Slashdot Mirror
Dead Salmon's "Brain Activity" Cautions fMRI Researchers
AthanasiusKircher sends in a Wired writeup on what should surely be a contender in the next Improbable Research competition: wiring a dead salmon into an fMRI machine and showing it pictures of humans designed to evoke various emotions. "When they got around to analyzing the voxel... data, the voxels representing the area where the salmon's tiny brain sat showed evidence of activity. In the fMRI scan, it looked like the dead salmon was actually thinking about the pictures it had been shown. ... The result is completely nuts — but that's actually exactly the point. [Neuroscientist Craig] Bennett... and his adviser, George Wolford, wrote up the work as a warning about the dangers of false positives in fMRI data. They wanted to call attention to ways the field could improve its statistical methods. ... Bennett notes: 'We could set our threshold [of significance] so high that we have no false positives, but we have no legitimate results.... We could also set it so low that we end up getting voxels in the fish's brain. It's the fine line that we walk.'" The research has been turned down by several publications, according to Wired, but a poster is available (PDF).
Wiring red herring's brain? Will it think too?
And here I though I had exterminated the last of the zombie salmon.
They're definitely on track for an igNobel prize. Using a red herring instead of the salmon would have made it a near certainty. A kipper would normally be the best choice, apart from the lack of a head/brain.
Those who can make you believe absurdities can make you commit atrocities. - Voltaire
This story makes me reconsider my zeal to see Terri Schiavo die. If she was indeed experiencing brain activity despite her handicap, surely she would be considered more alive than a dead salmon.
Our consciousness is all just a series of nerve impulses and chemical reactions. If Terri was experiencing these reactions and impulses, I hate to say it, but we may have killed a human being and not just a vegetable.
God bless you, Terri Schiavo.
The point of the experiment was not to prove the type of fish.
Fish are capable of all sorts of feelings for humans.
WARNING!!! Pun approaching!!
It proves that an fMRI, like most machines, needs to be carefully operated and the mechanisms understood, as there are risks of false positives for results.
The paper is about intentionally observing a dead creature, and coming across a few false positives and why that happened.
[..] it looked like the dead salmon was actually thinking about the pictures it had been shown. ... The result is completely nuts -- [...] as a warning about the dangers of false positives [...]
Looks to me like the dark matter syndrome: "Our theories wrong? Our calculations off by an insane amount? Unpossible! That can never be. Nature must be lying!"
Has anyone even checked if a dead brain can still have flows of energy through its brain? I mean light patterns still reach the retinas, and can still trigger signals, depending on the state of the neurons there. How long was that salmon dead? I know that pigs can be frozen to be clinically dead for long times (90+ minutes), and still be revived without much damage.
I'd at least check if there are actual signals of current going trough the brain (with an OTHER (better) instrument, before dismissing it. Every unchecked assumption is a good chance for flaw in your study. You wouldn't want it to be dismissed by peer review, because of a faulty assumption.
Any sufficiently advanced intelligence is indistinguishable from stupidity.
No no he's not dead, he's, he's restin'! Remarkable fish, the salmon, idn'it, ay? Beautiful plumage!
It was probably a salmon of doubt.
The Tao of math: The numbers you can count are not the real numbers.
"It's OK to eat fish cause they don't have any feelings."
-- K. Cobain
Even vegetables put into an MRI machine for a functional scan can show some 'brain activity', simply because the fMRI doesn't actually show 'brain activity', it (in its typical configuration) shows blood oxygenation concentration levels in various places in the brain. The real problem is translating increasing or decreasing levels of oxygenation into brain activity. That's precisely what this study is showing: even a dead fish has changing brain-blood oxygenation levels. You need to remember to do the science and the math part of the problem, and make sure that the statistics are really showing meaningful relations.
The question remains as to what functionality is required to call a person "alive" or "brain dead". If you want to be as absolutely conservative as possible, anyone with a beating heart and working brain stem (corneal reflexes, heart-beat signal, breathing stimuli, etc) and can be considered alive, even if their entire frontal lobe has been entirely caved in removing any wisp of humanity and they aren't even capable of controlling their bowels or bladder or many other autonomic or homeostatic functions. Whether you think it's cruel to pull the plug on someone in this state is entirely up to personal beliefs and/or religious convictions. Medicine tries not to tread too deeply into this water, simply because it's not worth it to rehash the ethical dilemmas with no new science to change anyone's opinion. We leave it up to the individuals (through advanced directives, living wills, etc) and their families to choose.
Just don't be fooled into thinking that scattered activity in a bundle of nerves we happen to call a brain necessarily means she's "alive".
"Victory means exit strategy, and it's important for the President to explain to us what the exit strategy is." G.W.Bush
fMRI is a blunt instrument compared to what ultra high resolution spectroscopic MRI will show us in the future.
Current MRI is tuned to the proton nmr signal (and variations of it). As magnet technology advances and ginourmous gradients are achieved, it will be possible to obtain full spectroscopic data (chemical shift) in addition to positional data. Not only for the proton but for other isotopes that produce an NMR signal (of which all the CHONPS elements have at least one). As aquisition electronics speed increases it should eventually be possible to show this data in real time (molecules in motion). Of course it will be a trade-off between positional data resolution and spectroscopic data resolution, but this will be a very powerful technique. fMRI is just the tip of the iceberg and only a first step toward spectroscopic MRI proper.
That said (and without RTFA of course), I wonder how long the salmon was dead? What temperature was it stored at? The animal need not necessarily be alive for a stimulus to produce an effect. (Thinking of batteries and frog legs...) As long as the bulk of the cellular machinery is intact...
OK, I broke down and read the pdf. This report is coming from a psyhchology department! (I expected biology) I'd wait until the chemists and physicists weigh in to make any conclusions about this observation.
Looks to me like the dark matter syndrome: "Our theories wrong? Our calculations off by an insane amount? Unpossible! That can never be. Nature must be lying!"
I find it amazing that people who haven't even bothered to study the data or the reason for hypotheses like dark matter feel the need to make ass backwards comments about people who've literally dedicated their lives to it. What do you actually know about dark matter and the current state of the evidence? Do you even understand it at a layman's level let alone understand the insanely complex math? Have you heard of the bullet cluster? Do you know about the rotation curve of galaxies? Do you understand anything about the cosmic microwave background and its fluctuations? Do you understand the background theories you're ridiculing? Do you know why General Relativity fits the data we have collected so well? Have you even bothered to find out why scientists believe in these things? Dark matter and dark energy aren't just theories that a bunch of arrogant pricks pulled out of their asses. These are our best attempts to fit multiple kinds of data into a single theory of nature. Your attempt to imply it's just scientists refusing to believe the data is at best childish. At worst you're no better than a flat earther.
These posts express my own personal views, not those of my employer
Can we conclude from this data that the salmon is engaging in the perspective-taking task? Certainly not. What we can determine is that random noise in the EPI timeseries may yield spurious results if multiple comparisons are not controlled for. Adaptive methods for controlling the FDR and FWER are excellent options and are widely available in all major fMRI analysis packages. We argue that relying on standard statistical thresholds (p 8) is an ineffective control for multiple comparisons. We further argue that the vast majority of fMRI studies should be utilizing multiple comparisons correction as standard practice in the computation of their statistics.
And why wasn't this published? The very conclusion is that we should be more careful when trusting fMRI results and conduct more testing before jumping to conclusion.
I am the lawn!
"It's OK to eat the barrel of a gun cause then you don't have any feelings."
-- K. Cobain
I for one welcome our new zombie salmon psychotherapist overlords.
I can't believe I'm going to say this, but:
Fixed that for you.
Oh, was that my outside voice?
Atlantic salmon is called Salmo salar in biology-speak. It is the model species of the entire order Salmoniformes. Salmon doesn't get any truer than that. Pacific species belong to the genus Oncorhynchus. They are true salmons too. "Trouts" belong to both Oncorhynchus and Salmo (and another 5 genera). Some of these trouts have anadromous forms (that is, go to the seas and return to the rivers to spawn), for instance, the rainbow trout (called steelhead in its anadromous form) is Oncorhynchus mykiss and the brown trout (sea trout) is Salmo trutta.
Well, maybe what they saw wasn't a false positive? Maybe there is residual functionality of the brain some time after death, the same way you can electrically stimulate the muscles of a dead body to make them twitch. Is it that unthinkable that visual impulses have some effect on the brain, that death instantly renders every single braincell inoperable?
GAAH! MY PRINTER IS ON FIRE!!! PUT IT OUT! PUT IT OUT!
Yep. What little I remember of stats is that it is an extraordinarily delicate tool, every little theorem is couched in uber cautious qualifications. All the more reasons to be cautious of stat-based findings of math-impaired social scientists, and medicine isn't all that far ahead in terms math literacy.
Fuck systemd. Fuck Redhat. Fuck Soylent, too. Wait, scratch the last one.
That fish that you are eating is watching you... and feeling it.
No sir. What it proves is the existence of the sole.
I don't care if it's 90,000 hectares. That lake was not my doing.
It's OK to eat any animal because, by the time you eat it, it doesn't have any feelings. - A normal person
The poster highlights a very well-known problem in statistics that folks doing brain research are well aware of and almost always correct for. The issue is that, when you're doing a large number of statistical tests, like you are with brain imaging data, you're likely to get a lot of false positives. You can correct for this by using a very conservative significance threshold (i.e., "p-value"), directly controlling for the proportion of false positives using a statistic called the "false discovery rate," controlling for false positives via monte carlo simulation, etc. etc.
Most neuroscientists who do brain imaging are very familiar with these correction methods, and apply them with great success. If anything, neuroscientists tend to be too concerned with false positives, such that they end up actually missing real activations because they're over-correcting.
So it's actually really unfortunate that this study is getting so much popular media attention, because it's giving people the impression that researchers aren't aware of this problem and/or that that they aren't doing anything about it. That couldn't be further from the truth.
The mechanisms are the most important thing. What is fMRI actually measuring? It doesn't measure activity directly, since it's not built into the brain. Ergo, it measures activity indirectly by measuring something else entirely. But anything which also generates that something else will also be detected.
This is less a false positive than it is a complete confusion between direct and indirect observations. The falseness is not in the measurement but in the observer.
Sir Arthur Conan Doyle would have loved this finding, as he often has his most famous creation of Sherlock Holmes make snide remarks about the folly of poor observation and the absurdities that follow.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
No, west-coast farmed Atlantic salmon is a cheap substitute that is sometimes dyed red to disguise it as wild pacific salmon. Fortunately, Atlantic salmon exists outside of fish-farms and is a perfectly good fish in its own right.
Salmon only possess soles.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
you insensitive cod!
If they're zombies, wouldn't that be psychotic therapist?
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
Hey guys - I am the first author of the Salmon poster. If you have any questions that you would like us to answer then post it as a reply below and I will do my best to respond as soon as I can.
You can find some more information on the poster at the following link:
http://prefrontal.org/blog/2009/06/atlantic-salmon-index/
Best ~ Craig Bennett
No sir. What it proves is the existence of the sole.
Yeah, the measurements were right off the scales.
Crumb's Corollary: Never bring a knife to a bun fight.
AC - The paper has been rejected once so far. I won't mention the journal, but it was rejected on an editorial basis before it reached the peer review stage. I can only conjecture regarding why the editor decided to pass on the paper, but it was not (to my knowledge) rejected for any methodological deficiencies. We are currently in the review stage at a second journal and the reviewers had no trouble with our methods, only how we argue for multiple comparisons correction without stepping on too many toes.
As an interesting aside, the poster was also rejected at first. All the peer reviewers thought is was a joke and voted to exclude it from the conference. Once it went before the program committee they realized that, even though we had an odd approach, the conclusions of our data were sound and that we had a very good point to make.
* Dave Lister: Sometimes I think it's cruel giving machines a personality. My mate Petersen once brought a pair of shoes with artificial intelligence. Smart Shoes, they were called. It was a neat idea. No matter how blind drunk you were, they would always get you home. Then he got ratted one night in Oslo, and woke up the next morning in Burma. See, the shoes got bored just going from his local to the flat. They wanted to see the world, man, y'know? He had a helluva job getting rid of them. No matter who he sold them to, they'd show up again the next day! He tried to shut them out, but they just kicked the door down, y'know?
* Arnold Rimmer: Is this true?
* Dave Lister: Yeah! Last thing he heard, they'd sort of, erm, robbed a car and drove it into a canal. They couldn't steer, y'see.
* Arnold Rimmer: Really?!
* Dave Lister: Yeah. Petersen was really, really blown away by it. He went to see a priest. The priest told him, he said, it was alright, and all that, and the shoes were happy, and they'd gone to heaven. Y'see, it turns out shoes have soles.
The need for multiple comparison corrections is standard knowledge among cognitive neuroscientists. It is actually common practice for manufacturers of MRI machines to image inanimate objects as a test of the machine. You could easily get that data, rather than imaging a dead fish. Once you know the amount of noise, it would be easier to just simulate within a statistical program to determine the effects of not correcting. If the authors of the poster weren't aware of the value of multiple comparison corrections BEFORE they stuck a fish in the magnet, at least they learned a lesson everyone else gets in second year stat.
It detects the oxygenation of blood. The mechanism behind this is a different magnetic moment of oxygenated hemoglobin, oxygenated hemoglobin is diamagnetic vs paramagnetic while deoxygenated. This is called the BOLD effect (Blood Oxygen Level Dependent). The difference in the two conditions magnetic property affects the MRI signal lifetime in the near vicinity. This results in contrast developing between tissues with oxygenated blood vs tissue with deoxygenated blood. The idea behind fMRI is that when you use a certain part of the brain, it requires oxygenated blood, which will lead to contrast. Unfortunately, due to low overall signal strength/contrast-to-noise ratio, the image must be signal averaged. Hence if you were tapping your finger to see which part of your brain "lights up", you would have to repeat this action, and have your MRI scan be synced to your action so that the same part of the brian is being imaged over the same interval each time. It's tricky, but my understanding is that it's quite feasible. There are many other mechanisms for causing localized signal lifetime changes, without having RTFA, I can't be sure what they took under consideration.
ardeaem - At face value you are absolutely right. The majority of cognitive neuroscientists do use multiple comparisons correction in their research. Our commentary is targeted at the remainder of researchers who continue to use uncorrected statistics. The percentage is larger than you might believe, and my co-authors and I are of the opinion that we need to get our statistical house in order for the field to mature.
venicebeach - Again, good points. The trouble is that multiple comparisons correction is not the de dacto standard in any neuroimaging journal. Some journals, like NeuroImage and HBM, have become quite good about requiring correction in the results. Still, even they are not 100%. Other journals with a lower impact factor are quite a bit worse, with uncorrected statistics used in almost 50% of the studies. So, either people know about the problem and are willingly choosing to ignore it when they publish or they are unaware of the seriousness of the problem and need a salient reason to begin correcting. We believe it is the latter, which is why we published the Salmon.
As for the argument about it being counter-productive, I fully agree. We presented the poster at the Organization for Human Brain Mapping meeting last June, which was our target audience. I then uploaded the poster to my website so those researchers could grab a copy. The poster got picked up by a few weblogs and eventually spiraled into what you see on Slashdot. We were quite content to publish the paper in a sleepy corner of neuroimaging and wanted it to remain as a discussion piece among scientists.