NOTICE: Posting schedule is irregular. I hope to get back to a regular schedule as the day-job allows.

Monday, August 29, 2011

Monday Stuff... [Full link to blog for email clients.][FT:C44]

This past week, while teaching the medical students, we discussed the origin of gastric ulcers.  Until the last 25years or so, the medical field thought that stomach ulcers were caused by a combination of stress and the foods we ate.  Spicy foods, rough foods, certain combination of carbs all increase stomach acid.  Stress and lifestyle can also lead to increased stomach acid.  These factors, when combined, must be producing ulcers, right?  After all, what is the main complaint of people suffering from ulcers?  Pain with eating or ny time stomach acid is increased.

Actually, no,about 70-90% of stomach ulcers are associated with a bacterial infection.  Heliobacter pylori is the culprit, and it has been found to cause gastritis (inflammation of the stomach lining) and significantly contribute to ulceration.  What?  A bacterium living in the highly acid environment of the stomach?  No way!

Back in the 80's Australian pathologist Robin Warren and Australian physician Barry Marshall isolated the "acidophile" (acid-loving) bacterium H. pylori in the lab and put forth the highly controversial theory that a bacterium caused gastritis and ulcers (Marshall BJ, Warren JR (June 1984). "Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration". Lancet 1 (8390): 1311–5. doi:10.1016/S0140-6736(84)91816-6).  It was hard to get the medical establishment to take the theory seriously, in fact, it took 10 years for the National Institutes of Health to publish a consensus statement that ulcers could be successfully treated - even cured! - with antibiotics  (

To prove his point, Dr. Marshal drank a beakerful of H. pylori culture.  He became ill within days, and by ten days, endoscopy showed that he had full-blown gastritis with the beginnings of an ulcer.  A one-week course of antibiotics cured the condition.  Ergo, treating ulcers with antibiotics has become the accepted therapy of the 21st Century - not to mention that Warren and Marshall received the Nobel Prize for Medicine in 2005.

So... one of my students asked me: "Dr. R- Would you have made such a sacrifice in the name of science?"  

I paused.  Would I?  Like that?  No.  Probably not.  "Not even for the Nobel Prize?"  

Well, maybe, but understand, Warren and Marshall did not know that they would win the Nobel.  In fact, most recipients do not receive the Nobel until 20-30 years after they made their breakthrough. 

So again, no, likely not - after all, Mrs. Speaker would probably be very mad at me.

Still, I do know scientists who have sampled their own products - usually in the pharmacology realm.  The famous case of course is Dr. Timothy Leary and LSD, but I also know of at least one instance of a scientist testing a drug on themself that they hoped could some day provide relief from dementia and Alzheimer's disease.  In fact, I can say that based on my work with neural prosthetics, if I ever find myself in need of one, I would volunteer to test a brain-machine interface.

After all - isn't that part of what Science Fiction is based upon?  The noble, famous (on infamous) doctor slaving away in the lab, making the ultimate sacrifice for the betterment of Mankind?  (or at least to come up with a better Frankenstein Monster!).

On that note - Here's the latest installment in Monday Funnies:  Quantum Vibe - about a slightly mad scientist and his assistant.

I particularly like this recent one: "For most scientists, life is all about laboratories and endless incremental experimentation and publishing in journals."

But some do jump in with both feet, drink the culture, and make history.

Wednesday, August 24, 2011

That Medical Student Syndrome... [Full link to blog for email clients.][FT:C44]

...No, not that one [where the think they've got every disease they study]... the other one...

It's the one where students try hard to ask their professors a question that the professor can't answer.

To be fair, Medical Students aren't all like that.  I may have mentioned that I am currently working in the medical school curriculum, and some of my students may even be reading this.  They are smart and curious, it's a prerequisite for medicine, but some students can take it a bit too far - and they often know it.

Also, believe it or not, this is meant to be a humorous post.  In retrospect, I have found these incidences to be quite humorous.

Back to the Medical Students:  We have a program that emphasizes "Case-centered" learning.  Students are presented with a patient case, starting with the chief complaint, then the history, physical and test findings.  The info is provided in stages, just like an office or ER visit.  In between bits of info, the students have to brain storm possible causes, eventually leading up to the point where they can start diagnosing diseases.  Along the way they identify stuff they don't know and need to learn.  Students meet in groups of 6-8, with two professors.  One of the professors is a clinician, the other (me) is in a "basic science" field, our job is to keep the discussions within boundaries, help out (a little) when they are stalled, and act as an expert resource when asked.  What we don't do is lecture to them.  They do have some lecture courses, and some laboratory work in anatomy, histology, etc.

However, it was not always that way.  We used to provide nearly all medical school content through lectures and labs.  I attended those lectures nearly 30 years ago, and I used to teach them before the curriculum changed to the case-centered system we now use.

What does this have to do with Teddy's Rat Lab?  Be patient, let me explain a bit more...

In those lectures there was always one or two students - we called them "gunners" (" 'gunning' for the top") and apparently the term is still in use - that tried their darnedest to be at the top of the class.  Grades weren't enough.  All of the students - and professors - needed to know that they were "the" top student in the class.  In a sense, all of the med students are "gunners" compared to their undergraduate classmates, so you can just imagine what it takes to be thought a "Gunner" in a class of 108 others.

What this meant, is that in any lecture there would be questions.  Questions are good, they show that the students are thinking, and they reveal what needs better attention in the lectures.  However, out of every class, there was usually someone who would as THE IMPOSSIBLE QUESTION (or TIQ).  Mind you, I like questions.  I judged a classes interest on the students that came up after lecture with follow-up questions.  Since I taught the basic neurophysiology of ion channels and action potentials, I got questions from chemistry and physics majors wanting more info, or history and music majors that needed more background info.  But I dreaded TIQs.

Usually what happened was that a student had read something brand new in the New England Journal of Medicine and realized they had something that wouldn't be covered in a lecture that was based on material written 5 or more years ago.  TIQs were verbal traps for the professors (not realizing that the NEJM article was likely based on 20 years of research with which the professor is familiar!). When a student asked a TIQ and it was answered with "I don't know," the student had scored, or "counted coup" on the professor. Obviously, if the professor couldn't answer it (and the student could) then the Gunner was smarter than the professor, right?  The Gunners prided themselves on how many times they could score against the professors.

However, TIQs weren't necessarily impossible to answer, they just took time.   See, med school lectures were 50 minutes long.  I was allotted 4 lectures to cover 2 textbook chapters of material, giving mainly the highlights with the students required to read the rest for exams.  If I was 30 minutes into a 50 minute lecture with at least 15 minutes worth of material left and was then asked a TIQ, I had a problem.  So, what shoud I do?
  1. Take 10-20 minutes to answer the TIQ, dropping the rest of the lecture and making the students read the rest (or squeeze it into the next lecture)?
  2. Try to squeeze in a 5 minute version of the answer, confusing or boring the rest of the class?
  3. Tell them to see me after class (but we only had about 7 minutes actual time between the lectures)?
  4. Tell them to see me during office hours? (except I don't really have office hours, I don't have an office on that campus, and they would likely spend at least 40 minutes waiting and riding shuttles to get to my office).
  5. Or say "I don't know" (or the more appropriate "That's too complicated to explain in the time allowed" - but the students would interpret it as not knowing the answer).
I had about 10 seconds to decide:  #1 and #2 needlessly aggravated the whole class, #2 and #3 didn't provide sufficient time for a decent answer, #3 and #4 frustrated the ones asking the questions, and #5 made it look like the student was smarter than the prof.  I generally opted for #3 and #4, because I could answer the question given enough time, but I know professors that used #5 on a regular basis.

Students asking a TIQ and getting response #4 or #5 generally considered it a win.  Hey, they're back there virtually high-fiving each other.  However, professors talk to each other.  They kept track of who asked the most TIQs and if a particular student did so too often, they were "troublemakers."  Asking questions is the path to knowledge; asking THE IMPOSSIBLE QUESTION (repeatedly) is not.

And you know, I can't help but think that Dr. House, M.D. asked TIQs when he was in med school.

Don't read this the wrong way.  Questions are important! I like answering questions.  Without questions, we don't learn.  However, TIQs are counter productive.  Just because you can think up an Impossible Question, doesn't mean you should ask it (or at least not in a public forum), nor does it really call into question the previous education, experience and writings of the professor.

They are amusing, though, when I look back at the patterns of TIQs and responses and compare them with the types of questions that students must ask if they are going to learn.Especially in today's curriculum where they have to ask questions, then go look them up themselves.  Sometimes they must ask themselves the TIQs!

So, here's what it has to do with Teddy's Rat Lab blog...

The Aug. 8 blog discussed a number of the issues I have faced as a beta reader and scientific adviser to several friends and acquaintances who write science fiction.  I gave several examples of the types of things I would advise against an author using in their story - including an example of XY chromosome-liked genetics.

Boy, did I ask for it!  This blog is automatically posted on a bulletin board I frequent, and I often get questions and comments that show up only on that board. O that's when it started.  I Certainly got questions - and in fact, I'll share some as Mailbag posts in the week to come.  

Yes, I discovered that TIQs are not limited to Medical Students.  They weren't exactly impossible to answer, and I'm more amused by the occurrence than upset at them being asked, but I had correspondents going out of their way to come up with obscure instances of genetic conditions that could meet the conditions that I had advised against writing.  In my defense, I was trying not to be too specific about the author, novel, or specific passages within the novel.  In their defense, they brought up some valid cases, but they were not common, and still did not invalidate my advice in the blog. 

What I find amusing is that TIQs are apparently not limited to Medical Students, in fact they aren't really limited to science.  Sometimes we *have* to ask TIQs.  I suppose they are the consequence of inquisitive and curious people trying to gain a better understanding of what they've read.  At the same time, though, I can't help but think that the ones asking the TIQs - much like Dr. House for the first 50 minutes of each show - are somehow missing the Big Picture.

Until next time - keep asking questions, they are the only way we "feed" our brains!

Monday, August 22, 2011

Monday AWESOME! [Full link to blog for email clients.][FT:C44]

This week's Monday blog is less about the funny, and more about the awe-inspiring.  THIS is the stuff that made me want to study science.

Back in the 70's, the Time-Life Science series of books combined incredible artwork with understandable explanations of everything from the atom to the workings of the brain.  This combination of eye-catching visuals with science is a great way of catching nascent scientists - it certainly caught me.  Now we live in a digital multimedia age - and illustrating science takes something that will appeal to the 3-D CGI audiences of today.

Biovisions, at Harvard University is working on just that.

I cannot link the videos directly, but please follow the link, click the "X" at left to close the first page, then look at the videos in the middle of the page.  At the top is The Mitochondria.  Below that is The Inner Life of the Cell.  Both are incredibly awesome animations that depict real-life cellular mechanisms.  This is stuff that is *way* beyond Hollywood EPIC!  [The only thing that would make it better would be an epic soundtrack -]

When done viewing the two clips, click on "The Inner Life Series" button at the left, then select the super speed version of Inner Life (lower left) for a narrated explanation of the scenes in the 'music video.'  You can also go to the "All Media" link and view some other interesting video such as the Myosin video which illustrates the actin-myosin interactions underlying muscle contraction and intracellular transport.
This is neat stuff, and I can't wait to see what Biovisions produces next.

To continue both the concept of what makes scientists laugh - or cheer! - with getting back to regular blog posting, Wednesday's blog will feature "The Medical Student Syndrome" along with a peak at some of the strange and bizarre stories doctors hear from patients, then a few Mailbag blogs featuring the questions that readers have asked - or comments that deserve more than just a sentence of answer.  We'll return to "The Lab Rats' Guide to the Brain next week - just in time for me to be gone a few days to Dragon*Con. I promise to build up some backlog and get back to a normal posting pattern.

Until next time.  Treat your brain to some *AWESOME*!

Monday, August 15, 2011

Monday FUnnies (on *Monday*! this time) [Full link to blog for email clients.][FT:C44]

Today's Monday Funnies focuses on the humor of Eric Schulman.  The good doctor has written a number of humorous works that focus on the less than serious side of science. 

For example - from: "How to write a scientific paper": 

The real purpose of introductions, of course, is to cite your own work (e.g., Schulman et al. 1993a), the work of your advisor (e.g., Bregman, Schulman, & Tomisaka 1995), the work of your spouse (e.g., Cox, Schulman, & Bregman 1993), the work of a friend from college (e.g., Taylor, Morris, & Schulman 1993), or even the work of someone you've never met, as long as your name happens to be on the paper (e.g., Richmond et al. 1994).
You've written the paper, and now it's time to submit it to a scientific journal. The journal editor will pick the referee most likely to be offended by your paper, because then at least the referee will read it and get a report back within the lifetime of the editor. Referees who don't care one way or the other about a paper have a tendency to leave manuscripts under a growing pile of paper until the floor collapses, killing the 27 English graduate students who share the office below (Schulman, Cox, & Williams 1993).
Trust me - he's right on target!  The full text can be found here: - Note this was an actual paper published in the Annals of Improbable Research. [Formerly known as the Journal of Irreproducable Results until a bunch of lawyers got involved in science - a situation that should *never* be allowed!]

I highly recommend the "History of the Universe in 200 words" - especially once you see the result of running it through the automatic translation software:

or "Gunga Dean":


Now in administration,
Where I had great frustration,
A-servin' to the needs of faculty...
Of all the suited crew,
The worst one that I knew
Was our Arts and Science leader, Gunga Dean.

The complete collection of Eric Schulman's science humor essays can be found at

Enjoy, and exercise your brain - and funny bone!

Wednesday, August 10, 2011

Monday Funnies... on Wednesday [Full link to blog for email clients.][FT:C44]

[Note this blog was delayed to allow the timely posting of Monday's blog.]

This week's Monday Funnies spotlights two different sites.

First up is Doc Nickel and his Website Doc's Machine, featuring "The Whiteboard" comic strip.

Granted, most of the jokes in The Whiteboard are engineering rather than strictly science, Doc and Roger are inventors, engineers, and accidental scientists.  No one knows exactly where the character Doc (The Polar Bear) gets his funding, but his sources seem strangely familiar to me... Hmmm......

My favorite strips are... well, anything where Doc and Roger are inventing!

Inventing the wormhole gun:

Doc discovers super-speed (in more ways than one):


Next up, Dante Shepherd's "Surviving the World".

Dante does a great job poking fun at science and education/universities in general while also showing a bit of the serious side.  In this entry, he has a bit of advice for making science a bit more interesting.

Thanks, Dante, and in fact I think you and I are both working on that "better job of teaching science."  

By the way - don't blame me if you waste a lot of time reading the webcomics, although some of my online friends to take pleasure in getting newcomers hooked on certain sites we find....

You have been warned! 


Monday, August 8, 2011

The care and feeding of Science advisors and beta readers... [Full link to blog for email clients.][FT:C44]

I almost titled this "Betta" readers to play off of Sarah Hoyt's recent blog: Since this is a timely response to Ms. Hoyt, the Monday Funnies will appear on Wednesday this week.  I think you may enjoy this column in its place, if not, come back Wednesday for your dose of funny science.

What I have learned as a Science Adviser / Beta Reader.

First - don't put us in the same aquarium (Oh, sorry, that's 'Bettas' again!) [with apologies to Sarah Hoyt.]

First - I have learned that every author wants something different from a beta reader, but they often want the same thing from a Science Adviser.

I have often heard or read despairing comments from readers that see early versions of a manuscript "Didn't the Author even *show* this turkey to Beta Readers? It's *full* of typos!"  As Sarah Hoyt mentions in her blog, she doesn't want her beta readers to be copy editors - she wants them to advise her on the "readability," "likability", "believability" and overall sense of the manuscript.  Their job is not to mark every typo or grammar error, but to tell the author when the plot has too many wholes, when a character is inconsistent, or the progression of events is not understandable.  In this respect, the reader despairing of typos in an "Advance Readers Copy" is out of luck.  Copy editing is not done at that stage.

However, they do have a valid point when it comes to science advising.  The role of a science adviser *is* to pick up on the inconsistencies.  Examples: (a) "Light years" as a measure of time; (b) space drives that produce 400 gravities of thrust in one section, and 4000 gravities in another; (c) males as "carriers" for an X-chromosome-linked disease that affects only women; (d) viruses treated with antibiotics.  I have seen variations of these errors in many published books as well as manuscripts.  [By the way - the answer to (c) is that if the disease was on the X chromosome, the male would not be a "carrier," he'd have the disease since he does not have a second X chromosome to carry a normal gene to counter the disease gene.  For (d), antibiotics treat "biotic" infections - i.e. bacteria.  Viruses are not "biotic."]

The science adviser is supposed to catch inconsistencies.  What the science adviser is *not* expected to do is to change anything that would alter the essential plot or characters.  Early in my tenure as an adviser to SF authors I had an exchange with an author that went something like this:
Me: "Hey __ - scientifically that's "an epithelial colonization with papules and pustules."
Author: "Speaker - my characters are grunts.  To them its a bad rash with pus blisters.  Now, if I need dialogue between the scientists who are *creating* the disease, I'll write it differently."
The story is more important than the science.  That is not to say that accuracy is not important, after all, the hallmark of *good* SF is a good foundation in science, but there needs to be understanding that other parts of good SF include speculation beyond current capabilities, and above all, it has to be a good story.

Which brings me to Lesson Two that I learned as a beta reader and a science adviser:  Make it understandable.

I know plenty of scientists that are excellent at what they do.  They publish papers, get research grants, give seminars - but they can't explain what they do to someone without the same level of education that they received.  A science advisor has to first explain the concept to the author, then be able to guide the process of getting the idea into the story.  Note: you are *not* writing it for the author, you are helping them by saying "no, this is not consistent", "this doesn't read well", "this doesn't make sense."  In addition, you can say "this is not accurate" and provide the appropriate information.  It's not easy, and anyone that wants to try to position themselves as a science advisor needs to first *read* a lot of SF, then see how well they can explain their own work in SF terms.

SF authors *want* the reader to feel that the science is accurate enough to allow "willing suspension of disbelief." This is important to any form of SF, fantasy, speculative or adventure fiction.  Readers are often willing to accept one (or two) unbelievable things if the rest of the science is accurate.  For examples, I would draw your attention to Jack Campbell's "The Lost Fleet" series.  There are two major "gotchas" in his Space Opera - first is the existence of a faster-than-light drive, second is ships maneuvering at significant fractions of light speed.  Yet the rest of his space battles entail the slow ballistic trajectories of missiles and bombs dropped onto fixed outposts such as moons and planet-bound cities.  Likewise, David Drake postulates a "sailing culture" for his RCN Lieutenant Leary books, yet he includes many realistic issues such as not having elevators on a spaceship due to various stress which would jam the elevator shafts.

It's a mix of  the unbelievable, with science and engineering which is quite believable and understandable that aids the author in setting up the plot.  It is the adviser's job to check the accuracy and understandability of the science to a much greater degree than that of a beta reader.

The third thing I have learned is to be careful in how you send your comments back to the author.  Some authors prefer that you take the manuscript, mark your changes/comments in line, then send it back.  To do so, you need a unique marker that the author can find using the search functions of their word processor. Authors I know use "###" or "///" for the purpose.  Make sure you mark both the beginning and the end - and be careful to distinguish between corrections and comments.  I once wrote a paragraph of side explanation to an author.  I was surprised to find the complete paragraph in the final version of the book.  I asked the author about it, saying "It was only meant as a comment for you."  His response "Oh, I didn't realize.  However, it fit, so I put it in."  From this I learned that comments to the author - particularly long, involved ones - should be sent separately, so as not to confuse the poor author suffering from brain strain as they try to reconcile five sets of beta reader comments.

The most important thing I have learned as both a beta reader and science adviser is to find out what the author wants from you.  Do they want "gobbledygook" and "handwavium" that they can use to give the impression of science to a particular scene?  Do they want (allow) their scientist/engineer character to have a 500-word infodump to which the grunt characters can respond "Huh?"  [Don't laugh, I know a best-selling author that allows his scientist co-author a single 500-word exposition per book!]  Do they simply want the scientists to read a passage and comment on whether it "feels right?"  It is very important for the scientists to not only have read other SF, but also that author's own works to get a feel for style and composition.  Also, keep in mind that even if the author actually says "I need gobbledygook" they don't really mean nonsense such as "unobtanium" or "full-sprocket framistan with punctate lobes."  No, what they usually want is science in terms that their readers will recognize as being realistic, without requiring a PhD to read it. 

The down side of being a science adviser and beta reader is that when those other readers are saying "Why didn't somebody catch this mistake" they are talking about you.  So it behooves the beta to look for the big issues, the ones that leap out of the page and hit you between the eyes.  Perhaps the author will decide they don't matter, at which time it is best to leave it alone.  But if you approach the task as recreational reading because "Wow, I get to read it *first*!" then you'll probably miss things that you would pay more attention to if you had a checklist from the author of items that they want you to review.  On the hand, you *do* get to read it first, and sometimes that can make a difference to understanding how the author's mind, and the craft of writing actually work.

And when you're a neuroscientist that is interested in how the creative mind works, that can be more rewarding as seeing your name in the acknowledgments.  

Sunday, August 7, 2011

Fair warning... [Full link to blog for email clients.][FT:C44]

Just to give y'all fair warning - my schedule has become very full over the past couple of weeks and I may need to take a break from the blog this week and/or next.  Once the current block of teaching concludes in 3 weeks I'll have more time, but I plan to use this time to work ahead on the Guide and possibly get some other projects completed. 

Monday Funnies will continue to post as scheduled, it's the Wed/Fri Guide posts that may have to be postponed.  Rather than leave the blog blank I may look at some of the early posts or other material and see if it is worth editing and re-posting - or I may find some special content for filler. 

Thanks for your understanding.


Friday, August 5, 2011

Ethanol, the Science behind the story... [Full link to blog for email clients.][FT:C44]

In the prior blog I provided an example of alcohol effects on the brain in story form.  Today I present the science behind that story, courtesy of Guest Blogger Karni Mata.  K. Mata takes her name from the Goddess of Rats, or in her case, Goddess (mother) of Lab Rats, due to her position as a laboratory manager.  K. has a doctorate in Psychology and works with me on several matters of interest to the readers of this blog.  She was a bit too shy to come out here and introduce this blog herself, but believe me, she has very thoroughly researched the topic and is Teddy's Rat Lab's resident expert.

And now... the Science Behind The Story:

Alcohol.  Ethanol.

It's a fuel, a disinfectant, an anesthetic, and a foodstuff.

The molecule ethanol - EtOH - consists of two carbon atoms, six hydrogen and one oxygen.  It has the characteristics of both a hydrophilic (water-soluble) and hydrophobic (oil/lipid-soluble) compound and easily penetrates the skin, the mucous membrane lining of nose and mouth, the stomach lining, and distributes widely through the blood and body.  A set of six enzymes - collectively called alcohol dehydrogenase - breaks it down, and the level of ethanol in the blood remains elevated until it is either broken down by this metabolic method (i.e. "metabolized") or it is excreted via sweat, breath and urine.  The primary breakdown product of ethanol is "acetaldehyde" which is responsible for the headaches, upset stomach, and overall discomfort of a hangover.  A further breakdown product of acetaldehyde makes "acetone" and "methyl ketone" which produce a sour taste, and are responsible for the bad breath and body odor of alcoholics and the chronically intoxicated.

The name - acetaldehyde - may seem familiar, especially if you have ever heard of the preservative "formaldehyde."  In fact, acetaldyhyde is a 2-carbon structure, while formaldehyde has only one carbon.  When a person drinks wood alcohol - methanol (ethanol is "grain alcohol") - the same alcohol dehygrogenase breaks down the single-carbon methanol molecule into the single-carbon formadehyde.  There is a large amount of alcohol dehydrogenase in the retina of the eye.  This is one reason why excess ethanol affects vision, and why drinking wood alcohol can cause blindness as the formaldehyde kills and "preserves" the sensitive neurons of the retina. 
Alcohol affects multiple brain systems working overall as a central nervous system depressant. It may seem that alcohol stimulates a person since his or her speech becomes more animated and free, social inhibitions are reduced, and emotional responsivity is increased. However, it actually decreases the brain’s ability to function, resulting in cognitive effects such as hazy thinking and foggy memory, sensory effects such as dulled hearing and impaired vision, and physical effects such as weakened muscles and uncoordinated movement. Depression of self-control and judgment occurs as well, leading to poor reasoning and decision-making.

Within seconds of consumption, it alters the action of neurotransmitter systems. The neurotransmitter dopamine, involved in systems of reward, is initially increased causing euphoria. This feeling of pleasure can be accompanied by increased self-confidence and sociability. These dopamine surges in the brain sends signals that alcohol is important and valuable, and induce the brain to want more. High amounts of GABA neurotransmitters are released, increasing the action of inhibitory neurons, causing many systems to decrease activity, dulling the senses and pain and reaction time. Additionally, glutamate, an excitatory neurotransmitter, is less active, contributing to feelings of relaxation and sluggishness. A fourth neurotransmitter, serotonin, is increased in the presence of alcohol which may increase positive mood. It is also a neurotransmitter that when increased will raise the levels of dopamine and GABA, intensifying their effects.

As the limbic system, a group of several brain structures that work together is affected, emotions become more intense. Hypothalamus dysfunction can increase the intensity of feelings of attraction, or aggression, or sadness depending on the situation one is in. Sexual desire can increase, but the ability to perform sexually is decreased. Additionally, the amygdala is compromised, where emotional control, motivation, and interpretation of nonverbal emotional expression are processed. In the hippocampus, memory processes are also hampered. The thalamus relays information from the sensory organs to the cerebral cortex where they are processed into meaning. When this neural pathway is slowed down, the ability to respond quickly to information from the environment is slower and less accurate, resulting in longer reaction times which seriously hamper the ability to drive.

As blood alcohol rises, the frontal lobes are affected. This is where higher mental processes including thought, reasoning and decision making are largely processed. A dangerous consequence is that an intoxicated person may decide to drive even if he or she knows, when sober, that they should not.

As blood alcohol concentration levels increase in the cerebellum, fine motor coordination is reduced and speech is slurred. The ability to judge distances, and when to stop, is also impaired. The brain stem areas that control movement and balance are also affected resulting in a staggered gait and clumsiness. When blood alcohol levels become very high, the medulla in the brain stem, which regulates life support functions, becomes compromised. The body sends signals that poisoning is occurring, leading to vomiting (poison = toxin; someone drunk is “intoxicated”). Because inhibitory neural pathways are more active, swallowing, breathing and heart rate can also be affected, leading to unconsciousness and even death.

There are benefits from alcohol.  The mild depressant action of just one or two drinks relieves stress and enhances mood.  Many of the alcohol preparations, such as red wine, contain beneficial antioxidants.  Ethanol does have some caloric content - it is produced as a partial breakdown of glucose.  It is also used as a "solvent" to dissolve many medicines that would be poorly absorbed by the stomach and intestines.  It also serves as a considerable "disinfectant" when added to water and food of questionable purity. 

Still, as illustrated in the case of poor Joe from our last blog, it has its dangers as well. In comparison with other intoxicants - such as marijuana - Society as a whole has decided that the dangers of excessive ethanol consumption are acceptable.  Only time will tell if Society makes the same decision about other intoxicants.

In the next blog we'll discuss some long-term consequences of ethanol use, as well as a discussion of problems strictly associated with (and indicative of) alcoholism.

Until then, take care of your brain - and if you take it out for a few drinks after work - do so with caution!
(and again - many thanks to K. Mata for today's blog!).

Wednesday, August 3, 2011

All Boozed Up... [Full link to blog for email clients.][FT:C44]

16:55.  BAC 0.00-0.01

"Hey, Joe!  You coming with?  Finally?  We've been asking for a month.  Me and the guys are headed to Harry's for wings and beer.  You've put us off long enough, so you'd better show this time."

"Thanks, Buddy, I know I promised, but I can't stay long, I've got a date later."

"What?  You?  Mister all-work-no-play has a date?"

"Well, kind of a date, my brother's wife's sister's friend.  They keep conspiring with my mother to get me married off."

"It's the grandkids, Joe, I keep tellin' ya - once ya give 'em grandkids they'll stop!  Anyway, we're heading out in five.  See ya at Harry's"

17:30.  BAC 0.03

"Hey Harry!  Another round!  Joe, you need another bottle of... what *is* that stuff?"

"Hardcore IPA, Buddy, I like it, full body, nice rich taste.  If you guys would stop drinking that horse piss you call 'light beer' you might find that you like a *real* beer!"

"Not for me, you might like those strong brewskis but I still gotta drive home to the wife.  At least it finally got you out of the office and socializing with us for a change, so I guess I can't complain.  Harry!  Another bottle for Joey!"

17:50. BAC 0.07

"Damn, I'm gonna be late - I've got to catch the train and meet her at Le Bon Temps at 6:30.  Let's see 10 minutes to walk to the station, catch the eighteen-hundred, 20 minute ride, another ten minutes to the restaurant.  Yeah, I can do this, and the walk will do me good.  Hey!  Guys!  See you on Monday!"

About this time, if you are as old as I am, you're probably expecting a narrator to pop up and say 'I am Joe's Liver' or something like that.  Sorry to disappoint.  Sure, I'm the narrator, but nothing quite so specific as to describe Joe and his liver on a night like this.  No mistaking - it will be a night to remember, unfortunately, Joe won't remember it, or at least not remember *most* of it.

Joe is a typical guy in his 20's-30's.  His weight borders on 200 pounds (90 kg).  He spends all day in an office and doesn't exercise enough.  He likes a beer or two in the evening.  Socially he drinks wine, and occasionally something stronger.  Tonight will be one of those nights.  He's already had two beers: 11 oz bottles each, of a high-alcohol-content beer, and it is started to have an effect.  He's socially relaxed, confident - too confident - and his judgment is starting to suffer.  His blood alcohol content (BAC) is 0.07% - 0.07 grams of ethanol per milliliter (mL) of  blood - and he's already over the legal limit to be able to drive in most countries (except U.S., Canada, U.K., Mexico).  He *is* above the legal limit for Colorado.  Luckily he doesn't live there and is using public transportation tonight.

18:30. BAC 0.06.  Aldehyde 0.01

"Made it.  Whew, I'm a bit sweaty, ugh, need some deodorant or something.  Good, the vending machine has that spray cologne.  Where is she?  It was six-thirty, right?  Bartender!  Gin-and-tonic, with lime.  Thanks."

Forty minutes after he finished that second beer, Joe's BAC has dropped by 0.01%.  If he stops now, the alcohol dehydrogenase in his body will convert the rest of the alcohol in his blood to acetaldehyde in another 4 hours.  If he sleeps for about 4-6 hrs after that, the aldehyde will be cleared from his bloodstream as well (0.01% per hour) and he probably won't notice any lasting effects in the morning other than strong body odor from the aldehyde in sweat.

He's still not noticing much of an effect of the alcohol because at 200 pounds, but 5 feet 10 inches in height, Joe has enough fat in his body to "buffer" some of the alcohol before it reaches  his brain.  Unfortunately, he skipped lunch and has no food in his stomach except 1 chicken wing and a handful of snack mix. 

18:45.  BAC 0.08.  Aldehyde 0.01

"Damn, she's still not here.  Did I get the time wrong?  Bartender!  I'll take another, easy on the tonic this time around!  Oh - and another bowl of bar-mix, I had a meeting at lunchtime and my date is late."

Joe has consumed two beers, one gin-and-tonic and is working on a second.  That would ordinarily constitute 4 standard doses of alcohol.  The stand measurement for alcohol consumption is one shot (1.5 oz, 44 mL) of liquor - 80 proof (40% alcohol by volume) - or 5 ounces (148 mL) of wine (9-15% alcohol by volume) - or one 12 ounce (355 mL) can of beer (4-6% alcohol by volume) .  However, these are 'standard' measures, and vary with the actual alcohol content.  Joe's 'Hardcore IPA', for example was 9% ethanol-by-volume and two bottles gave him at least three 'standard doses' of ethanol - it's a good thing he didn't order 'Tactical Nuclear Penguin' (32% alcohol - the equivalent of about 6 beers).
18:55.  BAC  0.10. Aldehyde 0.02

"Bartender, ano-  Oh!  Hello!  You're must be Tracey, right?  Cheryl told me a lot about you!... No, I haven't been waiting long.  Wow, she didn't tell me how pretty you were.  I think I'm in love already!  Bartender, get the lady whatever she wants.  Sure, I'll take one to the table."

19:06.  BAC 0.11. Aldehyde 0.02

"Would you like some wine? They have this lovely Australian Syrah... Bordeaux?  Sure. let's see, hmm, the lighting is sure low, either that or I'm going to need to borrow your glasses ... Yes, sir, the 1998 Bordeau.  Oh, sorry about knocking over the salt - just a pinch over... what was that old superst... uh. legend?  A pinch of salt over the left shoulder?  Yeah.  That's it."  
Joe is legally intoxicated in any jurisdiction by this time.  His vision is just a bit blurry, his coordination a bit off, and he is making - and correcting - small slips of the tongue and memory.  He hides it well, having had a bit of practice in college, but he hasn't drunk this much in several years.  At his current Blood Alcohol Concentration, it will take over 7 hours to clear the ethanol from his bloodstream and more than 11 hours to metabolize the aldehydes.  We *will* have a hangover in the morning.
20:33.  BAC 0.18.  Aldehyde 0.04

"What the hell, Jake!  No one told me she was a Vegan!  How was I to know she'd get sick at the sight of Steak Tartare?  Then she stuck me with that damned Bordeaux.  I hate French wines!  ... What do you mean what did I expect in a French restaurant?  Up yours, Buster!  Oh, sorry, Lady, and I am *not* drunk! ... 'nother sh-sh-sh-shot of Jack, Jake.  Hah!  Jack-Jake!  Thass funny, that is!  Yeah, 'nother Jake-Jack and make it a double!"

Joe is now in trouble.  Two strong beers, two-and-a-half gin-and-tonics, three glasses of wine and at least one shot of whiskey has raised his BAC to levels that are clearly affecting motor control, judgment, speech, and vision.  If he tries to stand he will discover that the high concentration of alcohol in his blood has actually allowed ethanol to enter the cerebrospinal fluid and the fluid of the inner ear, increasing the effects on the brain as well as directly affecting balance (by suppressing hair cells in the semicircular canals), blood pressure, heart rate, etc. 
If he stops now, he'll have a miserable morning, but will have detoxified by the afternoon.  Unfortunately the night is not yet over...

21:57.  BAC 0.22.  Aldehyde 0.06

"Hoo-ey, that's good stuff!  You say your brother makes it up in the mountains?  Wow, never had it before!  Sure glad you came along, sweetie, the nerve of that guy, cutting me off!  I'm going to call his b-b-b-boss in the... the... wassname... yeah! mornin'  Yeah, wha' kinda beertender does he think he is?  Oops, sorry darlin, din' mean ta trip ya.  Hoo.  You shore are purty, darlin'!  Wheah?  Ah'm fum Tay-has, din' ah tell y'all tha'?"

Joe's BAC is now in the dangerous levels.  If he keeps drinking, he will lose consciousness, lose memory, lose his bladder function and if he ends up in a position in which it is hard to breathe, he could suffocate.  He does not understand his own actions, or what is wrong with his behavior.  He may find himself attracted to his 'Darling' but will likely be unable to do anything about it.  To say that his judgment is impaired is too mild.  At this point, Joe has no judgment -after all, he just drank the 2 shots of moonshine (70% alcohol - the equivalent of 3-4 standard drinks).
 "Wha's tha' you say, Darlin'?  Your place?  Wha' Ah thought we *were* at yore place?"

23:59.  BAC 0.28.  Aldehyde 0.09

Joe has lost consciousness.  When he awakens he will still be highly intoxicated.  He will also have The Mother of All Hangovers.  He will have no memory of the evening after the failed dinner date.  He will remember only that it went badly, but not why.  He will not know where he is, how he got there, or what he has done.  That may be rather fortunate for him.

07:30.  BAC 0.17.  Aldehyde 0.13

"Damn!  Too loud!  Stop that noise!  Ohhhhhh, my head!  What?  Where am I?  What happened?....

"Oh no!"

------ On Friday, "The Science Behind the Story"

Monday, August 1, 2011

Monday Funnies [Full link to blog for email clients.][FT:C44]

The Hungarian biochemist Albert Szent-Gyorgyi won the Nobel Prize for Medicine in 1937.   His research focussed on Vitamin C.  We once defined a vitamin as:  "A substance that makes you ill if you don't eat it!"

A couple of my favorite (paraphrased) Szent-Gyorgyi quips are:

"Under the most precise conditions of environmental and behavioral control - the lab animal does what it damn-well pleases!"

"A drug is that substance, which when injected into an animal, produces a research paper."

Truer words were never sp- ..., well, paraphrased.

Today's Monday Funnies is about humorous quotes about science.

SciScoop (, lists a page of science jokes and quips, but I didn't find them to be particularly scientific - more commentary and less humorous.  Basic Funny Jokes ( is a bit more on-topic.  There is also a list organized by topic at:

My favorites:

"We can lick gravity, but sometimes the paperwork is overwhelming." - Wehrner von Braun

"When a distinguished but elderly scientist states that something is possible, he is almost certainly right. When he states that something is impossible, he is very probably wrong." - Arthur C. Clarke

"The essence of life is statistical improbability on a colossal scale." - Richard Dawkins

"Basic research is like shooting an arrow into the air and, where it lands,
painting a target." - Homer Burton Adkins

"The most exciting phrase to hear in science, the one that heralds new
discoveries, is not 'Eureka!' but rather 'hmm....that's funny...' " - Isaac Asimov

"Your theory is crazy...but it's not crazy enough to be true." - Neils Bohr

There are many more out there, and as time is short - I challenge you to find them. My apologies for irregularities in the posting schedule, but I am teaching for the next six weeks,therefore a good portion of my daily work has shifted to work in the evenings, at home.  This has somewhat limited the time available for blogging.  I promise to stick to the main schedule as much as possible, and to work on that backlog of comments on last week's blog posts.

I leave you with this final (humorous) thought: "I know that this defies the law of gravity, but, you see, I never studied law." - Bugs Bunny