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.

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Op vrijdag 31 oktober 2008 20:34 schreef Aslama het volgende:

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Het was begonnen met deze post . Hier werden concretere bewijzen gevraagd. Ik kan nu uit je post opmaken dat het niet om bewijzen gaat. Het is 'redelijkerwijs waar of onwaar'. 'Redelijkerwijs' is niet meetbaar, waardoor er altijd een kans bestaat dat het anders is.

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In de quote in je vorige post waar ik op gereageerd heb zijn er te veel woorden als suggest, probably etc. Het is duidelijk dat het artikel niet hetzelfde waarheidsniveau heeft als wat een experiment kan hebben bijv. om te verifiëren dat het DNA van een kind een combinatie is van die van de ouders.

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Daarnaast denk ik dat de voorkeur/ vooroordelen/subjectiviteit hoe dan ook medebepalend zijn voor de houding t.o.v. een theorie. Iemand die een kritische houding neemt t.o.v. de evolutiethoerie neemt niet zo snel alles aan van een hypothese in de evolutietheorie als een evolutionist. Een evolutionist zal minder snel kijken naar de bezwaren van de evolutietheorie. Hij zal geneigd zijn de hypothese te verdedigen.

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Ik bedoelde de fase waarin het betreffende artikel is gekwalificeerd bv. hypothese of verificatie.

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Op donderdag 6 november 2008 22:12 schreef Droogreden het volgende:
Vraagje tussendoor:
Hoe word met de evolutie theorie de volgende zaken verklaard.
- Ogen, neus, oren en tong.

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- Het bestaan van een grote diversiteit aan zeer complexe emoties.

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- Het evolutionait nut van zaken als depressies of het willen plegen van zelfmoord.

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Op zaterdag 8 november 2008 02:13 schreef Apollyon het volgende:

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Hmmm ... ik zou zeggen : 'Geloof versus Evolutie' [Dan vat je alle voor/tegen en andere standers]
En 'Evolutie in Progressie' [Aangezien zelfs de ontwikkeling van je eigen PC een hele evolutie ondergaat]

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Octopuses share 'living ancestor'

Many of the world's deep-sea octopuses evolved from a common ancestor that still exists in the icy waters of the Southern Ocean, a study has shown.

Researchers suggest that the creatures evolved after being driven to other ocean basins 30 million years ago by nutrient-rich and salty currents.

The findings form part of a decade-long global research programme to learn more about life in the world's oceans.

The first Census of Marine Life (CoML) is set to be completed in late 2010.

The project, which began back in 2000, involves more than 2,000 scientists from 82 nations.

The research into the evolution of deep-sea octopuses was part of a programme called the Census of Antarctic Marine Life (CAML), explained Don O'Dor, CoML's co-senior scientist.

"Many of these octopuses were collected from the deep sea by a number of the CoML's different projects," he told BBC News.

"All of that material was brought together and made available to Dr Jan Strugnell, a biologist at the British Antarctic Survey (BAS) in Cambridge, and she used this material to carry out DNA studies.

"She was looking at the relationship between these different deep-sea octopuses and how they originated.

"She has been able to trace the timeline for their distribution back 30 million years to a common ancestor."

The species could all be traced back to a shallow-water octopus called Megaleledone setebos, which is only found in the Southern Ocean.

Dr O'Dor added that the BAS researcher's work also enabled her to identify how changes in the region's ocean played a pivotal role in the development of the new species, especially the emergence of a "thermohaline expressway".

"When you get an increase in sea ice, fresh water forms ice crystals and leaves behind high-salinity, high-oxygen water, which is denser than the surrounding sea water, so it sinks," he explained.

"It gets mixed by sea currents and flows into all of the deepest parts of the ocean.

"At the time this process started, there was no oxygen at the bottom of the ocean, so it brought oxygen into these areas, and we can now see that the octopuses moved out from the Antarctic into deeper water."

Dr Stagnell's work also showed how the creatures adapted to the new deep-sea environment.

One example was the loss of their ink sacs, because there was no need for the defence mechanism in the pitch black waters.

As well as being one of the CoML's highlights, the research is also being published in the journal Cladistics on Tuesday.

'Unprecedented project'

The deep-sea octopus study, along with dozens of other projects, form part of the census's fourth progress report, which will be presented at the World Conference on Marine Biology, which begins in Valencia, Spain, on Tuesday.

The overarching objectives of the global collaboration between CoML's scientists include:

Advancing technology for discoveries

Organising knowledge about marine life, and making it accessible

Measuring effects of human activities on ocean life

Providing the foundation for scientifically based policies

Dr O'Dor said that the main focus of the CoML for the remaining two years was to "synthesise" the data.

"Many of our projects have already completed their fieldwork and we have a lot of information," he observed.

"What we are now trying to do is to bring all that information together in a form that allows the public to understand how much we have learned about the ocean and what lives in it."

As far as improving our understanding of life beneath the waves, Dr O'Dor said: "It has been successful beyond what I imagined when I first became involved.

"It will provide a baseline. We are not going to know everything about what is happening within the oceans, but we have samplings of most marine habitats.

"We are moving into this period of global warming, which is resulting in the acidification of the oceans, melting of the polar ice cap.

"We can use the first census as a benchmark to see what happens in the oceans over the next decade or more."

Meeting formally for the first time at the five-day gathering in Valencia will be the CoML's Science Council, which will take an overview of the 10-year Census.

"Over the past few years, there has been huge public interest in biodiversity because there is a legitimate concern about the changes being caused by humans," commented Patricia Miloslavich, the Census's co-senior scientist.

"The Science Council will (consider) what people have said about areas that have not been explored or taxonomic groups that have been overlooked in the past," she told BBC News.

"We have had this first census that has given outstanding and amazing results for many ecosystems and regions.

"But now that we have been able to identify where there are some gaps, we would like to explore these areas."

Dr Miloslavich added that the Science Council will also develop the objectives of the second census, which will run from 2010 until 2020.

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Op donderdag 13 november 2008 08:49 schreef wijsneus het volgende:
Princeton Scientists Discover Proteins that Control Evolution

"Evolutionary changes are supposed to take place gradually and randomly, under pressure from natural selection. But a team of Princeton scientists investigating a group of proteins that help cells burn energy stumbled across evidence that this is not how evolution works. In fact, their discovery could revolutionize the way we understand evolutionary processes. They have evidence that organisms actually have the ability to control their own evolution."

http://io9.com/5083673/pr(...)at-control-evolution
http://www.princeton.edu/(...)l?section=topstories

Oh noes! Darwin had het mis! Zie Je Wel

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The other problem that often occurs is that one of the investigators opens his mouth and reveals that he is completely out of his depth, and that the team has absolutely no conception of how evolution actually works. This time, there is no exception.

"The discovery answers an age-old question that has puzzled biologists since the time of Darwin: How can organisms be so exquisitely complex, if evolution is completely random, operating like a 'blind watchmaker'?" said Chakrabarti, an associate research scholar in the Department of Chemistry at Princeton. "Our new theory extends Darwin's model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness."

Dear gob. Is this an indictment of Princeton, of chemists, or is Chakrabarti just a weird, isolated crank? That first sentence is not even wrong. Darwin answered the question of how complexity can arise, so no, we haven't been puzzled by that general question; evolution is not completely random, so that part is a complete non sequitur; randomness easily generates lots of complexity, so even if we accept his premise, it invalidates his question; and how does he reconcile his assertion of "completely random" with his use of the simple metaphor of the "blind watchmaker", which implies non-randomness? That's a sentence that contradicts itself multiple times in paradoxical ways.

Anyway, I'll be looking for the paper. My bet would be that it says nothing like the claims made for it by the press release, or that it will be an embarrassing error of interpretation by the authors.

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Op donderdag 13 november 2008 11:40 schreef wijsneus het volgende:
Uiteraard - maar de pers zit er bijna altijd naast als het gaat om evo-nieuws toch? Niets raars aan.

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Wat wel gaaf is dat evolutie dus blijkbaar selecteerd op eigenschappen die voordelig zijn voor evolutie zelf. Positieve feedback zeg maar.

leuk, leuk, leuk!