PDX Biopsy

(Those who faint when reading about blood may want to skip this one.)

On Tuesday, I went down to London to have the biopsy for the PDX trial in which I’m taking part. The biopsy happened at the Royal Marsden hospital in Chelsea on Wednesday morning. It was a CT-guided needle biopsy, which means that they use a CT scanner in near-real-time to guide a hollow needle towards the lump to be sampled, and the sample extraction needle is then passed down that needle to take multiple samples.

At least, that’s what happens when it all goes well. :-)

The target, I found out on the day, was an isolated tumour in the top corner of my left lung. As they were biopsying my lungs, which are not a stable target, I had to both stay very still, and achieve a consistent size of “held breath”, so that when they moved the needle or did a scan, everything was in pretty much the same place. I was placed on the CT scanner table, and they used a lead-or-similar grid placed on my chest to find the optimum point of entry. They then injected generous quantities of local anaesthetic (a process which itself stings) and started inserting the needle. After each movement, they stopped, slid me into the scanner, told me to take a standard breath, and used the scan to see where the needle was and whether the track needed correction.

All went fairly smoothly until the needle passed through the outer wall of the lung itself. At this point, I started bleeding into my lung, which (although I tried to suppress it) led to significant amounts of convulsive coughing. They had to use suction to remove the liquid from my mouth. One nurse said afterwards that she thought they might well have abandoned the procedure at this point. In someone as young as me, this complication at this point is fairly rare. Of course, coughing so much, I was not able to hold still or take the standard breath, and it was dangerous to move the needle any further.

After a couple of minutes, I managed to get the coughing under control, although later I opened my eyes for a short time and saw blood spatters all over the inside of the CT machine! Once I was stable again, they were able to continue inserting the needle and were able to get 8 good “cores” of sample for use in the PDX trial.

However, a final whole-chest scan revealed that all that jerking about had given me a small pneumothorax, which is where air gets into the pleural space, between the lung and the chest wall. So I had to stay there for longer while they inserted a second needle into a different part of me and attempted to suck out the introduced air. This took less long, and was mostly successful. Any remaining air should, God willing, be reabsorbed in the next week or so.

Towards the end, I asked what my heart rate was; they said “66″. That’s the peace of God in action, I thought. The nurses joked that we should measure the heart rate of the surgeon! :-)

I was sent to the recovery room and then to the Clinical Assessment Unit. After 3 hours, they did a chest X-ray, then after another 2 hours another one, to check that I was stable and the remaining tiny pneumothorax was not growing. It wasn’t, so they let me go home. But I have another X-ray in a week, here in Sheffield, to make sure everything is OK and I’m fine to fly to the USA the following Monday :-)

Awesome Article on Browsers

James Mickens on top form, on browsers, Web standards and JavaScript:

Automatically inserting semicolons into source code is like mishearing someone over a poor cell-phone connection, and then assuming that each of the dropped words should be replaced with the phrase “your mom.” This is a great way to create excitement in your interpersonal relationships, but it is not a good way to parse code.

Read more.

Patient-Derived Xenografts

In my last post, I mentioned that I’ve been asked to take part in an interesting study to help develop a new form of cancer therapy. That therapy is based on Patient-Derived Xenografts (PDX). It works roughly like this:

  1. They extract a sample of your tumour, and divide it into two bits.
  2. They take one half, and implant it under the skin of an immune-deficient (“nude”) mouse. The immune deficiency means the mouse does not reject the graft.
  3. If it grows in the mouse, once it’s large enough they remove it and implant it into a second “generation” of four mice.
  4. They keep going for four generations, so at the end you have about 64 mice. It turns out that if you can get a tumour to grow for this long, it is acclimatised to the mice and will grow forever if required.
  5. Next, they take the other half of the sample and do a deep genetic sequence on it, along with one of a normal bit of me.
  6. They “diff” the two sequences to find all of the mutations that my cancer carries.
  7. Some of those mutations will be “driver” mutations, responsible for the cancer being cancerous, and others will be “passenger” mutations, which happened at the same time or subsequently, but are just along for the ride. They try and work out which are which.
  8. If they can identify the driver mutations, they look and see if they have a treatment for cancers driven by that set of mutations.
  9. If they do, they feed it to the mice.
  10. If it works in the mice, they give it to me.

As you can imagine, there’s a lot that can go wrong in this process. The biopsy samples could be bad, the tumour may not grow in the mice, or it may not grow for long enough, they may not be able to figure out which mutations are drivers, if they can there may not be an agent targetting that pathway, if there is it might not work in the mice, and if it does it might not work in me! So it would be wrong to trust in this for a “cure”. As before, my life is in the Lord’s hands, and he alone numbers my days. But I hope that even if it does not result in a cure for me, the knowledge gained will help them to cure others in the future.

I have significant involvement only at the beginning and (if we get there) the end. To start the process, it was necessary to provide a tumour sample via biopsy. That happened in London yesterday, and the rather eventful experience will be the subject of my next post.

Cancer Update

Last November, and again this month, I had CT scans, and it turns out my cancer (Adenoid Cystic Carcinoma) has been growing. (If you haven’t known me for long and didn’t know I have cancer, the timeline and in particular the video might be a useful introduction.) I now have lumps of significant size – 2cm or larger – in both of my lungs and in my liver. It has also spread to the space between the lung and the chest wall. It normally doesn’t cause much bother there, but it can bind the lung to the wall and cause breathing pain.

For the last 14 years, we have been following primarily a surgical management strategy. To this end, I have had approximately 5 neck operations, 2 mouth operations, 2 lung operations, and had half my liver, my gall bladder and my left kidney removed. Documentation about many of these events is available on this blog, linked from the timeline. Given that I’m still here and still pretty much symptom-free, I feel this strategy has served me rather well. God is good.

However, it’s now time for a change of tack. The main lump in my left lung surrounds the pulmonary artery, and the one in my liver is close to the hepatic portal vein. Surgery on these might be risky. So instead, the plan is to wait until one of them starts causing actual symptoms, and to apply targetted radiotherapy to shrink it. Because my cancer is “indolent” (a.k.a. “lazy”), it can have periods of activity and periods of inactivity. While it seems more active at the moment, that could stop at any time, or it could progress differently in different places.

There is no general chemotherapy for ACC. However, at my last consultation I was asked to take part in a clinical trial of a new and interesting therapeutic technique, of which more very soon.

A friend texted me a word of encouragement this morning, and said he and his family had been reading Psalm 103. It’s a timely reminder of the true nature of things:

The life of mortals is like grass,
    they flourish like a flower of the field;
the wind blows over it and it is gone,
    and its place remembers it no more.
But from everlasting to everlasting
    the Lord’s love is with those who fear him,
    and his righteousness with their children’s children –
with those who keep his covenant
    and remember to obey his precepts.

Psalm 103:15-18

10 Year Blogaversary

10 years ago today, I started blogging.

At the time, I thought I was rather late to the blogging party. In hindsight, it seems not. Since then, through one change of host (thanks, Mozillazine!), there have been 1,463 posts (including this one), and 11,486 comments. Huge thanks to everyone who’s read and/or commented (well, if you commented without reading, not so much) in the last 10 years. It’s uncertain whether I or the blog will last another 10 (the Lord is in control of that) but here’s to however long it is!

Who We Are And How We Should Be

“Every kingdom divided against itself will be ruined, and every city or household divided against itself will not stand.” — Jesus

It has been said that “Mozilla has a long history of gathering people with a wide diversity of political, social, and religious beliefs to work with Mozilla.” This is very true (although perhaps not all beliefs are represented in the proportions they are in the wider world). And so, like any collection of people who agree on some things and disagree on others, we have historically needed to figure out how that works in practice, and how we can avoid being a “kingdom divided”.

Our most recent attempt to write this down was the Community Participation Guidelines. As I see it, the principle behind the CPGs was, in regard to non-mission things: leave it outside. We agreed to agree on the mission, and agreed to disagree on everything else. And, the hope was, that created a safe space for everyone to collaborate on what we agreed on, and put our combined efforts into keeping the Internet open and free.

That principle has taken a few knocks recently, and from more than one direction.

I suggest that, to move forward, we need to again figure out, as Debbie Cohen describes it, “how we are going to be, together”. In TRIBE terms, we need a Designed Alliance. And we need to understand its consequences, commit to it as a united community, and back it up forcefully when challenged. Is that CPG principle still the right one? Are the CPGs the best expression of it?

But before we figure out how to be, we need to figure out who we are. What is the mission around which we are uniting? What’s included, and what’s excluded? Does Mozilla have a strict or expansive interpretation of the Mozilla Manifesto? I have read many articles over the past few weeks which simply assume the answer to this question – and go on to draw quite far-reaching conclusions. But the assumptions made in various quarters have been significantly different, and therefore so have the conclusions.

Now everyone has had a chance to take a breath after recent events, and with an interim MoCo CEO in place and Mozilla moving forward, I think it’s time to start this conversation. I hope to post more over the next few days about who I think we are and how I think we should be, and I encourage others to do the same.

Using Deja Dup (Ubuntu Built-In Backup) with rsync.net

This is one of those posts which is trying to save other people the hassle I’ve had.

Ubuntu One is shutting down. So I want to switch some backups over to use my rsync.net account. With U1, I used Ubuntu’s built in backup system, which is based on a program called Deja Dup. I would like to use that program with rsync.net too.

However, Deja Dup auto-prepends a “/” to the beginning of the path you give it. (There’s a bug on this behaviour.) And I don’t have root on the rsync.net server. (A good thing.)

So, in order to use Deja Dup with a server where you don’t have root, you need to find and give it a full path. Execute:

ssh 42@ch-s001.rsync.net pwd

(where 42 is your user number, and ch-s001 your server name) to find out the path to your home directory, and then, in the Deja Dup settings, prepend that to the name of the directory you want to store your backups in. You’ll also need to set up passwordless login.

You’ve Been Trolled

(Troll (v.): to say something with the aim of provoking an angry reaction which benefits you.)

On , an American company called Honey Maid (company slogan: “This is Wholesome”) released a new commercial. It features a number of families and children in a very positive light, including a family of two men. Here’s the video:

Soon after came the calls for a boycott.

A few days later, a Facebook friend linked to this video, which you absolutely should watch in full:

So, if you were someone who called for or joined this protest, what did you achieve here? Let’s consider. You got to look angry and intolerant – even if you didn’t use language like that depicted in the video, everyone will assume that you did. You got to look weak – it’s now clear that even companies whose core market is supposed to be the All-American family with traditional values have no problem taking an explicit stand for same-sex marriage, because they think it’ll be a net win for their sales figures. And you got to look fearful and patronised – what they did is the approximate equivalent of patting you on the head and saying “There, there, dear, don’t be scared, it’ll all be alright in the end.” You gave the company a ton of free publicity, and they got to look enlightened and forward-looking.

And the crowning achievement of the trolling, the pièce de résistance, was the fact that there was a shot of a mixed-race family somewhat later in the original, and they included that in the “bits people didn’t like” section of the follow-up video, right after showing the gay couple. So you all look racist, too – even if none of you had any issues with the promotion of that type of family.

I’m pretty sure they didn’t think of this after the commercial was published; it was set up in advance. They knew this was going to happen, and you played right into their hands. As bits of marketing go, I have to say “well played”.

So, here’s my advice. Public expressions of outrage (something you picked up from the other side’s playbook anyway) clearly don’t work any more, if they ever did. When a company like Honey Maid can troll you to get a quite predictable reaction and lots of free publicity, here’s the lesson: you need new tactics. This isn’t working.

21st Century Nesting

Our neighbours have acquired a 21st century bird’s nest:

Not only is it behind a satellite dish but, if you look closely, large parts of it are constructed from the wire ties that the builders (who are still working on our estate) use for tying layers of bricks together. We believe it belongs to a couple of magpies, and it contains six (low-tech) eggs.

I have no idea what effect this has on their reception…

Copyright and Software

As part of our discussions on responding to the EU Copyright Consultation, Benjamin Smedberg made an interesting proposal about how copyright should apply to software. With Chris Riley’s help, I expanded that proposal into the text below. Mozilla’s final submission, after review by various parties, argued for a reduced term of copyright for software of 5-10 years, but did not include this full proposal. So I publish it here for comment.

I think the innovation, which came from Benjamin, is the idea that the spirit of copyright law means that proprietary software should not be eligible for copyright protections unless the source code is made freely available to the public by the time the copyright term expires.

We believe copyright terms should be much shorter for software, and that there should be a public benefit tradeoff for receiving legal protection, comparable to other areas of IP.

We start with the premise that the purpose of copyright is to promote new creation by giving to their authors an exclusive right, but that this right is necessary time-limited because the public as a whole benefits from the public domain and the free sharing and reproduction of works. Given this premise, copyright policy has failed in the domain of software. All software has a much, much shorter life than the standard copyright term; by the end of the period, there is no longer any public benefit to be gained from the software entering the public domain, unlike virtually all other categories of copyrighted works. There is already more obsolete software out there than anyone can enumerate, and software as a concept is barely even 50 years old, so none is in the public domain. Any which did fall into the public domain after 50 or 70 years would be useful to no-one, as it would have been written for systems long obsolete.

We suggest two ideas to help the spirit of copyright be more effectively realized in the software domain.

Proprietary software (that is, software for which the source code is not immediately available for reuse anyway) should not be eligible for copyright protections unless the source code is made freely available to the public by the time the copyright term expires. Unlike a book, which can be read and copied by anyone at any stage before or after its copyright expires, software is often distributed as binary code which is intelligible to computers but very hard for humans to understand. Therefore, in order for software to properly fall into the public domain at the end of the copyright term, the source code (the human-readable form) needs to be made available at that time – otherwise, the spirit of copyright law is not achieved, because the public cannot truly benefit from the copyrighted material. An escrow system would be ideal to implement this.

This is also similar to the tradeoff between patent law and trade secret protection; you receive a legal protection for your activity in exchange for making it available to be used effectively by the broader public at the end of that period. Failing to take that tradeoff risks the possibility that someone will reverse engineer your methods, at which point they are unprotected.

Separately, the term of software copyright protection should be made much shorter (through international processes as relevant), and fixed for software products. We suggest that 14 years is the most appropriate length. This would mean that, for example, Windows XP would enter the public domain in August 2015, which is a year after Microsoft ceases to support it (and so presumably no longer considers it commercially viable). Members of the public who wish to continue to run Windows XP therefore have an interest in the source code being available so technically-capable companies can support them.

Mozilla Voices

I invited people to email me; here’s what they have been saying.

I fear that Mozilla showed a weakness, when we replied to that initial complaint. We showed people we care about what they had to say about Brendan, and about politics. I think we shouldn’t. …

Although technically we are still good, I fear that our community is strained right now. We need to forget all politics, and focus on the mission. Only the mission. We shouldn’t care about other things. Hopefully we will pull through…


Recent events have made me very angry, and the more I think about it, the angrier I get. …

Brendan understood that for Mozilla to be successful in its mission, participants needed to check their prejudices at the door and work together to build this great thing. And he himself compartmentalized his prejudices away from his work life.

He awarded others this tolerance, but in the end was not awarded it himself by others.


While I am myself a strong supporter of equal marriage rights, I am shocked by what was done to Brendan. It was truly vindictive and intolerant, completely unbecoming of a movement that claims to fight for tolerance.


I am not sure what you will do with the feedback you get, but if you can, in the middle of the rest, express that there exists a point of view that the leadership does not listen well enough and needs to open up lines of communication to the leadership from employees, the community and even non-community users, that idea would be worth communicating.


I feel that Brendan was unfairly persecuted for expressing his views even though it seems evident he never allowed any personal views to affect his ability to function.

People have been justifying bashing his position on the basis that equality is normally and editorially required for any position of power. Unfortunately these people are either bordering on misinformed or purely idiotic.


I am surprised at how mean people can be toward Brendan. It is a big loss for Mozilla.

I have been using Firefox since it was called Phoenix. I have installed it on many PCs. I learned Javascript on Firefox. I was loyal to Firefox during the difficult years when it had memory and speed issues. I was generally impressed with Mozilla’s stance on the Open Web. Now, I am not so impressed with Mozilla.


Somebody has been forced to resign from Mozilla because of his beliefs/ideas/opinions. That is exactly the opposite of what Mozilla states to be its “mission” …


I find it horrific that this backlash is a repeat of what you experienced two years ago. And it’s deeply affected me in my impression of how welcomed Christians are at Mozilla.


If you want your voice heard, or just want to talk in confidence (say if so), please email me.

Your Ire Is Misdirected

Hi. My name is Gervase Markham. I’m a supporter of traditional marriage, and I work for Mozilla. In fact, as far as being on the record goes, I believe I’m now the only one.

Many people who agree with me on this issue are very upset about what happened to Brendan Eich, our co-founder and, for two weeks, CEO of the Mozilla Corporation. Brendan was appointed and then, after 10 days under the Internet’s lens of anger based on his donation in opposition to the redefinition of marriage, stepped down and stepped away from Mozilla – to our great loss.

I am assured by sources I trust that Brendan decided to leave of his own accord – he was not forced out. My understanding is that the senior management of Mozilla (many of whom disagree with him on this issue) worked very hard to support him, even if I would not agree with all the actions they took in doing so. However, he eventually felt that it was impossible for him to focus on leading if he was spending all of his time dealing with the continued, relentless news and social media storm surrounding the donation he made. In other words, he wasn’t forced out from the inside – he was dragged out from the outside.

So, here’s my plea: please don’t be angry with Mozilla. Mozilla and what it does and stands for is too important to the future of the free web to allow this to do it damage. It was us who brough innovation back to the web browser market and started the process which led to the awesome web you use today. And now, we’re trying to do the same with the closed smartphone market. I believe that connecting billions of people in the developing world to the web at minimal cost and with full fidelity will lead to the next great advance in human flourishing, as people can use the information they discover to make their own lives better. That’s our goal.

If you can’t find it in your heart to forgive them (the course I would recommend), then your anger is best directed at those outside Mozilla who made his position untenable. The press that twist and sensationalize without investigation, social media which magnifies and over-simplifies without consideration, and those who rush to judgement without understanding. I’m not going to name names or organizations. But as far as Mozilla itself goes, please, please continue to support us.

I am determined to work to make all Mozillians of whatever beliefs – and whatever actions they take outside of Mozilla in support of those beliefs – confident that, if they can work with other Mozillians as Brendan did so well for 15 years, Mozilla is a place for them. How successful we’ll be at that depends on how our community deals with what just happened – but it also depends on you. If you jump to paint Mozilla in the colours of ‘the opposition’, that will become a self-fulfilling prophecy. And the world will be poorer for it.

Mozilla is caught in the middle of a worldview war. Let’s not make the free web a casualty.

Recent Events

It’s possible some people may want to discuss or give their view on recent events but, given the strength and tone of opinion expressed already, may not feel safe doing so in public. If that’s true of you, please feel free to email me at gerv@mozilla.org. I’m available to talk.

I may produce anonymous summaries of what people are saying to me so that others can understand how people are feeling; I want everyone to feel their voices can be heard. But if you want that not to happen for you, just say.

If you need it, you can find my PGP public key here.