12 days of evolution

I find the Dropbox ads a little annoying.  I mean, the content is only two minutes so a 30 second commercial feels quite long.  Still, on Youtube, here are 12 days of evolution.

THE bounty Hunter

I have long been a fan of Piraro's Bizarro comic.  The subject of this one fits my blog so here is a shrunken version of it.  To see it full size, go to Piraro's blog.  Stay a while.

Misconceptions? About evolution? About Creationism?

Jim Stump names and corrects 10 misconceptions about evolution here.  At AIG, Avery Foley tries -and mostly fails, to correct those corrections.

Most glaring, is Foley's counter regarding the second law of thermodynamics.  After correctly discussing open- and closed- systems, Foley quotes astronomer Dr Danny Faulkner (with my bolding):

However, merely being an open system does not automatically mean that entropy decreases. Life depends upon a huge number of complex biochemical reac-tions continually operating. These biochemical reactions operate opposite to the direction that they would naturally proceed. That is, living things synthesize simpler molecules into more complex ones. The inputs are matter and energy (required to bond the more complex molecules), which is why living things are open systems. However, these inputs are insufficient in themselves to circumvent the second law of thermodynamics. The di-rection of the chemical reactions normally is decay from the more complex to simpler molecules, the opposite of what living things require to exist. Given this, the appeal to an open system to rescue the day for evolution is not demonstrated and amounts to hand-waving and gross extrapolation.

I don't understand what Faulkner is saying.  Is he saying that all living things break the second law of thermodynamics.  It sure looks as if he -an astronomer so knowledgeable about physics in general, but not necessarily about biology - is saying that.  Let me help him.
For humans, or plants, or fungae, or archaea, or other animals, synthesizing complex molecules happens all the time  Plants take in water and carbon dioxide and produce sugar.  We use sugar and other organic compounds and make hemoglobin and more.  Yes, plants are also using the sun's energy so they are clearly benefiting from an open system but what about us?  Well, as a newborn, I was around 3 kg.  I feel I was at a physical peak at around age twenty-five.  I don't know when my mental peak was but I sure forget a lot of stuff now so I think I have passed it.  Let's stick with twenty-five.  At that time, I weighed 76kg. Ah, those were the days.
...Anyway, during those twenty-five years, I ate food.  A lot of food.  Far more than 73 kg of food.  From age fifteen to twenty-five, I ate more than 151 kg per year. What did I do with that food?  I was a serious athletes in those days and used the food as energy burned while swimming twelve hours a week, and as the building blocks for muscles of great power and endurance.
I excreted and exhaled most of that mass.  I made the air around me, with my exhalations, warmer and wetter and spread carbon dioxide far and wide, so that it dispersed and settled at the global average concentrations. While concentrating complex molecules in my body, I increased global and universal entropy.  I radiated heat. I released liquids.  I released gases.  And I did so to a greater extent than I locally decreased entropy in my body.  Again, in that last year, I ate 150+ kgs of food, but gained less than 5 kg of mass.

Foley is also concerned with Stump's explanation for how new information can be added to DNA.

He argues that genetic mutations and gene duplication can create new information, but they don’t. All they do is work on already existing information.

Again, I am not sure what Foley is saying.  If I rearrange a word, have I created a new word or not?  'From' and 'Form' are two different words which change the information content of a sentence.

Let's dig in.  Duplication mutations have been observed copying an entire gene.  More localized mutations have been observed changing parts of that gene. The new gene has been observed to have new functions.  How is this not new information?
From Sci Am 1, 2.  From Talk Origins. From Stump's original article.

Is evolution a theory in crisis?

...the vast majority of scientists are evolutionists (although some do doubt evolutionary ideas) ...have been indoctrinated to think that way. They interpret the evidence through the lens of evolutionary ideas because they have an evolutionary worldview. What we do point out are the huge problems with evolutionary ideas that should make it a theory in crisis! The evidence is much better explained through the lens of God’s Word and is consistent with a biblical worldview.

I don't think evolution is a theory in crisis, but I am not about to argue a philosophical point.  I do want to point out that to my knowledge, no evolutionary scientist has had to sign a form promising to only view evidence according to a specific worldview or lose their job.  Foley has.  Everyone at AIG has.  Here is that statement.  There is no such oath for evolution proponents.  Creationists are not automatically guilty of deliberate misrepresentation of the facts but are automatically more highly suspected of such misrepresentation.

On the fossil record and transitionals:

A fully formed and functional creature is discovered, and it’s labeled a “transitional” or “intermediate” creature because it’s interpreted that way based on assumptions about how life formed and how old the fossil is. A biblical creationist will go and look at the exact same fossil and reach an entirely different con-clusion, that this is a fully formed organism that belonged to one of the original kinds God creat-ed, because we have an entirely different starting point—the true history revealed in God’s Word.

Here is another example of creationists and evolutionists looking at the same evidence - only the evolutionist looks at all the evidence.  When we find a 'fully formed organism' or fossils thereof, we also note that it is only found among a set of specific other animals, looking for all the world as if some animals had roamed the earth and gone extinct and new animals appeared and gone extinct then the fossil in question appeared and gone extinct then we appeared in the fossil record. This does not in any way resemble a 6-day Creation story.
About the fossils themselves - we have a beautiful set of seven transitions from fish to amphibian.  One such fossil was found by making predictions based on an ancient Earth and evolution principles.  Tiktaalik is a big problem for creationists like Foley.

Via the Sensuous Curmudgeon.

AIG: All cats are one kind

At AIG, they've partially answered a question I've had for a long time.  Some time ago, Ken Ham stated that kinds could be similar to the modern genus or even family level of relationship (His statement is highlighted at that link and also mentions the information below.  I only found it after the quoting below so I'm leaving this post alone - it now has internal confirmation).  And yet, I'd never seen an example to be studied and considered.

In an article mostly about errors in illustrating Bibles, Bodie Hodge states:

Putting too many individuals of a kind on the Ark: We often see lions and tigers and other cats entering or exiting Noah’s Ark.1 There is only one cat kind (cats can interbreed with each other), so Noah only took two cats on the Ark. Of course, they had the genetic information which can account for the cat variations we see today (as a result of various selection processes over time). The same with dogs—there is only one dog kind, so Noah only needed two dogs on the Ark, no dingoes, wolves, coyotes, and so on. The same goes for the bear kind, ceratopsian kind, sauropod kind, elephant kind, horse kind (zebras are part of the horse kind—they are a variation of the horse that is post-Flood), and so on. Learn more about kinds.

"There is only one cat kind

(cats can interbreed with each other),

so Noah only took two cats on the Ark."

Wikipedia tells me that there are 41 species of Felidae known today.  From massive saber toothed tigers (which aren't tigers, if it needed to be said) to pack-hunting lions to the solitary short-tailed lynx of North America, all are one Biblical kind.  That's a lot of variety for one kind, for 'micro' evolution to accomplish.  And even more to accomplish in a few thousand years.

How long did Cats have to evolve to this variety?  If the flood occurred four thousand years ago, that sets an upper boundary, but we can shrink it immediately to three thousand, six hundred because settlers in North America learned about local cats and the Native Americans did not note in oral legends any new species appearing recently.

Neither did European, Indian or Asian written records.  This puts a reasonable but negotiable upper limit at fifteen hundred years, plus or minus a little. What about the cats in North America?  It's hard to say but once the continents separated, it is unlikely for later transfer of species.

We are looking at 41 species to evolve and some to die out in under 2,000 years.  And none to evovle since then.

This is the problem with Creationist kinds.  They require evolution to occur at rates far faster than ever observed and also for evolution to stop even while we see it occurring today at rates historic records tell us are reasonable.

The Peppered moth controversy

I follow a blog that discusses evolution-creationism arguments and has a 'creationist wisdom' feature.  Most recently, the blog looked at an editorial in the Dalton Daily Citizen.

In this editorial,the author mentioned Pepper Moths and complained that the moths were pinned or glued to trees for the photos.

And you might also check out the textbook peppered moth story — dead moths being affixed to a tree trunk in order to stage photographic “proof” of evolution. The list goes on and on.

I can only imagine the author thinks photographing butterflies and moths is easy.  I've been lucky a few times but many times have ended up running through a field with the camera ready, trying to catch up to the insect on the wing.  It never ends well.

From Hoaxes.org:

Since the mid-1960s most Biology textbooks have included the story of the peppered moth, accompanied by Kettlewell's two photos (or ones very similar to them). The ubiquity of the images made it that much more shocking when the public learned the photos were staged. Finding black and white moths posed beside each other in a natural setting would have been almost impossible, so to create the photos Kettlewell pinned dead moths to tree trunks. Moth experts knew the photos were staged because live moths would not have had extended wings. But no textbook ever disclosed this detail to readers.

The thing about the peppered moths study is it simply shows small-scale evolution, the sort creationists claim to accept.  Look at changes in peppered moth colouration or changes in maturation in cod or tusk length in elephants and you see the beginnings of a transition.  Look at ring species like salamanders in the Western US or gulls species about the north pole and you see a bigger step.  Genetics and fossils show the larger scale steps.  For creationists to complain about peppered moths is to see their inconsistency - "Micro evolution is okay, but this micro evolution must have been faked."  Which is it?
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Added a few hours later:
Paul Braterman has a wonderfully detailed account of the history of Peppered Moth research.

Sci Am has 170 years of articles on Evolution

It is as the title says.  It is part of their Celebrating 170 years of Scientific American and of course, they are likely to have 156 years or less of evolution article as Darwin's theory was proposed only that many years ago.

I'm just dumping the link here.  I currently have four different Chrome windows open on a variety of subjects and need to clean up my desktop a little in order to get some real work done.

This weak a blog post will not surprise Marian66, who discussed the evidence for the Big Bang and more in the comments to this article:

Your vile rejection of God is duly noted. You sound like a teen who thinks he knows it all. But you have no idea what you are talking about. Your poorly structured and written blog points to that. You are blind, friend. But I will pray for you. Again, when the day comes, and it will come, when you stand before God, you are not going to get a second chance to accept him.

OT: a response to Parnell's "homosexuality is different from other sins"

Added later:
I wanted to mention that I found Parnell's article on Facebook.as a suggested post after I clicked on a friend's post, 9 sins the Church is okay with.  The 'sins' in that post were strange and not all that connected to the Bible as far as I could tell.  Anyway, I'm writing this introduction to specify that I haven't been hunting for Christian blogs or news to attack. It was suggested to me on Facebook.

---Original ---
Jonathan Parnell, at his blog, Desiring God, wrote about the difference between homosexuality and other sins of the Bible.  His blog does not have a comments section but he does have a Twitter handle.  I wanted to discuss his post and this blog is the closest in theme I have to use.

Jonathan Parnell, "Why homosexuality is not like other sins"

"the unrighteous will not inherit the kingdom of God? Do not be deceived: neither the sexually immoral, nor idolaters, nor adulterers, nor men who practice homosexuality, nor thieves, nor the greedy, nor drunkards, nor revilers, nor swindlers will inherit the kingdom of God."
...
"At this moment in history, contrary to the other sins listed here, homosexuality is celebrated by our larger society with pioneering excitement. It’s seen as a good thing, as the new hallmark of progress."

"To be sure, the masses increasingly make no bones about sin in general. " -the end of this paragraph does mention, "in the church" but I feel Parnell needs to emphasize the hypocritical aspect of attacking homosexuality now.

In a long paragraph, Parnell names several other sins.  I have elided details to leave the names:

"But as far as I know, none of those sins is applauded so aggressively by whole groups of people who advocate for their normalcy. Sexual immorality .... Adultery .... Accusations of greed .... There’s no such thing as a drunk agenda yet. Most aren’t proud to choose a beverage over stability, and there aren’t any petitions that the government should abolish the driving restrictions of inebriated individuals. Reviling others .... Swindling, ...conniving scammers."

To paraphrase Parnell, "None of those sins is punished or attacked in church sermons as vigorously as homosexuality". Divorce and remarriage are common among Christians - this seems to be a form of immorality accepted by church-folk.  As for Greed and swindling, the wonderful John Oliver devoted 20 minutes to discussing the greed of a large number of church leaders.

But the bigger problem with Parnell's list is that he doesn't see anything different about homosexuality compared to the rest of the listed sins. Briefly, to a non-Christian in a secular society, homosexuality is victimless.

Homosexuality, or more properly, the opportunity for homosexuals to now get married, is a sign of love and desire for a stable long-lasting relationship.  Adultery is a sin that works to break up such relationships and usually happens in a moment of weakness.  Greed is a sin requiring more deliberation and outright evil.  It is the act of desiring more money than one has earned.  Drinking alcohol, and by extension, using other drugs, is of questionable morality but driving or attempting professional work while drunk causes a threat to all around that person.

I have heard some Jews describe some of the religious laws they follow as tests.  I think it was Van Halen that required bowl of brown M&Ms in their backstage room.  They didn't particularly care about the M&Ms; they cared that someone had read their contract and had followed their rules.  In the Bible, wearing clothes of mixed fabrics is forbidden, but as my Jewish friends explained, it was there as a test, a sign of their willingness to submit to God's authority.
Many Christians eat pork and bacon.  Many eat shrimp.  Many get tattoos. These are forbidden but they are different from sins of theft and violence.
And so is homosexuality.  This is why homosexuality is not like other sins.  It is victimless or the only victim might be the perpetrator.  A man who drinks alone and heavily but does not try to drive a vehicle or perform surgery is harming himself but no one else. This is different from murder.

 Homosexuals might or might not be harming themselves - you're welcome to the opinion that they are - but they are not harming others.  Their actions are different from murder.

As an aside, I note that Parnell's list of sins is quite lightweight. There are lots of things in the Bible described as sins.  Indeed, the translations of the Bible I read for this post do not use the word 'sin' in 1 Corinthians 6-9 (where his quote comes from). A quick search of Google suggests there are 125 sins described in the Bible. Parnell isn't interested in comparing homosexuality to murder or lying, which are Commandments.   The one he and I most agree on from his list is thievery as a sin. I would describe swindling as a form of thievery.

Greed, or in other Bible translations, 'covetousness' , can be damaging but is the heart of the Capitalist system of economics.

In Parnell's list, sexual immorality and homosexuality are both mentioned.  As a non-Christian, consensual sex between or among adults is seldom immoral of itself.  Adultery, which damages marriage and breaks vows one chose to make is usually immoral to some degree.

"As Christians, we believe with deepest sincerity that the embrace of homosexual practice, along with other sins, keeps people out of the kingdom of God. And if our society celebrates it, we can’t both be caring and not say anything. "

Then also speak up against greed and swindling, especially when done by clergyfolk.  Speak up against divorce and remarriage.  Speak up against the lies of creationists.  If Christians want the moral upper-hand, they need to speak up against sins that are crimes against others with at least as much vehemence as they do against homosexuals.

Creationism in Korea

The Marmot's Hole is the place for English news in Korea.  Today, it featured a post, caught in the screen shot from Feedly above, that disappeared.  Then, a new post, covering overlapping content appeared.

Yonsei University, one of the oldest universities in Korea, is now offering a course on Creationism – the belief that the Universe and Life originate “from specific acts of divine creation.” The Hankyoreh has a good article on this and the (electrical engineering) professor’s description of his course is interesting:

And their quote, coming from the Hangyoreh (a local newspaper):

It isn’t about how creationism is correct and evolution is always wrong,… As a Christian studying and teaching engineering, I have often had to think about faith and science. My aim is to talk about these concerns with students – not to try to boost creation science,…scientists in the Christian faith “often experience conflict between the words of the Bible and their scientific understanding.” The course, he explains, is intended to “find the parts of the Bible that can be tested scientifically and aid Biblical understanding through a scientific approach to creationism and evolution.”

The Hankyoreh article does not make clear whether the class will defend creationism or defend theistic evolution or the like but that very uncertainty is driving some (like me) to fear the weasel words are hiding the intent of the class.

The comment section is already active with a commenter from England, Richard Forrest responding to creationists there.  I believe this Forrest is also active on Talk Origins, a evolution/creationism Google Group.

I shot my mouth off a few times there as well.

Archaeological evidence for a Looooonng stone age

From the Natural Historian:

Trillions of stone artifacts cover the surface of the African continent. The product of the manufacturing of stone tools by hunters and gathers over long periods of time, these stone artifacts literally carpet the ground in some places in Egypt and Libya.
Just how much Stone-Age produced rock could be strewn across the African continent?
Trillions and trillions of artifacts!
The trillion isn’t a typo. That number sounds absolutely fantastic, doesn’t it?  Let’s take a look at how these numbers were derived.
The results of a study just published (see references below) shows how incredibly dense stone artifacts can be in some places in Africa.   Working in a remote location in southern Libya, researchers took surveys from hundreds of one or two-meter square plots. From the tens of thousands of artifacts found in them, they estimated a minimum density of 250,000 stone artifacts per square kilometer is present in this portion of Libya.

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One of the interesting parts of the article was the timeline given by AIG.  It includes an Ice Age.  It does not contain a stone age.  I have always wanted a Creationist timeline of Biblical and world events to see if and how they put them together.  Such a timeline would not need to include volcanic eruptions in Austral-Asia unless records show they affected the Middle-East but perhaps  1) a suggestion for when humans arrived in Australia would be handy- along with evidence supporting the date.
2) Geologists and Paleontologists claim evidence for five or six extinctions and several Ice Ages.  I don't know the details but would like to see an explanation for only one extinction and only Ice Age.
3) The start and end dates for construction of the Egyptian pyramids.
4) known fossil layers - From Pre-Cambrian on.
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Back to the numbers of stone tools.  My Internet connection is not working right now so I am typing this in Wordpad.  When I am connected, I will try to find the link from Terry Mortenson of AIG who critiqued the original blog post.  If I do not, then note that two other bloggers that I do have links for have responded to Mortenson's reaction.  They are:
Age of Rocks

and Evoanth

From Age of Rocks:
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More importantly, Terry makes no serious or scientific attempt to explain why anthropologists and geoarcheologists have misidentified thousands of artifacts, which were actually created by random collisions with other clasts. He essentially mocks those who are familiar with the process of weathering and erosion and have long considered how to distinguish random chipping from human knapping. He writes:
Below quoting Mortenson:

As AiG geologist Dr. Andrew Snelling commented to me after seeing the pictures and reading the article, these are mainly gravels transported and deposited by moving water. In the process they were rounded or shattered to varying degrees… Dr. Snelling added, “Such ‘artifacts’ are not found all across Africa, as there is much of Africa that isn’t desert. And they are not seen anywhere across the USA that I am aware of, or in Australia.” (emphasis added)

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Age of Rocks points out that looking at a few photos and saying, "No, that's wrong" is not how science works.  Best would be if Snelling went and handled some of the rocks in location but an entirely acceptable alternative would be to read and respond to the actual published study.  AofR also notes that Snelling appears unaware of the Clovis people that lived in North America, including the USA and are known for their stone tools.
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Evoanth (not sure what this is a shortform of) notes this part of the Mortenson's rebuttal:

...these [artifacts] are mainly gravels transported and deposited by moving water. In the process they were rounded or shattered to varying degrees . . . In any case, they are not all artifacts (“stone-age” tools) scattered over this vast area. In fact, it is highly questionable if any but a few of them are.

Evoanth responds:

Stop the presses everyone. Stones can break naturally. This is something now archaeologist had ever realised! It changes everything.
Oh wait, yes they had. Scientists are fully aware that rocks can break naturally (such rocks are called geofacts) and have a whole raft of techniques for telling them apart from actual artifacts. 

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Evoanth then gives a list of four such techniques that you will have to visit the site to learn for yourself.
I have a really trivial example to post here.  Two, I guess.  First, in an animal behavior class in university, I studied bees that lived under a layer of glass.  The hive was basically two-dimensional except for bees climbing over each other.  There were no extra combs out of sight.  When I started my research, all I saw was a lot of bees moving aimlessly.   After twenty minutes, I saw my first waggle dance.  I noticed more waggle dances as time went on until I saw that there was one or more every minute.  My classmates and I would impress passers-by with, "Look, right there, a waggle dance..... There's another." And the spectator would see them but not be able to find any more until we pointed them out.
Second, and far more trivial.  I lived and worked near lakes and on boats throughout my childhood.  While painting a cottage near the water, a coworker asked me about a high-pitched hum he heard.  Without hesitation, I told him it was the whine of hydraulics in an Inboard/outboard boat motor.  He looked out and saw one just leaving its berth and the propeller mechanism was being lowered to cruising position.

I don't want to pretend to be an expert in any field but I do have sympathy for actual experts whose results are ignored or ridiculed with no real basis.  Rocks that break through chance have different characteristics than ones that are repeatedly smashed in one orientation. A geologist like Snelling might have the necessary background but he would do better to explain why the stones look more like ones washed along by a river than hand knapped into shape.

What is consciousness?

TL;DR:   Nobody really knows.

For a little more detail, there is an interesting article on research done at San Francisco State University.   Here is a big excerpt:

Consciousness, per Morsella's theory, is more reflexive and less purposeful than conventional wisdom would dictate. Because the human mind experiences its own consciousness as sifting through urges, thoughts, feelings and physical actions, people understand their consciousness to be in control of these myriad impulses. But in reality, Morsella argues, consciousness does the same simple task over and over, giving the impression that it is doing more than it actually is.
"We have long thought consciousness solved problems and had many moving parts, but it's much more basic and static," Morsella said. "This theory is very counterintuitive. It goes against our everyday way of thinking."
According to Morsella's framework, the "free will" that people typically attribute to their conscious mind -- the idea that our consciousness, as a “decider,” guides us to a course of action -- does not exist. Instead, consciousness only relays information to control "voluntary" action, or goal-oriented movement involving the skeletal muscle system.

I enjoyed Sleights of Mind, a book on how magicians perform illusions and how we trick ourselves.  It touches on similar subject matter.

The study of consciousness relates to evolution and religion in what our minds actually are. Is the mind part of an incorporeal spirit or entirely a product of the brain.  I think Morsella's research supports the latter concept.  Some background at Wikipedia.
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Added Sept 29, 2015:
BBC on Blindsight and consciousness.

Picking apart the experience may also reveal further clues about the power of unconscious mind. To understand how, imagine that you are part of a strange puppet show. You have been blindfolded, and your limbs are tied to invisible strings. Every so often, they are tugged here or there by a hidden puppet master, leading you through a complicated dance. To the audience, it looks like you are in full control of your actions, but you don’t have the foggiest idea of what you’ve just done.

The non-conscious mind acts as the puppet master, pulling the strings without their knowledge

That puppet show is essentially what happens when someone with blindsight navigates their way past obstacles – with the non-conscious mind acting as the puppet master. “It shows that awareness isn’t the whole story,” says Tamietto. “Very often we believe we have decided something, but our brain has made the decision for us before that – in many ways, and in many contexts.”

Fossil evidence

In a previous post, I wrote about what evidence we should expect to find and whether gaps in the evidence were deal-breakers.  in brief, I tried to show there are places where we shouldn’t expect a lot of evidence (Smaller plants and animals are generally less likely to fossilize, as are soft bodied plants and animals.  Soft body parts, such as organs are less likely to fossilize.  Chemical traces are similarly fragile and their lack does not mean they never existed).  This isn’t to mean that there is no evidence for evolution or that we should accept evolution, or any scientific theory, on bad evidence.  Only that pointing out a lack of evidence in one area does not mean other similar areas are also lacking.

Here’s an example.  I personally don’t know what transitional fossils there are between dinosaurs and mammals.  Similarly, I don’t know what early carnivore might have transitioned into canines, felines and mustelids (the group containing weasels, otters, wolverines and more).  Partly, this may be due to my own ignorance as I have not dug into evidence or fossils in these areas.  On the other hand, there is excellent, finely graduated evidence for transitions between fish and amphibians. There are good transitionals between an ancient land mammal and whales.  There are so many fossils showing a transition from dinosaurs to birds that I personally don’t know which ones best show bird ancestors.

I blamed my own ignorance above but I also see ignorant people on Twitter claim there is no evidence for fish to amphibians.  I wish they would investigate where they lack knowledge before proclaiming it wildly to make a claim.  I have admitted my own ignorance above but not as a claim or to promote a conclusion.

Alright, to the evidence!

1: Fossils

First, it should be noted that fossils are found in assemblages that support an ancient Earth and evolution over a long period.  There are (very few) fossils of soft bodied organisms that pre-date the Cambrian Explosion.  In 2014, in the Cambrian fossil beds, a vertebrate fish was found, the Metaspriggina. This early fish was jawless.  Another, similar fish existed: Haikouichthys. The Pikaia, a chordate, also lived during the Cambrian.

I have heard and read the claim that all phyla were present during the Cambrian so they must have been created.  Again, there are fossils older than the Cambrian era and a phylum is a big group.  I have given examples of a chordate and two vertebrate fish but there are no jawed fishes, no amphibians, no reptiles, no birds, dinosaurs, mammals, crocodiles, or turtles.  Sharks don’t have bones the way other vertebrates do so I am uncertain on this point, but I believe there are no examples of them, either.

So, we have a period of sealife only, a period where, among vertebrates, only amphibians existed.  A period of dinosaurs, a period of giant mammals, then a period, continuing now, with humans.  There are animal groups that bridge some of these eras - sharks, turtles and crocodiles existed with and even before dinosaurs- but the groups I first named are discrete.  In one group of fossils, there are no land vertebrates.  In another group, there are dinosaurs but no large mammals or people.

We don’t need to stick to vertebrates.  Another famous group of animals that existed at one point and not with animals of other periods are the Ammonoidea.

The evidence I have given is, I would say, weakly supportive of evolution.  This is a broad strokes, a long distance look, at the evidence and at this scale we can only say that a primitive group of fish existed, then more advanced fish, then amphibians, then other terrestrial vertebrates.

While it offers only weak support to evolution, it seems, ah, the first nail in the creationist coffin.  Comparing the broad strokes of the fossil record to the creationist claim that all creatures were created in one week and that specimens of all such species died in a single year during the flood shows great conflict.

I’m describing it thus to emphasize the difference between support for one explanation with conflict for another.  If a piece of evidence appeared that conflicted with evolutionary accounts, that would not mean that creationism must then be correct.  On this blog I primarily deal with Biblical Young Earth Creationists, but Hindus have their own creation beliefs as do other religions and there are probably other propositions as well.

Transitional Fossils

What is a transitional fossil?

It is:

• A snapshot of the existence of a single individual of a population
• It has features of two distinct groups
• Almost entirely lacking in organic molecules.
• Without DNA, it is impossible to say if it is the direct ancestor or not (a grandfather or a great-uncle)
• What they show is that a transition from group to group is possible .

In finding one, or a few, specimens, much can be determined of how the creature ate and lived, but not the range of its species’ survival.  Statistically, a fossil is likely to be made when the species is at peak population and geographic spread.  But when did the first individual of this group appear?  When did the last go extinct?  We can’t know.  This means that the fossil Archaeopteryxs, which are found later in the geological records than true birds appear, might still be the ancestor to true birds.  To my knowledge, scientists do not think so but the placement of the fossils is not definitive.   Archaeo has feathers but also a long bony tail and teeth.  there are other features which belong to one group or the other but are a little technical for me. Since Archaeo, many dinosaurs have been found with feathers.  Yet another new feathered dinosaur was recently found.

Some fossils do contain some organic molecules but these have so far been too degraded to run any tests suitable for identification or DNA comparison.

To be completely fair, transitional fossils do not mean that creatures must have transitioned from one species to another, but only that it is possible. Many creationists plaintively ask, "What good are feathers on an animal that can't fly?" From Creationtoday:

Reptiles have four legs, while birds have two legs and two wings. If the front legs turned into wings, the evolutionist has to believe that somewhere in the evolutionary spectrum they had to be half-leg, half-wing. This means, during that time, the creature couldn’t run or fly, and had a serious survival problem.

In this post, I am discussing evidence here, not arguing against specific claims, but briefly: Dinosaurs are not reptiles, many dinosaurs move on two legs.  One of the most famous dinosaurs has tiny, nearly uselessly small arms (T rex) which might be good evidence for evolution on its own.  There are lots of birds that have wings and run well but cannot fly.

Dr Kevin Padian, at the famed Dover Intelligent Design Trial, displayed some remarkable presentation slides on bird evolution that even show how the feathers evolved. His other slides are at the same site and show more transitions. The Fish to Amphibian transitional series is wonderful at least partially due to a creationist joke.

Creationist: There is a huge gap between A and Z.Evolutionist:  We found fossilized M.Creationist: There are now two big gaps.Evolutionist: We found fossilized F.Creationist: There are now three big gaps.

….

Padian’s slides show a full five or more transitional fossils between fish and amphibians.  Around the time of the trial, a new fossil was found, Tiktaalik, which filled in even more of the space between fish and amphibians.

Just last year, researchers raised a group of Senegal fish, bichirs, out of the water to see how they would adapt.  They already possessed gills and lungs and learned better how to walk and wriggle around out of water.

I should have a post on DNA evidence for evolution soon.

A first look at evolutionary morality

A common creationist argument against evolution is the existence of morality.  How and why do we use the terms good, evil, right, wrong, bad?

This video has the start of an answer.  I have elsewhere used a similar argument -without Dawkins' eloquence or the neat animations - and am glad to see it so clearly described.



As I see this, I think:

As a population, humans are comfortable with or capable of carrying perhaps 5% cheaters.  In the example above, if one person cheats once in a while, s/he gets a great benefit but no one suffers much of a loss.  Losing one fish a month isn't that bad.

This does explain how many people (I think nearly all) will cheat or steal in rare instances but few do so most of the time.

It doesn't really explain how we feel or experience good, evil or conscience.  In my opinion, this is an unconscious psychological effect.  Just as women are said to be attracted to different types of men depending on their menstrual cycle but not be aware of their change in judgement; just as apparently rational men and women irrationally treat tokens as less valuable than money ( see Dan Ariely on Youtube or his books.  The talk I haven't had time to find was one about casinos using tokens as guests don't attach the same significance to them.) despite their equivalent value, people feel pangs of conscience as a result of worry or nervousness.

I want to explore this further but this is where I am heading.

Evidence is a funny thing.

Here are a series of Tweets that have had extra details removed.  Most of the excised details are of the original poster's ID and the IDs she was responding to.

Tami ‏@Tam...yama  Jul 27

Genetic entropy &  information & code in DNA refute biological evolution.

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No mechanism exists that adds novel function info to DNA that allows, say, fish to evolve to amphibians or ...

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.. reptiles to birds ... or invertebrates to veryebrates. So my rejection of evolution is EVIDENCE-based.

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Here is my attempt at a full-length response regarding evidence.  I believe the results of the Lenski experiment show how a duplication mutation followed by local mutations can add novel functions to DNA.

Evidence is a funny thing.

I want to start this discussion with some examples of events where we don't expect evidence of their occurrence.  I will start with New Testament examples so even before that, let me start with a reminder that where evolution is concerned, neither I personally nor the theory of Evolution is anti-Christian or anti-religion.  The Roman Catholic Church has long accepted evolution with a wonderful sentence on the subject from Pope John Paul II.
 "The convergence, neither sought nor provoked, of results of studies undertaken independently from each other constitutes in itself a significant argument in favor of this theory."

In addition, around 13,000 (13,008 signatures, as noted on my Birthday - probably not related) clergy in the USA have signed a letter stating that they see no conflict between their religious beliefs and the theory of Evolution.

OK, miracles in the New Testament where we do not expect evidence.  First, the miracle of the Loaves and Fishes.

Jesus Feeds the Five Thousand13 When Jesus heard what had happened, he withdrew by boat privately to a solitary place. Hearing of this, the crowds followed him on foot from the towns. 14 When Jesus landed and saw a large crowd, he had compassion on them and healed their sick.
15 As evening approached, the disciples came to him and said, “This is a remote place, and it’s already getting late. Send the crowds away, so they can go to the villages and buy themselves some food.”
16 Jesus replied, “They do not need to go away. You give them something to eat.”
17 “We have here only five loaves of bread and two fish,” they answered.
18 “Bring them here to me,” he said.
19 And he directed the people to sit down on the grass. Taking the five loaves and the two fish and looking up to heaven, he gave thanks and broke the loaves. Then he gave them to the disciples, and the disciples gave them to the people.
20 They all ate and were satisfied, and the disciples picked up twelve basketfuls of broken pieces that were left over.
21 The number of those who ate was about five thousand men, besides women and children.

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It would be crazy for anyone, believer or not, to go to Bethesda, apparently on the Jordan River,  and look for evidence of the miracle but let's imagine someone tried.  They might find fish bones - but this is on the side of a river, so bones would hardly be surprising.  Maybe, if we wanted to stretch a point to a ridiculous extent, we could imagine looking for the bones of a thousand or so fish, all in the same location and all with enough good DNA in them to show they were somehow clones of each other.  That might show they were perfectly replicated in the miracle.
This excludes the possibility, though, of God choosing to make the fish pleasing each individual taste so all had their favorite, whether it be bass, trout, carp or well, fish that actually live in the Middle East rather than my native Canada.
So, we have a situation where finding the (far-fetched) evidence would defend the claims of the miracle but not finding the evidence does no injury to those claims.
The same might be said regarding evidence of Mary's virginity during her pregnancy.  'nough said.
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ADDED LATER:
Snopes on The Lost Day (This is about the claim that NASA engineers working to organize their satellites for long periods of time, had made a computer program to plan for a hundred or a thousand years.  But the computer broke down and the reason was, there was a missing day.  This is crazy as Snopes explains)

Regardless of the amount of time involved, the discovery of a "missing" period of time remains implausible. If the sun had indeed stood still for a day a few millennia ago, we would have no way of determining that fact through astronomic observations today. We have no frame of reference, no cosmic calendar or master clock to check against to see if we're overdrawn at the Bank of Time. The concept described here would be like giving someone a non-functioning clock and asking him to determine how much time had elapsed since the clock had stopped running. One could note the positions of the hands on the dial and make a reasonable guess about what the time of day was when the clock stopped running, but without knowing whether that time was A.M. or P.M., and without knowing the calendar date on which stoppage occurred, one could not possibly make any reasonable estimate about how long ago the clock stopped
Read more at http://www.snopes.com/religion/lostday.asp#I5UKJbwmB6WfiB9k.99

AIG agrees as does ChristianAnswers.
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The point is, a lack of evidence for an event is not evidence of a lack of that event.

So now we turn to transitional fossils and their apparent lack.
As before, although I just said we would look at evidence, let's first look at what 'transitional fossils' are or should be if they exist.  A transitional fossil is an example of a once-living creature that has features of two different groups.  I will use 'Archaeopteryx' as an example to demonstrate what a transitional fossil is and isn't.
archaeopteryx appears to have characteristics of both dinosaurs and birds.  There are some features that are too technical for me to comment on but a toothy beak (dino), long, bony tail (dino) and feathers (bird) are good starting points.
Was Archaeopteryx the actual transitional species?  There is no way to be sure but it seems likely not.  The stony remains that hold the shape of the original bones do not have DNA and I wonder if full DNA would even help - we would need good exemplars of several dinosaur species DNA to compare it with.  The stony remains can only tell us that an animal existed that had the features expected of a transitional species.  Is Archaeopteryx the grandfather or the great-uncle of modern birds? Impossible to say.
For one thing, it appears that Archaeopteryx is too young.  There are more fully bird fossils deeper and older than Archaeopteryx.  Does this mean Archeop (please forgive the short-form, I am becoming tired of the full name.  Expect more of the like to come.) didn't exist before birds.  No.  a transitional fossil is like a single photograph.  I have a photo of me paddling a canoe in Georgian Bay dated to 1999 but I existed for 32 years before that and at least 16 -as of this writing - more after that.  A transitional fossil doesn't lock in the full period of a species' existence.  And we wouldn't expect it to.  The more common a species is, among other factors, means a greater likelihood of fossilization.  When a species first evolves and as it goes extinct, the numbers are going to be smaller.

Now for the 'other factors' mentioned in the paragraph above.  Fossils are rare.  This is not a desperate hope stated by paleontologists to explain away the claimed lack of evidence but a fact.  Let me defend this fact.
First, soft bodied and small animals are less likely to be fossilized.  bones, especially large ones, are more likely to last long enough to be buried in sediment and be fossilized.  A soft bodied animal or soft tissue of a bony animal is more likely to be eaten or rot away.  Such fossils are found but in lesser numbers.  This is a (n entirely reasonable) fact.

Second, many animals die where fossilization is unlikely.  Yes, I did choose the 'weasel-word' "many".  I can't say whether this is a majority or not, but i believe it is.  It is at least a large number, however else you define it.  Fossilization in a jungle is rare - the warm, humid condition encourage the life of ants and other scavengers even smaller.  a remarkable fact I recently learned is that the first Chimpanzee fossil ever found we found only eight years ago (in 2006).  To my knowledge, there are only around six chimpanzee individuals that have fossilized that we know of.  Another example is that of buried soldiers from World War 2.  Many died and were buried in France and after decades past some Americans have wanted their heroes to come home.  The graves were dug up but often no bodies -and seldom even cloth or belt buckles - are found.  Forty years after a large bodied vertebrate, buried below the active biological layer of soil and the remains are gone.

In the TV show for the book, Your Inner Fish, Dr Niel shubin describes fossil collecting in the American North-East coast.  At one place with huge tides, he described going onto the sea bed at low tide, finding many new fossils, trying to collect a few before being forced away by the returning tide. The next day, many of the fossils seen the day before are worn away and new ones are visible.  The life of fossils on the rock surface in this region can be measured in days or hours.

I haven't actually defended evidence of evolutionary change in this blog post but I hope I have defended the state of evidence and shown that the fossil evidence, weak as it might be (I think it is actually pretty good although that might be the subject to a later post), is satisfactory and not a deal-breaker for evolution.

more feathered dinosaurs

Sci Am has the details.  Below is an image from the link - deliberately shrunk a little - if you want full quality, follow the link.

misconceptions about evolutionary trees

The article from NCSE can be found here.  The image below has been cropped; to see the full image and a lot more, follow the link.

Dang it, I can't find Dawkins' quote that went along the lines of 'The ----, a limbless worm, is our exact evolutionary equal and just as evolved as humans'.
...
Whadoyaknow?  I covered the same subject in 2012.  Dawkins said, "Lancelets are live creatures, our exact contemporaries.  They are modern animals who have had exactly the same time as we have in which to evolve.  Another telltale phrase is 'a side branch, off the main line of evolution.'  All living animals are side branches.  No line of evolution is more 'main' than any other, except with the conceit of hindsight. "
From Wikipedia.

Biblical defense of a flat (and square) Earth

In 1893, Professor Ferguson (professor of what, I don't know) drew a map representing what he thought the Bible required the Earth to look like.

The image is from Wikimedia. It comes with this caption:

MAP OF THE

SQUARE AND STATIONARY EARTH.

BY PROF. ORLANDO FERGUSON,

HOT SPRINGS, SOUTH DAKOTA.

Four Hundred Passages in the Bible that Condemns the Globe Theory, or the Flying Earth, and None Sustain It.

This Map is the Bible Map of the World.

A fragment of a footnote:

SCRIPTURE THAT CONDEMNS THE GLOBE THEORY

And his hands were steady until the going down of the sun—Ex. 17: 12. And the sun stood still, and the moon stayed.—Joshua 10: 12–13. The world also shall be stable that it not be moved.—Chron. 16: 30. To him that stretched out the earth, and made great lights (not worlds).—Ps. 136: 6–7. The sun shall be darkened in his going forth.—Isaiah 12: 10. The four corners of the Earth.—Isaiah 11: 12

The Sensuous Curmudgeon has also documented verses that defend the notion of a flat Earth -although in the Curmudgeon's case, it is for purposes of mockery. A fragment:

1Samuel 2:8
for the pillars of the earth are the LORD’s, and he hath set the world upon them.
1 Samuel 2:10
The adversaries of the LORD shall be broken to pieces; out of heaven shall he thunder upon them: the LORD shall judge the ends of the earth;
Job 9:6
Which shaketh the earth out of her place, and the pillars thereof tremble. [A reference to the usually unmovable earth, but it must be flat to sit on pillars.]
Job 37:3
He directeth it under the whole heaven, and his lightning unto the ends of the earth.
Job 38:4
Where wast thou when I laid the foundations of the earth?

Strange that not many Creationists defend this claim any more.

Were feathers added to Archaeopteryx fossils?

Dr Walt Brown says yes.  From the Center for Scientific Creationism:

Archaeopteryx means ancient (archae) wing (pteryx). But the story behind this alleged half-dinosaur, half-bird is much more interesting than its fancy, scientific-sounding name or the details of its bones. If Archaeopteryx were shown to be a fraud, the result would be devastating for the evolution theory.

Since the early 1980s, several prominent scientists have charged that the two Archaeopteryx fossils with clearly visible feathers (the Berlin and London specimens) are forgeries.1 Allegedly, thin layers of cement were spread on the mating surfaces (slab and counterslab) of two fossils of a chicken-size dinosaur, called Compsognathus (komp-SOG-na-thus). Bird feathers were then imprinted into the wet cement.

This apparently is from Brown's 2008 edition of In the Beginning; compelling evidence for creation and the flood (the link is to a different edition).

Things go wrong in the first paragraph.  If Archaeopteryx were shown to be a fraud, scientists would continue to use all the other feathered dinosaurs that have been found. Flying Dinosaurs has a long list of feathered dinosaurs.

From the Smithsonian:

In 2012, paleontologists found that a T. rex relative, Yutyrannus huali, had filamentous feathers. If a relative had feathers, why not the king of reptiles itself?
Until a specimen is found with preserved imprints of feathers, though, the jury is out.

Carl Zimmer has more:

Now Archaeopteryx is sinking back into the crowd of primitive birds and feathered dinosaurs. As Ed Yong has ably explained, a fresh wave of fossils are coming to light. They reinforce the argument that paleontologists have agreed on for a couple decades now: birds evolved from a lineage of dinosaurs called theropods. But it’s less clear now how exactlyArchaeopteryx fits into that evolution. It might still be closely related to the ancestors of living birds, or there might be non-flying theropods that were more closely related. Combine this with the recent discoveries of heavily feathered dinosaurs–feathered down to their feet, in fact–and the possibility emerges that dinosaurs evolved into flyers more than once. We look up in the sky today and see the results of only one of those transitions.

National Geographic goes even farther.

Over the past two decades, discoveries in China have produced at least five species of feathered dinosaurs. But they all belonged to the theropod group of "raptor" dinosaurs, ancestors of modern birds. (Related: "Dinosaur-Era Fossil Shows Birds' Feathers Evolved Before Flight.")

Now in a discovery reported by an international team in the journal Science, the new dinosaur species, Kulindadromeus zabaikalicus (KOO-lin-dah-DRO-mee-us ZAH-bike-kal-ik-kuss), suggests that feathers were all in the family. That's because the newly unearthed 4.5-foot-long (1.5 meter) two-legged runner was an "ornithischian" beaked dinosaur, belonging to a group ancestrally distinct from past theropod discoveries.

"Probably that means the common ancestor of all dinosaurs had feathers," says study lead author Pascal Godefroit of the Royal Belgian Institute of Natural Science in Brussels. "Feathers are not a characteristic [just] of birds but of all dinosaurs." (Related: "Dinosaur Feathers Changed With Age.")

So already Brown seems to be in trouble.  On to the second paragraph. "Several prominent scientists" seems to be light on actual paleontologists. Fred Hoyle and N. Chandra Wickramasingh are mentioned.  They are both mathematicians and astronomers but have no obvious background in the study of fossils.

At The War For Science, they note that no such cement has been found by other researchers.

Palaeontologists that examined the London Archaeopteryx arrived at a quite different conclusion - “Proof of authenticity is provided by exactly matching hairline cracks and dendrites on the feathered areas of the opposing slabs, which show the absence of the artificial cement layer into which modern feathers could have been pressed by a forger.”.

War For Science quotes (above) from this Science Mag article.

For more information, have a look at Kevin Padian's slides from the 2005 Dover Creationism trial. I used Chrome's highlighter extension to highlight some of the text near the slides which I feel carry all the relevant information.

How dinosaurs became birds

Scientific American has the goods.  An excerpt:

But it has become increasingly clear that the story of how dinosaurs begat birds is much more subtle. Discoveries have shown that bird-specific features like feathers began to emerge long before the evolution of birds, indicating that birds simply adapted a number of pre-existing features to a new use. And recent research suggests that a few simple change—among them the adoption of a more babylike skull shape into adulthood—likely played essential roles in the final push to bird-hood. Not only are birds much smaller than their dinosaur ancestors, they closely resemble dinosaur embryos.

definition of a theory

Here is a common creationist definition, although a little more honest than some:

After all, evolution is a theory, and in the dictionary I have, it states that a theory, among other things, is a hypothesis, a guess, a conjecture, a speculative opinion — hardly absolute fact.

From Craig Kappel

The unusual honesty is in the phrase, "among other things".  Let's look at two online dictionaries:

Merriam Webster:(Click to enlarge - or follow the link)

The scientific definition is not so clear at Merriam Webster and it could be the first or fifth one in the list.

Dictionary.com: (ditto)

Here, the scientific definition is the first one.

Even Google's own definition service puts the  scientific meaning first:

The word 'theory' can be a synonym for 'guess' or 'conjecture' or 'opinion' but it sure seems dishonest when the relevant definition is there and deliberately skipped over.

Added Sept 24: a nice graphic from York Daily Record.  I hamfistedly added an extra line and some text to it.

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Added later on Sept 24: At Science Alert, a video explaining the difference between hypothesis, theory, fact and law.
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Added later, On Aug 23, 2016, Piers Sellers on climate change and Theory:

Fundamentally, a theory in science is not just a whim or an opinion; it is a logical construct of how we think something works, generally agreed upon by scientists and always in agreement with the available observations. A good example is Isaac Newton’s theory of gravitation, which says that every physical object in the universe exerts a gravity force field around itself, with the strength of that field depending on its mass. The theory—one simple equation—does a superb job of explaining our observations of how planets orbit around the sun, and was more than good enough to make the calculations we needed to send spacecraft to the moon and elsewhere. Einstein improved on Newton’s theory when it comes to large-scale astronomical phenomena, but, for everyday engineering use, Newton’s physics works perfectly well, even though it is more than three hundred years old.

via pharyngula.

Dennett on how to argue

In the previous post, I described a barely remembered fragment of Daniel Dennett's advice on how to argue coherently.  Turns out, the post I recalled was about how to criticize with kindness and offered a excerpt from his book, Intuition Pumps and other tools for thinking.

From the "How to Criticize..." link:

How to compose a successful critical commentary:

1. You should 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.
2. You should list any points of agreement (especially if they are not matters of general or widespread agreement).
3. You should mention anything you have learned from your target.
4. Only then are you permitted to say so much as a word of rebuttal or criticism.

Good advice for us all.
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Not related but not quite worth a blog post of its own.
Vignettes of Famous Evolutionists.  Ah, the content is worth a post (or more) of its own, but I don't have much to add.  Follow the link to learn about masters of the field of evolution.