6 ms·

>"molecular biology and forward genetics have great traditions of reproducibility" Where is the evidence of this? There is plenty saying otherwise: http://www

• AlexCoventry 10y ago
  I actually cited the seminal cancer-biology editorial in the GP. I suppose cancer biology is often a form of molecular biology, but I meant more fundamental research into molecular structure and biological function, and in-vitro methods for querying and modifying the structure. CRISPR is a good example.
  • nonbel 10y ago
    CRISPR is a great example. Please see my other post on that topic in this thread, and if you are interested I will go find the refs that led me to that position.
    • AlexCoventry 10y ago
      I would certainly be interested to know the references, but I don't find your argument here convincing. Testing for insertion of a defensive gene by exposing the organism to a hostile environment is an extremely well-developed and reliable method in genetics. But I suppose there must be a million ways to screw it up so I can't rule your mutation scenario out based on what I currently know of the research. On the other hand, I find your skepticism and independent thinking refreshing.
      • nonbel 10y ago
        Thanks, not sure if I will get to it today. A lot can be found in my previous posts here on the topic if you want to search.
      • nonbel 10y ago
        Actually this thread should do: https://news.ycombinator.com/item?id=10967719 https://news.ycombinator.com/item?id=10967719 I see now I had an earlier discussion with tstactplsignore, back then they were seemingly incapable of understanding what I was saying (they kept thinking I denied the endonuclease activity).
        • AlexCoventry 10y ago
          http://www.nature.com/nchembio/journal/v10/n8/abs/nchembio.1550.html http://www.nature.com/nchembio/journal/v10/n8/abs/nchembio.1... claims that resequencing of a CRISPR-targeted gene showed dramatic increases in indel mutations, consistent with non-homologous end joining repair of the CRISPR cuts. (Supplementary table 5.) I assume the resequencing happened before the drug screen, otherwise the paper is badly written.
          • nonbel 10y ago
            Well, from your table S5 and table S12, as is usual we see that about 0.1 - 1% of the cells were mutants in the control group (ie they came pre-"modified"). Interestingly, from table S12 and my (selection for pre-existing mutants) model we can also explain a mysterious result they observed: "Silent co-mutations in the repair oligonucleotides were introduced into >99% of D54H mutant alleles and ~3% of the F482S allele (Fig. 2c). Carryover of these silent SNPs indicates that the alleles are the product of HR and not de novo mutagenesis. The lower rate of coappearance of silent SNPs in F482S is presumably due to the larger distance between the two SNPs in the oligonucleotide and is rather common to see with single-stranded oligonucleotide donors19." Rather than that ad hoc explanation, it is simply that the D54H cells had more silent only mutations to begin with (0.1% vs 0.0%). Regarding that 0.0%, an annoying thing is that they only report these percentages to one decimal place. I'm not exactly clear on the number of cells present before the CRISPR-Cas9 treatment, but it sounds like 10^8, and then they let them grow for 72 hr + 7-12 days (total of 10-15 days) after the treatment. They also don't tell us how many cells were left at the end... but anyway if we assume these cells divide once a day, and 0.1% are preexisting mutants we could calculate the possible number of mutants thus: Nt = 10^8 p = 0.001 d = 0:15 Nt*p*2^d After 12 days we can get ~400 million cells from those initial pre-existing mutants, and after 15 days over as 3 billion. Of course other factors would probably come into play that limit this growth, I'm just saying it would be no problem for that small subset of the population to become dominant during the experiment. That is even if the 99,900,000 "WT" cells were just growth arrested rather than died. So I find those results to favor the "selection for pre-existing mutants" explanation over the "gene modification" one.
• tstactplsignore 10y ago
  Your links are talking about preclinical trials and attempts to replicate specific high profile, controversial studies from specific subfields. We're talking about the entirety of basic research. The "evidence" for this is the incredible advances in our understanding of how the cell and the molecules of life work in the last 50 years. Every single experiment done in the modern life sciences would not be even possible to contemplate doing if all of the molecular biology it is based on was not extremely reproducible. Entire fields of modern biology like genomics, structural biology, genome editing, and more could not even be fathomed to exist if this were not true. Nobody tallies up how often biology "works", only how often a few experiments attempting to prove specific hypotheses don't work. Basic science in molecular biology and microbiology are extremely reproducible most of the time and nobody writing these articles questions that. No offense, but this is some creationist-tier science denial you have going on if you don't believe this, and it isn't the responsibility of the scientific community to educate people who've read one time many articles about reproducibility that science works.
  • nonbel 10y ago
    >"Entire fields of modern biology like genomics, structural biology, genome editing, and more could not even be fathomed to exist if this were not true." Yes, everything needs to be redone since at least the 1980s, and probably the 1940s (whenever NHST became the primary method of assessing what is correct or not). We have no idea what is actually going on. It is scary, I know. It took me years to accept. >"this is some creationist-tier science denial you have going on if you don't believe this" Ok, link to a specific paper and I will discuss it with you. In my experience, if it is biomed, no one will have ever published a replication of any results it contains. There will be no model capable of quantitative prediction of anything, and conclusions drawn will also almost certainly be fatally flawed due to the vagueness of their explanation.
    • tstactplsignore 10y ago
      Lol, I just realized you were that guy who denies CRISPR-Cas9 genome editing really works. It may be against the rules, but I just have to tell you that you are an insufferable idiot who brings down the quality of discourse on this site with your bizarro pseudoscience nonsense.