Darwin Unhinged: The Bugs in Evolution

Sure. I guess it would depend on what you mean by neo-darwinism. The evidence for common descent is as solid as evidence can get, and further research is always ongoing, trying to nail down the minutiae. Where do you think it crosses the line?

I know most on this site don’t subscribe to ‘god did it creationism’. Reading through the list one can see how that would tip over into pseudoscience.

I agree with you to some extent. To take creationism first, yes, I agree if you really mean creationism in the sense that it is commonly understood: i.e. biblical literalism or even Young Earth Creationism. I have no truck with that. If you mean created in its widest sense then that's a different argument because, as I would usually maintain, I think that the material world is a manifestation (creation) of mind. But that's a philosophical position and I am not at all sure of the scientific basis for the philosophy. 

As for neo-darwinism, I think there is reliance upon NS/RM not because the evidence is good but because it is a materialist requirement to keep out any thoughts of design. I'm not saying that NS doesn't happen - I'm sure it does - but it fails, in my view, to provide the real driving force for evolution, especially when considered with random mutation. The first article I posted which started this thread has plenty to say about that, as have subsequent discussions. Thus, I think that developments in epigenetics, the so-called "Third Way" and all this talk of panspermia are, in their own way, recognition of the weakness of neo-darwinism. Not that I'm claiming that they are endorsements for ID either but, again, I think that is because ID is a philosophical shift most trained scientists are very unwilling to make. Also, of course, because there is no agreement upon the nature of the intelligence in ID, as we have also discussed at length in this thread.

Thousands of new genes would have been necessary for the origin of animals, according to a new paper, summarized here. It's title is "Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty”. They conclude that “many new” genes were necessary during the origin of animals. According to the paper, for the origin of the Bilatera (animals with symmetrical left and right sides), an additional 1580 gene groups were required.

From the paper: 

"Thus, the first animal genome was not only showing a higher proportion of Novel HG [homology (gene) groups], but these also perform major multicellular functions in the modern fruit fly genome. The implication is that the transition was accompanied by an increase of genomic innovation, including many new, divergent, and subsequently ubiquitous genes encoding regulatory functions associated with animal multicellularity." 

From a commentary on this work by the paper's lead author:   

"...we looked at the novel genes in the first animal genome that weren’t found in older lifeforms. We discovered the first animal had an exceptional number of novel genes, four times more than other ancestors. This means the evolution of animals was driven by a burst of new genes not seen in the evolution of their unicellular ancestors."

Of course the paper’s authors assume that all these organisms share common ancestors and evolved by random mutation plus natural selection. However, actually these study results continue the insidious erosion in the credibility of Darwinism, exacerbating the problems of neo-Darwinism in explaining the Cambrian Explosion, and give more credibility to the advocates of panspermia.

As molecular biology and genetics progress, the more closely complex traits and diseases are looked at in detail, the harder it gets to find active genes that don’t influence them. It seems to be little-known and usually ignored that due to this RM + NS (Darwinism) as an explanation for evolution is becoming more and more untenable, since for so many traits so very many genetic changes over so very many genes would all have to happen in a coordinated way, but all these (mostly mutational) changes are assumed to be random in time and with respect to fitness. It just doesn't work. The foundations of the theory just can't accommodate the new data. The old combinatorial explosion problem.
   
From Veronique Greenwood at Quanta:    

"Mutations of a single gene are behind sickle cell anemia, for instance, and mutations in another are behind cystic fibrosis. But unfortunately for those who like things simple, these conditions are the exceptions. The roots of many traits, from how tall you are to your susceptibility to schizophrenia, are far more tangled. In fact, they may be so complex that almost the entire genome may be involved in some way…
...............................
When you look at the portions of the genome that genome-wide study findings have flagged as significant to individual traits, they are eerily well-distributed. Pritchard and his colleagues had been studying loci that contribute to height in humans. “What we realized was that the signal for height was coming from almost the whole genome,” he said. If the genome were a long string of ornamental lights, and every DNA snippet linked to height were illuminated, more than 100,000 lights would be shining all the way down the string. That result contrasted starkly with the general expectation that study findings would be clustered around the most important genes for a trait."

From a book review in the journal Cell Communication & Signaling:   

Abstract

"The evolutionary synthesis, the standard 20th century view of how evolutionary change occurs, is based on
selection, heritable phenotypic variation and a very simple view of genes. It is therefore unable to incorporate two
key aspects of modern molecular knowledge: first is the richness of genomic variation, so much more complicated
than simple mutation, and second is the opaque relationship between the genotype and its resulting phenotype.
Two new and important books shed some light on how we should view evolutionary change now. Evolution: a
view from the 21st century by J.A. Shapiro (2011, FT Press Science, New Jersey, USA. pp. 246.) examines the richness
of genomic variation and its implications. Transformations of Lamarckism: from Subtle Fluids to Molecular Biology
edited by S.B. Gissis & E. Jablonka (2011, MIT Press, Cambridge, USA. pp. 457) includes some 40 papers that anyone
with an interest in the history of evolutionary thought and the relationship between the environment and the
genome will want to read. This review discusses both books within the context of contemporary evolutionary
thinking and points out that neither really comes to terms with today’s key systems-biology question: how does
mutation-induced variation in a molecular network generate variation in the resulting phenotype?"

Excerpt: 

"If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions [6]. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits [7]: the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation..."

It's pretty basic - after much work the researchers still can't "come to terms" with the new data and explain complex innovation and adaptation (which are what evolution is really all about). This most likely is because the assumed fundamental mechanism must not be the actual fundamental mechanism. But of course the researchers can't explicitly recognize that and make a dent in the problem because being good Darwinists they must absolutely rule out any teleological forces and sources of information. The 2016 Royal Society meeting on problems in evolutionary biology was convened because of this and was posted about earlier in this thread.

A new ground-breaking and paradigm-breaking research study paper by Winston Ewert has just been published in Bio-Complexity. It appears to finally demolish the heirarchical tree-like common ancestry model of Darwinism, which has long been in trouble anyway. It not only does that but also at the same time establishes a strong empirical and analytical case for the superiority of a design-based overall structure to replace it. The least of this empirical case is an explanation of convergence, which has long been found to be inexplicably common in evolution. This work looks at the great array of species unbiasedly and attempts to come up with the best origin model, rather than a priori assuming a common descent tree structure because that is predicted by a now bankrupt theory - Darwinism. 

We have known for a long time that the common descent tree has major problems. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data.   

The Dependency Graph of Life

Abstract:

The hierarchical classification of life has been claimed as compelling evidence for universal common ancestry. However, research has uncovered much data which is not congruent with the hierarchical pattern. Nevertheless, biological data resembles a nested hierarchy sufficiently well to require an explanation. While many defenders of intelligent design dispute common descent, no alternative account of the approximate nested hierarchy pattern has been widely adopted. We present the dependency graph hypothesis as an alternative explanation, based on the technique used by software developers to reuse code among different software projects. This hypothesis postulates that different biological species share modules related by a dependency graph. We evaluate several predictions made by this model about both biological and synthetic data, finding them to be fulfilled.

A very short summary:

1) Modularization is a well-established design methodology in human engineering, especially software design.
2) Things that are developed with modularization can look as if they have a tree-like structure (heirarchical, common ancestry).  
3) A Bayesian methodology can be used to differentiate between modularized and tree structures.
4) For instances where the origins are known, the Bayesian methodology correctly separates trees and modularizations.
5) Using this methodology which is utilized in the work described by the new paper, it was found that genomes are organized very much more module-like than tree-like. The actual "tree of life" looks very much more like an modular dependency and reuse graphical scheme as followed in the engineering design process over time, than a common descent tree. 

From the paper:

"(In the dependency graph model of origin, as examples), all marine species depend on a marine module, and the echolocating species depend on the echolocation module.

The dependency graph is essentially a tree with extra flexibility; the modules can explain genes shared between species thought to be only distantly related by common descent.

A module is not restricted to reusing code from a single source, but can freely reuse from multiple sources. Compare this to common descent where each species must almost exclusively draw from a single source: its ancestral species.
....................................................................

The dependency graph hypothesis does not simply predict the same pattern as common descent, nor common descent with unspecified deviations from the general pattern. Instead, it predicts instances of module reuse across taxonomic boundaries.

Examples include the molecular convergence found in echolocating mammals or marine mammals. Others have argued that mammals in general show a similar level of convergence ."

A new ground-breaking and paradigm-breaking research study paper by Winston Ewert has just been published in Bio-Complexity. It appears to finally demolish the heirarchical tree-like common ancestry model of Darwinism, which has long been in trouble anyway. It not only does that but also at the same time establishes a strong empirical and analytical case for the superiority of a design-based overall structure to replace it. The least of this empirical case is an explanation of convergence, which has long been found to be inexplicably common in evolution. This work looks at the great array of species unbiasedly and attempts to come up with the best origin model, rather than a priori assuming a common descent tree structure because that is predicted by a now bankrupt theory - Darwinism. 

We have known for a long time that the common descent tree has major problems. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data.   

The Dependency Graph of Life

Abstract:

A very short summary:

1) Modularization is a well-established design methodology in human engineering, especially software design.
2) Things that are developed with modularization can look as if they have a tree-like structure (heirarchical, common ancestry).  
3) A Bayesian methodology can be used to differentiate between modularized and tree structures.
4) For instances where the origins are known, the Bayesian methodology correctly separates trees and modularizations.
5) Using this methodology which is utilized in the work described by the new paper, it was found that genomes are organized very much more module-like than tree-like. The actual "tree of life" looks very much more like an modular dependency and reuse graphical scheme as followed in the engineering design process over time, than a common descent tree. 

From the paper:

I can hear the ground breaking right where I stand. You ought to check check the credibility of the source.

From the

Encylopedia of American Loons

http://americanloons.blogspot.com/2016/0...t.html?m=1

Winston Ewert is Bill Dembski’s at least one-time research assistant and support staff at his Evolutionary Informatics Lab, which is not a lab. As such, he was Dembski’s coauthor (together with George Montañez and Robert J. Marks II) on the paper “Efficient Per Query Information Extraction from a Hamming Oracle”, a paper that has become somewhat legendary for its perfection of the art of obfuscation in the service of anti-science (it is discussed in some detail here), as well as “A General Theory of Information Cost Incurred by Successful Search”, which seems to be not really much better. Ewert’s reply to critics is discussed here; in fact, in December 2015 he finally admitted that the No Free Lunch theorems don’t work as an argument against evolution, but it is unclear whether he is willing to admit that he admitted this. (See in particular this and this for some details). He also writes posts for Uncommon Descent, in particular posts that display a notoriously poor understanding of (one almost suspects deliberately misleading claims on) probability, such as this.


Ewert is currently apparently affiliated with the Discovery Institute’s Biologic Institute, and has published his own stuff in their house journal Bio-Complexity...

I can hear the ground breaking right where I stand. You ought to check check the credibility of the source.

You are quoting the "Encyclopedia of American Loons" and telling someone else to check the credibility of their sources?

You are quoting the "Encyclopedia of American Loons" and telling someone else to check the credibility of their sources?

You only seem to post when I do. How odd. I know that purpose has appeal on this forum; please go ahead and defend Ewert's claims. Maybe you can find an overt way of not proving evolution is a product of time, chemistry, genetic mutation..., many have tried so give it a go.

You are quoting the "Encyclopedia of American Loons" and telling someone else to check the credibility of their sources?

Speaking of sources is there a link to the paper?

Speaking of sources is there a link to the paper?

Isn't it hyperlinked in the word "paper" in nbtruthman's post?

You only seem to post when I do. How odd. I know that purpose has appeal on this forum; please go ahead and defend Ewert's claims. Maybe you can find an overt way of not proving evolution is a product of time, chemistry, genetic mutation..., many have tried so give it a go.

You must not look at other parts of the forum if you think I only post in response to you.

Oh, I'm sorry, you now have proof that evolution is purely a product of time and random genetic mutation? You should let the scientific community know. I'm sure they'll be glad to know that you've discovered something that will resolve a topic of intense and ongoing study. 

Do you have anything to add other than a link to a site with no information about its author, and no reason to believe anything that that author has written? Or the normal, "this person was in some way affiliated with the Discovery Institute, so it simply must follow that everything they say is completely worthless."