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.



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Thursday, 11 May 2017

April foolish grammar

And following up on bad grammar, I just received this email:
From 1st April 2017 average water and sewerage charges in our region will be rising in line with inflation. This means Yorkshire Water bills will remain some of the lowest in the country.
I fail to follow the implication as stated.  Surely that should read:
From 1st April 2017 average water and sewerage charges in our region will be rising in line with inflation. Despite this, Yorkshire Water bills will remain some of the lowest in the country.



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Wednesday, 10 May 2017

from limp platitudes to inconsistent nonsense

Geoffrey Pullum fulminates yet again on the topic of Strunk and White.
50 Years of Stupid Grammar Advice 
“Keep related words together” is further explained in these terms: “The subject of a sentence and the principal verb should not, as a rule, be separated by a phrase or clause that can be transferred to the beginning.” That is a negative passive, containing an adjective, with the subject separated from the principal verb by a phrase (“as a rule”) that could easily have been transferred to the beginning. Another quadruple violation.


[h/t BoingBoing]

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Sunday, 7 May 2017

sequestering carbon, several books at a time LXX

The latest batch:


A couple of these were bought from the self-published/small publisher authors at Eastercon.

Friday, 5 May 2017

spam spam spam spam

I get email:
We are delighted to inform you that the Journal of Molecular and Applied Bioanalysis is a newly launched journal that aims to disseminate quality research and innovative ideas to the scientific community without any barrier.

We have read your article entitled “Programming Unconventional Computers: Dynamics, Development, Self-Reference”. We have found it really impressive. We request you to kindly contribute in the inaugural issue of the journal. We truly believe that your article will be benefit for the journal. You can submit an article in the form of Research, Review, short commentary, Clinical case study, Perspective, opinion, commentary and Book review etc. on or before 31st May 2017.
I am usually pleased when someone has read a paper of mine, especially if they find it “really impressive”.  However, I’m not so pleased if they think it is in any way even remotely connected with the topic of the stated journal.

Maybe, just maybe, they didn’t actually read it after all?

Maybe, just maybe, this is a newly launched spam journal?





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Thursday, 4 May 2017

David Runciman's review of Rosa Price's biography of Theresa May

 Fascinating book review – or rather, primer on the UK’s PM.
Do your homework 
William Hague promoted her to shadow secretary of state for education, a high-profile position for a newcomer but also traditionally a department that the Tories felt suited a female touch. The fact that Thatcher had been there before her didn’t mean the Tory high command was thinking of May as a future leader. It meant it was thinking of her as another woman. 
What is clear is that Osborne had little idea how much she loathed him. He had thought that their previous disputes were just part of the cut and thrust of high politics and easily put behind them. That’s precisely what she loathed about him. 
The public tends to see Johnson as the ultimate clown politician, all stunts and no substance. That’s not the way May sees it. For her it was Cameron, Osborne and Gove who were fundamentally unserious, because they were the ones who made promises they couldn’t keep. Johnson had the advantage of never having his promises believed in the first place. 
As so often in politics, the roles seem to have been handed out the wrong way round. May would have been a far better person than Cameron or Osborne to lead the Remain campaign, and had she done so Britain would almost certainly still be in the EU. But either Cameron or Osborne might do a far better job at negotiating Britain’s departure. What is the Brexit negotiation if not a game? If May is determined to treat it as something else, it could end badly for everyone involved.





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Wednesday, 3 May 2017

Gödel's co-authors

Copy-editor changed “Hofstadter, in his seminal book Gödel, Escher, Bach” to “Hofstadter, in his seminal book Gödel et al

Sigh.  




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Monday, 1 May 2017

Cavalier amateurism

The Brexit dinner: delusion at every course 
stepping back from the detail, perhaps the most shocking aspect of this sorry affair is the cavalier attitude shown by May and Davis: a caricature of Brexiteer amateurism.



[via Danny Yee's blog]

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