Thursday, April 30, 2015

Nature reviews Nessa Carey's book on junk DNA

Read it at" Genetics: We are the 98%. Here's the important bit ...
Finally, Junk DNA, like the genome, is crammed with repetitious elements and superfluous text. Bite-sized chapters parade gee-whizz moments of genomics. Carey's The Epigenetics Revolution (Columbia University Press, 2012) offered lucid science writing and vivid imagery. Here the metaphors have been deregulated: they metastasize through an otherwise knowledgeable survey of non-coding DNA. At one point, the reader must run a gauntlet of baseball bats, iron discs, Velcro and “pretty fabric flowers” to understand “what happens when women make eggs”. The genome seems to provoke overheated prose, unbridled speculation and Panglossian optimism. Junk DNA produces a lot of DNA junk.

The idea that the many functions of non-coding DNA make the concept of junk DNA obsolete oversells a body of research that is exciting enough. ENCODE's claim of 80% functionality strikes many in the genome community as better marketing than science.

Nessa Carey doesn't understand junk DNA

Nessa Carey is a science writer with a Ph.D. in virology and she is a former Senior Lecturer in Molecular Biology at Imperial College, London.

She has written a book on junk DNA but it's not available yet (in Canada). Judging by her background, she should be able to sort through the controversy and make a valuable contribution to informing the public but, as we've already noted Nessa Carey and New Scientist don't understand the junk DNA debate.

Casey Luskin has a copy of the book so he wrote a blog post on Evolution News & Views. He's thrilled to find someone else who dismisses junk DNA and "confirms" the predictions of Intelligent Design Creationism. I hope Nessa Carey is happy that the IDiots are pleased with her book [New Book on "Junk DNA" Surveys the Functions of Non-Coding DNA].

Friday, April 24, 2015

Human mutation rates - what's the right number?

There's some controversy over the rate of mutations in humans. The latest summary comes from science journalist Ewen Callaway, a Senior Reporter for Nature, writing on March 10, 2015: DNA mutation clock proves tough to set.



-mutation types
-mutation rates
Let's review what we know. The first thing we have to do is define "mutation" [What Is a Mutation?]. A mutation is any alteration of the nucleotide sequence of a genome. It includes substitutions, insertions, and deletions.

The mutation rate can be described and defined in many ways. For most purposes, we can assume that it's equivalent to the error rate of DNA replication since that accounts for the vast majority of substitutions. Substitutions are far more numerous than most insertions and deletions. (But see, Arlin Stoltzfus on The range of rates for different genetic types of mutations).

Thursday, April 23, 2015

Happy 10th birthday to YouTube!

The first video was posted to YouTube on April 23, 2005 [see YouTube]. I took this photo (right) a few years ago near my daughter's place in Playa Vista, California. It's a production facility, YouTube Space LA, on the site of the former Howard Hughes airport.

The main purpose of this post is to give me an excuse to post one of my granddaughter's favorite YouTube videos (below top). She's a big fan of YouTube and so is my two year old grandson—he likes videos of rocket launches (below bottom).

Friday, April 17, 2015

Does natural selection constrain neutral diversity?

Razib Khan is an adaptationist and he's discovered a paper that gets him very excited: Selectionism Strikes Back!.

Here's the paper and the abstract.
Corbett-Detig, R.B., Hartl, D.L., Sackton, T.B. (2015) Natural Selection Constrains Neutral Diversity across A Wide Range of Species. PLoS Biology Published: April 10, 2015 doi: 10.1371/journal.pbio.1002112

The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.
It is impossible for someone like me to evaluate this paper. Can someone take a look to see if it's valid?

How many selective sweeps must there every 50,000 years in order to remove substantial amounts of neutral diversity from junk DNA?

Mississauga Mayor Bonnie Crombie agrees to abide by Surpeme Court ruling banning prayers at city council

Shortly after being elected last Fall, the new Mayor of Mississauga, Bonnie Crombie, decided that the City Council would continue to say a prayer before each council meeting. She voted in favor of continuing the practice even though she heard the arguments against it and even though she knew that the Ontario Court of Appeal (in 1999) had ruled it illegal [Mississauga council debates removing Lord’s Prayer from meetings].
Crombie, who is Catholic, said she doesn’t have a problem with the recitation of the prayer. But, she does want to touch base with the municipality’s 11 councillors to get their opinions.

She has already heard lot of different ideas from her peers, such as leaving the practice the way it is to replacing it with a non-denominational blessing to even rotating a prayer from a different faith before each meeting.

"I don’t think there’s anything wrong with (reciting the prayer)," said Crombie. "But, I am asking each councillor about it and there is a diversity of opinion."


Larry Moran, who described himself as an atheist, is also a University of Toronto professor and an advisory fellow with the Centre for Inquiry Canada, an organization he said strongly supports the separation of religion and government.

He wrote a blog post condemning the practice in Mississauga earlier this year and Moran estimates about 30 per cent of Canadians aren’t religious. He strongly believes the Lord’s Prayer before council should come to an end.

"There is no reason to invoke any of the gods at a public meeting of any government body," said Moran. "It sends the wrong message to … citizens who don’t believe in those gods or who believe in other gods. Nobody has been able to tell me why religion has to be mixed in with government business."
Now Bonnie Crombie says she will obey the law—no mention of fairness or of consideration for non-Christians in the community. Oh well, at least she's not going to fight it and cost the city lots of money.

The Toronto Star reports that the mayor of Oshawa plans to ignore the Supreme Court decision. I bet he backs down after talking to the city lawyers [Oshawa mayor plans to keep Lord’s Prayer].
Brampton Mayor Linda Jeffrey stopped the practice of reciting the Lord's Prayer before council meetings earlier in the year and today Mississauga Mayor Bonnie Crombie indicated her council will now do the same, after the Supreme Court decision. At the beginning of the year she supported keeping the Lord's Prayer in Mississauga council meetings.

"Today’s ruling sets a precedent and the City of Mississauga will abide by the Supreme Court’s ruling," Crombie said.

At the beginning of the year Crombie supported keeping the Lord's Prayer in Mississauga council meetings, after Councillor Carolyn Parrish had pushed to remove it from council meetings.

Story-telling and the origin of eukaryotes

Austin Booth and Ford Doolittle have just published a paper that discusses the origin of eukaryotes (Austin and Doolittle, 2015). They point out that many of the stories about this event are not grounded in fact. Read the paper.
Writing for public audiences, and often even for themselves, biologists are not loath to make simplifying claims about uniqueness and importance that are rhetoric disguised as fact. Such generalizations serve purposes in the doing of science, but are often not themselves testable scientific claims and are subject to biases. Evolutionary biology may be especially vulnerable to hype, as suggested by the frequency with which revolutionary evolutionary claims in top-notch journals are debunked. Additionally, anthropocentrism, as it grades into "zoocentrism" and then "eukaryocentrism," surely remains a subtle distorter of objectivity.

Our aim here is to critique general claims about the uniqueness and special importance of eukaryogenesis, with an aim to making them more open to question and conceptual and empirical analysis. We ask (i) whether eukaryogenesis entailed such a "genuinely unlikely sequence of events" as to justify belief in its uniqueness as a process, (ii) if, as is often claimed, eukaryogenesis has a problematic or unique theoretical status in evolutionary biology, (iii) what intrinsic features might have conferred on eukaryotes their presumed "richer evolutionary potential," and (iv) if this greater potential might be just a presumption, an illusion reflecting eukaryocentric bias.
There are many useful ways of understanding evolution, and their articulations can be intellectually valuable and experimentally fruitful. We advocate a more self-conscious pluralism that would require not that we stop telling eukaryogenesis stories but that we do recognize them for what they are. We do not claim to know whether there is any best story, any theory by which the apparent differential success of eukaryotes can be objectively probed and causally rationalized. What we have questioned here is whether premises of existing theories have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was "special," any such notion has more than rhetorical value.

Booth, A. and Doolittle, W.F. (2015) Eukaryogenesis, how special really? Proc. Natl. Acad. Sci. (USA) Published online before print April 16, 2015 [doi: 10.1073/pnas.1421376112]

Wednesday, April 15, 2015

Canada bans prayers at city council meetings

The Supreme Court of Canada has ruled that prayers at the opening of city council meetings are not consistent with a secular society [Quebec town can’t have prayers at council meetings, top court rules].

The Supreme Court decision is at: Mouvement laïque québécois v. Saguenay (City). The decision appears to be unanimous (9:0) provided I'm reading it correctly.
The state’s duty of religious neutrality results from an evolving interpretation of freedom of conscience and religion. The evolution of Canadian society has given rise to a concept of this neutrality according to which the state must not interfere in religion and beliefs. The state must instead remain neutral in this regard, which means that it must neither favour nor hinder any particular belief, and the same holds true for non‑belief. The pursuit of the ideal of a free and democratic society requires the state to encourage everyone to participate freely in public life regardless of their beliefs. A neutral public space free from coercion, pressure and judgment on the part of public authorities in matters of spirituality is intended to protect every person’s freedom and dignity, and it helps preserve and promote the multicultural nature of Canadian society. The state’s duty to protect every person’s freedom of conscience and religion means that it may not use its powers in such a way as to promote the participation of certain believers or non‑believers in public life to the detriment of others. If the state adheres to a form of religious expression under the guise of cultural or historical reality or heritage, it breaches its duty of neutrality. The Tribunal was therefore correct in holding that the state’s duty of neutrality means that a state authority cannot make use of its powers to promote or impose a religious belief. Contrary to what the Court of Appeal suggested, the state’s duty to remain neutral on questions relating to religion cannot be reconciled with a benevolence that would allow it to adhere to a religious belief.
This seems so obvious to most people that it's a wonder why anyone ever thought that reciting prayers at city council meetings was justified.

Now, let's see how long it takes for other cities to stop the practice.

Hat Tip: Canadian Atheist

The Virtual Cell Animation Collection

I'm interested in science education in general and teaching biochemistry and molecular biology in particular. A recent publication in PLoS Biology caught my eye ...
Reindl, K.M., White, A. R., Johnson, C., Vender, B., Slator, B.M., and McClean, P. (2105) The Virtual Cell Animation Collection: Tools for Teaching Molecular and Cellular Biology. PLoS Biology 13(4): e1002118 DOI: 10.1371/journal.pbio.1002118
The paper focuses on the value of short animations for teaching biochemistry and molecular biology to advanced high school students and college students.

There's nothing in the paper about the scientific accuracy of the presentations or the pedagogical approach and this is unfortunate. The animations only show complex eukaryotic cells in spite of the fact that the American Society for Biochemistry and Molecular Biology recommends an evolutionary approach to teaching. The fact that the videos emphasize eukaryotes leads to some interesting descriptions of fundamental processes.

Look at the video on transcription regulation for example [Regulated Transcription]. The textbooks teach this using simple systems such as E. coli transcription then they move on to more complex prokarotic systems such as the lac operon. Then they cover the eukaryotic examples pointing out how they differ from the simple bacterial systems. This has always been a successful approach to teaching the basic concepts of transcription and transcription regulation. 1

Is the approach taken by the authors of The Virtual Cell Animation project better? I don't think so. What do you think? Does anyone out there teach transcription without introducing it first in bacteria?

Let's not forget my favorite example of biochemical misconceptions: the Citric Acid Cycle. Did you know that it's sometimes called the "tricarboxylic acid cycle" because three CO2 molecules are released for every pyruvate molecule? 2

The carboxylate groups on citrate, isocitrate etc. are shown as -COOH instead of COO- as in the textbooks. I don't know why they did this ... it leads to some extra protons being released in the reactions.

The authors make a very common mistake with succinate dehydrogenase. They show FADH2 as one of the products of the reaction whereas the IUBMB database shows that the real final product is QH2 [see Succinate Dehydrogenase]. I don't understand why biochemistry teachers can't check out a leading textbook (or the scientific literature) before producing a video.

Did you know that some of the reactions of glycolysis are irreversible? Check out the video on Glycolysis to find out which reactions have this interesting property. 3 There is no video on gluconeogenesis and that's surprising because the synthesis of glucose is far more important than glycolysis in most species.

I wonder if the editors of PLoS bothered to watch the videos or whether they just assumed that they were scientifically accurate and pedagogically sound? I'm guessing that they didn't see the need to review the videos and simply concentrated on whether all the words in the article were spelled correctly.

1. There's a separate video on the lac Operon. How many errors, flaws, or missed opportunities, can you spot?

2. Silly me. I always though it had something to do with the fact that two of the key intermediates (citrate and isocitrate) were tricarboxylic acids. Most of the others are dicarboxylic acids.

3. Maybe I'm quibbling. In my textbook I describe these reactions as "metabolically irreversible" because the activities of the enzymes are regulated. That's not the same as saying that the reactions are irreversible.

Saturday, April 04, 2015

Stupid Harvard press release illustrates the importance of author responsibility

Bonnie Prescott is a Senior Science Writer at the Beth Israel Deaconess Medical Center at Harvard Medical School. She has written a press release concerning pseudogenes and cancer: Evolutionary Relic: Pseudogenes in the human genome may lead to cancer development.

Here are the first five paragraphs ...
Pseudogenes, a subclass of long noncoding RNA (lncRNA) that developed from the human genome’s 20,000 protein-coding genes but has lost the ability to produce proteins, have long been considered nothing more than genomic "junk."

Yet the retention of these 20,000 mysterious remnants during evolution suggests that they may in fact possess biological functions and contribute to the development of disease.

Now, a team led by investigators at Harvard Medical School and the Cancer Center at Beth Israel Deaconess Medical Center has provided some of the first evidence that one of these noncoding "evolutionary relics" actually has a role in causing cancer.

In a new study published in the journal Cell on April 2, the scientists report that, independent of any other mutations, abnormal amounts of the BRAF pseudogene led to the development of an aggressive lymphoma-like disease in a mouse model, a discovery suggesting that pseudogenes may play a primary role in a variety of diseases.

The new discovery also suggests that with the addition of this vast "dark matter" the functional genome could be tremendously larger than previously thought—three or four times its current known size.
There are many things wrong with that description but I'm not going to elaborate. If you don't know what's wrong you probably won't be interested in this post anyway.

I want to discuss two rules that should be enforced for every press release.
  1. The press release must include the complete citation, including a link (doi). If This means delaying the press release for a day or two after the embargo is lifted then that's a small price to pay.
  2. The press release should always include a notice from at least one author affirming, in writing, that the press release is a complete and accurate report of the results and conclusions that have been published in the peer reviewed literature.
This press release did not contain a citation. In this case, the paper has been published online but there's no volume number or page number because it hasn't appeared in the journal. Here's the citation ...
Florian A. Karreth, Markus Reschke, Anna Ruocco, Christopher Ng, Bjoern Chapuy, Valentine Léopold, Marcela Sjoberg, Thomas M. Keane, Akanksha Verma, Ugo Ala, Yvonne Tay, David Wu, Nina Seitzer, Martin Del Castillo Velasco-Herrera, Anne Bothmer, Jacqueline Fung, Fernanda Langellotto, Scott J. Rodig, Olivier Elemento, Margaret A. Shipp, David J. Adams, Roberto Chiarle, Pier Paolo Pandolfi (2015)The BRAF Pseudogene Functions as a Competitive Endogenous RNA and Induces Lymphoma In Vivo Cell published online April 2, 1015. [doi: 10.1016/j.cell.2015.02.043]
There. That wasn't so hard, was it?

I can't read the paper because it's behind a paywall but the abstract suggests that the authors really do think their work applies to most pseduogenes. The press release quotes the senior author, Pier Paolo Pandolfi, and while his views aren't nearly as idiotic as the beginning of the press release it does suggest that he isn't a fan of junk DNA.

In order to confirm that the views expressed by Bonnie Prescott are an accurate representation of the views in the peer-reviewed paper, it would be nice to see a note at the bottom of the press release signed by multiple authors. It would state that they stand by the press release and that the views in the press release represent those views that have passed peer review.

I call this "Author Responsibility" and I think it should be a requirement in all press releases.

Hat Tip Dan Graur: Shouldn’t Press Releases from @Harvard be Less Asinine?

Friday, April 03, 2015

James Lunney doesn't get no respect - does he deserve it?

James Lunney has quit the Conservative Party of Canada and decided not to run in the next federal election. He's upset because he doesn't believe in evolution and lots of people, including me, are pointing out the stupidity of his views. Because those views are based on religion, he interprets this to be an attack on his faith.

Here's what he says on his website [Evolution Controversy].
Maybe it’s because I am tired of seeing my faith community mocked and belittled. To not respond is to validate my accusers and worse yet, imply that I lack the courage of my convictions to stand–up for what I believe. This is not a legacy I wish to leave behind. Many of you colleagues represent constituencies beyond the ones who elected you; I hope that no member of any faith community in Canada is compelled to defend the beliefs of their community in the future.

Freedom of Religion and conscience are fundamental freedoms in Canada. Bigotry cloaked in defense of "science" is as intolerable and repugnant as bigotry from any other source.

It is contrary to our multi-racial, multicultural and multi-faith character and the tolerance for diversity that defines us as Canadians.

I know members on all sides of the house are concerned about bullying in general and cyber-bullying in particular. The government has brought in new legislative measures to address some aspects of this brutal phenomenon and there are many social actions like the pink shirt initiative that seek to shield the vulnerable.

We are living in an era where knowledge is increasing at an astounding pace; there are so many technical advances it is hard to keep up and what we refer to in general as "science" has been parsed into more and more diverse pursuits of knowledge.
I urge you to read the entire article that he posted on April 1st 2015. See if you think he deserves the respect he craves. He sounds like a kook to me.

How many times have we heard this stuff before? And how many times have we seen this style of writing?
So is "Evolution Theory or Fact?

The late Stephen Jay Gould stated: "a fact is something that is proven to the extent that to not believe it is perverse"!

That translates to: a fact is something that my friends and I believe, AKA eminence-based science. There’s a lot of that in health-care, where it’s known as eminence-based medicine as opposed to evidence- based medicine. There are people in the medical world expressing concern about the immense influence of KOLs (Key Opinion Leaders) with influencing public policy and decision making in directing scientific inquiry

Darwin’s brilliant and convincing construct that defined a century and a half of scientific belief, is in crisis because of astounding advances in molecular biology and it’s all about THE CELL.

You have 80-100 trillion cells, 200 cell types, all reading the same genetic library, but as different as they are, working together in specialized communities to perform astonishing synchronized manufacturing, recycling, transport, packaging and delivery functions. Twenty-five thousand miles of blood vessels if you strung them end to end; that is a trip around the world at the surface.

Every cell is worlds within worlds of nanotechnology finely tuned and regulated.

Darwin’s elaborate construct is stalled at the cell; even the simplest prokaryotic cell is infinitely beyond the odds of ever coming together by random, undirected process.
Jame Lunney is attacking evolutionary biologists and their acceptance of the scientific evidence for evolution, which happens to be their area of expertise. It seems ironic that he accuses others of bigotry and bullying.

James Lunney is a chiropractor and he has a B.Sc. (science). He says, "I have a background in Science: my credentials modest as they are, are superior on this file to many in this chamber and most of my critics."

That explains a lot.

Thursday, April 02, 2015

Poor James Lunney resigns from the Conservative Party because of bullying over his religious beliefs

Some of you may recall James Lunney, Conservative Party Member of Parliament for Nanaimo-Alberni in British Columbia. He's a chiropractor who spoke out against evolution back in 2009 [James Lunney: Creationist, Chiropractor, Conservative].

More recently, he defended another MP who didn't believe in evolution. He was mocked and ridiculed in the popular press and now he has decided to resign from the Conservative Party and sit in the House of Commons as an Independent. That's not working out so well according to CBC News [James Lunney defends views on evolution in House of Commons].
One day after he announced he was leaving the Conservative caucus to better defend his religious beliefs, Nanaimo-Alberni MP James Lunney attempted to do just that from his new seat in the corner of the House of Commons reserved for independent MPs.

But despite his best efforts, he was unable to convince House of Commons Speaker Andrew Scheer that the "cyberbullying" and "crowd-shaming" that he claimed to have experienced after questioning the science behind evolution constituted a breach of his parliamentary privilege.
Imagine that! He was unable to convince Parliament that making fun of his silly beliefs is wrong! This is exactly how the Canadian public SHOULD deal with people who act like kooks.

Wanna hear about his beliefs? This is what he said in Parliament ....
Speaking to CBC News Power & Politics host Evan Solomon on Wednesday evening, Lunney said that he was tired of seeing his faith community bullied.


Lunney described evolution — or, as he calls it, "macro-evolution" is "a theory in crisis."

"Scientists are not able to speak their mind on that — at least half of them who feel this way, they're gagged by an old construct," he argued.

"There's a whole generation of kids being taught that what they're taught in Sunday School or in church is garbage, it's wrong, it's false, and it's simply a form of bullying that's no longer acceptable. It's not scientifically tenable, it's a disservice to science… it's not freedom of religion if your views are put down by your peers."
Freedom comes in several forms. If you live in a free society then you have to be prepared to accept criticism of your most cherished beliefs. You can't hide behind religion to protect you when you act like an IDiot. Pointing out the stupidity of a Member of Parliament is not bullying

As far as I'm concerned, this is exactly how freedom should work.

On the "ethics" of germ line DNA editing

Edward Lanphier, Fyodor Urnov, Sarah Ehlen Haecker, Michael Werner and Joanna Smolenski have published a comment in Nature with a provocative headline "Don’t edit the human germ line. They are asking scientists to agree " not to modify the DNA of human reproductive cells." The idea is that editing the genome of sperm or egg cells produces changes that will be passed on to future generations and this poses certain dangers.

Wednesday, April 01, 2015

Physiologists fall for the Third Way

I looked forward to this "conversation" because I was already familiar with Denis Noble and his strange views of evolution [A physiologist thinks about evolution]. Noble reiterated his view of modern evolutionary theory at the meeting. He thinks that modern evolutionary theory (The Modern Synthesis or Neo-Darwinism) is all about random mutation and natural selection. He thinks it is based on the views of Richard Dawkins in The Selfish Gene. Neither he nor Michael Joyner (an anaethesiologist at the Mayo Clinic) have learned about random genetic drift or Neutral Theory and neither of them have much knowledge of population genetics. In other words, they are pretty ignorant about evolution even though they feel entitled to attack it.