6 ms·

The Far-Reaching Ripple Effects of a Discredited Cancer Study

51 points by voisin 2y ago

andyjohnson0 2y ago
This seems to be the same article, but not paywalled: https://www.msn.com/en-us/health/other/the-far-reaching-ripple-effects-of-a-debunked-cancer-study/ar-AA1pHQ5J https://www.msn.com/en-us/health/other/the-far-reaching-ripp...
fedeb95 2y ago
society will be better when research gets the automation it deserves.
- BiteCode_dev 2y ago
  That wold require automating reproductibility or requestin and analysing datasets that are not provided.
  - fedeb95 2y ago
    1) they could in theory be provided 2) not necessarily: it's a matter of authority, that when ceases to exist, it ripples Edit: to an extent it applies to journalism. Nowadays, at best, you have citations that turn out to be fake and seldom who cites them gets updated
  - more_corn 2y ago
    Sounds like a plan. I think the ERROR project is doing exactly that. https://www.nature.com/articles/d41586-024-02681-2 https://www.nature.com/articles/d41586-024-02681-2 (posted here two days ago)
- contagiousflow 2y ago
  What tasks being automated will make research more epistemologically sound?
  - fedeb95 2y ago
    mainly, if a study turns out to be flawed, other studies based on it could be "revoked" automatically.
- arnaudsm 2y ago
  Depends how we implement it. We could make bad science way faster. ChatGPT paper spam is already a thing, and their authors don't care about quality
some_random 2y ago
The sciences are long overdue for a epistemological reckoning.
borgchick 2y ago
"surprise" of the day: scientists can also be greedy for money and fame
- more_corn 2y ago
  I’d look for a more complicated and nuanced explanation than that. Maybe, there are perverse incentives in scientific publishing (ever heard of publish or perish?), and insufficient checks and balances, and it’s hard to do the right thing and easy to do the wrong thing. The more nuanced explanation gives you more traction for incremental improvement. One historically easy way to get people to do the right thing is to make the right thing easier. People used to dump their used motor oil in the nearest stream. Now every auto shop is required to accept used motor oil and recycle it. Doing the right thing is so easy that you’d have to be crazy to do the wrong thing.
idunnoman1222 2y ago
What far-reaching ripple effect? some grifters grifted and got found out and some investors lost their money. This is not far reaching. I guess the guy writing the headline is a grifter too go figure
- ProjectArcturis 2y ago
  600 other papers cited it. Hundreds of other labs, professors, postdocs, and grad students had failed projects based on extending the research. Undoubtedly many of those people had their careers end in this hypercompetitive space due to this one paper.
  - idunnoman1222 2y ago
    Heres something that actually qualifies People trying to reproduce wild claims is just science https://www.vox.com/future-perfect/368350/scientific-research-fraud-crime-jail-time https://www.vox.com/future-perfect/368350/scientific-researc...
- fasa99 2y ago
  The impact didn't destroy society or anything, it damaged the field. It made people think "wow that's interesting, tumors have unique microbiomes". the article says: Meanwhile, research groups that, according to Salzberg, relied on the study’s data are dealing with the fallout, as are the journals that published the work. The publishers or journal editors of eight studies have begun reviewing the papers, according to spokespeople at Springer Nature, Frontiers, Wiley and the American Association for Cancer Research. The corresponding authors of these studies didn’t respond to requests for comment. Looking at the analysis critique, yes, the original paper had an awful analysis. It smacks of a wet lab or clinical administrator who knows nothing about bioinformatics, having work done by say a grad student who themselves are not experienced in the field but clever enough to stitch together a nice sounding pipeline and write a Nature paper about it, and perhaps a bit cocky. This, I have seen before first hand. The long and short of it is, they used a big database of all bacteria genomes, and guess what, if a human grinds in a wet lab sequencing a bacteria genome, sometimes a bit of human DNA slips into the bacteria genome assembly, particularly if this was done some 50,000 times for 50,000 bacteria. So their analysis made no consideration to removing alignments to the human (or any other contaminant) genomes. So maybe their system says "aha! this bacteria is Staph Aureus!" but actually the Staph Aureus sequence has a fragment of human genome because the sequencing project therein had light contamination. It's absolutely self evident that if they were sequencing bacteria DNA off tumors, they should have controlled for human DNA contamination, given that the tumor the bacteria is sitting on, that tumor has a lot of human DNA.
WarOnPrivacy 2y ago
Under-addressing bad behavior within trusted communities never stops biting us. The most pervasive human condition I know is: No one anywhere wants to clean their own house. I can't think of a life-bettering system that doesn't fall victim to it.

51 points by voisin 2y ago

This seems to be the same article, but not paywalled: https://www.msn.com/en-us/health/other/the-far-reaching-ripple-effects-of-a-debunked-cancer-study/ar-AA1pHQ5J https://www.msn.com/en-us/health/other/the-far-reaching-ripp...

fedeb95 2y ago

society will be better when research gets the automation it deserves.

BiteCode_dev 2y ago
That wold require automating reproductibility or requestin and analysing datasets that are not provided.
- fedeb95 2y ago
  1) they could in theory be provided 2) not necessarily: it's a matter of authority, that when ceases to exist, it ripples Edit: to an extent it applies to journalism. Nowadays, at best, you have citations that turn out to be fake and seldom who cites them gets updated
- more_corn 2y ago
  Sounds like a plan. I think the ERROR project is doing exactly that. https://www.nature.com/articles/d41586-024-02681-2 https://www.nature.com/articles/d41586-024-02681-2 (posted here two days ago)
contagiousflow 2y ago
What tasks being automated will make research more epistemologically sound?
- fedeb95 2y ago
  mainly, if a study turns out to be flawed, other studies based on it could be "revoked" automatically.
arnaudsm 2y ago
Depends how we implement it. We could make bad science way faster. ChatGPT paper spam is already a thing, and their authors don't care about quality

some_random 2y ago

The sciences are long overdue for a epistemological reckoning.

borgchick 2y ago

"surprise" of the day: scientists can also be greedy for money and fame

more_corn 2y ago
I’d look for a more complicated and nuanced explanation than that. Maybe, there are perverse incentives in scientific publishing (ever heard of publish or perish?), and insufficient checks and balances, and it’s hard to do the right thing and easy to do the wrong thing. The more nuanced explanation gives you more traction for incremental improvement. One historically easy way to get people to do the right thing is to make the right thing easier. People used to dump their used motor oil in the nearest stream. Now every auto shop is required to accept used motor oil and recycle it. Doing the right thing is so easy that you’d have to be crazy to do the wrong thing.

idunnoman1222 2y ago

What far-reaching ripple effect? some grifters grifted and got found out and some investors lost their money. This is not far reaching. I guess the guy writing the headline is a grifter too go figure

ProjectArcturis 2y ago
600 other papers cited it. Hundreds of other labs, professors, postdocs, and grad students had failed projects based on extending the research. Undoubtedly many of those people had their careers end in this hypercompetitive space due to this one paper.
- idunnoman1222 2y ago
  Heres something that actually qualifies People trying to reproduce wild claims is just science https://www.vox.com/future-perfect/368350/scientific-research-fraud-crime-jail-time https://www.vox.com/future-perfect/368350/scientific-researc...
fasa99 2y ago
The impact didn't destroy society or anything, it damaged the field. It made people think "wow that's interesting, tumors have unique microbiomes". the article says: Meanwhile, research groups that, according to Salzberg, relied on the study’s data are dealing with the fallout, as are the journals that published the work. The publishers or journal editors of eight studies have begun reviewing the papers, according to spokespeople at Springer Nature, Frontiers, Wiley and the American Association for Cancer Research. The corresponding authors of these studies didn’t respond to requests for comment. Looking at the analysis critique, yes, the original paper had an awful analysis. It smacks of a wet lab or clinical administrator who knows nothing about bioinformatics, having work done by say a grad student who themselves are not experienced in the field but clever enough to stitch together a nice sounding pipeline and write a Nature paper about it, and perhaps a bit cocky. This, I have seen before first hand. The long and short of it is, they used a big database of all bacteria genomes, and guess what, if a human grinds in a wet lab sequencing a bacteria genome, sometimes a bit of human DNA slips into the bacteria genome assembly, particularly if this was done some 50,000 times for 50,000 bacteria. So their analysis made no consideration to removing alignments to the human (or any other contaminant) genomes. So maybe their system says "aha! this bacteria is Staph Aureus!" but actually the Staph Aureus sequence has a fragment of human genome because the sequencing project therein had light contamination. It's absolutely self evident that if they were sequencing bacteria DNA off tumors, they should have controlled for human DNA contamination, given that the tumor the bacteria is sitting on, that tumor has a lot of human DNA.

WarOnPrivacy 2y ago

Under-addressing bad behavior within trusted communities never stops biting us. The most pervasive human condition I know is: No one anywhere wants to clean their own house. I can't think of a life-bettering system that doesn't fall victim to it.