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

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

#81
post #6

Or perhaps stop using Excel?

Excel is pretty efficient at ad-hoc text processing. You get real time feedback as you change rules and there are lots of handy functions to help you along. Its like a tabbed portable jupyter notebook.

Love this analogy. Yes, Excel is error-prone at its core. It's also the most widely-used and accessible IDE yet created. Those statements are correlated.

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

#82

Quote: "There’s no easy fix, either. Excel doesn’t offer the option to turn off this auto-formatting..." What kind of loopy Excel variant the article's author is using? It's right there in settings, you can easy stop auto-formatting. Yes, default installation has it on, but it can be turned off.

Can you explain where? I just booted up a relatively clean copy of Excel 2019 and can't find it after a couple minutes.

I see a few autoformatting options, but nothing corresponding to dates. The only options I see are similar to this:

https://www.journalofaccountancy.com/issues/2016/dec/how-to-...

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

#83
post #3

I think another question is that why isn't there a viable alternative to excel for this particular use case? Is there, perhaps, a market for niche spreadsheet applications that serve one particular market?

Educated guesswork: this isn't one particular use case, but a whole bunch of use cases with one thing in common: gene names are put in a table. Excel is the familiar, ubiquitous tool for tabular data.

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

#84
post #33

Earlier quoted context omitted.

> " To people calling, "why do they use Excel?" that's like asking "why must we be subjected to gravity?"" I respectfully disagree with this. Excel is fundamentally not suited to analysing *omics data. It's often the default program affiliated with a .csv filetype on people's computers, but trying to get an entire field of scientific research to rewrite itself based on its glorified bugs is...wrong, in my opinion. If…

Excel is not fundamentally suited, but it's fundamentally used. I wish you luck, but I long ago declared defeat against Excel. I can't prevent everyone from using it. I have come to accept that whatever Excel does is what I have to live with, because someone, somewhere out there hasn't heard the anti-Excel gospel yet.

This is the exact sort of thing that indicates market-power being concentrated to a point requiring severe, acute regulatory action.

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

#85
post #74

> For example, HECA used to have the gene name ‘headcase homolog (Drosophila),’ named after the equivalent gene in fruit fly, but we changed it to ‘hdc homolog, cell cycle regulator’ to avoid potential offense.” Ugh... everything is politics now.

As the sentence before the one you quoted explains, this is not done for politics. It is done because clinicians have to be taken seriously by the parents of the child having a mutation in that gene. Saying "your child has a headcase mutation" ends up causing defensive reactions instead of discussing treatment. Maybe that is an irrational reaction on the parents' part, but not everyone is super rational the first moment they learn their child has an illness.

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

#86

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.

We programmers also complain a lot about YAML, though maybe not enough and not as much as about Excel. But some YAML footguns like the country code for Norway being interpreted as a boolean are reasonably famous, and I think widely regarded as a bad idea.

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

#87
The problem is it isn't just dates. If you load a list of genomic variants (read: mutations) into Excel, then the standard way to describe whether a person has the variant or not is to use "0/0" for no, "0/1" for yes heterozygous, and "1/1" for yes homozygous. Guess what gets auto-converted into the first of January.

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

#88

The problem is that your average business user of Excel thinks type safety is a bug, not a feature. If Excel enforced types instead of guessing on your behalf, a lot of people would complain. And it would be really hard to explain why it is sometimes useful to have constraints to someone who normally sees Excel's flexibility as its main strength. I don't think I've ever seen a non coder use Excel in a sensible way: m…

Yeah excel produces hairballs so easily. From a coder perspective I've only seen excel workbooks that are bad or terrifying.

On the other hand a ton of people that don't write software for a living and have no interest in code manage to produce things that help them do their job and automate a ton of tedious stuff.

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

#89

My mind is blown that Excel's usability is so bad that the representation of the human genome itself has to adapt around it's undesired behaviour. As in, the history of genetics research is now irreversibly linked with the shortcomings of this one software product, which just happens to be incapable of describing the genetics of the organisms that created it.

My favorite is still that Excel can't handle dates before 1900

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

#90

Earlier quoted context omitted.

I read the article and parent is correct in part. However, equally the article touches on the fact that many people may use a spreadsheet and not all will be correctly trained to use their complex tools properly, in order to ensure data integrity. I consider this a failing not in software or Excel, but in education and professional standards. Scientists can be expected to understand and use their tools correctly, sin…

Is the simple renaming of 27 genes a good solve? I think it is. Any time you expect people to be trained, you’re planning for failure. Even a trained person can make a mistake or forget to do the manual steps. This eliminates the possibility.

I think it's the pragmatic approach, yes. I'm disappointed that the article (and so many of the comments here) are not addressing the root cause. The worst part is that not all of the people using it need to be trained - data validity enforcement ought to solve this outright.
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