Darwinian Evolution of Virtual Organisms

我们构建了一个虚拟生物进化的模型。 在该模型的初始版本中，“生物体”是布尔网络，其结构由可遗传但易发生突变的“基因组”指定。 每一个网络都经历一个“生命周期”，其中的“任务”是尽可能接近地生成研究者指定的目标函数。 选择生物体是因为它们在执行任务时的准确性。 这导致了生物体的进化，这些生物体在模拟目标功能方面非常有效。 当生物体受到环境干扰时，以注入的数字噪音的形式，它们可以在某些情况下通过发展排除噪音的能力来适应。 然而，我们出乎意料地发现，在其他情况下，生物体会通过将噪声的无关紧要的特征融入自己的结构中来适应，这样它就融入了生物体的功能，并且是其功能所必需的。 这个过程，我们称之为“噪音印记”，似乎类似于许多情况下，在文化进化的过程中，外来元素被带入人类文化。 在当前的项目期间，我们已经将模型并行化并在Beowulf集群（NIH Bethesda的Biowulf和我们实验室的专用48处理器集群）上实现，将计算能力提高了2-3个数量级。 利用这一额外的力量，我们正在构建一个“生物体”和“模因”（“文化”元素）共同进化的模型，后者通过在生物体中传播来复制，并作为“软件”来控制生物体与环境的相互作用，类似于人类基因组和人类文化的共同进化。 我们假设，这两个层次的进化过程可能会产生类似于生物体之间的“群体选择”的后果。我们推测，不断演变的模因可能分为“理性”的，在短期内从环境和“神话”的，体现永久的，不可观察的“真理”进化过程本身的基础上的经验信息的基础上采取行动的价值，在多代的时间尺度上支持生物体的生存。 这可能提供了一个类似的“科学”和“宗教”的文化元素共存于所有人类社会。 我们特别关注的是在紧密耦合的生物体对中可能发生的共同进化相互作用的类型，例如宿主/宿主对以及基因和模因之间的类似关系。 由于这样一对生物体有独立的生殖周期，尽管它们相互依赖，所以它们有“自由意志”以“重新谈判”它们的关系的方式进化。 我们希望看到这些转变，这似乎是一个有用的模型，许多权力和统治地位的变化，发生在人类文化中，是体现在计算模拟。

We have constructed a model of the evolution of virtual organisms. In the initial version of the model, the "organisms" are boolean networks, whose structure is specified by a "genome" which is heritable but subject to mutation. Each network is stepped through a "life cycle" in which the "task" is to generate, as closely as possible, a target function specified by the investigator. Organisms are selected for their accuracy in carrying out the task. This resulted in the evolution of organisms that were highly effective at simulating the target function. When organisms were subjected to environmental perturbation, in the form of injected, numerical noise, they could, under some circumstances, adapt by developing the ability to exclude the noise. However, we unexpectedly discovered that, under other cirumstances, organisms would adapt by incorporating extrraneous and irrelevant features of the noise into their own structure, such that it became enmeshed in the function of the organism and necessary for its function. This process, which we dubbed "noise imprinting" appears to be analogous to many situations in which extraneous elements are entrained into human culture during the process of cultural evolution. In the current project period, we have parallelized the model and implemented it on Beowulf clusters (Biowulf at NIH Bethesda, and a dedicated 48-processor cluster in our lab) increasing computational power by 2-3 orders of magnitude. Using this added power, we are constructing a model of the co-evolution of "organisms" and "memes" ("cultural" elements) the latter of which replicate by spreading among the organisms and act as "software" to control the organisms' interactions with the environment, analogous to the co-evolution of the human genome and human culture. We hypothesize that this two level evolutionary process may have consequences analogous to "group selection" among the organisms. We speculate that the evolving memes may divide into "rational" ones that act in the short term on the basis of empirical infromation from the environment and "mythological" ones that embody permanent, non-observable "truths" about the evolutionary process itself that are of value in supporting survival of the organisms over multi-generational time scales. This might provide an analog of the "scientific" and "religious" cultural elements that co-exist in all human societies. We are giving particular attention to the kinds of co-evolutionary interactions that can occur in tightly coupled pairs of organisms, such as host/commensal pairs and the analogous relationship between genes and memes. Since organisms of such a pair have separate reproductive cycles, despite their close interdependence, so they have the "free will" to evolve in ways that "renegotiate" their relationship. We are looking to see if these transformations, which seem to be a useful model for many of the shifts in power and dominance that occur in human culture, are manifest in the computational simulations.