2 ms·

if you are a cancer researcher, please share research assumptions that are debunked yet still commonly held. i’m compiling a list. these must be empirically s

if you are a cancer researcher, please share research assumptions that are debunked yet still commonly held. i’m compiling a list. these must be empirically supported. for instance, i believe negative conclusions based on knockout studies are misleading, but this is not empirically proven and would not qualify. (if you knock out a fire alarm and the house still functions, saying the alarm serves no purpose is flawed.)

dkural 4y ago
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.
- panabee 4y ago
  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.
  - dkural 4y ago
    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?
    - panabee 4y ago
      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.
      - panabee 4y ago
        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=20 https://twitter.com/simocristea/status/1646573238884122624?s...
  - anonymouskimmer 4y ago
    Do the studies typically claim "no function", or "not required"?
ly3xqhl8g9 4y ago
Levin, M. (2021), "Bioelectric Signaling: Reprogrammable Circuits Underlying Embryogenesis, Regeneration, and Cancer", Cell [1] is a general overview how cancer is a breakdown in communications leading to a down-scale of the self for the affected cell, see also Levin, M. (2021), "Bioelectrical approaches to cancer as a problem of the scaling of the cellular self", Progress in Biophysics and Molecular Biology [2]; for more articles [3]. In video format: "Why don't (today's) Robots get Cancer" [4] [1] https://www.cell.com/action/showPdf?pii=S0092-8674%2821%2900223-3 https://www.cell.com/action/showPdf?pii=S0092-8674%2821%2900... [2] https://www.sciencedirect.com/science/article/abs/pii/S0079610721000377?via%3Dihub https://www.sciencedirect.com/science/article/abs/pii/S00796... [3] https://drmichaellevin.org/publications https://drmichaellevin.org/publications [4] https://www.youtube.com/watch?v=L43-XE1uwWc https://www.youtube.com/watch?v=L43-XE1uwWc

dkural 4y ago

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.

panabee 4y ago
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.
- dkural 4y ago
  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?
  - panabee 4y ago
    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.
    - panabee 4y ago
      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=20 https://twitter.com/simocristea/status/1646573238884122624?s...
- anonymouskimmer 4y ago
  Do the studies typically claim "no function", or "not required"?

ly3xqhl8g9 4y ago

Levin, M. (2021), "Bioelectric Signaling: Reprogrammable Circuits Underlying Embryogenesis, Regeneration, and Cancer", Cell [1] is a general overview how cancer is a breakdown in communications leading to a down-scale of the self for the affected cell, see also Levin, M. (2021), "Bioelectrical approaches to cancer as a problem of the scaling of the cellular self", Progress in Biophysics and Molecular Biology [2]; for more articles [3]. In video format: "Why don't (today's) Robots get Cancer" [4] [1] https://www.cell.com/action/showPdf?pii=S0092-8674%2821%2900223-3 https://www.cell.com/action/showPdf?pii=S0092-8674%2821%2900... [2] https://www.sciencedirect.com/science/article/abs/pii/S0079610721000377?via%3Dihub https://www.sciencedirect.com/science/article/abs/pii/S00796... [3] https://drmichaellevin.org/publications https://drmichaellevin.org/publications [4] https://www.youtube.com/watch?v=L43-XE1uwWc https://www.youtube.com/watch?v=L43-XE1uwWc