A new biology for a new century.

Biology today is at a crossroads. The molecular paradigm, which so successfully guided the discipline throughout most of the 20th century, is no longer a reliable guide. Its vision of biology now realized, the molecular paradigm has run its course. Biology, therefore, has a choice to make, between the comfortable path of continuing to follow molecular biology's lead or the more invigorating one of seeking a new and inspiring vision of the living world, one that addresses the major problems in biology that 20th century biology, molecular biology, could not handle and, so, avoided. The former course, though highly productive, is certain to turn biology into an engineering discipline. The latter holds the promise of making biology an even more fundamental science, one that, along with physics, probes and defines the nature of reality. This is a choice between a biology that solely does society's bidding and a biology that is society's teacher.     

A New Biology for a New Century

Biology today is at a crossroads. The molecular paradigm, which so successfully guided the discipline throughout most of the 20th century, is no longer a reliable guide. Its vision of biology now realized, the molecular paradigm has run its course. Biology, therefore, has a choice to make, between the comfortable path of continuing to follow molecular biology's lead or the more invigorating one of seeking a new and inspiring vision of the living world, one that addresses the major problems in biology that 20th century biology, molecular biology, could not handle and, so, avoided. The former course, though highly productive, is certain to turn biology into an engineering discipline. The latter holds the promise of making biology an even more fundamental science, one that, along with physics, probes and defines the nature of reality. This is a choice between a biology that solely does society's bidding and a biology that is society's teacher.     

Uexküllian <Emphasis Type="Italic">Umwelt</Emphasis> as science and as ideology: the light and the dark side of a concept

The concept of Umwelt, in particular the interpretation originally developed by Jakob von Uexküll, played an important role in the development of biological thought of the first half of the twentieth century. The theory of Umwelt (Umweltlehre) was one of the most original ideas that appeared in German biology at that time. It was the first attempt to introduce subjectivity into a science about organisms; it laid down the foundations of behavioural research and inspired the development of ethology. However, the theory of Umwelt has also been used to support more sinister activities and even some dangerous ideologies. The concept of Umwelt is of interest not only to historians: within some intellectual circles, it is still broadly used today. Our aim was to analyse the notion’s historic development within the context of biological thought of the first half of the 20th century. In particular, we focus (1) on how the concept was adopted and adapted for various, often widely diverging purposes; (2) on interactions between the Umweltlehre and other contemporary worldviews. We argue that in order to understand the developments that occurred in twentieth century biology, one needs to properly appreciate the role which Umweltlehre played in these. Even more importantly, the Umweltlehre is a worldview that influenced not only science but also politics and social affairs. In this respect it functioned rather like a number of other scientific and ideological frameworks of that time, such as Synthetic Darwinism.     

Selenoproteins and the metabolic features of the archaeal ancestor of eukaryotes

In all three branches of life, some organisms incorporate the rare amino acid selenocysteine. Selenoproteins are relevant to the controversy over the metabolic features of the archaeal ancestor of eukaryotes because among archaea, several known selenoproteins are involved in methanogenesis and autotrophic growth. Although the eukaryotic selenocysteine-specific translation apparatus and at least one selenoprotein appear to be of archaeal origin, selenoproteins have not been identified among sulfur-metabolizing crenarchaeotes. In this regard, both the phylogeny and function of archaeal selenoproteins are consistent with the argument that the archaeal ancestor was a methanogen. Selenium, however, is abundant in sulfur-rich environments, and some anaerobic bacteria reduce sulfur and have selenoproteins similar to those in archaea. As additional archaeal sequence data becomes available, it will be important to determine whether selenoproteins are present in nonmethanogenic archaea, especially the sulfur-metabolizing crenarchaeotes.     

Do organisms have an ontological status?

The category "organism" has an ambiguous status: is it scientific or is it philosophical? Or, if one looks at it from within the relatively recent field or sub-field of philosophy of biology, is it a central, or at least legitimate category therein, or should it be dispensed with? In any case, it has long served as a kind of scientific bolstering for a philosophical train of argument which seeks to refute the mechanistic or reductionist trend, which has been perceived as dominant since the 17th century, whether in the case of Stahlian animism, Leibnizian monadology, the neo-vitalism of Hans Driesch, or, lastly, of the "phenomenology of organic life" in the 20th century, with authors such as Kurt Goldstein, Maurice Merleau-Ponty, and Georges Canguilhem. In this paper I try to reconstruct some of the main interpretive stages or layers of the concept of organism in order to evaluate it critically. How might organism be a useful concept if one rules out the excesses of organismic biology and metaphysics? Varieties of instrumentalism and what I call the projective concept of organism are appealing, but perhaps ultimately unsatisfying.     

Reminiscences from the first curator of the whitney-rothschild collection

Dr Ernst Mayr has been one of the seminal figures of 20th century biology. His essential contributions were in the development of the Modern Synthesis in evolutionary biology. His landmark book Systematics and the Origin of Species, was published in 1942 and has long been acknowledged as one of the key foundations of 20th century evolutionary biology. In many subsequent articles and books on evolution and the history and philosophy of biology during the past half century, he has continued to be a key contributor of ideas and inspiration to successive generations of evolutionary biologists. In the first of two ‘Roots’ articles, he describes the early stages of his career and the serendipitous events that furthered it. This article was first presented as a talk, on October 27, 1993, at the 50 year Jubilee celebration of the founding of the Whitney wing, the ornithological section, of the American Museum of Natural History in New York City. In next month's ‘Roots’ article, Dr Mayr will describe the events that led to the founding of the Society for the Study of Evolution in 1946, in St Louis, Missouri.     

The deep archaeal roots of eukaryotes

The set of conserved eukaryotic protein-coding genes includes distinct subsets one of which appears to be most closely related to and, by inference, derived from archaea, whereas another one appears to be of bacterial, possibly, endosymbiotic origin. The "archaeal" genes of eukaryotes, primarily, encode components of information-processing systems, whereas the "bacterial" genes are predominantly operational. The precise nature of the archaeo-eukaryotic relationship remains uncertain, and it has been variously argued that eukaryotic informational genes evolved from the homologous genes of Euryarchaeota or Crenarchaeota (the major branches of extant archaea) or that the origin of eukaryotes lies outside the known diversity of archaea. We describe a comprehensive set of 355 eukaryotic genes of apparent archaeal origin identified through ortholog detection and phylogenetic analysis. Phylogenetic hypothesis testing using constrained trees, combined with a systematic search for shared derived characters in the form of homologous inserts in conserved proteins, indicate that, for the majority of these genes, the preferred tree topology is one with the eukaryotic branch placed outside the extant diversity of archaea although small subsets of genes show crenarchaeal and euryarchaeal affinities. Thus, the archaeal genes in eukaryotes appear to descend from a distinct, ancient, and otherwise uncharacterized archaeal lineage that acquired some euryarchaeal and crenarchaeal genes via early horizontal gene transfer.     

The impact of genomics on research in diversity and evolution of archaea

Since the definition of archaea as a separate domain of life along with bacteria and eukaryotes, they have become one of the most interesting objects of modern microbiology, molecular biology, and biochemistry. Sequencing and analysis of archaeal genomes were especially important for studies on archaea because of a limited availability of genetic tools for the majority of these microorganisms and problems associated with their cultivation. Fifteen years since the publication of the first genome of an archaeon, more than one hundred complete genome sequences of representatives of different phylogenetic groups have been determined. Analysis of these genomes has expanded our knowledge of biology of archaea, their diversity and evolution, and allowed identification and characterization of new deep phylogenetic lineages of archaea. The development of genome technologies has allowed sequencing the genomes of uncultivated archaea directly from enrichment cultures, metagenomic samples, and even from single cells. Insights have been gained into the evolution of key biochemical processes in archaea, such as cell division and DNA replication, the role of horizontal gene transfer in the evolution of archaea, and new relationships between archaea and eukaryotes have been revealed.     

Charles Manning Child (1869-1954): the past, present, and future of metabolic signaling

Charles Manning Child's work focused on metabolic gradients and their influence on organismal development. Early in the 20th century, his work had considerable currency, but by the second half of the century he had become little more than a historical footnote. Yet today Child's ideas are once again topical. While there were issues of cause and effect that Child and his students were never able to address adequately, in hindsight the extent of his eclipse hardly seems warranted. In fact, the demise of Child's theories may have resulted from larger changes in the nature of biology in the early 20th century. Child frequently studied planarians, hydroids, and other animals that are capable of asexual, agametic reproduction, and his theories most clearly apply to such organisms. In contrast, Thomas Hunt Morgan, initially one of Child's competitors in studies of regeneration, later developed the field of transmission genetics based on fruit flies, which can only reproduce via gametes. Child's theories and model systems were largely casualties of the success of Morgan's mechanistic paradigm. Nevertheless, in modern biology metabolic gradients, recast in terms of redox signaling, have become central to understanding both normal and pathological development.     

Archaeal abundance across a pH gradient in an arable soil and its relationship to bacterial and fungal growth rates

Soil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abundance related to bacterial and fungal growth rates across the same pH gradient. We identified two distinct and opposite effects of pH on the archaeal abundance. In the lowest pH range (pH 4.0 to 4.7), the abundance of archaea did not seem to correspond to pH. Above this pH range, there was a sharp, almost 4-fold decrease in archaeal abundance, reaching a minimum at pH 5.1 to 5.2. The low abundance of archaeal 16S rRNA gene copy numbers at this pH range then sharply increased almost 150-fold with pH, resulting in an increase in the ratio between archaeal and bacterial copy numbers from a minimum of 0.002 to more than 0.07 at pH 8. The nonuniform archaeal response to pH could reflect variation in the archaeal community composition along the gradient, with some archaea adapted to acidic conditions and others to neutral to slightly alkaline conditions. This suggestion is reinforced by observations of contrasting outcomes of the (competitive) interactions between archaea, bacteria, and fungi toward the lower and higher ends of the examined pH gradient.     

Evidences of lateral gene transfer between archaea and pathogenic bacteria

Acquisition of new genetic material through horizontal gene transfer has been shown to be an important feature in the evolution of many pathogenic bacteria. Changes in the genetic repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens. However, horizontal gene transfer across the domains i.e. archaea and bacteria is not so common. In this context, we explore events of horizontal gene transfer between archaea and bacteria. In order to determine whether the acquisition of archaeal genes by lateral gene transfer is an important feature in the evolutionary history of the pathogenic bacteria, we have developed a scheme of stepwise eliminations that identifies archaeal-like genes in various bacterial genomes. We report the presence of 9 genes of archaeal origin in the genomes of various bacteria, a subset of which is also unique to the pathogenic members and are not found in respective non-pathogenic counterparts. We believe that these genes, having been retained in the respective genomes through selective advantage, have key functions in the organism’s biology and may play a role in pathogenesis.     

Regenerative medicine's historical roots in regeneration, transplantation, and translation

Regenerative medicine is not new; it has not sprung anew out of stem cell science as has often been suggested. There is a rich history of study of regeneration, of development, and of the ways in which understanding regeneration advances study of development and also has practical and medical applications. This paper explores the history of regenerative medicine, starting especially with T.H. Morgan in 1901 and carrying through the history of transplantation research in the 20th century, to an emphasis on translational medicine in the late 20th century.     

Archaea in boreal Swedish lakes are diverse,dominated by Woesearchaeota and follow deterministic community assembly

Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.     

U.S. racial and ethnic relations in the twenty-first century: are old divisions prevailing?

In this response to Valdez and Golash-Boza’s article, U.S. Racial and Ethnic Relations in the twenty-first century, I commend the authors for raising critical issues about the traditional lack of integration of race and ethnicity paradigms. However, I argue that, in an effort to make their claim about the distinction between the ethnicity and race paradigms, they end up oversimplifying some of the literature and overlook the ways in which race and ethnicity scholarship from the twenty-first century has made important advances towards paradigm integration. In my response I provide an alternate reading of some of the literature that the authors critique, focusing on the Mexican middle-class case. I then highlight scholars who are working towards race–ethnicity integration, moving past old paradigm divides. I conclude my response by introducing the concept of the “ethnoracial core”, which I believe moves us in the direction that Valdez and Golash-Boza are proposing.     

AIDS and transfer factor: Myths,certainties and realities

At the end of the 20th century, the triumph of biology is as indisputable as that of physics was at the end of the 19th century, and so is the might of the inductive thought. Virtually all diseases have been seemingly conquered and HIV, the cause of AIDS, has been fully described ten years after the onset of the epidemic. However, the triumph of biological science is far from being complete. The toll of several diseases, such as cancer, continues to rise and the pathogenesis of AIDS remains elusive. In the realm of inductive science, the dominant paradigm can seldom be challenged in a frontal attack, especially when it is apparently successful, and only what Kuhn calls “scientific revolutions” can overthrow it. Thus, it is hardly surprising that the concept of transfer factor is considered with contempt, and the existence of the moiety improbable: over forty years after the introduction of the concept, not only its molecular structure remains unknown, but also its putative mode of action contravenes dogmas of both immunology and molecular biology. And when facts challenge established dogmas, be in religion, philosophy or science, they must be suppressed. Thus, results of heterodox research become henceforth nisi — i.e., valid unless cause is shown for rescinding them, because they challenge the prevalent paradigm. However, when observations pertain to lethal disorders, their suppression in the name of dogmas may become criminal. Because of the failure of medical science to manage the AIDS pandemic, transfer factor, which has been successfully used for treating or preventing viral infections, may today overcome a priori prejudice and rejection more swiftly. In science, as in life, certainties always end up by dying, and Copernicus’ vision by replacing that of Ptolemy.     

Gene decay in archaea

The gene-dense chromosomes of archaea and bacteria were long thought to be devoid of pseudogenes, but with the massive increase in available genome sequences, whole genome comparisons between closely related species have identified mutations that have rendered numerous genes inactive. Comparative analyses of sequenced archaeal genomes revealed numerous pseudogenes, which can constitute up to 8.6% of the annotated coding sequences in some genomes. The largest proportion of pseudogenes is created by gene truncations, followed by frameshift mutations. Within archaeal genomes, large numbers of pseudogenes contain more than one inactivating mutation, suggesting that pseudogenes are deleted from the genome more slowly in archaea than in bacteria. Although archaea seem to retain pseudogenes longer than do bacteria, most archaeal genomes have unique repertoires of pseudogenes.     

Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales

The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies in model organisms, using the complementary approaches of genetics and biochemistry. Archaea have led to some exciting discoveries in the field of biochemistry, but archaeal genetics has been slow to get off the ground, not least because these organisms inhabit some of the more inhospitable places on earth and are therefore believed to be difficult to culture. In fact, many species can be cultivated with relative ease and there has been tremendous progress in the development of genetic tools for both major archaeal phyla, the Euryarchaeota and the Crenarchaeota. There are several model organisms available for methanogens, halophiles, and thermophiles; in the latter group, there are genetic systems for Sulfolobales and Thermococcales. In this review, we present the advantages and disadvantages of working with each archaeal group, give an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.     

Archaea and the cell cycle

Sequence similarity data suggest that archaeal chromosome replication is eukaryotic in character. Putative nucleoid-processing proteins display similarities to both eukaryotic and bacterial counterparts, whereas cell division may occur through a predominantly bacterial mechanism. Insights into the organization of the archaeal cell cycle are therefore of interest, not only for understanding archaeal biology, but also for investigating how components from the other two domains interact and work in concert within the same cell; in addition, archaea may have the potential to provide insights into eukaryotic initiation of chromosome replication.