genes – Techdirt (original) (raw)

Scientists Forced To Change Names Of Human Genes Because Of Microsoft's Failure To Patch Excel

from the code-is-law dept

Six years ago, Techdirt wrote about a curious issue with Microsoft’s Excel. A default date conversion feature was altering the names of genes, because they looked like dates. For example, the tumor suppressor gene DEC1 (Deleted in Esophageal Cancer 1) was being converted to “1-DEC”. Hardly a widespread problem, you might think. Not so: research in 2016 found that nearly 20% of 3500 papers taken from leading genomic journals contained gene lists that had been corrupted by Excel’s re-interpretation of names as dates. Although there don’t seem to be any instances where this led to serious errors, there is a natural concern that it could distort research results. The good news is this problem has now been fixed. The rather surprising news is that it wasn’t Microsoft that fixed it, even though Excel was at fault. As an article in The Verge reports:

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, 27 genes have been re-named in this way. Modifying gene names in itself is not unheard of. The Verge article notes that, in the past, names that made sense to experts, but which might alarm or offend lay people, are also changed from time to time:

“We always have to imagine a clinician having to explain to a parent that their child has a mutation in a particular gene,? says [Elspeth Bruford, the coordinator of HGNC]. “For example, HECA [a cancer-related human gene] 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.”

It is nice to know that we won’t need to worry about serious problems flowing from Excel’s habit of automatically re-naming cell entries. But it’s rather troubling that Microsoft doesn’t seem to have thought the problem worthy of its attention or a fix, despite it being known for at least six years. It shows once again how people are being forced to adapt to the software they use, rather than the other way around. Or, as Lawrence Lessig famously wrote: “code is law“?

Follow me @glynmoody on Twitter, Diaspora, or Mastodon.

Filed Under: autoconversion, dates, excel, gene names, genes, spreadsheets
Companies: microsoft

DailyDirt: There's So Much We Don't Know About Life…

from the urls-we-dig-up dept

Biology defies simple categorization — even though some think of the field of biology as glorified taxidermy. We even have a difficult time defining what life is. (Are viruses alive?) Fundamental questions about how life began and how life even continues are still elusive. We’ve just started to scratch the surface of collecting data that might help us understand more about ourselves and the ecosystem we live in. Here are just a few links on genomes and biodiversity that lead to more questions than answers.

• What is the ‘hypothetical minimal genome’ required for a living organism to exist? Researchers thought that maybe a living cell could get away with 256 genes, but it didn’t produce a viable living organism. So after a some trial & error iterations of editing simple bacterial genomes, it looks like 473 genes might be the smallest genome that life needs… to be called life. (And we still don’t know what a significant fraction of these genes do.) [url]
• Genome analysis is becoming more practical to do on a large scale, and for just $25,000, you could have your own personal genome — plus a battery of other medical tests that may or may not provide any meaningful results. Collecting all this health data, though, could start to provide some interesting correlations, and the company offering the service is named Human Longevity — so there might be something in aggregating this information that might help people live longer lives. [url]
• How many mammalian viruses exist? At least 320,000? And there’s probably no limit to the number. It’s important to note that not all viruses cause disease — bacteriophages keep us healthy by killing off bacteria that do cause diseases. So we don’t want to eradicate viruses, but it would be nice to know more about them. [url]

After you’ve finished checking out those links, take a look at our Daily Deals for cool gadgets and other awesome stuff.

Filed Under: bacteria, bacteriophages, biology, dna, genes, genome, hypothetical minimal genome, longevity, viruses

DailyDirt: Is It All In The Genes?

from the urls-we-dig-up dept

The Nature vs Nurture debate may never end, but it could become more interesting as researchers quantify the Nature aspects with genetics (and epigenetics and microbiome information and …). But we’ve really only just started to learn about the vast genetic world of biology. We still have a lot to learn from simple fruit flies, so we’re not about to crack the enormous number of genomes that exist (or that could even be synthesized). Here are just a few genomes that scientists have started playing with.

• Octopus DNA is unusually large, but that’s maybe not so surprising given how intelligent and complex these creatures are. In case you didn’t know, octopuses can regrow limbs, change their skin color for camouflage, expel a cloud of ink to escape predators, and manipulate their boneless bodies to their advantage — in surprising ways. The California two-spot octopus is the first cephalopod to have its genome fully sequenced, and while its genome is slightly shorter than the human genome, the octopus seems to have more genes than we do. [url]
• The genome of ixodes scapularis (aka the common tick) has been published, and it could lead to better ways to control these blood-sucking arthropods (and maybe Lyme disease, too). Tick saliva contains all kinds of possible pharmaceuticals (antimicrobials, analgesics, blood thinners, and immune suppressors) that help the bug feed on a variety of host animals. [url]
• Immortal HeLa cells have been useful in research because they were one of the first human cell lines to be conveniently grown outside of a person’s body. However, HeLa cells originally came from a patient’s tumor, so its DNA is filled with errors and is very different from normal human DNA. Cancer cells might even qualify as a new species — if researchers can agree on a definition of what “species” is. [url]
• A platypus is just a weird animal, so it’s not at all strange that its genome is weird, too. Platypus DNA codes for traits that are mammalian, reptilian and avian — and the animal itself lays eggs, produces milk for its offspring and has unusual sex chromosomes. [url]

After you’ve finished checking out those links, take a look at our Daily Deals for cool gadgets and other awesome stuff.

Filed Under: arthropod, biotech, cancer, cephalopod, dna, genes, genetics, genome, hela cells, ixodes scapularis, octopus, platypus, tick

DailyDirt: Creating Superfoods For Fun Profit

from the urls-we-dig-up dept

Feeding billions of people isn’t an easy task. Farming isn’t actually the hardest part. Food distribution and food waste are much more challenging than simply growing more food for people. It’s good that we have multiple biotech solutions for making plants and animals that are easier to raise and grow, but some of the concerns about genetically modified organisms (GMOs) aren’t totally unfounded. Turning back the clock on genetic research isn’t going to happen, but we should also keep an eye on what’s going on.

• Dupont and Caribou Biosciences are working on CRISPR technology to modify the genes of food crops, predicting that CRIPSR GMO foods will be on dinner plates by 2020. Genetically modified corn and wheat plants are already being grown in greenhouses, and many other plants are being tested, too: soybeans, rice, tomatoes, potatoes — even allergy-free peanuts. The resulting plants have no genes from other species, so it may be much easier to avoid GMO regulations with these kind of gene-edited crops. [url]
• Yum yum. A succulent red marine algae called dulse looks like translucent red lettuce, is high in protein, and tastes like bacon when cooked. This strain of dulse is patented, but the claims don’t mention its bacon-y goodness. So get back in the lab and start creating more bacon-flavored species, already! [url]
• Many scientists are hard pressed to find the harm in creating genetically modified organisms — because genes are genes. However, there are still concerns with monoculture crops and creating a food supply chain that is dominated by a handful of companies. [url]

Hold on. If you’re still reading this, head over to our Daily Deals to save an additional 10% on any item in our Black Friday collection — using the code: ‘EARLY10’ — just through this Sunday, November 22nd.

Filed Under: algae, bacon, biotech, crispr, dulse, farming, food, food supply chain, genes, genetics, gmo, plants
Companies: caribou biosciences, dupont

DailyDirt: Messing With Mice Brains

from the urls-we-dig-up dept

The genes that make humans distinct from other animals are being narrowed down. We have a lot in common with other mammals and especially other primates, but relatively tiny differences in a set of genes could explain how human language and intelligence evolved and developed. Understanding the complexity of human intelligence and genetics will likely take decades or longer — and we may never fully understand every aspect of consciousness. However, we’re making some progress and creating some smarter mice along the way. Check out a few of these experiments.

• Injecting human astrocytes (the most abundant cells found in the brain) into a mouse brain actually makes mice measurably smarter. This isn’t exactly the beginnings of the rats of NIMH, but the researchers are going to try rats next…. [url]
• Activating a certain gene called HARE5 (“human-accelerated regulatory enhancers”) leads to the development of bigger brains in humans — and perhaps other mammals like mice and chimpanzees. A mouse embryo treated with a human HARE5 sequence developed a 12% larger brain than a mouse embryo with a chimpanzee HARE5 gene. [url]
• Hundreds of mice have been genetically engineered to express the human version of the FOXP2 gene — a gene linked to speech and language. The resulting mice were able to learn a maze faster than control mice. And are you pondering what I’m pondering? [url]
• The ARHGAP11B gene could be a unique gene for developing modern humans’ massive neocortex. Adding this gene in mice gave them larger neocortices and brain folds (mice brains are usually tiny and smooth) — but the mice weren’t necessarily more intelligent. [url]

If you’d like to read more awesome and interesting stuff, check out this unrelated (but not entirely random!) Techdirt post via StumbleUpon.

Filed Under: animals, arhgap11b gene, astrocytes, brains, dna, evolution, foxp2 gene, genes, genetics, hare5 gene, intelligence, mice, neocortex, nihm

Will Patents Ruin The Most Important Biotech Discovery In Recent Years?

from the rhetorical-question dept

Although not many outside the world of the biological sciences have heard of it yet, the CRISPR gene editing technique may turn out to be one of the most important discoveries of recent years — if patent battles don’t ruin it. Technology Review describes it as:

> an invention that may be the most important new genetic engineering technique since the beginning of the biotechnology age in the 1970s. The CRISPR system, dubbed a “search and replace function” for DNA, lets scientists easily disable genes or change their function by replacing DNA letters. During the last few months, scientists have shown that it’s possible to use CRISPR to rid mice of muscular dystrophy, cure them of a rare liver disease, make human cells immune to HIV, and genetically modify monkeys.

Unfortunately, rivalry between scientists claiming the credit for key parts of CRISPR threatens to spill over into patent litigation:

> [A researcher at the MIT-Harvard Broad Institute, Feng] Zhang cofounded Editas Medicine, and this week the startup announced that it had licensed his patent from the Broad Institute. But Editas doesn’t have CRISPR sewn up. That’s because [Jennifer] Doudna, a structural biologist at the University of California, Berkeley, was a cofounder of Editas, too. And since Zhang’s patent came out, she’s broken off with the company, and her intellectual property — in the form of her own pending patent — has been licensed to Intellia, a competing startup unveiled only last month. Making matters still more complicated, [another CRISPR researcher, Emmanuelle] Charpentier sold her own rights in the same patent application to CRISPR Therapeutics.

Things are moving quickly on the patent front, not least because the Broad Institute paid extra to speed up its application, conscious of the high stakes at play here:

> Along with the patent came more than 1,000 pages of documents. According to Zhang, Doudna’s predictions in her own earlier patent application that her discovery would work in humans was “mere conjecture” and that, instead, he was the first to show it, in a separate and “surprising” act of invention. > > The patent documents have caused consternation. The scientific literature shows that several scientists managed to get CRISPR to work in human cells. In fact, its easy reproducibility in different organisms is the technology’s most exciting hallmark. That would suggest that, in patent terms, it was “obvious” that CRISPR would work in human cells, and that Zhang’s invention might not be worthy of its own patent.

Whether obvious or not, it looks like the patent granted may complicate turning the undoubtedly important CRISPR technique into products. That, in its turn, will mean delays for life-changing and even life-saving therapies: for example, CRISPR could potentially allow the defective gene that causes serious problems for those with cystic fibrosis to be edited to produce normal proteins, thus eliminating those problems.

Although supporters of patents will argue as usual that they are necessary to encourage the discovery of new treatments, CRISPR is another example where patents simply get in the way. The discoveries were made by scientists in the course of their work in fundamental science at academic institutions, not because they were employed by a company to come up with a new product. According to some, the basic application of CRISPR to human cells that everyone is fighting over may even be obvious. The possibility of legal action will doubtless discourage investment in companies working in this area, and thus slow down the flow of new treatments. As usual, the only ones who win here are the lawyers.

Follow me @glynmoody on Twitter or identi.ca, and +glynmoody on Google+

Filed Under: biotech, crispr, dna, emmanuelle charpentier, feng zhang, gene editing, genes, jennifer doudna, patent fights, patents
Companies: broad institute, editas medicine, intellia

Now It's Canada's Turn To Decide On The Patentability Of Genes

from the matter-of-life-and-death dept

It’s taken a surprisingly long time for countries to settle the question of whether something as fundamental as genes can be patented or not. And opinions still differ: last year, the US Supreme Court ruled that naturally-occurring genes couldn’t be patented, while more recently, Australia went the other way (although it’s possible that ruling could be overturned by higher courts there). Now a test case has been filed this week to establish the situation in Canada, as the Toronto Star reports:

Monday’s legal case, brought by the Children’s Hospital of Eastern Ontario (CHEO), deals with five patents held in Canada by the University of Utah on genes and tests for an inherited cardiac condition called Long QT syndrome.

Interestingly, the case is not about genes that play a role in developing breast cancer, which were the focus of attention in both the US and Australian court decisions. However, as with breast cancer, the effects of allowing gene patents in this area is the same — to drive up the cost of testing:

The two-tier test [for Long QT syndrome] currently costs approximately $4,500 (U.S.) per person, CHEO estimates, whereas researchers at the hospital believe they could administer the same process in-house for about half the cost.

“The collective impact (of this case) could easily be in the orders of millions of dollars for the healthcare system,” said Gail Graham, a clinical geneticist at the hospital.

This isn’t just about money: it’s a matter of life and death. The more expensive a gene-based test, the less likely it will be used by hospitals, which are struggling to make their limited budgets stretch as far as possible. And that means that medical conditions will be missed, with serious, possibly fatal, consequences.

Follow me @glynmoody on Twitter or identi.ca, and +glynmoody on Google+

Filed Under: canada, dna, genes, patents
Companies: cheo, children's hospital of eastern ontario, university of utah

Australian Court Disagrees With US: Claim Genes Are Totally Patentable

from the sucks-to-be-DownUnder dept

Last year, the Supreme Court made an important ruling in the Myriad Genetics case, effectively saying that genes aren’t patentable, even if you can separate them out from the rest of a strand of DNA. Myriad Genetics had isolated two key genes related to breast cancer, BRCA1 and BRCA2 and argued that only it could test for those genes, because of its patent. The Supreme Court soundly rejected that, noting that you cannot patent something in nature, and clearly Myriad did not “make” the genes. Unfortunately, as we’d noted just a few months earlier, a court in Australia had come to the opposite conclusion, saying that Myriad Genetics had legitimate patents on BRCA1 and BRCA2. That case was appealed, and there was some hope that after the US’s ruling, higher courts in Australia might see the light. Not yet apparently. An appeals court has agreed that genes are patentable Down Under, which means that such important genetic tests there are likely to be much more expensive and limited.

You can read the full ruling here if you’d like. The case can still be appealed to the Australian High Court, so perhaps it will take the same trajectory as in the US, where it needed the Supreme Court to finally point out the absolute insanity of patenting genes. Though, frankly, if Australia does keeps genes patentable, it might make for an interesting natural experiment to see how much innovation and research happens in both places — one with, and one without, patents.

Filed Under: australia, brca1, brca2, breast cancer, dna, genes, patents
Companies: myriad genetics

Using Spreadsheets In Bioinformatics Can Corrupt Data, Changing Gene Names Into Dates

from the careful,-now dept

A few years back, people were rather disturbed to find out about the famous Excel bug, whereby the multiplication of two numbers in Microsoft’s spreadsheet gave the wrong number. It turns out there are other circumstances in which Excel (and, to be fair, presumably other spreadsheets) can give incorrect results, but they are unlikely to be encountered in typical everyday tasks. However, in the specialized world of bioinformatics, which uses computers to analyze data about genes and related areas, careless use of spreadsheets can throw up a significant numbers of errors, as this paper in BMC Bioinformatics explains:

> Use of one of the research community’s most valuable and extensively applied tools for manipulation of genomic data can introduce erroneous names. A default date conversion feature in Excel (Microsoft Corp., Redmond, WA) was altering gene names that it considered to look like dates. For example, the tumor suppressor DEC1 [Deleted in Esophageal Cancer 1] was being converted to ‘1-DEC.’

Here we have the interesting interaction of two very different fields, where the name of a gene involved in esophageal cancer, DEC1, was interpreted by Excel to mean the date, 1 December. As the paper points out, these kinds of substitution errors are already to be found in key public databases:

> DEC1, a possible target for cancer therapy, was incorrectly rendered, and it could potentially be missed in downstream data analysis. The same type of error can infect, and propagate through, the major public data resources. For example, this type of error occurs several times in even the immaculately curated LocusLink database.

As that notes, a gene that might be relevant for treating cancer could well be missed because of this incorrect conversion to a date by Excel. Although it is unlikely that any serious harm has been caused by this — yet — it’s a useful reminder of the dangers of depending a little too heavily on the results of software without checking for corruption of this kind.

Follow me @glynmoody on Twitter or identi.ca, and +glynmoody on Google+

Filed Under: bioinformatics, data, errors, genes, spreadsheets

Company Offering Open-Source Biological Reagents Hopes To Recapitulate Free Software's Success

from the the-value-of-free dept

It’s well-known that monopolies can lead to price-gouging, which produces effects like this:

> I still have no idea how people can get away with charging several thousand dollars for a milligram of recombinant protein. That’s an amount that you can see with the naked eye, if your eyesight is really good, but even then, you can see it only just barely. If you had to make a recombinant protein in your undergraduate biology class, then you know that the cost of doing this is essentially the cost of highly refined sugar water (= culture media) plus the cost of highly refined salt water (= chromatography buffers).

That comes from a fascinating essay by John Schloendorn, founder and CEO of Gene And Cell Technologies, a regenerative medicine startup, which appears in Issue 4 of the BioCoder journal. But here’s the strange thing: the biological reagents market may show the classic symptoms of monopoly abuse, but as Schloendorn points out, there are very few actual monopolies here:

> The protections of the closed-source biologics vending industry are actually thin as paper and brittle as glass. For most of this stuff, they have no patents, no copyright, no government regulations, hardly a lobby to speak of, and no monopolies of any kind. They manage to lock biotechnology away from new entrants and to keep the cost of doing science in the stratosphere for establishment professionals, solely through the physical possession of the source DNA and by imposing contractual restrictions on those willing to sign them.

Schloendorn notes the parallels with the software market, which also suggests an obvious solution to the problem of exorbitant prices: open-source biological reagents. That is precisely what Schloendorn has created:

> I have synthesized, manufactured, tested, and fully validated a collection of open source plasmids [small circular DNA strands] coding for some of the very basic building blocks of biotechnology. I do charge an initial purchase price to pay for storage, ongoing quality control, and the provision of a reliable source of these molecules. But there is no proprietary barrier of any type on their use. You may grow them on your own, modify them, give them to others, sell them, sell products derived from them, and do whatever you (legally) want to do with them.

What’s fascinating here is to see the application of the business model commonly found in the world of open-source software — whereby the code is freely available, and customers effectively pay for a service that provides quality control — in the world of DNA. Given the easy profits that will be put at risk by this new offering, we can probably expect the same kind of scaremongering and lobbying from the incumbents that free software experienced when it became clear that it posed a serious threat to the traditional, high-margin world of closed-source code.

Follow me @glynmoody on Twitter or identi.ca, and +glynmoody on Google+

Filed Under: biological reagents, dna, genes, open source
Companies: gene and cell technologies