Bacteria, Circumcision and HIV. Oh my!

Basically every place on our bodies is loaded with bacteria. All of these communities are important (I’ve written about some of the ways before) and more and more research seems to be finding that our microbes play an active role in fighting (or causing) disease.

So maybe it’s obvious that microbes in our swimsuit areas could be involved in sexually transmitted disease. OK, maybe not “obvious” but it may be the case with HIV and the penis microbiota. Did you know that circumcision reduces the rate of HIV transmission to men by 50 – 60%? That’s a pretty significant reduction (no pun intended). There are two major (and non-mutually exclusive) hypotheses as to how circumcision accomplishes this – morphological and bacterial. [SIDENOTE: if you are unfamiliar with the technical aspects of circumcision, I suggest Wikipedia – which has a lot of information but contains an image or two that may not be safe for work – or this Mayo Clinic site.]   

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We’re not missing the penis bone, we just lost it

** Hey y’all – it has come to my attention that the article this post is criticizing might have been more of a tongue-in-cheek textual criticism than a literal hypothesis (like I treated it). Instead of it being “this is what we think is true” opinion, I think it’s more of a “this interpretation of the Bible is more justified by the natural world”. Read at your own risk and sorry for my confusion. – S.Hird **

During his Society of Systematic Biologists presidential address at this year’s Evolution meeting, Jack Sullivan mentioned a rather…unusual…article. (Well, letter, technically.) Congenital Human Baculum Deficiency, by Scott Gilbert and Ziony Zevit was published in the American Journal of Medical Genetics in 2001; it describes their hypothesis that Genesis 2:21-23 doesn’t mean Eve came from one of Adam’s ribs, she came from his baculum.

Walruses have bacula almost 2 feet long – it is required that a picture of a walrus accompany any discussion of bacula.

What’s that, you say? Baculum is the technical term for the penis bone. Many mammals have one – presumably to aid in sexual intercourse. For mammals that mate infrequently, prolonged intercourse ups the chances that a particular male sires some babies. For mammals that must mate quickly, the baculum provides immediate rigidity. And for all mammals, keeping the urethra straight while copulating is imperative, so maybe it’s there to prevent a kink in the works, so to speak. The truth is, there are a lot of hypotheses about what bacula do but – as you might imagine – they’re kind of difficult to test. Regardless, our nearest evolutionary neighbors, the great apes, all have bacula, as do most other primates. Gilbert and Zevit cite this– the fact that our baculum is missing – as evidence for their argument. Which goes like this:

  1. A rib seems like an unlikely origin for Eve because male and female humans have the same number of ribs.
  2. Ribs also lack “intrinsic generative capacity”, which penises have “in practice, in mythology, and in the popular imagination”.
  3. Most mammals – and especially primates – have bacula, humans do not.
  4. It is therefore “probable” that Adam’s baculum was removed to make Eve, and not a rib.

The authors then continue to support their argument with alternate translations of the Hebrew word for “rib” (which they say could mean “support beam”) and claim the raphe of the human male scrotum is what Genesis 2:21 is referring to when it says “The Lord God closed up the flesh.”** I’m almost convinced!

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Friday Coffee Break, Easter/April Fools edition

black coffee with chocolate easter eggs

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

To get this weeks coffee break started, Amy brings us a post about the Paleo diet.  A new book by Marlene Zuk aims to show that the Paleo diet is a misinterpretation of evolution.

Jeremy takes the time this week to wonder about the effect on sea level if all the ships in the ocean were removed.  Alternatively, XKCD also wondered what would happen if you removed all the sponges.

Sarah stumbled upon this gem of a PDF book which will hopefully prove useful as she transitions from student to post doc.  She also brings up the potentially scary idea that you may not own your own DNA.  At least if the current patent situation remains upheld.  What happens if a company can own a 15-base pair fragment of DNA?

CJ continues the discussion on DNA with an article on the recent sequencing of the HeLa genome and the continued controversy regarding the ownership and publication of an individuals genome.  We continue to venture on into a strange new world with these issues.

Which came first: The obese chicken or its obese microbiota?

Historically, medical research has focused on pathogenic bacteria when trying to understand the relationship between human health and microorganisms. This makes intuitive sense – since pathogens make us sick – but our bodies host way more nonpathogenic bacteria than pathogens and they function in keeping us healthy. Our gastrointestinal tract has trillions of bacteria in it and much recent work has been trying to understand these complex communities. Mice are a common model for understanding human gut microbes and health. Enter Obie, the obese mouse (Figure 1, left) and Lenny, the lean mouse (right).

Figure 1: Obie and Lenny

Obie and Lenny are genetically different at a locus in their genomes that codes for leptin – a hormone that inhibits appetite. Mice that can’t make this hormone become very hungry and morbidly obese. These two mice also differ in the composition of their gut microbiota – obese individuals (both mice and human) have different amounts of the main bacterial phyla in their gut and as a result, are able to more efficiently extract calories from food. In other words, if you give both of them the exact same amount of food, Obie is going to get more calories from it than Lenny, contributing to Obie’s weight problem. In humans, where the status of our “leptin locus” is not normally known and probably not as straightforward as the case of Obie and Lenny– it’s been hard to tell whether this shift in gut microbiota is the CAUSE of obesity or the EFFECT of obesity. That brings me to today’s paper: a short communication in The ISME Journal (that’s open access!) by Fei and Zhao that addresses this exact problem.

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Friday Coffee Break, Spring Break Style

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

beachcoffee

To get things started, CJ found a depressing study (depending on your perspective anyway) about how your attitude can affect your health.  It’s not what you would expect a study to find, but there are additional conflicting studies so take it as you will.  However, she follows it up with another article about how the privatization of space flight has a long way to go before we can all reach for the stars.

From Amy, a new variant in the African-American Y-chromosome leads to the speculation on how long ago the common ancestor of modern humans existed and/or whether there was potential interbreeding between Neanderthals and modern humans.

To follow that up, Jeremy found an interesting video that shows a morphing of the faces of human ancestry.

From Sarah, a rather fun blog post on Scientific American on how one individual looked for answers to questions and found lots of information, but failed to answer the original question.

Finally, to return to the spring break theme, the CDC reports in its weekly grand rounds about multi-drug resistant gonorrhea.

Herd Immunity

vaccination

Over the past several years there has been a growing trend of parents that are terrified of vaccinating their kids citing reasons such as the debunked link to autism or that it just isn’t “natural.”   A healthcare blog run by several infectious disease doctors called Controversies in Hospital Infection Prevention has run frequent stories reporting on the declining vaccination rates as well as problems that ensue because of that, most recently about the whooping cough epidemic in Washington and wondering why Jenny McCarthy has so much influence on national views on vaccinations.

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Friday Coffee Break, Turkish style!

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

From Jeremy and Noah:

Apparently this particular link is so impressive it gets two recommendations!  “OneZoom is committed to heightening awareness about the diversity of life on earth, its evolutionary history and the threats of extinction. This website allows you to explore the tree of life in a completely new way.”

From Sarah:

The quintessential list of items every graduate student should have (at least something similar in each category).  And also, in this story on NPR global warming could have a very detrimental effect on one particular species of  lizard the Tautara as egg temperature determines gender.

From Devin:

Australian scientists respond to massive government budget cuts for funding here and also here.

From Amy:

The evolution of drug resistent strains of gonorrhea or how the clap came back.

And finally from Jon:

Healthcare is very slow to adopt new technology but the flood of mobile technology might help make trips to the doctors office less painful with real time updates on when the doctor is available and to help patients check in.

Evolution of Diabetes?

Image

As a medical student and health care professional, if there is one disease that continually comes up in daily discussion, it’s diabetes.  As a disease, diabetes is one that I would not wish on anyone, not that I ever wish disease on anybody to begin, but I wouldn’t wish it on my worst enemy.  As a disease diabetes my initially seem fairly tame, but it has the potential to eventually affect just about every organ system in the body.

As I begin to plan my career as a future Family Medicine Physician, I know that I will be dealing with diabetes on a regular basis.  Any opportunity I have to learn more about the risk factors to look out for in order to help people avoid it, or to better manage it is one I need to take.  So I am following up on a previous post regarding the frequency of the 230Cys allele found in Native American groups as a potential adaptation to feast or famine and storage of energy in the form of fat to hold out during harsh conditions.

How is this relevant to diabetes?  Well, first of all, a little background.  Diabetes is a disease that has a huge global burden. Currently, around 285 million people worldwide are affected and that number could potentially climb to 430 million by the year 2030.  Diabetes also accounts for 12% of all health care expenditure.  It is also a highly genetically associated disease, at least Type 2 Diabetes.  Now, in type 2 diabetes the individual will have high levels of circulating insulin.  Insulin is a key regulator of fat storage.  It is released following meals in response to glucose from the meal and stimulates the uptake of that glucose into liver, muscle and fat.  It also acts to antagonize other hormones that would breakdown and use the stored glucose as energy.  So, this is where I got to thinking, if there is a gene that is linked evolutionarily to helping survive famine, is there a potential link between such genes and diabetes.

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Hands of Blue

Today’s post is going to be a little different from the standard of this site.  No, I’m not writing about Firefly, but I’ll get to that connection in a bit.  I would like to take the opportunity to give the readers of Nothing in Biology Makes Sense a brief glance into an aspect of medicine that few get the opportunity to experience.

I am talking about surgery, specifically, Cardiothoracic surgery, or surgery that takes place by opening up the chest of a patient and putting them on cardiopulmonary bypass in order to operate on the heart (doing coronary bypass, valve replacement, or placement of assist devices).  The reason I feel the need to post about this is because I know I have been given the opportunity that few people (physicians and medical students included) get the chance to experience first hand.  For the last 6 weeks I have been on my surgical rotation, and was lucky enough to be able to spend two of those weeks working with the Cardiothoracic surgeons observing and assisting with open heart surgeries.

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Estimating dates using HIV evolution patterns

In this post we see how we can track mutation rates to estimate when people were infected with HIV and even when the virus first crossed over into humans.

HIV is an evolution machine

Its polymerase enzyme is pretty sloppy and has an error rate of about 1 mistake for every 10 thousand nucleotide bases copied.

For a virus with a genome about 10 thousand bases in length, that means that basically every time HIV replicates itself, it makes a mistake.

Sometimes these errors result in a defective virus, but sometimes they give the virus some new property its predecessor didn’t have, such as resistance to an antiretroviral agent (the drugs we use to treat HIV). The high mutation rate of HIV has also led to extensive worldwide diversity in the epidemic, leading to groupings of related viruses called clades that are named with the letters A through K, and sometimes with two letters where it looks like two clades have recombined into a spliced version of HIV. The different clades are shown in this phylogenetic tree. Also shown are how they relate to other immunodeficiency viruses that infect other primates, as well as how HIV (more precisely, HIV-1) is related to a distinct virus that also infects humans and causes AIDS, called HIV-2, which is mostly confined to west Africa.

This extensive diversity also makes it very difficult to develop an HIV vaccine.

Although the high mutation rate makes things difficult for scientific and medical advances in HIV, it does allow us to see evolution in action, and can lead to some pretty interesting discoveries.

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