You ever have one of those weeks where you're just like: yeah. there might be a right-wing conspiracy?

I don't think Infinite Jest is itself depressing, but you'll want to avoid some of the books that came after. After reading Oblivion I didn't feel surprised that he killed himself.

From the wiki:

In general, Marshall Boswell claimed that this was Wallace's "bleakest" work of fiction. In Oblivion, he "uncharacteristically" provides "no way out" of solipsism and loneliness. Boswell further suggested that the collection "repeatedly undermines many of the techniques for alleviation" from loneliness, like communicating through language, that Wallace presented in Infinite Jest. "Oblivion," he writes, "remains unique in Wallace's oeuvre in its unrelenting pessimism."[26]

Fuck if even Brooks is seeing the light, maybe there is hope?

Chances are I'll still be in town doing the same old thing next April too. Keep us posted!

Implemented an algorithm from a paper, got invited out to drinks tonight by the author. Makes this a real pubski, rather than a labski, day for me!

Also, met with my adviser to discuss human patient data, kept calling our samples "animals". Old habits die hard?

Do they freeze alright? Their parent cells are so finicky that somehow I doubt mine would be happy with a drop of DMSO in solution.

And making microglia:

I made an embryoid body!

~2 months until I have the final cell type I'm looking at.

A month and a half of treating, sorting, maintaining, and cleaning my cells every day to finally get the CRISPR knockouts I'd been working towards:

Now to do this 6 more times.

One of the genes I'd been trying to knock out was in a tricky region to sequence. I asked my adviser if I should spend a month debugging the PCR (after a post-doc had tried and failed for a month), just show the protein had disappeared by an antibody assay, or sequence the whole genome and look at that one gene afterwards.

They said sequence the whole genome.

The golden days we live in. Time to start making designer babies.

Nom nom nom

I'm getting chunks of human brain today!

Thu / Sun both work for me, keep us posted

I'll be around, I'm down for a pubski in meatspace.

http://dailycaller.com/2017/08/17/bannons-time-is-up/

Daily caller, but it's Stone who's... a sight to behold:

Not understanding that “personnel is policy”, Bannon refused to fight for any of his allies or those who helped get Trump elected. It’s as if Steve felt the grubby business of patronage was below him.

Bannon delivered the Trump State Department into the hands of the Globalists.

Bannon failed to push the President to use his most potent rhetorical and political weapon-Term Limits -in his current fight with the Congress. ... which sent the clear signal to Republicans in Congress that you can thwart the President and there are no consequences.

Tough talking Anthony Scaramucci, whom I like and whom I think was treated rather shabbily, was, as I said, a political suicide bomber. He took out two RINOS: Preibus and Spicer

Thoughts:

- It's pretty annoying to see the guy described as having a PhD in systems biology from Harvard. Word from a friend is he dropped out after 2 years. And even if he had the degree, it doesn't really doesn't make him any more an authority on psychology or gender dynamics than the layman. Especially when half his links are blog posts.

- The guy's an idiot if he expected to keep his job after calling his female colleagues more neurotic and less stress tolerant. Especially coming from a biology background where environment is just as stressful but the gender ratio tips the other way.

- Saying "I'm just commenting on general trends, don't take it personally" doesn't make what comes after any less offensive or wrong. The same goes for "PC culture isn't going to like this but..."

- The arguments from inherent genetic differences tend to always ignore the social differences, past and present, that favor one group over another. Most positive initiatives (select training and outreach to women, under-represented minorites) are evolutions on previous affirmative action policies as a way of addressing the whole "it's not fair to those of us in the present who aren't responsible for the actions of others in the past" argument.

- It's hard to read this:

I’ve heard several calls for increased empathy on diversity issues. While I strongly support trying to understand how and why people think the way they do, relying on affective empathy—feeling another’s pain—causes us to focus on anecdotes, favor individuals similar to us, and harbor other irrational and dangerous biases. Being emotionally unengaged helps us better reason about the facts.

And not think that this guy doesn't play well with others.

"Nucleofector – Amaxa" and "Human Stem Cell Nucleofector Kit 1 – Lonza", I may need to play around with it though, as the protocol appears to have not worked very well (it was ~6M across 4 cuvettes, which may not be the optimal cell:cuvette ratio?...)

Wasn't this what Russians ridiculed Obama for as ineffective when he did it to them?

But maybe you are the person to innovate a "rifle scope" for CRISPR? Who knows?

Doubtful, I'm just using it to make separate cell lines, I have zero plans to optimize anything if I can get my 10 cells that look alright by the end of the year. But thanks, it's nice to hear encouragement.

So I'm doing CRISPR this week.

Starting with 30 million stem cells, I worked my way down to about 500,000 that survived electroporation, 2% of which actually showed a marker of Cas9 expression.

Of those, maybe 10% will survive this week and grow from single cells back into full colonies without losing their pluripotency. Of those, maybe 10% will actually have a change that I want (destroying gene function). I believe it'd be an order of magnitude lower if I actually wanted to actually wanted to make a mutation in a more targeted way.

So 0.0003% of my starting cells will actually be gene edited and usable afterwards. I personally only need about 10 in total to make it through the whole process, but it's hard to look at those numbers and feel we're a longgg way from designer babies.

There were some meetings between Trump officials and some Russians, but so far no more than you’d expect from a campaign that was publicly and proudly pro-Putin. And so far nothing we know of these meetings proves or even indicates collusion.

Is this guy actually retarded?

On the flip side, it's $600 for 30X WGS to find all those hundreds of off target mutations.

Joking aside, the weird part:

None of these DNA mutations were predicted by computer algorithms that are widely used by researchers to look for off-target effects.

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.

Quoting a friend here: The "S" in IoT stands for "Security"

TREMENDOUS.

But seriously, I'm curious, how many cells do you end up getting from each patient and what fraction of those actual survive the freeze / thaw procedure?

I honestly prefer this aspect, of a formal regulation agency approving tests that have decent support for them. You can already download your SNP data from 23andme and run it through the genetic gauntlet with other services, but this adds convenience and separates the well-supported from the less-well-supported associations out there.

FWIW, from 23andme's privacy statement

We will not sell, lease, or rent your individual-level information (i.e., information about a single individual's genotypes, diseases or other traits/characteristics) to any third-party or to a third-party for research purposes without your explicit consent.

Definitely something to keep an eye on in the future (though companies can already get your genetic info through the incentive of healthcare discounts iirc.

Past few months have been dealing a lot with chronic lower back pain, so here's something slightly different in the vein of productivity. For 2017 I bought a calendar that I can mark off my accomplishments for each day:

Each of those symbols corresponds to a different exercise for physical therapy, as well as rock rock-climbing and days of major lab work. I've found that seeing the calendar every morning helps prod me to do the maintenance that I'd otherwise skip. Because let's face it, PT is otherwise tedious and boring.

On the lists of politicians that you may surprisingly agree with: Bernie Sanders

Did you know that 2.5 millilon employees work in healthcare insurance and that a single payer option would probably reduce that in a huge way, creating a massive group of unemployed people? There are dozens of major insurance companies who, in the course of daily business operations, duplicate the work that is being done at competing companies. Obviously, Blue Cross' accounting department isn't going to do the accounting for Cigna, and so you get two accountants doind the same parallel work multiplied across all the companies. But if the US Gov't is going to do all the work in a single payer system, you'll have a massive cut in employment. No way around it. I don't think people realize that the sudden disappearance of probably 1.5 million jobs will be a reality in that case. Esepcially not Trump who has advocated for single payer and ran on a major employment focus.

FWIW, even countries with fully socialized medicine have their own private healthcare insurance industries (ex: UK). But even so, this strikes me as a backwards argument: health insurance is too expensive, so we should preserve the inefficiencies and bloat already present in the system.

So far, the clearest summary of the ACA's shortcomings has been that it addressed health insurance coverage without doing enough to address costs. So now you have fewer uninsured people waiting until the last minute to get treatment instead of preventative care, and fewer insured people being denied the coverage the payed for due to undisclosed domestic violence. But the drugs, the scans, and the doctor salaries are still roughly the same. And medicare still can't negotiate drug prices.

So the delta flow of money is still heavy in the direction of providers.

For me? Not to this date, no

Truth. And yet it's just one control and a few experiments short of being a landmark paper in the field of Alzheimer's imo.

Crazy research of the week:

In which researchers took skin cells from a fully grown human, converted them into stem cells, partially differentiated them into neurons, and put them into mouse brains to study the effect of the same environment on neurons from different species.

When I saw that paper, I had a woah moment. Holy shit are we living in the future.