Evolutie. Deel XV

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Op maandag 27 oktober 2008 22:15 schreef Aslama het volgende:

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Laten we het wetenschappelijk houden.

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Wat ik vroeg was de evolutie van het DNA: van niets tot miljarden baseparen die samen de code van het organisme vormen.
-Hoe kwamen de eerste baseparen tot stand.

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The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells

Most evolutionists agree to consider that our present RNA/DNA/protein world has originated from a simpler world in which RNA played both the role of catalyst and genetic material. Recent findings from structural studies and comparative genomics now allow to get a clearer picture of this transition. These data suggest that evolution occurred in several steps, first from an RNA to an RNA/protein world (defining two ages of the RNA world) and finally to the present world based on DNA. The DNA world itself probably originated in two steps, first the U-DNA world, following the invention of ribonucleotide reductase, and later on the T-DNA world, with the independent invention of at least two thymidylate synthases. Recently, several authors have suggested that evolution from the RNA world up to the Last Universal Cellular Ancestor (LUCA) could have occurred before the invention of cells. On the contrary, I argue here that evolution of the RNA world taken place in a framework of competing cells and viruses (preys, predators and symbionts). I focus on the RNA-to-DNA transition and expand my previous hypothesis that viruses played a critical role in the emergence of DNA. The hypothesis that DNA and associated mechanisms (replication, repair, recombination) first evolved and diversified in a world of DNA viruses infecting RNA cells readily explains the existence of viral-encoded DNA transaction proteins without cellular homologues. It also potentially explains puzzling observations from comparative genomic, such as the existence of two non-homologous DNA replication machineries in the cellular world. I suggest here a specific scenario for the transfer of DNA from viruses to cells and briefly explore the intriguing possibility that several independent transfers of this kind produced the two cell types (prokaryote/eukaryote) and the three cellular domains presently known (Archaea, Bacteria and Eukarya).

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-Hoe konden deze zich in chromosomen splitsen.

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-Beschrijf het proces dat ertoe leidt dat het aantal chromosomen in verschillende organismen anders werd.

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Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13-2q14.1 and Paralogous Regions on Other Human Chromosomes

Human chromosome 2 was formed by the head-to-head fusion of two ancestral chromosomes that remained separate in other primates. Sequences that once resided near the ends of the ancestral chromosomes are now interstitially located in 2q13-2q14.1. Portions of these sequences had duplicated to other locations prior to the fusion. Here we present analyses of the genomic structure and evolutionary history of >600 kb surrounding the fusion site and closely related sequences on other human chromosomes. Sequence blocks that closely flank the inverted arrays of degenerate telomere repeats marking the fusion site are duplicated at many, primarily subtelomeric, locations. In addition, large portions of a 168-kb centromere-proximal block are duplicated at 9pter, 9p11.2, and 9q13, with 98%-99% average sequence identity. A 67-kb block on the distal side of the fusion site is highly homologous to sequences at 22qter. A third ~100-kb segment is 96% identical to a region in 2q11.2. By integrating data on the extent and similarity of these paralogous blocks, including the presence of phylogenetically informative repetitive elements, with observations of their chromosomal distribution in nonhuman primates, we infer the order of the duplications that led to their current arrangement. Several of these duplicated blocks may be associated with breakpoints of inversions that occurred during primate evolution and of recurrent chromosome rearrangements in humans.

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Evidence for fusing of two ancestral chromosomes to create human chromosome 2 and where there has been no fusion in other Great Apes is:

1) The analogous chromosomes (2p and 2q) in the non-human great apes can be shown, when laid end to end, to create an identical banding structure to the human chromosome 2. (1)

2) The remains of the sequence that the chromosome has on its ends (the telomere) is found in the middle of human chromosome 2 where the ancestral chromosomes fused. (2)

3) the detail of this region (pre-telomeric sequence, telomeric sequence, reversed telomeric sequence, pre-telomeric sequence) is exactly what we would expect from a fusion. (3)

4) this telomeric region is exactly where one would expect to find it if a fusion had occurred in the middle of human chromosome 2.

5) the centromere of human chromosome 2 lines up with the chimp chromosome 2p chromosomal centromere.

6) At the place where we would expect it on the human chromosome we find the remnants of the chimp 2q centromere (4).

Not only is this strong evidence for a fusion event, but it is also strong evidence for common ancestry; in fact, it is hard to explain by any other mechanism.

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Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

Whole-genome duplication followed by massive gene loss and specialization has long been postulated as a powerful mechanism of evolutionary innovation. Recently, it has become possible to test this notion by searching complete genome sequence for signs of ancient duplication. Here, we show that the yeast Saccharomyces cerevisiae arose from ancient whole-genome duplication, by sequencing and analysing Kluyveromyces waltii, a related yeast species that diverged before the duplication. The two genomes are related by a 1:2 mapping, with each region of K. waltii corresponding to two regions of S. cerevisiae, as expected for whole-genome duplication. This resolves the long-standing controversy on the ancestry of the yeast genome, and makes it possible to study the fate of duplicated genes directly. Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions.

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The zebrafish gene map defines ancestral vertebrate chromosomes

Genetic screens in zebrafish (Danio rerio) have identified mutations that define the roles of hundreds of essential vertebrate genes. Genetic maps can link mutant phenotype with gene sequence by providing candidate genes for mutations and polymorphic genetic markers useful in positional cloning projects. Here we report a zebrafish genetic map comprising 4073 polymorphic markers, with more than twice the number of coding sequences localized in previously reported zebrafish genetic maps. We use this map in comparative studies to identify numerous regions of synteny conserved among the genomes of zebrafish, Tetraodon, and human. In addition, we use our map to analyze gene duplication in the zebrafish and Tetraodon genomes. Current evidence suggests that a whole-genome duplication occurred in the teleost lineage after it split from the tetrapod lineage, and that only a subset of the duplicates have been retained in modern teleost genomes. It has been proposed that differential retention of duplicate genes may have facilitated the isolation of nascent species formed during the vast radiation of teleosts. We find that different duplicated genes have been retained in zebrafish and Tetraodon, although similar numbers of duplicates remain in both genomes. Finally, we use comparative mapping data to address the proposal that the common ancestor of vertebrates had a genome consisting of 12 chromosomes. In a three-way comparison between the genomes of zebrafish, Tetraodon, and human, our analysis delineates the gene content for 11 of these 12 proposed ancestral chromosomes.

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De novo chromosome formation in rodent cells

A hybrid cell line was produced by the fusion of an EC3/7 mouse cell with a Chinese hamster ovary cell. The EC3/7 cell carries a dicentric chromosome with a functional marker centromere. This marker centromere contains human, lambda, and bacterial vector DNA sequences and a dominant selectable gene (aminoglycoside 3'-phosphotransferase type II; neo). In the hybrid, the marker centromere separated from the dicentric chromosome and formed a full-sized chromosome (lambda neo). The newly formed chromosome is stable, even under nonselective culture conditions. This functional chromosome, which is the result of an amplification process, is composed of seven large, different-sized amplicons. Each amplicon contains multiple copies of human, lambda, neo, and mouse telomeric DNA sequences. Individual amplicons are separated from each other by mouse major satellite DNA sequences. The marker centromere was localized to a terminal amplicon by anticentromere immunostaining. The number of amplicons in the newly formed chromosome is remarkably consistent. This finding suggests that the length of the newly formed chromosome is highly constrained.

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Het lijkt me duidelijk dat het DNA zelf niet het bewijs van evolutie is: ALS het DNA evolueert DAN evolueert het organisme, omdat het DNA de code is van het organisme.

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Op woensdag 29 oktober 2008 20:40 schreef Aslama het volgende:
Onderstreepte woorden zeggen het al: geen bewijs. Daarnaast bestaan er inderdaad verschillende theorieën over bepaalde tussenstappen rondom dit onderwerp die aanduiden dat men het niet over een bewijs heeft, laat staan een duidelijk bewijs.

Het heeft voor mij niet zoveel nut om deze theorieën te bekritiseren aangezien deze nog niet vaststaan:

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Many students reject evolutionary theory, whether or not they adequately understand basic evolutionary concepts. We explore the hypothesis that accepting evolution is related to understanding the nature of science. In particular, students may be more likely to accept evolution if they understand that a scientific theory is provisional but reliable, that scientists employ diverse methods for testing scientific claims, and that relating data to theory can require inference and interpretation. In a study with university undergraduates, we find that accepting evolution is significantly correlated with understanding the nature of science, even when controlling for the effects of general interest in science and past science education. These results highlight the importance of understanding the nature of science for accepting evolution. We conclude with a discussion of key characteristics of science that challenge a simple portrayal of the scientific method and that we believe should be emphasized in classrooms.

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het kan weer net iets anders worden en dan mag ik deze weer bekritiseren.

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Om dezelfde reden wil ik nog niet ingaan op de rest van je post. Daarnaast heb ik niet zoveel tijd om al de quotes en links te bestuderen. Liefst wil ik zoveel mogelijk een reactie in je eigen woorden: het leest vaak gemakkelijker als deze de essentie van de theorieën bevat.

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Op donderdag 30 oktober 2008 10:14 schreef Aslama het volgende:

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Betreffende woorden die gebruikt worden in het artikel passen bij een hypothese: in de wetenschap wordt het een hypothese genoemd. Als b.v. de overgang van RNA naar DNA door een experiment geverifiëerd is dan zijn we zeker een stap verder. In biologie kun je d.m.v een experiment verifiëren dat bijv. de chromosoom van een kind een combinatie is van de chromosomen van de vader en de moeder.

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Some scientific explanations are so well established that no new evidence is likely to alter them. The explanation becomes a scientific theory. In everyday language a theory means a hunch or speculation. Not so in science. In science, the word theory refers to a comprehensive explanation of an important feature of nature supported by facts gathered over time. Theories also allow scientists to make predictions about as yet unobserved phenomena

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Zodra de methode duidelijk is gekwalifiseerd, is het zinvoller om in de materie te verdiepen, niet eerder. Dan weet je ook op welk waarheidsniveau je praat.

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Human beings, like other organisms, are the products of evolution. Like other organisms, we exhibit traits that are the product of natural selection. Our psychological capacities are evolved traits as much as are our gait and posture. This much few would dispute. Evolutionary psychology goes further than this, claiming that our psychological traits—including a wide variety of traits, from mate preference and jealousy to language and reason—can be understood as specific adaptations to ancestral Pleistocene conditions. In Evolutionary Psychology as Maladapted Psychology, Robert Richardson takes a critical look at evolutionary psychology by subjecting its ambitious and controversial claims to the same sorts of methodological and evidential constraints that are broadly accepted within evolutionary biology.

The claims of evolutionary psychology may pass muster as psychology; but what are their evolutionary credentials? Richardson considers three ways adaptive hypotheses can be evaluated, using examples from the biological literature to illustrate what sorts of evidence and methodology would be necessary to establish specific evolutionary and adaptive explanations of human psychological traits. He shows that existing explanations within evolutionary psychology fall woefully short of accepted biological standards. The theories offered by evolutionary psychologists may identify traits that are, or were, beneficial to humans. But gauged by biological standards, there is inadequate evidence: evolutionary psychologists are largely silent on the evolutionary evidence relevant to assessing their claims, including such matters as variation in ancestral populations, heritability, and the advantage offered to our ancestors. As evolutionary claims they are unsubstantiated. Evolutionary psychology, Richardson concludes, may offer a program of research, but it lacks the kind of evidence that is generally expected within evolutionary biology. It is speculation rather than sound science—and we should treat its claims with skepticism.