When did nylon-eating proteins actually evolve the ability to eat nylon?

It has been widely advertised that nylon eating genes evolved after 1940. I have no problem with that claim in principle since new antibiotic and malaria resistances have evolved since 1940. Even though I can easily accept the possibility of post-1940 nylon-eating evolution in principle, where is the slam dunk evidence that this is actually the case? Did a significant portion of the ability for bacteria to digest nylon take place after 1940 (or 1935 when nylon was first created)?
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Evolution and Functional Information

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Here, one of my brilliant MD PhD students and I study one of the “information” arguments against evolution. What do you think of our study?

I recently put this preprint in biorxiv. To be clear, this study is not yet peer-reviewed, and I do not want anyone to miss this point. This is an “experiment” too. I’m curious to see if these types of studies are publishable. If they are, you might see more from me. Currently it is under review at a very good journal. So it might actually turn the corner and get out there. An a parallel question: do you think this type of work should be published?

 

I’m curious what the community thinks. I hope it is clear enough for non-experts to follow too. We went to great lengths to make the source code for the simulations available in an easy to read and annotated format. My hope is that a college level student could follow the details. And even if you can’t, you can weigh in on if the scientific community should publish this type of work.

Functional Information and Evolution

http://www.biorxiv.org/content/early/2017/03/06/114132

“Functional Information”—estimated from the mutual information of protein sequence alignments—has been proposed as a reliable way of estimating the number of proteins with a specified function and the consequent difficulty of evolving a new function. The fantastic rarity of functional proteins computed by this approach emboldens some to argue that evolution is impossible. Random searches, it seems, would have no hope of finding new functions. Here, we use simulations to demonstrate that sequence alignments are a poor estimate of functional information. The mutual information of sequence alignments fantastically underestimates of the true number of functional proteins. In addition to functional constraints, mutual information is also strongly influenced by a family’s history, mutational bias, and selection. Regardless, even if functional information could be reliably calculated, it tells us nothing about the difficulty of evolving new functions, because it does not estimate the distance between a new function and existing functions. Moreover, the pervasive observation of multifunctional proteins suggests that functions are actually very close to one another and abundant. Multifunctional proteins would be impossible if the FI argument against evolution were true.

The Arrival of the Fittest: a book review

Andreas Wagner’s book,The Arrival of the Fittest has been mentioned many times (just try a site search as I’ve just done) since it was published. Petrushka pointed it out in a comment

For anyone interested in whether RMNS can create stuff, I recommend a relatively new book, Arrival of the Fittest. I just bought the Kindle version an haven’t finished, but it has a lot to say about how goldilocks mutations occur.

Much later Mung writes:

Reminds me of petrushka, who is always plugging Andreas Wagner’s Arrival of the Fittest, but will never post an OP on it for discussion.

So I’ve taken the hint and bought the book at last. I can see why people have recommended it. Continue reading

Testing Evolutionism (the alleged theory of evolution)

Testability is the main thing a concept needs in order to be considered science. If your claims cannot be tested then science doesn’t care about them. Enter evolutionism, also mistakenly called the theory of evolution, ie the concept that all biological diversity evolved via natural selection, drift and neutral construction starting from some much simpler biological replicator, which in turn evolved from much simpler molecular replicators.

None of that can be tested. Not only that the sub-claims are also untestable. Biology is full of biological systems, subsystems and structures. These too need to have testability, yet they do not. Evolutionists hide behind father time and think that excuses them from the testability criteria science requires. All that does is prove theirs is not a scientific position.

No one knows how ATP synthase arose and no one knows how to test the claim that natural selection, drift and neutral construction did it. Dembski tried to help by formulating a conditional probability but he was shrugged off. Evolutionists are fine failing on their own and don’t need no steenking help from Dembski!

So how can we test your claims, evolutionists? And why, in the absence of testability, do you think your position qualifies as science?

 

 

Eugene Koonin – Evolution Skeptic?

The edifice of the Modern Synthesis has crumbled, apparently, beyond repair.

– Eugene Koonin (2009)

Does this make Eugene Koonin an evolution skeptic?

The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the Modern Synthesis is gone.

I’m still struggling to incorporate Alan Fox’s allegation that I am an evolution skeptic. I still don’t really know what it means to be an evolution skeptic. Eugene Koonin rather obviously rejects the view of evolution held by Alan Fox. Is Eugene Koonin an evolution skeptic?

Or is this just another example of Creationist quote mining. Maybe it’s both.

What say you, “skeptics”?

The Origin at 150: is a new evolutionary synthesis in sight?

Jerry Falwell Jr, a Trump appointee.

I’m sure the name Jerry Falwell Jr means more to US members than it does to me. A friend passed on a link where I read:

Donald Trump appoints creationist college president to lead higher education reform taskforce

According to Salon:

The focus will be on “overregulation and micromanagement of higher education,” according to university spokesman Len Stevens. This would be consistent with Falwell’s past positions, in which he has opposed federal regulations on funding and accreditation for American schools of higher learning.

Following the appointment of (Calvinist?) Betsy DeVos as Education secretary, should we be concerned for the future of public education in the US?

Is anatomy the evidence that theropod dinosaurs evolved into birds? No!

On another forum the claim was strongly put that the anatomy of theropod dinosaurs was so similiar to moderrn birdds that its excellent evidence for birds to have evolved from dinosaurs. So some evolutionists  say birds today are really the end game of dinosaur evolution.

yEC say birds wewre created in their kinds on creation week and were on the ark in kinds. So were creatures we call dinosaurs and so these theropod ones.

So its impossible birds evolved from theropod dinos.

The only evidence they have is the anatomy of theropods . Some say they had feathers.

I have another hypothesis. That it is only a convergence of bone structures(anatamy) for the same needs. It is not that these dinos have bird bones but thart birds don’t have bird bones. they both only have bones to join body with physics. the theropods needed to be liught on their feet and the only answer is size and structure of bones to allow this. birds have the same need and so have the same bones. Yet its physics that determoines the bone structure and not a biological ancestry. there is no ancestry. they were created in whole right away. Perfect. its just the right and only conclusion .

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Darwin’s House of Cards

In this provocative history of contemporary debates over evolution, veteran journalist Tom Bethell depicts Darwin’s theory as a nineteenth-century idea past its prime, propped up by logical fallacies, bogus claims, and empirical evidence that is all but disintegrating under an onslaught of new scientific discoveries. Bethell presents a concise yet wide-ranging tour of the flash points of modern evolutionary theory, investigating controversies over common descent, natural selection, the fossil record, biogeography, information theory, evolutionary psychology, artificial intelligence, and the growing intelligent design movement. Bethell’s account is enriched by his own personal encounters with of some our era’s leading scientists and thinkers, including Harvard biologists Stephen Jay Gould and Richard Lewontin; British paleontologist Colin Patterson; and renowned philosopher of science Karl Popper.

Darwin’s House of Cards: A Journalist’s Odyssey Through the Darwin Debates

Of course, no real skeptic will want to read this book.

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Introns

In the 1970s, when scientists compared the sequences of DNA in genes with the sequences of RNA encoded by those genes, they made a puzzling discovery: the DNA of most genes in animals, plants, and other eukaryotes contains too much information. The extra segments of largely useless information were named introns, and they must be cut out of RNA before the protein is made. Exons are the portions of the gene that remain in the RNA after the introns have been removed.

  • Relics of Eden

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Junk DNA munged

Salvador seems to have successfully hijacked the early embryonic mutations thread and turned it into a discussion of junk DNA. So I thought I’d share my thoughts on the subject of junk DNA. Why care?

Various strains of creationism hold that the earth and life started out perfect, then came the fall, and it all went downhill from there. Both young earth and old earth forms can easily accommodate the presence of junk in DNA. So the presence of junk DNA does not mitigate against the creationist position. But what of it’s absence?

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