(Reprinted from Recursivity.)

As each year draws to a close, we can expect being treated to the annual ritual of self-congratulation by intelligent design advocates. Why, they have accomplished so much in the last year! The movement is simply overflowing with ideas! And honest, god-fearing people! And real scientists! And publishing successes! Not at all like those dogmatic, liberal, communistic, intolerant, censoring, Nazi-like evolutionists!

2014 is no different. Here we have the DI's official clown, David Klinghoffer, comparing himself to Leon Wieseltier (in part because, he says, their surnames sound similar -- I kid you not) and the Discovery Institute to The New Republic.

Actually, there are two big similarities I can think of: when TNR tried to come up with a list of 100 "thinkers" whose achievements were most in line with things that TNR cares about, science didn't even merit its own category. But theology did! And TNR's Wieseltier wrote a review of Nagel's book that demonstrated he didn't have the vaguest understanding of why Mind and Cosmos was nearly universally panned. Wieseltier even adopted intelligent design tropes like "Darwinist mob", "Darwinist dittoheads", "bargain-basement atheism", "mob of materialists", "free-thinking inquisitors", "Sacred Congregation for the Doctrine of the Secular Faith", and "scientistic tyranny". Don't let the door hit you on your way out, Leon.

Klinghoffer claims "In the evolution controversy, it's supporters of intelligent design who stand for ideas (disagree with us or not) and idealism." Well, that's something that we can actually check. Since ID is so brimming with ideas, let's look at ID's flagship journal, Bio-Complexity, and see how many papers were published this year. ID supporters are always complaining about how their groundbreaking word is censored by evil Darwinists. If true (it's not), then in Bio-Complexity they have no grounds for complaints: nearly all of the 32 people listed on the "Editorial Team" are well-known creationists and hence automatically friendly to any submission.

How many papers did Bio-Complexity manage to publish this year? A grand total of four! Why, that's 1/8th of a paper per member of the editorial team. By any measure, this is simply astounding productivity. They can be proud of how much they have added to the world's knowledge!

Looking a little deeper, we see that of these four, only one is labeled as a "research article". Two are "critical reviews" and one is a "critical focus". And of these four stellar contributions, one has 2 out of the 3 authors on the editorial team, two are written by members of the editorial team, leaving only one contribution having no one on the editorial team. And that one is written by Winston Ewert, who is a "senior researcher" at Robert J. Marks II's "evolutionary informatics lab". In other words, with all the ideas that ID supporters are brimming with, they couldn't manage to publish a single article by anyone not on the editorial team or directly associated with the editors.

What happened to the claim that ID creationists stand for ideas? One research article a year is not that impressive. Where are all those ideas Klinghoffer was raving about? Why can't their own flagship journal manage to publish any of them?

As 2015 draws near, don't expect that we will get any answers to these questions. Heck, not even the illustrious Robert J. Marks II can manage to respond to a simple question about information theory.

Ohio House Bill 597 dead, for now

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The authors of House Bill 597, the anti-common core science distorting bill introduced in the Ohio legislature, is dead for now. According to the Cleveland Plain Dealer (via NCSE), the bill won’t be debated or voted on this term. However, according to the bill’s author, Republican State Representative Andy Thompson, the issue will be revived in the next term of the Legislature. I’ll note that the Bill’s co-author, Republican Speaker Pro Tem Max Huffman, will be term-limited out of the Legislature and thus won’t be around to shepherd it.

As I argued previously on the Thumb, the Bill also enshrines a distorted representation of science education, focusing students on memorizing facts rather than learning the processes of science (see here and here and here). I’ll be interested to see if that same distortion appears when the issue is revived, if it is in fact revived.

Phylogenomic Fallacies

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This is the fourth in a series of articles for the general public focused on understanding how species are related and how genomic data is used in research. Today, we talk about some common fallacies in phylogenomics.

Where do humans fit on the evolutionary tree of life? This is an important topic in evolutionary biology. A lot of people believe humans are the most important and highly-evolved organisms, but in reality, all modern species are equally evolved. Our natural tendency to assume that humans are evolutionarily superior has led to a few misconceptions about phylogenetic trees.


To understand the first misconception, let’s look at a phylogenetic tree of plants (from “The Amborella Genome and the Evolution of Flowering Plants”). Eudicots and monocots are two classes of flowering plants, or angiosperms, and the plants in black are non-flowering plants. The term “basal” refers to the base of a phylogenetic tree, and a basal group is a species that branches closer to that base. The authors chose to label the angiosperms that are not eudicots or monocots as “basal angiosperms.” But this label is arbitrary; all the angiosperms are equidistant from the common ancestor and thus equally evolved. We sometimes tend to give more weight to branches that contain the species of interest and call other branches basal, almost assigning them a lesser importance. In this case, the species of interest is plants that consist of many foods that humans eat; a species is often deemed more important as it relates to humans. But modern species are equally evolved from a root common ancestor regardless of when their branch diverged from the common ancestor. To avoid confusion, it might be best to eliminate the “basal” term altogether.

This type of thinking also leads us to place humans at the end of phylogenetic trees. However, this placement is arbitrary and trees can be drawn in many equivalent ways. For example, compare a tree of primates with the branches rotated. The tree on the left, with humans at the top of the tree, is one you might see more often. But both of these trees are actually identical, and the relationships between species that can be inferred from the tree on the right is the same as the relationships in the tree on the left. Species at the tip of a tree are equidistant from the root common ancestor, so they can be considered evolutionarily equivalent.

primate tree 1.png

primate tree 2.png

Similarly, a common misconception is that humans evolved directly from monkeys. Monkeys, though, are modern species just like we are and have been evolving and changing over time. The common ancestor we share with monkeys may have looked much different than monkeys do now. This assumption that modern species represent an ancestral state of human evolution is what T. Ryan Gregory calls the platypus fallacy. Gregory uses the example that we can’t examine the traits of platypuses and think that humans at one point in their evolution possessed these same traits. We can no more infer the traits of human ancestor species from platypuses than platypuses can infer the traits of their ancestors from us.

Human-centered thinking is very prevalent in our society, affecting our laws, religions, and customs. While it probably influences all of us on a personal level, it can lead to false conclusions and misconceptions in science, like thinking that humans are the most highly evolved species. But all modern species are evolutionarily equivalent because they have been evolving for the same amount of time. Eliminating this fallacy will enable us to better understand the evolutionary process.

For more information on basal groups, check out: “Which side of the tree is more basal?, Krell, Frank et al. Systematic Entomology (2004).

This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

Libellula pulchella forensis

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Libellula pulchellaeight twelve-spotted skimmer, Elmer’s Two-Mile Creek, Boulder, Colorado. See here for eight-spotted skimmer, L. forensis.

Update, 12/11/2014, 12:30-ish MST: A Lexington Herald-Leader editorial has a [f]ew questions for Answers in Genesis, not least,

Why does God need so much taxpayer help?

Really, has God been so lame spreading the good news that AIG must “counter the myths floating around about the Bible-upholding Ark Encounter,” on a digital video board in New York’s Times Square?

Does God need to be defended with the demagogic language AIG and its founder Ken Ham use in the holy war against “intolerant liberal friends,” “secularists,” “Bible-scoffers,” and, the most telling, “agitators outside the state?”

The editorial concludes,

Perhaps Answers in Genesis should give up thanking God that intolerant liberals “can’t sink this ship,” and ask the deity instead whether it can be built without more government handouts.


I noted in a comment to another article that, according to reporter Joe Sonka, writing in Insider Louisville, The Lost Ark: Kentucky will not grant tax incentives to Ark Encounter,

Kentucky’s Tourism Arts & Heritage Cabinet Secretary Bob Stewart informed representatives of the proposed Ark Encounter tourist attraction today that their project will not be eligible for up to $18 million in tax incentives from the state, due to their refusal to pledge not to discriminate in hiring based on religion.

and further that

Stewart cited AiG CEO Ken Ham’s Nov. 19 fundraising letter that accused the Beshear administration of religious persecution and reaffirmed their desire to discriminate in hiring based on religion. He also cited other statements throughout the year from AiG officials claiming the purpose of the park is to evangelize and indoctrinate its visitors.

Mr. Stewart wished Ark Encounter well but noted,

“Certainly, Ark Encounter has every right to change the nature of the project from a tourism attraction to a ministry,” wrote Stewart. “However, state tourism tax incentives cannot be used to fund religious indoctrination or otherwise be used to advance religion. The use of state incentives in this way violates the Separation of Church and State provisions of the Constitution and is therefore impermissible.”

Mr. Sonka appends to his article two letters: The first is from Bob Stewart, the secretary of the state’s Tourism Cabinet, to James Parsons, an attorney for the Ark Park, and outlines the state’s reason for denying the tax incentives. The second is from Mr. Parsons to Mr. Stewart; it looks as though they may have crossed in the mail. Mr. Parsons observes that Ark Encounter is (now) wholly owned by Answers in Genesis and argues that it should therefore be treated as a religious nonprofit. He continues with a lot of material that only a lawyer could love and concludes,

For all these reasons, if you insist on the newly imposed condition in your Letter [sic], it will amount to unconstitutional viewpoint discrimination[,] and my client will have no choice but to seek redress in federal court. [Boldface in original document.]

Viewpoint discrimination generally refers to limiting speech in a public or semi-public space; I would like to hear from a lawyer as to whether that concept can reasonably be extended to a case such as this or whether Mr. Parsons is just whistling past the graveyard.

Thanks again to my Indefatigable Informant for the tip.

The Hebrew Bible says that God made humans from dust,* but maybe it was a slurry of clay and water. That is a tentative conclusion you might draw from an experiment that used a (very) high-powered laser beam to zap a suspension of clay in an aqueous solution of formamide, a very simple organic compound. The result has been reported in the press, but there is a somewhat more-precise article in Science magazine. (You may find the abstract of the original article here and the supporting information here. I did not get access to the full article.)

In a nutshell, a team at the J. Heyrovský Institute of Physical Chemistry in Prague used a laser that can produce up to 1 kJ in a 300 ps pulse,** irradiated the suspension, and produced adenine, cytosine, guanine, and uracil, which are the bases of the RNA molecule. And apparently not a drop of thymine, one of the bases of DNA. The experiment is supposed to simulate the bombardment of the early Earth by comets and presumably supports the hypothesis that an RNA world came first.

* Actually, Job, Isaiah, Psalms, and I imagine elsewhere say clay, as in, “We are the clay, and you are our potter.” (Don’t get excited; I consider the fact to have no significance whatsoever.)

** I am a laser physicist and wrote my thesis on laser-produced plasmas, so you must forgive me for somewhat stressing the laser, which to this day gives me a certain amount of pulse envy.

Meditation on The Mind’s Eye

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I am a physicist, with a specialty in optics, so I was especially interested in The Mind’s Eye, by Oliver Sacks (not to mention the less well known The Island of the Colorblind). The Mind’s Eye is a fascinating book about the visual system, many of the things that can go wrong with it, and what we learn from them. It is also the book in which Dr. Sacks reveals that he suffers from prosopagnosia, or face blindness; is not a surgeon because he cannot visualize; and functions only with great difficulty now that he has monocular vision as a result of a retinal cancer. I have great difficulty recognizing faces, but nothing approaching prosopagnosia, and it is a marvel to me that he could cover it up for the better part of 80 years.

Coyote Buttes

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Photograph by Vivian Dullien.


Coyote Buttes, Arizona.


Credit: Abnormal Interests. Creative Commons copyright CC BY-NC-SA 3.0 US.

Kang Lee, a 2014 Ig Nobel Prize* winner, asks, “Have you ever seen the face of Jesus on toast? No? … Your brain is completely normal if you see nonexistent faces in everyday objects. In fact, if you don’t, your brain may actually lack the essential ingredients for a vivid imagination.”

The research was actually mildly interesting, if unsurprising. I could not read the original article, which was published in a proprietary journal, but I found synopses here and here. The gist, at any rate, seems to have been that when observers think they see a face, even in random noise, the face-recognition area in their brain lights up.

OK, it is normal to see patterns where none exist. More-imaginative people see more patterns. Fine.

But too many people who ought to know better think that such patterns are real.

*The Ig Nobel Prizes were awarded in September, but I did not catch up with them till a broadcast on NPR the other day. Dr. Lee added, by the way, “And I have some good news for you, for those without a good imagination, I just found out, you can buy a Jesus toaster on eBay .…” You may see him at about 19 min into the tape. For the record, seeing patterns where none exist is known as pareidolia.

Joe Sonka reported the other day in Insider Louisville that Ken Ham has now attacked his old friend, Steve Beshear, the governor of Kentucky. As Mr. Sonka puts it, Mr. Ham “penned a fundraising letter last week claiming the governor is launching a ‘massive attack’ on their religious freedom and persecuting his organization ‘because of our Christian message.’” Mr. Ham blames atheists and “secularists” for putting pressure on state government officials and avers that “our freedom of speech and freedom of religion … are now under attack.”

In the simplest possible terms,

  1. Nonprofit religious organizations, such as Mr. Ham’s own Answers in Genesis, may legally discriminate in hiring on the basis of religious belief.
  2. For-profit organizations, such as Mr. Ham’s own Ark Encounter, may not legally discriminate in hiring on the basis of religious belief.
  3. You may not try to get around (2) by hiring people to work at Ark Encounter and pretending that they are employees of Answers in Genesis.
  4. If you try to get around (2) in that manner, then Kentucky’s Tourism Arts and Heritage Cabinet will ask you to pledge in writing that Ark Encounter will not discriminate in hiring on the basis of religion before they will reinstate your tax incentives.

In other words, Ark Encounter’s tax incentives will be restored, if only they pledge in writing that they will not discriminate in employment. Ark Encounter has so far declined to give such assurance, which makes a body speculate that they just might be thinking of laundering all Ark Encounter employment through Answers in Genesis in order to circumvent the law.

Is it any wonder that the Freedom from Religion Foundation has petitioned the Internal Revenue Service to investigate the nonprofit status of Answers in Genesis and its affiliate the Creation “Museum”?

Analyzing the Genome with Statistics

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This is the third in a series of articles for the general public focused on understanding how species are related and how genomic data is used in research. Today, we talk about the challenges of using statistics to analyze phylogenomic data.

Suppose you were a door manufacturer trying to figure out the average height of a population living in a certain country. You might conduct an experiment where you ask a group of people to report their height. You would then assemble those measurements in a data set. But in order to study this data set and draw conclusions you would need to analyze it using statistics. For example, how tall should your door be in order to fit 95% of people in the country? How many people do you need to survey to accurately represent the total population? These questions can be answered with statistical analysis.

Because acquiring data from experiments can be costly and time-consuming, we often use small data sets to represent a larger population of interest. In our height experiment, we would not be able to ask every single person in the country his or her height. We would choose a group of people under the assumption that they accurately reflect the population as a whole. However, when we are trying to map out the evolutionary history of organisms using data from sequenced genomes (phylogenomics, which we talked about last time), we need to change our method of analysis.

Let’s look at the treeshrew, for instance. It looks like a rodent but actually shares some internal similarities with primates (studied by Sir Wilfrid Le Gros Clark in the 1920s), like brain anatomy and reproductive traits. To figure out if the treeshrew is more similar to rodents or primates, we could sequence its genome and, using statistics, compare its genes to those of rodents and primates. But typical statistical models are based on subsets of populations, while by definition, genomic sequencing gives us a complete data set - all of the treeshrew’s genes. These typical models may not be suitable for interpreting genomic data.

The treeshrew. Source: Wikipedia

Before reaching a conclusion about the tree shrew, or any set of data, scientists must consider precision and accuracy. Multiple measurements of the same quantity are precise if they are similar to each other. Another way of saying this is that their variance is small. On the other hand, measurements are accurate if they are close to the true value of what they are trying to measure. For genomic data, we need better statistical tools to ensure that the accuracy of our conclusions matches the precision characteristic of these huge data sets.

Larger data sets provide more precise conclusions than smaller ones. For example, when we ask more people to report their height, we are more confident that our sample represents the variability of the actual population. Similarly, we analyze more genes in the treeshrew’s genome to increase our confidence that our conclusion is precise. However, our results might not necessarily be accurate; big data sets may lead us to draw incorrect conclusions with high confidence. The treeshrew’s genome contains some genes that are more similar to rodents’ genes and some that are more similar to primates’ genes (Fan et al., Nie et al., and Xu et al.), and with so much data we could find that the treeshrew is most similar to either group with high confidence. We need analysis tools that will tell us which genes give the correct answer.

Why are conclusions from data sometimes inaccurate? Statistical biases are external factors that produce consistent error in our measurements. Biases have many sources, including faulty experimental design, violation of assumptions made in analyzing the data, and errors in the data collection process. Bias in our height experiment might arise if we unintentionally ask the height of more women than men, causing our estimate of the average height to be lower. But in the case of phylogenomics, we are likely to have biases because of our relative lack of knowledge about the genome: we don’t always know which genes to analyze or the correct way to model the data. For example, some models assume that evolution followed the same pattern throughout all time, but this most likely was not the case.

Furthermore, the process of genome sequencing and analysis itself may create error, especially in the reconstruction of the genome and the alignment of genes for comparison. If we are comparing the genome of the treeshrew to the genomes of primates and rodents, it is difficult for us to know which genes are correlated between species when we are looking at a data set of billions of points. We might use a probability model to determine correlated genes, but all models are at least somewhat incorrect and introduce bias. In smaller data sets, biases are offset by a low precision and relatively small confidence in reaching conclusions. However, in genomic-size data sets, even small biases can be amplified and lead to high confidence in the wrong answer and incorrect phylogenetic trees.

When analyzing phylogenomic datasets, we need to use analyses that are appropriate for large data sets. This will unlock the potential of phylogenomic research to draw unbiased conclusions, like figuring out the correct phylogenetic classification of the treeshrew (still a topic of controversy among evolutionary biologists). However, phylogenomics is such a young field that these tools do not yet exist. When they are developed, we can increase our chances of correctly classifying species’ relationships and discovering the true history of evolution.

For more detail, check out: “Statistics and Truth in Phylogenomics”, Kumar, Sudhir et al. Molecular Biology and Evolution (2011).


Fan, Yu, et al. “Genome of the Chinese tree shrew.” Nature communications 4 (2013): 1426.

Nie, Wenhui, et al. “Flying lemurs-The’flying tree shrews’? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade.” BMC biology 6.1 (2008): 18.

Xu, Ling, et al. “Evaluating the Phylogenetic Position of Chinese Tree Shrew ( Tupaia belangeri chinensis) Based on Complete Mitochondrial Genome: Implication for Using Tree Shrew as an Alternative Experimental Animal to Primates in Biomedical Research.” Journal of Genetics and Genomics 39.3 (2012): 131-137.

Our next installment will cover some misused terminology in phylogenomics. This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

… because it (gasp!) uses the word, “abortion.” But wait – there is a glimmer of hope: The new superintendent, who was ordered to offer a plan for redacting the textbooks, says that the books comply with the law already and instead plans to hold a public discussion.

Meanwhile, as a service to the affected high-school students, Rachel Maddow has posted the offending page on a blog, ArizonaHonorsBiology.com, which her show apparently owns. If you are curious or have a prurient interest, you may also see the verso of The Page, as well as several other pages on human reproduction.

For the record, the book is Reece, et al., Biology: Concepts and Connections.

Lenticular clouds

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Interesting cloud formation, Boulder, Colorado. The camera is facing south, and the wind is coming from the west, or right.

One hour later, in Golden,

Philae craft lands on comet

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Rosetta headquarters announced a few moments ago that the Philae lander is now sitting on the surface of the comet and transmitting data. Unfortunately, the European Space Agency is not exactly releasing a trove of pictures. I know this is not biology, but where did you think those hydrocarbons came from in the first place?

Phylogenomics: Deciphering a Billion-Piece Puzzle

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This is the second in a series of articles for the general public focused on understanding how species are related and how genomic data is used in research. Today, we talk about phylogenomics, the application of whole genome sequencing to understand evolutionary relationships among species.

DNA Chemical Structure. Source: Madeleine Price Ball

The haploid human genome is 3.2 billion DNA bases long, and each base can be one of four nucleotides: A, T, C, and G. Uncoiled, the DNA in a single human cell would be 2 meters long, and the DNA in a human body would stretch from the sun to Pluto multiple times. With 3.2 billion bases, each person’s genome is unique, and this plays an essential role in shaping our physical and mental individuality. However, despite being unique, each human genome is very very similar, due to our shared ancestral heritage. Similarly, species that share a recent ancestral heritage also have similar genomes. Species that are distantly related are likely to demonstrate significant differences in their genomes. This is why, as we discussed last week, evolutionary biologists compare traits and genes to determine the relationships of different species.

Unfortunately, some genes give us the wrong answer about how species are related. A section of a gene can be identical for two species due to independent mutations. After all, any given base can only mutate into one of three other bases. Chances are the same mutation could happen twice, or multiple mutations can produce the same sequence. Consider two species that are distantly related; one contains an AGA fragment, while the corresponding fragment in the other species is TGT, i.e. they differ in 2 out of 3 positions. As these species evolve, by chance the first species may experience a change in the first position such that AGATGA, and the second species may experience a change in the third position such that TGTTGA. Now, these two sequences look the same so you might think the species share a recent common ancestor; however, it is only an accident of biology that they appear closely related. Because some fragments may be identical due to independent mutations and not shared ancestry, estimating species relationships with using whole genomes is better than just a few genes. The more information we have, the more likely we are to figure out species’ relationships correctly.

The cost to sequence whole genomes has fallen from $100 million to $1000 in just the past twelve years. It now takes days to sequence a genome compared to the 13 years it took for the first human genome. The challenge now is not to obtain the data but to compare all the billions of base pairs in one genome to those in another. Current sequencing methods, while fast, can only read the genome by dividing it into millions of short fragments, which must be reassembled like an enormous puzzle. Researchers then have to figure out which genes correspond to one another in different species’ genomes. These comparisons are challenging because genes in one genome might be in a different order, on different chromosomes, or missing completely in another species’ genome.

Biologists are beginning to use genomic information to understand how species are related and measure how fast or slowly different genes evolve. Then in turn allows us to understand how evolution happens. For example, using genomic information we can figure out how genes mutate, characterize and diagnose genetic diseases, and track harmful pathogens. But before that can happen, we need to address the difficulties of analyzing these large genomic datasets. You might think that more data is always better, but having a lot of data can lead us to have very high confidence in the wrong answer. In a pool of thousands of genes, we need to find the ones that tell us the right answer.

Next week, we’ll discuss statistical challenges associated with big data analysis, especially as it relates to phylogenomics. This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

Or, as Right-Wing Watch puts it, Neo-Confederate Republican Michael Peroutka Wins Maryland Election. Mr. Peroutka operates the family foundation that donated the allosaurus fossil to the Creation “Museum,” as we reported here. I will not synopsize the Right-Wing Watch article, but I think that you will find that being a neo-Confederate is the least of Mr. Peroutka’s problems; if he is not completely crackers, he is giving a convincing imitation.

I started this post thinking I’d write a review of Andreas Wagner’s recent book “Arrival of the Fittest: Solving Evolution’s Greatest Puzzle” (links below), an engrossing book about how biological innovation arises from the structure of metabolic, genotype, and protein networks, and how robustness–the stability of phenotypes in the face of underlying genetic variability–is critical in evolutionary innovations. But there are several excellent reviews already out there, so another would be redundant. I’ll mention only a couple of points I think worth emphasizing below the fold.

Delicious sex chromosomes

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Plants have sex? Yes, they totally do.

A brief overview: 
Plants have female reproductive organs (carpels) and male reproductive organs (stamens), but several different ways of determining sex. There are two main groups of seed-producing plants.

Gymnosperms are plants without covered seeds, and include those that produce cones. Gymnosperms and are split with about 75% exhibiting monoecy (having male and female sex organs on the same plant), and 25% exhibiting dioecy (having separate male plants and female plants).

Photo by Muhammad Mahdi Karim, via Wikimedia Commons

Phelsuma laticauda

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Photograph by Tony Gamble.

Photography contest, Honorable Mention.


Phelsuma laticauda – gold dust day gecko.

Kent Hovind in trouble again

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I haven’t got time to investigate further, but Hovind watchers might be interested that Mr, Hovind (Dr. Dino) has been charged with filing a lien on property that had already been forfeited. Or something. A Forbes columnist, Peter Reilly, suggests that the government is piling on, and I suspect he is right; you may read about it here.

Acknowledgement. Link provided by the truly indefatigable Dan Phelps.

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