Tag Archives: blogging

Academic Blogging

Natalia Cecire has a good post on academic blogging over at Arcade. Tne ensuing discussion is excellent.

Here’s what I posted to the discussion:

Excellent post, Natalia, and excellent discussion all.

I come at this subject from a different angle. I was trained as an academic, held an academic post, then failed to get tenure. Since then I’ve done this and that, while maintaining an active intellectual life. The advent of the web was a godsend to me, for it opened up new lines communication. Now I could easily find out about things and stuff and contact any scholar with an email address. I was once again in the mix, though a somewhat different mix, to be sure.

It’s within that context that I see my blogging. I do most of my blogging at my own blog, New Savanna, which is a mixture of various things. I could easily break it into 3 or 4 more tightly focused blogs, but why do that? (Perhaps readers would be less confused.) I post photos, personal essays (not so many of those), and material on a wide variety of topics at varying levels of sophistication and intellectual development.

I’m particularly fond of the work I’ve been doing on cartoons, most of which is analytic and descriptive. I regard that as being as important as anything I’m doing, but I don’t see how I could do that work in a formal academic venue. As far as I know, there’s no place to publish largely analytic descriptive work on cartoons. So I blog it. Most recently, a series of four posts on Porky in Wackland and eight on The Greatest Man in Siam. While some of those posts get just a tad heavy here and there, for the most part they’re pretty straightforward and accessible. Anyone who’s interested in that material can read those posts. And there’s a substantial community of folks interested in animation that isn’t being served by academia.

So, I’m a public intellectual without the reputation that seems to be part of the implicit understanding of the term. Continue reading

Fungus, -i. 2nd Decl. N. Masculine – or is it?: On Gender

ResearchBlogging.orgIn an attempt to write out my thoughts for others instead of continually building them up in saved stickies, folders full of .pdfs, and hastily scribbled lecture notes, as if waiting for the spontaneous incarnation of what looks increasingly like a dissertation, I’m going to give a glimpse today of what I’ve been looking into recently. (Full disclosure: I am not a biologist, and was told specifically by my High School teacher that it would be best if I didn’t do another science class. Also, I liked Latin too much, which explains the title.)

It all started, really, with trying to get my flatmate Jamie into research blogging. His intended career path is mycology, where there are apparently fewer posts available for graduate study than in Old English syntax. As he was setting up the since-neglected Fungi Imperfecti, he pointed this article out to me: A Fungus Walks Into A Singles Bar. The post explains briefly how fungi have a very complicated sexual reproduction system.

Fungi are eukaryotes, the same as all other complex organisms with complicated cell structures. However, they are in their own kingdom, for a variety of reasons. Fungi are not the same as mushrooms, which are only the fruiting bodies of certain fungi. Their reproductive mechanisms is rather unexpectedly complex, in that the normal conventions of sex do not apply. Not all fungi reproduce sexually, and many are isogamous, meaning that their gametes look the same and differ only in certain alleles in certain areas called mating-type regions. Some fungi only have two mating types, which would give the illusion of being like animal genders. However, others, like Schizophyllum commune, have over ten thousand (although these interact in an odd way, such that they’re only productive if the mating regions are highly compatible (Uyenoyama 2005)).

Some fungi are homothallic, meaning that self-mating and reproduction is possible. This means that a spore has within it two dissimilar nuclei, ready to mate – the button mushroom apparently does this (yes, the kind you buy in a supermarket.) Heterothallic fungi, on the other hand, merely needs to find another fungi that isn’t the same mating type – which is pretty easy, if there are hundreds of options. Other types of fungi can’t reproduce together, but can vegetatively blend together to share resources, interestingly enough. Think of mind-melding, like Spock. Alternatively, think of mycelia fusing together to share resources.

In short, the system is ridiculously confusing, and not at all like the simple bipolar genders of, say, humans (if we take the canonical view of human gender, meaning only two.) I’m still trying to find adequate research on the origins of this sort of system. Understandably, it’s difficult. Mycologists agree:

“The molecular genetical studies of the past ten years have revealed a genetic fluidity in fungi that could never have been imagined. Transposons and other mobile elements can switch the mating types of fungi and cause chromosonal rearrangements.Deletions of mitochondrial genes can accumulate as either symptomless plasmids or as disruptive elements leading to cellular senescence…[in summary,] many aspects of the genetic fluidity of fungi remain to be resolved, and probably many more remain to be discovered.” (Deacon, 1997: pg. 157)

At this point you’re probably asking why I’ve posted this here. Well, perhaps understandably, I started drawing comparisons between mycologic mating types and linguistic agreement immediately. First, mating-type isn’t limited to bipolarity – neither is grammatical gender. Nearly 10% of the 257 languages noted for number of genders on WALS have more than five genders. Ngan’gityemerri seems to be winning, with 15 different genders (Reid, 1997). Gender distinctions generally have to do with a semantic core – one which need not be based on sex, either, but can cover categories like animacy. Gender can normally be diagnosed by agreement marking, which, taking out genetic analysis of the parent, could be analogic to fungi offspring. Gender can be a fluid system, susceptible to decay, mostly through attrition, but also to reformation and realignment – the same is true of mating types. (For more, see Corbett, 1991)

As with all biologic to linguistic analogues, the connections are a bit tenuous. I’ve been researching fungal replication partly for the sake of dispelling the old “that’s too complex to have evolved” argument, which is probably the most fun point to argue against creationists with. However, I’ve mostly been doing this because fungi and linguistic gender distinctions are just so damn interesting.

If anyone likes, I’ll keep you updated on mycologic evolution and the linguistic analogues I can tentatively draw. For now, though, I’ve really got to get back to studying for my examination in two days. Which means I’ve got to stop thinking about a future post involving detailing why “Prokaryotic evolution and the tree of life are two different things” (Baptiste et al., 2009)…

References:

  • Corbett, G. Gender. Cambridge University Press, Cambridge: 1991.
  • Deacon, JW. Modern Mycology. Blackwell Science, Oxford: 1997.
  • Reid, Nicholas. and Harvey, Mark David,  Nominal classification in aboriginal Australia / edited by Mark Harvey, Nicholas Reid John Benjamins Pub., Philadelphia, PA :  1997.

Uyenoyama, M. (2004). Evolution under tight linkage to mating type New Phytologist, 165 (1), 63-70 DOI: 10.1111/j.1469-8137.2004.01246.x
Bapteste E, O’Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, & Martin W (2009). Prokaryotic evolution and the tree of life are two different things. Biology direct, 4 PMID: 19788731

Mapping Linguistic Phylogeny to Politics

Note: Most of the content in this post is refuted wonderfully in the comment section by one of the original authors of the paper. I highly recommend reading the comments, if you’re going to read this at all – that’s where the real meat lies. I’m keeping this post up, finally, because it’s good to make mistakes and learn from them. -Richard

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I had posted this already on the Edinburgh Language Society blog. I’ve edited it a bit for this blog. I should also state that this is my inaugural post on Replicated Typo; thanks to Wintz’ invitation, I’ll be posting here every now and again. It’s good to be here. Thanks for reading – and thanks for pointing out errors, problems, corrections, and commenting, if you do. Research blogging is relatively new to me, and I relish this unexpected chance to hone my skills and learn from my mistakes. (Who am I, anyway?) But without further ado:

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In a recent article covered in NatureNews in Societes Evolve in StepsTom Currie of UCL, and others, like Russell Gray of Auckland, use quantitative analysis of the Polynesian language group to plot socioanthropological movement and power hierarchies in Polynesia. This is based off of previous work, available here, which I saw presented at the Language as an Evolutionary Systemconference last July. The article claims that the means of change for political complexity can be determined using linguistic evidence in Polynesia, along with various migration theories and archaeological evidence.

I have my doubts. The talk that was given by Russell Gray suggested that there were still various theories about the migratory patterns of the Polynesians – in particular, where they started from. What his work did was to use massive supercomputers to narrow down all of the possibilities, by using lexicons and charting their similarities. The most probable were then recorded, and their statistical probability indicated what was probably the course of action. This, however, is where the ability for guessing ends. Remember, this is massive quantificational statistics. If one has a 70% probability chance of one language being the root of another, that isn’t to say that that language is the root, much less that the organisation of one determines the organisation of another. But statistics are normally unassailable – I only bring up this disclaimer because there isn’t always clear mapping between language usage and migration.

Continue reading

Regularities in Cultural Evolution

I recently came across a post over at GNXP on the rise and crash of civilizations. It’s a really interesting discussion on a new paper by Currie et al. (2010), Rise and fall of political complexity in island South-East Asia and the Pacific. Here is the abstract:

There is disagreement about whether human political evolution has proceeded through a sequence of incremental increases in complexity, or whether larger, non-sequential increases have occurred. The extent to which societies have  decreased  in  complexity is  also unclear. These  debates have  continued  largely  in the absence  of rigorous, quantitative tests. We evaluated six competing models of political evolution in Austronesian-speaking societies using phylogenetic methods. Here we show that in the best-fitting model political complexity rises and falls in a sequence of small steps. This is closely followed by another model in which increases are sequential but decreases can be either sequential or in bigger drops. The results indicate that large, non-sequential jumps in political complexity have not occurred during the evolutionary history of these societies. This suggests that, despite the numerous contingent pathways of human history, there are regularities in cultural evolution that can be detected using computational phylogenetic methods. [My emphasis].

I don’t have much to add on the subject as I think Razib covered most of the relevant points, plus I haven’t even finished reading the paper yet (I’m hoping to get back into research blogging later this week). I will, however, post one of their figures that shows the dynamic between the rise and fall of political complexity, and how it shows regularity (btw, RJMCMC means Bayesian reversible-jump Markov chain Monte Carlo… if that helps you in any way):

Where does the myth of a gene for things like intelligence come from?

As a linguist I struggle with genetics, I am, however, as an evolution geek, very interested in it. This creates all sorts of problems and high levels of anxiety when talking about FOXP2 and other genes, due to fear that I misunderstand the very highly complex interactions which exist between genes, environmental effects or cascading effects which cannot be summed up in a simple “x gene causes x trait in humans” paradigm.

I would like to point everyone towards a new blog Dorothy Bishop’s written over at guardian science blogs:

Where does the myth of a gene for things like intelligence come from?

Which is about busting the widespread belief (for idiots like me) that individual genes determine traits such as intelligence, optimism, obesity and dyslexia. I find it interesting that this is presented in the blogs section and not as a mainstream article.

She points out on Twitter this morning that the Jedward pic was not her idea. (I add this point because I found it weirdly comforting)

And it’s also lovely to see that at the bottom of the pile of comments is a well articulated reply by Dorothy to individual users.

I love blogging, because there exists  the ability for individuals to reply to claims made about them, primary sources (papers &c.) are cited and checkable and there’s none of the unnecessary dumbing down found in mainstream media. Here’s an article by Ben Goldacre expanding on this subject (which incidentally includes work by Dorothy Bishop).

Here is a parable about how, as a blogger, my claims were checked, discussed and ultimately concluded to be bollocks. (I don’t have a contrastive parable about what would have happened if I’d instead made these claims in the mainstream media but many stories of this nature can be found here.)

If you read the blog post I wrote about links between Autism and SLI you would have seen me make this claim:

the CNTNAP2 gene has been found in independent samples to be associated with both ASD and SLI. This is interesting because it could show that gene mutations which cause improved social abilities could have also caused changes in our linguistic ability on a syntactic or phonological level.

This blog post cited the work of Dorothy Bishop quite heavily and she took the time out to come and tell me problems with it. Here’s what she said:

As you anticipated, I think there are some problems with the implications you draw from the work. There are two issues. The first is that the variants of CNTNAP2 associated with language level are not mutations. You would usually only use that term in the case where most people had the same DNA sequence in a gene, but rare individuals had a different DNA sequence. FOXP2 is a case in point: there is a family, the KE family, who have a mutation affecting around half the family members, where the DNA sequence is changed. For most people in the general population, and for most people with SLI, the FOXP2 sequence is the same.

The CNTNAP gene is very different. The DNA sequence has different versions in different people, and one version, which is pretty common in the general population, is associated with a small decrease in language abilities, but most people with this version would not be recognised as having any language impairment. Most researchers now think that SLI is probably the result of the combined effect of many genes, each of which may nudge language ability up or down a bit. In this regard, language ability is rather like height: there are rare mutations that may make a person drastically tall or short, but most variation in height arises from combined effect of many small influences of genes that show DNA variation in the normal population.

The second issue concerns the evidence for CNTNAP2 being involved in both SLI and autism. Many people in the field do think this means that the same gene that can cause SLI can also cause autism, and that the only difference is that people with autism have additional difficulties going beyond language – what I have termed the ‘autism as SLI plus’ model. I supported that model in the past, but there are some facts that are hard to square with it. First, although many people with autism have structural language problems (affecting grammar and phonology) similar to those in SLI, not all of them do. So people with high-functioning autism or Asperger syndrome may have well-developed skills in syntax and phonology, while still having difficulties with pragmatics. The second point, which is a big problem for a simple genetic account, is that whereas the relatives of people with SLI often have some difficulties with structural language, we don’t usually see that in relatives of people with autism, even if the person with autism has poor language skills. It was this latter point that I was particularly keen to try and explain in my paper. The bottom line is that to explain the pattern of data we need to think in terms of interactions between genes (technically known as epistasis). So there are genetic variants that increase risk of autism, and others that increase risk of SLI. Most of these will have an individually small effect. However, if you have a risk variant for a gene influencing SLI (such as CNTNAP2) in the context of having a genetic risk for autism, the effect on language will be much worse. According to this model CNTNAP2 doesn’t affect both social cognition and language; rather it affects language, but that effect will get multiplied if the person also has risk factors for autism.

Which is SOOOO interesting.

I’d really like to thank her for replying, it’s really lovely to know that high-flying academics are willing to help out when a sincere blogger tries to understand something and falls on their arse.

Some Links #17: The Return of Whorf

The famous Klingon linguist, Whorf, has returned with his theories on linguistic relativity (I know, terrible joke).

The Largest Whorfian Study Ever. The Lousy Linguist looks at the paper Ways to go: Methodological considerations in Whorfian studies on motion events. As you can probably guess, the paper deals with the methodological issues surrounding linguistic relativity. It’s all interesting stuff, bringing to light important questions about how the brain handles language. I’m fairly lay when it comes to this topic, so for more background on the current events, see similar posts over at Language Log: Never Mind the Conclusions, What’s the Evidence? and SLA Blog: Linguistic Relativity, Whorf, Linguistic Relativity.

But Science Doesn’t Work That Way: Miller & Chomsky (1963). Many of you who read this blog will be familiar with the position taken by Melody’s post over at Child’s Play: against a strong nativist position in language acquisition. It’s the first part in a series of posts so I’ll reserve judgement on her conclusions until she’s finished. But much of her post is drawn from a brilliant paper by Scholz and Pullum (2005): Irrational Nativist Exuberance. Key paragraph:

Do we really want to say that phonemes are ‘innate’?

I haven’t yet addressed how we know — with all but certainty — that the model Miller and Chomsky used had to be a poor approximation of human learning capabilities.  It has to do with phonemes.

Experiments have shown that people are remarkably sensitive to the transitional probabilities between phonemes in their native languages, both when speaking and when listening to speech.  If Miller and Chomsky’s assessment of probabilistic learning is correct, then the problem of “parameter estimation” should apply not only to learning the probabilities between words, but also to learning the probabilities between phonemes.  Given that people do learn to predict phonemes, Miller and Chomsky’s logic would force us to conclude that not only must ‘grammar’ be innate, but the particular distribution of phonemes in English (and every other language) must be innate as well.

We only get to this absurdist conclusion because Miller & Chomsky’s argument mistakes philosophical logic for science (which is, of course, exactly what intelligent design does).  So what’s the difference between philosophical logic and science? Here’s the answer, in Einstein’s words, “No amount of experimentation can ever prove me right; a single experiment can prove me wrong.”

PLoS Blogs. Yet another blogging network. This time it’s with the Public Library of Science. The most notable move, for me at least, is Neuroanthropology. That move hasn’t seemed to impact upon their ability to produce good articles, the latest of which being in regards to Uner Tan Syndrome (I’m sure there was a documentary about this on BBC…).

Hap Map 3: more people ~ more genetic variation. Razib has a cool read on the new HapMap dataset. The current paper (Integrating common and rare genetic variation in diverse human populations) looked for variants across the genome in 11 populations, consisting of 1184 samples. It’s been especially useful with less common variants. As with previous versions, you can also explore the data. Here’s the conclusion from the paper:

With improvements in sequencing technology, low-frequency variation is becoming increasingly accessible. This greater resolution will no doubt expand our ability to identify genes and variants associated with disease and other human traits. This study integrates CNPs and lower-frequency SNPs with common SNPs in a more diverse set of human populations than was previously available. The results underscore the need to characterize population-genetic parameters in each population, and for each stratum of allele frequency, as it is not possible to extrapolate from past experience with common alleles. As expected, lower-frequency variation is less shared across populations, even closely related ones, highlighting the importance of sampling widely to achieve a comprehensive understanding of human variation.

Mathematics: From the Birth of Numbers. Someone gave this in to the charity store I work at: it’s a brilliant book by Jan Gullberg on (surprise, surprise) the history of mathematics. The first chapter was on mathematics and language, so I had to pick it up, and not just for that chapter alone, as there are plenty of gaps in my mathematical knowledge I’m sure this will clear up.

Guardian Science Blogs

Some smart moves by the Guardian. They’ve created their own mini science blog network, containing some top names and proven bloggers. There are currently five blogs: Punctuated Equilibrium, Political Science, The Lay Scientist, Life and Physics. The fifth blog, in case you were concerned about my ability to count, is going to rotate between various bloggers, the first of which being the brilliant Mo Costandi of Neurophilosophy. I would normally subscribe to each of these blogs individually, so it’s nice to see them all under one digital roof of science-blogging goodness.

Btw, here’s the RSS feed for all the blogs: http://www.guardian.co.uk/science/scienceblogs/roundup/rss.

Massive Science Blogging Aggregator

If you are quite keen on keeping up with the ever-changing science blog ecosystem, then a must visit website is the newly created ScienceBlogging.org:

Created by Anton Zuiker (MisterSugar), Bora Zivkovic (A Blog Around The Clock) and Dave Munger (Word Munger), the site aggregates all the major science group blogs, blogging networks, aggregators and services. Great stuff. They also have a blog.