I’m channel hopping but it seems to me there’s nothing that I want to watch. I feel like stopping but it’s easier to just sit and drop off.

“Did you know that if you focus really intently on something that takes as much energy as running across North America?”

Last week I helped out on my division’s stand for Science Week. The University of Manchester held a Science Fair for local schools to take part in some simple experiments and find out some new things about “science.” Our stand had a few games including a “Pin the Hormone on the Organ,” and tests to diagnose dogs with diabetes. I’ll just leave that there, I don’t think you need any more information right?..

So, whilst giving our little spiel the question (well statement? I mean I guess it’s a question as it starts with “did you know” but it doesn’t really seem to be asking anything worth while. Is it a rhetorical question? This is why I chose science, English is hard!) above was asked (stated? Goddamn not this again!). My colleague, a practicing clinician, experienced researcher and Head of the Division of Diabetes, Endocrinology and Gastroenterology, nodded politely and said “no I hadn’t heard that.”

Staring at something intently? Like maybe a screen? Is this some nonsense thought up to encourage kids to watch TV or play video games? Well I wasn’t one to let this chubby 10-year old get away with it… Thanks to DiabetesPro literally the day before I saw this little story, “Screen time linked to increased diabetes risk in children.” So, I could shoot down that child with facts!

Obviously, I didn’t as I’m not (that much of) a jerk. But I still think it made interesting reading, and as I don’t have any kids I am in the perfect place to tell people how to raise their children. 1 hour of TV a day folks!

Children who spend 3 hours a day watching TV have increased fat mass, skin folds and insulin resistance. So basically 9-10-year olds are getting pre-diabetic. Even when taking into account factors like physically activity, gender, adiposity (fatness) and socio-economical markers, there is still more insulin resistance in the kids who watch more TV.

It’s likely that the large amount of TV isn’t solely to blame, but the habits which arise from it. Children who consistently watch TV, particularly eating meals in front of the TV, snack more whilst watching TV. Moreover, this policy statement from the American Academy of Pediatrics suggested that children spend 8 hours a day engaging in some sort of media, and teenager more than 11. This included phones, computers and everything else, whilst admitting that a lot of this may overlap and therefore be exaggerated. But still they recommended limiting children’s screen exposure to less than 2 hours a day.

At the moment, it’s all correlative, so could be nonsense until more comprehensive studies are carried out, but stopping your kids snacking whilst watching TV 3 hours a day is probably a good idea.

 

Today’s quote is by Blakfish

I have to keep going, as there are always people on my track. I have to publish my present work as rapidly as possible in order to keep in the race

The other day I received an email from EMBO Molecular Medicine informing me that they have received a manuscript with me as an author. This paper is one I’ve snuck on from my work in San Diego. So, a few days later, when I saw a talk from an EMBO chief editor I thought that’d be too good to pass up. It was titled ‘Transparent Publishing & Open Science: how to share reproducible data’ but the part I was most interested in is the editorial process.

If you’ve never had the joy(?..) of submitting a paper, here’s how it is supposed to go.

  1. Discover something.
  2. Write a manuscript explaining what you’ve discovered.
  3. Edit the manuscript in-house, with all authors contributing to a final draft. (The authors are basically anyone who has contributed to the work in the manuscript, with the first author being the person who has contributed the most. Other authors are listed to the amount of contribution they have made, with the supervisor/senior member is usually the last author. For example, the paper “Why won’t Arsenal spend any money on players?” would be authored by Wenger, A., Usmanov, A., Moshiri, F and Kroenke S.)
  4. Submit to a journal.
  5. An editor at the journal assesses the merits of the manuscript and if it’s good enough, they then send the manuscript to 2 or 3 referees (also called reviewers).
  6. These referees critique your work, comparing it to previously published work, checking your conclusions are valid and providing feedback and improvements to the paper.
  7. Based on the referees’ comments the editor decided to; accept your manuscript as it is, tentatively accept it on the basis that you make a few changes, suggest a whole bunch of changes and reserve the right to reject it later, or outright reject it.

Here’s how it really goes.

  1. Set out to change the world.
  2. Spend far too long trying to discover something huge.
  3. Get towards the end of your contract and panic about what to publish.
  4. Work long, stressful hours. *
  5. Focus on getting the necessary results to finish your paper.
  6. Scrabble together a manuscript full of hyperbole.
  7. Have said manuscript demolished by your supervisor. *
  8. Re-write manuscript.
  9. Repeat 6 and 7
  10. Have manuscript destroyed by co-authors. *
  11. Repeat 6 and 9
  12. Argue about positioning of authors.
  13. Include any and all collaborators to keep them happy.
  14. Include idiots who may have attempted to contribute at some point.
  15. Ensure all authors have the chance to look through the manuscript, but ignore any changes they suggest.
  16. Submit to a high impact journal.
  17. Get rejected. *
  18. Submit to a journal with a lower impact
  19. Get rejected.
  20. Repeat 17 as necessary, until your manuscript is sent to reviewers.
  21. Get rejected. *
  22. Back to 17.
  23. Receive corrections from referees, outlining complicated experiments which take a lot of money and time to carry out. Most of these will be unnecessary additional experiments. *
  24. Attempt corrections, update manuscript and resubmit.
  25. Get rejected. *
  26. Re-write paper fully to include corrections, and make it seem like these were always part of the plan and not hurriedly added on after referees’ comments.
  27. Submit to terrible journal with a low impact.
  28. Receive corrections from referees, and get manuscript tentatively accepted.
  29. Carry out additional experiments, and make changes to the manuscript.
  30. Eventually get accepted. *
  31. Pay huge fees to publish your work.

* If necessary “cry” can be inserted here.

Also this process may well take longer than I have suggested here. I’ve not gone into how awful referees or editors can be. (Although I’ve talked about referees before.)

However, that’s not what the EMBO journals are all about. They have a high rejection rate at first, which means that they can put a lot of effort into the papers which they do like. The first questions they ask are “Is it publishable?” and “what is the minimum changes to make it publishable?”

Afterwards, they carry out “cross referee commenting”, which means that the referees can see what other reviewers have written. They can comment on each other’s comments, and communicate with each other. This means that the reviewers have a dialogue with each other and can give you more constructive feedback.

Furthermore, they keep track of the comments, and these can be accessed after a paper has been published. Officially this is great as it means you can get up to 4 expert reviews on each paper. Not only is this good because of the expertness, but because you get an insight into the what referees look at, and the types of comments successful manuscripts get. This is crucial to early-career scientists as they are unlikely to see many of them up close and personal. It encourages you to take a more attentive look at your own work to see if you can pass muster.

And unofficially it’s great because it means referee’s are held accountable for any mean things they say. You probably won’t call someone a “dick weasel” if it’s going to be stuck on the internet forever.

Also, they encourage an open dialogue between reviewers and the researchers. This even comes down to allowing the authors to respond to referees’ comments and defend their paper, before an editor makes their decision.

Ah, the paper’s been rejected… erm ignore all of that nice stuff I wrote above

Today’s quote is from Ernest Rutherford.

I think part of being a parent is trying to kill your kids

So, I’ve covered a couple of things before about obesity; specifically watching Dr Giles Yeo and leptin. If you don’t know type 2 diabetes is kinda my jam, and obviously obesity can play a big role in causing type 2 diabetes. So obviously I was interested in this article stating that a modern lifestyle is to blame for making y’all chubby.

I’ve covered before (in those links above) that your genes play a massive role in if you put on weight. But Dr Yeo compared them to poker. “You can win with a bad hand, and you can definitely lose with a good hand.” And this study seems to show that especially.

Basically the incidence of the mutated genes isn’t increasing. So why are we getting fatter?

Walter and folks looked at the genes of almost 9000 patients born between 1900 and 1958. They compared 29 mutations, which have been linked to obesity, to generate a Genetic Risk Score (GRS) combining all changes. I won’t go into too much info, as it uses very complicated maths. Basically mutations can take away or add to the risk of obesity, so the GRS is a sum of the positive and negative influences. Get it?

The first cohort of subjects were the oldest, so basically people born before we began feasting for every meal. Interestingly, here was no significant connection between the GRS and the BMI of people. Even though the incidence of mutations and the value of the GRS was the same as for people born later, for some reason people didn’t get fat. As you work your way through the cohorts, looking at people born later, the association increases. This means that the GRS starts to mean more as you get younger patients. Also, the older people got the more likely they were to be obese, potentially due to the increased availability of high-calorie foods, and the sedentary lifestyle old folks tend to have.

This suggests that the modern environment plays a bigger role in whether or not you develop obesity.  So, what’s the happy haps?

The authors suggest a few things. The average calorie intake in the States has increased by a whopping 22% (in woman; only 7% in men – still bad though). Sugar-sweetened drinks increase the risk hugely, and consumption of these bad boys has increased rapidly. I’ve just watched a live cast from Physiology 2016, where Prof John Blundell showed that when given a choice people choose energetically dense food.And now we live in a time when folks can access calorific food simply, and cheaply. Another reason may be because we’ve gotten lazy. Although Prof Blundell mentioned that even exercise cannot undo a high calorie diet. Demereth et al carried out a similar study, but had a more complicated explanation; epigenetics!

I have talked about epigenetics before, but probably in real life rather than here as it’s a bit of a head scratcher. Simply put your DNA contains all the data needed to make you. However, to stop DNA from just being accessed all of the time you need something to control it. This can involve modifying the DNA directly, usually by sticking something onto it. This can increase or decrease the rate of which genes are transcribed (i.e. made) (kind of…). Crucially epigenetics don’t actually change the DNA, just the way it is read. And obesity can cause quite a few epigenetic changes. This means that the expression of the proteins involved in obesity and other nasty things can be changed, simply by becoming obese. It’s like an ironic* perpetual motion machine.

Think of your DNA like a fancy library, like one with a museum. All of the day-to-day books for children and idiots are accessible all the time. But those old, fragile books are kept under lock and key, and can only be used in a controlled environment. Now the easiest way to get access to the books is to bribe the librarian with a pile of greasy donuts. Most of the time anyway; perhaps sometimes the librarian shuns your treats and tells you to do one.

Now imagine your big fat grandad has gone around opening and locking doors and eaten the keys. That’s right, epigenetic changes can pass from one generation to the next. Someone at ENDO 2015 said it can pass over two generations, but I can’t remember who, so let’s just let that hang there…

(Since I originally wrote this piece, this came out. The study shows that incidence of Type 2 Diabetes is increasing, and that the percentage of younger people getting the disease is increasing. If you don’t know, obesity and Type 2 Diabetes usually go hand in hand.)

*American ironic. Not proper ironic

 

Today’s quote is from Stephen King.

The Build

Bluedot is over, and our project was a success! We spent a very tiring weekend explaining to everyone how astronauts exercise, whilst blowing up balloons, giving out stickers and setting off bottle rockets. A few people did ask how we managed to build it all, so I figured I’d write a little something about our apparatus here.

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So, after The Physiological Society approved my outreach grant I went on a spending spree. I purchased bike pumps, lengths of tubing, balloons, brackets, screws and nipped to the local B&Q. I’m a bit in love with the wood cutting machinery at B&Q. It’s is basically a big circular saw connected to a frame which takes up an entire wall. It can cut wood to any size you want. As I’m awful at saws, I was excited to measure things up and pass it off to the folks at B&Q.

I came home with a car full of treats, and starting drilling away. I basically made a big box of wood, which can be taken apart, and rebuilt, quickly. I drilled holes to allow the tubing to pass through, and hide it away inside the box. I used a jigsaw to cut a little square in the lid, so insert a big upright bike pump, and led a tube out of the front of the box. Simples.

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Using a loads of rubbish from labs I connected tubes together, and built a little stand for the empty bottles to sit in. Charlotte drank herself through roughly 900 bottles of Pepsi Max to give me a load of empty bottles.

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I had to toy around with a couple of things to actually bung up the bottles. I originally planned to jam a cork in, drill though it, snap a sterile pipette and jam that through. Then connect my tube to  the other side of the stripette and Robert’s your dad’s brother!

However, I soon realised that sellotape wrapped around the tube would work just as well. And when I saw as well, I mean better. And a roll of sellotape is much simpler to carry around then all of that junk.

So there you have it. Although if you’re making it at home, you can do it much simpler, by drilling a small hole through a cork, jamming it into a two little bottle with 200-300 mL water in, then feed the needle from your bike pump through, pump away and enjoy!

I’ve put a lot of my life into making it possible to fly in space at all.

Everyone knows exercise is important right? It helps you lose weight, increase muscle mass, makes you feel good, decreases health problems and according to The Oatmeal eat obscene amounts of amazing terrible food. But I bet you didn’t know how important exercise is to astronauts, did you?

Think about it. Crew members on the International Space Station can spend months in “microgravity,” or as you probably call it “floaty floaty space times.” Because of this they do not use their muscles properly. It’s hard to imagine, but just by standing up and walking around you actually use a lot of your muscles, and prevent them from just wasting away. So, just imagine what happens in space when all of this day to day exercise is cut out.

Crew members can lose up to 25% of their muscle mass after a stint on the International Space Station. Which you’ll recognise as about 25% more than you ideally want to lose. Sarcopenia, a disease literally meaning “poverty of the flesh”, occurs when you lose about 1% of your muscle mass. And generally to over 50s!

Some of you weedy, gym-phobic jerks are probably all like “so what? I don’t got me no muscles and I been doing just fine.”

Firstly, you are not fine, that was an appalling sentence and you should apologise for it. Secondly, skeletal muscle (the type of muscle you think of when you generally think of muscles) is the biggest organ in your skinny little joke of a body. Skeletal muscle makes up all of you. In only the most extreme circumstances is there something in your body bigger than muscle.

Mostly, it’s fat. Which is pretty darn gross.

Aside from the obvious, muscle wastage can lead to lots of problems. Rates of Type 2 Diabetes increase, and those suffering from sarcopenia often undergo complications following surgery. It can even cause bone loss. It sucks, is what I’m trying to say.

Futhermore, remember how you can’t be an astronaut because;
A) you’re not smart enough
B) ain’t lucky enough
C) and most importantly here, you would fail all of the physical challenges given to trainee astronauts

These folks are literally the best we have to offer. They’re so good at what they do, they get to dick about in space doing it.

“So, exercise right? That is what fixes it right? Right?”

Better, but stop saying “right?” Asking rhetorical questions in a seemingly relaxed, but secretly pain-stakingly crafted manner is my thing you twerp.

And yes. Although, remember that microgravity I talked about before? What type of exercise can you do when things weigh nothing and you just float around? It’s not like you can just strap someone onto a treadmill can you?..

Luckily those folks at NASA are crazier than you think. They have manufactured a treadmill (called COLBERT) with two bungee cord straps and braces. This means that crew members can be harnessed and attached to the treadmill. This means they can run just as normal.

But why would you run, when you can ride a bike in space? Like I said them NASA smarties are also a little bit zaney. CEVIS is basically a box with pedals on it. Again, you get strapped into it, but it means you can ride whilst you float around.

So, that’s your cardio done. As microgravity affects everything it is important that crew members exercise all muscle groups. Enter ARED, the advanced resistive exercise device; a goddamn beast of a machine. ARED uses piston-driven vacuum cylinders to simulate exercise. Crew members lift bars to push the cylinders closed, like a bicycle pump. What is so special about ARED is the flexibility. Not only can the amount of vacuum be changed to increase the amount of “weight” but the machine can be altered to mimic lots of different exercises.

Having trouble picturing any of this? Well how about you get yourself over to The Bluedot Festival. It’s a new festival at Jodrell Bank, showcasing the best in music, art and science. And we’ve been chosen. We’ll be there all day Saturday and Sunday showing people how to #exerciselikeanastronaut. Yeah, I stick hashtags on things now. On the ISS crew members attempt to exercise for 2 hours a day. We’ll be knocking out a week’s worth of exercise in just two days.

So, come along and check us out. And then stick around for 65daysofstatic, Caribou, Everything Everything, Polinski, DJ Shadow and so many more artists. Brian Cox and Robin Ince will be there, and everyone loves him right? Come on, it’ll be fun. We can blow up some things*.

 

* things may include balloons.

Today’s quote is from Chris Hadfield.

Talk Less, Smile More

I went to a workshop titled “Shut Up and Write!”, in an attempt to write my paper/make some figures/proofread my mates thesis. When I arrived they introduced us to the Pomodoro technique.

Yep, that means tomato.

The two hour session was split into four 25 minutes sections, with 5 minute breaks in between. We were asked to write down some achievable goals, turn off our phones, and disconnect from the internet. We then spent 25 minutes writing in silence, before a silent 5 minute break. Another 25 minutes, and a 10 minute break where we  could  talk amongst ourselves, have a walk and get a cup of tea. A third 25 minute writing session, then a 5 minute break where we talked about our progress and how our goals were going. Before a final 25 minutes writing.

We were encouraged to write down any distractions we had, and then continue writing.

Write down distractions? Don’t get carried away, and focus on scribbling your real work. That rings a bell… If you didn’t click that, it was a link to my thesis-writing blog. I accidentally stumbled onto a version of the Pomodoro technique whilst I was writing my thesis. I would try and write as much as I could, but whenever I felt distracted I would update my blog with whatever gibberish I could  think of.

As well as updating my tea count obviously.

So with that in mind, I decided to blog about my experience at the workshop, old school style. Enjoy!

As I’ve never been here before, I have literally no idea as to my goals. I’ve settled for;

  1. Finish my papers
  2. Proofread Sophie’s first chapter

That’s doable in like 2 hours yeah?

Anywho Quadrupède is on, my phone is off, and Lappy Jr is disconnected from the internet. Work time!

Time for my first five minute break. This is going pretty well. Obviously I’m only been doing 25 minutes, but still I think its going well. I didn’t even really want to stop for the five minute break.

Do you have any idea how long five minutes is when you have to sit there in silence doing nothing?!

Writing time.

Unfortunately the Quadrupède album isn’t actually that long, so I’ve had to change up my music. I guess I could try writing without it, but I’m not experimenting too much now. I’m already pretty sure it’ll turn out listening to music improves writing. I’ll just have to wait for the evidence and see what model gets created in the future. I mean I’m already pretty good at almost stumbling upon tried and tested techniques.

I thought there would be tea available, and am as disappointed as you can expect as Englishman to be without tea. If (when, let’s be realistic) I do this at home, I’ll definitely have a proper tea break.

We’re allowed to talk in this break, but as no-one knows anyone we’re all very awkward and most folks are mumbling. Anyway, time to stretch my legs, it’s not good for your cardiovascular system to sit for an hour anyway.

And my pedometer app is moaning at me.

I’ve ended up listening to my Happy Songs playlist on Spotify, which basically got me through my thesis.

Totally forgot how much I like that one Kidstreet song.

This is going really quickly. And it seems to be working. I’ve managed to get my paper finished, and now I’m reading Sophie’s thesis. I’m not entirely sure I’ll get this chapter done, but I’ll try my damndest.

Time for the final session.

Sophie is much better at writing than I am.

 

So, it works! I am definitely a fan of Shut Up and Write! At the organisers have asked if anyone would be willing to host their own workshop. I totally am, although it may well be in my man cave. There’s a very real chance I’ll use it as an excuse to book a room, and hide away for a couple of hours. I never really  get chance to write at work, as I feel obliged to spend my time in the lab. So locking myself away in a room for a designated time is probably a good idea.

 

Today’s quote is from Lin-Manuel Miranda, as I am totally obsessed with Hamilton at the moment.

 

 

Sometimes you can do things for others that you can’t do for yourself.

A bit of a strange one today.

I received an email just before instructing me that my subscription to a complimentary service has expired. Apparently I had received a two week free trial to DiabetesPro; a free service to health professionals who “need to keep current with what’s happening”. Needless to say I’d never heard of it.

So I trawled back through my emails and it turns out the American Diabetes Association have developed a mobile app to keep you up to date with the latest going on in Diabetes. I assume it’s for medics, but I signed up regardless. Why wouldn’t I?..

“So, you cares?” I hear you asking.

I don’t know, why did you follow the link here in the first place. Don’t hold accountable for your actions!

Oh, wait, I guess I should as I invited you. The point of this was to write about how often I actually use these services. So as well as DiabetesPro, I get updates from the Endocrine, Biochemical and Physiological Societies, PracticeUpdate, Diabetes UK and for some reason the latest in Stem Cell Research and Immunology from Bio-Techne.

I am also on the mailing list for the Lipids MAPS conference, so I receive updates about their conferences, and Keystone Symposia.

A quick look through my Twitter tells me that I follow over 20 accounts dedicated to updating me (and others I assume…) about the latest developments in various topics. That doesn’t even include journals that I follow, or scientists that I know constantly post their latest papers.

A post from Nature summarised some data about whether or not Twitter buzz leads to more citations, and it doesn’t! Interestingly sharing on Mendeley is apparently closer, and as you know, I love me some Mendeley. Apparently, it’s because sharing and analysing things amongst scientists is better than letting the general public have a go at it. Which makes sense really, considering how little some chumps know.

Somewhat crazily in 2012, 20% of biomedical articles were tweeted at least once, and that’s going up, so I assume by the time I get my babies out, I’ll be falling behind if I don’t post it. Who am I kidding, I’ll be posting my Ryan et als like they’re going out of fashion!

Which they might well possibly be considering no-one cares about phosphatidylinositol (4,5)-bisphosphate.

Which brings me onto my next thing. I get updated from Google Scholar every time one of my papers get cited. Unfortunately, as I’ve recently changed my research area (for the second time) I don’t have much to do with the inositol lipids anymore, I tend not to even read those papers. Rude I know.

Similarly, Researchgate lets me know when my papers have been cited, but more importantly it lets me know when people I follow publish more papers. This is useful as I follow my collaborators, competitors and friends a distant third.

I guess there’s also LinkedIn. Look how well I kept a straight face. Get over yourself LinkedIn, you’re dumb.

So, do I use any of these? The Endocrine Society’s “Daily Briefing” is great. The biggest benefit is that it often links to a simply written article. If you want to read the actual papers it clearly supplies references, but other than that a few paragraphs summing up the study is ideal.

Similarly, PracticeUpdate sums up a lot of studies. You know those people who constantly have multiple tabs open on multiple web browsers? Yeah that’s me. And it’s almost definitely PracticeUpdate’s fault. I open at least a tab a day, aiming to read them later, but I rarely get it done.

I have never cited a paper I’ve found on Twitter. I think it’s because when I’m trying to write a paper I don’t generally check Twitter. (I’m a Facebook nerd, not just a better person than you.) I also tend to read papers I find interesting, and not necessarily for their science. Show me a paper about a bunch of nonsense and I’ll probably read that and share it. Even if my friend shares one of their papers I don’t think I’ve ever shared it.

“Why wouldn’t you help your friends?” you scream, somewhat obtusely. Firstly, I’ve just told you it doesn’t help, but I will from now on though! Especially on Mendeley.

 

Today’s quote is from A.M. Homes.