Archive for the 'Scientific Practice' category

Echo Chambers

Sep 22 2010 Published by under Scientific Practice

In the late 70's, French anthropologist Bruno Latour set off to do some interesting fieldwork. He spent time observing the daily rituals and customs of scientists in situ, in the laboratory of Roger Guillemin, discoverer of TRF, at the Salk Institute. The results of his anthropological study was a book called "Laboratory Life" which was published in 1979. It was one of the first descriptions of the day to day functioning of a science lab and of the act of doing science itself. Anyone that has worked in a lab will recognize the descriptions of laboratory dynamics, the role of funding in scientific research and in the selection of what scientific questions are considered important, the role of the PI's prestige in determining which data gets published where and how "believable" it is, how hypotheses sometimes become unspoken assumptions without any real data to back them up, and in general how scientific facts become constructed by the human enterprise of science. Latour's conclusion is somewhat extreme – that all scientific facts are socially constructed. I think most scientists would agree that this is not the case, that while many of the observations that Latour makes can influence scientific conclusions, in the end there is a real fact that is eventually shed light upon by the science and is continuously refined by the process of scientific consensus. Nevertheless, its a great book (a bit dry at times) that everyone should take a look at. However, there are some cases where scientific facts have been almost entirely socially constructed, and have even persisted for over a thousand years, despite large evidence to the contrary. One of my favorite examples relates to the structure and function of the human heart.

In the second century C.E. the Roman physician Galen wrote what became the seminal medical text for the next thousand years or so. In it he described the human heart as the source of the body's heat and described the heart as having two chambers, the right was associated with the liver and contained "nutritive blood" which was made by the liver and consumed by the different organs. The left chamber was involved in making vital spirits which were distributed to organs by arteries. Both the left and the right chambers were supposed to be connected by tiny pores in the heart's septum where both types of humors could mix. It's not clear to me how Galen drew these conclusions about the structure opf the heart. Although he never did dissect human hearts, he did dissect hearts of multiple animals, and its pretty obvious in these that, like human hearts, they have four chambers. Maybe he was trying to fit the evidence to his prevailing world view. Galen's book was translated into multiple languages and went unquestioned in medical circles for centuries. Even Avicenna, the famous medieval Persian physician deferred to Galen when it came to the structure and function of the heart, and any evidence of pulmonary circulation or the fact that the heart actually had four chambers was usually ignored because it contradicted the accepted cannon, and Galen's "facts" just propagated from textbook to textbook.

Fig 1. Galen's conception of the heart and blood.

It wasn't until the Renaissance when the practice of studying human anatomy from direct observation (rather than from texts) became popular. Yet even then, some anatomical drawings, allegedly drawn from real life still show the heart with two chambers and pores in the septum. Take a look at this drawing by Leonardo Da Vinci. For the most part it's an anatomically accurate description of the heart and organs. But look at the heart – it has two chambers and tiny pores in the septum. Again deference to authority still seemed more important than actual observation.

Fig 2. Anatomical drawing of the heart by Leonardo Da Vinci. Notice the two-chambered heart and the pores in the septum.

Finally in 1543 Andreas Vesalius published one of the first modern anatomy texts, De Humani Corporis Fabrica, in which all anatomical descriptions were drawn from real cadavers, and where it is recognized that the heart has four chambers and no septal pores. This is a beautiful and compelling book. My university library has an original copy of this book which is bound in human skin. It's a wild and creepy experience to leaf through it.

Despite a revised anatomical picture of the heart, there was still confusion about its function. This was settled about 100 years later when English physician William Harvey published his seminal study on blood circulation. Harvey started from modern anatomical views of the heart and performed a series of comparative experiments in hearts of various animals, and concluded that the heart was actually pumping blood. He further measured the capacity of the heart and multiplied it by the heart rate and figured that there was no way that the liver and heart could produce so much blood to be consumed by the organs in a single day. Thus, he proposed that blood actually circulated from the lungs to the heart to the body, then back to the heart and again to the lungs. He showed that blood vessels had valves which would ensure unidirectional circulation. This he demonstrated by a variety of simple experiments, one which you can do yourself. Right now! So: 1) Find a vein on your arm or back of your hand. 2) Press on it with a finger on the end closer to your body,  use another finger to squeeze the blood out. You will see that as soon as you do this it will fill up immediately. 3) Press now on the side of the vein closer to your fingertips. Squeeze the blood out. You will see that the vein remains empty until you release your other finger and then fills up. This is because venous blood blood flows towards the heart, as opposed to the Galenic view that both types of blood flow to the organs to be consumed.

Fig 2. Harvey's little vein experiment. From "De Motu Cordis".

Thus with actual observation, an integrative scientific approach and demonstrable experiments, as well as information from the latest literature, Harvey was able to overturn a thousand year-old "fact". It's not that he he had fancy new equipment not available to Galen, but rather lived in a time where a scientific world view was prevalent. And it was just a matter of time. If he hadn't resolved the discrepancy between theory and data, someone else would have.

This is obviously an extreme case where deference to authority distorts scientific facts. But in reality this occurs all the time in more subtle ways in modern scientific practice. Part of learning to do science is to be able to identify these types of biases and avoid them as much as possible.

Further Reading

Bruno Latour (1986, 2d Ed.), "Laboratory Life: The construction of scientific facts".

Andreas Vesalius (1543). "De humani corporis fabrica". (click link for browsable version!)

William Harvey (1628). "De motu cordis" (On the motion of the heart and blood).

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Neuronistas vs. Reticularistas

Sep 06 2010 Published by under Scientific Practice

Every couple of years I teach an upper-level seminar course which focuses on historical controversies in neuroscience. Typically we read some classic scientific papers describing how a specific bit of knowledge first came to be and then we read some contemporary papers from the scientific literature which either overturn this long-held dogma, or revisit it with more modern experimental techniques. Ideally we'll discuss papers which look at the same question but come up with completely opposing conclusions. We then try and see why this is so – whether it is differences in experimental techniques, or cherry picking of data by a lab looking to support their pet hypothesis.

One of the first discussions we have in class is about a heated controversy that occurred over 100 years ago regarding the fine structure of the nervous system. During the second half of the 19th century, anatomists had been unable to distinguish much in the way of structure in neural tissue. It was simply too dense, too complicated and indistinct, and it was difficult to conclude anything useful about its anatomy from available anatomical and microscopic techniques. In 1872, Italian anatomist Camillo Golgi developed a method to stain brain sections using silver impregnation such that only a few of the brain cells, or neurons, in the tissue were stained, but were stained completely, allowing one to observe their complete structure in relative isolation from other cells. This discovery brought Golgi a good deal of recognition throughout Europe and he became well established at the University of Pavia. One of the conclusions that Golgi drew from observing his anatomical sections was that neurons appeared to have a series of complex appendages, also known as processes, that formed a continuous web, which he called a reticulum, with each other. Thus, the cytoplasm within each neurons was continuous with all other neurons in a given brain region, and somehow neural information flowed through these webs to produce brain function. This idea became fairly entrenched within the scientific circles of the time.

Fig 1. Golgi's interpretation of the hippocampus, a region in the mammalian brain. Notice how all the cells appear to be connected in a reticulum.

Meanwhile in Spain, an obscure anatomist named Santiago Ramón y Cajal had refined Golgi's technique so that neurons were stained even more clearly and he had reached a very different and controversial conclusion. Before I tell you about that, let's first examine how neuron function is currently understood. In today's thinking, the canonical view of a neuron is that it has two types of processes, dendrites and axons. Dendrites are the part of the neuron that receives information from other neurons via specialized junctions known as synapses, while axons are what send information to other neurons via electrical impulses known as action potentials. In a synapse, the end of an axon from one cell ends, releases signaling chemicals known as neurotransmitters, which travel through a gap between the axon terminal and the dendrite of the next neuron. The neurotransmitters activate receptors in the dendrite and ultimately generate further activity. What Cajal claimed to have seen was that in some cells he could see axons terminating in areas where another cell was known to be, but the cell was not stained by the silver stain. From looking at these free terminals, he concluded that neurons were not continuous with each other, but rather individual units, and that somehow, these free terminals made contacts with the dendrites of other neurons to transmit neural information. These contacts were later named synapses by Sherrington, a British physiologist and friend of Cajal. Cajal never actually saw a synapse – the distance between the axon terminal and the dendrite is way too small to be seen by a light microscope. But rather he inferred their existence by studying free terminals. Using these observations he was able to create composite wiring diagrams that showed the flow of information within a given brain region. More importantly, he established that neurons were polarized, with information traveling from dendrites to axons, as opposed to the reticular view, in which information travelled through a web of axons, and dendrites simply were thought to supply nutrients to the reticulum.

Fig 2. The hippocampus according to Cajal. Notice how a circuit diagram is drawn, showing neurons as individual units with information flowing between them.

Cajal published most of his early work in Spain and his views were not widely disseminated through European scientific circles or even accepted by many of his contemporaries. In an attempt to increase dissemination of his work he began to publish in French to reach a wider scientific audience. However the idea of a neural reticulum had taken hold, not only within Italy, but throughout Europe, and for the few that had read Cajal's work, they deeply mistrusted it. Desperate for recognition, Cajal joined the German Anatomical Society and took his slides and a borrowed microscope to their annual meeting in Berlin. Scientific meetings back then were similar to the ones today – there were a series of keynote talks and presentations of papers, followed by scientific demonstrations in a great hall. Rather than posters, people used to bring microscopes and specimens and set up in little tables as people would come by and discuss their findings. Richard Rapport writes in his book "Nerve Endings" that at this meeting Cajal was mostly ignored and scoffed at as he sat in his little table. Thus Cajal took it upon himself to find Albert von Kölliker, one of the most preeminent Swiss neuroanatomists at the time, and dragged him over to his microscope. Kölliker, like most bigwigs today, always had a posse of people following him around, and they all gathered around to see his reaction to this weird Spanish guy's claims. After listening to Cajal explain his theories and clearly demonstrating supporting evidence with his slides, Kölliker realized Cajal had performed a major breakthrough in our understanding of the nervous system. Kölliker worked hard over the next several years to promote and extend Cajal's findings. The idea, that individual neurons are the fundamental units of the nervous system was later dubbed the "Neuron Doctrine". Within 30 years, more and more evidence poured forth supporting the neuron doctrine, establishing it as one of the central tenets of modern neuroscience. In 1906 both Golgi and Cajal received the Nobel Prize for their contributions toward our understanding of the nervous system.

Golgi never did give up the idea of a neural reticulum. Despite the growing evidence against it, he kept generating more and more evidence supporting his views. Which is not hard to do. If you have ever looked at a Golgi stain, it is very easy to see how one would conclude that neurons are continuously connected through their dendrites. Even if only a small percentage of neurons are stained, dendrites are often so extensive that they appear to be completely tangled together between cells. And Cajal never did see connections between neurons, he just inferred their existence by looking at free axon terminals. So both sets of conclusions, based on the available technology were in their own way valid. It just happened that Cajal was right and Golgi refused to give up his pet hypothesis, finding examples to support his view and ignoring those that didn't.

Apparently Cajal and Golgi did not talk to each other when they received their Nobel Prizes.  It is worth reading the Nobel Prize acceptance speeches given by Golgi and Cajal to illustrate the very different approaches of both scientists. It also goes to show that science 100 years ago was, in many ways, much like science today. Furthermore, as any good scientific theory does, the neuron doctrine has significantly evolved in 100 years. In a future post I will write some of the modern challenges that the neuron doctrine has faced over the years.

Further Reading

Ramón y Cajal, S. (1906) The structure and connexions of neurons. Nobel Lectures.

Golgi, C. (1906) The neuron doctrine – theory and facts. Nobel Lectures.

Highly recommended and entertaining book on Cajal and the Neuron Doctrine:

Rapport, R. (2005) Nerve Endings: The discovery of the synapse. Norton, 240 Pages, ISBN: 0393060195

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Autism and socioeconomic status

Jul 20 2010 Published by under Scientific Practice

I've been thinking about this for the past few days. I recently read an interesting article published last week in the journal PLoS One. I am by no means an expert in autism or epidemiology, but here is my take. In this study Durkin and colleagues show that there is a link between socioeconomic status and the prevalence of autism spectrum disorder. The authors took surveillance data from the CDC which evaluates prevalence of autism throughout the country. Overall they evaluated data from over 550,000 eight-year olds in a two-year period and found about 3500 individuals that would qualify as autistic. Using census data they sorted these cases into three groups based on socioeconomic status. Surprisingly they found that there was a very significant correlation between prevalence of autism and socioeconomic levels such that wealthier areas had relatively more cases of autism (see Figure 1). They further show that this gradient is present across all races and ethnicities examined. One possibility is that this effect may be due to the fact that wealthier communities might have better access to health and diagnostic services. In support of this claim the authors state that in fact the gradient is steeper if you only take into account cases where there was a previous diagnosis of autism before the surveillance data was collected. Meaning that children from wealthier families were more likely to receive a diagnosis during early childhood than children from poorer families. This would lead to diagnostic bias and may explain the correlation between wealth and autism. It also means that autism may be underdiagnosed in young children from socially disadvantaged communities, denying them the possibility of early intervention and treatment. Which is another reason for making health care accessible to all.

Figure 1. Prevalence per 10001 of ASD by three SES indicators based on census block group of residence.

That being said, the authors then looked at the group of children that had not previously received a diagnosis of autism but were picked up in the surveillance data. In this case any diagnostic bias should disappear. What they found was that even in this group there was a significant correlation between autism prevalence and socioeconomic status. The authors conclude by saying that "factors associated with socioeconomic advantage might be causally associated with the risk for developing autism." Which totally baffles and surprises me. I guess that one possible factor that may lead to this correlation might be maternal age, as socioeconomically advantaged women tend to have children at an older age. Or it could be something to do with differences in the type of prenatal care received that we don't fully understand. However the authors mention in passing something called the "hygiene hypothesis". Now I'm not sure how much actual evidence there is for supporting this hygiene hypothesis, but what it states is basically that the more you are exposed to a variety of diverse pathogens during early childhood, the less likely you are to develop chronic immune disorders such as allergies, asthma or inflammatory bowel disease. Some have used this view to explain higher prevalence of these disorders in developed countries or correlations between socioeconomic status and immune disorders. The reason this is interesting is that there are some well-established correlations between chronic abnormal regulation of immune system function and several neurodevelopmental disorders including autism. Many molecules which are active in the immune system are also known to regulate normal signaling in the brain and this may explain the association between chronic immune disorders and abnormal brain development. This is of particular interest to me since part of my research involves looking at the role of some of these immune molecules during early brain development. It is important to mention that when I say abnormal immune function I am not referring to the immune reactions which result from vaccination. Immune reactions to vaccines are short-term, and it has been very clearly established that there is no link between vaccines and neurodevelopmental disorders, including autism. What I am talking about is long-term alterations in the levels of various immune system molecules including regulators of inflammation and the so-called MHC markers. So wouldn't it be interesting if the link between socioeconomic status and autism prevalence was somehow related to the increased prevalence of immune disorders in economically advantaged groups?

Of course this is just a hypothesis, which has no actual proof. In fact I can find several holes in it. For example there is no evidence that someone from a lower socioeconomic status, living in the United States would be necessarily exposed to more pathogens than someone with a high socioeconomic status. I mean, wealthy kids eat as much dirt as poor kids. If you don't believe me go to a playground in a fancy neighborhood and in a poor neighborhood and observe the kids. They get exposed to all sorts of junk either way. But by making hypotheses scientists are then able come up with ideas for experiments that would either prove or disprove them. What I like about this paper is that it made me think a little outside the box, to come up with ideas and associations that I would not otherwise had come up with. And this is something that is important to do. I have several colleagues who do basic research into the mechanisms of autism and other neurodevelopmental disorders. And everyone is doing very different research, ranging from population-wide human genetic studies, to studying molecules which regulate the communication between brain cells to looking for structural abnormalities using brain scanners. And all of these individuals are doing great science and are very careful with their results and interpretations. Yet despite the fact that they are all studying the same disorder, it's almost as if they live in totally different, internally-consistent worlds. So in essence, they are all "correct" and all their results are "true", but if you look at them together then their theories start to look a little more shaky. At least not so consistent with each other.

It's a little like the movie Rashomon by Japanese director Akira Kurosawa. For those of you who don't know Kurosawa, he is one of my favorite movie directors and you should see all his movies, particularly the Seven Samurai, which is beyond great. But anyway, Rashomon is a murder mystery taking place in medieval Japan. A woman has been raped by a bandit in the woods and her husband, a samurai, has been stabbed and killed. The movie tells the story of the bandit's trial and three witnesses recall the events. The first witness is the bandit, the second is the woman, the third is the dead samurai (channeled through a medium). Although the basic facts are the same –the bandit raped the woman and the samurai was killed with a knife– the three stories differ from each other. At the end of the movie we hear a fourth version, from a woodcutter who witnessed the entire thing as he hid in the woods. For some reason he had chosen not come forward during the trail even though his story would resolve all the inconsistencies between the three other stories. Presumably, his version, as a disinterested party, represents the actual events. However at the very end we become suspicious of even his story since we start to suspect that the reason he did not come forward was because he has actually stolen the murder weapon, a bejeweled knife, after witnessing the events. So even he is not a totally disinterested party.

So what's my point? My point is that even the best hypotheses and ideas in science always have some spin, and that this spin will introduce bias. And it takes a study that makes everyone think outside of the box to bring these various hypotheses together and separate the spin from the facts. Good scientists will gladly let their pet hypotheses evolve or be discarded if evidence shows up to disprove them. Bad scientists will keep looking for specific data supporting their views while ignoring overwhelming amounts of data that don't support their views. As far as this relationship between socioeconomic status, chronic immune disorders and autism, we'll see how that one plays out.

Further reading (some may require subscription or a trip to a university library):

Durkin MS, Maenner MJ, Meaney FJ, Levy SE, DiGuiseppi C, et al. (2010) Socioeconomic Inequality in the Prevalence of Autism Spectrum Disorder: Evidence from a U.S. Cross-Sectional Study. PLoS ONE 5(7): e11551. doi:10.1371/journal.pone.0011551

H. Okada, C. Kuhn, H. Feillet and J.-F. Bach (2010) The 'hygiene hypothesis' for autoimmune and allergic diseases: an update. Clin Exp. Immunol. ;160(1):1-9.

Cohly HH, Panja A. (2005) Immunological findings in autism. Int Rev Neurobiol.;71:317-41. Review. PubMed PMID: 16512356.

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