Nom nom nom
On the flip side, it's $600 for 30X WGS to find all those hundreds of off target mutations. Joking aside, the weird part: An interesting, though definitely somewhat odd finding. If it's true, it'd undermine the current model of how CRISPR/Cas9 finds where and where not to cut in the genome. On the other, that goes against a lot of what's already been observed in cell lines taken out of the body. But maybe things really are really different in vivo. In any case, CRISPR therapies are valued in the hundreds of millions of dollars each, so I have the feeling it won't be long until the answer to that is worked out. And even if the canonical Cas9 fails, there's also a dozen variants lined up with different mechanisms to reduce off target effects.None of these DNA mutations were predicted by computer algorithms that are widely used by researchers to look for off-target effects.
Got discharged from PT, feels good to not be in pain for two hours a day. Turns out foam rolling your IT is a thing and can alleviate 80% of a half-year's worth of pain within half a week. I'm a little annoyed that the orthopedic physician I saw never mentioned it, but they get a by for being a student trainee I guess... Been going through a series of drug books, Acid Test, Methland, and now Dreamland. All have been fascinating, but damn if the history of almost every drug hasn't been plagued with social strife. Shit's fucked. Headed home now, spent the last three weeks holed up in lab trying to get datas. It went okay... culminating in an experiment Monday that showed not just a negative effect, but an inverse effect from what I was expecting. More controls are needed to actually figure out wtf's going on, since cell culture can be pretty easy to mislead when the conditions across different cell lines, like the population density half a week back, vary in subtle ways. In any case, flying back to California and trying not to think about it for a couple weeks. Time to visit Berkeley + SF and make the rounds of all the friends who I haven't seen in a year.
Rationalizing last night as this could be my generation's Nixon. It's not going well. I've had better nights of sleep. Wondering if this means I should start grant applications asap before the NIH starts getting starved again.
"We bailed out the guys on Wall Street" ... who paid us back. "QE will save us" ... well ...: This might sound like a small distinction if you're not a monetary policy obsessive. But it's absolutely essential to understanding what the Fed was doing, and the rationale behind it. (Among other things, holding onto the debts, rather than canceling them, was a key part of how the Fed planned to contain inflation down the line.) Stein's description is so far off, it's as if someone asked Stein how to play basketball, and she answered that teams scored points by kicking the ball off the backboard. I'm not going to pretend I'm an economic expert, but that entire interview seemed like a hand-wavy: "they got their's, why can't we get ours" without much attention to the risks and complications involved in these interventions. Yeah, because GM food is effectively non-existent in the EU. Estimates that include only the cost of generating labels put the change at $2/year. Estimates that include the cost of restructuring the US's food processing pipeline to track GM crops from start to finish put the change at $800/year. The animal studies go up to two years, which is quite long term in the field of toxicology. The trouble with doing multi-year nutritional studies in humans is that it's insanely expensive and challenging to run a controlled trial with a large group of people on that diet for that long. The sane solution is to examine animal and epidemiological data, and use prior knowledge to hone in on diseases or populations you may believe are at risk. See... (Can't copy-paste, so pages 138, 143, 147, 154) And on and on... All evidence points to glyphosate / RoundUp being safer than previously used herbicides, and Cry / Bt toxin being safer than other insectides. It's not ideal, but you'd be hard pressed to find people knowledgeable enough for those positions who haven't had some involvement with the industry during their career. Have you known anyone to go directly into the FDA right out of college and stay there for the rest of their life? RoundUp crop patents started expiring last year. I have no issue with a company patenting a genetically engineered organism or a process to make or use one. Farmers are free to choose what they see as advantageous, and patents open up trade secrets and encourage new developments. We've literally had this exact same conversation before. Check out hybrid vigor if you need a refresher. (1) There's no such thing as proof in science, only evidence supporting or rejecting a hypothesis; (2) that's pretty decent evidence supporting their safety when combined with other methodology; (3) the entire point of your link is that GM is a category of technology, and as such each product should be evaluated individually, but in every one of these discussions that we have, you simply argue against GMOs as a whole. Read up on Bt. Read up on RoundUp. Read up on PPO-less apples and PRSV-resistant papayas. Read up on the farming practices each and encourage and each replace. It might change your perspective. But my mini-essays sure don't feel they're doing anything. So I'm going to stop trying after this.Dr Jill Stein explains how to abolish student debt.
This is wrong. Flat wrong. Quantitative easing was an unconventional monetary policy tool the Federal Reserve used to try and revive the economy after the financial crisis once it had emptied its normal bag of tricks. There have been vigorous debates about whether it was wise, or whether it worked. But it did not involve buying and canceling debt owed by the banks. Quite the opposite—it involved buying and holding onto debts owned by the banks (or other investors, for that matter), such as Treasury bonds and mortgage-backed securities.
Europe has always had GM labelling and food didn't get more expensive.
Those studies are 90-110 days long. Is that long term?!
How about the revolving door I mentioned before, that doesn't bother you?
How about patenting of living organisms?
If you care so much about the farmers why make them buy the seed every year?
the last 2 decades of GMO consumption does not constitute as proof of their safety
Halfway done with writing my thesis proposal. Re-re-re-injured my knee last week. Someone else in my lab defended this week on cartilage signaling, and the background on arthritis fallout in the years after joint injuries has me worried. But maybe this is my chance to become a cyborg?
So how about that Ann Arbor / Boston meetup?
I took apart one of our old instruments last week:
Not really a side, because it's still in lab, but I've been trying to convert my lab to use as much open software as possible. I've been re-writing a lot of old MatLab code in Python, setting up IPython notebooks, and converting or disorganized set of protocols into a git-version-controlled repository of Markdown documents. I came across this talk on a similar workflow being set up in neuroscience imaging, which got me excited: And in the process learned about one of the most futuristic research campuses I've seen: I'm hoping that when I finally go to publish a paper, the analysis will be completely NumPy / IPython / Jyupter / Docker-powered. I'm currently stuck on how to distribute an eventual 50+ GB of data without having to pay extraordinary costs for hosting...
I'll point out that transplants / grafts between identical twins do work without rejection. And that was basically the only type of transplant surgery that occurred before the discovery of immunosuppressants. Isograft: Past that, I've seen papers testing all kinds of coatings and shapes on implanted devices. They delay, but never prevent the inevitable. Personally I suspect that it's not just what cells touch, but how their neighbors respond to that touch that dictates rejection. But that's largely speculation. Home-grown stem-cell-derived tissues might one day be a thing, but until then, we're stuck with sticking metals under our skin. Which I personally regard as dumb when medically unnecessary.That's a 1:1 replacement, blood type and all biomarkers matching perfectly, and the body still knows it ain't natural
An Isograft is a graft of tissue between two individuals who are genetically identical (i.e. monozygotic twins). Transplant rejection between two such individuals virtually never occurs.
- Cook: Been doing it! A decent bit more than crockpots. Going to get a vegetarian cookbook when I head home so I have something a bit more convenient than a phone to use for recipes in the kitchen. - Science: Been doing it! Project is coming along very well. I'm at a point where I'm trying to both mine more information from the data sets I have (using something more complex than "sort by fold change") and finish off collecting data from a few more samples. Internally I'm hoping to have something submitted for review by the end of 2016, but I'm not sure how reasonable that is. Doing proteomics on brain stuff is definitely an untapped fountain of information, almost everything I've been finding has yet to be studied at a systems level or even noted anywhere that they even play a role in the brain (let alone diseased brains). I was thinking that once this all goes through and I've had a few rounds of peers critiquing it, I'll make a post on here explaining things from the basics on up. - Draw: Didn't do it to any appreciable degree, maybe next year. Also mk: Looks like there's a bug in closing a bold tag on this post
So what does that make mknod?a nod to pg
_____E YOURSELF!
You know, I think it would be worth a bit more if it came with an accompanying donation. But when the barrier to entry is a click of a button, the potential meaning seems limited. Talk is cheap...
My department had its retreat this week and it really cemented in my views about its biases. We had a rather forced event where we interacted with other researchers and tried to come up with impromptu collaborations. I wasn't exactly enthused with the idea to begin with, but I felt it devolved into churching out more and more non-sensical combinations of hype-y technologies without any attempt to carefully think about a biological question. I've spent the few days since trying to reflect and think about what other biases or viewpoints I might encounter at other universities and how they contrast with my own tech-obsessed environment. That said, here's this week's set of instrument pictures: First time I've seen a TEM before, it looked like it was built in the 80s
August was a hot, humid write-off, but September has been going a lot better for me. After 8 months of struggling with a technique, I finally generated my first dataset, and so far, it looks awesome! I talked to a post-doc working on a similar project yesterday and it looks like my results fit the narrative she's been working on. And they have brain slices available for follow-up validation and have some knock-out mice to see if what we're seeing effects to disease progression. Hopefully this will lead to insight into a new Alzheimer's-associated pathway! I'm also taking a neurotechnology class this semester and it feels rough, but manageable so far. My coloring book from the summer hasn't been for naught, and I'm starting to feel more comfortable hearing people discuss efferent, afferent, plasticity, and cortical layers without switching to immediately definition-lookup time. My optics knowledge is trailing pretty far behind though, and the class yesterday on 2-photon microscopy was mostly: "I understand this neurobiology, but have no idea what went into making these images." Thursdays are mini-rotations in all the labs that work on the methods discussed in the class, so hopefully I'll have a few photos to show you all in future weeks.
I want to QFT most of what you wrote, but to save space, I'll just add my own opinions on one of your points: I've taken to accepting that sometimes the language I use will be received as offensive and changing it around others even when I know I disagree with them. Some people have been offended by "you guys" instead of "you all" or even the use of assumed gendered pronouns before I've explicitly asked the other person what their preferred pronoun is. Sometimes I disagree. I don't consider "bitch" a sexist insult. I care little way one or the other about "undocumented" vs. "illegal". I consider "3rd world" to be a somewhat archaic term from the generation before mine and prefer "developing" instead. I see "jew" as offensive only in some contexts. I dislike the use of "faggot" (and consider it a pejorative for "gay"), but I equate "retard" to "stupid" / "moron" / "dumb" / "idiot" as all having varying degrees of intensity of the same idea. For all of them though, I have learned to recognize when the bother those around me and adjust the words I use in accord with keeping a respectful conversation.2.) Change when you're told a new term, and don't get mad when you're corrected. You don't live the life of a person of colour, or a trans person, or someone with a developmental disorder. That makes it hard to keep up, because you're not steeped in it, all day every day. Also, lots of people have different reactions to different words.
Was walking through Allston when a hail storm hit, then got surprise dumped and saw George Church walking on the street on my way home
You look like a completely different person! What's the book?
TL;DR: state the encodingIf you completely forget everything I just explained, please remember one extremely important fact. It does not make sense to have a string without knowing what encoding it uses. You can no longer stick your head in the sand and pretend that "plain" text is ASCII.
At one end of the possibilities: A repeat of the 1967 Mulford Act when Ronald Reagan banned open carry in California in response to the Black Panthers there. It's hard to predict how such a movement would turn out today though. Doubtless it would get bad press from Fox, maybe it would lead to conflicts with overzealous police, possibly it could lead to a change in law?...
I'm hoping to take a course on neurotechnology in the fall though, so in the mean time I'm trying to sharpen up my very vague understanding of how brains work. I've been making slow but steady progress up the structure of the brain. Unfortunately memorizing has never been my strong point, and already much of the anatomy is dissolving into "a bunch of nuclei here, some nerves there, tracts running this way and that."
Yeah I'm picturing a "Click to subscribe to my youtube channel!" situation. I'm curious to watch this play out as well.
Re-read Infinite Jest. Would definitely recommend it to those pre-occupied with drugs, entertainment, tennis, or have had friends go through detox. It's pretty long though (Took me 1.5 months to read both times) and can be a tough nut to crack open at first.
Academic writing is all about audience. The primary publication is something akin to a proof, and precise language is important there. I'll be damned in most naming conventions aren't terrible, but if I say "white blood cell", that means one thing to the layman, but to the academic, that means one of several things. More often it's a page-limit that removes explanatory sentences and crunches phrases down into polysyllables. At a certain point, you have to pick what to define and what not to. I would assume a scientific audience knows molecular orbital theory but maybe not Raman scattering. But then again, I'm not going to re-list the rules of quantum mechanics if I'm writing to physicists and I consider that to be common knowledge among them. Still a good read and shared, the "Curse of Knowledge" is definitely one I encounter a lot.People often tell me that academics have no choice but to write badly because the gatekeepers of journals and university presses insist on ponderous language as proof of one’s seriousness,
Frank (2014) was one of the most disappointing movies I've seen in a while. Literally every character other than Fassbender's was simply not likeable. And when did it become a thing to start inserting Twitter / Blogger / Facebook pop-ups directly into the movie frame? It's tacky and immediately takes me out of the experience of the movie. One of the same main actors showed up in Ex Machina (2015) a few days later, still playing the same socially inept computer nerd! I'd recommend it anyways though, since it's a mindfuck and a great experience to watch.
Boston marathon, freezing rain
I strive for a level of compassion so extreme that it is near-indistinguishable from sarcastic condescension. That twinkling love in a person's eyes that one might see in an elder at peace with the world, but seems to appear so rarely in ages 5-65.
It's a good thing that the only things that apparently matter in the world are (1) social networks, (2) apps for middle-men, and (3) luxuries for people with too much money. Wat. Uber is cheap because Uber subsidizes their rides in new areas and relies on surge pricing to make up the difference in pay to drivers. If you spent $7b on delivery via Uber cars, you have a bunch of cars without adequate storage, traveling more frequently back to their source for pick-ups. I can't imagine what society is more efficient with a hundred separate cars doing a task that can already be done by one truck. Past that, the warehouse technology wouldn't be changed one bit. ... In the U.S. we’re well behind. More wats Who owns Android again? Oldly enough, the most sane thing the author wrote. It's one possibility, the other is complete failure. Only time will tell.Specifically, I think, likely the disruptive force for Amazon, who’s been the most disruptive force in retail in America, is going to be Uber. It came to me, when I took an Uber ride in southern Florida and it was $4. In Chicago, you can hire a car and a driver for 90 cents a mile. If you spent the same amount on Amazon, as Amazon does on its shipping services, that’s seven billion miles of flexible delivery in the U.S.
The other big trend in retail is something pretty boring. People won’t talk about click and collect, ordering online, picking up in-store. It ends up that stores are fantastic and flexible warehouses.
The bottom line is the mobile economy is not friendly to Google’s business model.
I’m going to fly through this. The first year, Apple’s going to be the biggest watch company in the world. Who does this hurt? It hurts everybody. Not just watch companies, but all aspirational price point brands. Teen retailers have been getting killed. They’re staring at their navel. Is it a product? Is it a brand problem? It’s an Apple problem. These brands get hurt.