OLE! Now we have fun with molecular phylogeny.
http://www.arn.org/docs/wells/jw_critic ... ry1103.htm
Yet biologists have known for years that some bacteria, algae and single-celled animals do NOT have the same genetic code as most other organisms.
Yes of course this is not in dispute. However one needs to examine what the exceptions are. In mitochondria and some microorganisms the genetic code is slightly different. Given that bacteria predates all other forms of life it can shown phylogenically that all eukaryotic life forms resulted from the one time mitochondria and a larger cell became symbiotic.a
AttentionKMartShoppers wrote:Darwinists claim that the exceptions are unimportant, since they "know" that the aberrant organisms are descended from organisms that had the standard code.
Incorrect, the theory is that the two codes existed concurrently and that higher life forms arose from one of the groups.
AttentionKMartShoppers wrote:But the code itself was supposed to be the primary evidence for such descent, and no comparable evidence is offered to replace it.
The code itself is not the evidence it is the comparative analysis of many species.
AttentionKMartShoppers wrote:Clearly, the Darwinists' "knowledge" in this case is philosophical rather than empirical.
The analysis of the sequences is far from philosophical.
AttentionKMartShoppers wrote:The non-universality of the genetic code is not a minor quibble, but part of a general pattern. In 1991, Phillip Johnson argued in Darwin On Trial that common ancestry the so-called "fact of evolution" is not an empirical hypothesis for Darwinists, but a logical consequence of their naturalistic philosophy.
What organisms have this variation in code? Have you done any research into that? For instance mitochondria which uses one code is present in all higher life and the mitochondria in all these lifeforms all use the same code. The somatic DNA also uses the same code in all higher lifeforms. What are the chances of this?
AttentionKMartShoppers wrote:As such, it is immune to empirical disconfirmation. Even when evidence cited as primary support for the idea turns out to be false, the idea survives.
What evidence is this?
AttentionKMartShoppers wrote:We see this in molecular phylogeny (in which the contortions needed to protect the common ancestry of the major kingdoms make Ptolemaic epicycles look downright elegant), the fossil record (in which the absence of a common ancestor for the major animal phyla is still dismissed as an artifact of incomplete collection, even though 150 years of collecting have shown that the Cambrian explosion is real), and vertebrate embryology (in which dissimilarities in early embryos that do not support the doctrine of common ancestry are explained away, on the grounds that early development evolves more easily than we thought).
Now the author is babbling, he is no longer talking about the genetic code.
AttentionKMartShoppers wrote:The truth is that MOST of the evidence cited in support of common ancestry at the levels of kingdoms, phyla and classes has had to be explained away to protect the idea of common ancestry.
What is the evidence for this truth?
AttentionKMartShoppers wrote:But if most of the evidence must be explained away, then it's clear that we're dealing with a philosophical doctrine rather than empirical science.
Again what evidence is this based on?
AttentionKMartShoppers wrote:Of course, common ancestry may be true at lower levels of the biological hierarchy. For example, everyone would probably agree that all human beings are descended from common ancestors. And even many biblical creationists regard the ability of members of the cat family to hybridize as evidence that they share a common ancestor. In the absence of evidence, however, why should we accept as "fact" the idea that ALL organisms are descended from a common ancestor?
Why is it acceptable here but no further? Where is this line being drawn? Isn't this line arbitrary?
Save the trees!
Tamzek implies that Darwin's tree of life looks simple and "tree-like" apart from the 'molecular thicket' at the root, however this is not the case. It is well recognized in systematics that very often phylogenetic trees based upon one gene or protein sequence, will lead to one tree, while a tree based upon some other biomolecule look quite different.
Different but not quite different. Do some analysis yourself and you will begin to see why. If all you read are opinions you are at least 2 degrees away from the actual data.
AttentionKMartShoppers wrote:And even more often, trees based upon biomolecules are at odds with trees created on macromorphological characteristics or the fossil record (and trees based upon different macromorphologies often differ from one another a well).
This is the source of the whale debate. But as you can see the argument is about which ungulate gave rise to whales not wheather whales are descended from land mammals or not.
AttentionKMartShoppers wrote:Tamzek claims that the Eukaryote tree is well resolved through Baldauf et al. (2000)99, however this paper escapes typical problems of conflicting trees because it creates one tree using a massive dataset of many protein sequences to statistically obscure the differences between the trees based upon individual proteins.
The tree of life is not complete nor will it be completed any time soon.
AttentionKMartShoppers wrote:By creating one "flimsy" tree through many genes, common ancestry cannot be strongly verified through independent converging lines of genetic evidence (admittedly, this is a good technique for creating a phylogeny if one already assumes common ancestry is true, however, as a test of common ancestry, it shows molecular evidence provides little support). In fact, it was found that single-gene phylogenies only "support subsets of the combined protein tree." In other words, the different genes, when taken independently, do not converge to make a nice neat tree.
Care to expand on this? There are many cases of molecular analysis of multiple genes converging.
AttentionKMartShoppers wrote:Tamzek claims that the results of this article indicate that Eukaryote phylogeny is coming along "just fine", and that this paper provides a "perfectly traditional and tree-like" phylogeny of the Eukaryotes. As said before, the neatness of this tree is purely the result of statistical techniques and the combined dataset used in the paper. Regardless, Baldauf et al. actually found that their tree has "striking differences from SSU rRNA phylogeny"99, and noted that past studies have also encountered conflicting trees. When faced with differing trees, Darwinists usually manage to retain common ancestry by explaining these discrepancies through differing rates of evolution, differing selection pressures, lateral gene transfer, or even convergent or parallel evolution.
Do you expect that genes will change at the same rates? Do you expect environmental factors not to have an impact on gene selection?
AttentionKMartShoppers wrote:However, nonetheless, nice neat Darwinian trees are often hard to come by, and predictions from common ancestry fail, leaving us with epicycle after epicycle. Resorting to lateral gene transfer might not be necessary99, but this paper shows that nice neat Darwinian trees are still elusive for the alleged ancestry of Eukaryotes.
Nice neat trees are difficult, however general phylogenies and empirical analysis helps give clues which might have otherwise been overlooked.
AttentionKMartShoppers wrote:Other organisms, whose alleged phylogenetic trees have run into the "thicket" problem, because nice neat Darwinian trees could not be produced by the observed character distributions, include (but are by no means limited to) relationships of major reptile groups62, amniote groups (particularly with the placement of birds)69, major placental mammal groups64, 72, whales (both as an order within class mammalia63, and its sub-groups 65, 66), songbirds74, bats (as an order within class mammalia and its sub-groups)64, 67, 69, rodents64, 68, 72, lagomorphs (rabbits)69, 72, artiodactyls sub-groups72, insectivores64, 72, chimps (their position within the order primates)69, sea urchins72, many major plant groups71, angiosperm sub-groups69, 71, marsupials (in relation to monotremes and placentals)72, osteichthyans (in their alleged relationship to tetrapods)69, some deuterostome phyla69, and many Eukaryote groups (e.g. fungi70, 99, plants99, and metazoa99).
Have you actually looked at the data to see what these problems may be? You may be surprised how this particular article is blowing these problems out of proportion.
AttentionKMartShoppers wrote:Schwabe and Warr73 found that proteins such as relaxin, insulins, adrenocorticotropic hormone, somatostatin, histocompatability antigens, neural glycoproteins and microglobulin are distributed in both animal and non-animal groups in ways which differ markedly from Darwin's alleged tree of life.
This I will research more.
AttentionKMartShoppers wrote:Early in the molecular revolution there was some hope that molecular phylogenies of mammalian orders would match those created by morphology64, 72, however as more data came in, the tree became less and less "Darwinian". In fact, in 1998, de Jong noted that:
"the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows."72
More data is better than less, if you have an alternative explanation please share. For now there is much to be learned and that is what science is about.
AttentionKMartShoppers wrote:Systematist Colin Patterson also did a review of congruence between trees generated by morphology and trees created by molecular data and found that "congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology"69. His study concluded that after reviewing trees based off of molecular and morphological data, their hopes of verifying morphologically derived trees were "dampened."69 This does not square well with Tamzek's claim that "[molecular] phylogenies are reliable and in reasonably good accord with phylogenies generated from other data." In closing, this reoccurring "thicket" problem shows that the tree of life, if all life is even inter-related, is surely very different from its portrayal in textbooks.
Of course it is simplified for the sake of teaching, only a professional who understands the intracacies can fully appreciate the areas which require further study and debate.
You bet ya.
AttentionKMartShoppers wrote:http://www.darwinismrefuted.com/myht_of ... gy_05.html
Again a repeated statement, the more we analyze the more we can paint a more conclusive picture.
AttentionKMartShoppers wrote: …cientists started analyzing a variety of genes from different organisms and found that their relationship to each other contradicted the evolutionary tree of life derived from rRNA analysis alone.302
Have you had a chance to analyze the actual data?
No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced. Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various [groups] to the makeup of the primary groupings themselves.303
This is true.
A year ago, biologists looking over newly sequenced genomes from more than a dozen microorganisms thought these data might support the accepted plot lines of life's early history. But what they saw confounded them. Comparisons of the genomes then available not only didn't clarify the picture of how life's major groupings evolved, they confused it.
It appears microorganisms have diverged greatly, more than anyone could have imagined.
AttentionKMartShoppers wrote:And now, with an additional eight microbial sequences in hand, the situation has gotten even more confusing.... Many evolutionary biologists had thought they could roughly see the beginnings of life's three kingdoms... When full DNA sequences opened the way to comparing other kinds of genes, researchers expected that they would simply add detail to this tree. But "nothing could be further from the truth," says Claire Fraser, head of The Institute for Genomic Research (TIGR) in Rockville, Maryland. Instead, the comparisons have yielded many versions of the tree of life that differ from the rRNA tree and conflict with each other as well...304
Again I would encourage you to look at the data yourself instead of taking the opinion of others.
Inconsistencies among trees based on different molecules, and the bizarre trees that result from some molecular analyses, have now plunged molecular phylogeny into a crisis.305
As far as we can tell junk DNA does not encode for genes and therefore not subjected to selective pressures. And therefore not subjected to comparative analysis. This may or may not change in the near future. Who knows what new discoveries lie ahead.
Imagine the sequences like cooking instructions. Each letter represent a different step. You can see that the recipe for the cow and sheep is identicle. The whale is almost the same.
However the ones for the monkey, kangaroo, and bat are different.
And if you delve further into the differences a significant pattern emerges.
Doesn't this ignore "junk" DNA, among other things?
AttentionKMartShoppers wrote:But, alas, as we know...BGood, a man went to college to be an engineer...will attempt to single handedly refute my three sources...
Not surprisingly, none of the three sources actually gave any empirical evidence, I strongly suggest you look at the data and use that to refute points. Opinions although valued in everyday life are immaterial in science.
It is not length of life, but depth of life. -- Ralph Waldo Emerson