MetaFilter posts tagged with Genetics

Researchers calculate that life began before Earth existed

Confess, Fletch — Thu, 18 Apr 2013 09:29:42 -0800

Geneticists have proposed that if the evolution of life follows Moore's Law, then it predates the existence of planet Earth.

Intelligence Tests

kliuless — Thu, 11 Apr 2013 10:40:00 -0800

Is Psychometric g a Myth? - "As an online discussion about IQ or general intelligence grows longer, the probability of someone linking to statistician Cosma Shalizi's essay g, a Statistical Myth approaches 1. Usually the link is accompanied by an assertion to the effect that Shalizi offers a definitive refutation of the concept of general mental ability, or psychometric g." Myths, Sisyphus and g - "Over the years I have not encountered a single endorser of Shalizi's article who actually understands the relevant subject matter. His article is loved for its reassuring conclusions, not the strength of its arguments. I am sure many 'thinkers' resisted Darwinism, the abandonment of geocentrism, and even the notion that the Earth is a sphere, for similar psychological reasons." Nuthin' but a 'g' thang

So I've always had the intuitive hypothesis that there are different types of intelligence; that different people tend to process information in different ways, whether due to habit or nature. But then there are all those people who say that intelligence can be boiled down to a single factor, the mysterious "g" (which I assume stands for either "general intelligence" or "gangsta"). Since this went against years of casual observation, I was somewhat pleased to see the eminent Cosma Shalizi write an essay debunking the notion of "g". But then I saw this blog post defending the notion of "g", and claiming that Shalizi makes a bunch of errors. Basically, the disagreement revolves around the question of why most or all psychometric tests and tasks seem positively correlated with each other. Shalizi points out that this correlation structure will naturally lead to the emergence of a "g"-like factor, even if one doesn't really exist; his opponent points out that if no "g" exists, it should be possible to design uncorrelated psychometric tests, which so far has proven extremely difficult to do. The latter post, by a pseudonymous blogger calling himself "Dalliard", contains a bunch of references to psychometric research that I don't know about and have neither the time nor the will to evaluate, so I'm a bit stumped. Normally I'd leave the matter at that, shrug, and go read something else, but I realized that my intuitive hypothesis about intelligence didn't really seem to be explicitly stated in either of the posts. So I thought I'd explain my conjecture about how intelligence works. In a nutshell, it's this: What if there are multiple "g's"? ...just imagine several dozen hyperplanes, and project them all onto one hyperplane... Remember that psychometric tests are simple mental tasks, but most of the mental tasks we do are complex, like computer programming or chess or writing. And for those tasks, learning and practice matter as much as innate skill, or more (for example, see this study about the neurology of chess players). Therefore, everyone can be "smart" in some way, if "smart" means "good at some complex mental task".

also btw To Make Mice Smarter, Add A Few Human Brain Cells (previously)

China is engineering genius babies

Tom-B — Mon, 18 Mar 2013 15:09:28 -0800

I just attended a debate in New York a few weeks ago about whether or not we should outlaw genetic engineering in babies and the audience was pretty split. In China, 95 percent of an audience would say, “Obviously you should make babies genetically healthier, happier, and brighter!”

Some people just can't let sleeping frogs lie...

heyho — Sat, 16 Mar 2013 11:17:55 -0800

Extinction got you down? Try de-extinction! Our species has played a role in the extinction of ... many other species. But now some scientists are proposing a radical turn of the tables: Bringing lost species back from the dead. How to Resurrect Lost Species. Today's example: Rheobatrachus silus was a bizarre gastric-brooding frog that swallowed its eggs, brooded its young in its stomach and gave birth through its mouth. The frog species became extinct in 1983. Well, it may not stay that way for long, thanks to the Lazarus Project. And wait, there's more! A lot more. Revive & Restore, with the support of TED and in partnership with National Geographic Society, is convening a day-long conference (today) to showcase the prospects of bringing extinct species back to life, along with a discussion of the ethical issues that will raise. Can it be done responsibly? Should it be done at all? The full-day conference brings together a range of speakers to dive into the emerging idea of de-extinction.

“who’s managing our fisheries?”

the man of twists and turns — Sat, 09 Mar 2013 13:17:52 -0800

Blood and Brains - can vampires survive a zombie apocalypse? Southern Fried Science is a group blog focused on marine science, environmental science, and conservation. It covers topics like: Turtle excluder devices: analysis of resistance to a successful conservation policy Chronicle of a Death Forestalled: the Gulf of Mexico oil spill that didn’t happen How not to apply for a job working with sharks America’s lust for gigantic breasts leads to impotence: the population genetics of captive-reared turkeys 10 Myths About Social Science The Importance Of Word Choice: Terms With Multiple Meanings For Scientists And The Public Dolphin-safe tuna: conservation success story or ecological disaster? SFS has been featured on MetaFilter before: The science of Aquaman, How to brew beer in a coffee maker, using only materials commonly found on a modestly sized oceanographic research vessel. Also one of the bloggers is a mefite.

It's Not in Your Brain, It's in Your Genes

kinetic — Fri, 01 Mar 2013 03:38:50 -0800

The psychiatric illnesses seem very different — schizophrenia, bipolar disorder, autism, major depression and attention deficit hyperactivity disorder. A study funded by the NIMH and published in The Lancet, as reported by the New York Times indicates that five seemingly-different psychiatric diseases share several genetic glitches. The findings strengthen an emerging view of mental illness that aims to make diagnoses based on the genetic aberrations underlying diseases instead of on the disease symptoms. While this research is considered the tip of the iceberg, doctors have had some success in treating the genes that involve calcium channels, which are used when neurons send signals in the brain.

Models and their Mothers

zarq — Wed, 27 Feb 2013 11:10:20 -0800

Models and their Mothers by Howard Schatz. Interview. The "Howard" link above goes to his online portfolio. Last year, his book "With Child" looked at pregnancy and motherhood. More photos at his site. (both links nsfw) Schatz, previously on mefi.

Bigfoot DNA as mysterious as the elusive cryptid

filthy light thief — Mon, 18 Feb 2013 12:13:13 -0800

November 24, 2012: analysis of extensive DNA sequencing of 'a novel hominin hybrid species, commonly called “Bigfoot” or “Sasquatch” ... suggests that the legendary Sasquatch is a human relative that arose approximately 15,000 years ago as a hybrid cross of modern Homo sapiens with an unknown primate species.' The press release claimed that the research was "currently under peer-review," except that no scientific journal would publish the research, until now: DeNovo, an open access scientific journal. But DeNovo isn't really open access, as it costs $30 to view the article, the paper itself is brand new, the domain was recently purchased, and the website features generic stock photos. Ars Technica digs deeper, summarizing some of the "open access" article, and providing a link to a particularly insightful clip on YouTube, with an odd water mark. Wasn't the research done by the Texas geneticist, Melba Ketchum? Who is Erickson? Adrian Erickson was a rich fellow who lost millions trying to get bigfoot footage for a documentary. That documentary was to include footage of, as Ars Technica science editor John Timmer wrote, "a very shaggy carpet sleeping in the woods," was supposedly of a female Sasquatch named Matilda. Sadly, it's not the unseen, rumored Matilda footage that was supposed be "the best video of Bigfoot since the Patterson-Gimlin clip from 1967. Ketchum apparently purchased Erickson's work, and blogger Robert Lindsay, who knows more of Matilda's story, says Ketchum's research is good (though he reviewed some "bootleg copies" of the paper). Huston Chronicle science blogger Eric Berger has been following Ketchum's Bigfoot DNA story for a while, from the press release (noting that Ketchum's company, DNA Diagnostics, got an “F” from the Better Business Bureau, and that some of the DNA samples came from blueberry bagel-loving Bigfeet in Michigan), and the publication of the paper, and most recently, he got feedback from geneticists. Bonus: as noted in the Ars Technica article above the fold, the Sasquatch DNA article notes "seen on the television series Monster Quest." But it doesn't clarify which one, so you can watch a bunch of the episodes about the various Sasquatch/Bigfoot creatures here in this YouTube playlist.

Bring me more genomes

catlet — Sat, 26 Jan 2013 07:10:30 -0800

"If the history of public health has until now been embodied by the map—as in British physician John Snow’s famous map, which allowed him to curb the London cholera outbreak of 1854 and to found, in doing so, the modern field of epidemiology—Snitkin was embarking on a new kind of epidemiology: one founded on the phylogenetic tree." Writing for Wired, Carl Zimmer describes how Evan Snitkin and Julie Segre used genome sequencing to halt a bacterial outbreak at the National Institute of Health's Clinical Center. (via The Feature)

East India Company?

Guernsey Halleck — Fri, 25 Jan 2013 01:56:02 -0800

A recent genetic study suggests that around 2200 BC explorers from India arrived and settled on the continent of Australia. "Unlike their European successors, these earlier settlers were assimilated by the locals. And they brought with them both technological improvements and one of Australia’s most iconic animals." [SLEconomist]

Some Budding Yeast I Used to Grow

grouse — Thu, 24 Jan 2013 10:05:51 -0800

A biologist researcher laments the present difficulty of getting funding for yeast experiments. In song form. With a stop motion animation video. And music by Gotye.

Make Babies

vidur — Wed, 12 Dec 2012 18:30:02 -0800

"Older parenthood will upend American society." "Is waiting to have kids a big mistake?" "Why do women believe they can delay children for so long?" "Older men are more likely than young ones to father a child who develops autism or schizophrenia, because of random mutations that become more numerous with advancing paternal age."

"The Double Helix has more in common with Truman Capote's In Cold Blood than, say, The Decline and Fall of the Roman Empire."

ocherdraco — Thu, 08 Nov 2012 13:36:24 -0800

"The Turn of the Screw: James Watson on The Double Helix and his changing view of Rosalind Franklin": Maggie Koerth-Baker's brief interview with Watson, co-discoverer of the structure of DNA, about his "infamous" treatment of Franklin in his book The Double Helix, on the occasion of the publication of an annotated and illustrated edition of the same.

Breast cancer rules rewritten in 'landmark' study

Blasdelb — Mon, 05 Nov 2012 00:58:09 -0800

What we currently call breast cancer should be thought of as 10 completely separate diseases, according to an international study which has been described as a "landmark". The categories could improve treatment by tailoring drugs for a patient's exact type of breast cancer and help predict survival more accurately. The study in Nature analysed breast cancers from 2,000 women [Abstract] . It will take at least three years for the findings to be used in hospitals. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups [Abstract] The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (copy number variants and single nucleotide polymorphisms) and acquired somatic copy number aberrations (CNAs) were associated with expression in ~40% of genes, with the landscape dominated by cis- and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP and MAP2K4. Unsupervised analysis of paired DNA–RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, oestrogen-receptor-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the ‘CNA-devoid’ subgroup and a basal-specific chromosome 5 deletion-associated mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome.

Hacking the President’s DNA

homunculus — Fri, 26 Oct 2012 20:55:26 -0800

Hacking the President’s DNA. "The U.S. government is surreptitiously collecting the DNA of world leaders, and is reportedly protecting that of Barack Obama. Decoded, these genetic blueprints could provide compromising information. In the not-too-distant future, they may provide something more as well—the basis for the creation of personalized bioweapons that could take down a president and leave no trace."

Microbial Bebop

Egg Shen — Mon, 08 Oct 2012 15:51:52 -0800

When looking for inspiration, most songwriters to go well-used emotional wells – triumph or loss, love or heartbreak. But Peter Larsen, a biologist at Argonne National Laboratory, looked to the microbes of the English Channel. He used seven years’ worth of genetic and environmental data, converting geochemical and microbial abundance measurements into notes, beats, and chords.

Eating the plate instead of the food

CheeseDigestsAll — Mon, 08 Oct 2012 09:25:29 -0800

With the possible exception of the Nobel awards, physicists seem to get all the press these days, whether they're doing quantum level work at the LHC, or cosmology via the latest satellite data. Biologists, not so much. It's too bad, because Richard Lenski is running one of the great evolutionary experiments of our time, and it's producing interesting results. Lenski and his team have raised 55,000 generations of E. coli, the equivalent in human terms, of over a million years of evolution. These bacteria normally feed on glucose, a sugar, which is stabilized in solution by sodium citrate, not a chemical that E. coli can typically metabolize. In Lenski's lab, however, one strain has evolved to eat the citrate, not the glucose. Because Lenski deep-freezes samples every 500 generations. They were able to track the mutations that led to this change. One of my favorite science journalists, Carl Zimmer, has been following this work for over a decade with reports like the one above. Lenski, who was awarded a MacArthur grant in 1996, combines ecology and genetics to create experiments that illustrate the role of population dynamics in evolution, and his research supports the "punctuated equilibrium" model suggested by Steven J Gould and Niles Eldridge. In addition to lab work showing evolution occurring "in the flesh", Lenski has also published work using computer simulations that advance understanding of evolutionary mechanisms.

O soapy flavour / Why pollutest thou my food? / Thou me makest retch

dephlogisticated — Wed, 12 Sep 2012 14:44:32 -0800

A genome-wide association study has linked a dislike of cilantro with a variant of a single nucleotide in a cluster of olfactory receptor genes. The palatability of cilantro has previously been a divisive subject on the blue. While the association was strong in European populations, it did not hold in most of the other populations in the study, and furthermore, could account for only a small subset of those who found cilantro to have a "soapy" taste. It is possible that other such gene variants are involved.

ENCODE: the Encyclopedia of DNA Elements

Westringia F. — Thu, 06 Sep 2012 07:52:35 -0800

In 2001, we learned the sequence of our genome; now, we have amassed a vast amount of knowledge about what those sequences actually do. Yesterday, the data from the ENCODE project went live. ENCODE, the Encyclopedia of DNA Elements, is a project to identify and annotate all functional elements of the human genome, including transcription, transcription factor association, chromatin structure, and histone modification. It is a major achievement that was announced in a fanfare of publications. An elegant and accessible description of the project was posted by science writer Ed Yong on his Discover blog Not Exactly Rocket Science. The data is publicly explorable through a very nice interface, including an iPad app and a virtual machine. ENCODE constitutes a vast amount of data that will have a significant impact on research in genetics, bioinformatics, and medicine. Ewan Birney, the lead data analysis coordinator, discusses in Nature how the vast amount of data was wrangled, and has posted additional thoughts on his blog.

Otzi was More Neanderthal than You

Schmucko — Sat, 18 Aug 2012 13:59:18 -0800

Ötzi the Iceman died around 3,300 B.C., yet his body was preserved frozen in the Alps until 1991. DNA sequencing of Neandertals (who died out about 35,000 years ago) suggests modern humans with ancestry outside of Africa carry a few percent of Neandertal genes due to interbreeding. Now (in a blog post knocking down a re-interpretation of the Neandertal DNA evidence) paleontologist John Hawks previews an upcoming publication of his examining Ötzi's DNA::

If we took as a baseline that Europeans have an average of 3.5 percent Neandertal, Ötzi would have around 5.5 percent (again, the actual percentage would be highly model-dependent). He has substantially greater sharing with Neandertals than any other recent person we have ever examined.

Previously (Ötzi), Previously (Neandertals)

Spiders, a post about them

Brandon Blatcher — Fri, 10 Aug 2012 06:36:57 -0800

The fear of spiders is hardwired into most of humanity, despite the creatures often being beneficial to people. For some reason, it's the odd and scary stories about spiders that stick in our heads.

The Orgins of the Melungeon

edgeways — Thu, 24 May 2012 15:12:47 -0800

A relatively small group of people from Appalachian, the dark-skinned Melungeons (previously) have been a source for speculation and conjecture for many years. Exactly who where their ancestors? Portuguese? Turks? Roma? Cherokee? A recent DNA study (108 page pdf) posted in the Journal of Genetic Genealogy (site link) says otherwise (WaPo article).

Hit me Einstein, one more time!

Brandon Blatcher — Sat, 19 May 2012 05:51:44 -0800

When a Blow to the Head Creates a Sudden Genius

The Perfect Milk Machine

Joe in Australia — Tue, 01 May 2012 23:11:01 -0800

The Perfect Milk Machine: How Big Data Transformed the Dairy Industry

The Case For Enhancing People

jason's_planet — Fri, 30 Dec 2011 12:13:22 -0800

Just as Dante found it easier to conjure the pains of Hell than to evoke the joys of Heaven, so too do bioethicists find it easier to concoct the possible perils of a biotech-nanotech-infotech future than to appreciate how enhancements will contribute to flourishing lives. One of the chief goals of this symposium is to think about the indispensable role that virtue plays in human life. The chief motivating concern seems to be the fear that biotechnologies and other human enhancement technologies will somehow undermine human virtue. As we will see, far from undermining virtue, biotech, nanotech, and infotech enhancements will tend to support virtue; that is, they will help enable people to be actually good.