Drew Berry: Animations of unseeable biology

[rhody]

We have no way to directly observe molecules and what they do -- Drew Berry wants to change that. At TEDxSydney he shows his scientifically accurate (and entertaining!) animations that help researchers see unseeable processes within our own cells.

Watch the TED video, atty, pathagorean, aperion, pay special attention around 6:35. Two strands of DNA bundled and interface between the micro tubules (made up of about 200 different types of proteins). The tubules act as a signal broadcasting system, and as an attention sensing system and a are mechanical, 8:02). As Berry's ends his talk, he says exploring at the frontiers of science is "Mind Blowing". Uh... yeah, I wholehearted agree, this is warping my mind to think that something like this is happening in my bodies billions of cells right now.

I wonder what Roger Penrose would have to say about Berry's comments of the function of micro tubule's. I wonder if he would be pleased, surprised...

Rhody...

 

[JorgeLobo]

This is an animation. As consistent with relevant data and instructive as it may be, it is an interpretation. We still have no way to directly observe. It is hype to claim that it allows us to "see" the unseeable.

 

[apeiron]

Two strands of DNA bundled and interface between the micro tubules (made up of about 200 different types of proteins). The tubules act as a signal broadcasting system, and as an attention sensing system and a are mechanical, 8:02).

Great animations. Note that it is the kinetochore - http://en.wikipedia.org/wiki/Kinetochore - which has the rich complexity. Microtubules are just general purpose structural elements not information processing devices as such.

I know Hameroff played them up as first potential cellular automata computers, then quantum coherence harnessing computers, but that is crank science.

The take home message from this video perhaps should be that if so much complex informational control and dynamic activity can be taking place on the molecular scale in every cell, why is it so surprising that whole brains, tying together 100 billion cells, connected to an outside world, should have an immensely rich play of states.

On the one side you have science talking about staggering biological complexity. On the other, you have crackpots saying nothing really happens until some particular molecular structural sub-unit - which has a self-assembling half life of about 10 minutes in the thermal turmoil of a cell - "lights up" with quantum coherence. And somehow everything becomes conscious.

 

[Ryan_m_b]

Albert's Molecular Biology of the cell used to (I'm not sure about the most recent edition) come with a CD with animations, some of which were in that TED talk. I think artistic and accurate animations like this are vitally important, not just for researchers but also for kids. I think more videos like this should be used in lower and upper school curriculums so as to encourage fascination with biology and chemistry. I may be biased but I think something like this would inspire far more than 2D symbolic cartoons of photosynthesis.

 

[nobahar]

I recently came across some really cool protein structures, and I was thinking we could have a protein structure thread. Members can post structures they find that they think are remarkable. It always amazes me, at least; and as ryan says, I think it gets people interested in biology.

 

[rhody]

I think more videos like this should be used in lower and upper school curriculums so as to encourage fascination with biology and chemistry.

I agree Ryan, and if biology is not their gig, then perhaps computer simulation and gaming would be up their alley.

The take home message from this video perhaps should be that if so much complex informational control and dynamic activity can be taking place on the molecular scale in every cell, why is it so surprising that whole brains, tying together 100 billion cells, connected to an outside world, should have an immensely rich play of states.

For once we are on the same page aperion, nice for a change, (just kidding). Seriously, after seeing that and reading about the brain for the past 3o years I feel safe in saying we know a lot about what and where things take place in people and animals who are healthy and diseased. The mixing bowl involving the progression, diversion and combinations of how and why the parts function the way it does, IMHO we have a long way too go. Consider the vision areas in the brain for instance, http://kyb.tuebingen.mpg.de/fileadmin/user_upload/files/publications/attachments/bartels1998_colorarea_%5B0%5D.pdf, which has characteristics of the known V4 region. The point being is that the visual mapping effort (because it was so new) resulted in disagreement between researchers who had overlapping studies and were reporting different results. I don't think the period of 1994 to present, a mere eighteen years is sufficient to claim success in how a large part of the brain (the visual area) works. We have made some progress for sure, but as this graphical illustration hints, we have a long way to go to reach a "set of first principles" regarding its function.

Rhody...

 

[Ryan_m_b]

I think more videos like this should be used in lower and upper school curriculums so as to encourage fascination with biology and chemistry.

I agree Ryan, and if biology is not their gig, then perhaps computer simulation and gaming would be up their alley.

In response to this http://fold.it/portal/ seems pertinent.

 

[apeiron]

Consider the vision areas in the brain for instance, http://kyb.tuebingen.mpg.de/fileadmin/user_upload/files/publications/attachments/bartels1998_colorarea_%5B0%5D.pdf, which has characteristics of the known V4 region. The point being is that the visual mapping effort (because it was so new) resulted in disagreement between researchers who had overlapping studies and were reporting different results.

Well everyone involved agrees that the visual hierarchy is indeed a hierarchy .

The controversy here only concerns whether the "colour centre" is split so that hemifields are handled separately, as appears the case in primates, or are instead integrated into one location, as appears the case with humans.

Primates were investigated first (the studies that proved the notion of hierarchical organisation of course). The expectation was that humans would follow suit, but we don't seem to.

You are thus getting into a wrangle over the fine detail of the brain's hierarchical organisation. And you are seeing the usual lumpers vs splitters argument - some argue for more modular stories, some more distributed.

 

[rhody]

In response to this http://fold.it/portal/ seems pertinent.

Cool,

Foldit is an online game in which humans try to solve one of the hardest computational problems in biology: protein folding.

Amazing what the human visual cortex can do when applying itself in a focused fashion to the problem.

Rhody...

 

[rhody]

...the usual lumper vs splitters argument...

lumpers versus splitters... how humbling, I kind of like that.

Rhody...

 

[apeiron]

lumpers versus splitters... how humbling, I kind of like that.

Talking about advances over past 20 years, a key one is our understanding of the principles of scalefree networks - a model of hierarchical organisation which successfully combines the lumpers and the splitters!

Both can now be right if they take option B.

But in science, it still takes two sides to make a discovery seem like a discovery. Someone must be wrong to allow the other to be right - and take the prize.

 

[rhody]

I wonder what Dick Feynman would say about all this ? I for one, really miss that guy, sigh... I know, Feynman neuro diagrams, lol.

Rhody...

 

[Ygggdrasil]

Bah, who needs animations when you can directly image the motions of molecular motors in real time. For example, see Kodera et al. 2010. Video imaging of walking myosin V by high-speed atomic force microscopy. Nature, 468: 72. http://dx.doi.org/10.1038/nature09450[/URL]. Check out some of the videos that come with the paper:

http://www.nature.com/nature/journal/v468/n7320/extref/nature09450-s3.mov

The movie I linked above shows myosin V (the "v" shaped molecule), a motor protein that walks along myosin filaments (the linear tracks in the movie). These images were taken using atomic force microscopy, a technique that uses a sharp tip to "feel" around a sample and create a topological map of the sample. It has recently been possible to acquire AFM images very quickly, enabling the above imaging of molecular motor proteins. Of course, the technique seems fairly difficult to implement and has some limitations (for example, you can't peer inside cells with it), but being able to directly watch motor proteins through their catalytic cycles will certainly aid in understanding the details of the mechanisms.