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.

Advertisements

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.

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.

 

 

Women are from Earth, men are from Earth; deal with it!

Sorry it’s been so long. I’ve been all kinds of busy preparing for heading back to England. I’ve been booking flights, sorting out my accommodation for the last couple of weeks, making a list of things to do before I go, looking for jobs, writing papers, and (I wanna say dancing, but it’s not come up that much, and my dancing is fairly poor at the best of times, so let’s go with…)  drinking at the zoo?..

As my Timehop is so keen to point out, this time 3 years ago I was on a plane to San Francisco to go hang out in the Tenderloin. Admittedly, this holiday was amazing; I travelled to Truckee, got to hike thoughout the Donner Memorial Park in my (fake) Converse (which was a dreadful idea), hit up Portland, had an awesome Couch Surfing experience, fell in love with Powell’s bookstore, went to La Jolla, had a dreadful experience with a breakfast burrito, went to Lipid MAPS, schmoozed some labs, ate carnitas, wandering through the Tenderloin in the wee hours, and threw up in a urinal at San Francisco Airport. It was a great holiday, and basically got me my postdoc.

So, in what I’m sure you’ll agree is a beautiful little send off, the Lipid MAPS conference (which got me my postdoc in the first place) is now giving out registration fee waivers to students and postdocs. I put together a short little abstract, but was abruptly told that the waiver is for those underrepresented in science; namely minorities, females and those with disabilities. As a straight, white, European male, I am, if anything, completley overrepresented in science. All I’d need to be is old, and I’d basically be Captain/King O’ Science*.

Strangely enough, the two woman in my lab told me that that was rubbish, and that reverse-sexism is not the correct way to correct years of people being dicks to women.

Being the great big leftie that I are, I completely disagreed. I then realised all that the nonsense I learnt at the weird little equality and equitability seminar I “helped” teach, was actually relevant. This comic from Everyday Feminism explains it perfectly.

If you’re too lazy to click on a link, or find feminism stupid, I’ll explain, and you can do one, respectively. Us white men have depended on women, minorities and the like to get where we are now. Therefore, equality isn’t just given everyone an equal playing ground, but allowing everyone to reach the same level. Science has an appaling record when it comes to treating woman equally, and the way Henrietta Lacks was treated is disgusting. This isn’t even getting into  the terrible experiments on syphilis. There’s even an entire Wikipedia entry dedicated to “Unethical Human Experimentation in the United States“; the majority of which involve, or focus entirely on, minorities.

And I haven’t even mentioned the N-word.

Oh crap, the N-word I meant is nazis, not the other entirely- offensive–regardless-of-the-amount-of-black-friends/family you have-word.

But yeah, the nazis suck.

They then told me horrible stories about how sexism has affected them, including the need to move to an entirely different country! I’m not going to tell these stories here as they’re private, but it’s awful to think of the struggles people better at science than me go through, just to get the same oppurtunity. And all I did was turn up with a poster…

When I worked with the Manchester Access Programme, the point was to encourage folks unlikely to go to university, to actually go. My BioPathways interview was basically talking about how awesome science research was, but when I re-watch it, my friends Suzy and Liz (who was in charge) no longer work in research science. I’m not saying this is due to sexism, but it’s awful the amount of females who drop out.

I feel I should probably end this on a happy note, so if you look at this picture of me at Lipid MAPS 2012 looking like a scrunty grobbler. Follow the middle palm tree down, until you see a checkered shirt. In my defence, my pale English complexion couldn’t deal with the 2PM heat.

EDIT: After I wrote this, I saw this being shared around. Apparently a reviewer claimed the study would be better done if a man had looked at it or preferably get credited as a co-author. Whilst they haven’t explained which journal it is, it’s a member of the PLoS family; a journal we’re currently writing a manuscript for. I think all of the authors are men, so I wonder if we’ll get told to add a female co-author…

* I’m totally aware I have refered to myself as “King O’ Science” a lot of times, and Charlotte has defintiely called me “Captain Science” but they’re pretty sarcastic** really.

**Not ironic. No matter how much you incorrectly call it that ‘murica.

Today’s quote is from George Carlin.

One day I will find the right words, and they will be simple.

I know it may seem like I’ve been a bit lazy with this recently, but I’ve been a bit distracted. I’ve had a hell of a lot of writing to do recently, so I’m afraid this has been on the backburner. So, this is really just about keeping you up to date with what I’ve been doin.

I’ve written a couple of posts for Proteintech, and another for Diabetes UK. If you want to give them a read, here they are. Just choose your topic from Movember, proteins with dumb names or the discovery of insulin. I’ve also written one about “Diabetic Superfoods” which should be up soon. (Here it is.)

A couple of weeks ago I went to symposium on proteomics; basically Mass Spectrometers and the like. Big, scary, expensive machines. Big, scary, expensive machines that I want to use. Myokines ain’t going to discover themselves! Interestingly, they mentioned small pilot grants, so I’ve been busy getting an abstract written for that. If they like it, then we can submit a proper grant. The fun thing about that is that we have a load of samples pretty much ready to go, so once (if) they’ve given (give) us money, then we can just send them a pile of media, and be all like “science time turkeys!”

And lastly, the Endocrine Society, of which I am now a member, were asking for abstracts for the annual symposium next March. It’s in San Diego, so looks like I’ll be going. So that was another abstract to get in.

Add to that me trying to organise my PhD paper to fit to a journal’s ridiculous word and figure limits. As well as writing up my postdoc work, reviewing another recently submitted paper, and playing host to about a hundred (well 7) people, and that results in one busy Alex.

I also went a fairly stupid “Diversity in the Classroom” workshop. Don’t get me wrong, I’m totally pro-diversity and equality, but this workshop was handled appallingly. Also, it suggested that people who don’t believe in evolution shouldn’t be made to feel dumb. In a biology class. About evolution. Face it, evolution happens, and if you don’t believe in it you really should get the hell away from science, as apparently you have no idea what counts as evidence.

Today’s quote is from Jack Kerouac

Locals, locals, all standing still

So, I’ve been in America for a year now, and I’m celebrating by making figures and drinking whiskey. I’ve pretty much finished a paper from my PhD work (save the proof-reading…) so that’s nice. I just need to finish my figures, and get it to my old supervisor so she can add her data, and hopefully get it off somewhere as soon as possible.

It’s made me realise the difference between the first year of my PhD and the first year of my postdoc. Obviously I’m better at science now, but I feel like I’ve done quite a lot of work this year. Admittedly I could have done more, but not much more. I’m beholden to the number of biopsies we can carry out, and they’ve been fairly infrequent. Regardless I think I’ve covered more ground here. I’ve learnt new assays, and how to manage primary cells and a couple of new cell lines, as well as being able to get to my feet on a surfboard. Western blots are still annoying though.

Luckily there’s a good measure of my progress; submitting abstracts. Not for anything particularly interesting, but still a chance to show off my work. Towards the end of the first year of my PhD I helped organise the Young Physiologist’s Symposium at Manchester, and we were short of abstracts. But, I couldn’t do anything about it. Unless people we interested in learning that insulin increases glucose uptake (In my hands most of the time anyway…); something even Wikipedia doesn’t think requires a reference.

Now it’s time for the UCSD Postdoc Research symposium, and I have so much data I can’t put it here in case someone gazumps our science before publication. Just need a couple more experiments and I’m going to get a pretty good abstract in. I know it’s unlikely but I’m almost certain I deserve an oral presentation. Especially considering the standard of the talks I’ve seen since moving out here. Seriously, for an accent that sounds like you’re sooo interested in everything, you could at least muster some enthusiasm California.

And I’m almost certain my year here has benefited diabetes more than my three in Manchester. Turns out PIP2 isn’t that useful hey?

It is. It totally, totally is.

 

Today’s quote is by Meet Me In St. Louis (probably Toby Hayes)