An Honest Intelligent Design Proponent?

It's unusual to find a proponent of Intelligent Design Creationism who makes an honest attempt to evaluate scientific facts. Jonathan McLatchie (Jonathan M) seems to be one of those rare birds. I'm not going to refer to him as an IDiot.

Here's a bit from his latest post on Evolution News & Views (sic [Perspectives on ENCODE and Junk DNA].

The debate thus hinges on whether activity such as transcription, transcription factor association, and histone modification are signs of true function. My own view is that such activity is suggestive of functionality, but not proof. Therefore I would be cautious about claiming that these results show 80% of the genome to have function in the sense that we normally use that word.

On the other hand, the observation that the genome is buzzing with activity underscores what proponents of ID have been saying for years: not knowing what something does doesn't constitute evidence that it's doing nothing. Moreover, it wasn't long ago that Laurence Moran and PZ Myers were telling us that the genome is not even pervasively transcribed and that this amounted to evidence that the majority of our DNA is junk.

That's pretty good for someone who posts on a blog that also publishes stuff from Jonathan Wells and Casey Luskin. I wonder if they talk to each other?

On the other hand, it's not perfect. I've been arguing for years that there is good solid evidence that most of our genome is junk. I have never used the argument from ignorance that Jonathan attributes to me.

Also, I have never denied that the genome is pervasively transcribed. Instead, I have argued that pervasive transcription is something that one expects given what we know about DNA binding proteins and transcription. I've pointed out that the vast majority of our genome is transcribed very rarely—about one transcript per day in 100 cells—and this is consistent with accidental transcription. This is noise. The product is junk RNA and is has no function [Useful RNAs?] [Junk RNA] [Pervasive Transcription] [How to Frame a Null Hypothesis] [How to Evaluate Genome Level Transcription Papers ].

I discussed this thoroughly when I reviewed Jonathan Wells' book The Myth of Junk DNA [Junk & Jonathan: Part 6—Chapter 3]. Perhaps Jonathan McLatchie hasn't read my earlier posts?

Contrast McLatchie's post with that of Jonathan Wells [A Dishonest Intelligent Design Proponent?].

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Breaking News ... New Atheists Aren't Very Sophisticated

Richard Swinburne is Emeritus Professor of Philosophy at the University of Oxford (UK). He's a noted Christian apologist who has written many books defending the existence of God. According to Wikipedia, his two most important "sophisticated" priniciples are:

• Principle of Credulity - with the absence of any reason to disbelieve it, one should accept what appears to be true (e.g., if one sees someone walking on water, one should believe that it is occurring)
• Principle of Testimony - with the absence of any reason to disbelieve them, one should accept that eye-witnesses or believers are telling the truth when they testify about religious experiences.

What this means is that when it comes to religious experiences that confirm your beliefs you should abandon skepticism. I don't think these principles apply to people who have seen leprechauns or been abducted by UFOs. It probably doesn't apply to Muslims or Hindus, either. It seems like a "sophisticated" way of shifting the burden of proof.

As you might imagine, Swinburne is really unhappy with the New Atheists because they ignore all his sophisticated apologetics and simply ask for evidence of God. That's not playing fair. They probably haven't read any of his books.


There ought to be a rule for people who claim to have sophisticated arguments for the existence of god(s). They should have to describe at least one of them.

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[Hat Tip: Uncommon Descent]

What Is Evolution?

Most non-scientists seem to be quite confused about precise definitions of biological evolution. Part of the confusion is because the word "evolution" has many different meanings, depending on the context. When we talk about biology we are thinking about biological evolution and that's the term I want to define here. What do biologists mean when they refer to biological evolution?

This is a slightly modified version of a post from January, 2007 which, in turn, is a moified version of an essay that appears here. An even earlier version is on the TalkOrigins Archive.One of the most respected evolutionary biologists has defined biological evolution as follows:

Biological (or organic) evolution is change in the properties of populations of organisms ..., over the course of generations. The development, or ontogeny, of an individual organism is not considered evolution: individual organisms do not evolve. The changes in populations that are considered evolutionary are those that are ‘heritable' via the genetic material from one generation to the next. Biological evolution may be slight or substantial; it embraces everything from slight changes in the proportions of different forms of a gene within a population, such as the alleles that determine the different human blood types, to the alterations that led from the earliest organisms to dinosaurs, bees, snapdragons, and humans.

Douglas J. Futuyma (1998) Evolutionary Biology 3rd ed., Sinauer Associates Inc. Sunderland MA p.4

Why Do Students Skip Lectures?

There's an interesting article on student attendance at lectures in the latest issue of BAMBED (Biochemistry and Molecular Biology Education): Engagement of students with lectures in biochemistry and pharmacology.

The authors surveyed students to find out why they skipped classes at Monash University in Melbourne, Australia. The answers they give are not surprising, especially for the 8AM biochemistry lecture. However, the really interesting finding is that there's hardly any correlation between the number of lectures attended and a student's final grade in the course. The slight difference could easily be due to motivation and not ability to master the material.

This is a common finding in studies like this and the paper provides several references to the pedagogical literature. (In fairness, there are some studies that show a more significant correlation—students who skip classes get a much lower grade than those who attend.)

Here's my take on the issue of skipping lectures. If the lecture doesn't provide any value in terms of your final grade then why waste time going to class? Why bother giving the lecture?

I'd like to see a study comparing attendance in a course that has adopted student-centered learning where the class time is devoted to explaining difficult concepts and helping students think critically. The exams and assignments would have to measure whether students have mastered the concepts and learned how to think critically about the subject. In an ideal course, a student shouldn't be able to pass if they've skipped most of the lectures. What would attendance look like in such a course?

If students are skipping your lectures and still getting good grades then it's time to change your course. If you can't, or won't, do that then just cancel the lectures. You could record them and put them online if it makes you feel better. Your students are clearly not getting anything of value from sitting in the classroom.

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Monday's Molecule #189

Last week's molecules were cis Δ⁹-octadecanic acid (oleic acid) and trans Δ⁹-octadecanic acid (elaidic acid). Last week's winner was John Runnels. He should email me.

Name this week's molecule. Be sure to give an unambiguous name—it can be the common name or the IUPAC name. Why is this molecule important in some species?

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

An Online Course for Intelligent Design Creationists

About 99% of all books and posts by Intelligent Design Creationist consists of criticisms of evolution—which they mistakenly refer to as "Darwinism."

What this usually reveals is that the typical IDiot doesn't understand evolution. But there's at least one Intelligent Design Creationist who recognizes that this is a problem. Jonathan McLatchie (Jonathan M) recommends that his colleagues take an free online course in order to learn about evolution [Free Online Course: Introduction to Genetics and Evolution]. He writes,

Critics of modern evolutionary theory have an intellectual responsibility to strive to understand the paradigm that they are critiquing, preferably to a level where they can clearly articulate the key propositions of evolutionary theory and offer a standard defense of them.

Richard Hoppe, at the Panda’s Thumb blog, drew my attention to a free online course on the subject of genetics and evolution. You can, as I have done, sign up for (and read about) the course at this link.

...

I particularly recommend that those among us who don’t have a strong biology background take this course. It is very important that we ID proponents make sure we have a robust grasp of what evolutionary theory is saying and why it says it, so that no one can say we haven’t given it a fair hearing.

Wouldn't it be nice if most IDiots followed Jonathan McLatchie's advice? In just a few months they could learn that modern evolution and genetics includes all sorts of things that Darwin never knew! Imagine what a relief it would be if they stopped referring to us all as "Darwinists" and started to understand that evolution is a fact.

Not holding my breath.

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Visiting the Grand Canyon

Last week we took a helicopter from Las Vegas to Hoover Dam and the Grand Canyon. Check out the photos on Ms. Sandwalk's blog: The Magic Canyon Ride.

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Online Training of Competent, Employable, Bioinformatics Professionals

I think that undergraduate education at most universities is done very badly. There are far too many courses that consist of professors giving standard lectures to large classes with evaluations focused on "memorize and regurgitate" exams. Most courses pay no heed to student-centered learning even though there has been sound pedagogical research showing that student participation leads to better learning. Most courses and programs provide no "value-added" component that takes advantage of being physically located in an enriched scholarly environment. Most courses do not teach critical thinking.

Given the horrible status of most university courses, it's not surprising that they can be replaced by online courses where the student never needs to set foot on a university campus to get the same quality of education. This is not an endorsement of online courses, it's a comment on the poor quality of campus-based courses.

David B. Searls is an "independent consultant" who published an article in PLOS Computational Biology: An Online Bioinformatics Curriculum.

Carnival of Evolution, Number #52: the Network Edition

This month's Carnival of Evolution is hosted by Sam Wise at SOS Presents%mdash;the Carnival of Evolution #53. Read it at: Carnival of Evolution, Number 52 — the Network Edition

Welcome to the 52nd edition of the Carnival of Evolution, hosted here at The Genealogical World of Phylogenetic Networks blog.

For those of you not familiar with the Carnival of Evolution, at the beginning of every month the Carnival provides a collection of some of the most interesting of the recent blog posts about biological evolution. The Carnival is hosted by a different blog every month: last month's Carnival can be found at The Stochastic Scientist blog; and next month's Carnival will be hosted by the Sorting Out Science blog at the beginning of November.

The theme for the presentations this month is, of course, phylogenetic networks. You can skip straight on to the blog posts if you are familiar with such networks.

There's some cool stuff this month, including a summary of the ENCODE/junk DNA fiasco.

The next Carnival of Evolution (September) will be hosted by Sorting out Science. If you want to volunteer to host others, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before. Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution.

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Reddit: We are the Encyclopedia of DNA Elements (ENCODE) Consortium.

There's been a lot of talk recently about the discussion on reddit concerning the ENCODE publicity fiasco.

Here's the forum ...

AskScience Special AMA: We are the Encyclopedia of DNA Elements (ENCODE) Consortium. Last week we published more than 30 papers and a giant collection of data on the function of the human genome. Ask us anything!

It's interesting to see how some of the consortium members are responding to criticism. My personal view is that none of them seem to be very knowledgeable about genome biology and the work that has been published over the past 40 years.

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Monday's Molecule #188

Last week's molecule was N-formylmethionyl-tRNA_f^Met [Monday's Molecule #188]. Only three people came close. The winner was Mikkel Rasmussen.

Name these molecules. One of them has a well-known common name that you have to include in your answer. The other one also has a common name but you don't have to find it. You have to give the complete formal names of each molecule. Do you know the significance of these two molecules?

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Douglas Axe Explains Molecular Evolution

There are several dozen scientists and graduate students in my department studying various aspects of protein evolution, structure, and folding. They've published dozens of papers but, apparently, they never realized that what they're studying is impossible. Douglas Axe, a leading Intelligent Design Creationist, sets them straight.

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[Hat Tip: Evolution News & Views: Axe: Vive la Différence]

Where Am I?

My granddaughter, Zoë, took a picture of me getting a hot dog. Can you guess where I am?

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Where Am I?

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Ewan Birney: Genomics' Big Talker

My copy of Science arrived in the mail last week and I wasn't surprised to see the article by Elizabeth Pennisi on ENCODE Project Writes Eulogy for Junk DNA. Pennisi has long been skeptical about junk DNA. She advocates the position that what makes us human is hidden in the "dark matter" of the genome. She has never lost an opportunity to promote those scientists who claim to have discovered function in junk DNA so it was natural for her to fall hook-line-and-sinker for the recent ENCODE publicity campaign [see Science Writes Eulogy for Junk DNA].

What did surprise me was a three-page spread on Ewan Birney: Genomics' Big Talker, written by Elizabeth Pennisi. This is extraordinary. I don't know of another example where a leading science journal has promoted a young scientist in this manner. Of course, it's doubly extraordinary because, in this case, Science is promoting a scientist who just made some serious mistakes interpreting his own data! The man who is so prominently featured in the Sept. 7, 2012 issue of Science magazine is coming under serious criticism for letting publicity rule his science. He has almost single-handedly¹ damaged the reputation of 400 scientists in the ENCODE Consortium and he did it, in part, because he was not knowledgeable about his own field of expertise! [see ENCODE Leader Says that 80% of Our Genome Is Functional and The ENCODE Data Dump and the Responsibility of Scientists]

UPDATE:A reader has reminded me that Science published two pages (online) on Felicia Wolfe-Simon at the time of the arsenic affair. Hmmmm ... is this the beginning of a pattern?