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

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There are tens of thousands of genes in the human genome: minuscule twists of DNA and RNA that combine to express all of the traits and characteristics that make each of us unique. Each gene is given a name and alphanumeric code, known as a symbol, which scientists use to coordinate research. But over the past year or so, some 27 human genes have been renamed, all because Microsoft Excel kept misreading their symbols as dates.

The problem isn’t as unexpected as it first sounds. Excel is a behemoth in the spreadsheet world and is regularly used by scientists to track their work and even conduct clinical trials. But its default settings were designed with more mundane applications in mind, so when a user inputs a gene’s alphanumeric symbol into a spreadsheet, like MARCH1 — short for “Membrane Associated Ring-CH-Type Finger 1” — Excel converts that into a date: 1-Mar.

This is extremely frustrating, even dangerous, corrupting data that scientists have to sort through by hand to restore. It’s also surprisingly widespread and affects even peer-reviewed scientific work. One study from 2016 examined genetic data shared alongside 3,597 published papers and found that roughly one-fifth had been affected by Excel errors.

“It’s really, really annoying,” Dezso Modos, a systems biologist at the Quadram Institute in the UK, told The Verge. Modos, whose job involves analyzing freshly sequenced genetic data, says Excel errors happen all the time, simply because the software is often the first thing to hand when scientists process numerical data. “It’s a widespread tool and if you are a bit computationally illiterate you will use it,” he says. “During my PhD studies I did as well!”

Examples of gene symbols being rendered as dates in Microsoft Excel.
GIF: The Verge

There’s no easy fix, either. Excel doesn’t offer the option to turn off this auto-formatting, and the only way to avoid it is to change the data type for individual columns. Even then, a scientist might fix their data but export it as a CSV file without saving the formatting. Or, another scientist might load the data without the correct formatting, changing gene symbols back into dates. The end result is that while knowledgeable Excel users can avoid this problem, it’s easy for mistakes to be introduced.

Help has arrived, though, in the form of the scientific body in charge of standardizing the names of genes, the HUGO Gene Nomenclature Committee, or HGNC. This week, the HGNC published new guidelines for gene naming, including for “symbols that affect data handling and retrieval.” From now on, they say, human genes and the proteins they expressed will be named with one eye on Excel’s auto-formatting. That means the symbol MARCH1 has now become MARCHF1, while SEPT1 has become SEPTIN1, and so on. A record of old symbols and names will be stored by HGNC to avoid confusion in the future.

So far, the names of some 27 genes have been changed like this over the past year, Elspeth Bruford, the coordinator of HGNC, tells The Verge, but the guidelines themselves weren’t formally announced until this week. “We consulted the respective research communities to discuss the proposed updates, and we also notified researchers who had published on these genes specifically when the changes were being put into effect,” says Bruford.

As Bruford makes clear, the art of naming genes is very much driven by consensus. Like the lexicographers charged with updating dictionaries, the Gene Nomenclature Committee has to be sensitive to the needs of those individuals who will be most affected by their work.

This wasn’t always the case, mind. In the early, frontier days of genetics, gene naming was often a playground for creative scientists, leading to notorious genes like “sonic hedgehog” (yes, named for that Sonic) and “Indy” (short for “I’m not dead yet”; a reference to the gene’s function, which can double the life span of fruit flies when mutated).

Now, though, the HGNC has taken matters firmly in hand, and current guidelines don’t cede much ground to whimsy or ego. The focus is on practical concerns: how do we minimize confusion? For that reason, gene symbols should be unique, and gene names should be brief and specific, says the committee. They cannot use subscript or superscript; can only contain Latin letters and Arabic numerals; and should not spell out names or words, particularly offensive ones (a rule that should hold true “ideally in any language”).

And while the decision to rename genes is not taken lightly, it’s not unusual, says Bruford. Many gene symbols that can be read as nouns have been renamed to avoid false positives during searches, for example. In the past, CARS has become CARS1, WARS changed to WARS1, and MARS tweaked to MARS1. Other changes have been made to avoid insult.

“We always have to imagine a clinician having to explain to a parent that their child has a mutation in a particular gene,” says Bruford. “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.”

But Bruford says this is the first time that the guidelines have been rewritten specifically to counter the problems caused by software. So far, the reactions seem to be extremely positive — some would even say joyous.

After geneticist Janna Hutz shared the relevant section of HGNC’s new guidelines on Twitter, the response from the community was jubilant. “THRILLED by this announcement by the Human Gene Nomenclature Committee,” tweeted Hutz herself. “Finally!!!” responded Mudra Hegde, a computational biologist at the Broad Institute in Massachusetts. “Greatest news of the day!” said a pseudonymous Twitter user.

Bruford notes that there has been some dissent about the decision, but it mostly seems to be focused on a single question: why was it easier to rename human genes than it was to change how Excel works? Why, exactly, in a fight between Microsoft and the entire genetics community, was it the scientists who had to back down?

Microsoft did not respond to a request for comment, but Bruford’s theory is that it’s simply not worth the trouble to change. “This is quite a limited use case of the Excel software,” she says. “There is very little incentive for Microsoft to make a significant change to features that are used extremely widely by the rest of the massive community of Excel users.”

Bruford doesn’t seem bitter about the situation, though. After all, she says, it wouldn’t do to wait on a hypothetical Excel update to fix these problems when a long-term solution can be introduced by scientists themselves. Microsoft Excel may be fleeting, but human genes will be around for as long as we are. It’s best to give them names that work.

Correction: The story has been corrected to clarify that Excel users can save spreadsheets that retain their formatting, avoiding the mistake where gene symbols are changed into dates. We regret the error.

Source : TheVerge ScienceRead More

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Too bright to breed

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Night light from coastal cities overpowers natural signals for coral spawning from neighboring reefs.

PHOTO: NOKURO/ALAMY STOCK PHOTO

Most coral species reproduce through broadcast spawning. For such a strategy to be successful, coordination has had to evolve such that gametes across clones are released simultaneously. Over millennia, lunar cycles have facilitated this coordination, but the recent development of bright artificial light has led to an overpowering of these natural signals. Ayalon et al. tested for the direct impact of different kinds of artificial light on different species of corals. The authors found that multiple lighting types, including cold and warm light-emitting diode (LED) lamps, led to loss of synchrony and spawning failure. Further, coastal maps of artificial lighting globally suggest that it threatens to interfere with coral reproduction worldwide and that the deployment of LED lights, the blue light of which penetrates deeper into the water column, is likely to make the situation even worse.

Curr. Biol. 10.1016/j.cub.2020.10.039 (2020).

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SpaceX launches Starlink app and provides pricing and service info to early beta testers

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SpaceX has debuted an official app for its Starlink satellite broadband internet service, for both iOS and Android devices. The Starlink app allows users to manage their connection – but to take part you’ll have to be part of the official beta program, and the initial public rollout of that is only just about to begin, according to emails SpaceX sent to potential beta testers this week.

The Starlink app provides guidance on how to install the Starlink receiver dish, as well as connection status (including signal quality), a device overview for seeing what’s connected to your network, and a speed test tool. It’s similar to other mobile apps for managing home wifi connections and routers. Meanwhile, the emails to potential testers that CNBC obtained detail what users can expect in terms of pricing, speeds and latency.

The initial Starlink public beta test is called the “Better than Nothing Beta Program,” SpaceX confirms in their app description, and will be rolled out across the U.S. and Canada before the end of the year – which matches up with earlier stated timelines. As per the name, SpaceX is hoping to set expectations for early customers, with speeds users can expect ranging from between 50Mb/s to 150Mb/s, and latency of 20ms to 40ms according to the customer emails, with some periods including no connectivity at all. Even with expectations set low, if those values prove accurate, it should be a big improvement for users in some hard-to-reach areas where service is currently costly, unreliable and operating at roughly dial-up equivalent speeds.

Image Credits: SpaceX

In terms of pricing, SpaceX says in the emails that the cost for participants in this beta program will be $99 per moth, plus a one-time cost of $499 initially to pay for the hardware, which includes the mounting kit and receiver dish, as well as a router with wifi networking capabilities.

The goal eventually is offer reliably, low-latency broadband that provides consistent connection by handing off connectivity between a large constellation of small satellites circling the globe in low Earth orbit. Already, SpaceX has nearly 1,000 of those launched, but it hopes to launch many thousands more before it reaches global coverage and offers general availability of its services.

SpaceX has already announced some initial commercial partnerships and pilot programs for Starlink, too, including a team-up with Microsoft to connect that company’s mobile Azure data centers, and a project with an East Texas school board to connect the local community.

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Erratum for the Report “Meta-analysis reveals declines in terrestrial but increases in freshwater insect abundances” by R. Van Klink, D. E. Bowler, K. B. Gongalsky, A. B. Swengel, A. Gentile, J. M. Chase

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