Archive for the 'Science and Medicine' category

Temples and Timelines

 | February 25, 2010 5:55 pm

Newsweek has a fascinating article about an archaeological site at Göbekli Tepe in Turkey that is well worth a look.

The site is the oldest religious temple ever discovered.  Preliminary carbon dating has determined that some of the artifacts date from 9,400 BC, which makes the place about 11,500 years old. (Which, just to be clear, is 7000 years before the Great Pyramid and 6500 years before Stonehenge.)  The article further explains:

The ruins are so early that they predate villages, pottery, domesticated animals and even agriculture – the first embers of civilization.  … [It] may be the very first thing that human beings ever built.

And yet, the site is amazing.  The pillars show beautiful stone carvings and there are examples of sophisticated engineering techniques.  The stone circles are nearly 30 yards across with pillars that stand more than 17 feet tall.  Many of the stones (some weighing up to 50 tons) were first quarried and then transported half a kilometer to the site, where they were erected.  What staggers me, though, is that the stone circles were roofed.

This quote from Ian Hodder, head of archaeology at Stanford University, summarizes my response pretty well:

[Göbekli Tepe] is unbelievably big and amazing, at a ridiculously early date.  The huge stones and fantastic, highly refined art [changes everything].  It overturns the whole apple cart.  All our theories were wrong.

This doesn’t happen often.  Scientists don’t admit mistakes and call for established theories to be overturned.  But when faced with such a revolutionary piece of evidence, you have little choice.

Göbekli  is literally an outlier in every way.  It shows engineering, organization, and artistic sophistication that seems to materialize out of nowhere.  The only other comparable examples won’t appear for five thousand years.

To really put this in perspective, consider the timeline below.  Arrayed across the bottom axis are the reigns of several ancient civilizations: the Chinese, Romans, Egyptians and Mesopotamians.  In addition to this information, I’ve also placed the approximate dates of the the ice age, stone age and examples of religious and cultural monuments (the oldest of which dates to about 3500 BC).

When compared with Göbekli, the great civilizations and monuments of the ancient world seem to to huddle in an upstart mob at the right of the chart.  Even the very oldest of the examples, a Mesopotamian palace, is separated from Göbekli by the same span of time that divides the ancient age from the modern day.

Such an amazing and sophisticated example at such an early date, literally, boggles my mind.  It's absolutely amazing.  And, paradoxically, the amazement and wonder helps to explain why Göbekli has remained essentially unknown.  A discovery of this magnitude demands enormous attention and dedication.  It takes almost as much as it gives, particularly from those that discovered it; and not every scientist is willing to give that kind of commitment.  Thus, I completely understand the response of the man who discovered the site.

[Unable to interpret what he saw], the [American] archeologist who stumbled on [on the site] in the 1960s simply walked away.

But, even so, the evidence at Göbekli has the potential to completely transform the history of civilization.  And I, for one, look forward to seeing what emerges.

Timeline-Gobekli-Tepe

Note: You can view a high resolution PDF of the timeline by clicking on the image, or here.

Hannibal, Napoleon, and Joseph Charles Minard

 | February 22, 2010 5:49 pm

Charles Minard - Railroad Routes

No study of the history of scientific communication can be complete without mention of Joseph Charles Minard, a 19th Century French civil engineer and cartographer.

At the end of his life, Minard created two very famous examples of statistical charts, called flow maps, that every scientist, engineer and student should be familair with.  The first showed Hannibal’s crossing of the Alps (218 BC, Second Punic War), and the second describes Napoleon’s disastrous invasion of Russia (1812-1813).

Both examples are beautiful works of art and masterful examples of evidence.  But they are also more than that, they tell cohesive and interesting stories.  In this post, I thought it might be interesting to take a closer look at the history of Hannibal and Napoleon, and highlight the ways which Minard’s charts help us to explain their eventual outcome.

(Note: High resolution, PDF versions of the two maps are available for download.  These versions have been translated from the original French.  To download, either click on the images, or here for the Hannibal invasion of Northern Italy, and here for the French Invasion of Russia.)

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Working With Words, Numbers and Images: A Reading List

 | February 14, 2010 2:10 pm

There are three tools that a professional, scientific or technical writer needs to make use of: words, numbers and images.  In many cases, such as an effective illustration or chart, all three will be used.

The following books introduce principles and examples of how to use these tools to their fullest extent.  Some of the titles are historical and others are academic.  In every case, though, they highlight strategies that can be used to more effectively communicate ideas.  Additionally, each one is also an interesting and fantastic read.

Math and the Mona Lisa Math and the Mona Lisa by Bulent Atalay. For more than 500 years, the name of Leonardo Da Vinci has been synonymous with brilliance.  His careful observation of nature, collection and analysis of evidence, and use of mathematics to explain his observations represented a radical shift that foreshadowed the modern scientific method.In this book, Bulent Atalay explains why Leonardo was a remarkable artist, engineer and scientist.  He looks at the hidden patterns, geometric concepts and impeccable perspective in order to probe the mind that dreamt of helicopters, unsinkable ships and underwater exploration.
Leonardo's Notebooks Leonardo’s Notebooks, edited by H. Anna Suh.  To understand a man, you must read him in his own words.  This volume provides an opportunity to sample Da Vinci’s writings on anatomy, botany, architecture, sculpture and the physical sciences.  The key illustrations from his notebooks have also been reproduced.
Galielo at Work: His Scientific Biography by Stillman Drake.  Like Leonardo, Galileo was a scientific titan.  As Stephen Hawking aptly summarized, “Galileo, perhaps more than any other single person, was responsible for the birth of modern science.”But why?  What was it about his innovative combination of experiment and mathematics that was so important.  How did he analyze data?  How did he present it to others?This book attempts to answer those questions.  It lays aside the philosophical implications of Galileo’s rift with the Catholic church and instead looks at how Galileo focused his mind on physical quantities and the mathematical relationships between them.
The Visual Display of Quantitative Information The Visual Display of Quantitative Information by Edward Tufte.  Communicating complex ideas is difficult.  One of the most important tools in that struggle are charts, graphs and illustrations.  Unfortunately, however, these important figures often receive less attention than other aspects of a manuscript.In this book, Tufte provides inspiring examples of graphics that are beautiful to behold and illuminating to ponder.  He also includes shockingly bad examples and explains why they are so dangerous.
Visual Explanations by Edward Tufte Visual Explanations by Edward Tufte.  In his earlier work, Tufte showed how important it is for numbers to be communicated clearly and without distracting  ornamentation.  In this volume, he turns his attention to a slightly different series of questions: What is the best way to show cause and effect?  Or to demonstrate evolutionary change?But the most important question he asks is far more universal: How can an information display be be used to reveal the truth?  To answer this, he analyzes a cholera epidemic in 19th century London and explains how poor communication contributed to the explosion of the Challenger space shuttle.
Beautiful Evidence by Edward Tufte Beautiful Evidence by Edward Tufte.  Like in his previous books, Tufte again tackles the question of how to best reveal truth through the graphical display of information.  But where earlier books focused on principles, Beautiful Evidence is about how seeing turns into showing.  To explore that theme, this book is filled with hundreds of spectacular examples and thoughtful commentary on what makes them unique.
Now You See It by Stephen Few Now You See It by Stephen Few.  The human mind is amazingly adept at seeing and understanding patterns.  An informed eye can distinguish between authentic and forgery and arrive at startlingly accurate calculations with minimal effort.  But even though we are capable of recognizing the hidden influences in the world around us, we can also be mislead and exploited far too easily.  We become awash in a sea of data of our own making.This book attempts to explain how the mind interprets and sees information.  As the author explains in the introduction, “[This book] provides tools to dive into the ocean of information, net the best of it, bring it back to shore and sort it out.”  In essence, it’s a book about seeing and distinguishing patterns on a conscious level.
Visual Thinking Visual Thinking by Rudolf Arnheim.  It’s long been known that “seeing is believing.”  This book explains why seeing is also synonymous with thinking.
Maps and Civilization Maps and Civilization: Cartography in Culture and Society by Norman J.W. Thrower.  The history of exploration and discovery is also the history of cartography.  As mankind sailed out of sight of shore, he needed to learn techniques for representing his position and understanding the natural forces that he might encounter.  This book tells the history of mapmaking and how advances in cartography impacted civilization.
The Elements of Graphing Data The Elements of Graphing Data by William S. Cleveland.  In this book by William Cleveland, he presents the nuts and bolts (the how-to) of graphing data.  Then he goes on to explore the science in which his principles are based..
Visualizing Data Visualizing Data by William S. Cleveland.  Whereas The Elements of Graphing Data is primarily  focused on the principles of quality display and exploration of many types of common statistical charts, Visualizing Data takes the next logical step.  It introduces a number of new chart types and techniques for creating insightful and clear graphics.
Fiasco: American Military Adventure in Iraq by Thomas E. Ricks Fiasco: The American Military Adventure in Iraq, 2003 to 2005 by Thomas E. Ricks.  Serious endeavors require careful forethought and nuanced planning; and few enterprises are more serious than the business of war.  This controversial book looks at the missteps and mistakes of the American military as it justified, planned and executed the 2003 Iraq War.It contains haunting examples of how information can be distorted and obfuscated by both well-meaning individuals and those with insidious hidden agendas.  It also explains how the adoption of American corporate culture and leadership by PowerPoint lead to serious miscommunication and early failure.
Challenger Launch Decision The Challenger Launch Decision: Risky Technology, Culture and Deviance at NASA by Diane Vaughan.  The Challenger explosion on January 28, 1986 changed the course of manned space flight forever.  But how did it happen?  What factors lead to it?  Might it have been prevented?In The Challenger Launch Decision, Diane Vaughan attempts to answer those questions.  In the process, she reveals that the Challenger explosion wasn’t the result of intentional wrongdoing but rather a slow-creeping definition of “normal” and comfort with the status quo.

Image Gallery: The Notebooks of Leonardo Da Vinci

 | February 5, 2010 12:31 am

DaVinci - HandsWhen I graduated from college and had to choose between a career in industry or academics, I found it to be an easy decision: I stayed in academics.  I like to have my head in the clouds and enjoy the intellectual lifestyle.  (I actually consider the label of “absentminded” to be a compliment.)

It should come as no surprise, then, that one of the most enjoyable aspects of writing a book has been the opportunity to research my subject.  My reading list has included books on analytic design, illustration, anatomy, typesetting, scientific communication, web technologies, LaTeX, the history of science, statistics and informational graphics. And as I worked my way through it, I took some extremely interesting side trips.  One of the most intriguing, however, was an extended tangent through the notebooks of Leonardo Da Vinci.

Da Vinci died in the year 1519, nearly five hundred years ago.  Yet, the modern world remains fascinated by him.  His name adorns the side of best selling books and conspiracy fiction; and his drawings have become cultural icons.  As an example of his popularity:

In October of 2009, Martin Kemp, a professor of art and history at the University of Oxford, found a portrait of an Italian girl.  Up until Kemp took an interest, it was widely accepted that portrait had been painted sometime in the nineteenth century by an unknown artist.   After a great deal of investigation and the use of a multispectral camera, however, Kemp discovered something startling.  The painting had actually been done by Leonardo and nearly overnight, it went from a value of 19,000  British pounds to over 100 million.

I’m no different than the masses.  Leonardo fascinates me.  He had a very distinctive way of seeing the world and an engaging style.  Maybe that’s why it’s so easy to lose yourself in the details of his work.  Given my interest, a thorough study of Leonardo’s notebooks seemed only natural.

What I didn’t foresee, however, is that I would start to digitally collect his sketches; and in the past several months, I’ve put together a rather eclectic mix from across the internets.  Earlier today, I realized that the images might be of interest to others as well; thus, I’ve created a special online gallery for them.  It can be found under “Art and Photography” –> “The DaVinci Notebooks”  To get there more quickly, you could also just click here.

Enjoy!

Statistics With R – Part 1: An Old Dog Learns New Computing Tricks

 | November 8, 2009 10:21 pm

When doing math or numerical analysis, the knowledge of the technique is far too often tied to the tool performing the calculation.  Consider an engineer whose understanding of the Fast Fourier transformation is inseparably tied to the fft function in Matlab.  Of course this hypothetical engineer understands what the results mean (more or less) but may not be able to duplicate his analysis if Matlab were taken away.

In most cases, it is likely that no deeper understanding will be required.  But what happens if the computer makes a mistake?  Or the program becomes unavailable?  Both situations are entirely possible.  Computer algorithms aren’t perfect and occasionally arrive at results make little sense; and hardware has been known to fail.

When the engineer understands how the computer arrived at the answer, however, he can recognize, understand, and ultimately correct those cases where the results are unexpected.  This is an important reality check that can prevent costly disasters later down the line.  Or, if the hardware is unavailable, he can use an alternative tool or software package to duplicate the analysis.

But while such a situation can arise with any type of numerical software, it’s most likely to happen to users of a statistical package.  I find this extremely ironic since a proper understanding of statistics is essential to live in the modern world.  (Much more so than an understanding of the Fast Fourier transform, at any rate.)  The rules of probability, the normal curve, correlation, and multivariate statistics can have a direct impact on how we live our lives.  They are used in making important decisions in finance, medicine, science and government.  A misunderstanding of stats and the methods of science (from which statistics is inseparable), underlies the most divisive issues of our day: abortion, stem cell research, and global warming.

Moreover, neither side has a monopoly on ignorance or misunderstanding.  People fail to distinguish between correlation and causality, or insist in using the word “average” as a slur.  Nearly as bad are those that – like the hypothetical engineer described above – only understand statistics within the narrow context of their stats package.  Casual statisticians are nearly as dangerous as the wholly uninformed.

The Statistical Package for the Social Sciences (SPSS), is one of the biggest perpetrators of this crisis.  Which is hugely ironic, because I happen to love SPSS.  SPSS is probably the first statistical package that has placed advanced statistical methods within the grasp of the novice user.  I’ve been a happy user for nearly a decade (ever since I was introduced to the program in high school).  But there is no doubt that I’ve come to understand statistics within the context of SPSS and its GUI.

Please don’t misunderstand me, I have a pretty good grasp of basic statistics.  I can sling probability with the best of them and take relish in describing when to use the Fischer Exact test instead of a Chi-Square; but advanced statistics are a completely different matter.  Advanced stats scare me.  I can certainly use these more complicated methods.  I’ve analyzed and written about multi-variate models and even ventured into Analysis of Variance (ANOVA).  But I have to rely on SPSS and the aid of my institution’s biostatistician to help me recognize when there is a problem.

Which is why, in a time of tight budgets, losing the institution’s SPSS license has been a crushing blow to my productivity.  (Whoever made that decision should be hauled out and shot!)  Because I don’t have my statistics software any more, there are certain aspects of my job that are much more difficult to do.  And unfortunately, there is only logical conclusion to draw: I’ve become a victim of the statistical ease of SPSS.

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Heart Arrhythmias and MRI

 | March 24, 2009 1:41 pm

image After nearly 18 months of work, my research group finally published our big study!  It should appear in the journal of the American Heart Association, “Circulation” on April 7, 2009.  This also means that I can finally talk about what I’ve been doing for the last long while.

Atrial fibrillation (AF) is the most common – and perhaps most insidious – form of heart arrhythmia (a change in the normal electrical patterns of the heart) in existence.  It affects millions of people and while it isn’t life-threatening in its early stages, it eventually leads to stroke or heart attack in many of those people who are afflicted with it.

Unfortunately, the current ways of treating AF are completely inadequate.  The class of medication used for treatment (anti-arrhythmics) often cause more problems than they prevent, and interventional treatment is still highly experimental.  It is, therefore, all but a guarantee that the AF will become more serious over time.  Patients cannot be as physically active as they used to be and eventually must adjust to the symptoms of the disease.

A great part of the reason why AF is so difficult to treat is that we lack a good understanding of what causes it.  About fifteen years ago, some researchers in France recognized that the random spots of electrical activity within the pulmonary veins (which return blood to the heart from the lungs) were a likely source of the arrhythmia.  As a result, there is an entire arm of interventional treatment designed to destroy these spots and isolate the pulmonary veins so that bad electrical signals are unable to influence the heart as a whole.  While this is effective in some people, it doesn’t work for everyone.

More recently, other researchers found that AF actually changes the underlying tissue of the heart (a process known as remodeling), which results in other electrical and mechanical adaptations.  These changes make the arrhythmia more serious as well as difficult to treat.  Even though the changes are a sign that the person has a more advanced form the arrhythmia, the only way to ascertain the degree of change is to invasively measure electrical changes from the inside surface of the heart.

That is, until about a year ago.  In the Circulation paper, we describe a method to determine how much the heart has remodeled by using MRI.  We also showed that the degree of change is the single best indicator of how the patient will respond to treatment.  While this may seem obvious, it isn’t something that could be measured easily or safely before.  Now, we have a tool which allows us to see how the heart changes over time in response to AF.  This will lead to a better understanding of the disease, and provide insight in how to treat it.

The image below shows an example of just how good this detection can be.  The first column of images (A) shows a three dimensional model of the human left atrium.  In the top row, we are looking at the back (or posterior) view of the left atrium.  The pointy bits projecting to the left and right are the pulmonary veins.  In the bottom row, we are looking at the atrial septum – part of the wall that divides the heart into left and right sides.  The really interesting information is in the second column (B) which shows a 3D model where two different types of tissue have been identified.  Healthy tissue (shown in blue) and diseased tissue (shown in green).

This particular patient has some diseased tissue, though overall the heart looks fairly healthy.  What is striking, however, is how well this diseased tissue compares to the measurements made by invasive mapping (taken during a catheter intervention).  On the back side (top) we can see a donut of unhealthy tissue, and on the right side (in the septum), we can see a hook of unhealthy tissue.  The location and shapes of these tissue are mirrored on the invasive maps (C).  And all of this can be determined without exposing a patient to radiation or needing to cut them open!

Bioen02 - Circulation Revision - Figure 1 - High Quality

These types of MRI techniques open a whole new branch of research that can be done on the heart that has important implications for more than AF research.  The remodeling and changes observed in AF can be seen in atrial tachycardia and even some types of ventricular arrhythmias.  Moreover, it appears to be related to other conditions, like coronary artery disease or ischemia (from smoking, for example).  More on that later, though.  If interested, you can find the complete text of the Circulation article here.

Atrial Fibrillation Study Published

 | October 20, 2008 12:32 pm

I am happy to note that the first of my papers with the Atrial Fibrillation Group at the University of Utah was published!  The full text can be found here.  While I know that I have an obvious bias, the paper is still very important.  It describes the University of Utah's methodology for visualizing tissue damage following the ablation.  Further, it lays the groundwork for the next studies: the detection of low voltage tissue prior to ablation, and the determination of what ablation parameters will result in the induction of scar.  All in all, a nice little paper.

As an add on interest, we found that the degree of enhancement (or damage) seemed to relate to how well people did following the procedure.  There are a lot of theories flying around as to why this might be the case.  My own personal theory is that targeted ablation induces a change in diseased tissue.  I was also happy to notice that we aren't the only people who see it as such.  Our study was of sufficient interest that it was accompanied by editorial comment, as a highlighted article.  Not bad, if I might be allowed a smug moment.

For those that care about such things, here is the citation:

McGann CJ, Kholmovski EG, Oakes, RS, Blauer JJ, Daccarett M, Segerson N, Airey KJ, Akoum N, Fish E, Badger TJ, DiBella EV, Parker D, MacLeod RS, Marrouche NF.  New magnetic resonance imaging-based method for defining the extent of left atrial wall injury after ablation of atrial fibrillation. J Am Coll Cardiol.  2008 Oct 7; 52(15): 1263-71.  PMID: 18926331.

If you'd like to take a look at the full article, you can get the accepted draft from the Science and Technology page.

AF and Smoking

 | August 17, 2008 11:14 am

Several weeks ago, while working on the revisions for a larger study, I noticed an important trend. Patients who suffer a recurrence of atrial fibrillation following catheter ablation quite often have a history of smoking. "That's interesting," I thought at the time. I then successfully stopped thinking about it, so that I could think about other important things. The ability of men to focus only on the task at hand being what it is. While spending time at Dr. Marrouche's party last night, I ran into Brent Hill. Brent is the research coordinator for the Division of Cardiology. While talking, I mentioned the finding. He got quite excited about it. So excited, in fact, that he thought about co-opting the idea for his thesis. Some additional ideas that he shared:

  1. By what mechanism does smoking cause a recurrence of AF following the procedure? Might it be due to smoking induced ischemia?
  2. Is the effect mitigated by the number of cigarettes which the person smokes per day?
  3. Would offering smoking cessation materials help to increase the effectiveness of the ablation procedure?

Interesting things to think about! I think the next step is to formulate a number of specific hypotheses and draw up a formal proposal. At that point, it would be interesting to approach Marrouche and get his take on it.

Update

Though it may have been interesting to further think about and develop a map of how AF and smoking relate, I do not think that will ever be a possibility; unfortunately. Due to a number of personal reasons, I have decided that it is time for me to leave the AF group. I have greatly enjoyed the time that I have been able to work with the people in the group, but it is possible that my future lies somewhere outside of medicine. I will be posting a "Swan Song" shortly which describes my thoughts of how the various projects interconnect, but that will be my last thoughts on atrial fibrillation and its treatment.