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Caveat lector: This blog is where I try out new ideas. I will often be wrong, but that's the point.

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30.8.12

Allen Institute for Brain Science

Yesterday I gave a talk at the Allen Institute for Brain Science (twitter) about my work on brainSCANr and how it integrates with their Allen Brain Atlas.

view from my hotel room
For those of you not familiar with the organization it was started by Paul Allen, co-founder of Microsoft. So far he's invested about $500,000,000 of his own money to allow the Institute to prosper. They've got several concurrent projects going on, namely looking at gene expression in the human and mouse brain, connections between regions, and so on.

They made a splash about 5 years ago with their Nature paper, "Genome-wide atlas of gene expression in the adult mouse brain" and then again in 2009 with their Nature Neuroscience paper, "An anatomic gene expression atlas of the adult mouse brain". It's my understanding they've got a huge new Nature paper coming out soon as well.

And they recently just hired consciousness neuroscience research extraordinaire Cristof Koch away from Caltech to be their Chief Science Office. Although shorter than we'd hoped, it was really nice to be able to sit and chat with him about my research and future directions.

Why are these papers so cool? Honestly it's mostly because of the amazing technology driving their massive data collection efforts. They've got an enormous facility with hundreds of scientists and automated robotic data collection systems just tearing through terabytes of data.

They were also really interested in my work with Uber... it was a pleasant surprise to meet a group of scientists who understood the importance of working with software engineers, data visualization people, and so on.



data collection facilities

It's clear Paul Allen and the Institute have built a very data-driven, tech heavy team. Their goal is not only to collect all this data, but to share it with everyone.

These are my people.

Over dinner last night there was a lot of excited talk about the future of data in neuroscience. I've said it before--and it's nice to sit with a group of scientists who agree--that I think it's arrogant to believe that the person who knows what best to do with the data that I collect is me.

And that philosophy is built into the Institute.

Don't get me wrong, they are doing amazing things with their data internally, but they really do hope that researchers will take their data and run with it and do things they couldn't imagine (which is I guess why I was invited).

They've put together what is probably the most user-friendly neuroscience data site I've seen that allows researchers to explore and play with data.

tool to explore point-to-all gene expression correlation maps
trying to get a handle on all the information!
brain data art
loving the OHBM Space Needle art

I really believe these kinds of endeavors will be the future of neuroscience: data-focused and engineering-heavy with a huge scientific team running in parallel to take part in the data exploration and to guide hypothesis-driven research.

I can't wait to see more efforts like this start popping up in the next few decades.


ResearchBlogging.org
Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, Chen L, Chen L, Chen TM, Chin MC, Chong J, Crook BE, Czaplinska A, Dang CN, Datta S, Dee NR, Desaki AL, Desta T, Diep E, Dolbeare TA, Donelan MJ, Dong HW, Dougherty JG, Duncan BJ, Ebbert AJ, Eichele G, Estin LK, Faber C, Facer BA, Fields R, Fischer SR, Fliss TP, Frensley C, Gates SN, Glattfelder KJ, Halverson KR, Hart MR, Hohmann JG, Howell MP, Jeung DP, Johnson RA, Karr PT, Kawal R, Kidney JM, Knapik RH, Kuan CL, Lake JH, Laramee AR, Larsen KD, Lau C, Lemon TA, Liang AJ, Liu Y, Luong LT, Michaels J, Morgan JJ, Morgan RJ, Mortrud MT, Mosqueda NF, Ng LL, Ng R, Orta GJ, Overly CC, Pak TH, Parry SE, Pathak SD, Pearson OC, Puchalski RB, Riley ZL, Rockett HR, Rowland SA, Royall JJ, Ruiz MJ, Sarno NR, Schaffnit K, Shapovalova NV, Sivisay T, Slaughterbeck CR, Smith SC, Smith KA, Smith BI, Sodt AJ, Stewart NN, Stumpf KR, Sunkin SM, Sutram M, Tam A, Teemer CD, Thaller C, Thompson CL, Varnam LR, Visel A, Whitlock RM, Wohnoutka PE, Wolkey CK, Wong VY, Wood M, Yaylaoglu MB, Young RC, Youngstrom BL, Yuan XF, Zhang B, Zwingman TA, & Jones AR (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445 (7124), 168-76 PMID: 17151600
Ng L, Bernard A, Lau C, Overly CC, Dong HW, Kuan C, Pathak S, Sunkin SM, Dang C, Bohland JW, Bokil H, Mitra PP, Puelles L, Hohmann J, Anderson DJ, Lein ES, Jones AR, & Hawrylycz M (2009). An anatomic gene expression atlas of the adult mouse brain. Nature neuroscience, 12 (3), 356-62 PMID: 19219037

7.8.12

The Adventures of Ned the Neuron!

I've been itching to announce this for months, but I've been biting my tongue. Now I can finally let the neuron out of the bag.

Ladies and gentlemen I'm proud to introduce to you a joint project between my wife Jessica Voytek and our friend Erica Warp: The Adventures of Ned the Neuron! To get the important pitch out of the way first, please go contribute some money to their Kickstarter campaign to help them get started if you want to help.


Also, please consider following their company on Facebook. I promise they're not spammy.

For several months now Jessica and Erica have been working on their company, Kizoom, to develop the first of what I hope to be many science education eBooks for kids. The fact that this is being built using open or semi-open tools and platforms is also pretty amazing.


Note that I'm in no way connected to this company, though the obvious disclosure is that my wife and I are financially entwined and, as unbiased as I try to be, I of course cannot be completely so. I mean, I'm writing this post, aren't I? But... as a new father I'm coming to appreciate more and more the joys of well-written, scientifically accurate educational materials.

So who are Erica and Jessica and why should you trust what they write?

Erica earned her PhD in neuroscience from Berkeley working on spinal cord development. She published three super cool papers during that time, one each in Nature, PNAS, and Current Biology. I promise you she knows her brains.

Jessica is the primary author on our brainSCANr paper which we published in The Journal of Neuroscience Methods earlier this year. She earned her Masters degree in Information Management and Systems at Berkeley, which she completed while very pregnant with our son. Not only does she know her brains, she's also technically and artistically very savvy.


The two of them have been working hard on this baby of theirs (that's them celebrating after submitting their NIH grant). They have managed to put together a book that is fun and interactive for kids (their target audience) while being educational and totally neuroscientifically accurate.

No neuro nonsense. Just good science and good fun.

So many of us neuroscientists complain about the poor public understanding of our field that it's time for us to stop being critics and start trying to make the changes we want to see. And that's what I love about Kizoom and The Adventures of Ned the Neuron: two very smart neuroscientists and techies are putting themselves forward and trying to make science more approachable to the most scientifically vulnerable group.

Kids.

Erica wrote the story and drew the early artwork while Jessica has been working on getting the whole thing coded up, animated, etc. Basically the techy nerd work.

What's impressed me the most is that, throughout all of this had work, they've also been doing a lot of science outreach and communication for kids. Jessica worked for the Girl Scouts for years, including developing a cookie booth finder to help people locate the nearest Girl Scout troop selling cookies in their area!


In May Jessica and Erica volunteered at a Girl Scout event to teach young women about neuroscience and the brain with the help of Ned the Neuron!


We also recently learned that, out of the thousands of abstracts and poster submissions to the Society for Neuroscience Conference this October, their poster "User experience design for children's neuroscience education" has been selected as one of nine in the new "Dynamic Posters" session.

What's that? Well, according to the email they received,
A dynamic poster is an electronic version of the current paper-based format, displayed on an LCD screen rather than a poster board. However, it’s more than just an e-poster, which is typically an electronic - but still static - PDF version of a paper poster. Embedding multimedia content is encouraged such as videos, slides, animated charts or graphs, scrolling text, or a 3D rotation of a model. A dynamic poster presentation is designed for face-to-face interaction: like a regular poster presentation, the dynamic presentation will be driven by the primary author while attendees visit the poster. Some text elements of the poster will always be viewable for browsing by people walking by or waiting for their turn to speak with the presenter. Other parts of the poster will be operated by the presenter, who can click on and play a video or enlarge a graph to better illustrate a method or result.
I definitely applaud the Society for Neuroscience for finally taking this kind of tech-based approach.

I wish I could convey to you in words the emotional love the both of them have for this project. I'm really proud to have seen it grow from nothing into a nearly completed project. Please check it out and consider helping if you can.

Thanks everyone.

ResearchBlogging.org
Voytek JB, & Voytek B (2012). Automated cognome construction and semi-automated hypothesis generation. Journal of neuroscience methods, 208 (1), 92-100 PMID: 22584238
Warp E, Agarwal G, Wyart C, Friedmann D, Oldfield CS, Conner A, Del Bene F, Arrenberg AB, Baier H, & Isacoff EY (2012). Emergence of patterned activity in the developing zebrafish spinal cord. Current biology : CB, 22 (2), 93-102 PMID: 22197243
Marriott G, Mao S, Sakata T, Ran J, Jackson DK, Petchprayoon C, Gomez TJ, Warp E, Tulyathan O, Aaron HL, Isacoff EY, & Yan Y (2008). Optical lock-in detection imaging microscopy for contrast-enhanced imaging in living cells. Proceedings of the National Academy of Sciences of the United States of America, 105 (46), 17789-94 PMID: 19004775
Wyart C, Del Bene F, Warp E, Scott EK, Trauner D, Baier H, & Isacoff EY (2009). Optogenetic dissection of a behavioural module in the vertebrate spinal cord. Nature, 461 (7262), 407-10 PMID: 19759620

1.8.12

The deception ratchet

The recent admission by Jonah Lehrer of fabricating quotes in his latest book has caused a lot of schadenfreude, bloviating about the "state of journalism", etc. People are writing a lot about what this "means".


I've been critical of Jonah Lehrer in the past because of his seemingly blind exaltation of neuroscientific findings but noted that this is a symptom of the state of cognitive neuroscientific research in general. After all these years, I believe I've finally identified the major root source of my scientific frustration.

Lies of omission. Intentionally leaving out critical information with the intent to deceive.

Again, this post isn't about Lehrer, it's about how Lehrer reflects the state of neuroscience. Specifically, this post is about the pervasiveness and problems associated with lies of omission. While I will discuss this in a neuroscientific and science reporting context, I think it is a more generalizable issue.

In that post linked to above, my friend and fellow neuroscientist Dan left a very insightful comment mirroring a discussion I had on twitter with Noah.





Dan said:
1. [Lehrer] wrote many blog posts, long-form articles, and books. In all cases, he had the luxury of space to add nuance to his articles (my point in an earlier comment).
2. He clearly isn't a scientist but he's shown that he can read and understand a large swath of scientific literature. He read enough that he must of come across articles that contradicted his ideas.
3/4 Is the big question. We know significant research exists that contradicted many of the stories he wanted to tell. When he came across those contradictory findings, did he convince himself that they weren't good science or did he actively ignore them to cherry pick the studies that fit his stories?
Dan's points 3/4 are basically talking about lies of omission. While Lehrer admitted to fabricating some quotes and then lying to cover up that fabrication, my deeper concern is how easy it is to commit a lie of omission and how hard such a lie is to uncover.

How can you possibly prove someone didn't know something when the accused can so easily feign ignorance?

Every time I hear about the insula being the "disgust" part of the brain, or oxytocin being the "love chemical", or dopamine being the "addiction chemical", I cringe. Normally I would say this is my curmudgeonly annoyance at oversimplification, but as Dan noted anyone who spends even a minute doing a search of the literature on PubMed will find tons of contrary evidence against the tidy narratives often reported in media accounts.

For example, the insula is also associated with a whole barrage of behavioral and cognitive functions.

There are two issues wrapped up here: one journalistic and one scientific.

Journalists are, in theory, supposed to fact check, but how can they check facts on scientific minutia in which they are not trained? Who is culpable? And are scientifically savvy journalists who follow the press release about a new scientific finding at fault if they don't address the complexities (when the allure of a neat behavioral narrative is so strong)?

Now the second problem comes down to evidence fishing. I'm sure many neuroscientists who have analyzed their data have encountered an anomaly. Maybe an unexpected brain area showed significant activation to your task. Maybe your treatment group had an unusual response. How do you handle these discrepancies?

The wrong way is to go to PubMed, search for the name of the brain area and the name of your task or drug or whatever, find some abstracts that talk about the two, and just go ahead and cite those and pretend like it's common knowledge that the insula "processes disgust" and leave it at that.

But I promise you this happens. A lot. I've seen it happen.

In both cases, journalist and scientist alike have committed sins of omission. The savvy journalist knows that their story is too simple, but man it makes for such a better story. The scientist just needs to add that little citation to show that their annoying finding is already known and therefore not worth discussing (because it doesn't fit their paper's narrative).

In a fantastic review of self-deception in unethical behavior, Tenbrunsel and Messick "...identify four enablers of self-deception, including language euphemisms, the slippery slope of decision-making, errors in perceptual causation, and constraints induced by representations of the self."

Honestly I can't recommend this paper highly enough; it's easy to read and fascinating.

The part that is most relevant to the discussion at hand, however, is on the ethical "slippery slope" that I'm calling "deception ratcheting":
The second component of the slippery slope problem is what we call the “induction” mechanism. Induction in mathematics is as follows. If a statement is true for N = 1, and if the statement for N + 1 is true assuming the truth of N, then the statement is true for all N. The way this works in organizations is similar. If what we were doing in the past is OK and our current practice is almost identical, then it too must be OK. This mechanism uses the past practices of an organization as a benchmark for evaluating new practices. If the past practices were ethical and acceptable, then practices that are similar and not too different are also acceptable. If each step away from ethical and acceptable practices is sufficiently small, small enough not to appear qualitatively different, then a series of these small steps can lead to a journey of unethical and illegal activities.
This happens in journalism just as it happens in science. If, as a scientist (or journalist), you witness some lazy brushing away of a surprising finding then you, too, will be more likely to do the same. And when your future students (or assistants) see you doing the same, then they become more comfortable with deceptions and lies of omission as well.

Tenbrunsel and Messick argue that such systematic, generational drift is caused by our large-scale errors in attributing causation to deception:
Acts of omission are a third reason as to why perceptions of causes are in error. Whereas lies of commission are direct misstatements of the truth, lies of omission are acts of deception that occur because someone withholds information that deceives the target. A failure to take an action, i.e., disclose the truth, makes it more difficult to ascertain responsibility, not only for others but also for oneself. Consider the situation in which you are selling a car. Is it your responsibility to inform the buyer that the car has had several unexplained malfunctions or is it the buyer’s responsibility to ask? Phrases or euphemisms such as “buyer beware” reveal the answer: moral responsibility shifts from the agent to the target under situations characterized by acts of omissions. Ritov and Baron’s (1990) work provides empirical support for this intuitive motion, demonstrating that acts of omission are viewed as more acceptable than acts of commission. Acts of omission, then, because they blur the assignment of responsibility, can create self-biased perceptions of causes, shifting blame from self to others. In such circumstances, it is highly likely that individuals’ propensity to engage in unethical behavior increases, because shifting responsibility to others allows one to divorce oneself from the moral implications of their actions.
Errors in perceptual causation allow us to distance ourselves from the ethical issues at hand. We erroneously believe that we cannot fix the problem, because it is a people and not a system issue. We also falsely believe that it is someone else’s problem, either because they are to blame or because the responsibility is someone else’s, not ours. While different from hiding the ethical implications of our own actions, this form of self-deception removes the ethical decision from our backyard, thus watering down the ethical demands of the situation.
The whole style of writing popular amongst the "Big Idea" crowd pushes for errors of omission in favor of a tight story. This is such a minor sin--one for which you almost certainly cannot be caught--that the allure to commit the lie probably overwhelms any inner voice of caution. But once you take that first deceptive step, you are statistically more likely to be willing to baby step your way farther and farther in service of that tight story.

Until in the end you're plagiarizing your own copy, making up quotes, and lying to fellow journalists.

By this point you should be asking yourself, "how well does this Tenbrunsel and Messick paper represent our state of knowledge on this topic?"

So caveat lector. Listen to the notes that are being played, but listen more carefully to the notes that are not being played.

And for you writers and scientists out there, beware the easy allure of the deception ratchet.

ResearchBlogging.org
Ann E. Tenbrunsel, & David M. Messick (2004). Ethical Fading: The Role of Self-Deception in Unethical Behavior Social Justice Research, 17 (2), 223-236 DOI: 10.1023/B:SORE.0000027411.35832.53
Chang LJ, Yarkoni T, Khaw MW, & Sanfey AG (2012). Decoding the Role of the Insula in Human Cognition: Functional Parcellation and Large-Scale Reverse Inference. Cerebral cortex (New York, N.Y. : 1991) PMID: 22437053