Thursday, December 3, 2015

Cycle 5 - getting the hang of chemotherapy

Chapter 13 - Starting to get the hang of chemotherapy [Friday 4 December]
At the start of each cycle, my infusions of "E" and "C" are accompanied by loads of steroids, which produce various side-effects including Hmmm, maybe this isn't a nice topic to open a blog post with... Let's skip over the details and just say that after five rounds of experimentation, I've figured out how to take preemptive Senna and Movicol to manage this one.

In cycle 5, my chemotherapy doses have been reduced for the second time. Apparently this is normal: they start off with doses that they think are likely to be too big for the patient, then watch for side-effects and reduce the doses by roughly 20% at a time. My dose of capecitabine (the toxin I take daily in pill form) was 1300 mg twice daily in cycle 1 and is now 800 mg twice daily.

Whereas in cycle 4 I felt washed out for almost the whole cycle, in cycle 5, I perked up from last Saturday (day 10) to today (day 16), which is great. Ramesh and I spent a day at Torrin's primary school (day 9) helping out with "Maths day". You can see Torrin enjoyed having his parents in school! I went down to London last Wednesday (day 7) for a meeting at Google Deep Mind about using machine learning to enhance climate science and to see Book of Mormon; and then again this Wednesday to give a talk about Why Making Good Energy Policy is Difficult in the House of Lords.

Here is a graph of my haemoglobin and white blood cell measurements. The green and blue lines delimit the "normal range" for each indicator. The brown line at the bottom indicates infusion days that begin each 3-week cycle. The yellow line shows whether I was taking capecitabine.

The interesting features are: (1) the low haemoglobin [June] that kicked off the investigations that led to my cancer being diagnosed; (2) bouts of neutropenia (low white blood counts) at the end of most of the chemo cycles; (3) monocytes are baby neutrophils, so high monocyte counts are a good sign of (temporary) recovery.

What else is going on?

The Huntingdon Road safety campaign #EddingtonSafety has not produced any positive results yet, but we haven't given up hope.

The children have been ill a lot recently; Eriska has followed up a lengthy snotty cold by contracting hand, foot and mouth disease. The doctors tell me to avoid contact if possible, which is sad, because it's nice to cuddle her.

Last night we had an evening out at a new Thai restaurant, Thaikhun, in Cambridge. Yum. Tonight we are planning a night out - thanks very much to Nanny for the babysitting! - to see Bridge of Spies at the cinema.

Monday, November 9, 2015

Time off for bad behaviour

Chapter 12 - a welcome break between cycles 4 and 5

Today I went to the clinic for my pre-infusion check-up and to my delight my symptoms [exhaustion] have been bad enough that, again, I get to have a one-week delay and indeed more than one week off from chemo drugs. Hurray!

Other cancer news... I had a second CT scan during cycle 3, and heard the results today. The purpose of the CT scan was to try to measure the progress of the cancer. Some people have cancers markers that can be measured weekly (e.g. the concentration of something in the blood), but I was told in the first couple of months that I don't have any markers, and the cancer didn't really show up at all on the first CT scan, so there was little expectation that the second CT scan would give much information. However, three things did show up:
a) the elasticity of the stomach has changed; in scan 1, the stomach didn't distend when I drank the obligatory 4 glasses of water; in scan 2 it distended much more. This is deemed a promising sign of the chemotherapy working as intended.
b) the lymph nodes that showed up enlarged in scan 1 are a bit smaller in scan 2.
c) there is a new secondary in a vertebra in my spine.
So, a 2-1 score, overall.

Other non-cancer news... We were privileged to have two memorable movie-nights-out: Last night we went to London for the UK premiere of HUMAN, the awesome new film by Yann Arthur-Bertrand [a big thank-you to Nanny for baby-sitting all day!]; and a couple of weeks ago a local Cambridge start-up [FeatureSpace] invited us to the Cambridge premiere of Spectre. Fun!

Yann Arthur-Bertrand presents HUMAN Ramesh and David dressed up as Bond girl and Bond

Sunday, November 1, 2015

The fourth cycle of chemotherapy

Chapter 11 – Mid-way through cycle 4

Cycle 3 finished without any problems, except for ongoing pain in the infusion vein in
my left arm. Sometimes the thought that I voluntarily connect my vein for several hours to a plastic tube passing litres and litres of chemicals strikes me as terribly odd and queasy-making.

Cycle 4, right arm.

Today is day 11.
This time I haven't had much in the way of runny noses and coughing, but feeling-weak-and-washed-out has lasted much longer than the canonical "first 4 or 5 days" that I was hoping for. I feel breathless and exhausted when I walk up two flights of stairs. It's a lot like when I had anaemia (a few months ago) but going by the blood test I had 14 days ago, I think it is unlikely that I'm anaemic. Presumably the whole body is just being successfully beaten up by the chemo. My leg muscles ache as if I have got sports injuries in all of them.

I've been keeping myself busy (1) giving one lecture for a new MPhil course in the department;
and (2) working with other local parents on The Campaign for Safer Cycling
and Walking to and from the North West Cambridge Development
I have made five youtube videos and learned how to put them into a playlist.

I've been using Facebook and Twitter, and our Petition has gathered over 300 signatures, including roughly 100 from University members.

I've been a bit manic about this campaign, and haven't rested enough. Today I stayed in bed all day.

So:  last cycle I kept my mind off cancer by working on the climate-cooperation Comment in Nature, which seems to have fallen on deaf ears; this cycle, I kept myself busy by campaigning for Cambridge University to actually build decent walking and cycling links, like it said it would do in its grand fluffy sustainable plans for the development. I've probably overdone it a bit. I don't have much oomph in my tanks. But I am optimistic that Cambridge University will hear our message and do the right thing.  If they don't then I genuinely fear that one of the children at the new University of Cambridge Primary School is going to be killed on Huntingdon Road.

As day 11 gives way to day 12, I find I have a steadily growing sore spot on my lips.
Tomorrow I will go to see my GP and ask him if all this aching body stuff is
normal, and is there any way to stop my lips from falling apart?

Then on day 13 I will put on my gown and will go to the Senate House to make
a "remark" at a "discussion".

Monday, October 12, 2015

The third cycle of chemotherapy

Chapter 10 – Mid-way through Cycle 3
As I said in my last post, my doctors suspended my chemo pills for a little over a week, and delayed the cycle-3 infusion by one week. Wow, it was lovely! Within 24 hours of stopping the pills I could feel my body's self-healing working again. The mouth ulcers healed up. My runny nose stopped being runny. I would be in great shape if it weren't for the chemo!

In the one-week gap, the hospital arranged for me to have an extra gastroscopy for the benefit of a research project I'm enrolled in. The project (called OCCAMS) is about attempting to measure the progress of a cancer by measuring tiny DNA signals in the blood. (Whereas some of my friends with cancer have cancer-markers that can be measured on a weekly basis, to reveal how things are going, in my case we are flying blind - there is no measure of cancer-up or cancer-down.) To help them use my blood in the study, they wanted to genome-sequence a sample of my cancer cells. So I popped in to a special research ward for an extra gastroscopy, which went smoothly. I'm looking forward to learning which mutation started the cancer - one fascinating thing I learnt about cancer is that a single gene, called TP53, is mutated in more than 50% of human cancers! Conceivably, knowing about the genome of my cancer might help me look into novel targeted therapies that might work better than the blunderbuss that is conventional chemotherapy.

Cycle 3 has been going a bit better than cycle 2. I have developed a runny nose and a cough again, but not quite so runny and cough as last time. My left-arm vein, which they infused me in for cycles 1 and 3, is sore and tender. I feel quite tired a lot of the time, but I have been getting some good work done. The pinnacle of the last year, from the work point of view, came last Friday when I went down to London for a press briefing for a Nature Comment piece that I wrote with Stoft, Cramton, and Ockenfels. As I said on my other blog, I view this article as the most important thing I have ever written. When I wrote Sustainable Energy - without the hot air, I wanted to improve and transform the public discussion of energy options, and I was delighted with the outcome; but that was just a book about energy arithmetic, and lots of other people have explained energy arithmetic before me and since me. Our Nature Comment, in contrast, makes a point that very few people are making, and if people listened carefully to our argument, I think it could be a game-changer for international negotiations.

I was really happy with how the press briefing went, and the Comment was published today. I'm grateful to the staff at Nature for recognising that we had an important message and helping us express it clearly in one and a half pages.

Anyway, halfway through cycle 3... What's coming up this week is a pneumonia vaccination, a check-up with my GP, a flu vaccination, and a CT-scan at the hospital to measure the unmeasurable (i.e., my cancer, which as far as we know doesn't show up on CT scans).

Apart from these four exciting outings, I'll mainly hunker down and work at home.

I'm eating well, and have a good appetite for snacks during the day as well as mealtimes. I've got my old juicer working and have been making lovely apple and carrot and ginger juice daily. I still feel tired and grey much of the time, and I do find myself wondering whether I'd be better off stopping chemotherapy.

At some point I think I will put some effort into researching the latest news about targeted cancer therapies. I've heard about quite a few - monoclonal antibodies, aspirin, warfarin... - but right now I can't be bothered to do the reading.

Instead I'm working on another work project - a completely different project, all about statistics, international standards, and how poor statistical protocols incentivise falsification of data.

Monday, September 21, 2015

Neutropaenia and other side-effects

Your normal neutrophil count is between 2,000 and 7,500 per cubic millimetre of blood. When you don't have enough neutrophils you are said to be neutropaenic.
A Red Admiral in our garden on a very sunny Sunday. Notice her black and white stripey antenna!

Chapter 9b - the medicine cupboard is not big enough
In the first few days of chemotherapy, we designated a bedside cupboard for the nasty medicines, and fitted a padlock to it. Eriska is fascinated and loves to rattle and pull the lock. 
As my side-effects multiply, the proliferation of prescribed medicines is remarkable. 
During cycle two (of which I have reached day 19 of 21) I had a perpetual runny nose, and I felt washed out more of the time. As in cycle 1, I was prescribed antibiotics for a week. At about 7 days, I developed a couple of sore patches on and inside my lip. One of them was simply caused by my accidentally biting myself while enjoying a delicious meal provided by a kind neighbour. They were the sort of sore patches that I'd normally expect to heal up and go away, but they stayed and grew and became steadily more painful. So, last week, I went to my GP, who prescribed mouthwash 2 and goop 1, and who encouraged me to phone the hospital; the hospital said "come on in", so, after a lovely bike ride, I spent most of the next day waiting to be seen, and then was given mouthwash number 3 and a new antiviral medicine and was advised to use goop number 2. The antiviral thing is five tablets per day, on top of the 8 tablets per day of capecitabine (cytotoxin), 4 tablets per day of omeprazole (to reduce stomach acidity), and 2 iron pills per day (to reverse my anaemia).   
The viral infections have been making me feel quite glum - aching teeth, sore ulcers both keeping me awake at night; ulcers sometimes very painful while eating; general grottiness.  
Today I went in to the hospital for my end-of-cycle check-up and told them how I was feeling. The doctor prescribed mouthwash number 4 (to replace mouthwash 3) and mouth-spray number 1, and put me on a new course of antibiotics (2 pills per day). He also recommended using over-the-counter goop number 3. And told me to stop taking the chemotherapy pills for a few days, to give me a chance to recover.  (Hurray!) 
It turns out my neutrophil count has dropped in the last 12 days to 0.48 billion per litre. (Normal range is 2-7.5 billion per litre.) So I'm especially vulnerable to infection, and my next chemo cycle is being postponed a week, because of both the neutropenia and the slow-to-heal mouth ulcers.  I've been told if I have any signs of having a temperature, I should not even wait to phone the emergency number, I should just go straight to the hospital as quick as possible.  

To cheer myself up, I aim to read a Lord Peter Wimsey novel. 

Sunday, September 13, 2015

What do you tell the children?

This is my second post about life with stomach cancer and palliative chemotherapy. I wrote my first post on day 15 of the first 21-day cycle of chemotherapy, and now here we are on day 11 of the second cycle.

Chapter 8 - What do we tell the children?  

What do we tell the children?  Eriska's only 1, so the main things we say to her, the human vacuum cleaner, are along the lines of "please spit that out". "Daddy's prognosis" is not yet in her vocabulary. Torrin, however, is 4, and understands "ill"; and just a few days ago, indeed, he was talking about how when an insect "got killed", he and his friend might bury it in the ground and write on a sign above the insect an explanation of "how the insect got killed". (It wasn't clear what cause of death was in Torrin's mind, but I think it's not out of the question that human agency might have played a part.)
I'm always keen on openness and honesty, and I am hoping that normalising what is going on will help make it less painful and difficult. But I don't think that our 4-year-old really understands time, weeks, months, years, or the future. Going to the new school on "Monday" is a difficult concept, unless Monday is tomorrow (which it now is), in which case I think we can just about communicate it. Anything that is not today or tomorrow is, I think, incomprehensible. So we don't think it would be wise to say "the doctors say Daddy's likely to die in a year or two". We also felt worried about mentioning the notion that what's wrong is "in Daddy's tummy" lest other people's tummy-aches become a source of anxiety. (Nevertheless, we told Torrin where the doctors were looking with their camera when I had the laparoscopy, and showed him the three scars after the operation.)
Some lovely friends gave us some straightforward advice about what to say, and we have taken it: we simply say "Daddy is ill, and the doctors are giving him medicine to try to make him feel better."
Girton playground - photo by Torrin G MacKay
We've also told Torrin that the medicine makes me feel tired. And he's met some extremely kind staff at the hospital who told him that the medicine will probably make my hair fall out, and who let him play with the electric up-and-down buttons on the bed in an examination room.
And I decided to try to make the "illness" and "medicine" a bit less nebulous by telling Torrin that there is a lump on the side of my tummy, and that the medicine is trying to make the lump smaller.
At some point I'd really like to normalise the whole situation, talk about returning to the earth, and take Torrin to the woodland burial park (on a non-burial day) to play there and make it a familiar place where we have been together.
And then keep on living.    But I think it will be a while before that's possible.
Meanwhile, here is what Torrin said to me yesterday morning: he burst into my bedroom and said "Daddy, it's wakey-up time, and today we are going to have a party to celebrate your illness!" 
That's the spirit!

Chapter 9 - cycle two, day eleven

For my second cycle of chemotherapy, I have switched from "EOX" to "ECX", which means that my "day one" infusion involves a longer infusion of "C" (cisplatin) in place of "O" (oxaliplatin).
The good news is that this switch has eliminated, as hoped, most of the pain and grisliness of the first few days of the cycle.
The bad news about cycle two is that I've felt washed out for the whole of the first ten days of the cycle. Today, day eleven, is the first day that I have felt at all perky. I've had a runny nose for most of the ten days, and I've been feeling as exhausted as I felt when I had anaemia, a couple of months ago; but now I'm not anaemic.
During cycle one, I had a lot of days when I had fun, made plans, and did good work.
For the first ten days of cycle two, I'm disappointed to have done far less. I've achieved a few tasks: I've bought dozens of favourite books via amazon, to turn into presents for Torrin and Eriska. [The website oldchildrensbooks was very helpful in tracking down books for which I had no memory of author nor title.] I've fixed stabilisers on one of Torrin's bicycles, at his request. I met Conrad Wolfram - lovely chap - and Simon Peyton-Jones - lovely chap too - and discussed an ambitious software project that I'm working on with two colleagues from DECC.
If the future cycles wash me out as much as cycle two, I'm going to be sad.  Anyway, hopefully today is the beginning of a fresh spell of perkiness.  

Friday, September 11, 2015

New release of Dasher4.11 for windows

To my delight, Ada Majorek (who works for Google in California) has taken on the challenge of enhancing Dasher to make it work better for real users. 
Here are instructions for obtaining an updated Dasher4.11. (for windows)

 Latest improvements:
 1 you can turn off status bar with language selection. 
 2 It will also ask you if you want to save changes on exit unless you uncheck "Confirm unsaved files".  
 3 Also try "Composition application" style. 
 4 removed Control text from control box to reduce clutter.

How to "install"
 Download and Copy
to "C:\Program Files (x86)\Dasher\Dasher 4.11"
(feel free to rename to dasher.exe, but save original dasher.exe first)
 Download and Copy
to "C:\Program Files (x86)\Dasher\Dasher 4.11\system.rc"

Source changes:

I will be dropping new binaries here: 

If anyone would like to help maintain and improve Dasher, please get in touch (e.g. through github or by commenting here).
PS - I just tried the latest version of Dasher for Android, and found that it is awesome - it has lots of features (in its Control mode) that have not yet made it into the windoze version.

More details for anyone else who wants to join in the development

Ada says:
There is original source under

I sync with original repository whenever I see changes.
So far there were only non-conflicting changes. I believe ipomoena repository is latest code.

Eventually I would like to push my changes back to GNOME repository. Maybe after it stops crashing at exit.

I will copy/paste discussion about features to github tracker.
We can hone final design in there. One by one. 

I know nothing about main installations for windows. I converted Visual Studio solution file so it builds dasher.exe, but installation targets are broken.

Do you know how to fix install targets?

Thanks Ada!!!

Tuesday, September 1, 2015

How to take apart and fix a Brio electric locomotive

Favourite electric engine number 7 started working only intermittently. Electrical fault? Carpet fluff in the gears? This photo blog details how I fixed it.

Thursday, August 27, 2015

Unexpected signs of malignancy

Chapter 1
Bedside manner is an interesting thing. How should a doctor tell you things about yourself? How should you pass on information to friends? How should I write this blog post?
My doctor told me something on Thursday 16th July 2015, and I'm going to write about it here. I noticed that my doctor told me in a slightly oblique way, flying past the central topic a few times, using slightly technical language, and emphasising how unexpected the information was. Somehow, this emphasis on the unexpectedness of the information made it comfortable to absorb.
Here's why I was visiting the doctor: I'd been to see him two weeks before, because I was feeling unreasonably exhausted - even walking up one flight of stairs was difficult; he had done a blood test, found that I had anaemia, and had referred me to the hospital for an endoscopy, which I'd had on the 9th of July. (Looking at the stomach was motivated by a history of stomach pain over the past couple of years.) The endoscopy doctor had told me, on the day of the endoscopy, that I had a stomach ulcer. The Thursday-16th-July meeting was for me to hear more about the results of the endoscopy.
My doctor got straight to the point: tests had been done on biopsies from my endoscopy; the letter from the hospital said the ulcer showed signs of malignancy, most unexpectedly.
"Malignant adenocarcinoma", he said.
That's a cancer of the glandular tissue, he said.
"So you need to go for a CT-scan tomorrow, to get more information. There's no reason to think it has spread at all. And in the absence of information about the grade (histology) and the stage (degree of spread) it's hard to say what treatment will be recommended; but almost certainly stomach surgery will be involved, soon. I need to take blood today for a kidney-function check before the CT-scan. Then next week after the CT scan, a multidisciplinary team will meet to discuss all the results and make a plan."
He also said "you could drive yourself crazy reading about this on the internet"; he encouraged me not to do that, but to wait to hear what the hospital team said.
So that was it. Unexpectedly off to hospital for an unexpected CT scan (cool!) to investigate an unexpected cancer on a mildly surprising stomach ulcer.
Many friends to whom I have told my news in the last month have said "you must be devastated"; but I didn't feel devastated. I just felt "ok, that's the way things are"; I started adjusting my plans to take into account the new information. Friday's trip to London had to be cancelled. Which Summer holiday plans would we need to change? Which engagements might I need to cancel? Should I stop trying to raise research funds to build up a new research group?
I found Ramesh in the village hall and we walked home together, pushing Eriska in her pushchair.
I did a little bit of reading on the NHS website about adenocarcinoma of the stomach. The probability of surviving stomach cancer is not great, as this Tufte graphic makes clear.
"But hey, if only 20% survive 5 years, I aim to be in that 20%", I figured.
Naively I thought "almost certainly stomach surgery will be involved" implied I should be planning for a couple of days in hospital some time in August. A friendly doctor disabused me of this notion however - the normal treatment for early-stage stomach cancer is surgery to remove some or all of the stomach and all nearby lymph nodes, and it typically takes at least a 10-day stay in hospital until the digestive system recovers sufficiently from this insult to work at all; during those 10 days, you are fed through your vein and a vacuum tube is put down your nose to ensure that nothing gets beyond the oesophagus. Hmm, that doesn't sound fun.
I found an internet discussion group for people who've had stomach surgery for cancer treatment. Lots of positivity about the eventual return to near-normality.

Chapter 2 Off I went for the CT scan. What a wonderful Siemens machine! A whizzing circle. And a nice clinical scientist who set up the injections and told me that as it went in it would feel as if I had wet myself, but don't worry, you won't have. (She was right.)
On Wednesday 22nd July I met some members of my multidisciplinary team. They said that the CT scan had not resolved the degree of spread; it looked like several lymph nodes near the stomach might be cancerous, and perhaps one lymph node near the aorta; and there might be something in the liver but probably not; so they wanted to do more scans and a laparoscopy to pin the situation down. An MRI scan of the liver, to check that there was nothing there. A PET-CT scan of the chest to investigate the lymph node near the aorta - this would require special finance-paperwork because it is a non-standard test. And a laparoscopy, which means inflating the abdomen with CO2 and putting a camera in for a look around, under general anaesthetic. These things would probably take two weeks to complete, because the scanners are in demand.
After these investigations, the team would then recommend one of two courses of action: either
1. treat stomach cancer with chemotherapy and surgery from mid-august (start of chemo) to roughly november 17 (surgery) followed perhaps by more chemo; all with the intention of cure. The surgery would remove some or all of the stomach (and based on what I'd read, and the location of my ulcer, I reckoned probably 'all' was the right thing to expect)
2. just chemotherapy, no surgery; with the intention to improve/extend quality of life but not to cure. [don’t bother with surgery because too much spread].
So the one fairly certain thing seemed to be that I would be in for chemotherapy fairly soon.
After meeting the gastric consultant and nurse specialist, I met a dietician, then the dashing surgeon who was going to do my laparoscopy and (under plan 1 above) my stomach surgery.
His bedside manner was very direct. After the laparoscopy, he said, we will know whether it is good news or "doom and gloom". And in the good news scenario, he would remove my stomach. Yes, the whole thing. He wasn't bothered with hedging about any possibility of removing just part of it.

Chapter 3
We nipped away for a brief holiday. The scheduling of the two scans and the laparoscopy was chaotic but in the end all three took place very neatly on Monday 3rd and Tuesday 4th August. And as I came round from the general anaesthetic on the Tuesday afternoon, the dashing surgeon came in with a bundle of photos he'd taken and with his direct bedside manner.
"You remember I said the results could be anything between good news and doom and gloom? Well, I'm afraid it's doom and gloom."
There are secondaries all over the peritoneum. He showed me two of the pictures, which showed a thin white layer of tissue covering much of the diaphragm. He said he reckoned that without chemotherapy I might have roughly 12 months to go, and the chemotherapy might extend things by 6 months or so, but was unlikely to make me last more than 24 months.
My main reaction was "hurray! I get to keep my stomach!"

Chapter 4
At this point I started telling more friends and colleagues the situation. I emphasized "I am feeling fine and enjoying eating well in order to build strength." Ramesh and I both felt determined to have some fun. On 5th August I wrote "There is still an option of having palliative chemotherapy, but I am not sure whether that will be a good choice, since it would eat into weeks or months of valuable time now in exchange for perhaps just a few months of extra time later; I’ll talk to oncology specialists at Addenbrookes today and see how they see the pros and cons." One of my main reasons for hesitating was my perception that I was feeling fine right then, and August and September seemed a fantastic opportunity for having some fun. Chemotherapy would spoil that opportunity. Was it worth it? Could I delay the chemotherapy a few weeks?
I met my gastric consultant again, and met the head of chemotherapy at Addenbrookes, who confirmed the surgeon's rough estimates about life-expectancy. He recommended that I take the chemotherapy immediately, even though the median extension of life by chemotherapy was only about two months; I asked about the loss of quality of life during the chemotherapy; he said the loss of quality was "only 20% or so", and that the expected return (in terms of the area under the quality-of-life curve) was greater.
What about the PET-CT scan and the MRI scan? The MRI scan had shown nothing in the liver. And the PET scan didn't show anything - apparently my cancer doesn't show up at all. And they said that it hardly showed up under the original CT scan either.
I agreed to their recommendation of "EOX" chemotherapy. I had one week of rest to recover from the laparoscopy (which left the tummy surprisingly sore for several days), then the following Thursday I was back in the hospital for...

Chapter 5 - the biggest red syringe I've ever seen
It looked like something out of an Austin Powers comedy. The nurse kindly squeezed it in. Then put me on the drip to put in the second cytotoxin. Then two hours later sent me home with my huge bag full of pills.

Oh, before I tell you about the chemo, I should insert a little addendum to Chapter 4.

Chapter 4b - the last minute hesitation
It wasn't "denial" or wishful thinking, but in the final day before starting chemotherapy I found myself really concerned about the possibility that the whole thing was a big false positive. After all, they had told me that the CT scan showed very little, the PET scan showed nothing, and the MRI scan showed nothing. The only 'positive' evidence we had to go on was a histologist's report from the gastroscopy saying "malignant adenocarcinoma" and the photos and expert judgement of the surgeon that what he saw was definitely secondaries all over the peritoneum. But what if I have an unusual-looking peritoneum? And could the histology results have been mixed up somehow? A bad histologist? Specimens mixed up? It would be stomach-churningly terrible to undergo chemotherapy if in fact I didn't have cancer! I hadn't seen any data with my own eyes that really convinced me. I was only agreeing to treatment because I trusted the NHS staff. But I really wanted to feel more convinced myself. (My head of department had just told me a few days before about a friend of his who had a misdiagnosis of cancer.) Thankfully a friendly doctor suggested what to do - certainly, he said, samples would have been taken from the laparoscopy too, and they should have been tested by now; I could ask about the histology results. So I did that, and was told that those biopsies were indeed cancerous too. As I said, I wasn't in denial. It's just that to believe things you need either data that you understand or you need complete trust. I still wish I had seen more of the raw data with my own eyes. I like data. Anyway, with both the independent histology findings, I was happy to go ahead.

Chapter 6 - Chemotherapy - it's not nice, but I think I shouldn't complain. It's much worse for some people. Here is a probably-too-detailed account of Side-effects and other recent history.
1. During my first (EO) infusion I had no side-effects for the first 90 minutes, but during the final 30 minutes or so, I had cramps in my infusion arm, and weird sensations in the out-facing surface of that arm (see point 4 below).
2. Some of the infusion arm’s veins were painful and I still noticed slight vein pains (if I looked for them) on day 13.
3. I experienced some of the predicted (neuropathy) side-effects: my fingertips had sharp pins and needles sensations, especially in cold situations; this lasted a few days; my feet also had cold-induced pins and needles, for two days. My tongue was very cold-sensitive for the first couple of days and remained somewhat cold-sensitive (feeling like a puffy sock) for about 5 days. After 7 days the tongue returned to normal.
4. I don’t know if it is part of the neuropathy syndrome, but my infusion arm’s out-facing surface remained strange for about 7 days. During the first 4 days the skin and hairs were very sensitive to the touch; it felt like being stroked with a cheese grater - all over the arm, and especially the hand. By day 7, this cheese grater sensation was mainly confined to the back of the hand.
5. I didn’t have strong feelings of nausea.
6. I took steroids for 2 days as instructed. My stomach had some ups and downs which were eased along by senna and lactulose.
7. My mood became quite dark on days 1-3, then I perked up again by day 5 onwards.
8. I feel tired a lot of the time, and spend lots of time snoozing and sleeping.
9. I got a sore throat on day 11 (Sunday 23rd) and then sore throat and cough on day 12; the oncology clinic instructed me to get antibiotics from my GP and to suspend taking the "X" (capecitabine) for a couple of days while I get over the cold. This cold reached its worst on Wednesday 27th, and now (early hours of Friday) I think I am getting over it. (Increased vulnerability to infections is one of the expected side-effects of the chemo.)

How I felt about the side-effects.
I didn’t enjoy the pins and needles feeling, but if it always were to go away after 5 days, that would be ok. However, the medics have indicated that the neuropathy is expected to worsen over subsequent cycles. So I am going to talk to my doctors about switching to a less-neuropathic alternative to oxaliplatin at the next cycle this Thursday coming. The down-sides of the alternative are “longer infusion, more chance of nausea”.

Chapter 7 - What's next
There are probably going to be eight cycles of chemotherapy. Each cycle lasts three weeks, starting with a Thursday infusion, followed by 21 days of pill-taking. Eight threes is twenty-four, which is roughly six months. Given how I've felt during the first 14 days, I expect I will feel fairly tired for much of the next six months, and I'll probably spend most of it at home or near home. So the having-fun plan is focussed in the Cambridge area for the near future, with aspirations to do some having-fun further afield [perhaps on a Scottish island or two] about February, March, or April.
I'm still feeling fine, and as I shake off the cold I am beginning to feel really perky again. I've got a great appetite. My time spent snoozing is happy time, usually accompanied by radio 4 comedies. I'm spending a lot of time listening to music and transferring music from CDs to my computer and my smartphone, so that I can have favourite music wherever I am.
The biggest weight on our minds is the question how to prepare for helping our children (aged 4 and 1) through whatever the next year or three throw up.
Here we are... we are all happy!

I'll add another blog post here at every three weeks or so, to keep you updated.
Thank you to our dear friends and relations for your support!

Wednesday, April 15, 2015

Newcastle-under-Lyme School, Form 5 beta, 1982/3

My form teacher and biology teacher (Bill Beatson) sent me this nostalgia-inducing photo of my class. We were 4th years? No, 5th years. The school had just started turning from a state school into a private school; all but two of this form were state-funded pupils.

Tuesday, January 27, 2015

Public transport & cycling orbital for Cambridge

I have long thought that West Cambridge (and Northwest Cambridge, now that it is being built) should be connected by fast public transport to Cambridge railway station and to Addenbrookes hospital. The rough map above shows a proposed route running (from NW Cambridge) East to the Science Park and the new Chesterton Junction Railway Station; and (from West Cambridge) south alongside the M11 to Trumpington and the guided busway. This route would connect to both the Trumpington and Madingley Road Park-and-Ride sites.
If there were a nice cycle-path along these routes too, it would provide pleasant commuting options for people who live outside Cambridge to get to work at the West Cambridge, NW Cambridge, or Science Park sites.
The part alongside the M11 could have a nice view of the Cambridge wind farm that I visualised in June 2009. A 36-turbine wind farm would produce enough power, on average, to power the University's Departments and Offices (not including the Colleges). I think that an arc of turbines alongside the M11 could make an interesting icon.

Monday, January 19, 2015

Bye bye Ubuntu Linux - Hello MacBook Air

Today I unpacked a MacBook Air. I have used Ubuntu Linux happily for a long time, but it seems to be time to migrate.

Favourite software on ubuntu:

mutt for mail
mgp (magicpoint) for presentations

I'll record my progress on this blog-post.

Kind friends made excellent recommendations.


I installed MacPort and it provides a functionality very similar to apt (apt-get install blah). And I found that many packages are supported by Port, some of which I had never expected to see again! xcode had to be installed for port to be able to do its thing.
sudo port selfupdate
     sudo xcodebuild -license
     sudo port install gnuplot
     sudo port select --set python python27
     sudo port install ghostview 
     sudo port install gv
     sudo port install make
     sudo port install convert
     sudo port install imagemagick
     sudo port install magicpoint
     sudo port install mutt
     sudo port install unison
     sudo port install xv
     sudo port install xephem
     sudo port install ruby
     sudo port install tcl
     sudo port install xeyes
 sudo port install tk
 sudo port install rails
 sudo port install wget
 sudo port install mercurial git 
 sudo port install ffmpeg figlet lynx mysql ncftp stunnel unrar tcsh csh sh git-core  signing-party  ntop tcping bash bash-completion file xdu tree 
 sudo port install acroread
 sudo port install xpdf
 sudo port install dasher

To get "locate" to work, I did this:
     sudo launchctl load -w /System/Library/LaunchDaemons/
Tom taught me about caffeinate -i to stop the machine from going to sleep. It is already installed.
To get focus to follow mouse (into terminals at least) I tried this, but it didn't seem to work.
  defaults write FocusFollowsMouse -bool true
  defaults write wm_ffm -bool true
  defaults write FocusFollowsMouse -string YES


I installed Quartz because xdvi said it needed X11 in order to run. It says I need to log out and in to get X11 to work. Not sure what that means.


I used system preferences to crank up the key-repeat speed to the maximum. I switched off most of the audible notifications; to switch off the "outgoing mail sounds like a jet engine" nonsense, I had to go into mail preferences.


I need to figure out whether going with MacTeX is a good idea or should I find a version in Port and stick with that? Instructions for MacTeX
cd /Volumes/packages/MacTeX/
installer  -pkg MacTeX-2011.mpkg -target /

/usr/local/texlive/2014/bin/x86_64-darwin/tlmgr update --self
/usr/local/texlive/2014/bin/x86_64-darwin/tlmgr update --all


I want shift-3 to give # not £ so I went into keyboard preferences, selected "show keyboard options in menu bar" and then added US as well as UK to the list of available keyboards, and switched to US.

Things I still need

Keyboard shortcuts in Apple's Mail programme - can I get it to feel like mutt? Why doesn't "mark as junk" come up as an option? How to move mail's focus between the message and the list of messages? What is the keyboard shortcut to close just one terminal window? (not all terminals! which is what cmd-Q does) Why does
emacs filename & 
not work? How can I get the command line completion feature that I had in tcsh? (e.g. ls !$TAB)

Tim's recommendations

Some of my productivity choices:

Although it comes with an emacs, I use Aquamacs :

Flip windows around with keypresses:

After you have got used to the mac a bit, Quicksilver :

And a key macro (e.g. for inserting dates and times):

Tom's recommendations

My biggest tip is that, if in doubt about how to do something, try dragging and dropping.

My second biggest tip is to make use of Time Machine. Hassle free overnight recovery from a lost or stolen machine.

As for software:

* A better terminal:
* A package manager:
* Like Divvy:
* Like emacs: ;-)
* For all those random notes: (not been updated in ages but works really well for me)
* Offsite backup: 
* A forgetful programmers friend:
* Like Word: 

And some important command line tricks:

* Drag a file or folder onto the terminal
* Drag the little icon at the top of a document window onto the terminal
* Copy, then type pbpaste in a terminal  (e.g. pbpaste | wc)
* ls | pbcopy  — then paste
* caffeinate -s (for when your computer is too sleepy)
* open index.html
* open random-word-doc.docx

Seb's recommendations

Using search is usually quicker than navigating to find stuff. Cmd-space (Spotlight) to find apps (including switching to open ones), files, emails, etc. Or use the search box in ‘file open/save’ dialogs. (Quicksilver is a fancier search/launcher system, which I don’t use)
Cmd-Tab switches applications, but use Cmd-~ to switch windows within each application.
Delete is Fn-backspace  (both for text and things like files in Finder).
If you download an app from the internet which hasn’t got Apple approval, the first time you launch it, override the fact that Apple “protects” you from it by “right clicking” (two-finger-click or ctrl-click) and ‘Open’. Thereafter it will open normally. You can turn off this security feature completely if you want.

Time Machine is indeed excellent for backup - and as the name suggests you can go back to older version of files if you need to. You either plug in an external drive, or configure it to use a device on your home network (Apple Time Capsule or non-Apple equivalent NAS device, just check it offers Time Machine support).

Personally I would be wary of iPhoto - it has some nice features but I don’t trust it either to look after my photos or give them back to me when I want to stop using a Mac.

I don’t know if ti’s still the case, but to get backspace to work properly in Terminal when ssh’d to a Linux box, in Terminal Prefs, I had to select rxvt as terminal type, uncheck 'Delete sends Ctrl+H', (

Everything below this point is third party stuff you need to install (mostly free):

nvALT is an updated version of notational velocity (which Tom mentioned) - for keeping text-based notes. Works well for me too, and you can store the notes in Dropbox so you can access them on your smartphone too.

pwSafe - password safe (not Mac-specific, but there’s a mac version) (syncs to phone etc too)

Making disk images - Carbon Copy Cloner. Good as an extra backup, and also if you lose you Mac or, heaven forbid, it dies, you can plug the disk into a friend’s Mac and boot up your system straight off it.

An alternative online backup: Arq (looks nice, haven’t got round to trying it yet).

Ripping DVDs: makemkv