of the vaccines. Part of the reason is because all the mechanisms used for reporting things like side-effects, effectiveness, etc. have a litany of confounding variables which haven't been controlled for which could be far better corrected for/isolated with good studies. For example, when it comes to vaccine side-effects, I don't think there exists a true a…

> I had this happen to me - started experiencing severe chest pain 2 days post-Pfizer. Subsequently saw a cardiologist after months of pain and his comment to me was "I'm seeing young people like you daily and your cases are going widely underreported" Orthogonal to the original conversation but have your cardiologist consultations yielded anything? I also have chest pain for now more than 2 months after the second d…

For me it took 6 months before the pain was reduced to "infrequent", I'm back to exercising almost to the full extent now as I was in July.

I received a diagnosis of pericarditis and had persistent tachycardia, mildest strain and my heart rate would shoot to 170 BPM not going below 85 while lying down. Now I'm back to normal and my resting heart rate is now 50-55 BPM.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#223

Post by rvnx » Fri, Jan 21, 2022, 5:51 AM UTC

geoduck14 wrote: post #217

rsfern wrote: post #203

Earlier quoted context omitted.

I don’t think they are allowed to ask those questions. They certainly aren’t allowed to discriminate in hiring or employment based on disabilities https://www.eeoc.gov/laws/guidance/your-employment-rights-in...

>I don’t think they are allowed to ask those questions They are DEFINITELY not allowed to ask.

for example, from a startup interview process: Calico, subsidiary of Alphabet: https://www.calicolabs.com/careers?gh_jid=5785761002

> "We are required to measure our progress toward having at least 7% of our workforce be individuals with disabilities. To do this, we must ask applicants and employees if they have a disability or have ever had a disability. Because a person may become disabled at any time, we ask all of our employees to update their information at least every five years.

Identifying yourself as an individual with a disability is voluntary, and we hope that you will choose to do so."

Re: Covid-19 vaccines and treatments: we must have raw data, now

#224

Post by throwawaygh » Fri, Jan 21, 2022, 6:07 AM UTC

nextos wrote: post #189

throwawaygh wrote: post #163

Earlier quoted context omitted.

> This is already a solved problem... raw data is made accessible only through an ethics committee. Summary counts from transcriptomes are publicly available, though. Right. 1. I'm not sure you understand the extreme position being taken by rvnx in this thread. 2. Presumably the patients agreed that their transcriptome data could be shared in this way, and you didn't change your data handling post-facto without their…

Of course patients need to agree. It's actually even simpler. When you recruit patients into a study they sign an agreement that is broad and usually includes data sharing terms. Properly anonymized, of course. Said agreements have previously gone through ethics committees which tend to be extremely strict. They are rarely changed afterwards, since this requires agreement of patients, which is impractical to obtain i…

I think we are in violent agreement on substance.

Your comment is somehow relevant to the article and insightful wrt the topic but also off-topic in this thread.

The type data you are suggesting should be shared -- and, more importantly, the consent assumptions -- are not related to the current discussion.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#225

Post by throwawaygh » Fri, Jan 21, 2022, 6:10 AM UTC

ceejayoz wrote: post #202

rvnx wrote: post #200

Earlier quoted context omitted.

Yeah, useful selectors for researchers, and still no identity. We learnt that somewhere there is a man/woman that is depressed and has weight management issue. We can take policy actions in order to improve the situation and monitor how this affects life of people (e.g. how much antidepressants are used in a year, are the food policies effective, what conditions are often linked to sudden cardiac arrest, etc). And "R…

No, you’re missing the point. Asking people in the study if it’s OK to release their data means the resulting data set is skewed. People with certain conditions and other variables will be more or less likely to agree, leaving a non-representative sample of the actual study. It will no longer be random.

Exactly.

Actually, set aside consent entirely.

The problem is NOT "how do we de-anonymize". That is super easy.

The problem is "how do we de-anonymize IN A WAY THAT LEAVES RESULTS OF RELEVANT STATISTICAL TESTS INVARIANT". Much harder. Remove a bunch of probably non-random points and make any logisitic regression on that dataset return the same result within some delta. There are trivial impossibility theorems. Really, really trivial. "Left as freshman exercise and if you can't some up with an example maybe step back and stop talking about this topic" trivial.

Now, add back consent. "how do we delete a subset of data that is likely not uniformly distributed with respect to risk variables and also de-anonymize the remaining subset of data.... AGAIN, IN A WAY THAT LEAVES RESULTS OF RELEVANT STATISTICAL TESTS INVARIANT". The position is untenable.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#226

Post by throwawaygh » Fri, Jan 21, 2022, 6:21 AM UTC

cogman10 wrote: post #131

throwawaygh wrote: post #114

Earlier quoted context omitted.

> So tell me, what harm have I done to myself by sharing this information? None, and yet you still aren't willing to put your name behind the statement "I'm healthy as a fiddle and never use drugs except the occasional beer". Also -- and this will apparently come as a surprise to you -- people who have STDs, abuse drugs/alcohol, or have genetic disorders in their family don't necessarily want that info shared on the…

Frankly, putting up my name with my medical history has far less to do with having the two linked and far more to do with "I'd rather not have a future employer have an easy link to my social media information". Oh genetic disorders, you didn't ask about that earlier. My family is a carrier for cystic fibrosis. Is that something that's supposed to be super terrible to share? I'm not the GP, but frankly I think it's a…

> "I'd rather not have a future employer have an easy link to my social media information"

So, to be clear, your right to post random ass thoughts on the internet under a pseudonym is sacred... but it's totally reasonable to RENEGE on EXISTING privacy agreements with real world actual existing real human patients about intimate health records?

Just so long as we're clear about the enormous esteem you hold yourself in and the absolute contempt you have for others' privacy...

Re: Covid-19 vaccines and treatments: we must have raw data, now

#227

Post by epgui » Fri, Jan 21, 2022, 6:24 AM UTC

srcreigh wrote: post #196

epgui wrote: post #173

Earlier quoted context omitted.

I'm a biochemist, and I'm as pro-vaccine as they come. The BMJ is a highly reputable journal. It's unfortunate that the anti-vaxx idiots are misinterpreting or decontextualizing their content, but that's the anti-vaxx's fault and it's what they've always done.

Would it be so hard to state the limitations of their investigation, and clearly explain that a few key misconceptions are incorrect? Based on their original censored article, it seems like they're heavily invested to make things seem problematic, and carefully avoid any indication that the status quo is acceptable. I don't think it's purely misinterpretation when anti vax people become generally skeptical of govt an…

They were not putting into question the safety of vaccines, that issue was tangential. I know the article has the literal words "patient safety" and raises potential safety concerns, but that all has to be read in full context: advocating for better data controls and better rigour in research.

It might seem obvious to you that the article would be misinterpreted or parts of it taken out of context by a lay public, but scientific publications are meant to be read mainly by other scientists, and this paper was written with that specific public in mind.

Even if this was intended as official public health communication, which it wasn't, public health communication is an absolute nightmare of a minefield. There's absolutely nothing you can ever say that won't be misinterpreted or misunderstood by some people, and the game is all about minimizing the potential for that. It's easier said than done. (And again, this paper was meant to be shared among expert colleagues in the field.)

Re: Covid-19 vaccines and treatments: we must have raw data, now

#228

Post by throwawaygh » Fri, Jan 21, 2022, 6:25 AM UTC

rvnx wrote: post #223

geoduck14 wrote: post #217

Earlier quoted context omitted.

>I don’t think they are allowed to ask those questions They are DEFINITELY not allowed to ask.

for example, from a startup interview process: Calico, subsidiary of Alphabet: https://www.calicolabs.com/careers?gh_jid=5785761002 > "We are required to measure our progress toward having at least 7% of our workforce be individuals with disabilities. To do this, we must ask applicants and employees if they have a disability or have ever had a disability. Because a person may become disabled at any time, we ask all o…

That wording is literally from a US Department of Labor form: https://www.dol.gov/sites/dolgov/files/OFCCP/regs/compliance...

Just stop. This is embarrassing.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#229

Post by throwawaygh » Fri, Jan 21, 2022, 6:32 AM UTC

nextos wrote: post #210

wombatpm wrote: post #198

Earlier quoted context omitted.

A broad agreement will most likely NOT make it past the institution review board. Any experiment with human subjects has strict rules around consent and data sharing agreements. The legal exposure is huge.

Broad meaning sequencing data (e.g. RNA) from tissues will be made available in public repositories, and accessible via application to committee. I have had helped draft at least 6 studies with materials coming from our own clinical trials and deposited all data myself. Went through institution review boards without an issue, just like many other equivalent studies. Perhaps your experience is different because of loc…

> Perhaps your experience is different because of location?

AFAIK this is also possible in the US. Probably more hoops to jump through? I don't know anything about the EU. (But also this discussion is basically totally unrelated to the original article or this thread.)

Re: Covid-19 vaccines and treatments: we must have raw data, now

#230

Post by andreskytt » Fri, Jan 21, 2022, 6:32 AM UTC

nradov wrote: post #141

invokestatic wrote: post #59

I’m a software consultant for Pharma companies and have worked on projects that used the same kind of study design as the Pfizer COVID vaccine (Kaplan-Meier). “Raw data” is submitted to the FDA in the CDISC format. This format contains a lot of pretty sensitive medical information, including which diseases a patient has, their medical history, what drugs they take, etc. This is supposed to be anonymized, but if the p…

What is the specific basis for your belief that patient re-identification is possible? The federal government has provided clear guidance on de-identification which should eliminate that as a serious concern. https://www.hhs.gov/hipaa/for-professionals/privacy/special-...

MIT researchers have been able to assign cafeteria bills to individuals with 80% probability. With any identification information as well as timestamps removed. Correlating datasets gets pretty powerful pretty fast. Also, if the data is made public, we are basically betting, that it is not possible to deanonymize in the future. Given the rate of technological development, I’d be very reluctant to make that bet.