22 September 2016

gene and race

So there was this discussion on non-racialism at this book launch last night ...
and a member of the audience asked that typical question about the obvious genetic basis to race.

I was working up to try and answer there, but found it a bit hard to get my thoughts together in time. So below is working toward how I'd like to answer that in future. I'll correct/refine it with time, hopefully, and corrections and comments from you, the anonymous or not anonymous public, are as welcome as always.

 Attempt One:

Once our very early, singular human population separated geographically (after what appears to be a series of survival bottlenecks), they evolved separate and particular traits according to the now well understood processes of natural selection and genetic drift. 

Even while populations were largely separated, there was still sufficient movement and interaction to allow for genetic information to pass between populations. This, most importantly, would have included the successful spread of immune response adaptations and anti-parasite counter-measures vital to early population survival. [which is why all so called races have within their populations a spread of proteomic pathways for immune function that are common between races] 

As populations interacted and genetic information spread, there are a few mechanisms by which certain traits persisted within local populations, despite the relatively thorough statistical mixing of other genetic traits. The  mechanisms that ‘preserved’ local ‘race type traits’ include environment specific adaptations (like skin colour) that were continuously selected for within separated populations by survival pressure, and culture-specific sexual selection criteria - that proceeded along with cultural evolution. There are more mechanisms i think, but these two come to mind for now.

Via these mechanisms, an aggregation of certain traits (the sexual selection model accounts for why these are most often just externally visible) would accumulate within populations, while allowing the fortunate mixing of other vital genetic survival strategies without which local populations would most likely have fallen from parasite/pathogen load/stress.

This explains why, with the exception of this small percentage of ‘race type traits’, when looking at particular sequences, we often see more genetic diversity within races than between them — for example, there will be a particular immune system function that is expressed in different ways by several different protein pathways (lets call them A,B,C,D) and each race will have individuals carrying sequences for A,B,C,D. For the larger pathways, two individuals from different ‘races’ carrying the sequences necessary for A will often have more in common genetically with each other than with members of the same race carrying sequences for B, say.

[Immune function has been a big driver for evolution throughout the entire animal line, and so its not for nothing that it gets emphasised when discussing genetic variation.]

Even as our populations experienced civilisational shifts that allowed for more interaction between populations and more and more geographical displacement, patterns of mechanisms like the culture-specific sexual selection mentioned above - now intimately coupled with power, violence, etc. - still worked to keep certain traits prominent within local populations. 

Anyway, I think that's the type of traits the dude from yesterday mentioned. That small percentage of genetic traits, often highly visible, that we based the myth of race on.

 added later:

Of course, the other reason that immune system is so important when discussing us, is that in the very brief evolutionary time since we split up, nothing much else changed.

Sure some of us lightened our skins and straightened our hair, but these were almost insignificant changes when seen against our vast evolutionary history.

The most significant changes to humankind since our ‘forking’ is that the big brains that we evolved before we split led to us being super successful wherever we went - and that success was met in turn by a multitude of parasites rushing in to live off a newly found ecosystem - us.

So, most of our real evolution as humans, neglecting the very very minor surface tweaks, have been in complex immune system responses to those parasites since we became successful. That is why we are closer to members of other races that share our immune pathways than those of our race that don’t - immune system complexity makes up most of our evolution since we got here.

07 June 2016

Are We Shifting to a New Post-Capitalist Value Regime?

RT @mbauwens (Michel Bauwens): Are We Shifting to a New Post-Capitalist Value Regime? https://t.co/l1tn1LEs0R (one of my best lectures)

"We will argue that there is consistent evidence that the structural crises of the dominant political economy is leading to responses that are prefigurative of a new value regime, of which the seed forms can be clearly discerned."

https://www.youtube.com/watch?v=CltUp19s9lc - video lecture. 45mins. worth the watch.
... notes to follow

25 May 2016

race and inequality links flow both ways

Racism is also emergent en-masse because it allows a population to subconsciously rationalise their privilege. So instead of just causing social injustice, racism is also a result of social injustice. The more you see racially implemented social privilege, the more you have to apply racist models to subconsciously justify that privilege - when you have it.

07 May 2016

principles of hierarchical-temporal-memory

HTMemory and Sparse Distributed Networks. Lots of progress in understanding the neocortex - how intelligence works in the brain - and modelling that for a cortical approach to machine intelligence

UPDATE: broken link: Video moved to http://numenta.com/learn/htm-videos-from-jeff-hawkins.html.

Direct link on youtube: https://youtu.be/6ufPpZDmPKA

05 May 2016

JeffHawkins OnIntelligence HTM Sparse-Distributed-Representations GroK Numenta
WardCunningham FederatedWiki

and over there..
CraigVenter - SyntheticBio -

09 March 2016

Getting WikidPad running on Mac OS-X El Capitan

WikidPad, the excellent personal wiki tool and my knowledge-base of choice hasn't been working on my mac ever since my fresh install of El-Capitan, some time ago. There was some issue with the package installer for wxPython not running on El-Capitan, and just too much real work demanding my attention ... 

So I made do with the version on my Ubuntu desktop, and by accessing the sync'd plain text wiki files directly from my text editor - Sublime Text - on my mac. Good enough to survive with - but just barely so.

Today I decided that the time had come to end the pain, and so here is a brief log of the fix - to help anyone else that needs this, including quite possibly my future-self.


To start off with I chose to use an older version 2.8 of wxPython, because of numerous reports I'd seen on the WikidPad forums of errors while running under wxPython3
And as always, I use the latest release of Wikidpad - in this case version 2.3beta13_01.

- I used wxPython2.8-osx-unicode-

2) Change security on your mac to installs from all developers. You get a weird message saying that the package doesn't exist if you don't. 

3) The wxPython installer package now runs a little further before failing with another weird error to the same effect: 
The Installer could not install the software because there was no software found to install.

This apparently happens because wxPython is using a legacy script, and the bundled installers were deprecated and are (as of El Capitan release) unsupported. 
The solution was found on the following stack-overflow page: http://stackoverflow.com/questions/34402303/install-wxpython-in-osx-10-11

I'll repeat the instructions here. Use the name of your wxPython file in place of wxPython-ABC below (for the file we chose above replace wxPython-ABC with wxPython2.8-osx-unicode-

3.0) Let's assume that you have already mounted the dmg and you have moved the pkg folder to a working folder ~/repack_wxpython.
cd ~/repack_wxpython
cp -r /Volumes/wxPython/wxPython-ABC.pkg .
3.1) Use the pax utility to extract the payload file (pax.gz) from Contents/Resources to a folder that will become the root of your new package.
mkdir pkg_root
cd pkg_root
pax -f ../wxPython-ABC.pkg/Contents/Resources/wxPython-ABC.pax.gz -z -r
cd ..
3.2) Rename the bundle's preflight/postflight scripts, to preinstall/postinstall scripts, as required for flat packages, in a scripts folder.
mkdir scripts
cp wxPython-ABC.pkg/Contents/Resources/preflight scripts/preinstall
cp wxPython-ABC.pkg/Contents/Resources/postflight scripts/postinstall
3.3) Create the flat package using the pkgbuild tool:
pkgbuild --root ./pkg_root --scripts ./scripts --identifier com.wxwidgets.wxpython wxPython-ABC-output.pkg

4) Once that is complete, install wxPython from the new output package. If you use the version I did, that will be wxPython2.8-osx-unicode-universal-py2.7-output.pkg. Finally, wxPython should install!
5) Now, download WikidPad source from http://wikidpad.sourceforge.net/. The direct link for the version I used is http://downloads.sourceforge.net/wikidpad/WikidPad-2.3beta13_01-src.zip

6) Run WikidPad from source:
cd to directory where you unzipped the source - in my case:
cd ~/apps/wikidpad/WikidPad23 
then launch WikidPad with the following:
arch -i386 python2.7 WikidPad.py 

7) At this stage I got a python error from wxPython:
File "/usr/local/lib/wxPython-unicode-", line 3917, in Bind
    assert callable(handler)

8) Instead of tracking this down properly, I used a temporary fix by commenting out the assert: 
- open "/usr/local/lib/wxPython-unicode-", line 3917
- comment out line 3917
  assert callable(handler) 

9) Wikidpad opens and runs! .. but will only work on wikis using the Gadfly db - No SQLite wikis run. I saw the following error when trying to open my wiki:
ERROR: required data handler "original_sqlite" unknown to WikidPad

10) To fix this, I had to use homebrew to install sqlite3 with universal support:
brew install sqlite3 --universal

11) Then soft link the sqlite3 dynamic library into the WikidPad source folder
cd ~/apps/wikidpad/WikidPad23/
sudo ln -s /usr/lib/libsqlite3.dylib libsqlite3.0.dylib

12) Try running again from source ....
cd ~/apps/wikidpad/WikidPad23
arch -i386 python2.7 WikidPad.py

... and WikidPad should launch fine now.