Tuesday, August 18, 2009

Why do DNA supporters feel jilted? Or, an examination of simple CpG methyltransferase treatments

No, this really doesn't have a lot to do with my FriendFeed-related post from last week, Why do FriendFeed users feel jilted? Or, an examination of erotic impulses. But in a way it does, because this is yet another case in which something which has been assumed to be true is suddenly called into question.

But let me back up a bit.

I don't really talk about my day job much in this blog, but there has been a big tempest brewing in the biometric arena since February of this year. In that month, the National Academy of Sciences released a report entitled Strengthening Forensic Science in the United States: A Path Forward.

While the report itself is only available via purchase, a free executive summary is available for download by all. And that executive summary has some interesting statements on what we call "forensic science":

...in some cases, substantive information and testimony based on faulty forensic science analyses may have contributed to wrongful convictions of innocent people. This fact has demonstrated the potential danger of giving undue weight to evidence and testimony derived from imperfect testing and analysis. Moreover, imprecise or exaggerated expert testimony has sometimes contributed to the
admission of erroneous or misleading evidence.

Which forensic sciences are being questioned? Well, ALL of them...save one:

Often in criminal prosecutions and civil litigation, forensic evidence is offered to support conclusions about “individualization” (sometimes referred to as “matching” a specimen to a particular individual or other source) or about classification of the source of the specimen into one of several categories. With the exception of nuclear DNA analysis, however, no forensic method has been rigorously shown to have the capacity to consistently, and with a high degree of certainty, demonstrate a connection between evidence and a specific individual or source.

Or, most of the forensic sciences aren't scientific.

It should be noted that forensic science practitioners have a differing view. Here are excerpts from a position statement issued by the Scientific Working Group on Friction Ridge Analysis, Study, and Technology (SWGFAST).

SWGFAST is concerned that the NAS report may be used to misrepresent the true state of the practice and science of friction ridge comparisons. The NAS report has already been cited in a legal motion to exclude forensic evidence.... It would be unfortunate if the report is represented as a definitive analysis of forensic science practices as opposed to a presentation of concerns derived from a select group of interviews and limited literature review....

Unfortunately, the lack of practicing examiners on the NAS Committee itself may have led to misunderstandings about the practice of the discipline and an unbalanced reliance on certain research and sources. As an example, the Committee comments on the “...common lack of scientific expertise among judges and lawyers…” [p. 1-14] yet relies, though not solely, on the opinion of a single jurist when addressing the scientific underpinnings and reliability of fingerprint examinations [p. 1-7]....

The NAS states “With the exception of nuclear DNA analysis, however, no forensic method has been rigorously shown to have the capacity to consistently, and with a high degree of certainty, demonstrate a connection between evidence and a specific individual or source [p. S-5]. SWGFAST respectfully disagrees. History, practice, and research have shown that fingerprints can, with a very high degree of certainty, exclude incorrect sources and associate the correct individual to an unknown impression. Furthermore, fingerprints discriminate between monozygotic twins, and DNA currently does not.

This particular statement from SWGFAST is interesting.

SWGFAST acknowledges that subjectivity is inherent in the friction ridge examination process. Subjectivity (informed judgment) is inherent to every human activity. Therefore, it naturally follows that it is also present in any scientific endeavor where the human is the instrument and the decision cannot be separated from the method. In fact, subjectivity is found in the informed analysis of DNA, a discipline the NAS regards throughout the report as the gold standard of forensic science. During the encoding phase of DNA entry to a search system, a human examiner subjectively determines the presence and the degree to which individual markers are present in the sample. Additionally, the examiner also compares peak heights of the unknown sample with known samples presented as likely candidates for a match, the quality of which can also sometimes vary in degraded samples. A great deal of subjectivity exists specifically in the interpretation of mixtures of DNA profiles and low copy number analysis. All of these factors point to the same subjective elements in the determination of the relevance of features in DNA analysis that are present in the selection and evaluation of friction ridge skin features.

Despite the efforts of SWGFAST and others, a view is emerging that DNA forensic science represents, in SWGFAST's words, a "gold standard," and all other forensic sciences, ranging from fingerprint identification to bullet casing analysis, are of a lower order.

So, if someone comes into court and presents DNA evidence (and ignoring the SWGFAST concerns, as well as possible contamination of samples), people are inclined to accept that the DNA evidence is true.

But what if the DNA evidence is...um...faked? Here is the abstract of an article from FSI Genetics - an article with the innocuous title "Authentication of forensic DNA samples":

Over the past twenty years, DNA analysis has revolutionized forensic science, and has become a dominant tool in law enforcement. Today, DNA evidence is key to the conviction or exoneration of suspects of various types of crime, from theft to rape and murder. However, the disturbing possibility that DNA evidence can be faked has been overlooked. It turns out that standard molecular biology techniques such as PCR, molecular cloning, and recently developed whole genome amplification (WGA), enable anyone with basic equipment and know-how to produce practically unlimited amounts of in vitro synthesized (artificial) DNA with any desired genetic profile. This artificial DNA can then be applied to surfaces of objects or incorporated into genuine human tissues and planted in crime scenes. Here we show that the current forensic procedure fails to distinguish between such samples of blood, saliva, and touched surfaces with artificial DNA, and corresponding samples with in vivo generated (natural) DNA. Furthermore, genotyping of both artificial and natural samples with Profiler Plus® yielded full profiles with no anomalies. In order to effectively deal with this problem, we developed an authentication assay, which distinguishes between natural and artificial DNA based on methylation analysis of a set of genomic loci: in natural DNA, some loci are methylated and others are unmethylated, while in artificial DNA all loci are unmethylated. The assay was tested on natural and artificial samples of blood, saliva, and touched surfaces, with complete success. Adopting an authentication assay for casework samples as part of the forensic procedure is necessary for maintaining the high credibility of DNA evidence in the judiciary system.

By the time the New York Times got a hold of this, the title of the resulting article was "DNA Evidence Can Be Fabricated, Scientists Show."

A few points from the New York Times article merit consideration:

  • The Times noted that the lead author of the paper, Dr. Dan Frumkin, is "a founder of Nucleix, a company based in Tel Aviv that has developed a test to distinguish real DNA samples from fake ones that it hopes to sell to forensics laboratories." So Dr. Frumkin unquestionably had a financial motivation to pursue this line of scientific study - the cynical can claim that he is creating market demand for his product.

  • That having been said, it isn't like Frumkin is creating something that is not there. "John M. Butler, leader of the human identity testing project at the National Institute of Standards and Technology, said he was 'impressed at how well they were able to fabricate the fake DNA profiles.' However, he added, 'I think your average criminal wouldn’t be able to do something like that.'" Yet the very fact that criminals COULD do this is enough to potentially call DNA evidence into question.

  • Unless, of course, you have the Nucleix product. "Nucleix’s test to tell if a sample has been fabricated relies on the fact that amplified DNA — which would be used in either deception — is not methylated, meaning it lacks certain molecules that are attached to the DNA at specific points, usually to inactivate genes." (We'll return to this point a little later.)

  • What are the implications of this? Well, there are two. In addition to the possibility that fabricated DNA could be placed at crime scenes, the Times article claims that there are possible privacy violation issues. "[I]t may be possible to scavenge anyone’s DNA from a discarded drinking cup or cigarette butt and turn it into a saliva sample that could be submitted to a genetic testing company that measures ancestry or the risk of getting various diseases. Celebrities might have to fear “genetic paparazzi,” said Gail H. Javitt of the Genetics and Public Policy Center at Johns Hopkins University."
Now I have to admit that my biology and chemistry knowledge is restricted to high school courses, and I am unqualified to evaluate the likelihood of someone fabricating DNA. And I'd be willing to bet that most people who read this blog post are similarly unqualified. But that isn't going to stop public perception from jumping to conclusions...and one of the most likely conclusions is that DNA is now relegated to junk science - something that can be challenged in court even if the sample weren't tampered with in the lab. For what it's worth, I've already made the following prediction:

Within 30 days, at least one defense lawyer will cite the FSI Genetics paper in an attempt to throw some evidence out.

I made that prediction in the comments area to the "CSI: Ambiguous Sentences" blog post at Uncertain Principles. The post itself questioned the relationship between the lead author of the study that said that the DNA can be faked, and the company that just happens to be able to detect fake DNA.

But I found another comment to the post to be interesting. Remember the claim that I printed earlier that you can detect fake DNA because it is not methylated? Well, another commenter (Sigmund) questioned that statement:

But of course any competent molecular biologist will point out that it is simple to use a simple CpG methyltransferase treatment to methylate the amplified DNA.

Now I have no idea whether Sigmund knows what he's talking about - it would take me great effort to figure out how many neutrons are present in a water molecule - but if this means that "any competent molecular biologist" can plant a fake DNA sample at a crime scene that can remain undetected as fake...well, one of our so-called universal truths has just been dashed.

Here are some other reactions that I found. CrimProf Blog:

I suspect that most geneticists would not at all be surprised about the possibility that DNA crime scene evidence could be fabricated. It would be interesting to hear more independent opinions about just how easy or difficult the fabrication process would be....

B12 Solipsism:

...what about court-ordered DNA tests to get a wrongfully accused death-row murderer out of jail, and then the DNA turns out to be fake?

A commenter at the same post:

The relativist nature of knowledge precludes the notion of gold standard of proof in science.What seem to be true today might turns out to be erroneous in the future.

Which brings us back to the beginning of this post, and the FriendFeed post. We have a heartfelt belief in something - FriendFeed is a wonderful independent site, DNA is the gold standard of forensic science - and then something comes along to shatter our belief.

This would be an appropriate time to refer to the seven stages of grief - but perhaps my assumption of seven stages is wrong, and there's really five stages, or ten, or perhaps grief doesn't exist and everything is an illusion.

I hate relativism.
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