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Report Finds Microsoft Excel Causes Errors in 20 Percent of Genomics Studies

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Microsoft Excel, that ubiquitous tool for data crunching, has been playing an unexpected role in the scientific world. The program has been screwing with data in genomics studies. A new report in the journal Genome Biology estimates that around 20 percent of scientific papers published in leading genome-focused journals that include gene lists from Excel contain errors due to the program’s default autocorrect settings, Slate reports.

The problem is, several genes have symbols that look a lot like dates. The program has a tendency to convert gene symbols like SEPT2 (Septin 2) and MARCH1 (Membrane Associated Ring-CH-Type Finger) into what Excel thinks is proper date form—turning them into 2-Sept and 1-Mar instead. In some, SEPT2 became “2006/09/02.”

"Inadvertent gene symbol conversion is problematic because these supplementary files are an important resource in the genomics community that are frequently reused," the paper’s authors write. They reviewed the supplementary gene list Excel files from 18 journals, examining studies published between 2005 and 2015—Excel’s gene-typo issue was first reported in 2004—for date formatting within lists of genes. The analysis was performed by a program that flagged supplementary materials that seemed to be lists of genes, then searched them for date formatting. Out of more than 35,000 supplementary files, they confirmed 987 files with gene errors that were published as part of 704 studies.

Overall, 19.6 percent of papers in the 18 journals contained gene name errors caused by Excel’s autocorrect function, but some journals were worse than others. High-impact journals, typically the most respected outlets to publish research in, actually had more affected gene lists, which the researchers speculate may be because studies published in these journals are more likely to have larger and more numerous data sets.

The highest proportion of gene lists with errors (more than 20 percent) came from the journals Nucleic Acids Research, Genome Biology, Nature Genetics, Genome Research, Genes and Development, and Nature; conversely, the journals Molecular Biology and Evolution, Bioinformatics, DNA Research, and Genome Biology and Evolution showed errors in less than 10 percent of genomics papers.

While this isn’t the worst scientific error to end up in a journal, since it’s pretty clear that 2006/09/02 isn’t a gene symbol, it’s also fairly disturbing that this many papers could make it through the editing process without anyone noticing that they contained lists of nonexistent genes.

The researchers highlight Google Sheets as a potential alternative for Excel, because it doesn’t suffer from the same symbol-date mixup, and it seems that when you open Sheets documents in other programs like Excel, the data is protected from Excel’s default autocorrection. They suggest that journal editors and reviewers should look out for these errors, pasting gene name lists into blank files and sorting them so that any dates that have been mistakenly inserted will become apparent.

[h/t Slate]

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Why DNA Is So Hard to Visualize
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Picture a strand of DNA and the image you see will likely be similar to the artist’s rendering above. The iconic twisted ladder, or double-helix structure, was first revealed in a photo captured by Rosalind Franklin in the 1950s, but this popular visualization only tells part of the story of DNA. In the video below, It’s Okay to Be Smart explains a more accurate way to imagine the blueprints of life.

Even with sophisticated lab equipment, DNA isn’t easy to study. That’s because a strand of the stuff is just 2 nanometers wide, which is smaller than a wavelength of light. Researchers can use electron microscopes to observe the genetic material or x-rays like Rosalind Franklin did, but even these tools paint a flawed picture. The best method scientists have come up with to visualize DNA as it exists inside our cells is computer modeling.

By rendering a 3D image of a genome on a computer, we can see that DNA isn’t just a bunch of free-floating squiggles. Most of the time the strands sit tightly wound in a well-organized web inside the nucleus. These balls of genes are efficient, packing 2 meters of DNA into a space just 10 millionths of a meter across. So if you ever see a giant sculpture inspired by an elegant double-helix structure, imagine it folded into a space smaller than a shoe box to get closer to the truth.

[h/t It’s Okay to Be Smart]

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Scientists Remove Disease-Causing Mutations from Human Embryos
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Researchers have successfully edited the genes of viable human embryos to repair mutations that cause a dangerous heart condition. The team published their controversial research in the journal Nature.

The versatile gene-editing technique known as CRISPR-Cas9 is no stranger to headlines. Scientists have already used it to breed tiny pigs, detect disease, and even embed GIFs in bacteria. As our understanding of the process grows more advanced and sophisticated, many researchers have wondered how it could be applied to human beings.

For the new study, an international team of researchers fertilized healthy human eggs with sperm from men with a disease called hypertrophic cardiomyopathy, a condition that can lead to sudden death in young people. The mutation responsible for the disease affects a gene called MYBPC3. It’s a dominant mutation, which means that an embryo only needs one bad copy of the gene to develop the disease.

Or, considered another way, this means that scientists could theoretically remove the disease by fixing that one bad copy.

Eighteen hours after fertilizing the eggs, the researchers went back in and used CRISPR-Cas9 to snip out mutated MYBPC3 genes in some of the embryos and replace them with healthy copies. Three days later, they checked back in to see how their subjects—which were, at this point, still microscopic balls of cells—had fared.

The treatment seemed successful. Compared to subjects in the control group, a significant number of edited embryos appeared mutation- and disease-free. The researchers also found no evidence that their intervention had led to any unwanted new mutations, although it is possible that the mutations were there and overlooked.

Our ability to edit human genes is improving by the day. But, many ethicists argue, just because we can do it doesn’t mean that we should. The United States currently prohibits germline editing of human embryos by government-funded researchers. But there’s no law against such experimentation in privately funded projects like this one.

The same day the new study was published, an international committee of genetics experts issued a consensus statement advising against editing any embryo intended for implantation (pregnancy and birth).

"While germline genome editing could theoretically be used to prevent a child being born with a genetic disease, its potential use also raises a multitude of scientific, ethical, and policy questions,” Derek T. Scholes of the American Society of Human Genetics said in a statement. “These questions cannot all be answered by scientists alone, but also need to be debated by society."

Ethicists and sociologists are concerned by the slippery slope of trying to build a better human. Many people with chronic illness and disability live happy, complete lives and report that they’re limited more by discrimination than by any medical issues.

Disability studies expert Lennard Davis of the University of Illinois says we can’t separate scientific decisions from our society’s history of violence against, and oppression of, disabled and sick people.

“A lot of this terrific science and technology has to take into account that the assumption of what life is like for people who are different is based on prejudice against disability,” he told Nature in 2016.

Rosemary Garland-Thomson is co-director of the Disability Studies Initiative at Emory University. Speaking to Nature, she said we are at a cultural and ethical precipice: “At our peril, we are right now trying to decide what ways of being in the world ought to be eliminated.”

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