Summer reads (papers)

Over the last few weeks of holidays I’ve started to store some papers I’d like to read. Now I’ve got all my devices and apps full of references, open and with no particular order, which is causing me a bit of stress (obsessive-compulsive disorder alert). I thought it may be useful to write a post with all the references so that they’re out of my daily activities and I can find all of them fast in few days. Plus, they may be interesting for other people. Here they are:

Inherent forms and the evolution of evolution (S. A. Newman):

John Bonner presented a provocative conjecture that the means by which organisms evolve has itself evolved. The elements of his postulated nonuniformitarianism in the essay under discussion—the emergence of sex, the enhanced selection pressures on larger multicellular forms—center on a presumed close mapping of genotypic to phenotypic change. A different view emerges from delving into earlier work of Bonner’s in which he proposed the concept of “neutral phenotypes” and “neutral morphologies” allied to D’Arcy Thompson’s analysis of physical determinants of form and studied the conditional elicitation of intrinsic organizational properties of cell aggregates in social amoebae. By comparing the shared and disparate mechanistic bases of morphogenesis and developmental outcomes in the embryos of metazoans (animals), closely related nonmetazoan holozoans, more distantly related dictyostelids, and very distantly related volvocine algae, I conclude, in agreement with Bonner’s earlier proposals, that understanding the evolution of multicellular evolution requires knowledge of the inherent forms of diversifying lineages, and that the relevant causative factors extend beyond genes and adaptation to the physics of materials.

Making and breaking symmetry in development, growth and disease (D. T. Grimes):

Consistent asymmetries between the left and right sides of animal bodies are common. For example, the internal organs of vertebrates are left-right (L-R) asymmetric in a stereotyped fashion. Other structures, such as the skeleton and muscles, are largely symmetric. This Review considers how symmetries and asymmetries form alongside each other within the embryo, and how they are then maintained during growth. I describe how asymmetric signals are generated in the embryo. Using the limbs and somites as major examples, I then address mechanisms for protecting symmetrically forming tissues from asymmetrically acting signals. These examples reveal that symmetry should not be considered as an inherent background state, but instead must be actively maintained throughout multiple phases of embryonic patterning and organismal growth.

Genomics of developmental plasticity in animals (E. Lafuente & P. Beldade):

Developmental plasticity refers to the property by which the same genotype produces distinct phenotypes depending on the environmental conditions under which development takes place. By allowing organisms to produce phenotypes adjusted to the conditions that adults will experience, developmental plasticity can provide the means to cope with environmental heterogeneity. Developmental plasticity can be adaptive and its evolution can be shaped by natural selection. It has also been suggested that developmental plasticity can facilitate adaptation and promote diversification. Here, we summarize current knowledge on the evolution of plasticity and on the impact of plasticity on adaptive evolution, and we identify recent advances and important open questions about the genomics of developmental plasticity in animals. We give special attention to studies using transcriptomics to identify genes whose expression changes across developmental environments and studies using genetic mapping to identify loci that contribute to variation in plasticity and can fuel its evolution.

The evolution of phenotypic correlations and ‘developmental memory’ (R. A. Watson, G. P. Wagner, M. Pavlicev, D. W. Weinrich, R. Mills):

Development introduces structured correlations among traits that may constrain or bias the distribution of phenotypes produced. Moreover, when suitable heritable variation exists, natural selection may alter such constraints and correlations, affecting the phenotypic variation available to subsequent selection. However, exactly how the distribution of phenotypes produced by complex developmental systems can be shaped by past selective environments is poorly understood. Here we investigate the evolution of a network of recurrent nonlinear ontogenetic interactions, such as a gene regulation network, in various selective scenarios. We find that evolved networks of this type can exhibit several phenomena that are familiar in cognitive learning systems. These include formation of a distributed associative memory that can “store” and “recall” multiple phenotypes that have been selected in the past, recreate complete adult phenotypic patterns accurately from partial or corrupted embryonic phenotypes, and “generalize” (by exploiting evolved developmental modules) to produce new combinations of phenotypic features. We show that these surprising behaviors follow from an equivalence between the action of natural selection on phenotypic correlations and associative learning, well‐understood in the context of neural networks. This helps to explain how development facilitates the evolution of high‐fitness phenotypes and how this ability changes over evolutionary time.

Evolutionary significance of phenotypic accommodation in novel environments: an empirical test of the Baldwin effect (A. V. Badyaev):

When faced with changing environments, organisms rapidly mount physiological and behavioural responses, accommodating new environmental inputs in their functioning. The ubiquity of this process contrasts with our ignorance of its evolutionary significance: whereas within-generation accommodation of novel external inputs has clear fitness consequences, current evolutionary theory cannot easily link functional importance and inheritance of novel accommodations. One hundred and twelve years ago, J. M. Baldwin, H. F. Osborn and C. L. Morgan proposed a process (later termed the Baldwin effect) by which non-heritable developmental accommodation of novel inputs, which makes an organism fit in its current environment, can become internalized in a lineage and affect the course of evolution. The defining features of this process are initial overproduction of random (with respect to fitness) developmental variation, followed by within-generation accommodation of a subset of this variation by developmental or functional systems (‘organic selection’), ensuring the organism’s fit and survival. Subsequent natural selection sorts among resultant developmental variants, which, if recurrent and consistently favoured, can be inherited when existing genetic variance includes developmental components of individual modifications or when the ability to accommodate novel inputs is itself heritable. Here, I show that this process is consistent with the origin of novel adaptations during colonization of North America by the house finch. The induction of developmental variation by novel environments of this species’s expanding range was followed by homeostatic channelling, phenotypic accommodation and directional cross-generational transfer of a subset of induced developmental outcomes favoured by natural selection. These results emphasize three principal points. First, contemporary novel adaptations result mostly from reorganization of existing structures that shape newly expressed variation, giving natural selection an appearance of a creative force. Second, evolutionary innovations and maintenance of adaptations are different processes. Third, both the Baldwin and parental effects are probably a transient state in an evolutionary cycle connecting initial phenotypic retention of adaptive changes and their eventual genetic determination and, thus, the origin of adaptation and evolutionary change.

Bonus tracks:

Why the reward structure of science makes reproducibility problems inevitable? (R. Heesen):

Recent philosophical work has praised the reward structure of science, while recent empirical work has shown that many scientific results may not be reproducible. I argue that the reward structure of science incentivizes scientists to focus on speed and impact at the expense of the reproducibility of their work, thus contributing to the so-called reproducibility crisis. I use a rational choice model to identify a set of sufficient conditions for this problem to arise, and I argue that these conditions plausibly apply to a wide range of research situations. Currently proposed solutions will not fully address this problem. Philosophical commentators should temper their optimism about the reward structure of science.

Null hypothesis significance testing: A review of an old and continuing controversy (R. S. Nickerson):

Null hypothesis significance testing (NHST) is arguably the most widely used
approach to hypothesis evaluation among behavioral and social scientists. It is also
very controversial. A major concern expressed by critics is that such testing is
misunderstood by many of those who use it. Several other objections to its use have
also been raised. In this article the author reviews and comments on the claimed
misunderstandings as well as on other criticisms of the approach, and he notes
arguments that have been advanced in support of NHST. Alternatives and supplements to NHST are considered, as are several related recommendations regarding
the interpretation of experimental data. The concluding opinion is that NHST is
easily misunderstood and misused but that when applied with good judgment it can
be an effective aid to the interpretation of experimental data.