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ORIGINAL: swan42

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ORIGINAL: unclemonkey

ORIGINAL: Agahnim

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The ideas of adaptation and natural selection (or “micro evolution”, to use creationist lingo)

“Micro-evolution” is NOT creationist lingo. An evolutionist coined it. The sole purpose of the terms “micro” and “macro” evolution are to provide a false sense of continuity between simple adaptation and microbe to man evolution. The terms are nothing more than one of evolutionists’ many deceptive word games.

While “micro-evolution” (simple adaptation) is compatible with the creationist worldview “macro-evolution” definitely is NOT.

Misuse

The term 'microevolution' has recently become popular among the anti-evolution movement, and in particular among young Earth creationists. The claim that microevolution is qualitatively different from macroevolution is fallacious as the main difference between the two processes is that one occurs within a few generations, whilst the other is seen to occur over thousands of years (ie. a quantitative difference). Essentially they describe the same process.

The attempt to differentiate between microevolution and macroevolution is considered to have no scientific basis by any mainstream scientific organization, including the American Association for the Advancement of Science.[2]

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Clearly there is no such thing as macro-walking. Just because we can take a few steps here and there (micro-walking) there is no reason to assume we can actually start at one place and end up in a location many miles away... thats what the macro-walkers would love for you to believe!

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ORIGINAL: Jhud
Really? Humans created some several thousand years ago sheep, cattle, and goats out of thin air? What evidence do you have for this?

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Obviously, since writing developed after 4000BC there are no 'human records', but there is still plenty of evidence.

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Oh, I beg your pardon-- I wouldn't have guessed that someone of your esteemed expertise would be confused by the word "husbandry":
a. The act or practice of cultivating crops and breeding and raising livestock; agriculture.
b. The application of scientific principles to agriculture, especially to animal breeding.
They were not "created out of thin air," but bred out of animals that imprinted readily (dare I presume that you are at familiar with ethologic and genomic imprinting?)

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A journey of a thousand miles begins with a single step. Oh yes, thanks for the softball.

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ORIGINAL: Jhud

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Oh, I beg your pardon-- I wouldn't have guessed that someone of your esteemed expertise would be confused by the word "husbandry":
a. The act or practice of cultivating crops and breeding and raising livestock; agriculture.
b. The application of scientific principles to agriculture, especially to animal breeding.
They were not "created out of thin air," but bred out of animals that imprinted readily (dare I presume that you are at familiar with ethologic and genomic imprinting?)

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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No this is not a confirmation of anything. Jhud you are simple regurgitating a self-consistent statement. There will be many self-consistent statements one can make that based on a premise either ID or Evolution because both attempt to describe the real world around us.

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ORIGINAL: drmark
There are numerous real-world benefits of biology, none of which contradict creation science.

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Null mutations in human and mouse orthologs frequently result in different phenotypes.

Liao BY, Zhang J.

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.

One-to-one orthologous genes of relatively closely related species are widely assumed to have similar functions and cause similar phenotypes when deleted from the genome. Although this assumption is the foundation of comparative genomics and the basis for the use of model organisms to study human biology and disease, its validity is known only from anecdotes rather than from systematic examination. Comparing documented phenotypes of null mutations in humans and mice, we find that >20% of human essential genes have nonessential mouse orthologs. These changes of gene essentiality appear to be associated with adaptive evolution at the protein-sequence, but not gene-expression, level. Proteins localized to the vacuole, a cellular compartment for waste management, are highly enriched among essentiality-changing genes. It is probable that the evolution of the prolonged life history in humans required enhanced waste management for proper cellular function until the time of reproduction, which rendered these vacuole proteins essential and generated selective pressures for their improvement. If our gene sample represents the entire genome, our results would mean frequent changes of phenotypic effects of one-to-one orthologous genes even between relatively closely related species, a possibility that should be considered in comparative genomic studies and in making cross-species inferences of gene function and phenotypic effect.

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Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9830-5. Epub 2005 Jul 5. Links

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences.

Hughes JR, Cheng JF, Ventress N, Prabhakar S, Clark K, Anguita E, De Gobbi M, de Jong P, Rubin E, Higgs DR.

Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom.

An important step toward improving the annotation of the human genome is to identify cis-acting regulatory elements from primary DNA sequence. One approach is to compare sequences from multiple, divergent species. This approach distinguishes multispecies conserved sequences (MCS) in noncoding regions from more rapidly evolving neutral DNA. Here, we have analyzed a region of approximately 238kb containing the human alpha globin cluster that was sequenced and/or annotated across the syntenic region in 22 species spanning 500 million years of evolution. Using a variety of bioinformatic approaches and correlating the results with many aspects of chromosome structure and function in this region, we were able to identify and evaluate the importance of 24 individual MCSs. This approach sensitively and accurately identified previously characterized regulatory elements but also discovered unidentified promoters, exons, splicing, and transcriptional regulatory elements. Together, these studies demonstrate an integrated approach by which to identify, subclassify, and predict the potential importance of MCSs.

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You've yet to demonstrate any contributions unique to the hypothetical predictions of so-called common descent theory.

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Actually, I for one find it amazing that a 3000 year old nomadic semite was able to make "self-consistent statements" about nature and the universe that still hold true to today

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Actually, I suspect Moses was "only" in his early 100's when he wrote down his amazing statements, although that was about 3000 years ago.

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Prog Lipid Res. 2007 May-Jul;46(3-4):171-99. Epub 2007 Apr 4. Links
Comparative genomics and evolution of eukaryotic phospholipid biosynthesis.

Lykidis A.

Genome Biology Program, DOE-Joint Genome Institute, Walnut Creek, CA 94598, USA. alykidis@lbl.gov

Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.

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Comparative genomics and evolution of eukaryotic phospholipid biosynthesis.

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ORIGINAL: drmark
Plenty of misinterpretation of evidence you mean.

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ORIGINAL: drmark
I could substitute "creative design" jargon for every usage of "evolutionary" jargon and the conclusions would be exactly the same!

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Jargon is not the only difference between ID and Evolution. When you account for the differences the conclusions (and predictions) would not always be the same. This is why my previous mention of Einstein and Newton should resonant. We can attribute 3 details about physics that are exemplary of interesting and well-done science.

1. Outside of average human experience
2. The old theory is approximation of the new theory
3. We reserve the right to replace the current theory with a better one in the future

That's science.

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

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and demonstrably so.

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ORIGINAL: drmark

Jack, do these people really not get it or what? I could substitute "creative design" jargon for every usage of "evolutionary" jargon and the conclusions would be exactly the same! This is science??

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ORIGINAL: Jhud
Generally, when I read stuff like this, it appears evolution is mostly assumed and doesn't necessarily add to the understanding of how phospholipids actually work, or how such knowledge could actually be utilized.

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ORIGINAL: Jhud
Amen, which is why if ID explains certain aspects of biology better than evolution does, we reserve the right to replace evolution with a better explanation like ID.

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PLoS Comput Biol. 2005 Oct;1(5):e45. Epub 2005 Oct 7. Links
Protein molecular function prediction by Bayesian phylogenomics.Engelhardt BE, Jordan MI, Muratore KE, Brenner SE.
Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America. bee@cs.berkeley.edu

We present a statistical graphical model to infer specific molecular function for unannotated protein sequences using homology. Based on phylogenomic principles, SIFTER (Statistical Inference of Function Through Evolutionary Relationships) accurately predicts molecular function for members of a protein family given a reconciled phylogeny and available function annotations, even when the data are sparse or noisy. Our method produced specific and consistent molecular function predictions across 100 Pfam families in comparison to the Gene Ontology annotation database, BLAST, GOtcha, and Orthostrapper. We performed a more detailed exploration of functional predictions on the adenosine-5'-monophosphate/adenosine deaminase family and the lactate/malate dehydrogenase family, in the former case comparing the predictions against a gold standard set of published functional characterizations. Given function annotations for 3% of the proteins in the deaminase family, SIFTER achieves 96% accuracy in predicting molecular function for experimentally characterized proteins as reported in the literature. The accuracy of SIFTER on this dataset is a significant improvement over other currently available methods such as BLAST (75%), GeneQuiz (64%), GOtcha (89%), and Orthostrapper (11%). We also experimentally characterized the adenosine deaminase from Plasmodium falciparum, confirming SIFTER's prediction. The results illustrate the predictive power of exploiting a statistical model of function evolution in phylogenomic problems. A software implementation of SIFTER is available from the authors.

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The scientists are assuming evolution and from that assumption they get useful information. If evolution were the incorrect assumption then they should get incorrect information, should they not? As it stands, they can trace the evolution of phospholipid biosynthesis through several genetic trees and use this information to propose function of previously unannotated genes. Where is anyone doing this type of work using ID? Nowhere, they are using evolution.

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"The Designer Did It" is not an explanation, and given the complete absence of scientists using ID to annotate genomes it is also useless.

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ORIGINAL: unclemonkey
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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Comparative evolutionary genomics of the HADH2 gene encoding Abeta-binding alcohol dehydrogenase/17beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10).Marques AT, Antunes A, Fernandes PA, Ramos MJ.
REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal. alexandra.marques@fc.up.pt

BACKGROUND: The Abeta-binding alcohol dehydrogenase/17beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10) is an enzyme involved in pivotal metabolic processes and in the mitochondrial dysfunction seen in the Alzheimer's disease. Here we use comparative genomic analyses to study the evolution of the HADH2 gene encoding ABAD/HSD10 across several eukaryotic species. RESULTS: Both vertebrate and nematode HADH2 genes showed a six-exon/five-intron organization while those of the insects had a reduced and varied number of exons (two to three). Eutherian mammal HADH2 genes revealed some highly conserved noncoding regions, which may indicate the presence of functional elements, namely in the upstream region about 1 kb of the transcription start site and in the first part of intron 1. These regions were also conserved between Tetraodon and Fugu fishes. We identified a conserved alternative splicing event between human and dog, which have a nine amino acid deletion, causing the removal of the strand betaF. This strand is one of the seven strands that compose the core beta-sheet of the Rossman fold dinucleotide-binding motif characteristic of the short chain dehydrogenase/reductase (SDR) family members. However, the fact that the substrate binding cleft residues are retained and the existence of a shared variant between human and dog suggest that it might be functional. Molecular adaptation analyses across eutherian mammal orthologues revealed the existence of sites under positive selection, some of which being localized in the substrate-binding cleft and in the insertion 1 region on loop D (an important region for the Abeta-binding to the enzyme). Interestingly, a higher than expected number of nonsynonymous substitutions were observed between human/chimpanzee and orangutan, with six out of the seven amino acid replacements being under molecular adaptation (including three in loop D and one in the substrate binding loop). CONCLUSION: Our study revealed that HADH2 genes maintained a reasonable conserved organization across a large evolutionary distance. The conserved noncoding regions identified among mammals and between pufferfishes, the evidence of an alternative splicing variant conserved between human and dog, and the detection of positive selection across eutherian mammals, may be of importance for further research on ABAD/HSD10 function and its implication in the Alzheimer's disease.

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