Debunking myths on genetics and DNA

Tuesday, August 30, 2011

Aliette de Bodard on writing, science, and language

The first time I read about her was on the SFWA website. She was the featured author and she instantly drew my attention because here was a young, very talented writer, whose mother tongue was French but who wrote in English. Well, turns out, that's not the only amazing thing about Aliette de Bodard. A Hugo, Nebula, and Campbell nominee, Aliette has won the BSFA Award for Best Short Fiction, as well as Writers of the Future. Her short fiction has appeared on Asimov's, Interzone, and other prestigious magazines, and her novels, Servant of the Underworld, Harbinger of the Storm, and the forthcoming Master of the House of Darts, are published by Angry Robots.

Needless to say, I am so honored to have Aliette on my blog today!

EEG: I'm truly impressed by your bio: you're half French and half Vietnamese, you were born in the US and grew up in Paris. You're a computer engineer and you write beautiful, lyrical stories about fantastic worlds that mix Aztec, Chinese, and Vietnamese cultures. And, may I add, you're a fabulous cook, at least judging from your blog! If you were to define yourself in only a handful of words, what words would you choose?

ADB: Urk, what I am not is concise... I'm a very intensely curious and open-minded person, and a bit of a contrarian (if there is a majority vote, you can be sure I'll be looking for good reasons to set myself against it). Also, occasionally, I write speculative fiction!

EEG: From your bio: "Aliette admits to being a proud maths geek, though most of that hasn’t seeped into her fiction." First of all: math geeks rock! I do understand the need to "step away from it," but I also wonder if it goes out one way and comes back the other way around, meaning: has it ever happened to you that you were sitting at your day job desk and you came across a concept that spurred a great idea for a story?

ADB: I don't think it's actually happened--I do try to keep my day job separate from my writing, both for my serenity of mind, and also because I don't want to run into confidentiality issues that might become problematic later. I do get a lot of exposure to scientific articles, and that provides a lot of the background that goes into my stories--the edge of "tech-speak" and the confidence that I know what I'm talking about, both of which might not seem like much but are actually crucial to establishing reader trust. I think the last time the wires crossed was a couple years ago, when I was reading an article on remotely-distributed computers; and I immediately had this vivid image of a computer gestalt spread across several ships--and, because I'm a nasty person, I immediately imagined what would happen if the radio communications that kept the gestalt together were cut... (this later grew into the short story "Horus Ascending," which was published by IGMS).

EEG: In general, do you think that the two worlds -- writing and engineering -- are two completely different compartments in your life or do you feel you couldn't do one without the other?

ADB: I definitely couldn't do one without the other: for one, I have this hankering for science, which I don't think writing would satisfy; and for another, I'm a moderately social person, and I think I'd go insane if I didn't have a day job where I'm regularly asked to interact with other people. Writing is tremendous fun, and something I could let go of as easily as, say, breathing, but it does need something in the way of a complement for me, and that's what engineering provides.

The two worlds do interact with each other, except it's not in terms of ideas crossing the boundaries (OK, I lie. Sometimes I'll write scientists in a lab, and it's good to know how scientists really function by virtue of having been there. Also, it helps to have a grounding in basic and not-so-basic science when writing science fiction, if only because it speeds up the research by several orders of magnitude: a lot of time when I'm looking up stuff in an encyclopaedia, I just skim to get the gist, because most of them refer to stuff I either know or have touched upon). Mostly, what I get from the engineering is a sense of method: I will build my stories fairly methodically, on something closely approaching a V-cycle of development. I.e., try to do as many substantial modifications to the story outline, rather than to the first draft, because the more developed the story is, the harder it is to fix. I think a lot of the analytical mind I picked up from science is something I use in my writing, and especially when I'm taking stories apart to see why they don't work.

I do have a set of different compartments for both activities, though, because I strongly need them to be separate. My day job is my day job, and I'm not going to start brainstorming my novel in the middle of a meeting; similarly, the work stuff is all well and good, but barring leftovers or emergencies, I need my mind to be clear of it when I write. I also have a need for this because of the language problems: so much of what I do in my everyday life is in French; but, in order to write, I have to think exclusively in English. I need to be in what I call "the bubble" in order to call up the English language faster, and the bubble thing won't work if I start crossing wires with my French-speaking day job. So, by necessity, I have to keep them both separate, and anything I can do to reinforce separation actually helps my writing. It sounds a bit counter intuitive, but that's just the way my mind works...

And, of course, it always helps to have writing skills when you have to write an engineering proposal with convincing arguments.

Fascinating. I am myself bilingual, but I never thought about that problem because luckily my everyday language is also my writing language. It's truly amazing that you can isolate yourself that way and create such beautiful, magical worlds. Thank you for sharing your stories with us and thank you for answering my questions.

To find out more about Aliette's books, visit her webpage, where she blogs about writing and, among other things, yummy Asian dishes that make you wanna ask, "Can I come over for dinner tonight?"

Photo: Canon 40D, exposure time 1/30, focal length 80mm.

Sunday, August 28, 2011


Okay, it's not perfect, but the darn little thing (ahem, no, not so little!) kept wiggling away whenever I pointed the camera!

Edit: Thank you all for your concern but no, the storm wasn't dangerous. I left when it got closer. However, as it turns out, what was in fact dangerous was the bear that's been spotted roaming around the neighborhood. I didn't see it, though. I'm probably too skinny for bears. The poor guy must've gone looking for dinner somewhere else.

First photo: focal length 41mm, shutter speed 10 seconds, 100 ISO. Second photo: focal length 35mm, shutter speed 4 seconds, 100 ISO.

Saturday, August 27, 2011

Tell me a joke, please!

I'm scheduled to give a 1-hr talk on Tuesday. I'm very nervous: I've never given a talk that long. Typically conferences give you a 10-20 minute slot, so you zip through a dozen slides, try to be convincing enough to make people happy while hand-waving enough to skip the dirty details.

But heck, one whole hour?
I suppose that means I'm growing up.

So, I'm told the way to start is to break the ice with a joke. Except I'm terrible at jokes. Nobody ever laughs when I tell one. Maybe it's my accent. Do I need a particular "joke-voice" I'm not aware of?

Or maybe it's the topic. HIV is not a funny subject to discuss.

In a talk that long, aimed at a general audience, I will have to start introducing the pandemic. Last June marked the 30th anniversary of the discovery of the AIDS disease. According to UNAIDS, at the end of 2010, there were over 34 million people leaving with HIV/AIDS worldwide. There are 2.6 million new infections per year, and 1.8 million deaths per year.

Those are some stunning numbers.

What's even more stunning--no, wait, let me use another word. Appalling. Two thirds of all infected people live in Sub-Saharan Africa. While in the western world the average life expectancy (how many years we "hope" to live) has steadily grown in the past 5 decades, and it's well beyond 60, in countries like Botswana people aren't expected to live past their 35th birthday. There are parts of Africa where villages have been wiped off of an entire generation and kids are raised by their grandparents. In these countries, teenagers have a 50% chance of contracting AIDS in their lifetime.

Why is this virus so deadly?

For one thing, HIV attacks the immune system. It's like striking under the belt: in order to reproduce itself, the virus uses the very same cells that are supposed to defend us from it.

But the virus's most effective weapon is its genetic variability. The way our immune system works, it takes a few days for our sentinels to recognize the "attacker" and put together a big enough platoon of soldiers to deploy a counterattack. Typically, a macrophage will recognize a viral particle, destroy it, then bring the "debris" to a T-cell. The T-cell carries the pathogen to the thymus in order to start a process called T-cell activation: once the pathogen is presented, T-cells able to recognize it and destroy it are mass-produced and sent off on a clean-up mission.

Problem: by the time the platoon leaves its quarters, the enemy has changed.


They are called T-cell escapes: mutations that appear in the viral genome and disguise the virus. The proteins on its surface change shape. They fold in a different way, and suddenly the T-cell is no longer able to grab the virus. The darn little thing slips away unharmed.

That's the challenge that HIV has posed for the past thirty years. Vaccines are typically made of a deactivated strain that, injected inside the body, elicits the proper immune response. But when you have a virus this variable what are you going to use as a strain? This enemy has a million different faces, and as soon as the immune system finds a weapon against it, the virus comes up with a new disguise to escape it.

Wait, not all hope is lost. We can beat the monster with its own weapons. How? Well, I've got to leave something for my talk, right? So read next post or come to the talk. And if you do come, please tell the jokes for me. Or give me a crush course.

Edit: the talk went well. Nobody laughed, but I didn't attempt telling jokes. So that was good, I really didn't want people laughing when I was NOT telling jokes. Nobody fell asleep either, which, for a 1pm talk was quite an achievement. Yay.

Photo: seagull. Canon 40D, focal length 17mm, exposure time 1/500. Tonemapped for pretty background.

Friday, August 26, 2011

Wanna be likeable? Zip your mouth!

I saw this post on BPS Research Digest: Prolific gossipers are disliked and seen as weak and couldn't help but spread the word. This is the original paper:

Is gossip power? The inverse relationships between gossip, power, and likability

The paper, by Sally Farley, from the University of Baltimore, looked at 128 individuals who were asked to rate how likeable (or not) people they knew as either gossipers or non-gossipers were.

It appears that gossiping "ain't so cool" after all.

Although, the statistician in me has me wondering: "What about bias?" Whenever people fill out questionnaires like this one, how can researchers ensure that they will answer truthfully? Especially in a study like this, where we all know that "morally" gossiping is bad, is the likelihood of a "moral bias" (as in people tend to answer that gossiping makes one less likeable because they know that's what they are supposed to think) real?

Photo: fall leaves. Canon 40D, exposure time 1/60, focal length 85mm. 

Wednesday, August 24, 2011

Intelligent people live longer... really?

I came across this abstract from a 2008 Nature essay:

Why do intelligent people live longer? 

We must discover why cognitive differences are related to morbidity and mortality in order to help tackle health inequalities.

The statistics show that children with high IQs tend to live longer than those with less intelligence. What the statistics don't tell us is why. What thing or things do intelligent people do that can delay mortality? Ian Deary explains how cognitive epidemiologists are trying to answer the question, and potentially contribute to the redistribution of health.

Prof. Deary is the director of the Centre for Cognitive Epidemiology of the University of Edinburgh. I never met him, but I looked up his research and what he does, and it is certainly impressive. The essay looks at a number of retrospective studies where the IQ was measured earlier in life, and the longevity of the subjects was measured. The article goes on trying to give possible explanations in order to, like the abstract says, "help tackle health inequalities."

The title seemed provocative enough to spark some discussion, so I thought I'd start by giving my two cents. I won't get into the whole issue of "how do we measure intelligence," as that is not my field (though I'd love to hear from experts). Instead, I tried to read the paper from a purely statistical point of view. And this is the part that got me puzzled:

"First, what occurs to many people as an obvious pathway of explanation, is that intelligence is associated with more education, and thereafter with more professional occupations that might place the person in healthier environments. Statistical adjustment for education and adult social class can make the association between early-life intelligence and mortality lessen or disappear."

You see, to a statistician that statement settles the argument. If correcting for education and social class makes the association disappear, then the association is spurious. Instead, the Nature essay deems it an "over-adjustment."

Whenever you are trying to fit a statistical model you have to make sure that your independent variables are truly independent. Example: suppose I take a population of ten Asians and ten Caucasians, follow them for forty years, and learn that after forty years all Caucasians are dead and all Asians are still alive. I might naively conclude that Asians live longer than Caucasians. Now suppose I tell you that eight out of ten Caucasians were smokers. Well, smoke turns out to be what statisticians call a confounding factor, in other words, a variable that's correlated to both the dependent and the independent variables. Not including it in the analysis leads to spurious relationships. In my made-up example, if I stratify my analysis between smokers and non-smokers and repeat the statistical test, this time I will find no significant difference in the longevity of Caucasians versus that of Asians.

In the case of intelligence and longevity, "income/social class" is an obvious confounding factor. We all know that a healthy lifestyle is expensive. A diet high in vitamins and fibers, the time to exercise, medications, regular medical check-ups: sadly, in today's world, they are all privileges for the well-off. Furthermore, the earlier you make healthy lifestyle choices, the better your odds later in life. So, income at birth also weighs in: children born in poor environments may not have access to vaccinations, medications, healthy foods, and other more general healthy lifestyle choices, all things that will affect them as adults. I may be missing something crucial, but it really doesn't seem like an over-adjustment to me.

In a way, we're saying the same thing. There is an association. But: is the association causal or is it masking an underlying, stronger association? The essay seems to suggest that the association is indeed indicative of something else, but somehow it leaves the question open-ended, concluding: "The things that people with higher intelligence have and do that makes them live longer may be found and, we hope, shared, towards the goal of better and more equal health."

Still, I would really like to see a similar study with education and social class folded in. Because if it turns out that the true underlying drive for a better and longer life is income, well, in that case I do have a suggestion to answer the above question: let's make health care and healthy life styles more affordable to people.

Picture: Colors at the Pike Place Market, Seattle. Canon 40D, focal length 70mm, exposure time 1/40.

Sunday, August 21, 2011

The Neuropathology of Zombies

One thing that fascinates me the most when I pick up a book is what inspired it. When you talk to authors you often hear that it was one particular image, or a "what if" question that they couldn't shake off, or one sentence they overheard at dinner.

Or, something that came across their autopsy table.
Well, it could happen that way too, couldn't it?

I've posed the question to my friend Peter Cummings, MD, a forensic pathologist based in New England, and the author of the textbook Atlas of Forensic Histopathology, as well as of the novel The Neuropathology of Zombies. The title of his novel intrigued me so much that I had to find out how he'd come up with the idea of dissecting... zombies.

I'm thrilled to have Dr. Cummings as a guest on my blog today!

EEG: Peter, from your blog I gather you come across some pretty dramatic cases. Is writing a way of "letting it all out" or, in your line of work, you come to a point where you reach a certain degree of detachment because "you've seen it all"? 

PMC: Excellent question. I think it’s important to have an outlet, regardless of what it is. In a way, you have to re-enter life. This is a very difficult job. It’s emotionally draining and physically it is very hard work. Having an outlet is the key to survival because there are days, sometimes weeks, where it really gets to you. You never know what case or series of cases it will be, or what will set it off, but it happens and you have to be aware or you’ll get eaten up. It’s also important to have understanding friends and families who are there to support you. Having said that, there is a degree of detachment and desensitization that go along with the work, and a hell of a lot of "gallows humor."

EEG: Is that how you deal with what you see on an every day basis? 

PMC: I don’t know. I mean, we're a pretty self-selecting group of people. You don’t go into forensic pathology unless you really want to do forensic pathology. So dealing with it is part of the genetic make-up of the forensic pathologist, I think. Like I said, some days it gets to you and you have to walk away and go work on your book, or go play soccer, or just go home and play with your kid. There are a lot of positive things about the work as well. I enjoy talking with families and helping them understand what has happened to a loved one. It’s very rewarding when you know you’ve helped them or made them feel better while they are going through one of the worst moments in their lives. I also get to help prevent death by getting families screened for inherited heart diseases or by understanding disease or injury patters. Helmet laws, safe sleeping practices for infants, seatbelt laws these are all things that have come from the morgue. We try to understand death so we can prevent it. That kind of positive drive is why most of us do this job. 

EEG: So, what inspired you to write a novel?

PMC: I was burnt out after completing the textbook and felt that I needed to do something creative. It was late October and someone mentioned to me that November was "write your novel month." It started as kind of a dare, and then I just ran with it. I hadn’t really noticed the zombie craze, and was never really into it, but one night there was a zombie movie on TV and I watched and really dug it. I watch horror movies continually through October and was getting a bit bored with the usual films and thought to myself, “Why not watch some zombie movies?” They were all new to me. Needless to say I loved them! So my idea was hatched. It wasn’t until I started doing some research for the book that I noticed the zombie craze sweeping the planet.

I started writing a novel about 2 years ago called The Magic City Murder. It was somewhat autobiographical in some ways and very vaguely paralleled a murder in my home town that happened when I was a kid. I was about half finished when I became bored with it. The plot revolved around our Dr. Benjamin Hawk, a well meaning forensic pathologist typical of the genre. I felt that the self-deprecating, self-loathing forensic pathologist character had been done before and was pretty well used up in the forensic thriller genre. So I put Hawk away for a while. I had always loved the X-Files character Scully and have always been a bit disappointed that no one ever developed a character in that direction: a forensic pathologist who investigates the paranormal. I think it’s a unique idea with some exciting potential. It was that thought that brought Hawk out of the desk drawer and back to life. So, in a way, my work contributed to that. I also think that my job allowed me to be very descriptive regarding the autopsies, I do it every day!

EEG: Cool, the X-files meet forensic pathology. I'm hooked! (I downloaded my copy last night.) And I confess to being morbidly addicted to very descriptive autopsies... in fiction! In real life? I faint as soon as I see a drop of blood. But that's exactly what fiction's for, right? To take us to places we would never go in real life.

PMC: The thing I love about zombies is the mashing together of monsters and science. There seems to be a particularly large numbers of neuroscientist infatuated with the waking dead, which is exciting because it's a great way to get kids excited about science, and in particular neuroscience.  I put a lot of science in my book and tried to tell a good story filled with interesting tid bits about how the brain works. Maybe I'll scare someone into learning something!

EEG: I sure hope you do! Thank you so much for answering my questions, and do keep the Dr. Hawk books coming!

I hope you all enjoyed meeting Dr. Cummings as much as I did. You can find out more about his work and his books on his website, where he blogs about forensic pathology, life, and, well, death.

Photo: dawn. Canon 40D, focal length 70mm, exposure time 1/13.

Friday, August 19, 2011

Green living

Though the main focus of this blog is genetics and science, I hope you'll allow me a slight change of topic today. I am honored to have as a guest blog my friend Jeff Casalina, who is an energy renewal specialist with the Department of Energy. Jeff is currently working on a book proposal on energy and transportation fuel renewal, and has kindly accepted to tell us about his vision for a greener and planet-friendly way of living. I hope you will enjoy what he has to say. It's something we can all promote and contribute to.

Question:   Of the following life necessities—food, water, air, clothing and shelter—which is your most immediate need?  Answer:  Air, of course!  But, what is your second most pressing need?  (Hint:  think sub-zero temperatures.)  You guessed it…shelter!  You might be hungry and thirsty, but when you are stuck in a raging snow storm or tornado, shelter is your immediate concern. 
We think of our shelter on so many levels—protection from elements, comfort, security, prestige, investment—but what about sustainability? 
Sustainability in housing can be defined in several amenities.
Simplicity-  How many times have you been on vacation and rented a small cabin or cozy hotel room and thought, “I could really live in something like this.  I don’t really need the big house and all that stuff.”   Simplicity equals low cost and energy efficiency.  The smaller the house, the less resources, heat, light, water and impact to the environment. 
Energy Efficiency-  The “low hanging fruit” of the fossil fuel tree has already been picked.  Regardless of what you have heard about oil shale and tar sands and vast deposit of natural gas, what are left are small pockets, remotely located and/or stuff requiring costly or environmentally damaging extraction methods.  (Please view the documentary, Gas Land.)  It’s time we get off it.  Every house has the potential to generate all of its own energy.  Solar water heating, solar and wind generated electricity are all common technologies, and every house has enough roof area to accommodate sufficient solar panels.   Energy efficient appliances and lighting reduce demand.
Design-  All new construction should incorporate passive solar design and earth sheltering.  Passive solar design uses south-facing windows to accept the sun’s rays.  Dark colored, high mass materials absorb the sun’s warmth during the day and re-radiate it at night.  A properly designed overhang keeps the high summer sun off the windows.  Earth sheltering, particularly on the north side, protects against cold north winds and provides basement-like coolness in summer.
Water Efficiency-  All new construction should incorporate water conservation.  A possible water conservation feature is separate gray water (shower and bathroom sinks) and black water (toilets and the kitchen sink).  Gray water can be used to water your garden.  Other water saving features include: waterless urinals and dual flush toilets (one button for number one, the other for number two) low-flow showerheads and rooftop catchments systems.  Every house, even in New Mexico, should be able to capture enough usable water.
 Impediments to sustainability are exuded by our consumer culture.  We are constantly bombarded by advertising that implies that bigger is better, and fancier is sexier.  Resist!  Turn off the TV.  Read and educate yourself on the topics that will make this a better planet (and you much happier).  Collectively, our individual efforts will devolve the consumer culture.  
And if you think about it, our ultimate home is Planet Earth, the one shelter we all share. Let's all pitch in and take care of it, if not for ourselves, for our children. Just like the Native American proverb says, We don't inherit the Earth from our Ancestors, we borrow it from our Children.
Thanks, Jeff. I can't wait to read your book! 
Photo: Seattle Arboretum. Canon 40D, focal length 61mm, exposure time 1/6. 

Wednesday, August 17, 2011

Fermat's last theorem

Today is Pierre de Fermat's 410th birthday. Google is celebrating it with a witty doodle that states: "I have discovered a truly marvelous proof of this theorem, which this doodle is too small to contain." It's a parody of the statement Fermat scribbled on the margin of a copy of the mathematical journal Arithmetica. The theorem he was referring to was later dubbed "Fermat's last theorem" and it made history. The proof was published in 1995, 358 years after Fermat first conjectured it.

Fellow math geeks out there, it's confession time: come on, admit it, we've all been fascinated by Fermat's last theorem. Why? Because of its simplicity! We were in high school (if not even younger) when we became old enough to understand it: x^n + y^n = z^n has no non-trivial integer solutions for any integer n>2. It had the innocent (and deceiving) appearance of an extension of the Pythagorean theorem, which we all knew. And the cherry on top was Fermat's tempting bait, right there: he'd found the proof, but darn it, it didn't fit the margin of the journal. So of course, we all thought good ol' Pierre was full of it and all we had to do was find four integers (x,y,z, and n) to disprove his claim.

It was so simple we all dreamed glory and fame spending countless night hours attempting to either prove it or find the four magic numbers.

And we all failed.

Why? Because we didn't have the tools in high school, nor we had them in our first years of college.

Luckily, Andrew Wiles proved it while I was still in college or else I may not have graduated. It took modular forms and elliptic curves to prove it, and even with all those tools, he had quite some obstacles to circumvent.

Pierre de Fermat is one of my old time heroes. Wiles started working on the proof in 1986 and published his final paper in 1995. And yet it will always be known as Fermat's theorem.
Nonetheless, hats off to Sir Wiles. I'm sort of jealous, though glad the proof ended up being far more complicated than we all envisioned back in high school.

Photo: oak leaf at the beach. Canon 40D, focal length 85mm, exposure time 1/30.

Friday, August 12, 2011

The case of "junk DNA" and why it shouldn't be called junk: Topology.

(This is part 4 of 4 in a series dedicated to the concept of "junk DNA". Links to the previous parts: Part 1, Part 2, and Part 3).

This is DNA:

This is also DNA:

Image from Wikimedia Commons

 The point I'm making: we often think of DNA as a code, a string of four letters repeated over and over again. Yet DNA is so much more than that. DNA is a three-dimensional structure, and as such it has a topology. In biology, the way molecules fold and spread into space is just as important as their chemical composition. The HIV virus, for example, can escape antibodies thanks to the way it hides its "docking" sites: as a consequence, the antibodies "bounce off" its surface and are unable to "grab" it. Some changes in the way certain proteins fold can change their functionality.

Which brings me back to "junk" DNA. I have already mentioned how several disease association studies (studies that look at which particular sites in the DNA increase the chance of getting a certain disease) have found significant correlations with mutations in the non-coding part of the genome. This may seem surprising since once the DNA is spliced, all the non-coding bits are thrown away. So, technically, those mutations should have no bearing on our biology.

Last time I discussed how a possible explanation lies in epigenetics, the mechanisms that activates pseudogenes that would otherwise be non-coding. If a pseduogene has a "defective" mutation and it gets "turned on" (and thus it becomes a coding gene), then the mutation will affect the individual's chance of expressing the disease trait.

Today I want to talk about another possible explanation. The mutation may never become a coding one, but it may very well change the topology of the chromosome where it sits. And some changes in topology may indeed affect our phenotype or, in other words, our biology.

As you know, our DNA is packaged in 23 pairs of chromosomes. DNA needs to be "un-packaged" so that the information can be read. This process, called transcription, is done through an enzyme called RNA polymerase. The enzyme "links" the chromosome and "unwinds" the DNA so that it can turn into RNA. Here's a nice animation of how the process works:

You can see how the topological structure of the chromosome plays an important role: a mutation that changes the architecture of the chromosome may very well affect the way the RNA polymerase enzyme attaches to it, which, in turn, may result in a defective transcription. Think of a pesky piece of torn plastic bag jamming your duffel's zipper. Ugh. Not good. The zipper may jam or it may skip some teeth, some nucleotide bases that won't be read, resulting in the wrong information. And wrong information often translates into defective proteins and defective proteins may results in diseases. Or, it may result in some advantageous trait. The original mutation is indeed in the "junk DNA," but it ends up being no junk at all.

In summary:
  • The vast majority of our DNA is non-coding, meaning that it gets thrown away after transcription and hence is not translated into proteins.
  • Most of the information contained in this part of the genome is redundant: many of our genes are repeated over and over again, but often the copies are "turned off."
  • This redundancy is what allows Mother Nature to "fix" potential mistakes, but also to find new evolutionary escapes.
  • The non-coding part of the DNA doesn't remain non-coding throughout our lifetime. Traumas and stress and other life changes can activate or deactivate certain genes.
  • Even though the non-coding part of the genome has no bearing in the making of proteins, it can change the 3-dimensional structure of the DNA and still affect the biological processes taking place in the body.
It's true that the term "junk DNA" has now become historical, and the more we learn about this mysterious part of our genome, the less likely we are to take the term literally. Still, it has led to many misconceptions. Like all new concepts, it takes a while to grasp its importance and understand it. It reminds me of a quote from population geneticist J.B. Haldane:

"Theories have four stages of acceptance:
        i. this is worthless nonsense,
        ii. this is interesting, but perverse,
        iii. this is true, but quite unimportant,
        iv. I always said so."

Picture: White anemone, Seattle Aquarium. Canon 40D, focal length 85mm, exposure time 1/5.

Monday, August 8, 2011

DNA and the criminal law

One of the things that makes DNA so fascinating is its widespread use not only in science and technology, but also, as you all know, in forensic law. I had the pleasure to discuss DNA evidence with my friend Mark Pryor, an assistant district attorney in Texas and a fellow writer. His novel, THE BOOKSELLER, is currently on submission to publishers and is represented by Ann Collette of the Helen Rees Agency.

I asked Mark to explain what happens after the DNA evidence has been gathered and a suspect has been identified.

 MP: Usually the detective writes an affidavit while consulting the prosecutor. The affidavit is used to lay out the probable cause that the defendant did the crime, then it is presented to the judge.  If the judge thinks there is probable cause, he causes the warrant to be issued.  
EEG: When will  you approve a detective's affidavit based on DNA evidence?

MP: Depends.
I know, poor answer.  But here's why: DNA is used to put someone in a certain place.  That's all.  In a rape case it can put the defendant inside the victim, literally, or just in her vicinity.  So usually we need more than just DNA, unless there is NO reason for the defendant to have been at the scene of the crime.  So your DNA being present when your husband is murdered in your house isn't helpful.  But my DNA there would be, although by itself it's still probably not enough for a warrant.  What would happen is that a detective would pay me a visit and find out if I had a good reason for being at your house.  Remember, DNA by itself can't tell you when someone was at a location, just that they were there.

The one time it would be enough by itself would be in a stranger-on-stranger rape case, where the victim got a good look at her attacker but didn't recognize him, didn't know him.  Even in a date-rape type scenario, where consent is usually the issue, a positive DNA hit will lead the detective to interview the accused before seeking a warrant, most likely.

EEG: What about the opposite scenario: when can DNA evidence be challenged?

MP: It's very hard to argue with DNA.  It's science, and good science, so it's not going to work if you just say, "That's wrong."  What you might be able to do is show an error in the testing.  One interesting case I've seen: semen from a rape/murder was tested against that of the suspect.  It came back negative.  Years later, a detective reopened the case and was convinced it was that suspect, so she resubmitted the sample.  Sure enough, they'd screwed up the testing and it was his.
Now that of course presents a problem when this case comes to trial because the defense lawyer will no doubt argue, "They messed up once, maybe they did twice."  Or even suggest we rigged the result.  

EEG: Interesting. As a scientist, I do know lab contamination is a reality, even when people are extremely careful. Ideally one should always repeat the same analysis multiple times, though DNA testing is still too expensive to allow for that. On a good note, in the five years I've been in this field, I've seen the technology in DNA typing improve exponentially, and the costs lower every year. I'm fairly confident that ten years from now the technology will be much more affordable and errors will be negligible.

Do you believe in the CSI effect, in other words, the fact that after the rise in popularity of shows like CSI prosecutors have a harder time convincing a jury?

MP: Oh yes.  I've blogged about this very thing, in fact. People have much higher expectations of prosecutors these days, and it's definitely something I have to address while picking juries, to make sure they understand what role DNA evidence might or might not play.  For example, I had a murder case recently--it'll be featured on 48 Hours on October 1 of this year--where that was an issue while picking the jury.  This was a cold case, from 1985, and I knew people associate cold cases with DNA, mostly because that's how they are usually solved.  But that wasn't our case. We didn't have DNA and during voir dire I wanted the jurors to understand that there are some instances when DNA testing is pointless.  In our case, the victim and defendant had been dating and so it was not disputed that he'd been at her apartment, where the murder took place.  If they'd collected samples, fingerprints etc., his would likely have been there, but if we'd presented that evidence it would have been a big "So what?" because, as I said above, DNA just tells you someone has been at a location.  Which we all knew.  

Even so, after explaining this, one potential juror insisted we would need to present her with DNA evidence before she'd convict.  I put the hypothetical to her: "What if we had the whole thing on video and you could clearly see the defendant committing the crime?"  She replied that she'd still need DNA.  Needless to say, that disqualified her from the jury panel.  And in the case itself, the defense made a big deal about how we had no DNA evidence of the defendant's guilt!  But those are the types of challenges we face.  DNA is a fantastic development, it's a wonderful tool, for law enforcement but we need to educate people as to its limitations, to the reality of what it tells us about a crime.

EEG: I couldn't agree more. CSI is a wonderful show, but unfortunately too many people watch it thinking they are learning science or forensic law. Watch it for the fun, folks!

Thank you, Mark, for taking the time to answer my questions. I look forward to the 48 Hours show in October!

To find out more about Mark and his book, visit his website, DA Confidential, where he blogs about writing and prosecuting crimes.

Photo: metal knots. Canon 40D, focal length 47mm, exposure time 1/125.

Monday, August 1, 2011

Las Conchas fire

Monsoon season is finally here, though this year it came a little too late.

Las Conchas fire started on June 26 and it swallowed nearly 50,000 acres in a mere 24 hours. The sky was dark and the sun an angry red.

From the infrared map we watched it grow like a cancer until it reached 156.6 thousand acres, dwarfing El Cerro Grande fire.

Our houses didn't burn this time. But the beautiful forest blanketing the Jemez Mountains is gone. Patches of surviving green remain here and there.

Do me a favor: next time you go on a hike, hug the trees along the trail for me.

Picture: burnt trees. Canon 40D, focal length 85mm, exposure time 1/5.