Nothing in Biology Makes Sense Except in the Light of Evolution
TL;DR: The Copernican world model has been shown to be a "mere theory" as mentioned in this paper, not a "fact," and it has not been verified by direct observations even to the extent the sphericity of the earth has been observed.
Abstract: As RECENTLY AS 1966, sheik Abd el Aziz bin Baz asked the king of Saudi Arabia to suppress a heresy that was spreading in his land. Wrote the sheik: "The Holy Koran, the Prophet's teachings, the majority of Islamic scientists, and the actual facts all prove that the sun is running in its orbit ... and that the earth is fixed and stable, spread out by God for his mankind. ... Anyone who professed otherwise would utter a charge of falsehood toward God, the Koran, and the Prophet." The good sheik evidently holds the Copernican theory to be a "mere theory," not a "fact." In this he is technically correct. A theory can be verified by a mass of facts, but it becomes a proven theory, not a fact. The sheik was perhaps unaware that the Space Age had begun before he asked the king to suppress the Copernican heresy. The sphericity of the earth had been seen by astronauts, and even by many earth-bound people on their television screens. Perhaps the sheik could retort that those who venture beyond the confines of God's earth suffer hallucinations, and that the earth is really flat. Parts of the Copernican world model, such as the contention that the earth rotates around the sun, and not vice versa, have not been verified by direct observations even to the extent the sphericity of the earth has been. Yet scientists accept the model as an accurate representation of reality. Why? Because it makes sense of a multitude of facts which are otherwise meaningless or extravagant. To nonspecialists most of these facts are unfamiliar. Why then do we accept the "mere theory" that the earth is a sphere revolving around a spherical sun? Are we simply submitting to authority? Not quite: we know that those who took time to study the evidence found it convincing. The good sheik is probably ignorant of the evidence. Even more likely, he is so hopelessly biased that no amount of evidence would impress him. Anyway, it would be sheer waste of time to attempt to convince him. The Koran and the Bible do not contradict Copernicus, nor does Copernicus contradict them. It is ludicrous to mistake the Bible and the Koran for primers of natural science. They treat of matters even more important: the meaning of man and his relations to God. They are written in poetic symbols that were understandable to people of the age when they were written, as well as to peoples of all other ages. The king of Arabia did not comply with the sheik's demand. He knew that some people fear enlightenment, because enlightenment threatens their vested interests. Education is not to be used to promote obscurantism. The earth is not the geometric center of the universe, although it may be its spiritual center. It is a mere speck of dust in cosmic spaces. Contrary to Bishop Ussher's calculations, the world did not appear in approximately its present state in 4004 B.C. The estimates of the age of the universe given by modern cosmologists are still only rough approximations, which are revised (usually upward) as the methods of estimation are refined. Some cosmologists take the universe to be about 10 billion years old; others suppose that it may have existed, and will continue to exist, eternally. The origin of life on earth is dated tentatively between 3 and 5 billion years ago; manlike beings appeared relatively quite recently, between 2 and 4 million years ago. The estimates of the age of the earth, of the duration of the geologic and paleontologic eras, and of the antiquity of man's ancestors are now based mainly on radiometric evidence-the proportions of isotopes of certain chemical elements in rocks suitable for such studies.
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TL;DR: A novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes is described.
Abstract: Recent advances in proteomics technologies such as two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of biomolecular interaction networks. Initial mapping efforts have already produced a wealth of data. As the size of the interaction set increases, databases and computational methods will be required to store, visualize and analyze the information in order to effectively aid in knowledge discovery. This paper describes a novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes. The method is based on vertex weighting by local neighborhood density and outward traversal from a locally dense seed protein to isolate the dense regions according to given parameters. The algorithm has the advantage over other graph clustering methods of having a directed mode that allows fine-tuning of clusters of interest without considering the rest of the network and allows examination of cluster interconnectivity, which is relevant for protein networks. Protein interaction and complex information from the yeast Saccharomyces cerevisiae was used for evaluation. Dense regions of protein interaction networks can be found, based solely on connectivity data, many of which correspond to known protein complexes. The algorithm is not affected by a known high rate of false positives in data from high-throughput interaction techniques. The program is available from ftp://ftp.mshri.on.ca/pub/BIND/Tools/MCODE
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4,599 citations
TL;DR: This work has demonstrated the power of the phylogenomics approach, which has the potential to provide answers to several fundamental evolutionary questions, but challenges for the future have also been revealed.
Abstract: As more complete genomes are sequenced, phylogenetic analysis is entering a new era — that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.
1,165 citations
TL;DR: An account of the recent explosion of actinobacterial genomics data is provided and an attempt to place this in a biological and evolutionary context.
Abstract: Summary: Actinobacteria constitute one of the largest phyla among Bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context.
1,026 citations
TL;DR: Research by demographers, epidemiologists and other biomedical researchers suggests that further progress is likely to be made in advancing the frontier of survival — and healthy survival — to even greater ages.
Abstract: Human senescence has been delayed by a decade. This finding, documented in 1994 and bolstered since, is a fundamental discovery about the biology of human ageing, and one with profound implications for individuals, society and the economy. Remarkably, the rate of deterioration with age seems to be constant across individuals and over time: it seems that death is being delayed because people are reaching old age in better health. Research by demographers, epidemiologists and other biomedical researchers suggests that further progress is likely to be made in advancing the frontier of survival — and healthy survival — to even greater ages.
876 citations
TL;DR: The authors exploit newly available massive natu- ral language corpora to capture the language as a language evolution phenomenon. But their work is limited to a subset of the languages in the corpus.
826 citations
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01 Jan 1974TL;DR: A new book that many people really want to read will you be one of them? Of course, you should be as discussed by the authors, even some people think that reading is a hard to do, you must be sure that you can do it.
Abstract: Come with us to read a new book that is coming recently. Yeah, this is a new coming book that many people really want to read will you be one of them? Of course, you should be. It will not make you feel so hard to enjoy your life. Even some people think that reading is a hard to do, you must be sure that you can do it. Hard will be felt when you have no ideas about what kind of book to read. Or sometimes, your reading material is not interesting enough.
3,241 citations
TL;DR: This study shows that there is a considerable amount of genic variation segregating in all of the populations studied and that the real variation in these populations must be greater than the authors are able to demonstrate.
Abstract: S pointed out in the first paper of this series (HUBBY and LEWONTIN 1966), A no one knows at the present time the kinds and frequencies of variant alleles present in natural populations of any organism, with the exception of certain special classes of genes. For human populations we know a good deal about certain polymorphisms for blood cell antigens, serum proteins, and metabolic disorders of various kinds but we can hardly regard these, a priori, as typical of the genome as a whole. Clearly we need a method that will randomly sample the genome and detect a major proportion of the individual allelic substitutions that are segregating in a population. In our previous paper, we discussed a method for accomplishing this end by means of a study of electrophoretic variants at a large number of loci and we showed that the variation picked up by this method behaves in a simple Mendelian fashion so that phenotypes can be equated to homozygous and heterozygous genotypes at single loci. It is the purpose of this second paper to show the results of an application of the method to a series of samples chosen from natural populations of Drosophila pseudoobscura. In particular, we will show that there is a considerable amount of genic variation segregating in all of the populations studied and that the real variation in these populations must be greater than we are able to demonstrate. This study does not make clear what balance of forces is responsible for the genetic variation observed, but it does make clear the kind and amount of variation at the genic level that we need to explain. An exactly similar method has recently been applied by HARRIS (1966) for the enzymes of human blood. In a preliminary report on ten randomly chosen enzymes, HARRIS describes two as definitely polymorphic genetically and a third as phenotypically polymorphic but with insufficient genetic data so far. Clearly these methods are applicable to any organism of macroscopic dimensions.
1,169 citations
TL;DR: It is shown that for all the wealth of observation and experiment, the techniques of population genetics have not allowed us to ask directly the most elementary question about the genetic structure of a population: at what proportion of his loci can the authors expect a diploid individual to be heterozygous?
Abstract: cornerstone of the theory of evolution by gradual change is that the rate of A evolution is absolutely limited by the amount of genetic variation in the evolving population. FISHER’S “Fundamental Theorem of Natural Selection” ( 1930) is a mathematical statement of this generalization, but even without mathematics it is clear that genetic change caused by natural selection presupposes genetic differences already existing, on which natural selection can operate. In a sense, a description of the genetic variation in a population is the fundamental datum of evolutionary studies; and it is necessary to explain the origin and maintenance of this variation and to predict its evolutionary consequences. It is not surprising, then, that a major effort of genetics in the last 50 years has been to characterize the amounts and kinds of genetic variation existing in natural or laboratory populations of various organisms. The results so far have told us a great deal about cytological variation such as polymorphisms for inversions and translocations, about frequencies of rare visible mutations at many loci, and about frequencies of chromosomes that are deleterious when homozygous together with the degree of that deleterious effect. In addition, we know of some striking singlelocus polymorphisms. These results are familiar to all students of population genetics and evolution, and have been well reviewed by DOBZHANSKY (195 1 ) and more recently by MAYR (1 963). Yet, for all the wealth of observation and experiment, the techniques of population genetics have not allowed us to ask directly the most elementary question about the genetic structure of a population: At w h t proportion of his loci can we expect a diploid individual to be heterozygous? Put in another way, this is the question of how much genetic variation there is in any given population. That this question remains unanswered is best shown by a statement of MAYR (1963) at the end of more than 100 pages of review of our present knowledge.
635 citations