Computational biology of plant development: Towards a deductive science

植物发育的计算生物学：走向演绎科学自21世纪初以来，通过分子遗传学，显微镜的进步和计算模型的结合，对植物发育的机械理解开始出现。令人惊讶的是，不同结构的发展可能是由不同背景下表达的相关机制引起的。例如，叶子的发育导致它们的各种形状，以及它们在支撑茎上的定位，是涉及植物激素生长素及其转运蛋白PIN蛋白之间相互作用的常见分子机制的表现。这种机制和其他机制的普遍性（例如，植物器官之间的空间竞争）表明，植物中不同发育过程的本质可以归结为少数基本原则，并从中推导出来。对这些原则的探索是我所提出的研究的首要目标。我计划通过设计数学上有充分依据的方法来表示和模拟异质植物结构的发展。作为一个起点，我将使用以前在我的实验室开发的嵌入静脉的叶子模型。由此产生的方法将被应用于解决花头的图案：花状花序（花簇）的特点，植物在紫菀科，如非洲菊，向日葵和雏菊。在这些头部中发现的螺旋图案的显著规律性和数学特性在几个世纪以来吸引了跨学科的兴趣，但图案机制仍然未知。基于与生物学家同事合作获得的独特数据和我实验室设计的计算模型，我相信我们可以解决这个长期存在的问题。该解决方案将提供一个出发点来解释一个相关的现象，发展的维管结构的花头。结果将被推广到更广泛的生物结构。总的来说，这项工作将构成一个步骤，以广泛适用的一般原则来表征植物中的不同过程和结构。拟议的研究具有内在的跨学科性质，将计算机科学和数学方法应用于源于生物学的问题，并涉及与植物科学家的合作。基于实验数据的计算模型将被设计并用于探索研究中的自组织发展过程中的因果关系。新兴结构的几何方面将该研究计划与计算机图形学联系起来。

Computational Biology of Plant Development: Towards a Deductive Science Since the early 2000s, a mechanistic understanding of plant development has begun to emerge through a combination of molecular genetics, advances in microscopy, and computational models. Surprisingly, the development of diverse structures may result from related mechanisms expressed in different contexts. For instance, the development of leaves leading to their various shapes, and their positioning on the supporting stem, are manifestations of a common molecular mechanism involving the interaction between the plant hormone auxin and its transporters, the PIN proteins. The universality of this and other mechanisms (e.g., competition between plant organs for space) suggests that the essence of diverse developmental processes in plants can be reduced to, and deduced from, a small number of fundamental principles. The quest for such principles is the overarching objective of my proposed research. I plan to proceed by devising mathematically well-founded methods for representing and simulating the development of heterogeneous plant structures. As a starting point, I will use the models of leaves with embedded veins that were previously developed in my lab. The resulting methods will be applied to address the patterning of flower heads: the flower-like inflorescences (flower clusters) characteristic of plants in the aster family, such as gerbera, sunflower and daisy. The conspicuous regularity and mathematical properties of the spiral patterns found in these heads have attracted interdisciplinary interest over centuries, yet the patterning mechanism has remained unknown. Based on unique data obtained in collaboration with biologist colleagues and computational models being devised in my lab, I believe that we can solve this long-standing problem. The solution will provide a point of departure to explain a related phenomenon, the development of the vascular structure of flower heads. The results will be generalized to a wider spectrum of biological structures. Taken together, this work will constitute a step towards characterizing diverse processes and structures in plants in terms of broadly applicable, general principles. The proposed research has an inherently interdisciplinary character, applying methods of computer science and mathematics to problems originating in biology, and involves collaborations with plant scientists. Computational models based on experimental data will be devised and used to explore causal relations in the self-organizing developmental processes under study. The geometric aspects of the emerging structures link this research program to computer graphics.