Darwinian Evolution of Virtual Organisms

我们已经建立了一个虚拟生物进化的模型。在该模型的最初版本中，“有机体”是布尔网络，其结构由“基因组”指定，“基因组”可遗传但易突变。每个网络都经过一个“生命周期”，其中的“任务”是生成尽可能接近研究者指定的目标函数。选择有机体是因为它们能准确地完成任务。这导致了生物在模拟目标函数方面非常有效的进化。当生物体受到注入的数字噪声形式的环境扰动时，在某些情况下，它们可以通过发展排除噪声的能力来适应。然而，我们出乎意料地发现，在其他情况下，生物体会通过将噪音的外部和不相关特征纳入其自身结构来适应，从而使其与生物体的功能融为一体，并为其功能所必需。这个过程，我们称之为“噪音印记”，似乎类似于在文化进化过程中，外来因素被带入人类文化的许多情况。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）上实现了它，将计算能力提高了2-3个数量级。利用这种额外的力量，我们正在构建一个“有机体”和“模因”（“文化”元素）共同进化的模型，后者通过在生物体之间传播来复制，并充当“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中的“群体选择”的结果。我们推测，进化模因可能分为“理性”模因和“神话”模因，前者基于来自环境的经验信息在短期内起作用，后者体现了关于进化过程本身的永久的、不可观察的“真理”，这些真理对于支持生物体在多代时间尺度上的生存具有价值。这可能提供了一个“科学”和“宗教”文化元素共存于所有人类社会的类比。我们特别关注在紧密耦合的生物体中可能发生的共同进化相互作用，例如宿主/共生对以及基因和模因之间的类似关系。由于这样一对生物体尽管彼此密切依赖，但它们有各自的生殖周期，因此它们有“自由意志”以“重新协商”它们关系的方式进化。这些转变似乎是人类文化中发生的许多权力和支配地位变化的有用模型，我们正在观察这些转变是否在计算模拟中得到体现。特别令人感兴趣的是，基因和文化的共同进化可能会推动生物进化朝着更长的生殖后寿命的方向发展（因为文化的传授不能在一个生物生殖周期内完成）。我们将在共同进化模型中寻找类似的现象。

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. Of particular interest is the possibility that the co-evolution of genes and culture may drive biological evolution in the direction of longer post-reproductive life span (because the teaching of the culture cannot be completed within one biological reproductive cycle). We will look for similar phenomena in the co-evolution models. Since the previous report we have developed an additional simulation model to study specifically the way in which irrational risk-taking evolves. In a stochastic model of natural selection, organisms that "gambled" increasing the variance of their fitness without increasing (or even decreasing)its avereage value were found to be at a disadvantage. However, when the effects of cultural or other epigenetic inheritance were included in the model, that pattern shifted dramatically, so that risk-taking behavior of no immediate benefit to the organism was nevertheless strongly sselected over multiple generations. The original version of this model concerned asexual organisms (or equivalently, traits coded on the Y chromosome). The risk model is now being extended to full sexual reproduction, and we are trying to see if the same generic effect of "cultural" evolution exists in the abstract boolean network model. During the current project period we have also begun to explore an additional hypothesis concerning the evolutionary role of the "Tragedy of the Commons" in which competition among rational actors for a limited resource may lead to a situation which is optimal for none of them. A very simple (but real-world relevant) model of fishermen trying to maximize their individual catches was found to lead to a steady state of fish depletion. Despite being a competitive equilibrium of the "hidden hand" this state is inferior in every regard (total yield, number of fish, number of fisherman) to a regulated regime -- i.e. all players could benefit if the fishermen "voluntarily" restricted their catch. Analysis of the equations shows that this situation depends on the fact that the scarce resource -- fish -- is a living (i.e. reproducing) species. Since this situation exists in nature, one might expect that evolution would take advantage of this opportunity for optimization. A non-social species in which each animal restricts his foraging would not be evolutionarily stable -- a cheater could do better. However, if individuals take ownership of parts of the resource by defending territories, then an optimal state could be stable. This suggests that the common evolution of territoriality or hierarchy (pecking order) may be as a mechanism to provide "stewardship" of living resources. A similar process might exist in cultural evolution, where complicated forms of territoriality and hierarchy are the norm. This leads to paradoxes, such as the possibility that the stability of feudal forms of governance/economy may reflect a better ability -- in a long-term steady state -- to husband resources for the benefit of all individuals than the more liberal free competition which is manifestly more successful in an era of growth. Further analysis of this model system may lead to collaborations with social scientists. In particular, the behavior of the "Commons" model is at variance with classic economic "proofs" of the optimality of market competition. We are examining analytically the basis of this discrepancy, which probably arises from the assumption of "ownership" which does not exist, or takes the form of territoriality, in natural systems.