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: Don't Make My Brown Eyes Blue!

from the urls-we-dig-up dept

Eye color isn't a simple single gene trait. In a rare 1% of the population, some people have two different colored eyes or eyes with multiple colors (aka heterochromia iridum). Most people have brown eyes, but it's easy to change your eye color with contact lenses to any color you want -- even scary unnatural monster eyes. Eye color doesn't seem to have much meaning -- as long as you don't teach kids otherwise -- but genetic studies will probably find some interesting correlations in the future.

• DNA analysis of ancient humans can determine eye color from 24 locations on the human genome. As long as enough DNA remains to be analyzed, researchers can determine hair and eye color for specimens that are hundreds of years old. [url]
• About 17% of the world's population has blue eyes, and if you don't like contact lenses to change your eye color -- you can turn your brown eyes blue with lasers. There's actually no blue pigmentation for blue eyes, so a laser ablation technique can remove brown pigments and change a person's eye color permanently. [url]
• All blue-eyed people have a single, common ancestor who lived about 6,000-10,000 years ago. Originally, everyone had brown eyes. [url]

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Filed Under: biology, dna, evolution, eye color, farsightedness, genetics, heterochromia iridum, mutations, myopia, nearsightedness, vision

DailyDirt: Age Is Just A Number

from the urls-we-dig-up dept

They say age is "just a number" -- but it'd be nice if that number could be a little higher before people were expected to die. The aging process has been studied for a long time, but no one has found the silver bullet that stops people from getting older (unless there are some immortals hiding among us). Still, medicine is making some slow progress towards understanding how we age -- and how we might prevent ourselves from aging.

• Researchers may have found a way to make mice live much longer -- by removing certain cells (senescent cells) from their bodies. Take a healthy mouse, start removing these senescent cells twice a week, and that mouse will live about 25% longer and stay healthier compared to an untreated mouse with identical genetics and a controlled diet. There could be serious side effects for doing this in people, but maybe start taking scientific "cleanses" seriously.... [url]
• There's a correlation with having more children and longer telomeres... for a sample of women from rural Guatemalan communities. Longer telomeres are associated with cell replication and longevity, but aging is a not a simple process. And obviously, there's a limit to the effect or else mothers of a dozen or so kids would live a surprisingly long time (plus the data could look a bit better). [url]
• If longer telomeres really does the trick, though, for leading to longer, healthier lives, then there might be a way to lengthen them artificially. It's too late for Roy Batty, but maybe not for us (or Rick Deckard). [url]
• There isn't just one theory about how cells age, but there's more doubt for the mitochondrial theory of aging that proposes that accumulated mutations in mitochondrial DNA lead to age-related mitochondrial defects. There may be other forms of genetic regulation, like epigenetic regulation, that lead to the effects of aging. [url]

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Filed Under: aging, biology, biotech, dna, genetics, health, lifespans, longevity, medicine, mitochondrial dna, senescent cells, telomeres

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 Vs. CRISPR

from the urls-we-dig-up dept

The reality of designer babies seems to be more and more likely -- especially now that gene editing tools like CRISPR are becoming more refined and widespread in labs around the world. Legitimate concerns over a modern form of eugenics are being raised, and the ethical debates are getting less theoretical as the science pushes the boundaries of what can be done. People might be able to activate or delete genes without fully understanding the results, and the advances that can eliminate genetic disorders could also eliminate certain minorities or traits that are not necessarily disabilities.

• British researchers will be performing gene-editing experiments on human embryos, but they're not going to be making full-term babies -- yet. Britain's Human Fertilisation and Embryology Authority is the first regulator to approve this kind of genetic tinkering (although plenty of countries don't require permission at all), and British lawmakers have previously voted in favor of allowing babies to be made from the DNA of three parents to prevent genetic disorders. (So perhaps a modified clone of Benedict Cumberbatch will actually become Khan Noonien Singh someday.) [url]
• Genetic discrimination is going to be a thing soon. A kid was removed from school because he has genetic markers for cystic fibrosis (and not the actual condition). A lawsuit is now working its way through the system to determine if the Genetic Information Nondiscrimination Act of 2008 (GINA) or the Americans With Disabilities Act will apply to future such cases of discrimination. [url]
• Someone might have the genes for a particular trait, but it may never be expressed. Researchers have discovered a way to activate some genes that are inaccessible and non-functioning -- but so far only in mice. Are you pondering what I'm pondering? [url]

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Filed Under: ada, biology, biotech, crispr, designer babies, dna, eugenics, gattaca, gene activation, gene editing, genetics, germline, gina

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]

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Filed Under: algae, biology, chloroplast, coywolf, dna, evolution, genome, life, nature, sacoclossan, tardigrade, taxonomy

Kuwait Creating Mandatory DNA Database Of All Citizens, Residents -- And Visitors

from the makes-you-want-to-spit dept

A growing number of articles on Techdirt attests to the fact that the use of DNA is becoming commonplace in many fields, thanks to the continuing drop in the costs of gathering and analyzing genetic material. As those costs fall, of course, so the temptation to roll out the use of DNA more widely increases. It looks like Kuwait has the dubious honor of being the first nation to require everyone's DNA -- including that of visitors to the country. The Kuwait Times has a frighteningly matter-of-fact article about the plan, which is currently being put into operation. Here's how the DNA will be gathered:

Collecting samples from citizens will be done by various mobile centers that will be moved according to a special plan amongst government establishments and bodies to collect samples from citizens in the offices they work in. In addition, fixed centers will be established at the interior ministry and citizen services centers to allow citizens give samples while doing various transactions.

Those who are not citizens of Kuwait will be sampled when they apply for residence permits:

Collection will done on issuing or renewing residency visas through medical examinations done by the health ministry for new residency visas and through the criminal evidence department on renewing them.

As for common-or-garden visitors to the country:

Collection will be done at a special center at Kuwait International Airport, where in collaboration with the Civil Aviation Department, airlines and embassies, visitors will be advised on their rights and duties towards the DNA law.

"Rights and duties" basically means: "no DNA, no way Kuwait", since the article says elsewhere:

the test will be mandatory for visitors

The DNA will not be used for medical purposes, such as checking for genetic markers of disease, which will avoid issues of whether people should be told about their predisposition to possibly serious illnesses. Nor will the DNA database be used for "lineage or genealogical reasons." That's an important point: a complete nation's DNA would throw up many unexpected paternity and maternity results, which could have massive negative effects on the families concerned. It's precisely those kinds of practical and ethical issues that advocates of wider DNA sampling and testing need to address, but rarely do.

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Filed Under: dna, dna database, genetic database, kuwait, privacy, tourism

DailyDirt: Imagine There's No Cancer...

from the urls-we-dig-up dept

In 2015, an estimated 1.6 million patients were diagnosed with cancer and over half a million died from it. We've previously pointed out some cancer research that could lead to promising new treatments, and it looks like we're making significant progress in the fight against the many forms of this deadly disease. Using the body's own immune system to fight cancer is a growing strategy that seems to be working. Check out a few of these minor successes.

• Jimmy Carter announced that his cancer treatments are going well, and his latest brain scans don't show any tumors. Carter has been getting radiation treatments and doses of Keytruda, an immunotherapy drug, to fight off cancer. Immunotherapy drugs are promising, but it's not well understood how they work just yet. Presumably, as we figure them out, we'll be able to target different kinds of cancer and improve the treatment. [url]
• Sequencing the genes of cancer cells can help determine drugs that could specifically target tumors. Hundreds of cancer drugs have been tested in clinical trials, and a few are extending the life expectancy of patients. As long as the drug prices don't skyrocket unexpectedly, many people might be able to benefit from this advance in biotech. [url]
• The FDA has approved a virus that can attack cancer cells. This living virus, sold as Imlygic, is an engineered version of herpesvirus, and it's probably the first of a class of viral anti-cancer treatments. [url]

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Filed Under: biotech, cancer, cancer research, dna, drugs, health, imlygic, immunotherapy, jimmy carter, keytruda, medicine, pharmaceuticals, treatment, tumor

DailyDirt: What's In Your... DNA?

from the urls-we-dig-up dept

Biotechnology doesn't have quite the same milestones of progress as Moore's Law, but as we unravel how biology works, we're going to have incredibly powerful tools to change the world. Sure, we're going to need to figure out the ethical ramifications of a GATTACA-esque future where designer babies are possible and replicants/clones can be grown for replacement parts. But it might take a while still before we're engineering lifespans and curing the disease of aging.

• Remnants of an ancient virus have been found in human stem cells' DNA, and this kind of viral material was once considered "Junk DNA" -- but may actually play a critical role in human development. Apparently, human embryonic stem cells require certain bits of DNA to act like stem cells (ie. be pluripotent, able to turn into over 200 different kinds of cells in the human body) -- and those critical bits of DNA are from a retrovirus that infected our ancestors' DNA millions of years ago. [url]
• Chromosomal proteins are intertwined with DNA, and these proteins play a critical role in determining when DNA is triggered to do its job. It's still not completely known how these chromosomal proteins evolved, but changes in these proteins can cause harmful mutations and cancer -- as well as improved cell performance. Learning more about these proteins and how they interact with DNA could lead to a much better understanding of certain diseases -- and even more fundamental clues to how life has evolved. [url]
• CRISPR is an incredibly important biological tool, allowing scientists to edit DNA much more easily than ever before... and it's a tool that can be used to delete HIV from human DNA. HIV is a retrovirus (so it puts its own genetic information into a host's DNA), and being able to remove it from a living cell could someday provide a cure -- and lead to other effective treatments for various intractable viral infections. [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, cancer, chromosomal proteins, crispr, dna, genetics, junk dna, stem cells, viruses

Familial DNA Searches May Make You Think Twice About Signing Up With Private Genetic Services

from the running-in-family dept

Using DNA found at the scene of a crime to identify the guilty party is pretty routine these days, but, as Mike discussed many years ago, police have been getting more aggressive in going much further: carrying out "familial" DNA searches on privately-held genetic databases. That link is to a recent Wired article that concerns the case of Michael Usry, who became a suspect in a 1966 1996 murder case because of his father's DNA:

Detectives had focused on Usry after running a familial DNA search, a technique that allows investigators to identify suspects who don’t have DNA in a law enforcement database but whose close relatives have had their genetic profiles cataloged. In Usry's case the crime scene DNA bore numerous similarities to that of Usry’s father, who years earlier had donated a DNA sample to a genealogy project through his Mormon church in Mississippi. That project’s database was later purchased by Ancestry, which made it publicly searchable -- a decision that didn’t take into account the possibility that cops might someday use it to hunt for genetic leads.

Using general similarities as the yardstick rather than more exact matches means that false positives are more likely -- as in this case, when Usry's own DNA proved he had nothing to do with the murder. Those similarities were only found because his father's DNA was in a privately-held genetic database that the police could access. That's unusual, but becoming more common as services like Ancestry.com and 23andMe gather many more DNA samples.

According to an article on Fusion.net, Ancestry now has over 800,000 samples, while 23andMe has a million customers (Ancestry says that a more up-to-date figure is 1.2 million members in its database). Those are significant holdings, and it's only natural that the police would try to use them to solve crimes; both companies confirm that they will turn over information from their databases to law enforcement agencies if served with a suitable court order. A more recent post on Fusion.net notes that 23andMe has produced its first transparency report (direct link, but Techdirt readers outside the US may have to use the Google cache version for reasons that are not clear.) The report shows that a total of four requests were received from the US authorities, concerning five 23andMe customers, and indicates that the company was successful in denying those requests, without giving details.

Although understandable, this kind of access is problematic for people who sign up for these services, for reasons made clear by the Usry case. The DNA that goes into the database affects not only the donor, if a rough match to crime materials is found by the police, but many close relatives whose genetic make-up is necessarily similar. As a result, it's entirely possible that completely innocent people might have to go through the traumatic experience of being a suspect just as Usry did before more precise tests ruled him out.

That's unfortunate, because it adds a complicating factor to the decision about whether to provide DNA to interesting and innovative services like Ancestry.com and 23andMe: doing so means future generations might be put at risk of erroneous police interest. The only way to prove their innocence would be to hand over their DNA to the authorities for detailed testing, which then raises the question of what happens to it afterwards.

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Filed Under: dna, government, law enforcement, surveillance, transparency
Companies: 23andme, ancestry.com