[HN Gopher] Comment on 2015 mRNA paper suggests data re-used in ...
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Comment on 2015 mRNA paper suggests data re-used in different
contexts
Author : picture
Score : 131 points
Date : 2025-01-16 17:24 UTC (5 hours ago)
(HTM) web link (pubpeer.com)
(TXT) w3m dump (pubpeer.com)
| owlninja wrote:
| I guess I'll bite - what am I looking at here?
| IshKebab wrote:
| Faked scientific results.
| sergiotapia wrote:
| what happens to people who do this? are they shunned forever
| from scientific endeavors? isn't this the ultimate betrayal
| of what a scientist is supposed to do?
| Palomides wrote:
| if caught and it's unignorable, usually they say "oops, we
| made a minor unintentional mistake while preparing the data
| for publication, but the conclusion is still totally valid"
|
| generally, no consequences
| dylan604 wrote:
| There's a difference of having your results on your black
| plastic cookware being off by several factors in an
| "innocent" math mistake vs deliberately reusing results
| to fraudulently mislead people by faking the data.
|
| Most people only remember the initial publication and the
| noise it makes. The updated/retractions generally are not
| remembered resulting in the same "generally, no
| consequences" but the details matter
| gus_massa wrote:
| The people in the area remember (probably because they
| wasted 3 months trying to extend/reproduce the result
| [1]). They may stop citing them.
|
| In my area we have a few research groups that are very
| trustworthy and it's safe to try to combine their result
| with one of our ideas to get a new result. Other groups
| have a mixed history of dubious results, they don't lie
| but they cherry pick too much, so their result may not be
| generalizable to use as a foundation for our research.
|
| [1] Exact reproduction are difficult to publish, but if
| you reproduce a result and make a twist, it may be good
| enough to be published.
| the__alchemist wrote:
| An (agarose?) gel.
|
| There are partial holes in at at one end. You insert a small
| amount of dyed DNA (etc) containing solution each. Apply an
| electrical potential across the gel. DNA gradually moves along.
| Smaller DNA fragments move faster. So, at a given time, you can
| coarsely measure fragment size of a given sample. Your absolute
| scale is given by "standards", aka "ladders" that have samples
| of multiple, known sizes.
|
| The paper authors cheated (allegedly) by copy + pasting images
| of the gel. This is what was caught, so it implies they may
| have made up some or all results in this and other papers.
| hummuscience wrote:
| This is protein on a western blot but the general idea is the
| same.
| shpongled wrote:
| Close - this is a SDS-PAGE gel, and you run it using
| proteins. The bands in the first two rows are from a western
| blot (gel is transferred to a membrane), where you use
| antibodies against those specific proteins to detect them.
| The Pon S row is Ponceau S, a dye that non-specifically
| detects all proteins - so it's used as a loading control, to
| make sure that the same amount of total protein is loaded in
| each lane of the gel.
| doctorpangloss wrote:
| Is it conceivable that the control was run once because the
| key result came from the same run? I can see a reviewer
| asking for it in all three figures, whereas they may
| drafted it only in one
| gus_massa wrote:
| The horizontal label is fine, it says Pon S in all
| images. (I guess a wrong label would be obvious to detect
| for specialists.)
|
| The problem are the vertical labels
|
| In Figure 1e it says: "MT1+2", "MT2" and "MT1"
|
| In Figure 3a it says: "5'-CR1", "CR2" and "3'-UTR"
|
| In Figure 3b it says: "CR2", "CR3" and "CR4"
| shpongled wrote:
| Based on the images, it is inconceivable that these are
| from the same run (see the dramatically different levels
| of TRF-S in each gel. One column/lane = one sample). This
| isn't something that would be included because of a
| reviewer - loading controls are required to meaningfully
| interpret the results (e.g. the data is useless without
| such a control).
| owlninja wrote:
| I love HN - thanks!
| NotAnOtter wrote:
| Additional context to be speculative of OP's intentions.
| Within the academic world there was a major scandal where a
| semi-famous researcher was exposed for faking decades of data
| (Google: Pruitt). Every since, people have been hungry for
| more drama of the same shape.
| f1shy wrote:
| This guy made some videos about it
|
| https://m.youtube.com/@PeteJudo1/videos
| barbazoo wrote:
| Would this imply that someone faked data in a paper they
| published?
| UltraSane wrote:
| Hard to explain how else it could happen.
| boogieknite wrote:
| any reason hanlons razor doesnt apply here? honest question,
| im just a regular 4 year degree off to work guy
| the__alchemist wrote:
| There are perverse incentives in scientific publishing, and
| there are not many alternative explanations.
| Lammy wrote:
| So sick of Hanlon's Razor. It's just a gift to the
| actually-malicious. If the outcome is the same then
| intentions don't matter.
| marxisttemp wrote:
| IMO it's only applicable to humans. Hierarchies attract
| malicious actors.
| JadeNB wrote:
| > So sick of Hanlon's Razor. It's just a gift to the
| actually-malicious. If the outcome is the same then
| intentions don't matter.
|
| I think that's only true for a single incident. If
| someone does injury to me, I'm just as injured whether
| they were malicious or incompetent, but mitigation
| strategies for future interactions are different.
| dec0dedab0de wrote:
| I consider it a reminder to stop and think before getting
| swept up in outrage.
|
| Sure, bad actors will maintain plausible deniability, but
| I would rather let some people slide than get worked up
| over mistakes or misunderstandings.
| Lammy wrote:
| Letting the people slide is not the same thing as letting
| the action/outcome slide. I do think it's reasonable to
| let intent inform one's feelings toward the person, but
| if it's easy to accidentally do fraudulent science then
| the system should still be criticized and the systemic
| problem should still be addressed.
| readthenotes1 wrote:
| Here's how the razor applies: There is no real malice
| behind all the fraud in science publications. The authors
| aren't usually out to specifically harm others.
|
| However, in the long run it is stupid because of two and a
| half reasons:
|
| - it reduces people's trust in science because it is
| obvious we cannot trust the scientists which in the long
| run will reduce public funding for The grift
|
| - it causes misallocation of funds by people misled by the
| grift and this may lead you actual harm (e.g., what if you
| catch Alzheimer's but there is no cure because you lied
| about the causes 20 years ago?)
|
| 1/2- there is a chance that you will get caught, and like
| the former president of Stanford, not be allowed to
| continue bilking the gullible. This only gets half a point
| because the repercussions are generally not immediate and
| definitely not devastating to those who do it skillfully.
| selimthegrim wrote:
| The former president of Stanford is the CEO of Xaira now.
| o11c wrote:
| "Adequately" is doing a lot of heavy lifting in Hanlon's
| Razor. A good corollary to keep in mind is "Never attribute
| to stupidity what is better explained by malice." I usually
| apply this to politics, but science publishing is 90%
| politics, so it still fits.
| asddubs wrote:
| Yeah, I have mixed feelings about hanlons razor. Giving
| people the benefit of the doubt is good, and some people
| don't do it enough, but there's also a lot of people that
| overextend the benefit of the doubt to the point that
| they're almost doing damage control for fraudsters
| emeraldd wrote:
| Could this be a repeat of the Xerox image duplication bug?
| https://www.dkriesel.com/en/blog/2013/0802_xerox-
| workcentres...
| jldugger wrote:
| In different documents?
| doodda wrote:
| Here's me, clicking and expecting to read about someone fleecing
| Spotify by setting up fake bands.
| philipwhiuk wrote:
| Whereas actually Spotify funds artificial bands because they're
| more profitable
|
| https://harpers.org/archive/2025/01/the-ghosts-in-the-machin...
| dylan604 wrote:
| The news here is that modern pop music has become so same
| same that people can't tell an "AI" generated music from real
| music.
| imzadi wrote:
| tbf, I don't think any of these are pop songs. It's ambient
| music and lofi chill stuff.
| dr_dshiv wrote:
| Is there an obvious way to tell that these are exactly the same?
| Or is this a pixel level comparison that is not mentioned?
| jldugger wrote:
| Look at the "scratch" on the right end of the leftmost dash.
| That "noise" shouldn't be replicated, right?
| Lammy wrote:
| Try looking at the artifacts, not the actual bands. There's a
| little black hairline on the top right corner of the leftmost
| band, and a similar line toward the left of the middle band.
| tom_ wrote:
| Ironically there was a whole post about basically exactly this
| the other day: https://news.ycombinator.com/item?id=42655870
| striking wrote:
| There's a video that's quite convincing:
| https://youtu.be/K0Xio5yo_x8
|
| It inverts the second image and passes the first and third
| images under it, and when there is a complete overlap the
| combined images make a nearly perfectly gray rectangle, showing
| that they cancel out.
| barbazoo wrote:
| The page has another comment with an animation where they're
| overlaying the images to show how similar (same?) they are.
| colechristensen wrote:
| Any image manipulation program like photoshop with layers, you
| put the suspect images on top of one another and use filters to
| subtract one layer from the other (I'm not sure which filter
| operation works best, it might be multiply or divide) and then
| work to align the two layers. Differences and similarities
| become extremely obvious.
|
| You can also get the raw pixel information by converting to a
| bitmap and comparing values, but it's easier visually because
| it's pretty trivial for a simple image modification to change
| all of the pixel values but still have the same image.
| munificent wrote:
| The linked video makes it pretty clear by subtracting one image
| from the other and showing the difference:
| https://www.youtube.com/watch?v=K0Xio5yo_x8
| philipwhiuk wrote:
| Can someone change the title to:
|
| "Comment on Nature paper on 2015 mRNA paper suggests data re-used
| in different contexts"
|
| The current title would suggest music to most lay-people.
| tones411 wrote:
| Agreed
| kylebenzle wrote:
| Disagreed. Title is fine.
| hinkley wrote:
| "We are no longer called Sonic Death Monkey. We are on the
| verge of being called Kathleen Turner Overdrive, however this
| evening we will be Barry Jive, and the Uptown Five."
| ActionHank wrote:
| As someone clueless about music and mRNA I've got to say this
| wouldn't help me much.
| fabian2k wrote:
| Even for people familiar with the field this title is a bit
| hard to parse at first without context. "bands" really needs
| either gels or gel electrophoresis as context.
| dang wrote:
| Ok, we've changed it. Submitted title was "Same three bands
| appear in three different presentations with different labels".
|
| picture (the submitter) had the right idea--it's often better
| to take a subtitle or a representative sentence from the
| article when an original title isn't suitable for whatever
| reason, but since in this case it's ambiguous, we can change
| it.
|
| If there's a better phrase from the article itself, we can
| change it again.
| Kye wrote:
| >> _" Same three bands appear in three different
| presentations with different labels"_
|
| This has the makings of a Highlander episode. Three groups of
| immortals forming bands in different generations.
| philipwhiuk wrote:
| Thanks :)
| lxe wrote:
| Not just same bands, but same noise and artifacts too. They
| copypasted the data?
| smusamashah wrote:
| They have a playlist of 3500 videos showing images like this one
|
| https://youtube.com/playlist?list=PLlXXK20HE_dV8rBa2h-8P9d-0...
| k2enemy wrote:
| I was curious how the video creators were able to generate so
| many videos in such a short timeframe. It looks like it might
| be automated with this tech:
| https://rivervalley.io/products/research-integrity
| jvanderbot wrote:
| A desperate need for automated experiment verification and
| auditing is needed. Something as simple as submitting exif +
| archiving at time of capture, for crying out loud.
|
| A imgur for scientific photos with hash-based search or
| something. We have the technology for this.
| w10-1 wrote:
| The opportunity here is to automate detection of fake data used
| in papers.
|
| I could be hard to do without access to data and costly
| integration. And like shorting, the difficulty is how to
| monetize. It could also be easy to game. Still...
|
| The nice thing about the business is that market (publishing) is
| flourishing. Not sure about state of the art or availability of
| such services.
|
| For sales: run it on recent publications, and quietly ping the
| editors with findings and a reasonable price.
|
| Unclear though whether to brand in a user-visible way (i.e.,
| where the journal would report to readers that you validate their
| stuff). It could drive uptake, but a glaring false negative would
| be a risk.
|
| Structurally, perhaps should be a non-profit (which of course can
| accumulate profits at will). Does YC do deals without ownership,
| e.g., with profit-sharing agreements?
| captn3m0 wrote:
| Elizabeth Bik (who is known for submitting such reports to
| journals) has a nice interview about this problem[0], which
| covers software as well.
|
| > After I raised my concerns about 4% of papers having image
| problems, some other journals upped their game and have hired
| people to look for these things. This is still mainly being
| done I believe by humans, but there is now software on the
| market that is being tested by some publishers to screen all
| incoming manuscripts. The software will search for duplications
| but can also search for duplicated elements of photos against a
| database of many papers, so it's not just screening within a
| paper or across two papers or so, but it is working with a
| database to potentially find many more examples of
| duplications. I believe one of the software packages that is
| being tested is Proofig.
|
| Proofig makes a lot of claims but they also list a lot of
| journals: https://www.proofig.com/
|
| [0]: https://thepublicationplan.com/2022/11/29/spotting-fake-
| imag...
| sega_sai wrote:
| At least this paper has only 43 citations over last 10 years,
| which is really nothing for Nature, which means it's basically
| irrelevant. (Obviously it is still a good idea to identify
| cheaters)
| egberts1 wrote:
| Copypasta.
| 5mk wrote:
| I've always wondered about gel image fraud -- what's stopping
| fraudulent researchers from just running a dummy gel for each
| fake figure? If you just loaded some protein with a similar MW /
| migration / concentration as the one you're trying to spoof, the
| bands would look more or less indistinguishable. And because it's
| a real unique band (just with the wrong protein), you wouldn't be
| able to tell it's been faked using visual inspection.
|
| Perhaps this is already happening, and we just don't know it...
| In this way I've always thought gel images were more susceptible
| to fraud vs. other commonly faked images (NMR / MS spectra etc,
| which are harder to spoof)
| dylan604 wrote:
| Isn't this the plot for pretty much every movie about science
| research fraud? When Richard Kimble was chasing his one arm
| man, it led to the doctor using the same data to make the
| research look good. I know this is not the only example.
| kylebenzle wrote:
| "Whats stopping?" nothing, and that is why it is happening
| constantly. A larger and larger portion of scientific
| literature is riddled with these fake studies. I've seen it
| myself and it is going to keep increasing as long as the number
| of papers published is the only way to get ahead.
| hinkley wrote:
| You switched the samples! In the pathology reports! Did you
| kill Lentz too!?
| fabian2k wrote:
| Gel electrophoresis data or Western/Southern/Northern blots are
| not hard to fake. Nobody seeing the images can tell what you
| put into each pocket of your gel. And for the blots nobody can
| tell which kind of antibody you used. It's still not totally
| effortless to fake as you have to find another protein with the
| right weight, this is not necessarily something you have just
| lying around.
|
| I'd also suspect that fraud does not necessarily start at the
| beginning of the experiments, but might happen at a later stage
| when someone realizes their results didn't turn out as expected
| or wanted. At that point you already did the gels and it might
| be much more convenient to just do image manipulation.
|
| Something like NMR data is certainly much more difficult to
| fake convincingly, especially if you'd have to provide the
| original raw datasets at publication (which unfortunately isn't
| really happening yet).
| dxyms wrote:
| Or from my own experience, suddenly realize you forgot to
| make a picture of the gel (or lost it?) and all you have are
| the shitty ones.
| cosmojg wrote:
| Ooh, I love that this website exists, and major props to whoever
| made that visualization!
| bdangubic wrote:
| damn you spotify ... :)
| snowwrestler wrote:
| There is so little content and context to this link that it is
| essentially flame war bait in a non-expert forum like HN.
| mrshu wrote:
| For reference, the title of the paper this appeared in is "Novel
| RNA- and FMRP-binding protein TRF2-S regulates axonal mRNA
| transport and presynaptic plasticity"
|
| Google Scholar reports 43 citations:
| https://scholar.google.com/scholar?q=Novel+RNA-and+FMRP-bind...
|
| The images still seem to be visible in both PubMed and Nature
| versions.
|
| PubMed version: https://pubmed.ncbi.nlm.nih.gov/26586091/
|
| Nature version: https://www.nature.com/articles/ncomms9888
|
| Nature version (PDF):
| https://www.nature.com/articles/ncomms9888.pdf
| neilv wrote:
| If you just looked at all the undergrads trying to find ways to
| cheat on their homework, exams, and job interviews, it'd be easy
| to imagine that university lab science conducted by those same
| people is also full of cheating whenever they thought they could
| get away with it.
|
| But I've wondered whether maybe _some_ of the fabrications are
| just sloppy work tracking so many artifacts.
|
| You might be experienced enough with computers to have filing
| conventions and workflow tools, around which you could figure out
| how to accurately keep track of numerous lab equipment artifacts,
| including those produced by multiple team members, and have
| traceability from publication figures all the way to original
| imaging or data. But is this something everyone involved in a
| university lab would be able to do reliably?
|
| I'm sure there's a lot of dishonesty going on, because people
| going into the hard sciences can be just as shitty as your
| average Leetcode Cadet. But maybe some genuine scientists could
| use better computer tools and skills?
| NotAnOtter wrote:
| Pruitt? Is that you?
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