Beneficial mutations still occurring in Lenski's long-running experiment

I'm a little busy with InNoWriMo these days but I had to leave a short note about Richard Lenski's bacterial evolution experiment which has been running since 1988.
Panda's Thumb
Ars Technica
Lenski's own blog.

From the Ars Technica link:

In 1988, Richard Lenski's lab started an experiment—50,000 generations of bacteria later, the experiment is still going. Lenski has watched the bacteria evolve to compensate for the stresses of harsh culture conditions, and he's been able to track the exact changes that allow them to do so. In the process, Lenski's learned a few things about the nature of evolution itself.

In his latest progress report on the bacteria, the lab set up a competition, pitting bacteria that had been adapting for different periods of time against each other. He found that those at the 50,000 generation mark not only beat the ones at 10,000 generations, but these bacteria also come out ahead of the ones at 40,000. The continual improvements suggest that, when it comes to fitness, these bacteria are nowhere close to reaching a point where improvement levels off.

In early November, I went to a Free Methodist church in Barrie, Ontario and heard a talk about creationism.  The speaker was summarizing things Carl Weiland had said (and maybe more -I don't know if Weiland covered this specific subject) and one thing he claimed was that evolutionists claim 100% of all species today are in stasis -that is, no evolutionary change is being observed today.  From the Panda's Thumb link - which is quoting a gated article in Science:

Most recently, the colonies have demonstrated that, contrary to what many biologists thought, evolution never comes to a stop, even in an unchanging environment.

I don't know any scientists that think evolution comes to a stop but there it is.  I don't know what that means.

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.

At Answers in Genesis, Georgia Purdom thinks evolution is shooting itself in the foot. She cescribes research by Sean Carroll

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 Creation.com, 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.

Yes, Christianity is at least a little anti-science

I'm going to weasel a little in this post but let's start with the premise.  Many Christian websites and leaders suggest that atheists consider them anti science. For example, CARM, Faithfacts, Answers in Genesis.

I personally find creationists and organizations, like the above AIG, to be anti science but I think I can start with the easy claim that most Christians should find many Christians anti science.  Here's the weaseling: Evolution-wise, Christians come in three main groups: Evolution-accepting, Young Earth Creationist and Old Earth Creationist.  I don't know how big any of these groups is or percent of the total they take up but it seems that Christians must see at least two major portions of their religion as anti science.

Away with the weaseling.  Here are more, and more concrete data:
Many evangelicals believe prayer cures mental health issues.  Related: Should Christians take Antidepressants? At this church, people had to be reminded to get vaccinated and not merely trust to God to protect them from disease.. Note that I have left out what I think are fringe beliefs about blood transfusions and the few parents who have recently been given jail time for refusing to take their children to the hospital.

I can't say for sure about individual Christians, but Christianity itself, these days, is no sure proponent of science.
---
Added much later: And creationists outright state their opposition to science:

"For example, as a Christian, my faith becomes the focus if evolution is the subject. Facts are notwithstanding."
Mike Fair, R-Greenville, represents District 6 in the S.C. Senate.

To be fair, Mike Fair is not any kind of scientist (nor am I) but his statement is typical of creationists - evidence doesn't matter.

Similarly, many creationists at AIG seem to think taking chemotherapy is denying God.  They are denying the power of science to help people (AIG, Facebook)
From the Facebook link:

"yes, it means the Holy Spirit has been unable to show you how evil the Cancer industry is, and Alleopathy in general. Chemotherapy is the biggest sham ever pulled on world. almost all MD's believe in evolution, revealing their blindness-- how could we trust their ideas and ways with something as serious as cancer?"

and

" If you believe in the Book of Enoch, then you know it was not God who gave us the knowledge of medicine, but the fallen angels. And what better way to take man's faith in God away than to make them masters of their own survival? Why do we need God when we have medicine, science, and technology? Soon we will master God's code (DNA) and will become God's ourselves. Wow! Sounds very familiar (Satan's promise to Eve?). Be careful who and what you put your trust and faith in. As has been stated before, God does not need medicine to cure us."

--

The Dawkins Proof: Rise in violence?

First, a link to Barns' own website where a free PDF of the book is available.

Barns tries to both suggest that Dawkins (and atheists in general) is goodly because of his Godly heritage, and at the same time offer statistics that show violent crime is on the increase as religiosity is on the decrease.  I think he is contradicting himself.  Perhaps Barns is trying to avoid smearing Dawkins with unfounded claims of evil while calling atheists in general evil.

In past posts I have discussed how evolution can support moral behavior and I probably discussed a few instances where highly religious types did evil things.  Humans can find many ways to be evil and I think the results of Zimbardo's horrifying experiment at Stanford best describes how and why. See also SMBC's take on it.

Still, Barns does use statistics to make his point so I can't push away his claims without looking at them.  While, I guess I have to at least discuss them without looking at them as his link does not work.  The link, copied from the PDF available above, has some bits at the end that seem superfluous or explanatory but even with them removed, the result is a 404 error (Not Found).

http://www.homeoffice.gov.uk/rds/pdfs/100years.xls (downloaded 29/03/07)

So, I cannot directly argue against his claims of greatly increased violence but I can look elsewhere for similar or contradicting results.

The Royal Statistical Society, presumably of England or Britain, where Barns got his data, states that many Britons mistakenly believe that violent crime has increased when it has in fact decreased.

Crime: 58% do not believe that crime is falling, when the Crime Survey for England and Wales shows that incidents of crime were 19% lower in 2012 than in 2006/07 and 53% lower than in 1995. 51% think violent crime is rising, when it has fallen from almost 2.5 million incidents in 2006/07 to under 2 million in 2012.

Barns' stats were of the hundred years ending around 2000 so the above doesn't directly address his results, although they do his background claim.  Atheism continues to grow even while violence is declining.

What about the hundred years Barns does describe?  Pinkers' fantastic book, The Better Angels of our Nature (this book is filled with graphs and charts that are surprisingly readable on a Kindle), meticulously, carefully and in minute detail, describes how violence has declined over the past several hundred years. Pinkers' TED Talk on the subject. Wikipedia on the book.

Without being able to see his work, I must reject Barns' claims.  His claims seem indefensible and simply wrong.
---Added on Sept 3, 2013:

At a religion themed blog I found this question: Does reading the bible lead to violent crime?  That site links to data showing that violent crime has fallen greatly and the religious blog ponders this fact:

After all, it seems violent crime has been falling in the past few decades.  Those have been the decades in which American children no longer prayed or read the Bible in their public schools, officially at least.
Religious conservatives have long bemoaned the social dangers of kicking God out of public schools.  Is it only fair, then, to blame God for all the rapes, burglaries, and assaults that haven’t been happening lately?
That doesn’t seem like a comfortable suggestion for most religious conservatives.  Yet thoughtful conservatives must recognize that they have long warned about the dangers of removing traditional religion from public schools.  Some of those warnings, at least, seem to have been flipped on their heads.  Without mandatory Bible-reading in public schools, American society has grown noticeably less violent. 

... [big ellipsis] ...
...violent crime has plunged in industrialized nations around the globe in the past twenty-five years.  As the article describes, talking heads have ascribed this happy circumstance to an array of possible causes: more abortions, fewer young men, better policing, even better violent video games.
Back in the 1950s, when the US Supreme Court had not yet “kicked God out of public schools,” violent crime skyrocketed.  To be consistent, we must ask: Did all that violent crime result from students reading the Bible?  Saying the Lord’s Prayer?  If conservatives predicted that removing Bibles from schools would cause more violent crimes, must they now acknowledge that the USA is a safer place without all that school Bible-reading?

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Added March 20, 2014
These lists of the most peaceful countries and the (lack of) importance of religion by country show a lot of overlap.  The former list is of the annoying new-page-for-each-country sort but most of its countries show up as finding religion unimportant.

I still can't understand how or why the least religious countries of fifty years to a century ago were also the most violent.  I'm thinking of Russia, China and North Korea.  Nazi Germany is not in that list because reports vary on how religious the country and its leaders were.  The leadership at least (mis)used Christian imagery and doctrines to motivate the people there.

I know a tiny bit more about North Korea than the other two countries and it sure seems North Korea, while not at all Christian, follows a perversion of Confucianism.   Elders are revered, with the Great leader now considered a God.
Perhaps in these (hopefully outlier) countries, the problem is that the change to proclaimed atheism was made by the leaders, while in the most peaceful and least religious countries of today, citizenry made the change.

Of course, a large chunk of the countries are in the far north - Denmark, Sweden, Norway and Finland, for example.  Could it be the cold that makes people both non-religious and peaceful?

Off-topic: further defence of Atheism

I have been, and will continue to, critique an Apologetics work titled The Dawkins Proof.  Normally I try to leave religion out of the discussion here and focus on evolution v creation.  I would like readers to accept that I am attacking some versions of Christianity not for their religious claims so much as their poor logic.  On the other hand, I have critical views of the Roman Catholic Church as well, but tend to leave it alone on this blog.  The Catholics, whatever their other crimes- and there are many- do accept evolution after all.

With that poorly argued excuse, let me quote an excerpt from H L Mencken's Memorial Service (For the full list, follow the link).

Nin
Persephone
Istar
Lagas
U-urugal
Sirtumu
Ea
Nirig
Nebo
Samas
Ma-banba-anna
En-Mersi
Amurru
Assur
Aku
Qarradu
Ura-gala
Ueras
You may think I spoof. That I invent the names. I do not. Ask the rector to lend you any good treatise on comparative religion: You will find them all listed. They were gods of the highest standing and dignity-gods of civilized peoples-worshiped and believed in by millions. All were theoretically omnipotent, omniscient, and immortal. And all are dead.

At some point soon, I will be looking at Barn's rebuttal to Dawkins' equating religions to "mind viruses".  Barns doesn't believe such mind-viruses, or possibly memes, could exist and asks how untrue claims could exist for long periods of time. My response is contained in the (partial) list above.  There are many such Gods who were well-accepted by many and I think Barns would agree with me that these could fit the definition of 'mind virus'.

The evolution of compassion

Creationists often claim that evolutionists either cannot be caring, or in caring demonstrate that they were created.  Barns (The Dawkins Proof) is at his clearest here:

The logical outworkings of atheism lead to a belief system that he [Dawkins] is unable to live by.  Its radical materialism destroys the notions of right, wrong and justice- indeed the reality of any concept or idea relating to values and standards...Standards of good and evil are not material - they are something beyond the natural, physical world and therefore, if Dawkins is right, they cannot exist. When Dawkins says that theism is a force for evil he is denying his own assertion about the fundamental nature of existence. (Reading on a Kindle so I cannot give a specific page but this is from the last few paragraphs of Chapter two.)

Barns is clear, but wrong.  Notions and standards of good, evil and justice are immaterial but that does not mean they do not exist or are without value. Imaginary numbers are immaterial but have great value in math.  Good and evil are tougher to explain, but justice is inherently about math, measurements and balance.    There are plenty of philosophical frameworks that attempt to rationalize and codify the concepts of good and evil, usually involving easy-to-understand but hard-to-actually-use criteria like 'acts that maximize happiness' or 'acts that deliberately inflict suffering'.

This is dodging Barn's point and the point of this essay.  Measurable or not, material or not, can our instinctive understanding of good and evil come from a source other than God?

Yes, they can.

Let me give two explanations, one somewhat more theoretical and the other more currently practical, although still under investigation.  The two can be seen as 'Distant Past' and 'Modern Example predicted by Distant Past' or as independent of one another.

First, explanations for altruistic behavior come from Dawkins' own The Selfish Gene (Wikipedia) and from Game Theory.  From the Wikipedia article on The Selfish Gene:

"In describing genes as being "selfish", the author does not intend (as he states unequivocally) to imply that they are driven by any motives or will, but merely that their effects can be accurately described as if they were. The contention is that the genes that get passed on are the ones whose consequences serve their own implicit interests (to continue being replicated), not necessarily those of the organism, much less any larger level.
This view explains altruism at the individual level in nature, especially in kinship relationships: when an individual sacrifices its own life to protect the lives of kin, it is acting in the interest of its own genes. Some people find this metaphor entirely clear, while others find it confusing, misleading or simply redundant to ascribe mental attributes to something that is mindless. For example, Andrew Brown has written:
"Selfish", when applied to genes, doesn't mean "selfish" at all. It means, instead, an extremely important quality for which there is no good word in the English language: "the quality of being copied by a Darwinian selection process." This is a complicated mouthful. There ought to be a better, shorter word—but "selfish" isn't it.[2]"

My own, imperfect, understanding of altruism in The Selfish Gene is that any behavior that increases the number of copies of my DNA is going to be promoted.  So who has my DNA? My son has the most, but so do my nieces and nephews, and my cousins and their children... in increasing numbers but decreasing percentages.  I am not sure if this means I should accept some tiny loss for helping anyone with some of my characteristics?  If I help brown-eyed, left-handed, lazy people, am I in some way promoting my own DNA?  I am not sure if evolutionary explanations can be stretched quite that far.

The mathematical modelling of Game Theory can be.

A short, non-technical explanation of Game theory:

Much of evolution and natural selection can be summarized in three short words: “Life is games.” In any game, the object is to win—be that defined as leaving the most genes in the next generation, getting the best grade on a midterm, or successfully inculcating critical thinking into your students. An entire field of study, Game Theory, is devoted to mathematically describing the games that nature plays. Games can determine why ant colonies do what they do, how viruses evolve to exploit hosts, or how human societies organize and function.
...
In the end, the students learned what social insects like ants and termites have known for hundreds of millions of years. To win at some games, cooperation is better than competition. Unity that arises through a diversity of opinion is stronger than any solitary competitor.
...
Morally, of course, games can be tricky. Theory predicts that outcomes are often not to the betterment of the group or society. Nevertheless, this case had an interesting result. When the students got carte blanche to set the rules, altruism and cooperation won the day. How unlike a “normal” test where all students are solitary competitors, and teachers guard against any cheating! What my class showed was a very “human” trait: the ability to align what is “good for me” with what is “good for all” within the evolutionary games of our choosing.

A popular account of another study:

Although this is obviously a very simple mathematical model and reality will never be as linear, Santos, Santos and Pacheco’s results gives us a total new perspective on how to look at ways of increasing cooperation/altruism and, consequently, also on how to create more successful societies, concerning issues as crucial to our survival as the protection of the environment or fairer social relationships, contributing in this way to the construction of a more peaceful world with less conflict and destruction.

As I understand the results, there are many situations where the winning strategy for a game could be egoistical behavior, but this is not always the case so any blanket statement that acceptance of evolution should mean selfish behavior is wrong.

As a side note, many of the games requiring selfless behavior to get ahead have multiple rounds.  People can see and recall what happened before and react to the justice or injustice of the game.  Apes show a similar understanding of justice.

How would this work?  What mechanism would be used to model fairness and justice?  Mirror neurons.

From Wikipedia:

A mirror neuron is a neuron that fires both when an animal acts and when the animal observes the same action performed by another.^[1][2][3] Thus, the neuron "mirrors" the behavior of the other, as though the observer were itself acting. Such neurons have been directly observed in primate and other species includingbirds. In humans, brain activity consistent with that of mirror neurons has been found in the premotor cortex, the supplementary motor area, the primary somatosensory cortex and the inferior parietal cortex.

These neurons assist us in feeling what others feel, in having empathy.  Empathy then is not (merely or exclusively) immaterial; it has solid, material roots in specific parts of the brain.

I do need to be careful.  These neurons can be used by hunters to understand prey activity or to model the activities of enemies to better fight them.  There is nothing inherently 'good' about them or their evolutionary origins.  Still, tools can start with one purpose and be used for others.

More from Wikipedia:

Empathy [edit]
Stephanie Preston and Frans de Waal,[47] Jean Decety,[48][49] and Vittorio Gallese[50][51] and Christian Keysers[3] have independently argued that the mirror neuron system is involved in empathy. A large number of experiments using fMRI, electroencephalography (EEG) and magnetoencephalography (MEG) have shown that certain brain regions (in particular the anterior insula, anterior cingulate cortex, and inferior frontal cortex) are active when people experience an emotion (disgust, happiness, pain, etc.) and when they see another person experiencing an emotion.[52][53][54][55][56][57][58] However, these brain regions are not quite the same as the ones which mirror hand actions, and mirror neurons for emotional states or empathy have not yet been described in monkeys.
More recently, Christian Keysers at the Social Brain Lab and colleagues have shown that people who are more empathic according to self-report questionnaires have stronger activations both in the mirror system for hand actions[59] and the mirror system for emotions,[57] providing more direct support for the idea that the mirror system is linked to empathy. Some researchers observed that the human mirror system does not passively respond to the observation of actions but is influenced by the mindset of the observer. [60] Researchers observed the link of the mirror neurons during empathetic engagement in patient care [61].

Again, caution is needed.  From an interview with mirror neuron researcher and enthusiast, V.S. Ramachandran:

The other important thing I want to say is that mirror neurons are obviously the starting point for things like empathy, but that’s all it is—I mean, you need much more. If mirror neurons are involved in things like empathy and language and all of that, then monkeys should be very good at these things. One of the things I argue, and others have argued, is that mirror neurons are important in transmitting skills from generation to generation. I need to put myself in your shoes to observe what you’re doing, and to mime it accurately. Mirror neurons are important in that.

Evolution has lead to many successful strategies and many of these are horrific, from the dumping of huge numbers of young in the hope that some will survive as salmon do to the killing of a competitor's offspring to encourage their mothers to mate as lions do.  Still, some of these strategies appear more moral, more 'good'.

I am not sure that the behaviors of bees or ants fit this description.  Individuals of both groups will die to protect their colonies but do so with so little free-will that the result is nearly as abhorrent as more selfish behavior would be.  Still, other social animals often do show admirable behaviors.  Gulls and prairie dogs give alarm calls to warn neighbours of approaching danger (and even here is another trait recognizable in humans: some fraudulently give the alarm call to scare neighbours away from valuable food).

Acceptance of evolution is not the same as atheism so I could have avoided the whole argument by reminding readers that many evolution proponents are also Christians.  Still, the groups, atheists and evolution proponents, are closely linked.

How to argue

Daniel Dennett has a book out, "Intuition Pumps And Other Tools for Thinking", that offers advice on how to argue.  Doctorow, of Boing Boing, quotes a bit that I agree with and one that I, as the point of this blog declares, do not.

Wonderful advice:

1. Attempt to re-express your target's position so clearly, vividly and fairly that your target says: "Thanks, I wish I'd thought of putting it that way."

Not-quite-so-wonderful advice:

A good moral to draw from this observation is that when you want to criticise a field, a genre, a discipline, an art form …don't waste your time and ours hooting at the crap! Go after the good stuff or leave it alone.

I gotta admit that I have heard the latter bit of advice from others and I am entirely willing to believe myself in the wrong.

This blog is dedicated to taking out the obvious bits of crap.  I want to hear the good arguments for Creationism and feel that trying to clear out the crap is worthy - at least of a blog that is updated once a month, if that.

My reivew of Chapter two of The Dawkins Proof

This part one of two for this chapter.  My friend Patrick disagrees with me about this book and I want him to  have room to place his comments next to this post.  He wanted to comment on my review of chapter one but his comment was too long for Blogger to allow.  He then did his commenting on a Wordpress blog post of mine.  I hope that by breaking up my review of chapter two, he will have room to comment here.

Patrick and I are friends and in no way in a teacher-student relationship, but this is my blog and he is 'just a commenter'.  I worry that there may be an asymmetry in our power here and that may affect the discussion. Still, he has agreed to use this forum.  If a perceived imbalance of power occurs, I hope we find a way to work it out.

Still to come: Part two of chapter two -this is becoming too long and my review are likely to become much shorter.  Review of chapter three (this one is about evolution so I suspect it will be long as well), then a 'tangents' post.  Patrick and I, over the course of our arguments, leave the book behind on occasion and I want a place to keep these digressions without losing focus on the book.

This pattern should continue to the end of the book: three chapter review posts and a tangents post...

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This chapter is titled Powerful arguments.

Barns starts by arguing against Dawkins' claim that Christian areas of the US are more violent or have more crime. He feels that the standards Dawkins uses may not show what Dawkins thinks they show. Barns, without defending or offering any counter claims has, for the moment, clouded the issue enough that I cannot rebut him. I do have a copy of The God Delusion and will have to see what else Dawkins said on the subject.

“Oppressed Atheists”

In The God Delusion, Dawkins claimed that atheists in the US are oppressed.  Barns disagrees and offers counter evidence of Christians being persecuted.  His first example is of Dr. Michael Dini, a professor of biology, who required his students to affirm that they supported evolution.

Barns asks, “But what if the origin of human species did involve God?  That idea was ruled out of the question by Dini...”

This is an example of Barns mistaking his version of Christianity for all of Christianity..  Dini himself is a devout Christian.  From the New York Times.

“Another student, Brent Lawlis, 21, from Midland, Tex., said he hoped to become an orthopedic surgeon and had had no trouble obtaining a letter of recommendation from Dr. Dini. ''I'm a Christian, but there's too much biological evidence to throw out evolution,'' he said.”

and:

''He's [Dindi] a devout Catholic,'' said Greg Rogers, 36, a pre-med student from Lubbock. ''He's mentioned it in discussion groups.''

Mr. Rogers, who returned to college for a second degree and who said his beliefs aligned with Dr. Dini's, added: ''I believe in God and evolution. I believe that evolution was the tool that brought us about. To deny the theory of evolution is, to me, like denying the law of gravity. In science, a theory is about as close to a fact as you can get.''

Perhaps Barns is worried about scientifically illiterate Christians.  He seems to be defending the perpetuation of ignorance, rather than Christianity itself.

Barns then looks at  Richard Sternberg who published an article favouring the theory of ID.  Even before we dig into the facts of the case, note that ID proponents claim their work is not religious so I am not sure how attacking it is an attack on religion. Barns is probably correct in connecting ID to Creationism; that is, he is not lying but ID proponents are.

Barns repeats Sternberg’s claim that “attempts were made to force him out of his position” as editor of the journal.  And yet, he had already handed in his resignation letter six months ago. See Expelled Exposed.  His actual work in choosing who would review the article is also in question.

I found this comment of Barns interesting. “No doubt Souder is a supporter of ID - he would hardly be pursuing investigation of this issue if he were an opponent.”  I don’t know; I think many people are able to recognize injustice even when it is done by members of one’s own group.

In Wealthy Theists, Barns looks at Dawkins’ discussion of the .“Templeton Prize”

“Yet he never mentions funding awarded to atheists.  The expenditure of the Templeton Foundation is insignificant compared to the vast state of funding given to university scientists.”

After connecting Intelligent design to Creationism, Barns should be careful of discussing the Templeton Foundation.

The Templeton Foundation, a major supporter of projects seeking to reconcile science and religion, says that after providing a few grants for conferences and courses to debate intelligent design, they asked proponents to submit proposals for actual research.

"They never came in," said Charles L. Harper Jr., senior vice president at the Templeton Foundation, who said that while he was skeptical from the beginning, other foundation officials were initially intrigued and later grew disillusioned.

"From the point of view of rigor and intellectual seriousness, the intelligent design people don't come out very well in our world of scientific review," he said.

Back to Barns and funding for atheists: “According to Dawkins, these scientists are largely atheistic and they are free to use that funding(...) to pursue their science based on an atheistic philosophy.”

First, clearly, funding to universities is not the same as funding for atheists or “atheist philosophy”. Secondly, what precisely is ‘atheist philosophy’? Is there any science that feels required to add “...and with the grace of God,...” to every conclusion?  Newton was famously devout but his equations and laws do not require any action from God for them to work. Atheists and theists alike can use them.  Even Dawkins admits to not being completely an atheist and would agree that no scientific experiment disproves God.  I think he would say, “God is never disproven but neither is he ever required.”

The Dawkins Proof Delusion

I think Dawkins’ views on evolution are, as my limited understanding allows, correct. While I generally agree with his views and talking points for atheism, I am not in nearly as complete agreement and I do see that he is not always consistent. For example, he once suggested that fantasy books might lead children into irrational thinking but also, I think, wrote a glowing forward to Philip Pullman’s The Golden Compass.

Barns' The Dawkins Proof is an attempt at rebutting The God Delusion.  One major problem he has is that he is one the types of people that Dawkins chides mainstream Christians for accepting.  That is, Barns is a creationist, and so at least one of his foundational claims is already torn away.  I would have significant trouble attacking the views of a Roman Catholic or member of the United Church of Canada as their views, in many respects, match mine -and, as far as evolution is concerned, Dawkins' as well.

Below you will find my general complaints about and thoughts about the book and a more specific review of Chapter one (Nothing Beyond the Natural Physical World).  I will post my comments on later chapters as I prepare on them.  I hope to better organize these thoughts but I was concerned the friend who suggested I read the book might get tired of waiting.  If you really want further introduction, look at a previous post.

Barns has a number of recurring problems:

1) He is a lumper: He counts all Christianity as having the same views -including, apparently Creationism.  I am not sure if he is a YE or OE Creationist.

He discusses “The Christian Viewpoint” but there is no “The Christian Viewpoint”. My particular interest is in evolution and there are Christians who are Evolutionists, Old Earth Creationists, Young Earth Creationists and even Old Universe- Young Earth Creationists.  There are Christians who feel Saturday is the Sabbath and those who do not keep it holy are breaking a Commandment....

2) He has a good definition of evolution but doesn’t understand what it means.  Only a few pages after he gives a definition he seems to have forgotten it.

3) He doesn’t define things.  I am specifically referring to ‘Mind’ and ‘rational thought’ or maybe ‘logical thought’

Regarding “Rational Thought” and “logic”: He thinks that because the concepts of logic or rational thinking are  immaterial, atheists cannot believe or use them and still be consistent in their atheism.

Are imaginary numbers “immaterial”?  Their name alone suggest they are not real, yet they have real usefulness in mathematics.

4) He thinks ‘physics’ explains all phenomena - or that atheists do or think it should.

SMBC’s take on physics, chemistry, and biology :

Three Body Problem at Wikipedia

5) His evidence and claims for God come exclusively from the Bible.  That can be a valid source but it needs both internal and external confirmation.  In other texts, internal confirmation requires two parts. First a quote from a character, “I am strong”. and second, a described instance of the character being strong.  In the Bible, God is described as perfect and merciful but also as driving Adam and Eve out of Eden in a rage and destroying most of humanity.  Considering that he made Adam and Eve, the fact that he became angry with their actions is a logical as me being angry with a wood carving I made and found wanting.

External confirmation relates to finding supporting evidence for the Bible’s claims in other sources.  This kind of confirmation can be challenging.  Yes, Egypt is mentioned in the Bible and in other sources, but London is mentioned in Harry Potter and in other sources.  No, it is the extraordinary claims that need support and in many cases such support does not exist.

These two forms of confirmation are entirely absent from The Dawkins Proof.

6) Three levels of defense: I don’t think Barns successfully meets the first level much less the next two.  These levels are (weak): show atheism is wrong, (middle) show religion is right, and (strong) show (my form of) Christianity is right.  As we can see from my final parenthesis, there may be four levels here.

Barns is a creationist and writes as if he is describing the Christian view when a large number of Christians, possibly a majority, accept evolution.  Indeed, the most famous Christians-who-are-also-respected-scientists seem to be Catholics. I am referring to Kenneth Brown (possibly least famous of the group but notably an expert witness as the Dover Trial), Guy Consolmagno (Vatican astronomer, an interview with him is at the bottom of the link) and Francis Collins (Genome Project leader) and their views of the natural world are practically those of atheists.  Here is my example:

When we look at the phenomena of lightning strikes, we cannot say that all lightning is always unguided and always controlled by local meteorology.  All lightning that has been artificially created or that has occurred in locations with observational equipment has appeared to follow rules.  Two views that have no practical difference are 1) Atheistic - lightning is an entirely natural event and entirely explainable within materialistic viewpoints and 2) God made the universe so lightning can happen and can choose- but might not- to influence when and where it strikes and if He has done so, has done so within the expectations of modern meteorology. God is not necessarily absent but neither is he necessarily required.

1) Nothing beyond the natural, physical world

“Non-material things such as God, spirit, mind, Laws, justice do not exist...”

This is a recurring theme for Barns. Somehow he equates the existence of laws or mind with the existence for God.  Laws are immaterial, sure, but no-one claims that legal-type laws (not scientific laws) have real existence.  They are agreements between groups of people but are not the same around the world or even viewed the same way by people even inside of one country.

Scientific Laws do exist but seen as descriptions of reality, not controls that existed before reality.

A huge problem for Barns here is “mind”.  He offers no definition for the concept I am uncertain what exactly I need to argue.  I do understand the idea of mind/body dualism but think it is known to be flawed.  We, Barns and I, need to read Wikipedia and Mirriam-Webster on the subject, but although I am not an expert, and perhaps nobody really is, it is clear that brain damage or various drugs affect mind.  I loved “sleights of mind” a book about stage magic and directing consciousness -this is not mind exactly, but most people don’t understand their own consciousness either. Added later. More from a friend on mind/body dualism. Added even later(!): Brain decoder can eavesdrop on your inner voice

He states: “...nothing special about human life.”

Yes, I agree with this scientifically but as a human would protect the life of a human over that of my cat, for instance.

He states “...no concept of “ought”. “

Why not?  I may get into this more when discussing Barns’ misunderstanding of evolution, so briefly:

Game theory shows how various strategies, often tested in game playing, can improve success.  It seems obvious that selfish people or cheaters will succeed over altruistic, honest people, but many iterations of game theory show this is not so or not always so.  Behavior can be built into genes.  The best way to live a long, healthy life is to be honest and altruistic.

He states “there is no such thing as “mind”.”

See above.

“What is God like?”

Barnes offers quotes from the Bible, which are clearly evidence of nothing.

From my introduction:

His evidence and claims for God come exclusively from the Bible.  That can be a valid source but it needs both internal and external confirmation.  In other texts, internal confirmation requires two parts. First a quote from a character, “I am strong”. and second, a described instance of the character being strong.  In the Bible, God is described as perfect and merciful but also as driving Adam and Eve out of Eden in a rage and destroying most of humanity.  Considering that he made Adam and Eve, the fact that he became angry with their actions is a logical as me being angry with a wood carving I made and found wanting.

External confirmation relates to finding supporting evidence for the Bible’s claims in other sources.  This kind of confirmation can be challenging.  Yes, Egypt is mentioned in the Bible and in other sources, but London is mentioned in Harry Potter and in other sources.  No, it is the extraordinary claims that need support and in many cases such support does not exist.

These two forms of confirmation are entirely absent from The Dawkins Proof.

“It is not surprising, then, that all cultures are theistic in some way.”

It is not clear where this assertion comes from.  Here is a valid idea of why cultures start with some degree of theism:   Some few hundred years ago, there was no explanation for disease and afflictions like Bell’s Palsy, rainbows, rainfall and weather patterns, or lightning.  Many gods from many different cultures have been given the power to use lightning.  Now, we cannot say that God does not personally control all lightning bolts but we can say He is unnecessary. See also: "I still say a church steeple with a lightning rod on top shows a lack of confidence."- Doug MacLeod

Indeed, it is not at all surprising that cultures start with a theistic bent, but that is evidence of nothing.