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Evolution is driven by junk?

Smidlee

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A new and improve ToE called "Genetic Drive" hypothesis.
http://www.murdoch.edu.au/News/Shaking-up-the-theory-of-evolution/http://

Murdoch University scientists have developed an improved theory of evolution – a groundbreaking hypothesis which finally reconciles evolutionary theory with the fossil record.
Yeah, since it is easier for man put to a camel through a eye of the needle than to make the fossil record to fit the ToE.
Without this DNA junk, a species is effectively frozen and faces eventual extinction.
Boy, you gotta love "junk" science. Of course this statement about extinction is true except when it not. For example
The coelacanth, which had been found off the coast of South Africa and Indonesia, had inactive or low levels of TEs and had been in stasis for 400 million years.
and
Like the coelacanth, the tuatara was characterised by very few jumping genes and has been unchanged for 220 million years.
yet they are somehow still around without all the extra junk. Evolution covers everything; both A and not-A equals evidence of evolution.
While jumping gene activity in the 235 species of primates had quietened down a lot since its peak about 40 million years ago, the high presence of identical TEs in the primate genome pointed to an improved ability to diversify, adapt and survive.
Of course evolution seems to be a lot quieter these days and had a lot more power back in the good old days.
This new hypothesis does make a little sense . As the more junk a junkyard has the more likely a tornado can build a new car.
He said some species - such as bats which “came out of nowhere” in the Eocene Period – suddenly appeared in the fossil record.
It's almost sounds like magic or..... maybe the c-word.
 
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crawfish

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Here, I fixed your link: Latest news | Murdoch University in Perth Australia

Goodness knows, let's stop the process of developing hypotheses and refining theory. After all, if we don't completely understand something from the start, then we're obviously on the wrong track.

Even in an incomplete state, the ToE has enough fact to completely discredit YEC science.
 
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Dark_Lite

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It's almost sounds like magic or..... maybe the c-word.

It's kind of funny you quote that, but conveniently forget the part right above it. Allow me to quote in context:

The Article said:
An explanation for many unanswered questions
Dr Greene said Genomic Drive theory provided an explanation for many unanswered questions such as why species suddenly appeared in the fossil record, why some groups of organisms were species rich and others species poor and why some species changed little over millions of years.

Successive waves of TE activity in a lineage potentially explained alternations of rapid evolution and stasis.

He said some species - such as bats which “came out of nowhere” in the Eocene Period – suddenly appeared in the fossil record.

This was in keeping with evidence that TE or jumping gene activity occurred in sudden episodic bursts.

So in reality, this is actually providing an answer for your magic.
 
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shernren

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I hate university-sponsored flattery. Quite frankly, we researchers come up with "new theories" every other day. It's what we're paid to do. Don't butter them up with words like "exciting", "groundbreaking", or "biggest advances", because they often aren't anything of the sort.
 
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The Barbarian

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The coelacanth, which had been found off the coast of South Africa and Indonesia, had inactive or low levels of TEs and had been in stasis for 400 million years.

That is, if you don't count greatly increasing in size, changing from a small freshwater fish to large deepwater fish comprising two new species.

I'm not sure that counts as "stasis."




 
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Smidlee

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The coelacanth, which had been found off the coast of South Africa and Indonesia, had inactive or low levels of TEs and had been in stasis for 400 million years.

That is, if you don't count greatly increasing in size, changing from a small freshwater fish to large deepwater fish comprising two new species.

I'm not sure that counts as "stasis."




We know that dogs comes in many shapes and sizes.
 
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Smidlee

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Here, I fixed your link: Latest news | Murdoch University in Perth Australia

Goodness knows, let's stop the process of developing hypotheses and refining theory. After all, if we don't completely understand something from the start, then we're obviously on the wrong track.

Even in an incomplete state, the ToE has enough fact to completely discredit YEC science.
When a theory has to change so much and the more fact has to be forced to fit the theory (like trying to force a 300 lb. woman in a size 4 dress) the more the theory needs to be questioned.
 
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crawfish

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When a theory has to change so much and the more fact has to be forced to fit the theory (like trying to force a 300 lb. woman in a size 4 dress) the more the theory needs to be questioned.

That is exactly why I rejected YEC "science" long ago.
 
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lucaspa

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A new and improve ToE called "Genetic Drive" hypothesis.
http://www.murdoch.edu.au/News/Shaking-up-the-theory-of-evolution/http://

Yeah, since it is easier for man put to a camel through a eye of the needle than to make the fossil record to fit the ToE.

First, Smidlee, notice that these scientists are trying to overthrow ideas about evolution. That's how scientists gain fame: challenging a theory. But also notice that they are not saying they overthrow evolution. Why not? Because they can't.

As it happens, these particular scientists are fighting against a strawman of evolution:
"Dr Greene, a Senior Lecturer in Molecular Genetics, said current evolutionary theory, which assumed biological lineages evolved by the slow accumulation of adaptive mutations, did not tally with the fossil record."

Phyletic gradualism (which is what this is) in large populations has been recognized since the 1940s to be only a minor mode of evolution. Instead, biological lineages evolve by allopatric and sympatric speciation. This leads to punctuated equilibrium. However, as every paleontologist knows, there are examples from the fossil record where we can see the accumulation of adaptive mutations.

What they are arguing for are large leaps across the genetic landscape by transposable elements. However, you can make large leaps across the phenotypic landscape without these. For instance, a change in a single base in the gene Ubx converts a multilegged body plan (centipede) to just 6 legs: Page not found : Nature Publishing Group

Of course evolution seems to be a lot quieter these days and had a lot more power back in the good old days.

Oh no. If you do a PubMed search with the search term "evolution" and do a search 3 months back, then 6 months, then a year, then 5 years, then 10 years, you will see that the rate of publications on evolution is increasing. What's more, the principles of natural selection are being applied to a much wider set of problems than ever before.

This new hypothesis does make a little sense . As the more junk a junkyard has the more likely a tornado can build a new car.

This is where you have been tripped up by the whimsy of scientists in assigning names. Scientists originally looked at genes -- those stretches of DNA that coded for proteins. Then they looked at the stretches of DNA before the genes that were involved with controlling when the genes were turned on or turned off. Transcription control, it is called.

But there was a lot of DNA that was neither in genes or the areas of transcription control. On whimsy, some scientists called this "junk" DNA. Initially, they thought that the "junk" DNA had no function. As it turns out, of course, much of that DNA has functionality. Much of it makes small RNAs, which have control functions in a cell's metabolism. Other parts are necessary for proper folding and unfolding of DNA. Some is involved in what are called "splice variants" or different forms of proteins by including or excluding different exons.

What you have done is take that name "junk DNA" out of context to make an inaccurate rhetorical argument. The question is whether you knowingly or accidentally committed false witness.

The hypothesis generated by Oliver and Greene looks, to me, like a lot of hype. Notice that they published in BioEssays, which is a journal specifically to air hypotheses and, particularly, hypotheses without much evidence.

For instance, I find this statement "Species without junk DNA risked extinction. Dr Greene said species that were devoid of TEs were more at risk of extinction because they simply lacked the capacity to adapt, change and diversify. " highly questionable.

Bacteria and archaea have only a little "junk" DNA, but they count for over 90% of living organisms and about 90% of all species.

"The coelacanth, which had been found off the coast of South Africa and Indonesia, had inactive or low levels of TEs and had been in stasis for 400 million years. " is also questionable. Greene apparently has never heard of stabilizing selection. He appears knowledgable about transposons, but not very knowledgable about evolution.

All in all, before you start to crow, I suggest you wait a couple of years and see how well this hypothesis stands up to testing.

BTW, even if the hypothesis is valid, it is not going to be "creation" as you use the word. It is simply going to be a material method for making many large scale changes to a genome as opposed to many small scale changes and very rare large scale changes.
 
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lucaspa

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We know that dogs comes in many shapes and sizes.

Yes. And the genetic shows us that dogs are now at least 4 species, not one. The language has not yet caught up with the biological reality.

BTW, is your avatar really a sinking ship as the result of hostile action? If so, how appropriate for a creationism supporter.
 
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troodon

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Genetics isn't my thing, but this hypothesis and their example don't make sense to me. If the coelacanth has low levels of these transposable elements, doesn't it stand to reason that the most recent Sarcopterygian ancestor to all Tetrapods also had relatively few transposable elements? And yet its descendants were able to rapidly adapt to a terrestrial environment, something their hypothesis says shouldn't happen.

Granted, the modern coelacanth has had hundreds of millions of years to mutate its genome and (I suppose) add non-coding junk to its DNA, which would decrease its relative proportion of TEs... but if that's the case, then high TE levels are an effect of being evolutionary static, not a cause.
 
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lucaspa

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lucaspa

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Genetics isn't my thing, but this hypothesis and their example don't make sense to me. If the coelacanth has low levels of these transposable elements, doesn't it stand to reason that the most recent Sarcopterygian ancestor to all Tetrapods also had relatively few transposable elements? And yet its ancestors were able to rapidly adapt to a terrestrial environment, something their hypothesis says shouldn't happen.

Good catch. Yes, if coelacanths were the direct ancestor. However, in their defense modern coelacanths are not the direct ancestor. They are an offshoot within the same family that was the direct ancestor.

So Greene would say that the species (possibly the genus) that is the direct ancestor did have transposable elements but that the genera that are coelacanths either did not have them or lost them (see below).

Granted, the modern coelacanth has had hundreds of millions of years to mutate its genome and (I suppose) add non-coding junk to its DNA, which would decrease its relative proportion of TEs... but if that's the case, then high TE levels are an effect of being evolutionary static, not a cause.

Another good catch. Yes, low TE levels (which Greene says would cause stasis) would be an effect of stasis, not a cause.

There are several problems with Greene's hypothesis. One is that Greene apparently feels that TEs are the only way to increased DNA. However, this paper shows that gene duplication (which does not require TEs as far as I know), is part of evolution:
Coelacanth genome sequence reveals the evolutionary history of vertebrate genes — Genome Research

This PNAS paper indicates that humans and coelacanths share at least one transposon! A family of conserved noncoding elements derived from an ancient transposable element — PNAS

"Recently, Bejerano et al. (11) reported a clear case of a CNE family derived from instances of an ancient transposable element. This CNE family (referred to as LF-SINE) has ≈245 copies in the human genome that are derived from an ancient SINE element. Interestingly, this SINE element (LF-SINE) appears to have been active recently in the genome of the coelacanth fish, implying that the transposon family has remained active for >400 million years."

I wonder how much data Greene's BioEssay paper really had.
 
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LightHorseman

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shernren

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The hypothesis of junk DNA being useful is actually nothing new. In fact, the very first time the term "junk DNA" was coined was in the context of some work by Susumu Ohno in the 1980's, a guy with many colorful genetic theories. The idea of his paper was that "junk DNA" couldn't possibly be purposeless (or else it would have been gotten rid of), and he then went on to identify some "uses" of junk DNA: it serves as buffers for frameshift mutation errors (if a frameshift has equal probability of occurring anywhere in the DNA sequence, then the more junk you have, the less likely it is that a frameshift will hit an important gene), and it serves as "drydocks" where inactive copies of genes can safely undergo massive mutations in order to be remodeled.

The other context was in gene sequencing. Trying to sequence the entire human genome in the 1980's would have been prohibitively expensive and slow. Researchers noticed that there was a model organism - the fugu pufferfish - which had about one quarter the amount of DNA that humans have. Surely, they reasoned, humans don't have four times the different number of proteins that pufferfish have! Furthermore, in the context of "bauplans" or developmental plans for the body, pufferfish and humans are both tetrapods and thus really not that different. Getting the same results for a quarter of the work is a good business proposal, and so it was only natural that all the other stuff in human DNA that researchers didn't want to touch back then would be called "junk".
 
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