HIV Aids - HIV's 3D structure revealed

Author

HIV's 3D structure revealed

DavidT

2006-01-27, 10:53 am

http://news.bbc.co.uk/1/hi/health/4642940.stm

Do "vesicles" look like this?

DavidT

2006-01-27, 10:53 am

"Cryo EM has allowed Prof Fuller's team to take a closer look at what
happens after HIV invades our cells at a resolution of about two
thousandths of a millionth of a metre, enough to show the shape of the
protein building blocks but not to see component atoms.

Using inactivated forms of HIV that keep the same shape but can be
handled safely, his team focused on the infectious stage of the
viruses' life cycle to help ensure they were the same size. While the
viruses were bathed in a thin layer of supercooled water, so they did
not dry out, they were gradually tilted in a series of steps and
separate images taken.

By using a computer to combine hundreds of separate images, each taken
at a different tilt, the team could examine the three- dimensional
structure of each virus in detail that is usually only obtainable with
X-rays. The result is a tomogram, rather than a two-dimensional image,
so they were able to examine the 3D anatomy of the virus or use a
computer to make a slice by slice image. "We now have determined
three-dimensional structures for around 70 HIV virus particles," said
Prof Fuller "The result, the first tomograms of authentic HIV, teaches
us how a variable structure assembles to produce an infectious agent."

http://www.telegraph.co.uk/connecte...ixconnrite.html

Chris Noble

2006-01-27, 10:53 am

DavidT wrote:
> "Cryo EM has allowed Prof Fuller's team to take a closer look at what
> happens after HIV invades our cells at a resolution of about two
> thousandths of a millionth of a metre, enough to show the shape of the
> protein building blocks but not to see component atoms.
>
> Using inactivated forms of HIV that keep the same shape but can be
> handled safely, his team focused on the infectious stage of the
> viruses' life cycle to help ensure they were the same size. While the
> viruses were bathed in a thin layer of supercooled water, so they did
> not dry out, they were gradually tilted in a series of steps and
> separate images taken.
>
> By using a computer to combine hundreds of separate images, each taken
> at a different tilt, the team could examine the three- dimensional
> structure of each virus in detail that is usually only obtainable with
> X-rays. The result is a tomogram, rather than a two-dimensional image,
> so they were able to examine the 3D anatomy of the virus or use a
> computer to make a slice by slice image. "We now have determined
> three-dimensional structures for around 70 HIV virus particles," said
> Prof Fuller "The result, the first tomograms of authentic HIV, teaches
> us how a variable structure assembles to produce an infectious agent."
>
> http://www.telegraph.co.uk/connecte...ixconnrite.html

The abstract for the scientific article is available here:

http://www.ncbi.nlm.nih.gov/entrez/...l=pubmed_docsum

It is worth reading. Here's a small quote:"Concentrated, high-titer
(w109 infectious units per ml) preparations of HIV-1 particles with
minimal contamination of cellular vesicles were obtained as described
previously (Welker et al., 2000). The quality of the preparation can be
judged from Figure 1A"

On the website they have included a cool animation in the supplementary
information where they rotate virus particles in 3D.

The same group has previously published this article which is
avalialble free.

http://www.pubmedcentral.gov/articl...bmedid=12660176
http://www.pubmedcentral.gov/picren...88&blobtype=pdf

It has very nice cEM pictures of HIV. Indeed, I have posted links to it
many, many, many times.

Chris Noble

GMCarter

2006-01-27, 10:53 am

On 24 Jan 2006 05:24:30 -0800, "DavidT" <david199@volcanomail.com>
wrote:

>http://news.bbc.co.uk/1/hi/health/4642940.stm
>
>Do "vesicles" look like this?

Yes. Of course, these are all lysosomes. Aren't they, Mr.
Iconoclusterfuk?

Oh. I think he'd previously waved his magic wandlet and answered that
query!

wilyretrovirus

2006-01-27, 10:53 am

David,
thanks for the link.

I really depend on the BBC for all the information I need regarding HIV
and AIDS. I especially like the way they use quotation marks in their
headlines...REALLY makes a person feel confident that they're getting the
in-depth analysis. Yes, 3-D structure of HIV is 'revealed'. Why
'revealead'? Don't they have the balls to say it without quotation marks?
They had another story we commented on here about the origin of AIDS
'discovered'. Hmmm...'discovered'? Why can't they say it without
quotation marks? I'm sure I'm just nitpicking though.

Which "HIV" is it? Is it the original 'wild' type? Is it one of the
many, many, many possible mutant strains. We ALL know how incredibly
rapidly "HIV" mutates now, don't we? How were they even able to get hold
of these pesky little guys before they decided to mutate again? Oh well,
I ask too many questions.

Well, after all that computer modeling/enhancement, I'm finally dead
convinced that HIV is most assuredly real, infectious and a deadly threat.
I'll be running up to one of my many local HIV testing clinics to make
sure I don't have those little buggers running around in my body doing all
sorts of damage. If I come up positive, maybe you guys can give me a
little advice on what the best drugs are to take these days. Gosh, if I'm
positive, my rapidly-mutating HIV could already be resistant to several
drugs. I KNOW, because I read about that! Guys, I'm scared. Right
<wink>.

Chris Noble

2006-01-27, 10:53 am

wilyretrovirus wrote:

> Which "HIV" is it?

NL4-3 which is availaible for purchase at
www.aidsreagent.org/UploadDocs/0114_005.pdf

Have you read any of the scientific articles by the group that did the
research?

Some of them are availaible over the internet for free.

Chris Noble

DavidT

2006-01-27, 10:53 am

>"I really depend on the BBC for all the information
>I need regarding HIV and AIDS. "

Well it is more authoritative than "Virusmyth".

Anyhow, Chris gave some links to the actual data/papers, but I guess
you haven't bothered to look at those.

Iconoclaster

2006-01-27, 10:53 am

>"Do "vesicles" look like this?"

No. NOTHING in the real world looks like this. It's just a computer
image, stitched together from hundreds of other images. A new stunt by
the comic duo briggs & Fuller. Financed by the Wellcome Trust.

Iconoclaster

2006-01-27, 10:53 am

From the article:

"Unlike most of its fellow viruses, infectious HIV varies wildly in size
over its life cycle, from just under 100 nanometres to 350 nm."

WoooHaaaaaaahahahahahahahahahaha!!

My dear gullible friends: "Unlike most"? There is NO virus in existence
that varies in size by a factor 3. Vesicles do. Materials that have to
be transported out of a cell must do so by budding from the cell mambrane.
So they take some of the membrane lipids with them as a vesicle. Of
course the size of this vesicle depends on what is being transported. But
a virus capsid has a fixed size, so the envelope around it should also be
of one size only.

Iconoclaster

2006-01-27, 10:53 am

>"Yes. Of course, these are all lysosomes. Aren't they, Mr.
Iconoclusterfuk?"

Not lysosomes, Mr. carter. Transport vesicles. I've worked with them.
They come in many sizes.
You'll never really learn any of this stuff, won't you?

Iconoclaster

2006-01-27, 10:53 am

>"Have you read any of the scientific articles by the group that did the
research?"

I can't answer for Wily, but I certainly did. Waste of time, as usual.
But at least I got a good laugh out of it.

"Portrait of a killer: the anatomy of HIV"
Actually, it looks quite huggable to me.
It's a collection of bric-a-brac, stitched together.

Iconoclaster

2006-01-27, 10:53 am

You call a study by a clown like Fuller, financed by Wellcome Pecuniary
Trust more authoritative than VirusMyth? Nice Photoshop work, though.
Maybe Disney would be interested.

GMCarter

2006-01-27, 10:53 am

On Wed, 25 Jan 2006 20:45:07 -0500, "Iconoclaster" <wgods@xs4all.nl>
wrote:

>Iconoclusterfuk?"
>
>Not lysosomes, Mr. carter. Transport vesicles. I've worked with them.
>They come in many sizes.
>You'll never really learn any of this stuff, won't you?

LOL. Finally, you answer the question--and then come up with this?

They aren't as big as 100 nm, let alone 350. And I'd LOVE to see a
slide showing the typical conical structure inside--among LOTS of
them. Budding from a cell. Which is not a funciton of transport
vesicles.

I'm sure with all your VAST experience and PROFOUND knowledge, this
will be an easy matter for you to show since clearly everyone in the
world is duped by something so obvious that only you have seen.

George M. Carter

GMCarter

2006-01-27, 10:53 am

On Wed, 25 Jan 2006 20:31:00 -0500, "Iconoclaster" <wgods@xs4all.nl>
wrote:

>
>No. NOTHING in the real world looks like this. It's just a computer
>image, stitched together from hundreds of other images. A new stunt by
>the comic duo briggs & Fuller. Financed by the Wellcome Trust.

I see. So LOTS of labs that have produced pictures like this are ALL
financed by Wellcome Trust, using photoshop to create the vast global
conspiracy of HIV's existence.

I see....

wilyretrovirus

2006-01-27, 10:53 am

"I see. So LOTS of labs that have produced pictures like this are ALL
financed by Wellcome Trust, using photoshop to create the vast global
conspiracy of HIV's existence."

Not *quite* the truth, but you're getting "warmer", George.

wilyretrovirus

2006-01-27, 10:53 am

From the article:

"Unlike most of its fellow viruses, infectious HIV varies wildly in size
over its life cycle, from just under 100 nanometres to 350 nm."

>WoooHaaaaaaahahahahahahahahahaha!!

>My dear gullible friends: "Unlike most"? There >is NO virus in
existence
>that varies in size by a factor 3

If we're expected to believe all the other "Alice in Wonderland" claims
about "HIV", why shouldn't we believe this one as well?

DavidT

2006-01-27, 10:53 am

As you have admitted, your paper reading "skills" don't extend beyond a
"superficial skimming" with your wall eye.

Death

2006-01-27, 10:53 am

"Iconoclaster" <wgods@xs4all.nl> wrote in message

> You call a study by a clown like Fuller, financed by Wellcome Pecuniary

http://www.boydgraves.com/

Chris Noble

2006-01-27, 10:53 am

Iconoclaster wrote:
> From the article:
>
> "Unlike most of its fellow viruses, infectious HIV varies wildly in size
> over its life cycle, from just under 100 nanometres to 350 nm."
>
> WoooHaaaaaaahahahahahahahahahaha!!
>
> My dear gullible friends: "Unlike most"? There is NO virus in existence
> that varies in size by a factor 3.

Never say never.

http://www.ncbi.nlm.nih.gov/entrez/...db=3Dpubmed&do=
pt=3DAbstract&list_uids=3D14963166&query_hl=3D2&itool=3Dpubmed_docsum
http://www.pubmedcentral.gov/articl...&pubmedid=3D14=
963166
http://www.pubmedcentral.gov/picren...&blobtype=3Dpdf

"The virions showed the broad range of diameters typical of
retroviruses."

"cEM permits reliable measurement of virus diameter, avoiding the
problems associated with viral membrane collapse when using
conventional techniques (11, 17). The diameters of viruses were
measured to the outer edge of the lipid bilayer. The three preparations
exhibited mean particle diameters of 130 =B1 18 nm (n =3D 150), 129 =B1 18
nm (n =3D 150), and 141 =B1 14 nm (n =3D 300), with virus diameter ranging
between 50 and 210 nm. The mean diameter is significantly smaller than
that observed after negative staining (180 nm) and similar to that
observed after freeze drying (125 nm) (11). Data from preparations 1
and 2 were combined (Fig. 3) and exhibit a size distribution of a
breadth similar to that of HIV-1 (2) (Fig. 3). The large range of
diameters observed is typical of retrovirus preparations (2, 9, 17). In
most retroviruses, the Gag protein shell assembles either at the plasma
membrane or on an internal membrane and the lipid bilayer plays a
significant role in the assembly process (1). Assembly of Gag protein
and nucleic acid in vitro in the absence of a lipid bilayer leads to
the production of particles that are more homogeneous in size (16, 18).
Betaretroviridae species, in contrast, assemble their Gag protein
shells in the cytoplasm. The dramatic range in diameters seen within
retrovirus preparations, therefore, does not result solely from the use
of the lipid bilayer as an assembly platform."

Once again Iconoclaster's "textbook science" comes straight out of the
wrong orifice.

Chris Noble

wilyretrovirus

2006-01-27, 10:53 am

Chris,

I'm curious to see what Iconoclaster has to say about this.

Until then, I don't think the size of a make-believe virus ends up being
terribly important.

Chris Noble

2006-01-27, 10:53 am

Iconoclaster wrote:
>
> No. NOTHING in the real world looks like this. It's just a computer
> image, stitched together from hundreds of other images.

You mean like Computed Tomography?

http://en.wikipedia.org/wiki/Computed_axial_tomography

Take a whole lot of projections from different angles and reconstruct a
3d model. Or in your words "just a computer image, stitched together
from hundreds of other images."

I wonder what a CT scan of your brain would show. Perhaps a large x-ray
opaque conical core?

Chris Noble

GMCarter

2006-01-27, 10:53 am

On Thu, 26 Jan 2006 08:01:20 -0500, "wilyretrovirus"
<purfling@nospam.yahoo.com> wrote:

>"I see. So LOTS of labs that have produced pictures like this are ALL
>financed by Wellcome Trust, using photoshop to create the vast global
>conspiracy of HIV's existence."
>
>
>Not *quite* the truth, but you're getting "warmer", George.

By all means, do feel free to clarify.

GMCarter

2006-01-27, 10:53 am

On 26 Jan 2006 15:14:44 -0800, "Chris Noble" <ChrisJNoble@hotmail.com>
wrote:

>I wonder what a CT scan of your brain would show. Perhaps a large x-ray
>opaque conical core?

ROFLMAO

Iconoclaster

2006-02-08, 12:57 am

Mr. Noble, I've heard from various sources you're a con artist, but now I'm
sure of it.

First you cite 3 references. Two of the links don't work, and the
remaining one leads to a paper pointing out that continuous poisoning with
HAART drugs is much better than allowing interruptions.

Then you include some text, supposedly from these references, that deals
with particles that are uncritically assumed to be "HIV", and shows that
these "somethings" vary in size.
Well, my point was that no virus varies significantly in size. This is
only claimed for that magical virus, "HIV", because otherwise they cannot
explain the phenomenon of a heterogeneous collection of vesicles with
varying payloads.

Iconoclaster

2006-02-08, 12:57 am

<sigh> I KNOW what a CAT scan is. But a computer-generated scan of an
unidentified object depicts STILL an unidentified object. And I still
don't see what this kindergarten computer project contributes to the
characterization or even the identification of a fantasy virus rumored to
cause a large number of diseases.

GMCarter

2006-02-08, 12:57 am

On Mon, 30 Jan 2006 21:07:20 -0500, "Iconoclaster" <wgods@xs4all.nl>
wrote:

><sigh> I KNOW what a CAT scan is. But a computer-generated scan of an
>unidentified object depicts STILL an unidentified object. And I still
>don't see what this kindergarten computer project contributes to the
>characterization or even the identification of a fantasy virus rumored to
>cause a large number of diseases.

Get infected. Find out for your own personal self!

wilyretrovirus

2006-02-08, 12:58 am

"Get infected. Find out for your own personal self!"

With a retrovirus? Hardly worth noting.

A make-believe retrovirus at that? Well, I know two people who've been
"infected" for more than 20 years with this make-believe retrovirus. They
don't take any of the nasty drugs to combat this viral ghost, and they're
fine. Just like Brian Mailman and his "smallpox".

The people I've known who've been "treated" for a make-believe virus are
dead, save for one, whose face is sunken-in, belly is extended, has veiny
arms and legs and runs to the bathroom every half-hour or so.

Chris Noble

2006-02-08, 12:58 am

Iconoclaster wrote:
> Mr. Noble, I've heard from various sources you're a con artist, but now I'm
> sure of it.
>
> First you cite 3 references. Two of the links don't work, and the
> remaining one leads to a paper pointing out that continuous poisoning with
> HAART drugs is much better than allowing interruptions.

PEBCAK.
All links work perfectly well.

All three links point to one single article that deals with
Cryoelectron microscopy of mouse mammary tumor virus. J Virol. 2004
Mar;78(5):2606-8.

One was to the abstract on Pubmed PMID: 14963166
http://www.ncbi.nlm.nih.gov/entrez/...l=pubmed_docsum

The other two were to the full article that is available free on
pubmedcentral.
http://www.pubmedcentral.gov/articl...bmedid=14963166

None of them mention HAART.

>
> Then you include some text, supposedly from these references, that deals
> with particles that are uncritically assumed to be "HIV", and shows that
> these "somethings" vary in size.

The papers are about mouse mammary tumor virus! Did you read the
titles?

> Well, my point was that no virus varies significantly in size. This is
> only claimed for that magical virus, "HIV", because otherwise they cannot
> explain the phenomenon of a heterogeneous collection of vesicles with
> varying payloads.

Your point was a load of bullshit.

MMTV varies significantly in size. Look at the results.
Or will you simply deny the reality?

Try lying more convincingly next time.

Chris Noble

GMCarter

2006-02-08, 12:58 am

On Tue, 31 Jan 2006 09:39:24 -0500, "wilyretrovirus"
<purfling@nospam.yahoo.com> wrote:

>"Get infected. Find out for your own personal self!"
>
>With a retrovirus? Hardly worth noting.

That's what you believe.

>A make-believe retrovirus at that? Well, I know two people who've been
>"infected" for more than 20 years with this make-believe retrovirus. They
>don't take any of the nasty drugs to combat this viral ghost, and they're
>fine. Just like Brian Mailman and his "smallpox".

I think you're probably lying about this.

Regardless, we've been through this. MOST (over 90%) of infected
people develop AIDS. If they don't take ARV ever, their chances of
dying of infection are quite high. And many, many do, every single
day. Most of them probably would like to have had access to treatment.

If you're infected and don't want ARV, that's your choice.

George M. Carter
00000000000000

wilyretrovirus

2006-02-08, 12:58 am

>A make-believe retrovirus at that? Well, I know two people who've been
>"infected" for more than 20 years with this make-believe retrovirus.
They
>don't take any of the nasty drugs to combat this viral ghost, and
they're
>fine. Just like Brian Mailman and his "smallpox".

I think you're probably lying about this.

==================================================
No, George,
it's JUST these kinds of things that have made me question the "logic"
behind the HIV=AIDS paradigm.

C'mon, let's not pretend there's no such thing as long term
non-progressors, ok?

The friends I knew who died were on AZT monotherapy. Sound plausible
enough?

I don't lie to try and *prove* something, Georgey. This is all perfectly
plausible, even in the realm of the orthodoxy.

GMCarter

2006-02-08, 12:58 am

On Tue, 31 Jan 2006 17:32:11 -0500, "wilyretrovirus"
<purfling@nospam.yahoo.com> wrote:

>They
>they're
>
>I think you're probably lying about this.
>
>==================================================
>No, George,
>it's JUST these kinds of things that have made me question the "logic"
>behind the HIV=AIDS paradigm.

No, it merely reinforces your insane and foolish beliefs.

>C'mon, let's not pretend there's no such thing as long term
>non-progressors, ok?

LOL. Please cite ANY time where I ever suggested LTNPs do not exist.

>The friends I knew who died were on AZT monotherapy. Sound plausible
>enough?

Not in the slightest. I've known people that died on AZT monotherapy.
On full ARV. On no ARV at all.

That does not mean HIV does not exist or cause AIDS.

>I don't lie to try and *prove* something, Georgey. This is all perfectly
>plausible, even in the realm of the orthodoxy.

Of course it is. MOST infections have a spectrum of results among an
infected population ranging from no clinical effects to potentially
death.

Which is why it is not an argument supporting denialist idiocy.

George M. Carter

wilyretrovirus

2006-02-08, 12:58 am

>>C'mon, let's not pretend there's no such thing as long term
[vbcol=seagreen]
>LOL. Please cite ANY time where I ever suggested >LTNPs do not exist.

You didn't, doofus. BUT, you said that I was lying...was it about knowing
two people that have lived with "HIV" for over 20 years, med-free and
well? That's called a long-term-non-progressor, pumpkin.

[vbcol=seagreen]
>Not in the slightest. I've known people that >died on AZT monotherapy.
>On full ARV. On no ARV at all.

Huh? You say it doesn't sound plausible that I knew two people who died
on AZT monotherapy, yet YOU say you've known people that died on AZT
monotherapy. Can you explaing your "logic"/"thinking"?

Iconoclaster

2006-02-08, 12:58 am

>"Get infected. Find out for your own personal self!"

I tried. In every way I could imagine, except sex with other men (which
is OK, but doesn't work for me). Still in good health. Do you... do you
think there may be something wrong with the infectious HIV theory?

Chris Noble

2006-02-08, 12:58 am

Iconoclaster wrote:
> Well, my point was that no virus varies significantly in size.

http://www.ncbi.nlm.nih.gov/entrez/...t_uids=11858708

"We have studied the organization of mature infectious Rous sarcoma
virus (RSV), suspended in vitreous ice, using transmission electron
microscopy. The enveloped virions are spherical in shape, have a mean
diameter of 127 nm, and vary significantly in size."

Is Iconoclutter going to argue that Rous sarcoma virus does not exist?

The study was supported by an NIH grant. Perhaps it is part of a vast
government plan to make HIV look more plausible?

Chris Noble

Iconoclaster

2006-02-08, 12:58 am

>"All links work perfectly well."

They do now. But just go back to your post of Jan.26, and click on the
links. Two of them don't work, and the third is irrelevant.

But let's stick with the links you give in your latest post of Jan. 31st.
They do work.
This paper, being from the same comic duo Briggs - Fuller, also mentions
the variability in size of MMTV. Small wonder: They're the same guys of
the "HIV in 3D" paper. And yes, also in this paper they mention HIV as a
comparison. Never before did I see such a line of reasoning toward a
preconceptual result. The comparison of the size distributions of HIV and
MMTV in fig. 3 should make anybody suspicious of this work. Comparison
with a virus that has never been obtained in pure form? Hm, peculiar...
It is not so surpring that the size of a lipid envelope varies with the
payload. If 2 cores of whatever must be accomodated, a bigger vesicle is
required.
A virus capsid is produced by self-assembly, according to strict geometric
principles. Usually around a nucleic acid structure. But that's not
absolutely necessary, as some virus preparations show empty protein
capsids. So building up the core around the RNA (as the authors suggest)
is not required.
What the virus core drags along from the host cell when it buds from the
mebrane may indeed be variable.
As the authors also had "HIV" on culture, they may have handled their MMTV
culture in the same sloppy way that is customary in "HIV science.
No, this paper does not look convincing to me. And I doubt it will
convince other colleagues.

Chris Noble

2006-02-08, 12:58 am

Iconoclaster wrote:
>
> They do now. But just go back to your post of Jan.26, and click on the
> links. Two of them don't work, and the third is irrelevant.
>
> But let's stick with the links you give in your latest post of Jan. 31st.
> They do work.
> This paper, being from the same comic duo Briggs - Fuller, also mentions
> the variability in size of MMTV. Small wonder: They're the same guys of
> the "HIV in 3D" paper. And yes, also in this paper they mention HIV as a
> comparison. Never before did I see such a line of reasoning toward a
> preconceptual result. The comparison of the size distributions of HIV and
> MMTV in fig. 3 should make anybody suspicious of this work. Comparison
> with a virus that has never been obtained in pure form? Hm, peculiar...
> It is not so surpring that the size of a lipid envelope varies with the
> payload. If 2 cores of whatever must be accomodated, a bigger vesicle is
> required.
> A virus capsid is produced by self-assembly, according to strict geometric
> principles. Usually around a nucleic acid structure. But that's not
> absolutely necessary, as some virus preparations show empty protein
> capsids. So building up the core around the RNA (as the authors suggest)
> is not required.
> What the virus core drags along from the host cell when it buds from the
> mebrane may indeed be variable.
> As the authors also had "HIV" on culture, they may have handled their MMTV
> culture in the same sloppy way that is customary in "HIV science.
> No, this paper does not look convincing to me. And I doubt it will
> convince other colleagues.

Do you have any comments that directly address aspects of the paper.

Your entire argument boils down to "it can't be HIV becasue HIV doesn't
exist". Preconceptual thinking.

Here is another study on MuLV again showing considerable variation in
size.

http://www.pubmedcentral.gov/picren...96&blobtype=pdf

So lets recapitulate the evidence so far:

Iconoclaster: Well, my point was that no virus varies significantly in
size.

Me: Here are three papers showing that virions of Rous sarcoma virus,
mouse mammary tumor virus and murine leukemia virus all vary
significantly in size.

Iconoclaster: Well, my point was that no virus varies significantly in
size.

Simply saying "because I said so" doesn't go far in science. Do you
have any papers to support your claim?

Chris Noble

GMCarter

2006-02-08, 12:58 am

On Tue, 31 Jan 2006 21:38:18 -0500, "Iconoclaster" <wgods@xs4all.nl>
wrote:

>This paper, being from the same comic duo Briggs - Fuller, also mentions
>the variability in size of MMTV. Small wonder: They're the same guys of
>the "HIV in 3D" paper. And yes, also in this paper they mention HIV as a
>comparison.

Yes. And the size they show is partly due to the presence of two
cones. Makes the virion somewhat larger.

And even the smallest size doesn't look like a transport vesicle, like
you'd like people to believe.

George M. Carter

GMCarter

2006-02-08, 12:58 am

On Tue, 31 Jan 2006 18:51:16 -0500, "wilyretrovirus"
<purfling@nospam.yahoo.com> wrote:

>
>
>You didn't, doofus. BUT, you said that I was lying...

Yep. You probably are. Mostly to yourself.

Let alone I have no reason to believe any claims an anonymous poster
makes.

George M. Carter

GMCarter

2006-02-08, 12:58 am

On Tue, 31 Jan 2006 20:08:45 -0500, "Iconoclaster" <wgods@xs4all.nl>
wrote:

>
>I tried. In every way I could imagine, except sex with other men (which
>is OK, but doesn't work for me). Still in good health. Do you... do you
>think there may be something wrong with the infectious HIV theory?

Do you...do you think maybe you just didn't get infected?

Doing nothing but whacking off to porn is pretty safe, dear.

DavidT

2006-02-08, 12:58 am

>Simply saying "because I said so" doesn't
>go far in science. Do you have any
>papers to support your claim?

I wouldn't hold your breath Chris...

Brian Mailman

2006-02-08, 12:58 am

GMCarter wrote:
[vbcol=seagreen]
> On Tue, 31 Jan 2006 20:08:45 -0500, "Iconoclaster" <wgods@xs4all.nl>
> wrote:
>

Including unprotected sex with a known HIV+ person? Including injecting
blood from a known HIV+ person?

B/

Bennett

2006-02-08, 12:58 am

Iconoclaster wrote:
> It is not so surpring that the size of a lipid envelope varies with the
> payload. If 2 cores of whatever must be accomodated, a bigger vesicle is
> required.
> A virus capsid is produced by self-assembly, according to strict geometric
> principles. Usually around a nucleic acid structure. But that's not
> absolutely necessary, as some virus preparations show empty protein
> capsids. So building up the core around the RNA (as the authors suggest)
> is not required.
> What the virus core drags along from the host cell when it buds from the
> mebrane may indeed be variable.
> As the authors also had "HIV" on culture, they may have handled their MMTV
> culture in the same sloppy way that is customary in "HIV science.
> No, this paper does not look convincing to me. And I doubt it will
> convince other colleagues.

All your points above simply go to explain why HIV might vary in size.
I'm not sure why you're stating them since they very neatly refute why
HIV should be expected to remain one fixed size virion.

It's been published several times that HIV capsids can assemble without
nucleic acid, but it's also clear that RNA dramatically improves the
efficiency of the capsid formation process. Much of the work involved
in working out what the cores look like and how the maturation process
works (from spherical core to conical core) comes from in vitro work of
capsid assembly - the rest from EM's of cultures at various timepoints
in viral replication and/or mutagenic studies (e.g. to see how a
mutation affects virion size and shape and function). My PhD was on
HIV virion production, specifically the role of viral RNA in capsid
protein interactions and packaging of the genomes.

I've seen no evidence anywhere that HIV is handled in a "sloppy" way
other than the hearsay of the dissidents. It's a nice meme to bring up
to "refute" all HIV virology with no concrete evidence or logical
argument.

Influenza has pleomorphic virions, measles can be filamentous or
spherical, bacteriophage m13 has a capsid that can extend or shrink in
size in direct proportion to the genome being encapsulated (a
phenomenon utilised in certain DNA cloning/mutagenesis techniques).
Hep B (which you have elsewhere stated you think is a real entity) has
viral particles that are so unusual among the muck that is produced
they have their own name (the Dane particle).

To me HIV isn't unusual, it's par for the course. To state simply that
viruses shouldn't vary in size is silly, as they plainly do and by your
own words above have good reason to do so.

Cheers

Bennett

Chris Noble

2006-02-08, 12:58 am

Bennett wrote:
<snip>
> To me HIV isn't unusual, it's par for the course. To state simply that
> viruses shouldn't vary in size is silly, as they plainly do and by your
> own words above have good reason to do so.
>
> Cheers
>
> Bennett

I think Iconoclutter's argument comes down to:

Around 40 years ago I worked with Turnip Yellow Mosaic Virus.

Virions of TYMV are nice and regular.

Therefore all viruses are nice and regular.

Chris Noble

Iconoclaster

2006-02-08, 12:58 am

>"Doing nothing but whacking off to porn is pretty safe, dear."

Oh, you don't know my history. Not my fault; it's all on the web. I've
never done anything safe in my life. I only passed on the stupid things -
like taking drugs.

Chris Noble

2006-02-08, 12:58 am

Iconoclaster wrote:
>
> I tried. In every way I could imagine, except sex with other men (which
> is OK, but doesn't work for me). Still in good health. Do you... do you
> think there may be something wrong with the infectious HIV theory?

Where I live I get bitten by mosquitoes all the time. Still in good
health. Do you... do you think there may be something wrong with the
infectious malaria theory?

Chris Noble

GMCarter

2006-02-08, 12:58 am

On Thu, 02 Feb 2006 21:16:21 -0500, "Iconoclaster" <wgods@xs4all.nl>
wrote:

>
>Oh, you don't know my history. Not my fault; it's all on the web. I've
>never done anything safe in my life. I only passed on the stupid things -
>like taking drugs.

Clearly, claiming you're some kind of authority on absolutely anything
at all is one of the most unsafe things you've ever done. May your
students have utterly forgotten every syllable you ever spoke.

George M. Carter

Bennett

2006-02-08, 12:58 am

Chris Noble wrote:

> I think Iconoclutter's argument comes down to:
>
> Around 40 years ago I worked with Turnip Yellow Mosaic Virus.
>
> Virions of TYMV are nice and regular.
>
> Therefore all viruses are nice and regular.

It would makes things easier it they were that's for sure!

Viruses like that are great starting points to understand virology and
the easiest way to teach students about the topic. Once they
understand the basics of virion structure and why it has to be that
way, they can then move onto the "exceptions". For example, once they
understand that virus capsids are "either icosahedral or helical" it's
not so hard to accept a spherical or conical core as they (should)
still appreciate that a geometric fit must exist between the capsid
proteins, even if they personally don't know what that geometry is.

Serious question for Iconoclaster...I wonder if he knows WHY viruses
like TYMV are so nice and regular. My kick-off question on the
virology teaching sessions I used to do was "Why are viruses
symmetrical?" The proper answer opens up half a dozen key elements of
virology and molecular biology.

Hint: the proper answer is not "because they are made according to
geometric rules", as that's way too simplistic. You have to ask
yourself why the rules exist... I have taught students who got this
first time with no hints. I would not have been one of them... ;-)

Cheers

Bennett

Chris Noble

2006-02-08, 12:58 am

Bennett wrote:
> Chris Noble wrote:
>
>
> It would makes things easier it they were that's for sure!
>
> Viruses like that are great starting points to understand virology and
> the easiest way to teach students about the topic. Once they
> understand the basics of virion structure and why it has to be that
> way, they can then move onto the "exceptions". For example, once they
> understand that virus capsids are "either icosahedral or helical" it's
> not so hard to accept a spherical or conical core as they (should)
> still appreciate that a geometric fit must exist between the capsid
> proteins, even if they personally don't know what that geometry is.
>
> Serious question for Iconoclaster...I wonder if he knows WHY viruses
> like TYMV are so nice and regular. My kick-off question on the
> virology teaching sessions I used to do was "Why are viruses
> symmetrical?" The proper answer opens up half a dozen key elements of
> virology and molecular biology.
>
> Hint: the proper answer is not "because they are made according to
> geometric rules", as that's way too simplistic. You have to ask
> yourself why the rules exist... I have taught students who got this
> first time with no hints. I would not have been one of them... ;-)
>
> Cheers
>
> Bennett

I find the whole idea of a symmetrical virus capsid rather implausible.

Do these viruses all read Euclid's geometry.

Most university students can't tell you what symmetry operations are
contained in the 532 space group. How do these viruses know? Are they
smarter than most humans?

Get a group of people and ask them to build a regular icosahedron. See
how many are smart enough to do it. And viruses do it all the time?

They must be pretty smart little buggers!

Chris Noble

GMCarter

2006-02-08, 12:58 am

On 4 Feb 2006 13:36:10 -0800, "Chris Noble" <ChrisJNoble@hotmail.com>
wrote:

>
>They must be pretty smart little buggers!

They ARE the intelligent designers.....

HAIL!

Thou shalt have no VLP before me....

Bennett

2006-02-08, 12:58 am

GMCarter wrote:
> On 4 Feb 2006 13:36:10 -0800, "Chris Noble" <ChrisJNoble@hotmail.com>
> wrote:
>
>
> They ARE the intelligent designers.....
>
> HAIL!
>
> Thou shalt have no VLP before me....

:-D Well, when a virus can hijack and cell and replicate using only 3
genes, it makes you wonder... 3 versus 30,000. Which organism has the
more intelligent design?

Cheers

Bennett

Gary Stein

2006-02-08, 12:58 am

"Bennett" <njb35@cantab.net> wrote in message
news:1139164086.969309.226850@g43g2000cwa.googlegroups.com...
> GMCarter wrote:
>
> :-D Well, when a virus can hijack and cell and replicate using only 3
> genes, it makes you wonder... 3 versus 30,000. Which organism has the
> more intelligent design?

Indeed...................

I also notice the complete absence of Claster every time Bennett can spare a
few minutes to post here on MHA. Gee Claster what's up with that afraid of
Bennett are you?

I say we all refuse to reply to Claster until he address's the questions
raised by Bennett and Chris in this thread.

Gary Stein

Gary Stein

2006-02-08, 12:58 am

> Iconoclaster wrote:
>
No while Turnip Yellow Mosaic Virus does not vary significantly in size you
can not make the assumption that this is the model all virus follow.

Quite the opposite is true as Bennett explained elsewhere in this thread and
you have yet to answer.

Gary Stein

Brian Mailman

2006-02-08, 12:58 am

Gary Stein wrote:

> I also notice the complete absence of Claster every time Bennett can spare a
> few minutes to post here on MHA. Gee Claster what's up with that afraid of
> Bennett are you?

You know how scary the English are.

B/

Gary Stein

2006-02-08, 12:58 am

"Iconoclaster" <wgods@xs4all.nl> wrote in message
news:531b7ccbe00c5ae7ddf19cf3b6d878a3@localhost.talkabouthealthnetwork.com...
> <sigh> I KNOW what a CAT scan is. But a computer-generated scan of an
> unidentified object depicts STILL an unidentified object. And I still
> don't see what this kindergarten computer project contributes to the
> characterization or even the identification of a fantasy virus rumored to
> cause a large number of diseases.
>
>

So the first CAT scan of a live brain could not have been used to
characterize those portions of the brain never before seen in a live
patient. Nor could it be used to show the levels of resolution that had
never before been seen in either a living or dead brain.

Of course the above is not the case your silly strawman argument could be
used against every advancement in imagining since the discovery of the
microscope. New imaging tools that provide new levels of, magnification,
increased resolution, new spectrums, different visualizations discover new
never before seen facts about the items they image and discover entirely new
never seen before entities separate from the original item imaged. Are you
seriously claiming that all these discoveries of previously "unidentified
object depicts STILL (are) an unidentified object".

If so please explain yourself and focus on all the things discovered by
modern imagining devices that according to you are still unidentified. I am
sure that most of the biologists, virologists, microbiologists,
microchemists, microprocessor designers, etc etc will all be happy to retire
and through up there hands and admit that everything they based the last 100
years of science on has simply vanished because Iconclaster that renowned
scientist says they have.

Gary Stein

Chris Noble

2006-02-08, 12:58 am

Gary Stein wrote:
> "Iconoclaster" <wgods@xs4all.nl> wrote in message
> news:531b7ccbe00c5ae7ddf19cf3b6d878a3@localhost.talkabouthealthnetwork.com...
>
> So the first CAT scan of a live brain could not have been used to
> characterize those portions of the brain never before seen in a live
> patient. Nor could it be used to show the levels of resolution that had
> never before been seen in either a living or dead brain.
>
> Of course the above is not the case your silly strawman argument could be
> used against every advancement in imagining since the discovery of the
> microscope. New imaging tools that provide new levels of, magnification,
> increased resolution, new spectrums, different visualizations discover new
> never before seen facts about the items they image and discover entirely new
> never seen before entities separate from the original item imaged. Are you
> seriously claiming that all these discoveries of previously "unidentified
> object depicts STILL (are) an unidentified object".
>
> If so please explain yourself and focus on all the things discovered by
> modern imagining devices that according to you are still unidentified. I am
> sure that most of the biologists, virologists, microbiologists,
> microchemists, microprocessor designers, etc etc will all be happy to retire
> and through up there hands and admit that everything they based the last 100
> years of science on has simply vanished because Iconclaster that renowned
> scientist says they have.
>
> Gary Stein

The main paper
http://tinyurl.com/cl9ef
shows very clear traditional transmission electron micrographs of HIV.
The HIV virions clearly have gp120 spikes and conical cores. They look
like no vesicles reported in the history of science. The method by
which a number of 2D EM projections are used to reconstruct a 3D model
is excatly the same mathematics that are used in Xray CAT scans. The
only difference is that electrons are used rather than xrays.

Iconoclaster's contrived objection to this technique sounds a lot like
the alleged response of the Church to Galileo's observation of the
moons of Jupiter using a telescope. They aren't moons they are just
unidentified objects!

Chris Noble

Chris Noble

2006-02-08, 12:58 am

Chris Noble

2006-02-08, 12:59 am

Gary Stein wrote:
> No while Turnip Yellow Mosaic Virus does not vary significantly in size you
> can not make the assumption that this is the model all virus follow.
>
> Quite the opposite is true as Bennett explained elsewhere in this thread and
> you have yet to answer.
>
> Gary Stein

I have already cited several articles dmonstrating that retroviral
particles vary significantly in size.

Here is another one published in 1976 (and available free online!)

http://tinyurl.com/9l45x

Figures 8, 9 and 10 show size distributions of MuMTV, RSV and FeLV
virions as determined by electron microscopy. All show large variations
in size.

I am still waiting for Iconclutter to come up with a coherent response.

Chris Noble

Chris Noble

2006-02-08, 12:59 am

Gary Stein wrote:
> "Bennett" <njb35@cantab.net> wrote in message
> news:1139164086.969309.226850@g43g2000cwa.googlegroups.com...
>
> Indeed...................
>
> I also notice the complete absence of Claster every time Bennett can spare a
> few minutes to post here on MHA. Gee Claster what's up with that afraid of
> Bennett are you?
>
> I say we all refuse to reply to Claster until he address's the questions
> raised by Bennett and Chris in this thread.
>
> Gary Stein

Iconoclaster makes a claim " There is NO virus in existence that
varies in size by a factor 3."

I post several articles demonstrating that other retroviruses such as
Rous Sarcoma Virus do indeed have size distributions like this.

Iconoclaster doesn't respond to these articles here.

Iconclaster makes the same claim on Denialist forums that viruses do
not vary in size.

How can we describe Iconoclutter's actions?

Chris Noble

Iconoclaster

2006-02-08, 12:59 am

>>"But a computer-generated scan of an
unidentified object depicts STILL an unidentified object."

That's what I said...

>"New imaging tools that provide new levels of, magnification, increased
resolution, new spectrums, different visualizations discover new
never before seen facts about the items they image and discover entirely
new never seen before entities separate from the original item imaged."

That's what you came up with.
<Gawd! And this guy dares to mention strawman arguments>
The first CAT scan of a brain showed more details than were ever seen
before. But everybody still knew it was a brain they were looking at. It
was not an unidentified object.
The first scientists who saw bacteria through a microscope did indeed see
unidentified objects. But they were identified shortly thereafter, by
other methods. And up to today, nobody identifies bacteria by looking at
them under the microscope. There are many other methods for that (cf.
Bergey's Manual).
But the situation with "HIV" is quite different. Everybody knew beforehand
what HIV looks like, and what they're supposed to believe. So now they
took a tomogram of an UNIDENTIFIED OBJECT, and declared triumphantly it
was a scan of HIV. But what one is supposed to see had already been
prescribed by the HIV-priests.

I am in awe of the accomplishments of scientists of the past 100 years.
But for the present crop of pharma-whores I have very little respect.

Chris Noble

2006-02-08, 12:59 am

Iconoclaster wrote:
> unidentified object depicts STILL an unidentified object."
>
> That's what I said...
>
> resolution, new spectrums, different visualizations discover new
> never before seen facts about the items they image and discover entirely
> new never seen before entities separate from the original item imaged."
>
> That's what you came up with.
> <Gawd! And this guy dares to mention strawman arguments>
> The first CAT scan of a brain showed more details than were ever seen
> before. But everybody still knew it was a brain they were looking at. It
> was not an unidentified object.
> The first scientists who saw bacteria through a microscope did indeed see
> unidentified objects. But they were identified shortly thereafter, by
> other methods. And up to today, nobody identifies bacteria by looking at
> them under the microscope. There are many other methods for that (cf.
> Bergey's Manual).
> But the situation with "HIV" is quite different. Everybody knew beforehand
> what HIV looks like, and what they're supposed to believe. So now they
> took a tomogram of an UNIDENTIFIED OBJECT, and declared triumphantly it
> was a scan of HIV. But what one is supposed to see had already been
> prescribed by the HIV-priests.
>
> I am in awe of the accomplishments of scientists of the past 100 years.
> But for the present crop of pharma-whores I have very little respect.

There have been electron micrographs of HIV available in the literature
for people to look at since 1984. All it takes is the energy to go to
your local library.

All of these have been TEMs which show a 2D projection through a thin
slice or SEMs that show suface. The novel aspect of electron tomography
is getting a 3D model which enables us to see the 3D structure of the
virion in much better detail.

It also enables us to see the conical RNA containing cores that are
found in other lentiviruses such as Equine Infectious Anemia Virus but
are not found in transport vesicles.

These tomograms, and the electron micrographs and immunoelectron
microcroscopy that preceded them, make your contention that they are
just transport vesicles totally laughable and ridiculous.

Chris Noble

Iconoclaster

2006-02-08, 12:59 am

From the abstract:
"Using an approach grounded in geometric probability, we estimate the size
of the viral core from the projection data. We show that the size of the
core is not tightly controlled and that core size and virion size are
positively correlated."

Hm, interesting. I wish I had the complete paper, to see how they show
that the core size is not tightly controlled. With all viruses, it is.
Just follows from the rules of geometry. But... they say they *estimate*
the size of the core? That certainly leaves room for discussion.

Do I deny the existence of Rous sarcoma virus? No, I don't. It's Stefan
Lanka who denies the existence of the whole retrovirus class as exogenous
viruses. I do believe in RSV. In 1911 they still did good research. But
I dread the state of science by the year of 2011.

Iconoclaster

2006-02-08, 12:59 am

>"Simply saying "because I said so" doesn't go far in science. Do you have
any papers to support your claim?"

Sure. But they're older, and not on the web. Here's a classic:

D.L.D. Caspar & A. Klug (Sir Aaron to you): Physical principles in the
construction of regular viruses, Cold Spring Harbor Symp. Quant. Biol.
27, 1 (1962)

And:
A. Klug, W. Longley, R. Leberman: Arrangement of protein subunits and the
distribution of nucleic acid in Turnip Yellow Mosaic Virus. I. X-ray
diffraction studies, J. Mol. Biol. 15, 315 (1966)

J.T. Finch & A. Klug: Arrangement of protein subunits and the distribution
of nucleic acid in Turnip Yellow Mosaic Virus, J. Mol. Biol. 15, 344
(1966)

Iconoclaster

2006-02-08, 12:59 am

>"I wouldn't hold your breath Chris..."

Wrong again.

Chris Noble

2006-02-08, 12:59 am

Iconoclaster wrote:
> From the abstract:
> "Using an approach grounded in geometric probability, we estimate the size
> of the viral core from the projection data. We show that the size of the
> core is not tightly controlled and that core size and virion size are
> positively correlated."
>
> Hm, interesting. I wish I had the complete paper, to see how they show
> that the core size is not tightly controlled.

Just go to your local library.

> With all viruses, it is.
> Just follows from the rules of geometry. But... they say they *estimate*
> the size of the core? That certainly leaves room for discussion.

Here you go with your absolute statements which just like the statement
"all swans are white" are simply falsified by the observation of a
black swan. There are some viruses where the number of capsomers and
their geometrical arrangement in the capsid are narrowly defined. This
is not true in all viruses. In particular it is not true in
retroviruses.

You may be surprised to learn that real scientists study the capsid
assembly of retroviruses by observing them and not by issuing papal
bulls from the safety of their armchairs

> Do I deny the existence of Rous sarcoma virus? No, I don't. It's Stefan
> Lanka who denies the existence of the whole retrovirus class as exogenous
> viruses. I do believe in RSV. In 1911 they still did good research. But
> I dread the state of science by the year of 2011.

Can you produce a single paper that looked at the size distribution of
RSV virions that did not find a significant size variation? This isn't
to much to ask is it? I mean you don't expect people to believe you
without any evidence do you?

Chris Noble

Chris Noble

2006-02-08, 12:59 am

Iconoclaster wrote:
> any papers to support your claim?"
>
> Sure. But they're older, and not on the web. Here's a classic:
>
> D.L.D. Caspar & A. Klug (Sir Aaron to you): Physical principles in the
> construction of regular viruses, Cold Spring Harbor Symp. Quant. Biol.
> 27, 1 (1962)
>
> And:
> A. Klug, W. Longley, R. Leberman: Arrangement of protein subunits and the
> distribution of nucleic acid in Turnip Yellow Mosaic Virus. I. X-ray
> diffraction studies, J. Mol. Biol. 15, 315 (1966)
>
> J.T. Finch & A. Klug: Arrangement of protein subunits and the distribution
> of nucleic acid in Turnip Yellow Mosaic Virus, J. Mol. Biol. 15, 344
> (1966)

You appear to have some major problems with logic.

You made the statement that no viruses vary significantly in size.

Giving examples such as TYMV that do have regular sizes does not prove
your statement.

On the other hand when I give you several examples of viruses that do
show significant size variations it directly falsifies your claim.

To use an analogy again. You say all swans are white and produce 3
photographs of white swans. I produce 3 photographs of black swans. Is
the statement "all swans are white" true or false.

It is a demonstrable fact that not all viruses are as regular as TYMV.

Can you get in contact with Sir Aaron Klug and ask him to confirm your
claim that no virus varies significantly in size?

You may want to ask why he has his name on HIV research.
http://tinyurl.com/e262f

Chris Noble

Iconoclaster

2006-02-08, 12:59 am

>"All your points above simply go to explain why HIV might vary in size.
I'm not sure why you're stating them since they very neatly refute why HIV
should be expected to remain one fixed size virion."

I'm stating them because I want to keep things in perspective. No sense
in denying obvious facts.
The point I'm trying to drive home is that the core size of even an
enveloped virus should be fixed, based on the size of the protein
subunits. (Never mind what anybody says who is just "estimating" sizes).
Now the whole virion, including the lipid envelope, could vary somewhat,
depending on what additional garbage is taken along from the cell. But a
factor 3, as Briggs and Fuller allege, is a bit much. I consider the
envelope of lesser importance, and hardly consider it part of the virus.
Of course you may counter that it is indeed important for the infection
process, because it holds the surface proteins that attach itself to the
cell to be infected. Well, maybe so. The picture for retroviruses is
still far from complete. Anyhow, there is also a group-specific antigen
of smaller size, inside a retrovirus. That is released once the virus
disintegrates.

>"It's been published several times that HIV capsids can assemble without
nucleic acid, but it's also clear that RNA dramatically improves the
efficiency of the capsid formation process."

If we replace "HIV" by "RNA-viruses", I'm in complete agreement. This has
indeed been shown for various kinds of viruses. Does that mean there is a
virus named HIV that follows this same rule? Hardly.

>"Much of the work involved in working out what the cores look like and
how the maturation process
works (from spherical core to conical core) comes from in vitro work of
capsid assembly - the rest from EM's of cultures at various timepoints in
viral replication and/or mutagenic studies (e.g. to see how a mutation
affects virion size and shape and function)."

You make it all sound so easy and straightforward. Just like an NIH
grant proposal. I'd really like to see this work on in vitro capsid
assembly. I've always been very suspicious of these conical-shaped cores.
But, of course, I couldn't really criticize work I haven't even seen.

>"I've seen no evidence anywhere that HIV is handled in a "sloppy" way
other than the hearsay of the dissidents."

You would if you'd just put a virological publication from 40 year ago
next to one written last year, and compare.
First of all, don't you think it's sloppy to discuss al kinds of
biological properties of a virus that has not even be isolated? (No, poor
excuses such as "molecular cloning": won't do). If they could isolate
Rous sarcoma virus, Murine leukemia virus, Avian myeloblastis virus, Mouse
mammary tumor virus, etc., decades ago, then why couldn't Montagnier and
Gallo isolate HIV virions the same way?
Modern publications treat HIV as an established entity, without admitting
that the foundation is lacking.

>"Hep B (which you have elsewhere stated you think is a real entity) has
viral particles that are so unusual among the muck that is produced they
have their own name"

Yes indeed. Hep B does not fit any of the virus classes. Very unusual.
But HIV is rumored not to be unusual at all. You say this yourself. It's
supposed to be just an ordinary retrovirus, just like RSV or MMTV...
But then, about this "ordinary retrovirus" hair-raising stories are told,
wilder than the tales about Charlemagne. HIV is too unstable to be
isolated, but it "hits like a truck" (Gallo). It infects only a few CD4+
T-cells, but destroys the whole cellular immune system. It hides, and
refuses to be found inside the host. It waits 10 years or more before it
strikes and kills the infected person. While it sits there, quietly, its
proviral DNA integrated in the genome of the host, it manages to produce
millions upon millions of offspring. Yet, these virus particles cannot be
found, except when you add blood plasma from the patient to an immortal
cell culture, and say "hocus pocus".
Cores of retroviruses are spherical or tubular. Yet, those of HIV have a
conical shape, or even look like coffins (Fuller).
The genome of retroviruses is puny compared to that of influenza- or
herpes viruses. Yet, HIV mutates its XXX off, and is even able to become
resistent to drugs it does not even interact with...
I could go on and on. But if I do, I'll wind up writing a sonnet about
it.
But... HIV is just an ordinary retrovirus, of course. Nothing unusual.

Cheers, Wilhelm

Iconoclaster

2006-02-08, 12:59 am

>"Virions of TYMV are nice and regular.
Therefore all viruses are nice and regular."

No-o-o-o. Not all viruses look the same. But the assembly rules are
universal.
And within one and the same virus species, all particles are the same (And
spare me the argument about filamental forms. I know about them).

Iconoclaster

2006-02-08, 12:59 am

>"Do you... do you think there may be something wrong with the infectious
malaria theory?"

No.
I'd be careful with those mosquitoes, though. Some plants get tumors
after insect stings.

Iconoclaster

2006-02-08, 12:59 am

>"Serious question for Iconoclaster...I wonder if he knows WHY viruses like
TYMV are so nice and regular. My kick-off question on the virology
teaching sessions I used to do was "Why are viruses
symmetrical?"

Well, that's old Watson and Crick stuff, Professor Bennett. Viruses
contain only enough nucleic acid to code for just a few proteins of
limited size. So the large structure of the capsids must be built up
from these protein subunits by a self-assembly process. Each of these
subunits must have the same environment. And the only way you can arrange
them, each having the same environment, is a regular structure of high
symmetry. It's very much like the cubical class in crystallography.
Caspar and Klug later extended this idea, which led to the icosahedral
model.

Iconoclaster

2006-02-08, 12:59 am

>"Get a group of people and ask them to build a regular icosahedron. See
how many are smart enough to do it. And viruses do it all the time?"

Elementary, my dear Wa... eh, Noble. Not only viruses can do it. Even
water molecules do it. Ever looked closely at snow crystals? Pretty
symmetric, huh? Molecules of one kind (even proteins) floating around
freely, interact with each other in such a way that they each attain the
same immediate environment. And the structure that achieves that goal is
one of high symmetry.

Iconoclaster

2006-02-08, 12:59 am

>"I also notice the complete absence of Claster every time Bennett can
spare a few minutes to post here on MHA. Gee Claster what's up with that
afraid of Bennett are you?

Hey, wait a minute! Are you sure you can read? I have written long posts
in reply to those of Bennett, in this thread and others, whenever *I* have
a few minutes to spare.
I'm not always on this forum. I have other things to do as well. And,
now that you mention it: We haven't seen YOU for quite a while, here in
the snakepit. Were you scared of anybody? Wilyretrovirus, perhaps?
Death? (no pun intended).
It's always a pleasure, discussing things with Bennett. Which is not
something that can be said of the three stooges (of which you're one).

Iconoclaster

2006-02-08, 12:59 am

As the only thing you ever do is parroting the other stooges, I just refer
you to my answer to Mr. Stein.

Iconoclaster

2006-02-08, 12:59 am

"Infectious HIV particles contain a characteristic cone-shaped core
encasing the viral RNA and replication proteins..."

They forgot to add: "Because we say so!"
What good is an abstract (especially from those clowns Briggs and Fuller)
if I can't even look at the Materials and Methods section?
Why is there heterogeneity in size and shape? Sloppy methodology? Can't
tell from the abstract.
With sloppy methodology I don't mean the scan technique, but the
preparation of the material to be scanned.

Iconoclaster

2006-02-08, 12:59 am

>"Figures 8, 9 and 10 show size distributions of MuMTV, RSV and FeLV
virions as determined by electron microscopy. All show large variations
in size."

Ah! Finally a paper that makes sense. No bullshit about HIV, No genetics
or clinical claptrap. Just straight measurements. They even have the
brilliant idea of using a centrifuge.
I have only read quickly through the complete paper, but I need some time
to go through it seriously. I'll get back to it tomorrow.

Chris Noble

2006-02-08, 12:59 am

Iconoclaster wrote:
> TYMV are so nice and regular. My kick-off question on the virology
> teaching sessions I used to do was "Why are viruses
> symmetrical?"
>
> Well, that's old Watson and Crick stuff, Professor Bennett. Viruses
> contain only enough nucleic acid to code for just a few proteins of
> limited size. So the large structure of the capsids must be built up
> from these protein subunits by a self-assembly process. Each of these
> subunits must have the same environment. And the only way you can arrange
> them, each having the same environment, is a regular structure of high
> symmetry. It's very much like the cubical class in crystallography.
> Caspar and Klug later extended this idea, which led to the icosahedral
> model.

Still not getting there. You have basically just restated your
"geometrical rules" non-explanation without adding any phyisical
explanation.

I for one would not give your attempt a pass.

Chris Noble

Chris Noble

2006-02-08, 12:59 am

Iconoclaster wrote:
> Therefore all viruses are nice and regular."
>
> No-o-o-o. Not all viruses look the same. But the assembly rules are
> universal.

Can you find a single reference that shows that retroviruses such as
Rous Sarcoma virus assemble according to your version of universal
rules?

> And within one and the same virus species, all particles are the same (And
> spare me the argument about filamental forms. I know about them).

Why do just keep on repeating the same claim over and over again? Do
you think repetition makes it more true?

I have provided you with numerous citations that experimentally show
that many viruses have virions that vary significantly in size.

You on the other hand just keep on repeating the same claim with no
evidence.

Chris Noble

Chris Noble

2006-02-08, 12:59 am

Iconoclaster wrote:
> I'm not sure why you're stating them since they very neatly refute why HIV
> should be expected to remain one fixed size virion."
>
> I'm stating them because I want to keep things in perspective. No sense
> in denying obvious facts.

Then why do you keep on denying the obvious fact that virions of
retroviruses like RSV vary significantly in size?

> The point I'm trying to drive home is that the core size of even an
> enveloped virus should be fixed, based on the size of the protein
> subunits.

The size of the capsid is determined by the number of protein subunits
that are incorporated. There is no absolute "law" that restricts the
number of these units.

<snip>

> But, of course, I couldn't really criticize work I haven't even seen.

Why not? You do it all the time.

Chris Noble

Chris Noble

2006-02-08, 12:59 am

Iconoclaster wrote:

> Cores of retroviruses are spherical or tubular. Yet, those of HIV have a
> conical shape, or even look like coffins (Fuller).

Lentiviruses have cone shaped cores. EIAV has cone shaped cores. This
is how HIV was originally determined to be a lentivirus. Because it
looks like EIAV and not like vesicles.

> The genome of retroviruses is puny compared to that of influenza- or
> herpes viruses. Yet, HIV mutates its XXX off, and is even able to become
> resistent to drugs it does not even interact with...

Where on earth did you get this idea that mutation rates get bigger
with genome size? Mutation rates are determined by the fidelity of the
viral polymerases. Observed mutation rates (substitutions per site per
replication) are inversely correlated with genome size.

Where on earth do you get the idea that HIV does not interact with
ARVs? ARVs interact with viral enzymes such as reverse transcriptase.

> I could go on and on. But if I do, I'll wind up writing a sonnet about
> it.

I have no doubt that you can go on and on. The only limitation is the
voices in your head that keep on suplying you with your "scientific
knowledge".

Chris Noble

Chris Noble

2006-02-08, 12:59 am

Iconoclaster wrote:

> Molecules of one kind (even proteins) floating around
> freely, interact with each other in such a way that they each attain the
> same immediate environment.

Umm you mean like micelles that self-assemble from surfactant
molecules? They show a wide distribution of sizes. They don't exist in
only a single geometric arrangement.

http://en.wikipedia.org/wiki/Micelle

Chris Noble

Iconoclaster

2006-02-13, 10:55 am

Right. I'm back. You didn't really tink I wouln't go after you, Mr.
Noble? How come you were not there, a couple of weeks ago when I was
hunting for you? Even my fellow dissidents complained that it was so dull
in the snakepit.

About the paper in J. Virol. 1976 now:
Yes, it's 30 years old, and they don't write them like that anymore. I
used to (alone, not with 7 people), but that was also 30 years ago.
Anyhow, it's a delightful paper where they perform real mesurements on
real objects. The previous 3 you cited were the usual present-day
bullshit, written by trained apes who would't know a centrifuge or a
spectrophotometer if it fell on their heads from a third story window.
But this one is nice. What does it tell us?
The authors demonstrate that the size distributions of several
retroviruses, as seen in EM's correspond closely to those found in
sedimentation-purified solutions. In the process, many physical
properties of these viruses are determined, such as sedimentation
constants, diffusion constants, Mol. weights, particle sizes, and
percentage water of hydration. Yes, you can get all those data if you
perform real measurements with physical techniques, instead of just
sending an RNA sample off to a service lab to be sequenced, and looking up
the sequence in a gen bank, so that you can write another meaningless
paper, together with 12 other losers who also happen to work in the same
lab.

What about the size distributions you mentioned?
Well, I don't think anybody expected one sharp needle in figs. 8, 9, and
10. Even if you give a class of students a solid object and let them
measure the length of it, you don't get one result but a distribution of
length measurements. In this case, there are doublets in the sample. On
the other hand, we can expect envelopes containing smaller material. It
all depends on the purity of the samples. But from the smallest to the
largest size, what did they observe? A maximum spread from 100 to 180 nm
at the most. That's a long way from the factor 3 or even 3.5 those yo-yos
at Oxford are claiming for "HIV"! And if you cut off at 5% in the
histograms, the size distributions become even a lot sharper.
In a 1976 paper one cannot expect any hogwash about "HIV", fortunately,
because that had not been invented yet. Actually, I was so happy with
that paper that I printed it out, and it's hanging above my bed right now.
(Much better than Carter's porno pics).

But... Meanwhile, Mr. Noble: You have, with much fanfare, put up a
gigantic strawman argument.
Making a big deal out of the question whether a virus could come in
various sizes just tends to take the casual visitor's attention away from
the central points we are discussing here. All this picayune bickering
does not hide these facts:

HIV DOES NOT EXIST, IS NOT SEXUALLY TRANSMITTED, DOES NOT DEPRESS CD4
T-LYMPHOCYTES, AND DOES NOT CAUSE ANY OF THE 29 AIDS-INDICATOR DISEASES.

And remember: I don't have to prove these negatives. You and all the
prostiscientists and the pharmaceutical industry and all their money have
to prove the claims they have made.

Iconoclaster

2006-02-13, 10:55 am

>"There have been electron micrographs of HIV available in the literature
for people to look at since 1984. All it takes is the energy to go to
your local library."

Total crap. The whole dissident world has been crying for these EM's.
None found. Only some pictures with lots of cell debris and a few black
spots that are supposed to be the virus.
And, of course there are the fansasy artist's renditions in full blazing
color...

Iconoclaster

2006-02-13, 10:55 am

>"There are some viruses where the number of capsomers and their
geometrical arrangement in the capsid are narrowly defined. This is not
true in all viruses. In particular it is not true in retroviruses."

Oh yes, also for retroviruses. Capsids that are self-assembling (with or
without nucleic acid inside) have a narrowly defined geometry. The
subunits must all be equivalent (or "quasi equivalent" as Caspar and Klug
pointed out).
Only for "HIV" the true believers want to make this kind of exception.
That's all right. You may give a non-existing object any kind of
properties your blythe mind may come up with. But leave the retroviruses
that really exist alone, please!

Iconoclaster

2006-02-13, 10:55 am

>"On the other hand when I give you several examples of viruses that do
show significant size variations it directly falsifies your claim."

You did no such thing. Three of those papers were crap. Only the
excellent 1976 paper came up with size distributions for 3 known
retroviruses. But these distributions were by no means as broad as the
factor 3 present-day virus-hacks want to sell us.
Those measurements and purifications were a tour de force, by the way.
It's amazing they got distributions that were relatively sharp.

O have an idea: Why don't you try these same methods they used 30 years
ago on HIV? I could use a good laugh.

>"Can you get in contact with Sir Aaron Klug and ask him to confirm your
claim that no virus varies significantly in size?"

I probably could, but haven't seen him for years.

>"You may want to ask why he has his name on HIV research."

Cigarette money, I guess. He's the 7th author, out of 8. All this
genetics shit is definitely not his bag. Maybe he drove the getaway car.

Iconoclaster

2006-02-13, 10:55 am

>"Still not getting there. You have basically just restated your
"geometrical rules" non-explanation without adding any phyisical
explanation."

Oh come on, Mr. Noble! You must be joking. All these subunits are
identical, and have the same binding sites. So they must be arranged in
equivalent positions.

But that may not be the exact answer that's in youyr script...

Chris Noble

2006-02-13, 10:55 am

Iconoclaster wrote:
<debloviated>
> But... Meanwhile, Mr. Noble: You have, with much fanfare, put up a
> gigantic strawman argument.
> Making a big deal out of the question whether a virus could come in
> various sizes just tends to take the casual visitor's attention away from
> the central points we are discussing here. All this picayune bickering
> does not hide these facts:
>
> HIV DOES NOT EXIST, IS NOT SEXUALLY TRANSMITTED, DOES NOT DEPRESS CD4
> T-LYMPHOCYTES, AND DOES NOT CAUSE ANY OF THE 29 AIDS-INDICATOR DISEASES.
>
> And remember: I don't have to prove these negatives. You and all the
> prostiscientists and the pharmaceutical industry and all their money have
> to prove the claims they have made.

Unfortunately science does not work in this fairytale manner. You
cannot just say for instance "Viruses don't cause any disease" and sit
back in your armchair and demand that everyone else prove to you
personally that viruses do indeed exist and do indeed cause disease.

There are a number of kooks that populate physics newsgroups that go
around saying "Einstein was wrong". Nobody takes any notice of them
because they can never come up with a coherent argument why "Einstein
is wrong".

Likewise the arguments you come up with that supposedly demonstrate why
HIV does not exist are false.

You demand to see electron micrographs of HIV. You say they aren't
viral because they look like transport vesicles. When you are asked to
produce electron micrographs of vesicles that look any thing like the
electron micrographs of HIV you admit that you can't.

Then you say that these electron micrographs can't be of a virus
becuase viruses do not vary significantly in size. I present you with
several examples of viruses with virions that do vary significantly in
size and you just keep on repeating the same bullshit.

Before that you said that HIV cannot exist because viruses don't
generally mutate. This is demonstrably false. All RNA viruses have high
mutation rates.

Every time you attempt to come up with an argument as to why HIV does
not exist you end up displaying your own ignorance.

Your final tactic is a tactical retreat and to demand that everyone
eles has to prove to you personally that HIV exists. I am sorry but you
are not the supreme arbiter of viral existence. The validity of
evolutionary science does not depend on whether the so-called
Intelligent-Designer scientists can be convinced.

Chris Noble

Chris Noble

2006-02-13, 10:55 am

Iconoclaster wrote:
> geometrical arrangement in the capsid are narrowly defined. This is not
> true in all viruses. In particular it is not true in retroviruses."
>
> Oh yes, also for retroviruses. Capsids that are self-assembling (with or
> without nucleic acid inside) have a narrowly defined geometry. The
> subunits must all be equivalent (or "quasi equivalent" as Caspar and Klug
> pointed out).
> Only for "HIV" the true believers want to make this kind of exception.
> That's all right. You may give a non-existing object any kind of
> properties your blythe mind may come up with. But leave the retroviruses
> that really exist alone, please!

Can you come up with a single paper that demonstrates that the number
of protein subunits in retroviral capsids are narrowly defined?

I have produced a number of papers that demonstrate that core size in
retroviruses do indeed vary significantly in size.

You would do well to stop evoking the name of Sir Aaron Klug as if it
supports you argument. He was one of the signatories of the Durban
Declaration.

Chris Noble

Iconoclaster

2006-02-13, 10:55 am

>"Can you find a single reference that shows that retroviruses such as Rous
Sarcoma virus assemble according to your version of universal rules?"

Haven't looked for any. But they should; otherwise the rules would not be
*universal*, now would they?
(heh! heh! heh!)

>"I have provided you with numerous citations that experimentally show
that many viruses have virions that vary significantly in size."

No, you didn't. The first three sucked. The fourth (from 1976) was
excellent, but the fairly narrow size distributions don't come anywhere
near the monstrosity that is claimed for "HIV".

Why do you repeat yourself all the time?

Chris Noble

2006-02-13, 10:55 am

Iconoclaster wrote:
> "geometrical rules" non-explanation without adding any phyisical
> explanation."
>
> Oh come on, Mr. Noble! You must be joking. All these subunits are
> identical, and have the same binding sites. So they must be arranged in
> equivalent positions.
>
> But that may not be the exact answer that's in youyr script...

You can take a set of iidentical lipids and put them in water. They may
well self assemble to form micelles. They make even form roughly
spherical micelles. But they form micelles of varying sizes.

Everytime you use the "must" in your explanations you point to your own
ignorance. It is like saying that objects fall down because they must.

Chris Noble

Iconoclaster

2006-02-13, 10:55 am

>"Then why do you keep on denying the obvious fact that virions of
retroviruses like RSV vary significantly in size?"

What, again?! I'm not going beyond the point where I recognize the
results of the 1976 paper you cited.
For RSV the whole distribution ranges from 105 nm to about 175 nm. But
that includes everything present in the sample, including doublettes and
small crap.
Let's not forget that this must have been very difficult work to carry
out.
But you're trying to cover up the fact that I've taken my stand against
the truly ridiculous claim by Briggs and Fuller that "HIV" could vary in
size by a factor 3. They couldn't pay me enough to believe that. How
about you?

Chris Noble

2006-02-13, 10:55 am

Iconoclaster wrote:
> show significant size variations it directly falsifies your claim."
>
> You did no such thing. Three of those papers were crap.

Crap? Because you say so? Isn't it a bit obvious that you reject any
papers that contradict your beliefs. This is the thing about Denialism.
You keep following the same trajectory you are locked into you end up
denying all aspects of science.

> Only the
> excellent 1976 paper came up with size distributions for 3 known
> retroviruses. But these distributions were by no means as broad as the
> factor 3 present-day virus-hacks want to sell us.
> Those measurements and purifications were a tour de force, by the way.
> It's amazing they got distributions that were relatively sharp.
>
> O have an idea: Why don't you try these same methods they used 30 years
> ago on HIV? I could use a good laugh.
>
> claim that no virus varies significantly in size?"
>
> I probably could, but haven't seen him for years.

Well go on. Just do it.

While you are at it contact the university of Leiden and see if you can
arrange to do experiments on HIV there.

>
> Cigarette money, I guess. He's the 7th author, out of 8. All this
> genetics shit is definitely not his bag. Maybe he drove the getaway car.

Why did he sign the Durban Declaration?

Is this genetics shit your bag? You keep on trying to convince someone,
perhaps yourself, that RNA viruses don't generally mutate.

Chris Noble

Chris Noble

2006-02-13, 10:55 am

Iconoclaster wrote:
> Sarcoma virus assemble according to your version of universal rules?"
>
> Haven't looked for any. But they should; otherwise the rules would not be
> *universal*, now would they?
> (heh! heh! heh!)

And all swans are white.

The other paper I cited for RSV is this one.

http://tinyurl.com/axs9o

You have not read the full article but you have dismissed it as being
crap. This is just dishonest.

"Cores are not uniform in size or shape"

> that many viruses have virions that vary significantly in size."
>
> No, you didn't. The first three sucked.

According to you.

> The fourth (from 1976) was
> excellent, but the fairly narrow size distributions don't come anywhere
> near the monstrosity that is claimed for "HIV".
>
> Why do you repeat yourself all the time?

I may repeat myself but I also support my statements with evidence.

You do not.

Chris Noble

Chris Noble

2006-02-13, 10:55 am

Iconoclaster wrote:
> retroviruses like