Skip to main content


A new type of mathematics

From TEDxMontreal:

John von Neumann: The Computer and the Brain 

Nature article on 2-photon microscopy: Visualizing hippocampal neurons with in vivo two-photon microscopy using a 1030 nm picosecond pulse  (January, 2013 - free online access) by Ryosuke Kawakami, Kazuaki Sawada, Aya Sato, Terumasa Hibi, Yuichi Kozawa, Shunichi Sato, Hiroyuki Yokoyama & Tomomi Nemoto

Singularity University:
- David Dalrymple's antidisciplinary, non-institutional science and technology project for digital replication of the functionality (“mind”) of simple nervous systems (“brain”)
Recent posts

It ain't what you don't know that gets you into trouble. It's what you know for sure that just ain't so.

-- Mark Twain

So far, most of the posts in this blog have been focused on building a 'bottom-up' understanding of how the brain works - from how DNA works up to how individual neurons work. Lots of good science to base all of this stuff on. It is difficult to go further 'up the stack' in this way, however.  How do neurons work together to do useful things? How are small-scale networks of neurons structured and how do the neurons interact in order for us to do simple things like rhythmically tap a finger?

Are we there yet?
Every decade or two the scientific community gets wildly optimistic that we will be able to fully understand how cognition works and be able to replicate the process in some non-biological system. It's been named many things over the years - cybernetics, artificial intelligence, computational intelligence, cognitive computing (see for a nice overview).  And yet, with all of the money tha…

Magnetoreception - a gift from Mars?

I've been finding lately that if you look deeply into just about any aspect of life it quickly becomes fascinating. Like migration, for instance...

The story starts with something called 'magnetotactic bacteria' - bacteria that have DNA that creates tiny magnetite (Fe[sub]3[/sub]O[sub]4[/sub]) particles that can act as tiny compasses...

From Magnetotactic bacteria
Magnetites from magnetotactic bacteria MV-1 are elongated. The elongation adds to the magnetic pull of these tiny compasses and thus helps the bacteria locate sources of food and energy. This team of authors found that the elongation was accomplished by the addition of six faces, shown in red in the figure [above]. "The process of evolution on Earth has driven magnetotactic bacteria to make perfect little bar magnets, which differ strikingly from anything found outside biology," says coauthor Joe Kirschvink

And it turns out that birds, sea turtles and salmon also have these tiny magnetite crystals... F…

Diffusion Imaging - Mapping the Connectome

From The Human Connectome Project Is a First-of-its-Kind Map of the Brain's Circuitry:
Working with $30 million and just half a decade, the Human Connectome Project aims to create a first-of-its-kind map of the brain’s complex circuitry, detailing every connection linking thousands of different regions of the brain. ...
The project aims to tap state-of-the-art brain scanning technologies, including diffusion imaging, various MRI methods, and magnetoencephalography to map not just how messages move through the brain, but how various regions work together via networks and networks of networks to achieve the complexity that is the human mind. With map resolutions down to the voxel – small swaths of grey matter containing about one million neurons each – researchers estimate the HCP will generate about one petabyte of data, which will require its own supercomputer to process.

All that scanning, data gathering, and analysis should pay off though, HCP researchers say. The end result will …

Junk DNA: "Listen to your junk man - he's singing"

"Listen to your junk man - he's singing ... All dressed up in satin, walking past the alley..." - Bruce Springsteen, New York Serenade

Junk DNA is looking mighty fine lately. Only a few years ago, the non-coding regions of DNA that make up over 95% of the genome were looked upon as the uninteresting desert wastelands between the regions of DNA involved in protein synthesis. How times have changed!

'Junk' DNA not junk but key to complexity

There's a very nice video on Gene Regulation(free) from Science Magazine that discusses the pivotal roles that these non-coding regions of DNA play in our genome.

As John Mattick of The University of Queensland states at the end of the video:"We're just realizing that we've only got to first base and we have a long way to go, and most of the journey forward is going to be dissecting, analyzing and rebuilding an understanding of the massively parallel and extremely sophisticated RNA regulatory circuits, which rea…

Connecting the dots... "Let us begin anew"

As I've learned more about bio-systems, starting from water molecules and working up to synapses and networks of neurons, I've come to appreciate how incredibly powerful and compact the molecular computing substrate that life is built on top of is. Our most powerful supercomputers take days to calculate how one protein molecule folds, when the simplest bacteria can perform millions of these operations in parallel in seconds. What these simulations give us, however, is insight into exactly what special characteristics each of the proteins has in all of the various shapes it can assume. Building up from this low level understanding, hopefully we will be able to understand what the larger-scale purpose is for each of the various signaling chains and genetic transcriptions that are taking place, and perhaps we may one day be able to model these complex molecular interactions using state machines and logic that allows us to achieve a functionally equivalent set of operations withou…

"Once more into the breach, dear friends, once more!"

The more I read about "Cognitive Computing", the more disenchanted I get with most of the work being done under this banner. There is an awful lot of hype going on here: everything from university researchers that claim how simple it is to create a silicon chip that accurately emulates millions of neurons and projects to create silicon prosthetics for some of the major centers in the brain to overly ambitious claims stating how close we are to getting computers to 'think' and thus to the resulting 'singularity'. Most 'cognitive computing' efforts seem to miss the point that there is more happening here than simple electrical signaling over a network. So coming across the following articles and podcast was like a breath of fresh spring air:

Complex Synapses Drove Brain Evolution:

ScienceDaily (June 9, 2008) — One of the great scientific challenges is to understand the design principles and origins of the human brain. New research has shed light on the…