Tag: Mitochondrial DNA

Categories
Anthropology Archeology Forensics Genetics Science

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

Photo: <a href="http://gigaom2.files.wordpress.com/2013/05/dna-strand.jpg">GigaOm</a>

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.

Categories
Forensics Science

Resting on shaky ground: did DA Doorley mislead a jury on faulty DNA evidence?

Photo: <a href="http://www.yalescientific.org/2013/05/qa-does-the-y-chromosome-rot/">YaleScientific.com</a>

Some truths are axiomatic. They’re ideas we hold as being so solidly true, we never bother to examine them too deeply.

The concept of “DNA evidence” as the fool-proof smoking gun is one of these axioms. We understand that your personal DNA encoding is responsible for determining your sex, hair color, eye color and even your risk of having a heart attack. We know that, when a person interacts with a crime scene, there’s a distinct possibility that they may leave behind substances from which DNA can be sampled and a match found. There’s even new technology aimed at potentially reconstructing your face from DNA, to help police search you out.

But is DNA evidence presented in court really so iron-clad? What exactly constitutes a “match” by forensic standards, and how close can that match be to the true criminal? These questions were put to the test just recently in the appeals trial for Howard Wright, charged with the 1995 rape and murder of Patricia Daggett. The conviction was ultimately upheld on a 3-2 vote, but the two judges that dissented point out that the DNA evidence was nowhere near as conclusive as they contend then Assistant District Attorney Sandra Doorley made it seem. Indeed, based on court documents, it very clearly was not. The dissent reads in part:

As the majority notes, the People “presented evidence that . . . defendant’s DNA could not be excluded from various pieces of evidence recovered [from the victim’s vehicle].” At trial, the People’s forensic expert, who analyzed defendant’s DNA sample, described the two types of DNA testing used in this case—mitochondrial DNA analysis and YSTR DNA analysis…

The People’s forensic expert acknowledged the two above-mentioned types of DNA analysis at trial, but she did not speak at length about a third type of DNA analysis—autosomal..

How could an analysis of DNA evidence not point solidly to a single individual? The dissent notes that the sample could not have ruled out the victim’s husband, nor could it rule out the second alleged accomplice in the crime, Christopher Gifford. And what are these three types of DNA testing?

The DNA of DNA forensic testing

To unravel this mystery, we first need to understand that not all DNA in your body is the same. There are two types: nucleic DNA and mitochondrial DNA.

Nucleic DNA is a combination of information from your genetic parents, which is passed to you, and is responsible for the you-building that we all understand. Mitochondrial DNA is passed more or less unchanged from your genetic mother to you. Mitochondrial DNA does not contain enough information to be used to pinpoint a specific individual, but can be used to broadly exclude individuals who simply do not match.

That leaves us with nucleic DNA. But here again, there are two different types of testing, YSTR and autosomal. YSTR tests are performed on the Y chromosome and therefore only possible in male individuals. But since the Y chromosome is passed intact from father to son, all individuals of a specific paternal line – which could potentially be quite vast – will have similar or exactly the same YSTR results.

Autosomal DNA testing is the closest thing in the forensic arsenal to the “smoking gun.” In autosomal testing, 22 out of the 23 pairs of chromosomes that make you what you are can be tested. The 23rd pair is, of course, the sex pair for which YSTR is used. Here is the evidence which sometimes boasts a 1-in-a-billion accuracy.

Then what of Mr. Wright’s sentence?

Regardless of which method of testing is used, the results boil down to a statistical analysis and professional judgement of the facts of the case. And none of these types of evidence is easy to get in the first place. DNA like all living material is delicate and easily destroyed at the scene of the crime, by investigators or even by the lab.

Mitochondrial and YSTR testing can certainly be used to exclude a suspect from consideration, assuming that their DNA signatures differ significantly enough. But they don’t do much to identify a specific suspect, especially as in this case, where multiple persons involved in the crime all fit the same basic profile. Only autosomal DNA testing can positively identify a single individual, but that requires a working, undamaged sample of all 22 required pairs.

The dissent for Mr. Wright’s appeal says that the People’s forensic expert never spoke “at length” about autosomal DNA evidence. Was that because that evidence was not conclusive, or not possible to obtain? Nobody says.

Other evidence presented in the case, as recounted by the appeal ruling, is deeply suspicious but circumstantial. Wright was seen in Daggett’s car with her prior to the murder; the prosecution proved that Daggett was raped in the car; eye witnesses saw Wright in Daggett’s car the next day. None of these facts would have been usable for a conviction on their own, without DNA evidence. But the DNA analysis was itself dubious and inconclusive: it implicates three potential suspects, one of whom was never on trial.

The real problem here is not whether the DNA matched one individual suspect. The real problem seems to be that the fate of our justice system was in this case settled by a 3-to-2 decision in which the majority seems to whistle past a very large graveyard. The majority waves a fairly vague hand at the DNA evidence and concludes, based on circumstantial evidence, that a “reasonable person” might have found Mr. Wright guilty. In the absence of the DNA, is that really true?

If sympathy for the convicted is hard to come by, it is worth considering the implications of a 3-to-2 decision in the opposite direction. Had the flimsiness of the DNA evidence been the thing that overturned the conviction of Howard Wright, how many more men in how many more jails might have been set free, possibly erroneously, on the basis of dubious forensic evidence gathering?

Categories
History Science

Richard III and evolution, how one identified the other.

King Richard III

His power challenged and overthrown, pierced by “humiliation wounds,” his legacy to be tarnished by his successors, Richard III’s lifeless body was draped over the back of a horse, to be carried to parts unknown. For hundreds of years, nobody has ever known just where the last Plantagenet King finally laid down to rest.

Uncovering that mystery took detective work. It took a lot of convincing of skeptical colleagues. It took forensic analysis and most definitively of all, it took mitochondrial DNA evidence:

 DNA from the skeleton matched a sample taken from a distant living relative of Richard’s sister. Geneticist Turi King said Michael Ibsen, a Canadian carpenter living in London, shares with the skeleton a rare strain of mitochondrial DNA. She said combined with the archaeological evidence, that left little doubt the skeleton belonged to Richard.

What is mitochondrial DNA and why is it so authoritative? The answer is an amazing bit of cellular evolution that takes place millions of years before the first humans even thought to stab each other with sharp metal things.

Mitochondria are the fuel cells of the cellular world. Every cell in your body has several mitochondrion, whose role it is to convert energy from glucose into a form that the cell can use, called ATP or Adenosine Tri-Phosphate.

But what is really interesting about mitochondria is that they behave like a separate living organism within the cell. They have their own discrete nucleus with its own DNA, their own cellular wall that performs the same functions as the wall around the main cell, ..and they even reproduce in the classic cell splitting bacterial way:

Bacterial and mitochondrial reproduction. Image courtesy Berkley University

This has led scientists to believe that mitochondria are in fact their own separate species of symbiotic life. Somewhere along the line, scientists believe that a proto-mitochondria was enveloped by another type of cell and rather than being killed, ended up helping the host cell out. Scientists have observed bacteria being absorbed by amoeba in this same fashion. The result was a form of inter-species cooperation that is beyond ubiquitous. All forms of eukaryotic life – cells which have nuclei, which is to say every cell in your body, your dog’s body and every plant or tree – have mitochondria. That leaves only bacteria and archaea without mitochondria.

So, why does this all matter in the discovery of a long-dead king? Because mitochondria reproduce asexually, are contained in the ovum (an egg cell) and are therefore passed from mother to child exclusively. Whereas the rest of your DNA is half your mother, half your father, your mitochondrial DNA is all momma. And because it is copied asexually, it is very, very consistent over hundreds and even thousands of generations. The DNA that make your mitochondria work are probably not all that different from relatives so far back, your Ancestry.com profile doesn’t even include them.

Thus after hundreds of years, a controversial noble’s irrefutably ignoble resting place beneath a modern-day parking lot was discovered.