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Tiny DNA circles are key drivers of cancer, study finds

med.stanford.edu

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Re: Tiny DNA circles are key drivers of cancer, study finds

#31

Post by dkural »

panabee wrote: post #22
dkural wrote: post #10

Earlier quoted context omitted.

A knock-out study will work as well as the precise definition and measurement of the phenotype you're looking for will allow. The point you're making is well understood by geneticist. There's about 22K genes in the genome, if your typical genetic screen returns a list of a 0 to 1K positives, no one is claiming that the 21K genes are absolutely uninvolved in the phenotype.

i have read many studies that claimed a gene had no function in a pathway after performing knockout and observing no effect. there are many great research papers, but there are also many flawed ones.

I completely agree there are many flawed scientific papers in general. I am wondering about your specific category of flawed papers.

Could you point to one concrete example where you believe a paper is flawed in its conclusion, where they've claimed a gene has no function in a pathway under the given experimental conditions, after performing a knockout?

Re: Tiny DNA circles are key drivers of cancer, study finds

#32

Post by anonymouskimmer »

robocat wrote: post #23
jtbayly wrote: post #4

Earlier quoted context omitted.

Reading this gives me an understanding for how some of my friends feel when I talk about technology. “Make sure to set the dip switches on your SCSI drive and confirm your cable is USB 4+ PD.” Lol

Yeah, status seeking by using uncommon words or concepts, often noticeable in geek-culture. The same thing occurs in many cultures. “Well-educated” people in England might use more sophisticated[1] language and drop[2] references in Greek, Latin, or other languages of le très bien formées. “Elucidate” feels like a status signal in the OP’s comment. Personally one has been working on counter-signalling[3] by using sim…

Sometimes I want to use more common words but the right one to use just doesn't come, so I'm left using a less common word.

I find it odd that you're referring to yourself as "one".

Re: Tiny DNA circles are key drivers of cancer, study finds

#33

Post by anonymouskimmer »

panabee wrote: post #22
dkural wrote: post #10

Earlier quoted context omitted.

A knock-out study will work as well as the precise definition and measurement of the phenotype you're looking for will allow. The point you're making is well understood by geneticist. There's about 22K genes in the genome, if your typical genetic screen returns a list of a 0 to 1K positives, no one is claiming that the 21K genes are absolutely uninvolved in the phenotype.

i have read many studies that claimed a gene had no function in a pathway after performing knockout and observing no effect. there are many great research papers, but there are also many flawed ones.

Do the studies typically claim "no function", or "not required"?

Re: Tiny DNA circles are key drivers of cancer, study finds

#35

Post by panabee »

dkural wrote: post #31
panabee wrote: post #22

Earlier quoted context omitted.

i have read many studies that claimed a gene had no function in a pathway after performing knockout and observing no effect. there are many great research papers, but there are also many flawed ones.

I completely agree there are many flawed scientific papers in general. I am wondering about your specific category of flawed papers. Could you point to one concrete example where you believe a paper is flawed in its conclusion, where they've claimed a gene has no function in a pathway under the given experimental conditions, after performing a knockout?

thanks for demanding intellectual rigor on HN.

because the papers seemed invalid, i didn't save them. i'll try to find them.

even if i share a few, it's possible most papers do not commit this mistake, and i was simply unlucky to stumble upon a few and generalized from an invalid sample size.

which is why i disqualified the opinion by saying it was not empirically supported.

for what it's worth, i discussed this opinion beforehand with several post-docs from respected schools and did not get pushback. this isn't proof either, but merely clarifies that the comment wasn't a thoughtless one.

in the meantime, do you mind sharing one widespread assumption you believe is false? it sounds like you're very informed, so it would be great to learn from you.

Re: Tiny DNA circles are key drivers of cancer, study finds

#36

Post by panabee »

panabee wrote: post #35
dkural wrote: post #31

Earlier quoted context omitted.

I completely agree there are many flawed scientific papers in general. I am wondering about your specific category of flawed papers. Could you point to one concrete example where you believe a paper is flawed in its conclusion, where they've claimed a gene has no function in a pathway under the given experimental conditions, after performing a knockout?

thanks for demanding intellectual rigor on HN. because the papers seemed invalid, i didn't save them. i'll try to find them. even if i share a few, it's possible most papers do not commit this mistake, and i was simply unlucky to stumble upon a few and generalized from an invalid sample size. which is why i disqualified the opinion by saying it was not empirically supported. for what it's worth, i discussed this opin…

FYI here's the tweet that motivated the desire to compile a list of wrong but common assumptions (empirically debunked): https://twitter.com/simocristea/status/1646573238884122624?s...

Re: Tiny DNA circles are key drivers of cancer, study finds

#37

Post by [deleted] »

woleium wrote: post #24
robocat wrote: post #23

Earlier quoted context omitted.

Yeah, status seeking by using uncommon words or concepts, often noticeable in geek-culture. The same thing occurs in many cultures. “Well-educated” people in England might use more sophisticated[1] language and drop[2] references in Greek, Latin, or other languages of le très bien formées. “Elucidate” feels like a status signal in the OP’s comment. Personally one has been working on counter-signalling[3] by using sim…

idk man, elucidate is pretty common if you spend a lot of time reading scientific papers (I'm assuming oop does).

[deleted]

Re: Tiny DNA circles are key drivers of cancer, study finds

#38

Post by robocat »

wrycoder wrote: post #28
robocat wrote: post #26

Earlier quoted context omitted.

Exactly the point: well-educated people use words that appear in scientific papers. Showing you are well-educated is a common status signal amongst many well-educated people. Some people are lingual chameleons[1]: their language patterns completely change depending on their social surroundings. And many people are liguistic artistes[2] who choose their language to paint an image of themselves. However, failure is rif…

Well-educated people use more precise language than the average person. Otoh, the article uses words like roly-poly and willy-nilly, which I found jarring in the context of a moderately technical article from Stanford Medical.

https://www.chronicle.com/article/why-academics-stink-at-wri...
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