I've been thinking a lot about fundamental concepts in biochemistry. One of them has to be energy—where do cells and organisms get the energy to grow and divide?
Most of the metabolism section of biochemistry courses in North America are taught from an anthropomorphic, fuel metabolism perspective. That's understandable since the purpose of such courses is mostly to prepare students for the MCAT exam. (Medical school entrance exam.) I prefer an evolutionary approach to teaching biochemistry but that's not very popular these days.
By the time the course is over, students will have learned that humans get their energy from food, especially glucose. The next step is to ask where the glucose comes from. The simple answer is that food (i.e. glucose) comes from plants. The next question is where do plants get the energy to make glucose? The answer is, of course, sunlight. This should lead to an explanation of photosynthesis but that rarely happens in introductory biochemistry courses.
This description leads to the classic "food chain" as shown in the figure (above) from FT Exploring Science and Technology [The Flow of Energy Through Plants and Animals]. This is conceptually sound biochemistry as far as it goes. As long as students understand how sunlight can be used to make ATP and how ATP can be used to make macromolecules (including glucose), then they will understand that humans ultimately get their energy from sunlight. I would be happy if all biochemistry students could explain this food chain at the molecular level.
But in order to make sure that students really understand this process, I go one step further. I explain that there are many species of bacteria that are chemoautotrophs. Chemoautotrophs are incapable of photosynthesis yet they are able to grow and divide in the absence of any organic compounds. Their carbon source is CO2, just like photosynthetic organisms. These bacteria have a basic metabolism that teaches us what primitive life forms must have been like. Knowing how they get their energy helps students understand evolution.
Where do chemoautotrophs get their energy? I'm interested in knowing how many readers have taken biochemistry and are able to answer that question. Please let me know in the comments before you read the answer in these posts [Carbon Dioxide Fixation in the Dark Ocean] [Core Concepts: Pathways and Transformations of Energy and Matter] [Ubiquinone and the Proton Pump].
The last Monday's Molecule was the pyrrolysine, 23rd amino acid. The winner was Michael Florea [Monday's Molecule #201].
Today's molecule is an enzyme. Homologous enzymes are found in all species. They play an essential role in metabolism. The green part binds the substrate and the subsequent reaction reduces a bound FAD prosthetic group (yellow). Electrons are then passed to an FAD molecule in the purple part in the orientation shown on the left. Notice that the yellow FAD molecules are close together. (The two purple parts on the left should be joined but the connection can't be resolved in the structure.) This electron transfer results in a shift in conformation to the conformation of the purple structure shown on the right. Note that the FAD molecule has shifted to a less exposed position. The purple protein then dissociates and carries electrons to an membrane-bound enzyme that transfers electrons to ubiquinol (QH2). Name the green protein and the purple protein.
This week I'm trying a new format in order to avoid moderating comments. Email your answers to me at: Monday's Molecule #202. I'll hold off posting your answers 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 email message.)
Lately there's been a flurry of activity in the American press about the value (or lack of value) of science. There have also been attempts by various organizations to enhance science education.1 Most defenders of science and science education will eventually end up trying to explain how science directly benefits the economy, usually in the form of return on investment. In other words, we need to do science because eventually the result will be used by somebody to make a profit.
I posted an example of this a few days ago [Zack Kopplin Defends Science].
I think this is a dangerous strategy. There are several ways of responding to the "what's in it for me" question without bringing up indirect economic benefit. These strategies are common when defending public support for the arts, for example. They're also used when defending research in the humanities.
Phill Plait of Bad Astronomy hits the nail on the head as far as I'm concerned [Wall Street Journal Editorial Board Member Gets Schooled on Science Funding]. His defense of science should be the primary talking point whenever anyone questions the value of learning about the natural world. Here's what Phil Plait says in response to Zack Kopplin's "return on investment" defense of science when Stephen Moore asks why the government is funding research on sex in snails.
How’s that for return on investment?
And that’s just a pedestrian, look-at-what’s-directly-in-front-of-you kind of thinking. We research the Universe around us because we are curious, inquisitive, intelligent animals. We don’t know what snail mating habits might teach us. That’s why we study it. Maybe it’ll lead into insight on how animals behave, or a new chemical secreted during the process, or to insight on the environment where snails live. Maybe none of that.
But that’s not the damn point. We study science because we want to learn about the real world. If we wanted to stick our heads in the sand, as people like Moore would have us do, he wouldn’t even have the venue he has to say ridiculous things like he just did.
Science is about exploration and discovery, and making sure we don’t fool ourselves. It’s among the noblest of all human endeavors, and something we should be both pursuing to our fullest abilities as well as defending from those who would drag it down.
Right on, Phil! Science leads to knowledge and knowledge is always better than ignorance. That's reason enough to fund science research and reason enough to support science education.
As sure as night follows day, there are going to be comments from people who advocate the "return on investment" strategy for defending science research. The argument frequently boils down to the fact that most politicians don't care about knowledge. All they want to see is how science can help business or improve the health and physical well-being of our citizens. Because these politicians are ignorant of the real value of knowledge, we must cow-tow to their ignorance and defend science on their turf.
That's what's happening in Canada with our Conservative government. In my field (biochemistry & molecular biology), many of my colleagues think we have to justify our research by showing how it will improve health. The current buzzword is "translational research." If you don't engage in the kind of research that Conservatives want, then you won't get funded.
Unfortunately, that may be true in today's climate. That doesn't mean we have to fool ourselves into thinking that that "translational research" be our primary goal. We recognize that the ignorance of our Conservative government is a problem, not a virtue. It's a problem that has to be fixed ... in the long term. Our goal should be to educate the next generation of politicians so we don't have to be embarrassed by them in the future. Let's at least have some people like Phil Plait who will speak out for basic curiosity-motivated research. We'll never succeed in convincing politicians and the general public of the value of knowledge if we don't even try.
Let's make sure we start with our students. Let's at least ensure that when we have them in our clutches as undergraduates we make sure that they understand science and the importance of knowledge. If we don't do that then we have nobody to blame but ourselves when future societies demand that science generate a return on investment.
Looking at my own university, it's obvious that we are not doing a very good job in our courses. I fear for the future of science.
1. In the USA "science" often gets lumped in with "technology," "engineering," and "mathematics"(=STEM) as though they had the same goals.
Regis College is a Jesuit College at the University of Toronto. One of their main jobs is to train students for the priesthood in the Roman Catholic Church.
Earlier this year it offered a course on "Responding to 21st-Century Atheism." This attracted the attention of Huffington Post who published a story about it on January 27, 2013 [Regis College, Catholic Institution, Offers Course On Atheism]. This provoked some traffic in the blogosphere [e.g. Jesuit college teaches atheism!].
I thought this was pretty interesting so when Regis College announced a one-day workshop I signed up and sent in my $50. Yesterday I spent more than seven hours at Regis College: six hours of lectures and an hour to eat my peanut butter sandwiches.
Join Professors Scott Lewis, S.J., Gordon Rixon, S.J., and Jeremy Wilkins from the faculty of Regis College as they explore responses to the challenges presented by contemporary atheism. This one day seminar will discuss the role of Scripture, tradition, and theology to address the questions about human living posed by today's culture and climate of disbelief.
Saturday, April 13, 2013 from 9:00 am to 4:00 pm. Cost $50.00
I mentioned a few days ago that Stephen Meyer's new book Darwin's Doubt is about to be released [see Two Books on the Cambrian Explosion]. I'm planning to read it as soon as I can get a hold of a copy—probably sometime in August in Canada.
You are all going to have to read this book because, according to Casey Luskin, it is "going to be another landmark for the ID movement" [Three (or Four) Reasons Everyone Should Read Darwin's Doubt]. Luskin has read it. Here are his three reasons why the book is important and worth reading.
- Arguments for intelligent design in the Cambrian explosion have certainly been made before. But Darwin's Doubt will be by far the most in-depth and mature development of those arguments to date, addressing in detail many ideas and rebuttals and theories advanced by evolutionary scientists, and showing why the theory of intelligent design best explains the explosion of biodiversity in the Cambrian animals.
- When published, Darwin's Doubt will be the single most up-to-date rebuttal to neo-Darwinian theory from the ID-paradigm. In this regard, one exciting element of Darwin's Doubt is that Meyer reviews much of the peer-reviewed research that's been published by the ID research community over the last few years, and highlights how ID proponents are doing relevant research answering key questions that show Darwinian evolution isn't up to the task of generating new functional information.
- As many ENV readers already know, we now live in a "post-Darwinian" world, where more and more evolutionary biologists are realizing that neo-Darwinism is failing, so they scramble to propose new materialistic evolutionary models to replace the modern synthesis. (These models include, or have included, self-organization, evo-devo, punc eq, neo-Lamarckism, natural genetic engineering, neutral evolution, and others.) In this regard, Darwin's Doubt does something that's never been done before: it surveys the landscape of these "post-neo-Darwinian evolutionary models," and shows why they too fail as explanations for the origin of animal body plans and biological complexity.
I know that it's a bit annoying to have to read all this hype when the book won't be available for several months. The Intelligent Design Creationists want you to know that any criticism of what they are saying about the book is unethical unless you've read it yourself. However, it's not the least bit unethical for them to make outlandish claims about what's in the book months before we can verify whether those claims are correct.
This is creationist ethics. It's not supposed to make sense.
Intelligent Design Creationists love to refer to their opponents as "Darwinists." We all know why they do it. It's a rhetorical device designed to belittle those who accept evolution. The term makes it look like evolutionary biologists worship a man who died 130 years ago and it implies that we still believe in nineteenth century science. The term "Darwinist" also makes it easy to associate modern scientists with social Darwinism. That's a common strategy employed by creationists of all stripes. I get it. It has nothing to do with scientific debates about evolution.
But sometimes rhetoric gets in the way of understanding. There seem to be a few (very few) Intelligent Design Creationists who genuinely want to understand the issues—even if their motive is still to push a scientific view of creationism. They pop up from time to time on the Intelligent Design Creationist websites. Andyjones seems to be one of them. (I'm giving him the benefit of the doubt.)
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.
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.]
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
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.
- 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."
- 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"
- 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."
- 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."
- Masumi Nozawa (National Genetic Institute, Mishima, Japan)
(I don't know anything about his work. Can anybody help?
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.
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.
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.
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:
- Using highly purified messenger RNA (mRNA) the amount of DNA suggested that the genome had between 15,000 and 20,000 genes.
- 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.
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.
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.
- Pervasive Transcription—especially the idea that this isn't new.
- Most Transcripts Are Very Rare—what does this say about their possible function?
- The Specificity of DNA-Binding Proteins—non-specific (i.e. nonfunctional) binding is an essential property of RNA polymerase and regulatory proteins.
- The Meaning of Darwinism—why abuse of this term confuses creationists.
- Evidence for Junk—there is plenty of data supporting the concept of junk DNA
I've been thinking a lot about fundamental concepts in biochemistry. One of them has to be energy—where do cells and organisms get the energy to grow and divide? 
