Where Does Pattee’s “How Does a Molecule Become a Message?” Belong in the History of Biosemiotics?

Recalling the title of Yoxen’s classical paper on the influence of Schrödinger’s book, I analyze the role that the work of H. Pattee might have played, if any, in the development of Biosemiotics. I take his 1969 paper “How does a molecule become a message?” (Developmental Biology Supplement) as a first target due to several circumstances that make it especially salient. On the one hand, even if Pattee has obviously developed further his ideas on later papers, the significance of this one springs out right from the title, the journal and date of publication and, of course, its content. On the other, this paper in particular has been somehow rediscovered recently and not only within the frame of biosemiotics (eg, in history and philosophy of biology by E.F. Keller). Following the parallelism with Yoxen’s perspective, I contend that Pattee’s work was relatively influential with respect to a good amount of attempts to rethink living systems within theoretical biology around the 70s. This influence diminished together with the decay or even collapse of those attempts under the impact of molecular biology as it was being developed those years. Eventually, Pattee’s work has been taken up again. Notwithstanding, it is quite clear that Pattee himself was not intending to contribute specifically to Biosemiotics and that he was probably unaware of any such discipline, at least until recently. Then, we should as well ask (as Yoxen wonders with respect to Schrödinger) to which extent Pattee’s influence has been a direct one or rather an indication of the relevance of his ideas and the resonance of his hypotheses with those of biosemiotics. For this task I will sketch a few points of convergence and divergence and examine the work of some authors who either address directly this issue or have contributed significantly to build up the history of Biosemiotics.     

The prominent absence of Alfred Russel Wallace at the Darwin anniversaries in Germany in 1909, 1959 and 2009

It is well known that the contribution of Alfred Russell Wallace (1823–1913) to the development of the “Darwinian” principle of natural selection has often been neglected. Here we focus on how the three anniversaries to celebrate the origin of the Darwin–Wallace theory in Germany in 1909, in 1959 in the divided country, as well as in 2009, have represented Charles Robert Darwin’s and Alfred Russell Wallace’s contributions. We have analyzed books and proceedings volumes related to these anniversaries, and the main result is that Wallace was almost always ignored, or only mentioned in passing. In 1909, Ernst Haeckel gave a talk in Jena, later published under the title The worldview of Darwin and Lamarck (Das Weltbild von Darwin und Lamarck), but not as the Darwin–Wallace concept. Haeckel mentions Wallace only once. In two important proceedings volumes from the 1959 anniversaries, Wallace was ignored. The only fair treatment of Wallace is given in another book, a collection of documents edited by Gerhard Heberer, for which the author selected nine key documents and reprinted excerpts (1959). Three of them were articles by Wallace, including the Sarawak- and Ternate-papers of 1855 and 1858, respectively. An analysis of the dominant themes during the celebrations of 2009 shows that none of the six topics had much to do with Wallace and his work. Thus, the tendency to exclude Alfred Russell Wallace is an international phenomenon, and largely attributable to the “Darwin industry”.     

Role of the hemA gene product and delta-aminolevulinic acid in regulation of Escherichia coli heme synthesis.

We initiated these studies to help clarify the roles of heme, delta-aminolevulinic acid (ALA), hemA, and hemM in Escherichia coli heme synthesis. Using recombinant human hemoglobin (rHb1.1) as a tool for increasing E. coli's heme requirements, we demonstrated that heme is a feedback inhibitor of heme synthesis. Cooverexpression of rHb1.1 and the hemA-encoded glutamyl-tRNA (GTR) reductase increased intracellular levels of ALA and heme and increased the rate of rHb1.1 formation. These results support the conclusion that heme synthesis is limited by ALA (S. Hino and A. Ishida, Enzyme 16:42-49, 1973; W. K. Philipp-Dormston and M. Doss, Enzyme 16:57-64, 1973) and that the hemA-encoded GTR reductase is a rate-limiting enzyme in the pathway (J.-M. Li, C. S. Russell, and S. D. Cosloy, Gene 82:2099-217, 1989). Increasing the copy number of hemM, whose product is believed to be required for efficient ALA formation (W. Chen, C. S. Russell, Y. Murooka, and S. D. Cosloy, J. Bacteriol. 176:2743-2746, 1994; M. Ikemi, K. Murakami, M. Hashimoto, and Y. Murooka, Gene 121:127-132, 1992), had no effect on either ALA pools or the rate of rHb1.1 accumulation. The hemA-encoded GTR reductase was found to be regulated by ALA. Some of our results differ from those reported by Hart and coworkers (R. A. Hart, P. T. Kallio, and J. E. Bailey, Appl. Environ. Microbiol. 60:2431-2437, 1994), who concluded that ALA formation is not the rate-limiting step in E. coli cells expressing Vitreoscilla hemoglobin.     

Evolutionary Anatomy of the Primate Cerebral Cortex, 2001 et S.J. Gould : regards croisés

Evolutionary Anatomy of the Primate Cerebral Cortex, 2001 and S.J. Gould: crossed paths. The book Evolutionary Anatomy of the Primate Cerebral Cortex (Falk and Gibson, 2001) is a report of the congress in honor of H.J. Jerison held in USA (1998). Gould wrote the foreword of that book and Jerison its epilogue. For some participants, Gould’s successive works on organisms' evolution have given an important background to their own research. Jerison and Gould met for the first time something like 40 years ago and all along they have shared common scientific interests. In this article, we shall attempt an overview of Evolutionary Anatomy of the Primate Cerebral Cortex, one of the themes close to an ‘influential’ (fide Gould) book entitled: Evolution of the Brain and Intelligence (Jerison 1973). Tendencies in the organization of the brain volume of Vertebrates, and especially in still-living or fossils mammals, is a major question (cf. recent publications and the debate in Nature). If Jerison was a leader for the encephalization concept (sensu 1D, 2D), Gould clearly introduced modern research (nD) on encephalization. From him, the representation through hyperspace could describe the complexity of the paths followed by Vertebrate brain evolution. From this, the new concept of neurotaxonomy (see Thireau et al., Bull. Soc. Zool. France 122 (4) (1997) 393–411) relates encephalic organisation to species taxonomy. So, in the future, paleoneurologists should be using some results from the neurotaxonomy of existing species, for help in completing interpretation of endocranian casts. Throughout this article, special attention is given to Gould’s arguments, proposed in his foreword to Falk et Gibson, 2001. Each of these deserves to be discussed, thus benefiting evolutive neurobiology, and should be completed by the reading of his major contribution to modern biology: The structure of Evolutionary Theory (Gould 2002). To cite this article: L. Thireau, J.-C. Doré, C. R. Palevol 2 (2003).     

Ability of Acidaminococcus fermentans to oxidize trans-aconitate and decrease the accumulation of tricarballylate, a toxic end product of ruminal fermentation.

Mixed ruminal bacteria convert trans-aconitate to tricarballylate, a tricarboxylic acid which chelates blood divalent cations and decreases their availability (J. B. Russell and P. J. Van Soest, Appl. Environ. Microbiol. 47:155-159, 1984). Decreases in blood magnesium in turn cause a potentially fatal disease known as grass tetany. trans-Aconitate was stoichiometrically reduced to tricarballylate by Selenomonas ruminantium, a common ruminal bacterium in grass-fed ruminants (J. B. Russell, Appl. Environ. Microbiol. 49:120-126, 1985). When mixed ruminal bacteria were enriched with trans-aconitate, a trans-aconitate-oxidizing bacterium was also isolated (G. M. Cook, F. A. Rainey, G. Chen, E. Stackebrandt, and J. B. Russell, Int. J. Syst. Bacteriol. 44:576-578, 1994). The trans-aconitate-oxidizing bacterium was identified as Acidaminococcus fermentans, and it converted trans-aconitate to acetate, a nontoxic end product of ruminal fermentation. When S. ruminantium and A. fermentans were cocultured with trans-aconitate and glucose, tricarballylate never accumulated and all the trans-aconitate was converted to acetate. Continuous-culture studies (dilution rate, 0.1 h-1) likewise indicated that A. fermentans could outcompete S. ruminantium for trans-aconitate. When mixed ruminal bacteria were incubated in vitro with 10 mM trans-aconitate for 24 h, 45% of the trans-aconitate was converted to tricarballylate. Tricarballylate production decreased 50% if even small amounts of A. fermentans were added to the incubation mixes (0.01 mg of protein per mg of mixed bacterial protein). When A. fermentans (2 g of bacterial protein) was added directly to the rumen, the subsequent conversion of trans-aconitate to tricarballylate decreased 50%, but this effect did not persist for more than 18 h.(ABSTRACT TRUNCATED AT 250 WORDS)     

BOOK REVIEWS

Book reviewed in this article:
C hadwick , D. H. 2002. A beast the colour of winter .
K aranth , K. U. and N ichols , J. D. 2002. Monitoring tigers and their prey: a manual for research managers and conservationists in tropical Asia .
K leiman , D. G. and R ylands , A. B. 2002. Lion tamarins: biology and conservation .
L ott , D. E. 2002. American bison: a natural history .
L umpkin , S. and S eidensticker , J. 2002. Smithsonian book of giant pandas .
M artin , R. and H andasyde , K. 1999. The koala: natural history, conservation and management .
T aylor , A. B. and G oldsmith , M. L. 2003. Gorilla biology: a multidisplinary perspective .
Z eveloff , S. I. 2002. Racoons: a natural history .     

5-Aminolevulinic acid synthesis in Escherichia coli.

A hemA mutant of Escherichia coli containing a multicopy plasmid which complemented the mutation excreted 5-aminolevulinic acid (ALA) into the medium. [1-14C]glutamate was substantially incorporated into ALA by this strain, whereas [2-14C]glycine was not. Periodate degradation of labeled ALA showed that C-5 of ALA was derived from C-1 of glutamate. The synthesis of ALA by two sonicate fractions which had been processed by gel filtration and dialysis, respectively, was dependent on glutamate, ATP, NADPH, tRNA(Glu), and pyridoxal phosphate. tRNA(Glu) stimulated ALA synthesis in a concentration-dependent manner. Pretreatment with RNase reduced this stimulation. The amino acid sequence of the cloned insert, derived from the nucleotide sequence (J.-M. Li, C. S. Russell, and S. D. Cosloy, J. Cell Biol. 107:617a, 1988), showed no homology with any ALA synthase sequenced to date. These results suggest that E. coli synthesizes ALA by the C5 pathway from the intact five-carbon chain of glutamate.     

Glucocorticoid receptors in human fibroblasts derived from normal dermis and keloid tissue

Hydrocortisone stimulates proliferation and System A amino acid transport in cultured human fibroblasts, while decreasing production of collagen. Fibroblasts isolated from keloid tissue have an unusual glucocorticoid response; they are hyporesponsive with regard to proliferation and collagen production but hyperresponsive with regard to the induction of System A amino acid transport (Russell, J. D., Russell, S. B., and Trupin, K. M. (1978) J. Cell. Physiol. 97, 221-229; Russell, S. B., Russell, J. D., and Trupin, J. S. (1982) J. Biol. Chem. 256, 9525-9531). We show here that despite these differences, the glucocorticoid receptors of keloid cells do not differ from those of normal dermal fibroblasts in steroid specificity, dissociation constant (Kd), total number of binding sites (Bmax), or nuclear binding of glucocorticoid-receptor complexes. A single glucocorticoid binding species of molecular weight 93,000 was found in both cell types. A monolayer assay for glucocorticoid receptor binding is described which facilitates analysis of multiple strains of cultured cells. This assay gives the same specificity and dissociation constants as the conventional cytosol assay, but it is more sensitive. The magnitude of induction of System A amino acid transport was found to be directly proportional to glucocorticoid receptor occupancy in both keloid-derived and normal fibroblasts. This induction requires serum, which can be replaced with 1 nM insulin.     

Does nothing in evolution make sense except in the light of population genetics?

“The Origins of Genome Architecture” by Michael Lynch (2007) may not immediately sound like a book that someone interested in the philosophy of biology would grab off the shelf. But there are three important reasons why you should read this book. Firstly, if you want to understand biological evolution, you should have at least a passing familiarity with evolutionary change at the level of the genome. This is not to say that everyone interested in evolution should be a geneticist or a bioinformatician, but that a working knowledge of genetic change is an essential part of the intellectual toolkit of modern evolutionary biology, even if your primary focus is the evolution of behaviour or the diversity of communities. Secondly, this book provides excellent examples of another important tool in the biologist’s intellectual toolkit, but one that is rarely explained or illustrated to such an extent: null (or neutral) models. The role null models play in testing hypotheses in evolution is a central focus of this book. Thirdly, as an accomplished work of advocacy for a strictly microevolutionary view of evolution, this book provides grist for the mill for the important debate about whether population genetic processes are the sine qua non of evolutionary explanations.     

Philosophical foundations for the hierarchy of life

We review Evolution and the Levels of Selection by Samir Okasha. This important book provides a cohesive philosophical framework for understanding levels-of-selections problems in biology. Concerning evolutionary transitions, Okasha proposes that three stages characterize the shift from a lower level of selection to a higher one. We discuss the application of Okasha’s three-stage concept to the evolutionary transition from unicellularity to multicellularity in the volvocine green algae. Okasha’s concepts are a provocative step towards a more general understanding of the major evolutionary transitions; however, the application of certain ideas to the volvocine model system is not straightforward.     

Pattern Cladistics and the ‘Realism–Antirealism Debate’ in the Philosophy of Biology

Despite the amount of work that has been produced on the subject over the years, the ‘transformation of cladistics’ is still a misunderstood episode in the history of comparative biology. Here, I analyze two outstanding, highly contrasting historiographic accounts on the matter, under the perspective of an influential dichotomy in the philosophy of science: the opposition between Scientific Realism and Empiricism. Placing special emphasis on the notion of ‘causal grounding’ of morphological characters (sensu Olivier Rieppel) in modern developmental biology’s (mechanistic) theories, I arrive at the conclusion that a ‘new transformation of cladistics’ is philosophically plausible. This ‘reformed’ understanding of ‘pattern cladistics’ entails retaining the interpretation of cladograms as ‘schemes of synapomorphies’, but in association to construing cladogram nodes as ‘developmental-genetic taxic homologies’, instead of ‘standard Darwinian ancestors’. The reinterpretation of pattern cladistics presented here additionally proposes to take Bas Van Fraassen’s ‘constructive empiricism’ as a philosophical stance that could properly support such analysis of developmental-genetic data for systematic purposes. The latter suggestion is justified through a reappraisal of previous ideas developed by prominent pattern cladists (mainly, Colin Patterson), which concerned a scientifically efficient ‘observable/non-observable distinction’ linked to the conceptual pair ‘ontogeny and phylogeny’. Finally, I argue that a robust articulation of Antirealist alternatives in systematics may provide a rational basis for its disciplinary separation from evolutionary biology, as well as for a critical reconsideration of the proper role of certain Scientific Realist positions, currently popular in comparative biology.     

Species, Demes, and the Omega Taxonomy: Gilmour and The NewSystematics

The word ``deme' was coined by the botanists J.S.L. Gilmour and J.W.Gregor in 1939, following the pattern of J.S. Huxley's ``cline'. Its purposewas not only to rationalize the plethora of terms describing chromosomaland genetic variation, but also to reduce hostility between traditionaltaxonomists and researchers on evolution, who sometimes scorned eachother's understanding of species. A multi-layered system of compoundterms based on deme was published by Gilmour and J. Heslop-Harrison in1954 but not widely used. Deme was adopted with a modified meaning byzoologists leading the evolutionary synthesis – Huxley, Simpson, Wright,and Mayr. Connections are shown between Gilmour's ideas around definingthe deme, his role in founding the Systematics Association, and his chapter``Taxonomy and Philosophy' in the book The New Systematics. Thishistorical episode raises questions about the role of carefully-definedwords in scientific practice.     

Janaki Ammal,C. D. Darlington and J. B. S. Haldane: scientific encounters at the end of empire

Right from the beginning, genetics has been an international venture, with international networks involving the collaboration of scientists across continents. Janaki Ammal’s career illustrates this. This paper traces her scientific path by situating it in the context of her relationships with J. B. S. Haldane and C. D. Darlington.     

More on how and why: cause and effect in biology revisited

In 1961, Ernst Mayr published a highly influential article on the nature of causation in biology, in which he distinguished between proximate and ultimate causes. Mayr argued that proximate causes (e.g. physiological factors) and ultimate causes (e.g. natural selection) addressed distinct ‘how’ and ‘why’ questions and were not competing alternatives. That distinction retains explanatory value today. However, the adoption of Mayr’s heuristic led to the widespread belief that ontogenetic processes are irrelevant to evolutionary questions, a belief that has (1) hindered progress within evolutionary biology, (2) forged divisions between evolutionary biology and adjacent disciplines and (3) obstructed several contemporary debates in biology. Here we expand on our earlier (Laland et al. in Science 334:1512–1516, 2011) argument that Mayr’s dichotomous formulation has now run its useful course, and that evolutionary biology would be better served by a concept of reciprocal causation, in which causation is perceived to cycle through biological systems recursively. We further suggest that a newer evolutionary synthesis is unlikely to emerge without this change in thinking about causation.     

Design,synthesis, and biological activity evaluation of a series of pleuromutilin derivatives with novel C14 side chains

In this work, according to the ‘me-too me-better’ design strategy, a peculiar side chain different from lefamulin at C14 position of pleuromutilin was introduced. A series of novel thioether pleuromutilin derivatives containing cyclohexane in the C14 chain was synthesized by ten-step synthesis reaction. All derivatives were characterized by Nuclear Magnetic Resonance (NMR) and High Resolution Mass Spectrometer (HRMS). Furthermore, majority of derivatives displayed moderate antibacterial activity in vitro. However, the compound 2C and 2J exhibited comparable or superior antibacterial activity to lefamulin. The summarized structure-activity relationship not only made the variety of pleuromutilin derivatives more diverse, but also provided new ideas for its design and development.     

Induction of the cell cycle in baby rat kidney cells by adenovirus type 5 E1A in the absence of E1B and a possible influence of p53.

From previous studies on the induction of DNA synthesis in quiescent primary baby rat kidney cells by adenovirus type 5 (Ad5) E1A deletion mutants, we concluded that induction is prevented only when cellular proteins p300 and pRb are both uncomplexed with E1A (J.A. Howe, J.S. Mymryk, C. Egan, P.E. Branton, and S.T. Bayley, Proc. Natl. Acad. Sci. USA 87:5883-5887, 1990). We have now examined induction by these same mutants in virus lacking the E1B region, so that cellular p53 was no longer complexed to the E1B 55-kDa protein. E1A mutants that fail to bind pRb induced DNA synthesis at a significantly lower level in Ad5 lacking E1B than in Ad5 containing E1B. Apparently, therefore, uncomplexed p53 can partially replace p300 in cooperating with pRb to suppress DNA synthesis in baby rat kidney cells.     

BOOK REVIEWS

Book reviewed in this article:
Recent Advances in Anaerobic Bacteriology (1987). Edited by S.P. Borriello, J.M. Hardie, B.S. Drasar, B.I. Duerden, M.J. Hudson & R.J. Lysons.
Current Topics in Medical Mycology (1988). Volume 2. Edited by M.R. McGinnis
Advances in Biotechnological Processes Vol. 6 (1986). Edited by Avshalom Mizrahi
The Health Service Use of Ethylene Oxide Sterilization. Edited by G.A.J. Ayliffe, N.F. Cripps, C.E.A. Deverill & R.H. George
Biotechnology of Waste Treatment and Exploitation (1987). Edited by John M. Sidwick & Roger S. Holdom
Animal Cell Technology, Principles and Products (1987). By M. Butler
Methods in Aquatic Bacteriology (1988). Edited by B. Austin
Homeostatic Mechanisms in Microorganisms (1988). Edited by R. Whittenbury, G.W. Gould, J.G. Banks & R.G. Board
Lecture Notes on Medical Virology (1987). By D.J. Jeffries
Urinary Tract Infections (1987). By J.R. Dalton & E.J. Bergquist
Quality Control and Assurance in Clinical Laboratories (1988). Edited by A.D. Farr
Disinfection in Veterinary and Farm Animal Practice (1987). Edited by A.H. Linton, W.B. Hugo & A.D. Russell     

On the nature and origin of cellular complexity: The combinatorial–eukaryogenetic scenario

The ideas on the nature and origin of the cell nucleus published by K.S. Merezhkowsky in his book The Theory of Two Plasms as the Basis of Symbiogenesis, a New Study on the Origins of Organisms (1909) are still relevant. In this book, Merezhkowsky (1909, p. 86) wrote, “Part of my theory related to the nucleus, its nature and origin will be the subject of a separate paper, which will present facts serving as the basis for the ideas, which are here only touched upon briefly.” For various reasons, he was not able to publish the paper intended. Therefore, I here attempt to interpret Merezhkowsky’s original concepts on the nature and origin of the cell nucleus in a modern context.