Friday, September 18, 2009

Response to Comfort's forward of the Origin of Species Part 1.

Over the next several postings (until I'm done), I will be reviewing this document by Ray Comfort.

On the outset, let me first tell the parts of the document that I will not be reviewing. I will start right off by skipping the first thirteen pages. These pages, as you can verify yourself from the link above, contain a history of Charles Darwin, as well as a timeline of his life. The facts of Darwin's life are objectively verifiable, and to a large extent are correct as presented in this document. I could quibble about the language used, but by and large, I have no major objection to the initial sections of this document.

Furthermore, I won't bother reviewing the section from the 43rd page to the end, starting with the section titled "Atheist Penn and the Time Bomb." These statements contain Ray Comfort's personal opinions and as such cannot objectively be evaluated. Suffice it to say, he draws the false assumption that evolution and atheism are synonymous (despite the fact that he himself names a number of scientists who accept or accepted both evolution and the existence of God; something which he does not even consider a possibility anywhere in his 50-page discourse), and the last pages of his manuscript are him saying that he sees atheism, and all the other major religions as bad, and Christianity as good.

This is going to be a long project, and anticipate the first posting tomorrow, in which I will start talking about the first few pages of the document.

I say that I will probably only get to the first few pages on that particular posting because the first page alone of this document is so crammed full of distortions, half-truths, outright lies, and straw-man arguments that much more than that would result in a ridiculously long posting.

At any rate, anticipate the first posting tomorrow.

What would Hitler do?

By far, one of the most egregious claims made by creationists is that somehow the theory of evolution is responsible for the Holocaust.

Now for the purposes of this discussion, I will set aside two undeniable facts:

1) the claim is pure, unadulterated, bullshit.

and

2) it would have no effect whatsoever if Hitler had quoted Darwin in every third sentence of Mein Kampf. One very evil person's opinions do not, in themselves, constitute an argument against any given position.

I'm going to set both of these aside for the moment and ask something a little more fundamental: if, indeed, Hitler were motivated purely by Darwin's theory of evolution, does the Holocaust even make sense?

Of course, one could posit that Hitler's approach is based upon a misunderstanding of the theory of evolution, but that can hardly be blamed on the theory. So, in the interest of full disclosure, in this little thought-experiment, I will make one assumption which I'm sure will be considered reasonable: Hitler actually understood the theory of evolution beyond the typical creationist straw-man versions of it. In other words, he understood what the theory of evolution actually says, rather than what creationists say it says.

So, if one was a dictator, motivated purely by an understanding of evolution, what would one do? In short, how, as a maniacal dictator, would one go about maximizing one's evolutionary potential? Well, in order to do that, one needs to first look at nature and ask what the most successful organism on the planet is, and see if there is any way we can mimic its behaviour.

Creationists are fond of claiming that human beings are the pinnacle of evolution. We're the most successful species on the planet, according to their version of evolution. This is, by any standard pertinent to what evolution actually says, false.

By any standard pertinent to evolution, the lowly e. coli bacteria is among the most successful organisms on the planet. Bacteria in general (and yes, I know, I'm talking about a whole kingdom here, rather than a species) are now, and always have been, the dominant organisms on this planet. They kick the asses of the entire animal kingdom in terms of reproductive rate, adaptability, and number of individuals, biomass, and environments exploited. By these standards, the only standards pertinent to evolution, all of the eukaryotic branches of the tree of life combined (that includes plants, animals, sponges, anything multicellular, and absolutely every living thing you can possibly see without a microscope) cannot even come close to matching the success of the e. coli species of bacteria alone.

A dictator, familiar with what the theory of evolution actually says would know this. Such a dictator would also know that it is beyond our technical capabilities to cause the human race to revert to the prokaryotic stage.

So, given this limitation, what is a dictator to do?

Well, short of reducing the human generational time to a matter of hours, rather than years (also beyond our capabilities), the next best option would be to increase the level of biological diversity as high as you possibly can. Actually, the most sure-fire way of guaranteeing a population's extinction would be to reduce the gene pool of your populus. Since extinct populations generally don't evolve any further, it seems unlikely that a dictator familiar with what the theory of evolution actually says would take this course of action. Put simply, if Hitler were actually motivated by the theory of evolution, the absolute last thing he would ever, ever want to do is create a "master race." In fact, were he motivated by what the theory of evolution actually says, he would know a "master race" of any kind; whether black, white, fuchsia, mauve or green; should be avoided at all costs.

There are any number of ways in which the genetic diversity of a population can be maximized, and while none of them are particularly palatable options, they're certainly not what Hitler did.

First off, some form of breeding program is a must. Not to breed out specific characteristics, mind you, the way that you do with dogs. The objective here would be to create the human equivalent of a mutt. Women will have to be required to produce offspring with different men of different ethnic backgrounds. This breeding program will have to go on for generations. After 6-10 generations or so (when we're breeding mice, we generally go with 6), it will be virtually impossible to tell that you have "races" at all in your population.

Next, from any country you conquer, the population which survives the conquering process will have to be included in the above-described breeding program. For example, it would be to your benefit to make sure that the gene for sickle-cell anemia exists somewhere in your population, as this has as a benefit a near-immunity to malaria. This gene exists almost exclusively in African populations. There's also a family in Greece which has a mutation which allows them to more efficiently process low-density lipoproteins. As a consequence, they have no family history of heart attacks. In tibet, a population has a gene which allows them to survive better at higher altitudes. Since none of these exist inherently in Germany, and very few exist in the caucasian races, limiting your genetic diversity to one race is, frankly, stupid.

Like I said, this will likely have to carry on for many generations, so you'll also probably have to do something about that whole "mortality" thing.

Now, we can argue about the ethics of this approach, and I agree, I'm not terribly keen on it myself. However, I think that there's one thing we can all agree on:

It's not what Hitler did.

Thursday, September 17, 2009

The latest creationist PR

Ray "bananaman" Comfort, and his former child actor associate Kirk Cameron are trying again to indoctrinate the masses, and I have the distinct feeling that it's going to blow up in their faces.

Nobody is trying to censor them, nobody is trying to stop them. We're not against free speech.

We are, however, against lies.

That said, they have recently announced their latest PR scheme.



To correct all of the lies presented in just the first few minutes of this video would be impossible in just about any other forum. So I'm doing it here.

I also plan to make this posting available to a number of a-list bloggers in the hope that they will spread this to the widest audience possible.

So, let's begin. Each comment will be preceded with a timecode, and a quote from former child actor Kirk Cameron. The video above is exactly that which was posted, so you can verify their comments against it at any time.

Let us begin.

0:00 Former Child Actor Kirk Cameron: "Are you concerned about what's happening to our country?"

No.

0:05 Former Child Actor Kirk Cameron: One by one, we're being stripped of our God-given liberties.

No evidence exists that your liberties were given by God. All liberties you enjoy were passed on to you by the founding fathers of this country. Founding fathers who said, among other things:

"Christianity neither is, nor ever was, a part of the common law."

Vol. 1 Whether Christianity is Part of the Common Law (1764). Published in The Works of Thomas Jefferson in Twelve Volumes

"All persons shall have full and free liberty of religious opinion; nor shall any be compelled to frequent or maintain any religious institution."

Thomas Jefferson Draft Constitution for Virginia (June 1776)

0:11 Former Child Actor Kirk Cameron: Our kids can no longer pray in public.

Outright Lie #1. Nobody has yet been arrested for praying in public. Every attempt to do so, ever, has been thrown out of court under the very first amendment which protects your right to present any religious view you feel is appropriate.

0:13 Former Child Actor Kirk Cameron: They can no longer freely open a bible in school.

Outright lie #2. Students are not prohibited from opening a bible in school. They're not prohibited from praying in school. They're free to do both activities, provided, naturally, that they don't disturb the rest of the class, as clearly demonstrated by this document, endorsed by the ACLU and the National Association of Evangelicals (and imagine what a challenge it is to get those two groups to agree on anything).

Where the limit of religious expression lies is when the teacher begins to present or endorse religion on the public dollar. That's the deal we made in the constitution: if it's paid for with taxes, religion stays out of it.

Of interest is the following passage of the same document, endorsed by both the ACLU and the National Association of Evangelicals:

Students have a right to distribute religious literature to their schoolmates on the same terms as they are permitted to distribute other literature that is unrelated to school curriculum or activities. Schools may impose the same reasonable time, place, and manner or other constitutional restrictions on distribution of religious literature as they do on nonschool literature generally, but they may not single out religious literature for special regulation.


Yep. Sure seems like they're restricting access to bibles.

Remember, this was endorsed by the ACLU, the organization that fundamentalists are always insisting is trying to force religion out of schools.

0:15 Former Child Actor Kirk Cameron: The Ten Commandments are no longer allowed to be displayed in public places.

Outright lie #3. The ten commandments are allowed to be displayed in public places. They're not, however, allowed to be displayed on public property, nor should they be. You are perfectly, and openly permitted to display a copy of the ten commandments, or the wiccan rede, or the scrolls of Mohamed, on your front lawn, or on the front of your church, or on your office door, but you can put none of them on the steps of a public courthouse.

Speaking of the ten commandments, we're just barely over a quarter-minute into this video, and Former Child Actor Kirk Cameron has already openly, blatantly and remorselessly lied three times. Isn't there a commandment somewhere in there about "bearing false witness?"

0:22 Former Child Actor Kirk Cameron: and the Gideons are not even allowed to give away bibles in schools.

No, the Gideons were not prohibited from giving the bibles away. They were not stopped from handing out the bibles, or condemned by the school for doing so. In fact, the school released a statement saying that the Gideons had violated no laws whatsoever. What actually happened was that the parents of students who were given the bibles got upset, and they have absolutely every right to be upset. Imagine if you found out that Muslim extremists were handing copies of the Koran to your children, or that pagans were teaching them all about the wiccan rede, or hindus were giving copies of the Bhagavad Gita. Honestly, don't you think that would upset you just a little?

Outright Lie #4, in just over 20 seconds.

0:24 Former Child Actor Kirk Cameron: Did you know that a recent study revealed that in the top 50 universities in our country, in the fields of psychology and biology, 61% of professors describe themselves as atheists or agnostics?

Not an outright lie, but a very misleading use of statistics.

The study in question shows that:

Respondents were asked to select the statement that comes closest to expressing their views about God. Only 10.0 percent chose the statement, “I don’t believe in God,” while 13.4 percent chose the statement, “I don’t know whether there is a God, and I don’t believe there is any way to find out.” About 23.4 percent of respondents to our survey, in other words, are either atheists or agnostics.


A pretty far cry from the 61% Former Child Actor Kirk Cameron is quoting here, isn't it? The only time when that number comes up is when you deliberately restrict it only to the Psychology and Biology professors. In other words, subjects where the religious views of the professor would be completely and utterly irrelevant to the subject matter.

So, even if 61% of biology and psychology professors are atheists, so what?

Let's follow Former Child Actor Kirk Cameron's so-called "reasoning" to the next step.

0:38 Former Child Actor Kirk Cameron: No wonder atheism has doubled in the last 20 years among 19 to 25-year-olds.

Since I really don't see why this is a concern, at all, I won't bother fact-checking this one. Suffice it to say, if it's true, so what? If it's not, then Former Child Actor Kirk Cameron is lying again. I could honestly care less.

However, he associates the "high" number of atheists college professors (and not just any professors, specifically those in biology and psychology, which is a tiny minority of the college professors in total) with the increase in atheism. This is unlikely to be true, as it is still only a minority of americans who possess a post-secondary education. In order for this statement to in any way be linked to the one which proceeds it (itself, at the absolute least, a disingenuous statement of the actual statistics), one would have to establish that a sizable portion of those who become atheists during this time were college educated in psychology or biology, and were taught by the 61% of professors who profess to be atheists or agnostics.

In short, they have not established any type of causal relationship, but have implied (and at the absolute least, flirted with saying outright) that such a relationship exists.

Not quite a lie, at any rate, but close enough that it barely makes a difference.

0:43 Former Child Actor Kirk Cameron: An entire generation is being brainwashed by atheistic evolution without even hearing the alternative, and it's radically changing the culture of our nation.

This is a loaded statement which needs to be broken down.

"An entire generation"

At the absolute most, using the numbers that Former Child Actor Kirk Cameron himself uses, we're looking at the tiny fraction of "the whole generation" who go to the top 50 universities in the US, who are educated by the 23% of atheists in those universities, in a subject where their religious views would possibly have been pertinent (which, incidentally, would pretty much always exclude both psychology and biology), who were sufficiently convinced by those arguments to convert to atheism. Once all those necessary caveats and addendums are included, the number can hardly be considered "an entire generation" by even the loosest definition of the term.

"is being brainwashed by atheistic evolution"

So, once we narrow it down to just the professors of biology and psychology, it pretty much stands to reason that they're going to be taught evolution in some capacity or another. Psychology these days has, as one of its central principles, how evolution has molded the human psyche. Stands to reason that evolution is going to be mentioned at least once or twice.

Biology has, as its central principle, evolution. Theodosius Dobzhansky once said that "nothing in biology makes sense, except in the light of evolution."

Now, note again how Former Child Actor Kirk Cameron slyly presents two ideas, atheism and evolution as if the terms were associated, or possibly even synonymous? Dobzhansky was an evangelical Christian who could not, by any reasonable definition of the term, be considered an atheist. Francis Collins, head of the NIH and head of the human genome project is both an evangelical Christian, and an evolutionist. Kenneth Miller is Catholic, believes in God, and testified against Intelligent Design at Dover. The last three popes (not counting JP1 who died before he had a chance to make a statement on the subject) all supported evolution. I don't think I'm assuming too much by saying that all three believed in God.

Again, not quite a lie, per se, but at the absolute least Former Child Actor Kirk Cameron is being disingenuous.

"without even hearing the alternative."

Once we're only looking at the tiny fraction of the generation educated in biology and psychology, both hard sciences which should be addressed scientifically, there is no alternative to evolution. None has ever been presented which passes even the most basic of scientific rigor. Scientists have spent the last several decades asking one simple question: what is the scientific theory of creation, and what experimental test would differentiate it from evolution?

No answer so far. Until there is one, there is no place for the creation hypothesis in either biology or psychology classes.

"And it's radically changing the culture of our nation."

So the tiny fraction of students who are post-secondary educated in the subjects of biology and psychology are radically changing the culture. Note again, Former Child Actor Kirk Cameron craftily implies a causal relationship here where none has been established.

Now, I'm going to skip a few sentences here. Suffice it to say that Former Child Actor Kirk Cameron states outright that the only possible way for someone to love that which is right, just and good is to love God. I'm a huge fan of that which is right, just and good. Former Child Actor Kirk Cameron doesn't qualify. Anyhow, since Former Child Actor Kirk Cameron clearly believes this to be true, and there's no objective way to demonstrate that he's lying, I'll instead focus on those things which are objectively false rather than his statements of faith.

Depressingly enough, that doesn't reduce my workload much.

1:24 Former Child Actor Kirk Cameron: Now when my friend Ray Comfort heard about this, and that the book was public domain, he actually wrote a 50-page introduction to the book which gives the history of evolution, a timeline of Darwin's life, Adolph Hitler's undeniable connection with the theory, Darwin's racism, his disdain for women, and Darwin's thoughts on the existence of God, and put them in the book.

Suffice it to say, virtually none of the above assertions are true, all of them are utterly irrelevant to the veracity of the theory of evolution. It would have no bearing whatsoever on whether evolution is true if Hitler quoted Darwin every third sentence of Mein Kampf rather prohibiting libraries from carrying "6. Writings of a philosophical and social nature whose content deals with the false scientific enlightenment of primitive Darwinism and Monism (Haeckel)".

It would make absolutely no difference whatsoever if Hitler supported Darwin's work rather than, like a creationist, Hitler asserted fixity of kinds:

The fox remains always a fox, the goose remains a goose, and the tiger will retain the character of a tiger. - Adolf Hitler, Mein Kampf, vol. i, ch. xi

Or, as Former Child Actor Kirk Cameron does here, Hitler argued against secular schooling:

Secular schools can never be tolerated because such schools have no religious instruction, and a general moral instruction without a religious foundation is built on air; consequently, all character training and religion must be derived from faith . . . we need believing people. - Adolf Hitler, Speech, April 26, 1933

Hitler's position on the subject is irrelevant to whether that position is actually valid. Former Child Actor Kirk Cameron is trying to claim that evolution must be wrong because Darwin was a racist, or Hitler supported it. This is logically equivalent to claiming that the theory of gravity is wrong because Newton was an asshole, and falling out of a tall building can kill you. It's an argument from consequence, and a clumsy one at that.

Setting aside that it is false by any standard of the time that Darwin was racist or possessed a disdain for women, and that the absolute best you can claim with regards to Hitler is that he applied a horrendous misinterpretation of evolution (tell me again how gas chambers constitute "natural selection?"), all of these points are utterly and completely irrelevant to whether evolution is actually true.

1:48 Former Child Actor Kirk Cameron: it also lists the theory's many hoaxes.

Again Former Child Actor Kirk Cameron slyly implies that somehow the hoaxes (which do exist) were ever considered evidence upon which the theory of evolution rests. They are not and never were. In fact, the reason why many such hoaxes were discovered is because they could not be reconciled with the theory of evolution.

And, by the way, Former Child Actor Kirk Cameron, who found these hoaxes? Here's a hint: it wasn't the creationists of the time. It was the evolutionist biologists whose well you're trying oh-so-hard to poison.

1:51 Former Child Actor Kirk Cameron: It exposes the unscientific belief that nothing created everything.

No scientist, no science, and certainly absolutely no science whatsoever to which Darwin's Origin would in any way have been pertinent to the subject matter makes any such claim. Former Child Actor Kirk Cameron has now lumped evolution in with cosmology, and presented a straw-man version of the latter. Then, for reasons which surpass absurdity, this straw man is being placed in an introduction to the Origin of Species, a text which long predates the science of cosmology, and therefore has absolutely no relevance to it.

1:56 Former Child Actor Kirk Cameron: It points to the incredible structure of DNA

Actually, the structure of DNA is remarkably simple.

2:00 Former Child Actor Kirk Cameron: And the absence of any species-to-species transitional forms actually found in the fossil record.

Outright lie #5. There is no shortage of transitional forms in the fossil record. What is absent is an actual definition of what creationists actually mean by a "transitional form." Former Child Actor Kirk Cameron is fond of trotting out a picture of a "crocoduck" as if such a creature (were it to exist) wouldn't be about the most dramatic disproof of evolution imaginable.

But we don't even need to look at the fossil record to find species-to-species transitional forms. We've observed speciation by any possible definition which is pertinent to evolution in the laboratory, and in nature in the tiny part of natural history on this planet that humans have been around for.

2:06 Former Child Actor Kirk Cameron: It then presents a balanced view of creationism.

If their view of evolution presented above is the measure of "balance..."

2:10 Former Child Actor Kirk Cameron: with information from scientists who actually believe that God created the universe.

Again, we have Former Child Actor Kirk Cameron slyly (and dishonestly) implying that acceptance of evolution, and belief that God created the universe, are somehow mutually exclusive propositions.

2:15 Former Child Actor Kirk Cameron: Such as Albert Einstein,

Albert Einstein openly accepted the theory of evolution. Therefore, the first example Former Child Actor Kirk Cameron gives refutes the false dichotomy he is trying to construct.

2:17 Former Child Actor Kirk Cameron: Isaac Newton

How are Isaac Newton's views even remotely pertinent in a book which would not be published until 130 years after his death?

2:20 Former Child Actor Kirk Cameron: Copernicus

Again, how can you possibly know Copernicus's views on evolution, or cosmology when he died over 400 years before either was published?

2:21 Former Child Actor Kirk Cameron: Bacon

Who died 200 years before "Origins" was published.

2:21 Former Child Actor Kirk Cameron: Faraday

Whose area of research was electrodynamics, whose life long predated any work on cosmology, and who never expressed any opinion one way or the other on Darwin's theories.

2:22 Former Child Actor Kirk Cameron: Louis Pasteur

Who accepted evolution, and believed that God created the universe. Former Child Actor Kirk Cameron's false dichotomy presents itself yet again, and his own example disproves it.

2:23 Former Child Actor Kirk Cameron: and Johann Kepler.

Who died 200 years before Origin was published.

So, just to recap, each of the scientists he cites all believe in God and for all of them, at least one of the following is also true:

1) they also believed in evolution.
2) they died long before any scientific theories of cosmology or evolution (which Former Child Actor Kirk Cameron doesn't seem to realize are two different things) existed or
3) their area of research had absolutely nothing to do with any subject to which Darwin's "Origin of Species" is an even historically relevant text.

So... why mention any one of them in a forward to "Origin of species?"

2:45 Former Child Actor Kirk Cameron: In one day, the gospel, and a clear presentation of Intelligent Design...

Waitaminitwaitaminit!!!!!

I thought that intelligent design had absolutely nothing to do with creationism, and certainly nothing to do with the Christian gospel. After all, that's what the defendants at Dover, as well as the Discovery Institute insist is the case. Perhaps you should try getting your stories straight before you start handing out books.

2:57 Former Child Actor Kirk Cameron: And we're working with Campus Crusade for Christ, Answers in Genesis, and the Alliance Defense Fund to get copies of Darwin's Origin of Species into the hands of this generation.

Or the tiny fraction of this generation who go to the top 50 schools and study biology and psychology.

3:06 Former Child Actor Kirk Cameron: And all we want to do is present the opposing, and correct view rather than being censored, which is exactly the case, at present.

It takes someone truly delusional to claim that allowing the two Hovinds (Kent and Eric) to present their views in videos which are freely available, allowing Ken Ham to operate a museum which is utterly devoid of substance, and allowing Former Child Actor Kirk Cameron to make a video which contains blatant falsehoods constitutes "censorship."

3:15 Former Child Actor Kirk Cameron: These students aren't stupid. They should be presented with both sides of the argument and allowed to make up their own minds, right?

Except that Former Child Actor Kirk Cameron, and his associate Ray Comfort have never presented their side of the argument. They, and every creationist I have ever seen, always construct a negative argument. Evolution is wrong, therefore creationism wins by default. This is, put simply, false, and it is a false dichotomy. They never present "both sides" of an argument. They attack one side of the argument and make the absurd leap that they've somehow supported their own.

They fail to recognize one very simple fact: disproving one position in no way constitutes any evidence whatsoever in support of another.

For some reason, creationists have a great deal of difficulty with this very simple concept.

The rest of the video is basically a request for donations.

Am I the only one who's always found it a little strange that God always seems to need money?

Wednesday, June 25, 2008

Conservapedia gets Schooled.

So, some of you may have heard of Andrew Schlafly, who once described his Conservapedia as "unbiased, from a conservative viewpoint." Classy.

At any rate, their own website chronicles the effective ripping apart of an attempt by Schlafly of the rather elegant work done by Richard Lenski, who, for the last several years, has done long-term studies on the evolution of E. coli. In particular, he managed to breed E. coli which is capable of growing in a media where the only available food source is citrate, a food source not normally used by E. coli. He showed that this was a novel pathway in these bacteria which was not present in their ancestral population. He even identified the mutations necessary to bring it about.

Anyhow, I can't guarantee how long this page will remain up. Conservapedia has a way of censoring their own website, but will include a link to Dr. Lenski's demolishing of Schlafly's attacks, and I want to include here, the full text of Lenski's final response.

Dear Mr. Schlafly:

I tried to be polite, civil and respectful in my reply to your first email, despite its rude tone and uninformed content. Given the continued rudeness of your second email, and the willfully ignorant and slanderous content on your website, my second response will be less polite. I expect you to post my response in its entirety; if not, I will make sure that is made publicly available through other channels.

I offer this lengthy reply because I am an educator as well as a scientist. It is my sincere hope that some readers might learn something from this exchange, even if you do not.

First, it seems that reading might not be your strongest suit given your initial letter, which showed that you had not read our paper, and given subsequent conversations with your followers, in which you wrote that you still had not bothered to read our paper. You wrote: “I did skim Lenski’s paper …” If you have not even read the original paper, how do you have any basis of understanding from which to question, much less criticize, the data that are presented therein?

Second, your capacity to misinterpret and/or misrepresent facts is plain in the third request in your first letter, where you said: “In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000.” That statement was followed by a link to a news article from NewScientist that briefly reported on our work. I assumed you had simply misunderstood that article, because there is not even a mention of proteins anywhere in the news article. As I replied, “We make no such claim anywhere in our paper, nor do I think it is correct. Proteins do not ‘appear out of the blue’, in any case.” So where did your confused assertion come from? It appears to have come from one of your earlier discussions, in which an acoltye (Able806, who to his credit at least seems to have attempted to read our paper) wrote:

“I think it might be best to clarify some of Richard's work. He started his E.Coli project in 1988 and has been running the project for 20 years now; his protocols are available to the general public. The New Scientist article is not very technical but the paper at PNAS is. The change was based on one of his colonies developing the ability to absorb citrate, something not found in wild E.Coli. This occurred around 31,500 generations and is based on the development of 3 proteins in the E.Coli genome. What his future work will be is to look at what caused the development of these 3 proteins around generation 20,000 of that particular colony. ...”

As further evidence of your inability to keep even a few simple facts straight, you later wrote the following: “It [my reply] did clarify that his claims are not as strong as some evolutionists have insisted.” But no competent biologist would, after reading our paper with any care, insist (or even suggest) that “3 new and useful proteins appeared in the colony around generation 20,000” or any similar nonsense. It is only in your letter, and in your acolyte’s confused interpretation of our paper, that I have ever seen such a claim. Am I or the reporter for NewScientist somehow responsible for the confusion that reflects your own laziness and apparent inability to distinguish between a scientific paper, a news article, and a confused summary posted by an acolyte on your own website?

Third, it is apparent to me, and many others who have followed this exchange and your on-line discussions of how to proceed, that you are not acting in good faith in requests for data. From the posted discussion on your web site, it is obvious that you lack any expertise in the relevant fields. Several of your acolytes have pointed this out to you, and that your motives are unclear or questionable at best, but you and your cronies dismissed their concerns as rants and even expelled some of them from posting on your website. [Ed.: citation omitted due to spam filter] Several also pointed out that I had very quickly and straightforwardly responded that the methods and data supporting the evolution of the citrate-utilization capacity are already provided in our paper. One poster in your discussions, Aaronp, wrote:

“I read Lenski's paper, and as a trained microbiologist, I thought that it was both thorough and well done. His claims are backed by good data, namely that which was presented in the figures. I went through each of the figures after Aschlafly said that they were uninformative. Actually, they are basic figures that show the population explosion of the bacterial cultures after the Cit+ mutation occurred. These figures show that the cultures increased in size and mass at a given timepoint, being able to do so because they had evolved a mechanism to utilize a new nutrient, without the assistance of helper plasmids. ... Lenksi’s paper, while not the most definite I’ve seen, is still a very well-researched paper that supports its claims nicely.”

(As far as I saw, Aaronp is the only poster who asserted any expertise in microbiology.) As further evidence of the absence of good-faith discussion about our research, in the discussion thread that began even before you sent your first email to me, I counted the words “fraud” or “fraudulent” being used more than 10 times, including one acolyte, TonyT, who says bluntly that I am “clearly a fraudulent hack.” In the discussion thread that also includes comments after my first reply, the number of times those same words are used has increased to 20, with the word “hoax” also now entering the discussion. A few posters wisely counseled against such slander but that did not deter you. I must say, it is surprising that someone with a law degree would make, and allow on his website, so many nasty comments that implicitly and even explicitly impugn my integrity, and by extension that of my collaborators, without any grounds whatsoever and reflecting only your dogmatic adherence to certain beliefs.

Finally, let me now turn to our data. As I said before, the relevant methods and data about the evolution of the citrate-using bacteria are in our paper. In three places in our paper, we did say “data not shown”, which is common in scientific papers owing to limitations in page length, especially for secondary or minor points. None of the places where we made such references concern the existence of the citrate-using bacteria; they concern only certain secondary properties of those bacteria. We will gladly post those additional data on my website.

It is my impression that you seem to think we have only paper and electronic records of having seen some unusual E. coli. If we made serious errors or misrepresentations, you would surely like to find them in those records. If we did not, then – as some of your acolytes have suggested – you might assert that our records are themselves untrustworthy because, well, because you said so, I guess. But perhaps because you did not bother even to read our paper, or perhaps because you aren’t very bright, you seem not to understand that we have the actual, living bacteria that exhibit the properties reported in our paper, including both the ancestral strain used to start this long-term experiment and its evolved citrate-using descendants. In other words, it’s not that we claim to have glimpsed “a unicorn in the garden” – we have a whole population of them living in my lab! [ http://en.wikipedia.org/wiki/The_Unicorn_in_the_Garden] And lest you accuse me further of fraud, I do not literally mean that we have unicorns in the lab. Rather, I am making a literary allusion. [ http://en.wikipedia.org/wiki/Allusion]

One of your acolytes, Dr. Richard Paley, actually grasped this point. He does not appear to understand the practice and limitations of science, but at least he realizes that we have the bacteria, and that they provide “the real data that we [that’s you and your gang] need”. Here’s what this Dr. Paley had to say:

“I think there’s a great deal of misunderstanding here from the critics of Mr. Schlafly and obfuscation on the part of Prof. Lenski and his supporters. The real data that we need are not in the paper. Rather they are in the bacteria used in the experiments themselves. Prof. Lenski claims that these bacteria ‘evolved’ novel traits and that these were preceded by the evolution of ‘potentiated genotypes’, from which the traits could be ‘reevolved’ using preserved colonies from those generations. But how are we to know if these traits weren’t ‘potentiated’ by the Creator when He designed the bacteria thousands of years ago, such that they would eventually reveal themselves when the time was right? The only way this can be settled is if we have access to the genetic sequences of the bacteria colonies so that we can apply CSI techniques and determine if these ‘potentiated genotypes’ originated through blind chance or intelligence. But with the physical specimens in the hands of Darwinists, who claim they will get around to the sequencing at some unspecifed future time, how can we trust that this data will be forthcoming and forthright? Thus, Prof. Lenski et al. should supply Conservapedia, as stewards, with samples of the preserved E. coli colonies so that the data can be accessible to unbiased researchers outside of the hegemony of the Darwinian academia, even if it won’t be put to immediate examination by Mr. Schlafly. This is simply about keeping tax-payer-funded scientists honest.”

So, will we share the bacteria? Of course we will, with competent scientists. Now, if I was really mean, I might only share the ancestral strain, and let the scientists undertake the 20 years of our experiment. Or if I was only a little bit mean, maybe I’d also send the potentiated bacteria, and let the recipients then repeat the several years of incredibly pain-staking work that my superb doctoral student, Zachary Blount, performed to test some 40 trillion (40,000,000,000,000) cells, which generated 19 additional citrate-using mutants. But I’m a nice guy, at least when treated with some common courtesy, so if a competent scientist asks for them, I would even send a sample of the evolved E. coli that now grows vigorously on citrate. A competent microbiologist, perhaps requiring the assistance of a competent molecular geneticist, would readily confirm the following properties reported in our paper: (i) The ancestral strain does not grow in DM0 (zero glucose, but containing citrate), the recipe for which can be found on my web site, except leaving the glucose out of the standard recipe as stated in our paper. (ii) The evolved citrate-using strain, by contrast, grows well in that exact same medium. (iii) To confirm that the evolved strain is not some contaminating species but is, in fact, derived from the ancestral strain in our study, one could check a number of traits and genes that identify the ancestor as E. coli, and the evolved strains as a descendant thereof, as reported in our paper. (iv) One could also sequence the pykF and nadR genes in the ancestor and evolved citrate-using strains. One would find that the evolved bacteria have mutations in each of these genes. These mutations precisely match those that we reported in our previous work, and they identify the evolved citrate-using mutants as having evolved in the population designated Ara-3 of the long-term evolution experiment, as opposed to any of the other 11 populations in that experiment. And one could go on and on from there to confirm the findings in our paper, and perhaps obtain additional data of the sort that we are currently pursuing.

Before I could send anyone any bacterial strains, in order to comply with good scientific practices I would require evidence of the requesting scientist’s credentials including: (i) affiliation with an appropriate unit in some university or research center with appropriate facilities for storing (-80ÂșC freezer), handling (incubators, etc.), and disposing of bacteria (autoclave); and (ii) some evidence, such as peer-reviewed publications, that indicate that the receiving scientist knows how to work with bacteria, so that I and my university can be sure we are sending biological materials to someone that knows how to handle them. By the way, our strains are not derived from one of the pathogenic varieties of E. coli that are a frequent cause of food-borne illnesses. However, even non-pathogenic strains may cause problems for those who are immune-compromised or otherwise more vulnerable to infection. Also, my university requires that a Material Transfer Agreement be executed before we can ship any strains. That agreement would not constrain a receiving scientist from publishing his or her results. However, if an incompetent or fraudulent hack (note that I make no reference to any person, as this is strictly a hypothetical scenario, one that I doubt would occur) were to make false or misleading claims about our strains, then I’m confident that some highly qualified scientists would join the fray, examine the strains, and sort out who was right and who was wrong. That’s the way science works.

I would also generally ask what the requesting scientist intends to do with our strains. Why? It helps me to gauge the requester’s expertise. I might be able to point out useful references, for example. Moreover, as I’ve said, we are continuing our work with these strains, on multiple fronts, as explained in considerable detail in the Discussion section of our paper. I would not be happy to see our work “scooped” by another team – especially for the sake of the outstanding students and postdocs in my group who are hard at work on these fronts. However, that request to allow us to proceed, without risk of being scooped on work in which we have made a substantial investment of time and effort, would be just that: a request. In other words, we would respect PNAS policy to share those strains with any competent scientist who complied with my university’s requirements for the MTA and any other relevant legal restrictions. If any such request requires substantial time or resources (we have thousands of samples from this and many other experiments), then of course I would expect the recipient to bear those costs.
So there you have it. I know that I’ve been a bit less polite in this response than in my previous one, but I’m still behaving far more politely than you deserve given your rude, willfully ignorant, and slanderous behavior. And I’ve spent far more time responding than you deserve. However, as I said at the outset, I take education seriously, and I know some of your acolytes still have the ability and desire to think, as do many others who will read this exchange.

Sincerely,
Richard Lenski

P.S. Did you know that your own bowels harbor something like a billion (1,000,000,000) E. coli at this very moment? So remember to wash your hands after going to the toilet, as I hope your mother taught you. Simple calculations imply that there are something like 10^20 = 100,000,000,000,000,000,000 E. coli alive on our planet at any moment. Even if they divide just once per day, and given a typical mutation rate of 10^-9 or 10^-10 per base-pair per generation, then pretty much every possible double mutation would occur every day or so. That’s a lot of opportunity for evolution.

P.P.S. I hope that some readers might get a chuckle out of this story. The same Sunday (15 June 2008) that you and some of your acolytes were posting and promoting scurrilous attacks on me and our research (wasn’t that a bit disrespectful of the Sabbath?), I was in a church attending a wedding. And do you know what Old Testament lesson was read? It was Genesis 1:27-28, in which God created Man and Woman. It’s a very simple and lovely story, and I did not ask any questions, storm out, or demand the evidence that it happened as written at a time when science did not yet exist. I was there in the realm of spirituality and mutual respect, not confusing a house of religion for a science class or laboratory. And it was a beautiful wedding, too.

P.P.P.S. You may be unable to understand, or unwilling to accept, that evolution occurs. And yet, life evolves! [ http://en.wikipedia.org/wiki/E_pur_si_muove] From the content on your website, it is clear that you, like many others, view God as the Creator of the Universe. I respect that view. I find it baffling, however, that someone can worship God as the all-mighty Creator while, at the same time, denying even the possibility (not to mention the overwhelming evidence) that God’s Creation involved evolution. It is as though a person thinks that God must have the same limitations when it comes to creation as a person who is unable to understand, or even attempt to understand, the world in which we live. Isn’t that view insulting to God?

P.P.P.P.S. I noticed that you say that one of your favorite articles on your website is the one on “Deceit.” That article begins as follows: “Deceit is the deliberate distortion or denial of the truth with an intent to trick or fool another. Christianity and Judaism teach that deceit is wrong. For example, the Old Testament says, ‘Thou shalt not bear false witness against thy neighbor.’” You really should think more carefully about what that commandment means before you go around bearing false witness against others.


We scientists have been playing softball with creationists for long enough. I think it's about time we started hitting back.

Tuesday, June 24, 2008

How Genesis 1 should read.

Chapter 1

1. In the beginning God created Dates.

2. And the date was Monday, September 7th, 4177 BC.

3. And God said, let there be light; and there was light. And when there was Light, God saw the Date, that it was Monday, and he got down to work; for verily, he had a Big Job to do.

4. And God made pottery shards and Silurian mollusks and pre-Cambrian limestone strata; and flints and Jurassic Mastodon tusks and Picanthopus erectus skulls and Cretaceous placentals made he; and those cave paintings at Lasceaux. And that was that, for the first Work Day.

5. And God saw that he had made many wondrous things, but that he had not wherein to put it all. And God said, Let the heavens be divided from the earth; and let us bury all of these Things which we have made in the earth; but not too deep.

6. And God buried all the Things which he had made, and that was that.

7. And the morning and the evening and the overtime were Tuesday.

8. And God said, Let there be water; and let the dry land appear; and that was that.

9. And God called the dry land "land;" and the water called he the Sea. And in the land and beneath it put he prehistoric carboniferous forests yielding anthracite and other ligneous matter; and all these called he Resources; and he made them Abundant.

10. And likewise all that was in the sea, even unto two hundred miles from the dry land, called he resources; all that was therein, like manganese nodules, for instance.

11. And the morning unto the evening had been a long day; which he called Wednesday.

12. And God said, Let the earth bring forth every moving creature, with or without wings or feet, or fins or claws, vestigial limbs and all, right now; and let each one be of a separate species. For lo, I can make whatsoever I like, whensoever I like. But he didst verily also make ring species, just to confuse matters.

13. And the earth brought forth abundantly all creatures, great and small, with and without backbones, with and without wings and feet and fins and claws, vestigial limbs and all. And verily were ring species made, just to confuse matters.

14. But God blessed them all, saying, Be fruitful and multiply and Evolve Not.

15. And God looked upon the species he hath made, and saw that the earth was exceedingly crowded, and he said unto them, Let each species compete for what it needed; for Competition is My Law. And the species competeth, the cattle and the creeping things; and the dogs ate the brontosauruses and God was pleased. And grass didst verily outrun the velociraptors, and God was pleased.

16. And God took the bones from the dinosaurs, and caused he they to appear old; and cast he them about the land and the sea. And he took every tiny creature that hadst been eaten by dogs, and which hadst not survived the Competition, and caused them to become fossils; and cast he them about likewise.

17. And just to put matters beyond the valley of the shadow of a doubt God created radiometric dating, and didst verily set the ratio of radioactive isotopes to make the world appear mightily old.

18. And in the Evening of the day which was Thursday, God saw that he had put in another good day's work.

19. And God said, Let us make man in our image, after our likeness, which is tall and well-formed and pale of hue: and let us also make apes, which resembleth us not in any wise, but are short and ill-formed and hairy. And God added, Let man have dominion over the monkeys and the fowl of the air and every species.

20. So God created Man in His own image; tall and well-formed and pale of hue created He him, and nothing at all like the apes. And verily didst God create Endogenous Retroviruses and transposons. And placed they he these in Humans and all apes, which resembleth Man not at all.

21. And created He the redundant pseudogenes, such as the Hemoglobin pseudogene, and placed they he in the genome in the exact chromosomal location in all Humans which corresponds to the Apes, even though they resembleth us not at all.

22. And verily didst He break the gene for Vitamin C synthesis, and placed it verily within the genome for Humans, as well as apes which resembleth us not at all. For Scurvy was His will, but only for Humans and Apes and Monkeys, even though they resembleth us not at all.

24. And God saw everything he had made, and he saw that it was very good; and God said, It just goes to show Me what the private sector can accomplish. With a lot of fool regulations this could have taken billions of years.

25. And the evening of the fifth day, which had been the roughest day yet, God said, Thank me it's Friday. And God made the weekend.

Monday, June 23, 2008

Get Intelligent Design into the Classroom in 6 easy steps

1. Actually come up with a theory of Intelligent Design. It must make positive, testable predictions beyond "Evolution is wrong, therefore Intelligentdesignerdidit." It must make predictions of the form "if intelligentdesignerdidit, then when we perform experiment x, we will observe y." Observing something other than y must disprove the theory of Intelligent Design.

2. Perform experiments. The results of those experiments must not be explainable by the theory of evolution, or by any other explanation other than an intelligent designer. In the course of these experiments, you must make a concerted effort to conclusively disprove that an intelligent agency had any hand in the creation of life, and for every single experiment, there must be a result predicted which would disprove the action of an intelligence.

3. Repeat step 2. A lot.

4. Publish the results obtained in a peer-reviewed scientific journal.

5. Repeat steps 2-4. A lot.

6. Sit back, relax and enjoy a beer, and keep your Nobel prize polished to a healthy shine while ID is automatically inserted into science textbooks everywhere, and becomes the new standard in science education in biology.

Do these six things and no scientist on earth will object to ID being inserted into science class. Evolution has done this many times over. That's why it's in science textbooks right now. If ID did the exact same thing, it'd be in the science texts within the next 20 years, easily.

So, who's up for it?

Thermodynamics for Creationists

Okay, so in a recent discussion, the second law of thermodynamics came up. Honestly, I can't believe that I'm having to point this out again, but the truth of the matter is that the second law of thermodynamics in no way prohibits evolution. All the second law of thermodynamics states is that the total entropy of the universe must increase over time.

So let's start with the basics. What is entropy?

The thermodynamic definition of entropy is k*ln(multiplicity)

Okay, what is multiplicity?

let' start with a simple conceptual example (which, surprisingly enough, turns out to have a real world thermodynamic version (the two state paramagnet))

Let's say you flip four coins.

How many possible ways are there for it to come up all tails? 1
How many ways are there for it to come up with exactly one heads? 4
How many ways for two heads? 6
How many ways for three heads? 4
And for all four heads? 1

Those numbers are what are called multiplicities.

Let's look at that again. Define a microstate as the specific state. ie, tails-heads-tails-tails would be one microstate. heads-tails-tails-tails would be a different microstate; but they're both part of the same macrostate (one heads). The fundamental assumption of thermodynamics is that in any given macrostate (all tails, one heads, and so on), the microstates are indistinguishable from each other. So, assuming that your coins are fair, the probability of a microstate is equal to any other.

In other words, multiplicity is effectively a measure of probability. multiplicity of some macrostate/multiplicity of all possible macrostates of a system gives the probability of that specific macrostate.

Back to our definition of entropy.

S = k*ln(multiplicity)... log is a monotonic function, so bigger it is, bigger S will be. k is boltzman's constant.

This is what entropy, essentially, truly is. The reason we say it tends to increase is because, as long as the fundumental assumption of statistical mechanics holds, higher entropy states directly correspond to higher probability states. ie, the high entropy states are literally the most likely states of reality. However, the key point here is total entropy.

Systems can easily take a entropy drop in one area so long as there's a corresponding entropy increase elsewhere. In fact, that's pretty much exactly how your refrigerator works.

First, consider if you have two systems, one with multiplicity A, the other with multiplicity B. What's the total multiplicity? A*B, right?

so therefore the two entropies would be the sum, since ln(A*B) = ln(A) + ln(B)

accept that so far?

Great. Now, let's define temperature. Temperature is not actually defined as being proportional to the energy of an object. That's a nontrivial fact about temperature. Temperature nowadays is defined thermodynamically as the reciprocal of the partial derivative of entropy with respect to energy with volume and number of particles (and external magnetic field and other such things) held constant when relevant.

Now, what does that actually mean? it means an object for which a slight change in energy would net a huge change in entropy (in the same direction) would have a low temperature, while big change in energy causing small change in entropy would have a high temperature, right? This also works backwards, if two objects, one hot one cold, both undergo a change in temperature of an equal quantity, the cold one will have a greater change in entropy than the hot one. That's pretty much the definition of the term. Again, if you're having trouble with this, I recommend you pick up a good thermodynamics text. I recommend Kittel and Kroemer's "Thermal Physics." I don't know which edition it's in now, but you should be able to find it on Amazon.

So place those two objects together. What's going happen? Well, the highest probable states are those that correspond to the highest entropy, right?

So... if energy goes from the cold object to the hot object, a lot of entropy will be lost from the cold object, while only a little entropy will be gained by the hot object. So a net decrease in entropy.

In the other direction, there'd be obviously a net increase in entropy. This is why energy goes from hot to cold. And it's a nontrivial fact, as I mentioned.

All of this is to point out the obvious: local decreases in entropy are not only possible; but they happen as a matter of routine in nature. Take crystal formation for example, or the operation of your refrigerator. All the second law of thermodynamics states is that the entropy of the universe has to go up. It doesn't matter if the entropy of a living being, or even of the entire planet earth drops, as long as there's an increase in entropy elsewhere.