Anthropology Archeology Forensics Genetics Science

DNA in Doubt: our increasingly-complicated relationship with the stuff of life

It used to be so uncomplicated. DNA is the stuff that makes you who you are. It’s what makes you look the way you do, makes you susceptible or resistant to certain types of illnesses, even sets your biological clock. DNA is the stuff of life.

Except when it’s not. As science probes the depths of the genomes of all forms of life on Earth, we are confronted with an increasingly-convoluted relationship between DNA and it’s expression – nature and nurture, in other words – that in turn makes our previous use of DNA increasingly dubious.

Sammy Malone: DNA forensic expert
Y’know, Sammy Malone: crime fighter.

It isn’t all bad news: our more sophisticated understanding of genetic information means we’re getting close to finding cures for disease, genetically-tailored health care and amazing discoveries in the worlds of biology and anthropology. But our colloquial understanding the nature of DNA has not caught up to the scientific understanding. The result of this gap can often be abusive at best and flat out destructive at it’s worst.

Nowhere is that fact more certain than in the world of forensics. As DFE discussed last year, local law enforcement has seen the same forceful push-back on DNA evidence presented in criminal cases that has swept the nation in the last few years. The assumption most of the public has in the infallibility of DNA to finger guilty parties is entirely wrong. And whether intentionally or not, many cases have been tried and many people convicted on evidence that is nowhere near near as declarative as prosecutors would have you believe.

A new grant to Syracuse University is aimed at finding a solution to a fundamental problem in forensic DNA evidence-gathering: mixed DNA samples. Regardless of what type of tissue law enforcement is sampling from – blood, semen, hair, skin – it’s still just a pile goo at a crime scene. That pile of goo is a bit of a hothouse flower: organic chemicals don’t last long outside the body. And biological evidence can easily get mixed up with other that of individuals not even involved in the crime. Taken together, you can see that this is a bit of a dumpster dive.

So clearly, the biggest challenge in DNA forensics is getting a clean, uncontaminated and complete sample of DNA. How challenging? Basically, the odds of meeting all three criteria are just a few degrees north of ever french kissing a unicorn. Pretty low.

The SU plan is to light up cells with dyes and black light in a way that lets them tell whether the two cells contain the same DNA. The next step would be to extract them by DNA signatures: all of Specimen X, followed by Specimen Y and so on. That’s where SU’s brain power is supposed to hopefully kick in.

And even as the scientific community grapples with the problem of commingling DNA and incomplete samples, a novel and highly-dubious use of DNA evidence is being tested in law enforcement, winkingly called “Familial DNA.” This concept means that, even if you’ve never been DNA tested for any reason, your DNA may get linked to a crime, simply because there is DNA in a database from a cousin or other relative.

What? That’s right. If a DNA sample taken at a crime scene is similar enough to a relation of yours, police may use this fact to posit that the DNA must be yours. In a Six Degrees of Separation type of scheme, you are implicated to be involved in the crime simply because you have similar DNA to what was found on scene.

This deeply-troubling practice runs directly afoul of the Birthday Paradox, a statistical quirk that radically and unexpectedly reduces the odds that a match will be found in a group, rather than individually. For a much more elegant explaination than I might summon forth, read Southern Fried Science. This statistical fact makes DNA databases generally misleading in the first place, but once you expand the search to include people who aren’t even in the database, the potential results are genuinely disturbing.

In the world of anthropology (the science, not the store), our deepening understanding of mitochondrial DNA is completely redefining our understanding of human migration. Perhaps not for the better, depending on your favourite theory.

At issue is the long-held belief that those who would become Native Americans traveled across the Land Bridge and very quickly populated the whole of the Pacific shore. This fairly linear theory of American anthropology has brought multiple theories and timelines into clash for decades. Are the Clovis points really the most ancient relics? No. But are the Clovis people still the oldest people in the Americas? Well, maybe…

What the newest mitochondrial DNA evidence, taken from the bones of a mother and child discovered near the Bering Sea, suggest that perhaps part of the problem with identifying the path of Native Americans is that there simply isn’t just one path.

Instead, the mitochondrial evidence points to a highly-diverse group of Asian immigrants coming across the famed land bridge. Rather than a single set of tribes or related individuals crossing the great divide, it may have been hundreds. This new evidence suggests that the reason archeological evidence of human inhabitation seems so scattered is because human habitation was in fact very scattered.

If there is a lesson in the week’s DNA news stories, it is that science is a double edged sword for those that would hold onto it’s truths too tightly. However reliable a scientific fact has seemed in the past, there is always new research that casts doubt upon it.

Rochester Science

Live forever? @UofR boffins may be getting closer.

The goal of soon stopping the aging process entirely is something Ray Kurzweil swears by, and for this he gets a lot of criticism. But U of R scientists have recently discovered that a protein named SIRT6 extends the lifespans of mice, and this is a step towards its application in our own bodies. Although this may seem like a menial leap, the team plans on using their research to eventually extend a person’s life and treat cancer.

This makes me wonder what societal changes will be made about the collective perception of an average lifespan. In my lifetime, will it be normal for me to live out 120 years before passing away? Will that be the norm? I’m not sure what to expect, but with great jumps in medicine and the exponential growth of technology, I’m wondering if I really will see these breakthroughs in my life.

Enhancing the way cells repair DNA increases lifespan, U of R scientists found. By overexpressing the SIRT6 protein, DNA repair by cells can take place for an extended amount of time. Old cells are 38 times less efficient at repairing critically broken DNA than younger ones, and SIRT6 lowers this number. Vera Gorbunova, one of the U of R scientists, sums the idea up well:

“Our research looked at DNA repair and found a reason for the longevity, and that is SIRT6’s role in promoting more efficient DNA repair.”

With a recent poll showing that nearly half of Americans either feel they look their age or older than their age, it’s clear U of R scientists are headed in the right direction. Medicine is evolving into a practice that caters to the needs of the masses and to the wants of the masses as well. Whether fiddling with our lifespan is ethical or not is beyond my capacity for a philosophical discussion, but I’m excitedly waiting for the day I can enhance the way my cells repair DNA, entirely avoid any terminal illnesses like cancer, and maybe even live well past 120.


Girl, look at that genome! Working out reprograms your DNA, science discovers

Just over 2 months ago, we rang in 2012. For many of us, that meant resolutions and goal setting. The most common nationwide new year’s resolution is hands down becoming physically fit. Gyms recognize this trend and often offer new member new year specials or trial periods or various other marketing tactics to drive home the point of attaining a new you for the new year.

Working out changes your body. Endurance builds, muscles strengthen, metabolism grows – and your DNA loses chemical modifications. Wait, what?

A paper published in Sweden just this week studied the methylation status of genes in small biopsies taken from the thigh muscles of healthy young adults before and after working out on an exercise bike. The biopsies showed that some genes involved in energy metabolism were demethylated in the promoter regions by the workout – the parts of DNA that facilitate the transcription of particular genes.

The amount of demethylation in the genes varied on a person by person basis depending on the intensity of the workout. In other words, individuals who had cycled the hardest showed the greatest amount of gene demethylation in their biopsies.

Interestingly enough, similar demethylation processes have been observed in cultured muscle cells upon receiving large doses of caffeine.  According to Juleen Zierath, a member of the team providing research for the paper,

“Caffeine releases calcium from the sarcoplasmic reticulum, an organelle found in muscles. It sort of mimics a contracting muscle. Calcium might, therefore, be the cellular trigger that activates the demethylation pathway.”

So what does this all mean? Well, your body works differently after demethylation, as different genes begin to get expressed. Its like changing the settings on your phone: it’s the same phone, but now it operates differently. In this case, the change happens in the muscles.  Just like caffeine makes you physically feel more awake, demethylation sort of “wakes up” your muscles, making them respond more quickly than they would have before exercise.

Despite the fact that demethylation happens in response to caffeine, this doesn’t necessarily mean we should change our resolutions from working out more to drinking more coffee.  To achieve the same effect on muscles that exercise does, one would need to consume approximately 50 cups of coffee per day, a near lethal amount!

Although it is unclear exactly how these methyl groups were removed from the DNA tested, demethylation is quickly becoming a topic of scientific popularity. It is expected to undergo many tests and experiments so we can have a full understanding in the next 3-6 months of why the process happens and what exactly it does.  In the meantime, I’ll continue to enjoy both my morning caffeine fix and evening gym workout.

Rochester Technology

How 16-year-old DNA evidence may solve a cold case murder in Greece

Thanks to scientific advances, a 16-year-old unsolved Rochester murder case may soon be closed. Back in the summer of 1995, Timothy Milgate was found stabbed and shot to death in his home in Greece. Although trace amounts of DNA from Milgate’s killer were found at the scene of the crime, they were too small to be tested. Until now.

Nearly 17 years later, 6 pieces of evidence found at the scene of Milgate’s murder have been sent to New York City to be analyzed using a new procedure called high sensitivity DNA testing.  High sensitivity (HS) DNA testing, also referred to as low template (LT) DNA, low copy number (LCN) “touch DNA” and trace DNA testing, is a reliable, state-of-the-art technology used to detect and recover small amounts of DNA.  Although it is fairly young, high sensitivity DNA testing is an extremely well-regarded, powerful tool which can help law enforcement’s ability to identify or exclude individuals suspected of crimes.

High sensitivity DNA testing can be broken down into two stages: a further purification process which allows the trace DNA to be seen more clearly, and an amplification process which increases the all-around sensitivity of the DNA, thereby increasing the amount of DNA information that can be obtained, even from very small traces as in the Milgate case. According to New York City Chief Medical Examiner,

“These methods have been extensively validated, reviewed by regulatory committees, and published in peer-reviewed journals. Analysts are specially trained in these methods and have frequently testified to High Sensitivity DNA results in New York City, as well as outside jurisdictions. “

What was considered impossible in 1995 is now a valid method of research in 2012. For Milgate’s surviving friends and family, these new technological advancements bring hope that justice will be served, even if it is almost 20 years later.