Wednesday, August 14, 2013
45 Years Ago
We're celebrating our 45th wedding anniversary by taking a cruise in the Baltic. We were in Oslo, Norway on our anniversary day (August 9) where we met our friends Dag and Robin from graduate student days. They are als0 marride 45 years so we celebrated with champagne at their house. More about that later.
Monday, August 12, 2013
University of Rostock
The University of Rostock was founded in 1419. It’s said to be the oldest university in the Baltic Sea area. The main university building is a prominent landmark in Rostock but I was more interested in the Zoology building off to the side.
Looks like I just missed an important conference. Does everyone know who Willi Hennig is?
Looks like I just missed an important conference. Does everyone know who Willi Hennig is?
Warnemünde and Rostock
Yesterday our boat stopped at the habor in Warnemünde, Germany. There was a lot of activity of the quay in Warnemünde because a number of tall ships were in the harbor.
We took the train to the medieval town of Rostock—a key port in the Hansiatic League (Hansa=guilds). The architecture was similar to that in other leading cities of the Hansiatic League, notably Bruges.
We took the train to the medieval town of Rostock—a key port in the Hansiatic League (Hansa=guilds). The architecture was similar to that in other leading cities of the Hansiatic League, notably Bruges.
Sunday, August 11, 2013
Cruising
We've been on this boat for three days and we'll be on it for another 8 days as we cruise the Baltic Sea. Internet access costs 70 cents ($0.75 US) per minute so posts will be short and infrequent.
Friday, August 09, 2013
Wednesday, August 07, 2013
Carnival of Evolution #62: The Whig History
When it comes to the history of evolutionary theory, a whiggish image could look something like [the figure below]
I leave it to the readers to come up with a female version (including, for example, Maria Sibylla Merian, Rosalind Franklin, Barbara McClintock, Christiane Nüsslein-Volhard).
Arranging July's posts that I found interesting or entertaining as well as the few submitted by others according to a Whig history of evolutionary theory in the following is purely ornamental and does, of course, not imply any whiggishness on the side of the contributors.
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! 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. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.
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Tuesday, August 06, 2013
Carnival of Evolution #61: Crustie Lovin; Edition
Hello, and welcome to the Carnival of Evolution #61. For this edition, I’ve chosen to celebrate what I perceive as an inexplicably underappreciated group of animals: the Crustacea. Of the major arthropod groups, I notice that crustaceans often get the short end of the stick. Everyone can name insects and recognise spiders, but besides seafood, crustaceans seem to be a question mark with most people. Insects and spiders have movies and songs written about them; crabs are the logo for cancer, the vernacular name for an STD, and they are an astrological sign.
Insulting. Crustaceans are awesome. There may be over a million insect species, but crustaceans take the cake when it comes to disparity, or morphological diversity, a measure in which no other taxon can match them.
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! 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. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.
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Monday, August 05, 2013
Carnival of Evolution #60: Party like it’s 1953
Ladies and gentlemen, this is a special edition of the Carnival of Evolution. It’s the big six oh!
In honor of that achievement, we shall share this carnival’s space with other events celebrating their sixtieth anniversary.
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! 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. Please alert Bjørn or the upcoming host if you see an article that should be included in next month's. You don't have to be the author to nominate a post.
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Monday's Molecule #212
Today's molecule is an important part of a major pathway. Give the common name and identify the pathway. Explain briefly why this pathway is important.
Email your answers to me at: Monday's Molecule #212. I'll hold off posting your answers for 24 hours. The first one with the correct answer wins. I will only post the names of people with 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.)
Sunday, August 04, 2013
Dear Denyse, Stop Digging
Further to Cornelius Hunter’s “Evolutionist: We do not promote any ‘spiritual ideologies,’” (in which he recounts that recent findings about RNA structure conservation suggest that even more of the mammalian genome is functional than supposed, hence there is less “junk DNA”:
I’ve never clearly understood Darwin’s fans attachment to junk DNA. It makes a good “anti-God” statement, as long as you are certain that the stuff is not and never could be any use. But that is precisely what is now widely contested. And it was a trap they need not have fallen into.
But a simple illustration will show that even if most of the information in DNA were never used, it would still be valuable. Let us say I have a directory of members of a club I belong to. I never use most of the phone numbers. Many numbers may never be used by anyone.
Does lack of use make that proportion of the directory junk?
Friday, August 02, 2013
Goodbye Dumpster
Jerry Coyne posted this video and I thought it was so funny I just had to put it on my website blog.
What Would Jerry Coyne, Daniel Dennett, and Richard Dawkins Do at Ball State University?
I'm trying to understand how the rules announced by President Jo Ann Gora would work in practice.
Let's think about how they might affect three prominent atheists. Jerry Coyne is an evolutionary biology professor at the University of Chicago. He is a prominent atheist and he defends the position that science and religion are not compatible. He does not have to adhere to the Ball State University rules because the University of Chicago is a private school.
Daniel Dennett is a philosopher at Tufts University (private). He is a prominent atheist and no friend of religion.
Richard Dawkins was a professor and evolutionary biologist at Oxford University in the UK. He did not have to worry about following the Ball State University rules because they don't apply outside of the USA.
Let's imagine that all three became professors at Ball State University. They would have to pay attention to the rules outlined by President Jo Ann Gora. Here are the relevant passages from her recent message.
Most professors have graduate students. They do not hide their opinions from their graduate students. Nor do they hide them from their colleagues or the administrators in their university.
These professors aren't shy about expressing their points of view on blogs, twitter, Facebook, newspapers and just any other means of communication.
Now let's imagine that they are teaching an undergraduate course about atheism and religion in a humanities department at Ball State University. How is that supposed to work? Are they supposed to go out of their way to avoid "privileging one view as more legitimate than others"? And if so, are any of the students going to be fooled? They can all access the internet.
It's clearly a ridiculous rule unless it also applies outside of the classroom. Does it mean that professors at a public university must avoid criticizing religion at all times?
Let's think about how they might affect three prominent atheists. Jerry Coyne is an evolutionary biology professor at the University of Chicago. He is a prominent atheist and he defends the position that science and religion are not compatible. He does not have to adhere to the Ball State University rules because the University of Chicago is a private school.
Daniel Dennett is a philosopher at Tufts University (private). He is a prominent atheist and no friend of religion.
Richard Dawkins was a professor and evolutionary biologist at Oxford University in the UK. He did not have to worry about following the Ball State University rules because they don't apply outside of the USA.
Let's imagine that all three became professors at Ball State University. They would have to pay attention to the rules outlined by President Jo Ann Gora. Here are the relevant passages from her recent message.
Creation science, intelligent design, and other worldviews that focus on speculation regarding the origins of life represent another important and relevant form of human inquiry that is appropriately studied in literature and social science courses. Such study, however, must include a diversity of worldviews representing a variety of religious and philosophical perspectives and must avoid privileging one view as more legitimate than others.All three professors have written extensively about religion and their views are widely known. They attend conferences and give public lectures. They do not pull any punches when they talk about the evils of religion. Nobody would ever say that they go out of their way to avoid endorsing one perspective over another. Academics have opinions and they are not afraid to express them.
As a public university, we have a constitutional obligation to maintain a clear separation between church and state. It is imperative that even when religious ideas are appropriately taught in humanities and social science courses, they must be discussed in comparison to each other, with no endorsement of one perspective over another.
Most professors have graduate students. They do not hide their opinions from their graduate students. Nor do they hide them from their colleagues or the administrators in their university.
These professors aren't shy about expressing their points of view on blogs, twitter, Facebook, newspapers and just any other means of communication.
Now let's imagine that they are teaching an undergraduate course about atheism and religion in a humanities department at Ball State University. How is that supposed to work? Are they supposed to go out of their way to avoid "privileging one view as more legitimate than others"? And if so, are any of the students going to be fooled? They can all access the internet.
It's clearly a ridiculous rule unless it also applies outside of the classroom. Does it mean that professors at a public university must avoid criticizing religion at all times?
President of Ball State University Forbids Teaching Intelligent Design
Thursday, August 01, 2013
The Junk DNA Controversy: John Mattick Defends Design
The failure to recognize the implications of the non-coding DNA will go down I think as the biggest mistakes in the history of molecular biology.
John Mattick
abc AustraliaJohn Mattick has just published a paper dealing with the controversy over the ENCODE results and junk DNA. As you might imagine, Mattick defends the idea that most of our genome is functional. He attempts to explain why most of the critics are wrong.
The title of the paper is "The extent of functionality in the human genome" (Mattick and Dinger, 2013). It's published in the HUGO Journal. Recall that HUGO (Human Genome Organization) gave Mattick a prestigious award for his contributions to genome research. (See The Dark Matter Rises for a discussion of these contributions.)
UPDATE: Mike White also discusses this paper at: Having your cake and eating it: more arguments over human genome function.
Mattick's paper begins by mentioning three of the papers that were critical of ENCODE results: Dan Graur's paper (Graur et al. 2013), Ford Doolittle's paper (Doolittle, 2013), and the paper by Niu and Jiang (2013).
He begins by addressing one of Dan Graur's points about conservation.
John Mattick
abc AustraliaJohn Mattick has just published a paper dealing with the controversy over the ENCODE results and junk DNA. As you might imagine, Mattick defends the idea that most of our genome is functional. He attempts to explain why most of the critics are wrong.
The title of the paper is "The extent of functionality in the human genome" (Mattick and Dinger, 2013). It's published in the HUGO Journal. Recall that HUGO (Human Genome Organization) gave Mattick a prestigious award for his contributions to genome research. (See The Dark Matter Rises for a discussion of these contributions.)
UPDATE: Mike White also discusses this paper at: Having your cake and eating it: more arguments over human genome function.
Mattick's paper begins by mentioning three of the papers that were critical of ENCODE results: Dan Graur's paper (Graur et al. 2013), Ford Doolittle's paper (Doolittle, 2013), and the paper by Niu and Jiang (2013).
He begins by addressing one of Dan Graur's points about conservation.
Wednesday, July 31, 2013
The Dark Matter Rises
John Mattick publishes lots of papers. Most of them are directed toward proving that almost all of the human genome is functional. I want to remind you of some of the things that John Mattick has said in the past so you'll be prepared to appreciate my next post [The Junk DNA Controversy: John Mattick Defends Design].
Mattick believes that the Central Dogma means DNA makes RNA makes protein. He believes that scientists in the past took this very literally and discounted the importance of RNA. According to Mattick, scientists in the past believed that genes were the only functional part of the genome and that all genes encoded proteins.
If that sounds familiar it's because there are many IDiots who make the same false claim. Like Mattick, they don't understand the Central Dogma of Molecular Biology and they don't understand the history that they are distorting.
Mattick believes that there is a correlation between the amount of noncoding DNA in a genome and the complexity of the organism. He thinks that the noncoding DNA is responsible for making tons of regulatory RNAs and for regulating expression of the genes. This belief led him to publish a famous figure (left) in Scientific American.Mattick has many followers. So many, in fact, that the Human Genome Organization (HUGO) recently gave him an award for his contributions to the study of the human genome. Here's the citation.
Theme
Genomes
& Junk DNA
The Award Reviewing Committee commented that Professor Mattick’s “work on long non-coding RNA has dramatically changed our concept of 95% of our genome”, and that he has been a “true visionary in his field; he has demonstrated an extraordinary degree of perseverance and ingenuity in gradually proving his hypothesis over the course of 18 years.”Let's see what this "true visionary" is saying this year. The first paper is "The dark matter rises: the expanding world of regulatory RNAs" (Clark et al., 2013). Here's the abstract ...
The ability to sequence genomes and characterize their products has begun to reveal the central role for regulatory RNAs in biology, especially in complex organisms. It is now evident that the human genome contains not only protein-coding genes, but also tens of thousands of non–protein coding genes that express small and long ncRNAs (non-coding RNAs). Rapid progress in characterizing these ncRNAs has identified a diverse range of subclasses, which vary widely in size, sequence and mechanism-of-action, but share a common functional theme of regulating gene expression. ncRNAs play a crucial role in many cellular pathways, including the differentiation and development of cells and organs and, when mis-regulated, in a number of diseases. Increasing evidence suggests that these RNAs are a major area of evolutionary innovation and play an important role in determining phenotypic diversity in animals.This is his main theme. Mattick believes that a large percentage of the human genome is devoted to making regulatory RNAs that control development. He believes that the evolution of this complex regulatory network is responsible for the creation of complex organisms like humans, which, incidentally, are the pinnicle of evolution according to the figure shown above.
The second paper I want to highlight focuses on a slightly different theme. It's title is "Understanding the regulatory and transcriptional complexity of the genome through structure." (Mercer and Mattick, 2013). In this paper he emphasizes the role of noncoding DNA in creating a complicated three-dimensional chromatin structure within the nucleus. This structure is important in regulating gene expression in complex organisms. Here's the abstract ...
An expansive functionality and complexity has been ascribed to the majority of the human genome that was unanticipated at the outset of the draft sequence and assembly a decade ago. We are now faced with the challenge of integrating and interpreting this complexity in order to achieve a coherent view of genome biology. We argue that the linear representation of the genome exacerbates this complexity and an understanding of its three-dimensional structure is central to interpreting the regulatory and transcriptional architecture of the genome. Chromatin conformation capture techniques and high-resolution microscopy have afforded an emergent global view of genome structure within the nucleus. Chromosomes fold into complex, territorialized three-dimensional domains in concert with specialized subnuclear bodies that harbor concentrations of transcription and splicing machinery. The signature of these folds is retained within the layered regulatory landscapes annotated by chromatin immunoprecipitation, and we propose that genome contacts are reflected in the organization and expression of interweaved networks of overlapping coding and noncoding transcripts. This pervasive impact of genome structure favors a preeminent role for the nucleoskeleton and RNA in regulating gene expression by organizing these folds and contacts. Accordingly, we propose that the local and global three-dimensional structure of the genome provides a consistent, integrated, and intuitive framework for interpreting and understanding the regulatory and transcriptional complexity of the human genome.Other posts about John Mattick.
How Not to Do Science
John Mattick on the Importance of Non-coding RNA
John Mattick Wins Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research
International team cracks mammalian gene control code
Greg Laden Gets Suckered by John Mattick
How Much Junk in the Human Genome?
Genome Size, Complexity, and the C-Value Paradox
Clark, M.B., Choudhary, A., Smith, M.A., Taft, R.J. and Mattick, J.S. (2013) The dark matter rises: the expanding world of regulatory RNAs. Essays in Biochemistry 54:1-16. [doi:10.1042/bse0540001]
Mercer, T.R. and Mattick, J.S. (2013) Understanding the regulatory and transcriptional complexity of the genome through structure. Genome research 23:1081-1088 [doi: 10.1101/gr.156612.113]
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