Educating an Intelligent Design Creationist: The Specificity of DNA Binding Proteins

I'm replying to a post by andyjones (More and more) Function, the evolution-free gospel of ENCODE. This was the fourth post in a series and I'm working my way through five issues that Intelligent Design Creationists need to understand. The first two were "Pervasive Transcription" and "Rare Transcripts."

Educating an Intelligent Design Creationist: Introduction
Educating an Intelligent Design Creationist: Pervasive Transcription
Educating an Intelligent Design Creationist: Rare Transcripts

The Specificity of DNA Binding Proteins

It is absolutely essential that you understand the basic biochemistry of DNA binding proteins if you want to interpret the ENCODE results and the controversy surrounding junk DNA. You might think this is a given since almost everyone involved in the discussion has had some exposure to biochemistry in undergraduate courses. Unfortunately, most of these courses don't teach that stuff anymore¹ so we've raised a generation of scientists who were never exposed to the facts.

Next Generation Science Standards

The Next Generation Science Standards are a set of recommendations for teaching science to public school children in the USA. The standards were made up by representatives from the National Research Council and 26 states. The standards have been extensively reviewed and many drafts were posted on the web.

You can look at the final version at DCI Arrangements of the Next Generation Science Standards.

Let's look at the High School Section on Biological Evolution : Unity and Diversity. Let me know what you think.

HS-LS4 Biological Evolution: Unity and Diversity

Students who demonstrate understanding can:

HS-LS4-1. Communicate scientific information that common ancestry and biological evolution are supported by multiple lines of empirical evidence. [Clarification Statement: Emphasis is on a conceptual understanding of the role each line of evidence has relating to common ancestry and biological evolution. Examples of evidence could include similarities in DNA sequences, anatomical structures, and order of appearance of structures in embryological development.}

HS-LS4-2. Construct an explanation based on evidence that the process of evolution primarily results from four factors: (1) the potential for a species to increase in number, (2) the heritable genetic variation of individuals in a species due to mutation and sexual reproduction, (3) competition for limited resources, and (4) the proliferation of those organisms that are better able to survive and reproduce in the environment. [Clarification Statement: Emphasis is on using evidence to explain the influence each of the four factors has on number of organisms, behaviors, morphology, or physiology in terms of ability to compete for limited resources and subsequent survival of individuals and adaptation of species. Examples of evidence could include mathematical models such as simple distribution graphs and proportional reasoning.] [Assessment Boundary: Assessment does not include other mechanisms of evolution, such as genetic drift, gene flow through migration, and co-evolution.]

HS-LS4-3. Apply concepts of statistics and probability to support explanations that organisms with an advantageous heritable trait tend to increase in proportion to organisms lacking this trait. [Clarification Statement: Emphasis is on analyzing shifts in numerical distribution of traits and using these shifts as evidence to support explanations.] [Assessment Boundary: Assessment is limited to basic statistical and graphical analysis. Assessment does not include allele frequency calculations.]

HS-LS4-4. Construct an explanation based on evidence for how natural selection leads to adaptation of populations. [Clarification Statement: Emphasis is on using data to provide evidence for how specific biotic and abiotic differences in ecosystems ( such as ranges of seasonal temperature, long-term climate change, acidity, light, geographic barriers, or evolution of other organisms) contribute to a change in gene frequency over time, leading to adaptation of populations.]

HS-LS4-5. Evaluate the evidence supporting claims that changes in environmental conditions may result in: (1) increases in the number of individuals of some species, (2) the emergence of new species over time , and (3) the extinction of other species. [Clarification Statement: Emphasis is on determining cause and effect relationships for how changes to the environment such as deforestation, fishing, application of fertilizers, drought, flood, and the rate of change of the environment affect distribution or disappearance of traits in species.]

HS-LS4-6. Create or revise a simulation to test a solution to mitigate adverse impacts of human activity on biodiversity. * [Clarification Statement: Emphasis is on designing solutions for a proposed problem related to threatened or endangered species, or to genetic variation of organisms for multiple species.]

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Educating an Intelligent Design Creationist: Rare Transcripts

I'm replying to a post by andyjones (More and more) Function, the evolution-free gospel of ENCODE. This was the fourth post in a series and I'm working my way through five issues that Intelligent Design Creationists need to understand.

Educating an Intelligent Design Creationist: Introduction
Educating an Intelligent Design Creationist: Pervasive Transcription

Andyjones says he didn't know that many of the unusual transcript are very rare. That's a shame because it's one of the very important things you need to know in order to have an intelligent opinion about junk DNA. Here's a question from andyjones ...

The second point is interesting, but I have to ask the question: given the fact that we don’t know everything about the genome, isn’t it precisely those parts that are rarely transcribed that would give most difficulty when it comes to determining their functions?

The simple answer to your question is "yes" but that doesn't mean we don't have clues. The best explanation depends on how rare the transcripts are and on whether there's another, equally reasonable, explanation that accounts for their existence. What we can say right now is that the presence of these rare transcripts is consistent with junk DNA. We can also say that there's no reasonable functional explanation for huge numbers of transcripts that are present at less that one copy per cell. Think about that for a minute. It means that right now there are only two scientifically reasonable explanations: (1) junk DNA/RNA, and (2) we don't know if they have a function. It is scientifically incorrect to say that these transcribed regions are functional and therefore junk DNA is refuted.¹

Evolution and Junk DNA in Chicago

I just signed up for the SMBE Conference in Chicago in July. There's lots of cool talks about evolution but, in the end, I decided I just couldn't miss the session on "Where did 'junk' go?" with Wojciech Makalowski as organizer. Here's the blurb ...

Late Susumu Ohno once said "So much junk DNA in our genome" and the phrase junk DNA was born. For a long time mainstream scientists avoided these parts of the genome. However, over the years the picture slowly started to appear suggesting that the junk DNA hides a genomic treasure. With the completion of the current ENCODE project, junk DNA effectively disappeared because there's no longer useless DNA in the genome. This symposium will discuss the current understanding of these not-so-long-ago obscure areas of the genome, with special attention to transposable elements' activities and their evolutionary consequences. The integral part of the symposium will be general discussion of Ohno’s idea and its place in today's biology.

I'm familiar with Makalowski's way of thinking—it resembles the opinions of many Intelligent Design Creationists even though Makalowski is not a creationist [see Junk DNA: Scientific American Gets It Wrong (again)]. Back in 2007 he said,

Although very catchy, the term "junk DNA" repelled mainstream researchers from studying noncoding genetic material for many years. After all, who would like to dig through genomic garbage?

We know who's been invited to talk.

1. Josefa Gonzalez (Institut de Biologia Evolutiva, Barcelona, Spain)
   "Adaptation is the key concept in Evolutionary Biology. Understanding adaptation has important scientific and social implications since adaptation underlies processes such as the ability of species to survive in changing environments, resistance to antibiotics and cancer chemotherapies and host-pathogen interactions, among others.
   However, adaptation is to date a very poorly understood process largely because the current approaches to the study of adaptation are often exclusively based on a priori candidate genes or on searching for signals of selection at the DNA level giving us an incomplete and biased picture of the adaptive process.
   
   In our lab we aimed at understanding the molecular process of adaptation and its functional consequences. Towards this end, we study recent transposable element (TE)-induced adaptations in Drosophila melanogaster."
2. Valer Gotea (National Human Genome Institute, Bethesda, USA)
   "... it is not surprising that TEs [transposable elements] have a significant influence on the genome organization and evolution. What once was called junk now is considered a treasure. Although much progress has been achieved in understanding of a role that TEs play in a host genome, we are still far from a full understanding of the delicate evolutionary interplay between a host genome and the invaders"
3. Dan Graur (University of Houston, Houston, USA)
   "This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect."
4. Dixie Mager (University of British Columbia, Canada)
   "The fact that transposable elements (TEs) can influence host gene expression was first recognized more than 50 years ago. However, since that time, TEs have been widely regarded as harmful genetic parasites-selfish elements that are rarely co-opted by the genome to serve a beneficial role. Here, we survey recent findings that relate to TE impact on host genes and remind the reader that TEs, in contrast to other noncoding parts of the genome, are uniquely suited to gene regulatory functions. We review recent studies that demonstrate the role of TEs in establishing and rewiring gene regulatory networks and discuss the overall ubiquity of exaptation. We suggest that although individuals within a population can be harmed by the deleterious effects of new TE insertions, the presence of TE sequences in a genome is of overall benefit to the population."
5. Masumi Nozawa (National Genetic Institute, Mishima, Japan)
   (I don't know anything about his work. Can anybody help?

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Spontaneous Degradation of DNA

I heard a crash in my outer office. I knew what had happened. My cool space-filling model of DNA is 33 years old and it is spontaneously degrading as the plastic connectors become brittle. This is very, very, sad.

I don't think it can be replaced because I can't find anything similar on the internet. Besides, I figure it would cost over three thousand dollars at today's prices.

I can't bear to look at it anymore. It will have to go in the garbage.

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Carnival of Evolution #58

This month's Carnival of Evolution is hosted by Bradly Alicea (e.racer) at Synthetic Daisies. Read it at: Carnival of Evolution, #58 -- Visions of the Evolutionary Future

What does the future look like? For some, the future is the place of constant progress and a place where dreams become reality. For others, the future is a scary, dystopian place. When actualized, however, future worlds fall somewhere in between these two visions. Can we make accurate projections about the future? As I pointed out in a Synthetic Daisies post from February [1], futurists and technologists have a pretty dismal track record at projecting future scenarios, and often get things notoriously wrong.

With visions of the future in mind, this month's Carnival of Evolution (#58) theme is the future of evolution. While a significant component of evolutionary biology involves reconstructing the past [2], we are actually (with error, of course) also predicting the future. Yet can we do any better than futurists or technologists? It is hard to say, and if you have opinions on this I would be glad to hear them. However, this month's CoE will address five themes that may (or may not) help us understand where the complexity of life is headed.

This is an amazing edition of Carnival of Evolution with lots of commentary to put the posts in context. If you haven't read it yet then get on over there right now!!!

If you want to host a Carnival of Evolution please contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! So far, there's nobody in the queue for May or June. Bjørn is threatening to name YOU as host even if you don't volunteer! 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 although you now have to register to post a submission.

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Come With Us to Watch "The Unbelievers"

Here's an announcement from HotDocs (The Canadian International Documentary Festival).

The Unbelievers follows evolutionary biologist Richard Dawkins and theoretical physicist Lawrence Krauss across the globe as they speak publicly to sold-out halls, advancing a thoughtful dialogue about the importance of science and reason in the modern world. Dawkins, the world’s most famous atheist, and Krauss, director of the esteemed Origins Project, are dedicated to furthering the (r)evolutionary idea that science, above all else, should inform man’s understanding of the universe. Filmmaker Gus Holwerda follows these “rock stars of reason” as they embark on a most modern crusade to encourage people to cast off antiquated ideologies and assume a purely rational approach to important current issues. Refusing to engage with those who advance divisive and extreme fundamentalist positions Dawkins and Krauss show how sometimes sensitive and provocative ideas can be discussed respectfully and with intellectual rigour. Fans, including Ricky Gervais, Cameron Diaz, Stephen Hawking, Woody Allen and Werner Herzog, share their impressions and support, while arenas full of admirers and the curious eagerly receive them. As engaging as the subjects themselves, The Unbelievers offers an exciting glimpse into two of the world’s most influential minds at work.

The opening night is Monday, April 29. Richard Dawkins and Lawrence Krauss will be there for a conversation after the show. This event is sponsored by one of Canada's big banks (Scotiabank) as part of their Scotianbank Big Ideas series. Tickets for that event sold out before I even became aware of it and you can't even buy rush tickets right now.

My colleagues, Craig Smibert and Alex Palazzo, invited me to the movies on Wednesday May 1, 2013. We'll be making our way to the TIFF Bell Lightbox for the 3:00 pm show. Maybe we'll have lunch before the movie ... would anyone like to join us? I really like the Oliver & Bonacini restaurant (LUMA) that's in the building. It's bit pricey but it's worth it. There are tons of good restaurants in the theatre district.

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Educating an Intelligent Design Creationist: Pervasive Transcription

I'm replying to a post by andyjones (More and more) Function, the evolution-free gospel of ENCODE. This was the fourth post in a series and I'm working my way through five issues that Intelligentt Design Creationists need to understand.

Educating an Intelligent Design Creationist: Introduction

Pervasive Transcription

The idea that most of the human genome is transcribed dates back to the early 1970s. Workers isolated RNA from various sources and hybridized it to DNA (Rot analysis). They measured the amount of DNA that was complementary to this RNA and discovered two things:

1. Using highly purified messenger RNA (mRNA) the amount of DNA suggested that the genome had between 15,000 and 20,000 genes.
2. Using heterogeneous nuclear RNA (hnRNA) a much larger percentage of the genome was covered. This included the repetitive DNA fraction that we now know consist mostly of defective transposons.

These discoveries lead to intensive investigation of these non-coding DNA sequences and contributed to the discovery of introns and splicing. That accounted for a great deal of the mass of nuclear RNA that never made it into mature mRNA. Still, there was lots of RNA being synthesized that couldn't be accounted for. The data showed that this fraction was very complex (lot's of sequences) but that individual RNAs were not very abundant.

The main references quoted these days are Milcarek et al. (1974), Hugh et al. (1975), Holland et al. (1980), and Varley et al. (1980) but there were dozens of papers. The work was summarized in great detail in the first edition of Gene Expression by Benjamin Lewin. Most molecular biologists knew of these results.

Andyjones commented on this finding ...

... some people have known since the mid 70s that most DNA is transcribed into RNA, but sat on it because apparently they didn’t realise its significance ...

Now, to my mind the first point only underlines my original point about the cult of Darwinism (word defined according to the old-school, traditional and popular usage); that it can get in the way of the practice and dissemination of science, a dysteleological worldview which stagnates interest in trying to find function, something which has only recently been picked up again by ENCODE, and only then, Larry claims, because they don’t understand evolution.

It's true that most scientists were puzzled by this pervasive transcription but gradually they learned that a lot of it was introns and the rest was probably spurious transcription or junk RNA. They reached this conclusion because most of the transcripts were of very low abundance and were turned over (degraded) very rapidly.

I don't know where andyjones got the idea that scientist "sat on" the data. He seems to have made it up.

Andyjones says ....

The idea that (almost) everything gets transcribed sometimes but only by accident, is an explanation, but it is one that requires no investigation, and inspires no investigation. It is much more convincing to an already-convinced Darwinist than to anyone else. A Darwinist says, nah, there’s nothing here to be understood, stop looking. But to others, that would be a presumptuous ‘evolution-of-the-gaps’. Anyone who has reason to suspect teleology (meaning: engineering intent) is going to look just that little bit harder, and is going to see the importance of pervasive transcription just that little bit earlier.

Many scientists wanted to find a function for all of this RNA but they failed to do so. Meanwhile, other studies showed that much of our genome was probably junk DNA. This is about the time that scientists discovered pseudogenes (early 1980s) and discovered that half our genome was transposon pseudogenes (defective transposons). Experiments showed that a lot of pervasive transcription came from those regions of the genome suggesting that the transcripts were not functional.

It's simply not true to claim that the junk RNA explanation was not based on solid evidence and it's not true to claim that it stifled investigation. It's also ironic that andyjones thinks that the "Darwinists" would give up looking for an explanation when they (Darwinists) were doing the exact opposite! It's those who prefer natural selection (Darwinists) who most wanted there to be a function for this RNA. They still do.

I wonder if we should not be a little angry that this was not popularised in the 70s! My fiancee, who has a recent biology degree, is now annoyed that this fact was kept from her … The Darwinian establishment seem to have buried it, exactly the kind of thing I wanted to warn against.

The existence of hnRNA was widely known in the 1970s. It was discussed in graduate courses when I was a student. By the late 1970s we were teaching this material to undergraduates.

By 1990, the general consensus was that most of the rapidly degraded nuclear transcripts were probably introns although it was still an open question. That's the view that Benjamin Lewin popularized in his textbook Genes IV in 1990. The next decade showed that this was wrong because hundreds and hundreds of ESTs (expressed sequence tags) were being sequenced and most of them could not be assigned to a known gene.

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Holland, C. A., Mayrand, S. & Pederson, T. (1980) Sequence complexity of nuclear and messenger RNA in HeLa cells. J. Mol. Biol. 138:755–778.

Hough, B. R., Smith, M. J., Britten, R. J. & Davidson, E. H. (1975) Sequence complexity of heterogeneous nuclear RNA in sea urchin embryos. Cell 5:291–299.

Milcarek, C., Price, R. & Penman, S. (1974) The metabolism of a poly(A) minus mRNA fraction in HeLa cells. Cell 3:1–10.

Varley, J. M., Macgregor, H. C. & Erba, H. P. (1980) Satellite DNA is transcribed on lampbrush chromosomes. Nature 283:686–688.

Educating an Intelligent Design Creationist: Introduction

Andyjones is a frequent contributor to Uncommon Descent, one of the main Intelligent Design Creationist websites. I don't know very much about him except that some people refer to him as a physicist and he seems to be based in the United Kingdom..

Andyjones and I debated the results of the ENCODE project in a series of posts ....

Function, the evolution-free gospel of ENCODE
ENCODE & Junk and Why We Call Them IDiots
(More) Function, the evolution-free gospel of ENCODE
ENCODE, Junk DNA, and Intelligent Design Creationism

He has now replied to my second post and I think I detect a real desire to learn about the issues [see (More and more) Function, the evolution-free gospel of ENCODE]. This could just be my imagination but please bear with me while I try to explain the facts to andyjones.

Andyjones begins with ...

Larry’s ‘reply’ (to my first post) appears to have replicated and evolved into a real reply (to my second post) with some real information. Well, a little information. When I say information, I don’t just mean grammatically correct and unambiguous English text, I mean things that offered ‘surprisal’ and improved my ability to understand the world and to function better in this debate. I learnt three things: firstly, some people have known since the mid 70s that most DNA is transcribed into RNA, but sat on it because apparently they didn’t realise its significance; secondly, where DNA is transcribed but a function is not known, it is generally transcribed only relatively rarely; and thirdly, that RNA polymerase (RNAP) binds at sites other than recognised promoters.

Later on he adds two other issues that he wants to learn about so that makes five in total. I'll devote a seperate post to each one.

1. Pervasive Transcription—especially the idea that this isn't new.
2. Most Transcripts Are Very Rare—what does this say about their possible function?
3. The Specificity of DNA-Binding Proteins—non-specific (i.e. nonfunctional) binding is an essential property of RNA polymerase and regulatory proteins.
4. The Meaning of Darwinism—why abuse of this term confuses creationists.
5. Evidence for Junk—there is plenty of data supporting the concept of junk DNA

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One Public School System in Ontario

I petition the Ontario Legislature to adopt legislation to establish a single, non-sectarian, publicly funded school system made up of English and French language school boards.

Sign the Petition.

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Monday's Molecule #201

The last Monday's Molecule was L-gulose and the winner was Bill Gunn. It was a special anniversary (#200) so I reposted my original Monday's Molecule from November 13, 2006 [Monday's Molecule #200]. I don't think it was any easier this year than it was seven years ago. That's a shame since biochemistry students should have had no problem getting the right answer if they understand the basic concept behind drawing structures of carbohydrates.

Let's see if you can do any better with the same molecule from November 20, 2006. It's a common molecule, although I think it's not taught in most introductory biochemistry courses. It's in most of the textbooks.

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.)

Zack Kopplin Defends Science

I watched Real Time with Bill Maher a few days ago and was delighted to see a young student named Zack Kopplin defending science. This clip has been making the rounds under various titles such a "snail logic" and "you are not a scientist." You know that it hit home when even the Intelligent Design Creationists are blogging about it [Non-Scientist Says, "You're Not a Scientist"].

The ignorant conservatives refer to a grant on snail sex as an example of waste. The grant, Genomic Consequences of Asexuality, has John Logsdon as one of the co-principle investigators. We know John through his blog, Sex, Genes, and Evolution, and because he was a post-doc with Ford Doolittle. We also know that the evolution of sex is a serious problem and that New Zealand snails are an excellent model organism for testing many theories.

The thing that puzzles me is why conservative pundits like Steve Moore have any credibility at all. None of their arguments many any sense. If even a young student like Zack Kopplin can shoot them down then why do these ideas keep coming up in the US Congress?

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Tweeting a Conference

Imagine that you are speaking at a conference. You spent a long time preparing your talk and you have wonderful slides to illustrate your most important points. Imagine that half your audience doesn't seem to be paying attention. Their heads are down and they seem to be messaging on their smart phones or tablets. How do you feel about that?

Now imagine that there's a second screen behind you. One of them shows your wonderful slides but the other shows a continuous stream of tweets about your talk. That's the situation that PZ Myers encountered at a recent meeting [Good ideas and bad ideas]. PZ thinks this is a good idea, he says ...

One particularly interesting technological development was that there were two screens at the front of the room: one big one for the presenter to use, and a smaller one on which a twitter wall was displayed — all the silent conversations using the “#skeptech” hashtag were continuously displayed, which meant there was a constant flow of commentary from the audience sharing the stage with the speaker. It was rather cool — I’d like to see more of it at more conferences. It certainly made that hashtag explode with content.

I think that's a very, very, bad idea. I'm not sure that I would agree to be a speaker if I knew that the audience was going to pay more attention to their own tweets than to anything I was saying.

I wonder if PZ will incorporate this technology into his course lectures?

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Not Everyone in the USA Hates Evolution!

I lived in New Jersey for six years. I've lived in North Carolina for several months and my daughter lived there for six years. She now lives in California. We visit and vacation in New York (state) quite often. All these states are different but North Carolina is more different than the others.

Jerry Coyne has posted a graph showing why (see below) [Acceptance of evolution vs. religiosity in the U.S.]. It reminds me that some parts of the USA are much more like Canada and Europe. It reminds me that I shouldn't assume that Texas (or North Carolina) represents the whole country.

It also reminds me of a conversation I once had with a well-known defender of evolution. That person expressed serious concerns about a possible second civil war if trends continue the way they are going. (It might not mean war, but the point is that the Union is fragile and there are many good reasons for splitting the country.)

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Alvin Plantinga Explains Why Naturalistic Evolution Is a Self-Defeating Proposition

Alvin Plantinga is a philosopher who is widely admired in the Intelligent Design Creationist community. They believe that his arguments offer strong support for theism and, more importantly, point out the logical inconsistencies of science and atheism. Yesterday (April 5, 2013) the main Intelligent Design Creationist website posted a short video of Alvin Plantinga giving a lecture where he shows that naturalistic evolution is logically inconsistent [In Two Minutes or Less: Plantinga on Naturalistic Evolution as a Self-Defeating Proposition]. They must think it's very important. They refer to the video as something that should "win a prize for elegant brevity." We should pay attention if we hope to counter these arguments.

Watch and learn. This is a philosopher who other philosophers seem to respect. It's the very best that the other side has to offer in the field of epistemology and philosophy of science.


Here's more stuff that I've written about Alvin Plantinga and his views. It's part of a larger discussion about the credibility of the entire field of philosophy of science.

What Do Philosophers Really Think About Arguments for the Existence of God(s)?
Boudry vs Plantinga
The Flying Spaghetti Monster Steals Meatballs (What's the Purpose of Philosophy?)
A Sophisticated Theologian Explains Why You Should Believe in God
Is Evolution Guided or Unguided?
Fideism

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