Bacteria don't have to be icky
Feb 7, 2010, 10:30a
(This is the second in a 3-post series on biology. The first post gave background on the various levels at which biologists analyze organisms. This post discusses bacteria and an interesting behavior that they have called chemotaxis. The last post will present a web app that's an interactive simulator of this behavior. Yes, I had originally thought this would all ... more »
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A name change
Jan 3, 2010, 2:55p
I was reading an essay about art and neuroscience out loud to Becca. The more I read, the more insightful it appeared it could have been, yet the more like computer-generated spam it actually sounded. Becca said "That person sounds like they have a lot of interesting ideas, interspersed with nonsense." For some reason, that made me think about my ... more »
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omar
- Jan 4, 2010, 5:25a
This is nonsense
david
- Jan 26, 2010, 10:21p
this is silence. oh, wait.
A Note about Biology
Dec 25, 2009, 3:11a
(This is the first in a 3-post series on biology. I begin with some background, mostly to provide context for the second post, which is about a behavior in bacteria called chemotaxis. The third post will introduce a web app that simulates bacterial chemotaxis, and will be explained in gratuitous detail. I made it over a year ago, and ... more »
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Ruggero
- Jan 4, 2010, 3:26p
Excellent post.
Biological systems are far more complex than any of the system we've been able to come up with so far.
So far.
There'll be a time when the products of our minds will be more complex and smarter than us all. And probably at that time it won't make much sense anymore to talk about 'products of our minds' and 'us' because they will merge one into the other. If you think more carefully, this actually already happened. Do you wear contact lenses? Do you have a tooth filled? Do you have a hip replacement? Do you know of Oscar Pistorius? Technology is rough, but it's slowly integrating with biology. And not only at the macroscopical level. The most interesting works are in nanotechnolgy, where the distinction between an engineer and a chemist (or a biologist) becomes pretty hard to make.
Biological systems of course are still much smarter than robots. This is partly because biology writes information on DNA (about 3 nm), where current technology only goes down to 32 nm. And partly because we don't know how to handle matter properly yet. What is DNA if not a self-assembly material?
'Cleaner' substrates? There's nothing really clean even in engineering, believe me. 'Simpler' would sound much better.
Is there a basic biological principle we are missing? I don't know. I only know that there's a lot more to know about the language used in nucleic acids. If the principle is there, it has to be written down somewhere.
A question: does a virus chemotax?
nikhil
- Jan 4, 2010, 8:00p
As far as I know, a virus doesn't have any ability to actively move through space. A bacterium, on the other hand, uses flagella as propellers to execute a biased random walk through space. So I guess that a single virus wouldn't be able to chemotax. I haven't really looked into it though, and perhaps the right experiment hasn't even been tried, so I could be wrong.
Sundar
- Jan 10, 2010, 5:44p
Nice post, I do find biology interesting when written this way. I hated it because I did not want any part of dissection and infact, refused to in high school.
PS - engineers do not always deconstruct human made devices, sometimes it is also nature like "Big bang" - unless you are differentiating between engineers and scientists
nikhil
- Jan 15, 2010, 12:44p
yep, i'm distinguishing engineers, who build things, from scientists, who try to understand how non-human-made things (nature, socieities, human minds) might work.
oh how vegetarian of you :)
Cell phones, gestures, and 3G
Dec 23, 2009, 11:14a
(I'm sitting on a plane as I write this, flying to LA for Christmas. It's a 6 hour flight, and since I seem to be slightly phone-obsessed at the moment, I figured I'd pass the time by putting my thoughts down, since there's nothing on TV and I'm bored. Be forewarned - my blog is not turning into yet another ... more »
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omar the french duke
- Dec 23, 2009, 11:42a
I type this now on the google phone virtual keyboard. I was very skeptical of virtual keyboards but I must say this one is growing on me.
I too am baffled by the lack of pinch.
You should fiddle with the new phone when you get a chance. It is vastly improved.
Sachin
- Dec 24, 2009, 11:47a
Obviously I'm highly biased towards the iPhone. But I will start by saying I too am very impressed by the new Android phones. I think Android will give Apple a run in the coming years and ultimately might win because it's open. (although rumors claim the new iphone in 2010 is the first true redesign, 3G and 3GS were just refreshes. so Android is sorta competing with 2.5 year old tech in terms of software and gestures)
Ok, i'm going to battle 2 points to this article (i could argue more)
1. I find the Palm Pre gestures 100% UNNATURAL. I remember saying that the first time i every used one. The various swipes, card metaphor, etc are 100% learned. NO ONE can pick up this phone and just use it. When both my mom and my dad got their iphones, i remember not getting a chance to show them anything. (I think both times I was leaving down right after we went to the apple store). I never had to teach them anything, they got it naturally. And they are old!
I think your bias towards the palm gestures is largely because it's the first touch device you've used. That's always going to feel more natural than something you see later. But all the palm gestures are modal, which i find to be terrible. you have to swipe to enter this "card view" before you can swipe up cards to quit. Having these modes will confuse normal people. What mode am I in? Why does this gesture work in mode X but not mode Y?
2. The keyboard. You really can't diss a virtual keyboard unless you've used it for like a week and gotten used to it. I can type so freakin fast on my iPhone, much faster than I've seen people type on their bb. now when I do use a BB or other physical keyboard phone, it's seems too laborious. Having to push down hard enough for the physical click slows me down. If i'm already touching the key, register it and let me move on. And then correct for my mistakes. It's such a better experience.
And of course the touch screen gives you more free screen space, but that's a separate issue. It is nice that the keyboard itself can change based on what you are typing. web address, email address, phone number, they each have their own layout. I think optimization of keyboard layout and correction on touch screen phones is going to be huge in the coming years.
and on a random aside, switch to posterous, dammit. You'll get way more page views, and i'll be notified of new comments via email. and all the other random stuff...
Sachin
- Dec 24, 2009, 11:50a
You need a lot of faith to type a long comment here. I kept mine on my clipboard just in case it didn't appear in a few minutes :)
omar
- Jan 1, 2010, 7:51a
nikhil's blogging technology is so last decade
nikhil
- Jan 3, 2010, 11:58a
actually, my blog uses technology circa 1998. so it's actually from 2 decades ago!
Tugging Bubbles in a Box
Dec 15, 2009, 10:15a
Last weekend, I went to San Francisco for a friend's wedding. While there, I was thrust back into a world I left 3 years ago, the world that is my California. It is a world of engineering and of business, the world of working and thinking in Silicon Valley. It is a world raft with rapid, superficial, constructed, and possibly ... more »
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Making DNA look simple
Nov 19, 2009, 8:47p
UPDATE #2: Users can now change the scale bar to any length they'd like in the Exon-Intron Graphic Maker. The default had been 100 bases, but for people working with genes much longer than worm genes (such as human genes), the scale bar would disappear into single-pixel oblivion. So now users can set the size of their scale bar ... more »
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Tron
- Jul 25, 2009, 10:27p
Thank you very much for making this available.
belle
- Aug 5, 2009, 7:16a
this is the best thing since sliced bread!! thank you just saved me thousands of hrs
dude,
- Nov 3, 2009, 6:33p
awesome.
jasonII
- Nov 12, 2009, 8:59a
Thanks, this works great. A few things though. Some of us work on large (18kb) genes. Is there any way to change the scale bar? Also, being able to indicate alternative spice events would be nice.
nikhil
- Nov 18, 2009, 9:29p
Thanks for the request jasonll. I've updated the graphic maker so you can now change the size of the scale bar, to be something more appropriate for your 18kb genes. Not sure what the convention is for indicating alternative splice sites - why not just make 2 separate gene models? I guess if there are several it would be nice to consolidate them into one image. If you have any ideas about what this would look like, lemme know.
nikhil
- Nov 19, 2009, 11:54p
Alan Marnett over at Benchfly.com asked me to write a blog post for them about the Exon-Intron Graphic Maker. It's just like this post, slightly revised. Storing the link here for safekeeping.
http://www.benchfly.com/blog/making-dna-look-simple/
omar
- Nov 29, 2009, 11:07p
dude this has advanced my research significantly
To Be Conscious in a Body, Frozen
May 16, 2009, 11:21a
It's hard to tell if a thing is conscious. You know, if there is something that it feels like to be that thing. I know it feels like something to be a person, and I think it doesn't feel like anything to be a shoe (unless perhaps I've been smoking some salvia), or to be a dead person. But what ... more »
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Tom Stocky
- May 19, 2009, 6:26a
Wow, ingenious is right -- thanks for sharing this.
omar
- May 19, 2009, 9:41p
dear god. this is ingenious, but i am just thinking about this person who is locked in. i think they are likely totally insane. or almost. how could you not be, with no ability to communicate with the world?
when i read the diving bell book, at one point i was reading on the bart. it made me feel so claustrophobic that i almost threw up and had to get off the bart and breathe.
just reading your blog post is making me nauseous.
hope you are well!
Ruggero
- Aug 14, 2009, 3:02p
Is a worm conscious?
nikhil
- Aug 17, 2009, 7:22a
short answer: i don't know whether a worm (e.g. C. elegans) is conscious.
long answer: hmm, what a damn tricky question.
there are a few issues. first, it seems that it is in principle impossible to know if something other than yourself is truly conscious. if you define consciousness to be the phenomenon of having a subjective experience of the world (which is how i use the word most of the time), it seems plausible that another creature could act as if it were conscious even though it had no subjective experience. it would answer your questions, behave "normally", and even say "yeah, i'm conscious", but there may in fact be nothing that it is like to be that creature; in other words, the creature may act as if it has subjective experience without ever having any - it would fake it. and in principle, it seems impossible to know when something might be faking it.
this applies equally to other humans as to other organisms, such as the worm C. elegans. in general, though, when it comes to humans, I seem to make a sort of similarity argument: i'm conscious, and other humans seem to be a lot like me, so they're probably also conscious. so in practice we make assumptions that seem to be consistent with common sense, but in principle confirmation of consciousness in another creature seems unknowable.
second, let's just forget the first problem and say that yes, there exists a behavior that can only exist if a creature is conscious. so if the creature can act in a certain way, then i conclude that it is conscious. which behavior would I use as the test for consciousness? in practice, being able to respond sensibly to questions seems like a nice test, but as in the article above, verbal response seems sufficient but not necessary. also, it doesn't extend very well beyond humans, as we seem to be the only species that has a highly-expressive language (at the very least, we don't have good ways of communicating with other creatures in their own language, if they have one). intuitively, i think my dog is conscious, yet I communicate with her in extremely simple ways. and i can imagine that even if i couldn't communicate at all with my dog, she might still be conscious. my conclusion that my dog is conscious is based largely on empathy and similarity of response - she responds to things (e.g. hunger, anger, treats) in a way that i also respond to those things.
so now on to worms. i have nearly no empathy with worms, and there lives are so different than mine that it's really hard to tell based on intuition alone whether they're conscious. but you can do things in worms that are easier to do than in any other organism: you can identify genes, molecules, cells, and groups of cells that are required for certain behaviors. so if consciousness is due to some physical process (a big assumption), studying worms might be a good way to find pieces involved in that physical process - assuming, of course, that they are conscious (to some degree) to begin with.
i guess this is a very long-winded way of saying that i don't know whether a worm is conscious. there is a specific type of learning that is correlated with awareness in humans (a variant of Pavlovian classical conditioning), and i'm in the process of testing to see whether the worms can do this type of learning. if they can, it would be one small piece of speculative evidence that worms (specifically C. elegans) might be conscious. my hope is that over time we'll discover more behavioral tests that are correlated with consciousness in humans, and that worms could then also be tested. if i accumulate enough pieces of speculative data, the whole argument might become a lot more convincing. that's one strategy, at least.
Ruggero
- Oct 15, 2009, 12:53p
thanks for the very accurate answer.
let's assume that C. elegans is conscious (which i believe is true). is a bacterium conscious? is the fact that a system possesses a neural net that makes it conscious? or isn't just their reaction to a behavioural test? if the reaction makes it conscious then also a bacterium is conscious, since it replies to external stimuli as any other creature. aren't neural nets only there because of the size of the systems and therefore the necessity of a faster communication between parts than that achievable chemically?
nikhil
- Oct 18, 2009, 3:26p
i don't think that just because an organism has a neural net it's also conscious. like i said, i believe you need to find a behavior or some other observable that correlates well with awareness or consciousness. the presence of a neural net could be an example of such an observable, but given that there are many examples of nonconscious states in humans who have neural nets (e.g. vegetative states, dream-less sleep), i don't believe a neural net is sufficient. a neural net may be necessary, as there don't exist any examples of conscious creatures without neural nets, but that is less helpful in identifying those creatures which are conscious.
(as an aside: i prefer using the word "organism" or "creature" over the word "system", as i think "system" masks the complexity found in biology that is not found in standard engineered "systems")
i want to be clear - i don't believe that just any behavioral response is sufficient to show that a creature is conscious. people talk in their sleep and sleepwalk all the time, ostensibly without any consciousness at that moment (or at least very low levels). it's actually pretty interesting to record yourself sleeping - i got a nightvision camera that can do this, and i do all sorts of strange things in my sleep. one night i woke up holding a light bulb in my hand, with no memory of how it got there. the light bulb had been lying on my nightstand, so i just put it back, but it was a bit bizarre...
what i'm working with so far is a specific behavior called trace conditioning. i think i've blogged about it before; it's a specific type of pavlovian conditioning that involves specific time delays between the paired stimuli. i may blog about it in more detail at a later point. right now i'm working under the assumption that if an organism can trace condition, than this is sufficient for consciousness. this assumption is based on the fact that trace conditioning is well-correlated with awareness in humans, while other forms of conditioning are not. neither a bacterium nor a paramecium (a larger single-celled creature) are capable of trace conditioning (though no one has ever tried, as far as i know). no one has shown that c. elegans can trace condition. getting trace conditioning working in c. elegans is actually my main research project, and if i can show that they trace condition, then that's a tiny shred of evidence that it may be conscious.
for your last question, size does not necessitate the presence of a neural net / nervous system. paramecium are much larger than bacteria (~300 microns at its longest length, comparable to baby C. elegans larvae), and they are single cells without any neurons. they do have ion channels and they conduct electric currents, which only goes to show that you don't need a neural net to conduct currents. even plant cells have been shown to conduct currents, so many cells likely have this property. neurons are generally defined by shape (a cell body with at least one process reaching away from it) rather than by their ability to conduct.
hope this is helpful (and not too confusing).
Visualizing a Worm's Neural Network
Apr 21, 2009, 11:17p
For almost a year and a half, I've been working in Bob Horvitz' lab at MIT studying the nematode C. elegans. A microscopic worm of diminutive proportions (weighing in at only 1 millimeter in length), a single creature is just smaller than the size of an eyelash. These worms have been studied since the 1970s and much is known ... more »
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Sundar
- Apr 22, 2009, 6:31p
Very cool, nice to see you doing great work. thanks for the chrome plug:)
Ruggero
- May 15, 2009, 12:46a
Simply fantastic.
Matej
- Sep 5, 2009, 4:33p
I'm involved in neural networks in computing (artificial NN in chips) and this is very interesting for me.. Nice!
Carlos
- Nov 30, 2009, 4:10a
Excellent iniciative!
You have 2 time travels: Choose wisely
Jan 13, 2009, 8:37p
If you could travel to any 2 points in time, to where and when would you go?
This question popped into my mind as I was wandering the snow-cleared paths of MIT today. I had taken a break from my lab to contemplate the fine points of associative and non-associative learning (with little luck), when I saw a few plump ... more »
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anonymous
- Jan 21, 2009, 6:41p
i would like to travel back to time before the universe was created..
nikhil
- Jan 21, 2009, 7:18p
ahh... but where would you land? what would be your GPS coordinates? if your GPS coords didn't exist at that point in time, i'm not sure you'd be able to successfully travel to then..
Basil Rush
- Dec 21, 2009, 12:57p
Forwards definitely to start with, then perhaps backwards to take corrective action if forwards scared me.
I'd love to know what happens to us all in a thousand years time. Whether we survive another ice-age, whether we ever understand that elegans worm properly let alone develop some strong-AI.
I'm not sure I'd spend much time researching what happens to little old me. Though if I end up in the future and there's some way of extending my life further I suspect I'd have to take the opportunity.
Now the grid reference and exact date are going to take some serious consideration.
Controlling robots with your mind
Nov 8, 2008, 12:15p
It's the stuff of which sci-fi dreams are made. Mind control, well, not of another person, but of a robot. Want your laundry done? Tell your robot to do it. But not just tell it, think it.
That's the idea, anyway.
Before I applied to grad school, this stuff really intrigued me. While working at Google, so often I ... more »
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Sachin
- Nov 9, 2008, 9:50p
Movies hosted on Posterous.com
http://nikhil.posterous.com/
Garry
- Nov 14, 2008, 11:36a
Wow, this is remarkable work.
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