Intro to ERVs: Why EVERYONE should care about ERVs!

I wasnt going to talk about this until later, but a commenter/troll left a comment on my last post:

Umm, Do retroviruses have any clinical relevance whatsoever?

Top ten killers in USA per CDC:

Heart disease: 652,091
Cancer: 559,312
Stroke: 143,579
Chronic lower respiratory diseases: 130,933
Accidents: 117,809
Diabetes: 75,119
Alzheimer’s disease: 71,599
Influenza/Pneumonia: 63,001
Nephritis, nephrotic syndrome, and nephrosis: 43,901
Septicemia: 34,136

Do you see any retroviruses on this list? Do you now understand why you toil away at 10 bucks/hour? Your work has not an iota of relevance to the real world.

Sure its flame-bait, but thats all Creationists have, so thats what you are going to be confronted with when you bring up ERVs with a Creationist.

ERV readers, I has a second weapon for you.

ERVs are the cause/effect of a ton of diseases, from MS to juvenile diabetes to all kinds of cancers!!

Endogenous retroviruses are not just a neat example of how we can use genetics to establish, without a doubt, that humans and primates and other organisms share a common ancestor. While that is cool enough on its own… ERVs get even cooler! ERVs have practical implications that effect you and me and your kids and your grandma– everyone!

Once again, there is a cool book on this topic, online, for freeeeee if you would like more details and references, but I want to talk about how I use ERVs so you all will have a nice counter example whenever you encounter an online troll while discussing the evolutionary importance of ERVs.

I am interested in how ERVs relate to cancer. There are lots of ways retroviruses can cause cancer– either they encode for an oncogene, or they insert into a tumor suppressor gene, or upregulate the transcription of an oncogene– lots of things can go ‘wrong’ for the host when retroviruses are involved. You all might remember a few years ago, the SCID patients who were successfully treated for their disease with retroviral gene therapy… only to succumb to leukemia a few years later.

With endogenous retroviruses, well, they obviously didnt insert into a really bad location, because you and me and everyone have these guys, and we are still doing okay. But they are still dangerous. If ERVs are left unchecked, free to make more viruses, the new guys they make could plop into a bad location and cause disease.

So its not just where a retrovirus inserts, but how our genome controls it after it inserts.

One way our genomes have evolved to control mobile DNA, like ERVs, is epigenetics. Its a way our genome can shut off genes it doesnt want expressed. Numerous studies have noticed that in cancers, there are little bits of ERVs hopping around! Sometimes they even make particles! Why? Cause when you have cancer, when you are on chemo, your epigenetic profiles are all messed up, and dead/mutated ERVs are allowed to ‘live’ again!

If you could give cancer patients drugs to help their epigenetic profiles get back into order, their ERVs will go silent again, and the chemo/radiation can do their job, killing the cancer, without ERVs bopping around the genome causing more cancer!

YAY!

So heres the deal– Creationists like William Dembski insist that humans are specially created. ERVs do not exist, scientists are making it all up, whatever. Yet here I am, a graduate student, using evolution and ERVs to help treat cancer. There are hundreds, thousands more of us around the world, trying to figure out how to control ERVs to help treat everything from infertility to breast cancer to schizophrenia!

What do Creationists do all day, again?

Comments

#1 Blake Stacey
May 14, 2008

/me does the free book dance
#2 ShavenYak
May 14, 2008

Even if the idiot troll hadn’t been mistaken about the relevance of retroviruses to cancer, his list is of the top 10 killers in the USA. Worldwide, AIDS does make the top ten, and the sheer numbers of people dying from it make it well worth researching. Except, of course, that most of those people aren’t white, which I’m guessing means to that jackass, they aren’t worth the research.

And I’m pretty sure Abbie isn’t in this for the pay, anyway.
#3 Mark
May 14, 2008

I noticed you mentioned the possibility of controlling ERVs to treat schizophrenia. Is there any similar work being done to treat bipolar disorder? I’m just curious since I am bipolar. If so, do you know where I can read about it? Thanks!
#4 Jason
May 14, 2008

great post Abbie!

I read that and thought to myself, “If that dude had a clue…” well, that and I kept thinking about Rous Sarcoma Virus, Hepatitis B and C, Herpes-cervical/analrectal/oral/neck cancer…

but whatever. They believe what they want.
#5 Joshua Zelinsky
May 14, 2008

The troll’s comment was also terribly anti-intellectual. The troll implied strongly that things are worth studying for their own sake and moreover that if something doesn’t have applications then it can be simply ignored. That seems about par for the course for these sorts of commentators…
#6 Robert O'Brien
May 14, 2008

The practicality (or lack thereof) of your ERVs has no bearing on whether they exist, of course, but until you or someone else actually cures cancer using them and/or common descent I remain unimpressed.
#7 Joshua Zelinsky
May 14, 2008

Marginally connected you link to your old post about what Dembski does all day. Since it is now clear that Galapagos Finch is Robert Marks not Dembski should that post be updated?
#8 Jason
May 14, 2008

I’m sorry in advance – feeding the troll.

Robert – that’s fine, but your understanding of basic science research is as chilling as it is misinformed.

Medically relevant research is almost certainly contingent on biological principles fleshed out in a basic science lab. I study, from a genomic perspective, the evolution of drug resistance. Because I study yeast, and not staph, are you unimpressed?

Look: Rous Sarcoma Virus causes cancer. Had that been a human disease, and not one of chickens, I’m sure you’d be a lot more concerned.

But you should still care because
1) it could still happen to us
2) therapeutic options and strategies can result from enhanced understanding of ERV insertion.

2a) Imagine being able to restore a lost tumor suppressor into a tumor.
-or-
2b) Imagine being able to defend/vaccinate effectively for diseases spread by retroviruses.

Understanding enough of viruses to control something like genomic insertion… that doesn’t happen on its own; mechanistic elucidation comes from basic science.
#9 Robert O'Brien
May 14, 2008

Jason,

How many people living outside, say, the polar ice caps dispute evolution when it is defined as “change in allele frequencies over time?” Precious few, I suspect. Your work with yeast and the hypothesis that humans and apes are descended from a common ancestor are separate issues in my book.
#10 Rev. BigDumbChimp
May 14, 2008

The troll’s comment was also terribly anti-intellectual.

Creationists being anti-intellectual?

Never
#11 Major Transition
May 14, 2008

Robert:

Humans are apes, as originally classified by Linnaeus. What you meant to type is that humans share common ancestry with other great apes. And this has been established via several lines of independent evidence: comparative biochemistry, comparative embryology, comparative morphology, comparative ethology, biogeography, and in the fossil record.
#12 Robert O'Brien
May 14, 2008

Humans are apes, as originally classified by Linnaeus.

That is not my understanding. He used homo for humans and simia for other primates:

http://upload.wikimedia.org/wikipedia/commons/b/bb/Linnaeus_-_Regnum_Animale_(1735).png

In any event, I do not accept the lumping together of apes and humans (other than at the primate level). “Non-human apes” is redundant, as far as I am concerned.
#13 Bernard Bumner
May 14, 2008

Your work with yeast and the hypothesis that humans and apes are descended from a common ancestor are separate issues in my book.

Alas, your book is obviously made from wipe-clean plastic pages, and probably contains very little aside from a story about a boy and his ball… Try reading a new book, maybe one on biology?

If you want to know about the relevence of evolutionary science to yeast research then you might want to look at the great annotated yeast genome databases, and possibly ponder the work of Nurse, Hunt, and Hartwell which took the Nobel Prize for Medicine in 2001.
#14 Rrr
May 14, 2008

Robert O’Brien: Your work with yeast and the hypothesis that humans and apes are descended from a common ancestor are separate issues in my book.

So, tell me quick: When can I buy your book, Rob? Is it a free download? Or maybe it’s still being edited for that bi-decadely ID Journal?
#15 Robert O'Brien
May 14, 2008

If you want to know about the relevence of evolutionary science to yeast research…

This is not difficult, so try to follow along. I want to know about the relevance of the purported common descent of apes and humans to yeast research.
#16 Major Transition
May 14, 2008

“In any event, I do not accept the lumping together of apes and humans”

Why not? Humans and chimpanzees are more closely related to each other than either are to gorillas. This is why some systematists have argued that chimpanzees should be changed from Pan to Homo. We are separated from chimpanzees by roughly 7 million years; by comparison some species of Drosophila are separated by multiples of this. I can’t see any good scientific reasons for not classifying humans as apes.
#17 Bernard Bumner
May 14, 2008

This is not difficult, so try to follow along. I want to know about the relevance of the purported common descent of apes and humans to yeast research.

The relevance is that the evidence for human evolution is self-consistent with the wider evidence for all eukaryotic evolution. The selfsame evidence which demonstrates the one, demonstrates the other, and underpins much of modern biology. If the evidence for common ancestry of humans and other apes is flawed, then it also necessarily invalidates much of what is known about the evolutionary history and biology of other eukaryotes, including yeast.

The fact of common ancestry is not some revelation which exists in an vacuum.
#18 Bernard Bumner
May 14, 2008

Oh, I should add that more generally, the shared ancestry of modern eukaryotes has obvious and important implications for all areas of comparative biology, whether it be fundamental cell biology, genomics, proteomics, or any other.
#19 Robert O'Brien
May 14, 2008

Humans are exclusively bipedal animals whose hands are “freed up” for complex manipulation; whereas, chimpanzees are characterized by quadrupedalism. (Yes, I am aware that they have been known to walk upright for brief periods but that is not their “natural” form of locomotion.) There is also the issue of human intelligence versus that of chimpanzees. (Although, some atheists make me wonder about that distinction.)

In fine, I think more should be taken to account than just genetic commonality.
#20 Jason
May 14, 2008

Bipedalism does not change the underlying genetics and biochemistry. Having 95+% similarity in the genomes suggests commonality of function ‘under the hood’.

You’re using behavior to define arbitrary boundaries?

Are penguins not birds because they only swim and do not fly? Or are emus, kiwis and ostriches not birds, either? They walk, and cannot fly or swim.
#21 Bernard Bumner
May 14, 2008

In fine, I think more should be taken to account than just genetic commonality.

Which it is, and hence the recognition of the fact that humans come from a distinct lineage within the homo genus, which is defined via those characteristics which are unique to human apes and their ancestors.

Phylogenetics have been used to refine taxonomic classification, but this is still ultimately a descriptive system of cataloguing. Semantic tricks will not change the nature of the biology: saying that humans aren’t apes will not change a single percentage point of that genetic relatedness.
#22 Major Transition
May 14, 2008

“Humans are exclusively bipedal animals whose hands are “freed up” for complex manipulation…There is also the issue of human intelligence versus that of chimpanzees”

These are derived characteristics in the human lineage, but they don’t invalidate the genetic data. If chimpanzees and gorillas are classified as apes then it would be absurd to exclude humans since chimpanzees are more closely related to humans than they are to gorillas. This would also make the ape clade paraphyletic, which is undesirable.

For example, cetaceans are aquatic animals with anatomies greatly modified for living in the water. This does not mean that we should privilege these derived characteristics over their other characteristics which indicate that they are mammals. Some lineages evolve phenotypically more radically than other lineages – as a result of exploiting new environments, for example – but this is not a basis for excluding them from monophyletic groups that they belong to.
#23 mgarelick
May 14, 2008

10 dollars an hour? Righteous bucks, man. (Name that stoner.)
#24 Robert O'Brien
May 14, 2008

If you (biologists) find that classification useful, then you are welcome to it. Just as you are welcome to common descent. Even if I were in the position to compel you to repudiate common descent I would not; your acceptance of common descent “neither picks my pocket nor breaks my leg.” I, however, have no use for it.
#25 Major Transition
May 14, 2008

“If you (biologists) find that classification useful…”

Yes, it is generally best practice to define taxonomic groups as clades (monophyletic groups). There are some cases when it might be handy to break this rule – prokaryota, for example, is a useful grouping even though it is paraphyletic. But I originally thought that you were objecting on a scientific basis, but now I see that you’re not. Carry on.
#26 Bernard Bumner
May 14, 2008

If you (biologists) find that classification useful, then you are welcome to it. Just as you are welcome to common descent. Even if I were in the position to compel you to repudiate common descent I would not; your acceptance of common descent “neither picks my pocket nor breaks my leg.” I, however, have no use for it.

Well, fine. I don’t necessarily invoke the common ancestry of apes when, for instance, I’m choosing what coloured shirt I’m going to wear. There are literally thousands of situations where I have no use for this mater of biological fact.

However, biologists not only have use for such a fact, but would be forced to recognize that fact even were it not useful. It is the only logical conclusion to be drawn from a huge body of supporting evidence.

Now then; you might choose to ignore such evidence and conclusions, but it doesn’t make you right. It does make you somewhat intellectually dishonest, because it represents a conscious decision to turn away from an expert consensus in favour of a personal revelation. Still, if it makes no difference to you, then you have only your own conscience to worry about.
#27 Andy
May 14, 2008

Forget all this. The dude’s argument is toast: I work in a cancer lab and still get paid $10/hour.
#28 michael fugate
May 14, 2008

Robert,
Since you are a christian, I am having difficulty seeing the difference it makes to you if your god was the creator of all living things separately or the creator of one living thing that evolved into all other living things – either way they all share a common ancestry.
#29 Bernard Bumner
May 14, 2008

Forget all this. The dude’s argument is toast: I work in a cancer lab and still get paid $10/hour.

Not including the 100s of hours unpaid overtime, I presume?

If scientists were really paid what we’re worth to society, then we’d all be too drunk on champagne and bloated on caviar and fois gras* to do any actual science.

*I’m not sure that vegetarianism is really an option for money-crazed decadence.
#30 David Marjanovi?
May 14, 2008

That is not my understanding. He used homo for humans and simia for other primates:

Firstly, he used Homo (genera get capital letters!) for humans (Homo sapiens) and chimpanzees (Homo troglodytes).

Secondly, he wrote in a private letter that he was unable to find any “genus-level characters” that would justify separating Homo from Simia; he just did it because he was afraid of the scandal Simia sapiens would have produced — his classifying of humans as primates and mammals already triggered a big enough scandal, and Linnaeus was a pious creationist who explicitly rejected Buffon’s theory of evolution.

Humans are exclusively bipedal animals whose hands are “freed up” for complex manipulation; whereas, chimpanzees are characterized by quadrupedalism. (Yes, I am aware that they have been known to walk upright for brief periods but that is not their “natural” form of locomotion.) There is also the issue of human intelligence versus that of chimpanzees. (Although, some atheists make me wonder about that distinction.)

And?

If you dye your hair pink, are you no longer a human?
#31 Monado, FCD
May 14, 2008

about 15% of people have mouse mamillary tumor virus in their DNA, which makes them more likely to develop breast cancer. Conversely, 40% – 60% of breast cancer in humans includes the mouse virus. I don’t know if it’s an ERV, but I suspect it is.
#32 Joshua Zelinsky
May 14, 2008

Bernard, it is arguably a good thing too since this way the people who become scientists are the people who are in it to do science not the people who want to make a lot of money.
#33 Jeb, FCD
May 14, 2008

@23:

Jeff Spicoli!
#34 Dr. Duke
May 14, 2008

Monado, there is no such thing as a mamillary tumor virus. And the idea that 15% of people have Mouse Mammary Tumor Virus anywhere in their body is not well established. Likewise for any link to breast or other cancers. The linkage between cancers and viruses such as Epstein Barr virus, Simian Virus 40, Human Papilloma Virus type 16 and others if FAR stronger than the link between the Mouse Mammary Tumor Virus and cancer. Has anyone ever cultured the MMTV from a human? Has anyone found where it is integrated into the human genome? Or do they only have PCR products of fragments?
#35 Dr Benway
May 14, 2008

This is not difficult, so try to follow along. I want to know about the relevance of the purported common descent of apes and humans to yeast research.

Silly question. It’s like asking, “How does the purported common property of “gravity” for planets and golf balls apply to modern ballistics?
#36 ERV
May 14, 2008

Duke–
The fastest way to start a fistfight at a retrovirus conference: Scream “MMTV CAUSES BREAST CANCER!!!” into a packed auditorium.

LOL!!

One of my lab-mates studies MMTV in humans– its a contentious topic
#37 Eric Saveau
May 14, 2008

I see Phlegming is back. And still no response to the question I posed. Nor, as I scan the comments, to anything previously or currently said to him by other commenters. If I were at all cynical, I might get the impression that he is simply a vainglorious anti-intellectual bomb-thrower with nothing of any substance to contribute to this or any discussion.

And that his penis is horrifyingly small.

*blink*
#38 Joe
May 14, 2008

but until you or someone else actually cures cancer using them and/or common descent I remain unimpressed.

Me, I’m just gob-smacked by the concept of using ERVs to cure common descent.
#39 Brian
May 14, 2008

Do you see any retroviruses on this list? Do you now understand why you toil away at 10 bucks/hour? Your work has not an iota of relevance to the real world.

Clearly spoken by someone who has never been a grad student. It doesn’t matter what relevance your work has. You’re paid crap and get very little recognition, unless you have the greatest PI ever.

Probably preaching to the choir hear. *shrug*

(A tad touchy on the relevance to the real world thing, since my interest lies in beyond standard model physics…. lol)
#40 jeff
May 15, 2008

Probably preaching to the choir (and the incurably inrectotestulated), but think for a second about the people you know who have had cancer and are not dead. WHY are they not dead ? (Cuz’ gawd hain’t kild em yet, DUH !) Much, if not most, of the credit goes to “irrelevant” non-useful basic science.

X-rays : rocks make film turn foggy, even in complete darkness : I WONDER WHY ?

Nuclear Magnetic Resonance (NMR) : if we put a nucleus in a magnetic field, we can tickle it with radio waves and make it jiggle : THAT’S SO COOL, WHAT ELSE CAN WE DO ?

Anti-matter : Dirac’s equation seems to describe electron spin okay, and it agrees with relativity, but there’s this extra particle, that’s sort of the opposite of an electron : WHAT’S UP WITH THAT ?

Ask any of your un-dead cancer friends what (after prayer, of course !) was the biggest break that kept them from dying, and I’ll bet you’ll find it comes down to early detection. Apart from skin cancer, the early detection of cancer relies very heavily on imaging techniques such as CT scan(xrays), MRI(NRM), PET scan(antimatter) that grew out of poorly funded, useless, highly esoteric science that was done purely for the sake of curiosity and fascination, and _clearly_ had nothing to do with curing disease.
#41 Steven
May 16, 2008

“Do you see any retroviruses on this list? Do you now understand why you toil away at 10 bucks/hour? Your work has not an iota of relevance to the real world.”

If she was in it for the money she could be a dishonest hack creationist tool and syphon money from the credulous till she was blue in the face.

Silly Abbie. She wants to understand the world, contribute to human knowledge and perhaps help people.

Hell it is for her.

Fantastic BBQ though.
#42 Fleming
May 16, 2008

Whoa! What a testy bunch!

Ok, I’ll make it even easier:

Q: Are any Human endogenous retroviruses a top 10 cause a death in the US?

A: No.

Q: Is there ANY well-known disease CAUSED by a Human endogenous Retrovirus?

HERV’s do NOTHING. They are genetic debris just loitering in the human genome. Junk DNA. Sure, they seem to be relevant to evolution, you twerps, but I am talking about DISEASE.

They have no clinical relevance whatsoever. They are MEDICALLY IRRELEVANT. That is why grad students get paid $10/hour to study them, as opposed to making $10/hour shining shoes at the Bus Depot.
#43 Eric Saveau
May 16, 2008

The return of Phlegming! Excellent!

So, with regard to your comment – The quest for an HIV vaccine is an utter failure. All scientists who have been part of this inept quest should really be fired.

- I once again repeat my question: And replaced with whom? Or are you saying that no one should even make the attempt?
#44 007
May 16, 2008

FYI, this guy is a notorious troll: Wavy Davy (creationism – see Panda’s Thumb), Hank Barnes (AIDS denial – see Aetiology), the list of pseudonyms goes on. He’s really a personal injury lawyer from San Francisco named D. David Steele. His unique sense of logic always forces him to make little lists in his posts like the Q & A above.
#45 trrll
May 18, 2008

They have no clinical relevance whatsoever. They are MEDICALLY IRRELEVANT. That is why grad students get paid $10/hour to study them, as opposed to making $10/hour shining shoes at the Bus Depot.

Riiiiiight. So why is it that grad students also get paid $10/hour to study cancer and heart disease?
#46 Monado
May 25, 2009

Duke, ERV, in that case, I look forward to further developments. Teach the controversy!
#47 Hu
May 26, 2009

X-rays : rocks make film turn foggy, even in complete darkness : I WONDER WHY ?

To pick a nit, that’s how radioactivity was discovered, soon after Roentgen had discovered X-rays while researching cathode rays (electrons in a vacuum tube). Anyway, Roentgen wasn’t trying to cure or diagnose any disease, so your point stands.