The end draws near – the PhD viva

Submitted PhD thesis

Submitted PhD thesis

A few months ago, I submitted my PhD thesis. After all of the preparation and writing, submitting was somewhat of an anti-climax. This is because submitting those nicely bound volumes means nothing unless someone is going to read and examine them to determine if the work they contain will earn you the degree and the right to call yourself Dr.

In the UK, these examinations often happen some time after submitting, in a process known as the viva. These exams involve the examiners coming to the university/institute and conducting a private, face-to-face examination of your knowledge and the work presented in the thesis, often over a number of hours.

All this is purely explanation of the main point:

I had my PhD viva on Monday and I passed!

I passed with the most common outcome; minor corrections. This means that whilst I have passed, the examiners would like some changes to be made before the final version of record is submitted. It is only when they are happy with those changes that I will officially earn the degree.

For now, I’m beginning to come down from the celebrations and start working towards the corrections. So it is still not yet the end; I think the real closure will happen when the award letter and certificates are in my hands.

3 years and 9 months

Submitted PhD thesis

Submitted PhD thesis

Yesterday, I submitted my PhD thesis! The culmination, to the day, of 3 years, 9 months of work, distilled into 145 pages. It means that I can now return to “normality”, having become somewhat of a hermit over the last month whilst I pulled out all the stops to get it completed.

It’s a great relief, and I hope I don’t need to write a document that long again for a while. It’s also not over yet though. For those who don’t live in the academic bubble, I just thought I’d explain what this means, and after what point I’ll officially “get” the degree.

What happens next?

Currently, the university is looking after my two submitted copies, until two people (one within UCL and one from outside) can be found to conduct an examination. They will then read the thesis and after that, the 3 of us will sit down in a room and they’ll question me on it – this is the oral exam or ‘viva’.

The outcome of this meeting will decide whether or not I am awarded a PhD. The most common outcome is “minor corrections”, where the examiners will award the PhD on the condition that various mistakes are corrected or additional information added before the final version of record is produced. This is version that will end up in the library at UCL. Once the examiners have approved those corrections; then I’ll be Dr James. So it’s not over yet, but the end is in sight ūüôā

Katherine Esau – Ada Lovelace Day 2013

This is the first year that I’ve participated in¬†Ada Lovelace Day, and I decided to pick a woman from history, related to my own field and who I’d not heard of previously, so that I’d have to do some research. I came across the plant anatomist and later electron microscopist, Katherine Esau.

Katherine Esau

Katherine Esau working at the electron microscope - Copyright Cheadle Center for Biodiversity and Ecological Restoration

Katherine Esau working at the electron microscope – Copyright Cheadle Center for Biodiversity and Ecological Restoration

Katherine Esau was born in the city Yekaterinoslav, in the then Russian Empire (now Dnipropetrovsk, Ukraine) in 1898. It was in Russia that she received her early education, until 1917, when the Russian revolution and later German occupation of Ukraine prevented her from completing her studies at the Golitsin Women’s Agricultural College, Moscow.

Esau and her family fled to Germany, moving to Berlin. Here, she was able to continue her studies by enrolling at the Berlin Landwirtschaftliche Hochschule (Agricultural College), completing them in 1922.

Later in 1922, the Esau family moved again, this time to California, USA. It is here that Esau made home for the rest of her life. After some short term jobs, her research career began in earnest with a job at Spreckels Sugar Company. Her project was to develop a sugar beet resistant to curly top disease, a virus carried by beet leafhoppers. This research led to her gaining a position doing similar research as a graduate student at UC Davis in 1927.

Unfortunately (or perhaps fortunately, given Esau’s later success), this project turned out not to be viable at UC Davis, and Esau’s attention was turned to plant anatomy and the effect of the curly top virus on the plant. For this research she was awarded a PhD in 1931.

Esau stayed within the University of California for the rest of her career, first at Davis and later at Santa Barbara, and continued researching the same themes; plant anatomy and virus-plant interactions. In particular, Esau studied the phloem, the tissue that distributes nutrients throughout plants and how viruses such as curly top use this to spread, as well as studying healthy plant anatomy.

My interest in Esau comes from her later work, setting up an electron microscopy laboratory and using this technique to study virus-diseased plants. These are techniques not a million miles away from those I use to look at cells today. Much of this work was carried out after Esau retired, as despite retiring in 1965, she continued to work for many more years, including supervising PhD students.

In addition to her research and teaching, Esau also wrote and illustrated two key textbooks in plant anatomy; “Esau’s Plant Anatomy” and “Anatomy of Seed Plants”, both of which continue to be on university reading lists today, amongst many other books and publications.

During her career, Esau picked up many awards for her work, including the National Medal of Science in 1989, Certificate of Merit from the Botanical Society of America in 1956, and election to the National Academy of Sciences in 1957. She became only the sixth woman to be elected to the Academy. She was also president of the Botanical Society of America and now gives her name to one of their awards, the Katherine Esau Award,¬†given to “the graduate student who presents the outstanding paper in developmental and structural botany” at their annual meeting. UC Davis also runs a post-doctoral fellowship in her name.

As part of her autobiography and oral history in 1991, David Russell asked her about women in science and her experience:

When I first arrived in the United States, many people expected me to do just ordinary things, housework and getting married and so forth‚ÄĒthe same routine. But I was more ambitious.

and

I never worried about being a woman. It never occurred to me that that was an important thing. I always thought that women could do just as well as men. Of course, the majority of women are not trained to think that way. They are trained to be homemakers. And I was not a homemaker.

However, on promotion and her former boss, Esau says;

I now learn from people that he actually did not like to have a woman in the department. He did not treat me right, but I didn‚Äėt notice it. I thought that was the way it was done. I never even questioned it. For example, he was very reluctant to give promotions. Nowadays they often jump one step, and people just go right through the appointments very quickly. But at that¬†time, we went six years in each grade. Six years. It never changed. But then when a new director arrived on the campus, he looked at my record and said that I was not getting enough salary. So he raised my salary, but our chairman, Dr. Robbins, would not do it.

And thus demonstrating, in her own words, why we need initiatives such as Ada Lovelace Day and Athena SWAN.

References and further reading

Biographical Memoir from the National Academy of Science
Autobiography and oral history from UC Santa Barbara
Katherine Esau digital archive from Cheadle Center for Biodiversity and Ecological Restoration
Katherine Esau on Wikipedia (this article could do with some love!)

About Ada Lovelace Day

Ada Lovelace¬†(1815-1852) is known as the world’s first computer programmer for her work with Charles Babbage on his Analytical Engine. She gives her name to a Ada Lovelace Day, in mid-October each year where we “celebrate¬†the achievements of women in science, technology, engineering and maths” (STEM). The day is generally marked by people creating and sharing blogposts, videos and other material about an inspiring woman in STEM.

Electronic Lab Notebooks

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Every time I have to write a report, prepare a presentation or meet with my boss, I curse the fact that I can’t just “Ô£Ņ+F” through my lab book and find those conditions/results/images that I’m looking for.

Of course, with an electronic lab (note)book (ELN), that would be perfectly possible. I see that there are plenty of options; purpose-built or general, local or web/cloud, free or commercial.

At the moment, I’m contemplating a locally hosted WordPress blog, because it is what I know already and it’s easy to set up, but I’m totally open to other solutions. All I know is that I’d like it to be both local and free.

Does anyone have any experience with using Electronic Lab Notebooks and have any advice or preference? I’m all ears.

Also, how about image tagging, like iPhoto or Lightroom but for micrographs? I can’t count how many times I’ve looked for “the kinda round one” or “the one with the weird speckles”…

Joining professional societies

As a PhD student in the life sciences, there are plenty of professional/scientific societies vying for me to join them. These range from the very general, covering all science such as the AAAS, through the general biology (Society of Biology) down to specific fields (Biochemical Society) or techniques (Royal Microscopical Society). Most seem to come with a student rate, subscription to the society’s journal and some obscure postnomial letters. Perhaps most importantly, becoming a member often entitles you to apply for travel funding, as hapsci¬†pointed out.

On the other hand, joining a society requires outlay of some (normally small for student) membership fee, pestering your PI to sign a form stating you are student of a relevant discipline and for the travel grants, anticipating when you want to travel as some societies require you to have been a member for some time prior to asking them for money.

So I’m putting it out there; is it worth joining these societies as student, and if so, how many?

Is using an academic title automatically an ‘argument from authority’?

We are bombarded with ‘expert opinions’ every day in the media, both printed and broadcast, and many of these people are presented to us with their title: Prof, Dr, PhD, FRS and the like. An example might be this recent story on sleep deprivation and stroke from the Guardian, which is followed throughout.

My questions are: does including their “rank” in the scientific hierarchy automatically say to the audience “you should believe this person for they are more qualified than you“, is this committing an ‘argument from authority‘ and does this even matter at all?

The first question translates basically to whether or not an academic’s title is optional. On the one hand, they’ve earned the degree/accolade by working pretty damn hard and deserve to be called by it. In 3 years time, when (hopefully) I finish my PhD, I’ll be pretty cheesed off if ‘Dr’ doesn’t get written down in the right places. On the other hand, within science (certainly biology/biochemistry), people don’t much use their titles. At the institute where I work, titles are basically relegated to the telephone directory and a handful of email signatures. They certainly don’t appear on published papers, so why in the press release and press coverage. (As an aside, this is different in the medical world such as the BMJ, The Lancet and NEJM, where author qualifications are published). If they aren’t on the paper itself, I think that says to me that they aren’t needed in the press coverage, but I’ll admit that it’s an open question.

Does the inclusion of these titles confer authority on to whatever quote their holder is giving? I think they probably do. This might not be the intention in science reporting but it has that effect. Why else would people be so keen to use the title Dr, if not to be accepted as an expert in a field?

A better question is whether worrying about presenting a well-qualified expert as an authority figure actually matters? As noble as the Royal Society’s motto might be (nullius in verba – On the word of no-one), equally nobody has time to fact check everything, and qualifications and titles are often a pretty good heuristic for reliability. As Paul Nurse (or perhaps “the Nobel laureate Sir Paul Nurse PRS) recently put to James Delingpole (3m30s), when you go to a doctor, you trust their clinical judgment. You might do your own research and disagree with the consensual position, but that would be a very unusual position to take.

The problem – as there is with all such rules of thumb – is that it is open for exploitation. I alluded earlier to those who ‘pass off’ having more qualifications than they have, often in order to lend their opinion legitimacy, often for monetary gain in the form an endorsement by an expert. Weirdly, this means that every time a title such as Dr is used legitimately, it adds weight to all those using the same title illegitimately.¬†A reverse problem can also occur – someone with a legitimate qualification, in a relevant field presents a maverick view rather than scientific consensus and can be spectacularly wrong, but still taken “on authority”. Think Andrew Wakefield and the disproven MMR/Autism link for an example.

On balance, I’m not sure that there is a right answer to the use of academic titles. To me they are a mark of respect and achievement, not authority and certainly don’t mean that everything the holder says is true and sacrosanct, but I’m not sure that is always how they are taken.

“James Streetley BSc (Hons) MRes

Science is Vital

Supporters at the rally

Supporters at the rally

Yesterday, I attended (and helped marshall, as evidenced here) the rally for an important campaign called Science is Vital. It is a campaign against any proposed cuts to the science budget, when the spending review is published later in the month. I urge anybody who hasn’t already done so to: check out their website which details all the reasons why continued investment in science is a necessity, sign their petition and write to their MP about the campaign.¬†It was a fantastic afternoon and great to meet up with so many people that I’ve heard about or briefly tweeted @ them but never spoken; even if it was under unfortunate circumstances with the prospect of cuts hanging over all our heads.

This campaign is more than just a self-interested group getting antsy about a policy they don’t like. Yes, many of the people who have signed the petition are scientists who are understandably worried about their own careers. I am also worried about what the state of biomedical science will be when I start looking for my first position after finishing my PhD in 3 years time.

This is about more than that though. We are saying

We already don’t have enough money to do all the research we need, with only around 20% of grant proposals finding funding, and yet we greatly ‘punch above our weight’, in almost any metric you pick; number of World-class universities, citations per researcher, papers produced against spend. We can’t get more efficient. We are already at the limit.

And it isn’t the scientists that will be the biggest losers in this. They can move to other world-leading institutions in the US, Japan, India, Australia, Germany and others. It is society that loses out, as we have to become reliant on the work of other countries to fulfil our scientific, technological and engineering needs.

The Campaign for Science and Engineering has plenty more on the economic reasons why science funding is a poor judgment, so if you like facts and figures, head here. The Science is Vital campaign has also collated photos and other reports from the event and the Pod Delusion has podcasts of all the speakers and some reporting from the rally. The rest of my own photos from the event can be found in this Flickr set.

Regulation of Old Wives’ tales-type medicine?

Handing out diplomas

This morning, Voice of Young Science stood outside the Department of Health on Whitehall, assessing passers-by and awarding them diplomas in “Traditional Medicine of Old Wives’ Tales”.

The reason for this is a little bit protracted, but bear with me and I’ll explain why they were doing it, and why it is important to take notice.¬†The story started over a year ago when the Department of Health published this document, a consultation on the statutory regulation of a number of Traditional Medicine Systems. This seems to have sent alarm-bells ringing for a number of people, for a number of reasons:

  • the proposed registration scheme doesn’t require a practitioner to have any training
  • the scheme doesn’t require evidence of efficacy (that the treatments work), merely that they are traditional
  • registration from a Government body such as the Department of Health or a subsidiary implies endorsement and legitimises these treatments.

These concerns are found in the Sense about Science submission to the consultation (from October 2009) and in the flyer for today’s event.

It is the first point which VOYS have taken the most issue with: lack of training and the implication that “[traditional]¬†practitioners have the knowledge, skills and attributes of qualified medical practitioners”. This leads on to today’s exploits, which aim to show just how little knowledge is required to proclaim Old Wives’ Tales-type traditional medicine – so little knowledge, that even I got a Diploma:

My traditional medicine Diploma

I’m not entirely sure what the significance of today is, as other than the original consultation, I haven’t been able to find any more on the matter from the Department of Health, not even a response to the consultation. There has also been a little bit of criticism over the choice of “Old Wives'” as the type of traditional medicine portrayed here, as ageist, sexist and failing to take account of historical context, when conventional medicine wasn’t exactly evidence-based. I also think that the way today’s event was done, it looked more about the ease of obtaining a qualification rather than about regulation in traditional medicine.

However, none of these snaggles should stop us from being seriously worried at the point made today though. Regulation and accreditation of alternative medicine only serves to legitimise this sort of pseudoscience and helps it to gain another foothold in society, similar to the platform that traditional medicine courses in universities has provided. We must make every effort to ensure that money isn’t wasted on regulations that could ultimately hinder medical care.

Preaching to the choir

Last night, I attended my first British Library Talk Science event: “Science in UK Government: Where’s the Evidence?”, and made it to the second half of the night’s Westminster Skeptics. A bumper night for science, evidence and critical thinking, one might think.

Actually, I think we have a bit of a problem. Of the many people tweeting at the BLTS event (#blts) I recognised many of the names and Twitter handles. I could even put a few to actual faces. Going across town to Westminster Skeptics, I met up with many of the regulars for the Q&A session and a chat afterwards, some of whom have become friends over the last 7 months of my attending and interacting on Twitter, others I could just place either faces or Twitter handles again. And as Jack of Kent pointed out, the Simon Perry, our speaker last night, is not someone who has made his name elsewhere and become a skeptic, but rather made a name as a skeptic.

The long-winded point I am attempting to make is; has skepticism become an echo chamber, where we all know each other and agree with one another? Rather than wandering around the country, talking to each other in pubs, should we be focusing more effort in starting dialogue with others outside of the skeptic fold. In no way am I insinuating that the Skeptics in the Pub movement is a bad thing; it is fun, social and motivates skeptics, but I’m not sure of its value in publicising the skeptic values and position.

We’ve had a warning about this before, as Evan Harris found out to his (and our) dismay. If you had looked on Twitter around the first week of May, I think you would have thought Evan was a dead cert to hold his Oxford West and Abingdon seat. As a community, we were making so much noise at each other that to us, Evan appeared more popular than he turned out to be. This was something he remarked upon last night as “observer bias”; when you are both observing and involved in something, your perception is distorted.

I also think this fits in with JoK’s recent post “The Image of Skepticism“. Coming across as one insular group can also hurt our credentials. The development of skepticism into a close-knit group with its own in-jokes (homeopathy-dilution jokes, skeptic Top Trumps) can make us look like “the nasty party”. We also run the danger of having the possibility to develop a “herd mentality”, where individuals don’t appraise the evidence, but take it as a given because other skeptics (or those in authority) have already adopted a viewpoint.

I’m not sure what the answers to these points or questions are, but I do think that recognition of some of these problems in the growing skeptic community is important. Do other people feel the same way? Or am I off by a country mile here?

Night at the museum

Once a month, on the last Wednesday, the Science Museum opens its doors at night for adults only until about 10pm. Not only are the general exhibits open, but there are also special events and a recurring silent disco (in between the space exhibits!) and a pub quiz. Another notable additions include a number of bars and DJs being set up in exhibition spaces which adds to the relaxed atmosphere. Each month also has a theme and last night’s was “Genius”.

This was my second Science Museum Lates and the first one I’ve brought my camera along to, so here are a few photos documenting what we got up to last night:

Adult table football (Sadly I don't have any pictures of us)

Firstly we played this somewhat hilarious game of 5-a-side “table football” where we were all attached to sliders along scaffolding tubes for 5 minutes. Not entirely sure how this relates to genius; I guess through the tenuous link of “footballing genius” to remind us that a genius doesn’t have to be about academic intellect, but it was fun none the less. We lost 6-2!

Fun with the bubblewall

More bubble wall fun

Then it was off to play like children in the LaunchPad, as you can see we were particularly fascinated by the bubble wall thing! Before going to see a demonstration of Newton’s laws, as they related to rockets!

Newton's 3rd law in action via a human rocket.

Culminating in a hydrogen balloon explosion. ūüėÄ

After all that LaunchPad fun it was off to test our brains in a massive genius-themed pub quiz (complete with colouring competition!). We didn’t win either I’m sad to report – despite a valiant colouring attempt mounted by 2 of our teammates followed by a brief look around the plastics and the Islam exhibition rooms.

A few more of my photos are in this Flickr set and photos from myself and other participants across the other Lates nights are all in the Flickr group ‘Science Museum Lates’.

My only complaint (if you can call it that…) is that with so much going on, there is so little time to look at the exhibits! Maybe it should be another hour longer! Otherwise this is a great idea and definitely gets people into the museum who wouldn’t otherwise have gone, hopefully teaching a bit of informal science too and being a great fun night out.

The next one is 30th June – theme TBC I think. See you there!