Response to Evolution "News"

I don't know why I wasted my time. My edits are in bold italics. Response to 

http://www.evolutionnews.org/2015/09/waiting_for_mut099631.html

Many (hardly any) scientists now recognize the insufficiency of the classic Darwinian story to account for the appearance of new features or innovations in the history of life. They focus on other theories to account for remarkable differences between genomes, the appearance of novel body plans, and genuine innovations like the bat's wing, the mammalian placenta, the vertebrate eye, or insect flight, for example (In the same way that General Relativity improved on "Newtonian Theory" and made Mercury's orbit work?). They realize (Inspired by their religion, they believe) that the traditional story of population genetics (changes in allele frequencies in populations due to mutation, selection, and drift) cannot account for "the arrival of the fittest" and not just the "survival of the fittest." (Hugo DeVries, 1904). <--  Wow, they're reaching DEEP into the historical academic work

One of the reasons many (this tiny fraction of )scientists acknowledge the insufficiency of Darwinism is because they know the refuse to admit that the accounting won't works. The mutation rate, the generation times, the strength of selection versus genetic drift, the population sizes, and the time available don't match up just fine.

Here's where they deliberately misinterpret journal results and compare apples to oranges to make the reader think there's something wrong with science. At its core, this is part of a larger argument from ignorance approach, paraphrased as: 'Science isn't right. Therefore God did it.'

For example, supposedly humans last shared common ancestry with chimps about six million years ago. Since that time, we have accumulated significant differences with chimps -- genetic, anatomical, physiological, behavioral, and intellectual differences, among others. The genetic differences between humans and chimps are much more than the (shrinking) 1.2 percent difference in base pairs that is so often quoted in the media. (Yes, there are different ways of measuring similarity.) Add small insertions and deletions and the differences climb to about 3-5 percent,depending on whose estimate is used. Add another 2.7 percent for large scale duplications or deletions, another 6 percent for new Alu elements (a kind of mobile genetic element) and some unknown number for rearrangements of the DNA, other insertions of mobile genetic elements, or new genes, we have more than 11.7 percent of our genome with unique features not present in chimps. (Only when you struggle to exaggerate moves and deletions. For reference, here is the preliminary analysis as published in Nature.) 

There is only so much time for these differences to have accumulated. Mutations arise and are propagated from generation to generation, so the number of generations limits how many mutations can accumulate. The estimated mutation rate is about 10^-8 per base pairs per generation, and we have an average generation time of somewhere between 10 and 25 years. Our estimated breeding population size six million years ago is thought to have been about 10,000 (these are all rough estimates based on numbers currently in use -- see the papers cited below). Based on these numbers, one can estimate how many years it would take to acquire all those mutations, assuming every mutation that occurred was saved, and stored up. (Since the mutation rate is extremely small and uniformly distributed, this assumption is valid.)

But there's a difficulty -- it's called genetic drift. In small populations, like the 10,000 estimate above, mutations are likely to be lost and have to reoccur many times before they actually stick (WTF? It's not like a specific change keeps trying. Many are just lost). Just because of random effects (failure to reproduce due to accidental death, infertility, not finding a mate, or the death of all one's progeny), a particular neutral mutation may have to arise many times before it becomes established in the population, and then many more years before it finally becomes fixed (that is, before it takes over the population and replaces all other versions).

What a strange misinterpretation of the process! The author seems to think that the mutations which fail to reproduce keep trying until they stick. Bizarre! Clearly, lost mutations are simply lost. Just like the 99.9% of all species which have gone extinct. Very few succeed.

How long before a single, new mutation appears and becomes fixed? An estimate from a recent paper (by a Young Earth Creationist) using numerical simulations is 1.5 million years. That is within the range of possibility. (By assuming that there is only a single specific desirable mutation being considered by nature at any given time.) But what if two specific mutations are needed to effect a beneficial change? Their estimate is 84 million years. Other scientists have done this calculation using analytical methods, but their numbers are even worse. One report calculates 6 million years for one specific base change in an eight base target typical of the size of a DNA binding site to fix (In the abstract, the author points out that the sequence needn't be perfect to be valuable, reducing the time to 60,000 yrs), and 100 million years to get two specific mutations. (That work was later amended to 216 million years.) Extrapolating from other published data merely confirms the problem.

Astonishing dishonesty! A brief review of the linked article (100 million years) contains the following quote: "Fortunately, in biological reality, the match of a regulatory protein to the target sequence does not have to be exact for binding to occur. Biological reality is complicated, with the acceptable sequences for binding described by position weight matrices that indicate the flexibility at different points in the sequence. To simplify, we assume that binding will occur to any eight-letter word that has seven letters in common with the target word. If we do this, then the mean waiting time reduces to ∼60,000 years."  Why would Evolution "News" need to misrepresent the author's conclusions in their linked article? Did they think nobody would read it?

Durrett makes a good analogy to the mistake Michael Behe made to reach is 216 million year figure in the linked article: "Behe is not alone in making this type of mistake. When Evelyn Adams won the New Jersey lottery on October 23, 1985, and again on February 13, 1986, newspapers quoted odds of 17.1 trillion to 1. That assumes that the winning person and the two lottery dates are specified in advance, but at any point in time there is a population of individuals who have won the lottery and have a chance to win again, and there are many possible pairs of dates on which this event can happen. The probability that it happens in one lottery 1 year is ∼1 in 200 (Durrett 2009)  

Another paper came up with much shorter time frames by assuming that any 5 to 10 base pair binding site could arise anywhere within 1 Kb of any promoter within the genome. 

Yet in all likelihood many more than two binding sites would be required to change anything significant, and those binding sites must be appropriate in location and in sequence to accomplish the necessary changes. They must work together in order for a specific adaptive change to happen.  (Again, the authors seem to think that these changes are prescribed and can't be happening at random, in parallel, and at different sites.) 

Genes operate in networks, and to shift a gene regulatory network would require many mutations, and not just random ones. Remember there are anatomical physiological, behavioral, and intellectual differences to explain, multiple traits each requiring multiple coordinated mutations. Unless one invokes luck on a large scale, those traits would not have come to be. (Again, all this presumes humanity is the intended end-state. It is because it is.) 

I'm not betting on luck. (Of course you're not). 

Image: Homo georgicus, reconstruction, photo by 120 (Own work (photograph), model by Élisabeth Daynes) [CC BY-SA 3.0], via Wikimedia Commons.

Well that was as much fun as beating my head against a wall. The basics mistakes are as follows:

1. Cite ancient journals from 1904 as if they're still relevant
2. Misrepresent the number of changes
3. Cite letters to journals which explicitly refute the point you're claiming they make (oops?!)
4. Presume that the genetic changes were prescribed
5. Assume intelligent humanity was the universe's desired end-goal
6. Ignore that a neutral genetic change will not survive without a second change that's necessary to the benefit. Indeed, we could have millions of such single-mutations waiting on a second mutation to confer a benefit.