dr-stav

[dr-stav]

It's me!

Alex Stavrinides, PhD, Isothermal microwave biology, currently at Liverpool John Moores University, UK.

Doing the Liverpool Santa Dash with my 2 year old daughter and 5000 more Santa suited runners. (Twitter - @AlexStavrinides)

[dr-stav]

[dr-stav]

Surviving the Ph.D Viva - some help

I was going to send this as an internal message to someone who is preparing for their PhD viva, but thought maybe it would be good to have it public - if you wish to reblog it, share or repost to other sites, feel free but please give a link back for credit.  It's the nice thing to do.

As I'm back at work, thought I would share how I preped for my viva.  If you want to skip to a Tl;Dr version, pick out the bold texts.

By this point, if a thesis is going to viva, then the leaving the lab at 3am, sitting at the home office while the sun comes up, drinking bottles of Jura whisky and chewing on the coffee cup should be over.  60-70 hour weeks should be ending and a pat on the back chat should be looming.  This is what I did and how I approached finishing my PhD.

Months ago, while scratching my head over why I was getting certain effects, wanting to spitball ideas and just have a good discussion, I put into a discussion seminar for the whole school of Biomedical and Pharmaceutical Science and invited loads of other who I thought would give me a hard time.  I asked them to be tough on me, explained in a 45 min presentation my work and braced for the firestorm.  One or two experts really gave me a hard time and questioned me with viva style questions which I had to defend.  I had spoken to a couple of them previously so they could have more informed questions lined up.  With an auditorium of eyes focused on me, but being confident in being an expert in my research field, any scientific problems, errors, alternative hypothesis, overlooked results or areas for focus were pulled out there and then.  This work made the cut into the thesis but more importantly prepared me for oral defence.

There were a couple of web links that I found useful (but so was 5 years of teaching).  From a first person perspective, keeping the viva in context of “the external is someone who wants to talk about the work I have done, not someone who is there to destroy and pick at me” helped.  I have the philosophy of “I know my shit, now let me explain it to you.”  Hence my pre viva Facebook post about “I taught shitty school kids, this fella is not going to abuse me.”  Besides, if he does, there is my supervisor in the room for inappropriate questioning, and the police at the end of a phone line if I really have to defend myself.  But I was sure my viva was going to be a little more civil than 15yr olds on detention on a Thursday evening before Christmas holidays.

Tip 1, they have read my viva - all 247 pages of core text, 65k words, >250 references and the supporting appendix.  He won't want me to go through each page and it would be boring to present.  So my PPT is a summary of why I think it is worthy of PhD status, not MPhil, MSc or BSc. 

I wasn't aware of the externals depth of knowledge before I met him, so I kept the PPT light on text.  That way I could modify my language without either having condescending or too complex language on the screen.  The text I did add was almost as check markers for points I wanted to raise. I opened with a couple of slides that would put me at ease and set out how I wanted to present the research and how I’d like to interact in the viva.  As my partner was 37 weeks pregnant and due to give birth at any time, a picture of a stork and an excuse about my phone being on loud broke the tension straight away.  I highlighted the slide which I thought was the “Queen slide” - the one graph that says "screw you" to previous dogmas or thoughts.  It was a subtle highlight – I changed the slide background colour from green leaves to a serious grey leaves – but it set the graph apart from the other key data sets I was presenting.  This is where I suspected the most dialogue would occur.  I chunked the PPT to keep it accessible throughout out, as I was expecting interruptions and wanted to be able to pick up or skip sections without requiring run up slides to make a point.

The end of the presentation was emphasising the impact my research has in academic and industrial context, and it’s versatility to challenge other ideas and possible misnomers in the research field.  I concluded the PPT but held back 6 hyperlinked slides that I thought were going to be either catch-me-out questions, FAQ’s or additional support if needed.  I hyperlinked each with simple numbers (a key jotted on the cover of my version of the thesis helped remind me) – this stopped the external asking “well, now I see it, what does that hyperlink about xxxxx mean????”

I admit that I had done a lot of other work on the run up to the viva so didn’t give it my full attention until I looked at a calendar and thought “oh shit!  It’s in 8 days!”  The week before the viva, I used a FAQ link for the “Nasty Viva” (http://pages.cpsc.ucalgary.ca/~saul/wiki/uploads/Chapter1/NastyPhDQuestions.html) – tough questions or common questions people fluff under pressure.  I kept reading it to make sure I could give concise answers then got my partner to test me the evening before.  Youtube has various examples of people defending their own viva’s but the link I found most useful was a series of videos from an external explaining what he was looking for.  Click here -> http://youtu.be/jsE1mi8Lz4o.  Grab a coffee, take a few notes and enjoy his lecture.

As expected and as agreed at the start of the viva, the external was free to interrupt or question at any point through the presentation.  He had a list of questions that he had prepared through reading the thesis.  If the questions were answered in the PPT, he could tick them off, or if they were linked or relevant, we were free to explore the answers there and then.  I had prepared maybe a 30-40 mins worth of slides, but expected some to be glossed over and some dwelled on.    This has been my research for many, many months so I can recall a lot of the justifications, exceptions and quirks, blind allays and various other developments that either were edited out of the thesis or just a side note to the core text.  This actually helped the external pick up on a lot of the subtleties that he had actually over looked in reading the thesis and appreciate why it was novel, innovative and justifiable as a PhD.  It also stimulated a lot of excitement in discussions.   The “Queen slide” was discussed in detail for a good portion of the time with a lot of white board use to explain how a mechanism had been fundamentally altered and in a fashion that was unique, novel and of imperative importance to the understanding of protein structures.  Tip 2; I would suggest ismake sure that a white board is available.  A lot of the work I do requires either complex mental modelling or doodling to explain.  The doodles won oodles.

The rest of the viva was a pleasure.  I actually got to discuss my research with someone who has a very respectable background in my knowledge area!  We had a fantastic discussion about why this thesis is important – a very nice ego boost but after having a supervisor who is less then knowledgeable in the intricacies of what I have done, it was fantastically refreshing.  To my own credit, and those who had supported me through drafting and redrafting a dyslexic thesis, he commented on the high quality of the thesis from the start and the volume of research conducted and concluded, and how it opens up research fields that were previously inaccessible.  He described it as an “extremely important and thorough text which others would build upon for years to come” and so passed it without corrections.  Had it not have been for the hard work previously, the viva could have been very different – goes to show that the bulk of the PhD is already done, the viva is just a polish (“you can’t polish a turd” comes to mind). 

If you, your supervisor and team around you are confident in your thesis and quality of your results, then the viva will be a pleasure, a good discussion and a fun experience.  If you’re shaky on your work, then prepare as best as you can but expect it to be a harder ride. 

But in context, your life will never be in as much threat as trying to keep 15 year old kids with ASBO’s in detention on a Thursday before Christmas.

Hope this helps.

[dr-stav]

Science slogan needed!

I have an abstrat and research to launch.  

Premise - Isothermal Microwave Irradiation.  

Designed, prototyped and experimented with a novel microwave reactor.  Based on a enzymatic principle, saw initial rate increase by over 200% and total product yield by 25%.  Based on microbial fermentation, growth retardation but same end product yield.

Catch; need a strap line to allure people to the seminar.  Must include microwave and biology.  

So far, not so good; 

“Microwave zapping biology, biocatalysts and bugs (but not kittens)”

“Breaking the “If you can’t nuke it, it not worth eating” mantra for microbial cuisine.”

“Microwave biology; more than just reheating coffee”

Any ideas?  I don't do sexy science.

[dr-stav]

Biofuels based X Prize

I’ve read, recorded and regurgitated enough policy documents, arguments over requirement, thoughts on policies, provocation by lobbies, NGO’s, charitable bodies and activists.  As far as I am concerned, today is still a capitalist society and money still talks.  Any benefit of any carbon system will be based on the £, $, € or Yen.   Having another policy report hitting my email inbox is very nice to tell me that there is still the need for biofuels, reduction of GHG’s  etc, but there is never an incentive or mandate to say who, how or what will get us there.   A vague smudge of “this is what’s out there…….” Is often quoted before everyone goes back to the status quo and burns some more oil and views the alternative as a pet project.

So lets move it into the money driven markets.  Very simple concept of A -> B within a certain time limit, lowest amount of KJ’s used solely from a biomass basis and at the lowest cost. 

Kilojoules used to move a set weight, per gram of GHG released, per unit distance travelled, per unit of time, per unit of feed biomass (as it were).  Sounds complicated but something a number can be pinned against to say that this one has ranked better than that one.

This would have to have a real world element and a public relationship flag point.  As fuels would be diverse, engines would be flexible but the aim and measuring factors would be the same.  Industry, universities, private companies, bedroom dreamers and shed based inventors could all have a go.  There could be  collaborations with others, partners or have a go it solo.  A carrot of financial help, someone who will give a firm commitment to exploit it (not just by lip service) and the prestige of a tangible prize.

For arguments sake it could be tasked with rounds (aerial performance with a plane, aquatic with a boat and land based with a car).  Each has to span a tangible, recognisable space (English Channel, Grand Canyon or Sahara desert) and have to carry a nominal weight (4 people for example).  Those with technologies or battery of technologies can win different prizes for engine innovation, fuel production, innovative step or tech/scientific merit.

I develop technologies in this area.  We have a Formula Student sports car group that would be up for a challenge and like every other institute, a requirement for funding.   Hitting research objectives, publishing papers, patents, presenting conferences is all well and good, but it doesn’t even register against the consumption of fossil fuels being burnt or impact on the general status quo population.

Publicity, and a clear number value for any given fuel/process that clearly shows how good a system is against an enthusiastic target would be required (particularly) for fossil fuel companies to really say “yep, your value is close to or greater than our fossil fuel value.  We can see real merit and financial incentive to follow your process.”  Talking to the blue chip wallet has much greater scope than kicking at the oil giants knees.  

The oil companies have already adopted it once for oil remediation after the Gulf of Mexico accident so they’re not scared of the concept.

 I believe an X Prize competition may give a shot at getting there.

[dr-stav]

Question for scientists; Re molecular temp.

Question for biochem/biophys scientist (or anyone with knowledge/experience).

Dielectric heating of fluids.  Is there an accepted method of determining localised temperature of a particular microscopic hot spot over the bulk temperature?  As any hot spot will incur a temperature gradient, what is the limiting distance between molecules structural centre and closest point of temperature recording?

Don't want to answer through Tumblr?  Find me through Twitter (@AlexStavrinides) or LinkedIn to message me for an email address 

[dr-stav]

Steve Jobs - a non-fans final thoughts.

I confess, I am not a Apple fan.  I never have been.  I do like their functionality and lustful bling factor, but I also dislike or at least sceptical about their image - style over substance, running costs and efficiencies, image hype over core usability and compatibility - and on a more personal note, I don't believe I fit into their users stereotype.  I'm simply not trendy enough or drink the right coffee at the right coffee shop.  Nope, I bash data, hide in labs, play with microbes and enzymes and become a social leper by being viciously vocal about others scientific inaccuracies.

As such, I have admired Steve Jobs but I have never been a worshipper at the feet of his key note speech, product launch or press release.  This has not been through any bitter resentment of not being in the cool, trendy group, more over his products haven't directly impact my life (I use a Creative mp3 player for my music, various Linux and MS based computers due to work compatibilities, I speak into my HTC/Android phone and prefer Google products over iEverything for, well, everything else).

But the impact he has had on my life has been indirect.  I have always respected, entertained and enlightened by the thoughts and writings of Douglas Adams, ever since being introduced to his books in my early teens.  Douglas had a real art of transferring some of the most entertaining synaptic pathways that have ever fired around a humanoids cranium into a digital form for printing and broadcasting, and invariably through the intermediate stage of an Apple Mac.    To most compilers of words, the tools they use maybe a foot note, a credit or side note.  Adams however had a passion for these alternative boxes to the march of 80's IBM grey and beige boxes.  And when Adems did write about them, it was from what would be now put into the stereotype of a "Fanboy."

Had it not been for Steve Jobs, would Adams have had the same passion for writing?  Would a lot of the photographers I follow through Twitter, Tumblr and Flikr have the same artistic flair and child-like furore every time they snap, edit and post their brief snap shots of life?

Steve Jobs passing won't have the major impact that this mornings post apocalyptic press releases may portray, but without Steve, my flippant and playful curiosity over the infinite probability drive may never have started in a classroom, when once told to bring a book to read in Year 8 English class.

If Steve Jobs had never built Apple 1..........

If Duglas Adams hadn't bought a Mac........

If Hitch Hikers Guide had never been written.......

If my teacher never asked me to pick a book.........

If I had never been sparked into studying science.........

.......... it would be very unlikely I would be married to beautiful wife, have such an adorable loving child, be finishing my Ph.D., and writing a note on Tumblr about Steve Jobs.  Through an interplay of many different influences, quirks of time and joyful leaps of thought, although I was never his greatest fan, Steve Jobs has had an inevitable impact in my work just like many others, Apple fans and sceptics alike.

[dr-stav]

Every atom in your body came from a star that exploded. And, the atoms in your left hand probably came from a different star than your right hand. It really is the most poetic thing I know about physics: You are all stardust. You couldn’t be here if stars hadn’t exploded, because the elements - the carbon, nitrogen, oxygen, iron, all the things that matter for evolution and for life - weren’t created at the beginning of time. They were created in the nuclear furnaces of stars, and the only way for them to get into your body is if those stars were kind enough to explode. So, forget Jesus. The stars died so that you could be here today.

Lawrence Krauss (via screwinginmoderation)

[dr-stav]

How much God appreciates you.

Just a thought.

Assuming a God (pick a god of your choice) is going to dedicate some time to thinking solely about you, your problems, hope and fears.  How much thought would they give you??  Time wise??

Annual thought allocation could be thought of a second per person per year - assuming this is a God who only protects human and isn't interested in any other of his creations to distract his mind.  Therefore, 365 days per year x 24 hrs x 60 minutes x 60 seconds gives 31,536,000 per year (we wont argue over part days or leap years).

Divide our 31 million seconds by the approximately 6 billion inhabitants (apparently all humans are Gods creation, therefore he will even think of us athiests too) would give a personal time allocation of 0.005256 seconds per person per year (assuming the use of the short scale billion).  With the average life expectancy of around 80 years, this would equate to 0.42048 seconds over an average life span.

As an 80 year life expectancy would tally 2.5billion seconds, this would represent 1.9x10-9% of an average life (or 0.0000000019%).

With inequality in the world (bad bad people like dictators, v's the quiet, well behaved, v's those whom are in need) I'm sure that the distribution of God's concentration would resemble a normal distribution curve, therefore it is more likely that there are inhabitants of this world that would be taking a lions share of his concentration - your time allocation.

So take comfort, the God that so many theists are subservient to would only be interested in you for half a second, but there are people around you that would much prefer to give you their time.  Likewise, I would prefer to give much more of my time to my family, friends, research and those around me.

Just a thought.

Edit;  To put this into perspective, a 0.4 second time frame would be 9.7e-19% of the age of the Universe at this current time point. (0.0000000000000000097% to those whom dislike exponentials)   

[dr-stav]

"The Second Law of Thermodynamics has been sentenced to 26 months for inciting disorder. #Riots" "However, Tom Watson believes the 2nd Law of Thermodynamics was covering for the Zeroth Law, and promises to expose the conspiracy. #HackGate" "The Third Law of Thermodynamics gave almost no response to the allegations against its colleagues." "The First Law of Thermodynamics has resigned, but in line with the principle of conservation of position is still on the books."

http://twitter.com/#!/mtpt

[dr-stav]

It's been a while.

After some mental time in experimental crisis, the end is getting to be in sight, although it's coming at me all too fast!  Ph.D is nearly in the bag.  But more realistically, it's currently across 6 Word Documents, 15 Excel spreadsheets, over a hundred HPLC logs and a data base of thermal and microwave profiles.

Allotting time for sleep around the experiments appears to be more of an issue than the experiments themselves.  Take any given 24 hour period, remover, say 2 hours for commuting and replenishing milk and coffee at the shop, remove 16 hours for the experimental data tracking and sampling, and suddenly life is squeezed into a 4 hour period.  Minus time for breakfast and maybe a shower, and suddenly it become apparent why the ashen look appears on my face.   Once up and running, the practical work is repetitive, but all consuming.  Usually, a day or two later with an excel spreadsheet, several data analysis cpackages and a coffee later, I'm usually slightly enlightened on what went on.  Not always, but sometimes.  the theories that spread from the data could be world changing, but as any conservative scientist will say, the data has to speak and not the assumption built on the data.

Note;  If anyone from Berkeley Uni, the NREL or Jaguar supercomputer group wish to have a Skype call, please let me know.  Thanks.

Did I mention I'm nearly 30?  After the work I've packed into the past 8 years (career changes, outdoors work, teaching, research, setting up a business and alike), I have had the good grace of (without sounding egotistical, vain or worse, narcissistic) maintain a few shreds of youthful looks.  A healthy life style, diet and plenty of enjoyment has aided this.  With talking to a couple of sales reps and speaking about my experiences, the rep suggested that I had already achieved a lot in a short time.  Remarking that I was looking forward to my holiday and my 30th birthday, she responded with "really? I thought you were much younger!"

1)  Thank you.  After looking at a lot of my peers (and a lot of people younger than me) it is nice to see that the years haven't caught up with me.  I haven't been aged by smoking, excess boozing, high fat diets or drying out under sun beds and Club 18-30 holidays.

2)  Does that comment diminish my accomplishments? Actually being older dilutes the number of achievements per year.  should I be doing something to increase my concentration of achievements per year??    

Anyway, as the HPLC pump keeps pumping, and the data keeps transferring, Blogging should be lower on the priorities.  With an exciting prospect landing on my doorstep in October, all is to play for. Now where is the Excel function for..............  

[dr-stav]

As it's the Grand Depart tomorrow, thought I would re-blogg and share.    Thanks to the original blogger and source.

velodelphia:

All you need to know about the Tour de France (July 2 - July 24 2011)

[dr-stav]

Sample, rinse, repeat.

An afternoon of repeated sampling with 10 min repetitions so a brief opportunity to blogg.  Frequently think that with the time I spend hunched over reactors and analysis kit, that maybe my office chain just requires a note "I'm not here.  I'm doing science."

Recent work has taken me into the some of the greatest depths of polysaccharide digestion sciences, where to fully explain what's going on, a super computer is handy.  Mention a single aspect, numerous avenues open up and the scope for investigation become staggering, often with some very unique opinions, theories or ideas.

As for the details and what I want to discuss, well that has to wait.  With a patent on the way and several journal reports pending, all will cascade shortly.

[dr-stav]

Viral plugs, hacking and "is it me?"

Just a note about the recent Tumblr hacks and security issues.   I am a geek, a cyclist, a kayaker and have interests in various things (photography, whisky, travel, computing, design work to name but a few) and as such, I will never use this blog to post in appropriate images, use it for lewd comments or put anything behind any kind of password protected paywall/firewall/privacy wall.  If anything of that nature does appear, it's not me!  

With the current scams going around, if anything untoward does appear, please send me a message (email, Tumblr note, Tweet or Facebook) and I'll strive to rectify.

Thanks. 

[dr-stav]

"In the case of Vino, doping didn't transform him from packhorse into thoroughbred. He had the potential to be a thoroughbred from the moment he was squirted out of his mother's Soviet womb..."

Just the thought of there being an almighty Communist Mother womb.  From a cycling forum, re; Vinokourov

[dr-stav]

This is something with a bit of history.   I picked up this frame from my parents house a few weeks ago.  It's a used 1971 Claude Butler Gran Sport.  Tons of charactor and begging for a new lease of life.   From what I've heard, my Uncle collected this as a disregarded bike from someones back yard in the middlands in the '70's.  Done up with the intention of touring, it was too small for him, so passed onto my mum.  With my parents and my uncle touring the fjords of Norway the cycling was split between this bike and the 1936 Grub tandem we also have in the family.

Over the years, the bike has been neglected and pillaged for parts, many of which still sit in a box somewhere in the attic/garage of my parents.  To do a complete authentic rebuild would absorb a lot of my free time (something I'm vastly lacking at the moment) but with a head badge featuring the 1948 Olympics (CB bikes used) it would be fantastic to get her spinning again. For the original spec, have a look at this link: http://homepage.ntlworld.com/nkilgariff/CBcats/Cat_71/p3_GranSport.jpg

http://homepage.ntlworld.com/nkilgariff/CBcats/Cat_71/p4_GranSport.jpg 

[dr-stav]

turning-world:

Details of Coppi’s Bianchi, in the Bianchi factory

In honour of the Rapha Cycle Club’s exhibition on Fausto Coppi, which comes down tomorrow, at the end of this fantastic Giro, here are a few pictures of one of Coppi’s bikes.

It’s on display in totally original condition and has acquired an amazing patina after years of use and as the materials gradually perish.