Tuesday, March 06, 2007

If this sentence is representative of the book...

I always admired Latin as a written language. Our professor might only ask us to translate a page of Latin into English, but it would take us five pages of English. The Romans were so efficient.

The Romans would be impressed with this sentence from Rebecca Culshaws book that a reader brought to my attention, as it addresses both HIV and ERVs. Culshaw took a page from the Creationist play book and published a pop culture book instead of a journal article, with you know, science. But dont let her PhD in math and direct-to-consumer publication fool you! This chick knows SCIENCE!:

"Furthermore, such apoptosis-inducing proteins as gp120, tat, and nef are present in other retroviruses including human endogenous retroviruses, yet these retroviruses are not thought to induce apoptosis to anywhere near the extent that HIV supposedly does."
OOOOOOOOOOOOOOOOOOOOOOW! How did she do that??? I mean, UD is great at fitting a lot of wrong information into compact language, but theyve had decades and decades to practice! Deniers havent had nearly as long, and look what they can do!

Heres the short reply:
"Well all Staph bacteria secrete toxins, but not all toxins are harmful to humans, therefore Staphylococcus aureus is harmless. Har har har!"

Heres the long reply:

Retroviruses in general just require three genes-- gag, pol, and env (hence my blog subtitle). Other genes like tat, nef, vif, vpr, etc are just accessories for some viruses. Retroviruses in general also have extremely compact genomes, which means to get alllll of the genes it wants, usually there are 'alternate reading frames' and 'alternate splicing patterns' for the same stretch of DNA. Take a look at this pic: (ugh click on it and look at it. thank you blogger.)

See how the boxes are overlapping? You can get more than one protein out of the same stretch of DNA just by starting a base pair later or cutting the proteins up differently. I would not expect ERVs to maintain the sequences necessary to keep the accessory proteins functional. And, a quick PubMed search agrees with me.

'erv env'-- 27 hits
'erv gag'-- 10
'erv pol'-- 20

'erv tat'-- 1 hit, a review (no data) from 1996, doesnt address tats in ERVs
'erv nef'-- 0
'erv vif' --0
'erv vpr'-- 0

As I said, ERVs are a young field, so 27/10/20 vs 0 might not be as impressive as 295876249674234 vs 0, so lets pretend that there are lots of transcribable/translationable tats and nefs in our genomes, we just havent found them yet. Then you have epigenetics to deal with.

There are ways your cells keep certain parts of your DNA from being expressed. You can methylate DNA to keep it from being transcribed, or make modifications to 'histones' to wrap DNA tighter (no transcription) or looser (more transcription). ERVs are wound up TIGHT! Like I said in Part 5 of 'ID vs ERVs', you do NOT want ERVs to become active because of the damage they do! Parts are okay if theyve been co-opted for other uses, but retroviruses are dangerous! Even the envs that are active are only active at very specific times and places when it is safe from an immunological attack.

The reader then brought up an excellent point that I didnt even think of:
Do you know if any HERV has a 'gp120'? ERVs have well-conserved envelope genes, from what I gather, but can they be processed into a gp120 (even assuming that they're transcribed and translated)?

DOH! Of course!

Okay all retroviral envs are cleaved into a transmembrane and subunit piece-- but not all retroviruses cleave into gp120, gp41. gp100, gp135, etc etc etc.

I currently know of no ERV that specifically cleaves into a gp120 SU. gp120-gp41 splicing is not characteristic of all retroviruses in the first place, so when you add in a few million years for an ERV env to mutate, you REALLY would be surprised to find that particular splicing pattern.

What the HELL is Culshaw talking about??

My local library doesnt have this book. Im not buying it... Unless enough people are interested in helping me take it down a la 'Politically Incorrect Guide to Darwinism'. Or maybe one of the Deniers who lurk here will send me a copy?


Chris Noble said...

It is extremely obvious when a creationist regurgitates what they've read from creationist sources. You can ususally tell that they have never opened a biology textbook in their life but are simply repeating what they just read in "Darwin on Trial" or something similar.

The same is true for HIV "rethinkers". Culshaw gives the impression that everything she "knows" about virology epidemiology and diagnostics she "learnt" from reading "rethinker" websites.

Human Immunodeficiency Virus and Acquired Immunodeficiency
Syndrome: Correlation But Not Causation

The presumably specific genes of the HIVs (12, 188) are alternative reading frames of essential genes shared by all retroviruses (3, 7, 12, 23, 90, 148).

3. Institute of Medicine (1986) Confronting AIDS (N .A.S., Washington, D.C.).
7. Institute of Medicine (1988) Confronting AIDS-Update 1988 (N.A.S., Washington, D.C.)
12. Gallo, R.C. & Montagnier, L. (1988) Sci. Am. 259 (4), 41-48.
23. Duesberg, P.H. (1987) Cancer Res. 47, 1199-1220.
90. Baum, R.M. (1987) Chem. Eng. News 65 (47), 14-26.
148. Clavel, F. (1987) AIDS 1, 135-140.

What is the bet that Culshaw never bothered to check these references or read anything published since.

ERV said...

1987! Good god! I would believe she hasnt read a paper published since then-- check out her book intro on Amazon.com. One of her 'complaints' against HIV research is that papers came out too fast, and her papers got sent back to her with 'please review literature' notes.

I would be horrified if I was incompetent enough to get that note. But of course, she blamed her inadequacies on other researchers publishing too fast *rolleyes*

Chris Noble said...

Here is Bialy's more recent version of the "HIV lacks an AIDS-specific gene" story.

5. What is there in the genetic structure or organization of HIV that distinguishes it functionally from other retroviruses such as HTLV-I and II that are not said to cause AIDS?

The citing of apparently different orfs in these viruses is not convincing since a functional genomic analysis can produce similar orfs for almost all of the human and animal retroviruses with sequences deposited in GenBank (G. Moreno and J. Collado, Bioinformatics Unit, International Center for Nitrogen Fixation, UNAM, analysis available on request).

Apparently Bialy reckons that if you play around on a computer with the the genomes of endogenous retroviruses you can get ORFs for tat, nef, vif, vpu etc.

It's not clear whether he thinks that HIV-Tat, Nef, Vif etc are real or just some sort of computer generated virtual proteins. The other claim that I hear regurgitated from "rethinkers" is that HIV has just 3 genes - gag,pol,env.

ERV said...


So HIV is only gag, pol, and env--- but other HIV genes like tat/nef/etc can be found in ERVs? LOL!

In either case, its ridiculous to think that any ERV would have much in common with a modern infectious virus (eg accessory proteins, cleavage patterns, etc)-- and they dont.

Whats their explanation for why nothing that supports their view has been published? Usual Creationist scream of persecution?