Science

Inferring tumor evolution from single-cell genomes

Series on Tumor Evolution

Everything is better if you do it with a Nested Effects Model – even inferring tumor evolution.

Let me introduce to you Oncogenetic Nested Effects Models, or for short OncoNEMs, which we just published in the new Single Cell collection of Genome Biology (see here). They exploit the fact that tumors accumulate mutations while they evolve, which leads to (noisy) subset relations between clones – exactly the type of pattern NEMs were made for.

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Science

“Look at me, I was a terrible supervisor”

“I was a terrible PhD supervisor. Don’t make the same mistakes I did,” writes Sian Townson in the Guardian.

Lots of points I agree with:

Research points to high levels of depression among PhD students.

I am not surprised. This is one of the reasons Cambridge has such an active counseling service and, as far as I can see, there is little stigma attached to using it.

I also share her observation about the lack of training for supervisors:

[Academic practice courses] taught me some technical rules and requirements but nothing about the practical processes involved in teaching, mentoring and career-building a fellow human.

I have lamented this fact before in my post “Why science needs continuous leadership support”.

She is also right when saying

I failed to see that even as mature, independent people, my students still needed clear achievable milestones and objectives and celebrations when they reached them.

Especially the celebrations can be hard to do. There is always a Next Goal, a Next Paper.

Like my supervisors before me, I was technically successful – all my students passed on time and within budget – but in practice they struggled, feeling lost, unsupported and sometimes depressed.

She is making an important point here: there can be a big difference between how successful you and your students look on paper, and how you feel about it.

But nothing she writes here sounds really worrying to me. First of all, if all your students graduate in time – that’s great! Well done!

PhD research is hard. You are pushing the boundaries of current knowledge. If you don’t struggle and don’t feel lost for a while, you are not pushing hard enough.

I am not sure what she means by ‘sometimes depressed’ – it’s too unspecific. Everyone has their ups and downs. As a supervisor I am not trained to and shouldn’t attempt to diagnose people’s mental health. This is a task for specialists.

However, her saying her student felt ‘unsupported’ is an issue – this is definitely something a supervisor can and should change.

Look at me, I failed

For my taste, there is to much “Look at me, I failed” in this article.

I was an utterly appalling supervisor and I didn’t even realise it.

What is this? Fishing for compliments? Does she want an answer like “Oh, no, you were not. You did the best you could.”

Or is this an indirect way of telling me I am blind? Maybe I only think that I am an Ok supervisor because I haven’t realised yet how appalling I actually am.

Sigh.

Her last sentence is

Perhaps you can learn from my example.

No, I can’t.

Because this is all about perceived shortcomings and weaknesses of supervisors. To learn, I’d need some positive examples about how these shortcomings and weaknesses were overcome in some concrete situations.

Without any positive advise, this is just Failure Porn.

Florian

 

 

Science

‘Five selfish reasons’ is one of Genome Biology’s Most Influential Articles of 2015

Genome Biology just sent an email around with 2015’s Most Influential Articles, according to Altmetric.com.

And, guess what, one of mine made the Top 10: Five selfish reasons to work reproducibly  from last December — really a late-comer to the competition.

And so, my fellow scientists: ask not what you can do for reproducibility; ask what reproducibility can do for you! Here, I present five reasons why working reproducibly pays off in the long run and is in the self-interest of every ambitious, career-oriented scientist.

Now I just need one of my research papers to have the same impact as my opinions, and I’d be sorted …

Florian

 

Science

First parasites, now online harrassment – how has transparency harmed you lately?

An interesting post at Political Science Replication:

Getting the idea of transparency all wrong

Following an article in the New England Journal of Medicine, which portrayed scientists who re-use data as parasites, we now hear more on this from Nature. Apparently, data transparency is a menace to the public. The Nature comment “Don’t let transparency damage science” claims that the research community must protect authors from harassment by replicators. The piece further infects the discussion about openness with more absurd ideas that don’t reflect reality, and it leads the discussion backwards, not forward. 

Read more at https://politicalsciencereplication.wordpress.com/2016/01/29/getting-the-idea-of-transparency-all-wrong/

Duty Calls, Science

I am a research parasite. Got a problem with that?

In case you wondered what’s wrong with biomedical research, just read this editorial on data sharing by Longo and Drazen in the New England Journal of Medicine, a leading journal in the field. What you will find is a desperate attempt to take data hostage and to enforce co-authorships for people who didn’t make any intellectual contributions.

But let’s take it one step at a time. What did Longo and Drazen actually say? They think there are major problems with sharing data fully, timely and openly.

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Science

Science Stories – Reproducibility

If you think I am serious about reproducibility, you should see my wife.

In this movie by the Royal Society she is explaining the issue to David Spiegelhalter. That is Sir David Spiegelhalter, FRS etc etc.

Published on 22 Dec 2015. We need mathematical help to tell the difference between a real discovery and the illusion of one. Fellow of the Royal Society and future President of the Royal Statistical Society, Sir David Spiegelhalter visits Dr Nicole Janz to discuss reproducibility in scientific publications.

 Way to go!

Florian

Science

“Five selfish reasons to work reproducibly” published

 

Wohoo! Genome Biology just published my piece on “Five selfish reasons to work reproducibly” (which I have talked about before).

And so, my fellow scientists: ask not what you can do for reproducibility; ask what reproducibility can do for you! Here, I present five reasons why working reproducibly pays off in the long run and is in the self-interest of every ambitious, career-oriented scientist.

Go check it out at http://www.genomebiology.com/2015/16/1/274

I am a bit sad, though, that they cut this über-geeky joke I used to illustrate how tightly the tools of reproducibility have to be linked with routine practice:

in-case-of-fire-1-git-commit-2-git-push-3-leave-building2

Florian

Career, Science

Why science needs continuous leadership support

Hello, my fellow PIs, here is a question for you: Did you get trained well for your job?

Silly question, of course you did. Years of study and examinations culminating in a PhD have obviously trained you well in all things science.

But that’s not what I mean. Details of experiments and algorithms –what you learn in a PhD– are only a small part of a PI’s job. Once you start leading a group, the tough nuts to crack are people-problems.

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Creativity

Lit with a ghoulish inner light — Three Oncologists for Halloween

The scariest picture I have seen this Halloween (or maybe even ever) is Ken Currie’s eerie portrait Three Oncologists:

The Three Oncologists are Professor RJ Steele, Professor Sir Alfred Cuschieri and Professor Sir David P Lane of the Department of Surgery and Molecular Oncology, Ninewells Hospital, Dundee. *

In the Guardian Kathleen Jamie writes:

It’s a portrait, but far from flattering. (…) The three men are lit with a ghoulish inner light; they seem to be haunting the threshold between life and death. (…)

Furthermore, they hold their tools or means: Steele raises his gloved and bloodstained hands, Cuschieri holds a surgeon’s implement, Lane carries a paper. Whose sentence is written there?

As we grow more able to say the word “cancer” out loud and more of us survive it, thanks in no small part to our surgeons and physicians, this painting will become a historical record of an emotional state, as well as honouring three esteemed medics.

But it will still send a shiver down the spine.

It sure will.

Florian