TUIT3A_1 - johnbuckleton.files.wordpress.com · Web viewWITNESS: Perhaps just before we start, it...

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

.DM:DF:CAT 21/04/17 SC 11A 231 TAYLOR XXNTuite

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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.


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?


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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, 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.


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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.


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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.


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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


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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.


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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.


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.


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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WITNESS AND EXHIBIT LIST: PAGE:

DISCUSSION 230

DUNCAN ALEXANDER TAYLOR, RECALLED 231

CROSS - EXAMINED BY MR DESMOND 242

THE WITNESS WITHDREW 266

DUNCAN ALEXANDER TAYLOR, RECALLED 266

THE WITNESS WITHDREW 278

DISCUSSION 279 -

280

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