Hi, believe it or not, I have actually done what the authors were attempting. I used saliva rather than blood as a source of DNA and extracted it using a Qiagen kit.
My Nanopore flow cell had nearly every pore working from the start. So I would say that is not normal. Maybe it was stored incorrectly.
Do you have a write up somewhere? If not, it would be amazing if you wrote one!
I was planning on doing a similar thing (also with saliva) once I finished moving in and had a bit more time after conferences. (But, of course, I’d have to go through and actually figure out all of the mechanics and so on.)
Thanks for the kind words! I have not written it up but would like to. A word of warning: by trying to get into sequencing, I eventually burned through ~20k USD of student loans (still unpaid) with little to show. Nanopore sequencing also requires some specialized equipment (at least a micro centrifuge and micropipette and possibly more) which is not cheap.
For sure, I think it’d be fun to show it can be done under 5k or so, which would be close ish. Can probably get older equipment from university surplus, but yeah, these are the “things that need to get figured out” :)
Adding on: Claude also gave me the following line which was necessary to get the model weights to download from HF. This might be obvious for anyone familiar with HF but it helped me so sharing here!
I think the real story here might be the line below:
"Durham University improved by 30 places year-on-year"
Seems a bit suspicious, no? What methodology change led to this result? How can a university that was previously not as well-regarded become the #3 in the country overnight?
Durham is the oxbridge reject university, and it’s a standard opener during freshers week to ask which college rejected them. Me, Corpus Christi Oxford reject, Durham alumnus.
What has seemingly happened here is that oxbridge have ramped up their intake of overseas students, who pay a vast sum compared to a U.K. student, thus pushing more U.K. talent to Durham, as you’ll always preferentially give the place to the kid paying six figures rather than the one on a state bursary.
Yes, and then when oxbridge reject you, you take your second choice, Durham. At any rate that’s how it worked 25 years ago, I think it’s much the same now.
My recollection from thirty years ago was a lot of people that were aiming for Oxford would have Durham as their backup plan. It's been hovering around there for a while although not so much in the the world tech people care about, for which Warwick and Imperial circle Cambridge far more closely.
There's a stereotype, possibly unfair but somewhat amusing, that Durham attracts some people who are less clever/bright than they and their families believe, who failed to get into Oxbridge despite expensive private education, personal tutors, every other privilege under the sun. Sometimes known as "rahs" possibly? ;
What's the provenance of this "30 places year-on-year" assertion anyways? (TFA won't load on my end.)
The Times filed Durham 7th @ 859 in FY24[1], 5th @ 898 in FY25[2]. They're now 3rd @ 906 for the current FY.
P.S. Chuckling at the perception that a university which ranked top 10 for at least the past decade being characterized as "not as well-regarded"...strikes me as indefensibly elitist.
> Durham University improved by 30 places year-on-year in its students’ evaluation of teaching quality, which was the main driver in securing its third place in the overall university league table
Which isn't quite the same as 30 places in ranking as OP suggests, however I agree with their point that moving 30 places on that metric could be fairly suspicious.
For example - when I was at university in the UK we got a speech telling us basically that we were going to get sent a survey from the times, and the higher we ranked the university, the higher the universities ranking would be, and that would make our degree more valuable. If the main reason they jumped from 7th to 3rd could be a metric that is potentially 'influence-able' by the university, it could be more of a change in comms-strategy than actual university quality.
The US culls 350 million male chicks per year, per this article. Wikipedia says billions of male chicks are culled worldwide, which seems plausible when accounting for EU, China, India, SA, SEA etc. The citation on Wikipedia looks legit to me as well.
Edit: Wikipedia does indeed cite several different figures, including a "billions" number which does not seem plausible. Thanks monster_truck for pointing this out, and apologies for my misunderstanding!
Male chicks are not feed nor raised but rather fed into a device quite similar to a wood chipper shortly áfter birth. You can read more about it here [1] or find some quite graphic videos on YouTube. This is addressed in the article:
"In polling, only 10% of Americans correctly identify that male chicks in the egg industry are killed shortly after hatching. A plurality mistakenly believe these chicks are raised for meat, and another 10% even think that male chickens can lay eggs. Most people are surprised, and often disturbed, to learn the truth: in the United States alone, approximately 350 million male chicks are routinely culled each year, typically by methods such as maceration (being ground up alive)."
There was also that time when a milk company wrote the names of the cows who produced the milk on the cartons and some feminist complained that all the names were female.
One of the Minecraft mods makes you actually do the video game equivalent (thus not over the correct time period) of how we actually get milk. Instead of just right click on any cow with a bucket (like vanilla Minecraft) that mod requires you to find a boy cow and a girl cow, ensure they're both happy (well fed, no nearby predators etc.), and after a short period nature takes its course and you get a baby cow. Next, steal the baby cow, you can kill it for food or just move it to somewhere mum can't reach it. She's recently given birth so her body will make milk but now there's no baby to drink it, so you can steal the milk.
I think 10% of people probably just say things for their own internal amusement. I have to think there's some overlap with the people who draw penises or write or write "jokes" in bathroom stalls.
East Asia has lots of highly walkable cities with great public transit -- even a few you might not have heard of. Not just Tokyo, Seoul, Shanghai, Beijing but also Shenzhen, Chongqing, and Hangzhou to name a few.
Sure, there are small areas like that (which are dense areas meaning a lot of people live there), but they are still a minority. Even within those cities there are places that are more walkable than others.
I have no idea how this tracks to births, but I did some studies before of Nordic homicide rate, and if you drop an actual Nordic citizen in similarly white homogenous states like new hampshire their murder rate isn't terribly worse than it is in a Nordic nation.
My hypothesis is there may be something like this effect happening, where once you control for nordic people in similarly white states I bet they'd have much closer to nordic birth risk.
Ham-fisting statistics to support some model of eugenics and racially perfect societies is an old tale.
We need to be very careful with statistics, because rarely does one or even a dozen cover the whole picture. For example, in the US we can see that black individuals are more likely to commit crime. We could easily run with that and draw some unfavorable conclusions.
But, they're also much more likely to be impoverished, more likely to live in communities with low infrastructure funding, more likely to live in communities with drugs, more likely to have much poorer access to education, and more likely to face barriers to employment.
OK but blacks in Seychelles (adjusting for purchasing parity, about the richest black nation in existence to the point they're not far from the black american GDP per capita) have a gini coefficient far better than the US (in fact almost same as Sweden) but still have a pretty similar infant mortality to blacks in the US. So I don't know about the thesis they just need to be made more equal to the rest of USA or something.
Definitely not interested in accepting eugenics either, just maybe we should acknowledge and be OK with the fact some demographics are just different and we shouldn't be forcing them to be like the nordics.
I don't think it's a matter of demographics being different, I think it's a matter of us wanting to believe some demographics are inferior because that makes us feel better. I mean, we're not describing positive, but different, traits, now are we?
In regards to Seychelles - are we looking at levels of education? Are we looking at income inequality? Are we looking at corruption? Are we even considered how developed the nation is? How long have they been developing? Have we taken a gander at any population pyramids?
Again, it feels like we're hamfisting these things to draw conclusions that we want to draw. I don't think just having white people fixes things, we need to look at what those white people are doing that actually works. Even money doesn't necessarily fix things, if you're already underdeveloped or you have high corruption.
I have a thesis that could be wrong. I have some very weak data. What you have is that would be an inconvenient hypothesis.
It is quite an inconvenient hypothesis. Unfortunately I have some weak data that leads the question to persist and no strong evidence against it. I see no reason why it can be dismissed.
It's not just that it's an inconvenient hypothesis, it's that it's an hypothesis we've already been trying for several hundreds of years. It's how we justified slavery, the holocaust, colonialization. These people weren't dumb, they genuinely believe black people were inferior, so they would therefore have the best quality of life by being slaves. You see, we're really helping them by taking them from their backwater countries of tribal war and giving them opportunities to do structured labor that their feeble minds could handle.
Time and time again, we prove those hypothesis wrong. As countries develop and equality is prioritized, we see more and more differences disappear.
Ultimately, I have no reason to believe we have achieved the apex of development or equality. Systemic racism is real, because racism doesn't just disappear. We implemented integration just a few decades ago in a lot of communities, and that disconnect and resentment that built doesn't just - poof! - disappear. It continues on and manifests in less opportunities for education, more drugs in communities, and a lot of second order effects that transcend generations.
We even still see black populations today distributed as we saw them during slavery. And that was 150 years ago. These things don't get solved, they just get better, a little bit at a time over very long periods of time.
I dismiss the hypothesis because we have already dismissed the hypothesis more times than we can count. And, I have no reason to believe this time it's different.
I feel like we're on the same page then -- my hypothesis isn't intended to drive policy which is what you appear to object to. I don't want to 'enslave' black people into a systemically racist society that tries to force them into different infant metrics.
If even sovereign, nord-level equal in income, relatively well off black nations have US-black level infant mortality then it's not really my place to tell them to be more like the white man and do something that drops it but has god knows what other unintended consequences. Maybe they benefit in some other way. I have no idea.
Indeed, unfortunately when it comes to children/babies everyone is busybodies and seems to think they can act on behalf of the child in their interest and trump the actual parents. The biggest actor in the US in this capacity is CPS themselves, who investigate and take black children at far higher rates than the others races, believing they can stomp on black parents to implement their idea of bettering the outcome of babies to closer match that of white ones.
I hope someday society can see your plan of less interventionism is the more correct one.
Sure, take a look at Bahamas or Seychelles, "rich" black countries almost as high GDP per capita as some of the nordic nations (PPP adjusted in Seychelles case). Still with infant mortality in the relative shitter.
Or compare hispanic to blacks at similar income in USA, they knock them out the park on infant mortality.
> Sure, take a look at Bahamas or Seychelles, "rich" black countries almost as high GDP per capita as some of the nordic nations. Still with infant mortality in the relative shitter.
The Seychelles Gini coefficient is higher than Sweden. There doesn’t seem to be data on the Bahamas.
Gini coeff is bullshit anyway. Just look at who's topmost at income equality (Ukraine) and also at the bottom of the list for wealth inequality. This makes no sense as a practical indicator. Especially for the racist take the other poster is making.
Having mostly flat income inequality can mean either of those -- everybody is rich and paying taxes and people with money are tax evading really good, so poor don't have access to healthcare.
Then again, just because country has allocated money for healthcare, the outcome depends on how many sick/old/poor people need it and how well it's used up, because corruption exists and isn't reflected in Gini coeff.
The Nordics is where American conservatives and liberals find unity on harmonious white homogenity.
> My hypothesis is there may be something like this effect happening, where once you control for nordic people in similarly white states I bet they'd have much closer to nordic birth risk.
Historically (at least up until the late 90s) Japan, France and maybe others had a much different point of death included as death at birth that skewed infant mortality numbers. I'd like to see more than a bullet point 3 to understand how/when that was changed.
The U.S. has beginning to end health care for pregnancy and child birth. Its infant mortality rate (5.4) isn’t really much higher than Canada (4.7), which has a socialized healthcare system.
Which seems kind of okay, except when you consider that we pay significantly more per-capita for healthcare as opposed to Canada. Yes, that includes if you take into account taxes, and it's not even close.
Sure, we're not the absolute worst, but we are the most expensive. And, for that, we get close to the worst results. Clearly, our healthcare system is broken in a variety of complex ways.
As far as I can tell, we pay more for healthcare for the same reason we pay more for schools and more for subways. We’re a low competence, low trust society, and have to compensate for it by making everything subject to litigation to the point where the country is effectively run by lawyers.
My six year old boy ran into a table and got a black eye. Took him to the doctor (because my wife made me), who physically examined him and saw he was fine. But ordered a CT scan anyway (which we got the same morning because this is America). No sane healthcare system would order a CT scan for this! But in our litigation-driven system, the doctor has to do it, because in the extremely unlikely situation that there was an undetected internal bleed, he’d get sued. And some expert would get on the stand and say the standard of care is to order a CT scan every time a six year old boy does a six year old boy thing.
I don't think this is the sole reason why, I think private sector inefficiency is a big reason why, too.
We have an extremely fragmented system that breeds inefficiency. Thousands of insurers, so hospitals have hundreds of billing specialists. Thousands of plans, so the complexity of what is and isn't covered explodes beyond belief. There's no streamlining, no centralization, no authority. Just bickering and "erm, ackshually" from every party. Every interaction has extremely high friction that comes with a massive, fragmented system.
It's like a microservice architecture with thousands and thousands of microservices. Except their contracts aren't always published, sometimes you need to call them on the telephone. And sometimes you just have to try requests and see if they get denied.
Also, I think a CT for head injury is fairly standard practice. I think they do that in Europe. Anyway I had some pain somewhere inconspicuous once and it was cancer, so. I don't think the issue is we image too much.
We very definitely image too much. There are apparently as many MRI machines in Massachusetts as there are in all of Canada. "We image too much" is a pretty common complaint in health policy discussions; Rayiner is not just making that up himself.
I don't know, maybe, but at the same time our cancer screening recommendations are pretty conservative and we're actively looking to lower the screening ages for some of them because enough are slipping through the cracks.
We do image a lot for injuries. Maybe it's to give radiologists something to do, I don't know.
First, when we're talking about imaging overuse we're generally talking about injuries and back/joint paint.
But it's also probably not true that we screen less aggressively than Europe. For instance, I think we start breast cancer screening earlier than Europe. There are European countries with better rates of colorectal screening, but that's a patient compliance issue as much as anything else (and 10 years from now standard of care is unlikely to be imaging-based for that screening for most pts).
>Also, I think a CT for head injury is fairly standard practice. I think they do that in Europe.
Chiming in here from a rich EU country. CT for head bumps at the ER is not standard unless the doctor deems it absolutely necessary in grave injuries since the public system is already clogged up. Only X-ray on the spot is standard.
When I had my bicycle accident they did no CT scan, only head Xray. They said they'll do a head CT only if concussion symptoms don't go away or worsen after a few days.
In poor EU countries, you don't even get an Xray if your skull isn't cracked wide open because there's already 100 people in the ER waiting with even bigger issues than you. My dad slipped and fell on a concrete floor and the ER sent him home after looking at him for 3 seconds telling him "it looks fine". If he went to a private hospital he'd get all the imaging he wants since he'd be paying out of pocket and they'll never say NO to money.
I feel like Americans live in a parallel universe where healthcare has infinite money so they throw expensive checks procedures at the wall since insurance pays anyway, but that's not the case in public systems where money is tight than the government demands frugality from hospitals and doctors.
I agree our private sector is inefficient. But our public sector is too (hence my transit and educational examples). We suffer from cost disease across our entire economy, both in public and private spheres.
My Nanopore flow cell had nearly every pore working from the start. So I would say that is not normal. Maybe it was stored incorrectly.
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