Tuesday, June 23, 2015

Milo Yiannopoulos destroyed by Emily Grossman in a debate

I just watched the 10-minute debate between Milo Yiannopoulos and Emily Grossman on the scandal surrounding Tim Hunt. It was stunning. Yiannopoulos uttered a stream of unsupported and inflamattory nonsense, and Grossman just dismantled him with facts. I know I would have lost my composure and temper in a debate with him, but Grossman magically remained professional and unfazed by his debate theatrics.

To be honest, I felt slightly bad for Yiannopoulos. Grossman so eloquently and forcefully showed him to be a fool and a clown, it's impossible to watch without sympathy for him. I even heard a rumor that Yiannopoulos cried after the debate and asked for it not to be aired. (Can anyone confirm if this is true or not?)

However, after the debate, in an attempt to recover and spin his poor performance for personal benefit, he wrote Why do feminists cook up stories about misogyny when they lose debates? This is the part where my sympathy for Yiannopoulos evaporates. When you lose a debate, admit it and move on. Write a blog post apologizing for stupid and offensive stuff you said, admit that Grossman destroyed you, and try to do better next time.

Friday, June 19, 2015

An argument FOR electronic lab notebooks

Most existing electronic lab notebooks (ELNs) are terrible. There is a good reason why the vast majority of scientists still use paper. But these are not arguments against ELNs - these are arguments against poorly-designed ELNs.

Below is my e-mail to a professor from a few months ago on this topic.
From: ProfessorX
Date: Sun, Jan 4, 2015 at 9:51 PM
To: Lenny, ProfessorLab

The attached article [How My Mom Got Hacked] is about the latest form of malware.   There is no way in the world that I could ever get authorization to pay the ransom to get any of out data back for reasons you will see.   So beware…..and keep a real note book.

From: Lenny
Date: Sun, Jan 4, 2015 at 11:24 PM
To: ProfessorX, ProfessorLab

Dear ProfessorX and lab,

I think this is a fascinating article and is in fact an argument for a digital lab notebook as Protocols.io envisions it.

ProfessorX, we have repeatedly discussed electronic lab notebooks (ELNs) over the past two years. You argue that the paper notebook has reliability and persistence that is not matched by the ELNs. You cannot access anything from the digital files on the floppies from the 90s, but you can still read your paper notebook from the 70s. You've also told me that the ELN business is the Afghanistan of startups. 

I agree with everything you point out, and these considerations have influenced our approach to the digital notebook since the birth of Protocols.io. I agree with everything you point out, but not with your final conclusion that the paper notebook is the best way of keeping records. It is indeed today, but that's just because the existing ELNs are shitty, not because the ELN concept is flawed.

Now for the details:

1. Formats change and startups fail, so you can lose all of your data.

Agreed. That's why we made sure that our protocols.io journal can be exported as .txt and PDF. You can export the whole thing, print it, put it on dropbox, thumb drive, and anywhere else. And it's good practice to do so periodically, as we do with all of the data that we generate. The important aspect is that your records belong to you and not to Protocols.io.

2. ELNs have not been adopted by biomedical scientists because the paper notebook is best.

Agreed that ELNs have not been adopted and paper is best today. However, that's because most ELN companies have been solving the wrong problem. Labguru, eCAT and LabArchives all think they are competing with each other. They are not; their real competition is the paper notebook, and paper wins by a long shot against them because all of them have a terrible product. The existing and dead ELNs all thought the problem they need to solve is the retrieval of information, which is infinitely better in digital format. No. The problem is the entry of the information in the first place. That's where the paper notebook shines in contrast to websites and desktop software. My takeaway here is that as a mobile company, if we really do this right, we can come close to and possibly beat the paper notebook for the entry of the information (e.g. ability to write over the gel image, directly on the iPad). If we do that, we have a shot at adoption.

3. Hard drives can die and computers can become infected, as outlined in this article.

Agreed. This is an argument for backups. Hence we have a daily snapshot of all user data going back a month and a monthly snapshot beyond that. As the article itself points out, this is also an argument for cloud storage. Chances of losing your notebook on a laptop or single hard drive are high, but chances of losing it entirely on our Amazon server or on Dropbox are lower than the chance of losing or burning your paper notebook (doesn't have to burn as the drowned notebooks during Sandy at NYU showed us).

4. The paper notebook stays in the lab and can be easily read by anyone forever.

I agree it stays in the lab forever, but disagree it can be easily read by anyone. Most notebooks can only be parsed by the person who wrote them. So when that student moves on, her inability to physically access the notebookeffectively makes the entire record useless. My PhD notes from 2003-2009 may be physically in the Berkeley Lab, but when I am in Boston for my postdoc, good luck trying to answer a reader's question without me, just from flipping through my notebook. In fact, a paper notebook can't easily be used by anyone, including the author. That's because looking for a primer number or some note, without the ability to search digitally, requires hours of flipping through the notebook.
When students or postdocs leave the lab, they should re-assign their digital lab notebook to the professor. At the discretion of the professor, the student continues to have access to the notebook after leaving the lab. So when ProfessorX gets a question about a 2007 paper from a previous student, he forwards it to that student, student logs in, does a quick keyword search, reads the relevant page, and answer the question precisely. That's how the protocols.io journal will work.

The inefficiency of the paper notebook, in the electronic age, is staggering. That's why both Novartis and Merck moved last year to ELNs for their chemists and are currently in the process of moving the biologists to ELNs as well. The arguments against the existing ELNs are arguments for a better digital lab notebook product, but they are not arguments that the paper is best. After all, we don't transcribe RNA-Seq or ChIP-Seq data into our notebooks. Nor do we transcribe our qPCR readouts from Excel. We are firmly in the digital age. We need a good ELN, be it from Protocols.io or someone else, and we need good practices to make sure the electronic records are accessible long into the future, without wasting trees.



P.S. I'd love to hear more arguments from everyone, for and against the ELN.