With all the clamor over sequencing the HeLa genome, Rebecca Skloot and her book ‘The immortal life of Henrietta Lacks‘ are making headlines again. I had been very impressed when I read it first (as you can see from my review in early 2012), but I am less enthusiastic now that I had some time to think about it.
The reason is the way Skloot fails to distance herself (and thus the reader) from the Lackses magical world-view.
‘I’m a Stem Cell and I Know It’ from the Frye lab at the Cambridge Stem Cell Institute.
Mike Eisen has joined the discussion about the HeLa genome:
Skloot’s piece glides from the issue of how to retroactively get Henrietta’s permission to experiment with and publish about her cells to the seemingly related issue of whether publication of the HeLa cell genome is an invasion of the privacy of Lacks’ living relatives. (…)
I find the way Skloot’s NYT piece moves back and forth between the historical transgressions against Henrietta Lacks and the contemporary threat to her relatives’ privacy incredibly misleading.
I doubt this was intentional – rather I think it reflects muddled thinking on her part about these issues. *
I think this is a very good point.
And when discussing how much threat the HeLa genome is to the privacy of her living (and future) relatives, it would actually be important to know if Skloot is right that a few minutes of analysis of the HeLa genome provide “a report full of personal information about Henrietta Lacks, and her family.”
I still doubt it.
But it’s a testable hypothesis. We just need to sequence other members of the Lacks family and see if their genomes are significantly closer to the HeLa genome than yours or mine or Skloot’s.
Now there’s an experiment waiting to be done.
I’ll start talking to the folks at the EMBL.
Florian
Arthropod Ecology wrote a great post on Ten tips when asking for a letter of recommendation.
What I would add: Be prepared to write a draft yourself!
All advisors are busy and for them it’s a lot of help if you draft your own letter. This is harder than it sounds. Most of us instinctively undersell their own performance. But if gives you the opportunity to define which particular feature of your CV or work the letter should focus on.
And if you draft the letters for more than one of your advisors, you can actually stress different bits in different letters to make sure they don’t all sound the same and cover your general awesomeness comprehensively.
Update 4/5/13: Make sure that the letters still look unique, even if you drafted them or supplied a list of bullet points. It looks a bit weird if all your letters contain the same sentences. And don’t trust your letter writers to reformulate what you sent them. Like all of us they will be busy (and/or lazy) and most likely just copy/paste what you sent them. So it’s up to you to feed them bits that sound different from each other.
Florian
On March 11th scientists at EMBL announced that sequencing of HeLa cells revealed havoc in biology’s most-used human cell line. Their sequence analysis reveals how the HeLa genome is different to the Human Genome Project reference. Their results are published in G3: Genes, Genomes, Genetics.
Since HeLa cells are indeed one of biology’s most-used human cell lines, this is a great resource for cancer research.
But wait, … ‘HeLa’ stands for ‘Henrietta Lacks’. It’s not an anonymous cell line. There is a real person (plus still living family) behind it. What does the Lacks family say to having their family’s genome exposed?
Theory papers almost never make it into top journals and this is why I have blogged about the paper ‘Detecting Novel Associations in Large Data Sets’ in Science by Reshef et al before (here and here). The reception in the statistics community was mixed and while Terry Speed seemed to love it, Rob Tibshirani started to point out weaknesses. And now other people have joined the discussion.
Jonathan Wolff takes a look at academic references in the Guardian. Some examples are really funny:
“Pound for pound she is the best philosopher in the department.” What can that mean? She’s not very good, but on the other hand she is really small?
He concludes:
[T]he value we get from academic references is minuscule compared to the effort involved on all sides.
That’s what I have always been thinking …
Florian
I have blogged about the ISMB workshop “From Postdoc to PI” before (here and here) and now the organizers published a paper about it in PLoS Comp Bio: “Don’t Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator” Nice!
Florian
There is an excellent discussion of an excellent post on marginal improvements over at biomickwatson. He calls for an embargo on short read alignment tools, because there now already 70+ of them out there.
I can’t help but say – I’m sorry, but isn’t this a waste of time, both yours and mine?
I have nothing against the authors of the new tool, whom I am sure are excellent scientists. [...] But still, rather than write another tool, why not contribute to the codebase of an existing tool? If BWA is not accurate enough for you, then branch the code and make it so; if Stampy is too slow, speed it up. *
That reminds me of my own rant against marginal improvements: ‘Spare me your method, show me your finding‘. What is true for aligners is true for the rest of bioinformatics too. I have seen thousands of microarray clustering, network reconstruction and enrichment analysis papers – all of them rephrasing the same small number of ideas.
You need to read the comments thread under Mick’s post. Well-argued and diverse opinions. I particularly liked this comment:
It is a false and wasteful economy to value a paper over the software it describes, but will the madness never end?
Florian
… and this time it doesn’t even have anything to do with breast cancer. Check out the latest news on replication in the social sciences on my wife’s new blog Political Science Replication:
“I don’t have a ready-made dataset.” – “We don’t have the R code for our paper available.” – “I’m travelling. I will definitely send the replication data when I can clean it up a bit.” These are just some of the answers I received when asking authors for their replication data in political science. Only few sent me replication-ready data and almost no one sent me their code or .do file. This is a serious case of replication frustration! *
Reading her post I realized that my own field, genomics, actually seems to put much more effort into reproducibility and replicability than the social and political sciences. Just think of all the big repositories for micorarrays and sequencing data. That should sort at least the availability of the original data. And the experimental data packages on Bioconductor can contain vignettes with all the code necessary to re-do the analysis (like in this example from my group).
I’m quite happy about these efforts, but then again … it’s still sometimes a pain in the neck to get full GWAS data sets or complete genome-wide RNAi screening data. And ‘we need to clean up the data first’ or ‘the first author is traveling’ are excuses I regularly hear when asking for data.
Still so much left to do, wherever you look …
Florian
PS: I wonder where she got the idea for the layout from …
If you are into cancer genomics, you might want to learn more about what my colleague James Hadfield calls “probably the best Cancer sequencing meeting in the world”. He provides summaries of talks and discussions over at his own blog:
http://core-genomics.blogspot.co.uk/2012/11/probably-best-cancer-sequencing-meeting.html
I agree with James. But of course we are a tiny bit biased – the meeting is at our own institute …
Florian
Welcome back! The last post discussed rules 1-3: the importance to do a postdoc, a concise CV and a unique research statement. Like the last post this one is inspired by a Career Development Workshop at ISMB 2012 that I contributed to (download the slides).
There is still one thing missing from a standard application pack:
Together with CV and research statement some places ask you to submit a teaching statement. So write one. But don’t be fooled, it’s pretty low on the priority list (for the hiring committee, even if maybe not for you). Academic employers want three things from you: money, papers, and … long time nothing … teaching. I’m not saying they won’t ask you to teach for many hours a week, but when it comes to you being evaluated its money and papers (in that order) which counts.
Starting your own group is one of the most important steps in your scientific career — and one of the hardest.
Being invited to a Career Development Workshop at ISMB 2012 made me write down some of the advice that I had got when I was on the jobmarket a few years ago (and even put some of it on slides).
In a diverse and interdisciplinary field like computational biology it is very quite hard to come up with general rules that fit everyone. This is why I went down the self-indulgent route and revisited the CV and research statement I had prepared 4 years ago. (You’ll find a copy in the slides.) Some things are Ok, some things I would improve now — you will see, I’ll comment on this later. Let’s start with the basics:
Update: as pointed out in the comments, the amusing error in this article has been "corrected" (or at least, "edited away"). Thanks for your interest.
Update: I note that this article is now "Highly Accessed" ;)
An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver
BMC Systems Biology 2011, 5(Suppl 3):S4
With thanks to…
Comedian Tim Minchin argues with a hippy named Storm. Not really a song about science, but … great british accents, great animation, great word-plays!
| “Knowledge is merely opinion! The human body is a mystery, science just falls in a hole when it tries to explain the nature of the soul” |
Another science that has trouble explaining the soul is physics. But they are good at banging things together. Small things:
