Saturday, October 31, 2009

The Unselfish Gene: Altruism and Zombies

The Unselfish Gene is the first published novel of science journalist Robert D. Burns, and it sounds like a lively mixture of pulpy science fiction-horror and genetics. The novel's blurb gives you a taste of that:
It's love and terrorism in the time of cholera. In the mid-21st century, a form of bird flu has killed billions and turned most of the rest into mindless, stumbling zombie-like invalids. The few humans who had immunity now face the threat of a comet on a collision course with Earth. Settlers from the Moon colony were spared the disease, but face their own threats to survival: radiation-induced mental illness, a limited gene pool and shrinking resources. The Moon settlers have launched a last-ditch mission to Earth to salvage human DNA and other crucial materials ... before the comet strikes. The salvage crew find the biggest threat to the mission is neither the zombies or the comet, but insanity within their own ranks.
Now if you are a biology geek like me, the first thing you think of when you hear the novel's title is Richard Dawkin's classic book on evolution The Selfish Gene. It turns out that that was indeed one of Burns's inspirations for the novel, as he told Irma Arkus in an interview on Hi-Sci-Fri (The interview begins at 22:17). They also discuss the evolution of altruism, the deleterious effects of radiation, and other sciency bits from the novel.

Read excerpts from The Unselfish Gene, and take a peek at the novel's illustrations.

Purchase The Unselfish Gene @ Amazon.com.

Bioscience books discussed on the Hi-Sci-Fi podcast:




David Sloan Wilson's Unto Others: The Evolution and Psychology of Unselfish Behavior.







Richard Dawkins' The Selfish Gene




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Friday, October 30, 2009

Creature Features

If you plan to stay in this Halloween weekend, you might want to plug your laptop into your TV, dim the lights and watch one of the many free SF-horror movies featuring terrible (in more ways than one) creatures.

Here are a few to get you started:

Movie: The Killer Shrews (1959) (Google video)
The science fiction setup: A doctor performs experiments to make humans half-size which have the unintended side effect of creating giant, venomous shrews.

Sometimes called one of the worst sci-fi movies ever made, you can get a taste of Killer Shrews from the trailer:


Movie: Giant Spider Invasion (1975) (Hulu.com, US only)
The science fiction setup: "NASA scientists Dr. Langer and Dr. Vance try to save Wisconsin from 15-foot flesh-eating spiders from another dimension."

Movie: Empire of the Ants (1977) (Hulu.com, US only)
The science fiction setup: "An aggressive land developer takes a boatload of prospective buyers to a reclaimed swamp in the southeast. While there, the group is attacked by a swarm of huge ants, the result of genetic mutation after exposure to atomic wastes."

These movies may be more silly than scary, but they'll keep you entertained for a few hours while you are waiting for trick-or-treaters.

You can find more free horror movies at Classic Cinema Online, YouTube, and Hulu.com

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Thursday, October 29, 2009

When it Changed - Science Into Fiction


UK publisher Comma Press has just released When it Changed, a cool-sounding new anthology where writers and scientists have teamed up to produce something that incorporates both their specialities. From their book's web site:
When It Changed is an attempt to put authors and scientists back in touch with each other, to re-introduce research ideas with literary concerns, and to re-forge the alloy that once made SF great. Composed collaboratively – through a series of visits and conversations between leading authors and practicing scientists – it offers fictionalised glimpses into the far corners of current research fields, be they in nanotechnology, invertebrate physiology, particle physics, or software archaeology. From Planck's Length (the smallest indivisible distance) to Plankton (potential saviours of the Earth's ecosystem), from virtual encounters between Witgenstein and Turing, to future civilisations torn asunder by different readings of the Standard Model, together these stories represent a literary 'experiment' in the true sense of the word, and endeavour to isolate a whole new strain of the SF bug.
Edited by award-winning author Geoff Ryman, the scientists involved include two biologists and a bioethicist:
  • Dr. Jennifer Rowntree, post-doctoral researcher, Faculty of Life Science, University of Manchester. Rowntree is a plant evolutionary ecologist whose reseach includes "genetics of plant-plant and plant-animal interactions and the value of genetic diversity in plant communities."
  • Dr. Matthew Cobb, Programme Director Biology, the University of Manchester. Cobb and his laboratory study how genes and environment shape animal behavior and communication. Most of his research has focused on pheromones and olfaction in fruit flies. Cobb was paired with writer Simon Ings, who wrote the story "Zoology" for the anthology.
  • Professor Steve Williams, Williams develops and uses magnetic resonance imaging techniques to study appetite regulation and gut-brain interctions.
  • Professor John Harris, Lord Alliance Professor of Bioethics, and Director of the Institute for Science, Ethics and Innovation, University of Manchester. He has written a number of books, including Enhancing Evolution: The Ethical Case for Making Better People and On Cloning.
When it Changed had it's UK debut at an apparent joint event of the overlapping Manchester Literature Festival and Manchester Science Festival (which runs through the weekend -TThere's a lecture on "Exploring neuroscience through literature" on Sunday, Nov. 1, which is right up Bio in SF's alley). You can read all about the October 24th panel on the Manchester Literature Festival Blog.

When it Changed will be released in the US in April 2010.

(via io9)

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Tuesday, October 27, 2009

Joan Slonczewski's Biology in Science Fiction Course

The Columbus Dispatch published a nice article about Kenyon College biology professor and science fiction writer Joan Slonczewski's Biology in Science Fiction course:

"It's well-known as being amazing," said Kenyon student Ferrell Garramone, an 18-year-old studio-art major from Nashville, Tenn.

"I took (advanced-placement) biology in high school, and it was just a drone. This is much better than reading a textbook."

The offering has plenty of required reading: six novels, including two by Slonczewski. And it includes pop quizzes, class presentations and homework assignments known as "mutant challenges."

[snip]

Kenyon students -- most with backgrounds in literature, philosophy and the arts -- relate to the approach.

"I think it epitomizes liberal-arts education," said Rachel Rubenstein, a 21-year-old American studies major from San Francisco. "It's interesting, and it's exciting."

There has been a lot of discussion of late about how to make science interesting and engaging to non-scientists. This seems like a great approach - not only do students learn about biology without being put off by a dry textbook, but the course also probably introduces science fiction to students who wouldn't read it otherwise. It's a win-win!

Slonczewski has put the class syllabus, quizes, related links, and study guide online. The class has started a related wiki, and many of the students' projects are online.

This year the course focuses on "Mutants". Some of the science fiction references that were used:
See the course syllabus for the full list.

(I find it oddly comforting that her students are required to have a calculator that doesn't look much different than the one I used in my own college days, way back in the 80s. I suppose the difference is that my good old Casio was the fanciest bit of technology I carried around with me, while students today probably all have cell phones with more computing power.)

Related posts about Joan Slonczewski:

SF Pet Fish: Guest Post at the Reef Tank

I have another guest post up at The Reef Tank blog, in which I talk about my favorite science fictional pet fish. Go check it out!

Image: Borg Hugh examines Livingston, Captain Picard's pet lionfish

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Monday, October 12, 2009

ALL THESE WORLDS ARE YOURS, EXCEPT...

" . . . relay this information to Earth. Tsien destroyed three hours ago. I'm only survivor. Using my suit radio – no idea if it has enough range, but it's the only chance. Please listen carefully. THERE IS LIFE ON EUROPA. I repeat: THERE IS LIFE ON EUROPA. . . "

~ 2010: Odyssey Two by Arthur C. Clarke
Europa, one of the Jupiter's large moons, holds a special place in the minds of science fiction writers and astrobiologists alike. What sets Europa apart from the other planets and moons in our solar system is that it is covered with a fairly smooth surface layer of frozen water, and its interior is much hotter than its surface, suggesting that there could be a zone of liquid water under that protective layer of ice where life might exist. That easily accessible source of water on its surface could also make Europa a handy refueling stop for space ships exploring the outer solar system – assuming there isn't the sort of life that destroyed the ill-fated spaceship Tsien in Clarke's 2010.

In the afterword to 2010, Arthur C. Clarke says his Europans were inspired in part by a 1980 article by Richard C. Hoagland – "The Europa Enigma" – which describes his "quite brilliant concept" that there might be life on Europa. Since then, NASA's Galileo exploration mission to Jupiter and its moons has provided more detailed information about the moon's surface:

Prior to the Galileo mission, scientists' knowledge of Europa was simply a small ice- covered moon with an exceptionally bright surface covered by faint curved and linear markings. Now, scientists see evidence of a young and thin, cracked and ruptured ice shell, probably moving slowly over the surface of a briny ocean that is 100 kilometers (62 miles) or more deep.
University of Arizona Professor of Planetary Sciences Richard J. Greenberg, a member of the Galileo Imaging Team, believes that Europa might even be able to support fairly complex life forms, as Discovery News reported last week:
Judging by how quickly Europa's surface ice is replenished, Richard Greenberg estimates that enough oxygen reaches the subterranean ocean to sustain "macrofauna" -- more complex, animal-like organisms. Assuming Europa life forms would need as much oxygen as Earth-like fish, Greenberg estimates the moon's ocean has enough oxygen to support 6.6 billion pounds of macrofauna.
Unconstrained by the limitations of biology, futurist/physicist Freeman Dyson has speculated a bit more wildly, suggesting that we should be looking for flowers on Europa's surface:
Life could be visible from orbiting spacecraft, however, if it made a home in cracks in Europa's shell that connect the surface to the interior, Dyson said.

Such life might take the form of flowers with a parabolic shape that focuses the dim sunlight falling on Europa on the interior of the plant. Flowers with such shapes [...] are found in Arctic climes on Earth, where the plants have evolved to maximise solar energy.

Europa flowers could be detectable through a phenomenon called retroreflection, in which light gets reflected back to its source, Dyson said. This optical effect is seen in light reflected from animals' eyes, and was used in the design of road signs and mirrors left behind on the moon by Apollo astronauts.

My first thought was that Dyson had wandered off into Larry Niven's Known Space, but on further consideration I think it's an interesting idea – assuming that Dyson was referring to life forms with a superficial resemblance to flowers, rather than actual Earth-type plants. Or as University of Washington astrobiologist John Baross explained:
As for Dyson's flower suggestion, he says it is "a very radical" idea. "On Earth, flowering plants evolved during the Cretaceous and became diverse by co-evolving with insects. . . . I would not include flowering plants to my list of life-forms to look for."

"Any photosynthetic system on Europa would have to live at a depth removed from the high radiation bombarding the ice surface and still get light," Baross says. "Having said this, it would be worthwhile to make more comprehensive observations and analysis of some of the surface features, including the deeply coloured ridges [...]," he says. "One might find evidence for biosignatures or very interesting chemistry."

More likely than surface flowers are organisms similar to those found around the deep sea hydrothermal vents on Earth. Frank Carsey and his colleagues at the Jet Propulsion Laboratory are designing robotic vehicles that will be able to cut through ice and explore the watery world beneath, initially in Antarctica, but with the hope of eventually exploring Europa's depths. Until we are able to send exploratory probes, the possibility of life on Europa is little more than educated speculation.


Free Short Fiction:
Further Background Reading:

Top Image: The Conamara Chaos. "a view of a small region of the thin, disrupted ice crust in the Conamara region of Jupiter's moon Europa showing the interplay of surface colors with ice structures." From NASA's Galileo Image Gallery. More details.
Middle Image: Europa and the Thrace Region. This image shows an image of the cracked surface of Europa. From NASA's Galileo Image Gallery.
Middle Image:"Metal Flower" http://www.flickr.com/photos/quepollo/ / CC BY 2.0
Bottom Image: Artist's concept of a cryobot and hydrobot that can melt through ice and then explore the water beneath. From "The Search for A Planetary Ocean on Europa" at JPL.
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Wednesday, October 07, 2009

Science Fictional Ribosomes

small subunit of the Thermus thermophilus ribosome"What you want is to add and subtract lengths of input DNA easily, and the feedback enzyme arrangement does this. When the feedback arrangement is in place, the molecule will open itself up for transcription much more easily, and more rapidly. Your program will be transcribed onto two strings of RNA. One of the RNA strings will go to a reader - a ribosome - for translation into a protein. Initially, the first RNA will carry a simple start-up code ––

~ Blood Music
by Greg Bear, 1985
This year's Nobel Prize in Chemistry went to three scientists - Venkatraman Ramakrishnan, Thomas Steitz, and Ada Yonath - for their study of the structure and function of the ribosome", the organelle assembles proteins from amino acids based on nucleic acid sequences. Since ribosomes are essential part of the cellular machinery, it's no surprise that writers who incorporate genetics and biotechnology into their fiction include it in their fiction. They even provided the name for the bioscience-based science fiction subgenre called "ribofunk".

This classic 1971 human reenactment of protein synthesis, made by the Department of Chemistry at Stanford, can give you a pretty good idea of how ribosomes work1. (Click for bigger video)
The much abbreviated version:
  • DNA sequences that encode proteins are used as a template for the transcription of messenger RNA (mRNA)
  • a ribosome attaches to the mRNA
  • protein synthesis begins at a specific sequence of three nucleotides - the AUG start codon - within the mRNA
  • a transfer RNA (tRNA) that has a sequence complementary to the start codon sequence (the anticodon) carries the amino acid methonine to the ribosome.
  • a tRNA with an anticodon complementary to the next three nucleotides in the mRNA - the next codon - also binds the ribosome, and the amino acid it carries added to the initial methionine
  • this process continues along the length of the mRNA until a stop codon is reached and the newly synthesized protein is released from the ribosome
Greg Bear's mention of ribosomes in Blood Music gets the process right. Other science fiction writers have used ribosomes much more fancifully in their stories. Take, for example, the 2003 short story "Junk DNA" by Rudy Rucker and Bruce Sterling:
"You’re about to tell me that Alan Turing anticipated the notion of DNA as a program tape that’s read by ribosomes. And I’m not gonna be surprised."

"One step further," coaxed Veruschka. "Since the human body uses one kind of ribosome, why not replace that with another? The Universal Ribosome–it reads in its program as well as its data before it begins to act. All from that good junk DNA, yes Janna? And what is junk? Your bottom drawer? My garbage can? Your capitalist attic, and my start-up garage!"

"Normal ribosomes skip right over the junk DNA," said Janna. "It’s supposed to be meaningless to the modern genome. Junk DNA is just scribbled-over things. Like the crossed-out numbers in an address book. A palimpsest. Junk DNA is the half-erased traces of the original codes–from long before humanity."
While they use lots of sciency terminology, the description of ribosome function doesn't make much sense. Of course ribosomes skip over "junk DNA" - they don't interact with DNA at all. And while some "junk DNA" may be transcribed into "junk mRNA", it appears that those sequences are degraded before they can be used to encode protein. I'm just not grokking how "junk DNA" that is primarily made up degenerate coding sequences2, could be translated into proteins that do anything more than muck up cells, even given an Universal Ribosome Turing-like machine.3

And I should say that "Junk DNA" is an entertaining story if you can gloss over the nonsensical biology details - read it for yourself for free at Asimov's Science Fiction.

I'm hoping that science fiction writers will embrace recent research exploring complex biochemistry of our cells to come up with some interesting variations on life as we know it. I just wish they would get their terms straight (of course, that's probably just me).

Oh, and if you know other SF that uses ribosomes as a plot device, mention them in the comments. I know there is an episode of Star Trek:TNG that does, but I couldn't come up with any other examples.

1. Note that the ribosomal components are not depicted to scale. They are also a bit more colorfully dressed than you find in your typical cell.

2. What most biologists call "junk DNA" is primarily made up of repetitive DNA sequences from transposable elements, not interesteringly "scribbled over" ancient genes.

3. While DNA-based Turing machines have been proposed (and even shown to work in rudimentary form), the "computations" are not performed by protein synthesis, which is the function of ribosomes I don't think that's the case, anyway. My understanding of Turing machines is a little fuzzy. Mark Chu-Carroll has posts about them here and here and here that I'm still thinking about.

My related posts:

Animation: "Animation of the small subunit of the Thermus thermophilus ribosome. RNA shown in orange, protein in blue." Taken from PDB 1FKA and animated by David S. Goodsell
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Monday, October 05, 2009

Telomeres, Aging, and Science Fiction

It was announced today that Elizabeth Blackburn, Carol Greider and Jack Szostack won the Nobel Prize in Physiology or Medicine for their "discovery of how chromosomes are protected by telomeres and the enzyme telomerase." While the winners' biochemical studies have been extremely important in our understanding of how cells divide, what has caught the attention of science fiction writers is the role that telomeres - or more precisely the loss of telomere sequences - plays in the process of aging.

A bit of biochemical background:

When Watson and Crick figured out the double-helix structure of deoxyribonucleic acid, or DNA, one of the cool aspects of their model was that the structure immediately suggested how identical copies could be produced when cells divide: the two strands of DNA could "unzip" and be used as templates to create a new double strand. Research into the actual biochemistry of DNA replication, however, discovered a problem. The enzymes that synthesize the duplicate strand of DNA - DNA polymerases - can only add nucleotides onto an existing nucleic acid sequence called a primer, which is made of RNA, rather than DNA.

When the DNA sequence that is being duplicated is a circle, like most bacterial chromosomes, the head of the growing DNA strand eventually meets up with its tail, completing the sequence. However, the DNA in the nuclei of eukaryotic cells - which includes fungi, plant and animal cells - is packaged into large linear chromosomes. Consider that every human starts out as a single cell but ends up with an estimated 10 trillion (1013) cells after many many cell divisions. If your chromosomes shrank every time a cell divided, they would be severely truncated by the time you were ready to pass on your DNA to your offspring and any functioning genes located near the ends of the chromosomes would be lost.

What chromosomes clearly needed is something to protect its ends during replication, and that "something" turns out to be a telomere. A telomere is a short DNA sequence on the end of the that is repeated many times and folds into a three-dimensional structure that protects the ends of chromosomes. Nobel winner Blackburn had compared telomeres to the plastic tips that prevent shoelaces from fraying.

Imagining biological aglets paints a pretty decent picture of what telomeres do, but doesn't really capture the dynamic nature of chromosome structure. An enzyme called telomerase can extend the repeating telomere sequence, but telomerase is absent from most adult cells, so a bit of the telomere sequence is lost every time a cell divides. Once its telomeres become too short, a cell loses its ability to divide and either ages or self-destructs.

If all that seems too complicated to visualize, check out this nice animated tutorial on "Solving the End-Replication Problem" or watch Elizabeth Blackburn's excellent recent lecture on telomeres and aging.

So how has telomere research been adopted into science fiction? I've looked at a couple of examples below.

Telomeres as Longevity Controls
"Look at me," said McGavin, spreading his arms again. "I'm sixty-two years old, according to my birth certificate. But my cells, my telomeres, my free-radical levels, and every other indicator say I'm twenty-five. And, if anything, I feel younger even than that."

Don's jaw must have been hanging open in surprise. "You thought I'd had a facelift, or something like that?" McGavin said, looking at him. "Plastic surgery is like a software patch. It's a quick, kludgy fix, and it often creates more problems than it solves. But rejuvenation, well, that's like a code rewrite — it's a real fix. You don't just look young again; you are young." His thin eyebrows climbed his wide forehead. "And that's what I'm offering you. The full-blown rejuvenation treatment."
~ Rollback by Robert J. Sawyer

A natural extrapolation from the correlation between the shortening of telomers and aging is that artifical means of keeping telomeres long would reverse - or at least halt - the aging process. That is one of the premises of Robert Sawyer's 2007 novel Rollback, in which the characters undergo anti-aging Rejuvination treatments that includes telomere lengthening. At least that's what the treatments are meant to do.
"We did succeed in lengthening your telomeres, Sarah, but for some reason the new endcap sequences are just being ignored when your chromosomes are being reproduced. Instead of continuing to transcribe all the way up to the end of your DNA, the replicator enzyme is stopping short, at where your chromosome arms used to end."
~ from Rollback by Robert J. Sawyer
I'm finding it hard to imagine how DNA replication would not occur in extended telomeres and be limited to the exact end of the original telomeres, since the extended telomeres should just be repeats of the same DNA sequence1, at least the way I would do it.

The easiest way to extend telomere length is by increasing the activity of the enzyme telomerase. Scientists at the biotech company Geron, for example, have shown that expression of telomerase in adult human cells can signficantly increase the life span of those cells in culture. Extending that to "cure" human aging has been suggested by others, and is not surprisingly the claimed mechanism of action of overhyped so-called "neutraceuticals" currently on the market, as well as some anti-aging drugs that are apparently in development.

It's important to keep in mind, however, that there is a potential downside to allowing cells to divide indefinitely. The adult cells that do express telomerase are usually tumor cells. That's not particularly surprising, since one of the characteristics of cancer cells is that they keep dividing when they aren't supposed to be. While introduction of telomerase can immortalize human cells in culture without causing changes associated with cancer cells , transgenic mice with increased telomerase expression only show an increased lifespan if they don't die from tumors during their first year of life. I don't think that would be acceptable for a human therapeutic treatement.

So while telomeres are an obvious target to increase human longevity, I think we're a long way from safe and practical anti-aging treatments.

1. I haven't read Rollback beyond a few excerpts, so the speculation is all mine and not reflective of the what's in the novel. But to get all pedantic, that a particular passage seems to muddle the action of DNA polymerase enzymes, which replicate DNA, telomerase, which is a reverse transcriptase (a DNA polymerase that uses an RNA template), and "transcription" which is the synthesis of RNA using a DNA template (i.e., not DNA replication). I guess it all sounds good and sciency if you aren't familiar with the terminology. Or maybe there's a better explanation in the text. Clearly I need to put Rollback on my "to read" list.

Telomeres as the Human Equivalent of Tree Rings

While it it's been well established that telomeres get shorter as cells divide and an individual gets older, it wasn't until fairly recently that it was demonstrated that telomere shortening appears to occur at a predictable rate. In 2002 scientists at Kyushu University in Japan published a method of roughly estimating human age from DNA samples (see Tsuji et al. (2002) doi:10.1016/S0379-0738(02)00086-5). That's a nifty scientific device to determine an individual isn't the age he claims to be - say, for example if the character turns out to have been (dun, dun, dun) cloned from an adult cell.

The logic goes like this: as people age, their telomeres get shorter. When a clone is made by transferring the nucleus of an adult cell into an egg, the telomeres are presumably at their adult length, rather than the longer length found in embryos. As the clone ages, its telomeres would always be shorter than uncloned individuals of the same age. Not only would the shorter telomere length give away the fact that the individual was a clone, but the clone's life would be shortened because his cells would stop dividing at an earlier age.

Science fictionally, that was the scenario used on Stargate Atlantis. In the episode "The Kindred" the Stargate Atlantis team discovers an imprisoned Dr. Beckett. That wouldn't have been particularly remarkable if Beckett hadn't died heroically several years before. The man they found looked like Dr. Beckett, had the memories of Dr. Beckett and even was genetically identical to Dr. Beckett - except that his telomeres were 30% shorter than they should have been for a man his age. Sadly, his cells are also rapidly degenerating so that he needs to be kept in stasis until the plot team really needs his help.
Clone Beckett looks at the analysis of his DNA.

Now that we've been cloning mammals for more than a decade, we can ask if that scenario is plausible. The first mammal cloned from an adult somatic cell, Dolly the sheep, did indeed have shorter telomeres than expected for her age, and she died young. However, that doesn't seem to hold true for all other cloned animals. There is evidence from cloned pigs and cloned cattle, for example, that the presence of telomerase enzyme during embryonic development can rejuvinate the length of telomeres in clones. And it's still unclear whether Dolly's shorted telomeres played any role in her death.

And to complicate matters, telomere length isn't only dictated by age. For example, psychological stress has been shown to reduce telomere length to the equivalent of 10 years of aging, and men generally have shorter telomeres than women of the same age. While telomeres may be a good measure of an individuals physiological age, I suspect that they will never provide more than an approximation of chronological age.

----

So to sum it all up: telomere length can affect both the aging and health of cells, in ways that aren't entirely understood. Ideal science fiction fodder!

My related posts:

Top Image: Crystal structure of parallel quadruplexes from human telomeric DNA. The DNA strand (blue) circles the bases that stack together in the center around three co-ordinated metal ions (green). Produced from NDB ID: UD001
by Thomas Splettstoesser for Wikipedia.
Middle Image: Cartoon of a telomere forming a loop at the end of a chromosome. From Wikipedia.
Middle Image: Chromosomes with telomeres stained yellow. From the Human Genome Program, US Department of Energy, 1997.
Bottom Image:
Clone Beckett looks at the analysis of his telomeres. Screen grab by Crystal @ Perspective.

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