Sunday, August 31, 2014

Barrington Court (NT)

We were at Barrington Court this last day of August under an autumnal sun, summer already forgotten.

The sun's come back in a semi-serious way

The author, not about to announce a new Apple product

Scary denizens of the Rose Garden pool

She's all pom-pomed out ...

Barrington Court in its fuzzy glory

Friday, August 29, 2014

Recent books

"Under the Skin" by Michel Faber. This is the (excellent) book which was recently art-house filmed with Scarlett Johansson. People say the book is better; I plan to watch the film sometime soon on my tablet, renting - for the first time - from the Google movie store. Moral: think twice before accepting lifts from strange girls with infeasibly large boobs and difficult-to-place accents.

Isserley in action 

"Theological Incorrectness: Why Religious People Believe What They Shouldn't" by Jason Stone.  As recommended by Razib Khan. In the spirit of Scott Atran's "In Gods We Trust" an evo-psych analysis chiefly interesting for its passing analyses of, for example, Buddhism. (Despite what western intellectuals believe, practising Buddhists in the heartlands of that religion deify the Buddha;  ditto with Taoism - which to western despair is full of gods and magic in the east).

"The Rosie Project" by Graeme Simsion. Purporting to tell the tale of the "wife project" undertaken by a partner-free genetics professor, this account of Aspie life is almost convincing. Sadly, success in love is seldom achieved in reality to those as far along the spectrum as our hero. But it's a great story nonetheless.

My next reading treat is that old favourite, "Ringworld" (Larry Niven).

Friday, August 22, 2014

The story on DNA sequencing

One company has transformed the economics of gene-sequencing. Here's the story of Illumina and a taste of where things go next. (h/t Razib Khan's site).

How important is this? Here's a clip from the article.
"... But then Follweiler, a retired financial services professional, found she had another tumor in her bowel. Her doctors opened her up, found it was too big to remove and sent her home. “I was basically throwing in the towel,” she said.

"But one of her physicians sent a tumor sample to Foundation Medicine, a startup backed by Bill Gates and Google Ventures that used Illumina’s sequencers to locate mutations in 236 genes that could help direct drug treatment. As a result of the test she was given Pfizer’s Xalkori, which has made the bowel tumor undetectable and has kept it that way for more than a year. “I feel no different than I felt two and a half years ago,” she says."
23andMe use the Illumina chip; my mother's saliva sample should be arriving at its North Carolina offices later this afternoon.

Family History

We were at the Bristol Records Office and the Bristol Registry Office yesterday hunting down information about my maternal grandfather, William Richard Porter and his mysterious brother George - long disappeared. Here's our data dump so far, mostly based on my mother's recollections (Beryl Seel).

We're still researching, so this may not be the final story.


William Richard Porter (son of George Samuel Porter)


George Samuel Porter ("Grandad Porter")

Born: ???
Died: June 1938 aged 75 ??? (or was it Alfred Hewlett died around that time, Beryl's maternal grandfather?)

Address: Salmon Street, Kingsdown, Bristol (now demolished)

Occupation: Docker

Married twice

1. m. ???  and had two daughters Winny and Maisie (died in childbirth with Maisie)
     - Maisie married Reg, a pianist with a band (controversially dyed his hair!).
     - Winnie married George Batten (sp?) they had two girls.

Maisie and Winnie lived next door to each other in Raglan Road, Bishopston, Bristol

2. m. ??? ("Ma Porter") and had three children
    - George Porter  (b. December 1893? - Barton Regis)
                      -- married a non-white girl; banished for ever: disappeared.

    - Florence Porter ['Flo', 'Florrie'] (b. 1895 or 1896? - Barton Regis)
                      -- fat woman, was married (no details), children??

    - William Richard Porter (b. 1st January 1898 - Barton Regis)


William Richard Porter known as Dick Porter.

Born:  (b. 1st January 1898 - Barton Regis)

Father: George Samuel Porter

Mother: ??? ("Ma Porter")

Wife: Linda Louisa Annie Hewlett.

Death: Oct 30th 1964 in Bristol (aged 66) throat cancer.

Military Medal: awarded in Bristol in 1918.
Private: No. 127338
Invalided out of forces - lost an eye rescuing an officer under enemy fire, hence the medal.

Occupation: Foreman, Wine and Spirits distributor, City Road, St. Pauls, Bristol.

Children: Ray, Beryl, Gordon.

Address: Ray, Beryl were born in a house on Constitution Hill. The family then bought the house at 14 William Street, St Pauls, Bristol.


Barton Regis was, from 1894 to 1904, a rural district in the English administrative county of Gloucestershire, adjacent to the City of Bristol, comprising:

  • Filton
  • Henbury
  • Shirehampton
  • Stoke Gifford
  • Westbury-on-Trym
  • Winterbourne


Bristol Record Office
'B' Bond Warehouse
Smeaton Road


Tuesday, August 19, 2014

Bacon reduced at Waitrose

Watched "Horizon should I eat meat?" on BBC2 last night (why is it not yet on YouTube?). The bottom line (so many puns) is that processed meats - bacon, sausages - are the killers: the nitrosamines they contain and produce are carcinogenic.

We predicted there would be a lot of half-price bacon and sausage on the shelves at Waitrose this morning!


Michael Mosley's self-experiment with extra meat rations was a trifle disingenuous. Presumably he is usually on the 5:2 diet - his physique certainly suggests that. If you then switch to seven day extra-meat-eating for a month, with generous bread rolls, fruit and veg, you are certain to gain 6-7 pounds (3 kg) as he did. Not sure it was the processed meat doing the damage here, doctor!

We got some great shots of a colonoscopy BTW .. I can hardly wait!


Steve Hsu has an accessible paper here on progress in identifying the many genes (alleles) of small effect which underlie quantitative traits such as height and intelligence. I've been reluctantly* convinced by his argument that fixing the many negative (dysfunctional) alleles in every person could remarkably increase intelligence. Read the paper, skip the harder maths and see if you agree.


* Why reluctantly? There are a number of brain attributes which presumably contribute to increased general intelligence: specific modes of brain modularisation, optimised brain architecture, increased brain size, larger number of neurons, efficiency of neurons, efficiency of neural-interconnect, density of neural-interconnect .. and so on.

Only some of these are capable of significant change - brain size, for example, is hard to increase given birthing constraints. Steve Hsu's linear additive model seems to imply that (in Sky Pro Cycling terms) there is the possibility of 'aggregation of marginal gains' which would impact all of the attributes mentioned above and more.

And so I have become a reluctant convert.

Monday, August 18, 2014

A Doctor writes ...

From my GP today:
Dear Mr Seel

Thank you for your letter regarding your family history and suggestion for enhanced screening. I think this probably would be a sensible idea and I am sure the family history would fall within the referral guidelines for the enhanced screening. If you would like to go ahead with this please let me know and I can arrange the referral. The enhanced screening involves an endoscopy which is a fibre-optic camera which can look inside the bowel.

If you would like to discuss this in more detail before me making the referral please arrange to speak to me.
Here are some of the highlights from Wikipedia.
"The pain associated with the procedure is not caused by the insertion of the scope but rather by the inflation of the colon in order to do the inspection. The scope itself is essentially a long, flexible tube about a centimetre in diameter, i.e. as big around as the little finger, which is less than the diameter of an average stool.

"The colon is wrinkled and corrugated, somewhat like an accordion or a clothes-dryer exhaust tube, which gives it the large surface area needed for digestion. In order to inspect this surface thoroughly the physician blows it up like a balloon, using an air compressor, in order to get the creases out. The stomach, intestines and colon have a so-called "second brain" wrapped around them, which autonomously runs the chemical factory of digestion. It uses complex hormone signals and nerve signals to communicate with the brain and the rest of the body. Normally a colon's job is to digest food and regulate the intestinal flora. The harmful bacteria in rancid food, for example, creates gas. The colon has distension sensors that can tell when there is unexpected gas pushing the colon walls out—thus the "second brain" tells the person that he or she is having intestinal difficulties by way of the sensation of nausea. Doctors typically recommend either total anaesthesia or a partial twilight sedative to either preclude or to lessen the patient's awareness of pain or discomfort, or just the unusual sensations of the procedure. Once the colon has been inflated, the doctor inspects it with the scope as it is slowly pulled backwards. If any polyps are found they are then cut out for later biopsy.

"Some doctors prefer to work with totally anesthetized patients inasmuch as the lack of any perceived pain or discomfort allows for a leisurely examination. Twilight sedation is, however, inherently safer than general anesthesia; it also allows the patients to follow simple commands and even to watch the procedure on a closed-circuit monitor. For these reasons it is generally best to request twilight sedation and ask the doctor to take his or her time despite any discomfort which the procedure may entail. Tens of millions of adults annually need to have colonoscopies, and yet many don't because of concerns about the procedure.

"It is worth noting that in many hospitals (for instance St. Mark's Hospital, London, which specialises in intestinal and colorectal medicine) colonoscopies are carried out without any sedation. This allows the patient to shift his or her body position to help the doctor carry out the procedure and significantly reduces recovery time and side-effects. Although there is some discomfort when the colon is distended with air, this is not usually particularly painful and it passes relatively quickly. Patients can then be released from hospital on their own very swiftly without any feelings of nausea."
Something to look forward to before Christmas! Here is what my 23andMe health report has to say about my Colorectal Cancer risk.
Nigel Seel
4.2 out of 100 men of European ethnicity who share Nigel Seel's genotype will develop Colorectal Cancer between the ages of 15 and 79.

5.6 out of 100 men of European ethnicity will develop Colorectal Cancer between the ages of 15 and 79.
And here's the caveat.
The 23andMe Odds Calculator only takes into account effects of markers with known associations that are also on our genotyping chip. Keep in mind that aside from genetics, environment and lifestyle may also contribute to one's risk for Colorectal Cancer.

Saturday, August 16, 2014

Can you be too super-secret?

In Terry Hayes' excellent and scary thriller "I Am Pilgrim", the hero works for a super-secret and totally deniable organisation called 'The Department'. Basically it audits the spies - with few restrictions on what it can do.

In China Miéville's wonderful "The City and the City" there's a super-secret organisation called Breach which has almost unlimited power in its bizarre domain.

Operatives of these super-secret organisations have a problem, it seems to me. Probably no-one has heard of their secret organisation, nor are they permitted to identify themselves with it.

So how then do they gain authority to interview people, task military/police assets and generally grab the logistical resources they need?


Semi-spoiler: I'm still wondering how easy it would be to create from scratch a synthetic version of a deadly virus. Once fabricated, the deployment mechanism in "I Am Pilgrim" seems horribly plausible.

Westhay Moor and Nature Reserve

We visited Westhay Moor Nature Reserve this morning, about 15 minutes from Wells on the Somerset Levels.

Ponies at Westhay Moor
Flies on the face
The author with birds
The author's wife with pony

Friday, August 15, 2014

The high priests are out again

From The Times today.
"A British writer is facing global protests from scientists for suggesting that there are biological differences between races that could explain the success of European nations and make African societies prone to poverty and violence.

"Nicholas Wade had expressed the hope that his book, A Troublesome Inheritance, would “draw some of the tension from this fraught subject by showing that the understanding of genetic differences between human groups does not lead to racism”.

"The book, which speculates on whether differences between societies and nations are based on genetic variations, has caused uproar in academia and allegations that its author is doing the very thing he said he was seeking to avoid and encouraging racism.

"In a letter to The New York Times books section, 143 geneticists from universities in Europe and the US protest that his book “juxtaposes an incomplete and inaccurate account of our research on human genetic differences with speculation that recent natural selection has led to worldwide differences in IQ test results, political institutions and economic development.”

"The scientists rejected “Wade’s implication that our findings substantiate his guesswork”, adding that “there is no support from the field of population genetics for Wade’s conjectures.”

"Besides a chapter speculating on an evolutionary basis for “Jewish intelligence” and passages suggesting that genetic traits had led Africans to fail to “develop the ingrained behaviours of trust, non-violence and thrift that a productive economy requires,” Wade examines whether a genetic variation could predispose young African-Americans towards aggressive behaviour.

"He notes that 5 per cent of African-Americans in a study had the mutation as against 0.1 per cent of Caucasians. African-Americans with the genetic variation were “significantly more likely to have been arrested and imprisoned.”

"He says “a large number of genes are evidently involved in controlling aggression” and that even if African-Americans were more likely to possess one particular mutation, Caucasians may carry other mutations."
I reviewed Nicholas Wade's book here.

In other news, leading scientists confirm that the sun does indeed circle the earth, and that the world was created in 4004 BC.

Why bother with 23andMe?

The genetics company 23andMe is no longer permitted (under a current US FDA ruling) to provide you with health advice based on sequencing your own DNA sample. In practice this is not an issue since you simply go to Promethease and import to them your raw data from 23andMe (as described here). For some reason this is not forbidden.

How useful are these reports? To be honest, I believe they're of bounded interest, and here's why.
"A number of commercial firms offer targeted or extensive genotyping to anyone who wants to submit a saliva specimen and pay a fee. Some of the reasons suggested for doing this include identification of ancestral background, relationship certification and most commonly, detection of genetic susceptibilities to disease.

"The latter are almost entirely based on GWAS that have associated specific single nucleotide polymorphisms (SNP) with an increased (or decreased) likelihood of developing a particular common disease. In almost all such GWAS-based analyses, the association with disease is highly statistically significant but of remarkably little predictive value. In other words, the relative risks of developing a disease based on having one of these markers is typically in the range of 1.1–1.4.

"Moreover, virtually no research has been done to examine the clinical utility of being identified as having one of these risk markers. For example, is someone with the 9p21-linked SNP that has no known biologic function but is associated with a slightly greater risk of developing an atherosclerosis-related condition more likely to alter their lifestyle, change their diet, or stop smoking? "
In addition, there are many other sources of error in the genetic code which can have profound medical implications - but are not SNPs - such as (from the same report):
"Translocation results from an exchange of parts of two chromosomes.

"Deletion is loss of chromosomal material.

"Duplication is the presence of two or more copies of the same region of a given chromosome. The redundancy may occur in the same chromosome or in a nonhomologous chromosome. In the latter case, a translocation will also have occurred."
So most health reports tell you that you have some SNPs which increase, or decrease your susceptibility to this or that condition, but in the current state of the research it's not known how many other SNPs or distinct genetic modifications could also affect the likelihood of acquiring it. Early days indeed!

One of the things 23andMe ask you is whether you permit them to keep your sample for ten years (I guess in liquid nitrogen or something). I imagine that in a decade the cost of a complete genome sequencing will have come down to something affordable and 23andMe will then be able to offer a much more sophisticated analysis/diagnostic service based on your complete genome (FDA willing!).

Assuming we will also by then understand a lot more about how the genome ties in to phenotypic traits such as health, intelligence, personality, appearance, sports potential and so on, the report in 2024 might be quite informative, and the one in 2034 even more so.

One generation down-track from now, everyone will have their genome transcribed for health reasons, and moreover we'll understand it. One of our remote descendants may well be interested in their ancestors, bewailing the fact that they never got genotyped.

But wait!


Steve Hsu has more to say here:
"... given sufficient phenotype|genotype data, genomic prediction of traits such as cognitive ability will be possible. If, for example, 0.6 or 0.7 of total population variance is captured by the predictor, the accuracy will be roughly plus or minus half a standard deviation (e.g., a few cm of height, or 8 IQ points). The required sample size to extract a model of this accuracy is probably on the order of a million individuals. As genotyping costs continue to decline, it seems likely that we will reach this threshold within five years for easily acquired phenotypes like height (self-reported height is reasonably accurate), and perhaps within the next decade for more difficult phenotypes such as cognitive ability. At the time of this writing SNP genotyping costs are below $50 USD per individual, meaning that a single super-wealthy benefactor could independently fund a crash program for less than $100 million.

"Once predictive models are available, they can be used in reproductive applications, ranging from embryo selection (choosing which IVF zygote to implant) to active genetic editing (e.g., using powerful new CRISPR techniques). In the former case, parents choosing between 10 or so zygotes could improve their expected phenotype value by a population standard deviation. For typical parents, choosing the best out of 10 might mean the difference between a child who struggles in school, versus one who is able to complete a good college degree. Zygote genotyping from single cell extraction is already technically well developed, so the last remaining capability required for embryo selection is complex phenotype prediction. The cost of these procedures would be less than tuition at many private kindergartens, and of course the consequences will extend over a lifetime and beyond.

"The corresponding ethical issues are complex and deserve serious attention in what may be a relatively short interval before these capabilities become a reality. Each society will decide for itself where to draw the line on human genetic engineering, but we can expect a diversity of perspectives. Almost certainly, some countries will allow genetic engineering, thereby opening the door for global elites who can afford to travel for access to reproductive technology. As with most technologies, the rich and powerful will be the first beneficiaries. Eventually, though, I believe many countries will not only legalize human genetic engineering, but even make it a (voluntary) part of their national healthcare systems. The alternative would be inequality of a kind never before experienced in human history."

Changing the router (again)

Back in May I went through the hell of retiring my BT Home Hub in favour of a spare one (v.2) which I had lying around. I wrote about the pain here. That replacement router was not a success. What is it with BT Home Hubs? Unstable, dropping the broadband line, refusing to allocate IP addresses ... .

I bought a Netgear N300 wireless ADSL+ Modem Router (DGN2200v4) on Tuesday and installed it yesterday. Good day - it was chucking it down with rain, which reliably knocks over the DSL line. The Netgear wizard was not so smart either, believing for some reason I was connecting to a cable modem. I tried to manually configure the Internet connection but to no avail. After some hours of messing around I re-engaged the wizard (via the "Advanced" pane) and this time everything worked. I remembered that the Sky Box WiFi connector needed to be re-homed; only later did I recall the wireless printer and my Kindle.

I may pay a price for ditching the Home Hub. I no longer provide the BT FON function and will most likely be shut out of using other people's BT WiFi when out and about. There again, BT will probably not notice.

Wednesday, August 13, 2014

David Hume nails Artificial Intelligence

"Reason is, and ought only to be the slave of the passions, and can never pretend to any other office than to serve and obey them."

David Hume, "Treatise on Human Nature", T 2.3.3 p. 415, 1739.
Razib Khan writes:
"In other news, my post on the Islamic State has been widely distributed, including being referenced in Ross Douthat’s column. I would have chosen a better title if I had known how it would blow up, but who knows such things. Most of the reaction has been positive, but a few have come up with this sort of feedback:

"The ease with which the author rationalizes ISIS' genocidal ways has left me pretty much speechless!"

The post was long, so this individual may not have read it in full. Or, they may have some issues with reading comprehension, I’m not the clearest writer sometimes (though often it is by design because sometimes I don’t want to be explicit about secondary or sideline issues). But it’s not an uncommon response over the years when I talk about controversial or difficult things. There are several definitions of rationalize, but the key is that often I write in a somewhat bloodless and detached manner about topics which people are emotional about. The problem here is with people who are emotional and allow their emotions to cloud all ability to reason. To understand something you need to engage in Epoche, detach yourself from your conventional perspective and attempt to fly over the landscape. Those who lack emotional self control can’t comprehend that sort of self control in others, and so impute emotional motives. This is unfortunate, since it helps turn everything into screaming match. On the other hand, I do agree with David Hume that reason serves emotions. But that service of reason is rendered null if the two aspects are muddled."

Putting Empiricism to one side, let's agree that Hume is absolutely right in the quote at the start of this post. People in the grip of emotion (often abhorrence or disgust, but it can go the other way) all too frequently apply their rationality in the service of justifying their feelings. So what is Razib Khan actually asking for? That the emotional drive we should engage when thinking about something analytically is that of enquiry, the urge to find out. Only there will truth lie (and apologies for the superficial gloss on Epoché).

Another application of Hume's law. People worry about the technological singularity, that the ultrasmart machines will take over the world and render humans extinct. But wait - it's those endangered humans who build the smart machines; the AI systems' objectives -  Hume's 'reason' - derives from our own human objectives. While this remains true, they're artefacts, and typically artefacts which can't self-reproduce. If our smart tools render us extinct (why? what passions drive them thus and from whence did they come?) they'll soon be streaks of rust on the landscape. The magic of entropy.

Start to worry only when we design automata which are capable of self-reproduction in a non-technological environment and are motivated to do so. Von Neumann might have had the worst idea in history!

Monday, August 11, 2014

Promethease from 23andMe

Take a look at this image (click on it to make it large enough – it’s from Population Genetics, 2nd Edition by John H. Gillespie, p. 3).

A gene - showing coding nucleotides and SNPs

It’s the reference allele (gene) which codes for the alcohol dehydrogenase enzyme in a particular species of fruit fly. Fruit flies need this enzyme to handle the alcohol in rotting fruit. There are 768 coding bases in this gene (a coding base, or nucleotide, is one of the four constituents of DNA commonly abbreviated to A, G, C and T).

Grouped in threes, the nucleotides code for amino acids: so at position 578 the sequence AAG codes for lysine. Change it to AAC and you get threonine instead. This change of a single base is called a SNP – a ‘Single Nucleotide Polymorphism’ pronounced ‘snip’. Two coding sequences in a population which differ in one or more SNPs are called alleles. Note that the string of amino acids listed in the image, when assembled together, constitute the alcohol dehydrogenase enzyme in variants depending upon which SNPs were present..

SNPs are happening all the time in DNA due to mutations, e.g. copy errors of various kinds. Mostly they so mess up the gene that it can’t function properly, the organism dies without reproducing and thus natural selection ‘purifies’ the genome. In some places, though, a SNP merely alters the function slightly and creates variation between individuals. Most traits such as height, intelligence and personality are under the control of many different alleles ‘of small effect’ so just looking at one SNP won’t tell you too much.

The human genome contains at least 30,000 genes constituted from three billion base pairs on 23 chromosome pairs. One of these pairs is the sex-determining chromosome pair: XX (you’re a girl) or XY (you’re a boy). In each chromosome pair you get one of the chromosomes from your father and the other from your mother. However, each of these chromosomes has itself been randomised from the two corresponding chromosomes in each of your parents through a process called recombination (except for the Y chromosome which has no female variant to pair with in its chromosome and is thus handed on unchanged).

Humans have at least ten million SNPs – the number increases with research. Many studies have looked at people with medical conditions and tried to work out if they have some specific SNPs which non-sufferers lack. When you have a genome analysis – as with 23andMe – they put your sample through a chip (made by a company called Illumina) which knows about a million SNPs reflecting those currently considered important and significant by the research community. You can download your personal raw data from the 23andMe website and here’s mine (text version; Excel spreadsheet version - download, don't try to preview, they're too large). Be warned, the raw data lists around a million SNPs and occupies 20/30 MB. It also takes a while to load. It’s also completely meaningless by itself.

Here’s some background on human genome SNPs. There’s a standard database called SNPedia which centralises what’s known and gives a reference number (such as rs1234 - a tutorial SNP) to each unique SNP. Here is what the 23andMe raw data looks like (just the first few entries!)
# This data file generated by 23andMe at: Tue Apr 23 09:13:29 2013
# Below is a text version of your data.  Fields are TAB-separated
# Each line corresponds to a single SNP.  For each SNP, we provide its identifier
# (an rsid or an internal id), its location on the reference human genome, and the
# genotype call oriented with respect to the plus strand on the human reference sequence.
# We are using reference human assembly build 37 (also known as Annotation Release 104).
# Note that it is possible that data downloaded at different times may be different due to ongoing
# improvements in our ability to call genotypes. More information about these changes can be found at:
# More information on reference human assembly build 37 (aka Annotation Release 104):
# rsid chromosome position genotype
rs4477212 1 82154 AA
rs3094315 1 752566 AA
rs3131972 1 752721 GG
rs12124819 1 776546 AA
rs11240777 1 798959 GG
rs6681049 1 800007 CC
rs4970383 1 838555 AC
rs4475691 1 846808 CT
rs7537756 1 854250 AG
rs13302982 1 861808 GG
rs1110052 1 873558 GT
rs2272756 1 882033 AG
So now we come to Promethease. This is a self-service program which links your raw data to the current scientific literature. For $5 you get a report which tells you what is known about the unique set of SNPs which define you (at least as far as 23andMe presently go - some way short of a full genome analysis which is still too expensive).

Promethease has a reputation as being difficult to use; it is not. Here’s the YouTube video which I watched and then knew exactly what to do. It was no problem at all.

And here’s the report I got back (zipped, 40 MB). It’s basically not too hard to interpret and the help links are good. I found Medical Conditions particularly informative once I looked at the help link to understand the graphics.

A I expected, there are few surprises. I was pleased to be in the 12% where exercise actually loses you weight. And of the SNPs currently known to be associated with Autism, I have only a few. Testicular cancer – not so good.

Do you want to know more?

Saturday, August 09, 2014

Secure backups after TrueCrypt

I had been using TrueCrypt (v. 7.0) for a while to archive my data onto USB drives. One drive (64 GB) with the car keys and another couple in the car itself. If the house burns down ...

A couple of days ago I was checking and found I couldn't open these TrueCrypt volumes. The message came back "Incorrect password or not a TrueCrypt volume". Bad news. TrueCrypt 7.2 (the 'broken version') succeeded in opening the archives - proving it wasn't a password problem or data corruption - but this latest version has had the encryption modules removed, apparently. Time to move on.

An Internet search reveals that there is nothing which really replaces TrueCrypt's 'volume' facility as I don't want to encrypt drives or entire USB devices. I tried some freeware with AES encryption (7-zip) but it's clunky and awkward. In the end I've paid my £26 and bought WinZip v. 18.5. The user interface is well-designed and pretty intuitive, and enormous (10+ GB) AES-encrypted archives can be created.

A downside is that file-names can be read-off when an encrypted zip-archive has been opened, although without the password the files themselves can't be accessed. For my purposes that's enough. I have spent hours and hours today reorganising my 30+ GB DropBox folder and creating multiples backups onto three different USB drives.

One small issue: it's not too clear how many licences I got for my money. I installed WinZip on the two house laptops and it hasn't complained - but some of the documentation suggests you only get the one licence.

Thursday, August 07, 2014

Another failed star drive

I was alerted to this piece of excitement by the XKCD cartoon.

Never heard of it. A quick google turned up a breathless Wikipedia article where the experimenters promised:
"a quantum vacuum plasma thruster-powered spacecraft weighing 90 tonnes would be able to reach Proxima Centauri in ~29.9 years at 4 newtons per kilowatt."
I'd definitely buy one of those!

Alas, famed mathematician John Baez put the boot in. Both theory and experiment are all over the place and they probably observed a heating effect.

Cataracts - bah!

Busy day today. Started with the opticians for an eye test: they were very thorough. It appears that my eyes have degraded yet again - new specs! - and that I have early-onset cataracts. The effect, apparently is to make the lenses of both eyes rather misty rather than clear and transparent. Here are the typical symptoms.

  • you may find it more difficult to see in dim or very bright light
  • the glare from bright lights may be dazzling or uncomfortable to look at
  • colours may look faded or less clear
  • everything may have a yellow or brown tinge
  • you may have double vision
  • you may see a halo (a circle of light) around bright lights, such as car headlights or street lights
  • if you wear glasses, you may find that they become less effective over time

I'm told to expect the operations (both eyes) in 3-5 years (just like my parents). Genes, huh.

After that excitement I joined Clare, very delayed, to hoover the church. I do this in a spirit of solidarity with my idiosyncratically-observant wife and for the exercise. I currently lose the hoover detritus but am open to offers from any spies who wish a DNA bomb to deliberately false-trail scene-of-incident genetic evidence.

Then I hit the gym to put it all behind me!

A recent post bemoaned my indecision as to how to use my spare time .. and Adrian's now-vacated bedroom as a study. I have decided to write some AI programs in JavaScript (calm yourselves - it's become a proper language these days!) which I can use to cheer up this very blog. Don't hold your collective breaths!

Wednesday, August 06, 2014

Displacement activities

Two days since Adrian left us to start his new job. By now a creative fever was meant to have overcome me. I was debating whether to plunge back into particle physics, engage with differential geometry, renew getting my head around population genetics, do some Python programming, learn how to use that genome analysis program that interprets your 23andme results .. or just get on and do some writing.

Instead I find myself camped on Amazon ordering mouse mats - and today an even greater displacement opportunity presented itself: we discovered a mouse had taken up residence in our pantry.

I write in the third hour of our hygiene operation ...

Yep, it's been there ..
My sister commented that Clare looked 'cheesed off' ..

Monday, August 04, 2014

You write the truth: who cares?

"A religion is sometimes a source of happiness and I would not deprive anyone of happiness.But it is a comfort appropriate for the weak - and you are strong. The great trouble with religion - any religion - is that a religionist, having accepted certain propositions by faith, cannot thereafter judge those propositions by evidence. One may bask at the warm fire of faith or choose to live in the bleak uncertainty of reason - but one cannot have both."
Robert A. Heinlein wrote these words in "Friday" (p. 306) published in 1982 - thirty two years ago. Last time I noticed, religion was still doing its magic.

There's a kind of self-importance writers have, that they possess important insights and truths, and that it is sufficient to take these to print and the world will be enlightened. I remember a while ago a smart music-scene reporter doing a feature on the band Oasis. The Gallagher brothers informed him they were going to be bigger than The Beatles. Our reporter answered that this was impossible: that band had been the voice of a vast, global social revolution - the sixties - but there was no such seismic shift right now. Then he shut up - he was wasting his breath. Good luck to those few authors who are truly the voice of a new generation, or the revolution!

As the judge said, "I may not be able to define pornography but I know it when I see it." Just as you know political correctness, or an author with an agenda, when you see it. Heinlein has many attractive virtues as a writer and as a social theorist but boy, does he have an agenda. I can't tell you how jarring it is to read "Friday" or "Methuselah's Children" or, God help us, "Stranger in a Strange Land" and be exposed to Heinlein's theory that men and women in an ideal state desire nothing more than to have no-strings sex with anyone they quite like. (He seldom features male-male sex for some reason).

The argument that his writing predates evolutionary psychology is a non-starter. Noticing how people normally react to marital infidelity would have been enough - or some introspection into his own emotions with regard to his beloved wife Ginny. Correction: it appears that Heinlein had open marriages with both his second and third wives (Ginny was number three). So guilty of sexual solipsism then. 

I'm disappointed in him!


I rather liked Peter Frost's recent article on how empathy (and its inverse, guilt) are particularly individualistic attributes of Europeans - it has been suggested that East Asians (Chinese, Japanese) express their prosociality through the more externalized traits of conformity and shame. Worth reading the article.


Gregory Cochran's recent post (Biology and Human Capital) attracted this comment from a Mr Boyle:
"It seems to me that the world should try to preserve the precious resource of Ashkenazi brains. I don’t follow the politics of the region all that closely but Arabs, Palestinians and the like are plentiful and not very talented. Jews however are rare and valuable. These basic facts to me argue for siding with Israel."
This is a scaringly controversial sentiment to express. It violates all our empathic instincts .. and the poster was immediately rebuked for 'autism'.  We can all think of scenarios where for the good of some section of humanity, other sections have to justifiably die. It's called backing one side in a war and we're all expected to do it under some circumstances - so perhaps it's disingenuous to beat up Mr Boyle for his unbearable frankness. Had he spoken instead of Israel being a first-world democracy in a third world region and thereby worth preserving as a beacon then I guess his remarks would have come across as more mainstream, at least in America.

For the record, Israel is of course worth preserving: I just wish they'd be smarter and more strategic about it.