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.
Studies found a fifth of genetic data in papers was affected by Excel errors
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,” Dezső Módos, a systems biologist at the Quadram Institute in the UK, told The Verge. Módos, 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!”
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”).
Gene names should avoid offense “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.
Why did Microsoft win in a fight against human genetics?
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.
Kuna maelfu ya jeni katika genome ya binadamu: twists ndogo ya DNA na RNA ambayo kuchanganya kueleza sifa zote na sifa kwamba kufanya kila mmoja wetu kipekee. Kila jeni lina jina na nambari ya herufi na tarakimu, inayojulikana kama ishara, ambayo wanasayansi hutumia kuratibu utafiti. Katika mwaka uliopita, jeni 27 za binadamu zilibadilishwa majina kwa sababu Microsoft Excel ilisoma vibaya alama zao kama tarehe. Tatizo hilo si lisilotazamiwa kama linavyosikika mwanzoni. Excel ni moja ya programu maarufu zaidi ulimwenguni na hutumiwa na wanasayansi kufuatilia kazi zao na hata kufanya majaribio ya kliniki. "Kama ilivyoelezwa hapo juu, ""Membrane Associated Ring-CH-Type Finger"" ni kifupi cha ""Membrane Associated Ring-CH-Type Finger"" (MARCH1) na ""Excel"" ni kifupi cha ""Membrane Associated Ring-CH-Type Finger"" (MARCH1)." Utafiti unaonyesha kuwa asilimia tano ya data ya maumbile ya binadamu huathiriwa na makosa ya Excel, na hii ni hatari sana kwa wanasayansi kuharibu data zao kwa mikono. Pia ni ya kushangaza kuenea na huathiri hata kazi ya kisayansi peer-kukaguliwa. Utafiti uliofanywa mnamo 2016 ulichunguza data ya maumbile iliyoshirikiwa pamoja na karatasi 3,597 zilizochapishwa na kugundua kuwa karibu moja ya tano ilikuwa imeathiriwa na makosa ya Excel. "Hiyo ni ya kuchukiza sana,"" Dezső Módos, mwanabiolojia wa mifumo katika Taasisi ya Quadram nchini Uingereza, aliliambia The Verge." Modo, ambaye kazi yake ni kuchanganua data mpya ya maumbile, anasema makosa ya Excel hutokea wakati wote, kwa sababu programu ni mara nyingi kitu cha kwanza mkono wakati wanasayansi mchakato wa data ya tarakimu. <unk>Ni chombo kinachopatikana sana na ikiwa wewe ni mchanganuo wa kompyuta usiojua kusoma na kuandika utaitumia,<unk> anasema. <unk>Wakati wa masomo yangu ya PhD nilifanya pia! <unk> Hakuna suluhisho rahisi, ama. Excel haina kutoa chaguo la kuzima hii auto-kufomata, na njia pekee ya kuiepuka ni kubadilisha aina ya data kwa safu za mtu binafsi. Hata hivyo, mwanasayansi anaweza kurekebisha data zao lakini kuuza nje kama faili ya CSV bila kuhifadhi umbizo. Au, mwanasayansi mwingine aweza kupakia data bila muundo sahihi, akibadilisha alama za jeni kuwa tarehe. Matokeo ya mwisho ni kwamba wakati watumiaji wenye ujuzi wa Excel wanaweza kuepuka tatizo hili, ni rahisi kwa makosa kuanzishwa. "Hili ni jambo ambalo limetokea kwa sababu ya kutofautisha majina ya jeni na majina ya watu, na kwa sababu ya kuanzisha ""Hugo Gen Nomenclature Committee"" (HGNC)." HGNC imetoa miongozo mpya ya jina la jeni, ikiwa ni pamoja na alama ambazo zinaathiri utunzaji wa data na kupata, na sasa, jeni za binadamu na protini zinazozungumziwa zitaitwa kwa jicho moja kwenye muundo wa Excel. "Kama ilivyoelezwa hapo juu, ""MARCH"" ni jina la alama ya kwanza ya MEP, ""MARCH"" ni jina la alama ya kwanza ya MEP, ""MARCH"" ni jina la alama ya kwanza ya MEP, ""MEP"" ni jina la alama ya kwanza ya MEP, na ""MEP"" ni jina la kwanza la alama ya MEP." Hifadhi ya alama za zamani na majina itahifadhiwa na HGNC ili kuepuka kuchanganyikiwa katika siku zijazo. "Jina la jeni 27 limebadilishwa kwa njia hii kwa mwaka mmoja, ""Elspeth Bruford, mratibu wa HGNC, anasema, lakini miongozo yenyewe haikutangazwa rasmi hadi wiki hii." "Tuliwashauri jamii za utafiti zinazohusika kujadili sasisho zilizopendekezwa, na pia tukawajulisha watafiti ambao walikuwa wamechapisha juu ya jeni hizi haswa wakati mabadiliko yalikuwa yakiwekwa katika athari", anasema Bruford. Kama Bruford anavyoeleza waziwazi, sanaa ya kutaja majina ya chembe za urithi huongozwa sana na makubaliano. Kama vile wasomi wa kamusi wanaohusika na kusasisha kamusi, Kamati ya Jina la Jini inapaswa kuwa nyeti kwa mahitaji ya wale watu ambao wataathiriwa zaidi na kazi yao. Hii haikuwa hivyo sikuzote, kumbuka. Katika siku za mapema, mipaka ya maumbile, jina la jeni mara nyingi lilikuwa uwanja wa michezo kwa wanasayansi wa ubunifu, ikisababisha jeni maarufu kama <unk>sonic hedgehog<unk> (ndiyo, jina kwa Sonic) na <unk>Indy<unk> (fupi kwa <unk>I'm not dead yet<unk>; kumbukumbu ya kazi ya jeni, ambayo inaweza mara mbili maisha ya nzi matunda wakati mutated). Sasa, ingawa, HGNC imechukua mambo kwa uthabiti mkononi, na miongozo ya sasa haitoi ardhi nyingi kwa whimsy au ego. Lengo ni juu ya masuala ya vitendo: jinsi ya kupunguza kuchanganyikiwa? Kwa sababu hiyo, ishara za jeni zapasa kuwa za kipekee, na majina ya jeni yapasa kuwa mafupi na ya pekee, husema halmashauri hiyo. Hawawezi kutumia subscript au superscript; wanaweza tu kuwa na herufi za Kilatini na tarakimu za Kiarabu; na hawapaswi kuandika majina au maneno, hasa yale yenye kuudhi (sheria ambayo inapaswa kuwa kweli <unk>kimsingi katika lugha yoyote<unk>). Majina ya jeni yanapaswa kuepuka kukasirisha - kwa njia bora katika lugha yoyote - Na ingawa uamuzi wa kubadili jina la jeni hauchukuliwi kwa urahisi, si jambo lisilo la kawaida, anasema Bruford. Ishara nyingi za jeni ambazo zinaweza kusomwa kama majina zimebadilishwa majina ili kuepuka matokeo mabaya wakati wa utafutaji, kwa mfano. "Kama ilivyoelezwa hapo juu, ""Mars"" ni jina la kwanza la mashine ya kupigia risasi, na ""Mars"" ni jina la kwanza la mashine ya kupigia risasi." Mabadiliko mengine yamefanywa ili kuepuka kudharau. "Lazima tufikirie daktari akimweleza mzazi kwamba mtoto wao ana mabadiliko katika jeni fulani", anasema Bruford. "Kwa mfano, HECA ilitumia jina la jeni ""headcase homolog (Drosophila) "" lililoitwa baada ya jeni sawa katika nzi wa matunda, lakini tulibadilisha kuwa ""hdc homolog, mtawala wa mzunguko wa seli "" ili kuepuka kosa linalowezekana. "" Lakini Bruford anasema hii ni mara ya kwanza kwamba miongozo imeandikwa upya haswa kukabiliana na matatizo yanayosababishwa na programu." Hadi sasa, majibu yanaonekana kuwa mazuri sana - wengine wangesema hata ni yenye furaha. Baada ya mtaalamu wa maumbile Janna Hutz kushiriki sehemu husika ya miongozo mpya ya HGNC kwenye Twitter, majibu kutoka kwa jamii yalikuwa ya shangwe. "NIMESHANGazwa na tangazo hili la Kamati ya Uteuzi wa Jeni ya Binadamu", Hutz mwenyewe alitoa ujumbe kwenye Twitter. <unk> Mwishowe!! !! alijibu Mudra Hegde, mwanabiolojia wa hesabu katika Taasisi ya Broad huko Massachusetts. "Habari bora ya siku!" alisema mtumiaji wa Twitter aliyejiita jina bandia. Kwa nini Microsoft ilishinda katika mapambano dhidi ya chembe za urithi za binadamu? "Bruford anasema kuwa ""kuna baadhi ya kutoelewana juu ya uamuzi, lakini inaonekana zaidi ni ililenga juu ya swali moja: kwa nini ilikuwa rahisi kubadilisha majina ya jeni la binadamu kuliko ilikuwa kubadilisha jinsi Excel kazi?""" Kwa nini, hasa, katika mapigano kati ya Microsoft na jamii nzima ya maumbile, ilikuwa ni wanasayansi ambao walilazimika kurudi nyuma? Microsoft haikujibu ombi la maoni, lakini nadharia ya Bruford ni kwamba haifai kubadilisha. "Hii ni kesi ya matumizi mdogo kabisa ya programu ya Excel", anasema. <unk>Kuna motisha kidogo sana kwa Microsoft kufanya mabadiliko makubwa kwa vipengele ambavyo hutumiwa sana na wengine wa jamii kubwa ya watumiaji wa Excel.<unk> Bruford haionekani kuwa na uchungu juu ya hali hiyo, ingawa. Baada ya yote, yeye anasema, haingekuwa kufanya kusubiri juu ya nadharia Excel update kurekebisha matatizo haya wakati ufumbuzi wa muda mrefu inaweza kuanzishwa na wanasayansi wenyewe. Microsoft Excel inaweza kuwa ya muda mfupi, lakini jeni za binadamu zitakuwa karibu kwa muda mrefu kama sisi ni. Ni afadhali kuwapa majina yanayofaa. "Kutengeneza: Hadithi imerekebishwa ili kufafanua kwamba watumiaji wa Excel wanaweza kuhifadhi karatasi za kupakia ambazo zinahifadhi muundo wao, kuepuka kosa ambapo alama za jeni zimebadilishwa kuwa tarehe. """ Tunahuzunika kwa kosa hilo.