Older blog entries for nutella (starting at number 249)

Yvonne C. Martin
My acknowledgment for Ada Lovelace day is Yvonne Martin, recognised as one of the pioneers of Computer Aided Drug Design. Yvonne started with Corwin Hansch's group in the early 1970s and (I believe) is still active (as a consultant). When I worked at the same company I always enjoyed conversations with Yvonne and always learned a great deal - especially how to be more pragmatic and less fluffy. Often she would tell me to stop wasting applying computers where they didn't belong. Long may she continue to publish!
Today I heard about Astrolabe's lawsuit related to the timezone database. That is crazy. Not just because of them trying to "own facts", but because of the people they are going after. When I worked in the same department, my desk used to be in the same room as ado, and, like everyone else in the department, I used to have an account on elsie, so I am sorry to hear that it has been taken down. When I was there ado was a great colleague - very smart, and very good at his job (done usually very quietly, and after normal hours). I had heard about his impending, and well-deserved, retirement, and I hope that this bad situation goes away very soon. I very much doubt that anyone from Astrolabe has actually met ado, or otherwise this wouldn't be happening.
Goodbye Mr. Jobs.
You will be missed.
robogato, thanks very much for the update. I had no idea the spam problem was that bad.

Also, good news on the tag fixes. I really appreciate your hard work. It would be a shame to see Advogato deteriorate or disappear.

Okay, now thanks to bad RSS feeds the Advogato front page is really messed up. The main target seems to have been the "Recent People Joining" list (which, thanks to the mess-up, now pretends to be empty). Of course, that has been the only way you can find out when the new spammers join (unless they actually create a diary entry). So, it looks as if we are screwed...

Advogato problems?
Am I the only one having problems reading the Recent Entries summary in Advogato? Fairly recently I've seen that summary become truncated due to someone crossposting a blog entry with an embedded video. Over the last few days someone's badly text-formatted crossposted entry caused havoc with the fonts for most of the summary below it. Today the summary gives up after one entry. I realise that the members causing the problems are likely unaware as hardly anyone apart from me seems to read Advogato directly these days.
I'm using Ye Olde Firefox 3.6.7 but I see the same behaviour with the work-mandated IE 7.0.

Cruising the library's "New" shelf yielded Jennifer Ouellette's The Calculus Diaries. I grabbed that because I am very much an amateur mathematician and so always hope for that "Aha!" moment from a new teacher, and I also like reading about the history of mathematics. The book is heavy on Diary (is she sponsored by Toyota?) and light on Calculus but some of the anecdotes were fun. For example, even though my job involves mathematical modeling of populations (people or cells or molecules) I had missed the 2009 paper by Munz and colleagues in Infectious Disease Modelling Progress called When Zombies Attack!.

Ms. Ouellette's coverage doesn't leap straight into Kermack & McKendrick's 1927 paper on the SIR model, but instead steps back to simple population modeling with Thomas Malthus (1798, unrestricted exponential growth) and Pierre-Fran├žois Verhulst (1838, logistic model). However, history is more rich than the space in the book will support, so it isn't pointed out that it took until 1920 before Pearl & Reed rediscovered the logistic equation and used it to model US population growth. The material that is really missing is when cool things start to happen, both mathematically and historically, when we moved away from linear algebraic models and over to multi-equation (compartmental) interacting nonlinear systems. Alfred Lotka buried that approach in his 1925 textbook (mainly applying it to chemical reactions) but it came more to the fore when Vito Volterra discovered it (apparently) independently and published it in 1926 when describing fish population dynamics (Dr. Lotka's letter to the journal, pointing out Prof. Volterra's oversight, is politely understated). While Kermack & McKendrick were applying Lotka-Volterra, it was made more rigorous by the work of Georgii Gause (1932) and Andrey Kolmogorov (1936). Then Kermack/McKendrick seems to be forgotten for a while, until it was popularized more recently by e.g. Prof. Roy Anderson. These days, in the medical world, this kind of model is not just limited to epidemiological disease modeling (and prevention strategies) but can also be used to model interactions between pathogens and cells within the body (e.g. the groups of Prof. Alan Perelson at Los Alamos and Prof. Martin Nowak at Harvard).

Also, thanks to Ms. Ouellette, having finished her book I am now reading Seth Grahame-Smith's Pride and Prejudice and Zombies (but not a Choc-ice to be found...)

No Pi for you!
I am using commercial program that is well-known in the field in which I work. It has a scripting language for building models in a flexible manner but most of the code I have written has been quite straightforward. More recently I had to come up with something a little more elaborate and it was only then I realised that the language is hanging firmly to its Fortran underpinnings. The two main clues were; 1) no definition of Pi, and 2) trigonometric functions limited to SIN, COS and ATN. This took me back more than 30 years to when I was programming in BASIC for an ICL 2900 machine. For my current script I needed arccosine and my maths teachers will not be surprised to know that I had forgotten the half-angle equivalence that allows you to calculate ACOS using ATN (thanks Wikipedia). For Pi, since I was already wimping out, I eschewed the usual 355/113, or even something like 833719/265381, and instead used Machin's approximation (as that also uses ATN).

This weekend I decided to watch O Lucky Man! for the first time in ages - it takes a good while to gird oneself up to deal with that one scene (you know which one). It was only while watching it this time that I noticed the strange resemblance between Alan Price and Steve Jobs. For those of you not familiar with Mr. Price, try the image here. Maybe I am imagining things as as putting "Steve Jobs" and "Alan Price" in The Google doesn't result in any "separated at birth?" theories. Maybe it's the Tyneside accent that puts people off...

So, the motherboard replacement, I mentioned in my previous entry, worked out just fine. A modest outlay has given me a completely working box again, and no leftover parts (well, okay, maybe a few screws). The CMOS battery was DoA (but that's not surprising for a five year old board) so the only real gotcha was that the behaviour of the audio ports didn't match the documentation in the manual. Thankfully I didn't have too much to lose, so trying my headphone jack in the "microphone" socket wasn't that risky. Actually, the problem may lie with the autodetection function of the Realtek driver. I'm not that fussed now that I have sound. I didn't realise that you could buy replacement latex mounting grommets for Antec fans, so mine are now held in place with wire ties and Blu-Tack.

"Are you from the past?"
I have been introducing my S.O. to The IT Crowd. When watching one of the shows from an early series she was puzzled when I pointed out the show was dated now because there was a LOLCat poster on the wall - but NOT because they had an Altair, a PET and a ZX81 on display.

Speaking of things becoming dated, I am wondering if Rich Lam's Vancouver couple photo will be the modern equivalent of Alfred Eisenstaedt's Times Square V-J Day picture. We'll see.

[Hah, it looks as if someone has broken the front page of Advogato with a misplaced HTML bold tag. Just like old times.]

With my S.O. abroad it didn't take me too long to revert to my old habits. I now have a disemboweled computer spread all over the bedroom rug. It's not as if she would disapprove if she were here, it's more that we've been busy doing things like measuring for curtains so that farting around with misbehaving hardware has been a low priority. Anyway, she gets to stay over there on a well-earned vacation and enjoy delicious XLB whenever she likes, while I get to fix a misbehaving box. This was one I built about five years ago with the main aim of being something for playing media (DVDs, CDs, photos, files etc.). It has a SmartPower power supply, smart fans and a silent (fanless) but fast video card. Recently it refused to boot and so after gutting it to a bare minimum I found that the motherboard (Asus A8N-E) wouldn't hold its CMOS settings. I fitted a new BIOS battery and reflashed the BIOS but still it forgets everything, even during a warm reboot. I don't see any damage to the motherboard but it seems likely that the NVRAM is dead, and that's beyond my fixit-fu. The board is about five years old, which means several generations have passed at computer evolution speed. It would be a shame to simply ditch it, as everything else works, so I looked around and found somewhere local that specialises in new end of life parts. They didn't have an A8N-E but they did have one of its cousins, an A8N-SLI SE, at a good price. So now I am reassembling the box and at first look it seems to work. Actually, I was surprised that it booted to the OS as the motherboard is not identical. Now I'll have to take care of some of the minor incompatibilities. The main one at the moment is that it doesn't have sound. I'll try and fix that or wimp out and drop in an old X-Fi card I have in the garage. When I popped the case I had forgotten how messy I had made it inside. The hard drives are some old SCSI disks so there's a long ribbon for them as well as the regular ones for the ATAPI DVD drives (I had two lying around). The reason it has survived is that the case is an Antec Sonata II which uses the magic of ducts[TM] to keep the airflow where it needs to go. That's essential as it does look like something that Harry Tuttle would delight in dealing with. I am glad that my life has changed so much that there's a time limit on how long I can scatter parts hither and yon, as the sane half of my life will be back soon and would treat my efforts with the dreaded raised eyebrow and half-smile.

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