Post on 20-Jan-2019
TRANSCRIPT OF PROCEEDINGS
SCR 2014 0007
SUPREME COURT OF VICTORIA
CRIMINAL JURISDICTION
MELBOURNE
FRIDAY 21 APRIL 2017
(3rd day of hearing)
BEFORE THE HONOURABLE JUSTICE EMERTON
DIRECTOR OF PUBLIC PROSECUTIONS v. CLINTON JAMES TUITE
VICTORIAN GOVERNMENT REPORTING SERVICE7/436 Lonsdale Street, Melbourne Vic 3000 - Telephone 9603 9134161889
Pages 230 - 280
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HER HONOUR: Morning, Dr Taylor. Good morning counsel.
.DM:DF:CAT 21/04/17 SC 11A 230 DISCUSSIONTuite
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<DUNCAN ALEXANDER TAYLOR, recalled:
WITNESS: Perhaps just before we start, it might help me and
hopefully help the court if I just summarise several
points there were still left open from yesterday and
perhaps have the material I sent last night relates to
each of those points.
HER HONOUR: Yes, that would be of assistance.
MR DESMOND: My friend - - -
HER HONOUR: Dr Rogers, do you want to - - -
DR ROGERS: I just want to clarify something with Dr Taylor
first.
HER HONOUR: Yes.
DR ROGERS: Dr Taylor, you sent a couple of papers by email to
me last night and indicated that you were working from
memory and you wanted to check whether you were correct
with sending the papers on the points that you were asked
about yesterday?---Yes, that's right.
I haven't given Mr Desmond copies of those papers because I was
waiting for you to, perhaps improperly, to email me this
morning to say "yes, they were the correct papers"?---Oh,
I see, okay. All right. Yes, they are the correct
papers, but if that now makes it difficult for Mr Desmond
to respond to perhaps what I am going to answer we can
defer the explanations to a later date.
HER HONOUR: Can we go through what the papers are just for the
record, please?---Certainly. So - - -
DR ROGERS: Can I just - - - ?---One of the - - -
Sorry?---Go on.
One of the papers that you sent me was called, "Population
genetic analyses of NGM STR loci"?---Yes.
And the authors, the first author is Bruce - - - ?---Bruce
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Bedoli.
Yes. The second is "Analysis of global variability in 15
established and five new European standard set STRs using
the CEPH human genome diversity panel" by Phillips and
others?---Yes, that's right.
And there was the addendum to the PCAST report, got that,
Mr Desmond has got that, and the fourth is - - - ?---Yes.
- - - a paper entitled "Factors affecting peak height
variability for STR data" by yourself and others?---Yes,
and there was also an additional paper matching and
partially matching DNA profiles written by Bruce Wier.
I don't have the Wier one here. I'll get a copy made for
Mr Desmond.
HER HONOUR: I received two of those - - - ?---Okay.
- - - five last night.
MR DESMOND: I got two.
HER HONOUR: I received the factors affecting peak height
variability and the addendum, but not the other
three?---Okay.
DR ROGERS: So there's, if I hand over these two to Mr Desmond
now, make copies for Your Honour and get the Wier article
done as well and I will have that brought to court.
HER HONOUR: All right. How is it proposed that the witness
deals this material in view of the fact that Mr Desmond
hasn't had these materials, although they were materials
that he called for, not by name, but as I understand it,
Dr Taylor has respond to a request from Mr Desmond.
DR ROGERS: Yes.
HER HONOUR: To provide material that shows this or that.
DR ROGERS: Yes.
HER HONOUR: And this the material.
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DR ROGERS: But my memory, Your Honour, is that the only one
that Mr Desmond wanted overnight was the PCAST addendum.
HER HONOUR: Right, okay.
DR ROGERS: So- - -
HER HONOUR: All right. Mr Desmond.
WITNESS: Shall I proceed then with the open items from
yesterday?
HER HONOUR: All right. Now can I just hear from counsel about
this, Dr Taylor.
MR DESMOND: My submission, Your Honour, would be, I have no
objection to either my friend leading or Dr Taylor giving
viva voce evidence-in-chief, as it were, on this fresh
material. I'm fairly slow to absorb information in these
sort of comprehensive reports. It wouldn't suit my
purposes to simply stand the matter down for an hour or
an hour and a half or whatever. My approach would be if
there was a need for some further pre-trial
cross-examination at a later date, whether it was
immediately before a jury trial commenced or at some
convenient date otherwise that would be the best
approach. It may be there would be no need, but I can't
just stand up and cross-examine on these just quickly
reading them. I need to cross-reference.
HER HONOUR: I think it would be useful to hear from Dr Taylor.
MR DESMOND: Yes, I don't object.
HER HONOUR: As to what the material is and how it answers the
queries that were raised.
MR DESMOND: Yes ma'am.
HER HONOUR: You don't have any difficulty with that?
MR DESMOND: No difficulty with that.
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HER HONOUR: All right, thank you. And Dr Rogers, would you
like to lead this evidence?
DR ROGERS: No, Your Honour.
HER HONOUR: You are quite happy for Dr Taylor simply to give
the explanation.
DR ROGERS: Yes, Your Honour. I have not spoken with
Dr Taylor, I have no idea what he plans to say, I have
just had that short email contact with him thanking him
for the documents.
HER HONOUR: Dr Taylor, I would like you will please to say
what it is that you want to say about these papers and
the issues that you feel were left open
yesterday?---Certainly. So one of the issues that was
left open was whether or not calibration data using
single source, what we call pristine DNA, generated in a
lab, or extracted within a lab, could then be applied to
mixed DNA profiles or case work DNA profiles. To respond
to that particular point, or to give some demonstration
of an empirical study that addresses that point was the
purpose of the paper, factors affecting peak high
variability for short tandem repeat data. All right. I
will just put that to one side for the moment and go
through the other open topics.
So that's about extrapolation?---What was that?
That's about extrapolating from single source to complex
mixtures?---Yes, that's right.
Thank you?---The second topic that was left open from yesterday
was whether or not it's a valid practice to multiply
likelihood ratios at each locus in order to obtain a
likelihood ratio for the entire profile and the request
was for some empirical data that demonstrated that this
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was a valid practice, so for that particular point I've
submitted the Bruce Wier paper entitled "matching and
partially matching DNA profiles".
Yes?---And then there was an extension to that conversation
when I mentioned that those loci are considered to be
unlinked because they are on separate chromosomes and the
extension was that in new DNA profiling systems there are
some regions that are, in fact, on the same chromosome,
so the question arose whether or not it was still valid
to multiply the locus likelihood ratios at those loci in
order to obtain an overall profile likelihood ratio and
in respond to that point are two papers I've submitted
entitled, "Population genetic analysis of the NGM STR
loci which was lead authored by Bruce Bedoli and then the
other paper with quite a long title authored by C
Phillips. Now, if you like, having just outlined the
purpose of those papers, I can go into more detail about
how those papers demonstrate the practices that we carry
out are fit for forensic use. I am happy to do that now
if you would like.
Yes, I think it would be useful to have that evidence now.
That might assist the parties in their reading of these
papers. Any difficulty with that?
MR DESMOND: No ma'am.
DR ROGERS: No, Your Honour.
HER HONOUR: Go ahead Dr Taylor?---All right. I'll start off
with the first point which is extrapolation of
calibration data based on single source profiles and then
to be extrapolated for use on mixtures and case work
samples, and this is, as I said before, using the paper
"factors affecting peak height variability for short
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tandem repeat data". Within that paper, or within the
work that led to that paper, myself and John Buckleton
and Jo-Anne Bright had a look at the peak height
variability that we obtained using STRmix for what we
call pristine single source DNA profiles, that is, single
source DNA profiles obtained from reference DNA, so it's
of good quality and not degraded, and by an analysing
those profiles, or a set of those profiles, we obtained a
certain level of peak high variability. Now within this
paper, amongst other things that we were looking at, we
were addressing two questions, one which was, can that
use of pristine reference DNA be extrapolated for use on
case work DNA, and secondly, could that use of single
source peak high variability model be extrapolated out to
mixed DNA profiles. Now, without trying to summarise the
entirety of the work, I'll perhaps just say that we found
that, yes, indeed as you would expect, the validation
data, or the pristine single source data could be
extrapolated out in these ways and when you are reading
you through this paper I would direct your attention to
the material on p.133 of that paper, that's the last
page, and about halfway through the discussion material,
the conclusion that we found is, "In general we found
that pristine DNA has approximately the same peak high
variability as case work samples, this result is
consistent with earlier work, and I reference some
earlier work which also found that pristine reference DNA
profiles could be used to develop models for case work
samples" so that addressed the first point. The second
point in conclusion we came to was looking at whether or
not single source profiles could be extrapolated out to
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mixed profiles, and I conclude that "Mixed DNA profiles
are likely to be no more variable in peak height and
perhaps less so than single source DNA profiles. There
are two points to consider here", and I won't read out
the points, but those points really go to the fact of why
we use single source profiles for validation rather than
mixed profiles, and that being that it's a lot harder to
extract the validation material we need from mixed
profiles because they are more complex and there's more
considerations we have to make, so this is why we
typically use single source profiles, but at the end
there I say, "Even given these two points the results
shown in figure 4 of this study do not indicate an
increase in peak high variability in mixtures compared to
single source profiles", so this indicates there are no
issues, validating systems, using pristine DNA to develop
and refine DNA profile behaviour models, so this is our
empirical demonstration of that ability to extrapolate
from single source to mixed profiles. Is there any
questions on that particular paper?
I presume in this, you conducted an empirical study here, you
actually did a whole lot of comparisons?---We actually
did comparisons on this pristine single source profiles.
We also did empirical studies on case work samples and on
mixed samples to compare them.
All right?---I am happy to leave it there unless there's any
questions and move on?
HER HONOUR: No. Any questions?
DR ROGERS: No, Your Honour.
HER HONOUR: No, thank you?---Okay. The next point I will
bring up relates to the Bruce Wier paper, which you don't
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have there but that looks, or that speaks towards the
ability to multiply individual locus likelihood ratios to
obtain an overall profile likelihood ratio. I feel like
at this point it might be good just to go through a very
brief section of population genetics just to explain how
these markers are used within forensic science and then
lead up to the result of paper. So, when we want to know
the rarity of a DNA profile in a population we will
generate a population database of individuals which is
some subset of the population and we will look at the
rarity of various alleles or components that make up a
profile within that database and use that to come up with
the rarity of the profile in the population. In order to
do that we make assumptions regarding the population, and
if we look at the simplest model, we say first of all
that we can multiply individually all frequencies within
a locus in order to determine genotype frequencies for
that locus, and that assumes requires what is known as
Hardy-Weinberg Equilibrium within the population, that is
to say that the population adheres to a number of
assumptions such as it is infinite in size, there is
random mating, there is no selection, there's no
migration and there's no mutation. Okay, so there's five
assumptions that underlie that simple model. We then
wish to multiply the genotype frequencies at different
regions in order to obtain an overall profile frequency
and that requires an additional assumption and that is
that the population is in linkage equilibrium and that
linkage equilibrium has the be additional assumption that
the population has undergone an infinite number of
generations since some disturbing population force such
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as a genetic selective sweep taking out individuals in
that population that contained certain types of DNA or an
admixture of two population that come together, or a
recent contraction and then expansion in population size,
so these sorts of disturbing forces will throw loci into
linkage disequilibrium. Now as you might expect with me
listing out those particular assumptions human
populations don't adhere to those assumptions, very
simply our population sizes aren't infinite, we don't
randomly mate with people in the population, we tend to
choose people from the same ethnic background or
religious background or geographical area. There is
selection, there is migration, there is mutation, so
human populations do violate the assumptions underlying
these simple models, and in fact whenever a population
database is compiled for use in forensic science, and
this would be the same for the databases that Victoria
have used for their calculations, those databases undergo
a validation procedure which looks for signs of
dependencies within a locus and between loci, so they
check the population for Hardy-Weinberg Equilibrium and
linkage equilibrium, now quite often they find there are
dependencies in the data, and that's okay, it's okay for
three reasons. One is that we expect a certain amount of
false positive indications of dependencies just based on
the way that the tests that are used work, it's fine
because we expect human populations to violate these
assumptions, and it's also fine, and probably most
pertinent to our particular discussion, because when we
carry out forensic calculations we incorporate what is
known as a co-ancestory coefficient, or sometimes in
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forensic science it is called an FST value, or a Theta
value, you may have heard this in evidence before, and
the use of this co-ancestory coefficient in the
particular models that we use to determine a profile
probability no longer require assumptions of
Hardy-Weinberg or linkage equilibrium. So that's the
background to population genetics. I can now turn to the
paper by Bruce Wier and in that paper what he did was
look at the levels of matching and partially matching DNA
profiles within a database and he came up with a set of
formula to calculate how many matches or partial matches
you expect within that database and he compared that to
how many matches you observe in that database. Now the
method that he used to come up with the expected number
of matches made the assumption that you could multiply
the matching probabilities across the different loci, so
what you would expect is that if the observed and the
expected - that observations of these matching and
partially matching profiles in the database, if there was
close alignment between them that, then that assumption
that you could multiply those locus matching
probabilities to obtain a total would seem to be a valid,
it would be a good description of how the population
genetics were working in these databases. So when you
come to read that paper on p.2 at the very bottom of the
page there is a passage which says that, "The values
shown in the figure" - and he is referring to figure 1
here - "for a Theta value of zero", so this is even not
taking into account that level of co-ancestory within a
population, "are those for the product rule, and they
assume that all ten of the alleles in the five locus
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profiles are independent. There is good overall fit of
these to be observed numbers with some sets of loci
having more matches than expected and some having less",
so this is indicating that the method that is used to
estimate the number of matches and partial matches is in
good alignment with a number that are seen, and by
implication then you can multiply these matching
probabilities across loci.
Okay?---That's the second topic dealt with. If you are happy
once again for me to continue I will take about the
linked loci now.
Yes, move on?---All right. With the linked loci there were the
two papers that I gave to you, the paper of Phillips and
the paper of Bedoli, and what they did was look at a
number of populations and they carried out some of these
tests for dependence or independence and particular tests
for linkage equilibrium or disequilibrium and they were
concentrating on two loci that are the closest together
on the same chromosome and they are two loci named VWA
and D12S391, both of which are you are PowerPlex 21
profiling kit. So they were interested to see whether or
not it was still valid that you could multiply the
individual locus likelihood ratios for these two regions
in particular because they had the highest chance of
violating that ability. All right. When you're reading
through the Bedoli paper, if you look at p.109, almost
the second paragraph of the page there is a passage that
says, "The tests for evidence of linkage disequilibrium
detected no more departures than would be expected by
chance", and then he details those results.
"Furthermore, there were no departures detected for the
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two sintenic (?) loci VWA and D12, even after a
correction. This observation is consistent with a
finding of Phillips, which is the other paper, and
supports that for identity testing multiplying the
genotype frequencies is justified for the loci DWA and
D12S391". So that paper has shown empirically that once
again you can multiply these locus matching probabilities
to obtain an overall likelihood ration for the whole
profile, even given these two loci which are on the same
chromosome, and the Phillips paper I have supplied
because it's referenced in this Bedoli paper and goes a
bit more into the population genetic detail. So that's
really all I had to say on those papers.
Good. Thank you, Dr Taylor. Mr Desmond, are you ready to
continue with your cross-examination.
<CROSS - EXAMINED BY MR DESMOND :
MR DESMOND: Yes, Your Honour. Doctor, just in reference to
that first issue, how many studies did you do on
individual pristine sources for that paper, when I say
you - - - ?---I'll just have a look.
You, the joint collaborators for the study?---Okay. So when we
looked at the case work samples we examined 136 case work
samples to compare to our models produced by the pristine
data.
But how many separate pristine samples were looked at for the
purpose of your model?---All right. So we looked at a
number of different pristine - - -
What's the number?---I - - -
You can have that on notice and supply the information, you
know, via email?---That's all right. There's table,
because we looked at a number of pristine data sets, in
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total it would be over 1,000 pristine samples, and then
136 case work samples and 93 mixed DNA profiles.
93 mixed, and the definition of mixed for that particular
purpose was it restricted to a minimum of three
contributors or was it two or more?---I think that was
from two to four contributors.
Two to four. At what rations, do you have the detail at what
ratios for each of the 93 broken into those for 2, those
for 3 and those for 4, which would be a long answer, but
does it contain that information?---Not within this
paper, but it references another paper which has all that
information set out in the table.
Sorry, this paper, I thought this paper was the primary source
for the comparison of the pristine sources to the then
case work?---That's right. We used the we used the mixed
DNA profiles that were also used in another study as the
comparison material in this study.
I just want to be clear. Your team was hands-on in actually
doing, working with the mixed samples and the case work
samples, or you were relying upon the results concerning
the mixed samples from an earlier study?---We were
hands-on. The mixed samples were from an earlier study,
or were from an earlier study that I conducted, so they
were mixed samples that I was hands-on in interpreting.
Do either of the papers detail the breakdown as to the number
of two, three and four that presumably add up to the 93
mixed samples and their ratios?---Yes.
Okay. The paper you've got or the paper it refers to,
references?---The paper refers to.
Can you give me the name of it?---Yes, I can.
So I can find it in due course?---That was a paper that was
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authored by myself called, named "Using Continuous DNA
Interpretation Methods to Re-visit Likelihood Ratio
Behaviour".
What's the publication details is that FSI or - - - ?---That is
in Forensic Science International Genetics 2014 Issue 11
p.144 to 153.
Okay, thanks. Just moving on to the, dealing with the
multiplication issue, and the assumption I think I've
noted what you said, you can multiply independent allele
frequencies, and this is an application of the
Hardy-Weinberg principle?---Yes.
And to do that there must be linkage equilibrium?---Well,
linkage equilibrium is between locus dependencies, so if
you are using a simple model where you just apply the
allele frequencies then you are making that assumption of
linkage equilibrium being present, but as I said, we
don't make that assumption in forensic calculations
because we use an FST value, or a Theta value in our
calculations.
Just dealing with first principles. Do you need linkage
equilibrium to apply, if I call it, the product rule,
that is the multiplication rule, across loci?---The
product rule assumption linkage equilibrium.
Linkage equilibrium, do you accept a definition a condition in
which genomes are composed of a random composition of
gamuts?"---Yes, okay, yes.
Linkage disequilibrium. Do you anticipate this definition, it
would mean that knowledge of a genotype at one locus
gives at least a statistical - I can't read my word,
statistical something as to the genotype of the other
locus?
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HER HONOUR: "Probability"?
MR DESMOND: Could be, Your Honour, you might be able to fill
in the word I am looking for, doctor?---"Probably" would
be all right, and yes, that's a reasonable definition.
Okay. All genotypes, do you say, sorry, all alleles, do you
say are they encountered in the population database, or
population databases?---Are you asking is every allele
that's in the population present in the population
database?
Yes?---No, no, they are not.
What about perhaps "extremely rare" alleles, some of those
might be missing from the population databases?---That's
right.
So just going back to linkage disequilibrium. That can exist
because either of population substructure or being of
physical linkage?---Yes.
Can you give me some example of physical linkage such as
degradation, I'm thinking?---When they're talking about
physical linkage in this context they're talking about
the two loci that you are interested in being physically
linked on the same chromosome. Like for example the VWA
and the D123 loci that I went through, they are linked
because they are on the same chromosome.
Sorry, were you finished?---I was just going to say other loci
are on separate chromosomes so they are not physically
linked, however they can still be in linkage
disequilibrium not because of the linkage, but rather
because of population sub-structure, which was the other
effect that you mentioned.
What if all alleles and genotypes across loci are affected by
matters such as degradation amplicon efficiency?---You
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are sort of mixing up concepts here. They have nothing
to do with the population genetics, they are properties
of a DNA profile, we are talking about linkage and
dependency issues within genotypes in the population.
Yes, but if they are matters that affect each individual loci
at different rates then there will be a disequilibrium,
whether they label it as physical or not, there would be
a disequilibrium, that's what I'm suggesting?---No, the
degradation, the problem is the DNA profile like DNA
amounts and degradation are a completely removed topic to
linkage disequilibrium. They have nothing do with it.
Ideally we should know the frequency of every genotype that
might be encountered. Do you agree with that?---That
would be wonderful.
How many genotypes at a locus, one could only say either
perhaps X or K?---You could make an approximation, but
without profiling the entire population you could never
know.
Well, I'm just putting a letter for the unknown, because the
answer is not known, I am calling it K?---Okay.
Can you give me the equation for K?---No, not off the top of my
head.
Thank you. Just given that we have addressed this this
morning, this issue of independence, reviewing
Chakraborty, which now I have to find where I put it. It
will just take me a minute - so if you might be easier if
you turn it up?---Okay.
This is going back to this paragraph 21?---Okay.
But I'm now on p.12 dealing with the paragraph, "In other
words" and you'll see about halfway down?---So this is -
- -
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Page 10, apparently, in your copy?---Okay, yes.
About halfway into that paragraph, "In the same document he is"
- that is a reference to you - "equation 6 reflects the
implicit in his assumption 2 is the supposition that
allele drop out events, these evidence items occur
independently across loci as well irrespective of their
amplicon sizes from which there is no validation date
from the developers of STRmix or proponents of any other
probabilistic genotyping inference procedures". The
clarification, and I am sure you understood it yesterday,
it's not that Chakraborty is saying "the product rule
does not apply", he's clearly not saying that's, he is
not challenging established math?---No, that's right.
What he is saying is that until there is evidence supporting
the proposition that it should apply in this particular
case, or situation, and he's defining that situation as
being where there is, that is, it's dependent upon the
amplicon sizes, so I'll read the top line on my page.
"Since it is almost universally recognised that allelic
drop outs are events mainly due to DNA degradation", I
won't go over that issue with you again, you spoke about
that yesterday, "it's reasonable to predict the drop out
event would occur more frequently for alleles with higher
amplicon sizes within as well as across the loci". So
you understand the proposition he's advocating there? I
know you don't agree with it?---Yes.
But you do understand it, he's saying it's because of this
amplicon size variation across the loci there's no
current evidence to support the proposition that the
product rule should apply. So my question is becoming,
can you identify or nominate, or if you already have tell
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me which it is, empirical support for the statement that
allele drop outs occur independently across loci
irrespective of amplicon size?---All right. I brought up
a couple of these points yesterday, but I'll bring them
up again. The multiplication of drop out probabilities
is an accepted practice for probabilistic genotyping and
has been so and is used in multiple different profiling
systems, I understand that's not addressing your point
about empirical proof of that.
I am more concerned with empirical proof specifically in the
construct of where that multiplication rule is applied
that's said to occur independently across loci
irrespective of amplicon size, that's the caveat I'm
putting on the rule?---All right.
All I am asking for, is there empirical data that supports that
particular assertion that allele drop outs do occur
independently across loci irrespective of amplicon
size?---Okay, so what he's saying is there as DNA
degrades across the profile high molecular weight peaks
are going to be smaller and therefore there are going to
have a higher, probability leave drop out than that low
molecular weight ones. You could also add to what
Chakraborty is saying there, which is to say if you have
two contributors in a profile and one has contributed a
lot of DNA and one has contributed a little bit of DNA
then the person that has contributed a little bit of DNA
is going to be more likely to drop out than the person
who has contributed a lot of DNA, so as well as - - -
Well I can't agree with that, I have to speak to
Chakraborty?---Well, my point is, as well having a
dependence on degradation, there's also a dependence on
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template amount. You could also imagine that if you had
amplification at particular loci that occurred very
poorly, or the peak heights at that locus would be low,
so again drop out might be expected to occur more at
those particular regions so.
I understand what you are saying?---Drop out on amplification
efficiency, so all these things are linked and I guess
the point I'm trying to make is all of those aspects
amplicon size, degradation, template amount, locus
inefficiencies, are all taken into account within STRmix
when it calculates drop out probabilities.
And you said that yesterday?---And if we were to look at
empirical - - -
Studies, data?---Support for the model. You could look in the
paper. Once again I am working from memory here but I
believe in the paper the validation of continuous
interpretation systems which is lead authored by myself
we have a section dedicated to drop out. Within that
section we look at the amount of observed drop out and
the amount of drop out expected from different models.
Some of those models don't take into account amplicon
size and these other factors and you find quite close
alignment with observed and expected levels of drop out.
We also do the same sort of test for STRmix which does
take those things into account, and again you of very
close alignment of observed and expected levels of drop
out, so that's empirical observation that those models
are performing quite well in explaining the drop out
phenomenon.
Well, I am suggesting to you that particular paper does not
offer support for the proposition that allele drop outs
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occur independently across loci irrespective of amplicon
size; what do you say?---Why do you say that it doesn't
prove it?
Well, with respect, you don't get to ask the questions?---I
can't see how having - - -
I understand this becomes sort of conversational, but you say
it does, I am putting you it doesn't?---Okay. I don't
know how we can prevent it from there then.
Well, we will just agree to disagree. But I am not restricting
you, if in the short term there's any other particular
empirical study you wish to rely upon for that
proposition just let the Crown know and they will make it
available to the defence, okay?---I will speak to my
colleagues and see whether they have any ideas.
Okay. Again, given I'm on this point, I might as well address
it now. Your response at p.9 of 20, do you have that
open, sir?---Yes.
The second bullet point concerning with Dr Chakraborty about
four lines in, you identify the mass parameters. So I
will read the relevant part of the paragraph,
"Dr Chakraborty has misunderstood the manner in which
STRmix takes drop out into account. STRmix assumes
independence of peak rights (in drop outs) within and
between loci, given the parameters that describe the
profile", which you collectively describe, or term as
mass parameters, and then you identify the mass
parameters, template DNA, amount degradation locus
amplification efficiency and replicate application
efficiency". Do you have a copy of the STRmix date for
the Tuite case hand with you? You have got a big file
open, sir?---Yes, I believe so.
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I am just, this is just by way of an example. The extended
data that was done by Victoria or you have your extended
data with - because you performed calculations with the
updated version?---I believe I have printed out all the
Victorian calculations as well so hopefully if you refer
to one of them I can find that material here.
For item 1-3 at page - do you have pages F200 F201, they are
handwritten in?---I don't have page numbers to those
effects because I printed out these results from the
computer files.
Are you able to find the commencement of the DCON for 1-3?---I
believe so. This would be the deconvolution, if we were
look to the top of the deconvolution page it would say
STRmix version 1.05 user BEB licence to VPFSD, analysis
Roman 2013 06/05, 1605, 25.
We're ad idem then. Now two-thirds of the way down that page
there's a heading termed "parameters"?---Yes.
Are these the best parameters?---Yes.
Are the mass parameters restricted to this information in this
section?---Yes, so we have the DNA amounts, the
degradation and the locus amplification efficiencies and
the inter PCR efficiencies, they are the mass parameters.
Just if you can turn up your page 9 again of your statement,
the first one you identify as a relevant mass parameter
is template DNA amount?---Yes.
Where is template DNA amount in the listed parameters?---That
is under the heading "DNA amount".
Okay, what is that an anagram - we don't get the
units?---That's, those values there that you have for the
DNA amounts, 997, 199, and 99, don't refer to any
specific nanogram or petagram type quantity of DNA, the
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DNA amounts are used within the context of the STRmix
calculation.
Well from your vow point it will probably be a dumb question
but I want an answer to it. What is the unit, how is
that measured, so that I can get some handle on what it
represents?---I suppose the closest that you would, the
closest description I could give would be that those
numbers describe the amount of fluorescence on the
electropherogram, which is used as an indication of DNA
amounts.
As I understand it, the parameters need to be inputted into
STRmix to facilitate your proposition that it is
appropriate to engage in this product rule?---So there
are certain - - -
Is that right or is that wrong?---Well, there are certain
aspects of the calibration that you have to give to
STRmix in order to carry out its deconvolutions. There
are other - - -
You finish?---Those are things such as the amount of peak
height you see within the laboratory or the stutter
ratios for your particular profiling kit, the mass
parameters are parameters that are explored within the
Markov Chain Monte Carlo process so they are not values
that you put into STRmix.
Well, I'll just read that sentence again from your statement.
"Chakraborty has misunderstand the manner in which STRmix
takes drop out into account. STRmix assumed independence
of peak heights and drop outs within and between loci
given the parameters that describe the profile"?---Yes.
You collectively the mass parameters. So looking at this page,
which just for transcript references, albeit you don't
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have it, is F2000, these are the parameters that describe
the profile for item 1-3, is that right?---Yes, this is
what STRmix has determined to be the mass parameters that
describe the profile.
If that was not imputed by - say DNA amounts were not imputed
by the case worker?---Correct.
At what stage of the STRmix process, or if you prefer the MCMC
process, or if you prefer the iteration process, at what
stage of the process, with whatever term best identifies
it, were those amounts generated, created or identified
by STRmix?---Yeah, the way that STRmix works is that
there are values for all of those mass parameters
throughout the STRmix analysis process, so throughout the
MCMC process. STRmix will start off with values for
those mass parameters that don't describe your observed
profile value very well at all, they start off in a
random place that's not a good description of your
observed data and through the course of the MCMC, and
this is the whole reason you use it, the values that
STRmix chooses for each of those mass parameters gets
better and better in way that it describes the profile
that you've given it.
So?---So there's values in every direction.
All right. But these are the end results of the MCMC process,
is what you are saying, these values here that are
recorded in the data?---These values are a summary of the
end result, so this is where STRmix ended up, it's a
summary of where it ended up.
A summary? I thought it looked at enumerable iterations,
amounts, rejects, rejects, rejects, increases, gets, it's
a hot and cold process until it determines this is the
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most favoured result dealing with DNA amounts, this is
the most favoured result that there was 997 amounts of
fluorescence for contributor one, is that wrong?---Well,
it never converges on a particular value, so it will just
continue to assign or estimate new values for DNA amounts
and it will continue to do that over the entire course of
the MCMC analysis.
Okay?---And that these summaries at the end are an average of
the amounts that it's been sitting on at the end of the
MCMC process, so there might be several hundred values
that are averaged in order to create this summary for
you.
Let's move on to the next item from your statement. This is at
p.9, degradation. And you've got degradation listed
there at F200 with different amounts for each contributor
expressed in the unit RFU per, what's that baseline point
again is it or peak points?---Base pair.
Base pair, thanks. Is that also an example of that, those
amounts were not imputed by the case worker, or they
were?---That's right. Those are values that were used by
STRmix, determined by STRmix as part of its analysis.
At what stage, MCMC?---Throughout the entire process.
Where did it get it from? Where does it get the information
that identifies say for contributor 3 there was .75 rate
or level of reflex - not reflex?---Relative.
Relative, thank you, fluorescence units per base pair?---We
would have started off at a random start, a random
position. In fact, I think that it starts off at zero
degradation and when you start off at the very early
iterations of the MCMC process it will have DNA amounts
and degradation and amounts and amounts for all the other
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mass parameters. It will use those to build up an
expected profile, it will compare that to your observed
profile, if they are very different from one another
obviously those mass parameter values are quite poor
descriptions of your observed data and so it will then
guess new values and it will build up another expected
profile and it will try to get closer to your observed
profile and to eventually it will get to a point where
the mass parameter values it's choosing produces an
expected profile that very closely aligns with your
observed profile and at that point the MCMC will have
been said to have converged on a good set of mass
parameters and that's what's been summarised in this
output here.
But can each of these contributors have 21 markers so?---Yes.
So where is the information as to what was the degradation per
marker per contributor?---Well, degradation a per
contributor effect, as in a contributor's DNA will have
degraded by a certain amount and that translates across
the loci.
But there's an amount of degradation at individual loci which
would have a rate - this is the traditional ski scope or
expediential curve, you may have a higher rate at the
end, the right-hand side, and not much degradation at the
left-hand side of the EPG?---Yes, that's right.
So they individually could have different rates, each locus can
have a different individual rate of degradation?---The
rate of degradation is how degradation acts across the
profile, you are talking, they could have a different
amount of degradation, if you are talking about absolute
amounts of degradation.
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Sure?---That's why part of the information that you provide to
STRmix to carry out an analysis is the molecular weight
of the different alleles and the different regions, so
STRmix takes into account the amplicon size and applied
the correct amount of degradation for each locus or each
region depending on its molecular weight.
Where does it say in this data dealing with 1-3 the amplicon
sizes of each marker?---All right. I'm not sure what
page is it for you, but after the parameters you have a
whole bunch of pages under the heading "genotype
probability distribution"?
Yes?---And if you go through all of those settings and then
after that is a section called "evidence input file".
Yes?---And you will see underneath the heading of evidence
input file about three lines down from that is a line
that says "locus, allele, height, size".
Yes?---So that's all the information that is provided to STRmix
in the preceding lines which describe the profile, so you
can the size is the last - - -
So it is where it has got size that is amplicon size, is
it?---Yes, that's right and that's in base best.
Okay. Is the amount of degradation per marker
detailed?---Well, as I said before, this degradation is a
rate, which means it applies, because it's a rate of
degradation per base pair that applies to any size
because base pair is part of that summary.
But if I ask the question, what was the amount of degradation
at D21 for contributor 3, does this product tell
me?---Well, you can do, you find out the molecular weight
of D21 and you know that that will be a certain number of
base pairs and then you've got a rate of 6 RFUs per base
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pair, so you multiply the amount of degradation per base
pair, by the number of base pairs, and that's the amount
of degradation.
Again, just looking back at your statement, the next issue was
locus amplification efficiencies and I can see the title
locus efficiencies in the data. The last one in the
sentence is replicate amplification efficiency, is that
re-named as inter PCR efficiencies in the output data?
---Yes, that's right.
And given I've got this particular example open for this
example, it's said to be PCR1-100 per cent what does that
mean?---Well, in this particular case there is only one
PCR, there is no replicates, so it is basically they are
just saying it's considering the inter PCR efficiency for
this one replicate to be 100 per cent. Which is
basically saying it is not considering inter PCR or inter
replicate efficiencies because there's no replicates to
do so.
We can see from 17 and 18 of your statement you did a
re-analysis using version 2.4.05?---Yes.
Did you that in South Australia, I take it?---Yes, that's
right.
So where, who has the data for that re-analysis, you or
Victoria?---I have that data.
All right. You are in a position to make that available to the
Crown, that is the extended output data for each of the
items that you looked at, so it can be provided to the
defence?---Yes, I can do that.
Thank you. Doctor, if you could open up your copy of "an
addendum to the PCAST report", please?---Yes.
Under the heading of "background" and then subheading of
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"forensic feature comparison methods", it's stated -
"PCAST chose to focus solely on forensic feature -
comparison methods" and then identified a specific method
defined by such elements as (ii) "the complexity of the
sample examined, (e.g. a DNA sample from a single person
versus a three person mixture in which a person of
interest may have contributed only one per cent)", and
then it moves on to shoe print issues. Is that part of
the change you were identifying yesterday, the reference
to "a person of interest" as opposed to a "minor
contributor" or not?---That is one reference to it, and
there is also a reference on p.8.
We will get to p.8 shortly. On p.2, the first complete
paragraph on p.2 is, "Importantly the test problems used
in the empirical study defined the specific bounds within
which the validity and reliability of the methods has
been established, for example, is a DNA analysis method
reliable for identifying a sample that comprises only one
per cent of a complex mixture". Clearly its stated there
in the addendum. You would agree that's an important
test problem that needs to be addressed?---Well, I would
agree that you need to carry out these empirical studies
as part of your validation. The mixture component is
what addresses those sorts of things.
Well you agree it's a legitimate question asked, that is, do
the empirical studies in effect establish an analysis
method is reliable enough for identifying a sample that
comprises, well clearly this is a small amount, only 1
per cent of a DNA mixture, that is assuming that is a
reference to a person of interest?---That's fine, yes.
They then go on to describe the evaluation of empirical testing
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for various methods and state, "To evaluate the empirical
evidence supporting various feature comparison methods
PCAST invited broad input from the forensic community and
conducted its own extensive review, based on this review
PCAST evaluated the seven forensic featured comparison
methods to determine whether there was appropriate
empirical evidence that the method met the threshold
requirements of 'scientific validity' and 'reliability'
under the Federal rules of evidence". And we then go to
bullet point 4, "In the remaining case DNA analysis for
complex mixtures, PCAST found that empirical studies have
evaluated validity within a limited range of sample
types". Do you agree with that statement in this
addendum by PCAST?---I agree that that's what's written.
No, I am asking you further, do you agree with that statement
that I've just read out that is in the addendum to the
original PCAST report which was done after further
consultation with those forensic scientists who wished to
make further submissions?---Well, I can't agree outright.
I agree PCAST found that empirical studies had evaluated
- - -
You are obfuscating doctor - - - ?---Within a limited range
- - -
That's not my question?---But that was restricted to published
material.
With respect, I suggest you are obfuscating. The question is
not what PCAST found, do you agree with it, yes or
no?---Can you perhaps just indicate specifically what I'm
agreeing with?
"In the remaining case DNA analysis of complex mixtures", so
that's the subject matter, "in this remaining category
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PCAST found that empirical studies had evaluated validity
within a limited range of sample types". Do you agree
with that?---I agree that that's what PCAST found by
looking at published material only.
HER HONOUR: I think it's ambiguous. You are asking the
witness whether he agrees that empirical studies have
evaluated validity within a limited range of samples
types.
MR DESMOND: Yes, as opposed to generally across the board. As
I understand it you say STRmix has been validated for
interpretation of complex mixtures whatever the range is
of sample types?---Well, it's certainly been validated
beyond the levels that PCAST recommend.
You see, the following paragraph is headed "response to PCAST
report". "Following the report's release PCAST received
input from stakeholders expressing a wide range of
opinions". Now STRmix is a stakeholder, and you
understand Mr Buckleton on STRmix's behalf provided input
as a stakeholder, is that right?---Yes, I don't know if
it was specifically on STRmix's behalf or just in general
on behalf of the forensic DNA community, but I understand
that he did meet and discuss that issue with these
people.
Well, they identify the issue here don't they? "Some of the
commentators raised the question of whether empirical
evidence is truly needed to establish the validity and
degree of reliability of a forensic feature comparison
method"?---Yes.
They talk about the FBI, which apparently clearly recognised
the need for empirical evidence, I won't read it out to
hasten the process, I'm not ignoring it, but ultimately
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in the bottom of that paragraph on p.3, "As noted below
the DOJ" - I think that's the Department of Justice -
"ultimately concluded that it had no additional studies
for PCAST to consider". They then go on to say "PCAST
received written responses from 26 parties including from
Federal agencies, forensic science and law enforcement
organisations, individual forensic science practitioners,
testing service provider, and others in the US and
abroad. Many of the responses are extensive and detailed
and thoughtful, they cover a wide range of topics, they
provide valuable contributions for advancing the field.
PCAST also held several in-person and telephonic meetings
with individuals involved in forensic science and law
enforcement. In addition PCAST reviewed published
statements from more than a dozen forensic science, law
enforcement and other entities. They are deeply grateful
for those who took the time and effort to opine on this
important topic" and then they suggest what follows is
they will focus on the three issues that were raised
during this post-report consultation period. You agree I
have fairly summarised the situation?---Yes.
The first issue, "are empirical studies truly necessary"? And
you will see again, to avoid reading out everything to
save time, towards the end of paragraph (ii) there's a
sentence that commences, "PCAST has great respect for the
value of examiners' experience and judgment, they are
critical factors in ensuring that a scientifically valid
and reliable method is practised correctly. However,
experience and judgment alone, no matter how great, can
never", and they emphasise the word "never" by
italicising that word, do you see that?---Yes.
.DM:DF:CAT 21/04/17 SC 11A 261 TAYLOR XXNTuite
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"Can never establish the validity or degree of reliability of
any particular method, only empirical testing of the
method can do so", and there's a footnote which you are
welcome to read, footnote 6. Do you agree with
that?---Yes, that seems reasonable.
Well, here's that very word "feasible", it's in the last
paragraph before the next issue is identified on p.4
commencing with, "Fortunately empirical testing of
empirical methods is feasible, there is no justification
for accepting that a method is valid and reliable in the
absence of appropriate empirical evidence". Given your
most recent answer, you would agree with that, I take
it?---Yes.
Okay. The next issue is "importance of other kinds of
studies". Just see whether I need to - no, I don't need
to go to that. Next issue on p.5 is "completeness of
PCAST's evaluation". "So finally we consider the
important question raised by the DOJ in September of
whether PCAST had failed to consider 'numerous published
research studies' which seemed to meet PCAST's criteria
for appropriately designed studies providing support for
foundational validity. PCAST re-examined the five
methods evaluated in its report for which the validity
and degree of reliability had not been fully established.
We considered the more than 400 papers cited by the 26
respondents, the vast majority had already been received
by PCAST in the course of the previous study. At the
suggestion of John Butler of ANYST (?) we also consulted
Interpol's extensive summary of the forensic literature
to identify additional potentially relevant papers. Our
enquiry was undertaken in response to the DOJ's concern.
.DM:DF:CAT 21/04/17 SC 11A 262 TAYLOR XXNTuite
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DOJ informed PCAST in late December that it had no
additional studies for PCAST to consider". We can then
skip the paragraphs about bite marks, footwear
microscopic hair, firearms and on p.8 the authors address
DNA analysis of complex mixtures, do you see that?---Yes.
He second paragraph. "Recently efforts have focussed on an
approach called probabilistic genotyping which uses
mathematical models involving a likelihood ration
approach and simulations to attempt to infer the
likelihood that a given individual's DNA is present in a
sample. PCAST found that empirical testing of
probabilistic genotyping had largely been limited to a
narrow range of parameters (numbers and ratios of
contributors). We judged that the available literature
supported the validly and reliability of PG for samples
with three contributors where the person of interest
comprises at least 20 per cent of the sample. Beyond
this approximate range, that is with a larger number of
contributors, or where the person of interest makes a
lower than 20 per cent contribution to the sample however
there has been little empirical validation". Now that
was the reference on p.8 you were taking me to earlier
where again the minor contributor was changed to the
person of interest that you mentioned yesterday?---Yes.
Allowing for that change, which you were correct about, do you
now agree with that statement or series of statements in
that paragraph, that is, in particular that for complex
samples with three contributors where the POI comprises
less than - there is a lower than 20 per cent
contribution, your studies have not been validated, there
is, I will use their phase, "there has been little
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empirical validation"?---I can say just from South
Australia's point we have done empirical valuation well
beyond those limits, so just to bring up the point yet
again, this is based purely on what's published, which is
what PCAST limited its scope to, there's ample in-house
laboratory validations that go beyond these levels and
just to bring up a point that I made yesterday, since
this PCAST report and the addendum there has been the
publication of the FBI validation of STRmix which goes
beyond three people when then less than 20 per cent for
the person of interest meeting PCAST's call and
requirement for additional published validation material.
You say that, but have you submitted the FBI report to PCAST or
are you just waiting on them to read it?---Well, I assume
now that they have their written their report that they
are not going to go back and continually refine and put
out addendums with each new study that is published, they
made a call in their report for additional material to be
published and it has been.
This would be a pretty important piece of information. I mean
the science, which you have acknowledged, and you say
properly is still an evolving science, but it's got to a
stage where it is appropriate to use PG at whatever
levels, you say you have got evidence to support it,
published empirical evidence to support it, and you don't
return to PCAST to get them to write one further
important addendum?---Well, you can imagine one further
important addendum for, just DNA will become 2, will
become 4, will become scores of important addendums for
each discipline that then published material, it's
simply, this group is never going to continually
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reconvene to re-publish addendums on a never ending
basis.
You just don't like, with respect, the umpire's decision, if we
consider PCAST the umpire? You may not consider it the
umpire, but you know what I mean by that?---They said
that further material is required to be published, and it
has been. I can also argue about internal unpublished
empirical validations which show that this is, the use of
probabilistic genotyping can be done on far greater
mixtures than what PCAST has responded to you, and by
adhering to what PCAST is saying with regard to empirical
studies.
And I am just using a figure, but many mean of the unpublished
or further materials you are either the author of or a
co-author of, not all of them, but much of the work in
support of PG, at whatever level, you're a joint author
for or of?---Much of the published material, yes, that's
true.
Which makes sense because you are in the field, you're doing
it, you understand that?---That's right.
Yes. Can we have a 10 minute break? My friend will be leaving
at 12 o'clock. It will probably give me a chance. I'll
still finish before 1.
DR ROGERS: It just appears that my learned friend is moving to
a different topic.
MR DESMOND: I am.
DR ROGERS: So this might be a convenient time also for
Dr Taylor to have a bit of respite.
MR DESMOND: I'm going to the code issue.
HER HONOUR: All right. We can take a 10 minute break if
that's all right with you, Dr Taylor?---Certainly.
.DM:DF:CAT 21/04/17 SC 11A 265 TAYLOR XXNTuite
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The court will resume sitting at five past 12.
<(THE WITNESS WITHDREW)
(Short adjournment.)
<DUNCAN ALEXANDER TAYLOR, recalled:
MR DESMOND: Dr Taylor, if you could open up p.12 of your
report and it's under point 30, it's that last paragraph
in paragraph 30 or point 30, "Finally, to provide an
equity of arms for the defence we provide (under
controlled conditions) access to the source code of
STRmix. The STRmix source code has been examined in this
matter and so in effect been opened for the defence
making criticisms of closed source all the more
irrelevant for this case". Would you accept that the
word "very" should be inserted between "under" and
"controlled", "under very controlled conditions"?---Well,
it's somewhat of a subjective question.
Yes. Do you accept it was a limited source code review that
was able to be embarked upon for a number of
reasons?---Well, it wasn't limited in that the way the
code was viewed the entirety of the code was provided.
The cost of the exercise, are you aware as to how prohibitive
that cost was?---No.
Are you aware of either the ongoing and current - of any, I
should say, ongoing and current either threat or in fact
institution of a legal suit by ESR by anyone
currently?---No.
Have you got a copy of Nathaniel, or Nathan Adams' statement
handy, doctor?---Yes.
If could you just open up to p.3?---Yes.
Results, item 6, second sentence, "However, due to the lack of
software development standards specific to the field of
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forensic DNA mixture interpretation we must consider this
an immature field from the perspective of software
engineering". Do you agree with that?---Well, I agree
there's a lack of software development standards specific
to the field of forensic DNA mixture interpretation.
Were you the code writer or joint code writer for STRmix, I
assume?---Initially I was the sole writer.
Yes?---Since that time, which is a number of years ago now,
we've employed other co-writers.
You'll see at the top of the next page he identifies the SWGDAM
guidelines and footnotes them at footnote 11, but he goes
on to say, this is Adams that "these guidelines do not
address minimum software engineering standards for the
development of PG software". You agree with
that?---That's right. Those standards are more about the
validation of software, not necessarily focused on the
way that they should be engineered or programmed.
His next sentence, "Many scholarly peer reviewed articles have
been published on the topic of probabilistic genotyping
but acceptance or even proof of a concept does not
directly translate to software quality. Scholarly
articles do not constitute formal software requirements
and specs against which software can be rigorously
tested". You would agree with that?---I would agree with
that but I would make the point here that this couple of
sentences and a number of points throughout Nathaniel
Adams' report is somewhat tangential to the actual crux
of the issue, that is, he's talking about the
professionalism of the code, the way it's structured, the
individual way that components of the code are programmed
to be more efficient or easy to update or maintain. That
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is certainly one consideration and that is one
consideration that is important within a software
development point of view, but perhaps the more pertinent
side of this for forensic application is does it give the
correct answer and we know that it does by virtue of
having recreated and validated various components of the
software so if - - -
Yes, well you make that point in your report?---If it gives the
correct answer, I suppose of secondary concern is how
efficiently or how quickly or how much memory does it use
in getting to that answer, which are all sort of
programming aspects which Nathaniel Adams is
concentrating on.
I understand the point you're making but it all presupposes
you're getting the correct answer?---Which we've tested
by comparison to hand calculations and know that we are.
Well, I'll get on to the hand calculations issue but it didn't
persuade PCAST, despite your rigorous explanations - when
I say "you", I mean you the group of PG
supporters?---Well, I don't remember PCAST specifically
talking about programming structure at all.
No. But you're talking about, "We get it right so the
programming issue is a secondary consideration because
fortunately we know we get the right conclusion or right
results". Well, I'm challenging you that you get the
right results as evidenced by at least PCAST, subject to
the caveat of three contributor mixtures, POI 20 per cent
at least okay but other than that, no?---Well, perhaps I
can refine what I just said. We know that the software
is implementing the mathematics that we expect it to
because when we implement that same mathematics by hand
.DM:DF:CAT 21/04/17 SC 11A 268 TAYLOR XXNTuite
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the calculations come out the same.
All right. Just on that issue of hand, I just want to put to
you - this is something Mr Adams provided to me in email
in response to your report?---Okay.
That addresses Adams and Chakraborty?---Okay.
"First, I appreciate that all parties involved appear to agree
that there are no software engineering standards specific
to probabilistic genotyping systems. However, I believe
the significance of this deficiency is either lost on or
ignored by Dr Taylor. Pen and paper 'double-checking'
the math approaches have long since be surpassed by
structured software quality controls and practices. Even
though STRmix is not a program of enormous complexity,
the number of failure points are too numerous for humans
to adequately check by manual procedural means". Do you
have a response to that?---My only response would be that
that is his opinion. We rigorously check numerous
aspects of the STRmix calculation.
Just quickly go back to that 20 per cent issue raised by PCAST,
given your now personal input into the Tuite items,
evidenced by the re-analysis, which of those, if any, do
you identify the POI, i.e. Mr Tuite, contributed at a
level of 20 per cent or more? You can have that on
notice and provide the answer in the fullness of time if
you'd prefer?---No, that's all right. So if we look at
the various samples which I re-analysed, which were items
1-1, through - 1-2, 1-3, 4-1, 5A-1 and 5B-1, there are
three, three person mixtures, okay. So we'll discount
the two person mixtures and the one person profiles as
being - - -
We're dealing with items 1-1, 1-2 and 1-3?---Correct.
.DM:DF:CAT 21/04/17 SC 11A 269 TAYLOR XXNTuite
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You know - you may not know, I can't recall now whether I
raised this with you in the previous pretrial -
Ms Taupin, one of the defence experts, and she's
convinced that one should appropriately have been viewed
as a four person mixture but, in any event, dealing with
items 1-1 to 2 and 3?---All right. With item 1-1 if
Tuite is one of the contributors he aligns best with
contributor two, which makes up 31 per cent of the
profile.
M'mm?---With 1-2, if Tuite is a contributor he best aligns with
contributor two, which is 12 per cent of the profile.
Yes?---And with 1-3, once again if Tuite's a contributor he
aligns best with contributor two, which is 45 per cent of
the profile.
Okay. Just getting back to the code issue - I'm still on p.4
of the report?---Okay.
He said he had not seen materials describing the formal
software test plan intended to demonstrate STRmix's
concordance with its formal requirements and
specifications. At least as at the time early last year
when Adams went over there was there a formal software
test plan in existence?---I believe there was. I don't
know how formalised it was but there was certainly a test
plan which indicated a number of validation points that
were carried out with each new version of STRmix
released.
He says, "I've seen limited direct evidence of testing of
STRmix largely limited to a check of the mathematics.
Any component not covered by these checks is
unnecessarily tested. Further, any component not
formally described or specified is untestable - without
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strict criteria for failure a proper test cannot be
constructed". Was he provided with anything other than
what he describes as the "check of the
mathematics"?---No, because that was the check that we
had done of the software at the time, the check of the
mathematics.
If you could go to p.5 7.1.1 "unchecked input". "The model
maker MCMC program utilises a variable called extreme
clip amount which is set by a user specified run time
parameter. I was unable to identify any checks or
constraints on this user specified value that would halt
operation of the program if the user entered a value that
would later violate an invariant of the model maker MCMC
program noted for the variable inhibitor extreme amount".
Do you take issue with that?---No, I don't take issue
with that and certainly in the early versions of STRmix
there wasn't the level of, I guess, user input checking
that occurs with current versions of STRmix.
7.1.3.1, "Get correlation probability". From the second line,
"The code executed within the catch block upon an
exception occurring however simply sets a variable named
correlation probability to zero. No further instructions
are present in this catch statement. This indicates that
upon any sort of otherwise unhandled exception occurring
during the execution of the get correlation probability
method the user will not be notified nor will the program
cease execution but a value will be zeroed and operation
of model maker code will continue". Do you take issue
with that?---A couple of issues. I suppose one point to
make is that we no longer use this correlation
probability in STRmix at all and haven't done so for some
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time. I appreciate that was in the version that Mr Adams
looked at. Secondly, the setting of those values to zero
was by design because later on in the program, and
obviously Mr Adams didn't see this particular point,
values of zero are used to indicate not to use that
particular result. It was programmed that way by design.
Okay. If you could turn to p.7, and 7.3.1 "Drop out prob" the
paragraph's headed, if you read that paragraph to
yourself, I'm going to take you to the end of it, "This
could be translated to a logical test that if failed
gives rise to a handled exception and notice to the user.
However, it exists in the code allowing for its own
execution and silent acceptance of an illegal operation
within the algorithm". Do you take issue with
that?---No. So what he's describing there is just an
additional check which is probably good programming
housekeeping. So, once again, that's the sort of the
thing that we've been building into STRmix since these
early versions.
If you could go to p.9, paragraph 8, "Finding algorithmic".
8.1.1, "Forced acceptances". "The model maker MCMC
module as well as its burning sub-module will force an
acceptance after a series of hard coded consecutive
failures. From the materials provided to me it is not
apparent why this limit exists or how it's calculated.
There's no apparent mechanism for notifying the user when
this limit is reached. Every 10,000 cycles without an
acceptance model maker appears to halve its
discriminatory power for future cycles. Further
investigation and evaluation of these behaviours is
merited in order to determine whether these limits are
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reached and how they affect the results of model maker".
Do you take issue with any of that?---Only that it's
perhaps this comment has perhaps come around through a
lack of understanding of the mathematics that's being
applied. So "hard coded consecutively failures" is
probably a harsh term that's causing issue here. That
just rejects, MCMC rejects and within the first part of
the burning, basically you want STRmix to find, to not
get stuck in any particular position but to keep moving
around until it finds a good set of mass parameters to be
sampling from so the idea with this forced acceptance is
just that it won't get stuck in these places early on in
the program. Once again, it's by design, that's a
feature that makes STRmix work.
If you could go to p.11, 8.2.6 headed, "Drop out probability"
and 8.2.6.1, "Intermediate variance". "An intermediate
variance value in a drop out calculation is set to
vary/expected peak height unless the expected peak height
is less than half of the detection analytical threshold.
If the expected peak height is less than half of the
detection threshold, the intermediate variance value is
set to variance/detection threshold/2. The comment
describes 'caps variance at 25 RFU'. There is no
indication that the detection threshold is set to 50 RFU
where half would be 25 RFU. It is not apparent that this
comment pertains to its neighbouring code or if it is
possibility an artifact from the development process".
Can you address his concern there?---Yes. He was
correct, it's an artifactual and development process.
Just to elaborate a little bit further so that you
understand what, in programming terms, what a comment is,
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it's a piece of programming, it's a piece of text that
you put into a code to assist people that are reading the
code as to what the code is doing. It's not actually
executed. So initially there was a detection threshold
of 50 RFU used within the early versions of STRmix and
that's where the comment came from, and as Mr Adams has
said, it's an artifact of the development process. We
updated the code but I neglected to alter the comment
describing the code.
If you go to the conclusion on p.12, "Given the materials I was
provided at the time I was able to review them and the
issues I identified I recommend that a comprehensive test
plan be developed and executed for STRmix". Do you agree
with that and has it been done?---We have very much more
formalised the test plan that we use for STRmix review
these days and we have put significant efforts into
professionalising the code and that addresses most of the
comments that Mr Adams has made in his report.
"While no formal standard exists for the development or testing
of probabilistic genotyping systems, it's important to
compare the actual operation of the software program
against its expected operation". That would make sense,
wouldn't it, that sentence?---Yes.
He goes on. "Without a set of formal requirements and specs
(descriptions of expected behaviour) and the results of a
comprehensive test plan (characterisation of actual
behaviour) it's very difficult to evaluate the operation
of STRmix. Subsequently the correctness of operation of
STRmix should be questioned". Do you have any response
in relation to that?---Only what I've said already that
the correctness as far as its correct application of the
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maths that we expect it to is something that we check in
our validation.
In your statement you speak of - well, you can correct me if I
am wrong here - there's a concordance study between
versions 1.05 and 1.08 and the newest version, at least
as I understand it, when you were writing your report,
version 2.4, is that right?---That's right, yes.
Adams has commented further to your report, "The purported
concordance between versions 1.5/1.08 and version 2.4
appears to be more anecdotal than scientific". What do
you say about that?---I would disagree.
"I appreciate that Dr Taylor and Dr Buckleton are of the
opinion that they have thoroughly checked all versions of
STRmix for correctness of operation but their repeated
issuance of bug fixes" - that's a computer term "bug
fix", isn't it? ---Correct.
"As well as lack of software engineering, quality controls and
practices" leads Adams to believe that you're out of your
element on this whole software programming issue. Do you
have a response?---Only that I disagree with what he
says.
Now, your re-analysis was done, I think we have established,
with version 2.4?---Yes.
Was that done pursuant to request by the Crown or you initiated
that re-analysis yourself?---I would have to check but I
perhaps - I believe it might have been myself suggesting
that I re-analyse it in a later version of STRmix that
has had a lot of code professionalisation carried out
that addressed a lot of Mr Adams' concerns.
I just want to put this to you. Prior to the defence becoming
aware of the re-analysis upon service of your statement,
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so let's say from, you know, well, your statement is
dated, if I can find it, September, it seems to be, so I
imagine we probably got it early September?---August.
Yours is dated in August?---Yes.
Nothing had been heard about version 2.4, do you accept that,
unless I suppose the lawyers decided to do their own sort
of research about ongoing developments?---What do you
mean by "nothing had been heard"?
Well, you put the parties on notice, "We're now using 2.4 and
I've actually used it in this case"?---Well, I suggested,
I said that there are, there have been numerous version
updates since the version that was used to originally
analyse the Tuite profiles and that the new versions
addressed many of the concerns that Mr Adams had with the
code and its professionalisation and that it might be
worth re-running these samples through the new version of
STRmix with all those coding improvements and user check
improvements to demonstrate that there was nothing
untoward about the early results.
I am raising it in this context. Do you accept that whatever
version was, the latest version that was in existence
when Adams was over in Adelaide, he was not provided with
any source code and supporting engineering documentation
for that version, if it happened to be 2.4 that then
existed, or not, or whatever version it was, to put him
on notice, look, I or we, we're going to re-analyse with
the latest version, there was no suggestion of that when
our science computer IT man is actually over there in
Adelaide all the way from the US, agreed?---Well,
considering I just said that my suggestion was in
response to Mr Adam's report, he couldn't possibly have
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been made at the time before he had written his report.
I understand that?---So why would I?
Exactly, but at least he was there as - to go through the
source code review again he would either have to be
subjecting himself to coming back to Adelaide under the
conditions, strict or otherwise, or even I'd suggest the
more restrictive conditions which were imposed if the
code was to be provided over in - I can't recall, Ohio, I
think that's where's he's based. Those were the two
options. Are you aware of that?---Not specifically, no,
but the point of him reviewing the code was to review the
code of the version of STRmix that was used in the Tuite
matter.
Yes, and now version 2.4 has been used in the Tuite
matter?---There would be no point reviewing a code for
versions other than that.
Now version 2.4 is being used in the Tuite matter, potentially
initiated by yourself, not even pursuant to a Crown
request and the defence haven't as yet, and I'd suggest
realistically don't have the opportunity because of the
limited resource of VLA, to review it, if that path was
decided to be taken. Do you understand?---If you decide
- - -
HER HONOUR: I think that question is a bit unclear.
MR DESMOND: I'll recast it.
HER HONOUR: As I understand it Dr Taylor has just run the
samples again using the most recent version.
MR DESMOND: Yes. The point I'm making is obviously we've not
tested the code, reviewed the code the most recent
version.
HER HONOUR: But Dr Taylor is not running the case on behalf of
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the Crown, he can't account for how the Crown is going to
use any of this material.
MR DESMOND: I understand that. All I can say, Your Honour, is
I have been served with a report that's got this
information. Until I've had a discussion with my friend
as to whether she and her learned junior propose to rely
upon that it is potentially out there. This is a Basha
hearing, I'm just - - -
HER HONOUR: All right.
MR DESMOND: - - - establishing - - -
HER HONOUR: I don't know that - - -
MR DESMOND: I'll be opposing it.
HER HONOUR: - - - any fault can be attributed to Dr Taylor.
MR DESMOND: It's not fault. I really want to establish the
defence have not, for whatever reason, had a review of
version 2.4, which seems to be the latest re-analysis
done in this particular case?---Okay.
Just pardon me, doctor. Yes, in fact, that completes that
issue and that completes my cross-examination. If Your
Honour pleases.
HER HONOUR: All right.
MR SONNET: No re-examination, Your Honour.
HER HONOUR: No re-examination. Thank you, Dr Taylor, that's
your evidence. You are excused and we will now shut down
the link.
<(THE WITNESS WITHDREW)
HER HONOUR: All right. Now, it was mentioned in the course of
yesterday that the trial date would be discussed today.
MR SONNET: Yes, Your Honour.
HER HONOUR: I have spoken to the Principal Judge about this
and he would like the matter to be mentioned before him
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on Tuesday 2 May 2017 at 9.30 am.
MR SONNET: 2 May at 9.30.
HER HONOUR: Registrar Pedley will be there. I should
foreshadow that His Honour will be looking to fix a trial
date this year, if possible.
MR DESMOND: I don't know what barristers will be appearing.
MR SONNET: Thank you for that indication, Your Honour. We
will make our case before the judge.
HER HONOUR: Yes. You will need to explain to him in some
detail I think about the availability of witnesses and
their importance.
MR SONNET: Yes.
HER HONOUR: In this particular matter.
MR SONNET: Yes, certainly Your Honour.
HER HONOUR: All right.
MR DESMOND: Can I just mention on that issue, Your Honour, in
recent times i.e. for this further pre-trial I have been
trying to contact Chakraborty again, and I'm having
difficulty. I do know last time I spoke with him, he's
apparently quite ill, I don't know what his current
health status is and I'm hoping that I'm not going to
have to replace him if he either becomes incapacitated.
HER HONOUR: You are going to need to have all this information
at your fingertips if you can at 9.30 am on Tuesday 2
May.
MR DESMOND: Yes. If the worst happens and he becomes
unavailable I will be certainly having by instructors
making application to fund a further report, because
we're otherwise without an expert on the math, but
hopefully we won't get to that situation, but I just fear
that could delay trying to find someone and then going
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through the process.
HER HONOUR: All right. On that basis I am going to extend
Mr Tuite's bail until 9.30 am on Tuesday 2 May 2017.
MR DESMOND: I should have indicated yesterday, Your Honour, he
reports twice a week to police, so it's not whatever the
adjourned period is, it's not like he's not reporting or
anything like that.
HER HONOUR: All right. Very good. Thank you.
---
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