XMRV -Comments in Retrovirology nr.3

[Guest guest]

References:

1) *Comment XMRV -Mouse DNA contamination

-Retrovirology*

Help ME Circle, 22 January 2011

See Co-Cure: http://bit.ly/ibnHjS

2) XMRV -Comments in Retrovirology nr.2

Help ME Circle, 22 January 2011

See Co-Cure: http://bit.ly/fDMsN6

~jvr

``````

RETROVIROLOGY

Research

Disease-associated XMRV sequences are

consistent with laboratory contamination

Stephane Hue1*, Eleanor R Gray1*, Astrid Gall2*,

Aris Katzourakis3, Choon Ping Tan1, Charlotte J

Houldcroft2, Stuart McLaren2, Deenan Pillay1,

Futreal2, A Garson1, Oliver G Pybus3

Kellam1,2and Greg J Towers1

1 MRC Centre for Medical Molecular Virology,

Division of Infection and Immunity, University

College London, 46 Cleveland St, London W1T 4JF,

UK

2 Wellcome Trust Sanger Institute, Hinxton,

Cambridge, CB10 1SA, UK

3 Department of Zoology, University of Oxford,

South Parks Road, Oxford, OX1 3PS, UK

````````````````

This study *Disease-associated XMRV sequences

are consistent with laboratory contamination*

by MJ et al, can be found at:

http://bit.ly/eo6e60

~jvr

````````````````

http://bit.ly/i5DWWx

Comments

is this really

the final straw?

aidan walsh

(21 December 2010)

nil

For the past year all efforts have been placed soley

on xmrv! let us all hope that this paper puts a final

end to this retrovirus infection theory!

there are numerous other serious ongoing research

with regards to the following...

c.pneumonaie, dr.charles stratton van der bilt

university...

drs. garth/nancy nicolson mycoplasma with 45% of

the hiv virus envelope, institute for molecular

medicine, california...

ciguetera 'epitope' toxins university of hawaii with a

link to low level radiation...

also a prominent neuro surgeon in the u.s.a. found

300 consecutive cfs/fibro patients with chiari

malformation and/or cervical spinal stenosis and last

dr.a.martin lerner on herpes viral ebv, cmv and hhv-6

causing heart muscle problems and successfully

treated with herpes antivirals...

it is now time to put the phycological babblers

behind and serious and long awaited research to

years of patient complete neglect.

this is not what medicine is all about!

i have met countless nurses and doctors whose lives

have been trashed by this disease and there is

absolutely nothing this disease cannot take from

you.

i call on the british prime minister/government in

2011 to give this disease the complete and urgent

funding it deserves and especially to all the children

who suffer day in and day out from this illness.

stop with your *all in the mind attitudes* and

put the money in to protect the spread of this and

safeguard the world's blood banks.

talk does not solve issues but serious funding will

find the cause(s) as dr. nancy klimas of miami,

florida once said:

*....i would rather have hiv than cfs*...

to all of you researchers who try to find answers may

god bless all of you...

to all mankind a merry xmas and health to everyone

in 2011...

sincerely

aidan walsh southampton,

united kingdom...

p.s. it is a monster of a disease and not ones

imagination...

Competing interests

None declared

``````

aysian knowledge is

not Scientific knowledge

Gerwyn

(13 January 2011)

PA institute

A consideration of Hue et al, 2010

The paper states:

*....To consider the provenance of XMRV we

sequenced XMRV from the cell line 22Rv1, which is

infected with an MLV-X that is indistinguishable from

patient derived XMRV....*

The virus expressed by the 22Rv1 cell line has been

sequenced and has the unique nucleotide sequences

in the env and gag regions which identify it as XMRV

123, therefore it is the same virus.

The cell line originates from a patient suffering from

prostate cancer in 1993(4).

Taking the evidence as a whole the explanation that

the origin of XMRV expressed by these cells in that

patient, in which case the difference in sequence was

not derived from replication in an immortalised cell

line but was representative of wild type XMRV in

1993 and yet Towers et al seem determined to

adhere to their speculative viewpoint that this is a

virus acquired by these cells, via passage through

mouse cell lines.

This seems irrational bearing in mind that there is no

known MuLV virus which has the characteristic 24 nt

deletion in the gag leader or the same sequences in

the env su region (1).

It continues:

*....Bayesian phylogenies clearly show that XMRV

sequences reportedly derived from unlinked patients

form a monophyletic clade with interspersed 22Rv1

clones (posterior probability >0.99).

The cell line-derived sequences are ancestral to the

patient-derived sequences (posterior probability

>0.99)....*

This is clearly been represented as objective

scientific evidence when in fact it is not, and directly

contradicts experimental scientific evidence.

This is an example of Baysian inference based on a

computer model and should not be portrayed as

objective or scientific (5, 6).

Baysian mathematics is a probability estimate of a

hypothesis being true. The Baysian methodology

rests on the idealised assumption that human beings

make decisions on a purely rational basis and that

knowledge can be gained by using reason and

inductive logic alone.

In a Baysian analysis an ideally rational (free of

political or emotional biases) individual assigns a

probability of truth to the hypothesis in question at

the beginning of the analysis, which is called a prior

position.

There then follows an analysis via the input of new

information, and the posterior probability of the

hypothesis being true (from the perspective of the

person(s) conducting the analysis) is inferred.

In other words the prior view can heavily influence if

not determine the posterior inferential probability of

truth.

The model does not work at all if the person

constructing the prior has an intransigent view

regarding the hypothesis in question.

A rational person (for example) would not simply add

information into the analysis which favours his/her

initial viewpoint and exclude that which does not.

If this does happen then the outputs, as well as

neither objective or scientific, are not even correct in

Baysian reasoning.

The following summary re Baysian methodology is

provided for the reader (5).

*Prior information may not be accurate - generating

misleading conclusions.

*The way of inputting prior information (choice of

prior) may not be correct, and highly subjective

*Prior data is a construct made by judgements

regarding relevance.

*There is no one *correct way* of inputting prior

information and different approaches can give

different results.

*Results aren't objective and cannot stand by

themselves.

We will turn to the information omitted from this

analysis later. This is an excerpt from the Stanford

encyclopedia of philosophy:

Quote

*....In Bayesian Confirmation Theory, it is said that

evidence confirms (or would confirm) hypothesis H

(to at least some degree) just in case the prior

probability of H conditional on E is greater than the

prior unconditional probability of H: Pi(H/E) > Pi(H).

E disconfirms (or would disconfirm) H if the prior

probability of H conditional on E is less than the

prior unconditional probability of H.

This is a qualitative conception of confirmation.

There is no general agreement in the literature on a

quantitative measure of degree of confirmation or

degree of evidential support.) hypothesis H could be

defined as Pi(H/E) ? Pi(H).

One potential problem with this proposal is that it

has the consequence that no evidence can provide

much evidential support to a hypothesis that is

antecedently very probable, because as the

probability of H approaches one, the difference goes

to zero.

So even if H is very probable at the time that

evidence E is acquired, we can ask how much

evidential support E would provide for H if we had no

other evidence supporting H....*

The key points from the above is that the Evidence

chosen, E, is both selective and subjective.

The other point is that E as chosen in this study

provides little evidential support for the

predetermined position of these authors that XMRV

is a contaminant.

Other lines of evidence are needed which have been

omitted from this analysis.

*....Furthermore, pol sequences apparently amplified

from PC patient material (VP29 and VP184) are

recombinants of XMRV and Moloney MLV (MoMLV) a

virus with an envelope that lacks tropism for human

cells....*

This is clearly presented as evidence that XMRV is a

contaminant.

It is known that the pol gene of XMRV consists of

polytropic and xenotropic sequences (1, 17).

It is also known that the human genome plays host

to Moloney Murine leukaemia Pol sequences (7) and

that acquisition of such sequences would actually be

evidence of a recombinant which would be expected

if XMRV was a human replicating MuLV class virus

(8].

XMRV has been compared to MoMulv by different

researchers and found to be very similar, but an

entirely different virus (1,9).

In fact the env proteins of XMRV and MoMulv only

have a homology of 54% (9). The reverse

transcriptase of XMRV has different biochemical

activity and three dimensional structure when

compared to MoMulv (10).

*....Considering the diversity of XMRV we show that

the mean pairwise genetic distance among env and

pol 22Rv1-derived sequences exceeds that of

patient-associated sequences (Wilcoxon rank sum

test: p=0.005 and p<0.001 for pol and env,

respectively). Thus XMRV sequences acquire

diversity in a cell line but not in patient samples....*

The hypothesis here seems to be that somehow a

sequence acquires sequence diversity in cell lines

while not doing so in the same cells in a living

human being. No mechanism is proposed.

The authors who first isolated and sequenced XMRV

concluded that the sequence variability in the POL

genes between the three sequenced clones was 5

orders of magnitude higher than could be accounted

for by PCR assembly and could only be explained by

the viruses being independently acquired by the

patients studied (1).

*....These observations are difficult to reconcile with

the hypothesis that published XMRV sequences are

related by a process of infectious transmission....*

These observations in fact can easily support the

other scientific evidence (omitted by this computer

simulation).

As already mentioned if the XMRV in the cell line

pre-existed in the patient with prostate cancer then

all the observations support that XMRV is an active

oncovirus.

Towers and others are clearly assuming that such a

virus can only be transmitted horizontally despite a

wealth of scientific evidence to the contrary.

Gammaretroviruses are transmitted from one

generation to the other (11,12) and cause cancer by

inserting into the GpG regions of tumour suppressing

genes leading to their silencing (13,14).

XMRV was originally discovered integrated into

Human DNA (1) and has shown to be integrated into

the tumour suppressing gene (NFATc3) (2) and has

demonstrated a distinct preference for integrating

into genes associated with cancer (15).

Finally we look at the rationality of the analysts

themselves both in terms of the evidence they

omitted from the analysis and how they came to

formulate the hypothesis in the first place.

XMRV was first isolated by Urisman and others in

2006 (1), when it was isolated from polyadenylated

RNA and also detected in samples taken directly

from embedded tissue samples.

Now polyadenylated RNA is extremely pure so would

not have contained any viral DNA. They amplfied

either viral mRNA and/or genomic RNA.

Either way a replicating virus must be involved as

naked genomic RNA is rapidly degraded. The authors

observed viral nucleic acid in the nucleus and saw it

integrated into DNA and saw nucleic acid clustered

just outside the nucleus. This is either cDNA or

MRNA. They also detected viral proteins.

The genetic makeup of the person was a variable,

linking the presence or absence of XMRV which was

only found in stromal cells and not in any epithelial

cells, thus displayed cellular tropism.

The sequence variability in pol was greater than that

for gag and 5 orders of magnitude higher than could

be accounted for by that created by PCR.

How does the theory that XMRV is a contaminant

account for these observations?

XMRV has been found integrated into genes

associated into genes implicated in causing cancer

(2) and indeed shows a distinct preference for such

sites (15). Antibodies to XMRV isolated from patients

with PCR have been found using serological methods

specific to that isolated virus (9) (16)

PCR is the least sensitive method for isolating XMRV

(or polytropic variants) (16) (9) (3). XMRV has been

detected with multiple assay methods many used

directly on patient samples.

LnCAP (the cells used in the Lombardi et al 2009

study) do not express XMRV cells naturally (16)

XMRV was not isolated by PCR but by DNA/RNA

hybridisation microarrays (virochip). Its sequence is

unique compared to other MuLV viruses be they

endogenous or exogenous which have their

sequences recorded in repositories.

Recovery of wild type XMRV by PCR using primers

constructed to detect the gag gene sequences of the

VP62 clone is impossible even in people known to be

positive using other PCR primers (19).

The XMRV from 22RV1 cells cannot be the source of

wild type XMRV. The 22RV1 cell line originated from

a prostate cancer patient in 1993 (4).

XMRV was isolated from a patient whose blood

sample was taken in 1984! (3, 17)

Thus was the hypothesis formed by this group a

product of scientific observation?

Clearly not.

It was a belief, and cannot be the product of rational

decision making.

Moreover the bulk of evidence relating to the

hypothesis of XMRV being a contaminant was

omitted from the analysis.

All this evidence supports the view that XMRV is an

infectious retrovirus. Is this omission consistent with

rational analysis?

I would submit that it is not.

Therefore this analysis at its best is neither

objective or scientific does not even adhere to the

principles of conducting a Baysian computer analysis.

It would be a sad day indeed if computer simulations

were given preference over experimental scientific

evidence.

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RR, Ganem D, et al: Identification of a novel

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Klein EA, Ganem D, Derisi JL, Chow SA, Silverman

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doi:10.1086/656146