Biotech "2020 2: This Time With Feeling" Mongoose

13.8K posts

Biotech "2020 2: This Time With Feeling" Mongoose banner
Biotech "2020 2: This Time With Feeling" Mongoose

Biotech "2020 2: This Time With Feeling" Mongoose

@BiotechMongoose

Genome engineerin' expert; Small carnivorous mammal; Punches =/= pulled

Somewhere in the Bay Area Katılım Mayıs 2017
884 Takip Edilen1.2K Takipçiler
Biotech "2020 2: This Time With Feeling" Mongoose
@madamscientist Another fun fact is that, in many versions of flowjo, when copying a flow plot to the layout window, the program's default was to not display all the events from the plot you copied (and finding the option to display all events was fairly tediois)
English
0
0
1
25
Rajini Rao
Rajini Rao@madamscientist·
@BiotechMongoose I've always felt that many of the digital artifacts and pixel replications considered to be fraud are actually issues of resolution but I don't have a technical understanding of this. The examples we see on here are seem too contrived and unnecessarily complicated to make sense.
English
1
0
2
739
Biotech "2020 2: This Time With Feeling" Mongoose
Sure, champ. You cracked the code. Thermo absolutely put fraudent data on their website and was gonna get away with it, but you solved the case. It's totally fraud and not a consequence of shitty integrated scanner resolution.
Sholto David@addictedtoigno1

Surprised to discover that Thermo Fisher appears to show a fake western blot for the validation of one of their p53 antibodies. I've added a diagram to show the very similar bands. This does not appear to be one of the "published figures", but their own internal data.

English
4
0
27
19.1K
Biotech "2020 2: This Time With Feeling" Mongoose
@Adrian_H Band three actually looks different on the end, pointing towards imager-resolution artifacts. Having good Westerns stopped happening unless one has access to a film developer and a good document scanner
English
3
0
3
1.1K
Dhurandhar B
Dhurandhar B@bornspectator42·
@BiotechMongoose This did make me nostalgic for Twitter of yore I have to say. But yeah as is usual meltdowns here are almost always about things breaking containment. Across borders of various kinds.
English
1
0
1
97
Biotech "2020 2: This Time With Feeling" Mongoose
This argument might hold water for bioRxiv, but math, physics, and engineering people use arXiv in a fundamentally different way than biosci uses preprints. They were getting swamped with hallucination-filled slop by randoms trying to farm citations for fooling investors!
Michael 英泉 Eisen@mbeisen

Too many threads on going on, so going to try to consolidate. I don't think anyone objects to the core principle nominally at play here that if you put science out into the world, you are responsible for that work. This is what science is. I don't want to get distracted by questions of authorship or how responsibility is apportioned amongst authors - that's an orthogonal issue. The expectation that you can trust the scientific outputs (and I'm intentionally broadening this beyond papers) of others is really a defining feature of science as a collective endeavor. And obviously, if a paper contains hallucinated references, fake citations, placeholder text, or obvious autogenerated junk, it’s hard to argue the authors exercised even minimal scholarly care. People have tried to paint me and the others who have expressed concern about the new arXiv policy as somehow questioning this. We're not. To me something deeper shift is represented by that move, and I think it warrants at least acknowledgment - and IMO deeper discussion. The value of preprint servers to the research community comes from them being fast, open, effectively unfiltered, and agnostic about correctness. A lot of great science is published first on arXiv and other preprint, and so is a lot of science that is poorly executed and often poorly presented. Since the existence of the later doesn't devalue the former, it's a bargain most people are happy with. One of the things that kept this model afloat was the fact that producing a paper required some non-trivial effort, and therefore people inclined to produce works that could en masse disrupt the ecosystem could not actually produce them at scale. AI has obviously shattered any remnant of connection between things that look like papers and scholarly output and effort (mind you, I think this is a good thing, but that's also a somewhat separate topic). **But the response to it has also broken something.** arXiv (and other preprint servers) have always had to impose some kind of screening to keep out obviously inappropriate stuff, and I think most of us agree that asking "Is this an actual work of science?" before posting something is a reasonable thing for a preprint server to do (provided that the definition of what a work of science is is intentionally fairly broad). However, the new policy is explicitly changing that bargain. The question is no longer "Is this a relevant scholarly work?" Rather it is becoming "Can we trust this authorial process?". That is a HUGE shift. Look, I understand why moderators feel existential pressure - the system isn't architected in infrastructure, processes or modes of use with a massive flood of AI-generated papers. But there are some real risks in the new direction. 1) The thing that makes preprint servers different from (and better than) journals is that there is no gatekeeping. The new policy threatens this. Once moderation becomes about inferring authorial integrity, the boundary between “quality control” and “editorial policing” gets blurry. The fact that one of the 'punishments' is to force people to go through peer review before posting to arXiv (an idea too absurd to even mock), suggests that current leadership has a comfortable relationship to journal peer review that makes the risk that arXiv will become a journal in every meaningful sense more of a risk. 2) “Incontrovertible evidence” sounds, well, incontrovertible, but moderation systems take on a life of their own via various forms of procedure, precedent and social signaling. Today it’s hallucinated references. Tomorrow it could become stylistic mimicry. Slippery slope here. 3) The policy misdiagnoses the real problem. As I've said elsewhere, the issue is not “AI use” but the system that leads people to think it will benefit them to push slop onto arXiv. LLMs may amplify the negative effects of metric-driven academia, but they didn't create it. To me we are at a fork in the road moment. There is a world within our grasp where an alignment of preprinting and AI actually breaks the toxic stranglehold that traditional publishing has on science. A world where actual communication (not the facsimile of it we have today) takes place between people, between machines and from people to and from machines, around data and ideas in science. But there is also a world where the preprint servers we love collapse in fear and a lack of imagination into irrelevancy and we lose to moment. I'm not saying this policy itself will cause that. But I am saying that it's not a good sign.

English
3
2
20
3.8K
Biotech "2020 2: This Time With Feeling" Mongoose
@mbeisen Math, physics, compsci, and engineering simply don't have the same problems with the publishing industry that bioscience does. ArXiv is bothered by people making ai-slop, making more ai-slop that cites only the slop, and "authors" using that to secure investor money.
English
2
0
6
352
Michael 英泉 Eisen
@BiotechMongoose You know what my problem is. Everyone has ignored the problems in science publishing for decades and now that the chickens are coming home to roost, they're only treating the symptoms rather than the disease.
English
2
1
12
906
Biotech "2020 2: This Time With Feeling" Mongoose retweetledi
Arthur Spirling
Arthur Spirling@arthur_spirling·
Setting up a rival to Arxiv where AI slop is not just acceptable but actively encouraged: no censorship, no one to tell you your claims are obviously fake. a whole ecosystem of people outdoing each other with no quality bar to hold them back. it’s called LinkedIn
English
16
163
2.1K
31.1K
Biotech "2020 2: This Time With Feeling" Mongoose
...and Zymo reagent that might result in failure to detect low-expressed genes (could be the reagent, could be their rna purification protocol) (No experience with their non-dry ice Dropbox option for mRNA, you gotta buy a reagent from them beforehand)
English
2
0
3
633
Biotech "2020 2: This Time With Feeling" Mongoose
$50 for 3'-focused seq (something like 400 bases max distance from polyA site), getting the fastq files is a pain, pipeline includes multimapped fractional reads for counts, analysis browser is only good as a toy exercise, and their cell lysate dropbox option was based on...
John Warrington@jmdubs6

the fact that @plasmidsaurus offers RNAseq for $50 is so outrageous... I had no plans to do RNAseq but now it's like, why not...???

English
1
0
8
4.5K
Biotech "2020 2: This Time With Feeling" Mongoose
So the thing about virtually all "Cas9 with some bullshit on it" approaches is that the bullshit tends to do whatever it does regardless of whether or not Cas9 is fully engaged with the actual target sequence.
Y Combinator@ycombinator

FinalDose is building the first programmable drug platform - a single smart drug molecule that finds diseased cells by their DNA and destroys them. They're starting with all cancers. Congrats on the launch, @Jeffliu6068Liu, @sklin_lite, and @liyaohuang2! ycombinator.com/launches/QKj-f…

English
2
3
95
10.8K
Biotech "2020 2: This Time With Feeling" Mongoose
Almost every time I come across a new method paper that seems to be a trivial addition to a solved problem presented as a ground-breaking novel whole method, it's a synthbio paper.
English
1
0
2
609