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 case of heroes.

A friend of mine shared this on her facebook wall today:

I'll be the first to come out as anti-war.  In my younger days, I identified as a pacifist, and while I no longer think such a concept is feasible or sustainable, I still vouch for peace and hate the glorification of war.  Violence can be necessary, and makes for excellent stories, but in reality it should never be celebrated.  I also am not much of a supporter of troops.  I don't hate them, but I don't feel that they need to be celebrated for serving in wars and conflicts that I believe to be unjust.  These are minor points, however, and I'm more interested in addressing a meme that this particular post exemplifies.  For the sake of this argument, I'm going to speak from a standpoint that supports our troops wholeheartedly.  I can't find an exact term for the meme, so I'll call it the "celebrity over soldier" meme.

The "Celebrity over soldier" meme is this idea that springs up every time a celebrity dies.  Someone decides to point out the great tragedy that this person is mourned while soldiers die and are ignored.  I understand the sense of outrage, especially if you know someone who serves or has served in the military, even more so if that person has suffered in the line of duty.  They served valiantly and protected us, doing something truly great for our country, yet they are forgotten over some random actor, singer, or politician.  Yet if we detach ourselves from the situation and observe the phenominon of mourning from an objective distance, it may be more clear.

Our mourning has no bearing on the objective importance of the death.  When my pet cat died over a year ago, I cried deeply for hours.  When a student in my high school, two years my junior, committed suicide, I felt panic over the notion of death but no tears.  The magnitude of my grief over this mere feline, an animal I would weigh as less important than that of a young human life, was far greater.  We do not mourn because tragedy has befallen someone else.  We mourn because tragedy has befallen us.  Is my cat, whose ashes still rest on my mantle, in any pain or suffering now?  Does he need my sympathy or sadness?  No, my sorrow was for myself, to live without him.

For a celebrity it is much the same.  Some may take it to extremes, but for most the grief is simple.  Celebrities are famous because they have made themselves a part of our lives in some small way.  Whitney Houston's version of "I will always love you" is a classic, and many have been moved by her music.  For me, the death of George Carlin in 2008 was a sad event, as I adored both his standup routine as well as his work in Dogma and Jay and Silent Bob Strike Back, among others.  We mourn them because they contributed something directly to our lives.  We may have their old material, but there will never be anything new.  They were a known quantity, and now they are gone.  We mourn for ourselves.

A dead soldier, heroic though his death may be, is a relative unknown.  There are hundreds of thousands of soldiers serving actively in the US and abroad, and we do not know them individually.  While we have holidays to celebrate their service, we do not know the names of every single soldier.  From a purely objective standpoint, we have not personally lost anything in their death.  If we did not at the very least know of them in life, mourning them in death is disingenuous.

Their service is not to be discounted, of course, but their death does not detract from our way of life; if anything, it promotes our way of life.  They fight to protect us and our interests, and it is that sacrifice that allows us to mourn for celebrities whose deaths mean they will no longer entertain us.  It is not sad, or wrong, or stupid for us to mourn the loss of Whitney (although honestly I think anyone who spends more than a few minutes thinking, "oh how sad" about any celebrity may need to rethink their priorities of what's important in their lives).  Those soldiers died to give us security, a security that means we can worry more about entertainment than whether we'll see the sun tomorrow.  That should be honored, certainly, but not mourned.  Mourning dead soldiers we never knew cheapens their sacrifice and makes their lives important only in their death.

Christmas

Maybe it's the years raised in a primarily catholic home talking.

Maybe it's the traditional (fake) Christmas tree, with its star trek ornaments mixed among armies of santas and hosts of angels.

Maybe it's the music, with all it's cheesy traditional goodwill.

Maybe it's seeing my uncle, my aunts, and my parents again.

I don't really know what it is exactly that does it, but I really like Christmas.  For some it's a celebration of the birth of their manifest deity, while for others the season celebrates the shortest day of the year and the return of the sun.  Be it Yule, or Christmas, or Hanukkah, or Kwanzaa, for many it's a deep religious celebration.  For me, and many others, it's a celebration of togetherness, of family and friends, and of love.  For all the stress, and rampant commercialism, and rampant religious fundamentalism, it still has that joyous allure for me, and while I'm right there with my fellow atheists in arguing for separation of church and state, and demanding we respect all the different traditions during this time while keeping the "christ" out of "christmas," as that special day nears I find myself caring less and less about the politics of it and more about that simple togetherness.

I'll be seeing my Uncle this Christmas Eve.  My uncle is fun, and I love seeing him every Christmas.  He's also a fundamentalist conservative Christian.  He's also a former hippie.  He's ridiculous in so many ways, yet I still love seeing him.  Every year there's worry of drama, of him finally confronting me, of me finally telling him that I'm an atheist and I don't give a damn about his stories of my miracle birth due to his prayers, or of us simply going at it over the dinner table as we argue one way or the other.  It hasn't happened yet, even though I've been a nonchristian for many years.  Does he know I'm not christian?  I think he may suspect it, but I doubt he realizes I'm a dyed-in-the-wool atheist.  Does it matter?  No, not really.  Even though there may come a christmas where we end up having that confrontation, I'm still happy to see him.  He's fun and I like him.  I like his wife, my aunt.  I like his sister, who is far more liberal and far more entertaining.  I like seeing them all, because it's Christmas.

This Christmas eve I'll be eating carrot pudding, watching A Christmas Carol (the original black and white version.  My family are purists for the classic), and enjoying one another's company.  Things will have changed.  This Christmas my grandmother won't be at her house.  I won't be obligated to take her portion of christmas dinner down to her.  She's not well and it won't be quite the same, but I'll still get to see her.  This Christmas will also bring newer blessings with it.  Tomorrow I drive to the airport to pick up my girlfriend, who will be spending Christmas with us.  She'll get to meet my parents for the first time, see the house I grew up in, and will be a new addition to my christmas tradition.  I like that.  My Christmas will be different, but it will not be bad.

Twenty years ago I cared about presents and loathed the ceremony of Christmas dinner.  I barely remember it.
Ten years ago I was still a catholic and was home for winter break after my first semester at Gonzaga.  I was going to be a famous writer one day and majored in English.
Five years ago I was so very, painfully new age, and I was just going back to school after a very long break, having left Gonzaga for various reasons.
Two years ago I was still religious, but only barely, and I had decided I loved science more than english.
A year ago I was an atheist, and knew that I loved science more than teaching.
Today I am still an atheist, and still remain committed to my goals from a year ago.  What is new is my beautiful girlfriend, who makes me feel like I can accomplish anything.

Looking around me, at the tree I decorated, at the life I had before and the life ahead of me, at the dining room table I grew up sitting at, I feel joyous.

Merry Christmas to some, and to the rest may you feel joy in whatever way you choose.

Don't give money to fetus-killers!

Ruh Roh.  Some funding from some bibles supported an organization that supports a program that happens to be put on by an organization that also sometimes provides abortions:

A Christian publisher is withdrawing copies of the "Breast Cancer Awareness Bible," from stores because the Bible helped raised money for the Susan G. Komen Foundation, which contributes to Planned Parenthood.

Oh, well, it's Planned Parenthood, and that's a bad name among Christians.  They probably put all of those funds to aborting fetuses and dancing naked in a wiccan circle, the heathens.  So I guess it's okay.

"Though we have assurances that Komen's funds are used only for breast-cancer screening and awareness, it is not in keeping with LifeWay's core values to have even an indirect relationship with Planned Parenthood," he said

Oh, so the money's all going to breast cancer screening and research?  Well...but it is Planned Parenthood, and they're evil bastards, what with the aborting and promoting promiscuity and whatnot.  Just fund some other company doing breast cancer screening and research.

"In all cases, Komen funding is used exclusively to provide breast cancer programs, including clinical breast exams conducted by trained medical personnel," stated the release. "It's important to note that Komen will only make grants to non-profit organizations. As many mammography providers are for-profit entities, we are only to fund mammography services through grants made to local non-profit service providers."



As long as there are vulnerable communities in need, said the release, "Komen will fund the facilities that can best meet those needs."

So you're saying that you really just went for the group that's going to do the most good in the community?  Well, okay then, but still, our Bible-money shouldn't go to such an evil, underhanded organization, no matter how much good it does!

The Komen Foundation issued a statement Thursday afternoon contending that there were "no dollars going to Planned Parenthood programs" from sales of the Bibles.

...crap.

So basically the Bibles were pulled from the shelves because a portion of proceeds went to an organization that redistributed said funds to nonprofits that would help with breast cancer screenings, awareness, and the all-important research....but that organization sometimes put funds into Planned Parenthood-sponsored breast cancer clinics.

How very righteous of them.

Antivaccination: how Low Can you Go?

Obviously lower than one might originally think, with books like this:

Since when were Measles "marvelous?"  It's one thing to make fallacious arguments about vaccinations, it's another to take those arguments and use them to teach children to embrace potentially life-threatening diseases.

Yick.

Flu Vaccine: Dishonest stat-skeptics

Well, I haven't found anyone else writing about this, probably because it's downright silly, but there's some people out there arguing that the seasonal influenza vaccine is only 1.5% effective.

Specifically, what happened is that a study published in the prestigious journal The Lancet revealed that flu shots provide only “moderate protection” against the flu, and in some seasons is altogether “reduced or absent.”

Specifically, the Lancet said the vaccine is about 59 percent effective. But when you break the numbers down statistically, what it really works out to is that the vaccine prevents flu 1.5 times out of 100.

That’s right. Using the Lancet’s own numbers, statistics show that the vaccine only works 1.5 times out of 100.

Wow.   Sounds pretty damning, and if it were actually true, I might have to rethink my position on the flu vaccine debate.  What we have here is very creative statistics.  The link they provide regarding the 1.5 times out of 100 effectiveness goes to a letter to the editor written by "J.L. Craig, BSN, PhD."  I'm fairly certain the individual in question is one Jennifer Craig, who has written several books against vaccinations and is now retired, so I haven't had much luck on a cursory search of PubMed to see what kind of research she did.  One of my favorite authors over at science-based medicine did a book review of a bunch of anti-vax books, and one of hers was critiqued (It's #6 if you care to get his impression).  She's very clearly anti-vax from her statements, and if this is the same individual then there's some clear bias going in.  That's fair, though, I have clear bias towards vaccination.  Let's look instead at the statistical ploy she uses in her letter:

... let’s examine the study to see how this spin transpired.

This was a meta analysis, meaning that the researchers used data from 28 previously published random controlled trials between 1967 and 2011. The control group, n=13,095, consisted of non-vaccinated adults who were monitored to see if they got confirmed influenza. Over 97 per cent of them did not. Only 357 got flu which means that 2.73 per cent of these adults got the flu in the first place.

The treatment group comprised adults who were vaccinated with a trivalent inactivated influenza vaccine. According to the study, 1.18 per cent got the flu.

The difference between these two groups (2.73 – 1.18) is 1.5 people out of 100. In other words, the flu vaccine did nothing for 98.5 per cent of adults in the studies.

Now in all fairness, she is technically correct.  In those studies 98.5% of people who had the flu shot were unaffected.  They were either already not going to get the flu shot or they got the flu even after having gotten the shot.  Only 1.5% of the people who got the flu shot benefited directly from it.

Does this mean that the flu shot was only 1.5% effective?  Well, no.  Let us say that, in some hypothetical world, a flu vaccine was developed that was perfect.  If you got this vaccine, you were guaranteed not to get the flu.  Not a single person got sick.  We would all agree that this shot was 100% effective.  If you got it, you wouldn't get the flu.  According to her statistical analysis and assuming the same morbidity from the study, the difference between vaccinated and unvaccinated would be (2.73-0.00) or 2.73 people out of 100.  So even with an absolutely, 100% perfect flu shot, it would still do nothing for 97.27 per cent of the population.  Does that mean the shot was only 2.73% effective?

The problem here seems to lie in the numbers.  Our puny mammalian brains have trouble comprehending numbers and making them work.  That's why it's easy for people to get confused by billions vs millions and for us to see a vaccine that cuts the number of infected people by more than half as "only 1.5% effective."  Statistics are easy to manipulate, and it's very easy to use numbers to make your case sound better.

What really gets me is Dr. Craig goes on to accuse the cdc of lying with statistics:

So where did the media get 60 per cent effective? It’s called lying with statistics. First you take the 2.73 per cent in the control group who got flu and you divide that figure into the 1.18 per cent of the treatment group who got the flu. This gives you 0.43.

You then say that 0.43 is 43 per cent of 2.73 and claim that the vaccine results in a 57 per cent decrease in flu infections. This becomes the 60 per cent effectiveness claim.

Erm, Hi.  Pot, Kettle.  Perhaps you've met?  If we really wanted to lie with statistics, we would argue that, since only 1.18% of vaccinated people get the flu, the flu shot must be 98.82% effective.  Now there's some blatant dishonesty for you.

One thing that's also difficult to work with here is that none of these studies involved working with the flu at pandemic levels.  60% efficacy only means a percentage of the population when flu levels are fairly low, but should they reach levels such as in 1918, where roughly 500 million were infected, that means 250 million people avoid the flu if they were all vaccinated.  (At the time that's roughly 30% of the population...that would mean, hopefully, that only 15% of the vaccinated population would get sick).  This is all hypothetical, of course.  More studies would be needed.  Further, the presence of protective immunity may also further reduce the number of people who get sick from the flu.  The higher the number of vaccinated people and the better the vaccine, the greater the herd immunity.  We like herd immunity, since it means the immunodeficient get some protection as well.

I will say one last thing: the mercola article is correct in pointing out that this lancet study showed zero efficacy in some seasons.  That happens.  It's always an educated guess as to which strains of influenza will hit us from year to year, and it would be unreasonably costly to vaccinate us from every flu strain we're aware of.  Even then, it might mutate into something we're entirely unprepared for.  That's part of why we will probably never beat the flu the way we beat smallpox.  I wouldn't ever argue that the flu vaccine is perfect, or even close to perfect.  The only argument I make is that it's the best defense we currently have against a virus that has a proven history of causing pandemic level infections in our population.  You may disagree, and that's fine.  I'm certain I'll get at least one comment arguing that the flu vaccine is bad or, at the very least, unnecessary, and that's fine, too.  My biggest beef is only when others take statistics that say "well, maybe it's only 60% effective instead of 78%" and instead argue that the flu shot has been proven to be pointless.  Don't do that.  It's dumb.

Further Reading:

Mark Crislip on Flu Vaccine Efficacy

WebMD Flu Vaccine FAQ