When Jurassic Park Becomes Real

The nerd in me is really jumping for joy. An article published today in the journal Nature entitled "Biocontainment of genetically modified organisms by synthetic protein design" discusses experiments performed at Harvard, Boston University, and the Fred Hutchinson Cancer Center in Seattle that explain how to develop genetically modified organisms (GMOs) that won't present a threat to the natural environment. I really think this paper is where science fiction becomes reality and we have dinosaurs to thank. Let me explain:

We've all seen the movie Jurassic Park. I'm talking about the original movie and not the shitty sequels where a T-Rex is brought to America ( just watch King Kong...the Simpsons did it...) and some crappy pterodactyls escape from a bird cage in the incomprehensible third movie. But the original is awesome and Chris Pratt is going to make the new one awesome too. Anyway, in the original movie there is a discussion between the main characters about how the dinosaurs can't escape from the island because of a built in fail-safe. The game warden Robert Muldoon mentions something called the 'lysine contingency' and we as the audience learn that the dinosaurs were genetically modified so they are unable to naturally produce the amino acid Lysine. Lysine is an incredibly important natural compound in our own bodies and the dinosaurs carry a mutation in the gene that help process and create it. With this defective gene in place, the dinosaurs in the movie must rely on diet-fed lysine in order to survive. Thus, if a dinosaur escapes it will just die because it cannot produce lysine on its own. (We should ignore the fact that lysine can be found in food and plants and the dinosaurs just eat the plants and other plant-eating animals and all is fine. 'Life finds a way' as the saying goes!)

Regardless, the important concept here is that the dinosaurs were engineered in the movie to keep these 'dino-GMOs' from escaping. In the real world there has been growing concern that GMOs could escape from the laboratory and grow unchecked in the wild. Such that they overtake the natural varieties of species already found on our planet, out-compete them in a Darwinian fashion, grow uncontrollably, and then apocalypse. I'm being a little hyperbolic here but it really is a legitimate concern, even for scientists, but it is blown out of proportion by people who don't see the value in any type of GMO whatsoever. Even in spite of the fact that we will need adaptable plants and foods as our climate changes and as an alternate strategy to combat hunger and famine.

But what this paper details is a methodology in which scientists engineered a type of 'lysine contingency' into E. Coli bacterial strains whereby they cannot out-compete their natural, wild-type bacteria. Specifically, mutations were induced in several proteins which forces said proteins to incorporate a synthetic or non-traditional amino acid into its structure in lieu of a natural amino acid. For example, a specific protein may require the amino acid tyrosine in a very specific location in its structure in order to function properly. The researchers engineered these proteins to instead substitute a non-traditional amino acid (let's call this tyrosine*). Proteins with tryrosine* still function and form properly but tyrosine* is only fed to the bacteria by researchers and not found or incorporated into proteins naturally. It is very similar to the 'lysine contingency' in Jurassic Park.

I know what you are saying, well what if these bacteria overcome this? Life finds a way, right? This is true. In fact, the experiments identify a small percentage of the engineered bacteria which do survive when the unnatural amino acid is removed from the food. The bacteria found a way to divide and grow and compete with the natural E. coli in the environment. However, some bacteria were engineered with additional mutations in several other genes in combination and these 'triple mutants' did not escape their habitat, nor out-compete their natural counterparts. This is the key point. Bacteria can be engineered to require important synthetic or non-traditional amino acids that are fed to them in the laboratory, but when that food is taken away they die. They don't mutate and escape. Life doesn't find a way.

I'm excited about this because it's a giant step in the direction of addressing the safety concerns of GMOs. A lot more work needs to be done, especially if this will be taken into plant crops like rice or wheat or corn, but it is a very important and elegant proof of concept. And for those staunchly opposed to GMOs...well this is a big blow.

The Dog Days of January

January is the armpit of winter. I feel January's only redeeming quality is making it easy to count how many days into the new year we are. New Year's Day is nice but it is over in the blink of an eye and usually half the day is spent nursing a sore head from the night before. The rest of the month drags by, storm after storm, until February approaches and the first scents of spring being to flutter by. It is days like these when I understand the desire to live in the south or on the west coast. Then I realize during the summer people are burning alive in Phoenix or Texas and I snap back to reality and my precious four seasons.

But January is not a total loss! There is plenty of opportunity to rummage through old boxes and bins and get rid of stuff that has accumulated over the years. I've also found it is a good time to plan that vacation you've been meaning to take, or to catch up on a novel you put down on the bed stand and left there for dead. Walden has been on my bed stand for a half year, bookmarked about thirty pages in. Sorry H.D.T. but I have too many science fiction anthologies to keep me up at night right now. In fact, Walden made it all the way back to my bookshelf last week. I was tired of seeing it next to my bed. It's a very rare occasion when I give up on a book. I do intend to read it someday but I just can't seem to get into it right now...maybe when I'm older and ready to follow my own damn advice.

I think the old adage that reading helps you as a writer is true. As I'm slowly developing my passion for storytelling I have come to learn  that the opposite is true too. As a writer I enjoy reading even more now. This surprises me because I've always been a voracious reader and have always loved to pick up a new book. But that excitement is even greater nowadays. I guess it really shouldn't surprise me though, I can't think of any musician who doesn't love to listen to music.

As a kid I would stay up until three or four in the morning reading Goosebumps, then Star Wars novels, then anything I could get my hands on. I read a lot of science fiction and fantasy (which is primarily what I write), but at times I have abandoned those genres for months at a time. I enjoy the long breaks and I get a chance to catch up on the classics and history or whatever else grabs my attention. I even enjoy biographies and non-fiction as my interests ebb and flow during the year.

But now when I read I'm also thinking about how the authors constructed their stories. I enjoy reading Harry Potter over and over again and identifying the little nuggets of information that Rowling left for you to discover and think about. For instance, in The Philosopher's Stone Harry reads the back of Dumbledore's chocolate frog card on his way to Hogwarts. Do you remember what it says? The card makes an almost nonchalant reference to Grindelwald, the dark wizard Dumbledore defeated in his youth and who ends up playing an important role in the very last book The Deathly Hallows. That took planning. It is those little juicy tidbits like that which keep me up at night as both a reader and writer. The master storytellers out there are inspiring and it makes reading even the smallest of stories that much more interesting to me. The point being: if you like to write, you have to read, read, read.

To me, staying up late and reading, engrossed in some far away world or teetering on the edge of history, is a great joy in life. I find it comforting to wake up suddenly, my book haphazardly laying across my chest, only to realize I've been passed out for hours. Usually I don't remember falling asleep (who does anyway) and inevitably I will need to search for my bookmark in the morning. It will usually be tucked into the sheets somewhere or hiding under the cat.

I'm not sure where all of this is going...just some random thoughts in the middle of winter. But if you are stuck in the dog days of January you should pick up a good book and let the month slip on by. Soon we'll all be in spring's warm embrace. Except Canada...ha!

The Guest of Honor: A (Scary) Christmas Story

Well its been a while since I last posted. I blame that on turkey and stuffing....not laziness or anything like that....

But today I'd like to share that a story of mine is being featured over at Dark Chapter Press! It's called 'The Guest of Honor' and it was a story I was asked to submit for their DreAdvent - a 24 day writing competition leading up to Christmas. If you like scary Christmas stories then you may want to check it by clicking right here, or at the link at the bottom of this post.

I hope you enjoy it! I don't know why but lately I've really enjoyed writing horror. It's not my forte but I'm really getting a kick out of it. I haven't abandoned my science fiction (or my novel) but it is fun to dive into something different every now and then. I promise to update more often now that life is settling down again. I haven't even had a chance to write up something about the new Star Wars trailer, which is pressing business...obviously.:)

The Guest of Honor

A New Story: The Fortune

I am very excited to announce that I was a finalist in the Dark Chapter Press September Flash Fiction competition! The story I submitted, The Fortune, is featured on their blog this week and drew inspiration from a creepy picture of an old, wooden pier. Please visit the Dark Chapter Press website and you can read my story!

Dark Chapter Press is a new horror publisher and I'm very honored to have placed as a finalist in their first two competitions. Unfortunately, I didn't have time to write a new story for their October competition. But if you love horror (and especially scary clowns) please browse their website because they will be featuring additional horror stories in the coming weeks and months!

On an unrelated note, it is also National Novel Writing Month (NaNoWriMo). I'm using this as excuse to finish up the first (and very rough) draft of a novel I have been working on for over a year now. If you'd be interested in being a guinea pig and reading my draft once it has been fixed and changed and edited, please let me know. I would really love some input from people to make it a better story. This would probably be sometime in the late spring. Please email me or drop me a message on Facebook.

Another link to The Fortune. I hope you enjoy it! Any and all feedback is appreciated.

Top 100 Scientific Articles

Quick post today because the work week has been crazy.

The scientific journal Nature just released several articles about the Science Citation Index (SCI). The SCI is a measurement of the number of citations (by other articles and research reports) a particular research paper or study receives. This purportedly reflects how important a particular research article is in related scientific fields. Both Thomas Reuters (which owns the SCI) and Google Scholar reported back to Nature on the top 100 most-cited scientific papers of all time. It's quite surprising how many methods and computational papers make the list. A second article discusses how researchers view their own work.

I'm still digesting the articles and what they mean to science and publishing in general, but I wanted to share this with anyone interested. I do find it surprising that the journal Nature only has two papers in the top 50....and the journal Science only gets as high as #63! Take that for what it's worth.

What's in a Name?

Have you ever called someone an Einstein? Or a Scrooge?

You may have even uttered the words ‘Call me Ishmael…’ at some point in your life. 

So what’s in a name? 

It is seemingly a simple question. A question that has been on my mind for some time. Frustratingly so, in fact, considering the powers that be in my research field cannot seem to settle on the nomenclature for the genes I am studying. It’s a mess, but that’s a story for another day…

The question may not be as simple as I once thought.

Names can be powerful, inspiring, and potentially fear-inducing. Sometimes a person or an idea can have multiple names. Some names transcend time – Cleopatra, Caligula, Hammurabi, Jesus, Budha. Whether or not you know it, the names of things can affect you every day. Take for instance the recent events in Syria and Iraq. Many governments and news outlets can’t even decide what to call the Islamic State. Is it ISIL? ISIS? ISIQ? Just the Islamic State? There have even been recent attempts to switch the acronym to QSIS (Al-Qaeda Separatists in Iraq and Syria) to differentiate the terrorist group from anything that remotely resembles Islam – because it most certainly does not.

I’m curious if individuals within the Islamic State have a similar problem when it comes to their own identity.  I doubt it, but if so, what would that mean? How can an enemy be understood if no one can even agree on what to call him/her/it/them? I don’t claim to have any answers on that but I think it is important to figure out.

I’m also not the only one who has thought about names. Click on this link if you are interested in a podcast about names and society. It's by the guys over at Freakonomics and it certainly dives into the topic at length.  

However, I’ve again treaded from my originally-intended topic: the literary motif of names and naming in fantasy stories. 

Even the most casual of fantasy readers are familiar with this. A great example is Lord Voldemort in the Harry Potter series. For most of the other characters in Harry Potter, ‘You-Know-Who’ or ‘He-Who-Must-Not-Be-Named’ are what Voldemort is known by. The mere speaking of his proper name is horrifying to most wizards and witches. There is a stigma associated with his name that induces emotional and sometimes physical reaction. In fact, J.K. Rowling builds a form of magic around the use of the name ‘Lord Voldemort’. Wizards using his proper name aloud can be tracked because of a taboo curse put on the actual spoken words. Not only does this add to both the stigma and mystique of Lord Voldemort but that’s just great story-telling! 

This does reflect the world in which we live though. When Hitler comes up in conversation there’s almost an immediate association with hurt and suffering. We also associate nicknames to people. Some are well-intended and others…..not so much.  And it’s the most frustrating thing to run into someone and temporarily have forgotten their name. (Something I need to work on.) I feel lost from the moment the conversation begins. 

The power behind names is a central theme in Patrick Rothfuss’ The Kingkiller Chronicles. The Dresden Files by Jim Butcher plays with the idea of full names and power, and there are elements concerning the names of people and places throughout The Lord of the Rings by Tolkien and The Sandman series by Neil Gaiman. Even in classics like Rumpelstiltskin - the queen must give up her child unless she can guess Rumpelstiltskin’s true name. 

I like the fact that theories of names and the power they derive are a staple in a lot of fantasy literature. It’s odd, but I find it comforting that buried in the depths of the Mines of Moria and obscured in the land of Faerie are hidden the true names of things. 

Are there such places in the real world where the true or first names of things are hidden? What did our primitive ancestors first call love, or the stars? Maybe that is why I’m drawn to the fantasy genre so much. The original name of a particular person or place or thing can draw a lot of power in those stories. I think the same is true for our own world. 

A Short Story: Where the Toys Go

Last month I submitted a 500-word story to an up-and-coming horror magazine and publisher called Dark Chapter Press. Dark Chapter runs a monthly horror flash fiction contest with inspiration for stories derived from photographs featured on their website. The August competition featured a photograph of creepy doll parts and it can be found here. I'm very excited to say that the story I submitted - Where the Toys Go - was selected as one of the runner-ups in the competition! They are featuring my story this week on their blog. Please click on the link below to read my story and the submissions of the other winners! There are also other horror stories featured on their website if you enjoy being scared. Horror writing is a new genre for me but I have to admit I am having a lot of fun with it. Enjoy!

Story: Where the Toys Go