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Stories filed under: "genome"

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]

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

DailyDirt: We Are Star Stuff And Genetic Mistakes…

from the urls-we-dig-up dept

The history of evolution has been largely erased by time and poor record keeping. Sure, we still have a few genomes that look remarkably similar to ancient organisms, and we can try to make some educated guesses about how life on earth developed. We might even be able to re-animate some extinct animals, but we’ll never be able to re-capture the full environment and complex ecology that no longer exists for our most distant ancestors. Still, it’s fascinating to study evolution and to try to witness it in action.

• The first multi-cellular organism lived about 800 million years ago, and no one knows how that happened exactly. The rise of multi-celled life relied on a protein (GK-PID) that happens to result from a mutation on a single gene. Without this minor change, life on earth could be little single-celled organisms (or not-so-little single celled creatures like Gromia sphaerica). [url]
• Since 1954, some Japanese researchers have kept fruit flies in the dark to breed them for 1,500 generations (and counting) to watch how mutations might help these flies adapt to living in total darkness. Sequencing the genome of Drosophila melanogaster specimens reveals dozens of possible genes that deviate significantly from normal flies and enable these flies to detect pheromones better (among other things). It might take a lot longer to witness the evolution of a new species (if we can agree on how to define a species, that is), but this dark-fly project also might not last much longer. [url]
• About 500 million years ago, an invertebrate animal mistakenly inherited twice its usual genetic material with a extra copy, and then that genetic doubling happened again in the next generation. These kinds of mistakes happen from time to time, and they’re sometimes unstable — but genome duplications can also lead to more complex cellular communication systems and novel protein developments. [url]

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Filed Under: biology, biotech, dark fly project, drosophila melanogaster, evolution, genome, gk-pid, gromia sphaerica, life, multi-cellular organisms, proteins, single celled organisms

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]

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

DailyDirt: Nature Doesn't Play By Our Rules…

from the urls-we-dig-up dept

Biology does whatever it can do, and it’s usually pretty messy about it. Just when people think they’ve figured out a nice hierarchical system for classifying plants and animals and microscopic organisms, we find out that there’s more going on and some things aren’t as clear cut as we thought. We could divide up life into several kingdoms and/or three domains, but taxonomy isn’t getting simpler with time. Life is a continuous spectrum that can’t be separated easily, and classifications could become even more complicated in the future. If you thought a platypus was weird, check out a few of these creatures.

• The tardigrade (aka water bear) is a strange eight-legged critter that is so resilient that it can survive in space — and it can inherit genes from its environment. Horizontal gene transfer from bacteria, fungi and Archaea has contributed to about 17.5% of the tardigrade’s genome, making it the record holder for an animal. For reference, the human genome has 5-8% of its DNA from foreign sources like retroviruses. [url]
• Solar-powered sacoclossans are herbivorous sea slugs that can absorb chloroplasts from their food and use these disembodied algae parts as both a form of camouflage (from the green color of the chloroplasts) and as a source of energy. These chloroplasts don’t get passed down to offspring, but young sacoclossans eat algae and obtain chloroplasts just like their parents did. [url]
• A new species of ‘coywolf’ is emerging in eastern North America from interspecies breeding, resulting in an animal with wolf, coyote and dog DNA. Millions of these animals populate a vast geographic area including rural and urban environments. These adapted coywolves can eat a variety of things — from discarded human foods to rodents and small mammals like cats — and hopefully these animals aren’t related to Michael Corvin. [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: algae, biology, chloroplast, coywolf, dna, evolution, genome, life, nature, sacoclossan, tardigrade, taxonomy

DailyDirt: Biotech's Own Exaflood?

from the urls-we-dig-up dept

Studying biology takes time. Computer software/hardware has a Moore’s law clockcycle that keeps things chugging along at a pretty good clip, but the biotech revolution is growing at a slightly slower pace. Sure, we’ve seen some cloning, genetically modified organisms and a wide variety of promising medical advances. Perhaps the biotech industry doesn’t have an exponentially-growing metric to rally around, but solid progress is leading to an enormous amount of accumulated data, knowledge and possibilities.

• Gene editing technology may become an incredibly important tool, but if the entire field becomes bogged down in a patent thicket, people may die needlessly. Researchers have developed an alternative to CRISPR-Cas9 techniques, but the patent fights and commercialization rights surrounding gene editing techniques will likely continue. [url]
• The “telomerator” is a genetic tool that will allow researchers to study the yeast genome and genetics in general. Genetically engineered microorganisms will be easier to make and study — and the resulting synthetic yeast genes can be designed to be better models for the biology of higher organisms, such as humans. [url]
• Genome sequencing creates a LOT of data — even just for human genomes, not counting all the other species out there. By 2025, predictions estimate that a billion people could have their individual genomes sequenced, and all of this information is going to need to be stored somewhere (other than in our bodies), digitally. [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: biotech, crispr, gene editing, genome, genome sequencing, gmo, telomerator, yeast

DailyDirt: Genetic Information Is Everywhere Now

from the urls-we-dig-up dept

The costs of analyzing DNA have come down significantly over time, so it’s becoming increasingly common to sequence DNA and discover all kinds of biological curiosities. It’s not quite as fast and easy as they make it look on detective shows on TV, but DNA analysis has made some pretty amazing advances. Here are just a few examples of genetic testing that you might have missed.

• It’s actually not that uncommon to find people who are chimeras — individuals with multiple genomes in their bodies. Twins can end up with a mixture of blood types that co-exist in their veins. Nearly all mothers retain some residual fetal cells from their children (and this is a form of microchimerism). We have a lot to learn about the genetic makeup of individuals, and it’s not as simple as one might have assumed. [url]
• The male fetal DNA from a mother’s son can often be found in her brain. Brain autopsies of 59 women showed that the majority of them had male DNA, giving evidence that fetal DNA can not only cross the placenta, but also the blood-brain barrier. [url]
• A blood test can now reliably detect an unborn baby’s sex at just 7 weeks old. The genetic material from the baby can be detected and analyzed, offering some advantages over more invasive tests such as amniocentesis. [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: biotech, blood test, chimerism, dna, fetal dna, genetic material, genome, microchimerism

DailyDirt: Looking At The Human Genome

from the urls-we-dig-up dept

The human genome contains an incredible amount of information that we are only starting to parse. Sequencing large amounts of DNA is getting cheaper and faster, so it’s only a matter of time before we’ll be able to collect a vast amount of genetic information and connect it with practical medical diagnoses and treatments. Here are just a few projects working on decoding our genetic blueprints.

• The international ENCODE project has been looking at the human genome to try to figure out what all the nucleotides do. Less than 2% of the genome is used for making proteins, and we’re just beginning to discover that about 80% of the genome is biologically active and isn’t just “junk” DNA. [url]
• The Genographic Project is asking the general public to participate in a genome analysis experiment to gather a broad sampling of DNA data. The results will be anonymous (but they’ll have your DNA…?) and dedicated to the public domain. [url]
• The 1000 Genomes Project currently claims to have the world’s largest, most detailed catalog of human genetic variation. The database includes sequenced genomes from over 1,092 people and should help medical researchers develop tests for genetic diseases. [url]

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

Filed Under: biology, biotechnology, dna, genome, human, medicine, science

Your Genome, Your Data

from the other-digital-revolution dept

The computing revolution is not the only one driven by constant scaling of technologies: the field of genomics — the study of DNA sequences — has also enjoyed rapid falls in basic costs over the last decade and a half. This means that whereas the first human genome cost around $3 billion to sequence, we are fast approaching the point where it will cost first a few thousand, and then a few hundred dollars to sequence anyone’s complete DNA. An interesting post on the Health Affairs Blog points out that neither the law nor society is ready for this.

Companies like 23andMe are already offering people the ability to find out about a range of important genes very simply, and for relatively low cost:

> The concern is that someone might learn of that same risk [for breast cancer] for $499 by spitting in a tube and hitting the “breast cancer result” button at 23andMe, a company that will test saliva samples for diseases as well as for DNA ancestry. No one should take an action, such as prophylactic surgery without confirming results from 23andMe, which reports on only the three most common mutations.

Against that background of possibly life-changing or even life-threatening decisions being made on the basis of results obtained from a blob of saliva, the Food and Drug Administration (FDA) is now looking to regulate this market. But in the opinion of the article’s authors, there’s a danger here:

> If regulators impose rules that allow us to obtain genomic data only as a medical service and through a health professional, however, access will never be cheap because it will always be bundled with expensive professional medical services. This is what Germany has done, and we should not follow their lead. By equating genome services to medical services, the German Government has reduced access, significantly limited the possible benefits to their citizens, and dramatically increased the costs.

The authors make a suggestive comparison:

> It’s as if [governments] had decided to cut off access to the World Wide Web in response to fears of pornography and copyright infringement. Imagine what the world would be like today if we had passed the Draconian Internet regulation bills proposed a decade ago when the Internet was as young as the nascent genomics sector is now. We would have sucked the water out of the pond that gave birth to the marvels of Google, Wikipedia and Facebook.

There’s another parallel, too. Just as with the Internet and its digital deluge, the imminent world of abundant, ultra-cheap genomic data could also could power the growth of a huge new economic sector:

> Our curiosity — and sometimes our health — will require ‘experts’ to do the science and to explain its implications. Some of these “genomicists” will be health professionals no doubt: genetic counselors, nurses, social workers, or physicians who learn the intricate math and follow the exploding technical literature. Others will be experts in genealogy, history, ethnicity, engineering and anthropology. New businesses are emerging to create interpretive software and interactive websites that walk us through tours of our genomic data. If you’re young and computer savvy; if you study genetics and read anthropology and history, you may have a job in a field that is just coming to life. That is, if we don’t screw it up by strangling this nascent field in its cradle.

The trick will be to allow these new businesses to aggregate and analyze DNA information while preserving individual privacy and control over genomic data that is unequivocally yours. That’s going to be hard, but the potential benefits in terms of improving people’s health make it worth striving for. For more information, check out the original post which goes into greater detail.

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Filed Under: data, dna, genome, privacy

Cocoa Genome Released… But Is It Really In The Public Domain?

from the the-public-domain-has-no-restrictions dept

Last week, a PR person working for Mars (makers of M&Ms and such) sent me an email about how scientists from Mars along with the USDA and IBM (among others) had sequenced the cacao genome and that “the results of the research will be made available to the public with permanent access,” at the accurately named Cacao Genome Database. Sounded interesting, but it was a busy week, and I wasn’t able to spend much time digging into it. I was intrigued, however, by the claim in the press release that the team had “released the preliminary findings of their breakthrough cacao genome sequence and made it available in the public domain“. It’s so rare to hear of some big companies doing research and release it into the public domain, that it, alone, seemed newsworthy, and something I wanted to explore.

Thankfully, before I even got the chance to, I saw Glyn Moody point me to Glen Newton’s analysis of the claims of public domain and open access for the data, only to discover it’s not true. While they are making the data available, it’s hardly public domain. You have to agree to a license that has some serious restrictions in it (and some contradictions). For example, it lists out the ways you can use it — and leaves out commercial use. Real public domain doesn’t care (and doesn’t require a license).

Then there’s this:

The User shall not transfer the information referred to in this agreement, or any copy of them, to a third party without obtaining written authorization from the Providers which will only be provided subject to the third party user entering into this same IAA.

I’m kind of wondering if this is just boilerplate that the lawyers threw into this not understanding what public domain means. But it seems pretty silly to (a) create a license for supposedly public domain data which (b) doesn’t allow you to tell anyone about what’s in the license!

There is a nice bit in the “license” where it says you can’t use the data in a patent application, but one would hope that the data being in the public domain would exclude it from being used in a limited fashion elsewhere anyway (sans license agreement). Separately, someone in the comments notes that the original license agreement said that if you used the data, you couldn’t publish any articles about your findings until some period in the future — but that clause was later removed (though, it’s unclear if those who signed in prior to the removal still need to live by that).

However, I do have a pretty serious question: is this data in the public domain? Last year, we pointed out how difficult it is to put something into the public domain. Here, we have a case where Mars, the main company behind the research, has put out a press release, which clearly states:

Today, Mars, Incorporated, the U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), and IBM released the preliminary findings of their breakthrough cacao genome sequence and made it available in the public domain.

Thus, one could easily read that and believe these findings are public domain. But, then, when you go to the actual site, it claims all sorts of license restrictions. So, if someone goes and copies all the data and puts it on their own site, is that legal? It certainly looks like the company put the info into the public domain via the press release, and once something is in the public domain, you can’t reverse that (well, unless you’re the 10th Circuit appeals court). So, it certainly looks like someone could make the argument that the license Mars is trying to put on this data is meaningless. The company has already declared it in the public domain, and thus, no license applies. But, here’s where the lack of any clear rules for how you officially make something public domain come into play. Would Mars claim that the press release “misrepresented” the company’s position?

I don’t mean to come down too hard on Mars. It’s actually quite nice that a company would do such research and try to make it “open” and try to prevent it from being locked up in patents. I really do commend such actions, and don’t wish to negate that point. But, I think the public domain is a really important thing, and if a company wants to put content into the public domain, they should be clear about what’s really in the public domain.

Filed Under: cocoa, genome, licenses, public domain
Companies: ibm, mars, usda