Wednesday, 9 October 2013

Barns tackles evolution and looks at mutations adding information

In chapter three of The Dawkins Proof for the existence of God and mostly shows that he understands just enough of Evolution to think he is an expert.

I have used book locations, Amazon Kindle's half-assed replacement for page numbers.  If you are using the PDF or hardcopy form, um, good luck.

On finches beak's and their variation (Location 485 of 1894):"Darwin did not propose a Theory of Variation but a Theory of Evolution.  The difference is this: our observation  of variation shows that living things can experience changes in the parameters that describe existing structures (e.g. shape and size of beak) but evolution teaches that extra complexity can be added to living things in the form of wholly new features and structures and that by this means all life on Earth descended from a very simple first organism."..."Changes in beaks do not involve extra complexity."
Note that Barns seems to think the only thing Darwin studied was finches and their beaks.  Origin of Species covers far more ground and explains far more. Besides there are a wide variety of beaks and some are obviously more complex than others.  The claim that changes in beaks do not involve extra complexity is only superficially reasonable and falls apart upon any kind of study.  For example, look at the differences in these beaks.  Some work best at crunching, others for tool use.  The former requires a strengthened beak but also different muscle attachments on the skulls.  The latter requires more sensitivity.  To suggest they are not differently complex is, well, wrong.

(Location 509 of 1894): "Species is usually taken to mean a set of organisms that will interbreed in the wild and produce fertile offspring.  On the basis of this definition it is perfectly possible for new species to form without evolution."  Here is where we see equivocation with the words 'variation' and  'evolution".  The genes have changed enough in a set of mosquitoes that they cannot interbreed - they are two distinct species but this is not evolution.  "What we see here is simply a group of mosquitoes turning into a different variety of mosquito.  This does not mean that they are in th eprocess of turning into something other than a mosquito.  As they have no biological structures this is just another example of variation."
(Location531): "It is important to understand the limits of natural selection.  It is only a selecting process.  It cannot add a new feature to an organism.... it is not a 'goal-seeking' process."
(Location570): "If, for example, you spend many years over many generations selecting for dogs that can dive and swim you may well get a dog that is very good at diving and swimming, but you will never, even if you spend millions of years doing it, turn that dog into a fish with scales and gills.  Yet this is exactly the sort of thing that evolution requires to happen."
 This is news to me.
(Location 586): Using the analogy of a bank vault (Dawkins') and 'Hunt The Slipper (Barns'), Barns points out that the games have a known endpoint toward which the player is working towards.  "But evolution has no long-term end in view..."
  His descriptions of evolution sometimes seem accurate then he shows he understands nothing.  In the case of evolution of the human eye, there is no endpoint, but a steady progression of improvement and there are organisms that display many of the steps needed to reach an eye as good as ours (and also to the better bird eyes and cephalopod eyes).  We don't need a goal, only value to improvement.  If something can see with only 1% of the ability I can (whatever 1% means), then something that can see 2% as well as I will do better at many tasks.  Both my eyes work but I need glasses.  If I were in a position where I had to choose to be blind or have one eye and no corrective lens, I would choose the one poorly working eye.  If I had to choose between one or two poorly working eyes, I would choose to have two eyes.  If I had to choose between no glasses and glasses, I would choose glasses.  But this is not a 'goal'.  Human eyes are not the endpoint of evolution!  There are eyes known to be better and they are not endpoints either.
(Location 616): Regarding DNA and mutations.  "Evolutionists believe that these accumulated errors have, via natural selection, caused a bacterium to become a man." 
Surely he too believes that accumulated errors have caused finch's beaks to change and mosquitoes to form new species.  He said as much above.  Also, he is offering an endpoint where none exists.  Yes evolution proponents believe that such errors caused a bacterium to become a man but also an elephant, an emu, a parasitic liver fluke, a mosquito.... There is no endpoint here.

(Around location 649): Barns follows standard Intelligent Design dogma in describing information and DNA.  Those claims can generally be described as "a  point mutation is not new information because the sum total of information has not changed.  A duplication mutation is not new information because existing information has simply been repeated." He never touches on what happens if a duplication mutation occurs then a point mutation affects one of the duplicated parts.  He discusses Dawkins' discussion of hemoglobin evolution and follows the ID pattern of demanding each and every step from the simplest protein to modern hemoglobin.

If it is not clear why this is dishonest, let me explain two reasons quickly. First, copying of one globin unit into two similar but non-identical units is an example of a duplication mutation and asking for further details is moving the goalposts.  If you ask for an example of X and get it, you cannot complain that the example does not include A~W.  Second, proteins don't fossilize so showing for a complete array of precursors is impossible even if the theory of evolution is correct.

(Location 673): "The argument of Dawkins' book depends entirely on there existing in nature a process by which extra instructions can be added to the genome."
  Note that Barns' has already mention duplication mutations by this point.
And he does so more around Location 695: "And according to evolution all have to be produced by chance mutations acting on chance duplicated genes."
(Location 703): Barns makes the long refuted claim that the huge majority of mutations are negative and have bad effects.  Under research conditions, the majority of mutations have no effect while some have negative effect and a much smaller but measurable number have positive effects.
Time to leave the book and look at experimental study of duplication mutations.

Talk Origins has had no new content added since 2006 but that just means that, in 2013, there is no reason to not be aware of the content.  They tackle the claim that mutations cannot add information here. An excerpt:
A mechanism that is likely to be particularly common for adding information is gene duplication, in which a long stretch of DNA is copied, followed by point mutations that change one or both of the copies. Genetic sequencing has revealed several instances in which this is likely the origin of some proteins. For example:
  • Two enzymes in the histidine biosynthesis pathway that are barrel-shaped, structural and sequence evidence suggests, were formed via gene duplication and fusion of two half-barrel ancestors (Lang et al. 2000).
  • RNASE1, a gene for a pancreatic enzyme, was duplicated, and in langur monkeys one of the copies mutated into RNASE1B, which works better in the more acidic small intestine of the langur. (Zhang et al. 2002)
  • Yeast was put in a medium with very little sugar. After 450 generations, hexose transport genes had duplicated several times, and some of the duplicated versions had mutated further. (Brown et al. 1998)
Talk Origins also looks at whether mutations can add something new.  To no-one's surprise, they found a few examples.
The Panda's Thumb took off when Talk Origins became static.  They look at experimental data on duplication mutations here. And here.

Scientific American has an article titled Scientists observe new genes evolving from mutated copies. Granted, Barns could not have known of this one as it was published in October 2012, but his claims predicted that such research would not produce results:
In a study in the journal Science, Andersson, Roth and their colleagues demonstrate the process in lab-grown Salmonella enterica. They grew one strain missing a gene key for expressing the essential amino acid tryptophan. The strain needed to rely on another gene, which had a primary job but also a weak ability to take on the missing gene's work. The researchers encouraged the bacteria to duplicate the overworked gene, and its copies gathered mutations—some of which enhanced tryptophan production. At the end of a year's time (3,000 generations later) the bacteria had one gene that did the original job and a second that had evolved a new primary function—manufacturing tryptophan.
Let's look at what other Creationist sources have to say about gene duplication.

It is important to note that the two genes in S. cerevisiae do not perform any new or different function than the one gene in K. lactis. This has been observed in other studies of supposed gene duplications—rather than resulting in “neofunctionalization” (new functions) the result is “subfunctionalization” (dividing of the functions among two or more genes).
Then she offers an analogy for the research.

Suppose I have a TV, and one day it loses the ability to produce sound, although it still has the ability to produce pictures. I go to a used TV shop and find the exact same make and model of TV as the one I have at home, though this one produces sound but not pictures. I purchase the broken TV, take it home, and put it beside my broken TV. The two broken TVs complement each other (they have different defects), and together make it possible for me to see the picture and hear the sound for any given TV program. However, my broken TVs are not doing anything new.
There's a big problem.  The two new genes cover the same area as the original but each now focuses on one part.  The original gene could perform both functions but now two specialists do the functions discretely and better.

Part of her conclusion:
What is clearly not shown in the article is evidence for molecules-to-man evolution. Instead, we observe just how powerless duplication and mutation really are for adding new information that leads to the gain of new functions. However, the authors of the article seem to think otherwise. Carroll states, “They [GAL1 and GAL3 in S. cerevisiae] became optimally connected in that job [their role in the galactose use pathway]. They’re working in cahoots, but together they are better at the job the ancestral gene held. Natural selection has taken one gene with two functions and sculpted an assembly line with two specialized genes.”
Note that she moves the goalposts here.  On the basis of one study, she condemns all of biology when the study in question merely shows that new information can be added. Note the abstract to her post ("Gene duplications followed by subsequent mutation of the duplicated genes are often cited by evolutionists as a mechanism for adding new information to the genome and providing new functions to the organism.") It's dishonest but that's what  you get from creationists.

I am impressed that Purdom gives a link to the abstract of Carroll's study. Note that he isn't saying anything about 'molecules to man', only that duplication mutations occur and add new information.

Jerry Bergman, at, asks, "Does gene duplication provide the engine for evolution?"
He starts by making a claim with no supporting evidence:
Statistical evaluation of the predictions of the gene duplication theory does not appear to be favourable to it. For example, the theory predicts a positive correlation between organismal complexity and gene number, genome size and/or chromosome number. All of these predictions are contradicted by the evidence.
I think that evolutionists believed that humans were the pinnacle of evolution and the most complex creature on Earth - a hundred years ago or so.  I don't have the full quote ready, but Dawkins said something like, "The lancet, a tiny worm, is just as evolved as we are."  No animal alive today can be considered more or less evolved than another.

Here is another ridiculous claim:
Male bees have a haploid number of chromosomes whereas female bees are diploid. This however, does not cause females to evolve faster, as predicted by gene duplication theory.
Since they are the same species they would be predicted to evolve at the same speed and any other claim is...I can't think of a polite word here.

I know that I have only nitpicked his post but some of it is very technical and all I can say is that the simple stuff he got wrong makes me unwilling to accept the complex stuff is correct.  It certainly looks like word salad.