Thanks Larry! If a species can lose its stomach, it must mean the mutation was neutral
|April 1, 2014||Posted by scordova under 'Junk DNA', Genetics, News|
Larry actually had some rare kind words for me. He said here
Cordova is correct.
Thanks for the kind words, Larry!
Larry goes on to argue that organisms can tolerate lots of mutations and still reproduce.
Yes, I agree, but reproduction is not the real thing in question, it is the existence of designs. I’ve argued even with creationists the issue isn’t whether mutations are “beneficial” or “deleterious” in the sense of differential reproductive success, the question is whether neutral evolution and real selection in the wild will tend to destroy design rather than build it.
What’s the simplest fix to the problem of irreversibly accumulating bad mutations (as I illustrated here)? Simple, renormalize the selection coefficients and declare being sick as the new normal. Problem solved!
To solve the problem of deleterious mutations, evolutionists will argue loss of function is reproductively “beneficial” or neutral. Think I’m kidding? If you were a shark, you’d lose your stomach over the idea:
Animals from lungfish and ghost sharks to platypuses have lost their acid-making stomachs over evolutionary time, and researchers have now traced the genetic changes behind these stomach upsets.
True stomachs with digestive glands that concentrate acid and release protein-cutting enzymes called pepsins evolved with vertebrates. The gastric glands arose some 450 million years ago but have dwindled away at least 15 separate times across the animal tree of life, explains Filipe Castro of the University of Porto in Portugal.
More than a quarter of known bony fish species digest food without a true acid stomach. Picking out what drove the evolutionary change is tricky, says Jonathan Wilson, also at Porto. For instance, pufferfishes now repurpose their organ to store food and bloat with water for menacing spines-out displays.
After scrutinizing genes of 14 vertebrates with and without stomachs, Castro and his colleagues determined that none of the stomach losers has high-functioning genes for maintaining a highly acidic zone in their digestive tracts.
The animals also lack or have low-functioning genes for secreting the peptic enzymes that slice and dice proteins under acidic conditions, the researchers report December 4 in the Proceedings of the Royal Society B.
Losing one’s stomach is neutral at best and “beneficial” at worst, thus no need to worry that mutations are deleterious — solution via redefinition of good and bad. Some have called this genius insight Survival of the Sickest, Why We Need Disease.
So was the DNA that coded for the now missing stomach junk DNA? Since nature has shown we can knock the stomach out and the organism still reproduces for millions of years, does this mean their stomachs are junk and so was the DNA that coded them? This obviously has relevance to the junk DNA discussion today where sometimes the benchmark for determining if something is junk is whether we can sacrifice it and the organism still reproduces.
Larry argues elsewhere:
Because a large percentage of gene mutations are neutral, and because most of our genome is junk, we can easily tolerate 130 mutations per individual per generation without going extinct.
But tolerating the mutation isn’t the real question, it’s how such a scrambling process can be compatible with development of novel complexity. Larry answers a question that is not being asked. The problem is about irreversible loss of function, it’s not about the ability to keep making babies.
In light of these considerations, the problem of deteriorating design remains as I pointed out in my claim that high mutation rates create high breakage rates.
Evolutionists think of “beneficial” in terms of reproductive success whereas IDists and creationists think of beneficial in terms of function. Unfortunately, as happens in some creationists papers and books like Genetic Entropy, the creationists sometimes fall into the trap of using the Darwinists notions of “beneficial.”
Behe’s rule of adaptive evolution illustrates the problem — most of the radical sorts of adaptive evolution observed in real time are examples of functional loss, not gain. Behe’s rule is experimentally confirmed, and this casts doubts that this mode of adaptation can be an explanation for evolution of function in the first place.
The problem is, when we can freely say losing one’s stomach is a neutral mutation, then we are free then to insist neutral theory is correct because it is fundamentally unfalsifiable on such terms.
I’ve proposed the proper way to falsify neutral theory is if we can show mutations are increasing unabated in deeply “conserved” regions. If we show this, then both selectionist and neutralist theories are falsified properly, and design is vindicated. Right now, it’s still a tad too expensive to carry such research out, but because the question of genetic deterioration has medical significance, I expect the ID proponents will have their answers in due time and John Sanford’s genetic entropy thesis will be vindicated.
1. Larry, couldn’t you have picked April 2 instead of April 1 to say something nice about what I said?
2. Thanks any way, Larry.
3. Here I suggested in 2007, there will be almost unabated growth of mild, almost undetectable defects accumulating in the genome.
JoeCoder, to my surprise, informed me that just last year:
Past 5000 years prolific for changes to human genome
Of 1.15 million single-nucleotide variants found among more than 15,000 protein-encoding genes, 73% in arose the past 5,000 years, the researchers report. On average, 164,688 of the variants — roughly 14% — were potentially harmful, and of those, 86% arose in the past 5,000 years. ‘There’s so many of [variants] that exist that some of them have to contribute to disease,’ says Akey
As I predicted, the deep sequencing made possible by Solexa technology is paving the way to vindicate ID claims over the competing theories of selection and neutral evolution in the past.
Thanks JoeCoder. You made my day, even if it means the human race is dying, at least I got something right.
4. I accept neutralism as a better description of evolution in the present day, but I reject it as an explanation of design and the fundamental structures of biology. Neutral evolution is real, it wins out over Darwinian selection, but it’s not the mechanism of design. Neutral evolution destroys design, it much less does it explain it.
5. Here is an excerpt form the paper in question. Note how the problem of harmful mutations is nicely renormalized away. Just redefine the loss of an organ as a good thing or neutral thing, and problem solved!
We propose that relaxation of purifying selection in pepsinogen genes and possibly proton pump genes in response to dietary changes led to the numerous independent events of stomach loss in gnathostome history. Significantly, the absence of the gastric genes predicts that reinvention of the stomach in agastric lineages would be highly improbable, in line with Dollo’s principle.
Translation, “we propose neutral evolution”. And lo and behold, on top of that we have fixation of this neutral trait in all those species who’ve lost their lunch.
6. The fundamental problem with evolutionary theory as compared to theories of physics is that the most fundamental concept “selective advantage” is not well-defined compared to physical notions like mass, charge, length, and time. The ambiguity, imho, is fatal to evolutionary theory. I tried to demonstrate the problem in this essay: Dennet’s Strange Idea is a bad idea for recognizing design. The article about sharks losing their stomachs serves to highlight this problem.
7. HT JoeCoder x10