Evolution: the Facts.

[randman]

On the contrary: Darwinism would predict that similar selection pressures placed on life forms would yield similar adaptations, and that this is going to be true, no matter what the life form's ancestors looked like in the past.

And, we can even isolate and measure those selective elements, if we do a careful enough study. We can survey the niches, observe transformations in survival strategies, and so on.

The fact that you would say otherwise tells us more about your lack of knowledge regarding the Theory of Evolution, than it does about the origins of life, or the powers of Intelligent Design.

Just not true. The opposite is the case actually. You are just not familiar with the development of these ideas.

When do you think, for example, front loading or related concepts came about?

 

[Wowbagger]

Just not true. The opposite is the case actually. You are just not familiar with the development of these ideas.

When do you think, for example, front loading or related concepts came about?

I know that the empirical facts behind "front-loading" were discovered through the work of evo/devo, rather than I.D.

"Front-loading" did not predict any empirical findings (that we didn't know already), in and of itself.

How can "front loading" tell us more about life, that Darwinism is completely missing out on?

Darwinism predicts that but it's extremely unlikely that marsupial and placental pairs would emerge in such a similar fashion.

Actually, Darwinism predicts it is MORE LIKELY that they WILL emerge in a similar fashion.

I remind you that selection pressures drive the change we see in genomes and ultimately in species, in the Darwinian view. When niches are similar, and selection pressures are similar, we SHOULD EXPECT emergence of similar traits...

...without the intervention of an Intelligent agent, I might add.

What explanation, what environmental pressures, for example, were brought to bear to evolve the mammalian ear independently?

Independently of what?

Are you aware that all the nitty gritty details of how the mammalian ear have been worked out by evolutionary biologists? So much so, that even a summary of the progress can be many pages long:
http://en.wikipedia.org/wiki/Evolution_of_mammalian_auditory_ossicles

Intelligent Design is not capable of delivering that level of detail, in regards to the ear's origins. NOT EVEN CLOSE.

 

[Dinwar]

Just not true. The opposite is the case actually. You are just not familiar with the development of these ideas.

I'm familiar with the FOSSILS--the actual records of the evolution. You start with pretty much any body shape, go into the water, start hunting fish, and your decendants have a bullet-shaped body. It happened with the first chordates, it happened with reptiles when they went back to the sea, it happened with mammals. And we have the fossil evidence that they were completely different lines.

Are you aware that all the nitty gritty details of how the mammalian ear have been worked out by evolutionary biologists?

And paleontologists. The mammalian ear is a well-documented transitional form, it turns out, and was established as a mammalian trait during the Permian/Triassic sometime. Bears didn't diverge from the rest of mammals until the Cenozoic, I believe.

 

[randman]

Wowbagger, real science welcomes dissent and does not misrepresent it as you have here with IDers. Nor argues that dissent is an attack on science itself.

 

[Wowbagger]

Wowbagger, real science welcomes dissent and does not misrepresent it as you have here with IDers. Nor argues that dissent is an attack on science itself.

Okay. I welcome dissent.

How are the arguments of your dissent higher quality than my own?

If I accused your dissent of being superfluous, how can you demonstrate otherwise?

What experiments can you propose to show when, where, and how the Intelligent Designer intervened with life?

What properties can we hope to isolate and measure of the Designer, itself?

Are all of your arguments merely denials of evolution's impact, or do you have positive evidence of a Creator to offer?

I welcome your dissent, but if it is going to win over the hearts of scientists, it has to argue itself better.

 

[randman]

Some of the experiments I would show, but once again am not going to veer off much from genetics for the sake of brevity, are being done in quantum physics but for other reasons and involve the origin of information. It's quite positive evidence.

Others have papers more in line with what you may be looking for. You should take the time to read some of them. The Discovery Institute has a nice link to some. Take a look at it.

I showed 2 papers by John Davison on the other thread. Why don't you look at them?

He was right in predicting greater complexity for the LCA, for example.

 

[Squeegee Beckenheim]

So it really is going to be a case of two separate threads derailed by randman with exactly the same discussion?

 

[Kotatsu]

What if we discover it's not involved with a function? Of course, people thought junk DNA had no function but that's been recently shown not to be the case. Incidentally, that undermines the claims that we can track phylogeny by seeing common errors in junk DNA. Prior evo claims were since junk DNA was non-functional, if we saw a similar mutation, it was good evidence for establishing a lineage. I think one time I debated for quite some time Cyto-chrome C or something like that running a program to show cladistics. Much of the evo argument there is thrown out the window if junk DNA is functional.

How? Most of the genes used for phylogenetic reconstruction is already functional, with a few additional regions traditionally seen as non-functional used in some animal groups. If we see a similar mutation in two given lineages, this is a good -- but not a 100% certain -- indication of close relationship regardless of if the gene is functional or not. In the five animal groups I've worked with over the last few years, about 25 different genes are commonly used for phylogenetics, and only one or two of those were previously thought to be non-functional. No one stopped using them when a function was found, as they typically give the same topology as genes known to be functional, although often at a different level of resolution.

Some great work just came out concerning sauropod head morphology, for example.

Could you give me a reference? We're about to start up a paleontology study group at my university, and this sounds very interesting.

 

[randman]

How? Most of the genes used for phylogenetic reconstruction is already functional, with a few additional regions traditionally seen as non-functional used in some animal groups. If we see a similar mutation in two given lineages, this is a good -- but not a 100% certain -- indication of close relationship regardless of if the gene is functional or not. In the five animal groups I've worked with over the last few years, about 25 different genes are commonly used for phylogenetics, and only one or two of those were previously thought to be non-functional. No one stopped using them when a function was found, as they typically give the same topology as genes known to be functional, although often at a different level of resolution.

You can read how TalkOrigins uses the argument of pseudogenes as a major argument for the darwinian paradigm. It's been a staple icon of "evidence" for many years and predictably, factually incorrect.

http://www.talkorigins.org/faqs/molgen/

 

[Kotatsu]

You can read how TalkOrigins uses the argument of pseudogenes as a major argument for the darwinian paradigm. It's been a staple icon of "evidence" for many years and predictably, factually incorrect.

This does not, however, answer my question, which was (here intensely paraphrased), "How does the fact that 'junk DNA' is found to be functional throw the use of shared mutations between lineages as evidence for common ancestry or relatedness out of the window?" Or, put in a different way, what is the qualitative difference between shared mutations or mutational patterns in two sections of perceived "junk DNA", compared to in two sections of DNA known to be functional, that renders support for a certain grouping of taxa nonviable when a given gene region is moved from one category to another? Why does it matter whether we know that a gene is functional or not when we try to reconstruct phylogenies?

 

[randman]

It does not address in this narrow point the issue of functional DNA. It just points out that a major piece of evidence for evolution was wrong. Junk DNA is functional. I don't want to rehash their failed argument because I never thought it was right. They'd find some mutation in junk DNA that they argued (not even correctly) was present in a group creatures they would then say had a common ancestor based on shared genetic sequences, and since it was not functional, it could not be related to similar features via design but could only be explained via Darwinism.

That was wrong. The genetic sequences are functional. Evos were wrong again, but whether they'll admit or not, we'll see. They took over 100 years under sustained criticism to admit Haeckel's drawings were forgeries. The internet helped because it became embarrassing for them, But they already back to repackaging him.

Evos don't like to abandon an effective tool for convincing people even after it's been shown to be wrong factually.

Functional sequences should likely be more similar, the more similar the function but perhaps not?

 

[Kotatsu]

It does not address in this narrow point the issue of functional DNA. It just points out that a major piece of evidence for evolution was wrong. Junk DNA is functional. I don't want to rehash their failed argument because I never thought it was right. They'd find some mutation in junk DNA that they argued (not even correctly) was present in a group creatures they would then say had a common ancestor based on shared genetic sequences, and since it was not functional, it could not be related to similar features via design but could only be explained via Darwinism.

I still don't see wherein the problem lies. Mutations or mutational patterns that are shared between lineages are evidence of shared ancestry whether the gene is functional or not. Discovering that a gene previously thought to be nonfunctional is in fact functional has absolutely no effect on this, and if you look over phylogenetic papers based on purportedly nonfunctional DNA alignments and just excise the word "non-functional", the phylogenetic trees will remain the same. The phylogenetic methods are the same regardless of what gene region you use -- or even if you use randomly generated, genuinely nonsense, DNA (1) -- even though e.g. the specific model of sequence evolution used in a Bayesian analysis may differ depending on the gene and/or the position in a gene.

As an example, let's look at 12S sequences in Phthirapteran lice, the group I work with. Let us assume that we believe 12S is non-functional. We have primers for this region, and sequence a whole lot from different genera of lice, and compare their primary and secondary structure. Apart from point mutations, we find certain patterns. For instance, compared with Columbicola columba, the 47 loop of both Halipeurus pelagicus and Naubates harrisoni are bloated and supports a secondary loop on the 5' side (Page et al., 2002). This suggests that H. pelagicus and N. harrisoni are closely related, but that C. columbae is not closely related to these two. We thus propose that these two species should belong in one group, whereas C. columbae should likely belong to another group.

Comparing this with morphology, we see that there is some sense in this. Eichler (1963) placed Halipeurus and Naubates in his Pseudonirmidae, whereas Columbicola is placed in Esthiopteridae. While Eichler is often sparse in his detailing of why he formed certain groups, this makes sense when comparing such structures as male genitalia, chaetotaxy, gross morphology of abdominal and thoracical tergites, and internal structures of the head. Comparing host relationships, we find that Columbicola is a parasite on pigeons and doves, whereas the other two are parasites on seabirds (Procellariiformes) (Price et al., 2003).

So let's look at other genes and on the actual genetic analysis of the 12S alignment. Fortunately, Page et al. (2002) provides such a comparison, which shows that for the alignment of 12S (which we assumed was nonfunctional), Naubates and Halipeurus are sister groups, and Columbicola is placed almost in the other end of the tree. They are placed more closely together (and Columbicola is paraphyletic) in a tree based on the secondary structure (discounting the actual sequences), but both the mitochondrial COI gene and the nuclear EF-1a gene place the two seabird lice together, and separate from the pigeon louse. Cruickshank et al. (2001) shows the same pattern, using a larger data set, regardless of whether parsimony, minimum evolution or maximum likelihood is used. Smith et al. (2004) show the same, again, with a different data set, and this result is stable whether you use only morphology, morphology and DNA, only DNA, or only protein-coding DNA, as well as stable under both maximum likelihood and Bayesian inference. Smith (2001) showed the same using only morphology.

Let us then assume that we find that 12S is actually functional. Where, more precisely, does this affect our conclusion? I argue that it does not make any difference whatsoever, and that your claim that "a major piece of evidence for evolution is wrong" is spurious, at best. Moving a given DNA region from the category "no known function" to "function known" does at no stage change the theory or practice of phylogenetic inference and reconstruction. The only difference would be in the perception of what level of resolution you would expect to get in your phylogeny based on a given gene region, as a protein coding region would be assumed to be more conservative than a structural region, which in turn would be assumed to be more conservative than a non-functional region. The only practical difference this would make is in the choice of gene regions used to look at the relationships within a given taxon, i.e., if I want to study within-genus relationships, I may first try some less conservative genes to sequence, as I would want to work with something that can give me resolution and structure at that level.

Now, I believe you are arguing, in the last section of the above quote, that if gene is functional, similarities between different lineages could very well be because of design rather than evolution. The reason the two seabird lice above have similar 47 loops in their 12S is because they live in a different environment from the pigeon louse, and thus this gene, if we assume its expression has a tangible effect on its survival, could have been designed to cope with these circumstances rather than those under which a pigeon louse lives. For instance, if we assume that 12S in some way gives the lice a higher tolerance to salt in the feathers they eat, it would make sense that lice on seabirds have this extended loop, while pigeon lice do not, whether they are related or not. Its existence would then not necessarily show a common ancestry, but just a similar feature for coping with the same problems of high salt content of the host plumage. This could then be either a result of design or of convergent evolution. Due to the complexity of molecular biology, which ensures that we can never be quite sure what a certain gene region is used for, this is at least superficially a reasonable argument.

However, this does not adequately explain the common patterns of random mutations and indels in a given gene. Why, for instance, do the ectoparasites of birds so often show phylogenies significantly similar to those of their hosts(e.g., Paterson et al., 2000; Page et al., 2004; Hughes et al., 2007)? Are the differences between the environment on two given closely related host taxa so different that there is a need for designed differences in their parasites? If so, why do these differences, when analysed phylogenetically, so often form nested hierarchies which are concordant with the nested hierarchies obtained when performing the same kind of analysis on their hosts? And why do these designed differences so often occur mostly in the third positions in gene coding regions, positions which are known to be subject to a certain amount of redundancy in the translation codes?

And if these differences are so large between closely related bird hosts that it warrants seemingly random changes in the design of their DNA, why is this not consistent over different kinds of lice on the same birds? Why can wing lice spread by phoresy (2), through shared nest holes, and from prey to predator species and establish new populations on novel hosts in some cases (documented from a large variety of bird louse groups) if their genetic design is based on their normal host? Instinctively -- and this is most likely a false dichotomy -- the DNA would either be designed for a specific host (and then lateral spread to novel hosts would never be viable), or it would be designed for a large amount of hosts or a generic host (and then there is no reason for co-phylogenetic patterns to occur).

The fact remains that these differences in DNA sequence do occur, whether we know that a specific region is functional or not. At the very most, finding a function for what was previously thought to be "junk DNA" changes the taxonomic level on which we expect to get resolution in a phylogenetic reconstruction, but it does in no way render previous phylogenetic reconstructions based on the assumption that the gene region was nonfunctional wrong, as both structural, coding, "junk" and all other kinds of DNA will at least under normal circumstances show the same kind of pattern, though perhaps at different levels due to the speed with which these changes get fixed in the population.

ETA:

To clarify, this is what I am getting at:

Incidentally, that undermines the claims that we can track phylogeny by seeing common errors in junk DNA.

Naturally, if there is no such thing as "junk DNA", we cannot track phylogeny by seeing common errors in it. However, this does not in any way mean that we cannot track phylogeny in non-junk DNA by seeing common errors in it. And if what was previously thought to be "junk DNA" is shown to be functional, any phylogeny based on that DNA sequence would simply switch from one category to the other, but this would not invalidate any phylogenies based on the gene region when it was still believed to be "junk DNA".


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References:
- Cruickshank, Johnson, Smith, Adams, Clayton, Page (2001). Mol. Phyl. Evol. 19, 202-215.
- Eichler (1963). Mallophaga. In: H. G. Bronn (Ed), Klassen und Ordnungen des Tierreichs, Leipzig.
- Hughes, Kennedy, Johnson, Palma, Page (2007). Syst. Biol. 56, 232-251.
- Page, Cruickshank, Johnson (2002). Insect Mol. Biol. 11, 361-369
- Page, Cruickshank, Dickens, Furness, Kennedy, Palma, Smith (2004). Mol. Phyl. Evol. 30, 633-652.
- Paterson, Wallis, Wallis, Gray (2000). Syst. Biol. 49, 383-399.
- Price, Hellenthal, Palma, Johnson, Clayton (2003). The Chewing Lice. Illinois Natural History Survey Special Publication 24
- Smith (2001). Zool. J. Linn. Soc. 132, 81-144.
- Smith, Page, Johnson (2004). Zool. Scr. 33, 239-259

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(1) In the sense that it does not code for anything as it is not taken from a known extant or extinct organism. This is regularly done to test phylogenetic theory and for method development.

(2) "Hitch-hiking" on Hippoboscid flies.

 

[Dinwar]

Wowbagger, real science welcomes dissent and does not misrepresent it as you have here with IDers. Nor argues that dissent is an attack on science itself.

Just want to point out, this is a continuation of randman's attempt to dictate the terms of the argument to us. He's attempted in numerous posts to tell us what science is and what it isn't. Also, this is nothing more than the "Teach the controversy!" argument. He's found some fringe crank, and demands that biology take that crank seriously.

That was wrong. The genetic sequences are functional. Evos were wrong again, but whether they'll admit or not, we'll see.

As was pointed out to you elsewhere, researchers don't tend to speak in terms of "junk DNA" anymore.

So it really is going to be a case of two separate threads derailed by randman with exactly the same discussion?

Looks like he's realized that he can't simply spout out garbage and dictate what terms mean in the other thread, so he's trying it here. Not a smart move on his part; this forum is more vicious than the other when it comes to this kind of behavior. Probably stems from the fact that a number of people who frequent it are researchers, and they take a dim view of being told what science is by someone who's demonstrable incapable of reading a journal article (look at his other thread for evidence--he's continuously claimed that a paper states the exact opposite of what the authors actually say).

 

[Dancing David]

Darwinism predicts that but it's extremely unlikely that marsupial and placental pairs would emerge in such a similar fashion. It's hard to get evos to see this at first because you guys are taught so much to reaffirm simple claims.

What explanation, what environmental pressures, for example, were brought to bear to evolve the mammalian ear independently?

If the lines that led to mamammls led to non-placental mammals, then marsupials (non-placental mammals) are likely to share common heritage. Therefore the ear structures are likely to have started with similarites in the two separate lines and then the similar ears developed.

Where did the mammalians ears deveolp independantly? They developed from a common ancestor.

 

[randman]

Naturally, if there is no such thing as "junk DNA", we cannot track phylogeny by seeing common errors in it. However, this does not in any way mean that we cannot track phylogeny in non-junk DNA by seeing common errors in it. And if what was previously thought to be "junk DNA" is shown to be functional, any phylogeny based on that DNA sequence would simply switch from one category to the other, but this would not invalidate any phylogenies based on the gene region when it was still believed to be "junk DNA".

I am not saying you cannot use arguments of similarity in functional DNA, just that evos have often argued that junk DNA was particularly a strong argument because the similarities were not related to function and so indicated a common ancestor apart from design.

Now, that argument based on pseudogenes is off the table.

I have argued that chemical maybe even quantum mechanical properties (DNA's local environment) would dictate certain types of mutations and errors, and there are papers in the literature talking about "convergent mutations" and so just because we see a similar genetic sequence does not actually mean it arrived there via common ancestry. Common ancestry is one explanation but it's important to recognize what the data does and does not confirm or rule out.

I would hope evos would learn to appreciate such thinking as it can help bring clarity to their arguments and beliefs and perhaps lead to their modification of their theories or their abandoning them for new paradigms, or at least avoid gross overstatements which often turn out to be wrong, such as assuming junk DNA was non-functional and spending quite a bit of time insisting pseudogenes were VERY strong evidence for Darwinism. You have to realize evos such as folks at TalkOrigins often presented this as definite proof of Darwinism.

Yet it never really was. It was a gross overstatement.

Real science is not about trying to make everyone believe something. It's about helping people understand things. It's really not important at all that anyone believes in Darwinism. No biologist or scientists that even does work as an evolutionist needs to believe it actually. They just need to understand the data and various theories and explanations of it, including Darwinism.

All too often evos debate and argue with a clear express intent focussed on belief rather than education.

 

[randman]

If the lines that led to mamammls led to non-placental mammals, then marsupials (non-placental mammals) are likely to share common heritage. Therefore the ear structures are likely to have started with similarites in the two separate lines and then the similar ears developed.

Where did the mammalians ears deveolp independantly? They developed from a common ancestor.

The issue for front loaders and men like Pierre Grasse is not whether they share a common ancestor but whether internal mechanisms such as the local environment for DNA (properties of chemicals and coded information, etc, etc,...) dictated the pattern or was it driven by mere random mutations being selected for due to environmental pressures.

Keep in mind there are lots of features that do not seem to serve to help the organism adapt to the environment that well. I know what an evo would say so you don't have to repeat it, but if you'd actually take a step back and listen to what men like Pierre Grasse emphasize and paraphrasing his words, being encouraged to look past this thinking of evolution as an easily understood process, etc,....., you might see what they are talking about.

It's quite astonishing when you begin to look at the data more objectively without the lens of insisting and assuming NeoDarwinian mechanisms explain everything.

They really do not. The patterns emerging do not indicate they were driven strictly by random mutations and the environment. Even looking at phylogeny, the pattern of how species seem to be grouped together, it's not what "evolution" in the sense of Darwinism would predict, but you have to take the time to look at the patterns and consider the arguments closely.

Lots of scientists, even some of great reputation, came and come to the same conclusions that NeoDarwinism just doesn't explain the data.

 

[randman]

Why, for instance, do the ectoparasites of birds so often show phylogenies significantly similar to those of their hosts(e.g., Paterson et al., 2000; Page et al., 2004; Hughes et al., 2007)? Are the differences between the environment on two given closely related host taxa so different that there is a need for designed differences in their parasites? If so, why do these differences, when analysed phylogenetically, so often form nested hierarchies which are concordant with the nested hierarchies obtained when performing the same kind of analysis on their hosts?

On nested hierarchies, keep in mind there is a tendency for evos to overstate their arguments, ignoring their weaknesses. Lots of time you will read some "fact" that is supposedly so but down the road it turns out to be an overstatement.

A few years back on another forum someone linked to a program that would create cladistics by plugging in a gene to look for among different animals. We were discussing convergent evolution and whether, for example, the placental mouse was really more closely related to human beings than it is to the Marsupial mouse.

I would advise caution in assuming the molecular data always shows what you think it does and what is predicted by NeoDarwinism. Let's wait to see what the studies and data really show.

 

[Squeegee Beckenheim]

It's really not important at all that anyone believes in Darwinism.

That's correct. The Theory Of Evolution remains true no matter whether people believe it to be true or not.

 

[Dancing David]

I'm familiar with the FOSSILS--the actual records of the evolution. You start with pretty much any body shape, go into the water, start hunting fish, and your decendants have a bullet-shaped body. It happened with the first chordates, it happened with reptiles when they went back to the sea, it happened with mammals. And we have the fossil evidence that they were completely different lines.

And paleontologists. The mammalian ear is a well-documented transitional form, it turns out, and was established as a mammalian trait during the Permian/Triassic sometime. Bears didn't diverge from the rest of mammals until the Cenozoic, I believe.

Not to mention the mammal, avian and reptile penises.

 

[Dancing David]

Wowbagger, real science welcomes dissent and does not misrepresent it as you have here with IDers. Nor argues that dissent is an attack on science itself.

Then stop the rhetoric and explain what an alternate theory explains better than the theroy of natural selection through reproductive success.