Darwin on Aristotle

Charles Darwin's famous 1882 letter, in response to a gift by his friend, William Ogle of Ogle's recent translation of Aristotle's Parts of Animals, in which Darwin remarks that his “two gods,” Linnaeus and Cuvier, were “mere school-boys to old Aristotle,” has been thought to be only an extravagantly worded gesture of politeness. However, a close examination of this and other Darwin letters, and of references to Aristotle in Darwin's earlier work, shows that the famous letter was written several weeks after a first, polite letter of thanks, and was carefully formulated and literally meant. Indeed, it reflected an authentic, and substantial, increase in Darwin's already high respect for Aristotle, as a result of a careful reading both of Ogle's Introduction and of more or less the portion of Ogle's translation which Darwin says he has read. Aristotle's promotion to the pantheon, as an examination of the basis for Darwin's admiration of Linnaeus and Cuvier suggests, was most likely the result specifically of Darwin's late discovery that the man he already knew as “one of the greatest ... observers that ever lived” (1879) was also the ancient equivalent both of the great modern systematist and of the great modern advocate of comparative functional explanation. It may also have reflected some real insight on Darwin's part into the teleological aspect of Aristotle's thought, indeed more insight than Ogle himself had achieved, as a portion of their correspondence reveals. This revised version was published online in July 2006 with corrections to the Cover Date.     

Aristotle on the Mechanism of Inheritance

In this paper I address an important question in Aristotle’s biology, What are the causal mechanisms behind the transmission of biological form? Aristotle’s answer to this question, I argue, is found in Generation of Animals Book 4 in connection with his investigation into the phenomenon of inheritance. There we are told that an organism’s reproductive material contains a set of “movements'' which are derived from the various “potentials'' of its nature (the internal principle of change that initiates and controls development). These “movements,'' I suggest, function as specialized vehicles for communicating the parts of the parent’s heritable form during the act of reproduction. After exploring the details of this mechanism, I then take up Aristotle’s theory of inheritance proper. At the heart of the theory are three general principles (or ‘laws’) that govern the interactions between the maternal and paternal movements, the outcome of which determines the pattern of inheritance for the offspring. Although this paper is primarily aimed at providing a detailed analysis of Aristotle’s account of inheritance, the results of that analysis have implications for other areas of Aristotle’s biology. One of the most interesting of these is the question of whether Aristotle’s biology is anti-evolutionary (as traditionally assumed) or whether (as I argue) it leaves room for a theory of evolution by natural selection, even if Aristotle himself never took that step.     

Exploring the genomes: From Arabidopsis to crops

Model systems have played a crucial role for understanding biological processes at genetic, molecular and systems levels. Arabidopsis thaliana is one of the best studied model species for higher plants. Large genomic resources and mutant collections made Arabidopsis an excellent source for functional and comparative genomics. Rice and Brachypodium have a great potential to become model systems for grasses. Given the agronomic importance of grass crops, it is an attractive strategy to apply knowledge from Arabidopsis to grasses. Despite many efforts successful reports are sparse. Knowledge transfer should generally work best between orthologous genes that share functionality and a common ancestor. In higher plants, however, recent genome projects revealed an active and rapid evolution of genome structure, which challenges the concept of one-to-one orthologous mates between two species. In this study, we estimated on the example of protein families that are involved in redox related processes, the impact of gene expansions on the success rate for a knowledge transfer from Arabidopsis to the grass species rice, sorghum and Brachypodium. The sparse synteny between dicot and monocot plants due to frequent rearrangements, translocations and gene losses strongly impairs and reduces the number of orthologs detectable by positional conservation. To address the limitations of sparse synteny and expanded gene families, we applied for the detection of orthologs in this study orthoMCL, a sequence-based approach that allows to group closely related paralogs into one orthologous gene cluster. For a total of 49 out of 170 Arabidopsis genes we could identify conserved copy numbers between the dicot model and the grass annotations whereas approximately one third (34.7%, 59 genes) of the selected Arabidopsis genes lack an assignment to any of the grass genome annotations. The remaining 62 Arabidopsis genes represent groups that are considerably biased in their copy numbers between Arabidopsis and all or most of the three grass genomes.     

Arabidopsis thaliana proteomics: from proteome to genome

Proteomics has become an important approach for investigating cellular processes and network functions. Significant improvements have been made during the last few years in technologies for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. As proteomics technologies advance and become more widely accessible, efforts of cataloguing and quantifying full proteomes are underway to complement other genomics approaches, such as RNA and metabolite profiling. Of particular interest is the application of proteome data to improve genome annotation and to include information on post-translational protein modifications with the annotation of the corresponding gene. This type of analysis requires a paradigm shift because amino acid sequences must be assigned to peptides without relying on existing protein databases. In this review, advances and current limitations of full proteome analysis are briefly highlighted using the model plant Arabidopsis thaliana as an example. Strategies to identify peptides are also discussed on the basis of MS/MS data in a protein database-independent approach.     

Arabidopsis: Sensitivity of growth to high temperature

Arabidopsis thaliana seedlings as measured by an electrolyte leakage assay, have been found to be extremely sensitive to high temperature stress as compared to a high temperature tolerant variety (Tracy) of soybean. Over 50% ion leakage occurred in Arabidopsis leaves during a 15-minute exposure to 50°C, indicating a heat killing time of less than 15 minutes. In contrast, the heat killing time for soybean at 50°C was over five times longer. When soybean or Arabidopsis seedlings in culture plates were exposed to 37°C for 2 hours and then returned to 23°C, they suffered no apparent short-term or long-term damage. Soybean seedlings given a 42°C, treatment for 2 hours also showed no damage. Arabidopsis seedlings after a 42°C treatment for 2 hours showed no apparent immediate damage, but 48 hours after return to 23°C severe damage symptoms were visible and after 96 hours all the seedlings were dead. Both soybean and Arabidopsis seedlings synthesize heat shock proteins (hsps) when exposed to 42°C for 2 hours. The hsps synthesized are of similar molecular weights, although the relative abundances of the different size classes are very different in the two plants. Even though hsps are produced in Arabidopsis seedlings after a 2 hour exposure to 42°C their presence is not sufficient for the seedlings to recover from the effects of rhe heat shock when returned to 23°C. Our results show that Arabidopsis has a heat sensitive genotype. This along with its other characteristics should make it a good model system in which to assay in transgenic plants, the functions of homologous and heterologous genes that might be candidates for determining heat tolerance in plants.     

From genome to function: the Arabidopsis aquaporins

Background

In the post-genomic era newly sequenced genomes can be used to deduce organismal functions from our knowledge of other systems. Here we apply this approach to analyzing the aquaporin gene family in Arabidopsis thaliana. The aquaporins are intrinsic membrane proteins that have been characterized as facilitators of water flux. Originally termed major intrinsic proteins (MIPs), they are now also known as water channels, glycerol facilitators and aqua-glyceroporins, yet recent data suggest that they facilitate the movement of other low-molecular-weight metabolites as well.

Results

The Arabidopsis genome contains 38 sequences with homology to aquaporin in four subfamilies, termed PIP, TIP, NIP and SIP. We have analyzed aquaporin family structure and expression using the A. thaliana genome sequence, and introduce a new NMR approach for the purpose of analyzing water movement in plant roots in vivo.

Conclusions

Our preliminary data indicate a strongly transcellular component for the flux of water in roots.     

Harvey,Aristotle and the Weather Cycle

It is well known that Harvey was influenced by Aristotle. This paper seeks to show that Harvey's quantitative argument for the circulation and his analogy of the heart with a pump do not go beyond Aristotle and may even have been inspired by passages in Aristotle. It also considers the fact that Harvey gives much greater prominence to a macrocosm/microcosm analogy between the weather cycle and the circulation of the blood than he does to the pump analogy. This analogy is prominent in both the preface to the king and pivotal chapter eight of De Motu Cordis, and may indicate a significant influence from the Renaissance natural magic tradition. The full implications of this analogy are critical for Harvey's conception of the nature of the circulation, especially the constant interconversion of venous and arterial blood and the passage of blood through the lungs. The tendency to assume that Harvey had a superior method since he made such an important discovery may have led not only to overestimation of the influence from the new science of the seventeenth century, but also to underestimation of influence from the magical tradition.     

Phosphoproteomics in Arabidopsis: moving from empirical to predictive science

Although protein phosphorylation is integral to the regulation of protein function in diverse biological responses, relatively little is currently known about the rules that govern phosphorylation in plants. This review will discuss how the data acquired by evolving phosphoproteomic methods are beginning to fill the gaps in our knowledge. In addition, ways are suggested in which new quantitative methods in conjunction with extrapolating from genomic data may provide a strategy to predict components of signalling networks that may be co-ordinately regulated.