Monday, June 22, 2015

48 Hours for DNA

Today's New York Times reports that
DNA matching that of two escaped killers was found in a cabin in the remote resort of Mountain View, N.Y., 15 heavily wooded miles west of the state prison in Dannemora, an official briefed on the investigation said on Monday morning.

The forensic evidence indicated that the men had been there within the last 48 hours, according to the official, who was not authorized to discuss the search and spoke on the condition of anonymity.

A pair of prison-issued underwear was also found in the cabin, the official said.
Andy Newman & William K. Rashbaum, DNA of Escaped Convicts Found in Cabin, Official Says, N.Y. Times, June 22, 2015 

It would interesting to know what "forensic evidence indicated that the men had been there within the last 48 hours." DNA itself carries no known signs of how long it has sat on some surface. If the DNA were in saliva on, say, an apple core left from a snack, would the extent of oxidation of the food allow it to be dated within a 48-hour period? Seventeen days have elapsed since the two men escaped.

Saturday, June 6, 2015

Maryland v. King and Fourth Amendment Doctrine

In Maryland v. King,1/ the Supreme Court upheld the practice of routine DNA sampling soon after arrest for certain crimes. The impact of the decision of the doctrinal framework for applying the Fourth Amendment to searches has been the subject of debate. The most extreme view is that is the opinion presages the collapse of the doctrine that criminal investigatory searches are per se unreasonable unless they fall within some well-defined exception to the requirement of a warrant based on probable cause.2/ Another destabilizing view is that the case establishes “that any suspicionless search of an arrestee is allowed if it will be useful to solve crimes.” 3/ Other observers were less alarmed.4/

A case having nothing to do with DNA suggests that King is not the death knell of either the reasonable-suspicion requirement for a search incident to arrest or the warrant requirement. In Riley v. California,5/ Chief Justice Roberts wrote that
As the text [of the Amendment] makes clear, “the ultimate touchstone of the Fourth Amendment is reasonableness." Our cases have determined that "[w]here a search is undertaken by law enforcement officials to discover evidence of criminal wrongdoing, ... reasonableness generally requires the obtaining of a judicial warrant." Such a warrant ensures that the inferences to support a search are "drawn by a neutral and detached magistrate instead of being judged by the officer engaged in the often competitive enterprise of ferreting out crime." In the absence of a warrant, a search is reasonable only if it falls within a specific exception to the warrant requirement. 6/
Applying this framework, the Court unanimously held that police generally need a warrant to search a cellphone, The mere fact that it was acquired incident to an arrest is insufficient to justify rummaging though its contents.Thus, if Riley is any indication, Maryland v. King changed neither the basic framework of Fourth Amendment analysis nor the parameters of searches incident to arrest.

Notes
  1. 133 S. Ct. 1958 (2013).
  2. Erin Murphy, License, Registration, Cheek Swab: DNA Testing and the Divided Court, 127 Harv. L. Rev. 161 (2013).
  3. Tracey Maclin, Maryland v King: Terry v Ohio Redux, 2013 Supreme Court Review 359, 403.
  4. David H. Kaye, Why So Contrived? The Fourth Amendment and DNA Databases After Maryland v. King, 104 J. Crim. L. & Criminology 535 (2014); David H. Kaye, Maryland v. King Per Se Unreasonableness, the Golden Rule, and the Future of DNA Databases, 127 Harv. L. Rev. F. 39, 40, 42-43 (2013); Orin Kerr, A Few Thoughts on Maryland v. King, The Volokh Conspiracy, June 3, 2013 (“while King is very important from a practical standpoint, there isn’t a whole lot of academically-interesting stuff happening in the King opinions.”).
  5. 134 S. Ct. 2473 (2014).
  6. Id. at 248 (citations and internal quotation marks omitted)

Wednesday, June 3, 2015

Spitting in Syracuse: Another Disgusting DNA Case

Police have linked restaurant and grocery store employees to expectoration in food or drink. The latest case is described in Syracuse.com, which reports how a server at the Chili's Restaurant in Clay, NY, was caught after the act and convicted of disorderly conduct. Now the affected customers plan to sue him -- and the corporate owners of Chili's.

Earlier, and even more unpleasant cases, come from Seattle and Albuquerque.


Saturday, May 23, 2015

No Relief for Jeffrey MacDonald After FBI Declares It “Exceeded the Limits of Science” with Hair Analysis

It was not yet 3:30 a.m. on February 17, 1970, when tragedy struck Captain Jeffrey MacDonald’s family at 544 Castle Drive, Fort Bragg, North Carolina. His pregnant wife, Collete, “had both her arms broken and was stabbed repeatedly in the chest and neck with a paring knife and an ice pick” (Anthony 2013).  Five-year-old Kimberley “was beaten across the head with a club and stabbed multiple times in the neck. Two-year-old Kristen was stabbed over 30 times in the back, chest and neck ... . MacDonald himself received relatively minor injuries except for a single stab wound that punctured his lung” (Ibid.)

MacDonald, who was a surgeon with the Green Berets, spoke of an attack “by four intruders — two white men, a black man and a white woman. He said the woman held a candle and chanted ‘Acid is groovy’ and ‘Kill the pigs’. On the headboard in the marital bedroom the word ‘PIG’ was written in blood.” (Ibid.) It was eerily similar to the depraved murders of Charles Manson’s followers in Los Angeles. “At Roman Polanski's home they killed the director's pregnant wife, Sharon Tate, and with her blood smeared the word ‘PIG’ on a wall.” (Ibid.) Indeed, Army investigators found an article on the Manson murders in the living room.

After an extended preliminary hearing culminated in a report exonerating Captain MacDonald, he left the Army with an honorable discharge and moved to California. But his father-in-law’s relentless pursuit led to the case being placed before a federal grand jury in 1974. An indictment came the next year. In 1979, federal prosecutors convicted him of the three murders. Appeals and post-conviction motions ensued. The case generated a “small library of books, a TV mini-series, countless documentaries and a forest of newsprint.” (Ibid.)

The latest opinion in this “wilderness of error” (to use the title of the most recent book on the case) is from a federal district court in North Carolina. The court issued this opinion last week, in the midst of an ongoing investigation into FBI reports and testimony about hair comparisons in thousands of cases before 2000. MacDonald’s case is now one of many in which the Department of Justice has confessed error in the presentations of its FBI laboratory personnel who compared hair samples from crime scenes to those of suspects.

Thus, last year, the Department advised MacDonald’s counsel that:
We have determined that the microscopic hair comparison analysis testimony or laboratory report presented in this case included statements that exceeded the limits of science and were, therefore invalid: (1) the examiner stated or implied that the evidentiary hair could be associated with a specific individual to the exclusion of all others—this type of testimony exceeded the limits of science; (2) the examiner assigned to the positive association a statistical weight or probability or provided a likelihood that the questioned hair originated from a particular source, or an opinion as to the likelihood or rareness of the positive association that could lead the jury to believe that valid statistical weight can be assigned to a microscopic hair association—this type of testimony exceeded the limits of science. (A copy of the documents upon which our determination is based is enclosed.) We take no position regarding the materiality of the error in this case.
According to the court, the FBI and the Innocence Project (IP) identified three errors based in the lab reports or trial testimony. None of them prompted the court to change an earlier order denying him post-conviction relief.

In light of the perception of award-winning journalists that the FBI “faked an entire field of forensic science” (Lithwick 2015), that the Bureau placed “pseudoscience in the witness box” (ibid.), and that it performed “virtually worthless” analyses (Blakemore, 2015), it is worth looking carefully at the descriptions of the self-reported “invalid” science. Not having the FBI-IP report cited by the court at my disposal, I rely solely on the court’s description of it. If this description is accurate and if the report on MacDonald's case is representative, one may want to exercise some caution with respect to the surprising number of FBI reports that are said to exude "junk science" (Editorial 2015).

Hair analysis figured into the MacDonald case in an unusual way. It was not performed to associate MacDonald with the crime scene. He was lying in the house, wounded and apparently floating in and out of consciousness. Hairs in the house — especially ones on or around the bodies of the victims — were significant only because they might have come from the invading Manson-like killers. But visual and microscopic inspections of various hairs from the house did not seem to support MacDonald's extraordinary story. Instead, the features seen in the hairs were consistent with hairs sampled from the MacDonalds themselves.

1

A bedspread on the floor of the master bedroom of the MacDonald home contained a hair entangled with a purple cotton thread. An FBI lab technician mounted the hair on a slide marked “Q96 H (from thread).” Paul Stombaugh, who was in charge of the Chemistry Branch of the Chemistry and Physics Section of the FBI crime laboratory, examined the Q96 thread and hair, and wrote:
Light brown to blond head hairs that microscopically match the K1 head hairs of COLLETE MACDONALD were found in specimens ... Q96.... The Q96 hair was found entangled around a purple cotton sewing thread like that used in the construction of the Q12 pajama top [belonging to defendant]. Further, this hair had bloodlike deposits along its shaft.
The 2014 report found no errors in this 1974 laboratory report or in Stombaugh’s testimony at the 1979 trial that “this hair—in conducting a comparison examination with the comparison microscope—microscopically matched the head hairs of Colette MacDonald.”

On cross-examination, however, defense counsel suggested that it was peculiar that the thread and the hair “were still wrapped around together after four years of having been in the laboratory custody.” He asked, “Doesn't it make a difference to you to find out what treatment or handling a hair would have had before you examined it in the laboratory?” Stombaugh replied that “The hair was not mounted sir, as were many other ones in this submission. We opened the vials up and identified what was inside. If they were hairs, we would mount it on a slide and then they were compared.” The following exchange then occurred:
Q. Mr. Stombaugh, the question was: weren't you concerned with what might have been done to that hair that might possibly lead you to a wrong conclusion unless you found out what they had done with it?
A. Sir, the only conclusion on the hair examination that I was going to make was its origin.
Q. That is pretty serious about whose hair it is. That is a fundamental question you were being asked.
A. That is correct.
This last exchange is what, in the eyes of the Inspector General and the FBI and IP reviewers, moved Stombaugh’s testimony beyond the limits of science—he said he was examining the hair to reach a “conclusion” of some sort about “its origin” and that this was a “fundamental question.” But he never presented any definitive conclusion of identity. Neither did he try to quantify the probability of identity. To be sure, he did state that the hairs had matching colors and microscopic features. But the reviewers did not deem this conclusion improper or unacceptable. Somehow the conclusion became “invalid” because Stombaugh explained that he was not overly concerned with how the hair had come to entangled with the thread. This event, he said, was not a problem for him to consider because his task was strictly limited to ascertaining whether there was a possible association between that hair and the sample of known hairs from the defendant. Considering this testimony about “the origin” in context, it hardly seems like an egregious example of “pseudoscience” or the like.

2

The second instance of “invalid science” reported in 2014 was a 1999 laboratory report of Robert Fram, an examiner in the FBI Lab Hairs and Fiber Unit. At this point in the post-conviction proceedings, the district court had ordered the FBI to ship the hairs to the Armed Forces DNA Identification Laboratory for mitochondrial DNA testing. Fram documented the contents of the slides and sample being packed up and sent. During this process, he examined a glass microscope slide marked “19 1/2 L2082 Q96 PMS,” which contained four hairs. He observed that:
A forcibly removed Caucasian head hair found on one of the Q96 resubmitted glass microscope slides . . . exhibits the same microscopic characteristics as hairs in the K2 specimen. Accordingly, this hair is consistent with having originated from KIMBERLY MACDONALD, the identified source of the K2 specimen.
Fram also stated in the report that “[h]air comparisons are not a basis for personal identification.”

Again, condemning these observations as erroneous seems harsh. Although the phrase “consistent with” is far from ideal, no one seems to doubt that the hair truly was “consistent with” the little girl’s, and MacDonald did not contend that it originated from anyone else.

3

In response to MacDonald’s original 1990 Petition for Post Conviction Relief, FBI laboratory analyst Michael Malone studied one hair found near Colette MacDonald. Malone was to become notorious for giving false or dubious testimony in other cases (Earl 2014). In this phase of the MacDonald case in 1991, however, he simply wrote that:
This hair [Q79] was compared to the pubic hair sample of JEFFREY MACDONALD (specimen K22). This hair exhibits the same individual microscopic characteristics as the pubic hairs of JEFFREY MACDONALD, and accordingly is consistent with having originated from JEFFREY MACDONALD.
Like Fram, he added a qualification. But where Fram cautioned that “[h]air comparisons are not a basis for personal identification,” Malone noted that “hair comparisons do not constitute a basis for absolute personal identification.”

Despite the addition of the word “absolute,” on their face, these statements do not seem to “state[] or impl[y] that the evidentiary hair could be associated with a specific individual to the exclusion of all others,” and they do not “assign[] to the positive association a statistical weight or probability or provide[] a likelihood that the questioned hair originated from a particular source.” Finding matching physical features is consistent with the proposition that the hair was MacDonald's. At the same time, “hair comparisons do not constitute a basis for absolute personal identification” -- the match does not exclude everyone else in the world. Thus, Malone's statements do not seem to be scientifically invalid (at least with respect to the two criteria in the DOJ's letter).

Rather, the legitimate concern is psychological -- without a literal statement that the observed similarities are also consistent with the possibility that the hair was not MacDonald's, the reader might give the match more weight than it logically deserves. This misconstruction of the report by a lay reader is certainly possible, and I would not want reports about hair matches to be written like Malone's and Fram's were. But this objection is different than dismissing the findings as invalid on the theory that the statements in the report logically imply that the only individual in world who could have been the source of the hair was MacDonald. In reaching the latter conclusion, the DOJ may have gone too far.

Microscopic hair comparison is only a rough indicator of identity. Many people could share the same characteristics. But this limitation does not make the field fraudulent. Many disease symptoms, for example, are overinclusive when used to make a diagnosis, but that fact does not render them invalid or worthless as diagnostic criteria.

Likewise, the consistency that Malone reported was not sufficient to establish to a near certainty that the hair was MacDonald’s rather than an intruder’s. In fact, the later mitochondrial DNA testing excluded MacDonald, his wife, and his children as the source of the hair. Consequently, Malone’s reported similarity could have been false (if Malone did not make accurate observations, or if he lied about what he observed). Or, perhaps the Q79 hair was physically similar to MacDonald’s, as Malone said, but it nevertheless originated from someone else. As MacDonald and Fram explicitly stated, physical similarity alone is probative but not definitive of identity.

References

Related Postings

Saturday, March 21, 2015

The Junk DNA Wars

This month, the New York Times' published a report on “the junk DNA wars” asking “Is Most of Our DNA Garbage”? 1/ Readers of the article (and an anonymous follow-up piece on the reactions appearing in science blogs) 2/ would come away thinking that there is a serious debate in the scientific community over the proposition that “junk DNA” is “mostly functional.”

Without defining terms like “functional” and “junk,” however, it is impossible to know what is in dispute and what is not.The follow-up piece is particularly frustrating. It observes that
Some scientists, like T. Ryan Gregory, a evolutionary biologist ... argue that if DNA is mostly functional, then it’s hard to explain why rather humble species, like the onion, have far more DNA than we do. ...
Those who disputed Gregory’s findings [sic — Gregory did not discover the long-standing C-value paradox 3/ ], including supporters of intelligent design, cited the Encode Project, an N.I.H.-sponsored attempt to catalog the functional elements of the genome. Encode scientists found that 80 percent of the genome had “biochemical functions,” suggesting that there was a lot less junk DNA than scientists had thought. But did “biochemical function” really mean anything?
For many scientists, it didn’t. A University of Toronto biochemist, Larry Moran, wrote that “the general public has been snowed by the Encode publicity campaign and by naïve journalists who have enthusiastically reported that junk DNA is dead.”
But the Times' writers did not explain why “many scientists” are not snowed by the 80% statistic. After reading some of the ENCODE papers and the surrounding (typically hyperbolic) publicity, I concluded that:
The ENCODE papers show that 80% of the genome displays signs of certain types of biochemical activity—even though the activity may be insignificant, pointless, or unnecessary. This 80% includes all of the introns, for they are active in the production of pre-mRNA transcripts. But this hardly means that they are regulatory or otherwise functional. Indeed, if one carries the ENCODE definition to its logical extreme, 100% of the genome is functional—for all of it participates in at least one biochemical process—DNA replication.

That the ENCODE project would not adopt the most extreme biochemical definition is understandable—that definition would be useless. But the ENCODE definition is still grossly overinclusive from the standpoint of evolutionary biology. From that perspective, most estimates of the proportion of “functional” DNA are well under 80%. 4/
In short, evolutionary biologists reject "biochemical function" as a criterion for recognizing "junk" because not every bit of biochemical activity affects the reproductive fitness of organisms. (Neither does chemical activity per se show any influence on phenotypes that are related to the healthy functioning of those organisms.) To the evolutionary biologists, the term “junk DNA” means parts of the genome in which the particular DNA sequences (the order of the base pairs) do not have evolutionary significance. The Times article defines “junk DNA” differently, and vaguely, as “pieces of DNA that do nothing for us.” This is not the scientific definition. In fact, the earliest papers on “junk DNA” proposed that much of it might “do something” for us.

The “junk DNA war” (or rather the confusion about the meaning of the term “junk”) has spilled over into the legal realm. A brief that leading genetics and genomics researchers submitted to the U.S. Supreme Court to clarify the privacy implications of forensic DNA typing tried to address it. 5/ These researchers observed that
  • In genetics, “junk DNA” denotes sequences that lie outside of genes and that are not under detectable selective pressure: that such DNA exists is not in doubt.
  • “Junk” DNA sequences could be biologically useful or interesting yet not be useful for disease diagnosis or prediction.
  • ENCODE data do not reveal that anywhere near 80% of the genome contains medically relevant information.
  • The ENCODE findings indicate that the system that regulates gene expression is exquisitely complex, but they do little to change the status of “junk DNA” in general.
As far as I know, these conclusions have not been contradicted by new studies, but I have not conducted a recent literature review and would be grateful to hear of relevant papers that undermine these observations.

Notes
  1. Carl Zimmer, Is Most of Our DNA Garbage?, N.Y. Times Mag., Mar. 5, 2015 
  2. Re: Is Most of Our DNA Garbage?, N.Y. Times Sunday Mag., Mar. 20, 2015
  3. See Sean R. Eddy, The C-value Paradox, Junk DNA and ENCODE, 22 Current Biology R898 (2012)
  4. David H. Kaye, ENCODE’S “Functional Elements” and the CODIS Loci (Part II. Alice in Genomeland), Forensic Science, Statistics, and the Law, Sept. 18, 2012 (note omitted)
  5. Brief of Genetics, Genomics, and Forensic Science Researchers as Amici Curiae in Support of Neither Party, Maryland v. King, No. 12-204, Dec, 28, 2012, reprinted in part in Henry T. Greely & David H. Kaye, A Brief of Genetics, Genomics and Forensic Science Researchers in Maryland v. King, 53 Jurimetrics J. 43 (2013), available at http://ssrn.com/abstract=2403063http://ssrn.com/abstract=2403063. Disclosure statement: I prepared an initial draft of the brief and coordinated the revisions to it.