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

#71

Post by mnw21cam » Thu, Aug 06, 2020, 2:14 PM UTC

ChrisLomont wrote: post #43

azalemeth wrote: post #23

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…

>based on its glorified bugs If someone types MARCH1, DEC1, OCT4, SEPT1 into a column, why should Excel not treat these as dates? Probably 99.999% of users would prefer this auto-understanding. To make users have to then select cell formatting and select date is a terrible UI decision. It's odd to call such a useful feature a bug. >Excel is fundamentally not suited to analysing *omics data But it's excellent for a ma…

> If someone types MARCH1, DEC1, OCT4, SEPT1 into a column, why should Excel not treat these as dates?

It should treat these as dates, unless told otherwise. But Excel goes one step further, and throws away the text you originally typed in. That means, if you type "DEC1" into a spreadsheet, see it looks stupid, and change the data type of that cell to "Text", then it's too late, and Excel will show "37226". It has destroyed the original data and replaced it with the numeric equivalent of the date.

The data type of the spreadsheet cells should be a display format only. The text you typed in (or loaded from a CSV file) should be preserved, and the data type of the cell should only dictate how that is treated and displayed, not how it is stored.

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

#72

Post by angel_j » Thu, Aug 06, 2020, 2:15 PM UTC

There must be a net benefit to using this software, right? Otherwise somebody in charge would make the decision to use something else, right? It’s not like they are forced to use MS excel, right?

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

#73

Post by numpad0 » Thu, Aug 06, 2020, 2:16 PM UTC

dkarl wrote: post #19

numpad0 wrote: post #5

Excel’s problem is it destroys the original keystrokes. Anyone know why? It makes little sense to me.

Because usability is measured by the naive expectations of the least sophisticated users.

But haven’t you seen the least sophisticated users trying to type in the same sequence until it sticks?

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

#74

Post by tomp » Thu, Aug 06, 2020, 2:16 PM UTC

> 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.

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

#75

Post by kang » Thu, Aug 06, 2020, 2:17 PM UTC

meow1032 wrote: post #47

jordigh wrote: post #7

To people asking, "why do they use Excel?" that's like asking "why must we be subjected to gravity?" The whole world's data ultimately comes from or ends up in an Excel spreadsheet. Sure, we might use other intermediate data storage methods, but in the end it's going to go into some scientist's or some politician's computer, and by golly it's gonna be in Excel. Trying to rally against Excel is like trying to rally ag…

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…

https://news.ycombinator.com/item?id=24070913

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

#76

Post by acidburnNSA » Thu, Aug 06, 2020, 2:17 PM UTC

meow1032 wrote: post #47

jordigh wrote: post #7

To people asking, "why do they use Excel?" that's like asking "why must we be subjected to gravity?" The whole world's data ultimately comes from or ends up in an Excel spreadsheet. Sure, we might use other intermediate data storage methods, but in the end it's going to go into some scientist's or some politician's computer, and by golly it's gonna be in Excel. Trying to rally against Excel is like trying to rally ag…

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…

I have a strong feeling that, if people really put an effort into reading and replicating more papers, we would find that a lot of what's being published is simply meaningless.

In grad school I had a subletting roommate for a while who was writing code to match some experimental data with a model. He showed me his model. It was quite literally making random combinations of various trigonometric functions, absolute value, logarithms, polynomials, exponents, etc. into equations that were like a whole page long and just wiggling them around. He was convinced that he was on a path to a revolution in understanding the functional form of his (biological) data, and I believe his research PI was onboard.

I guess "overfitted" never made it into the curriculum.

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

#77

Post by epistasis » Thu, Aug 06, 2020, 2:17 PM UTC

meow1032 wrote: post #47

jordigh wrote: post #7

To people asking, "why do they use Excel?" that's like asking "why must we be subjected to gravity?" The whole world's data ultimately comes from or ends up in an Excel spreadsheet. Sure, we might use other intermediate data storage methods, but in the end it's going to go into some scientist's or some politician's computer, and by golly it's gonna be in Excel. Trying to rally against Excel is like trying to rally ag…

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…

It's not usually computational biologists who are using Excel.

What if you want to share data with a wetlab biologist who want to explore their favorite list of genes on their own?

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

#78

Post by takluyver » Thu, Aug 06, 2020, 2:18 PM UTC

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.

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

#79

Post by BurningFrog » Thu, Aug 06, 2020, 2:18 PM UTC

jordigh wrote: post #7

To people asking, "why do they use Excel?" that's like asking "why must we be subjected to gravity?" The whole world's data ultimately comes from or ends up in an Excel spreadsheet. Sure, we might use other intermediate data storage methods, but in the end it's going to go into some scientist's or some politician's computer, and by golly it's gonna be in Excel. Trying to rally against Excel is like trying to rally ag…

If the gravity metaphor doesn't reach you, maybe this will:

The world speaks English. It's an illogical and absurdly spelled language. Esperanto is miles ahead on all logical measures. Yet we will never switch, both because the cost of switching is enormous, and because there is no way to coordinate/organize such a move.

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

#80

Post by rkachowski » Thu, Aug 06, 2020, 2:19 PM UTC

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.