01 December 2012

natural selection at the largest scale


Evolution / Natural Selection at the largest scale we could possibly ever know about - and the idea might of course be forever non-testable.

There's an earlier post on this here - http://jaysenn.blogspot.com/2006/10/natural-selection-of-universes.html

our tools are broken

Regular Reminder: Social networking tools and other information infrastructure that is not owned by us (copylefted) is almost by definition, fundamentally broken - because anything less, severely limits the extent to which we can use, experiment, and grow these into useful universal assets .. esp true in the long term.

the list of our broken tools include facebook, google search, and the operating systems windows, mac-osx, ios, and bits of android. (linux is completely ours)

21 November 2012

fedora 17 .. todo list post install

So, a few days ago, I installed Fedora17, partly because I wanted a straight gnome-shell experience, and partly because I hadn't seriously tried a rpm based distro yet. The short of it is, that I'm really enjoying the standard gnome-shell environment - especially how customisable it is compared to Unity. So much so, that I think I'll be working off this linux partition for a while to come.

That said, Fedora did take significantly longer to get the everything installed than either Ubuntu or Mint does, mainly because it does not come standard with any non GPL'd software in it's default repository - but with a fair amount of googling, all was eventually sorted.

Now, only after all of the searching and tweaking, and more searching and installing was done, have I come across a good, comprehensive how-to that would have saved me loads of time if I had only stumbled on to it earlier.

Smashing Web's Fedora 17 Post Installation guide covers just about everything you would want to add to a fresh Fedora install. Here's a list (not complete) of the packages I've used from there:

Appearance and customisation:
yum install faenza-icon-theme
yum install gnome-tweak-toolyum install dconf-editor

installed some of the gnome-extensions listed there (will list these later.. possibly)

a better software installer:
yum install yumex

to enable the RPM Fusion repository just install (this allows you to get at some of the packages below)
yum localinstall --nogpgcheck http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-stable.noarch.rpm http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-stable.noarch.rpm

add the adobe repository for downloading Acrobat Reader, by running this at the terminal
## Adobe Repository 32-bit x86 ## rpm -ivh http://linuxdownload.adobe.com/adobe-release/adobe-release-i386-1.0-1.noarch.rpm rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-adobe-linux ## Adobe Repository 64-bit x86_64 ## rpm -ivh http://linuxdownload.adobe.com/adobe-release/adobe-release-x86_64-1.0-1.noarch.rpm rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-adobe-linux

yum install flash-plugin nspluginwrapper alsa-plugins-pulseaudio libcurl

to play various Video formats:
yum install gstreamer gstreamer-plugins-good gstreamer-plugins-bad gstreamer-plugins-ugly
yum install ffmpeg ffmpeg-libs

dvd playback / ripping / players

yum install libdvdread libdvdnav lsdvd
rpm -Uvh http://rpm.livna.org/livna-release.rpm
yum install libdvdcss
yum install vlc
yum install mplayer mplayer-gui smplayer gnome-mplayer

and my music player of choice:
yum install clementine

BitTorrent client and IM client:
yum install transmission
yum install pidgin

yum install nautilus-open-terminal
yum install p7zip p7zip-plugins
yum install filezilla

yum install netbeans (no longer in repo - see below)
yum install eclipse
yum install spe
yum install geany
yum install cssed
yum install anjuta

To run yum you need to be in a terminal with root privileges.
just type:
su -
at a terminal, then enter your root password, and then paste in the yum install commands and wait for the installs to finish.

I found two commands that would not work from the howto. One was "yum install netbeans" - its been removed from the repo because it is no longer GPL compliant. Instead follow the instructions to install it here: http://www.matthewhughes.co.uk/netbeans-on-fedora-17/
The other was "yum install gnochm" - instead use:
yum install chmsee

20 November 2012

explaining epigenetics .. adding more nurture to the nature-nurture mix

A log-worthy RadioLab episode - Inheritance - Which includes a lovely explanation of epigenetics, explained through some beautifully told stories, as usual.
Listen, to find out how, for instance, mom's licking turns on a behaviour, via protein, via turned-on-gene ..

From the site: http://www.radiolab.org/2012/nov/19/:
"Once a kid is born, their genetic fate is pretty much sealed. Or is it? This hour, we put nature and nurture on a collision course and discover how outside forces can find a way inside us, shaping not just our hearts and minds, but the basic biological blueprint that we pass on to future generations."
the file is here ...

and streamed here

Another brilliant RadioLab's episode. Check out their podcast - it's some of the best produced radio, ever! .. methinks

07 October 2012

sugars, glucose, fructose, etc. etc.

possibly worthwhile 38 min audio doccie in this science and the city podcast
the mp3 for the episode is here http://ne.edgecastcdn.net/000210/podcasts/AThoughtForFood_SugarInTheMorning.mp3

Don't get too annoyed when you hear the (possibly) pro corn-syrup scientists talking their science in this interview - it still comes out that even though fructose and sucrose are roughly the same in organic chemistry, we've evolved to getting the majority of our sugars via glucose/carbohydrates. So we hear how the ratio fructose:glucose is significant, that we drink and eat way too much fructose via corn-syrup's extreme place in our intake, and how that's not a good idea.

The following gets affirmed and boosted too. the carb/sugar content in a can of soda is about equivalent to a full meal, so unless you replace a meal with that soda, or do enough exercise to burn off an extra meal, drinking cokes and such are going to be pretty bad as a long term behaviour.

That being said, one of the points being made is that the science is contested - despite the smoking guns, we don't yet have a complete mapping of the complex pathways involved.

grokking htm for ai

or .. Notes on Understanding Hierarchical Temporal Memory and its use in Artificial Intelligence and Knowledge Representation.

A few years ago I blogged about a TedTalk by Jeff Hawkins on how brain science will change computing. To summarize, the idea was that intelligence was more about prediction than behaviour, that the neocortex evolved to to basically be a mechanism to predict the future, and that it could be simply modeled as vast networks of hierarchical elements that predict their future input sequences - a hierarchical temporal memory (HTM) system.
Importantly, rather than the much more difficult task of modeling the entire brain, including the ancient and incredibly complex areas below the neocortex that deal with things like emotions and behaviours, one could approximate intelligent behaviour by modeling the much simpler cortex as a HTM - with simple repeated structure and algorithm.

Here's an update with more from Jeff Hawkins, and HTM ..

The following links are for a 2008 talk given by him on AI.. give it a watch
Jeff Hawkins on Artificial Intelligence - Part 1/5
Jeff Hawkins on Artificial Intelligence - Part 2/5
Jeff Hawkins on Artificial Intelligence - Part 3/5
Jeff Hawkins on Artificial Intelligence - Part 4/5
..some notes from the above:
- Work started by looking at what the structure of the brain could tell us about memory/knowledge storage.
- Memory - the bottom is close to the sensory system - retina for visual system, skin for touch, ears .. etc.
- Top nodes in the hierarchy get assigned to specific concepts/objects - like the individual neurons that fire every time you see or imagine Tupac and only Tupac (true story) 
- All nodes in the hierarchy are basically the same, and they all ..
    - look for temporal and spatial patterns/sequence
    - and pass the name of the recognized sequence up
    - pass the predictions they make down the hierarchy
- You get fast changing patterns at the bottom, slower changing as you move up the hierarchy.
- After training an HTM system (in silicon or neurons), you get something that learns hierarchical models of causes (statistical regularity) in the world - using bayesian techniques to build a belief propagation network.
- HTM's make the assumption that the world is hierarchical
- Predicting what can come from htm:
   - we cant, but ..
   - it could be much faster - neurons are slow
   - it could have other architectures - bigger bottom layers, fueled by big-data for example, or from large sensory arrays, etc. 

The latest thing I've come across from Hawkins' company Numenta, is their new Grok system (love the Heinlein reference). Grok is a cloud-based prediction engine that finds complex patterns in data streams and generates actionable predictions in real time. Check it out on Numenta's site, and their tech page
(more to follow.. soonish)

19 June 2012

mean world syndrome

Mean World Syndrome is a phenomenon where the violence-related content of mass media convinces viewers that the world is more dangerous than it actually is, and prompts a desire for more protection than is warranted by any actual threat.

10 June 2012

The Mappist

The first story on this mp3, The Mappist by Barry Lopez, is probably one of the better suggestions i can make for a spare 34 minutes sometime this sunday -- listen


This short story was produced for NPR's Selected Shorts - subscribe to their #podcast athttp://www.selectedshorts.org/podcast/ for an often superb stream of short #fiction. (beats the shit out of tv)

02 March 2012

the long road to a cell

Check out this truly amazing representation of the molecular machinery at work within each of our cells.
One thing that helps understanding these processes is to remember that at these scales, molecules are knocking around at much more than a million times per second - so it isn't that the right molecules miraculously find and fix themselves exactly where they belong in order to perform these very complex tasks (as these depictions sort of suggest), but rather that they are perpetually colliding at incredible speeds, and that it is only the (relatively) rare collision that is successful enough to allow the process to move forward.

All these random accidents accumulate, with the basic rule that what can persist, does, and on larger timescales seemingly miraculous complexity emerges.

Still, judging by the glimpse we get from this video, it's no wonder that evolution (a process that works with that same basic rule from above) took longer with these inner workings of a cell (2.8 billion years) than all the further developments on the tree of life combined (1 billion years)

.. give or take.

24 February 2012

more bonobo and less chimp

Above is SETI's Big Science podcast with an episode on us self-aware animals. Within is a fascinating bit on bonobos, our closest relatives, and their peaceful, matriarchal, and hyper-sexual society. The bonobo bit starts 16 minutes 30 seconds into the show but the whole show is worth the listen.

I'll try a bit of summary here.. Bonobos, instead of being male dominated with lots of violence in their societies like the chimpanzees, are matriarchal with little to no violence and aggression - they enjoy much more open relationships, with much less tension, much less fear of manipulation, and much greater cooperation. Chimps are excellent cooperators too, but their cooperation breaks down when emotions get in the way (like with us humans, emotion often constrains cooperation).

This reduced social tension and increased openness and trust is presumably linked to the bonobo's focus on play and their constant and indiscriminate sexual activity - between all members of the group with little regard for gender or age - sex as greeting and social bonding - sex for conflict resolution and sex for post conflict reconciliation.

Anyway, give it a listen - Vanessa Woods, the author of The Bonobo Handshake takes the comparison between our two closest cousins nicely further. The bonobo handshake, by the way, is when two females rub clitorises together with ever increasing frenzy until orgasm - this fosters great bonds between the females who cooperate to 'correct' any of the much larger males if they begin to exhibit chimp-like violence or aggression. Oh and males have their version of the handshake too.

Also came across this nice (though long) video interview with the author, here: http://www.youtube.com/watch?v=5CGMJiGe6u4


UPDATE: found this great related TedTalk here: Isabel Behncke: Evolution's gift of play, from bonobo apes to humans

"I just came back from a community that holds the secret to human survival. It’s a place where women run the show, have sex to say hello, and play rules the day.” 

"Chimpanzees are well known for their aggression. Unfortunately, we have made too much of an emphasis on this aspect in our narrative of human evolution. Bonobos are the other side of the coin."

03 February 2012

skinny legs, or jitterbug perfume?

Every 3 or 4 years, memory suitably dulled, the great purple divining rod pulls in a particular direction, and i am drawn to the spine of Tom Robbins' skinny legs and all (or its entry in my e-readers index) - the useful thing about time and losing one's memory, all the surprises and wonder remain intact.

multiple self .. and advertising

The brainstem and the mammalian brain. Deeper and wider than the new, beyond logic. That is where advertising works, not in the upstart neocortex. What we think of as 'mind' is only a sort of jumped-up memory machine, piggybacking on the older mammalian mind and the positively ancient reptilian brainstem, but our cortex and our culture tricks us into recognizing it as all of consciousness. The mammalian spreads continent-wide beneath it, mute and muscular, attending its ancient agenda. And makes us buy things. 
--mostly william gibson

... and from someone else:
"For it appears to be an inborn and imperative need of all men to regard the self as a unit. However often and however grievously this illusion is shattered, it always mends again."