Scientists rename human genes to stop MS Excel from misreading them as dates • Hacker News Board

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#321

Post by RugnirViking » Thu, Aug 06, 2020, 6:23 PM UTC

javier123454321 wrote: post #241

LatteLazy wrote: post #26

It's honestly amazing that Excel hasn't fixed this issue. It's pisses off an enormous number of users especially in basically any non-US country (even if 01/02 is a date, it isn't the second of January in most of the world...)

Honestly though, dates make more sense being month first, that way if you are trying to discover which one comes first, 10th of february or 10th of january, you only have to go to the first parameter in format 01/10 vs 02/10 instead of 10/01, 10/02. Logically, the most broad data item should go first.

Which is why most systems are yyyy/mm/DD when this matters

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#322

Post by airstrike » Thu, Aug 06, 2020, 6:28 PM UTC

travisoneill1 wrote: post #286

airstrike wrote: post #56

Earlier quoted context omitted.

Just type '01/02 or ="01/02" and get on with your life

Is that January 2, February 1, January 2002, or January 1902?

In Excel? It's January 2nd of the current year, which again is probably the most common use

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#323

Post by MystK » Thu, Aug 06, 2020, 6:30 PM UTC

throw_m239339 wrote: post #251

throwaway936482 wrote: post #187

Earlier quoted context omitted.

Excels usability isn't bad though. Which is why everyone uses it. It falls down in this (and lots of other cases) but if you want to see what good usability looks like, look at what people use.

Everyone uses Excel because it's a tool everybody learned at University or even highschool, nothing more, it's not because it's good at all. It's a terrible app but Microsoft managed to shove it everywhere in education. Same for Words. Unfortunately Libre Office and co tried to reproduce the terrible UX of both software, while coming up with inferior functionalities because they had to try to maximise compatibility w…

It may be a terrible app, but it's better than the competition. Does that mean it's the best one?

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#324

Post by rorykoehler » Thu, Aug 06, 2020, 6:31 PM UTC

njarboe wrote: post #312

rorykoehler wrote: post #225

Earlier quoted context omitted.

Tbh I think its a case for multidisciplinary research. You wouldn’t only hire one skill set to run a company, even a tech one, so why should research be any different? That’s probably where the deep insights are.

People that are just decent programmers can make at least twice (probable 3 or 4 times) as much money working for industry than for science in an academic environment. Most programmers that would work for less money because they are interested in science will be more interested in computer programming problems than basic programming to support a scientist. NSF won't give you $250k to hire a really good programmer to…

That's a problem we should aim to solve.

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#325

Post by rolph » Thu, Aug 06, 2020, 6:32 PM UTC

vikramkr wrote: post #285

rolph wrote: post #258

Earlier quoted context omitted.

there was a time when a gene was named to facilitate search through a bookshelf full of laboratory notes. you could look at a genes lable and know exactly where to find reference to the gene, the lable would indicate the stack number the shelf, the section the volume the page[s] and paragraph....lables such as Sonichedgehog dont do that anymore.

I've been in the room when deciding what to call a gene that the lab had just characterized/identified as interesting for the publication they were working on, and let's just say that making it easy to catalog and find the gene wasn't really on their mind. They'd actually been using a deliberately obfuscated name in conferences to prevent people from scooping their work on the gene before, which is pretty common.

conference is a different game but that doesnt change what happens in the lab, if you look at the overall picture you can see the potential for duplication of alphanumeric strings. this is why in conference lables must be developed as you have a wider context in conference than in your own lab. You can be scooped for research regardless of what lable is given to a gene, and for that matter even if you make publication first as not everybody has the same ethical framework of honesty or due accreditation. the time before computers were used reflexively was when we would record data, in cursive written in hardcover bound note books. a putative gene has a name that allows it to be found. later if things work nicely that putative is confirmed to be a gene and if things work ideally the locus can be established

https://en.wikipedia.org/wiki/Locus_(genetics)

around the late nineties the obsession with videogames and netspeak took hold, and the popular names began to crop up.

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#326

Post by sumtechguy » Thu, Aug 06, 2020, 6:32 PM UTC

shpongled wrote: post #159

kaesar14 wrote: post #151

Earlier quoted context omitted.

What's your source on it not being difficult to find biologists who are adept at using python, R, or C? Most biologists operating in private industry or academia have many years of training in their fields and many have learned their computational tools as they've gone on, meaning they've never received proper training. It seems dubious to claim that there's this neverending source of well trained biologists who are…

I would say the number of biologists who actually understand programming is extremely small. I've been programming for fun for ~15 years, and I'm about to finish a PhD in chemical biology (e.g. I started programming in C far before I started learning biology). You might occasionally run into someone who is passable - at best - with R or Python. But most of the code they might write is going to be extremely linear, an…

I write 'one off' programs all the time. Most of what I write I throw away, and I program for a living. Those are usually fairly linear. Which is fine. If I am writing something that will be re-used in 6 different ways and on a 5 person team. That is when you get out the programming methodologies. It is usually fairly obvious to me when you need to do it. For someone who does not do it all the time. They may not know 'hey stop you have a code mess'.

It one of the reasons why people end up with spreadsheets. Most of their data is giant tables of data. Excel does very well at that. It has a built in programming language that is not great but not totally terrible either. Sometimes all you need is a graph of a particular type. Paste the data in, highlight what you want, use the built in graph tools. No real coding needed. It is also a tool that is easy to mismanage if you do not know the quirks of its math.

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#327

Post by panda-giddiness » Thu, Aug 06, 2020, 6:32 PM UTC

Balgair wrote: post #178

meow1032 wrote: post #47

Earlier quoted context omitted.

I don't disagree completely with this, but just want to point out that it's kind of a bad smell to have computational biologists who are - as someone in the article puts it - computationally illiterate. I have met lots of these types over the years, and usually their methods are kind of a gong show. If you can't properly sanitize your data inputs on your column headers, why should I trust that you've treated the rest…

In grad school I had a friend that was doing olfactory (smell) research on rats with tetrode drives (wires in their brain). He was looking at the neuronal response to smells that they gave the rats and had a few signals to match up. There was the signal from the arduino running the scent gates, the amps that reported the weak neuronal currents, the nose lasers that gated the ardunio, etc. He was having a hard time ge…

> To the larger point, scientists are not programmers.

I mean, sort of. Some research is essentially just programming; other research can get by with nothing but excel. Regardless, it's unreasonable to ask most scientists to be expert programmers -- most aren't building libraries that need to be maintained for years. If they do code, they're usually just writing one-shot programs to solve a single problem, and nobody else is likely to look at that code anyway.

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#328

Post by whatisthiseven » Thu, Aug 06, 2020, 6:34 PM UTC

snowwrestler wrote: post #268

whatisthiseven wrote: post #206

Earlier quoted context omitted.

I keep seeing this sentiment when it comes to those in the natural sciences, but it makes no sense. I could replace "programming" in your above little bit with "mathematics" and it would be just as weird. Our modern world runs on computers and programs, just as our modern world and modern science built itself on mathematics and required many to use it. So too the new world of science may require everyone to know to p…

Most scientists are not great at math either. Again: these are tools that are means to an end. They only need to work well enough to get the researcher to that end. A lot of what are considered essential practices by expert programmers are conventions centered around long-term productivity in programming. You can get a right answer out of a computer without following those conventions. Lots of people did back in the…

Your point is maybe a little obtuse to me, because it sounds like you are arguing for "computers are tools that should be learned, but really no one does and who can blame them, they just want to science" and simultaneously arguing, "tools aren't science, and science can be done without them".

I feel like the later is obvious: of course the tools aren't science, but if you want to do real work and real science, your tools are going to be crucial for establishing measurements, repeatability, and sharing how one models their hypothesis onto real world mechanics.

Likewise, the former is just the same commonly repeated thing I just argued against and my reply is the same: so what? You building a kayak is not science and is irrelevant.

Scientists can't reach a meaningful conclusion without proper use of tools. All they can do is hypthesize, which is certainly a portion of science (and many fields are in fact stuck in this exact stage, unable to get further and come to grounded conclusions), but it is not the end-all of science, and getting to the end in the modern day science means knowing to program.

Of course there are exceptions and limitations and "good enough". No one is arguing that. The argument I am refuting is those who think "tools are just tools, who cares, I just want my science". That is the poor attitude that makes no sense to me.

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#329

Post by LatteLazy » Thu, Aug 06, 2020, 6:37 PM UTC

komali2 wrote: post #247

In excel, can you set the a column to not format to dates? I think you can do that in google docs for example. Why don't they do that?

It's actually worse. If you expressly set the format of a column to text, then put 01/01 in it, you still get Jan-01 and a field value of 46000ish.

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#330

Post by elwell » Thu, Aug 06, 2020, 6:38 PM UTC

takluyver wrote: post #78

Programmers love to complain about Excel, but we happily use YAML, which has essentially the same footgun: certain strings (like 'on') need quoting if you don't want it to interpret them as something else.

> Programmers love to complain about Excel

In Apache POI HSSF/XSSF (Java Excel API), the HSSF actually stands for "Horrible Spreadsheet Format".

As a fun example, note that we need isSheetHidden() and isSheetVeryHidden() functions. (http://poi.apache.org/apidocs/4.1/org/apache/poi/ss/usermode...)