Sunday, 28 May 2017

woodpecker spotting

We glimpsed a woodpecker on one of our birdfeeders this morning.  We couldn’t see it very well, as it was behind the feeder (so we have no idea how it was even hanging on), but it had a red head and a black and white body.  I confidently said “Lesser spotted”, then wondered if I was right.

Off to the RSPB website.

The Lesser spotted does have a red head and black and white body, but the RSPB site notes that it is the “least common of the three woodpeckers” in the UK, so it seems an unlikely identification.  Also, the one we saw had a longer beak that this:
Lesser spotted woodpecker

So maybe not.  The site says three woodpeckers.  I know of the Lesser and Great spotted, but what’s the third?  The RSPB site tells me it is the Green woodpecker:
Green woodpecker

Red head: check.  Long beak: check.  Black and white body: nope.  It definitely wasn’t that green.  But scrolling through the pictures on that page reveals the juvenile Green:
juvenile Green woodpecker, in a strangely semitransparent picture

Okay, that’s got more black and white markings, but it’s still seems rather too green.  But, maybe: it was only a short obscured glimpse.

I checked out the Great spotted, just for completeness.
Great spotted woodpecker

No red head, so definitely not.  But scrolling through the pictures on that page yielded:

juvenile Great spotted woodpecker

Red head: check.  Long beak: check.  Black and white body: check.  Okay, so I now, even more confidently, identify what we saw as a juvenile Great spotted woodpecker.

And being a juvenile explains why it was trying the bird feeder: it knew no better.


Saturday, 27 May 2017

by Jove!

You think you know something, then you see it from a whole new perspective, and it changes completely!

Jupiter from the bottom

Saturday, 20 May 2017

book review: Stiletto

Daniel O’Malley.
Stiletto.
Head of Zeus. 2016

Stiletto starts off where The Rook ends: Rook Myfanwy Thomas and the Checquy have declared a truce with Graaf van Suchtlen and the Grafters, and they have started the delicate process of working together. But not only are there centuries of well-stoked fear and suspicion on both sides impeding progress, there is a hidden faction actively out to sabotage the deal.

The bulk of the book alternates the viewpoint between Felicity Clements, a Chequay Pawn with aspirations to be a warrior Barghest, and Odette Leliefeld, a high ranking Grafter. After some typical Checquy-style horrors, Felicity is assigned as Odette’s bodyguard. Neither will be the same again.

I am slightly disappointed that this time round we don’t get Myfanwy’s viewpoint, except in a few scenes. And there is one scene from her point of view that doesn’t ring true for me. Myfanwy is at the Races investigating a gruesome murder, when she bumps into her brother Jonathan, and agrees to go up to his box to meet his friends later. After he leaves, she is attacked. The plot promptly proceeds to forget everything about this promised visit. Poor Jonathan, he must be worried sick!

Apart from this minor plot oversight (or maybe it is something incredibly subtle that will come back to haunt her later?) we get to see Myfanwy as others see her, in all her fearsome sarcastic efficiency. We are still in the wonderfully bizarre, dangerous, gross, complicated, surreal world of the Chequay, as two groups of people struggle to overcome perfectly understandable hatred and fear of each other, whilst surrounded by extraordinary and incomprehensible goings-on.

This is a great second book in the series. I hope it won’t be a four year wait for the third one! (There is going to be a third one, is there?)

Thursday, 18 May 2017

Semantic closure

Our paper “Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry” has just been published in the Journal of the Royal Society Interface.  We submitted in December, it was accepted after revision on 24 April, and appeared online yesterday! The advantages of web-based publishing.

Our “media friendly” summary is:
The ‘meaning’ of DNA lies in the act of translating a DNA sequence into a protein sequence. The mapping of DNA to proteins is identical in nearly all species, but some species have evolved alternative mappings. A new computer model uses an artificial chemistry to investigate evolutionary changes in these mappings, where the translating apparatus is encoded in the DNA and governs its own translation. As well as reproducing the known evolutionary mechanism of changing the meaning of DNA, the model predicts a novel mechanism for changing the mapping in biology that is not detectable by phylogenetic DNA sequence analysis.
Our slightly less friendly paper abstract is:
Abstract: We present a novel stringmol-based artificial chemistry system modelled on the universal constructor architecture (UCA) first explored by von Neumann. In a UCA, machines interact with an abstract description of themselves to replicate by copying the abstract description and constructing the machines that the abstract description encodes. DNA-based replication follows this architecture, with DNA being the abstract description, the polymerase being the copier, and the ribosome being the principal machine in expressing what is encoded on the DNA. This architecture is semantically closed as the machine that defines what the abstract description means is itself encoded on that abstract description.We present a series of experiments with the stringmol UCA that show the evolution of the meaning of genomic material, allowing the concept of semantic closure and transitions between semantically closed states to be elucidated in the light of concrete examples. We present results where, for the first time in an in silico system, simultaneous evolution of the genomic material, copier and constructor of a UCA, giving rise to viable offspring.
This is one of the key findings:

Figure 6. Semantic change without mutation of the genome.
Genome G0 (built in our artificial chemistry StringMol) encodes a bunch of “machines”, including E0.  E0 reads G0 and expresses the machines encoded on it.  The expression processes can make mistakes: one such mistake meant that E0 expressed E1 instead of another E0.  This “mutant” machine E1 then expressed E2 (without error).  And then E2 expressed itself, again without error. So the meaning of that part of the genome where the expressor is encoded has changed from E0 to E2.  All without the genome changing.  Which is cool.

The paper is open access and can be found at doi:10.1098/rsif.2016.1033.


Tuesday, 16 May 2017

frog's head

A frog sunning itself amid our pond weed:


Sunday, 14 May 2017

book review: The Slow Professor

Maggie Berg, Barbara K. Seeber.
The Slow Professor: challenging the culture of speed in the academy.
University of Toronto Press. 2016

There is an external view of academics as ivory tower effete dilettantes who spend all their time swanning around, thinking big thoughts, or just kicking back during the long vacations. There’s no real work involved, is there?

Then there is the reality: ever increasing bureaucracy, more scrabbling for more students, more worrying about “student feedback”, more scrabbling for ever reducing (per capita) research funding, more pressure to publish. I spent nearly two decades in industry, and have spent over a decade in academia: I can say with conviction that academia is much harder work and longer hours.

Bosses will say, but that’s because academia is vocational: you work so hard because you enjoy it. Well, we enjoy some of it, maybe even most of it, which is more than many people can say. But also if we don’t work so hard, we fall behind harder working peers, we don’t get promoted, we don’t get the research funding, we get in a death spiral. It’s a classic tragedy of the commons. And when we claim we are stressed because we have too much work to do, we are sent on time management courses (which we have no time for), rather than having workload reduced.

This thought-provoking little book (a mere 90 pages of text, to be digestible by the hurried academic, yet sufficiently dense with references to be academically rigorous), analyses the problem, and advocates slowing down, and savouring, the academic life. This is by explicit analogy with Slow Food and as a part of the Slow Movement in general. There are chapters on teaching, and research, and, crucial for academic learning, on collegiality. The call is for individual researchers to regain a sense of agency in the face of overpowering bureaucracy.

The authors write from the perspective of social scientists, but the findings and comments are equally applicable to other disciplines. The book documents much evidence of the problems, and suggests some approaches to mitigate these:
[p59] What does “time for the self” mean in the context of scholarship? For me, it means a shift from the dominant view of time as linear and quantifiable to time as a process of becoming. That is, rather than thinking of time as an accumulation of “lines on the CV” …, I am trying to think of time as an unfolding of who I am as a thinking being. Broadly speaking, I am trying to shift the focus from the product (the book, the article, the presentation) to the process of developing my understanding. This is not to say that books and articles and presentations don’t get written (although there may be fewer of them), but my experience of writing them changes in the sense that shifting my focus in this way eases some of the time pressure. I can keep at the back of my mind Readings’s question, which applies to our students as much as it does to us: “How long does it take to become educated?” … We tend to think of time as spent and gone. However, thinking of time as “constitutive, a becoming of what has not been before” … connects us to the scholarship that we do and goes against the corporate model.
How well this will go down with that “overpowering bureaucracy” remains to be seen. The issue with bureaucrats is they focus on those outputs, on those products, (presumably) because those are easy to measure, to count, to quantify. Students are to be assessed against learning outcomes: have they learned X, Y, Z? Yet students should grow and learn and change, through a process of becoming educated to think, and gaining meta-skills that can be adapted in a changing world. Research is to be assessed by publication and impact: how many journal papers and books? Yet researchers should grow and learn and change, through a process of reflection, and thinking, and experimenting. With much of academia, both teaching and research, most of the value lies in this process of becoming, hard to measure, even invisible in some cases. How much work are you really doing when reading a book, or staring at a screen, or just staring into space, thinking? Where’s the output, the result, the evidence of your work?

Learning and discovering and critiquing and thinking, like the rest of life, is a verb, not a noun.

I must read more about this Slow Movement. If I can find the time.



For all my book reviews, see my main website.