Yet another overly ambitious Todo list

2012 has passed (and I have to say, thank Eris it did), and 2013 is upon us. Say what you will about arbitrary counter resets and new year's resolutions; the start of a new year is a convenient time to reflect, to look back, and to look forward. Another motivation for this reflection is that I just completed my diploma thesis at long last; so naturally, there's the question of: What next?

And so I thought I'd record here what I'd like to do in 2013 - at a minimum, I may be able to go back to this post in a year's time and compare my goals then and now, and to get a sense of what I thought I might be able to accomplish in one year vs what I actually did accomplish. So here goes, in no particular order.

• Go snowboarding. Not a given, seeing as I live in a place where both mountains and snow are scarce to non-existent.
• Visit some of the European biohacking groups. High on my list are BiologiGaragen in Copenhagen, La Paillasse in Paris, brmlab in Prague, London Hackspace, MadLab in Manchester, and Cathal's lab in Cork.
• Explore Amazon's EC2.
• Push the Berlin biohacking efforts forward.
• Get back into the habit of going swimming regularly. Because swimming is awesome.
• Visit old friends who are scattered across the globe.
• Explore the European arctic further.
• Explore the science-y potential of the Stattgarten urban gardening project. That includes breeding, instrumenting, botanical drawing, microscopy, and more.
• More microscopy.
• Reading, lots of it.
• Convert my recently acquired apartment from a place where I keep my boxes of stuff into a place that feels like home.
• Get the University of Reading's self-cloning experiments kit and work with it.
• Explore the possibilities of genetic manipulation without a BSL1 license.
• Implement and test the transilluminator concepts that have been living in my drawer for way too long.
• Try Sanger sequencing.
• Try commercial sequencing.
• Learn more about metagenomics to a point where I can carry out a small metagenomics project.
• Collaborate with some of my favourite people on some interesting projects.
• Collaborate more in general.
• Implement and test the lab-in-a-backpack concept that has been living in my drawer for way too long.
• Moar bioinformatics.
• Draw and paint.

A tale of three cities

(Disclaimer: This post is about a toilet door. Yes. You read correctly. A toilet door that has come to mean a lot of things.)

Once upon a time, there was a group of people who had spent all their lives in a kingdom where women were considered commodities and things of value only if they pleased the eye. Believing that every human being should be regarded as such, they were frustrated with this, and so they decided to go out into the world and find a more accepting place. They came upon a fork in the road that led into three different directions; they decided to split up and promised to send each other word on what they found on the end of each road.

Each group came upon a magnificent city at the end of its respective road, full of technology and science and art and wonder, where strangeness and new perspectives and possibilities of being seemed to be around every corner. However, those three cities were not all the same; and the respective groups soon came to experience very different things in them.

All three of the groups were initially full of wonder, but the group that had stumbled upon the city of Primo soon found monuments in the city that depicted scenes they knew all too well from the place they had fled: scenes where women were depicted as things to be looked at and used, even to their visible discomfort. The group went to the city elders and expressed their discomfort at these monuments, and how it reminded them of the place they had just fled. The elders convened, and ruled that these monuments had been there before the newcomers had arrived, and that they were works of art that were not to be disturbed, that they were a part of the city's tradition, and that the newcomers should just learn to ignore them - even more, that the newcomers had come to this town as strangers, and if they wanted to be citizens, they had better learn to adapt. The group, which was made up of the more polite and shy people from the original trek, submitted to this ruling, and did as they were told - they tried to adapt so they wouldn't risk being expelled from this city of technology and science and art and wonder. But inwardly, they withdrew a little, and even though they still savoured the promises of the city, they never really felt like they were at home anymore; they kept to themselves more, and felt reluctant to contribute to all the exciting things that were going on in the city.

The second group, the one that found the city of Secundo, also found the same kinds of monuments in that city. Like the first group, they went to the elders, and like the first group, they received the same response. Only this group was made up of the more rebellious people, who felt they had taken enough shit in their lives, and that they hadn't set out for a better place, only to find one that made their hearts beat fast with joy, and then discover that it endorsed the same kind of crap as the place they had come from. This group stuck their heads together, and they decided to rebel. In a dark and stormy night, they snuck out, and they remade the monuments into something that wouldn't remind them of the place they had just left. When the monuments' defacement was discovered, there was an almighty shitstorm that left everyone involved covered in hostility and brown, smelly goo. If you, esteemed reader, want to find out what eventually happened to the city's inhabitants new and old, I advise you to check Twitter.

The third group found a city named Tertio at the end of their road. Like the other two cities, it was a marvellous place. But again, like the other two cities, it contained monuments like the ones in Primo and Secundo. And the third group, like the ones in Primo and Secundo, went to the city elders. Only in this city, the elders listened to the concerns of the newcomers. They recognized that newcomers to their city meant an enrichment, and that it was important that they, too, feel at home, so that they would contribute to the city's culture and help it thrive. The elders did not really understand what made the newcomers' group so upset about the monuments, but saw that if it was a big deal for them, then it was worth examining whether these monuments were really important enough to jeopardise the newcomers' company and potential. The elders came to the decision that the monuments were not worth that; they ruled that the citizens and the newcomers should sit down together and come up with new and more inclusive replacements for these old monuments. The ensuing meeting was long and fraught with frustration on both sides, but eventually, the old citizens and the newcomers discovered that there were other, equally beautiful monuments that would represent everyone's dreams. So they got to work and made the city an even more wondrous place. And everyone lived happily ever after, or something.

Life after the diploma thesis, or: my case against a PhD

I'm 34 pages into my diploma thesis (target is around 100 pages, including everything), and the deadline for handing it in is Decembre 28th. Time to think about life after the thesis.

I've been toying with the idea of going for a PhD, since I really, really want to do science. And if you want to do science, getting a PhD is the way to go, right?

But after mulling this over for quite a while, I've almost arrived at the conclusion that, no, for me, a PhD is not the right way to go. I'd like to lay out my reasoning and my plan here; who knows, maybe I'll get some useful input before making a final decision? Or maybe I'll make my decision anyway, and leave this as input to others who are in a similar situation.

One of the points that came up when talking about the issue with my parents was: making a living. Really. Me and my three siblings were raised by a single dad at the low-income end of the spectrum. Much as my older siblings, I started earning my livelihood when I was 17. I know that if I fail financially, my parents and grandparents would give anything to help me out, but they just don't have the resources themselves. Seeing as I've been working fairly successfully as a software developer and security consultant for the past 12 years, it would be foolish bordering on irresponsible to throw this away for an uncertain academic career by disappearing into the depths of a PhD programme. I hardly need to mention that software technology as well as IT security are fast-paced fields - if I decide to drop out for three years, I can't really expect to get back in afterwards.

Another point has to do with the above-mentioned work experience. I've been used to working as a freelancer, on my own terms; I've seen quite a bit of The Industry(tm). Meaning: I've seen too much to accept subordination easily. I've actually had squabbles about this with my thesis advisor, who nagged me about "taking my future seriously", all while I was juggling the responsibilities I had signed up for to pay rent and other unpleasantries (literally; we're talking contracts and penalties and fines here) and my thesis work which is taking place in an ivory tower. This makes me think that I wouldn't take kindly to the slightest hint of being used as a scientific wage slave. I pretty much know that every time my PhD advisor would be nagging me about this paper of theirs they want me to contribute to, I'd be thinking "You know, I made the decision to do this PhD at quite a monetary expense; don't you dare act like it's a privilege to do your work." So, whether these thoughts would be misguided or not, I'm guessing conflict would be pre-programmed.

Then there's the thing that from all I know, doing a PhD is a specialization exercise. Go deeper. But I don't want to go deeper, I want to go broader. This seems to be what makes me enthusiastic and happy and what makes me do good work: going broad. I don't really see how that fits in with what's expected of a PhD student.

So, taking all this into account, I've all but settled for going for an alternative. I'll try to make my own PhD. I'll try and see whether I can't do science on my own terms. There's a vague plan there that might me a combination of "transitioning to bioinformatics as a service" and "independent scientist". The idea is extremely vague, but I have a very roughly sketched plan. We'll see how it pans out.

Addition: Questions around personal genomics - sharing vs. privacy

There was something bugging me while writing my last post on some issues with personal genomics, because I seemed to remember I had another point that I wanted to bring up. Now it came back to me. The point was about the technicalities of sharing genomic data.

Now, the last post was mostly me bitching about the current mode of personal genomics, 23andme and all, and how I don't think it's a good idea to hand over your genomics data to some US-based company with very clearly stated commercial interests. (Just to summarize on that: Having commercial interests is not a bad thing in itself in my book, but I'm a bit of a tough sell if you want me to share my data for what seems like mostly your commercial interest, and doubly so if these data are not exclusively mine to disclose.)

But there is another point worth discussing around the topic of personal genomics which is a little more forward-pointing, maybe. Let's say we agree that personal genomics are here to stay. Let's say that getting your genome, or portions thereof, sequenced becomes part of  diagnostic routine, or even part of your routine medical examinations. That is, your genomic data or parts thereof become part of your medical record. How do we handle that?

As far as I can tell, there has been a certain separation of competences and sharing of data on a need-to-know basis even among your doctors. Professional discretion or not, it's fairly unnecessary in all but some freaky, borderline sci-fi cases, to share your cardiologist's findings with your dentist. And I think that's a good set of walls right there.

Now, with all these genome-wide association studies, lots of potential markers for all kinds of medical conditions and predispositions for behaviours showing up, I wonder whether we can come up with a scheme that empowers a person to share some, but not all of their genomic data with whomever they choose. Some results from a SNP genotyping may be relevant to a dentist. Some may be relevant to a gynecologist, such as a genetic predisposition for breast cancer, but others you may feel uncomfortable sharing with anyone but the persons you've elected to be trustworthy on certain subjects - say, markers that are associated with predisposition to addictions, or clear indications for Huntington's disease. At this point, I have to disclose, again, that my background is in computer security, and in this field, I've come to appreciate the concept of Defense-in-Depth. One of the things this concept teaches you is to only grant access on a need-to-have basis, and having grown up in a privacy-conscious environment, I think this is a good operating principle.

So, for me, the question is, how do we enable people to partially share their genomic information on a need-to-know basis? How do we implement this technologically, and how do we implement this UI-wise? I think that answering this questions is worthy of the engineer's attention, because a success at solving this problem means that we don't have to choose between privacy and the benefit of data sharing - that we may get to have both, with the individual having the power to make an informed and enforceable choice between these two extremes.

This may also have quite an impact on crowd-sourcing genomics projects that rely on people sharing data - they may benefit from individuals who are confident that they can make an informed and enforced choice concerning the disclosure of their genomic data.

Any ideas on how to achieve this are welcome, but I have a hunch that the much-condemned digital rights management (DRM) technology may actually see a use-case that is in the service of the informed individual, rather than being a servant to commercial interests.

If you have any suggestions regarding this, drop me a line/comment.

Some issues with direct-to-consumer personal genomics

There are a few issues on the personal genomics boo-hah that I've been meaning to write down, so, time for a brain dump. Context: The cost of sequencing DNA is dropping, fast, companies like 23andme have been offering direct-to-consumer SNP genotyping at affordable prices for quite a while now, and they even recently started offering exome sequencing for around 1000 dollars.

(Explaining the lingo: a SNP is a single nucleotide polymorphism - a single base in the genome where at least 1% of the population under study have a different "letter" than the rest. The exome is the set of all exons in the genome; very roughly speaking, it's the subset of the genome that codes for proteins and functional RNA. That doesn't mean the rest of the genome is junk, but the exome is a handy, sufficiently interesting subset that can already be sequenced at relatively low cost.)

And now, to the issues I mentioned. For me, the two major ones are "Analysis and interpretation" and "Information content and privacy".

Analysis and interpretation

One thing that irks me is this: at this point in time, with our current understanding of all things biological, personal genomics is little more than a geeky (although admittedly shiny) toy. Marketing it as anything more is just plain dishonest. Yes, there are some things genotyping and genome sequencing can tell us, but for a healthy individual, these are few and far between, to say the least. Do you smell snake-oil?

Apart from this problem of our still limited understanding, extracting information from sequencing data still requires a lot of work, with a little bit of voodoo on top of it. And I mean, a lot of work - expensive work, that needs to be carried out by skilled analysts.

On top of that, of course, there's the thing that a person's genomic information is only a small part of the picture. Methylation patterns, somatic mutations in a subset of an organism's cells, gene expression levels in response to stimuli or in dependence of the cell and tissue type, translation rates, protein-protein interactions, involvement of the immune system, or the gut microbiome are just examples for other parts that play a role in determining an organisms biological state. To borrow a metaphor from another field: If you're trying to reverse engineer a heterogenous distributed computer system, and you start out by dumping the firmware of one component - that would be the equivalent of exome sequencing. It's a part of the picture, for sure, but it's only a small first step towards understanding the entire system. Just something to keep in mind.

Information Content and Privacy

Another issue, and one that has kept me away from services like 23andme: Information content and privacy. I find it unnecessary to rehash the obvious privacy implications here, I just want to draw attention to two things:

Number one, 23andme in particular is an American company, that is under American jurisdiction. I'm sure you all remember some of the cases in the recent past where law enforcement agencies have approached Web 2.0 services with requests to hand over the personal data of individuals under investigation (off the top of my head, I recall cases involving Twitter, but I'm sure there are more). The SNP genotyping data that 23andme keeps in their databases is more than sufficient to match it against a biological sample and possibly get an ID this way.

(Additional note: DNA Forensics for law enforcement currently does not use SNPs for identification, but STRs. The reason for this is, um, legacy. The databases that have been built up over the last decades are based on STRs, and moving to a different marker system - one based on SNPs, for example - would mean a lot of cost and effort. However, that doesn't mean a law enforcement agency cannot also get their labs to do SNP genotying on a sample if this seems useful.)

Number two, which is the more important one in my decision to stay away from 23andme: My genome also contains a load of information about my relatives. That means, if I decide to submit my genomic information for storage on the servers of a company, without being able to reliably tell how long this data is going to stay there and where it will eventually end up or what it will be used for in 50 years' time, then I also make this decision for my parents, my grandparents, my siblings, and their children - even the ones that aren't born yet. And I have come to the conclusion that I just don't have the right to make this decision for them.

Update: Biotinkering, laws and regulations

Benjamin commented on the post "DIYBio and biotinkering - Laws and regulations in Germany":

The legal issues are pretty simple actually - you just cannot do any genetic engineering (including bacterial transformation) in your garage. Simple as that. Sorry.

Since writing the original post, I've learned that this is not completely true. You can do some genetic engineering even without a BSL 1 license - namely, "self-cloning". The legal text is a bit mushy on the subject, but essentially, you can genetically engineer known-to-be-safe organisms if you use only sequences that are naturally found in this organism, or one that is "phylogenetically close", provided you don't release the result into the environment.

I've talked it over with the office that is responsible for granting BSL licenses, and they suggested it may be OK for a biotinkerer to, for example, modify E. coli K12 with elements found in E. coli. The University Reading offers a kit, "The Transformer Protocol", which implements just that. It's aimed at teachers, students, and other experimenters who don't have access to a BSL 1 lab but want to learn about the basic procedures of bacterial transformation. The fine people of MadLab in Manchester have actually used this kit in one of their workshops recently.

Conceivably, it would also be within the bounds of this "self-cloning" provision to rearrange (inducible) E. coli promoters and E. coli genes to get externally inducible expression of some gene of interest - not exactly ground-breaking science, but probably fun, and a good way to get one's feet wet.

I think it would also be possible here to rearrange/recombine traits of different, say, apple cultivars (provided, of course, that you know which genes are associated with these traits, but that's a different problem). I'd want to talk this over with said office before I actually try it, though - better safe than sorry.
 

Some points on misogyny, misandry, patriarchy, feminism, and masculism

The following be a motley collection of points that keep rattling around in my head as I follow the current discussions around gender roles, feminism, masculism, and anti-feminist backlash.

Complex 1)

• Often-heard statement: There is no such thing as sexism directed towards men.
• Alternatively often-heard statement: sexism directed towards men is fundamentally different from sexism directed towards women, since these sexisms are merely "cloaked" versions of sexism directed towards women.
• Often-heard statement: Feminism has brought about the oppression of men and made them the laughing stock of humanity.

Wrong, all of it. And related. (Also, I do not ever want to hear the phrase "reverse sexism" again. It's moronic. Sexism denotes prejudice or discrimination based on sex. Sexism directed towards men simply denotes sexism against men, period, no need for verbal acrobatics.)

I found an interesting paper a while ago, entitled "Down So Long. Why Is It So Hard To Explain Gender Inequality?". While I do not agree with the entirety of this paper, it did provide some insights to me.

One of these interesting points was that misogynist and misandrist narratives have existed side-by-side throughout the history of patriarchy. The author of said paper gives a characterization of existing misogynist vs misandrist narratives, like thus:

Misogynist:

• Men are practical; women are childish
• Men are strong; women are weak
• Men are sexually open; women are sexually manipulative
• Men are independent and can lead; women are dependent followers
• Men are smarter and more knowledgeable; women think and know less
• Men are more rational, analytical, and thoughtful; women are more emotional and lack judgement
• Men are rule makers; women are ruled by circumstance and emotion.
• Men are outward lookking and socially responsible; women are narrowly concerned with families.

You'll find many of these views espoused in our cultural records of famous philosophers, writers, and scientists.

And now for the misandrist version:

• Men are childish [and need to be babied]; women are mature
• Men are brutish; women are gentle
• Men are sexually uncontrolled; women are sexually refined
• Men are bull-headed and power-hungry; women are cooperative
• Men are dense and obsessed with facts; women are intuitively insightful
• Men are withholding and insensitive; women are sensitive and expressive
• Men are morally weak; women are virtuous
• Men are cold and unfeeling; women are nurturing and concerned with others.

Needless to say, either of these narratives is an insult to many contemporary beings of at least average intelligence, whether male or female, especially if you take into account our (Western European) importance placed on individuality and self-fulfillment.

Thing is, due to the way patriarchy is set up, the misogynist narratives made it into our cultural record of philosophy, religion, and science, while the misandrist narratives didn't. For, well, millennia, the public sphere, including publishing on Culturally Important Subjects such as philosophy, theology, and science was an exclusively male domain, while the female domain was the home, which didn't usually produce written records. In a strictly gender-segregated society that has a separation of domains and power associated with it, it's hardly surprising that such opposing narratives will develop and proliferate. And make no mistake: The misandrist narratives created in this context were no less vicious or unfair than the misogynist narratives. Many of these traditional misandrist narratives are at the root of the issues that Men's Rights Activists are battling against - for example, the notion that men are emotionally impoverished and thus make poor parents, that men have a brutish and undiscriminating sexuality that needs to be defended against, that men are competitive and thus make poor team players if compared to the cooperative nature of women, etc. What we now have is simply a co-existence of misandrist and misogynist views that originated in the same power structure.

To sum up, Othering was prevalent throughout patriarchy's history on both sides of the two dominant categories, but the male form of Othering (including vilification, belittling, and what-have-you of the female Other) has made it into our culture and cultural understanding, while the female form was confined to oral tradition and didn't carry much cultural significance.

Taking this into account: while it's often heard (especially from Masculists) that Feminism has brought about a negative view of the masculine, I think what Feminism did was not to create these misandrist narratives, but to make them culturally visible by giving women, any women, a voice and making their view of the world part of our culture. 

I do think that both misandrist and misogynist views are utter bullshit and should disappear from the face of the earth, but I also think that blaming feminism for the existence and cultural significance of misandrist views means barking up the wrong tree. Giving 50% of the population a voice where they didn't have one before is a good thing - but it also creates some fallout as long as these Othering narratives are important and ingrained, and I think that this fallout is what the Masculist movement triggers on. This is a point where I agree with a premise of the Masculist movement - misandrist narratives are bullshit - but I don't agree with their conclusions - feminism is to blame, and we should just roll back to how things were before feminism appeared on the stage. Sorry, guys and gals, but that's just not going to cut it.

I also happen to think that nowadays, feminists tend to spend a lot of time refuting misogynist heritage, while masculists spend a lot of time refuting misandrist heritage. The point where I've got beef with the masculists is when they try to blame this misandrist heritage on feminism and fail to see the larger context: Feminism didn't create these misandrist views; a millennia-old patriarchical system did. (Though I concede that individuals flying under the banner of feminism may have enforced it).

For the most part, though, giving cultural significance to misandrist views was a side effect of giving women a voice. (To anyone who may want to counter now with: "But if women just go around spouting this kind of nonsense, then they don't deserve having a voice": Men have been going around spouting equivalent nonsense for millennia, and until very recently, nobody every disputed their legitimacy, so shut the fuck up and swallow it as the unfortunate side effects of a transitory status quo. No free lunch to be had on the road to a free and equal society.)

The point of this all is to say that Masculists are in fact on to something when they lament misandrist tendencies in some areas of public life. The point many of them seem to be missing, though, is that these misandrist tendencies today exist alongside equally old (and traditionally more powerful) misogynist tendencies, and that both these tendencies do not originate in feminism, but are a product of a much older societal system (commonly called patriarchy).

Complex 2) "But patriarchy is so widespread and has always existed, there must be some legitimacy to it!"

Also wrong. The very simple argument: Naturalistic fallacy.

Point in case: Slavery had existed for millennia (Ancient Greece anyone?), and still, the consensus in today's Western Democracies is that slavery is Wrong and inhuman and unacceptable. Human sacrifice had a long history - and still, it's considered inhuman and unacceptable and even incomprehensible in most modern-day societies. Just because something has existed for a long time doesn't mean that it's right or a moral blank cheque.

The more complicated argument: Patriarchy has not always existed, but the records of non-patriarchic societies are smudged and blurred. It's a commonplace to say that the victor writes the history - the first thing any victorious power has always done is to burn any existing libraries (if I recall correctly, this is nicely illustrated in the book "Glut. Mastering information through the ages" - which is a terribly interesting read in any case). But it also seems true in the case of patriarchy: If you look closely at the developments of myths, there are traces of non-patriarchic socities. Interestingly, they don't necessarily hint at matriarchic societies (a favourite of some Masculists, who seem unable to imagine a societal structure where there's no overarching domination of one sex/gender over another), but rather they hint at more egalitarian societies.

A point in case is the - no doubt transformed - myths of Amazon societies. Another is the myth of Lilith.

Lilith - Painting by John Collier

Lilith is a figure that appears in many myths as a female daemon, usually associated with sexual deviance, temptation, and vileness. However, some myths trace her back to a Sumerian, Babylonian, or Hebrew goddess of childbirth, children, women, and sexuality, whose transformation to a daemon can be interpreted as a societal transition to patriarchy and its need to control womens' sexuality. For example, in Hebrew mythology, Lilith is the first wife of Adam (as in Adam and Eve), who was created by God from the same earth as Adam, varyingly before, after, or at the same time as Adam. However, Adam and Lilith start bickering because Lilith refuses to submit to Adam on the grounds of being created from the same earth as and thus equal to Adam. In some versions of this myth, Lilith eventually chooses to get it on with archangel Samael and subsequently refuses to return to Paradise and Adam.
There are other myths that document the transition of female goddesses associated with liberal and self-determined femininity to daemons that embody threatening female sexuality, but I'm no scholar, so if this interests you, I suggest you go digging for yourself.
So. Point in case. While according to cultural records, patriarchy has "always been", you can find traces to the contrary if you pay close attention and take into account that records have always been modified to suit the dominant ideology.

As to the question of why patriarchy arose in the first place, I don't know - there seems to be little research investigating this. Something that seems to be consensus is that it's connected with the insight of humans into the correlation of sexual intercourse and progenity, an inheritance system (entailing something of substantial worth to be inherited, such as land, suggesting a link to humans becoming settlers), and the need to establish inheritance rights through kinship, which would have been a pretty much exclusively male issue. Establishing inheritance rights to something of worth through kinship, in an egalitarian system, may have led to the need for males to ascertain parent-child relationships, which- in the absence of genetic tests, which weren't available at the time - leads to a need to control female sexuality, which leads to a need to control female behaviour in general. And indeed, a prominent feature of patriarchies has been, and to this day still is, to control and subdue female sexuality. We still see this today in popular notions of "good girls" not initiating or desiring sex, or in tendencies such as slut shaming.

So. To summarize:

1) No more talk of "reverse sexism"
2) No more denying that there are misandrist narratives at work in our societies today
3) No more denying that there are misogynist narratives at work in our societies today
4) No more blaming feminism for the existence of these narratives
5) No more energy spent on arguing that patriarchy is "just natural" or "how things have always been, will always be, and should always be"
6) Hold your horses on generalizing or normative statements concerning female or male sexuality, because if you're tempted to make any, there's the reasonable assumption that you're blinded by your cultural background, and we're nowhere near a point where we can cleanly separate nature from nurture
7) No more judging of individuals - who inherently deserve respect all by themselves - on the grounds of traditionalist gender normatives.