Lenski vs conservapedia

No self-respecting evolution blog can go without mentioning the interactions of Dr. Lenski (of evolution in a tube note) with Mr. Schlafly of Conservapedia. Conservapedia is the religious right’s answer to Wikipedia, because they believe that Wikipedia is biased toward liberal ideas.

Mr. Schlafly (a non-scientist) sent a letter to Dr. Lenski to

request for your data underlying your recent paper….Your work was taxpayer-funded, and PNAS represents that its authors will make underlying data available. I’d like to review the data myself and ensure availability for others, including experts and my students. Others have expressed interest in access to the data in addition to myself, and your website seems well-suited for public release of these data.

For those of you unfamiliar with the process of modern science, peer-reviewed published articles are written in such a way that anyone with the knowledge and the equipment should be able to repeat the presented experiments. The articles also include enough information to prove the point that the authors are trying to make (of course interpretation is sometimes up for debate).

What Mr. Schlafly requested is completely unheard of, unless someone is being investigated for forgery (see Hwang Woo-Suk). What makes it worse is that he is nothing near a scientist. If this sort of practice was allowed to go on regularly, science would come to a grinding halt due to scientists having to constantly dig up old lab books and dust off their old 5 1/4 floppies. This is why no scientific competitor or lay person has the right to ask for this kind of data even though scientists are usually funded by public money.

Now for the good part. Dr. Lenski, after initially replying kindly, sent a scathing letter to Mr. Schlafly.  Rather than selecting specific quotes from the letter, I suggest you go read it yourself.  I promise at least one laugh.

Recently, it has come to my attention that some of the authors at Conservapedia have been using underhanded tactics and censoring people.  I guess I shouldn’t have been too surprised.

One step closer to a complete Tree of Life

The inability of scientists to create a complete Tree of Life (TOL) has been a talking point of ID proponents for some time. Indeed, a complete TOL based on DNA sequence alignments has yet to be completed. Instead of a single tree, usually ‘bushes’ of different clades are about as close as we have gotten. I don’t believe this is because it is impossible to make a complete tree that encompasses all known living organisms, it is simply another example of where the science is a work in progress. Molecular biology is in its infancy and the era of bioinformatics has just started. Nonetheless, IDers take our incomplete understanding as evidence against evolution (For the Discovery Institute’s take, see here and here).

These phylogenetic trees are made by taking DNA sequences from different organisms and aligning them with each other. Organisms that are closer evolutionarily will have more DNA in common and therefore the sequences will mostly match and be easily aligned. Organisms that are distantly related will have less similarities in their sequences. This is not an easy task and is fraught with error due to mutations that lead to an insertion of a piece of DNA, deletion of pieces of DNA, substitutions of DNA, etc.

In the June 20, 2008 issue of Science, Ari Löytynoja and Nick Goldman report a new and better way to align DNA sequences thereby creating better phylogenetic trees. Aligning DNA sequences is a mathematically complex process with several different algorithms designed to take into account small changes in the sequence. Don’t be scared, I am not going to bore you with the mathematical details (mostly because I don’t understand it).

According to the authors, the biggest problem with the current algorithms is that:

Traditional multiple sequence alignment methods disregard the phylogenetic implications of gap patterns that they create and infer systematically biased alignments with excess deletions and substitutions, too few insertions, and implausible insertion deletion–event histories”

Surprisingly, they found that simply adding more and more sequences from similar organisms did not increase the accuracy due to every additional sequence adding evolutionary time to the analysis and therefore more DNA deletions, insertions, or substitutions. This is where the authors say that their new method really shines due to its ability to utilize the phylogenetic relationship of sequences.

What does this all mean for the theory of evolution? Hopefully this will lead to better phylogenetic trees and bring us one step closer to that all important TOL. On the more technical side, the authors think that their new method will allow for a better understanding of the frequency of DNA insertions, deletions, and substitutions.

Year of Evolution in Philly

The Skeptick over at the Way of the Woo reminds us that this year is the 150th anniversary of the publication of “The Origin of Species” by Charles Darwin.  Philidelphia is celebrating the anniversary by having a “year of evolution.”  It looks like a wide variety of pro-science organizations and museums are participating, including the Academy of Natural Sciences, the Philly zoo, and many local museums.  Here is a list of the scheduled festivities.  I hope other cities around the nation and around the world will join in the fun.

Of course these events could not go on without the people at the Discovery Institute taking notice.  Anika Smith wrote a post entitled its Anno Darwini in Philadelphia.  In this post, Smith of course has to turn these celebrations into an anti-religious witch hunt:

It’s the final quote in the story that sounds an ominous note for dissenters from Darwin: “We will try to find ways of persuading people that it’s not in conflict with their faith,” Dr. Brown said.  Since the pro-evolution-only lobby ignores the scientific evidence that doesn’t support Darwin’s theory, they’ve decided to address what they can afford to acknowledge as a problem for many people: Darwinian evolution conflicts with their religious beliefs.

Just a couple things.  Darwinian evolution only conflicts with a small sect of religion: fundamentalists that take Genesis as literal fact and believe the earth is only 6,000 years old.  But modern geology, archeology, paleontology also all conflict with their religious beliefs.  Also, I have not seen any “scientific evidence that doesn’t support Darwin’s theory”?  All I see from the ID side is ignorance dressed up as complex explanations.

The evolutionary numbers game

In my last post, I brought up how Michael Behe used the fact that 40,000 generations of E. coli were necessary for Richard Lenski’s experiment to find an E.coli who could utilize citrate. In this post, I am going to run through some numbers to show how 40,000 generations is nothing to evolutionary time.  Of course my numbers are going to be rough estimates, but I think it will get the job done.

For the sake of argument, lets say the earth is 10,000 years old (yes, people do believe the earth is this young). If Behe’s math is correct, then E. coli have 2,000 generations a year or 20,000,000 generations over the time of the young earth. More realistically, the earth is 4.5 billion years old, or nearly 10 trillion generations of E. coli. Of course E. coli hasn’t been around the whole time the earth has, but it does put that 40,000 number into perspective.

Let’s say that a beneficial mutation, such as the ability to use citrate, occurs once every 100,000 generations. Given the 10 trillion number above, that would give 100,000 beneficial mutations. Keeping in mind that E. coli only has ~5000 genes, each gene could have changed 20 times.

The last set of numbers we will be addressing is the nearly unfathomable number of bacteria on the planet.  For reference, our bodies alone are estimated to have 1,000 trillion or 10^15 of bacteria (not all E. coli of course) of bacteria (Yes, I know, it is kind of gross). There are over 6 billion people on earth bringing the total of bacteria inside humans to 6 X 10^24.

Now that is a lot of bacteria, just inside people, but how about all over the planet?  Bacteria are everywhere: inside us, on practically every surface, throughout the ocean, and throughout the earth.  It has been estimated that there are 5 X 10^30 bacteria on earth.

10^12 generations of bacteria and 10^30 bacteria.  Those are mind-boggling numbers!  I know the numbers don’t really mean too much by themselves, but just keep them in mind when an IDer tries to convince you that something like 40,000 generations is a big deal.

Behe Doesn’t Believe in Evolution in a Tube

Michael Behe writes on June 6th a post entitled: Multiple Mutations Needed for E. Coli. This post came from his amazon blog, where he is trying to push his book. Behe is writing of course about Richard Lenski’s (et al.) recent publication in PNAS (Proceedings of the National Academy of Sciences). In the article, the authors describe an experiment that has been going on since 1988. Now that is persistence! Richard Lenski is the principal author and has kept the same 12 cultures of E. coli reproducing for the last 20 years. These cultures are grown in two food sources: glucose, which E. coli readily uses and citrate, which E. coli cannot use. After nearly 32,000 generations, one of the E. coli cultures developed, or evolved, the ability to use citrate.

This experiment provides an example of a living organism evolving a new trait in the tightly controlled setting. This type of result had not really been seen before (largely due to the long times necessary) and was something of a missing piece of evidence for evolution. Evolutionary type changes have been observed outside of the lab (isolated lizards, nylon eating bacteria), but not in a true experimental setup.

The changes in the isolated cultures of E. coli were not limited to the ability to utilize citrate. They also exhibited changes from the original cultures that include:

higher maximum growth rates on glucose, shorter lag phases upon transfer into fresh medium, reduced peak population densities, and larger average cell sizes relative to their ancestor.

10 of the 12 E. coli cultures also “evolved increased DNA supercoiling.” When challenged with other carbon sources, such as maltose or lactose, their growth rates differed. These changes are indeed important to keep in mind as more evidence of evolutionary change, but the clear advantage of the gain-of-function change illustrated by the new ability to utilize citrate is monumental.

Predictably, Behe does not seem to be too impressed by the experiment. He makes the point that E. coli divides rapidly and 20 years equates to 40,000 (even though the paper clearly states 31,500) generations and therefore is not that remarkable. This may seem like a lot of generations, but 20 years is not even a blink of the eye in evolutionary timescales. I will give an in depth analysis of the numbers in a later post. Besides, this experiment provides proof of concept that random mutations can lead to a gain-of-function change, one of evolution denier’s talking points, as Casey Luskin as said: “ID is far more interested in explaining the GAIN of biological function rather than loss of function.”

Lenski wanted to further explore how the E. coli were able to gain the ability to use citrate. Was it a single mutation event or was it a series of mutations? In order to determine which was true, he repeated the experiment with cultures that had gone through various numbers of generations, 12 in all. He found that when he took cultures after 20,000 generations, they more quickly were cit+. This led Lenski to conclude that there were multiple mutational events leading to cit+, one of which occurred before the 20,000 generation. An important finding, and one that shows that there can be silent, but beneficial, mutations. Behe disagrees:

If the development of many of the features of the cell required multiple mutations during the course of evolution, then the cell is beyond Darwinian explanation.

I am not sure how someone so educated and respected could say something so completely vacuous. In evolution, everything is carried over, whether it has an immediate benefit or not. Maybe one of the mutations that occurred allowed the mutant cell to grow slightly faster than the others. Maybe the mutation was silent and did not help or harm anything. Does Behe really believe that every mutation has to have a large phenotypic effect to be in accord with evolutionary theory?

Louisiana academic freedom legislation roundup

The Evolution News and Views blog from the Discovery Institute has put out a series of posts bragging about the success of academic freedom legislation. They seem to think that this is some big win for the side of ID (and irrationality).  Well, they are right. The newest strategy of ID proponents seems to attack evolutionary theory by pointing out its supposed flaws and weaknesses. ID of course can then swoop on in and become the alternate “theory”. This is exactly what these bills aim to accomplish which can be found here.

One of the provisions of the bill is that it should not be

construed to promote any religious doctrine, promote discrimination for or against a particular set of religious beliefs, or promote discrimination for or against religion or nonreligion.

This is exactly the reason these bills have been called stealth pro-ID bills. ID is not science; it is religion. However, it does masquerade as science allowing it to be taught in schools as science, which is why it is so dangerous. Furthermore, just because the bill says that it is not meant to be for any particular religion, or subset of religion, doesn’t mean that the teachers themselves won’t take advantage to spread their particular brand. I can remember several teachers in school who ignored the standard curriculum and textbook in favor of their own material.

Getting back to the construed language, here is what Sen. Ben Nevers, who introduced the bill, said when discussing why he proposed the bill:

They (The Louisiana Family Forum) believe that scientific data related to creationism should be discussed when dealing with Darwin’s theory. This would allow the discussion of scientific facts,” Nevers said. “I feel the students should know there are weaknesses and strengths in both scientific arguments.

As we all know, creationism is a religious doctrine.  Therefore, the that shalt not construe language is simply BS.

The bill aims to allow teachers to use alternative materials as teaching aids when discussing controversial subjects, including evolution. I am not really too sure what other science subjects are controversial, but I can make a few guesses though. Geology: the determination of the age of various fossils, including transition fossils. Astronomy: the red-shifted spectra of stars and galaxies that show the universe is ~13.7 billion years old. But why stop at science? History: the holocaust, crusades, slavery, etc. All of these subjects could be deemed controversial.

I find it odd that this type of bill, chiefly aimed against evolution, would be proposed in the face of more and more evidence arising for evolution. Within the last two years, we have seen the discovery of a key transition fossil (Tiktaalik), the observation of phenotypic changes in isolated lizard populations, and most recently, the spontaneous ability to metabolize a new carbon source in E. coli. At the same time, no real evidence has been produced in favor of ID/creation or evidence against evolution. This sort of absurdity is like if there was a murder investigation ongoing and new pieces of evidence had been appearing everyday to point to a particular person, but the detectives decide to focus on a person that has no motive and no evidence against them.

This bill, and others like it are dangerous because they have the possibility of removing any real academic standards. Education should be limited to the facts and not subject to interpretation or by any religious views.

What does the evidence say to the Discovery Institute?

The subject of today’s post is again about the denial of evidence for evolution by ID proponents. In the June 9th post, entitled: “Are Neo-Darwinists barking up the wrong tree?“, Casey Luskin and Logan Gage describes how some theists, including Stan Guthrie, are now embracing common ancestry. I applaud these people. However, the authors don’t buy it because of a lack of evidence for evolution. He says that we should ask “What does the evidence say?” I have been asking the same question for some time now, but IDers and I do not come up with the same answer.

One of the authors points is that the Cambrian explosion was too fast without any evolutionary precursors for the amount of new phyla seen. However, the Cambrian explosion was not the “geological instant” that it is made out to be. Does 70-80 million years seem like an instant? If you assume a generation to be 3 months, then that gives nearly 300 million generations of animals. Geological instant maybe, but a biological eternity.

Even if you were to accept that the Cambrian explosion was an act of God(Designer), you still have to accept that the creatures in existence back then are no longer around today. Where did all the new animals come from? This little detail seems to be missing from IDers analysis.

scientists have yet to uncover a scrap of evidence to suggest that they functioned as anything but commons fins

I have made this point so many times that I get blue in the face, but lack of evidence is not evidence that it is wrong. I am not too sure what kind of evidence they would want. Not too many pictures taken back then.

Anyway, as far as there not being a scrap of evidence, lets take a look at what the scientists who found the Tiktaalik fossils say about it:

Tiktaalik developed new mechanisms of head movement, respiration and body support that enabled this fish to exploit shallow water and even subaerial habitats. In support of this interpretation, ribs of the type that occur in Tiktaalik augment thoracolumbar rigidity and axial support, functions that are not necessary in an aquatic setting that is deep enough to support the body.

In regards to the fins that they simply dismisses out of hand, the authors point to:

Here we describe the pectoral appendage of a member of the sister group of tetrapods, Tiktaalik roseae, which is morphologically and functionally transitional between a fin and a limb. The expanded array of distal endochondral bones and synovial joints in the fin of Tiktaalik is similar to the distal limb pattern of basal tetrapods. The fin of Tiktaalik was capable of a range of postures, including a limb-like substrate-supported stance in which the shoulder and elbow were flexed and the distal skeleton extended.

I am not to sure how the authors can honestly say that there is not a “scrap of evidence.” Is it an honest mistake? Willful ignorance? Boldface lie?

They then goes on to poke holes in the Tree of Life (TOL) using the same arguments Luskin has used before. Rather than rehashing my criticisms of his analysis, I will just point you here. I do want to point out that Luskin and Gage refer again to a quote from WF Doolittle from June 1999, before the genomic era and the explosion of bioinformatic tools.

Both groups would do well to carefully scrutinize the scientific data and realize that there are good evidential reasons to question universal common ancestry.

Really? I haven’t seem it. All I hear from ID proponents is denial of evidence (read: Tiktaalik) or taking current unknowns as evidence against evolution (TOL).