Wrong, wrong, a thousand times wrong

First it was Todd Akin, who desperately needs some fundamental lessons in biology.

Now it's Senator Stacey Campfield, another republican, who decided to leave us with this nugget of wisdom:

“Most people realize that AIDS came from the homosexual community,” he told Michelangelo Signorile, who hosts a radio program on SiriusXM OutQ. “It was one guy screwing a monkey, if I recall correctly, and then having sex with men. It was an airline pilot, if I recall.”

“My understanding is that it is virtually — not completely, but virtually — impossible to contract AIDS through heterosexual sex.” 

Oh my, where to begin?

Let's start with where he's correct.  There's not a lot of correctness, so it shouldn't take time.  To say that AIDS, or more specifically the virus HIV which causes AIDS, comes from the homosexual community is almost accurate.  The first officially documented case of AIDS in the united states (or at least the most recognized) came in the early 80s, when five homosexual men were treated for pneumonia caused  by Pneumocystis carinii, an opportunistic pathogen (which is to say it only causes disease in certain circumstances, such as if the host were immunocompromised).  Most of the time, HIV was identified in homosexuals and drug users, leading many to initially believe that it was a disease that only affected gays.  That assumption lasted all of two years in the scientific community, when it became obvious that AIDS was not exclusive to homosexuals.

That's not to say this was the first case of HIV in the United States, but it's the first series of cases directly attributed to the virus.  There are theories about the original "patient zero" to bring HIV from Africa to the united states, but nothing conclusive.  The best hypothesis I've seen is that there were a series of well traveled gay men who happened to bring the disease back with them, which explains why it hit the gay community the hardest at first.  So yes, Senator Campfield, it seems at least somewhat reasonable to believe that AIDS originally came to the US from the homosexual community, but the assumption is flawed, as it implies that homosexuals are to blame for the disease.  As many of your ilk are prone, you are blaming the victims.  Strike One.

And there's the entirety of his factual understandings.  Oh, wait, there's one small additional tidbit.  The airline pilot in question refers to Gaetan Dugas, a man formerly considered "patient zero" to the US.  He probably wasn't, and again, there's absolutely no evidence that he had sex with a monkey.

The truth is that we don't have a definitive theory on how HIV originated.  We know fairly well that HIV originated from a strain of SIV (Simian Immunodeficiency Virus), but there are a lot of strands of SIV, each infecting a different primate.  Thanks to a lot of genomic data and analysis, researchers have been able to identify SIVcpz, the strain that specifically infects Pan troglodytes (The chimpanzee), as the culprit.  Of SIVcpz, the closest related viruses are found in Cameroon.  The specific jungle region identified is fairly far from the suspected origin of HIV-1, but there's a river that flows from the region of the SIV chimps to where HIV originated in Kinshasa.  While we don't have solid data on this, there's a lot of strong evidence to suggest that this was the origin of HIV, and it probably came from contact with infected chimp blood (possibly in feces or elsewhere in the river).

Either way, I doubt we'll know for certain exactly where it originated, but it's highly unlikely that it started with some man going all the way into the deep wilderness to have sex with a chimpanzee.  Bestiality may happen, but the likelihood here seems so insignificant as to be considered implausible if not impossible.  So there's strike two.

We know a lot about how HIV spreads.  While it is true that evidence suggests the person doing the penetrating has a lower chance of getting infected than the person being penetrated, infection can and does still occur in significant numbers for either party involved.  One of the biggest concerns in treating HIV in Africa is the threat of a child born to an infected mother.  Another is the common belief that Sex with a virgin will cure AIDS, which potentially has led to a significant increase in women infected with HIV by men.  It is not just stupid, but dangerously foolish to think that heterosexual sex cannot transmit the virus.  Strike Three.  You're out.  Or at least I seriously hope you will be.  Comments like this aren't just wrong.  They breed fear and distrust of others (homosexuals in this case) and promote unsafe behavior (not using protection for sex).  It's worse than the AIDS deniers, especially because this comes from a semi-powerful political voice.

Ugh.

I do this

4 months have come and gone, and I haven't made so much as a peep.  The last semester is in part to blame.  Between Organic Chemistry, Microbial Ecology, Analytical Chemistry, and my independent study, I was fairly swamped and didn't have enough brainpower to really think about any of the significant issues.  Of course, the last semester ended a month and a half ago, so I can't entirely blame that.  I know that the four or so people who actually read my blog on a regular basis are just crushed by my silence.

In any case, things have been busy here.  I took the GRE three weeks back, and that turned out very well.  With 90th percentile in verbal, 93rd in quantitative, and 87th in writing, I can feel comfortable knowing that my GRE scores will only serve to help me get into graduate school.  Also, over the last three weeks I've been doing a summer internship at UC Denver's Anschutz medical campus.  I have to say, the thing I'm most surprised about is the raw amount of reading I've had to do.  There are days where there just isn't a lot I can do on my particular project, so instead I read up about the basic principles surrounding it.  I now know more about miRNAs and gammaherpesvirus 68 (a mouse model for the virus that causes mono) than I ever thought I'd know.

Beyond that, though, it's fantastic.  I've gotten to learn how to do RT-PCR, and my first experiences working with RNA have gone surprisingly well, considering how easily it likes to degrade on researchers.  I've done my first cell cultures, and even got to set up a viral plaque assay.  While I walked into this program feeling overwhelmed by my lack of knowledge, I feel like I'm developing new skills every day.  I may not be stellar yet, and there's more than a few techniques I still haven't done and don't quite grasp, but I'm becoming more confident that research is really the career for me.  (Even if the amount of reading dense material is a bit insane).

Life outside of science is still good.  The girlfriend is still awesome.  The house (lacking air conditioning) is still unbearably hot.  My friends are still supportive and all I could ask for in friends.

Until next time, my friends.

The Virus and the Sanctity of Life

This paper, below, was a project for my Virology class.  I really wanted to go into more detail, but she specifically asked for around one page and I found, if I tried to talk about any other aspect of this debate, that I ran well over that limit.  So am I overall happy with the paper?  Well, no, not really.  Do I think it's reasonable for being limited to a page?  You bet'cha.  Let me know what you think!

Oh, the prompt was simply, "Are Viruses Alive?"  We had to take a side, though I'd like to place them pretty firmly in the "kinda sorta" category.

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                Characterizing viruses as alive or nonliving presents a very real challenge in modern biology; one must, before taking a stance, come with a functional definition of life that can clearly delineate living from the near-living.  This presents a problem, as we don’t really have a definition that accomplishes this.  We know to some extent how life functions, but have difficulty coming up with a clear, concise definition that excludes all things dead yet includes all living things.  The task would be easy if not for the strong societal connotation that “alive” bears.  You can see it permeated throughout our culture.  The 1980s movie Short Circuit focused heavily on this idea, featuring a robot that had argued for his own sentience with such clever catchphrases as “Number Five is alive!”  Humans are overly concerned with the notion of “living” when we actually tend to mean “sentient” or “self-aware.”  Rare is the person who cares if we kill a colony of bacteria, but human life or, to some, animal life bears greater significance.  This concern for the existence of sentient, feeling organisms seems to charge “life” and its variants with a connotation that can impede our efforts to define it. 

                We commonly consider an organism “alive” if it has a metabolism, responds chemically to its environment, maintains a separation from itself and its environment, and is capable of reproduction.  This definition carries with it many problems, as no single characteristic is exclusive to life, and some may, in fact, exclude forms of life.   A man who is infertile is not capable of reproducing more copies of himself (save at a cellular level), but is still considered alive.  A house has clear boundaries, but is quite dead.  A car has a form of metabolism, and nearly everything can respond chemically to their environment in some fashion or another.   A better definition of life must be more specific to have any relevance to biology.

 We know a few things about what we define as life.  All clearly categorized living things have a genome, a code of instructions that can be replicated by the organism.  This genome also undergoes a process to create proteins based on that genome (traditionally transcription followed by translation), which can be used for a variety of purposes.  These features function elegantly, but their function seems little more than that of a machine.  The genome is the programming code, the proteins created by that code are the gears (enzymes and cell signaling proteins), and while capable of some self-repair there comes a point when the machine is no longer capable of functioning.  In machines we might call it simply “irreparably damaged” or “junk.”  In life we call it “dead.”  A “living” machine must be organic and utilize a genome, certainly, but that makes it a category of machinery, not a classification separate from it.  Viruses are merely simpler organic machines.  They are capable of a set of processes defined by their genomic code, and have a point where they can no longer function.   By this presented argument, viruses are alive.  A bacterial spore has little to no function, but is still considered alive since it can be viable years after encysting.  If we accept these simple spores as alive, then a virus, which may like smallpox remain dormant for years and still be virulent, should be considered alive.  A prion, carrying no genetic code but being a peculiar infective result of that code, would not be considered alive.   It is a rogue cog in the machinery of life, causing significant damage yet holding no heritable, reproducible advantage or capability.