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Sticky: Becoming mobile-friendly

There's currently a lot of excitement among web designers about Google's announcement that they will penalise sites that don't work well on mobile devices. I've decided I need to comply with this although with less than total enthusiasm. Nearly all my pages now meet Google's new criteria (the only exception is my cycling pictures.)

The disadvantage of the change is that if you read my pages on a desktop or laptop the lines will be long (unless you adjust the width of your browser, of course). Perhaps I should have alternatives for people who are using those devices, though that would mean more complication and difficulty in maintaining both alternatives. And the variety of ways that web pages can be viewed has increased enormously, so it isn't possible to cater for all of them. Probably it's no longer a good idea to specify the width of one's lines as I did previously.

I'd be grateful for feedback on this.

Sticky: Changes to the blog

There has recently been a major update of the software I use for this blog (Serendipity). In the process of upgrading I had problems with the (pretty old) frontend theme I was using previously, hence this new one. It's plain and functional, which I like.

More important, it will now, I hope, be easier to search and navigate the blog. I'm particularly pleased to have the list of tags in the right-hand margin. I tend to come back to certain topics over the months and years but up to now I didn't have any easy way of linking posts on the same theme together. Now I have. I've already made a start on setting this up and I intend to increase the links in the future.

Book review: Cloning a Mammoth, by Beth Shapiro

Before reading this book I had not taken much interest in the possibility of reviving extinct splecies ("de-extinction"), supposing that it was largely confined to the realms of fiction like Jurassic Park, but this excellently written book has convinced me that I was wrong. Beth Shapiro explains, with admirable clarity and humour, why de-extinction matters and where the boundary lies between science and fiction. She is well placed to do this, heing professionally involved in the extraction of DNA from ancient bones for use in genetic engineering. [More]

Mark Horton gets it wrong in "Coast"

If you were watching "Coast" on BBC2 today you will have heard one of the presenters, Mark Horton, telling us that the Emperor Constantine made Christianity the official religion of the Roman Empire in 314. No, Mark, he didn't.

Constantine favoured Christianity and made it legitimate (together with all the other religions in the Empire). He played an important role in shaping how Christianity developed at this time. But it was not until the reign of Theodosius I (379-395) that Christianity became the official religion of Rome.

Book review: Hidden Gospels, by Philip Jenkins

In addition to the "canonical" texts of the New Testament there are numerous "apocryphal" writings that contain otherwise unknown sayings of Jesus or descriptions of his activities while alive. Some of these texts have been known for a long time, while others have come to light fairly recently. A notable example was the unearthing of the Nag Hammadi library in Egypt in 1945. Among the 52 mostly Gnostic texts found there was the gospel of Thomas, which is not a narrative of Jesus's life but contains sayings attributed to him.

Many scholars believe that the Gnostic texts, especially the gospel of Thomas, provide an alternative view of the early years of Christianity that is a valuable corrective to the mainstream teaching. Early Christianity, it is suggested, was much more diverse than what emerged later. It is often said that it was the influence of the Emperor Constantine that led to an "official" formulation of Christian belief and to the proscription of alternative views as heretical. Much of value is thought to have been lost at this time. [More]

Book review: Human, by Michael S. Gazzaniga

People who write about the brain in an evolutionary context tend to fall into one of two groups. Some seek for continuity between humans and other animals, while others concentrate on the differences between them. Gazzaniga belongs to the second group; he finds there is a qualitative as well as a quantitative difference separating us from other species.

The book covers a lot of territory, starting with brain anatomy and ending with the prospects for technology to modify the human brain by means of implants or genetic manipulation. On the way there is a lot about the neurological basis of social interactions, religion, and morality. [More]

FreeBSD as desktop

I've been using OpenBSD as a desktop for the last 7 months and have been pretty satisfied, although I still have ArchLinux as well. (Please see OpenBSD as desktop for details.) Most people who try a BSD for this purpose choose FreeBSD. I did install FreeBSD myself about 18 months ago but I encountered various difficulties and gave up after a week. But now I've had another go and this time my experience was much better. Perhaps this is because there is now a new version of FreeBSD (10.1) or because I'm more familiar with BSDs in general after using OpenBSD for a time.

Whatever the reason, I'm enjoying using FreeBSD in this way. I hope what I write here may be useful for any Linux users who are thinking of exploring the BSD world. I include some comments on the differences among FreeBSD, OpenBSD, and Arch.

To start with, I'll say what I want in a desktop, which may be different from what a lot of other people want. This will help to explain why I find the BSD idea attractive. In a word, it's KISS (Keep It Simple, Stupid), which is also the motto of ArchLinux.

What I want in a desktop
Perhaps I should have said "What I don't want in a desktop". I don't want Gnome, KDE. or any other desktop environment. I don't want complicated window managers either, with lots of widgets or decorations. My window manager is spectrwm; if I wasn't using that it would probably be dwm or ratpoison. If you are looking for more fancy stuff you probably won't use any BSD, although I'm sure that both FreeBSD and OpenBSD can provide it on request.

My hardware
Currently I'm using mostly Thinkpad T60s with 2GB ram. These are 32-bit machines, which means that they won't run PC-BSD, but FreeBSD and OpenBSD are fine. (Even if PC-BSD did run on 32-bit machines I wouldn't use it, because it installs a desktop manager by default and that isn't what I want.)

Installation of the base system is easy, although not quite as easy as for OpenBSD. Unlike with OpenBSD you are not offered the option of installing X, but this is easily done later via the packaging system (see below). Throughout, I relied on the excellent FreeBSD manual, available on line or you can download it to your system. This documentation is well-known for its high quality and I found it to be even better now than when I last encountered it.

Now you can install X and anything else you want, using the new and improved packaging system (pgk). This is much easier than installing everything via ports, which is what I did previously, although ports are, of course, available if you want them. Sound worked out of the box for me.

So far, so good, but I encountered a few difficulties setting things up as I wanted them. You will note that most of them concern third-party applications and not FreeBSD itself.

1. Blank black screen on exiting X
Af first when this happened I thought I needed to do a hard reset using the power button to get out. Then I found I could reboot by typing the command in the (invisible) terminal, although I couldn't see anything on screen. The real solution to this problem is to put this line in /boot/loader.config:


2. Entering "Sleep" when lid is closed
This worked out of the box for me wth OpenBSD but it seems to be a problem in FreeBSD, to judge by the discussion on the Net. I found that it was enabled for me with this command:

sysctl hw.acpi.lid_switch_state=S3

To make it happen on boot I inserted the line in /etc/rc.conf.local. I think some machines may need something other than S3, and the command may not work for all machines.

3. Fetchmail
I use fetchmail to collect mail from my ISP. In FreeBSD I got error warnings about certificates being incorrect, although the mail still arrived. The solution is given in the fetchmail man page: use these switches to eliminate the error messages:

fetchmail --sslproto 'SSL3' --sslcertck

4. Printing
My printer is a networked Brother HL5250DN. In OpenBSD printing worked fine with CUPS. In FreeBSD I set up CUPS without problems and a test page was printed, but I couldn't get lpr, lp, or lpq to work. This seemed to be because of a conflict with the native BSD printing commands, but stopping the BSD daemon didn't help. After a day's fruitless experimenting I followed the example of another FreeBSD user I found on the Net: I gave up on CUPS, used the BSD daemon following the setup instructions in the FreeBSD manual, and installed apsfilter. I then got good printing, using the generic Postscript driver. I'm happy with this because I don't like CUPS anyway.

Here is my /etc/printcap.

# APS1_BEGIN:printer1
# - don't delete start label for apsfilter printer1
# - no other printer defines between BEGIN and END LABEL
# APS1_END - don't delete this

5. Lyx on FreeBSD
I use Lyx a lot, for witing books and papers and for making slides with Beamer. When I loaded a Beamer file to edit it, Lyx complained that beamer.cls and a number of other files weren't on the system. I therefore installed the packaged texlive-texmf, which is supposed to provide the necessary files. But even after reconfiguring Lyx it still complained that the files were not there. After more on-line research I found I needed the tex-formats package as well. (It provides pdflatex.) FreeBSD has been criticised on DistroWatch for failing to install all needed dependencies for third-party packages.

FreeBSD works well as a desktop. So does OpenBSD, but I think FreeBSD may be marginally better for this purpose, because it is slightly more convenient to manage day to day (but note the criticism in the preceding paragraph). FreeBSD packages seem to be mostly a little more up to date than those in OpenBSD, though there are exceptions. As for keeping the base system up to date, I particularly like FreeBSD for its tool freebsd-update, which manages both security fixes and upgrades to minor and major versions. In OpenBSD I've used the -current branch, which works well but takes rather long to use and can occasionally break things, although that hasn't happened to me. None of these differences is decisive and both OSs are good choices for a BSD desktop. I'm still running both, on different machines.

Book review: The Enlightenment, by Anthony Pagden

The term "Enlightenment" refers to a period in European history from roughly the middle of the seventeenth century to the end of the eighteenth, during which radical changes in thought occurred that had a profound influence on politics, philosophy, science, and religion. But there are major disagreements among historians, not only about the dating of this event, but also about its significance. Was it a time of liberation, when ways of thinking that had blocked progress for centuries were cast aside, or did it bring about an over-reliance on the intellect and on reason and lead to a loss of moral certainty caused by the erosion of religious faith? Pagden's subtitle makes clear that he is favours the positive view. So do I, but I have to say that I was disappointed by this book. [More]

Speak as you spell?

This morning a BBC political correspondent, Norman Smith, pronounced "hyperbole" to rhyme with "sole" instead of "holy". I haven't heard this one before. One which I do often hear is "trope", which seems always to be pronounced to rhyme with "hope" instead of "dopey". (In any case, however you pronounce it, "trope" seems to me to be a pretentious usage that is probably better avoided in most cases.)

Book review; Neanderthal Man, by Svante Pääbo

Pääbo is famous for having shown that modern humans outside Africa interbred with the Neanderthals. Here he tells the story of how this discovery came about. Although the book is primarily an account of this work, it is also partly autobiographical and includes some excursions into the author's personal and emotional life. [More]

Writing Greek in Linux and BSD

Writing Greek text is quite difficult in Linux and BSD, especially if you want all the accents, breathings etc. used in Classical Greek. But I've found an easy way to do thjs via your browser (Firefox in my case). Simply point the browser at Type Greek. You can type your Greek text here and then cut-and-paste into LyX or Libreoffice.

For writing Greek using vim, please see Writing Polutoniko Greek With Vim and Latex

Book review: Do No Harm, by Henry Marsh

Henry Marsh is a neurosurgeon who has headed his department at a London hospital for many years and has worked in the Ukraine to help set up neurosurgery there. In this book he provides an extraordinarily vivid account of his work and its emotional impact both on himself and on his patients and their relatives. The book consists of a large number of short chapters, each of which tells a story usually linked to a particular kind of brain abnormality. Some chapters are autobiographical and tell us about events in Marsh's own life and how he came to study medicine and become a neurosurgeon.

Patients, Marsh says, invest their doctors with superhuman qualities as a way of overcoming their fears when undergoing surgery.

The reality, of course, is entirely different. Doctors are human like the rest of us. Much of what happens in hospitals is a matter of luck, both good and bad; success and failure are often out of the doctor's control. Knowing when not to operate is just as important as knowing how to operate, and is a more difficult skill to acquire.


Book review: The Big Fat Surprise, by Nina Teicholz

This book covers quite a lot of the same ground as Gary Taubes's The Diet Delusion, although with different emphases. Another similarity is that Teicholz, like Taubes, is a science journalist. This may give professional researchers who disagree with her an excuse to dismiss her conclusions, but she has undoubtedly done her reading of the original material with great thoroughness and she has interviewed a number of the best-known people in the field. More