Month: November 2017

Ep 90: Evolution strategies

Ep 90: Evolution strategies

Evolution strategies

In 1963, a couple of students were working in a wind-tunnel, attempting to find a way to figure out how to design surfaces to produce a given airflow. That was, and still is, a difficult problem. There are no simple formula. They decided to see if they could use the power of evolution to solve the problem, and it worked.

Here’s a link to the relevant section of “A Hitchhiker’s guide to Evolutionary Computation.”

What’s an Evolution Strategy

I mentioned evolutionary programming in this episode, but don’t provide much detail. For those who are interested, here’s a link that provides an introduction to the topic.

What’s Evolutionary Programming

Ep 89: How to make a mind—part4

Ep 89: How to make a mind—part4

How to make a mind—part4

It took our universe between 13 and 14 billion years to make minds like our own. It took our planet 4.54 billion years, and life between 3 and 4 billion. What if we took a process we know can produce minds, namely evolution, and simulated it. Maybe, if we could zero in on the right factors, we could manage to create something like a mind in much less time.

Here’s a link to a documentary on the evolution of our species.

Mankind Rising

Here’s a link to a newsgroup FAQ that was one of the first references I found on the subject of simulating evolution in order to solve problems. It’s still there, and it’s still good.

A Hitchhikers Guide to Evolutionary Computation

As most methods of simulating evolution run on computers, I’ve started a series of blog posts on how computers compute. Here’s a link to the first of two whole posts that have been written to date.

Build your own computer

ep 88: No species alone

ep 88: No species alone

No species alone

Large complex multicellular life and simple single celled creatures have been evolving together. Each species requires an environment similar to the one in which it evolved in order to grow and develop normally. That includes the other creatures that have been evolving along with it. Today, we talk about how mice, deprived of their usual microbial symbiotes, show changes in their behavior as adults—changes that cannot be reversed.

Here’s the paper on the experiment and the results.

Normal gut microbiota modulates brain development and behavior

Ep 87: The things you make me do

Ep 87: The things you make me do

The things you make me do

It’s strange but true. A microscopic single celled organism can change the behavior of animals that it infects. From a snail that climbs instead of hiding below, to rabies, to a disease that causes rodents to lose their fear of cats; behavior can be changed by a sickness to make it more likely that the disease will spread.

Here are some articles on toxoplasmosis, which can cause rats and mice to become unafraid of, and even become attracted to, cats.

The Parasite That Makes a Rat Love a Cat

Mind-Bending Parasite Permanently Quells Cat Fear in Mice

This tiny brain parasite seems to make rodents braver—and it likes humans, too

The only bug was in my Brain!

The only bug was in my Brain!

Previous post in topic
Next post in topic

In the previous post, I talked very briefly about a one instruction set computer. I didn’t go into details because I hadn’t had a chance to play with one yet. Well, I’ve played with it, and it isn’t as difficult as I was making it.

The one command I’m playing with is called subleq. That short for, “subtract and branch if less than or equal to 0.” Don’t worry if this doesn’t make sense yet; I’ll explain in painful detail in future posts.

If B

Build your own computer

Build your own computer

Next post in topic

We’re fast approaching topics like evolutionary computation and artificial neural networks on the show. Unless something crops up that is just too interesting not to make an episode over, we should get started with that by episode 89. It has been a long time since I last considered these topics, and I’ve been looking forward to finding out what new tricks have been found since.

My favorite approach is genetic programming, as described by John Koza. Mind you, after the recent episodes, I’m more aware than ever of its limitations, but it still strikes me as a rather elegant approach.

In genetic programming, you start with an initial, usually randomly generated, population of small computer programs. The programs are tested and evaluated, and each one is given a fitness score, based on how well each one is doing on the given problem. Some portion of the population that has done relatively well on the given problem, are perturbed—mutated and perhaps combined in an analog of sexual reproduction—to form the next generation of programs. The new population is sent through the whole process again, and the loop continues until one or more of the programs in the population are solving the problem to your satisfaction. Either that, or they entirely fail, and you have to back up and figure out what’s going wrong.

In gp, each possible command is called a “node.” The programs are composed of nodes that are specific to the given problem, tied together in a way that makes sense. I’ve always wondered if there might be some set of nodes that could, at least in theory, solve any given problem.

The set of all possible problems that can be solved by a computer is infinite, or as close to it as makes no practical difference. Even so, it turns out, the set of commands needed to solve any problem that can be solved by computer can be very small. In fact, if you’re unconcerned with how difficult it is to write a program, you can actually solve any computable problem with just one command.

Introducing the “one instruction set computer.”

A “one instruction set computer” or, “oisc,” is a method of computing that uses only one command. There are several approaches. Some of them use mathematics, and at least one, uses a command that simply moves data from one location to another. The oisc approach is most often used as a method for designing computer hardware, but we might be able to adapt it for evolutionary computation.

I’ve always wanted to be able to design a computer, at least conceptually—to be able to go from simple bit manipulation, all the way up to something that could run an arbitrarily complicated piece of software, like word processing or games. This is the first time that particular goal has been in sight. Before attempting to use such algorithms for evolutionary computation, I need to familiarize myself with how such things work.

So, let’s make a computer!

This would make far too many far too miserably lengthy and dull podcast episodes. Instead, I’ll blog about it.

I’ve no clue how long this will take, or if I’ll even finish. I make no promises, but it’s an interesting experiment.

Next post in topic

Ep 86: Just not complete without you

Ep 86: Just not complete without you

Just not complete without you

Symbiosis between animals and bacteria is very common. In some cases, animals will not develop fully without their microscopic partners—sometimes, they can’t even reproduce.

Here’s a paper on the bobtail squid, and the light producing organ that doesn’t develop fully without the correct strain of bioluminescent bacteria.

Bacterial symbionts induce host organ morphogenesis during early postembryonic development of the squid Euprymna scolopes

Here are a couple of articles on parasitic wasps, and the effects on their reproduction caused by their microscopic hitchhikers.

Removing symbiotic Wolbachia bacteria specifically inhibits oogenesis in a parasitic wasp

Essential but unhelpful wasp Wolbachia

And here’s an article that talks about the link between animal behavior and their microbial symbiotes.

Animal Behavior and the Microbiome

Ep 85: When your partner moves in

Ep 85: When your partner moves in

When your partner moves in

Many life forms live in partnership with other organisms. The cooperative relationship is called symbiosis. Sometimes, one of the cooperating creatures lives inside of the other, even inside the cells. When one creature lives inside of another one that it cooperates with, it is called endosymbiosis. Today, we take a look at a few examples.

Here’s a review of endosymbiosis, with many examples.


Here’s a couple of articles about Salamanders and algae—the only known vertebrate case of endosymbiosis where the symbionts live within the vertebrate cells.

Algae that live inside the cells of salamanders are the first known vertebrate endosymbionts

Scientists Just Found a Completely New Kind of Symbiotic Relationship

Here are a couple of academic papers on the recently discovered cellular symbiosis between salamanders and algae.

Intracellular invasion of green algae in a salamander host

Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate-algal symbiosis

Ep 84: The tickle me plant

Ep 84: The tickle me plant

The tickle me plant

Today, we talk about another fast moving plant, called mimosa pudica, AKA. Shame plant, shy plant, touch me not, or the tickle me plant. This little plant will curl up its leaves when they are touched.

Here’s a video that shows the tickle me plant in action.

Mimosa Pudica – The Sensitive Plant

Here’s an article on growing and caring for mimosa pudica as a house plant.

How to grow Mimosa Pudica

Ep 83: By request, the Venus flytrap

Ep 83: By request, the Venus flytrap

By request, the Venus flytrap

We move and eat via our nerves and muscles, but there are some plants that have no nerves and no muscles, and yet they still move and eat. Today, we talk about the Venus flytrap, and how it why it does what it does.

Special thanks to @StoneyJehker34, for the question and the topic.

Here’s a video showing the Venus flytrap in action.


Here are a couple of articles about this interesting little plant.

The Mysterious Venus Flytrap

Venus Flytraps Are Even Creepier Than We Thought

Here’s a paper on how the plant counts touches against its trigger hairs to decide how much substance to produce to digest its prey.

The Venus Flytrap Dionaea muscipula Counts Prey-Induced Action Potentials to Induce Sodium Uptake