Finals Week Mix Tape

It's been a while since last I wrote and wow do I have a backlog of sciencey stuff about which to nerd-out, but it's Finals Time around here. And that can mean only one thing.    

We need a mix tape.

I submit for your consideration my patented Finals Week Playlist, as appropriate for those taking finals as it is for those writing/grading them.  I think this is most effective as a Dance Party Break between bouts of studying/grading.  Explanations are provided for each entry; be warned that some selections involve adult language.

The Final Countdown (Europe)

I have yet to make it through a semester without having this end up on repeat during Finals Week (and the weeks leading up to Finals Week. let's be honest here).  It is inspirational and incorporates many things I loved about the 80s, including big hair and synthesizers.

Move in the Right Direction (Gossip)

It's a little poppy and a little motivational as far as Gossip go, but at the end of the semester (especially Fall semester, when daylight is scarce) poppy and motivational is what I need.  If you prefer your motivational music a bit more indy rock, sub in Standing in the Way of Control here.

Higher Ground (Red Hot Chili Peppers)

It is rare that I prefer a cover version to the original; the RHCP rendition of Stevie Wonder's hit is one of the few exceptions to my rule.  If you'd rather, pull up the version of this song from Center Stage and take a break from studying to twirl 'till you fall over.

Don't Stop Believing (Glee)

"If those high school kids can pull together a Glee Club performance with nothing but pluck and hard work then surely I can pass all these exams!"

Jump (Van Halen)
Deployment of David Lee Roth = automatic 10-fold boost in energy levels.  I'm serious. Try it.

Jump (Pointer Sisters)

Is it even possible to listen to one Jump without the others?  If it is, I don't want to know.

Jump (Kris Kross)
See comment above.  If you're not perked-up by now then I'm at a loss.

A Little Respect (Erasure)

Okay, now I'm really at a loss.

Heat of the Moment (Asia)

If you saw "Final Countdown" and thought, "Oh, that song by Asia!" then this is for you.  It's an appropriate bookend opposite Europe, to be sure.

Did I miss a crucial song? Have a piece of music you can't live without during exam time? Tell me about it in the comments.

May you all go forth and kick much behind on your respective exams (or rubrics, as the case may be).

Chin Cleft

What causes "butt chin?"

(my students' wording, not mine)

Back when my Anatomy students studied the mandible, folks became curious about chin clefts (referred to as "butt chin" by the student who finally asked about them).  A fine example of this may be viewed on one of my childhood heroes, the Muppet Show's own Statler:

Waldorf (left) and Statler (right, rockin' the chin cleft)

There are several things going on with Statler's chin, but let's focus on the cleft running along the midline.

It's worth noting that chins do not exist within a smooth/clefted binary - there is instead a variety of chins that can exist along the spectrum between smooth and clefted.  For an example of this spectrum, check out John McDonald's photographic survey of congressmans' chins here.

Conventional wisdom has told us that chin clefts were caused by a single gene.  More recent information suggests, however, that this is either a polygenic trait (McDonald, 2011) or a trait caused by a single gene with variable penetrance (Starr, 2004).  Let's translate that out of fancy-pants science-speak, shall we?


"... this is either a polygenic trait ..."
Many folks are familiar with how genes (the functional sections of DNA in each cell of the body) influence traits (the physical characteristics of the body).  If you're not one of these folks, I recommend checking-out this resource and/or watching this tutorial before continuing.  The simplest way to think of how genes lead to physical characteristics is with Mendelian traits, those that are caused by a single gene location.  For a Mendelian trait (for example, albinism), a person will have just 2 copies of the responsible gene - one from the biological mother and one from the biological father.  These 2 copies (alleles) of the gene will duke it out to determine the physical characteristic that manifests in the body.  If a trait is a Mendelian trait, it generally follows particular patterns of inheritance and manifests in a binary fashion - in the case of albinism, folks are generally albino or not albino.   If you've learned about physical characteristics that are caused by genes from a textbook or in a class, these were most likely Mendelian traits as they're the most straightforward examples to use for folks just learning about genetics.

Not all physical characteristics are Mendelian traits - that is, not all physical characteristics are caused by a single gene location and follow a predictable inheritance pattern.  Traits that are caused by multiple genes are referred to as polygenic traits.  Many of a person's most noticeable features - height, hair color, eye color - are examples of polygenic traits.  What this means is, for example, a person's eye color is the result of input from several genes.  Polygenic traits are also referred to as "continuous traits," or traits where there is a small grade of change between individuals.  As opposed to Mendelian traits which are generally binary (individuals in a population either have a particular trait or they don't), polygenic/continuous traits exist along a continuum.  Again, consider human height as an example.  If height were a Mendelian trait we might expect to see 2 possible characteristics within the human population - "tall" (all the individuals of the same relatively tall height, say 6 feet) and "not tall" (all the individuals of the same relatively shorter height, say 5 feet).  If we actually look at the human population this is not what we see - human height exist as a continuum where a person might be 5 feet 2 inches, or 6 feet 3 inches, or 4 feet 11 inches or anything in between (depending upon what that person's genes say).  For further explanation/an example of this, go here.

Okay, so what does this have to do with chin clefts?  Well, I stated earlier that current thinking is that chin clefting seems to be a continuous trait - this physical characteristic doesn't appear to be one that individuals in the population either have (to an equal degree) or don't have at all, but rather one that exists on a continuum from "no cleft" to "very clefted." This may point to it being a polygenic trait.

Another way to have a physical characteristic that is continuous is variable penetrance.


"... or a trait caused by a single gene with variable penetrance."
In genetics-speak, penetrance refers to the proportion of individuals carrying a particular copy/allele of a gene who actually display the physical characteristics that it causes.  If a gene is said to have "complete penetrance" that means that whenever a particular allele of that gene is present, the same physical characteristics are present throughout the population (so any individual with that allele will have the characteristic that goes with it).  If a gene is said to have "incomplete penetrance" that means that individuals who carry a particular allele of a gene don't always display the physical characteristic that it causes, or display them to the same degree.  This would allow for a trait that is controlled by only 1 gene location to also be continuous.  And again, since current information suggest that chin clefting is a continuous trait, this may be what is causing the continuum of chins that we see in the world.


The Upshot
Overall, the answer to what causes chin cleft seems to solidly be, "We don't know!" but current thinking points to it not being a Mendelian trait.

References

Beckman, L., Book, J.A., Lander, E. (1960) An evaluation of some anthropological traits used in paternity tests. Hereditas. 46(3-4): 543-569.DOI: 10.1111/j.1601-5223.1960.tb03100.x

Gray, H. (1918) "5b. 8. The Mandible (Lower Jaw)" in Anatomy of the Human Body. Retrieved on 23 February 2014 from http://www.bartleby.com/107/44.html

McDonald, J. (2011) "Cleft chin: The myth." Myths of Human Genetics. University of Delaware. Retrieved on 14 August 2013 from 

http://udel.edu/~mcdonald/mythcleftchin.html

"Penetrance" (2014) Genetics Home Reference. Retrieved on 23 February 2014 from http://ghr.nlm.nih.gov/glossary=penetrance

"Polygenic" (2014) Genetics Home Reference. Retrieved on 11 January 2014 from http://ghr.nlm.nih.gov/glossary=polygenic

Starr, B. (2004) "Ask a Geneticist." Understanding Genetics. TheTech. Retrieved on 11 January 2014 from http://genetics.thetech.org/ask/ask47.

Finding Answers, Part 2

We now return you to our continuing adventure in research, in which Your Humble Professor attempts to impart some wisdom on finding one's own answers.

In a previous adventure, we began discussing how one utilizes The Google to search for information in as safe and sane a manner as possible. In today's episode we'll talk about how to make sense of the results page and the resources provided therein.  I like to call this, 

"WHAT DO I DO WITH ALL OF THESE @#$%ING LINKS??!?"

In general, the goal here is to nab a few tools that help one evaluate the reliability of an informational resource.  This is a handy skillset not only for students of pesky teachers like me (who demand it of them constantly) but also of actual humans in the actual world.

Author's note: Please keep in mind that I was trained as a bench researcher.  I was taught to look for evidence and to back-up suppositions with data.  I <3 data.  Data, data, data.  This definitely shapes the way that I find and evaluate information in the world around me.  It can also make me a rather awkward dinner party guest.

Illustration by Jorge Cham, PHD Comics

Okay. So. You've gotten thyself to Google and used some awesome search terms and now you have a results page, which is a list of links to web resources that you may or may not find informationally useful.  First, let's acknowledge that It is a completely normal human impulse to start from the top and click on the first link on the list.  It must be the most relevant, the most important, the most reliable, the most wittily-written - why else would it be the first link???  

The thing is that several factors go into the order of links on a results page - in part this has to do with how well it matches your search terms and the overall quality/freshness of the website, but these aren't the only determinants.  Google also considers how many other websites link to a particular web resource (a measure known as PageRank) in placing a site on your results page. The point is that the first link on your results page may be the "best" resource for the information you're seeking ... and it may not.  

Check the domain
Before you start clicking, I suggest you scroll through your first page or 2 of results and perform triage.  One quick-and-dirty way to do this is to check the domain of each resource.  The domain is the suffix of a page's web address - for example ".com," ".org," ".edu".  The domain can give you a rough idea of who/what organization is responsible for the webpage (Webopedia has a list of some common domains here). There are also ways to alter your intial Google search so that the results are limited to only certain domains - for example, if you want results from only educational institutions, you could limit your search to pages whose addresses end only in ".edu".  While this can be a helpful practice, it is certainly not foolproof - just because a website is a ".org" or even a ".edu," that does not automatically make it informationally awesome.  A website that ends in ".biz" is not necessarily a poor resource.  However, performing such a check may allow you to be more targeted in your subsequent clicking, thereby making more effective use of your time and finger muscles.

Look for advertisements
Once you've settled on a link to click, take a look at where you end up.  In particular, pay attention to whether the website has advertisements or obvious sponsorship.  If so, consider how this might impact the information provided by the resource.  Finding that a website has ads or sponsors does not automatically make the information it contains inaccurate or biased;  knowing this is simply something to consider in evaluating the reliability/potential bias of the information it presents.

Check the "About" page
Many web pages have an "About" page that tells a reader more about the individual/group responsible for the resource.  Is this someone's personal webpage (and if so, what are that person's credentials? does the person seem reasonably qualified to share the information being imparted on the site?)?  Is this a resource created by a governmental organization?  Is the site produced by a group that might have an agenda such that the information could be biased?  Again, none of these automatically tanks a resource but knowing who is responsible is an important aspect of evaluating the reliability of the information it contains.

Check for citations
As you read through the informational portions of the site, check to see if there is acknowledgement of its own informational sources.  Are there in-text citations, footnotes or links? Are you, the reader, given the opportunity to view and evaluate the source material and draw an independent conclusion?  A resource that does this may inspire added confidence in a reader;  if nothing else, it gives you the ability to directly consult sources and make your own evaluation.

Trust your Dubious Eyebrow
We come now to the Holy Grail of resource evaluation tools, the researcher's best friend, that shining light in the darkness that is the internet: the Dubious Eyebrow.

"Oh really."

Everyone has a Dubious Eyebrow.  When it activates, pay attention.  This is your cue that something is not quite okay with the resource in front of you.  It's then up to you, the researcher, to determine what that is (is the resource's information not up-to-date?  is the writer unqualified to be writing on the topic? are all the cited sources fictitious?) and whether it's a deal-breaker for using that resource.  If yes, get thee back to your results page and try again.  If no, determine how big an impact the not-quite-okay has on the usability of the resource and what is still salvageable.

In Short
The suggestions above are guiding principles I suggest for navigating informational resources on the internet. For folks who aren't in the habit of critically evaluating their resources, it can seem a bit overwhelming at first.

No.

Rest assured that with practice, this is habit-forming.  The more often you engage in this process (when performing research for, say, a term paper), the easier/more natural it becomes and the more likely you are to unconsciously start employing it in every day life (when perusing articles friends have posted on Facebook or engaging in witty banter at the dinner table).

Acknowledgements

Credit for the knowledge I impart in this series goes to the following individuals, who have taught me pretty much all of what I know about informational research:  Yvonne Piper, R.N., F.N.P, M.L.I.S., Patricia Elzie, M.L.I.S., Joel Burton, M.A. and David Patterson, Ph.D.

Why?

Why does <insert name of body part here> look like that?

or

Why does <insert name of body part here> work like that?

These tend to come up when students learn about some feature of the human body that doesn't seem very sensical to them; favorite examples include the electron transport chain in aerobic respiration and urine production in the nephron.  When students ask these questions, my answer generally looks something like this:

Neil deGrasse Tyson said it best

... because, really, I don't know exactly why things look/work the way they do.  In these situations, I turn to evolutionary biology.

If folks think of the human body as a structure that was designed from the ground up, with goals in mind, features may indeed seem pretty nonsensical.  However, evidence suggests this was not a ground-up, goal-directed design process at all.  Evolution is more a "repurposing" - taking a feature that already exists and modifying it to perform another function.

Repurposing.

Even that is a not-entirely-accurate, wildly oversimplified way of explaining evolution, as those modifications are thought to be randomly-occurring.  In the words of Lynn Sagan in 1967, "... evolution is opportunistic and not foresighted."  What is already present may, with a few random mutations, become modified such that it performs a new function.  And that new function may increase the organism's likelihood of surviving and reproducing.  And that feature may not be the most elegant or streamlined way of performing that function, but if it works, it doesn't have to be pretty.  In the end, this process may produce some systems that resemble Rube Goldberg machines.

As I mentioned, my students often find the mechanics of the electron transport chain (ETC) to be crazy-making.  The part that confounds many is what they perceive as design flaws - "Why the heck would anyone set it up that way???"  And my answer is, "They probably wouldn't."  If we think about building a system with the goal of the ETC in mind (ultimately making a boatload of ATP), the current system looks positively nuts.  If, however, we think about the ETC as a repurposing of already-existing elements in a way that ultimately permitted this function, it may come off a bit different.

Scientific American published an article that speaks to this point of design vs. evolution in 2003.  It discusses how humans might look and function differently were we designed from the ground up.

References

Alberts, B., et. al. (2002) "The Evolution of Electron-Transport Chains." In Molecular Biology of the Cell, 4th edition. New York: Garland Science. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK26849/ 

Sagan, L. (1967) On the origin of mitosing cells. J Theoret Biol. 14: 225-274. http://www.gps.caltech.edu/classes/ge246/endosymbiotictheory_marguli.pdf

Joints ... & Lady Gaga

By now you've probably heard - Lady Gaga has cancelled the remainder of her Born This Way Ball Tour due to a hip injury.  Specifically, the issue is reported to be a labral tear at her hip joint, and some sources are speculating this may have been exacerbated by lupus (although it has not been confirmed that she actually has lupus, despite an apparent family history).

We just finished covering joints in my anatomy class, so let's talk about what might have gone down in Our Good Lady's hip, shall we?

Hip Joint Anatomy

The hip joint, also known as the acetabulofemoral joint, is the connection between the bone of the thigh and the pelvis (at the hip bone/os coxa).  Specifically, the head of the femur ("thigh bone") forms a ball and socket joint with the acetabulum (the cup-shaped indentation) of the hip bone, hence the name acetabulofemoral joint.  The hip joint is a synovial joint, which means it has a complex structure that includes supporting tissues, a joint cavity and synovial fluid, and it is also a diarthrosis, which means it is a freely moveable joint.

As a synovial joint, the hip joint is stabilized by a series of structures including ligaments and surrounding muscles.  There is also the labrum, a ring of fibrocartilage that helps the acetabulum (the depression in the hip bone) to grip the femoral head and make dislocation less likely.

Left hip joint, disarticulated

The consensus seems to be that folks who are especially active with their hip joints are at a higher risk of injuring a labrum - ballet dancers keep coming up as a prime example.  While she's not exactly a prima ballerina, I suspect folks who have seen Lady Gaga do her thing would agree she's quite active with her hip joints.  As such, I feel comfortable putting her in a category of folks who are more likely than most to tear a labrum.

When the labrum tears, depending on the severity of the tear symptoms can range from pain and stiffness to loss of mobility at the joint.  The treatment will depend on the severity of damage and the symptoms - for some this may be a course of anti-inflammatory medications and physical therapy, for others this includes surgical intervention.  Lady G falls in the latter category, suggesting her tear was on the more serious end of the spectrum.

Youch.

Lupus & Joint Function

Now for the lupus part.  Lupus erythematosus is a family of autoimmune conditions - "autoimmune" refers to the body's own immune system attacking and damaging/destroying a tissue or organ that it otherwise should leave alone.  As with many autoimmune disorders, the exact cause of lupus is not known.  The tissues/organs it attacks can vary, but one that is often cited is the joints - this often manifests as joint pain and swelling in affected individuals.  One not-so-common lupus-related complication cited in some resources is avascular necrosis, a condition of diminished blood supply to bones resulting in bone tissue death and structural failure of the tissue.  One of the most common areas affected by this complication is the hip joint.

In an interview in 2010, the Lady spoke of a family history of lupus and the fact that she had tested "borderline positive" herself.  Now whether this makes her more likely to experience a labral tear ... yeah, I don't know.  Folks with lupus are more likely to experience inflammation in and around their joints and from the arthritis-related research I've done in the past, joint inflammation can contribute to joint damage.  I have no idea if that includes increased likelihood of cartilage tears.  Given LG's profession and the recognized labrum-associated occupational hazards thereof, I suspect she could well have injured her labrum without the help/exacerbation of a pre-existing joint-related condition.  And as someone who is trained only academically in orthopedics, is not a clinician and did not specialize specifically in joints ... my professional opinion, along with $2, may just get you a cup of coffee.


References

Floyd, R.T., Adams, J.B. (2009) "Chapter 9: The Hip Joint and Pelvic Girdle." Kean University Kinesiology. Retrieved 24 February 2013 from 

http://www.kean.edu/~jeadams/docs/Kinesiology/Kines_Power_Points/Kines_Chap_9.pdf.

"Hip labral tear." (2011) Mayo Clinic. Retrieved 24 February 2013 from http://www.mayoclinic.com/health/hip-labral-tear/DS00920.

"Lupus." (2011) Mayo Clinic. Retrieved 24 February 2013 from http://www.mayoclinic.com/health/lupus/DS00115/.

"Systemic lupus erythematosus." (2012) ADAM Medical Encyclopedia/PubMed Health. Retrieved 24 February 2013 from http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001471/.

Dimples

What causes dimples?

A not-uncommon occurrence, when learning anatomy, is to learn something new about a particular part of the body and then wonder how that applies to what you observe on the bodies around you (e.g. your classmates, your family members).  My students have been studying the neck and facial muscles for the past few weeks so it's probably not surprising that someone asked about dimples.

Mario Lopez, known forever to my generation as AC Slater from Saved by the Bell
Also, dimples.

Dimples, shown in the photo above, are a (usually) naturally-occurring indentation in the flesh on a part of the body.  Folks are often most familiar with the facial variety.  I have been fantastically unable to find information detailing the proportion of the population that has them, or I'd throw you that figure here.  

According to the few peer-reviewed papers I was able to find in the medical literature (I was stoked that there were any), there is a correlation between dimples and an anatomical variation in particular facial muscles -- specifically, in the zygomaticus major muscles.

Gray's Anatomy

On each side of the face, the zygomaticus major muscle originates at the zygomatic bone of the face and inserts, effectively, at the corner of the mouth.  When it contracts, it pulls the corner of the mouth in a lateral and superior direction (as in a smile).  Most humans have a single zygomaticus major muscle on each side of the face (as shown in the image above).  Some studies of cadaveric tissue point to an anatomical correlation between having dimples and possessing a bifid (split in 2 parts) zygomaticus major muscle on each side of the face.  This muscle has the same origin and action as the single zygomaticus major, but inserts at 2 points on each side (one above the corner of the mouth, one below the corner of the mouth).  My guess (although I have not found it directly stated) is that the dimple would occur in the space between these 2 parts of the split zygomaticus major.  Some studies suggest that folks with dimples also have connections between the hypodermis and dermis in this region (referred to as "dermal anchoring") which may contribute to the indentation.  Dimple creation surgery seems to mimic such anchoring.

In short, the research points to a connection between dimples and an anatomical variation in one set of facial muscles, possibly accompanied by a variation in the attachment of skin to the underlying tissue.

References

Gassner, H.G., Rafii, A., Young, A., Murakami, C., Moe, K.S., Larrabee, W.F. (2008) Surgical anatomy of the face: implications for modern face-lift techniques. Arch Facial Plast Surg. 10(1): 9-19. doi: 10.1001/archfacial.2007.16.

Pessa, J.E., Zadoo, V.P., Garza, P.A., Adrian, E.K., Dewitt, A.I., Garza, J.R. (1998) Double or bifid zygomaticus major muscle: Anatomy, incidence, and clinical correlation. Clin Anat. 11(5):310-3.  DOI: 10.1002/(SICI)1098-2353(1998)11:5<310::AID-CA3>3.0.CO;2-T

Finding Answers, Part 1

When a student asks a stumpifying question mid-lecture, my first thought is generally, "Huh. I can't believe I haven't wondered that and looked it up by now."  My second thought is often, "I wonder why <insert name of student> didn't look that up him/her/zirself."  In some cases, it's likely that the question just dawned on that student in the midst of lecture and being in the very tech-free classroom that I insist upon, he/she/zie could not at that moment search for the answer and so decided to ask me.  In other cases, it might be that students aren't sure exactly how to go about finding such an answer (or it doesn't occur to them that they could).  Yes, the internet is a glorious treasure-trove of informational wonder ... but how does one parse the pile of links that inevitably result from Googling a topic?  Where else do people look?  Let's talk about this.  Let's talk about this in a series of related posts lest we all become completely overwhelmed.  

Credit for the knowledge I impart in this series goes to the following individuals, who have taught me pretty much all of what I know about informational research:  Yvonne Piper, R.N., M.L.I.S., Patricia Elzie, M.L.I.S., Joel Burton, M.A. and David Patterson, Ph.D.

Okay. So. I vote we start with The Googles.

by Hilariawesome

The default starting point for many folks when looking for answers on the interwebs is to high-tail it over to Google and enter their question/topic.  The upside to this is that these folks will then be deluged with links. The downside to this is ... well, that these folks will then be deluged with links.  Some of them may be informationally-dependable while others may not, and telling the difference can be challenging.  The order in which links fall on the response page says nothing for their informational reliability.  Folks who go the Google Route for answers have a bit of potential legwork ahead of them before they hit paydirt.

If you use Google (or another search engine) to find information, one way to decrease background noise is to be as specific as possible with your search terms.  For example, let's say I'm wondering if there is anatomical variation in biceps brachii muscles (known to many as "biceps"), so I have something on which to blame my poor ability to do biceps curls (sidenote: anyone else ponder this or is it just me?).  If I then head to Google and search using the terms "arm muscles," it's a pretty mixed bag - I get some sites that may have useful information (like anatomy resources) as well as links to fitness magazine sites and some advertisements.  If I make my search terms a bit more specific - "biceps" - then the results, while focused on a particular muscle, look quite similar.

If, however, I get more specific than that - "biceps anatomical variation" - suddenly my results look quite different.  My entire first page of results (except for Google's designated ad space) is a mix of scholarly articles, anatomy atlas references ... and of course there's always a link to a Wikipedia article.  By entering more, specific terms, one often gets a more targeted list of results.  Google Guide has a rather useful page that discusses this in more detail and provides examples. There are also fancy librarian-type search tricks one can use that are detailed in places such as this or presented as a tutorial here - if constructing Boolean search terms sounds like a hot way to spend an evening, this will be right up your alley.

Another option is to use Google Scholar, which searches only from scholarly articles, and if you so choose, patents and legal documents where appropriate.  Starting your search here narrows the sort of results you'll get right off the bat, which also helps to decrease the background noise of personal webpages and folks trying to sell you things. The potential downside is that the results you get may be less user-friendly (read: written for experts in a field for other experts in that field) than those you get from just-plain-Google.

That was long-winded.  High five if you made it all the way through.

In our next installment of Finding Answers, Your Humble Professor tackles how to evaluate the resources that show-up on that search results page.