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.

Your own opinions, not your own facts

UPDATE: Brean has deleted our comment thread.  I cannot say if this post is one-sided or biased but there is no longer an original record to refer back to.
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It takes more #faith to believe in #evolution than it does in #creation. http://t.co/8xojMIglNf
— Jacy Brean (@JacyBrean) April 21, 2015

I followed the link Brean provided and we had a cordial discussion in the comments of the blog post.

 Brean does not believe that there is enough evidence for Evolution.  I disagree but this is not my concern in this blog post.  My concern is the use of facts.

From the main post

  Even if it were possible for a human male to evolve, what are the chances of a female counterpart evolving at the same time in order for them to reproduce? 

The thing is, if Brean understood the theory, Brean would know this is not an issue.  Evolution works (or doesn't in Brean's view) on populations, not individuals.  My main rebuttal to this is at the bottom of the quoted sections.

From our discussion in the comments:

 I may maintain that there is not - and never has been - any observable evidence to support what has only ever been a theory, and a very flimsy one at that.

Brean seems unaware that although 'theory' is used in detective shows as 'guess', in science it is not. Evolution is (or isn't) a theory but it isn't "only" a theory.  To explain by example, let's look at gravity. There is a law of gravity.  There is no theory of gravity.  We know gravity works and understand that it works but we have no consensus on why it works.  The explanation is missing.  The theory is missing.
The same from Study.com

Outside of science, the definition of a theory is a thought that may or may not be true. In the science community, a scientific theory is defined as a hypothesis or a group of hypotheses about some phenomena that have been supported through research using the scientific method.

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 Another huge reason why I could never accept evolution is that it offers no hope for the future and no means to solve our problems in the here and now.
I do appreciate your taking the time to respond and respect, not only your views but also your right to express them.
Best regards

The theory of evolution offers hope for the future in the exact same way Germ Theory does. The exact same way the Particle Theory of light does. Heliocentric Theory, Cell theory... None of these offer or take hope away.  To offer a cliche, science is a tool and any tool can be used for good or ill. We cannot say that TNT or dynamite doesn't exist because we don't like bombs or missiles. We can't argue against nuclear physics because of the harm radioactivity can cause.
I left the second sentence in the quote to offer evidence that Brean was gracious and polite throughout.  I am frustrated by Brean's views but not by the tone they were given.

All my research an personal observation leads me to the only possible conclusion.
I have discussed the matter with various people, including scientists of many disciplines. None of them know how life began, or how life triggered the tiniest organism into being - and you are no exception.

Brean is a writer and presumably capable of research.  Brean claims to have discussed the subject with many scientists.  Yet, in asking when males vs females evolve we see that Brean doesn't know what evolution actually states.  Brean is unaware of the proper usage of the term 'theory'.  Brean specifically links lack of acceptance of the theory with its consequences.

In our discussion, I made a similar mistake.  In reading the timeworn attacks on evolution, I imagined I was speaking to a follower of Ken Ham's AIG Young Earth Creationism and made an argument based on that assumption.  Brean corrected me on my error and we moved on.  In an article promoting his book Intuition Pumps, Dennett stated that the way to properly argue a point was to do enough research to be able to describe the opponents position so well and clearly the opponent would thank him.  I jumped to an assumption and was corrected.  We see that Brean didn't understand the theory of evolution even while arguing against it.  Weinersmith seems correct when he said:

The more I read from creationists, the more I think they're not anti-evolution. They're anti-some crazy version of it their pastor taught.
— Zach Weinersmith (@ZachWeiner) April 4, 2012

I don't know if anyone actually reads this blog but I wonder at the etiquette of blog post argument. Brean had posted an opinion on the blog and promoted a link to it on Twitter so I think my decision to respond was not invasive. I am less comfortable about giving the link to the post at the top of my post. We each made three comments (one of mine was long and had to be broken into two. It really wasn't that long and I was surprised that I had to do that) with Brean politely closing the discussion down.  I have chosen not to post further there.  On another of my blogs, I had a blog post with a long comment discussion and stated that it was done.  I did not lock down comments and someone chose to keep commenting. There is breach of etiquette and there is rudeness ( and worse, is online rudeness) and I feel that commenter crossed a weak line in choosing to continue with comments.  I hope I have not.

Creationists and science - they do it wrong, sometimes dishonestly so

Creationists and evolutionists use the same evidence,

but evolutionists use all the evidence.

From Boingboing, of all places, comes a tale of an encounter with a creationist at the American Geophysical Union conference.  The author meet a man at the poster section.

A name badge declaring him to be Hugh Miller, the first author on the poster.He asked if I had any questions. I asked if he could just give me a quick summary of the work. He talked about performing mass spectrometry on samples of various dinosaur bones that produced age estimates ranging from 15,000 to 50,000 years. My spidey-sense tingled. I peered over his shoulder, searching for bullet points to figure out what was going on here.
That's when I read it: "humans, neanderthals, and dinosaurs existed together."

The author continues:

Now, here's the thing about Carbon-14 dating. This isotope has a very short half-life (the time necessary for the element to reduce in mass by half) of only 5730 years. Since it decays so quickly, it is useless for dating objects more than about 40-50,000 years old. The background levels of C-14 radiation in the laboratory have to be compensated for. 

The author points out

...often a technique called "bracketing" is used where the igneous rock on either side of the fossil is dated with radioactive isotopes that have half-lives on the order of millions of years. This give scientists a range of time in which the animal could have lived. The poster authors, Hugh included, were basing their attack on one technique in the geological toolkit, and disregarding all other evidence that would have undermined their conclusions.

Indeed, Ken Ham did the same thing in his televised debate with Bill Nye, saying:

In Australia there were engineers that were trying to search out about a coal mine, so they drilled down and they found a basalt layer, or lava flow that had woody material in it, branches and twigs and so on, and when Dr. Andrew Snelling, our PhD geologist sent that to a lab in Massachusetts in 1994, they used the potassium-argon dating method and dated it at 45 million years old. Well, we also sent the wood to the radiocarbon section of the same lab, and they dated it at 45,000 years old. 45,000 year old wood in 45 million year old rock. The point is, there is a problem.

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Jason Rosenhouse looks at how creationists abuse math in defense of their claims.

Sewell also argued that Darwinism runs afoul of the laws of thermodynamics. Evolution requires a decrease in entropy over time, whereas a cherished principle of physics says that is impossible. Since Sewell recognizes that the second law applies only to closed systems (which the Earth is not), it is unclear what the problem is. His claim that “natural forces do not cause extremely improbable things to happen” is pure gibberish. Does Sewell invoke spuernatural forces to explain the winning numbers in last night’s lottery?The fact is that natural forces routinely lead to local decreases in entropy. Water freezes into ice and fertilized eggs turn into babies. Plants use sunlight to convert carbon dioxide and water into sugar and oxygen, but Sewell does not invoke divine intervention to explain the process.

Historic and Observational Science

From AIG:

[I]t is useful to divide science into two different areas: operational science and historical (origins) science. Operational science deals with testing and verifying ideas in the present and leads to the production of useful products like computers, cars, and satellites. Historical (origins) science involves interpreting evidence from the past and includes the models of evolution and special creation. Recognizing that everyone has presuppositions that shape the way they interpret the evidence is an important step in realizing that historical science is not equal to operational science. Because no one was there to witness the past (except God), we must interpret it based on a set of starting assumptions. Creationists and evolutionists have the same evidence; they just interpret it within a different framework. Evolution denies the role of God in the universe, and creation accepts His eyewitness account—the Bible—as the foundation for arriving at a correct understanding of the universe.

and:

IF AN IDEA IS NOT TESTABLE, REPEATABLE, OBSERVABLE, AND FALSIFIABLE, IT IS NOT CONSIDERED SCIENTIFIC.

and:

 The denial of supernatural events limits the depth of understanding that science can have and the types of questions science can ask. We may define naturalism and materialism as:
Naturalism: a belief denying that an event or object has a supernatural significance; specifically, the doctrine that scientific laws are adequate to account for all phenomena.
Materialism: a belief claiming that physical matter is the only or fundamental reality and that all organisms, processes, and phenomena can be explained as manifestations or interactions of matter.
The problem with the above definition of science is that, even though naturalistic science claims to be neutral and unbiased, it starts with a bias. The quote from Dr. Todd on page 19 demonstrates that bias: only matter and energy exist and all explanations and causes must be directly related to the laws that matter and energy follow. Even if the amazingly intricate structure of flagella in bacteria appears so complex that it must have a designer, naturalistic science cannot accept that idea because this idea falls outside the realm of naturalism/materialism. Many scientists have claimed that allowing supernatural explanations into our understanding of the universe would cause us to stop looking for answers and just declare, “God wanted to do it that way.” This is, of course, false.

The ability to study the world around us is only reasonable because there is a Lawgiver who established the laws of nature. Most people do not realize that modern science was founded by men who believed that nature can be studied because it follows the laws given to it by the Lawgiver. Johannes Kepler, one of the founders of astronomy, said that science was “thinking God’s thoughts after Him.” Many founders of scientific disciplines, such as Bacon, Newton, Kepler, Galileo, Pascal, Boyle, Dalton, Linnaeus, Mendel, Maxwell, and Kelvin were Bible-believing Christians.  

... In a biblical worldview, scientific observations are interpreted in light of the truth that is found in the Bible. If conclusions contradict the truth revealed in Scripture, the conclusions are rejected. The same thing happens in naturalistic science. Any conclusion that does not have a naturalistic explanation is rejected.

...Making a distinction between two types of scientific study helps us to understand the limitations of naturalistic presuppositions in science:Operational (Observational) Science: a systematic approach to understanding that uses observable, testable, repeatable, and falsifiable experimentation to understand how nature commonly behaves.
Operational science is the type of science that allows us to understand how DNA codes for proteins in cells. It is the type of science that has allowed us to cure and treat diseases, put a man on the moon, build satellites and telescopes, and make products that are useful to humans. Biblical creationists believe that God has created a universe that uses a set of natural laws that operate consistently in the universe. Understanding how those laws operate is the basis for scientific thinking.
Some events defy natural laws. Christians refer to these things as miracles, but naturalistic science must find a way to explain these occurrences naturally. This approach rejects miracles in the Bible because they cannot be explained using natural laws. Such scientists occasionally try to explain the miracles in the Bible as natural phenomena, but this ultimately undermines the authority of God and His Word.
Historical (Origins) Science: interpreting evidence from past events based on a presupposed philosophical point of view.
The past is not directly observable, testable, repeatable, or falsifiable; so interpretations of past events present greater challenges than interpretations involving operational science. Neither creation nor evolution is directly observable, testable, repeatable, or falsifiable. Each is based on certain philosophical assumptions about how the earth began. Naturalistic evolution assumes that there was no God, and biblical creation assumes that there was a God who created everything in the universe. Starting from two opposite presuppositions and looking at the same evidence, the explanations of the history of the universe are very different. The argument is not over the evidence—the evidence is the same—it is over the way the evidence should be interpreted.

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That's a long set of excerpts.  Read more -there is a lot more - at the link.

I feel there are two main themes in the post and in the excerpted above.  The (artificial) distinction between observational and historic science and the inclusion of the supernatural in science. I also want to look at the claim that natural laws require a lawgiver.

This all-in-caps quote demonstrates the perceived difference between observational and historic science."IF AN IDEA IS NOT TESTABLE, REPEATABLE, OBSERVABLE, AND FALSIFIABLE, IT IS NOT CONSIDERED SCIENTIFIC."

I agree with this wholeheartedly.  If only I could find an example of so-called historic science that failed these criteria.
Let's look at the Greenland Ice Cores.  Superficially, looking at the long, thin cylinders and counting backwards through the layers is problematic.  We have not seen the snow fall on that location for more than a few decades and as the layer pile up and squeeze those below, there might be changes in the way those layers look, confusing the observer.
However, there are ways to repeat the tests and falsify them.  Let's look at falsification first.  The original creationist argument mentions "isotopes" once in one sentence and never again.  The method of looking for differences in the isotope ratios is not explored and yet it is a way to test the results.  The article also leaves out the presence of identifiable volcanic dust and ash.  When researchers find dust at 200 years-before-present, they can look for records of volcanic eruptions and compare the dates.  This is the definition of falsification.

Is it repeatable?  Yes.  There is lots of ice out there and researchers can drill more than one core and compare the results of one to another.

The same thing happens when we look at the insertion of viral DNA and how if an this happened to an ancestor all the descendants should have the inserted DNA in the appropriate place.  Researchers in a variety of locations and labs can look at viral DNA and compare that to the DNA in humans and other apes and confirm to deny that the DNA is the same.  Exceptions can be looked for.  No such exceptions have been found.

The Sensuous Curmudgeon covered similar ground in 2012.

Now for whether the supernatural can tested in a scientific way.  No, it can't.  When I teach ESL to young children, I sometimes amuse them by appearing to push a piece of chalk into one ear and pulling it out the other.  If you accept the supernatural, then even if you see that the chalk is hidden in my hand in one performance, you have to accept that the next time I do the trick, real magic occurred.

In my opinion, the best response to the science-testing-the-supernatural claim comes from Richard Hoppe and his look at Behe's suggested bacterial flagellum experiment.  Behe had suggested that bacteria lacking a flagellum be exposed to condition that would favor the evolution of a flagellum to see if one actually evolved.

Hoppe thought about the results of such an experiment.  

But then Hoppe notes that Behe states we can know nothing about the Designer and Its abilities.  He then imagines the experiment runs its course and bacteria flagellum appear...

. Does that mean that evolution works and ID is “disproven”? Not at all. After all, since we know nothing about the skill set and intentions of the putative designer(s), it’s possible that the designer(s) somehow ‘watched’ our culture, and sometime during the course of the generations ‘reached’ in and poofed a flagellum into existence on one of the bacteria.

If a flagellum appears, it means that evolution occurred the bacteria gained the flagellum through evolutionary processes or that The Designer chose to give them a flagellum.  If no flagellum appears, it means evolution did not occur or that it did occur and the bacteria were about to sprout flagella but The Designer chose to remove it. 

 Adding the supernatural to the mix means nothing can be scientifically determined. The argument turns into the brain-in-a-jar-on-a-desk-in-a-lab hypothesis.  If the supernatural is accepted, then nothing is settled.  We see what The Designer wants us to see and nothing else.  I try to keep this a religion-neutral blog but the only rebuttal that I can see Christians make to this point is that the Christian God is always honest and never deceptive.  If that is the case, then we can accept what our senses inform us of and the supernatural is not relevant.

"The ability to study the world around us is only reasonable because there is a Lawgiver who established the laws of nature."
The laws are what is observed, not required.  The quote above makes the same conflation that allows the joke about the judge outlawing gravity to be funny.  The law of universal gravitation has nothing in common with the laws of your country against murder.  The former is a fact of the universe and the latter is a arbitrary rule made by humans.
Further, Ham et al require the 'lawgiver' to mess around with the laws of nature.  In addition to claiming that any change to the laws of nature would destroy us all, they need the speed of light to change so light from distant stars can reach the Earth in six thousand years or less.  They need ice layers in Greenland to pile up so they appear to show one hundred thousand years  after only four thousand years passed.
They simultaneously state that the laws of nature are unchanging and they may have been different in the past.
Henry Morris made this claim - link is to Talk Origins:

Radiometric dating assumes that radioisotope decay rates are constant, but this assumption is not supported. All processes in nature vary according to different factors, and we should not expect radioactivity to be different.Source:
Morris, Henry M. 1985. Scientific Creationism. Green Forest, AR: Master Books, p. 139.

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In his debate with Bill Nye, Ham stated that the current diversity of life evolved from the far-fewer animals on the ark, simultaneously arguing against evolution and requiring evolution to occur at far faster rates than ever observed.

Nye argued that there are some 16,000,000 species on the planet today, and that if there was a Flood only 4,000 years ago, and only 7,000 representative species on the Ark to start with, there would have to have been 11 new species evolving every day over the last 4,000 years since the Flood.

Read from Darwin's library on the Beagle.

From Nature:

The cabin where Darwin worked and slept also housed the ship’s library, which he used for both reference and inspiration in his research. The library was dispersed at the end of the voyage, and its contents have been unknown. Now, 178 years later, science historian John van Wyhe of the National University of Singapore has reconstructed a virtual version of Darwin’s library, by cataloguing all of the printed sources Darwin made reference to in his travel notes.

If the link in the quoted section doesn't work, this should.