Science Tidbits: Sasquatch Genome, Human Evolution, and DNA Up Close

Some fantastic genetics news:

� Suspect Sasquatch Sequencing

Hoax? Viral marketing? or major scientific breakthrough? Texas company DNA Diagnostics,  headed by veterinarian Dr. Melba Ketchum, has announced that they have sequenced not one, but three different Sasquatch genomes. Dr. Ketchum has applied for a patent for a method of genetic analysis of wild and domestic animals, which suggests expertise in DNA analysis. Their claim is that not only that the Sasquatch is humanoid, but that they are hybrids between human females and "unknown" male hominins.

�Genetically, the Sasquatch are a human hybrid with unambiguously modern human maternal ancestry. Government at all levels must recognize them as an indigenous people and immediately protect their human and Constitutional rights against those who would see in their physical and cultural differences a �license� to hunt, trap, or kill them."

So not only some amazing claims but a strong message about ethics to go with them. 

 Over at Teen Skepchick they have dug into the details that are available about Ketchum and Robin Lynne, who put out the press release. It turns out Lynne has made a number of claims about a large Sasquatch family that she has interacted with on her property.

But her evaluation of the evidence is beyond reproach. Apparently she went out one day to her feeding box to find it locked, and when she opened it, the food was gone but there was an opossum inside. She naturally concluded that the Bigfoot family had put the creature in there and locked the box as a joke.

Apparently the original manuscript also claimed that they found "angel DNA" in the samples. The more I read the more this sounds like the work of some serious deluded individuals who may have analyzed a sample of wild animal DNA contaminated with human DNA. Or maybe this is truly a history discovery (but I think not).

Image: Bigfoot statue in Silver Lake, Washington. by Plazak on Wikimedia Commons licensed under the Creative Commons Attribution 3.0 Unported license. May not be scientifically accurate.

Now some more realistic science:

� Human Evolution Enters an Exciting New Phase | Wired Science 

 I don't think it should be a surprise to anyone that humans are evolving. Evolution is not a ladder where humans have reached the top and will never change again.

But a recent detailed study of 6500 human genomes - Americans of European or African descent - did turn up something unexpected: the explosion of the human population over the past 5000-10000 years has resulted in a "vast abundance of rare genetic variants".

"... the results suggest that humans are carrying around larger numbers of deleterious mutations than they did a few thousand years ago. But this doesn�t mean that humans now are more susceptible to disease, says Akey. Rather, it suggests that most diseases arecaused by more than one variant, and that diseases could operate through different genetic pathways and mechanisms in different people." 

One limitation of this study is that it only compared the protein coding sequences of the genomes it analyzed. 98% of our genomes do not encode proteins, so it's possible that whole genome analysis might have told a different story. In fact, I think it would be interesting to compare mutation rates in protein coding and non-coding sequences (some of which is functional, but much of which is junk).

Original paper: Fu, W. et al. "Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants" Nature Advance online publication, http://dx.doi.org/10.1038/nature11690 (2012).

� Scientists snap a picture of DNA�s double helix for the very first time �

Despite what you might see in science fiction movies and CSI-like TV shows, the DNA double helix is not usually visible under a microscope. In fact Enzo di Fabrizio and his colleagues at the University of Genoa were able to take high resolution photographs of double stranded DNA using an electron microscope in which the DNA double helix is clearly visible.

The image is actually not a single molecule of DNA - it's six DNA molecules wrapped around a seventh, since the energy of the electron beam can break a single DNA molecule. It's hoped that in the future a single DNA molecule can be imaged.

Original paper: Gentile F et al. "Direct Imaging of DNA Fibers: The Visage of Double Helix" Nano Letters Article ASAP (2012)

Image: The famous twists of DNA's double helix have been seen with the aid of an electron microscope and a silicon bed of nails (Image: Enzo di Fabrizio, from Gentile F et al.)

� GATTACA Rises: building structures out of DNA

Last, but not least, a team of French physicists lead by Jean Michel Arbona have designed a new computer model that describes how DNA can fold and knot and weave together into 3-dimensional structures known as DNA origami. See the video here for more details.

Science and SF Tidbits: Extreme Life, Using our Brains, Celebrating Dawn

Some recent bioscience and science fiction articles I found interesting:

� Ancient Microbes Found in Buried Antarctic Lake : Discovery News �

Some of the strangest forms of life on Earth live in the coldest and hottest environments. As long as there is a source of water, life is likely to be found. That's why any hint of water on Mars or Venus or other bodies in our solar system is big news.

Scientists recently found diverse bacteria thriving in an buried Antarctic lake, an environment devoid of oxygen, saltier than the ocean and a frosty -13�C. That hints at the possibility of life on frozen worlds like Europa.

� Scientists discover possible building blocks of ancient genetic systems in Earth's most primitive organisms

Has life always been as we "know it" today? Quite possibly not.

The genetic instructions in plant and animal life is currently based on DNA, with a deoxyribose based backbone. Before that, it's thought that life may have been RNA (ribose backbone) based. But what came before RNA? One hypothesis is that hereditary molecules were built from aminoethylglycine (AEG) peptide nucleic acids.

One problem with that theory is that AEG had never been found in nature - up until now. Scientists have found AEG inside cyanobacteria that live in extreme environments, such as hot springs. It's a far cry from finding AEG-based life, but the fact that AEG can be biologically synthesized makes that hypothesis less unlikely.

Image: Filaments of cyanobacterium Nostoc colonies. Uploaded by Thibul at fr.wikipedia. Shared under a CC-BY-1.0 license.

� Do we only use 10% of our brains?

Some myths keep being debunked over and over. One such idea is that we only use 10% of our brains, leaving some 90% just idling. In science fiction that often is used as an explanation why a character has psi powers or superintelligence: they have a mutation or took a drug that allows them to use that normally "unused" part of their brain, unlike us normal folk. It's annoying, because it's simply not true.

At BBC Future Claudia Hammond explains why the idea that the claim we only use 10% of our brains is a myth, albeit a persistent one. Various measures of brain function make clear that it's simply not true. And if you think more deeply about it, it doesn't really make sense from an evolutionary perspective either, as Hammond points out:

"It is true that nature can sometimes involve some strange designs, but to evolve to have a brain ten times the size we needed would seem very odd, when its large dimensions are so costly to our survival, leading on occasion to obstructed labour and the death of a mother during childbirth if no help is available."

� Celebrating Dawn by Octavia Butler

In honor of the 25th anniversary of the publication of Octavia Butler's Dawn, author N.K. Jemison reflects on the novel's significance and how Butler dealt with sexism and paved the way for African American science fiction writers:

"this fiction went right to the worst that I was seeing in the real world around me, but then she also suggested we can still do better, we can still survive, grow, change, improve"

Dawn is the first novel in Butler's Xenogenesis Trilogy. It takes place on a mostly depopulated Earth which has been invaded - or perhaps rescued - by aliens. The surviving humans must choose whether to adapt to an integrated hybrid human-alien society or fight for independence. If you haven't read the series you should do so!

Going to Mars: are we humans fit to make the journey and when we arrive will there be life there?

Inlet covers for sample analysis at Mars.
Image credit: NASA/JPL-Caltech/MSSS  

Are we humans prepared to travel to Mars? And if we are, will we find life when we arrive?

What has the Curiousity rover found on Mars? The Mars Science Laboratory team has made some tantalizing hints about a "historic" and "Earth-shaking discovery made in a Martian soil sample.

We won't actually know what they found until it's announced at the American Geophysical Union meeting in early December. Some intriguing possibilities are organic compounds, liquid water, or even microbial life. Hopefully the announcement will live up to the speculation.

(Update 11/27:  NASA's "historic news" turns out to be a misunderstanding. No big announcement forthcoming, alas.)

Even if it turns out that something less spectacular than life, any major finding is sure to inspire more calls for a manned mission to Mars. Humans, the argument goes, are more adaptable than mere machines. But I think the real appeal is to expand the boundaries of human territory and to say that we've been able to do it.

Artist's conception of manned exploration of Pavonis
Mons on Mars. Artist:Pat Rawlings for NASA

But some people have even bolder plans for Mars. Billionaire Elon Musk, founder of the private space flight company Space X, has proposed human colonization of Mars. He envisions a "self-sustaining civilization" of up to 80,000 on the red planet, with colonists paying an "affordable" $500,000 for the trip.

Of course the space ships are still under development. It's not clear when they would be ready for even a small-scale mission with a crew of ten.

And then there's the human factor. At least the first few manned missions to Mars are likely to be relatively rough compared to what later colonists are likely to experience. The journey would take anywhere from 150-300 days, with extended periods of weightlessness and - possibly more importantly - extreme isolation for the crew.

The astronauts aboard the International Space Station have been carefully monitored to help understand the physiological effects of living in microgravity. It takes a serious toll on the human body: bone and muscle mass are lost, vision can degrade, and some astronauts suffer debilitating space sickness.

But up until now stays aboard the ISS have be relatively short. It was just announced that two astronauts - American Scott Kelly and Russian Mikhail Kornienko - are scheduled to begin a year-long stay on the ISS in early 2015. Tests and experiments will be run to determine the physiological effects of such a long stay in space. That will hopefully give scientists a better idea if the human body will be able to tolerate a long journey to Mars under weightless conditions.

Concordia Research Station Source: StephenHudson on
Wikimedia Commons. Public domain.

And the effects of living in isolation with a small group are being tested in Antarctica. The scientists at Concordia Research Station in Antarctica are completely isolated for nine months of the year in the most extreme environment on Earth. Even in summer the outdoor temperatures rarely rise about -25�C. In the winter the temperature can fall to -80�C (-112�F) and there is darkness around the clock.

The scientists at Concordia are well aware that their experiences model the psychological pressures the crew of a manned mission to Mars will experience. In an article for the New York Times, physician and researcher Alexander Kumar explained what it's like to return to civilization after a stint there. He notes:

"I have learned a lot about Antarctica, myself and, of course, what might lie ahead on Mars. If we can make the journey, why would we go? And, as we have debated into the wee night hours, should we go?"

I think that's the ultimate question: even if we can make a Mars should we expend the resources and risk the lives of astronauts to do so? And would the discovery of possible life on Mars make a difference?

I admit I really like the idea of a human colony on Mars, but I'm not sure if that's just a romantic notion from having read too many science fiction novels. Even Kim Stanley Robinson's Red Mars, which shows the terrible difficulties - both human and technical - of colonizing Mars doesn't suggest we shouldn't try to go there in the first place. Even if it's hard I think we should go.

And heck, if given the opportunity, I think I would go, even if there aren't little green men. I guess I should be saving up so that I have a spare $500,000 when tickets go on sale.

Science and SF tidbits: middle-aged apes, fantastic cells, and SF genetics

Some recent reading about fictional biology:
� JIM: More Compelling Than GATTACA | DNA Science Blog �

If you are looking for a science fiction film with a scientifically plausible depiction of human genetic enhancement and cloning, you might want to check out JIM. Science writer/geneticist Ricki Lewis reviews the film and says:

"Although Jim, released in late 2010, shares with GATTACA the premise of widespread genetic enhancement, it�s much more subtle and nuanced. The film struck me with its stunning possibility, and the intentional gaps in the glimpse of future history still have me thinking a week later."

And watch a commercial for "Lorigen Engineering", which offers Better Kids, By Design�'

� Author Spotlight: Tom Crosshill 

Tom Crosshill's recent short story "A Well-Adjusted Man" takes a chilling look at the potential repercussions of erasing traumatic memories might have. In his interview with Lightspeed Magazine, talks about the psychology PTSD, the biochemistry of traumatic memories, and his inspiration for the story.

And some fantastic factual biology:

� Great apes go through mid-life crisis � Nature News

Psychologist Alexander Weiss and his colleagues wanted to find out if the human "midlife crisis" that hits somewhere between our mid-30s and 50s could have a biological basis. They decided to survey zookeepers about of the mood of the chimpanzees and orangutans in their charge. They found that our great ape cousins seem to have lower sense of well-being during their late 20s to mid-30s - the equivalent to human middle age.

It would have been nice if the study had included some quantifiable data, such as the level of stress hormones or other physiological measures. It's hard to know how much bias might be introduced by asking zookeepers to try to put themselves in the minds of their charges. But still, an interesting study.

Image: Orangutan Portrait by Chester Zoo on Flickr shared under a CC BY-ND 2.0 license.

� Introduction to Cells (Vimeo)

A dramatic video showing the beauty of cells. The video was created by science teacher Frank Gregorio who makes "introduction" science videos for middle and high school teachers to use in the classroom. I wonder how well it works to capture the imagination of fidgety teenagers?

� Paralyzed dogs walk again (video)

Jasper the dachshund regained some use of his formerly paralyzed hind legs after his spinal cord was injected with cells grown from the lining of his nose. Robin Franklin and his colleagues at the University of Cambridge, used nose cells (or more precisely olfactory ensheathing cells) because, unlike most nerve cells, the nasal nerve fibers continue to grow into adulthood. The injected cells grew new nerve connections restoring function to the dog's damaged spine.

While the treatment appears to have a lot of potential it will take a lot more research before it will be tested on humans. More about the study at the University of Cambridge.

� Chemical biology: DNA's new alphabet

Chemist Eric Kool is reengineering DNA with nucleotide bases not found in nature. He's one of a number of chemists and chemical biologists who are creating new types of DNA and RNA molecules that they hope can be used for studying the function of nucleic acids and that may have new biochemical properties. But Kool explains those aren't the only reasons:

".... researchers are still driven by what Kool calls the �science-fiction appeal� of designing or even improving on living systems. Earth's early life forms may have settled on their genetic alphabet simply because they were constrained by the chemicals available. [snip]
So if nucleic acids arose independently on another planet, would they have the same bases? Benner thinks not, unless the organisms were subjected to the same constraints. Some universal rules might apply, however."

And short of discovering extraterrestrial life, it's only by synthesizing and testing new molecules to see if they might be functional in living systems.

Thanksgiving special: inbred turkeys and feasts in space

Happy Thanksgiving everyone!

While you are feasting, you might consider the humble origins of the turkey:

� Tracing the taming of the turkey

At Double X Science Emily Willingham looks at the origins of today's turkeys, whose wild ancestors were carried from Mexico, to Europe and back again to North America.

Image: Turkey by wattpublishing on Flickr (www.WATTAgNet.com), shared under a CC-By-2.0 license. 

� Turkey trouble: Genetics gone too far?

At KQED Quest Barry Starr takes a hard look at the turkeys on factory farms and it's not pretty. Turkeys bread for to have lots white breast meat are likely in constant pain and are prone to heart attacks. He notes:

All of this raises the obvious ethical question. Just because we can breed this turkey, should we? The turkey lives a short, miserable life but we get an affordable, healthy source of protein. It is obvious which choice we�ve made as a society, but is it the right one?

A bit sobering to think about.

Meanwhile, NASA engineers suggest some interesting cooking techniques, astronauts celebrate Thanksgiving in space:

� Four Crazy Ways to Cook Your Turkey Using NASA Equipment

Gizmodo asked NASA engineers and science writers how they would use NASA's high tech equipment to cook a turkey. If you have a spare satellite dish or an Antares-class sounding rocket you could try out their recipes yourself!

� Astronauts get Thanksgiving feast in space

The astronauts on the International Space Station will be celebrating Thanksgiving with a holiday meal that includes irradiated smoked turkey and themo-stabilized yams - yum!. Even though it comes freeze dried and in foil packets it's still a special treat.

You can even follow NASA's recipe for cornbread stuffing if you want to eat like the astronauts do.

Finally, a Thanksgiving message from Commander Kevin Ford on the International Space Station, who talks about the holiday meal he and crewmates Oleg Novitskiy and Evgeny Tarelkin will be eating:

Science & SF Tidbits: Brain Music

Music from the brain and the brain on music:

� Scale-Free Brain-Wave Music from Simultaneously EEG and fMRI Recordings - PLoS One

Neuroscience + art = the music of our minds

A team of Chinese scientists has proposed a new method of translating the signals from EEG-fMRI brain scans into music. We'll have to wait and see if the music eventually is an aid to diagnosis or medical treatment as the authors hope, or if this turns out to be an off-beat art project:

"The brain music, as one of the human brain's intelligence product, embodies the secret of brain in an artistic style, provides the platform for scientist and artist to work together to understand ourselves, and it is also a new interactive link between the human brain and music. We hope the on-going progresses of the brain signals based music will properly unravel part of the truth in the brain, and then to be used for clinical diagnosis and bio-feedback therapy in the future."

Listen to the EEG music

Image: Illustration of the score of EEG-fMRI music from Lu J, Wu D, Yang H, Luo C, Li C, et al. (2012) Scale-Free Brain-Wave Music from Simultaneously EEG and fMRI Recordings. PLoS ONE 7(11): e49773. doi:10.1371/journal.pone.0049773 Shared under a CC-BY-2.5 license.

� Brain scans of rappers shed light on creativity � Nature News

What does a rapper's brain look like while he's freestyling? Neuroscientists at the National Institutes of Health had 12 rappers improvise while in an MRI machine. What they found was that brain activity in the medial prefrontal cortex increased, and activity in the dorsolateral prefrontal cortex decreased. What that may mean is that the parts of the brain involved in cognitive "executive functions" like planning, problem solving, attention and verbal reasoning might be relaxed during the creative process.

This could explain why the creation of music can seem to flow during improvisation without any conscious thought. As study co-author and alternative hip-hop artist Open Mike Eagle puts it:

�That�s kind of the nature of that type of improvisation. Even as people who do it, we�re not 100% sure of where we�re getting improvisation from.�

� Notes & Neurons: In Search of the Common Chorus

Performer Bobby McFerrin and cognitive neuroscientist Daniel Levitin teamed up at the 2009 World Science Festival to demonstrate how our brains are wired for music.

In this clip McFerrin "plays" the audience with the pentatonic scale:

At SIMF: Room needed on the Ark, for creatures great and small

I have a new post up over at Science in My Fiction - "Room Needed on the Ark" - that considers the following scenario: if Earth were in imminent danger of destruction and we had a space ark that could carry humans, animals, and plants to safety, how would we decide which animals to rescue? and how many individuals of each species we'd need to bring along?

Part of the answer depends, of course, on what the goal would be. Setting up a human colony on another planet might have different requirements than if the goal was to restore life on a ravaged Earth. To set up brand new self-sustaining ecosystems would likely require a wide range of animals and plants, whereas a self-contained and highly technological settlement might not.

And I think there is a bigger picture to look at. If we want to be able to save species from going extinct, or to have a repository to maintain genetic variety in crop plants, we need to be collecting samples and genetic material now (which is being done). So if we want to keep our precious gene banks from danger, do we spread them out in multiple countries? or do we build a DNA library on the moon?

So many questions! Read "Room Needed on the Ark" and share what you think.

Image: Startling Stories, November 1939