Book Review: Your Inner Fish

This past week I finished Neil Shubin's book Your Inner Fish. It was a book that I was highly looking forward to reading, as I had heard a lot about it and thought it was a really good idea. The basic premise of the book is to look at our present day physiology and trace aspects of it back through the fossil record using all the tools of modern evolutionary science (from the fossils themselves to comparative DNA studies and developmental biology).

I think my expectations may have originally been overly high, considering that the book combined many things that I am a big fan of: comparative anatomy and physiology, paleontology, and evolution. What I failed to realise was that this was a fairly short, well-written popular science book, and therefore did not go nearly into the detail that I wanted. Despite Shubin's general skirting of complex details in lieu of making general points, the latter half of the book I found to be highly engaging, as there were a number of fascinating factual gems and I felt he started to feel more comfortable expanding the detail of his discourse, given the basic knowledge set he had introduced in the first half.

Thus, my biggest criticism of the book is that it could easily have been longer and more detailed. As it stands, it is a well-written and easily accessible overview of how our bodies are shaped by our evolutionary history. It is interesting, being about a subject that we are all aware of (the human body), with an interesting perspective that not a lot of people acknowledge or think about. I hope every school library gets at least a copy or two, and I think biology teachers would do well to point them out to their students.

Edit: I just wanted to point out that the first half of the book was good too! I simply found the second half engaged me more, but I realise that my initial wording of this post made it seem like that was the only good part of the book.

Further Discourse on Demonizing Darwin

In my most recent Scientist Appreciation post on Friedrich Wöhler, I pointed out that Darwin, in my opinion, receives a disproportionate amount of discussion and demonizing by the religious right compared to other historical scientists. Regan responded to this by saying:

The biggest reason that Darwin is such a huge target is because the work he did and inspired totally invalidates the story of genesis.

Wohler's challenge to vitalism is different in the sense that there is nothing in the bible that says "And lo god created vitalism, and it was pretty neat", so it was easier to rationalize that concept into the theological worldview. The work that Darwin did and inspired can't be crammed into the bible no matter how hard you try. The bible says X happened, and the study of the processes of natural selection and evolution says Y happened. There is no possible way to reconcile the two.

I think the stranger scientist to be demonized by religion is Galileo. The bible doesn't even explicitly say the sun travels around the earth, and they still put him under house arrest until he died.

Since Regan's statements do not satisfy the quandary I meant to be presenting but are nevertheless factual and reasonable, I thought it worth writing another post on the matter to hopefully elucidate my original intent more clearly. As with most of my posts on subjects outside the realm of computational neuroscience, I have not made exhaustive study of the topics I cover here, so it is reasonably possible I am basing my discourse on incorrect information (of course, that is still possible when I am talking about computational neuroscience, just I tend to think it less likely). If you disagree with what I write, please do not hesitate to leave a comment or send me an email.

The thing is, revealed religious truths are awfully dependent on the ephemeral whims of people. Organized religions also tend to have a couple driving forces to deal with - there is both the scripture itself as well as clerical dogma. Before widespread printing of the Bible, these two forces in the Christian world were largely one and the same - Christianity was governed by one of a few theocratic hierarchies (the Catholic church in the west, and the Eastern Orthodox Church in the east). My historical knowledge of eastern Europe is weaker than my knowledge of western Europe before the 1900s, so I will primarily concentrate on the west. This merging of clerical dogma and scripture under the closed purview of the Catholic hierarchy meant that, for the most part, there was one accepted version of Christianity and alternative interpretations of the scripture (which could possibly lead to new dogmas) were not widespread (since few had access to scriptural learning) and, when they did occur, suppressed through threats of excommunication and the charge of apostasy. This situation could help explain the reaction to Galileo, as the view of Earth as the centre of the universe, while not explicitly scriptural truth, was heavily part of the clerical dogma. Given the philosophical stance of the Christian faith that humans are the favoured creation of an all-powerful god, Earth as the centre actually fits better. Combined with scriptural references like Joshua making the sun stand still, the conclusion that Earth was not the centre of the universe and rather revolved around the sun contradicted current dogmatic law based on the currently favoured interpretation of scripture. Galileo's conclusion, therefore, was, in some interpretations, contradictory to scripture, but, more importantly, was subversive to the power of the religious hierarchy. As time progressed and Galileo's view of the solar system became more and more undeniable, the religious dogma gradually shifted to accommodate. The story of Joshua was recast either to 'metaphor' or interpreted as the miracle of the Earth halting its rotation and orbit rather than the sun halting its motion, and the clerical dogma avoided comment on the issue before finally apologizing for Galileo's treatment a couple decades ago when someone must have realised they were still remiss in that regard. Of course, one reason the Catholic church is usually so slow to apologize or admit wrongdoing for anything is because, technically, their head guy is supposed to be divinely inspired by an omnipotent and timeless all-powerful being. As their god's agent on Earth, the pope should infallible (at least once he becomes pope). Admitting mistaken persecution of a brilliant scientist because his claims were deemed wrong makes the infallibility of a divinely inspired leader a little harder to argue.

Moving past Galileo and back to the time period of Darwin and Wöhler, however, schisms within the world of Christianity had been amplified by the translation of the Bible into many languages as well as widespread availability of printed material and an increase in literacy. Although there was still a certain amount of power concentrated in clerical hierarchies, there happened to be more of them now that the Church of England existed along with other Protestant branches like Lutheranism, and that division weakened their overall power. As was pointed out by Andrew, Darwin did not operate in a vacuum. Geology and paleontology were being developed by pioneering scientists like Georges Cuvier and James Sutton. Darwin was not the scientist who first developed the idea that extinct species had once lived on Earth without any evidence of mankind in a period of time far further in the past than one could feasibly trace the Biblical story. What he did was develop a theory that elegantly explained the appearane of the biological rule based on these observations as well as zoological observations in his current day. I would argue that it was the scientists who developed the fields of paleontology and geology who more directly contradicted the Biblical story of genesis.

Thus, the manner in which Darwin's work contradicts Biblical creationism must be seen more as a philosophical contradiction rather than a direct one, in which evolution can be seen as a naturalistic mechanism to explain the distribution and form of extant species. This explanation weakens the need for a divine explanation for the form of modern life, although it says nothing about the origin of life. Before vitalism had been demonstrated incorrect and we were able to generate organic substances from inorganic subtrates, an avenue for theological retreat remained widely open. By recasting genesis as a metaphor and enfolding evolution into "god's plan", the divine origin of life was much more easily defensible when there was no known natural mechanism for going from inorganic to organic. Without the abandonment of vitalism, theistic evolution is a much more viable outlook (although I would contend that one still has to answer how a benevolent and all-powerful god would deign to rely on such a largely unforgiving and unpleasant mechanism).

Evolution, it would seem, largely attacked the dogmatic idea of immutable forms, while the disproof of vitalism greatly weakens the idea of a divine origin for life. Both are aspects of the Biblical creation story, which is why I thought Wöhler's work also undermined religious dogma in a similar manner to Darwin's.

The tragedy that is our current government

As many of my readers are likely aware, the current Canadian Minister of Science, Gary Goodyear, recently horrified many by responding to a question of his belief in evolution (granted, a poorly worded question) with what is possibly the worst and most unsettling dodge possible:

I'm not going to answer that question. I am a Christian, and I don't think anybody asking a question about my religion is appropriate.

That response is highly troubling because the Minister of Science should not think a question about evolution is a question about religion. Apart from the troublesomely loaded word 'believe', the question had no religious content whatsoever, and it was Mr. Goodyear himself who invoked the religious aspect by conflating a 'belief' in evolution with questioning his Christianity. This has been well and thoroughly discussed, however, so I won't elaborate on this part of the story... what horrifies me is his attempt at a clarifying response:

We are evolving every year, every decade. That's a fact, whether it is to the intensity of the sun, whether it is to, as a chiropractor, walking on cement versus anything else, whether it is running shoes or high heels, of course we are evolving to our environment. But that's not relevant and that is why I refused to answer the question. The interview was about our science and tech strategy, which is strong.

His response continues to show only a shaky grasp at best of what evolution actually means. Reading further into this fellow's views, he also seems to think it is proper to solely undertake scientific research with a clear practical goal in place. This man is a terrible candidate for a Minister of Science.

Understanding Through Mathematical Concepts

My great aunt is a wonderful lady. A worldly intellectual in her own right, she can speak knowledgeably about Thucydides (which she read in the original Greek, not that wimpy translation stuff I read) and other literature of which I could not hope to compile an exhaustive list, as well as hold her own in a discussion of history and politics, especially if it involves Korea (where she was born and raised through much of her childhood before returning home to Canada). I am also a big fan of my great uncle, but since it was my aunt that made the comment I am going to discuss, I will have to wait for another day to sing his praises. I bring up my esteem for my aunt to put in context a comment she made one night when my girlfriend and I were at my aunt and uncle's for dinner, in which she stated something to the effect that she didn't understand how mathematics could hold any draw as a subject since it was such a dry and abstract thing. I think it was somewhat unfortunate for her that she made such a comment at a table with her husband (a retired aeronautical engineer), my girlfriend (who studies physics and mathematics), a Russian fellow who sails with my uncle and his wife (both who studied mathematics and computer science before moving to Canada), and me (a former aerospace student and now student of computational neuroscience), so she may have been a little unfairly outnumbered by those who had ties to mathematics. A great cry went up around the table and everyone tried to explain all at once that mathematics was, in fact, a wonderful thing. I don't think my aunt (a former graduate of the humanities) was trying to be confrontational at all, but I think she really was baffled (and, unfortunately, I don't think any of our answers really cleared anything up at the time, since the best we came up with was simply that it helps you to see the world differently without really giving any examples). I also don't think my aunt is alone. For many people, mathematics remains a dry and stuffy subject, handy for balancing the books and maybe work in research and design (but even then, there are a fair share of engineers who forsook mathematics upon achieving their degree and getting a job), but beyond that they don't have a concept of it.

While I am no mathematician, I still enjoy mathematics and dabble in it in my studies. I will therefore endeavour to give an example of how mathematical concepts can help explain aspects of the world using a personal insight about another subject that also commonly baffles people: speciation in evolutionary biology. Among critics of evolution, one of the commonly fallacious argument given is, "if evolution is true, why doesn't a dog give birth to a cat?" (or some other ridiculous combination). While that is probably the most ridiculous formulation of the argument, the basic idea that trips people up is understanding how one species can evolve into another. This lack of understanding often leads to the lamentable "middle of the road" half-cocked compromise in which a person accepts "microevolution" while claiming that he still doesn't believe in "macroevolution". To give some insight into how speciation works, at least from a conceptual standpoint, I turn to probability and calculus.

Take a circle with a spinning dial mounted in the middle. If you mark a spot on the circle (say the spot corresponding with '12' on a clock face) as the 0 mark, then you can spin the dial and it will land with some anticlockwise angle from 0 to 360 degrees. Since there are an infinite number of points on the circle, however, if you take your measurement to an arbitrary level of exactness (landing at 10.0000000000001 is different from landing at 10 exactly), the probability of landing at any distinct spot is essentially 0. The only way to obtain a non-zero probability is to talk about a range of possible angles. The probability is then simply the length of that range divided by 360 (thus, having the dial land within the first 90 degrees has a probability of 90/360 = 1/4). Thus, the circle can be divided into regions, each one representing a range of possible angles and thus having a non-zero probability. However, at the borders we see that which region we are in becomes a harsh cut-off over a seemingly negligeable difference. For example, if we divide our circle into four regions of equal size (each representing 90 degree increments), 89.99999999... would fall into region 1 while 90.0000000...001 would fall into region 2, despite an arbitrarily small difference between the two of them. Take the idea of that circle and now morph it in your head to represent an evolutionary lineage. The population of organisms at each moment in time represents one single location on the circle. A region represents a species, and thus a species is said to evolve into another if its region precedes the other. But remember that the demarcation line of our regions was essentially an arbitrary cutoff, a boundary imposed to provide meaning to the system. There is no drastic change in the dial's position when we go from region 1 to region 2, but rather the change can be as infinitesimally small as we want. Likewise, the change from species A to species B is not some drastic, single moment of monumental change such as a dog giving birth to a cat, but is rather a collection of tiny bumps in the dial position as it gradually creeps along the circle going from region 1 to region 2. However, when one compares the dial position from somewhere near the middle of each region, it looks to be very far apart.

This is no lofty or profoundly insightful thing I have come up with. I also recognize that I may have taken some liberties with the specific terms and workings of both mathematics and evolutionary biology, so for anyone who is actually in those fields and upset with me, I apologize (and you have full permission to admonish me in the comments). However, it is something that I have discovered a surprising number of people never really put together on their own. The concept of infinitesimal steps from calculus is a profound thing, and with it many other concepts in the world can be illuminated more fully. That, to me, is how mathematics is not dry or dull. Its concepts are wide reaching, elegant, and profound. If a person understands mathematics, there is a huge variety of subjects that suddenly become easily grasped.

Scientist Appreciation: John Maynard Smith

Oh dear, it's Friday again already. The scientist being appreciated this week is John Maynard Smith, aeronautical engineer turned evolutionary biologist. Part of what draws me to him is that I feel a slight kinship with him in terms of the change of fields (after all, I left aerospace engineering to pursue a degree in computational neuroscience). More to the point, though, is that Dr. Maynard Smith is a perfect example of the great impact a person can have on a traditionally descriptive field simply by applying mathematical reasoning. Instrumental in bringing game theory to bear on some of the more nuanced and difficult areas of evolution (such as cooperative behaviour), his best known game theory model is the Hawk-Dove game. I was first introduced to the works of John Maynard Smith by his mention in Richard Dawkins' The Selfish Gene, where his arguments and models are used extensively in framing the thoughts of, in my admittedly not entirely informed opinion, one of the greatest evolutionary biologists of the last century. Of course, like so many of my intellectual heroes, John Maynard Smith is now unfortunately deceased, leaving me without hope of ever getting to meet him and thank him for helping me see the beautiful obviousness of evolution by simply knowing how to look.

Some quick media reactions

I just wanted to put up some quick links to media I have watched/listened to when I should have been studying.

The first is from the most recent episode of Real Time. I was mightily cheered by this part of his show, especially since I spent four years living in small town western Pennsylvania and being appalled by the general political and religious atmosphere of the place. Perhaps things are changing.

The second is a link to a set of downloads for a conversation between Scientific American and Mark Mathis, one of the fellows behind that intellectual travesty that came out on the weekend (and that I keep linking to the site that debunks its claims). It is kind of difficult to listen to, since Mr. Mathis is fairly slippery, but perhaps I will get to a debunking post later. However, I've wasted too much time already on this.

The Evolving Brain

Most people are aware that their brains are (for the most part) split into two sides to create a right and left hemisphere. Furthermore, it is fairly common knowledge that (once again, for the most part) the right part of your body is controlled by the left side of your brain, and the left side of the body is controlled by the right side of the brain. This is more succinctly known as contralateral control. When signals to and from the brain do not cross over to opposite sides, it is instead known as ipsilateral control. What I have never heard a good explanation for, however, is why the human nervous system is primarily set up utilizing contralateral control. It seems to simply add an unnecessary complication to an already ridiculously complicated system. There is, of course, the possibility that contralateral and ipsilateral control offer virtually no selective difference to an organism, and it is therefore a 50-50 random chance sort of thing that just happened to end up favouring contralateral. However, that is a rather boring answer, and, like I said, leaves out the fact that contralateral is at least a small bit more complicated than ipsilateral, meaning there just might be something that made that complication actually worth while.

When my neuroscience professor mentioned Mauthner cells in one of my lectures, I realised that perhaps I had an answer. There is a reflex in fish and tadpoles called the Mauthner Cell C-Reflex. The Mauthner cell is the largest vertebrate neuron and it is activated by tactile stimulus to a creature's head. The signal from the Mauthner cell then innervates muscles on the opposite side of the body, quickly turning the head away from the stimulus for the fastest possible escape. Thus, here is a system in which there is a tremendous difference between contralateral and ipsilateral control. An ipsilaterally wired Mauthner cell would be a very bad thing, since it would turn its creature towards rather than away from the stimulus (which might very well be a predator).

Therefore, I wonder if the Mauthner Cell C-Reflex (or whatever reflex system was the precursor to it) was the first contralateral system in the vertebrate nervous system. Once it was wired up contralaterally, the whole somatosensory system followed, which of course led to other things until virtually the entire organism's nervous system was set up with contralateral control. By the time we crawled out of the oceans and lost our Mauthner cells it was too late to straighten things out.

Of course, this is just idle wondering into the murky evolutionary past, but I would love at some point to see if there actually is something to it. Of course, like most of my idle ideas, I will likely never actually get around to looking into it, but now that I've written it down, maybe it will stick with me for a rainy day when I'm in a researching sort of mood.

A Case for Inter-field Knowledge...

They say that the time of the generalist has come and gone, but to me that is a sad thing. Of course, every so often some new "hot" field develops from the merging of several other fields, and the buzz word "interdisciplinary" gets thrown around a lot these days. However, it really shouldn't be just a buzz word, and I have two short anecdotes that I think make that case.

The first is a horrifying tale from my first year psychology course last summer (which I had to take so I would be able to take some of the neuroscience courses I wanted to this year). Since it was a summer course it was not actually being taught by a professor, but rather by a PhD student in developmental psychology. The first couple lectures were devoted to neuropsychology, the quaint name given to the "branch of psychology" devoted to studying the actual physical make-up of the human brain (as opposed to several of the other branches, which is basically just making stuff up that sounds vaguely plausible. That, however, is a rant for another day). Anyway, now I had spent the previous four months realising that intelligence was what I wanted to spend the rest of my life studying, so I had done some modest reading about the brain. It was nothing fancy; I think the least pop-science style book I had read pertaining to the brain was Oxford Press's A Very Short Introduction to the Brain. Anyway, I make this clear because I want to point out how absolutely rudimentary my knowledge of neurophysiology was at this point. Imagine my surprise, then, when this young lady gets up in the front of the class and proceeds to dazzle everyone with several blatantly false statements. While I was a little disgruntled when she told a student that withdrawal of a limb from a painful stimulus was not a reflex, but rather the turning and oral searching of a baby was what was meant by the term reflex (granted, she was a developmental psychologist, so she dealt with infant reflexes more than the withdrawal reflex, but she should still know the definition of the reflex arc and some of the common examples), I was far more horrified when she answered another student's question as to how the myelin sheath helped make signals travel down the axon faster by saying it was "superconducting". Leaving out the blatant misunderstanding of what is meant by superconductivity, she clearly had no clue how myelin works. And this was the lady standing at the front of a class of several hundred students answering questions like she knew what she was talking about, because she was planning to get her PhD in a field that at least tangentially claims to study the brain.

How can a person possibly hope to bring insight to the question of how the brain develops and mediates thought without at least a rudimentary understanding of the underlying hardware? There is a reason they make computer science and software engineering students study digital electronics and lower level languages than Java or Python, because if you don't understand the underlying architecture of a system you are left writing all your MatLab scripts with for loops and uninitialized matrices rather than matrix algebra and left wondering why your program takes hours or even days to run.

Anyway, I had planned originally to also mention how my neuroscience textbook prompted this entire post because of its blatant reference to species selection at the beginning of the chapter on sexual selection, and I was going to spend some time dwelling on the importance of understanding evolution in all its brilliantly nuanced glory when doing anything in the life sciences (including neuroscience), but instead I seemed to have gone on a little too long with my rant about the lack of knowledge of my psychology lecturer. Clearly, I still bore an intellectual grudge.

Perhaps, though, I am being a little too harsh, since this very weekend an intellectual travesty far worse than what I have just described is going to be gracing selected theatres across this continent.

Also, please note that the majority of my "scientific" links were to various Wikipedia pages. I recognise that Wikipedia most certainly is not a scientific source, but the point I was making was how non-specialized this knowledge really is.