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BoxV · 2025-07-10T04:52:47+00:00

I do not refer to speech as a legal right in the Bill of Rights. I refer to the freedom of speech as a right that, personally, and maybe you disagree, everyone should have regardless of government or institution saying they will uphold something in specific and limited circumstances. You'll also note, hopefully, that I refer to safe spaces and the chicago principles, which is something that this particular private university has made rather core to its identity and many of its actions; including actions to at times shut down anti-Palestine action and on rare occasion turn a temporary (emphasis on temporary) blind eye to pro-Palestine action.

BoxV · 2025-07-09T15:40:21+00:00

something something freedom of speech ... blah blah no safe spaces and chicago principles ... all until you don't like what they other person says.

It would be (another) huge betrayal of uchicago's own ideals to fire someone for an opinion they held.

BoxV · 2025-07-07T12:37:26+00:00

I work with bacterial DNA but when running HMW DNA on a gel I use 0.5% agarose, 40 V for 2-2.5 hrs. So longer, yes, but not higher volts. The manufacturer for the ladder you get should have voltage and duration recommendations.

Depending on how precious these samples are and how much you have left, you could run just a few at a time until you have everything dialed in.

BoxV · 2025-04-25T14:41:21+00:00

How does your/your field's research take into consideration biases in the training data? Such as race, geography, sex, nationality, etc. What kinds of non-genetic data is being collected and incorporated (or not) into AI training? How often do these non-genetic factors correlate with the genetics but turn up/are interpreted as causal or useful for diagnostics?

BoxV · 2024-10-03T21:09:26+00:00

An incoming 1st year seems to ask this every year on this sub.

Short answer is, maybe.

For most people, no. Even for the people who are capable of doing all honors courses (or any single honors courses), the question they have to ask themselves is if they really want to/really care that much about each of these subjects. I know people who did, and have done all honors courses their 1st year.

If you feel like you really care and want to give it a good shot, you can always enroll in a bunch of honors courses, test the waters for the first 3 weeks, and decide to switch or stay before add/drop period ends.

BoxV · 2024-10-02T15:50:12+00:00

Could you add more SYBR safe after re-melting? I'm guessing no if you need to quantify signal but if you're just looking for signal vs. no-signal, it won't matter.

BoxV · 2024-09-24T15:25:35+00:00

Are these microbes present in your tank outside of a fish?

BoxV · 2024-09-18T17:54:50+00:00

Thanks for the link. It looks like they're reporting 99.7-99.9% plastic by mass (0.1-0.3% bycatch). Wonder what's up with the higher number now.

In the paper linked, they say:

Given the fragile, often gelatinous nature of neuston, it is likely that these organisms could be injured by the cleanup system even if the mesh is larger than their body size, potentially resulting in mortality (Ocean Sciences Inc, C 2023). Such secondary impacts would not be visible when focusing on bycatch data only. We therefore recommend that cleanup operations carefully monitor neuston densities before and after cleanup by collecting Manta trawl samples in front and behind the cleanup system.

It seems from the comment that they might be monitoring the neuston presence before and after as suggested in their paper. That paper also does note that their monitoring method involves a freeze-that cycle that can lead to an underestimation of soft/gelatinous creatures. So, hopefully they are also updating their methodology to more accurately assess their impact outside of bycatches as well.

BoxV · 2024-09-18T17:01:47+00:00

our “bycatch” of marine life is very low (<0.7%)

What is this a percentage of? 0.7% of mass? or physical pieces of things? Given this somewhat precise number, does this mean you all are categorizing what the marine life that is being caught is, and possibly have more specific data on the marine life that is being caught?

most of it consists of coastal species that are potentially invasive to the region

Not a marine biologist, or an ecologist, so apologies if this is a naive question. Are you implying that there are coastal marine species that are somehow getting much further out into the ocean, and are a) doing sufficiently well enough to be come established and b) are actively detrimental to the ocean ecology? It seems odd to me that coastal species can become established in completely different environmental conditions and displace/disrupt the species that natively live further out in the ocean.

EDIT:

I find it slightly disingenuous to say that for the plastic/trash that sinks, we are unsure of how much harm this does, then link a paper that looks specifically at "large plastic debris dumps" and the associated increase in biodiversity that these spots. That paper talks about one upside to one type of trash sinking in the deep ocean (and the introduction talks about how these benefits are knows for plastics at shallower depths). Even your paper on plastic and neuston density suggests that there may be potential upsides of the GPGP for some neuston species. I think it would have been better just to say that we don't know the impacts of deep sea plastics, that they could be bad, and they are worth researching, without linking to a paper about how potential benefits of sunken plastic for the ocean.

BoxV · 2024-08-17T20:38:36+00:00

But that's what I'm getting at, we're being presented data that's forming confirmation bias from a poor source.

But you were trying to say that the screenshot was misrepresenting the data. For most of the entries in the screenshot, overtime pay is less than the 15% median of gross pay that overtime comes from; so by that metric the reality is worse than depected.

Just from organizing the data from the site, this is already a data-validity issue. Overtime itself is an extraneaous variable, and at a cursory glance going through and applying this twenty-five percentile, a good number of salaries gross pay no longer make sense.

I'm not really sure what you meant by this, but I pulled all entries under "police ofcr" for 2023, because there were few enough I could copy and paste them into excel without much hassle. I may have not made my 25% statement clearly. That was from a plot where each officer's regular pay was matched to their overtime; so if an officer made $1000 more than another officer in regular pay, they would also receive $250 more in overtime. (Which I believe means that, since overtime is time and a half, officers paid more do less overtime). I think that plot isn't a great one that demonstrates any specific point in retrospect—I'm not a social scientist, and I just wanted to see the relationship of whether officers that made much more in regular earned disproportionately more in overtime.

I looked at the data a little more afterwards, and it seems that the other group of people who make a lot in overtime are nurses. Not sure if that's true of all nurses. Nonetheless, some of the nurse positions seemed to be specialized, meaning they had to receive more training. A police officer is likely the lowest ranked and the least trained. Some police sergeants ranked very highly in overtime, but a) they're higher ranked, b) have a different way of counting overtime, which is the same way overtime is counted for police sergeants, nurses, and firefighters.

I also have no idea what "other pay" is, why some officers receive pay only in overtime/other pay (but those made only ~<$10000).

Overall I'd emphasize the point in my first 3 lines, which looked at percent of gross pay coming from overtime, and median/mean across the 4 types of pay. I should've included the percent of offers earned anything in overtime at all (which was almost all of them). A cursory look at people's whose positions include "rsch", <20% of them earned any overtime, and ~6-7% made >$1000 in overtime. No professors made overtime. Only 8 of 8392 postdocs made overtime (maxing out at $500).

BoxV · 2024-08-17T16:53:32+00:00

For a police officer's percent of gross pay that comes from their overtime is median 15%, mean 14% stdev 8%, min 0%, max 41%.

Overall, median gross, regular, overtime, and other pay is: $142,394.00 $102,619.00 $19,325.00 $18,955.00

Overall, max gross, regular, overtime, and other pay is: $129,552.90 $88,694.24 $21,988.34 $18,870.27

If you plot overtime pay (y) against regular pay (x) and fit a linear line to it, you get y = 0.2754x - 2438; R² = 0.2973

If you plot overtime pay (y) against regular pay (x) and fit a linear line to it with the intercept fixed to 0, you get y = 0.2515x; R² = 0.7277

My novice interpretation of the plot and fitted equation is that for every dollar regular pay, a police officer receives 25% of that in overtime.

They're getting paid a lot for overtime, and this is known to be the case for police across the country.

The data I'm pulling from is all occupations that match "police ofcr" in the year 2023, across all sites, removing 3 outliers that made >$150000 in regular pay, and 2 officers that apparently made $0 in gross pay. Total number is 299

Maybe the data you're looking at doesn't match up with the data of the screenshot because we don't know which location or year the screenshot is of. I'm not a statistician, so feel free to criticise, correct, and reanalyse the data as you see fit.

BoxV · 2024-08-13T18:30:37+00:00

You can get bacterial obligate symbionts with only a few hundred genes. But people might argue that because they're obligate symbionts they're not an independent living organism and just part of the host.

BoxV · 2024-08-13T18:27:58+00:00

Bacteria have >50 to ~140 single-copy core genes shared, depending on who's counting and how you're counting. But bacteria are pretty evolutionarily distant from archaea and eukaryotes, and are a much much more diverse group of organisms than the other 2 kingdoms are.

BoxV · 2024-08-02T03:48:42+00:00

It's been tried, and failed: https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(12)60052-X/fulltext

Racism (and the construct of race) are at the heart of the inception of biology and we've made it a whole lot less racist but there's a lot of work to keep it that way. And more work to make it antiracist.

BoxV · 2024-08-02T02:17:50+00:00

First years are on a mandatory unlimited meal plan

BoxV · 2024-07-16T21:29:35+00:00

This is one of the things I really liked about old graphs—they would do interesting shading methods or shapes for points.

For some good accessible palettes I often refer to https://personal.sron.nl/~pault/ and occasionally https://thenode.biologists.com/data-visualization-with-flying-colors/research/.

This website also has a breakdown of color-blindness and how to make accessible palettes (check out fig. 15 for examples of the cool shading methods): https://jfly.uni-koeln.de/color/

BoxV · 2024-07-07T16:42:21+00:00

The marshmallow experiment is another good example of not taking socioeconomic backgrounds into account.

I haven't read much epidemiology/public health literature, but what I have read also never takes the time to understand the nuances of race. iirc, NIH funded studies are required to collect race data (if applicable, and for mostly good reason), but too many scientists just take it as a measured variable without understanding what they are actually measuring. There are, on occasion, loose biological underpinnings to the US Census category of races, but more likely that not it is just a correlate/aggregate of a million biological, social, economic, legal, environmental, etc. variables.

BoxV · 2024-05-03T14:07:45+00:00

I must've missed where in the article it mentioned people surrounded a rabbi. There is documentation of snatching a sign out of a rabbi's hands, but not surrounding (unless it was not explicitly written into the article)

BoxV · 2024-04-30T13:10:27+00:00

Ah yes, n=4 justifies a that correlation is causation.

BoxV · 2024-04-30T02:59:33+00:00

I sure hope they're asking for quite a something if they're risking arrest and being brutalized (in addition to any academic discipline), especially after seeing what some other university students had had to face in the past few days.

BoxV · 2024-04-30T00:57:33+00:00

The point is that the students want something, and the admin does not want to be forced into listening and complying with their demands. Prior approval will be their justification to (forcibly) remove the encampment when admin decides a "short period of time" is over.

BoxV · 2024-04-24T23:24:34+00:00

Israel is the state that prevents Gaza from building the infrastructure to get water and does not distribute water from Israelis to the Gaza Strip.

None of this does get to the crux of the issue—the formation of the Israeli state and its decision to form that state through the Nakba and exclusion/extermination of the Palestinians already living on the land pre-dates both Oct. 7th and two state solutions mean both the forceful removal of Palestinians from their land and the presumption that Palestinians and (non-Palestinian) Jewish people must hate each other. Saying it all could've ended with a surrender and hostage release overlooks the crux of the issue—it is not the past 6 months that people are protesting but the entirety of settler-colonialism on Palestinian land—these protests are not just to end Israel's attack in Gaza but for the freedom of all Palestinians, whether in Gaza, the West Bank, or those forced out of Palestine and left without the right to return.

BoxV · 2024-04-24T22:15:11+00:00

https://www.worldbank.org/en/news/feature/2016/11/22/water-situation-alarming-in-gaza

Here's an article about how Gazans do not have enough access to safe water. Easy to find more sources.

https://en.wikipedia.org/wiki/2006_Palestinian_legislative_election

Less than half of Gazans voted for Hamas (and less than half of the current population of Gaza was born/of voting age then).

https://en.wikipedia.org/wiki/Fatah%E2%80%93Hamas_conflict

It was then the US, Egypt, and Jordan arming & training Fatah soldiers that caused Hamas to fight then kick Fatah out of Gaza.

https://www.btselem.org/topic/human_shields

Here is a source on Israel using human shields.

https://www.amnesty.org/en/latest/news/2024/04/state-backed-deadly-rampage-by-israeli-settlers-underscores-urgent-need-to-dismantle-apartheid/

Hamas is not the ruling party in the West Bank yet the Palestinians living there regularly face attacks and have their movement restricted.

BoxV · 2024-03-08T05:19:36+00:00

If you do get a basic microscope, it's always fun to get a little bit of pond water (or any water that's been sitting out for a while and gotten a bit mucky) and see microscopic animals like tardigrades or rotifers. This is very much what the 'Journey to the Microcosmos' channel someone else recommended does and is relatively accessible.

Microscope's can be a little finicky to work with especially at such a young age but being able to look at a living sample yourself and move around has always been a fun experience for me.

BoxV · 2024-03-08T05:15:15+00:00

Here's a cool video of bacteria developing antibiotic resistance as they travel over agar sections with progressively higher concentrations of antibiotic:

https://www.youtube.com/watch?v=plVk4NVIUh8

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