Thursday, November 29, 2012

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 HelixNano 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.

Wednesday, November 28, 2012

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!

Monday, November 26, 2012

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.

Friday, November 23, 2012

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

Some recent reading about fictional biology:
JIM: the movieJIM: 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®'




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:

Orangutan PortraitGreat 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.

Wednesday, November 21, 2012

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:

Tuesday, November 20, 2012

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:

Monday, November 19, 2012

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

Sunday, November 18, 2012

Science & SF Tidbits: Speculative Genomics, Snot Whales, and Idiocracy (not)

Some fictional and speculative genetics and genomics for your reading pleasure:

Free Fiction:
The Authors: Flash Fiction Fest - Four Weeks of Flash Fiction from December House »

Publisher December House is posting several new short fiction pieces every day of November. Many of the stories have a "science fiction feel". Sean Craven's stories feature Henry Cleary; the Colonel, who's a rooster genetically engineered to have teeth and a long muscular tail; and many other science fictional biological oddities.

Craven has also been posting some thoughts on the biological background of his stories on his blog. If you are interested in some real odd biology, give them a read here: Salamanders and Snot WhalesThe Shade-Tree Biotechnician
Note that the stories are only available free through the end of November, so check them out soon.

Speculative genetics:
Brazil To Clone Wild Animals In Danger Of Extinction » io9
EMBRAPA, the Brazilian government's agricultural research agency, successfully cloned a cow in 2001. Since then they've been refining their cloning program to the point where they have now announced they are going to try cloning endangered species. Their list includes eight animals on the threatened species list, such as the maned wolf (Chrysocyon brachyurus), the jaguar (Panthera onca) and the black lion tamarin (Leontopithecus chrysopygus).

EMBRAPA has stated that their goal is to keep the cloned animals in captivity and only use them for restocking zoo populations and study, rather than releasing them to the wild. But it makes me wonder: is cloning a good use of resources in situations where the wild populations are at risk?

Cancer, Data and the Fallacy of the $1000 Genome » Forbes
Dr. Mark Boguski has a message: "The time of the $1000 genome meme is over. It served us well for years – driving advances in instrumentation, chemistry and biology. But now it is reducing clinical credibility. It’s time for it to leave the lexicon of healthcare; it has to go."

The fact is that genome sequencing for cancer patients is expensive (far more than $1000), not covered by insurance, available to a relatively limited number of people, and might not be that informative clinically. He argues that the focus should be on precision diagnostics, which involves "big data" and analytics. And because this article is in Forbes, that means that Boguski and colleagues have started a business - Genome Health Solutions - to do just that.

It seems to me that with potentially limited research funds it's not clear whether scientists should be striving to make genome available and affordable for everyone, or if it would be better if they instead focused on deeper analysis of the existing data - or, ideally, if both approaches are possible. Which would be better for the average cancer patient is still unclear.

Image: SNPs: Single Nucelotide Polymorphisms, Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science.science.energy.gov/ber/. Used with permission.

Neuroskeptic: We're Probably Not Getting Dumber »
While it may be popular to argue that the human race is evolving to be dumber Idiocracy-style, the good news is that we're probably not actually getting less intelligent as a species. We won't even become beautiful-but-dim Eloi. In the linked article Neuroskeptic explains how two recent articles claiming that humans are getting dumber are based on faulty assumptions.

Sci-Fi Political Thriller, Or Fact? - HuffPost Live »
Harvard geneticist George Church, SF author/futurist David Brin, and futurist Jamais Cascio, discuss the speculative possibility of "Hacking Obama's DNA". I'm glad the Huffington Post included a geneticist in the discussion!

Thursday, November 15, 2012

Science & SF Tidbits: Best science journalism and rosy futures

Recent reading:

AAAS - Winners Named in Science Journalism Awards »

The American Association for the Advancement of Science announced the winners of the 2012 AAAS Kavli Science Journalism Award Competition. The winners include:

Carl Zimmer, for publication in a "Large Newspaper" (New York Times)
Michelle Nijhuis, for publication in a magazine (Smithsonian)
 Sarah Holt and Laurie Donnelly for "In Depth Reporting" on TV (WGBH/NOVA)
See the announcement for the full list of winners and some back story about how their stories were written.

Image: little brown bat affected by white-nose syndrome. Image from the US Fish and Wildlife Service national Digital Library. (Public Domain). Read Nijhuis's "Crisis in the Caves" to learn more about how this fungal disease is decimating bat populations.

And for a more speculative point of view:

• 7 Best-Case Scenarios for the Future of Humanity »

Are you tired of apocalyptic futures where humanity is enslaved by aliens, or we destroy the environment or each other?  George Dvorsky looks at seven science fictional visions of the future that have a happy ending for humanity. Maybe I'm boring, but I were able to choose, I think I'd prefer a future not so different than today ("status quo") but with cleaner air and more green spaces ("bright green Earth") here on Earth, and colonies out in our solar system ("boldly go").  

I'm skeptical of post-human futures that involve uploading our minds to computers or otherwise transcending our physical bodies. Even if that were possible, I suspect that many (or even most) of us would be loathe to leave the real world behind. I personally like having corporeal form, even with all its flaws.

Wednesday, November 14, 2012

Cyborgs and enhanced humans - should we worry?

Humani Victus Instrumenta: Ars Coquinaria (1569)
Five or so years ago Nigel Ackland was involved in a terrible accident while working as a smelter. His  forearm was crushed, and eventually had to be amputated. He's had a series of prosthetic limbs, but the most recent version - the bebionic3 myoelectric hand - is by far the most advanced. The mechanical hand is so sensitive that he can now use it perform everyday tasks such as washing his hands, typing, peeling vegetables, and driving.

The video of Ackland using his hand shows how impressively well this technology works - and presumably more advanced hands are currently under development:



It's not just human limbs that can be replaced. For the vision impaired there are artificial retinas and plastic polymer replacement lenses under development. And hundreds of thousands of electronic cochlear ear implants have allowed the deaf or severely hearing impaired to hear.  Hip and knee joint replacements are almost routine.

Most of us, I think, agree that the restoration of physical or sensory abilities is a good thing. I know if I lost mobility or started to go blind I would seriously consider human-made body part replacements if they were available. That doesn't seem that different to me than wearing glasses.

But for me the ethics get murkier when you start considering modifications that change the way the brain works. While I think it would be great if there were an implant that prevented memory loss for Alzheimers sufferers, I'm conflicted by the thought that similar devices could be used to control someone's behavior.

And once the technology is readily available and affordable, a merely average human being will be able swap their working legs or heart or eyes with artificial replacements that could make them stronger or faster or able to hear or see better than their natural bodies could. But would that be ethical? Should we worry about the creation of cyborgs?

In science fictional futures featuring cyborgs, mechanical modification often come with a price: from Frederic Pohl's man engineered for Mars to Star Trek's Borg, something essentially human may to be lost when one's body parts or sensory inputs are enhanced. And Asimov played with the same idea in his story The Bicentennial Man, in which a robot gradually has his mechanical parts with more human-like ones, and eventually is legally declared a man.

Personally I don't believe that implanted electronics or mechanical parts are likely change our essential humanity.  But I think there are ethical concerns beyond the philosophical sorts of speculation about personhood. A recent New York Times story about bioengineering ethics points out that who has access to technology could become a serious issue:
Ethical challenges for the coming Age of Enhancement include, besides basic safety questions, the issue of who would get the enhancements, how much they would cost, and who would gain an advantage over others by using them. In a society that is already seeing a widening gap between the very rich and the rest of us, the question of a democracy of equals could face a critical test if the well-off also could afford a physical, genetic or bionic advantage. 
Already there are disparities between access to the latest and greatest medical technologies. It's not a stretch to think that such disparities would extent to voluntary modifications too. If ones place in society is dependent on one's health and physical prowess, technological innovation could increase the gap between the haves and have-nots.

And beyond that, there may be pressure on athletes, soldiers and even physical laborers to undergo modifications even if there is a potential risk to their health or well-being. Should biomechanical enhancements be banned the same way steroids and other performance-enhancing drugs are today?

I don't think there are any easy answers to these questions. But I do think that we should try to grapple with these issues as a society while the technologies are still in their infancy.

Perhaps the solution will be implants for everyone, and we wouldn't even recognize our descendents  a century or two from now.

Related non-fiction from Amazon.com:

Monday, November 12, 2012

Evolution of the Earth and aliens from a religious point of view

What would the discovery of intelligent extraterrestrials mean for humans? And is it even a likely scenario? Read on...

But first a brief interlude:

• Our Story in 1 Minute (YouTube)

This video shows the creation of the earth and evolution of life in under two minutes.  Lovely!
Of course the time scale isn't linear - it it was, the rise of life would pass in less than a blink.

OK, on to the more serious discussion:

• The Myth of the Evolution of ET - Ted Peters (SETI Talks)

In this video Professor Ted Peters of the Pacific Lutheran Theological Seminary talks at SETI Institute about the mythic elements surrounding discussion of extraterrestrial life.  In particular Peters takes on the assumption of some (many? most?) astrobiologists that extraterrestrials will necessarily be more "advanced" than humans, which is not consistent with what we know about evolutionary biology. He argues that if we do discover extraterrestrial life, it's more likely to be microbes than a technologically advanced society. 

It's a provocative position, as much of the excitement about SETI - the search for extraterrestrial intelligence - assumes that if there is life, it must be advanced. And if ETs turn out to be wise and technologically advanced, what does that mean for religion? And does it matter if life originated from God or nature?

You can read more about Peters' thoughts on aliens and evolution what that could mean for ethical first contact from a religious POV in his article for the Journal of Lutheran Ethics "Anticipating Detection of Life in Space: AstroEthical Scenarios".

Watch the video of Peters' talk - what do you think?

Image: View of North America from Apollo 16. Source: NSSDC Photo Gallery @ NASA.

Sunday, November 11, 2012

Science Tidbits: Beatles, Birds and Brains

Beatles Rubber Soul at Amazon.comWhat Beatles and birds may tell about brains:

The Beatles' Surprising Contribution To Brain Science : NPR »
It all started with an interesting observation by Georgetown neuroscientist Josef Rauschecker: if you asked him what order of the songs on his favorite Beatles album, he wouldn't be able to tell you. But he could sing along with a song and at the end he would be able to start humming the notes of the song that usually followed.

To try to figure out what was happening, he had volunteers listen to their favorite CD while in a brain scanner. It turns out the area of the brain that was most active wasn't associated with hearing, but the brain's motor system, which is usually involved in controlling our muscles.

Just like learning a sequence of dance steps or how to ski down a slope, our brain uses the motor control system to put together chunks of notes into the right order.

Listen to the whole story on NPR.

Wrens teach their eggs to sing »

fairy wren
Unborn fairy wren chicks must learn a special "password" note from their mother while still in the egg. After hatching will only be fed by their parents if they can produce the correct "begging call" - this prevents any relatively enormous cuckoo hatchling interlopers in their nest from being fed.

But some species of cuckoos are adapting: the cuckoo chicks may try out different calls until they find one that gets them a meal. Clever cuckoos!

Image: Juvenile female superb fairy wren. This work has been released into the public domain by its author, LiquidGhoul at the English Wikipedia project.

Human Brain Project -video overview (Vimeo)

The Human Brain Project is a collaborative effort between scientists across Europe to create a computer simulation of the human brain. They believe that working together is the key:

"We find that the major obstacle that hinders our understanding of the brain is the fragmentation of brain research and the data it produces. Modern neuroscience has been enormously productive but unsystematic. The data it produces describes different levels of biological organisation, in different areas of the brain in different species, at different stages of development. Today we urgently need to integrate this data – to show how the parts fit together in a single multi-level system."

Learn more about the Human Brain Project.

Friday, November 09, 2012

Free Friday Flick: Rendezvous with Rama short "trailer"

This week's recommended free movie is a short film inspired by Arthur C. Clarke's novel Rendezvous with Rama. The movie was a student project by Aaron M. Ross, who is now lighting director at Blue Sky Studios. He has gone on to work on visual effects on a number of animated movies, including Horton Hears a Who! and the Ice Age sequels.

Rendezvous with Rama - NYU 2001 from Aaron Ross on Vimeo.


The short "trailer" for a Rendezvous with Rama movie is a mix of live action and computer graphics. In the video showing how the film was created, you can see how Ross used actors attached to cables acting in front of a green screen to simulate the low gravity environment aboard Rama.

The short only covers the first part of the story, where a team of astronauts and scientists is sent to explore a mysterious massive cylindrical object travellng through our solar system.

This will have to satisfy fans until the long-discussed Morgan Freeman feature-length film of Rendezvous with Rama is actually made. Freeman has stated as recently as last February that he still intends for that to happen.

I would love to see a well-done movie version of the story. I think that special effect technology could actually capture the vast interior living space inside the cylinder, the circular sea, and the variety of "biots" that live and work there. But in Hollywood, it seems there's no guarantee a movie will be made until it's finished and scheduled for release - and maybe not even then.


In the mean time you could read the original novel, published in 1972 and winner of both the Hugo and Nebula awards. It does a great job evoking of the sense of wonder in exploring a truly unknown territory, even under dangerous conditoins.

Watch the Rendezvous with Rama short on Vimeo or YouTube.

Image: Artist's depiction of the interior of Rama at Wikimedia Commons. Original uploader was Monomorphic at en.wikipedia Released into the public domain by the artist.

Wednesday, November 07, 2012

Science & SF Tidbits: intelligent dinosaurs, printed meat, extreme voting

Some recent links:

• Extreme Voting: How Astronauts Cast Ballots from Space »
If you are in the US, did you vote in yesterday's election? The American astronauts on the International Space Station did, submitting their absentee ballots electronically.

Dinosauroids revisited, revisited | Tetrapod Zoology
If dinosaurs had evolved intelligence, rather than going extinct, what might they look like? Would they be like the Silurians on Doctor Who, essentially human shaped? or would they be clever as crows and appear more bird-like? It seems like most of the science fictional and speculative science depictions assume the former model: intelligent "dinosauroids" would look much like us humans, only scalier. Paleozoologist Darren Nash takes a look at the biological plausibility of the different models of intelligent dinos that have been proposed and takes a slightly different view. Read the article for more!

Image: Dinosauroid, Dinosaur Museum, Dorchester. Photograph by By Jim Linwood on Flickr. Shared under a CC by 2.0 license.

Primeval: New World >> Create a Fan Video
Primeval: New World is a Canadian spin-off of the UK paleo-science fiction series Primeval. The basic premise is that there are "anomalies" that appear that are essentially doorways to other times. If an anomaly opens between the Cretaceous and our own time, a bunch of velociraptors might just end up running down the street. So every week a team of specialists needs to catch any creatures that have come through the portal and fix any damage done.

As you might expect, both series rely heavily on CGI dinosaurs and other beasts. Primeval: New World has an interesting offer - they provide special effects and animated dinosaurs, you create the video and upload it to YouTube and they may feature it on their site (like this video). If you want to create your own dino movie, there is more information here.

First tasting of Printed Meat « NextNature.net »
University of Missouri biological physicist Gabor Forgacs uses 3-D bioprinting devices to "print" organs made of cells on extracellular matrix biogel scaffolds. But there may be other uses. As part of a TEDMed presentation, Forgac cooked and ate a printed piece of meat. Forgac's company, Modern Meadow, is working on developing lab-grown meat and leather products that could eventually be mass produced and sold.

What's not clear to me is whether this is really necessary. If industrial farming is the problem (and it is), why not use artificial leather and promote meatless meals, rather than growing likely expensive versions in the lab? I'm not sold.

Monday, November 05, 2012

Science & SF Tidbits: Life giving asteroid belts and the ethics of cloning

A couple of articles about what might help create life out there and what's possible for the creation of life right here:

Alien Life May Require Rare 'Just-Right' Asteroid Belts »

Astronomers Rebecca G. Martin and Mario Livio and have proposed that an asteroid belt that's just the right distance away from a system's sun and other planets may make life more likely. Why is that the case? Because asteroids may have helped bring water and organic materials to early Earth.

You may be thinking about the hypothesis that a meteor hitting the Earth caused the dinosaurs to go extinct. But maybe massive extinctions are ultimately a boon to life as well, opening up ecological niches for rapidly evolving critters to expand into.

Yes, it's (educated) speculation, based on the conditions on the only planet that we know has life - Earth, but it's interesting to consider. Considering that less than 4% of known solar systems appear to have an asteroid belt, if they are right that could reduce the chances of our finding life - at least as we know it - in other solar systems.

Image: There are several different scenarios for the evolution of asteroid belts. Depicted is our solar system where Jupiter (or a similarly-sized planet) orbits the sun just outside the asteroid belt. For other models see the NASA Scenarios for the Evolution of Asteroid Belts page. Image credit: NASA/ESA/STScI (not copyrighted and free to use)


Could Clones of 'Cloud Atlas' Be in Our Future? : Discovery News »

In the future depicted in the movie Cloud Atlas, fabricant" Sonmi-451 clones are servants, slaves and sex toys.They sound a lot like the "Gammas" and "Deltas" in Brave New World (only sexier).

Is it even technically possible to grow of an army of human clones in artificial wombs? According to the linked article, while there is ongoing research, it likely would not be really workable for a long time - and that's assuming that ethical considerations allow the development of the technology in the first place.

Discovery News also provides a video where geneticist Robert Lanza talks about cloning technology that can resurrect extinct animal species - and at least theoretically could be used to bring time-displaced genetic copies of dead people back to life too. 

Sunday, November 04, 2012

Science & SF Tidbits: Presidential DNA Biohacking, Alien Jellies, Non-fruity Dragons

Recent links of interest:

• The Lovely Lobed Comb Jelly (YouTube)
This video from the Monterey Bay Aquarium is an artful display of beautiful and eerily alien-looking bioluminescent comb jellies.

Image: "Frolicking" comb jellies at the Monterey Bay Aquarium by Steve Jurvetson (jurvetson) on Flickr, shared under a CC-BY-2.0 (Creative Commons Attribution) license.


• Hacking the President’s DNA (The Atlantic)
"So, in November of 2016, when a first-time visitor with the handle Cap’n Capsid posted a challenge on the viral-design site 99Virions, no alarms sounded; his was just one of the 100 or so design requests submitted that day"
This article in The Atlantic begins with a detailed scenario describing the rise of amateur biohacking that spins out of control into outright terrorism. With today's technology that is pretty much just science fiction. But the potential current threat that that the relatively straightforward molecular manipulation of viruses and bacteria and the ease of genome sequencing represents is taken very seriously by the government.

There are claims that the DNA of the President of the United States is carefully being protected, while DNA from other world leaders is being collected. And reports of the creation of synthetic organisms has added to the fear that genetically manipulated bugs could cause unstoppable pandemics. With the spread of "biohacking" culture, there is fear that even amateurs could become bioterrorists. While all of that sounds alarmist, the article does take a more realistic look at what bioscience is capable of today.

• ‘The Hobbit’: Peter Jackson’s unexpected journey to three films (Hero Complex at the LA Times)
Peter Jackson was interviewed about his upcoming film version of Tolkien's The Hobbit. When asked about the design of Smaug the dragon, he explained why he wanted a traditional look:
"The trouble with redesigning dragons is that if you really get fruity with it, it suddenly starts to look like some sort of monster from another planet — you very quickly can go into science-fiction territory,” Jackson said. “I don’t want to do that. I mean, people expect a dragon. ‘The Hobbit’ is one of the most famous dragon stories in the world, really. So I’m not trying to step away from the dragon. I just want to present the most venal, scary, decrepit, nasty dragon that I possibly can.”
I'm looking forward to see what they come up with. The greatest adventure indeed!

Saturday, November 03, 2012

OMNI Magazine free!

More than 200 scanned issues of OMNI magazine, originally published between 1978 and 1995, are now available for download at the Internet Archive. Totally free and presumably legal! (can you tell I'm excited?) While the science may be looking a bit dated now - and some of the UFO and "fringe" science was never very plausible to begin with - the short science fiction was and is fantastic.

I had a subscription to OMNI through high school and college, and up until that point most of my SF reading had been much older stories, like the Heinlein juveniles and the old Asimov robot stories. Maybe William Gibson's "Johnny Mnemonic" and "Burning Chrome" don't seem cutting edge today, but 30 years ago they weren't like any science fiction I'd previously read.

If you are looking for someplace to start, I'd suggest Best of OMNI Science Fiction #1 (1980). It includes GRR Martin's "Sandkings", Orson Scott Card's "Unaccompanied Sonata", plus stories by Isaac Asimov, Alfred Bester, Harlan Ellison, Robert Sheckley, Ben Bova, Roger Zelazny, Joe Haldeman and more.

Check out the fan-created Complete OMNI Index to find your favorites.

Image: Pierre Lacombe's cover of Best of OMNI #1.

Friday, November 02, 2012

Friday Free Flick: District 9: Violent Prawns

In 2009 director Neill Blomkamp's low budget science fiction movie District 9 was a surprise hit, and now you can watch the full film for free:

From Crackle: District 9

The story begins when a ship full of sickly aliens appears over Johannesburg, South Africa. The aliens end up living in a crowded slum neighborhood called "District 9". Thirty years later, the aliens - derogatorily called "prawns" - are to be evicted and moved to a more isolated internment camp, with the move managed by a private military company (you too can can train to join MultiNational United and arrest non-humans!). Unrest and violence ensues.

 The film's South African settings and depiction of the forcible re-settlement of the "prawns" into a segregated camp intentionally evokes on the historical enforced racial segregation of the apartheid era. But the racial issues are not just fictional; there has been significant criticism of the movie's depiction of Nigerian immigrants as gangsters and "savages".

So what about the biology? The aliens are called "prawns" because they have arthropod-like exoskeletons, just like Earthly insects and crustaceans like lobsters. The aliens are thought to look like the Parktown prawn, a South African cricket pest. And like ants or bees the "prawns" are mostly drone workers. The disease that affected the alien ship apparently killed off the higher castes, presumably including their queen.

When the bureaucrat overseeing the eviction and resettlement process is infected with alien goo and starts slowly transforming into an alien himself, he is forced to find help among the District 9 inhabitants. That forces him to become more sympathetic to their plight, so as he becomes less human himself he can better appreciate the "humanity" of the stranded alien population.


But truly the science depicted in the movie doesn't make a lot of sense. At it's heart District 9 is a violent action flick, with an unusual setting (at least for a Hollywood flick). If that's what you are mood for, check it out on either YouTube or Crackle.

If you would rather watch a high quality version, District 9 is also available for instant download at Amazon.com (for a price, of course).

Image: Libanasidus vittatus or Parktown prawn. Image by Paul venter from Wikimedia Commons, shared under a Creative Commons Attribution Share Alike license.

Thursday, November 01, 2012

Science & SF Tidbits: Nov. 1: Biology of Politics and Sci-Fi Sleep

Today's suggested links:

Science In My Fiction » Sleeping Fiction »

In science fiction, characters are rarely depicted as having a need for sleep. Sure they are put into suspended animation while traveling long distances or as the plot requires, but what is often overlooked are the biological functions of sleep. Studies have suggested that sleep may be important for learning, properly regulating our metabolism, our personalities, our health, our moods, and probably more.

A pretty common science fiction trope is that you can quickly learn by being fed information while sleeping. While there isn't good evidence that that is really possible, even now you can buy recordings that claim they can change your habits (like your desire to smoke) by simply listening while sleeping. So how might (science fictional) pills that replace the physiological need for sleep work - would they also be able to replace the psychological and learning processes that sleep provides as well? Something to think about.

Image: Astronauts Richard "Dick" Truly and Guion Bluford sleep on the space shuttle Challenger. Truly sleeps with his head at the ceiling and his feet to the floor. Bluford, wearing sleep mask (blindfold), is oriented with the top of his head at the floor and his feet on the ceiling. Source: NASA (public domain)

Nature News » Biology and ideology: The anatomy of politics

Do your genes or your physiological state affect the way you vote? Or is your environment and upbringing the deciding factor? Studies of the political and ideological leanings of twins suggest that there is at least some biological component to our politics. Whether that is more important than the influence of family, education and the way information is provided to us is still up in the air.

But I find the results of one study particularly interesting: people who have high levels of the stress hormone cortisol are less likely to vote at all. It makes me wonder if people who are under a lot of stress due to poverty, or because they live in an area affected by a natural disaster, or because their beliefs or lifestyle are different enough from their neighbors that they feel ostracized are indeed less likely to vote. That seems like it could significantly affect election results.

Read the linked articles for more details.