# DNA Says Evolution Unfolds According to a Plan

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Something funny is afoot in the biological sciences. Labs peering into DNA are seeing things that nobody expected. And because the received view of evolution failed to predict these findings, and because it has little room to incorporate them, a crisis is brewing for the theory. Something more than selecting random variants is going on in evolution.

The data coming out of DNA sequencing and analysis suggest that the something more has to do with a preferred direction in evolution. Phylogenetic descent seems now to be a developmental unfolding. Several discoveries point to this conclusion:

1. Junk DNA. This is not a particularly new discovery. It's been known for some time that all species carry around a lot of junk, DNA that appears to lie dormant. What aspect of evolution theory predicts that long stretches of inactive DNA would coast along inside organisms, seemingly contributing nothing to their survivability? Nobody saw it coming. It was an empirical surprise.

But in the context of ontogeny, the development of organisms, it is exactly what is to be expected. Each cell in the body of a complex organism inherits the same genes from the ancestral zygote, the original fertilized ovum. Despite all possessing the same genes, brain, liver, kidney, and skin cells, for example, distinguish themselves phenotypically. Each cell type looks and acts differently from the others. But, because they all inherit the same genes, there must be a lot of junk DNA in each type of cell. Brain cells don't need genes that function uniquely in liver cells, nor do kidney cells need genes that function uniquely in skin cells. But all the cells inherit all those genes from their common ancestor, the zygote, whether they need them or not.

When it comes to cell types in a body, an invariant genetic inheritance necessarily is the case, with lots of junk in each cell as a result. Ontogeny demonstrates that diverse morphologies, or phenotypes, need not correspond to any proportionate diversity of genotype. "Adaptive radiation" of cell types in a body proceeds just fine without genetic variation.

Evolution appears to operate similarly.

2. Conservation of DNA. Genetic material across species, though not invariant, turns out to be much less variable than observable differences among species would suggest. DNA is highly conserved across species. In their article, Regulating Evolution (Scientific American, May 2010) researchers Sean B. Carroll, Benjamin Prud'homme, and Nicolas Gompel comment,

For a long time, scientists certainly expected the anatomical differences among animals to be reflected in clear differences among the contents of their genomes. When we compare mammalian genomes such as those of the mouse, rat, dog, human and chimpanzee, however, we see that their respective gene catalogues are remarkably similar. [. . . .] When comparing mouse and human genomes, for example, biologists are able to indentify a mouse counterpart of at least 99 percent of all our genes.

The perplexed authors elaborate on the new findings:

. . . to our surprise, it has turned out that differences in appearance are deceiving: very different animals have very similar sets of genes.

The preservation of coding sequences over evolutionary time is especially puzzling when one considers the genes involved in body building and body patterning.

The discovery that body-building proteins are even more alike on average than other proteins was especially intriguing because of the paradox it seemed to pose: animals as different as a mouse and an elephant are shaped by a common set of very similar, functionally indistinguishable body-building proteins.

Surprise? Puzzling? Paradox? Why does evolution theory suffer so many bouts of the unexpected now that genomes are yielding their secrets? If the received theory of evolution were solid, wouldn't new genetic details have slots waiting for them in it? Shouldn't new genetic data bolster the theory, rather than generate surprises, puzzles and paradoxes for it to resolve?

Why didn't evolution theorists predict that phenotypic and genotypic differences across species would turn out to be so disproportionate, that so few genes would produce so many species? Nobody saw it coming. It was an empirical surprise.

3. Genetic switches. The differentiation of cell types in a developing organism is managed by homeobox genes. These genes function as master "switches" that trigger the expression and repression of other genes. By selectively turning other genes on and off at various stages of development, homeobox genes effectively control the varieties of tissues that will populate a body. This oversight function partly answers the riddle of junk DNA. Some genes that can appear dormant actually code for proteins whose phenotypic activity is the modulation of other genes. The regulatory genes are not junk.

Now, due to the work of Carroll, Prud'homme, Gompel and others, it looks like evolution uses regulatory genes in the same way.

Instead of spinning off variant cell types, the cycling on and off of genetic switches in the context of evolution spins off variant species. This discovery, of the importance of genetic switches in evolution and its helping to account for the low level of genetic diversity across species, was an empirical surprise. Nobody saw it coming.

The explanatory power of this discovery has produced a new discipline within evolutionary biology, called evolutionary developmental biology, or evo-devo, a science that gives regulatory genes a starring role in evolution.

4. Anticipatory genes. A new organism, a zygote, a fertilized egg carries many genes that ride along unexpressed—until they are needed by descendant cell types. The zygote anticipates, in its genetic catalog, the genes that remote descendant cells will need, even if those genes contribute nothing to the survival of the zygote itself or its immediate descendants. The zygote divides into two cells, and the two into four, and the four into eight, and so on. The cells that make up these early stages are said to be totipotent cells—they can bear descendants of any cell type. Later, after a degree of specialization, cells become pluripotent—they can give rise to several cell types, though not to all. And the specialization continues from there, with descendants inheriting from their ancestors the specialized genes they need, along with the rest of the genome.

This is to be expected in the context of a developing organism.

But it turns out that ancient species also carry genes that seem to anticipate the needs of descendants. A news article in Nature covering the sequencing of the genome of the Great Barrier Reef sponge Amphimedon queenslandica, reveals that the hoary creatures harbor a "tookit" of metazoan genes:

The genome also includes analogues of genes that, in organisms with a neuromuscular system, code for muscle tissue and neurons.

A curious finding. The article continues:

According to Douglas Erwin, a palaeobiologist at the Smithsonian Institution in Washington DC, such complexity indicates that sponges must have descended from a more advanced ancestor than previously suspected. "This flies in the face of what we think of early metazoan evolution," says Erwin.

Charles Marshall, director of the University of California Museum of Paleontology in Berkeley, agrees. "It means there was an elaborate machinery in place that already had some function," he says. "What I want to know now is what were all these genes doing prior to the advent of sponges.

The conundrum for normal evolution theory is clear. But, rather than propose that the genes needed by organisms with neuromuscular systems are in the sponge for the anticipatory purpose of providing those genes to descendants who will need them, the scientists invent an imaginary ancestor of the sponge that needed the genes. But the ghostly ancestor would have had to have arisen within a very narrow window. Fossil evidence of sponges goes back 650 million years; it constitutes, the authors note, "the oldest evidence for metazoans (multicellular animals) on Earth." So, what use would any species even more primitive than sponges have for the neuromuscular genes? Nobody saw it coming. It was an empirical surprise.

But the sponge genome is only one example. Research is finding case after case of ancestral species that harbor genes essential for remote descendants. Another example: It turns out that a species of unicellular protozoan carries genes essential for metabolic processes specific to metazoans. The researchers who discovered the surprise genes and published their data (PNAS – 2010 107 (22) 10142-10147) explain,

One of the most important cell adhesion mechanisms for metazoan development is integrin-mediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. [. . . .]
Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist
Amastigomonas
sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi.
[. . . .] Our data highlight the fact that many of the key genes that had formerly been cited as crucial for metazoan origins have a much earlier origin (emphasis added).

And the surprises just keep coming.

A news release (11/24/2005) issued by the journal Trends in Genetics announces that

Corals and sea anemones (the flowers of the sea), long regarded as merely simple sea-dwelling animals, turn out to be more genetically complex than first realised. They have just as many genes as most mammals, including humans, and many of the genes that were thought to have been "invented" in vertebrates are actually very old and are present in these "simple" animals.

The full text of the release is available at http://www.sars.no/resear ch/technau_Science.pdf

Newer (2007) sequencing and analysis results corroborate the anemone anomalies.

Another example comes from research at the European Molecular Biology Laboratory, which found human genes in a marine worm. The news release (11/24/2005) announcing the discovery is at http://www.embl.de/aboutus/communication_outreach/med ia_relations/2005/051124_heidelberg/index.html

Additional research has found that genes essential for human nerve cells to communicate with one another are present already in bacteria. This research is described in a NIH news release (6/1/2004) at http://www.nichd.nih...eases/genes.cfm

What is particularly striking about these findings, taken together—and what is particularly interesting to the star larvae hypothesis—is not only that they were unanticipated by the practitioners who engineered the current theory, but also that they make the evolutionary process look an awful lot like a developmental process, like a stage, or stages, in the life cycle of a developing organism.

The findings are paradoxical only for a theory that sees evolution as pure contingency. If evolution is recognized as the developmental unfolding of a life cycle, then the findings

• that much of its genome is unexpressed in any particular species,
• that phenotypic variation dwarfs genotypic variation (DNA is conserved),
• that genetic switches play key regulatory roles in phylogenetic descent and
• that ancestors carry genes needed in the future by remote descendants

are to be expected, because they are what we find when we study the differentiation of cells types in complex organisms.

To propose that evolution is programmed in a way similar to that in which the development of an organism is programmed is anathema to current evolution theory. The current theory has no room for teleology. But the new research findings point directly to such a conclusion. As happens in the history of science, scientists have to decide whether to stretch the normal paradigm to try to cover a growing collection of anomalous data or to construct a new paradigm based on the data.

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#### Popular Days

Something funny is afoot in the biological sciences. Labs peering into DNA are seeing things that nobody expected. And because the received view of evolution failed to predict these findings, and because it has little room to incorporate them, a crisis is brewing for the theory. Something more than selecting random variants is going on in evolution.

The data coming out of DNA sequencing and analysis suggest that the something more has to do with a preferred direction in evolution. Phylogenetic descent seems now to be a developmental unfolding. Several discoveries point to this conclusion:

1. Junk DNA. This is not a particularly new discovery. It's been known for some time that all species carry around a lot of junk, DNA that appears to lie dormant. What aspect of evolution theory predicts that long stretches of inactive DNA would coast along inside organisms, seemingly contributing nothing to their survivability? Nobody saw it coming. It was an empirical surprise.

But in the context of ontogeny, the development of organisms, it is exactly what is to be expected. Each cell in the body of a complex organism inherits the same genes from the ancestral zygote, the original fertilized ovum. Despite all possessing the same genes, brain, liver, kidney, and skin cells, for example, distinguish themselves phenotypically. Each cell type looks and acts differently from the others. But, because they all inherit the same genes, there must be a lot of junk DNA in each type of cell. Brain cells don't need genes that function uniquely in liver cells, nor do kidney cells need genes that function uniquely in skin cells. But all the cells inherit all those genes from their common ancestor, the zygote, whether they need them or not.

When it comes to cell types in a body, an invariant genetic inheritance necessarily is the case, with lots of junk in each cell as a result. Ontogeny demonstrates that diverse morphologies, or phenotypes, need not correspond to any proportionate diversity of genotype. "Adaptive radiation" of cell types in a body proceeds just fine without genetic variation.

Evolution appears to operate similarly.

Nope, not really a surprise for evolution. Or did we know just exactly what retroviruses and retrotransposons were doing before we knew of the junk DNA? The theory of evolution does not tell you what type of mutations happen, you need to look at the circumstances to find that out. Knowing what type of mutations happen in one organism plus the theory of evolution allows to predict similar effects in other junk organisms.

Junk DNA is however a surprise for any design theories. Some of that "junk DNA" really is junk, even if a lot of it isn't.

2. Conservation of DNA. Genetic material across species, though not invariant, turns out to be much less variable than observable differences among species would suggest. DNA is highly conserved across species. In their article, Regulating Evolution (Scientific American, May 2010) researchers Sean B. Carroll, Benjamin Prud'homme, and Nicolas Gompel comment,

For a long time, scientists certainly expected the anatomical differences among animals to be reflected in clear differences among the contents of their genomes. When we compare mammalian genomes such as those of the mouse, rat, dog, human and chimpanzee, however, we see that their respective gene catalogues are remarkably similar. [. . . .] When comparing mouse and human genomes, for example, biologists are able to indentify a mouse counterpart of at least 99 percent of all our genes.

The perplexed authors elaborate on the new findings:

. . . to our surprise, it has turned out that differences in appearance are deceiving: very different animals have very similar sets of genes.

The preservation of coding sequences over evolutionary time is especially puzzling when one considers the genes involved in body building and body patterning.

The discovery that body-building proteins are even more alike on average than other proteins was especially intriguing because of the paradox it seemed to pose: animals as different as a mouse and an elephant are shaped by a common set of very similar, functionally indistinguishable body-building proteins.

Surprise? Puzzling? Paradox? Why does evolution theory suffer so many bouts of the unexpected now that genomes are yielding their secrets? If the received theory of evolution were solid, wouldn't new genetic details have slots waiting for them in it? Shouldn't new genetic data bolster the theory, rather than generate surprises, puzzles and paradoxes for it to resolve?

Why didn't evolution theorists predict that phenotypic and genotypic differences across species would turn out to be so disproportionate, that so few genes would produce so many species? Nobody saw it coming. It was an empirical surprise.

Conservation of DNA is exactly what is predicted by evolution. You know, the whole "descent with modification" bit. But people just didn't believe it, they thought there would be more differences.

3. Genetic switches. The differentiation of cell types in a developing organism is managed by homeobox genes. These genes function as master "switches" that trigger the expression and repression of other genes. By selectively turning other genes on and off at various stages of development, homeobox genes effectively control the varieties of tissues that will populate a body. This oversight function partly answers the riddle of junk DNA. Some genes that can appear dormant actually code for proteins whose phenotypic activity is the modulation of other genes. The regulatory genes are not junk.

Now, due to the work of Carroll, Prud'homme, Gompel and others, it looks like evolution uses regulatory genes in the same way.

Instead of spinning off variant cell types, the cycling on and off of genetic switches in the context of evolution spins off variant species. This discovery, of the importance of genetic switches in evolution and its helping to account for the low level of genetic diversity across species, was an empirical surprise. Nobody saw it coming.

The explanatory power of this discovery has produced a new discipline within evolutionary biology, called evolutionary developmental biology, or evo-devo, a science that gives regulatory genes a starring role in evolution.

This is just the way life actually does work, but it could have turned out another way could it not?

4. Anticipatory genes. A new organism, a zygote, a fertilized egg carries many genes that ride along unexpressed—until they are needed by descendant cell types. The zygote anticipates, in its genetic catalog, the genes that remote descendant cells will need, even if those genes contribute nothing to the survival of the zygote itself or its immediate descendants. The zygote divides into two cells, and the two into four, and the four into eight, and so on. The cells that make up these early stages are said to be totipotent cells—they can bear descendants of any cell type. Later, after a degree of specialization, cells become pluripotent—they can give rise to several cell types, though not to all. And the specialization continues from there, with descendants inheriting from their ancestors the specialized genes they need, along with the rest of the genome.

This is to be expected in the context of a developing organism.

But it turns out that ancient species also carry genes that seem to anticipate the needs of descendants. A news article in Nature covering the sequencing of the genome of the Great Barrier Reef sponge Amphimedon queenslandica, reveals that the hoary creatures harbor a "tookit" of metazoan genes:

The genome also includes analogues of genes that, in organisms with a neuromuscular system, code for muscle tissue and neurons.

A curious finding. The article continues:

According to Douglas Erwin, a palaeobiologist at the Smithsonian Institution in Washington DC, such complexity indicates that sponges must have descended from a more advanced ancestor than previously suspected. "This flies in the face of what we think of early metazoan evolution," says Erwin.

Charles Marshall, director of the University of California Museum of Paleontology in Berkeley, agrees. "It means there was an elaborate machinery in place that already had some function," he says. "What I want to know now is what were all these genes doing prior to the advent of sponges.

The conundrum for normal evolution theory is clear. But, rather than propose that the genes needed by organisms with neuromuscular systems are in the sponge for the anticipatory purpose of providing those genes to descendants who will need them, the scientists invent an imaginary ancestor of the sponge that needed the genes. But the ghostly ancestor would have had to have arisen within a very narrow window. Fossil evidence of sponges goes back 650 million years; it constitutes, the authors note, "the oldest evidence for metazoans (multicellular animals) on Earth." So, what use would any species even more primitive than sponges have for the neuromuscular genes? Nobody saw it coming. It was an empirical surprise.

But the sponge genome is only one example. Research is finding case after case of ancestral species that harbor genes essential for remote descendants. Another example: It turns out that a species of unicellular protozoan carries genes essential for metabolic processes specific to metazoans. The researchers who discovered the surprise genes and published their data (PNAS – 2010 107 (22) 10142-10147) explain,

One of the most important cell adhesion mechanisms for metazoan development is integrin-mediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. [. . . .]
Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist
Amastigomonas
sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi.
[. . . .] Our data highlight the fact that many of the key genes that had formerly been cited as crucial for metazoan origins have a much earlier origin (emphasis added).

And the surprises just keep coming.

A news release (11/24/2005) issued by the journal Trends in Genetics announces that

Corals and sea anemones (the flowers of the sea), long regarded as merely simple sea-dwelling animals, turn out to be more genetically complex than first realised. They have just as many genes as most mammals, including humans, and many of the genes that were thought to have been "invented" in vertebrates are actually very old and are present in these "simple" animals.

The full text of the release is available at http://www.sars.no/resear ch/technau_Science.pdf

Newer (2007) sequencing and analysis results corroborate the anemone anomalies.

Another example comes from research at the European Molecular Biology Laboratory, which found human genes in a marine worm. The news release (11/24/2005) announcing the discovery is at http://www.embl.de/aboutus/communication_outreach/med ia_relations/2005/051124_heidelberg/index.html

Additional research has found that genes essential for human nerve cells to communicate with one another are present already in bacteria. This research is described in a NIH news release (6/1/2004) at http://www.nichd.nih...eases/genes.cfm

Again exactly what is predicted by the theory of evolution. New things don't just magically appear out of thin air; descent with modification requires the ancestors to have similar bits to the descendants. Does that make the genes "anticipatory"? No, the genes have to have a function in the organism in question. And the comparison to an embryo and adult is a false comparison, since the organism uses its genes none of those genes are anticipatory.

In short, you seem to have trouble understanding that theories and people predict different things. Would you also say that the above reflects badly on physicists and chemists, since physics and chemistry should be able to predict the details of an organisms functioning (since biology is just a subset of chemistry and chemistry just a subset of physics)? No, to be able to make predictions with a theory you sometimes need very specific information. The theory of evolution is not limited to the discovered earth life, it is a very broad theory and what can be predicted using it depends on the specific details of the life-forms in question. In particular, the mutation function depends on the details of the life in question, and the fitness function does likewise.

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Nope, not really a surprise for evolution.

Really? Who predicted it? Any DNA that is not expressed phenotypically cannot contribute to its own conservation and so would tend to be weeded out over the generations. Why is there so much junk in genomes?

Or did we know just exactly what retroviruses and retrotransposons were doing before we knew of the junk DNA? The theory of evolution does not tell you what type of mutations happen, you need to look at the circumstances to find that out. Knowing what type of mutations happen in one organism plus the theory of evolution allows to predict similar effects in other junk organisms.

I didn't say anything about what types of mutations will happen. Only that the predictive power of evolution theory stopped short of "Oh, by the way, now that you chaps are prying open DNA, we'll tell you what you'll find inside, because our theory tells us how genomes have come to contain whatever it is that they contain. By the way, you'll find gobs of DNA that is not expressed phenotypically." For a theory of genetic inheritance and genetic modification over time, evolution theory hardly stuck its neck out to predict what genetic sequencing and analysis would discover.

Junk DNA is however a surprise for any design theories. Some of that "junk DNA" really is junk, even if a lot of it isn't.

The only design theory I subscribe to is the normal scientific understanding of ontogeny, the unfolding of the adult "designed" into the zygote. I think evolution similarly is the unfolding of the life cycle of an organism. The findings coming out of genetic sequencing and analysis support that contention, because the findings correspond to what is found among the generations of cells in the body of a complex organism.

For the record, I am NOT a fundamentalist Creationist, ID advocate. I don't question that the fossils tell a story of common descent. But the rules governing the process of descent I do not believe are limited to those proposed by evolutionists.

Conservation of DNA is exactly what is predicted by evolution. You know, the whole "descent with modification" bit. But people just didn't believe it, they thought there would be more differences.

Why did they think there would be more differences? Why, in terms of evolution theory, should variation among genotypes not be proportionate to variation among phenotypes?

This is just the way life actually does work, but it could have turned out another way could it not?

I suppose it could have. But isn't it the job of science to say more than, "That's just the way it is" ?

Again exactly what is predicted by the theory of evolution. New things don't just magically appear out of thin air; descent with modification requires the ancestors to have similar bits to the descendants. Does that make the genes "anticipatory"? No, the genes have to have a function in the organism in question.

And what might be the function of neuromuscular genes in a creature more primitive than a sponge? -- for the reference, see my original post.

And the comparison to an embryo and adult is a false comparison, since the organism uses its genes none of those genes are anticipatory.

The comparison is between the descent of species on Earth and the descent of cell types in metazoan bodies. Ancestral cell types in a developing body (zygote, and the toti- and pluripotent types of the early embryo) carry unexpressed genes that are needed by descendant types (liver, kidney, etc). Ancestral species also carry unexpressed genes that are needed by descendants. The developmental program in both cases is built in. That's my contention.

In short, you seem to have trouble understanding that theories and people predict different things.

I don't think I have that problem, but even if so, I am content to let the data determine which contender has the better bead on what's going on.

Would you also say that the above reflects badly on physicists and chemists, since physics and chemistry should be able to predict the details of an organisms functioning (since biology is just a subset of chemistry and chemistry just a subset of physics)?

Physics and chemistry have done a fine job describing the workings of organisms in detail. But, yes, there are limits to those sciences' powers.

No, to be able to make predictions with a theory you sometimes need very specific information. The theory of evolution is not limited to the discovered earth life, it is a very broad theory and what can be predicted using it depends on the specific details of the life-forms in question. In particular, the mutation function depends on the details of the life in question, and the fitness function does likewise.

"mutation function" "fitness function" I find it amusing how Darwinians feel so free to invent new natural processes ex nihilo. It's like Hegelian metaphysics.

All you can possibly mean by "fitness function" is that whatever trait we find in an organism is that way because it was more adaptive than alternatives. Problem is, no one can define "trait", "adaptation" , "niche" , "organism" , or "gene." The vocabulary of evolution theory is mumbo-jumbo. See more on this problem at http://bit.ly/cQOdb2

BTW, I didn't mean to spam the biology forum when I posted originally. I was unaware of the speculation forum. Honest newbie error.

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Really? Who predicted it? Any DNA that is not expressed phenotypically cannot contribute to its own conservation and so would tend to be weeded out over the generations. Why is there so much junk in genomes?

A good question. Why though, should we presume to know it is junk? Even by your implied idea, this would not strictly be junk since it may instead be feed-stock for future teleological processes. As such, some sort of functional system must preserve the inventory, since random mutation and selection is known to weed it out useless systems since it requires more energy to preserve it and there is no reproductive advantage to inefficiency.

Modern biological experiments seem to confirm that non-functional systems are quickly eliminated, so it does seem clear that the traditional theory involving mutation and natural selection is a failure as an explanation for observed diversity, and by extension, these DNA sequences that don't have known function though are conserved.

I didn't say anything about what types of mutations will happen. Only that the predictive power of evolution theory stopped short of "Oh, by the way, now that you chaps are prying open DNA, we'll tell you what you'll find inside, because our theory tells us how genomes have come to contain whatever it is that they contain. By the way, you'll find gobs of DNA that is not expressed phenotypically." For a theory of genetic inheritance and genetic modification over time, evolution theory hardly stuck its neck out to predict what genetic sequencing and analysis would discover.

Indeed, hardly a scientific approach, and certainly nothing to be too impressed about.

The only design theory I subscribe to is the normal scientific understanding of ontogeny, the unfolding of the adult "designed" into the zygote. I think evolution similarly is the unfolding of the life cycle of an organism. The findings coming out of genetic sequencing and analysis support that contention, because the findings correspond to what is found among the generations of cells in the body of a complex organism.

No argument here.

For the record, I am NOT a fundamentalist Creationist, ID advocate. I don't question that the fossils tell a story of common descent. But the rules governing the process of descent I do not believe are limited to those proposed by evolutionists.

Yes those proposed by evolutionist are quite restrictive and without any clear scientific justification.

I suppose it could have. But isn't it the job of science to say more than, "That's just the way it is" ?

Absolutely it is.

And what might be the function of neuromuscular genes in a creature more primitive than a sponge? -- for the reference, see my original post.

I don't know of any. Odd that it would be preserved given construct of the modern synthesis. You seem to be on to something.

The comparison is between the descent of species on Earth and the descent of cell types in metazoan bodies. Ancestral cell types in a developing body (zygote, and the toti- and pluripotent types of the early embryo) carry unexpressed genes that are needed by descendant types (liver, kidney, etc). Ancestral species also carry unexpressed genes that are needed by descendants. The developmental program in both cases is built in. That's my contention.

There are examples that confirm this but there are many many examples that seem to go against it. Do we conclude that those examples where the development program is apparently not built in, where there are not unexpressed genes obviously present in ancestral forms are therefore not related?

I don't think I have that problem, but even if so, I am content to let the data determine which contender has the better bead on what's going on.

On the contrary, it seems you have a good grasp of the limitations of the current popular theory.

Physics and chemistry have done a fine job describing the workings of organisms in detail. But, yes, there are limits to those sciences' powers.

Indeed there are.

"mutation function" "fitness function" I find it amusing how Darwinians feel so free to invent new natural processes ex nihilo. It's like Hegelian metaphysics.

It is metaphysics.

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Don't have much time but there are a number of factual errors in the OP:

But in the context of ontogeny, the development of organisms, it is exactly what is to be expected. Each cell in the body of a complex organism inherits the same genes from the ancestral zygote, the original fertilized ovum. Despite all possessing the same genes, brain, liver, kidney, and skin cells, for example, distinguish themselves phenotypically. Each cell type looks and acts differently from the others. But, because they all inherit the same genes, there must be a lot of junk DNA in each type of cell. Brain cells don't need genes that function uniquely in liver cells, nor do kidney cells need genes that function uniquely in skin cells. But all the cells inherit all those genes from their common ancestor, the zygote, whether they need them or not.

This is not what junk DNA is. Essentially they refer to non-coding regions (though with the discovery of sRNA this has to be expanded somewhat). Genes that are silent (in a given tissue) are not junk DNA.

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Don't have much time but there are a number of factual errors in the OP:

This is not what junk DNA is. Essentially they refer to non-coding regions (though with the discovery of sRNA this has to be expanded somewhat). Genes that are silent (in a given tissue) are not junk DNA.

Perhaps the error is yours. You seem to have misread the context of the OP's illustration. the first paragraph referred to what is traditionaly called "junk DNA" the second paragraph described silent genes in particular cells. The third paragraph suggested that one possibility is that "Junk DNA" may be in a sense similar to silent genes in that this junk is actively conserved feed-stock for future needs. I welcome the OP's elaboration if I have this wrong.

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Junk DNA doesn't disprove anything about natural selection. If the DNA isn't hurting an organism there is no reason to assume that it will be weeded out. If the DNA seemingly doesn't code for anything anymore what is the reasoning behind that it would be weeded out. The idea of natural selection is that those who are most fit to survive will and those who are not won't. It's says nothing about how conservative the species must be.

The second point shows only our inexperience involving genetic sequences, not that evolutionary theories are wrong. Genetics does give support for evolution and just because some things shock us doesn't mean that evolution is wrong; it just shows that our knowledge is lacking.

The whole idea of genes anticipating anything is very wrong. Genes don't have an idea what's going on in the world nor do they know what will happen. Just because findings in certain animals are surprising doesn't mean that an entire theory is wrong, just some of our ideas concerning how animals may have developed along a timescale may have been wrong. A friend told me that Einstein's theory didn't predict black hole singularities, I'm not a physicist so I don't know if that's right, but just because there are singularities doesn't mean that relativity doesn't work.

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Really? Who predicted it? Any DNA that is not expressed phenotypically cannot contribute to its own conservation and so would tend to be weeded out over the generations. Why is there so much junk in genomes?

Natural selection isn't perfect. For example, the equation

$P(q) = \frac{1 - e^{-2N_esq}}{1 - e^{-2N_es}}$, where q is the initial frequency of the allele, Ne is the effective population size, and s is the selective advantage. This gives a probability for losing an allele, and note that a slight selective advantage is not even close to a guarantee that it won't be lost. See here for more details.

The result is that beneficial mutations could be lost and for many organisms reduced DNA is not really particularly crucial to their success. For bacteria that are tiny and reproduce quickly having extra DNA is much more of a hindrance than for eukaryotes that are much larger (so dedicate much less proportion of their mass to DNA) and reproduce slower (so that DNA doesn't have to constantly be replicating). Also, in some cases junk DNA serves a different role, as structural/spacing element. I think I've heard something about it being protective from certain types of viruses too, such that if the virus is inserted in the inert region of the DNA it isn't read, which forces the viruses to either be more selective about where to insert themselves, or to include the necessary bits for their genes to be expressed.

But the rules governing the process of descent I do not believe are limited to those proposed by evolutionists.

Well then provide evidence for your new process, either by direct observation or by correct predictions that can't be made with the currently accepted processes.

This is just the way life actually does work, but it could have turned out another way could it not?

I suppose it could have. But isn't it the job of science to say more than, "That's just the way it is" ?

And there is your problem. Evolution as a generic theory tells you what can happen, not what did, no more than any amount of knowledge of chemistry can tell you what your product was/will be unless you tell it the reagents and reaction conditions. Evolution is not some magical theory that needs no data, it needs data like any other theory to make specific predictions. Add in the specifics of mutation and fitness and then see if it still can't give you the answers.

Ancestral species also carry unexpressed genes that are needed by descendants.

Well that would be interesting. Can you give an example? Depending on the circumstances that is allowable by evolution, for example a gene could lose its ability to be expressed and later regain it, or junk DNA might be expressed and serve some function. But for that to happen frequently would require rethinking the theory.

Physics and chemistry have done a fine job describing the workings of organisms in detail. But, yes, there are limits to those sciences' powers.

Well then why didn't they tell the biologists about all the junk DNA and the other bits you complained about them not knowing? The fact is that those theories predict nothing unless you give them a circumstance. If I say, I have some gas, now tell me the temperature pressure and volume of it, the chemists would give me the finger. But if I tell them any three of the four they can tell me the fourth. Evolution is similar, it can't predict things from no data. Give it the necessary data and it gives the appropriate predictions.

"mutation function" "fitness function" I find it amusing how Darwinians feel so free to invent new natural processes ex nihilo. It's like Hegelian metaphysics.

All you can possibly mean by "fitness function" is that whatever trait we find in an organism is that way because it was more adaptive than alternatives. Problem is, no one can define "trait", "adaptation" , "niche" , "organism" , or "gene." The vocabulary of evolution theory is mumbo-jumbo. See more on this problem at http://bit.ly/cQOdb2

No, it is a measure of their reproductive success, measurable numerically unlike all the mumbo-jumbo you are suggesting. You can take two organisms identical in every respect except for one allele, put them in the same environment, and measure which is more successful. That gives you the comparative fitness of the two alleles in the context of the organisms other alleles and environment. You can change other variables too, if you like, and measure those effects. Conversely, mumbo-jumbo isn't measurable.

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Really? Who predicted it? Any DNA that is not expressed phenotypically cannot contribute to its own conservation and so would tend to be weeded out over the generations. Why is there so much junk in genomes?

Think of it like this:

IF you are with a group of people, how fast do you have to run to avoid being caught by a Lion?

You only have to run faster than the slowest in the group. You do not have to run faster than the Lion.

Yes, Junk, DNA has a slight disadvantae in that it consumes resources (DNA monomers), but these are failry pelntiful, in our food, and many organisms can make them themselves, so it is not a big problem. So, if the disadvantage from the Junk DNA is small enough that it doesn't overly effect an organims reproductive sucess, then it won't be selected out all that quickly.

However there is some advantage in having junk DNA.

First it can act as a buffer between coding regions. This way the physical and chemical processes that go on during the reading of DNA does not have as great an effect on other coding parts.

Secondly, as DNA is extremely twisted up to fit it into your cells (it is aproximately 2 metres in lengh, in each cell! ), so this junk DNA can be where DNA is able to twist up to allow access to the coding sections.

Thirdly, it act as a buffer against damage. If DNA is going to be damaged by a virus, or something else, then having sections that are non coding will mean that random damage has places to occur without it effecting any of the necesary places.

Finally, ther are likely many more reasons that Junk DNA could be conserved, we don't know all of them yet (but a long way).

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Perhaps the error is yours. You seem to have misread the context of the OP's illustration. the first paragraph referred to what is traditionaly called "junk DNA" the second paragraph described silent genes in particular cells. The third paragraph suggested that one possibility is that "Junk DNA" may be in a sense similar to silent genes in that this junk is actively conserved feed-stock for future needs. I welcome the OP's elaboration if I have this wrong.

Not as the OP describes it. Here:

Each cell type looks and acts differently from the others. But, because they all inherit the same genes, there must be a lot of junk DNA in each type of cell. Brain cells don't need genes that function uniquely in liver cells, nor do kidney cells need genes that function uniquely in skin cells.

Junk DNA is clearly referred to genes that have no function in a specific cell type (as opposed to another). Also note, while there are genes that are not expressed anymore in certain tissues, they may have very well been active during differentiation.

Also this is not quite accurate

What aspect of evolution theory predicts that long stretches of inactive DNA would coast along inside organisms, seemingly contributing nothing to their survivability? Nobody saw it coming. It was an empirical surprise.
.

It would only be surprising if the additional DNA came at a cost with no benefit. This appears to be somewhat true in e.g. prokaryotic and, even more pronounced, in viral genomes, where DNA size places a considerable cost on the organism. However, in eurkayotes genome size is much less limiting. So even in absence of benefits an increase would be considered neutral or near-neutral. Viral resilience have been put forth relatively early to explain an expansion of genome sizes in eukaryotes and, as mentioned, quite a bit of the junk DNA can actually be assigned to regulatory or structural functions. Once the cost restraint of DNA was lifted in higher eukaryotes expansion of genome size could lead to benefits that overcome the (in eukaryotes) relatively low additional cost for DNA synthesis.

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A good question. Why though, should we presume to know it is junk? Even by your implied idea, this would not strictly be junk since it may instead be feed-stock for future teleological processes.

I'm saying that "junk" is just that, the programmed evolutionary future, waiting to unfold.

This is not what junk DNA is. Essentially they refer to non-coding regions (though with the discovery of sRNA this has to be expanded somewhat). Genes that are silent (in a given tissue) are not junk DNA.

Call it what you like. Genes unexpressed, or non-coding, in the zygote are triggered into expression during the development of descendant cell types in metazoan bodies. The descendant cell types retain non-coding regions (i.e., those genes needed for other cell types -- e.g., some genes expressed in nerve cells are non-coding in skin cells. All cells in a body inherit the same genome, but different genes are active in different kinds of cells.)

And genes unexpressed, or non-coding, in ancestral species are triggered into expression during the evolution of descendant species. I provide several examples under heading 4 in the original post.

Junk DNA doesn't disprove anything about natural selection. If the DNA isn't hurting an organism there is no reason to assume that it will be weeded out. If the DNA seemingly doesn't code for anything anymore what is the reasoning behind that it would be weeded out. The idea of natural selection is that those who are most fit to survive will and those who are not won't. It's says nothing about how conservative the species must be.

Criticizing evolution theory for being tautological is, I think, still a legitimate avenue of criticism: Who survives? Those most fit, of course. Which are most fit? Those that survive, of course. It's a circular argument, like Plato's Euthyphro: What is good? That which pleases the gods. And what pleases the gods? That which is good.

The second point shows only our inexperience involving genetic sequences, not that evolutionary theories are wrong.

No, it shows that our EXPERIENCE involving genetic sequences now raises unsettling questions for the theory.

Genetics does give support for evolution and just because some things shock us doesn't mean that evolution is wrong; it just shows that our knowledge is lacking.

Sorry, but that's lame. My theory is about the knowledge we're gaining, not what's lacking. If we lack knowledge about how to shoehorn new empirical data into an old theory, maybe it's because the new data don't fit into the old theory.

The whole idea of genes anticipating anything is very wrong. Genes don't have an idea what's going on in the world nor do they know what will happen.

You're overgeneralizing. When you were a zygote, you possessed genes needed for muscle, nerve, kidney, etc. cells. Your genome anticipated the needs of descendant cell types.

Just because findings in certain animals are surprising doesn't mean that an entire theory is wrong, just some of our ideas concerning how animals may have developed along a timescale may have been wrong. A friend told me that Einstein's theory didn't predict black hole singularities, I'm not a physicist so I don't know if that's right, but just because there are singularities doesn't mean that relativity doesn't work.

I'm not a physicist either, but if the theory failed to predict something that it should have predicted, then the unpredicted finding must have forced a modification of the theory. Isn't that how science works? I think the unpredicted findings coming out of genetic sequencing and analysis call for a modification of evolution theory.

Natural selection isn't perfect. For example, the equation

$P(q) = \frac{1 - e^{-2N_esq}}{1 - e^{-2N_es}}$, where q is the initial frequency of the allele, Ne is the effective population size, and s is the selective advantage. This gives a probability for losing an allele, and note that a slight selective advantage is not even close to a guarantee that it won't be lost. See here for more details.

I'm not familiar with this formula. In what units is "s", the selective advantage, measured?

Well then provide evidence for your new process, either by direct observation or by correct predictions that can't be made with the currently accepted processes.

I'm not proposing a new process. I'm just proposing expanding the applicability of the familiar, observable process called ontogeny.

Well that would be interesting. Can you give an example? Depending on the circumstances that is allowable by evolution, for example a gene could lose its ability to be expressed and later regain it, or junk DNA might be expressed and serve some function. But for that to happen frequently would require rethinking the theory.

Under 4. Anticipatory genes. in the original post I provide several examples of anticipatory genes in ancestral species.

Well then why didn't they tell the biologists about all the junk DNA and the other bits you complained about them not knowing? The fact is that those theories predict nothing unless you give them a circumstance. If I say, I have some gas, now tell me the temperature pressure and volume of it, the chemists would give me the finger. But if I tell them any three of the four they can tell me the fourth. Evolution is similar, it can't predict things from no data. Give it the necessary data and it gives the appropriate predictions.

What data would you need to have about a sponge to predict that its genome would contain genes needed for neuromuscular metabolism, something far in the evolutionary future from the point of view of the sponge?

No, it is a measure of their reproductive success, measurable numerically unlike all the mumbo-jumbo you are suggesting. You can take two organisms identical in every respect except for one allele, put them in the same environment, and measure which is more successful. That gives you the comparative fitness of the two alleles in the context of the organisms other alleles and environment. You can change other variables too, if you like, and measure those effects. Conversely, mumbo-jumbo isn't measurable.

Well that's a fine thought experiment, but evolution theory is supposed to be about the real world. The situation you describe would never occur in the real world. If in your example one of the subjects got hit by lightning, it would tell us little about any supposed disadvantage due to alleles.

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Indeed, hardly a scientific approach, and certainly nothing to be too impressed about.

No argument here.

Yes those proposed by evolutionist are quite restrictive and without any clear scientific justification.

Absolutely it is.

I don't know of any. Odd that it would be preserved given construct of the modern synthesis. You seem to be on to something.

There are examples that confirm this but there are many many examples that seem to go against it. Do we conclude that those examples where the development program is apparently not built in, where there are not unexpressed genes obviously present in ancestral forms are therefore not related?

On the contrary, it seems you have a good grasp of the limitations of the current popular theory.

Indeed there are.

It is metaphysics.

!

Moderator Note

cypress, the topic of this thread is spelled out in the original post: a preferred direction to evolution. It is not an invitation for bashing of science/evolution (and unsubstantiated bashing at that). Please stay on topic.

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I'm saying that "junk" is just that, the programmed evolutionary future, waiting to unfold.

How would one test this hypothesis?

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I'm not familiar with this formula. In what units is "s", the selective advantage, measured?

It's all unitless. Would be a strange exponent if it wasn't.

I'm not proposing a new process. I'm just proposing expanding the applicability of the familiar, observable process called ontogeny.

Under 4. Anticipatory genes. in the original post I provide several examples of anticipatory genes in ancestral species.

None of those links have an example of what you said.

Ancestral species also carry unexpressed genes that are needed by descendants.

Which one of those genes is unexpressed in the ancestral organism?

What data would you need to have about a sponge to predict that its genome would contain genes needed for neuromuscular metabolism, something far in the evolutionary future from the point of view of the sponge?

You'd need an awful lot of data, perhaps all the possible ways to make neuromuscular structures, then comparison of that to all the sponge proteins, and then data on the usefulness of intermediates along the way. It would be pretty much impossible, kind of like predicting whether it's going to rain on Jan 1, 3010, but most people don't take that to mean that physics fails, even though in theory a physicist should be able to make that prediction with enough data.

However, it is essentially a necessity that the ancestral organisms carried genes used by their descendants, new function or no, since the odds of entirely new genes appearing are rather slim.

Well that's a fine thought experiment, but evolution theory is supposed to be about the real world. The situation you describe would never occur in the real world. If in your example one of the subjects got hit by lightning, it would tell us little about any supposed disadvantage due to alleles.

No, it would be a horrible thought experiment. That's how a researcher in a lab would measure fitness. Calling it a thought experiment just shows you completely failed to understand it, since as a thought experiment that would be worthless. Evolution doesn't need to measure fitness, and as the equation I gave shows, fitness is not the only thing that wipes out genes.

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Regarding non-expressed genes. This is what physiologically is expected from about every cell. Not even in prokaryotes can anyone expect to see every gene to be active. They are regulated by internal or external stimuli.

The basic premises in the OP are simply wrong.

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The basic premises in the OP are simply wrong.

At least it is thought provocative.

IMHO there is a way of thinking at least which is not entirely wrong.

I mean as I understand Evolution (I may be wrong here) we use to look at plants & animals as a sum of individuals, trying to explain that a change that occurs randomly into an individual will be transmitted to the specie. Maybe instead we have to look at Evolution as something wider that happens to the whole community, and stop considering plants & animals as individuals.

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Maybe instead we have to look at Evolution as something wider that happens to the whole community, and stop considering plants & animals as individuals.

My perception is that we do so. There are researchers who look at the behaviour and evolution of individual genes, who would doubtless subscribe to Dawkins Selfish Gene concept. There are others who explore the behaviour of the biosphere as an evolving entity and wuld view Lovelock's Gaia as more than a metaphor. And there is every shade in between. This is as it should be.

Meanwhile, the possibility that we might discover any teleological component to evolution is pushed into the background by the weak arguments of cypress and starlarvae.

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Actually evolution does not consider individuals per se (selfish genes are mostly interesting in terms of specific mechanisms), but always focuses on the population. The key is allele frequency. They are, by definition a description of the state of the population. There is no individual resolution. From that standpoint individual changes are almost always relatively inconsequential, with few exception. This may include extremely low population sizes, or enormous selective pressures, which would rapidly increase the frequency of the involved allele(s).

Actually, certain teleological elements in the broadest sense are somewhat possible. For instance, loss of certain functions may lock the future direction of a species (if the re-occurence of the mechanism by whatever means is highly unlikely), especially assuming an otherwise constant environment. Under these conditions (and probably some more that I did not think of right now, like e.g. the proportion of fixed alleles in the gene pool and whatnot), the possible directions of evolution may be limited to such a point that a certain endpoint appears inevitable.

Though I probably would not call it teleology in the classical concept (i.e. final cause) as it is more the consequence of certain mechanisms (or lack thereof). It would be a bit akin to invoke teleology to explain gravity, for instance.

Edited by CharonY
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How would one test this hypothesis?

How would one test the hypothesis that the descent of cell types in a developing organism proceeds according to a program?

However there is some advantage in having junk DNA.

First it can act as a buffer between coding regions. This way the physical and chemical processes that go on during the reading of DNA does not have as great an effect on other coding parts.

Secondly, as DNA is extremely twisted up to fit it into your cells (it is aproximately 2 metres in lengh, in each cell! ), so this junk DNA can be where DNA is able to twist up to allow access to the coding sections.

Thirdly, it act as a buffer against damage. If DNA is going to be damaged by a virus, or something else, then having sections that are non coding will mean that random damage has places to occur without it effecting any of the necesary places.

Finally, ther are likely many more reasons that Junk DNA could be conserved, we don't know all of them yet (but a long way).

I'm just proposing that DNA is conserved across species for the same reason that it's conserved across cell types in a complex organism.

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Knockdowns are very useful.

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I'm just proposing that DNA is conserved across species for the same reason that it's conserved across cell types in a complex organism.

Because it helps the organism in question survive and reproduce?

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Criticizing evolution theory for being tautological is, I think, still a legitimate avenue of criticism: Who survives? Those most fit, of course. Which are most fit? Those that survive, of course. It's a circular argument, like Plato's Euthyphro: What is good? That which pleases the gods. And what pleases the gods? That which is good.

No, those who survive, reproduce, and have their offspring reproduce. Mere survival isn't enough to cause an evolutionary change. Cherry picking a single statement and saying that is the whole of evolutionary argument is fallacy.

No, it shows that our EXPERIENCE involving genetic sequences now raises unsettling questions for the theory.

What questions?

.

Sorry, but that's lame. My theory is about the knowledge we're gaining, not what's lacking. If we lack knowledge about how to shoehorn new empirical data into an old theory, maybe it's because the new data don't fit into the old theory.

Still, accepting that we can't know entirely is part of science, I still don't see what doesn't 'fit' current evolutionary theory that is better explained in your theory.

You're overgeneralizing. When you were a zygote, you possessed genes needed for muscle, nerve, kidney, etc. cells. Your genome anticipated the needs of descendant cell types.

Which is already explained by a current theory without the belief in genetic precognition.

I'm not a physicist either, but if the theory failed to predict something that it should have predicted, then the unpredicted finding must have forced a modification of the theory. Isn't that how science works? I think the unpredicted findings coming out of genetic sequencing and analysis call for a modification of evolution theory.

And there have been many modification natural selection, hence the term neo-Darwinian that gets tossed around a lot. Parts of descent with modification didn't fit evidence of the time of Darwin, he became more Lamarckian. Then in the 1900's Mendel's pea experiments were 'rediscovered' and the use of allele frequency could better explain the change in animals that could genetic mixing; the theory was adapted. Theories change and evolution is not different. Assuming that evolutionary theory has never changed is ignorant as is the assumption that scientists refuse to believe anything in evolutionary theory could be wrong.

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Regarding non-expressed genes. This is what physiologically is expected from about every cell. Not even in prokaryotes can anyone expect to see every gene to be active. They are regulated by internal or external stimuli.

The basic premises in the OP are simply wrong.

That's easy to say in hindsight. But I suspect that if someone asserted the presence of significant amounts of noncoding DNA BEFORE it was discovered, the mainstream evolutionists would have dismissed the idea. "Why would there be noncoding DNA? It would just get in the way. And besides, where would it come from? "

IF it is "what physiologically is expected" why did no one expect it? If you have a reference to someone predicting the discovery of large amounts of noncoding DNA, I'd like to see it.

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The idea of the necessity of noncoding DNA was proposed as early as 1972, long before the human genome project or genome sequencing in general:

http://www.junkdna.com/ohno.html

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Because it helps the organism in question survive and reproduce?

"Conserved" just means that relatively little variation across genotypes corresponds to relatively large variation across phenotypes -- whether you're looking at cell types in a body or species.

DNA is conserved across cell types because all the cells inherit the same genome, which has to include genes for (genes that anticipate the needs of) each descendant cell type.

The (unexpected) conservation of DNA across phenotypically diverse species suggests that evolution works under similar constraints.

The idea of the necessity of noncoding DNA was proposed as early as 1972, long before the human genome project or genome sequencing in general:

http://www.junkdna.com/ohno.html

Ohno "predicted" it AFTER it was clear that genome size was not related to the complexity of the organism. I don't think that he, or anyone else, predicted that some amphibians, for example, would turn out to have genomes 30+ times the size of the human genome. That was another surprise with no basis in Darwinian principles.

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No, those who survive, reproduce, and have their offspring reproduce. Mere survival isn't enough to cause an evolutionary change. Cherry picking a single statement and saying that is the whole of evolutionary argument is fallacy.

But Ringer, you said "The idea of natural selection is that those who are most fit to survive will and those who are not won't." I thought you meant what you said.

Anyway, at least now you're getting away from the "fitness" nonsense. All we know is that the survivors survive. Calling the survivors "most fit" is just giving them another name.

What questions?

Why is it that evolution looks so much like a developmental process? Why is it

• that much of its genome is unexpressed in any particular species,
• that phenotypic variation dwarfs genotypic variation (DNA is conserved),
• that genetic switches play key regulatory roles in phylogenetic descent and
• that ancestors carry genes needed in the future by remote descendants ?

We know why these things hold in ontogeny, but why in evolution, which ostensibly is not programmed but wholly contingent?

Which is already explained by a current theory without the belief in genetic precognition.

I hope you don't think that by "anticipate" I mean that DNA has cognitive abilities. I just mean that genes needed by distant descendants are present already in ancestral genomes.

And there have been many modification natural selection, hence the term neo-Darwinian that gets tossed around a lot. Parts of descent with modification didn't fit evidence of the time of Darwin, he became more Lamarckian. Then in the 1900's Mendel's pea experiments were 'rediscovered' and the use of allele frequency could better explain the change in animals that could genetic mixing; the theory was adapted. Theories change and evolution is not different. Assuming that evolutionary theory has never changed is ignorant as is the assumption that scientists refuse to believe anything in evolutionary theory could be wrong.

Right. I know that the theory itself has evolved. All I'm humbly proposing is yet another modification.

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