Carl Zimmer and fused chromosomes

Man, the lengths creationists, and ID is a form of creationism, will go to hide and protect their unsupported claims.

Reactions to the Ham vs Nye debate

This post is not finished but I don't know when that will be.  I watched the opening of the debate live, then stopped and drove to my in-laws and watched the last hour or so.  Then I began watching again and have made it to one hour, thirty-nine minutes.  I do plan to see the fifteen or twenty minute gap.

A friend described those who found Nye the clear winner to be displaying confirmation bias.  I had made similar, but less eloquent, statements so I was pleased to see my own conclusion reinforced.  Still, Nye did a lot right.

I guess I need to give some specifics at the start.  On Feb 4, Ken Ham defended the proposition that Creation is the most viable model of origins in today's modern, scientific era against Bill Nye, who defended evolution.  The video is available at a few locations but I don't know for how long: try here, here and here.

My own impressions:

Ham is getting mileage from his previous debate -at Harvard in the '90s.

Ham has a degree in applied science -emphasis in environmental biology.

five minute intro: Ham begins the attack and offers scientists who accept creationism but do science. Of course, they don't appear to use creation science in their work. Then, he gets into his personal division of science into observational and historic focuses.

Nye takes his time to gain some acceptance by telling a pretty good, but long, joke.  Then he uses the example of CSI to tear down the idea of two kinds of science.  

Billions of people are religious but not creationists.

thirty minute talks.

Ham: More professional scientist claiming they are creationists without any appearance of using creationism in their work.

Ham and one of his scientist discusses Lenski's work: The ability to grow on citrate is not complex new ability.

Andrew Fabich: E-coli supposably evolving.  The information is already there - it's just a switch that's turned on and off.  There's nothing new. ... Later, Dr Lenski and his student read Fabich's claim in horror and have responded 1, 2, 3.  I have excerpted a few paragraphs from the third link below in my notes of reactions to the debate. (More about Dr Lenski.)

"Darwin was racist." From a book -not necessarily by Darwin - "The highest race of all, the Caucasians..." Everyone from the 1800's would appear racist to us today. Australians, Ham's own nationality, had some racist image problems even just a few decades ago.

I just remembered how to do screen shots: 

In discussing the difference between observational and historic science, Ham showed a video of Nye talking about creationists accepting many scientific wonders -including smoke detectors - while yet not accepting evolution.  Ham emphasized a few such wonders -including smoke detectors - and called then observational science.  And yet, I think smoke detectors use the half-life of radioactive elements and this must remain unchanged through history or the detector's results would be meaningless.

Nye:

Deep time. - ice cores.

Nine thousand year old tree.

"Your claim, for me, is not satisfactory." An elegant statement but not a thrilling one.

Nye on Ham's need for incredible speed in evolution to suit creationism's short time line:

Noah's ark and modern shipbuilding.

Around 1:20, Nye talks about the Big Bang Theory. This is important stuff and you need to explain the small details, but it takes a lot of time and comes off as a little dry at a debate.  I hope creationists were listening.

First 5:00 minute rebuttal
Ham:
"You can't observe the age of the Earth"
Radioactive decay - Uranium to lead, etc.

"The point is, there's a problem." - Yes, there is. The radiocarbon dating used on the wood can only give results up to around 50,000 years so a result in that range is equal to a pegged needle.  To suggest otherwise is dishonest. This claim can also be found at creation.com  and the original source, 'research' by Andrew Snelling is at the same site.   Gondwana Research looks into a similar claim here.

The more I think about this, the more impressed I am with Ham's daring, with his cajones (it seems less crude in a foreign language).  If Nye had understood how radiometric dating worked -and why didn't he, this was an obvious direction for a Young Earther to go? -he could have exposed clear dishonesty on Ham's part.

Dr Steve Austin used Potassium-Argon dating on a lava flow from Mt St. Helens.  The results varied greatly.

There is a big problem.  From Wikipedia: "Due to the long half-life, the technique is most applicable for dating minerals and rocks more than 100,000 years old. For shorter timescales, it is likely that not enough Argon 40 will have had time to accumulate in order to be accurately measurable."

slides from 1:32:00 - get them while on Windows computer.

Nye:
Didn't understand about radiocarbon dating - dang it!!! Attempted a rebuttal and moved on.
"Were the fish sinners?"
On Ham's claim that you cannot see the past, "but that's what astronomers do."

2nd rebuttal
Ham:
"What is a kind? ...  Predicted less than a thousand kinds on Noah's ark."
1:42 - planes in the ice on Greenland. Wow!  and Wow!
Bears have teeth very much like a lion or tiger.  Look at a panda's teeth - it looks like it should be a savage carnivore.
      Okay, I just searched with Google images for lion, bear, panda bear and Australian fruit bat teeth.  All have big scary canines.  The bears and bat all have grinding molars and the lion has only cutting teeth.  I guess he figures Nye can't do the search in time for his next turn to talk.

"The Chinese and the Egyptians built big boats. Research shows some had three layers interlocking so they wouldn't twist like that (like the Nye discussed a giant American wooden ship had twisted and leaked)."  Right, except the only place i can find news of three interlocking layers is at Creationist websites and there is substantial disagreement about whether the giant Chinese ships were actually built (some claim they were and did sail to India and elsewhere, others say they only floated in a sheltered lake, others say they may have existed on land and finally some say they were never built).

Horizon problem. Light and the expanding universe.

Nye:
1000 kinds makes Nye's criticism even stronger - instead of needing 11 new species to appear every day, now we need 35!
Nye claims some knowledge of shipbuilding and is skeptical that Noah could build the Ark with seven others.
"...explain to us why we should accept your word for it that natural law changed 4000 years ago, completely, and there's no record of it.  You know, there are pyramids that are older than that."
It is not reasonable to me to believe that everything changed 4000 years ago: species, the surface of the Earth, the stars in the sky and the relationships of all the other things on Earth to humans.

Evolution is not exclusively atheistic.

We need scientists and engineers.
---

Questions from the audience
1st question - Nye asks ham if he can predict something
2nd What was before the Big Bang?  Nye: I don't know - it is wonderful!
Ham: "There is a book..."
3rd dating techniques
Ham:....appendix is very important to the immune system -
...I did make predictions....one race, God made kinds
4th question - how did consciousness come from matter
Nye: "Don't know.  It's a great mystery. ...The joy of discovery."
Ham: There is a book" .. debaters both beyond debate subject....  Ham: after you die, you are gone, why bother with discovery?
5th question "What would change your mind?"
Ham:  long answer  "No one's ever going to convince me that the word of God is not true."
The model of the flood is subject to change but the fact of the flood is not subject to change.
Nye: We would need evidence. Bring on any of those things and you would change me immediately.
--
6th question: radiometric dating
Nye the science is strong on radiometric dating
Ham: showed slide from before "Hundreds of physical processes..."
This is a form of the Gish Gallop.  I know the coral reef claim is wrong and I'm pretty sure the meteor dust one is, too.  Note that Ham doesn't even try to defend any of them so what is Nye to do, attack 50+ in his next turn.  And even if he did, from the little info Ham offered, Ham could say, "No, I meant a different form of meteor dust buildup" or the like.

7th Question for Ham: Compare the rate of continental plates today to the rate 6000 years ago.
Ham: There was a catastrophic breakup.  Historic V observational science.
Nye: It must have been easier for you to explain this a hundred years ago.  The evidence of reversed magnetic fields supports old age slow plate movement evidence.

8th:  Favorite colour

9th: 2nd law of thermodynamics
Nye: Earth is not a closed system.We receive energy from the sun.
Ham: Energy or matter will never produce life.

10th: Could you be convinced the world is older than c10,000 years.
Ham: No
Nye: You want us all to take your claim based on nothing.  What can you predict?

11th: Is there room for God in science?
Nye: yes.
Ham: God is necessary for science.  observational v historic science. We assume laws of logic, nature the uniformity of nature. Where does that (as I've written it, "Where do they come from) come from?

12: Mr Ham, do you take everything in the Bible literally? Should we stone pig-touchers? Should men marry many wives?
Ham: Define literally.  If it's history, like Genesis, take it as literal.  The Bible shows marriage to multiple women causes trouble.
Nye: You pick and choose what to take literally.

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stopped at 2:28

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.

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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.

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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.