BIO-complexity最新文献

{"title":"The Types: A Persistent Structuralist Challenge to Darwinian Pan-Selectionism","authors":"M. Denton","doi":"10.5048/BIO-C.2013.3","DOIUrl":"https://doi.org/10.5048/BIO-C.2013.3","url":null,"abstract":"Here I first review the structuralist or typological world view of pre-1859 biology, and the concept that the basic forms of the natural world--the Types--are immanent in nature, and determined by a set of special natural biological laws, the so called ‘laws of form’. I show that this conception was not based, as Darwinists often claim, on a priori philosophical belief in Platonic concepts, but rather upon the empirical finding that a vast amount of biological complexity, including the deep homologies which define the taxa of the natural system, appears to be of an abstract, non-adaptive nature that is sometimes of a strikingly numerical and geometric character. In addition, these Types exhibit an extraordinary robustness and stability, having in many instances remained invariant in diverse lineages for hundreds of millions of years. Second, I show that neither Darwinism nor any subsequent functionalist theory has ever provided a convincing adaptive or functionalist explanation for the Types or deep homologies. Third, I discuss how recent advances have provided new support for the structuralist notion that the basic forms of life are immanent in nature. These include the discovery of the cosmic fine-tuning of the laws of nature for life as it exists on earth, and advances in areas of molecular and cellular biology, where it is apparent that a considerable amount of biological complexity is clearly determined by the self-organizing properties of particular categories of matter, rather than being specified in detail in a genetic blueprint as functionalism demands.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2013 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70593995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Entropy and Evolution","authors":"G. Sewell","doi":"10.5048/BIO-C.2013.2","DOIUrl":"https://doi.org/10.5048/BIO-C.2013.2","url":null,"abstract":"It is widely argued that the spectacular local decreases in entropy that occurred on Earth as a result of the origin and evolution of life and the development of human intelligence are not inconsistent with the second law of thermodynamics, because the Earth is an open system and entropy can decrease in an open system, provided the decrease is compensated by entropy increases outside the system. I refer to this as the compensation argument, and I argue that it is without logical merit, amounting to little more than an attempt to avoid the extraordinary probabilistic difficulties posed by the assertion that life has originated and evolved by spontaneous processes. To claim that what has happened on Earth does not violate the fundamental natural principle behind the second law, one must instead make a more direct and difficult argument.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2013 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70593955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Place of Life and Man in Nature: Defending the Anthropocentric Thesis","authors":"M. Denton","doi":"10.5048/BIO-C.2013.1","DOIUrl":"https://doi.org/10.5048/BIO-C.2013.1","url":null,"abstract":"Here I review the claim that the order of nature is uniquely suitable for life as it exists on earth (Terran life), and specifically for living beings similar to modern humans. I reassess Henderson’s claim from The Fitness of the Environment that the ensemble of core biochemicals that make up Terran life possess a unique synergistic fitness for the assembly of the complex chemical systems characteristic of life. I show that Henderson’s analysis is still remarkably consistent with the facts one century after it was written. It is still widely accepted even among researchers in astrobiology. I also review the evidence for believing that many of the properties of the same core set of biochemicals are specifically fit for the physiology of complex terrestrial beings resembling modern humans. I show that none of the recent advances in the field of extremophile biology, alternative biochemistries, or recent allusions to apparent defects in the fitness of nature for Terran life significantly undermine the core argument, that nature is peculiarly fit for carbon-based Terran life, and especially for the physiology of complex terrestrial beings resembling modern humans.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2013 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70594279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Time and Information in Evolution","authors":"W. Ewert, W. Dembski, A. Gauger, R. Marks","doi":"10.5048/BIO-C.2012.4","DOIUrl":"https://doi.org/10.5048/BIO-C.2012.4","url":null,"abstract":"Wilf and Ewens argue in a recent paper that there is plenty of time for evolution to occur. They base this claim on a mathematical model in which beneficial mutations accumulate simultaneously and independently, thus allowing changes that require a large number of mutations to evolve over comparatively short time periods. Because changes evolve independently and in parallel rather than sequentially, their model scales logarithmically rather than exponentially. This approach does not accurately reflect biological evolution, however, for two main reasons. First, within their model are implicit information sources, including the equivalent of a highly informed oracle that prophesies when a mutation is “correct,” thus accelerating the search by the evolutionary process. Natural selection, in contrast, does not have access to information about future benefits of a particular mutation, or where in the global fitness landscape a particular mutation is relative to a particular target. It can only assess mutations based on their current effect on fitness in the local fitness landscape. Thus the presence of this oracle makes their model radically different from a real biological search through fitness space. Wilf and Ewens also make unrealistic biological assumptions that, in effect, simplify the search. They assume no epistasis between beneficial mutations, no linkage between loci, and an unrealistic population size and base mutation rate, thus increasing the pool of beneficial mutations to be searched. They neglect the effects of genetic drift on the probability of fixation and the negative effects of simultaneously accumulating deleterious mutations. Finally, in their model they represent each genetic locus as a single letter. By doing so, they ignore the enormous sequence complexity of actual genetic loci (typically hundreds or thousands of nucleotides long), and vastly oversimplify the search for functional variants. In similar fashion, they assume that each evolutionary “advance” requires a change to just one locus, despite the clear evidence that most biological functions are the product of multiple gene products working together. Ignoring these biological realities infuses considerable active information into their model and eases the model’s evolutionary process.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2012 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2012-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70594146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Tetrahedral Representation of the Genetic Code Emphasizing Aspects of Symmetry.","authors":"Fernando Castro-Chavez","doi":"10.5048/BIO-C.2012.2","DOIUrl":"https://doi.org/10.5048/BIO-C.2012.2","url":null,"abstract":"<p><p>The genetic code is a mapping of 64 codons to 22 actions, including polypeptide chain initiation, termination, and incorporation of the twenty amino acids. The standard tabular representation is useful for looking up which amino acid is encoded by a particular codon, but says little about functional relationships in the code. The possibility of making sense of the code rather than simply enumerating its codon-to-action pairings therefore is appealing, and many have attempted to find geometric representations of the code that illuminate its functional organization. Here, I show that a regular tetrahedron with each of its four faces divided into sixteen equilateral triangles (for a total of 64 triangular 'cells') is a particularly apt geometry for representing the code. I apply five principles of symmetry and balance in order to assign codons to the triangular cells of the tetrahedral faces. These principles draw on various aspects of the genetic code and the twenty amino acids, making the final construct a positional balance of the amino acids and their functions rather than a re-analysis of them. The potential significance of this exercise, and others like it, is that this way of organizing the biological facts may provide new insights into them.</p>","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2012 2","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2012-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3445437/pdf/nihms396165.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30921180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Climbing the Steiner Tree--Sources of Active Information in a Genetic Algorithm for Solving the Euclidean Steiner Tree Problem","authors":"W. Ewert, W. Dembski, R. Marks","doi":"10.5048/BIO-C.2012.1","DOIUrl":"https://doi.org/10.5048/BIO-C.2012.1","url":null,"abstract":"Genetic algorithms are widely cited as demonstrating the power of natural selection to produce biological complexity. In particular, the success of such search algorithms is said to show that intelligent design has no scientific value. Despite their merits, genetic algorithms establish nothing of the sort. Such algorithms succeed not through any intrinsic prop- erty of the search algorithm, but rather through incorporating sources of information derived from the programmer’s prior knowledge. A genetic algorithm used to defend the efficacy of natural selection is Thomas’s Steiner tree algorithm. This paper tracks the various sources of information incorporated into Thomas’s algorithm. Rather than creating informa- tion from scratch, the algorithm incorporates resident information by restricting the set of solutions considered, introducing selection skew to increase the power of selection, and adopting a structure that facilitates fortuitous crossover. Thomas’s algorithm, far from exhibiting the power of natural selection, merely demonstrates that an intelligent agent, in this case a human programmer, possesses the ability to incorporate into such algorithms the information necessary for successful search.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2012-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70593390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lignin--Designed Randomness","authors":"M. Leisola, O. Pastinen, D. Axe","doi":"10.5048/BIO-C.2012.3","DOIUrl":"https://doi.org/10.5048/BIO-C.2012.3","url":null,"abstract":"0 0 1 282 1608 Biologic Institute 13 3 1887 14.0 Normal 0 false false false EN-US ZH-CN X-NONE Humans have long used wood as a structural material for some of the same reasons that trees use it—it combines great strength, flexibility and durability with a relatively low density. These desirable properties depend partly on lignin , a major chemical constituent of many plants, including trees. Lignin is the most abundant aromatic polymer on earth and the second most abundant organic polymer of any kind, exceeded only by cellulose. It is estimated that 30% of the earth’s non-fossil organic carbon is in the form of lignin. Considering its massive abundance and its high energy content (40% higher than cellulose, gram for gram), it is striking that no organism seems to have tapped it as an energy source. After posing this as an evolutionary enigma, we prepare to address it by reviewing what is known about the structure, biosynthesis and biodegradation of wood in general and of lignin in particular. Then, returning to the enigma, we ask whether it is more readily explained within a Darwinian framework or a design framework. The Darwinian account must somehow reconcile 400 million years of failure to evolve a relatively modest innovation—growth on lignin—with a long list of spectacular innovations thought to have evolved in a fraction of that time. How can one mechanism have been at the same time so effective and so ineffective? That tension vanishes completely when the design perspective is adopted. Terrestrial animal life is crucially dependent on terrestrial plant life, which is crucially dependent on soil, which is crucially dependent on the gradual photo- and biodegradation of lignin. Fungi accomplish th e bio degradation, and the surprising fact that it costs them energy to do so keeps the process gradual. The peculiar properties of lignin therefore make perfect sense when seen as part of a coherent design for the entire ecosystem of our planet.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"105 1","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2012-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70593530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway","authors":"A. Gauger, D. Axe","doi":"10.5048/BIO-C.2011.1","DOIUrl":"https://doi.org/10.5048/BIO-C.2011.1","url":null,"abstract":"Enzymes group naturally into families according to similarity of sequence, structure, and underlying mechanism. Enzymes belonging to the same family are considered to be homologs --the products of evolutionary divergence, whereby the first family member provided a starting point for conversions to new but related functions. In fact, despite their similarities, these families can include remarkable functional diversity. Here we focus not on minor functional variations within families, but rather on innovations --transitions to genuinely new catalytic functions. Prior experimental attempts to reproduce such transitions have typically found that many mutational changes are needed to achieve even weak functional conversion, which raises the question of their evolutionary feasibility. To further investigate this, we examined the members of a large enzyme superfamily, the PLP-dependent transferases, to find a pair with distinct reaction chemistries and high structural similarity. We then set out to convert one of these enzymes, 2-amino-3-ketobutyrate CoA ligase (Kbl 2 ), to perform the metabolic function of the other, 8-amino-7-oxononanoate synthase (BioF 2 ). After identifying and testing 29 amino acid changes, we found three groups of active-site positions and one single position where Kbl 2 side chains are incompatible with BioF 2 function. Converting these side chains in Kbl 2 makes the residues in the active-site cavity identical to those of BioF 2 , but nonetheless fails to produce detectable BioF 2 -like function in vivo . We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. Considering that Kbl 2 and BioF 2 are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution. [See published correction to this paper:  doi:10.5048/BIO-C.2011.1.e1 ].","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2011 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2011-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70593726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Stylus-Generated Artificial Genome with Analogy to Minimal Bacterial Genomes","authors":"D. Axe, P. Lu, Stephanie Flatau","doi":"10.5048/BIO-C.2011.3","DOIUrl":"https://doi.org/10.5048/BIO-C.2011.3","url":null,"abstract":"The difficulty of explaining evolutionary innovation on a scale that would account for the functional diversity of life and its components continues to dog evolutionary theory. Experiments are shedding light on this, but the complexity of the subject calls for other approaches as well. In particular, computational models that capture some aspects of simple life may provide useful proving grounds for ideas about how evolution can or cannot work. The challenge is to find a model ‘world’ simple enough for rapid simulation but not so simple that the real thing of interest has been lost. That challenge is best met with a model world in which real-world problems can be solved, as otherwise the connection with real innovation would be in doubt. Stylus is a previously described model that meets this criterion by being based on one of the most powerful real-world problem-solving tools: written language. Stylus uses a genetic code to translate gene-like sequences into vector sequences that, when processed according to simple geometric rules, form patterns resembling penned strokes. These translation products, called vector proteins, are functionless unless they form legible Chinese characters, in which case they serve the real function of writing. This coupling of artificial genetic causation to the real world of language makes evolutionary experimentation possible in a context where innovation can have a richness of variety and a depth of causal complexity that at least hints at what is needed to explain the complexity of bacterial proteomes. In order for this possibility to be realized, we here provide a complete Stylus genome as an experimental starting point. To construct it we first wrote a concise description of the Stylus algorithm in Chinese. Using that as a proteome specification, we then constructed the Stylus genes to encode it. In this way the Stylus proteome specifies how its encoding genome is decoded, making it analogous to the gene-expression machinery of bacteria. The complete 70,701 base Stylus genome encodes 223 vector proteins with 112 distinct vector domain types, making it more compact than the smallest bacterial genome but with comparable proteomic complexity for its size.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2011 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2011-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70593841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Can the Origin of the Genetic Code Be Explained by Direct RNA Templating","authors":"S. Meyer, P. A. Nelson","doi":"10.5048/BIO-C.2011.2","DOIUrl":"https://doi.org/10.5048/BIO-C.2011.2","url":null,"abstract":"Motivated by the RNA world hypothesis, Michael Yarus and colleagues have proposed a model for the origin of the ‘universal’ genetic code, in which RNA aptamers directly template amino acids for protein assembly. Yarus et al. claim that this “direct RNA templating” (DRT) model provides a stereochemical basis for the origin of the code, as shown by the higher-than-expected frequency of cognate coding triplets in aptamer amino acid-binding sites. However, the DRT model suffers from several defects. These include the selective use of data, incorrect null models, a weak signal even from positive results, an implausible geometry for the primordial RNA template (in relation to the universally-conserved structures of modern ribosomes), and unsupported assumptions about the pre-biotic availability of amino acids. Although Yarus et al. claim that the DRT model undermines an intelligent design explanation for the origin of the genetic code, the model’s many shortcomings in fact illustrate the insufficiency of undirected chemistry to construct the semantic system represented by the code we see today.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2011 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2011-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70593788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}