11 December, 2014

How birds lost their teeth, a theory...





In a recent publication of a landmark study where 40 species of birds DNA were sequenced and cross compared some really illuminating findings about probable evolutionary reasons for specific traits and relationships were revealed. One of the most interesting things is what was not realized about the origins of the birds beak.

"Although birds are descended from dinosaurs, they have no teeth. Most previous studies have suggested the common ancestor of modern birds lacked teeth, but other work has disagreed. The new findings add support to the idea of a toothless common ancestor, because all birds sampled share some mutations that turn off five genes for building teeth.

Researchers estimate that teeth, or at least enamel-covered teeth, disappeared about 116 million years ago in the ancestry of birds. They suggest beaks replaced teeth in a two-step process. But it's still not clear why beaks took over for teeth, said study author Robert Meredith, a biologist at Montclair State University in New Jersey."


Indeed, this line immediately brought up an idea of how it might have worked based on what we know about evolution and the forces that cause adaptations to flourish or to disappear as lineages continue to specialize into constantly varying niches. I'll start by stating that it should seem obvious that the common ancestor for birds...that from which the line descended as prior that they were classed more accurately as dinosaurs with features than birds is what we know from dinosaurs that they had teeth.

Even if the progenitor of the Avian line didn't have teeth itself it still descended from some land living dinosaur this is pretty clear from the many fossil finds of early proto Avian forms among the dinosaurs which have been found in China where it appears the Avian transition took off from 150 million years or so ago. We know for a fact that this ancestor did indeed have teeth as all early dinosaurs did...so how and why did birds loose them?

I think conservation of energy in the context of lineages exploring new survival niches created by the combination of access to feathers and trees tells the likely tale. The theories regarding bird flight that are most popular today advocate for a top down approach to evolution of birds, the theory being that animals attempting to gain the upper hand (literally) on their pray would do so from rock faces, vines and trees and bushes...stalking with feathered wings could provide gliding advantages that would allow a striking animal to both increase the glide length of their descent to the pray as well as slow the rate of fall allowing them a measure of increased success while hunting relative to those that do not take such advantages. A likely temporally significant adaptation was the formation of increasingly ossified skeletons to reduce the carrying weight of the animal and thus again increase glide distance and slow descent rate.

The genes of these individuals then propagated and the strategy continue to be employed from higher and higher vantage points selecting from those lineages individuals with either longer feathers or other advantages to such a mode of attack.

Eventually creatures like Archeoptrix ruled the forests where they took advantage of their feather laden hands and high vantage point to thrive but as those hands became wings and the descendants become capable of powered flight from the ground as their bones ossified. Mean while the strategy of hunting from the vantage point was replete with dangers...as these animals became less dense the animals they could target as prey continued to be lethal land living therapod or mammalian forms, the task of hunting was both dangerous (throwing yourself down from a high point is not exactly an optimal survival behavior trait) time consuming.

However something became more true the greater their ability to ascend the trees and later fly between them was unleashed. The new lineages were able to find different food sources away from those that their ancestors prayed upon, the vast access to nuts, seeds and fruit evolved around the same time as the angiosperm radiation continued apace, I posit provided a huge niche for potential exploration as a food source that up to that point no other large animal (besides the super massive therapod dinosaurs) were able to mine efficiently.





The early therapod descended avians who transitioned to more fruit and nut eating could satisfy their dietary requirements (which were increasingly more efficient compared to land living thanks to that high metabolism and low bone density they'd evolved) using these sources while not engaging in the dangerous activity of attacking much more bone dense and potentially lethal pray forms on the ground.

With food sources waiting in the trees the need to have teeth at great energy cost no longer presented itself as a requirement, the efficiency of eating nuts and berries with a beak would provide an advantage to exploiting those resources and so the first mutations in lineages to reduce tooth profiles likely allowed those lineages to more efficiently consume nuts and fruit while avoiding increased likelihood of death from not attacking ground pray. Several hundred or thousand generations later and the beak had spread as an adaptation across lineages exploiting this new (angiosperm radiation hit its stride around 160 million years ago right in the midst of the therapod to avian evolutionary shift) and relatively untapped regime.

So a multi step process of the energy efficiency for continuing to attack downward led to an increase in efficiency for attacking the static and safe food in the trees now evolving around them an increasing fruit and nut carrying capability, they had ascended to meet this static bounty rather than the dynamic and dangerous food they had descended from.
We know that birds in fact form a critical piece of the seed distribution puzzle for the angiosperms and so a synergistic relationship now formed explains the radiation and expansion of the flowering plants along with the dinosaurs and the insects who also enabled and thrived as the angiosperm radiation took place.

Update:

In a related discussion on this thread at Facebook a friend noted the insect radiation that was on going about the same time as a likely driving food source in the trees for early avian forms to use to supplant land based quarry. I assert this was indeed a factor but a lesser factor as insects still need to be captured at energy cost relative to fruits and nuts which are simply sitting there.
So step by step:

1) (~200 - 180 mya) Small feathered dinosaurs learn to ambush from increasing heights.

2) (~180 - 160 mya) Feathers evolve to enable greater height ambush without damage and better glide times. At same time Angiosperm radiation goes into full effect as insect synergy begins.

3) (~160 - 140 mya) Bone density reduction happens in early avian forms allowing yet higher ambush falls and glide times. Opportunity costs for teeth starts to dwindle as attack cost for land predators increases.

4) (~140 - 120 mya) Angiosperm radiation quickens as fruits and nuts evolve in force, insects explode provide secondary air born sources of food. Early avian cost for attack on ground exceeds cost for taking either insects or static fruits and nuts.

5) (~110 mya) True birds evolve specializing in either fruits and nuts and insects.




Links:

http://en.wikipedia.org/wiki/Origin_of_birds 

http://en.wikipedia.org/wiki/Flowering_plant

04 December, 2014

AOW: Shooting for the Moon instead of the Mountain




A recent Medium article exposes some of the drawbacks inherent in the business model of the TaskRabbit service.


 TaskRabbit is very much in the space that my Action Oriented Workflow mines for all possible work interactions but only for the subset of physical labor of a temporary and nature. They are a subset of the much larger space that AOW enables harnessing with both physical and knowledge work (this being the much bigger piece of the pie that WorkNetz will primarily focus on)...that said, one of the key features of the AOW technology  is the ability for delegated agents to REJECT work they do not wish to do OR to even simply never get work in their cue at all if they are not electing to receive it.

I saw this as a critical requirement of the system for two reasons:

1) If you give them the ability to reject they retain that sense of ownership, they are indeed their own boss and work on their own schedule as most people want and with Taskrabbits pivot are not denied.

2) Allowing people to reject work allows that work to move with alacrity to those who are available and want to do it, if you've got a global pool of options then this becomes MORE certain the larger your organization and or the larger your pool of possible contractors are.

:I explain why this is critical in my posts on Action Oriented Workflow but the sound bite can be had by flipping through this presentation deck I prepared last year to describe how AOW enable systems will work.

With the implementation of the autonomous work routing of the ADA (Action Delta Assessment) algorithm the determination of who gets a delegated action is done purely by the historical algorithm and those preferred nodes are virtual managers by virtue of the fact that their past performance has made them stars to the system and they still have the ability to re-delegate (reject work) that they get in their queue.

This virtual or dynamic management is the only type of management that should exist I posit, a real time assessment of ability to redelegate work trumps the manual distribution of labor that is done when people are in charge of teams of workers which is rife with opportunity for cronyism to skew results away from what would be ideal for the business. I elaborate on this in the AOW white paper.



When TaskRabbit was announced, I recognized it immediately as a play that was tacking toward what I'd already built with AgilEntity in the form of the AOW paradigm which generalizes the solution for any vertical physical labor or knowledge work. I considered describing WorkNetz the company I am working on now to present solutions built on the AOW paradigm as: "taskrabbit for everything" at some point...given this shift in their approach, which makes sense given that in any given geographical region, there is a low density of people who can mobilize, are skilled and willing to perform a specific physical task it is clear why as a target TaskRabbit was aiming too low, they built a rocket that only allowed them to reach for the mountain instead of the moon.



Solving the problem for one type of labor (physical) made sense as there would be no need to tackle the much harder problem of generalizing to all types of work actions irrespective of their nature as physical labor associated or knowledge work associated would be a much more difficult task one that I took on and completed when I completed the implementation of the Action Oriented Workflow technology in AgilEntity in 2005.

I chose to generalize the solution for any type of interaction and let the business decide how it is going to provide incentives to the agents it already has...what I defined as "in sourcing". This is critical as it prevents the attrition problem that is described in the article where once a person is set up with a tasker through the service why would they use the service a second time if they can get the direct contact information for that same tasker from the initial interaction? By enabling any existing business to turn all it's employees into an emancipated workforce of contingent laborers who are employees one can harness that existing workforce optimally to make action execution fluid and 24/7 possible and maintain this advantage even as the company grows from 10 to 10,000 "employees" distributed all over the globe.


Links:

https://medium.com/matter/hunting-task-wabbits-c60679bad0f6

WorkNetz AOW presentation slides

01 December, 2014

Master the Meta


About 6 years ago I wrote a blog post titled Mastering Multiple Mountains where I spoke about the interesting dynamic of interaction that happens between people with different levels of understanding of any given concept.

The difficulties of engaging an exchange of knowledge between these different levels of understanding are what make the art of diplomacy and consensus building an art. The need to constantly gauge the state of knowledge of the others participating in the conversation is required and is made more efficient the more any given conversant has multiple mastery of different areas of potential conversational exploration.

A corollary to this skill that I've been considering is highlighted by the advantage to communication enabled by those who master multiple mountains of knowledge and that is being able to consider a meta analysis of a given discussion. Meta analysis is slightly different from simply gaining knowledge across different areas and being able to then illuminate relative ignorance between oneself and others in discussion as was the scope of the earlier article. Meta analysis also involves being able to shift perspective from ones own state of knowledge to that of the other and then to restrict the 'view' to consider the reasons why the other may be taking a line of argumentation. It is related but tangent to that earlier article.

In all types of engagement being able to master the meta is a powerful tool in exposing where one may be led to ruin by the very veracity of the data that they hold as basis for their expressed knowledge even if that data and knowledge has veracity behind it, failing to engage in this shifting of perspective via meta analysis could lead to ruin.

For example being oblivious to the social mores that may be in place when discussing subject matter in public in certain cultures could lead to perceptions of great offense which in some places could make one subject to violent response without even realizing it.

Science fiction has often used this potential schism in social norms as fodder for story lines from Star Trek on but it is a critical failing of making assumptions about the perspectives and expectations of others irrespective of the state of knowledge that may be had by different participants in a conversation. So in attempts to relay information it is important to both recognize the differential knowledge sets that we have compared to those we are communicating with and also be able to inhabit those knowledge sets in order to guide our approach to building consensus...sort of a rudder in the water to the angling of a wind born mast on the boat of our path through the sea of ignorance toward a common island of truth.

10 November, 2014

Accelerating Humanities race to zero.



It's interesting to me how often people confuse the idea of being supported by government systems with the idea that those people are "lazy" or not being productive or creative in any way.

This is the height of the stupidity of such views. Ultimately we WANT to build a society where more people are able to survive without having to work if indeed that is what they want. This situation benefits all humanity as it ALWAYS has.

It is freedom FROM work that got us out of the daily subsistence survival JOB when we learned how to harness the patterns we saw in the environment with regard to locations for water and other sources of natural resource and flora and fauna we needed to survival.

That freedom FROM work got us to think about writing literature, induced us to build surpluses of our now readily gathered natural resources, created the first builders and engineers and craftsmen.

As our ancient ancestors all over the world became good at these things they discovered metal as a resource and learned to work it and used it to more efficiently mine the earth of plants and grain...which gave them even more time to think about ways to store and measure grain, mathematics was born.....writing and trade spread it all over the world.

The ease with which people could survive led to the emergence of art and philosophy and more invention.

So to sit back in technological hubris and with the assumption that there is something wrong with allowing people (any people) to have the choice of not working is not only completely wrong it is ABSURD.

It is freedom FROM work earned at hard edge of labor by our ancestors, built up into our technology and stored in the words of our languages and writing systems.... that has us living the way we do today in a significantly advanced society, mostly free from the grinding dangers of the environment...free of the daily act of survival in that environment and able IF WE WISH to create, to invent, to write, to pursue our ambitions or aims or to sleep our lives away.....THAT IS THE GOAL.

My driving aim having created the Action Oriented Workflow paradigm which takes the ability to enable people to free themselves from the NEED to work by leveraging technology,  is to get people to understand this....that we have to inverse this paradigm of thought that presumes freedom from work is some how bad or backward or "lazy".

Nonsense...absolute and complete nonsense, it is the polar opposite...it is how we got here as a species and if we want to improve,  it is the direction we MUST take all society otherwise with my brothers and sisters in technology rapidly moving toward replacing available sources of human work with automated or autonomous workers (my career for the last 16 years) we people will find ourselves in regimes of discord as displaced labor events accelerate. So leveraging technology to create workforce emancipation by converting systems to AOW driven systems, by building autonomous delivery and transportation systems (drones, robocars, robotrucks), by building autonomous manufacturing robots and facilities for mining and extraction fueled by electricity gathered at oceans of solar panels.

They've already been happening for the last 30 years and arguably since the industrial revolution but the return has over come the loss in terms of enabled freedoms for larger groups of humans (this is why the USG can now afford to support so many people on disability or other problems...again THIS IS GOOD....THIS IS THE GOAL.)

To think otherwise is to miss entirely the previous story of how we got here...which is not supposition it is 100% fact.

The relentless drive towards better ways to build hard drives, processors and networks is reducing the cost to massive compute power every year. Companies like Amazon, Apple, IBM, Salesforce.com, SAP, Microsoft and others are building "cloud" infrastructures that other companies are leveraging to make the task of building startups today significantly reduced compared to the past....today I can launch a startup entirely from my bedroom without need to buy a physical server, without need to touch a load balancer, a router  a switch...I don't need to hold a cd or a dvd to install my software on any of the machines I use....I can procure new machines as I need them and deallocate them as I don't need them and I can have them accessible across multiple geographic regions.

To build such a system just 10 years ago would have cost tens of thousands of dollars of physical procurement costs for hardware and hands on need to build it all together in some physical environment. The costs are all gone and I am much "lazier" with the work that would otherwise required dozens of people being done by one.

That has benefited us by allowing services built on such IAAS (infrastructures as a service) to extract value extremely efficiently...and then provide those services at low cost to consumers all over the world.

The race to zero is clear....in technology and it is clear that we can leverage technology to allow a race to zero in all areas of human existence...at least it was to me a dozen years ago and inspired why I started building AgilEntity and later inventing AOW. It's also why I've set forward to think about how technology used specifically can bring us to a world where humanity is coddled by a self healing infrastructure (SHI).

Getting people all people to a point where they can be lazy if they wish and thus be free to pursue an unbounded path in terms of creative expression is what we want.

May we get to zero with all deliberate speed.

Links:

http://sent2null.blogspot.com/search?q=aOW

http://sent2null.blogspot.com/search?q=SHI

01 November, 2014

New technique for in vivo gene modification, more like a CrispR-Cas9 supplement than a replacement



So some are cheerleading a new technique for inducing genetic modification.

The key issue that stands out with this new technique is indicated near the end of that article, it is NOT a permanent process.

First, the claim that the possibility of cancer formation exists with the process of Crispr / Cas9 is true but then the probability of formation is the same for a natural gene silencing operating which are constantly happening over the developmental life cycle of any organism.

That is why it is such an amazing technique to start, the mention of promoter addition as a possible bad thing doesn't make any sense to me (but I may not understand what they mean)...if you want to activate an inserted gene you need a promoter that is the switch essentially...to activate the inserted gene or by being found in a silencing operation is methylated.

In the final analysis to do all the things we want to do.

1) Repair existing genes in vivo (permanently).
2) Add in new genes in vivo (permanently).
3) Remove existing genes in vivo (of course permanently).

Crispr/Cas9 is a single stop solution that co-opts a robust natural system to employ those actions with risks that are comparable to the same actions being done naturally so there is no real disadvantage when you think of it from that perspective. Also, it stands as a multi prong approach...modulation of the associated protein configuration could radically improve specificity and reduce any possible side effects. A paper linked below details ways to extend the technique...it's more a toolkit for gene editing than just a one shot method like TALENS was before it.

I stand by my comment when I first heard of CrispR end of 2012, by 2017 Stockholm is calling Dr. Doudna (one of the principle researchers). It's a done deal.

I compiled a bunch of the seminal papers on the technology in my drive folder for those who haven't done a deep dive:

https://drive.google.com/folderview?id=0B9N6z_bRVUMmSklFbE9Da1hFa0U&usp=sharing

The article that does an excellent job of explaining what the problems are regarding oncogenesis risk and how those can be prevented (I think some have already been tried since this paper was written) are listed.

https://drive.google.com/file/d/0B9N6z_bRVUMmRWhwOHpxc2NhcUE/view?usp=sharing

:The short summary is that oncogenisis is not an inherent problem of the approach assuming it is applied 100% correctly but more a result of not ensuring uniqueness for the desired region of modulation (addition,removal or silencing). This would make sense as if you are trying to target a short sequence out of a strand of billions you need some way to disambiguate that one sequence from the many similar sequences that an improperly specific Cas9 program would produce. That said the authors (including George Church) indicate ways to get around these problems.

In the folder the paper that presented the use of CrispR with Cas9 to be a gene snipping tool is titled:

"Repurposing Crispr as an RNA guided platform for sequence specific control of gene expression"

https://drive.google.com/file/d/0B9N6z_bRVUMmMWU2VmxkdVZpWDg/view?usp=sharing

31 October, 2014

Dairy free "real" Milk on the way, thank GMO!

Science!!!

"Earlier this year, a synthetic dairy start-up called Muufri (pronounced “Moo-free") was founded by two bioengineers in California - Perumal Gandhi and Ryan Pandya. They’re working on perfecting an artificial cow's milk made from a special variety of yeast that has been genetically engineered to produce milk proteins.
Nicknamed an ‘out-of-body udder’, this system is designed to produce milk that retains the taste and health benefits of real milk, setting it apart from soy, rice, and almond milk varieties. Because as nice as soy-based ice-cream can be, it will never match the popularity of regular milk-based ice-cream, but what if Muufri ice-cream can get the taste just right?
"If we want the world to change its diet from a product that isn't sustainable to something that is, it has to be identical [to], or better than, the original product," Gandhi told Linda Qui at National Geographic. "The world will not switch from milk from a cow to the plant-based milks. But if our cow-less milk is identical and priced right, they just might.”

http://www.sciencealert.com.au/news/20142910-26413-2.html



--- That's one cruelty that hopefully can be eliminated from the captured animal prison system in a decade should this method be more efficient than getting milk from cows. Judging from their method I would say it is basically a guarantee...some advantages of deriving the proteins from yeast:

1) Well no cows! No cows in cages forced to stand and be milked by machines pulling their teets until they bleed. Now cows being abused by sadistic "employees" tasked with their charge (we've seen the abuse videos). No cows contributing to nitrogen off flows into rivers and lakes and thus contributing to acidification, no cows farting up a methane storm into the atmosphere already laden with green house gasses and other environmental fallout of the dairy industry.

2) Cow free cheese! Cheese is a product of churning milk fat with a culture of some sort until it produces cheese....if these GM yeast are producing all the right proteins than they should be perfect for producing all kinds of NON Dairy cheeses. Huge huge win....all the vegan's can start eating cheese again without pain of moral guilt.

3) Super clean production facilities....without cows or the bacteria issues associated with extracting milk from them...this milk is probably produced in an already semi pasturized state...if not fully clear of any harmless agents, after the yeast are separated from the proteins they produce and then mixed to the desired fat density  it should be drinkable straight away. In fact one can imagine the whole process being done in an apparatus that links production of the yeast proteins directly to filtering , directly to remixing , directly to packaging without any open air contamination points at all!! One mini machine with the right food for the yeast (all you need is sugar) and out the other end comes milk that you can't tell didn't come from a cow and that you can actually make cheese with ...which brings us too...

4) Butter! Churn butter milk and you separate the fats together into butterfat which is just those separated proteins linked up in a certain pallette pleasing way...likely would require salt but it would be butter and also produced potentially in a completely clean environment.

5) The efficiency of this process and the ability to possibly condense the process down to a machine that could produce butter, cheese and milk on the output end by inputting yeast , water and sugar on the input end is amazing. It could allow production of milk to happen pretty much any where....turning milk production into something that could be a craft (like beer production) and reducing costs over time.

6) Flavor possibilities, many flavorings were extracted years ago from natural fruits and seasonings...vanilla flavor for example could be added to the milk to produce a vanilla flavored kind or maybe the yeast can be further genetically modified to produce the flavor elements that are associated with given tastes ....banana milk? coconut milk? almond (essence of the oil mixed in). Many of the more expensive alternative "milk" products could likely be simulated better, cheaper and safer with modifications to this process.



The more I think about it the more excited about wanting to:

GET THIS STOCK! I become.

28 October, 2014

New Cognitive Flow Diagram and the possible need for artificial minds to sleep.

The Simple Dynamic Cognition Cycle flow diagram above is topologically identical to this one:



I published with an earlier post on the Salience theory of dynamic cognition and consciousness but this one shows the multiple feedback lines from the salience node as all left facing. The only one that is right facing feeds to Action. 
This is important because it shows that Salience evaluations directly modulate Action while also bypassing action for continued Sensation, some times a prediction is incorrect and is bypassed for continued approximation of stored memory with new sensation in the Comparison node which takes feedback from salience itself (emotional and autonomic).
I posit that cognition (the mind) happens between Sensation and Salience nodes and some times bubbles up Action, the "self" and consciousness are emergent reflections of this sea of comparisons in real time.

When we sleep the outer red flow arrows from salience to action are minimally triggered but subconscious cognition can still continue as memories are recalled for continued sub sensory evaluation, after all memories are basically copies of incoming sensation stored to make predictions as modulated by salience (tagged with emotional and autonomic import ratings) so if the Action is not driven that doesn't mean that comparison and salience evaluation aren't still on going particularly since autonomic salience must continue to be monitored as the agent "sleeps".

In the mammalian brain sleep seems to be important for low level memory consolidation and organization activities that would be inefficient to do during the wake state (they'd mar cognitive performance for obvious reasons you would be adding new sensations while trying to consolidate old ones). It should be possible to create an artificial cognition that doesn't need sleep (or needs less of it) by allowing consolidation to happen in parallel using an independent computational engine from the one processing real time sensation.

I hypothesize that in a dynamic cognition that correctly mirrors biological cognitive flow if an attempt to consolidate memories is not made the efficiency of cognitive processes will steadily degrade over time this would be due to the over loading of action delta data in the early virtual neuron layers of the sensory comparison and storage stacks for each dimensional modality.
In a sequential neural network the rate at which new data is fed into the system for training is deterministic and fixed, once trained new evaluations happen independent of continuous training, but in a real cognitive agent one has no control over when sensory data is coming into the system and one must handle it in that moment...doing so re weights low level network layers and thus reducing the efficiency of all the cognitive dimensional comparison tasks associated with those layers. The ability to accurately make predictions goes down as this noise piles up in lower layers of the cognitive stack. 

So I posit that some kind of offline consolidation will be needed to push sensed memories deeper into the virtual neuron stack and thus allowing future predictions to be more accurate, assuming of course that the DCC above is the only valid control flow that can emerge "mind". A different control flow and implementing architecture may be able to forgo this need.

The fact that the control flow described above between the 4 nodes may be a sign that it is correct as it seems to replicate the need for an analog of sleep. Again this is the simple diagram, the complex diagram has some particularly important symmetries identified that define how the cognitive engine would precisely flow between the different sensory modalities...getting those flows correct from the salience node is critical to emerging cognition. I will not be publishing the complex flow as I plan on working to implement it over the next 10 years or so...the significance of the simple diagram is that it presents the key innovation of salience evaluation as a fundamental requirement of dynamic cognition while describing exactly where it goes in the cognitive flow diagram.