chrisamiller

9 ms·

1.
by chrisamiller 1y ago
I don't mean this to sound snarky, but if a blog doesn't have a good ratio of signal to noise, you just unsubscribe from the feed. The solution is to be okay with missing some things instead of trying to drink from the firehose.
2.
by chrisamiller 2y ago
Our middle school has banned phones during school hours, and it's been great. Even though most kids own phones and have them in their backpacks, they aren't seen. There are less problems during classes and kids have to talk to eac
3.
by chrisamiller 2y ago
At any given time, I'm working on like 10 different projects. tmux lets me set up sessions for each of these projects, so that when I leave one and come back in a week, all the context is there (multiple windows, bash history, working
4.
by chrisamiller 3y ago
Are you claiming that declining fertility is due to plastic, rather than to increasing wealth, education of women, and access to contraception? If so, then I'm going to have to ask you for a) a source and b) a plausible mechanism.
5.
by chrisamiller 3y ago
Absolutely. We're not there yet, but it's not inconceivable.
6.
by chrisamiller 3y ago
The short answer is, we sequence their genomes, identify mutations that change a protein sequence and are highly expressed, then run those all through suites of algorithms that predict how well they'll be presented to the immune system
7.
by chrisamiller 3y ago
Look, I get the impulse, and might have agreed with you 10 years ago. At the end of the day, though, we have to work with non-computationally savvy people who (reasonably) want to look at their data sometimes. Not every lab tech or PI can o
8.
by chrisamiller 3y ago
It's too late, the genetics community already caved :-( [Scientists rename human genes to stop Microsoft Excel from misreading them as dates]( https://www.theverge.com/2020/8/6/21355674/human-genes-re
9.
by chrisamiller 3y ago
These are ballpark numbers to be sure, and yeah, my off the cuff comment didn't get that exactly right. I also simplified things quite a bit to try to get the broader point across - Thanks for following up!
10.
by chrisamiller 3y ago
This is a great example of where cancer treatment is headed and why it's so hard - namely that cancer isn't one disease, it's many thousands of diseases. This is a drug that targets lung cancer (~12% of cancers) and only one
11.
by chrisamiller 3y ago
I do cancer research, including using mouse models, so believe me, I know the difficulty :-) Getting promising drugs into humans is -hard-, and this research is interesting, but this press release is still kind of shitty.
12.
by chrisamiller 3y ago
I hate to be that guy, because it seems like there is some interesting science behind this press release hype. There are, however, many many miles between "effects in a mouse model" and "human therapeutic", let alone &qu
13.
by chrisamiller 3y ago
You're going to want to start with the PCAWG consortium, who looked very closely at viral involvement across a host of cancers. Their numbers: Cohort: 2,658 cancers across 38 tumor types Findings: Overall, 23 virus genera were detected
14.
by chrisamiller 3y ago
It's true that the whole problem of cancer therapy is "how do I target these cells over here, while avoiding the rest of your healthy cells, when they look mostly the same" And you're right that this is a really excitin
15.
by chrisamiller 3y ago
There is a lot of great work going on thinking about this very problem. One common theory goes like this: There are lots of tumor "driver mutations" that are causative and occur in lots and lots of patients. These would make grea
16.
by chrisamiller 3y ago
I'm as critical of pharma pricing as the next guy, but this really is a case where you're getting a custom vaccine design just for you, and the profit margins probably aren't very high. I certainly do think it'll come d
17.
by chrisamiller 3y ago
This isn't a preventative vaccine like that. It's something that has to be developed after you have cancer to target your tumor's specific mutational profile. So mass production (just churning out the same thing in bulk) i
18.
by chrisamiller 3y ago
That's not far off from the rates for producing custom order medical-grade peptides and/or mRNA vaccines, coupled with the expertise needed to design, administer, and monitor them. It's certainly not a case where they produce
19.
by chrisamiller 3y ago
There are lots of folks working on problems surrounding automation and reproducibility to enable science in this space. One such effort that I contribute to is [pVACtools]( https://pvactools.readthedocs.io/en/latest&#x2F
20.
by chrisamiller 3y ago
You're right that there are a variety of folks working on these things, both in academia and industry, but it's more complicated than "PhDs do this, others do that". It comes down to knowledge, ability, and experience, a
21.
by chrisamiller 3y ago
Part of my research involves designing these cancer vaccines. There are different delivery mechanisms, but the need to synthesize medical-grade peptides or mRNA vaccines is one of the major drivers of cost. The sequencing costs are pretty
22.
by chrisamiller 3y ago
The amount of energy needed to get out of earth's gravity well is incredibly high. It would be silly to try to boost a massive object like the ISS out.
23.
by chrisamiller 4y ago
That's a pretty expansive statement. Are you doing error-corrected sequencing to look for rare mosaic variants? Do you care about transcripts expressed at very low levels? Are you trying to tease apart subclonal variation in cancer?
24.
by chrisamiller 4y ago
In most cases* the raw data can be recreated from the aligned BAM/CRAM file, so it's often sensible to toss the raw FASTQs after alignment. But yeah, I go back to 10+ year old genome sequences more than some might expect. *In the
25.
by chrisamiller 4y ago
Money is absolutely an object. People are starting to do trials of early detection from circulating tumor DNA, and finding that the hit rate is alarmingly high. A decent portion of the population has some kind of malignancy, but most of the
26.
by chrisamiller 4y ago
I'm under no illusions that everyone is suddenly going to sacrifice quality of life to save the planet - humanity, writ large, is happy to burn coal until they choke to death on the fumes. So how do we stop the slow-motion disaster tha
27.
by chrisamiller 4y ago
There is already an unstoppable climate catastrophe happening. Many of the effects are already baked in for the next 50-100 years and it will disproportionately affect the poor. What we can still control is how bad it is. (An increase 1.5
28.
by chrisamiller 4y ago
This story lacks a lot of context. This linked article provides some of it: https://forbetterscience.com/2020/10/07/gregg-semenza-real-n... There's a big range between "grad student loaded the wrong
29.
by chrisamiller 4y ago
But that was after an embargo period of 12 months, during which a journal could paywall it. This forces immediate availability, which is a good thing.
30.
by chrisamiller 4y ago
It will force publishers to either add real value or be swept away by new models of publishing that aren't simply rent-seeking. It will take time to change, but this is another hole in the dike. It'll probably be messy for a coup

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