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ORIGINAL: Jhud
Well ya, and if that is what ID proffered, you might have a point.

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You would think that as a refutation you would offer ID comparisons of genomes and show how ID makes better predictions than evolutionary cmparisons. Don't these research projects exist? Or is the claim that ID produces better explanations just an empty claim.

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The term 'microevolution' has recently become popular among the anti-evolution movement, and in particular among young Earth creationists.

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ORIGINAL: Jhud
How would that refute a strawman?

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ORIGINAL: unclemonkey

ORIGINAL:swan42

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The term 'microevolution' has recently become popular among the anti-evolution movement, and in particular among young Earth creationists.

Where do you get this nonsense?

“Watch for equivocation, i.e. using the same term in different ways in the same article. It’s very common for evolutionary propagandists to define evolution as (1) simply ‘change in a population over time’, as well as (2) the idea that all life came from a single cell, which itself came from a chemical soup. Then they produce examples of ‘evolution’ (1) and use this to prove evolution (2), and then claim that Biblical creation is wrong! However the Biblical creation model does imply that organisms change over time—but these changes would always involve sorting or loss of already existing (created) genetic information, never the gain of new information. But evolution (2) requires the gain of new information. Even if information losing (or neutral) processes could continue for billions of years, they would never add up to a gain of information. Rather, to support evolution (2), evolutionists must demonstrate changes that increase information. If this theory were true, there should be plenty of examples, but we have yet to observe even one. Since evolution (2) is the only issue at stake in the creation/evolution controversy, we advise against referring to any mere change as ‘evolution’—not even ‘micro-evolution’—and reserving the term ‘evolution’ for (2).” - http://www.answersingenesis.org/docs2001/1115anthrax.asp

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Genomics. 2005 Dec;86(6):708-17. Epub 2005 Sep 19.

Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes.

Antunes A, Ramos MJ.

REQUIMTE, Grupo de Química Teórica e Computacional-Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal. aantunes@fc.up.pt

Nuclear inserted copies of mitochondrial origin (numts) vary widely among eukaryotes, with human and plant genomes harboring the largest repertoires. Numts were previously thought to be absent from fish species, but the recent release of three fish nuclear genome sequences provides the resource to obtain a more comprehensive insight into the extent of mtDNA transfer in fishes. From the sequence analyses of the genomes of Fugu rubripes, Tetraodon nigroviridis, and Danio rerio, we have identified 2, 5, and 10 recent numt integrations, respectively, which integrated into those genomes less than 0.6 million years (Myr) ago. Such results contradict the hypothesis of absence or rarity of numts in fishes, as (i) the ratio of numts to the total size of the nuclear genome in T. nigroviridis was superior to the ratio observed in several higher vertebrate species (e.g., chicken, mouse, and rat), and only surpassed by humans, and (ii) the mtDNA coverage transferred to the nuclear genome of D. rerio is exceeded only by human and mouse, within the whole range of eukaryotic genomes surveyed for numts. Additionally, 335, 336, and 471 old numts (>12.5 Myr) were detected in F. rubripes, T. nigroviridis, and D. rerio, respectively. Surprisingly, old numts are inserted preferentially into known or predicted genes, as inferred for recent numts in human. However, because in fish genomes such integrations are old, they are likely to represent evolutionary successes and they may be considered a potential important evolutionary mechanism for the enhancement of genomic coding regions.

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BMC Evol Biol. 2007 Jul 2;7:106. Links
Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure.
Desmond E, Brochier-Armanet C, Gribaldo S.

Unite Biologie Moléculaire du Gène chez les Extremophiles, Institut Pasteur, Paris Cedex 15, France. edesmond@pasteur.fr <edesmond@pasteur.fr>

BACKGROUND: As bacteria, motile archaeal species swim by means of rotating flagellum structures driven by a proton gradient force. Interestingly, experimental data have shown that the archaeal flagellum is non-homologous to the bacterial flagellum either in terms of overall structure, components and assembly. The growing number of complete archaeal genomes now permits to investigate the evolution of this unique motility system. RESULTS: We report here an exhaustive phylogenomic analysis of the components of the archaeal flagellum. In all complete archaeal genomes, the genes coding for flagellum components are co-localized in one or two well-conserved genomic clusters showing two different types of organizations. Despite their small size, these genes harbor a good phylogenetic signal that allows reconstruction of their evolutionary histories. These support a history of mainly vertical inheritance for the components of this unique motility system, and an interesting possible ancient horizontal gene transfer event (HGT) of a whole flagellum-coding gene cluster between Euryarchaeota and Crenarchaeota. CONCLUSION: Our study is one of the few exhaustive phylogenomics analyses of a non-informational cell machinery from the third domain of life. We propose an evolutionary scenario for the evolution of the components of the archaeal flagellum. Moreover, we show that the components of the archaeal flagellar system have not been frequently transferred among archaeal species, indicating that gene fixation following HGT can also be rare for genes encoding components of large macromolecular complexes with a structural role.

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ORIGINAL: unclemonkey

ORIGINAL: gluadys

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Nope. An evolutionary prediction would be that all descendants of cattle are related to cattle,

I think most would agree that humans and trout are distinctly different critters. According to evolution somewhere back down the line humans and trout are descendants of the same critter.

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Got anything other than a screwball interpretation of the fossil record to demonstrate the common ancestry of humans and trout?

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BMC Evol Biol. 2006 Nov 8;6:92. Links

Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family.

Levasseur A, Gouret P, Lesage-Meessen L, Asther M, Asther M, Record E, Pontarotti P.

Phylogenomics Laboratory, EA 3781 Evolution Biologique Université de Provence, Case 19, Pl, V, Hugo, 13331 Marseille Cedex 03, France. Anthony.Levasseur@up.univ-mrs.fr

BACKGROUND: There have been many claims of adaptive molecular evolution, but what role does positive selection play in functional divergence? The aim of this study was to test the relationship between evolutionary and functional shifts with special emphasis on the role of the environment. For this purpose, we studied the fungal lipase/feruloyl esterase A family, whose functional diversification makes it a very promising candidate. RESULTS: The results suggested functional shift following a duplication event where neofunctionalisation of feruloyl esterase A had occurred with conservation of the ancestral lipase function. Evolutionary shift was detected using the branch-site model for testing positive selection on individual codons along specific lineages. Positively selected amino acids were detected. Furthermore, biological data obtained from site-directed mutagenesis experiments clearly demonstrated that certain amino acids under positive selection were involved in the functional shift. We reassessed evolutionary history in terms of environmental response, and hypothesized that environmental changes such as colonisation by terrestrial plants might have driven adaptation by functional diversification in Euascomycetes (Aspergilli), thus conferring a selective advantage on this group. CONCLUSION: The results reported here illustrate a rare example of connection between fundamental events in molecular evolution. We demonstrated an unequivocal connection between evolutionary and functional shifts, which led us to conclude that these events were probably linked to environmental change.

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“Micro-evolution” is NOT creationist lingo. An evolutionist coined it.

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In fact, simple adaptation lacks a scientific definition. Natural selection is a better term.

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Since adaptation (microevolution) is a Darwinian concept, I don't see how it can sit well with creationism.

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But the really exciting evidence is in DNA.

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ORIGINAL: unclemonkey

ORIGINAL:gluadys

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But the really exciting evidence is in DNA.

YUP. It supports the concept of a common designer.

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ORIGINAL: unclemonkey

ORIGINAL:gluadys

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But the really exciting evidence is in DNA.

YUP. It supports the concept of a common designer.

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ORIGINAL: unclemonkey
YUP. It supports the concept of a common designer.

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No, it doesn't. A common designer can not explain why introns are more different sequence wise than exons when the human and mouse genomes are compared. A common designer paradigm can not explain why genes not related to morphology follow the same pattern as morphology.

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ORIGINAL: Jhud
Sure it can, the same way a common designer can explain what is similar and different in the text of a novel, and why novels follow certain identifiable patterns.

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How can a common designer explain why there are more differences in introns than exons? There are very few changes in the introns of humans and chimps, yet quite a few differences between humans and fish for the same gene. Why not copy the introns from fish straight over to humans? ID certainly allows this, does it not? Humans copy jellyfish genes into fish all of the time with no problems.

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ORIGINAL: Jhud
The question of course would be, do the introns found in a fish work the same way as the introns found in humans and apes? If not, then that would be 'why'.

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They do work in the same way. They are excised to produce mature mRNA. Outside of the splice sites the sequence can differ quite a bit making it a hotbed for neutral drift. So they do operate the same way, so why are they different?

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ORIGINAL: Jhud
They have ben tested to demonstrate they work exactly the same way when the genes are replaced?

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What's to test? The introns are not translated.

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ORIGINAL: Jhud
You said the introns work the same way; do they do the same thing in both genomes?

Same thing meaning, 'produce the same result'.

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ORIGINAL: Jhud
Well exactly, which confirms two things; first that there existed organisms that could readily be identified as potential 'livestock', and secondly, that intelligent design priciples could be used to modify said organisms - per Genesis, apparently.

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Adv Genet. 2008;60:655-97. Links
Comparative genomics for detecting human disease genes.

Moreno C, Lazar J, Jacob HJ, Kwitek AE.

Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.

Originally, comparative genomics was geared toward defining the synteny of genes between species. As the human genome project accelerated, there was an increase in the number of tools and means to make comparisons culminating in having the genomic sequence for a large number of organisms spanning the evolutionary tree. With this level of resolution and a long history of comparative biology and comparative genetics, it is now possible to use comparative genomics to build or select better animal models and to facilitate gene discovery. Comparative genomics takes advantage of the functional genetic information from other organisms, (vertebrates and invertebrates), to apply it to the study of human physiology and disease. It allows for the identification of genes and regulatory regions, and for acquiring knowledge about gene function. In this chapter, the current state of comparative genomics and the available tools are discussed in the context of developing animal model systems that reflect the clinical picture.