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The concept of developmental reprogramming and the quest for an inclusive theory of evolutionary mechanisms.

Evolutionary developmental biology has already made a major contribution to our understanding of evolutionary patterns, notably homology. However, while it has the potential to make an equally important contribution to our understanding of evolutionary mechanisms, and indeed to the integration of mechanism and pattern, it has not yet done so. This paper explores how this potential may be realized. In particular, I focus on the limitations of present-day neo-Darwinian theory, and indicate how a combination of the neo-Darwinian and "evo-devo" approaches provides a more inclusive view of evolutionary mechanisms with greater explanatory power. There is a particular focus on developmental reprogramming, which lies logically between mutation and selection, yet has been neglected in mainstream evolutionary theory. The inclusion of developmental reprogramming in the list of evolutionary mechanisms leads to a view that the direction of evolutionary change is determined by a combination of internal and external factors, rather than being controlled entirely by the environment.

Biological Evolution↗
PubMed1980

Predicting coding function from nucleotide sequence or survival of "fitness" of tRNA.

The sequence of a nucleotide region of f1 bacteriophage was determined on a bonded ultrathin acrylamide gel with a discontinuous buffer system by using the dideoxy-DNA sequencing method. This sequence and one other were analyzed for maximal base pairing with tRNAs. The results allow a prediction of the direction and phase of possible coding functions. The implication of sequence constraints on mRNA codon frequency, tRNA structure, the origin of protein synthesis, and triplet reading are discussed in terms of neutral, Darwinian, and genotypic selectionist perspectives of evolution. The model of F. H. C. Crick, S. Brenner, A. Klug, and G. Pieczenik [(1976) Origins of Life 7, 389-397] for the origin of the genetic code is used to interpet contemporary adaptive and functional nucleic acid sequences.

Anticodon↗
PubMed1983

Evolution: questions for the modern theory.

The blind spot of the present generation of evolutionists is failure to see the consequences and limits of natural selection. Darwinian natural selection is a costly process of differential elimination of individuals. The widely accepted misdefinition of natural selection as differential reproduction mistakenly hides the Darwinian process and its cost. And current theories of selfish genes, inclusive fitness, and kin selection are incompatible with Darwinian selection. Implicitly, if not explicitly, they postulate genes that favor themselves but reduce the Darwinian fitness of the individuals carrying them. Such genes would not survive; they would eliminate themselves by causing the selective elimination of their carriers. Critical questions that evolutionists should be asked are suggested. My own "unhappy conclusion" is that, because most biologists have forgotten what natural selection is, much current evolutionary and sociobiological theory presented by the most influential evolutionists is mistaken and dangerous. Anthropologists and sociologists are wise to distrust it.

Animals↗
PubMed1994

An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function.

Three short protein sequences have been guided by computer to folds resembling their crystal structures. Initially, peptide fragment conformations ranging in size from 9 to 25 residues were selected from a database of known protein structures. A fragment was selected if it was compatible with a segment of the sequence to be folded, as judged by three-dimensional profile scores. By linking the selected fragment conformations together, hundreds of trial structures were generated of the same length and sequence as the protein to be folded. These starting trial structures were then improved by an evolutionary algorithm. Selection pressure for improving the structures was provided by an energy function that was designed to guide the conformational search procedure toward the correct structure. We find that by evolution of only 400 structures for fewer than 1400 generations, the overall fold of some small helical proteins can be computed from the sequence, with deviations from observed structures of 2.5-4.0 A for C alpha atoms.

Algorithms↗
PubMed1994

Tempo and mode in the macroevolutionary reconstruction of Darwinism.

Among the several central meanings of Darwinism, his version of Lyellian uniformitarianism--the extrapolationist commitment to viewing causes of small-scale, observable change in modern populations as the complete source, by smooth extension through geological time, of all magnitudes and sequences in evolution--has most contributed to the causal hegemony of microevolution and the assumption that paleontology can document the contingent history of life but cannot act as a domain of novel evolutionary theory. G. G. Simpson tried to combat this view of paleontology as theoretically inert in his classic work, Tempo and Mode in Evolution (1944), with a brilliant argument that the two subjects of his title fall into a unique paleontological domain and that modes (processes and causes) can be inferred from the quantitative study of tempos (pattern). Nonetheless, Simpson did not cash out his insight to paleontology's theoretical benefit because he followed the strict doctrine of the Modern Synthesis. He studied his domain of potential theory and concluded that no actual theory could be found--and that a full account of causes could therefore be located in the microevolutionary realm after all. I argue that Simpson was unduly pessimistic and that modernism's belief in reductionistic unification (the conventional view of Western intellectuals from the 1920s to the 1950s) needs to be supplanted by a postmodernist commitment to pluralism and multiple levels of causation. Macro- and microevolution should not be viewed as opposed, but as truly complementary. I describe the two major domains where a helpful macroevolutionary theory may be sought--unsmooth causal boundaries between levels (as illustrated by punctuated equilibrium and mass extinction) and hierarchical expansion of the theory of natural selection to levels both below (gene and cell-line) and above organisms (demes, species, and clades). Problems remain in operationally defining selection at non-organismic levels (emergent traits vs. emergent fitness approaches, for example) and in specifying the nature and basis of levels, but this subject should be the central focus in formulating a more ample and satisfactory general theory of evolution on extended Darwinian principles.

Animals↗
PubMed1995

On the existence and implications of an inverse folding code in proteins.

The existence of a code relating the set of possible sequences at a given position in a protein backbone to the local structure at that location is investigated. It is shown that only 73% of 4-C alpha structure fragments in a sample of 114 protein structures exhibit a preference for a particular set of sequences. The remaining structures can accommodate essentially any sequence. The structures that encode specific sequence distributions include the classical "secondary" structures, with the notable exception of planar (beta) bends. It is suggested that this has implications as to the mechanism of folding in proteins with extensive sheet/barrel structure. The possible role of structures that do not encode specific sequences as mutation hot spots is noted.

Biological Evolution↗
PubMed1998

Working memory constrains human cooperation in the Prisoner's Dilemma.

Many problems in human society reflect the inability of selfish parties to cooperate. The "Iterated Prisoner's Dilemma" has been used widely as a model for the evolution of cooperation in societies. Axelrod's computer tournaments and the extensive simulations of evolution by Nowak and Sigmund and others have shown that natural selection can favor cooperative strategies in the Prisoner's Dilemma. Rigorous empirical tests, however, lag behind the progress made by theorists. Clear predictions differ depending on the players' capacity to remember previous rounds of the game. To test whether humans use the kind of cooperative strategies predicted, we asked students to play the iterated Prisoner's Dilemma game either continuously or interrupted after each round by a secondary memory task (i.e., playing the game "Memory") that constrained the students' working-memory capacity. When playing without interruption, most students used "Pavlovian" strategies, as predicted, for greater memory capacity, and the rest used "generous tit-for-tat" strategies. The proportion of generous tit-for-tat strategies increased when games of Memory interfered with the subjects' working memory, as predicted. Students who continued to use complex Pavlovian strategies were less successful in the Memory game, but more successful in the Prisoner's Dilemma, which indicates a trade-off in memory capacity for the two tasks. Our results suggest that the set of strategies predicted by game theorists approximates human reality.

Biological Evolution↗
PubMed1999

A structural view of evolutionary divergence.

Two directed evolution experiments on p-nitrobenzyl esterase yielded one enzyme with a 100-fold increased activity in aqueous-organic solvents and another with a 17 degrees C increase in thermostability. Structures of the wild type and its organophilic and thermophilic counterparts are presented at resolutions of 1.5 A, 1.6 A, and 2.0 A, respectively. These structures identify groups of interacting mutations and demonstrate how directed evolution can traverse complex fitness landscapes. Early-generation mutations stabilize flexible loops not visible in the wild-type structure and set the stage for further beneficial mutations in later generations. The mutations exert their influence on the esterase structure over large distances, in a manner that would be difficult to predict. The loops with the largest structural changes generally are not the sites of mutations. Similarly, none of the seven amino acid substitutions in the organophile are in the active site, even though the enzyme experiences significant changes in the organization of this site. In addition to reduction of surface loop flexibility, thermostability in the evolved esterase results from altered core packing, helix stabilization, and the acquisition of surface salt bridges, in agreement with other comparative studies of mesophilic and thermophilic enzymes. Crystallographic analysis of the wild type and its evolved counterparts reveals networks of mutations that collectively reorganize the active site. Interestingly, the changes that led to diversity within the alpha/beta hydrolase enzyme family and the reorganization seen in this study result from main-chain movements.

Biological Evolution↗
PubMed2000

A DNA enzyme with N-glycosylase activity.

In vitro evolution was used to develop a DNA enzyme that catalyzes the site-specific depurination of DNA with a catalytic rate enhancement of about 10(6)-fold. The reaction involves hydrolysis of the N-glycosidic bond of a particular deoxyguanosine residue, leading to DNA strand scission at the apurinic site. The DNA enzyme contains 93 nucleotides and is structurally complex. It has an absolute requirement for a divalent metal cation and exhibits optimal activity at about pH 5. The mechanism of the reaction was confirmed by analysis of the cleavage products by using HPLC and mass spectrometry. The isolation and characterization of an N-glycosylase DNA enzyme demonstrates that single-stranded DNA, like RNA and proteins, can form a complex tertiary structure and catalyze a difficult biochemical transformation. This DNA enzyme provides a new approach for the site-specific cleavage of DNA molecules.

Catalysis↗
PubMed2003

Making a robust biomolecular time scale for phylogenetic studies.

The further evolution of informational molecular sequences should depend on the number of viable alternatives possible for the sequences as set by selection, the unrepaired mutation rate, and time. Most biomolecular clocks are based on Kimura's nearly neutral mutation random-drift hypothesis. This clock assumes that informational sequences are in equilibrium, i.e., the nucleotides mutate at a uniform rate and the number of nucleotides unconstrained by selection remains constant. Correcting for deviations from these assumptions should produce a more accurate clock. Informational molecules probably formed from polynucleotides having some other function such as nitrogen or nucleotide storage, thus being initially functionally unselected. At any time the rate of development of functionality in a protein may be expected to be proportional to the number of viable alternatives of sequence in its potentially interacting regions. Assuming the rate of unrepaired mutations is constant, these clocks should exponentially slow as they evolve, each with a different rate toward individual equilibria. Also if the degree of selection changes, its clock rate should change. For a more precise clock two approaches are suggested to estimate these time dependent changes in evolutionary rate. An improved clock could improve estimation of phylogeny and put a time scale on that phylogeny.

Animals↗
PubMed2002

Changing philosophical perspectives on the management of children with physical disabilities--their effect on the use of powered mobility.

PURPOSE: Over the past decade, the emergence of a new philosophical framework has influenced approaches to service delivery in paediatric rehabilitation. Traditional approaches focused on the attainment of typical movement patterns as the ultimate goal of intervention. By contrast, contemporary approaches to intervention encourage children with physical disabilities to use their most efficient movement strategies to explore their environment and participate in meaningful activities. METHODS/RESULTS: Factors that facilitated this change in approaches to intervention are explored and include: the disability movement; the evolution of models of disablement; the shift from a medical model to a family-centred model of health care service provision; the emergence of a new theory to explain motor development and increased availability and quality of assistive technology. CONCLUSION: The clinical implications of this philosophical shift for the use of powered mobility with children with physical disabilities are explored. A collaborative approach to working with families throughout the process of selecting mobility options for their children is discussed.

Child↗
PubMed2002

Increased taxon sampling greatly reduces phylogenetic error.

Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little benefit of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic analysis. In this paper we examined five aspects of study design that may have led to these different perspectives. First, we considered the measurement of phylogenetic error across a wide range of taxon sample sizes, and conclude that the expected error based on randomly selecting trees (which varies by taxon sample size) must be considered in evaluating error in studies of the effects of taxon sampling. Second, we addressed the scope of the phylogenetic problems defined by different samples of taxa, and argue that phylogenetic scope needs to be considered in evaluating the importance of taxon-sampling strategies. Third, we examined the claim that fast and simple tree searches are as effective as more thorough searches at finding near-optimal trees that minimize error. We show that a more complete search of tree space reduces phylogenetic error, especially as the taxon sample size increases. Fourth, we examined the effects of simple versus complex simulation models on taxonomic sampling studies. Although benefits of taxon sampling are apparent for all models, data generated under more complex models of evolution produce higher overall levels of error and show greater positive effects of increased taxon sampling. Fifth, we asked if different phylogenetic optimality criteria show different effects of taxon sampling. Although we found strong differences in effectiveness of different optimality criteria as a function of taxon sample size, increased taxon sampling improved the results from all the common optimality criteria. Nonetheless, the method that showed the lowest overall performance (minimum evolution) also showed the least improvement from increased taxon sampling. Taking each of these results into account re-enforces the conclusion that increased sampling of taxa is one of the most important ways to increase overall phylogenetic accuracy.

Likelihood Functions↗
PubMed2002

Using tree shape.

Explore the source record for details and available documents.

Biological Evolution↗
PubMed2002

Tree balance, time slices, and evolutionary turnover in cretaceous planktonic foraminifera.

Studies of phylogenetic tree shape often concentrate on the balance of phylogenies of extant taxa. Paleontological phylogenies (which include extinct taxa) can contain additional useful information and can directly document changes in tree shape through evolutionary time. Unfortunately, the inclusion of extinct taxa lowers the power of direct examinations of tree balance because it increases the range of tree shapes expected under null models of evolution (with equal rates of speciation and extinction across lineages). A promising approach for the analysis of tree shape in paleontological phylogenies is to break the phylogeny down into time slices, examining the shape of the phylogeny of taxa alive at each time slice and changes in that shape between successive time slices. This method was illustrated with 57 time slices through a stratophenetic phylogeny of the Cretaceous planktonic foraminiferal superfamily Globotruncanacea. At 3 of 56 intervals between time slices, 93-92.5 million years ago (MYA), 89-88.5 MYA, and 85.5-84 MYA, the group showed steep increases in imbalance. Although none of these increases were significant after Bonferroni correction, these points in the history of the Globotruncanacea were nevertheless identified as deserving of further macroevolutionary investigation. The 84 MYA time slice coincides with a peak in species turnover for the superfamily. Time slices through phylogenies may prove useful for identifying periods of time when evolution was proceeding in a nonstochastic manner.

Biological Evolution↗