Sorry. Why don't you just--in terms of my hypothetical, why don't you just assume that you handled the swatch, swatches that were collected an hour, hour and a half before you got to the laboratory first and then the other sample second.
You did--plastic bag no. 1, you handled from the--that was the one that contained the swatches an hour, hour and a half old.
Right? Plastic bag no. 2 came from the samples that were seven hours in the plastic bag from the dirty surfaces.
Okay. So as I understand this now, somebody's taking what I would call a culture tube? Is that the right size?
Test tube. They're sticking that tube into a plastic envelope to capture the swatch into that tube?
A wet swatch. I would say one should change gloves between those two sets, yes.
KEY QUOTEWell, if you--I mean, the other thing about blood is, it's very visible, and one may look at the gloves and see whether or not there was any visible contamination that way.
You didn't change gloves. Are you saying, Mr. Sims, that that's the kind of laboratory practice that you would engage in?
Now, let's talk about--let's turn to--like to go actually to I think it's F, the one that's F. Yes. Now, samples that come from a victim and samples that come from a suspect, assume they're blood swatches.
All right. Let's try this. Would you agree that items of evidence collected from suspects should be handled separately from evidence samples?
I don't know the protocol by number, but if you read it to me, I'll let you know or you show it to me, I'll--
Well, now wait. We have to back up. When we're talking about examining them, there may be some cutting. I'm sorry. I agreed with you too quickly on that one.
And in your protocol, does it not state that in general, the examiner should examine only one item of evidence at a time.
And in particular, items of evidence collected from suspects should be examined separately from victim samples.
And that's a practice that your protocol indicates will guard against sample mix up and cross-transfer?
And you think that's an important precaution to take against cross-contamination, don't you?
So in terms of this logo which we don't intend to have--clip-art's limited and it's not supposed to look like men's room and women's room, all goes. But you agree with this principal that one should separate suspect, victim samples?
Now, wouldn't you agree that of extraordinary importance is the need to handle reference samples, be it from a suspect or victims, separately from evidence samples?
Just in terms of--would you try to keep separate the taking of any blood from a reference sample in terms of the time and place from the examination, cutting or handling of an evidence sample?
By that, do you mean, for example, preparing a swatch of the reference stain or the reference sample?
Well, I don't--I don't know if it's a cardinal rule, but it is an important concept, yes.
I do agree and I do practice that the DNA extraction will be separated in time from the reference samples against the evidence samples, but the PCR setup of evidence samples, it says, "should be performed at a separate time from the DNA extraction PCR setup of reference samples." I--I don't--I don't follow that. Usually what I do is, I put the evidence samples first in a set that I'm going to be doing the PCR analysis on and then I get to the evidence--I'm sorry--the reference samples last along the stream so that you don't start upstream with the reference samples. Instead, they're downstream from that process. But I do extract them separately, yes. I agree with that part of that.
All right. Let's start with this. So it is--you would agree that it is important that "DNA extraction--"
"DNA extraction of evidence samples be performed at a separate time from DNA extraction of reference samples"?
And this precaution will help prevent potential cross-contamination between evidence samples and reference samples?
Now, you're familiar with the California association of crime lab directors open proficiency tests in 1988 and `89?
And you have studied the factors that led to false positives by different DNA laboratories that participated in that open proficiency test?
All right. Are you aware--have you familiar--without going into the content yet, have you familiarized yourself with the circumstances surrounding false positives obtained by the Cellmark laboratory?
All right. With respect to false positives arising from RFLP testing, when a laboratory is handling, at the same time, reference samples from a suspect and evidence samples, are you aware of false positives ever arising in that context?
I--when you were that specific, I couldn't recall that. I--I am aware of sample mix-ups, but I wasn't sure of the actual what got mixed up with what.
Well, before you came in here to testify, Mr. Sims, you were watching this proceeding on television?
When Dr. Cotton was testifying, weren't you upstairs in the Prosecutor's office watching television in terms of her testimony?
I watched some of it in my hotel room and I watched a little bit of it when I was upstairs. But most of the time that I'm upstairs, I'm not watching the television.
In your reading in terms of forensic DNA testing, have you read literature concerning false positives on the CACLD tests?
Objection. It's irrelevant, calls for hearsay, 721 of the evidence code, your Honor.
Were the false positives in the CACLD tests a matter of concern to people in the forensic DNA community?
Objection. It's irrelevant, calls for hearsay, 721 of the evidence code, assumes facts not in evidence.
I believe it was a false positive, although it may have been a false negative. I'm not sure, but he did have a problem on one sample I recall.
Cellmark, my understanding, was using RFLP. Dr. Blake was using PCR DQ-Alpha in the--a different dot blot format than is used now.
Did you hear Dr. Cotton's testimony with respect to how the false positives arose in the CACLD tests?
In your review of the literature with respect to the CACLD open proficiency tests, did you become aware of a false positive arising when samples, evidence samples were handled--
With respect to handling reference samples the same time in the same area as evidence samples, all right?
Isn't that a particularly dangerous practice because the reference sample has a high concentration of DNA in the whole blood?
Objection. It's compound, same time and area, it's vague, same time and area, particularly dangerous practices.
Now, again, could you--when you describe the same--is it what, the same time and the same place? Is that what you're saying?
Yeah. You discussed before--remember you saying pouring out a reference sample and making a card in the same area--
And one of the reasons it's not a good idea is that the reference sample contains a high concentration of DNA in the whole blood?
A microliter of blood contains how many nanograms high molecular weight DNA would you estimate?
Yes. That would be about 20 nanograms, something like that, per microliter because it's about 20 microliter--or I'm sorry--about 20 micrograms per mil. So you're taking it down--that sounds right. About 20 nanograms per microliter whole blood.
And did you hear Dr. Cotton's testimony with respect to how much DNA was in the evidence lane of item 52 in her RFLP test?
All right. Are you aware of how much DNA was in the reference lane for 52 in the Cellmark RFLP test?
If there's cross-contamination of microliter particle blood to a swatch, that could cause as much as 20 nanograms, 25 nanograms high molecular weight DNA to be on a swatch?
In our laboratory, the limit we would test would be down in the--what we would call 300 picograms which is 0.3 nanograms.
Could you see the amount of blood that it would take to--for--from which one could get--what did you say? How many picograms could you do?
Well, I think, make it a little clearer, from a bloodstain that's about a millimeter by a millimeter, you could get about two nanograms. So that's 2,000 picograms. So I think that gives you an idea of how small we're talking about. It's--
The size of a particle of blood that could create--from which you could extract 300 picograms of DNA, would that be visible to the naked eye?
I think it would be visible, but it would be a speck. I mean, it's--it's--it's very small.
Now, and the amount of speck of blood that would give you two nanograms, it's pretty small too?
Well, now, again, that's about a millimeter by a millimeter, and that's pretty small, but it's very--it's visible, very visible.
Another precaution that one takes to prevent cross-contamination is not to do PCR processing on multiple samples at the same time?
The next process, once you've got it in the tube, is to go through the actual extraction of the DNA.
Well, in our laboratory, we do that by a procedure that involves placing the--or adding to that swatch, that stain a solution that has a soap, a detergent actually in it and an enzyme that chews up the protein, and that--that releases the DNA, and then that excess protein is removed by organic reagents, and then we do a purification step through a ultracentrifugation through a membrane.
Just visualizing it then, you take a piece of that extract, you put it in one of these little microfuge tubes?
And some of these tubes are the ones that you were talking about before that you were calling reagent blanks?
And when you're talking about some of those substrate controls, those would be those little tubes, but they would be the--the substrate control swatches, not the evidence specimen swatches?
All right. And you would also--you mentioned something, what you called a quality control, correct?
And then after you do what you call the extraction process, putting the swatches in the tubes and adding the ingredients, what's the next stage?
Well, then after you've got that process, you end up with a solution that has just the DNA. And so then the next stage would be the evaluation of the DNA as far as quality and quantity.
All right. Or sometimes we've have had a discussion of something called a yield gel, right?
And that's a method by which you get an assessment of the total amount of DNA in the sample?
All right. And just so we understand what a yield gel, yield gel tells you the total amount of DNA, but it doesn't tell you whether that DNA is bacterial or human?
That's correct, unless you do another procedure where you blot that gel and test it.
All right. And another procedure one can perform after the yield gel is a--what you call a southern transfer?
And by--that's literally one of those like the RFLP gels or those little agarose--it's a little agarose gel?
And those little bands, depending on how intense they are, give you some understanding of how much human DNA as opposed to bacterial DNA you have?
All right. Now, if you're doing a slot blot and you're doing 20--and you try to--withdrawn. Each stage of this procedure, whatever you're doing, you're going to do to all those different tubes?
After you do the slot blot or the yield gel or the southern transfer to that stage, what's the next stage?
Well, then you would move into the typing stage, and that would be, for example, the RFLP setup, which is the restriction, or if you did PCR, that would be the amplification of the DNA.
All right. And if it were PCR, the amplification of DNA, you take those test tubes and you stick it into that thermocycler machine?
All right. And if you were--and if you were doing "x" number of tubes to the extraction, the slot blot--then the next thing when you did the amplification, you would take it and do it with the same number of tubes, right?
Yes. I mean, assuming you're going to do that with all the tubes, right. I mean, in other words, you're treating them as a group, yes.
And when you amplify them up, sometimes that's referred to sometimes as amplification run?
Now, in terms of this process, is it a good precaution to limit the quantity of samples you do in a single run to a manageable number?
All right. How many of these samples did you do at one time, the most, in this case?
The--the greatest number of samples that I analyzed at one time--and this would include the stains and the substrate controls plus a QC sample and an extraction blank--these were all from the Bronco, and I believe the number is 21.
KEY QUOTEThat--I can tell you I think if you look on page 34 of my notes. Yes. That was on September 21st, 1994.
And you're familiar with the amplitype user guide recommendation in terms of samples?
15 sounds close to the right--but you have to recall that when you do this kind of test, you're really limited to the amplification of about 16 samples. Actually not the amplification, but the typing, you're limited to about 16 at a time. So that might be the number that they're discussing, because you would have to include a positive and negative control.
Now, would you agree that when performing all the operations that we talked about in terms of processing samples, it's important not to rush?
That the opening of a tube, popping of the tube and the creation of an aerosol has been known to cause cross-contamination in this process?
Do you know if the popping open of the tube can cause an aerosol which creates cross-contamination in this process?
Yes, I'm aware of that, and that's why we always spin our tubes down, so that won't create that aerosol problem. So we always spin a tube down before we pop it open.
Because just the touching of the top of these tubes and then the touching of the next one can cause that kind of--can cause cross-contamination?
Well, not so much from the outside of the tube. I mean, it's not that there's a problem with it on the outside. As long as you spin that down, that's the main thing, that you don't have any liquid up near the top of the tube. I think that's what you mean.
Your Honor, actually, looking at h and looking at the clock, before I go into H, this might be a good time to take a break.
Okay. Ladies and gentlemen, we are going to take our break at this point. Please remember all my admonitions to you; don't discuss the case amongst yourselves, don't form any opinions about the case, don't conduct any deliberations until the matter has been submitted to you, do not allow anybody to communicate with you. Mr. Sims, you can step down, and we'll take a 15-minute recess.
I would say one should change gloves between those two sets, yes.
That is a cardinal rule, isn't it?
On a good day, yes.
The greatest number of samples that I analyzed at one time...were all from the Bronco, and I believe the number is 21.
I lost the train anyway, so go ahead.