Science

At the movies: “My career in genomics: evolution “

Former postdoc Roland Schwarz of MEDICC fame has become a movie star.
Or at least the face of computational biology for the Wellcome Genome Campus:

In this film Roland Schwarz talks about his research using computers to model and understand evolution. This is one of a series of films providing a unique insight into different careers in the field of genomics.

Go here or watch it directly:

Florian

Career, Science

Forget about your animal friends – how to draft a recommendation letter

Marcia McNutt, Editor-in-Chief of Science, wrote a thoughtful Editorial about recommendation letters:

I noted an overall bias in the language used to describe the male candidates versus some of the female candidates. In some letters, women were described as “friendly,” “kind,” “pleasant,” “humble,” and frequently, “nice.”

[O]ne letter described how the candidate was so good to her elderly mother, yet still enjoyed life, spending time in nature with her husband and her animal friends. Another letter reflected amazement that the candidate managed to balance so efficiently being a student, a scientist, and a mother.

But isn’t it good being nice, humble and having lots of animal friends?

Not if that’s the only thing the letter says about you:

[A selection committee reading such a letter] cannot help but put a candidate at a disadvantage when compared to others who are praised for their self-initiated research projects, interesting uses of coursework to address new scientific problems, or careful background preparation for the research project proposed.

How does a better letter look like?

Very different words were used to describe the male candidates (and many of the females as well): “brilliant,” “creative,” “hard-working,” “insightful,” and “showing leadership.”

She ends her Editorial with a call to arms:

I urge all who write these important letters of recommendation to take a last look before hitting “send” to be sure that what you have written is free of bias.

Yup, I agree.

But let me add something:

Everywhere I have worked so far it has been common practice that the people on the job market provide drafts to their (always terribly busy) letter writers.

That already gives everyone an opportunity to avoid some of this bias.

When you describe yourself -whatever gender you are- use the words ‘brilliant’, ‘creative’, ‘hard-working’, ‘insightful’, ‘showing leadership’ and only then add ‘nice’ and ‘good team player’.

Leave out your animal friends.

Florian

Science

A unifying theory of cancer evolution: genomes in context

Finally a review article on cancer evolution that I really enjoyed. Maybe because it’s not a Review but an Opinion piece:Evolutionary dynamics of carcinogenesis and why targeted therapy does not work by Gillies, Verduzco and Gatenby (GVG for short).

Extra brownie points for a provocative title.

The first publication on tumor heterogeneity

First of all, GVG extended my knowledge of the history of tumor heterogeneity by citing a paper from 1930:

Ö. Winge, Zytologische Untersuchungen über die Natur maligner Tumoren, Zeitschrift für Zellforschung und Mikroskopische Anatomie, 6. JUNI 1930, Volume 10, Issue 4, pp 683-735,

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Science

Evolution in cancer: Yes! Darwin: No?

Series on Tumor Evolution

ResearchBlogging.org
Evolution is a fancy word for gradual change. In this general sense, all kinds of things evolve. The universe evolves, societies evolve, finches evolve.

The mechanisms and principles of these three evolutions are all different. For example, the finches change by Darwinian evolution, which is one particular type of evolution based on natural selection: There is diversity in traits between individuals in a population; because of their traits some individuals have more offspring than others; the traits are heritable and can be passed on to offspring. Over time the favorable traits will become dominant in the population – and with them the genotypes underlying them.

This is how it works for finches. How about cancer? Is that developing by Darwinian evolution too? Not so fast, say Sidow and Spies:

The forced application of terms and concepts from organismal population genetics can distract from the fundamental simplicity of cancer evolution,

write Sidow and Spies in their review ‘Concepts in solid tumor evolution‘ (TiG 2015) and they plan to set the record straight.

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Science

Hypnotizing the reader into accepting the authors’ conclusions

I just had a quick look at last week’s Nature Genetics Editorial Cause, correlation, conjecture.

[W]e have been struck again by the amount of repetition of claims and arguments in most research articles.

The main claims of the paper are detailed in the title, abstract, introduction, results, figures and discussion as well as in the methods as if to hypnotize the reader into accepting the authors’ conclusions. [My emphasis]

Repetitiveness shows lack of confidence. One more reason to remove it.

And the Nat Gen editors even mention a tool to better structure a paper:

Our recommendation in planning a research paper is to lay out the claims together with the supporting evidence and methods in a three-column table. The rows follow one another logically as one experiment or analysis follows necessarily from its predecessor.

It is unfortunate that the short article doesn’t contain an example of such a table. But I like the idea and might just try it next time we write a paper.

Florian

Cause, correlation, conjecture. Nature Genetics 47, 305(2015) doi:10.1038/ng.3271 http://www.nature.com/ng/journal/v47/n4/full/ng.3271.html

Creativity, Science

Healing Art of Pathology

Over at Connecting the dots … Jakob Scott describes an art (and book) project involving histology slides:

A project he began, called My Sarcoma, during which Ray painted over the top of his OWN histology images, transformed Ray from a sick and dying patient back into a living and vibrant artist.

From http://cancerconnector.blogspot.co.uk/2015/04/healing-art-of-pathology.html

An example of collaborative art:

Each of the paintings that Ray has made during this journey has had more than just Ray’s hands involved. Indeed, to make the paintings as you see them, a surgeon had to cut out his tumor, a pathologist had to stain and mount the tissue and a screen printer had to prepare the canvas.

Inspiring!

Florian

Science

Inferring tumour evolution 6 – What do we talk about when we talk about a clone?

Series on Tumor Evolution

What do you picture when you hear the word ‘clone’? A white-clad imperial stormtrooper from Star Wars: Attack of the clones? Or a fluffy sheep called Dolly? Both are good choices. Both are good, solid, well understood clones. But how is the situation in cancer? This is where it gets difficult. In most talks (at least the ones I sit in) the word ‘clone’ is used very loosely like it was a trivial concept. My goal for today is to show that reality is more complex than the ‘plain vanilla’ version that is often described on some introductory slide.

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Books, Science

Steven Weinberg and the smugness of hindsight

One of the more helpful pieces of advice I recommend to new starters in my team are Steven Weinberg’s “Four golden lessons“. Weinberg is a physics Nobel laureate and “considered by many to be the preeminent theoretical physicist alive in the world today” (says Wikipedia). I guess this means he knows his physics … and his four golden lessons certainly are helpful:

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Science

How normal is normal? Surprising mutations in normal-looking prostate tissue

Series on Tumor Evolution

ResearchBlogging.org

“Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue,” is the title of another recent paper that caught my attention.

I like long titles, because they often already contain the full story without the bothersome detail of the rest of the paper. Let’s look at the pieces of this one; two things stand out:

First of all, prostate cancer is generally multifocal, which means that cancer develops in different regions of the prostate, and the authors have found independent clonal expansions for these different foci. So it is not that the cancer started in one spot and then spread, these different tumors in the prostate developed independently from each other.

Morphologically normal is not always genetically normal

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Books, Science

The Emperor of All Maladies — now on Television

Science announces:

Based on the 2010 book by Siddhartha Mukherjee (Science, 22 April 2011, p. 423), this three-part documentary weaves together a sweeping history of cancer with intimate stories of contemporary patients. Told largely through interviews with researchers and oncologists, the series highlights Sidney Farber’s efforts to galvanize a national “war on cancer” in the 1940s, delves into the development of targeted drug compounds in the late 20th century, and explores the promise of personalized immunotherapies.

Science

When cancer goes BOOM – what is the difference between the Big Bang and clonal expansion models of tumor growth?

Series on Tumor Evolution

ResearchBlogging.org

And the prize for best paper title 2015 (so far) goes toooooooo……

Andrea Sottoriva, Christina Curtis and their coworkers for
A Big Bang model of human colorectal tumor growth.

Big Bang, Big Bang, … reminds me of (a) the prevailing cosmological model of how everything we know came about and (b) Sheldon Cooper. So maybe this is a genius paper that revolutionizes our basic understanding of cancer. It certainly is an eye-catching title.

What is the Big Bang model?

The Big Bang model is an alternative to the clonal expansion model, which is (has been?) the prevailing model of how cancer comes about.

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Science

Ripples in the pond …

Our PLoS Med paper (see yesterday’s post) on tumor heterogeneity and survival in ovarian cancer is getting some media attention – not the front page of the New York Times, but hey, beggars can’t be choosers.

For those of you in UK, here you can see me stutter and sweat on regional television (for all of ~3 seconds): http://www.bbc.co.uk/iplayer/episode/b052y909/look-east-east-25022015 (starts at 11.47 mins)

Cambridge News: http://www.cambridge-news.co.uk/Cambridge-scientists-discover-8216-patchwork-8217/story-26077501-detail/story.html

GenEng News: http://www.genengnews.com/gen-news-highlights/ovarian-cancer-more-deadly-if-genetically-motley/81250964/

Medical Xpress: http://medicalxpress.com/news/2015-02-patchwork-ovarian-cancer-deadly.html

News Medical: http://www.news-medical.net/news/20150225/Serous-ovarian-cancer-is-more-deadly-shows-Cancer-Research-UK-study.aspx

CRUK press release: https://www.cancerresearchuk.org/about-us/cancer-news/press-release/2015-02-24-patchwork-ovarian-cancer-more-deadly

Science

Tumor heterogeneity is bad for you

Series on Tumor Evolution

Heterogeneity everywhere! The lists of clonal and sub-clonal aberrations found here and there in many tumors get longer and longer. But is this whole heterogeneity business actually useful for anything?

Actually it is, as we show in a paper that just came out in PLoS Medicine: Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic reconstruction. And as a free bonus it comes with an editorial by Andy Beck from Harvard, who says “open access to large scale datasets is needed to translate knowledge of cancer heterogeneity into better patient outcomes” — right he is!

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