Evidence for God from Science

aa118816 wrote:Thanks for the post and you are correct that he seems to have changed his position,

aa118816 wrote:but in no way has he solved the suppossed puzzle and his source material is sparse. If you think you can recreate a complete phylogeny based on 150 bones, you are on drugs. His conclusions are based upon his commitment to methodological naturalism. If you read through the whole article carefully, you will only see speculation. I also wonder if he got an earful from his colleauges after his statement in 2001. A good example of this is Peter Ward completely changing his position after being hammered by his colleauges for many of his conclusions in Rare Earth and then Priviledged Planet.

Dan

aa118816 wrote:I also wonder if he got an earful from his colleauges after his statement in 2001.

Sirpa Nummela, J. G. M. Thewissen, Sunil Bajpai, S. Taseer Hussain and Kishor Kumar wrote:Nature 430, 776-778 (12 August 2004) | doi: 10.1038/nature02720
Eocene evolution of whale hearing

Sirpa Nummela, J. G. M. Thewissen, Sunil Bajpai, S. Taseer Hussain and Kishor Kumar

Abstract

The origin of whales (order Cetacea) is one of the best-documented examples of macroevolutionary change in vertebrates1, 2, 3. As the earliest whales became obligately marine, all of their organ systems adapted to the new environment. The fossil record indicates that this evolutionary transition took less than 15 million years, and that different organ systems followed different evolutionary trajectories. Here we document the evolutionary changes that took place in the sound transmission mechanism of the outer and middle ear in early whales. Sound transmission mechanisms change early on in whale evolution and pass through a stage (in pakicetids) in which hearing in both air and water is unsophisticated. This intermediate stage is soon abandoned and is replaced (in remingtonocetids and protocetids) by a sound transmission mechanism similar to that in modern toothed whales. The mechanism of these fossil whales lacks sophistication, and still retains some of the key elements that land mammals use to hear airborne sound.

Evolution does not predict that specific sequences have specific functions.

It is the variation in sequence that actually bolsters the theory.

This variation in gene sequences was predicted by evolution.

The non-harmful ones (mutations which do not alter protein function)will remain...

If it was designed why would this protein which works just as well in yeast cells as in humans have different sequences for each organism. Yes, the question makes sence.

Here are the sequences:

Mystical wrote:No, it is correct. Genes guide the encoding and development of proteins.

Evolution does not predict that specific sequences have specific functions.

Evolution doesn't predict anything.

It is the variation in sequence that actually bolsters the theory.

No, it doesn't. Variation in gene sequence doesn't say anything.

Mystical wrote:

This variation in gene sequences was predicted by evolution.

Evolution doesn't predict anything. Anthropomorphizing?

Mystical wrote:

The non-harmful ones (mutations which do not alter protein function)will remain...

Wrong, there are many protein-altering mutations which are not harmful and which remain.

Mystical wrote:

If it was designed why would this protein which works just as well in yeast cells as in humans have different sequences for each organism. Yes, the question makes sence.

No, it doesn't make sense. Why not? Funny, "Evolution" isn't even close to any explanation. I predict that he won't be figuring it out any time soon! Sounds like God to me.

Mystical wrote:

Here are the sequences:

Still don't mean a thing, my friend. Sorry.

If there is an apparant order to this variation it certainly does. Just as the word for love in french and spanish can be traced to its latin roots, the genes of your neighbor and yourself can be traced back to a common ancestor.

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. Darwinists claim that the exceptions are unimportant, since they "know" that the aberrant organisms are descended from organisms that had the standard code. But the code itself was supposed to be the primary evidence for such descent, and no comparable evidence is offered to replace it. Clearly, the Darwinists' "knowledge" in this case is philosophical rather than empirical.

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. 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. 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).

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. 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.

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?

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. 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). 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. 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.

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. 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.

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). 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.

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
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.

…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

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

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. 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

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

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.

AttentionKMartShoppers wrote: 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.

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.

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.

AttentionKMartShoppers wrote:Clearly, the Darwinists' "knowledge" in this case is philosophical rather than empirical.

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.

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.

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).

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.

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.

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?

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.

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).

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.

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.

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.

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.

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).

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.

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

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.

AttentionKMartShoppers wrote:http://www.darwinismrefuted.com/myht_of ... gy_05.html

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

Again a repeated statement, the more we analyze the more we can paint a more conclusive picture.

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

Have you had a chance to analyze the actual data?

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.

This is true.

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

It appears microorganisms have diverged greatly, more than anyone could have imagined.

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

Again I would encourage you to look at the data yourself instead of taking the opinion of others.
=D

AttentionKMartShoppers wrote: BGood again:

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?

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.

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...

BGoodForGoodSake wrote:

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.

BGoodForGoodSake wrote:

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?

sandy_mcd wrote:

BGoodForGoodSake wrote:

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?

It seems pretty obvious - take a common noun and a bunch of animals that pretty much look alike and put them in the same family (making sure to keep human beings separate). So you've got your cat family, your dog family, cow family, etc. Preferably stick with large well known mammals and ignore oddballs like cheetahs, hyenas. The less familiar you are with animals, the larger you can make your groupings, such as the fish family, the bug family.

AttentionKMartShoppers wrote:BGood, you, an engineer...are just tossing questions out against a guy....with a PhD in molecular and cell biology. This...is funny.

Today's responses brought to you by BGood and circular reasoning! W00T

BGoodForGoodSake wrote:

AttentionKMartShoppers wrote:BGood, you, an engineer...are just tossing questions out against a guy....with a PhD in molecular and cell biology. This...is funny.

Today's responses brought to you by BGood and circular reasoning! W00T

You see PhD and therefore forgoe any individual investigation?
Did you read any of the papers he cited in his essay?

The papers were basically just essay's of personal thoughts, which you happen to agree with.

Striving for the reinforcement of ones beleifs does not lead to scientific progress.

I suggest you actually look at the data, otherwise it is your loss.
=P

To start you off here is the data used to do molecular comparisons of various mammilian groups using the sequence from exon 28.
http://www.ncbi.nlm.nih.gov/entrez/quer ... t=Citation

Here is an article describing the difficulties in resolving descrepancies of phylogenic charts derived from various molecular comparisons. As you will surely notice upon closer analysis, it is not to the point of crisis.
lol
More data, and more analysis is what science is all about.
http://mbe.oxfordjournals.org/cgi/content/full/18/2/132


btw this is empirical data, no more opinions please.

AttentionKMartShoppers wrote:So, all my sources are just opinions...that's a neat way...poisoning the well are we? I guess it must be the best response to accusations of circular reasoning.

dougp59 wrote:Please visit my new anti-evolution website;

http://www.evolutionsucks.org

The battle against evolution intensifies!