john hawks weblog

paleoanthropology, genetics and evolution

mathematics

  • Civic allometry

    Sun, 2013-05-05 22:31 -- John Hawks

    An interesting article from Smithsonian magazine, about the mathematical study of cities: "Life in the city is essentially one giant math problem".

    Here's a passage quoting Geoffrey West, about the ways that different measures of a city exhibit allometry with population size:

    Remarkably, this phenomenon applies to cities all over the world, of different sizes, regardless of their particular history, culture or geography. Mumbai is different from Shanghai is different from Houston, obviously, but in relation to their own pasts, and to other cities in India, China or the U.S., they follow these laws. “Give me the size of a city in the United States and I can tell you how many police it has, how many patents, how many AIDS cases,” says West, “just as you can calculate the life span of a mammal from its body mass.”

    I've heard West speak about this population allometry. Obviously some of the most interesting cases are those where a city mismatches the expected relationships. But it is fascinating the way that so many aspects scale with a positive allometry -- getting proportionally greater as city size increases.

  • Math for biology

    Mon, 2013-04-08 00:36 -- John Hawks

    Edward O. Wilson, in the Wall Street Journal writes: "Great Scientist ≠ Good at Math".

    For many young people who aspire to be scientists, the great bugbear is mathematics. Without advanced math, how can you do serious work in the sciences? Well, I have a professional secret to share: Many of the most successful scientists in the world today are mathematically no more than semiliterate.

    Wilson takes himself as the canonical model. Razib Khan comments somewhat critically ("Does one need math for a career in science?"). I think that field biology requires working diligently and independently in the field in a way that some kinds of science do not, and personal qualities that set successful fieldworkers apart are pretty much orthogonal to math skill.

  • Turing and the apple

    Fri, 2011-11-11 18:18 -- John Hawks

    Folklorist Alan Garner has a poignant, short remembrance of Alan Turing:

    We had one thing in common: a fascination with Disney's Snow White and the Seven Dwarfs, especially the transformation of the Wicked Queen into the Witch. He used to go over the scene in detail, dwelling on the ambiguity of the apple, red on one side, green on the other, one of which gave death.

  • Monkey numerical distractions

    Fri, 2011-04-15 08:20 -- John Hawks

    This study has been out for a few weeks, and I've been meaning to put up a short comment about it: "Representational format determines numerical competence in monkeys", by Vanessa Schmitt and Julia Fischer [1]. The abstract:

    A range of animal species possess an evolutionarily ancient system for representing number, which provides the foundation for simple arithmetical operations such as addition and numerical comparisons. Surprisingly, non-human primates tested in ecologically, highly valid quantity discrimination tasks using edible items often show a relatively low performance, suggesting that stimulus salience interferes with rational decision making. Here we show that quantity discrimination was indeed significantly enhanced when monkeys were tested with inedible items compared with food items (84 versus 69% correct). More importantly, when monkeys were tested with food, but rewarded with other food items, the accuracy was equally high (86%). The results indicate that the internal representation of the stimuli, not their physical quality, determined performance. Reward replacement apparently facilitated representation of the food items as signifiers for other foods, which in turn supported a higher acuity in decision making.

    This seems so obvious in retrospect. An experimenter has to provide some kind of motivation or there will be no experiment. Providing food rewards in psychology tests on animals will conflate numerical cognition with food, rewards, and motivation. I'm surprised that a simple substitution of inedible items turned out to be so successful in relaxing this cognitive bias.

    As I'm thinking about the "numbers as technology" theme, I keep returning to the idea that most interesting technologies are cobbled together from heterogeneous parts. Cognitive technology is no exception. In this experiment, we see the interference between the food/reward aspects of cognition and the representation of number. To have an effective practice of number as applied to food items, an individual would have to overcome this interference.

    We might tinker with the system in different ways -- for example, we could set up a new system of behavioral rewards or we could change neurotransmitter regulation to decrease food salience. What is the dividing line between technical and natural solutions? Imagine a pill that improves monkey math by inhibiting dopamine receptors. The same inhibition might emerge by mutations to dopamine receptors -- a natural tweak that alters the threshold of technical interventions. A new reward system might seem purely technical -- in the experiment, it worked to substitute different kinds of food treats in different contexts. But then, "different" is itself a function of perception, which can be changed by changing visual and olfactory receptors. "Technical" is a matter of arranging heterogeneous things in such a way that their natural course of action achieves a desired end.


    References

  • Number as cognitive technology

    Tue, 2011-03-08 21:00 -- John Hawks

    Archaeologists often define technology in terms of material products. People make stuff, and that stuff is technology.

    But there's another way to think about the stuff we make: in terms of the information we need to make it. Technology is know-how, it's skill. It's something we learn how to do. Manufacturing may have physical side effects, but it's the cognitive software that lies at the heart of technology.

    This usage is true to the etymology of the word, "technology":

    from Gk. tekhno-, combining form of tekhne "art, skill, craft, method, system," probably from PIE base *tek- "shape, make" (cf. Skt. taksan "carpenter," L. texere "to weave;" see texture).

    I mention this because, if we take this perspective on technology, then some "technology" may never be instantiated in material -- it may reside purely in the mind. That is the contention that Michael Frank and colleagues made in a 2008 paper about speakers of a language that does not have cardinal numbers above two [1]. Frank and colleagues set out to find whether this curious lack of number words causes Pirahã speakers to deal with numbers in experimental contexts differently from speakers of other languages.

    The results showed that Pirahã speakers could complete number matching tasks, using strategies that were also widespread among non-Pirahã speakers in other contexts.

    A total lack of exact quantity language did not prevent the Pirahã from accurately performing a task which relied on the exact numerical equivalence of large sets. This evidence argues against the strong Whorfian claim that language for number creates the concept of exact quantity (and correspondingly, that without language for number, any task requiring an exact match would be impossible). Instead, the case of Pirahã suggests that languages that can express large, exact cardinalities have a more modest effect on the cognition of their speakers: They allow the speakers to remember and compare information about cardinalities accurately across space, time, and changes in modality. Visual and auditory short-term memory are highly limited in their capacity and temporal extent (Baddeley, 1987). However, the use of a discrete, symbolic encoding to represent complex and noisy perceptual stimuli allows speakers to remember or align quantity information with much higher accuracy than they can by using their sensory short-term memory. Thus, numbers may be better thought of as an invention: A cognitive technology for representing, storing, and manipulating the exact cardinalities of sets.

    At the moment, my twins are making great strides in math, at least compared to their skills six months ago. Then, their mastery of number depended on counting objects, which they tracked using fingers and toes. When they got to higher numbers, they would carry out operations by envisioning imaginary fingers and toes in their heads. Now, they have learned several different strategies to break up numbers and regroup or double them, allowing them to easily add and subtract two-digit numbers.

    It's pretty cool to see it unfold, but it's essentially based on learning a technology of number. Numbers can be patterned to accomplish addition and subtraction in many ways, and with some practice and memorization, kids can attain a very rapid pace of solving problems. It's something that most of us have in their schooling somewhere, and there's nothing magical about it -- we just have to learn some algorithms and practice them.

    The Pirahã are different from speakers of other languages with more cardinal numbers, because they do not have that particular shorthand. It's a significant aid to number processing, because words and concepts provide ways to escape the limits on human short-term memory. Frank and colleagues connect this research on number to other aspects of language and cognition:

    Where does this leave the Whorf hypothesis, the claim that speakers of different languages see the world in radically different ways? Our results do not support the strongest Whorfian claim. However, they are consistent with several recent results in the domains of color ([Gilbert et al., 2006], [Uchikawa and Shinoda, 1996] and [Winawer et al., 2007]) and navigation (Hermer-Vazquez, Spelke, & Katsnelson, 1999). In each of these domains, language appears to add a second, preferred route for encoding and processing information. In the case of color, language enables faster performance in search, better discrimination, and better memory when target colors can be distinguished from distractors by a term in the participant’s language. However, verbal interference – which presumably blocks access to linguistic routes for encoding – eliminates this gain in performance, suggesting that the underlying perceptual representations remain unmodified. Likewise in the case of navigation: The use of particular linguistic devices allows (though does not require, see e.g., Li & Gleitman, 2002) efficient compressive navigational strategies. But again, under verbal interference these strategies are not accessible and participants navigate using strategies available to infants and non-human animals.

    I would have written more subtle things about the Whorf hypothesis, and maybe I will some other time.

    I very much like the idea that language itself provides the gears of a cognitive technology -- I think that is a very powerful one that we should apply more broadly in the past. It is misleading to see minimal stone tools, or the organic tools of other primates, as the simplest basis of technology. Technology begins with habits of mind, developed as strategies to better process regularities in the social environment. The powerful thing about language is that it gets in from outside. Children encounter regularities that have already taken hold in experienced minds. As I discussed last week ("Language bootstrapping the brain"), the process of language learning can proceed surprisingly well within brains with very different structural equipment.

    One other observation of interest: Color and number words were "technologies" that were acquired surprisingly well by Alex the grey parrot. Talk about a very different kind of brain!


    References

  • Hangman strategy

    Thu, 2010-08-26 08:30 -- John Hawks

    You may have seen that story about "jazz" being the hardest Hangman word. Personally, I always figure that such a short word is hardly fair, but I'm not that good at Hangman. The inside story of how they figured out the hardest words is kind of interesting -- it involves a guy writing a Mathematica Demonstration to play Hangman and his daughter getting annoyed at never being able to beat the computer and its dictionary.

    (via Chad Orzel)

  • An (old) interview with Warren Ewens

    Sun, 2009-08-23 08:30 -- John Hawks

    I ran across an interview between Anna Plutinski and population geneticist Warren Ewens.

    I cannot say enough about Ewens' book, Mathematical Population Genetics. If you can work through it, you can do population genetics. It doesn't cover every au courant topic, but those will change next week anyway. And it's on Kindle now. Which I suppose probably looks pretty good on the DX, assuming the math displays well -- the book's format is just the right size for it.

    Anyway, this interview from 2004 was probably conducted around the time the book was released. It covers pretty much the gamut of his career. I have to select some part to quote for you, so I'll select the passage that would be most likely to come out of my own math in my genetics class:

    WE: Of course there is a strong possibility that the neutral theory is assumed not because it is appropriate but because the math of that theory is so very simple compared to the math applying for any selective theory.

    AP: Can I follow that up? Do you think that that has lead to models of phylogenetic change that is not very well supported by the evidence?

    WE: I think that that is quite possible. However, here we enter into another question. In mathematical population genetics theory you know from the very start that you are making big simplifying assumptions. You are in a very different position from a physicist, who might believe that his mathematical models describe reality exactly. No sensible population geneticist would make any claim along those lines. He or she is forced to simplify, because reality is so complicated that you don’t know it in any detail, and even if you did know it and used math describing it faithfully, the analysis would be impossible to carry through. So simplification is unavoidable. I do not know whether the use of the neutral theory is too much of a simplification and has lead us to incorrect and distorted views about the true evolutionary tree, it’s shape and dimensions, but I suspect that there has been quite a significant distortion.

    There is much more at the link, some history of association testing, genetic draft, a lot on Ewens sampling theory, and a touch about his work here in Madison.

  • People particles

    Wed, 2009-07-29 13:24 -- John Hawks

    Last week's Science included an article by Adrian Cho examining the way that social modelers use math to describe human behavior on a large scale ("Ourselves and our interactions: the ultimate physics problem?"). I'm sort of irritated at the way physics shows up in this. I mean, sure if -- for the purposes of a model -- we can treat people as interacting particles, then that shares a mathematical basis with (some kinds of) physics modeling.

    Behind it all lies the assumption that, at least within distinct types, people are like subatomic particles: basically the same. "We like to think that we are unique," says Alessandro Vespignani, a physicist at Indiana University, Bloomington, who works on networks. "But probably for 90% of our social interactions, we are not so unique."

    This isn't a very relevant criticism -- some models may assume that every individual is identical, but they need not do so. If there are well-characterized variations in behavior, a model can incorporate them directly. At some level this is what shopping centers do to predict the behavior of teenagers -- do you put the pink cell phones across from Hollister, or the blue ones?

    In any event, does that mean that every kind of mathematical model should be called "physics"? In practice, it seems to be people trained in physics who carry out this kind of work:

    Forays into "sociophysics" began in the early 1970s. Physicists proposed, for example, that individuals interact to form public opinion much as neighboring atoms make a crystal magnetic by aligning their magnetic fields; researchers analyzed the social phenomenon by adapting the Ising model used to describe such magnetic interactions. In the 1990s, many physicists turned to economics in the controversial subfield of econophysics (see sidebar, p. 408). Now, the movement seems to be gathering momentum, as complex-systems researchers have made solid contributions in the study of traffic, epidemiology, and economics. Some are now tackling more-daunting problems, such as the emergence of social norms.

    "The problems are more complicated than most natural scientists assume, but less hopeless than most social scientists think," says Dirk Helbing, a physicist-turned-sociologist at the Swiss Federal Institute of Technology Zürich (ETHZ).

    Sadly many traditional disciplines are safe harbors for the math-impaired. Disciplinary fence-building happens for understandable reasons -- not least, that "interdisciplinary initiatives" often cover administrative efforts to cut faculty or increase courseloads. The route to useful new mathematical models may be easier through cross-disciplinary institutes of various kinds, but even these are often subject to a kind of tunnel vision -- the founders of institutes have pretty specific ideas of what they value.

    Is there a future in particle models of humans, from an anthropology perspective? There's no doubt in my mind -- several of the high-ranking anthropologists and primatologists I know are deeply interested in network effects, hub/spoke models, and phase transitions. My only hesitation is that the models are being driven mainly by consistency. Models can produce outcomes that look like real social systems, and people who don't dig into the mathematical details can find this consistency very convincing. But consistency is not enough; untested models may be simpler, more realistic, or consistent with broader observations. So we need more people familiar with social systems to dig into the details of these models.

    References:

    Cho A. 2009. Ourselves and our interactions: the ultimate physics problem? Science 325:406-408. doi:10.1126/science.325_406

  • Decay processes of language lexicons

    Sat, 2009-02-28 12:00 -- John Hawks

    The Telegraph has a short article on Mark Pagel's research into reconstructing ancient languages:

    Dr Pagel has tracked how words have changed by comparing languages from the Indo-European family, which includes most of the past and present languages of Europe, the Middle East and the Indian sub-continent.

    He has been able to track the evolutionary history of Indo-European back using a computer and said that some of the oldest words were well over 10,000 years old even though the original Indo-European language is thought to date back no more than 9,000 years.

    "I can say with confidence that there are sounds or words that predate Indo-European," he said. "If you look at 'thou', 'I' and 'who', we can now tell they are probably at least 15,000 to 20,000 years old. The sounds used then for these meanings were probably very similar to those used today."

    Pagel is far from alone in reconstructing proto-Indo-European, of course, but he is introducing evolutionary methods to the problem -- called "glottochronology" -- in a unique way.

    The press release from IBM is actually more infomative (the project used an IBM supercomputer for its analysis):

    Looking to the future, the less frequently certain words are used, the more likely they are to be replaced. Other simple rules have been uncovered - numerals evolve the slowest, then nouns, then verbs, then adjectives. Conjunctions and prepositions such as: ‘and’, ‘or’, ‘but’ and ‘on’, ‘over’, ‘against’ evolve the fastest, some as much as 100 times faster than numerals. ‘Throw’ which is expected to evolve quickly, has a half-life of 900 years, there are 42 unrelated sounds for it across all the languages. In 10,000 years time, it will likely have been replaced in 10 of them – possibly including English, unless of course we all do our part to keep the word in circulation.

    “50% of the words we use today would be unrecognisable to our ancestors living 2,500 years ago. If a time-traveller came to us, and told us he wanted to go back to that period, we could arm him with the appropriate phrase book, and hopefully keep him out of trouble” explained Mark Pagel, Professor of Evolutionary Biology at the University of Reading.

    I'll have to wait to see the paper. I will be interested to get an idea of some of the dates they are proposing for language families and their relations.

    There are still questions that would pose problems for this method. If we have to rely on highly-conserved words to do chronologies of language relations deeper than 5000 years, we are limited to a very small subset of words in any given language. How likely are these conserved words to be borrowed -- causing similarities without recent ancestry? Are the probabilities of change across many languages over a short time (the source of the statistic) really comparable to the probability of change in a few ancient languages over a long time?

    UPDATE (2009-02-28): A linguistically-minded reader writes:

    Regarding this recent post in your blog, I was surprised to see you actually recommend the press release by IBM and the University of Reading ("The press release from IBM is actually more infomative ..."). Even an amateur linguist like myself can see that it's crap. There's been considerable discussion on Language Log, starting from the BBC interview, where Pagel was induced to make a right fool of himself, linguistically speaking (which doesn't say anything one way or the other about his computer expertise, of course).

    You can find the Language Log story here, along with comments. I always withhold judgment on a piece of work until I've read it myself, but I certainly sympathize with those who think the story was poorly reported in the press.

    Particularly the one with the headline "Handy phrasebook for Doctor Who".

  • Why biologists should care about math

    Sat, 2009-02-28 11:11 -- John Hawks

    I'd like to point readers to James Crow's article in the open access Journal of Biology. Titled, "Mayr, mathematics and the study of evolution," it's a brief summary of some of the important results from mathematical genetics -- sort of a follow-on to Haldane's "A defense of beanbag genetics".

    Coming fifty years after Haldane's effort, Crow has been able to include a lot more stuff -- in particular the consequences of the mathematical development of neutral theory, and the effects of computers, permutation tests, and molecular clock models in phylogenetics.

    I cannot help but quote this passage, which is direct:

    Ironically, Mayr himself unwittingly provided an especially compelling argument for mathematical analysis. His theory of “genetic revolutions” assumed that from a well integrated population, genetic drift in a small founder offshoot will sometimes produce a population with a new set of genotypes integrated in a new way. Intuitively, a small founder population seemed a particularly unlikely place to find a new favorable gene combination, and this was indeed shown to be the case in a very detailed mathematical analysis by Barton and Charlesworth [5]. If Mayr had had more respect for mathematical population genetics, he never would have made what most theorists regard as the mistake of proposing that small founder populations are a likely source of major evolutionary changes by genetic drift (Crow 2009:13.2).

    Lest you think this is an argument against the role of chance, Crow later describes the more au courant view of speciation:

    Until recently, mathematical theory had contributed little to the study of speciation. Mayr emphasized allopatric speciation and the prevailing model, due to Dobzhansky and Muller [9], prevailed. Recent mathematical studies [10] support it and favor the view that speciation genes correspond to normal genes, selected for their effects within the species. Furthermore, there is evidence that these genes evolve rapidly. Thus, hybrid incompatibility is a by-product of ordinary selection in geographically isolated populations (Crow 2009:13.4).

    This model of speciation recognizes chance and contingency, but not mainly from stochastic fluctuations in allele frequency (drift). Instead we have the stochastic processes of mutation and environmental change and the (possibly complex) epistatic interactions among selected alleles.

    There's more in the essay. Crow does refer to human evolution -- the out of Africa scenario and Neandertal genetics make appearances not entirely to my taste, but he notes that selective sweeps -- dear to my heart -- are an important feature of the recent landscape of mathematical genetics as well.

    Crow could have included a number of other mathematical developments, particularly the Price equation, Hamilton's contributions, and Maynard Smith's "evolutionarily stable strategies", all of which share his theme of the mathematical derivation coming first, and the non-mathematical descriptive formulations only coming later.

    References:

    Crow JF. 2009. Mayr, mathematics and the study of evolution. J Biol 8:13. doi:10.1186/jbiol117

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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.