The role of mathematical biology and Philip Maini’s podcast

Don’t let the image featured in this post fool you: this is about the role of mathematical biology. The observation comes from a podcast that we (at Pint of Science) released a few days ago featuring Prof. Philip Maini. Prof. Maini is the director of the Centre for Mathematical Biology at Oxford.

People have asked me (and my colleagues) about what the usefulness of theoretical/mathematical/computational biology. Here is a nice example:

Philip Maini and colleagues have worked on a mathematical model of neural crest formation. Around minute 3 of the podcast you can listen to Philip describe the biology of neural crest formation and the ‘verbal’ model that the experimentalist where working under. This model assumes that a certain factor (VEGF) is all it takes for the cells to move in the direction they do. Their mathematical model proved that, with the evidence at hand, the leading cells would consume all the available VEGF before the cells behind could make use of the gradient to go in the right direction. But not only did this mathematical model show what was wrong with the experimentalist’s assumptions, it also allowed them to explore what could be the guiding mechanism. Turns out that front cells and follower cells are different and that the following cells attach to the leading ones in order to find their way.

This shows 2 different ways that mathematical modelling proved to be useful: it allowed us to discard wrong assumptions and also to easily (and inexpensively) explore new hypotheses that can then, later, be confirmed experimentally.


Our letter to the New York Times criticizing Nicholas Wade’s book on race

On why you should be an expert in a topic on which you want to write a book about.

Why Evolution Is True

Sunday’s New York Times Book Review (already up) features a letter signed by 139 population geneticists, including myself. It is, in essence, a group of scientists objecting en masse to Nicholas Wade’s shoddy treatment of race and evolution in his new book A Troublesome Inheritance: Genes, Race, and Human History. 

The book was about the genetics of ethnic and cultural differences, and while it made a valid point that ethnic groups do show small but significant genetic differences across the globe, there was no evidence for Wade’s main thesis: that differences in behavior among groups, and in the disparate societies they construct, are based on genetic differences. While that might in principle be true, we simply have no evidence for that conclusion, and it was irresponsible of Wade to suggest that such evidence existed.

I was asked to review Wade’s book for a major magazine, but after reading it became so dispirited that I simply didn’t…

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What is a species?

Trait distribution
Trait distribution. With the X axis showing the value of the trait and the Y the frequency in a colony of asexual organisms.

With the increasing focus on the role of intra tumour heterogeneity in cancer, figuring out the types of tumour cells in a cancer becomes more important. But whereas we have a good idea of what a species is when it comes to sexual organisms, this question is harder when dealing with asexual ones.
One approach is to look at the genetic differences between two cells. If the differences are small then we can say that they belong to the same species. The problem with that is that genetic differences may not mean much. From the evolutionary point of view what matters is the phenotype: the way the cell looks, behaves and interacts with other cells and the environment.
This is closer to what we do with sexual species. If two individuals of different gender can mate and have offspring that can also mate then they are considered to be part of the same species.
Tamir Epstein is a research scientist with a PhD in physics and whose work involves him jumping between Princeton and Moffitt. He raised this issue and suggested an approach that I am trying to explore here.
If you start a colony of cells in a petri dish starting from one single cell there will be a lot of traits where the cells will be slightly different from the original one. We can describe this with a distribution like the one in the figure at the top of this post.
So here is a possible definition of species for asexual organisms courtesy of Tamir and (and myself to a smaller measure through the discussion): two organisms belong to the same species if for a relevant number of traits they can lead to the same distribution. That is, if you take two cells, place them under the same circumstances and let them grow, the resulting distributions should be identical.
I am guessing this is a start. In reality it is quite likely that finding two cells that can lead to equal distributions of traits will be tough so a degree of flexibility migh be necessary.

Guns, germs, steel…and fashion

I am still reading Mark Miodownik’s book Stuff Matters about materials. It’s a great book and I am doing my best to read it at a leisurely pace so that I can enjoy each chapter individually.

The chapter about glass is, as ever, very readable and interesting. In a way I was expecting Mark would talk at some length about the importance of glass for modern architecture. But Mark goes way back: how Romans and their primitive glass-making techniques might have contributed to change history. You see, at the same time that the Romans struggled to make glass that would be able to withstand even the tiniest shock, the Chinese has the capacity of  producing quality glass.

But while the Chinese were happy to drink from opaque vessels, the Romans loved to drink and see their wine. This led to further developments in glass making and could explain why European scientists created  microscopes and telescopes before anybody else.

The title in my post is based on the book by Jared Diamond: Guns, germs and steel. The idea of the book is that the West won the resources and geographical lottery. It turns that fashion might have also had something to do with it.

Stephen Fry on “How do we know what is true?”

Yes, it’s science

Why Evolution Is True

This is one of severa excellent videos Fry has narrated for the British Humanist Association.

Here Fry is talking about how we discover truths about the universe. As he says, “Science: there is no better method.”

Fry’s contrast between science and religion as ways of “knowing” the truth is explicit. To me, the distinction between science-based and spiritual healing is especially striking. How come religious people, who are so sure that revelation tells them what is true, shy away from equally revelation-based spiritual healing (except for Christian Scientists and other such misguided folk)?  Why won’t they put their trust in a healer who says that “faith” has told him how to cure their infection or their cancer? Why, when there is a choice, do they put their present lives in the hands of science?

After all, the matter of your fate in eternity is surely more pressing than your urinary tract infection. Why do you put the former in the hands of…

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