Peer Reviewed paper claiming evolution is wrong

[CapelDodger]

The Iders are all ablog about the paper. That suggest junk science

Junk interpretation seems more likely, but I spy an evolution from Darwinism to Genetic Darwinism as their latest talking-point. Irreducible Complexity just hasn't worked out; although still far from extinct it's on that trajectory.

 

[CapelDodger]

Before the first page is finished they claim it 'undeniably comforted racists' ...

Which chimes with the attack on Dawkins decribed here http://www.guardian.co.uk/science/2012/feb/19/richard-dawkins-disbelief-slave-trade-ancestor

In a very weird newspaper, but perfectly normal in its UK context. I don't see the "slave-owning gene" playing well in the US as a bad thing.

... 'sanctioned imperialism' and 'actively promoted eugenics'.

I won't argue the use that Darwin's insights were put to by people we now refer to as Social Darwinists (in all their manifestations). For imperialists it provided a scientific justification that they hadn't asked for but were happy to accept, and eugenics emerged before Darwin distinguished natural selection from selective breeding.

 

[ibbicay]

At first glance, I'm not convinced that paper was reviewed by anyone who studies evolutionary biology. The authors' other publications are also interesting, to say the least. Plenty of theory and speculation, to be sure.

Not that theory development doesn't play an important role in science, but at some point you have to actually check whether what you're saying reflects reality.

And no, I don't like the use of the term "Darwinism" either. I've seen it used in several different ways, and I haven't yet found it to be a particularly useful term.

 

[rjh01]

I just put the name of the paper into Google. Looks like most of the websites that discuss it are religious based. Not even any news sites discuss it. Looks like it will be preaching mainly to the choir.

 

[fishtumor]

Why isnt evolution found to be interesting by every one! Why shoot down such greatness!

 

[Acleron]

Why isnt evolution found to be interesting by every one! Why shoot down such greatness!

I think you will find it is intensely interesting to everyone. Just that the deluded feel threatened by it.

 

[Lowpro]

Can't access the paper through my school either =\ guess I'm stuck until it comes out somewhere...

I did see an interesting part of the Comments section though of one of the religious sites about one guy who of course is touting this paper as a victory, but he said something interesting which may deserve its own thread. It's a strawman argument, but one I haven't seen.

He says that evolution doesn't answer the question anymore because it's only focused on DNA, and not development in particular (this is a lie, but let me continue) and says the reason is because you, and I quote "Can't put a reptile's DNA in a fish egg and expect a reptile to develop, hence there's more to species diversity than just DNA, evolution isn't able to account for this, and therefor it doesn't answer the question of why wer're here, therefor God." He also said that this is why Baraminology works (lol) because if you can't put reptile DNA into a fish egg and get a reptile then there is a point where our species diversity cannot exist and the only answer are the baramins.

I've never heard this one before to be honest, I wonder if it's new. Evolution would never say that DNA is the end all be all of species (a geneticist might say it though ) but evolution-and development (evo-Devo) has a LOT to say about development. It takes more than DNA to build an organism, it takes proteins and environmental stringencies to promote the development of the organism too. But apparently evolution is "only caring about DNA" which is a lie, but apparently it's running around in the ID circles.

 

[Dinwar]

It's not new. randman tossed it out for a while, until some biochemists showed him that he was completely wrong. A LOT of evolution can be explained via DNA--but not all of it. There's also issues of WHICH genetic code to use (after all, the mitochondria and chloroplasts have their own).

The other issue is that this is yet again an example of Creationists insisting that we use modern organisms for discussing evolution. That's just plain stupid. Sure, modern fish (a paraphyletic group, by the way) and reptiles (another paraphyletic group) most likely can't make clones of each other in most cases (doubt anyone's tried every permutation possible, so this is speculation but not an entirely unreasonable one so I'll go with it). Problem is, that's likely because, as you suggested, there's been a few hundred million years' worth of evolution of celular structure separating them. Back when amphibians were first splitting off of fish it would have been much, much easier to clone one using the other's cells. When reptiles split off amphibians, again, it would have been much simpler to clone one using the other's cells. And they were vastly more similar, morphologically. Young Earth Creationists by definition have to reject the concept of common ancestry, however, and therefore cannot look at the history of any lineage in their reasoning--not because such examination is invalid, but because it violates their a priori conclusion.

In other words, it's a slightly different flavor of the same old dish.

 

[Lowpro]

Well I was more interested in that they actually try to separate it as DNA and development and saying "since evolution has a NOMA relation to development, it cannot POSSIBLY have the explanative power to development (they say this simply because they say it, not whether it's actually true...) therefor evolution doesn't have all the right answers, therefor God (or Baraminology, take your pick), which to me is what this paper MAY be trying to do, I don't know because I cannot read the damn thing -.-

I'm just find this to be a new tactic, at least to me. It's a curiosity.

 

[CORed]

Irreducible Complexity was a decent enough idea -- if someone designed life, then there might (note: not necessarily will) be some structures that could not have evolved as they are too complicated and thus incremental steps could not have arrived at them as there are no useful intermediates.


The only problem was they list all kinds of examples...which then start getting shot down one by one as scientists figure out how these things evolved.


Thus IC's "predictive power" begins to evaporate. At this point, no honest scientist would have any statistical reason to believe any remaining IC examples would continue to withstand scrutiny indefinitely.

Moreover, that so many examples on the list got shot down indicates the theory is very poor at defining methods of determining items in its class, also a red flag that it...needs some serious work.

Not really. Irreducible Complexity pretty much boils down to an argument from incredulity: I can't understand how this evolved, therefore God did it.

 

[Dinwar]

Thus IC's "predictive power" begins to evaporate.

IC had no theoretical basis for generating predictions to begin with.

In science, a prediction is not "Something may look created", or even "Something may not be stable if you remove any one part". Even in paleontology, which deals with some of the worst datasets in science, we expect predictions to be things like "If we dig in X lithology of Y geologic unit we will find critters Z, A, Q, and P". We can do that because we have a theoretical framework for understanding the driving force behind the changes we see--we know, for example, that decapods tend to migrate from Europe, north across the Iceland/Greenland area, then south along the Atlantic seaboard of the Americas; thus we can conclude that if we find Species A1 in Europe and A3 in Brazil, we can be reasonably certain of finding A2 in specific strata of Main (if those strata exist, of course--erosion plays havoc with our ability to find the blasted bugs!).

IC doesn't have that. Their theoretica framework consists of "Someone, somehow". Without providing specific details about who or how, they cannot create any specific and testable predictions that are significantly different from evolution. It's impossible--without knowing who or how literally ANYTHING goes, even evolution! And when anything can be the answer, there isn't any answer.

Of course, that's giving IC the best of it. In reality, ID (of which IC is a critical component) was an intellectually dishonest con-job designed specifically and intentionally to smuggle Creationism into public schools, in an organized attempt to undermine the secular nature of our government. This isn't hyperbole, nor is it speculation. The fact that IC was created to smuggle Creationism into public schools is a mater of public record (the Dover trial) and the fact that it's part of a larger scheme to turn us into the Christian version of Iran is outlined in The Wedge Document. So giving ID any credibility is actually imporper. The proper view of it is the same as the proper view of those emails about the Zimbabue prince who needs $5,000, but will give you millions of his fortune.

 

[Dr. Imago]

Junk DNA isn't all junk, though some of it sure is.

Just because we don't, per the current state of science, completely understand what something does doesn't mean it's "junk"...

http://www.sciencedaily.com/releases/2009/09/090921134702.htm

http://www.nytimes.com/2011/08/16/health/16cancer.html?pagewanted=all

http://www.artivist.com/index.php?o...e-secret-of-junk-dna&catid=498:food&Itemid=22

Personally, I'd like to know exactly what portion of our genome constitutes "junk DNA". And, no, I don't think these newer discoveries in any way support ID.

~Dr. Imago

 

[Acleron]

Just because we don't, per the current state of science, completely understand what something does doesn't mean it's "junk"...

http://www.sciencedaily.com/releases/2009/09/090921134702.htm

http://www.nytimes.com/2011/08/16/health/16cancer.html?pagewanted=all

http://www.artivist.com/index.php?o...e-secret-of-junk-dna&catid=498:food&Itemid=22

Personally, I'd like to know exactly what portion of our genome constitutes "junk DNA". And, no, I don't think these newer discoveries in any way support ID.

~Dr. Imago

Larry Moran has a useful series of blogs on junk DNA.

If I've understood and remembered Moran's text :-
When the size of the genome was known, long before it was sequenced, it was calculated from the known mutation rate that a lot would have to be junk otherwise the genome could not be passed on and not have too many errors. The sequenced genome contains for example areas with no start-stop codons. The amount found to be non transcriptable and not used for other known purposes was very roughly in accord with the earlier figure.

 

[Lowpro]

Right which is why I said "Junk DNA isn't all junk" Not too long ago a lot of what was understood was that it codes for proteins. Not all of it does, so it was given the colloquialism "junk" however now a lot more DNA is understood to have other functions, such as post-transcriptional regulation.

Some, such as viral remnants, are probably junk though as in it may still have no function and is there because getting in is thermodynamically favorable. Getting it out? Not so much.

Also, the blog that Acleron linked is pretty insightful

 

[Acleron]

Right which is why I said "Junk DNA isn't all junk" Not too long ago a lot of what was understood was that it codes for proteins. Not all of it does, so it was given the colloquialism "junk" however now a lot more DNA is understood to have other functions, such as post-transcriptional regulation.

Some, such as viral remnants, are probably junk though as in it may still have no function and is there because getting in is thermodynamically favorable. Getting it out? Not so much.

Also, the blog that Acleron linked is pretty insightful

I think you have to be careful, the prediction of junk was before specific regions were found not to have a function. The combination makes it more likely that a lot is really for no purpose.

Non-functional would imply that junk regions are not so well conserved as functional regions but I cannot find a confirmation of this.

The fact that there doesn't seem to be much evolutionary advantage in losing the non-functional regions nicely ties in with your comment about it not being favourable from a thermodynamic point of view. I wonder if there is a proof of that, would be handy when the creationist/IDers come out with their thermodynamic nonsense.

Do you know if there are fully function genes with start/stop codons that produce junk proteins? Their elimination from the genome would seem to be a much better advantage.

 

[Dinwar]

There's a hypothetical one: if there's a double-crossover that replicates a gene, and one gene isn't expressed (unlikely to be, as most of the time expression of both genes would kill the organism), that unexpressed gene can code for anything, from beneficial protiens to poisons, without impacting the organism's fitness in the slightest. It's one of several ways to develop irreducibly complex structures without a designer--yes, it wouldn't function in any of the intermediate forms, but since it didn't function ANYWAY it doesn't matter in the slightest.

 

[Lowpro]

I think you have to be careful, the prediction of junk was before specific regions were found not to have a function. The combination makes it more likely that a lot is really for no purpose.

Non-functional would imply that junk regions are not so well conserved as functional regions but I cannot find a confirmation of this.

The fact that there doesn't seem to be much evolutionary advantage in losing the non-functional regions nicely ties in with your comment about it not being favourable from a thermodynamic point of view. I wonder if there is a proof of that, would be handy when the creationist/IDers come out with their thermodynamic nonsense.

Do you know if there are fully function genes with start/stop codons that produce junk proteins? Their elimination from the genome would seem to be a much better advantage.

Depends on if the protein causes any harm. Generally a protein's half life is short (there are some that last days sure) and ubiquitous enzymes constantly degrade all types of proteins indiscriminately. If a junk protein were to form it needs to have a structure that can resist the breakdown.

There are many genes that have a mutation and form a nonfunctional protein (diseases such at TDO come to mind) but they are pathological in nature so the selection is against them. I don't know about an effectively "neutral" one.

 

[Lowpro]

Guess I'll post it here thought it deserves its own thread:

P.Z. discusses Evo-Devo

 

[Dinwar]

That’s the holy trinity of biology: evolution, ecology, development. Our goal ought to be to bring all three together in one beautiful balance.

Interesting, to be sure. Though two out of those three need paleontological input in order to say anything significant.

(Yes, I know what can of worms I'm opening there. )

 

[Lowpro]

Well paleontologists are kinda stuck between geology and biology aren't they? Maybe we need this biology trinity within another trinity, of paleontology and geology, and then that will be within a trinity of Earth Science and Physics and that will be....

By God it's a fractal..