johnnyb

I’m currently working through Robustness and Evolvability in Living Systems, and came across the following information which seems to be right in line with Denton’s evolution by natural law ideas: A final, especially counterintuitive feature of RNA sequence space is that all frequent structures are near each other in sequence space. Consider a randomly chosen sequence that folds into a frequent structure and ask how far one has to step away from the original sequence to find a sequence that folds into this second structure…For instance, for RNAs of length n = 100 nucleotides, a sphere of r = 15 mutational steps contains with probability one a sequence for any common structure. This implies that one has to search a Read More ›

A recent essay in PLoS biology bemoans that researchers are not using the term “evolution” nearly often enough in research papers. The essay lays out the horrendous possibilities that this could mean: A critical question is whether avoidance of the word “evolution” has had an impact on the public perception of science. To investigate this, we examined whether the use of the term “evolution” in the scientific literature affects the use of this word in the popular press, i.e., whether there is evidence for “cultural inheritance” of word use. We searched articles on antimicrobial resistance in national media outlets, such as The New York Times, The Washington Post, Fox News, and the BBC (Text S1). Our results showed that the Read More ›

It is often said that while there are many controversies within evolution as to the specifics of how evolution works, there is no controversy about the fact of evolution. Often times, when ID’ers talk about problems with evolutionary theory, they are accused of misrepresentation — that certainly there are controversies about aspects of evolution, but not controversies about the fact of evolution itself. Thus, any amount of doubt that might be brought on by these criticisms are washed away by the fact that these are mere quibbles over details.
Read More ›

Does Luria-Delbruck really mean that mutations are random? Or might it indicate something else?
Read More ›

Many people who argue against Intelligent Design’s position on transitional forms often don’t have any clue what it is that is actually being said. I’d like to take a moment to clear it up. If anyone disagrees with my commentary (especially ID’ers — I’d hate to misrepresent other’s opinions), please post below. My main point in writing is not so much a defence of the concept (though I do attempt that) but rather to show why it makes sense even in the absence of special creation, and why its use is not limitted to people who agree with special creation, but anyone who believes in a telic form of evolution.

Read More ›

In shocking news this morning, johnnyb was fired from his job for being irrelevant. When asked about why he was fired, ABC Co. gave the following response — “We looked at the operation of the company, and, while there were many programs attributed to him, and some people claimed that the network worked because of him, we ultimately decided that philosophically, these were all johnnyb-of-the-gaps arguments. In each case, someone from management was able to conceive of a way that these systems would be functional without a johnnyb.”

Read More ›

Do traceable lines of descent exist that might ultimately permit characterization of the genomes of organisms basal to the clades for the highest categories? The answer to this question increasingly appears to be no. Recent work on genomic structures demonstrate that all living organisms are genetic composites: mosaics and chimeras composed of bits and pieces of multiple genomes derived from multiple sources.
…
The base of the universal tree of life appears not to have been a single root, but was instead a network of inextricably intertwined branches deriving from many, perhaps 100 or more, genetic sources. The traditional version of the theory of common descent apparently does not apply to kingdoms as presently recognized. It probably does not apply to many, if not all, phyla, and possibly also not to many classes within the phyla. (from Malcom Gordon’s paper on monophyly)

When Intelligent Design advocates talk to evolutionists concerning the origin-of-life, the standard response is almost always something like “Evolutionary theory says nothing about the origin of life. Whether it was RNA world, or a special act of creation, evolution is an entirely different subject than abiogenesis.” However, I think that this argument is illegitimate. In fact, large-scale evolutionary theory depends thoroughly on specific notions of abiogenesis.

Read More ›

I think one of the biggest confusions about Intelligent Design is that it is a theory of origins. This has caused a tremendous amount of confusion on both sides of the fence. If Intelligent Design was a theory of origins, many of ID’s criticisms of ID would make much more sense. But I think that ID is really a theory of causation.

There is a growing body of experimental knowledge about the evolution of genomes, which shows that decidedly directed forces at work. The genome is best viewed, not as a happenstance gathering of parts, but as a holistic mechanism which functions as a whole. A good summary paper of these sorts of ideas is Mutation is modulated: implications for evolution. While the author does attempt to reconcile this directed view of evolution with Darwinism, ultimately it is the directed mutation, not the reconciliation with Darwinism, which is supported experimentally. Some interesting points about the genome: Tandem repeats can be used as tuning knobs to quickly and reversibly adjust biological function of genes The vertebrate immune system has “an integrated set of Read More ›