Wolfram Science

Dawei Li: A Subsequent Study of Visualized Sequence Comparison Based on Ten Types of Viruses

Dawei Li presented an investigation of the behavior of gene sequences transcoded to base 4 digits and evolved according to a ECA rule. He attempted to discover a new model of the propagation of virii using NKS methods, saying that Dr. Wolfram's approach provides a non-traditional visualized model for sequence comparisons.

He began with 4 hypotheses:
1 DNA is not random; it has a rule.
2 There is an uncertain mode of nucleotide organization that each DNA sequence follow.
3 Simple rules can produce complex behaviors in living organisms.
4 It is not only appropriate to DNA/RNA, but also to protein sequences

He selected rule 84 because of its nested structure and investigated its effect on many gene sequences in a selection of viruses, including some SARS strains. He displayed an array of algorithmically-colored graphs of evolutions, with similar colors indicating closer similar behavior. A detailed analysis of the transformations of various sequences in the virus DNA followed. The overall results seemed to be that regions that produces nested structures on evolution may be related to the reproduction of the virus.

He finished extremely early and the audience peppered him with questions about the implications of his project. Many people seemed skeptical, but intrigued.

Margaret Eppstein: Predicting Naturalization versus Invasion using Stochastic CA Models

Natural Sciences lecture series

Margaret Eppstein of the University of Vermont discusses invasion vs. naturalization in plant models

Margaret talked about what makes plants invasive. Several ideas already exist to explain some of the phenomena: the enemy release hypothesis, evolution of increased competitive ability, the biotic resistance hypothesis and propagule pressure. Models include both positive feedback effects, like pollinators and the presence of symbionts, and negative feedback effects like predators and pathogens. A characteristic like soil chemistry can be both a positive and negative feedback effect.

However, the standard Lotka-Volterra models typically used fail to account for frequency-dependent feedback effects, as well as typically making the assumption of a mean field, meaning that the use of space is ignored.

Margaret has developed a new model that incorporates propagule pressure, and both frequency dependent and independent effects, as well as spatial scale. Her results show that it's important to consider space when modeling whether an exotic species can establish when invading a new environment, as well as both frequency-dependent and independent interactions. This is then modeled as a stochastic CA with a configurable cell neighborhood.

This new model may be a practical way to assess the invasive potential of new species, or to estimate range limits of invasive species.

Erik Schultes, "RNA and NKS"

Schultes analyzes RNA folding patterns using the tools of NKS. The experimental variable is the informational content of the molecule. He has a robot for creating tailor made RNA sequences. The result of their experiment was that arbitrary sequences acquire sequence-specific folds. Also they used the technique of native gel electrophoresis. More compact sequences migrate faster.

He wants to examine the space of all possible sequences and examine the distribution of folds in RNA sequence space.

(It was a very interesting talk I don't think I've done justice to. Right afterwards I quickly ate some lunch and went upstairs to take a nap and let my brain rest up a bit.)

Abstract. His website is at hedgehogresearch.info.

Thomas Olivier, "Experiences with Computer Simulations of Primate Populations"

Talk in progress. He studied the genetics of monkeys in Kenya and elsewhere and does primate population simulations. The complex social structure is reflected the gene frequency distribution in the monkey populations. The attempt was to make a system useful for exploring questions from field research on primates. This entailed simulating individual life cycles maintaining kinship link and using kinship relation in process decisions. The data structures were intended to be usable for varied groups and to eventually model spatial effects.

His model produced gene distributions much like those found in real populations. These computer muodels turn out to be useful for analyzing the small local populations of animals that conservation biologists tend to work with.

Abstract. His website, Green Creek Paradigms, LLC. The CRITTRZ Population Simulation Kit is available from his web site.

Jane Molofsky, "Cellular Automata Models in Community Ecology"

Molofsky asks whether plant popultaions follow simple rules. Only the first and 2nd neighbors inluenced plant growth, however at higher density there were other effects.

She showed how playing with the mathematics of the effects of density, when run for multiple generations, yeilds banding patterns which looked very similiar to examples from the natural world which she had given at the begninning of the talk.

Abstract. Her web site.

Eric Mjolsness, "Toward a Searchable Space of Dynamical System Models"

Posted by Kathryn Cramer.

Mjolsness set out criteria for simple formal systems: expressive power, discrete labeled graph structure, & self-applicability. he showed a wide variety of examples from a number of disciplines and on multiple scales. He argued that the stochastic process operators can form the semantics of a language, and that operator algebra then leads to novel algorithms. This results in a searchable space of simple dynamical system models.

Abstract. Also, here is Eric Mjolsness's web site, which he  suggests you visit for more information, is here.