Defense’s Showing Of DNA Evidence Tests Envelope Of Jury’s Comprehension

By Mark Gutglueck
In the 13th week of the Charles Merritt murder trial, defense attorneys sought to deliver what they hoped would be their coup de grâce, scientific proof that three individuals other than Charles Merritt were in contact with the four McStay family corpses as they were crudely interred into two shallow graves in the desert area between north Victorville and Oro Grande.
In presenting that evidence, the defense team used three impressively credentialed experts in the realm of DNA collection, DNA processing and DNA analysis, each of whom demonstrated the integrity of the means by which the data presumed to be highly favorable to the defendant was derived.
Nevertheless, the absolutely arcane nature of the subject matter involving what even for those well-versed in scientific methodology is a barely comprehensible formula for the way in which genetic material is sequenced and differentiated left questions as to what degree members of the jury fully understood and appreciated the substance of the testimony they were hearing.
In the case of People vs. Merritt, prosecutors allege Charles “Chase” Merritt, had engaged in a series of thefts from Earth Inspired Products, the company owned and operated by his business associate, Joseph McStay. Through that company, Joseph was selling high end decorative water fixtures – artificial waterfalls and fountains – which Merritt designed and manufactured out of steel, glass, rock and other components based upon the specifications outlined by the company’s customers and passed along to Merritt by McStay. The prosecution’s theory, presented during the initial nine weeks of the trial that began on January 7 of this year, is that Merritt by early February 2010 was in a state of economic desperation brought on by his gambling addiction and utter lack of financial discipline. At that point, the prosecution maintains, Merritt fraudulently obtained access to the QuickBooks accounting system McStay had set up for the Earth Inspired Products enterprise and pilfered thousands of dollars by issuing himself a series of checks.
When he learned of what Merritt was up to, either shortly before or perhaps even on February 4, 2010, Joseph McStay traveled to Rancho Cucamonga, where Merritt was then living, and confronted him about his larceny, threatening to alert authorities, prosecutors allege. After Joseph McStay returned to San Diego County, the prosecution’s theory continues, Merritt that evening drove to the McStay residence in Fallbrook where he killed Joseph McStay, his wife Summer and their two sons, four-year-old Gianni and three-year-old Joseph, Jr.
Merritt then secreted the bodies for two days, in the meantime again fraudulently accessing Joseph McStay’s QuickBooks account for Earth Inspired Products, the prosecution maintains, and on February 4, 2010, February 5, 2010 and again on February 8, 2010 issued himself checks made out to himself for at total of $23,855.
Merritt then transported the corpses up into San Bernardino County’s High Desert, an area with which Merritt was familiar from having grown up in Hesperia and attended Apple Valley High School for three years in the 1970s, according to prosecutors. It was in that spot where on February 6, 2010 he buried all four along with the hammer he had used to bludgeon his victims in shallow graves he dug in a wash off a rarely-traveled dirt road, according to the prosecution. To confuse the situation, throw authorities off his track and delay a serious investigation into the matter, the prosecution maintains Merritt then drove the McStay family’s 1996 Isuzu Trooper, which yet contained the child seats for Gianni and Joseph, to San Ysidro, where he left the vehicle in a shopping center parking lot roughly a quarter of a mile from the Mexican border.
Suzanna Ryan, a crime laboratory and forensic laboratory manager employed either previously or currently with Bode Cellmark Forensics, Inc., Bode Technologies, Pure Gold Laboratories, and her own company and laboratory, Ryan Consulting, testified last week.
A portion of her testimony had outlined the function of the so-called M-Vac system, a device used for the collection of DNA evidence, which entails what is essentially a vacuum unit augmented with a hose, a line to spray sterilized water upon the item from which the collection is being made, a vacuum head, a containing unit and a filter, all of which are sterilized beforehand and used only once to prevent contamination. After spraying the item from which the possible DNA is to be collected with the sterile water, which is intended to serve as a buffer and liberating agent for DNA-containing material, and applying the vacuum to draw in the liquid from the subject item, the filter through which the liquid was drawn is dried, a portion of which is cut out and then subjected to a DNA analysis. Ryan testified that the M-Vac has been demonstrated to provide “20 times to 200 times more DNA than is collected by” traditional methods of DNA extraction used on porous materials.
Ryan testified that she utilized the M-Vac on eight items taken from inside the graves, as well as two items found outside the graves which she and the defense team collectively deemed to be of potential relevance to the case and then sent those items off to a laboratory run by Bode Technologies for analysis. It was subsequently determined that two of the items, a piece of cloth found outside of, and at a significant distance from the graves and a glove had no relevance to the case. Some level of DNA was detected on five of the eight remaining items, but at a level that was below Bode Technologies’ analytical threshold. She then recommended that the defense team provide the five items to another firm, Cybergenetics, which utilizes probabilistic genotyping to make interpretations of low level mixtures of DNA that are difficult or impossible to catalog or compare using manual methods of DNA analysis. Ryan testified that probabilistic genotyping is increasingly being used by both public and private crime laboratories as an acceptable method of interpreting minute quantities of DNA, partial DNA or DNA mixtures.
She said the science and methodology of probabilistic genotyping and the software utilized to accomplish it have been audited and accredited against the FBI’s quality assurance standards and has met the guidelines authored by the authoritative body, the Scientific Working Group On DNA Analysis Methods.
Jim McGee, one of the primary members of Merritt’s defense team, asked Ryan about what could be done to make sure that the process of analyzing items extracted from the gravesite for the DNA they might contain was not compromised by contamination or cross contamination from the DNA of the members of the sheriff’s department who excavated the graves. She said there was or should have been a protocol to eliminate the possibility of contamination and that DNA profiles of those working at the gravesite could be developed for comparison purposes, such that if one of the members of the sheriff’s department was the source of DNA on an item, the “results could be compared against department personnel to rule out contamination. If you know who has handled a particular item or come into contact with it, there should be a pretty easy way to then double check and make sure that person’s DNA is not on an item of evidence.”
Under both direct examination by Merritt’s defense attorney, James McGee, and cross examination by Supervising Deputy District Attorney Sean Daugherty, Ryan responded to questions about the survivability of DNA that had been buried in the earth as long as the items under consideration had been, alongside, above, under or proximate to the DNA-bearing bodies of the victims. Enzymes from the decaying corpses and their breakdown into what she termed decompositional fluid could eradicate the DNA, Ryan indicated, but she said DNA that was not directly in contact with the bodies or the decompositional fluid might remain intact.
Christina Nash, a senior DNA technical analyst with Bode Technologies at its corporate laboratory and headquarters in Virginia testified on Tuesday of this week.
She gave an overview of the processes used in the laboratory in handling submitted materials which are believed to contain DNA, stating that the company uses instrumentation on the material that has been collected including “genetic amplifiers.” Upon sufficient amplification, Nash said, “We then separate out the fragments we want to see,” consisting of a profile of alleles, which are forms of a gene, a basic genetic component located upon a DNA chain. She said each step of the process is documented as taking place “according to the validated and tested procedures we have to stick to to obtain consistent and reliable results.”
Bode’s instrumentation, which among other tasks utilizes electrophoresis to separate macromolecules based on size, will render, Nash said, a read out of the alleles and genetic markers in whatever quantity or intensity that they register, at levels both above, at or below the analytical threshold the lab has set. The lab will record results below its analytical threshold, but that in order for Bode to initiate an interpretation of those results, the markers have to register above the analytical threshold, which is measured in relative fluorescence units.
Bode, Nash said, received on March 12, 2018 multiple M-Vac filters that had been mailed to the laboratory, which she said were received and processed individually by technicians wearing protective clothing functioning in a secured and sterile laboratory environment. The DNA extraction, quantification, amplification and separation protocol was used, whereupon the product was subjected to a genetic analysis, which included seeking results at 21 locations along each DNA strand along with the two locations that indicate male sex identification. The electropherogram produced was used to visualize the peaks of the DNA profile. The raw data produced from the instruments was analyzed to determine how many alleles could be identified and if the profile was suitable for comparison to a known DNA sample. If such had been the case, she said, the data would have been submitted for such a comparison.
All standard operating procedures were utilized, Nash said and applied to the M-Vac filter from which potential DNA from an electrical cord had been collected. She said the data that came back was below Bode’s analytical threshold and the lab could not obtain any likely comparable data.
The procedure was applied to the panties found in the grave with Summer McStay. No DNA was detected by the laboratory’s instrumentation, Nash said.
When the procedure was applied to the left bra cup, Nash said, the DNA analysis did turn up data in that alleles at nine loci on the DNA strand were detected. The level of data was below the lab’s analytical threshold, and no comparison to any known profile could be performed given the laboratory’s standards.
When the procedure was applied to the sweatpants found in the grave with Summer McStay, there were no results and accordingly no interpretation could be made because the data fell below the lab’s set threshold.
Upon the procedure’s application to the M-Vac filter upon which was lodged possible genetic material from a white cord found in the grave wrapped around Joseph McStay, less than 0.01 nanograms of DNA was found, which included an allele at a location on the DNA strand indicating the contributor was a male. Nash indicated, nonetheless, that given Bode’s analytical threshold, there was not enough DNA present to say the sample represents a male’s presence, and Bode deemed it to not be comparable to any known samples overall, even though some of the allele peaks met an analytical threshold. The results were partial, and thus could not meet the laboratory’s guidelines.
No profile and neither male nor human markers were found on the M-Vac filter from an attempted extraction from a red strap found outside of the grave after it was subjected to Bode’s protocol.
When the procedure was applied to the M-Vac filter to a portion of the red strap found within Joseph McStay’s grave, there were results indicative of a partial profile that fell below Bode’s analytical threshold, Nash said, “of which we could not make any conclusion other than a potential male contributor. It was too low of a level to be confident. That is why we made this a partial [result].”
The processing of the filter that trapped DNA material from the cut right bra cup and its accompanying strap found outside the grave resulted in a partial DNA profile indicating a mixture of two contributors, at least one of which was male, according to Nash. “There was at least one male contributor, but it was at too low of a level,” she said. “It didn’t reach the threshold we have set, so we can’t be confident.” She said for her lab to perform a meaningful analysis beyond what she could report, “All of the alleles should be present.”
Based on the partial results that Bode found on five of the items, they were sent to Cybergenetics, which utilizes probabilistic genotyping to analyze problematic DNA samples, specifically where there is a mixture of DNA or DNA present in levels so low that it defies analysis using traditional means. Probabilistic genotyping utilizes biological modeling, statistical theory, computer algorithms, and probability distributions to calculate likelihood ratios and infer genotypes of a DNA profile.
Mark W. Perlin, who holds two doctorates and is a medical doctor, is the chief scientific and executive officer of Cybergenetics, based in Pittsburgh, Pennsylvania. He developed the algorithmic formulas used by Cybergenetics, known as TrueAllele, to derive the DNA profiles. Upon TrueAllele having been used to to identify the perpetrators of several crimes, Perlin and Cybergenetics were sued by the advocates of those convicted as a consequence of TrueAllele to force the disclosure of the algorithmic formula Perlin has fashioned to verify its authenticity and accuracy. After a prolonged court battle to protect what he considered to be proprietary information, Perlin relented, and TrueAllele has withstood all attempts to disprove its validity, such that it is now being recognized in ever-widening circles as a means of making DNA match-ups.
Perlin gave his analysis of the likelihood of there being a match-up between the DNA found on the five items in and around the grave and the four McStay family victims and Charles Merritt.
Very little in the way of comparison DNA from three-year-old Joseph McStay, Jr. was available because at some point during the three and a half years from the time the murders occurred until the graves were discovered in November 2011, his body had been dug up by predatory animals, most likely coyotes, such that only the top of his skull and eight bones had been recovered. Much more complete DNA profiles of his brother and parents are available. As a consequence, across all efforts to exclude Joseph McStay, Jr. as a contributor to the DNA on the items found in the grave, the lack of known alleles in his profile make ruling him out less statistically certain than with the others.
According to Perlin, the likelihood that the DNA extracted from the electrical cord found in the grave with Joseph McStay matches Joseph Joseph McStay is one in 115,000; that it matches Summer McStay is one in 499,000; that it matches Joseph Jr. is one in 2.1, that it matches Gianni McStay is one in 302,000 thousand; and that it matches Charles Merritt is one in 101.
Perlin said there is substantial statistical support for the conclusion that Charles Merritt is excluded as the contributor of the DNA on the electrical cord. Perlin said all five – the family members and Merritt – were “far removed from the matched statistics.”
With regard to the second piece of evidence he dealt with, the left bra cup, Perlin said there is substantial statistical support for the conclusion that all five were excluded from being the contributors to the DNA found on that item. The likelihood that the DNA on the left bra cup matches Joseph McStay is one in 239 million; that it matches Summer McStay is one in 487 trillion; that it matches Joseph Jr. is one in 15.7, that it matches Gianni McStay is one in 23.7 million; and that it matches Charles Merritt is one in 1.75 trillion.
“This is strong exclusionary support,” said Perlin. “It’s none of these people statistically.” Of Merritt, he said, “It is very unlikely he contributed DNA to that bra cup.”
The third piece of evidence Perlin took up was the white cord found in the grave with Joseph McStay.
A match between the DNA collected from the white cord and Joseph McStay, Sr.’s DNA is one in 16,400; for Summer McStay the ratio is one in 182 million; for Joseph McStay, Jr. one in 113; for Gianni McStay one in 4.24 billion; and for Charles Merritt one in 19 billion.
Of Merritt, Perlin said, “It shows statistically he is excluded.”
With regard to the DNA found on the red strap, Perlin said, “Again we get exclusionary statistics that point away from all five references. For Joseph McStay, Sr. the number is one in 1,550; for Summer McStay it’s one in 6.45 million; for the first McStay child [Joseph, Jr.] it’s one in 4.06; for the second McStay child [Gianni] it’s one in 4.39 million; and for Charles Merritt the exclusionary statistic is one in 1.76 million.”
With regard to the right bra cup Perlin said, “Again we have exclusionary statistics. On those numbers, the likelihood ratio match statistic for Joseph McStay, Sr. is one in 224,000; for Summer McStay it’s one in 2,850; for the first McStay child the exclusionary statistic is one in 20.6; for the second McStay child it’s one in 10,100; and for Charles Merritt it’s one in 3.06 million.
In her testimony under direct examination by McGee last week, Ryan had offered a counterpoint to suggestions made by the prosecution much earlier in the trial that it was Merritt who had driven the McStay family’s Isuzu Trooper to San Ysidro shortly after the family’s disappearance. With regard to the consideration that Merritt’s DNA had been found in the Isuzu Trooper, Ryan testified that the consideration that Joseph McStay was the major contributor of the DNA found on the steering wheel and gear shift of the vehicle suggested he was the last one to have driven it. That Charles Merritt was a trace DNA contributor on the same items, with Merritt’s DNA being present in a far greater quantity on the vehicle’s passenger side interior door handle, was an indication that Merritt was a passenger in the Isuzu and not the driver, Ryan said last week. Her belief that it was unlikely that Merritt had driven the vehicle from the McStay home in Fallbrook and left it at the parking lot in San Ysidro, where it was impounded on February 8, 2010, was based on her knowledge of experiments indicating that the last individual to handle nonporous items such as a pen and a steering wheel, if they do so for any extended length of time, are likely to displace the normal user of those items as the primary or major contributor of the DNA found on those items once they are subjected to an analysis.
“If someone drove a car for 90 minutes, the expectation would be that they would be the major contributor,” Ryan testified on Thursday of last week.
She also testified that trace amounts of DNA can be transferred to items the contributor of that DNA has not actually handled as a consequence of the person who directly handled the item in question having touched or been in contact with the trace DNA contributor.
Ryan testified that the presence of Merritt’s DNA in the Isuzu Trooper in minute quantities could reasonably be considered an instance of DNA transfer throughout the vehicle.
This week, Daugherty sought to subject her assertions with regard to the indirect distribution of DNA to question.
“Years ago you testified that the transfer of skin cells is actually questionable,” Daugherty said to her during cross examination.
“The transfer of skin cells is questionable?” Ryan said with skepticism at the premise of the question audible in her voice. “The secondary transfer of skin cells is questionable,” she repeated, sizing up the sentence. “I’m sure I said that sometimes it occurs and sometimes it doesn’t because that’s still the case today. We know that sometimes secondary transfer occurs. Sometimes it doesn’t. In fact, [with] primary transfer, sometimes we can detect DNA from somebody directly contacting something, and sometimes not.”
“Because that depends on a lot of different factors,” Dougherty said.
“Absolutely, yeah,” Ryan responded.
“The substrate being touched,” Daugherty continued.
“Yes,” Ryan responded.
“The shedder status of the person touching it,” Daugherty said.
“Yeah, but that’s a little controversial,” Ryan said. “Some people think there’s good shedders or bad shedders. There is definitely a concept of good shedders or bad shedders.”
“The type of contact and the duration,” said Daugherty. “The part of the body. Would that be a factor?”
“The duration,” Ryan said in affirmation. “What do you mean the part of the body?” she asked.
“In other words, the hand or leg vs. some other body part,” said Daugherty.
“Hmmm,” said Ryan. “I don’t know if there’s any specific studies that talk about differences in the amounts of DNA based upon body part.”
“Whether the person touching something used gloves,” Daugherty said.
“Yes,” said Ryan.
“And in this case, you have none of that information,” said Daugherty.
“That’s very true,” Ryan said.
“So you are assuming when you say that maybe there was some kind of handshake or something, you are making an assumption that handshake happened,” Daugherty said.
“Well, it doesn’t have to be a handshake,” Ryan said. “There can be secondary transfer from objects, as well,” Ryan said.
“But let’s take the handshake scenario again, okay? said Daugherty.
“Alright,” said Ryan.
Daugherty’s dwelling on handshaking stems from the defense’s contention, which was made during its opening statement on the first day of the trial, that the minute amount of Merritt’s DNA in the Trooper was a consequence of the defendant having shaken hands with Joseph McStay when the latter departed for home in Fallbrook after having driven to Rancho Cucamonga for what the defense says was a business meeting on February 4, 2010, which the prosecution says theorizes was not a friendly meeting but rather a sojourn by Joseph McStay to confront Merritt over fraudulent checks he had written against the Earth Inspired Products account.
“You have to assume that there was a handshake that occurred in order for someone else’s DNA or my DNA to transfer to another object,” Daugherty said.
“Okay, assuming we are discussing a handshake, yes,” Ryan said.
At that point, Daugherty propounded the idea that Merritt may have worn gloves while making the drive to San Ysidro or perhaps attempted to clean the car’s interior surfaces after making the trip.
“And you’re assuming in this case the Trooper wasn’t wiped down,” Daugherty said.
“Well, yes,” Ryan said. “I think the evidence supports that because there was DNA detected.”
“Does wiping down eliminate all DNA?” Daugherty asked.
“It would greatly reduce the amount of DNA present,” Ryan responded. “Even with a dry cloth it can greatly diminish and reduce the amount of DNA present. It might not get rid of every last bit of DNA.”
Daugherty then cited the consideration that there was a very low level of anyone’s DNA found on the inside driver’s side door handle in the Trooper to suggest that it had perhaps been wiped down.
After Ryan read from the investigative report relating to the analysis of the Trooper done by the sheriff’s department scientific investigations division, she said, “I would agree it is definitely a very low level of DNA.”
Daugherty asked if that was consistent with someone having cleaned or wiped the door handle.
“It could be, sure,” responded Ryan.
“There is also a very low level of Merritt’s DNA on the steering wheel,” Daugherty said.
“It’s a low level, but it’s not unusual to find a lower amount of DNA from a touched object,” Ryan said. “So, the other was about ten times lower than this particular sample.”
“You said you would expect if the person drove the vehicle 90 minutes that they would become the major contributor [of the DNA on the vehicle’s steering wheel],” Daugherty said.
“Right, and again that is going to be based upon the studies that were cited and the fact that it’s a harder surface. It’s not cloth, for example,” Ryan said.
“And an assumption the person didn’t wear gloves, right?” Daugherty asked.
“That was driving the vehicle?” Ryan questioned back. “Is that what you are asking? Sure, yeah.”
“And an assumption that the person didn’t try to wipe it down or clean it off in any way, right?” Daugherty asked.
“Right,” Ryan responded.
Ryan said that the concept of indirect transfer of DNA has recently come into vogue in the scientific community, based upon studies relating to it, which accounted in some measure for her having become more enlightened on the issue. She said studies have indicated that DNA transfer by touch has multiple levels including “secondary, tertiary and quaternary.”
As well versed, authoritative, experienced, composed, seemingly well-prepared and articulate as Ryan, Nash and Perlin were and as germane as the information they had to offer was, there remains a question as to how effective they were as witnesses. This is in large measure because of the profoundly intricate and oftentimes impenetrable nature of the advanced level of science related to DNA analysis, made more challenging still by the terminology and phraseology involved.
In addition to the recondite nature of the major issues being explored in most of this week’s testimony limiting the impact the content of that testimony might have had on the jury, the defense encountered other issues that may have undercut it with the jury. Throughout the trial, and particularly during the prosecution’s phase of the case, the defense on multiple occasions proved successful in expanding the context surrounding the evidence and testimony brought forth by the prosecution and the prosecution’s witness. This has often redounded to the prosecution’s disadvantage and in favor of the defense, often because it has left the impression with courtroom observers, and perhaps members of the jury as well, that the prosecution is being highly selective in its presentation, presenting only a portion of the whole story, and on occasion hiding the truth, particularly when the details left out mitigate in Merritt’s favor.
As the defense was putting its side of the case on this week, the prosecution on three occasion was able to lodge suggestions that it was the defense that is hiding the ball.
Daugherty, in his cross examination of both Ryan and Perlin, sought to imply that as defense witnesses they had obscured, hidden, ignored or overlooked evidence that related to the possibility that Merritt’s DNA was in the gravesite or the actuality it was contained therein.
After Ryan testified that she had advised the defense on what items to use the M-Vac on to obtain potential DNA evidence, Daugherty asked, “Your testimony on Thursday [April 4] was that you were the one who made the request for several items from the graves to be tested, right?”
“I mean it was in conjunction with the attorney,” Ryan responded, saying she had done so knowing there was low level DNA found on some items. “I did suggest, ‘Listen, we’re seeing some DNA, if we use the M-Vac we might have a better chance of getting results.’”
“And you made that decision on what you felt the perpetrator would actually grab or hold onto, etcetera, right?” Daugherty asked.
“Right, that was one of the thoughts, yes,” said Ryan.
“Where the actual perpetrator would [bring] friction or some kind of force to the object, right?” Daugherty asked.
“Right, yes,” Ryan said.
“And you also included Summer’s clothing because there was some kind of suggestion she had been sexually assaulted,” Daugherty said.
“I don’t know if she was sexually assaulted,” Ryan said. “I know her clothing were found, interestingly, not on her body.”
“And you felt those items might have been handled by the perpetrator.” Daugherty said.
“Right,” said Ryan.
“So you picked items like an electrical cord, right?Daugherty asked.
“Yes,” said Ryan.
“A couple of different electrical cords, right?” asked Daugherty.
“Yes,” said Ryan.
“And a tie-down strap, right?” Daugherty asked..
“Correct,” Ryan said.
Daugherty then brought out and laid before her the three-pound Stanley sledgehammer that had been used to bash in the skulls of the four members of the McStay family, which had then been discarded into the grave with Summer McStay and Gianni McStay.
“Did you request that item?” Daugherty asked.
“No, I did not,” Ryan said.
“That’s something the perpetrator would have handled, right?” Daugherty asked.
“Actually, to be honest, I don’t know if I requested this particular item or not,” Ryan said. “Yes, it would be something that was handled.”
“You certainly didn’t receive it, right?” Daugherty asked.
“That’s true,” Ryan said.
“And it isn’t on the list of items requested, right?” asked Daugherty.
“I don’t know,” Ryan said. “I don’t have the list of items requested. I definitely didn’t test it. One of the reasons I would say is that the M-Vac is better for porous items, things with ridges. So, it could have been tested, but we did not. You’re correct.”
“There are ridges on the handle,” Daugherty pointed out.
“There are some ridges on the handle, yes,” Ryan said.
Daugherty also questioned Ryan about an allele with a designated 24 marker, corresponding to Merritt’s, which Bode Technologies indicated had shown shown up on the left bra cup.
Daugherty verified with Ryan that Bode’s results were inconclusive and did not make any matches to anyone. He asked Ryan, “Did you compare the results to Mr. Merritt’s profile? The ones you got from Bode?”
“I did look but I can’t use the data because it’s below the analytical threshold,” Ryan responded.
“Did you look at the ones that were below the analytical threshold?” Daugherty pressed.
“I probably did,” said Ryan. “Yes.”
“Probably an important thing to do, right?” Daugherty asked.
“I looked at the data, yes,” Ryan said.
“So you looked at the results from Bode that were reported and they were below the analytical threshold, right?” Daugherty asked.
“Yes,” said Ryan. “Sure.”
“Did you look and compare those to Mr. Merritt’s known results?” Duagherty asked.
“If I did, it is not something I would testify about because it’s not based on their guidelines,” Ryan said. “Their guidelines are stating these results are partial, that they’re not useful for comparison purposes.”
“But they reported certain alleles at certain locations, right?” Daugherty said.
“Yes,” Ryan conceded.
“And some of those locations had alleles matching Mr. Merritt,” Daugherty said, without making reference to the second allele contained in the gene he was referencing.
“Objection, your honor,” McGee said. “Now it goes beyond the scope.”
“Sustained,” ruled Judge Smith.
Daugherty took the issue up with Perlin when he was on the stand.
On Wednesday, during his cross examination of Perlin, Daugherty brought up the presence of a 24 allele extracted from the left bra cup, according to the data delivered by Bode Laboratories. There is a 24 allele in Merritt’s DNA sequence.
Referencing a printout, Daugherty said, “23 here is a reported location.”
“That’s the allele of that peak,” Perlin responded.
“The allele of that peak,” Daugherty repeated. “24: See that?”
“Ah, yes, I do,” responded Perlin.
“Has a length of 333.8,” Daugherty said. “Is that accurate?”
“That’s what’s written here,” Perlin said.
“That’s what TrueAllele is saying, right?” Daugherty asked.
“That’s what the analyze program is providing as input, correct,” Perlin said.
“And a peak height of 7?” Daugherty asked
“Yes,” said Perlin.
“And the area under the peak which isn’t used is two,” said Daugherty.
“Correct,” said Perlin.
“The 23 is reported on the allele chart,” said Daugherty. “And the 24 is not, right?”
“Yes, based on genotype probabilities,” Perlin said.
“So you have two different representations of alleles with similar length, similar peak height, one’s reported and one isn’t,” said Daugherty.
“I’m trying to think of how to explain this to you,” Perlin said. “The data comes in as alleles. You see a pattern, an electropherogram. That data isn’t a genotype. It’s just data. It’s a reflecting of what’s in the biological sample. The computer then looks at that data, tries explaining it a hundred thousand different ways, follows the laws of probability, and when it’s done produces a genotype probability distribution based on prior prevalence of genotypes as well as how well those patterns constructed out of combinations of genotypes explain the data. That’s also listed in this case report. And then looking at those possibilities a list of alleles for data base search purposes, not for statistical or reporting purposes, is produced. So, an emphasis on alleles is basically holding the same point. The alleles come in as data with different heights. For a CODIS,[Combined DNA Index System, a DNA data base kept for known criminals by the FBI] search for a data base, it only knows about alleles. The FBI’s CODIS data base doesn’t know about genotypes and probability, so we have to put it in that form. What is important would be the genotypes, which is the distribution of allele pairs and their probabilities as well as the match statistics that are valid match statistics calculated from those genotypes when a comparison is made. So, it’s true there are alleles of the data that are not relevant to genotypes or match statistics in this processing. It’s true that there are alleles in a data base format that is designed to search the CODIS data base that doesn’t understand about probability, but that’s not what’s being reported for the purposed of inferring genotypes or comparing them to calculate a matched statistic.”
“The data’s not important,” said Daugherty.
“Your characterization of the alleles as being primary is an old way of looking at things,” Perlin said.
“And it’s the way it’s accepted in all but what?” Daugherty asked. “About ten labs that use TrueAllele?”
“They don’t look at the allele approach that you do, no,” said Perlin.
“Why did you use the allele term?” Daugherty asked. “For the purpose of conducting a data base search,” responded Perlin. “Since the FBI’s data base doesn’t use, yet, the concepts of allele pairs and probabilities, we have to put it into a 20-year-old form that’s just based on human review and thresholds. That’s how the data base functions. So, we have to retrofit it to an old approach from the FBI’s data base as anyone else would have to in order to even conduct a search. That search, if it returns profiles, would be the starting point for calculating accurate match statistics using genotype probabilities, but the alleles are not part of that. It’s genotypes, which are probability distributions over the allele pairs and the ratios of probabilities to calculate match statistics.”
“When you reported it in its older format as you characterized it, you didn’t report the 24 allele.”
“Are you referring to the allele list?” Perlin asked.
“Yes,” said Daugherty.
Perlin said what data he produced was contained in the report.
“Your testimony here is the data here, even though it is quite similar, 24 doesn’t explain the data,” said Daugherty. “That allele doesn’t happen.”
“If you look at the actual probabilistic genotype that was produced on page 297 you can see what the computer did actually produce based on the data it received, its model and the prior prevalence of alleles.”
“Of the four known samples that you were given, do you care to take a guess as to who is the only 24?” Daugherty asked. “Can you objectively infer who is the only 24?”
“I would have no idea,” said. Perlin “I wouldn’t speculate.”
“Do you have it on the sample?” Daugherty asked.
“The computer compares the known reference,” said Perlin. “We have whatever the computer produced.”
“Do you get the electronic data for the known samples?” Daugherty asked, irritation audible in his voice.
“We sometimes get it as lists and we sometimes get it as electropherograms,” said Perlin. “I can check to see which it was in this case.”
After looking at the sheaf of documents before him, Perlin said, “The reference samples were sent to us as reference tables, so it would be in text format,” Perlin said.
After further back and forth between Daugherty and Perlin, Daugherty sought to settle the discrepancy between the categorizations done by Bode Laboratories and Cybergenetics with regard to the left bra cup. He again angled to get Perlin to acknowledge that a portion of the DNA found at the gravesite corresponded to the defendant’s profile, but that pursuit diffused into a melange of technospeak that was impossible for a layman to parse.
“At that location the TrueAllele software called three different Alleles,” Daugherty said.
“TrueAllele does not call alleles at that location based upon a user viewing preference that’s higher than what the computer saw to unclutter the picture at 10 RFU [relative fluorescence units],” Perlin said. “That’s what you’re seeing. The computer considered more data than what is labeled in the boxes here.”
Daugherty than provided Perlin with a chart pertaining to the left bra cup that had been generated by Bode Technologies.
“I see a picture with gray bars and data and so on,” said Perlin. “I don’t know what it’s from. It’s not part of the TrueAllele system.”
“Does this case number here under sample name match the case number you received from Bode?” Daugherty asked.
“Yes, it’s the same sample name,” Perlin said.
“E03 is one of the samples you recognize?” Daugherty asked.
“Yes, it’s the same sample name,” Perlin said.
“Now you see here where it says bin for 15 allele, bin for 18 allele, bin for 20 allele? What’s a bin?” Daugherty asked.
“A bin, in this type of software, which is not ours, would be a range of sizes where, based on calibration data that’s done during a DNA testing run, would place a size an allele as being in the bin or not in the bin, based on whatever algorithms were used on the data.”
“And then when you get the data at Cybergenetics, you actually have a different bin?” Daugherty asked. “Three different bins for the data?”
“We don’t have bins in that sense,” said Perlin. “What we do, as I explained to you earlier, is that True Allele converts the sizing data, the pixels that are seen, using two different types of calibrations that are present in forensic runs, one run together with all the tests, and one called allelic ladder run in a different lane, but is part of the same machine and then it provides a number like 153.7, estimating what the length is of that DNA fragment. So, it uses more of the data, more of the calibration data, and a more sophisticated way to identify what are the sizes of the samples. The method that you’re showing here looks like perhaps it lacks the allelic ladder as part of an integrated math. But I don’t know. I don’t know what this is,”
“So the short answer is you don’t know what it is?” Daugherty asked the scientist.
“It looks like a primitive sizing algorithm from software I don’t use,” said Perlin. “I know some of what it is, but I couldn’t tell you the math behind what it’s doing.”
The defense also called Kathy Sanchez as a witness this week.
Sanchez is Summer McStay’s second cousin and the first cousin of Summer’s mother, Blnche Aranda.
Sanchez was utilized to undercut the prosecution’s contention that the McStay family was killed in their Fallbrook home. Investigators for the San Bernardino County Sheriff’s Department investigating the homicides believed that had been the scene of the murders and in obtaining a search warrant for the McStay premises stated that a cloth around Joseph McStay in the grave appeared to be a futon cover taken from the McStay home.
The defense contends the murders did not take place in the McStay home and that the claim that the material wrapped around Joseph McStay in the grave was the futon cover was a fabrication, and that the investigators knew so, because the futon covers remained at the McStay home after the family’s disappearance. The defense maintains that the investigation was botched and predicated on both mistakes and purposeful misrepresentations to propel a biased investigation into Merritt and Merritt alone forward.
Under questioning by McGee, Sanchez testified she had gone with Blanche Aranda at the invitation of Joseph McStay’s mother, Susan Blake, to help clean up the McStay family’s two-story home located at 3473 Avocado Vista Lane in Fallbrook at some point after the family’s disappearance in 2010. She was not precise as to the date, but remembered the weather as warm, placing the time at late spring or summer. She testified that she entered house through the back sliding door when Blake let her and her cousin in and that Tracy Russell, Summer’s sister, was also there.
She undertook to clean upstairs, she said.
“I was doing laundry,” she said, including the boys’ clothes, as well as “vacuuming upstairs” and cleaning the sink in the downstairs bathroom, cleaning the refrigerator. She said they had “straightened up the kitchen.”
While there, she said, she noticed a handprint on the outside of a window at the back of the house.
She testified that Susan Blake had said she had washed the futon covers, and that when she had retrieved one of the futon covers it was damaged. “It looked like it was falling apart,” she said, indicating she believed washing it had caused the cover’s fabric to start to unravel.
She attempted to put the futon covers onto the futon mattresses, which she said consisted of styrofoam with cotton wrapped around them. She said the fabric of the covers was “beige and woven.” Because the covers had shrunk from the washing, she said she struggled in trying to stuff the mattresses into them. “It wouldn’t fit,” she said, and related that she had folded the mattress “like a taco” to see if she could get it into the cover. She remembered that the futons had a large mattress almost but not quite the size of a small twin mattress as well as a smaller pillow. There were two mattresses and two pillows, she remembered, and two mattress covers and two pillow covers. The covers had zippers, she said. She had found the covers in the laundry room, she said.
On August 20, 2014, some four years later, Sanchez was interviewed by then-detectives David Hanke and Ryan Smith, who were investigating the homicides. They questioned her about her efforts with Arranda, Blake and Russell to clean the house and, in particular, the futon covers, a subject they went over several times. The interview took place in a vehicle. She said she provided drawings of the home as she remembered it to the detectives.
Under cross examination by Deputy District Attorney Melissa Rodriguez, Sanchez said she had not seen Susan Blake wash or dry the futon covers.
After Sanchez’s testimony, McGee called Ryan Smith, who is now a sergeant to the stand. Smith is the current case officer for the McStay family homicides and is the sheriff’s department’s liaison to the district attorney’s office during the trial. He has testified several times previously in the case.
Sergeant Smith testified that Sanchez was questioned by Hanke but that he had written the report.
McGee gave Smith the third degree about discrepancies between what Sanchez had said in the interview, which was recorded, and what he wrote in the report.
“How many times did you go back to the futon cover with Ms. Sanchez after you moved on to other topics? McGee asked.
“I believe its maybe four or five times we speak about the futons in this interview,” Sergeant Smith said.
The report states in part, “Sanchez located several cases for the futon upstairs in the unoccupied room These covers were not for the large portion of the futon and were only for the pillows.”
“That’s all you wrote on the futon cover, correct?” asked McGee
“I believe in the next paragraph I mention them again,” said Sergeant Smith, and he then read, “She observed several covers which she believed were for the futon on the top of the washer.”
“And that the drier was empty,” said McGee.
“Correct,” said Smith.
“But you kept out the important part, that she tried to put them on, right?” McGee asked.
“Objection, argumentative, relevance,” said Deputy District Attorney Melissa Rodriguez.
“Sustained,” said Judge Michael A. Smith.
“Why did you not put in your report that she was trying to put the larger cover on the mattress?” McGee asked.
“Objection, relevance,” said Rodriguez.
“And argumentative,” said Daugherty
“Overruled,” said Judge smith.
“Well, when I speak about the futon in Ms. Sanchez’s interview, I put that she tried. To quote my report, ‘They were not for the large portion.’ And I based that on her statements that it didn’t fit. And I also put, again referring to page two, the second paragraph, that ‘They were for the pillows.’ Again, that’s based on the totality of her interview.”
“So, she told you it was for the mattress, but you decided she was wrong and you wrote your opinion in the report instead,” McGee said.
“Objection, argumentative,” Rodriguez said.
“Sustained,” said Judge Smith.
Sergeant Smith said Sanchez’s drawings were booked into evidence.
“The reason you went over the futon issue with her several times is because she didn’t appear to be clear, did she, in terms of what she was putting covers on?” Rodriquez asked Sergeant Smith on cross examination. “Do you agree with that?”
“Correct,” Sergeant Smith said. “Her statement that the futon cover was tight and didn’t fit made us wonder if she actually got them on or not.”
On redirect examination, McGee assailed Smith with “You kept questioning Ms. Sanchez about the futon cover because her rendition of the facts, that it was in the house still didn’t match all the search warrants you guys wrote, saying the futon cover was wrapped around Joseph.”
“Objection, assumes facts not in evidence,” said Supervising Deputy District Attorney Britt Imes. “Not relevant.”
“Objection sustained on both relevancy grounds and assumes facts not in evidence,” Judge Smith ruled.
“Isn’t it true your department in the investigation of this case were tying the gravesite to the Fallbrook house, saying the futon cover was…” McGee began.
“Objection, argumentative, assumes facts not in evidence,” said Imes.
“Overruled,” said Judge Smith.
“…the futon cover was wrapped around Joseph?’ McGee finished.
“That was one of the suspicions, we had,” Sergeant Smith said. “I think I testified about this previously, as well. We can’t say for sure it was the futon cover wrapped around Joseph. I’m not aware of any specific positions. There are some comparisons that we made, and it is odd that the futon cover was missing. However, I’m unaware of any specific report saying this cover at the grave is the futon, because we weren’t able to say yes or no.”
“Did you review Sergeant [Joseph] Spears’ review on the summary of the physical evidence of the crime scene in the house?”
“Objection, relevance,” protested Rodriguez.
“Overruled,” said Judge Smith.
“No, I didn’t read Sergeant Steers’ report,” Sergeant Smith responded.
“So when you said you weren’t aware of any reports that said that, you hadn’t read them all,” said McGee. “Would that be fair to say?”
“Objection, argumentative,” said. Imes.
“It’s fair to say I haven’t read every report in the case,” said Sergeant Smith.
“Did you read all the search warrants?” McGee asked.
“Objection, relevance,” Rodriguez said.
“Sustained,” Judge Smith said.

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