Siddhartha Mukherjee tries to correct his book

There are lots of things wrong with Mukherjee's best-selling book The Gene. I've listed a few things that I know about [What is a "gene" and how do genes work according to Siddhartha Mukherjee?]. Others have come up with different problems.

The biggest problem is that Mukherjee misrepresents the current state of knowledge in genetics, biochemistry, and molecular biology. His misleads his readers by promoting silly viewpoints that conflict with the consensus view. He doesn't mention that there are other views that are well supported by tons of scientific evidence.

The best example is regulation of gene expression. He fails to explain the standard textbook understanding of transcriptional regulation by transcription factors—a view that's solidly backed by decades of work in biochemistry, developmental genetics, molecular biology, and genomics. Instead, he promotes a flaky epigenetic theory that, according to him, threatens to overthrow Darwinian evolution.

The seven biggest problems in science

Here's an interesting article about the biggest problems in (American) science: The 7 biggest problems facing science, according to 270 scientists. Most of them apply to science in other countries.

I've added brief comments under six of the headings. Those are MY opinions, not necessarily those of the authors. The comment under #6 is a direct quote from the article.

1. Academia has a huge money problem.
   There's not enough money to do high quality science, especially basic science.
2. Too many studies are poorly designed. Blame bad incentives.
   Some experiments are poorly designed. All scientists are under pressure to make their results seem important.
3. Replicating results is crucial. But scientists rarely do it.
   Replication is important—especially in medical studies—but I think this problem is exaggerated.
4. Peer review is broken.
   The system (peer review) isn't working well. That doesn't mean there's a better system.
5. Too much science is locked behind paywalls.
   This was never a problem in the past when you had to go to the library to read science journals. You could photocopy whatever you wanted. Now it's a problem because we want instant access from our laptops.
6. Science is poorly communicated to the public.
   "But not everyone blamed the media and publicists alone. Other respondents pointed out that scientists themselves often oversell their work, even if it's preliminary, because funding is competitive and everyone wants to portray their work as big and important and game-changing.
   
   'You have this toxic dynamic where journalists and scientists enable each other in a way that massively inflates the certainty and generality of how scientific findings are communicated and the promises that are made to the public,' writes Daniel Molden, an associate professor of psychology at Northwestern University. 'When these findings prove to be less certain and the promises are not realized, this just further erodes the respect that scientists get and further fuels scientists desire for appreciation.'"
7. Life as a young academic is incredibly stressful.
   This is not just a problem for my younger colleagues. It affects all of us. It affects morale in an academic department and it affects the way science is done.

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Science journal tries to fix problems with transparency and trustworthiness

The editors of Science recognize that they have a problem. They aren't very transparent or trustworthy. This is true. These same editors have been guilty of publishing and promoting lots of poor quality science over the past few years. Three examples come to mind ...

• Arseniclife: Science published a ridiculous claim that arsenic could replace phosphorus in DNA. That paper has been refuted but never retracted.
• Ardipithicus ramidus: Science fell for the authors' hype.
• ENCODE: Science falls for the hype promoted by ENCODE leaders. Editorial and feature writers announce the death of junk DNA

Don't worry. The editors have been working hard to fix the problem. After a year of study they announce their solution in the June 3, 2016 issue in the lead editorial: Taking up TOP. The author is the current Editor-in-Chief, Marcia McNutt.

She begins with ...

Nearly 1 year ago, a group of researchers boldly suggested that the standards for research quality, transparency, and trustworthiness could be improved if journals banded together to adopt eight standards called TOP (Transparency and Openness Promotion).* Since that time, more than 500 journals have been working toward their implementation of TOP. The editors at Science have held additional retreats and workshops to determine how best to adapt TOP to a general science journal and are now ready to announce our new standards, effective 1 January 2017.

So, what is TOP and how is it going to make Science more trustworthy? Does it involve firing some well-known writers and editors? Does it involve better reviewers?

Nope. TOP is just a way of making sure that raw data is available to other researchers.

... we believe the benefits of requiring the availability of data, code, and samples on which the authors' interpretations rest are worth the effort in compliance (and in some cases in adjusting data ownership expectations), while acknowledging that some special circumstances will require exemptions. This practice increases transparency, enables reproducibility, promotes data reuse, and is increasingly in line with funder mandates. We are also requiring the citation of all data, program code, and other methods not contained in the paper, using DOIs (digital object identifiers), journal citations, or other persistent identifiers, for the same reason. Citations reward those who originated the data, samples, or code and deposited them for reuse. Such a policy also allows accurate accounting for exactly which specific data, samples, or code were used in a given study.

That's not going to fix the main problem.

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Nature journal tries to fix the problem of a scientific literature that's too complex to understand

I recently posted some thoughts on the complexity of the scientific literature noting that many papers are simply too difficult to understand. This includes papers that are well within my areas of interest [How to read the scientific literature? and The scientific literature is becoming more complex].

Nature journal recognizes that there's a problem. A few weeks ago (June 16, 2016) they published a brief comment on Nature distilled.

They begin by describing the problem ...

Any journal that tries to publish the most important results that it is sent, in all fields of science, will run into the same problem. Every bit of our output, we hope, is useful and interesting to somebody somewhere. But even the most optimistic of our editors would concede that the pool of readership for each of these specific advances is only a small subsection of our audience, professional researchers included. To the outside world, science is science. To those who read Nature, science is a multiplicity of specialisms — and specialists.

We know that most of you are specialists, and that you don’t read most of what we present to you. You’re busy people. It is hard enough to follow the literature that you need to read. Even the titles of research papers in an unfamiliar field can look incomprehensible. But if you’re anything like us, one reason you got into science in the first place was curiosity about the world — and not just the tiny piece of it that you now focus on. Wouldn’t it be useful and interesting to keep better track of the rest? Or at least, the rest that is published in Nature, and therefore already judged to be important?

Let's make one thing clear. It's not just the complexity of a paper that's the problem and it's not just that the science isn't explained in easy to understand sentences. There's also the more serious problem of content. Sometimes the papers are hard to understand because the significance of the results is exaggerated and its importance is not placed in proper context.

The ENCODE papers are good examples of this problem. It wasn't easy to understand that they did but, more importantly, it wasn't easy to understand the significance of their results because the authors didn't explain their results very well. They made unsubstantiated claims.

Here's how Nature hopes to fix the problems they identified.

We think so, and this week we begin an experiment to see how many of you agree. We have revisited 15 recently published Nature papers and asked the authors to produce two-page summaries of each. The summaries remain technical — these are not articles suitable for the popular press — but they try to communicate both the research advance and why it matters. The authors of these papers have been enthusiastic — they want the broadest possible readership — and we thank them for their cooperation. Now we want to know what you think. The first three summaries are published online this week (see go.nature.com/1uhcy3x). The rest will be released in the coming weeks. Please take a look. Be brave — pick a topic that you expect to struggle with — and then fill in the online survey to let us know what you think. The rest will be released in the coming weeks. Please take a look. Be brave — pick a topic that you expect to struggle with — and then fill in the online survey to let us know what you think.

I looked at two papers that were about biology and I didn't think the summaries added anything to my understanding. That's partly because the papers weren't that hard to understand in the first place if you were just satisfied with knowing what they did.

Both papers raised lots of questions in my mind about the biological significance of the studies and whether they were accurate and reproducible. The author summaries didn't help much. [Non-coding recurrent mutations in chronic lymphocytic leukaemia and DNA-dependent formation of transcription factor pairs alters their binding specificity].

If the scientific literature is difficult to understand, and it is, then there's a problem with the authors. They aren't able to explain what they did in a reasonable manner and they aren't able to place their work in a proper context so we can evaluate the significance of the result. Asking them to try again (and doubling their citations) is probably not going to help.

The ENCODE authors couldn't do it.

It's a lot like asking the fox to guard the henhouse.

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How to read the scientific literature?

Science addressed the problem of How to (seriously) read a scientific paper by asking a group of Ph.D. students, post-docs, and scientists how they read the scientific literature. None of the answers will surprise you. The general theme is that you read the abstract to see if the work is relevant then skim the figures and the conclusions before buckling down to slog through the entire paper.

None of the respondents address the most serious problems such as trying to figure out what the researchers actually did while not having a clue how they did it. Nor do they address the serious issue of misleading conclusions and faulty logic.

I asked on Facebook whether we could teach undergraduates to read the primary scientific literature. I'm skeptical since I believe it takes a great deal of experience to be able to profitably read recent scientific papers and it takes a great deal of knowledge of fundamental concepts and principles. We know from experience that many professional scientists can be taken in by papers that are published in the scientific literature. Arseniclife is one example and the ENCODE papers published in September 2012 are another. If professional scientists can be fooled, how are we going to teach undergraduates to be skeptical?

Can scientists describe what they're doing to a fifth grader?

I'm working on a review of "The Gene" by Siddhartha Mukherjee. It raises a huge number of issues about science writing and the conflict between producing a bestseller and educating the public about science.

As part of the research for that blog post I've been reading all the reviews of his book and I came across an interview with Mukherjee on the Smithsonian website [Siddhartha Mukherjee Follows Up Biography of Cancer With “An Intimate History” of Genetics].

Here's an interesting answer to an important question ...

Evolution according to "New Scientist"

A recent editorial in the magazine New Scientist caught my eye. The title is "Long Live Evolution" and it offers support for "new ideas" about evolution. The online version is titled Darwin’s beautiful theory must itself be allowed to evolve. The author is not identified; I assume it's one of the editors.

Here's the opening paragraph ...
Nothing in evolution makes sense except in the light of population genetics.

Michael Lynch (2007)

Darwin's great theory must itself be allowed to evolve

THE theory of evolution is a splendid thing: an elegant and utterly logical explanation for how natural selection solves the problems of survival and creates the enormous diversity of life we see in the world around us.

There is no such thing as "THE" theory of evolution. Evolutionary theory is complex. It covers several mechanisms (natural selection, random genetic drift) and its core is population genetics—something that was unknown in Darwin's time.

We know that Darwin’s hypothesis of natural selection ... was correct, but we also know that there are more causes of evolution than Darwin realized ...

Douglas Futuyma (2009)
The New Scientists editor is describing the theory of natural selection but he/she even gets that wrong because most of life's diversity is probably NOT due to natural selection.

The irony here is that New Scientist then goes on to say ...

That brings to the fore areas that are not part of the canon of evolutionary theory: epigenetics, for example, which studies how organisms are affected by changes in the ways in which genes are expressed, rather than in the genes themselves.

Attempts to incorporate such elements into evolutionary theory have not always been welcomed, however. That is understandable, given how successful the theory has been without them. Occam’s razor applies: do not add complications unless they are absolutely necessary.

But another motivating factor is undoubtedly the fear that if scientists themselves are seen to suggest that even small details of the theory of evolution could be improved upon, its detractors will seize upon them with avidity. This is a well-founded fear: it happens all the time, with well-funded and highly visible front organisations distorting scientific discussion to create the false impression of disagreement about the basics of evolutionary theory.

It is a fear scientists need to overcome, lest the admirable defence of truth mutates into defensiveness and rigidity. It is one thing to counter reactionaries who reject evolution; it is quite another to be dismissive of or even hostile to scientists who have new ideas to offer.

I recommend that the editors of New Scientist purchase and read any introductory textbook on evolution before they write any more silly editorials. They will learn that "Darwin's great theory" has already been changed beyond anything that Darwin would have recognized. The fact that the editors of a prominent science magazine don't understand evolution is an example of one of the main problems that have led to so much confusion today over recent attempts to extend evolutionary theory.

If science journalists are going to write about whether epigenetics should be part of evolutionary theory then they better do their homework before criticizing prominent evolutionary biologists for being afraid of changing even "small details" of modern evolutionary theory. I suggest they start by reviewing some "small details" like Neutral Theory, random genetic drift, hierarchical theory, species selection, punctuated equilibria, sympatric speciation, group selection, directed mutation, cladistics, kin selection, selfish genes, endosymbiosis, and a host of other aspects of evolution that have been vigorously debated in the scientific literature over the past century.

Maybe after doing their homework they will realize that prominent evolutionary biologists who question epigenetics are not doing it because they fear change ... they're doing it because "epigenetics" has been debated for fifty years and it has little to do with modern evolutionary theory. Maybe the science journalists will realize that proponents of the "extended evolutionary synthesis" are as ignorant of modern evolutionary theory as they were before they did their homework.

The editorial ends with ...

Evolution is true. But it is also a living, breathing idea that must not be allowed to ossify into a dogma of the kind that it has done so much to sweep away.

Ironically, the most common "dogma" is the false idea that evolutionary theory hasn't changed since Darwin's time and the editor of New Scientist is a prime example of this kind of ossification.

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Research for a book

I'm on sabbatical this term, working on a possible book whose working title is "What's in Your Genome?: 90% of your genome is junk."

Here's some of the most important books I've read (or re-read) in the past few months.

I've also read a lot of papers and scribbled notes on what's important and what's bullshit not. The most difficult part about keeping up with the scientific literature is organizing it in some meaningful way so you can quickly find it again if you need to—something I do just about every day.

Everyone has their own method. What works for me is to keep an electronic reference with key words and links to a file folder on a particular topic. (I use EndNote.) Here are the folders with all the papers I've been reading in the past few months.

I don't know how other authors behave but for me the most difficult thing about writing a book is organizing my thoughts and planning how to present them in the most effective manner. I tend to write too much on too many topics so the initial drafts usually have to be pared down considerably. Keeping that in mind, what are YOUR favorite topics?

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John Oliver teaches us to be skeptical of scientific publications

We all know that the purpose of education should be to teach students how to think critically. We're not doing a very good job. Take biochemistry, for example. We spend a lot of time transferring information from lecture notes to student notes and then examining students on whether the transfer has worked. We think that teaching students to read the primary literature will make them better scientists when, in fact, teaching them to be skeptical of the primary literature is what's really necessary.

The ENCODE fiasco is just one of many examples where the scientific literature got it wrong. We need to make sure that our students appreciate the important parts of science; namely, the necessity of repeating experiments and the value of scientific consensus. Our students, and many of my colleagues, are prone to hype and promotion just like every one else but that's exactly what critical thinking is supposed to avoid. And it's exactly what proper science—no matter how you define it—is designed to overcome.

If students and scientists are having trouble with these concepts, imagine how difficult it is for the general public. How are they supposed to know that not every "breakthrough" is a real breakthrough and not every new study is correct?

John Oliver did an excellent job of explaining the problem on a recent (May 8, 2016) episode of Last Week Tonight. Watch it. It's worth 20 minutes of your time. The last bit on "Todd Talks" is classic.

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Another failure: "The Mysterious World of the Human Genome"

The Mysterious World of the Human Genome
by Frank Ryan
William Collins, an imprint of Harper Collins, London UK (2015)
ISBN 978-0-00-754906-1

This is just another "gosh, gee whiz" book on the amazing and revolutionary (not!) discoveries about the human genome. The title tells you what to expect: The Mysterious World of the Human Genome.

The author is Frank P. Ryan, a physician who was employed as an "Honorary Senior Lecturer" in the Department of Medical Education at the University of Sheffield (UK). He's a member of The Third Way group. You can read more about him at their website: Frank P. Ryan.

Nelson Lau responds to my criticism of his comments about junk DNA

I criticized Nelson Lau for comments he made about the junk DNA debate [Brandeis professor demonstrates his ignorance about junk DNA].

Here is his response,

Dear Dr. Graur and Dr. Moran,

Thanks for reading the commentary on my university’s communication page, hastily written for brevity and digestibility by me and our science communication officer, Lawrence Goodman. I was originally hoping the piece could focus on my latest research, but it turned into this sort of general Q&A chat. The commentary was written rather quickly and meant for a general audience perusing Brandeis research, so it is obviously not a peer-reviewed scientific publication.

I am well aware of both your reputations as fiery critics and experts of evolutionary biology, and you have somewhat of a following on the internet. Some of your earlier blog posts have been entertaining and even on point regarding how big projects like ENCODE have over-hyped the functional proportions of our genomes. So, it does NOT surprise me one bit that I would become your latest vitriolic target in your posts here, and here.

Could I learn more from you two about evolutionary biology theory? Indeed, I could. Can we revise our Q&A commentary to be more scientifically accurate while still being digestible to a general audience? Perhaps, if we have the time and I survive my tenure review, we may do so and take your input into consideration. Why respond and risk another snarky post from you guys? I could care less about your trivial blog critiques when I’ve received plenty of grants and paper rejections that cut much deeper into my existence as a young academic struggling to survive when the academic track has never been more challenging (<10% grant success rates at NIH, NSF, CIHR, etc).

I’m responding to ask that both of you reflect on the message your posts are sending to students and postdocs. As a young scientist, having a chat with my university PR rep, I have to now think twice about two senior tenured professors slamming my scientific credibility on your internet soapbox without a single direct email to me. How passive-aggressive!

Your message is saying that Academic science even less inviting to young scientists as it is, with faculty positions and grants falling way short of demand, and the tough sacrifices every young scientist is already making for the craft that we love. If we condone this type of sniping behavior, why would any young scientist want to learn and discuss with the older scientists of your generation?

The Science Blogosphere, Twittersphere, and the Open Data movements are the next generation of platforms for science communication, and I commend you two for being vocal contributors to these platforms quite early on. However, I also recently wrote a guest post on Bjorn Bremb’s blog arguing that for open data and discussion to work, we scientists need to uphold decorum and civility.

A direct email from you to me expressing your scientific concerns of our commentary would have been a better way to go. I am willing to stand corrected. Your blog posts, however, are disappointing and appear petty to me. Let’s all set a better example here for our trainees.

If you wish to post this response verbatim on your blogs, go ahead, since I had thought of posting this response on your blog’s comments section. But to follow my own advice, I’ll try a direct email to you first. And if I don’t hear back from you, I may then ask my friend Bjorn to help me post this on his blog.

Thank you for reading this till the end,

Nelson

Nelson Lau, Ph.D.
Assistant Professor - Biology

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Brandeis professor demonstrates his ignorance about junk DNA

Judge Starling (Dan Graur) has alerted me to yet another young biologist who hasn't bothered to study the subject of genomes and junk DNA [An Ignorant Assistant Professor at @BrandeisU Explains “Junk DNA”].

This time it's Assistant Professor of Biology Nelson Lau. He studies Piwi proteins and PiRNAs.

Lau was interviewed by Lawrence Goodman, a science communication officer at Brandeis University: DNA dumpster diving. The subject is junk DNA and you will be astonished at how ignorant Nelson Lau is about a subject that's supposed to be important in his work.

How does this happen? Aren't scientists supposed to be up-to-date on the scientific literature before they pass themselves off as experts? How can an Assistant Professor make such blatantly false and misleading statements about his own area of research expertise? Has he never encountered graduate students, post-docs, or mentors who would have corrected his misconceptions?

Here's the introduction to the interview,

Since the 1960s, it's largely been assumed that most of the DNA in the human genome was junk. It didn't encode proteins -- the main activity of our genes-- so it was assumed to serve no purpose. But Assistant Professor of Biology Nelson Lau is among a new generation of scientists questioning that hypothesis. His findings suggest we've been wrong about junk DNA and it may be time for a reappraisal. If we want to understand how our bodies work, we need to start picking through our genetic garbage.

BrandeisNow sat down with Lau to ask him about his research.

There's nothing wrong with being a "new generation" who questions the wisdom of their elders. That's what all scientists are supposed to do.

But there are certain standards that apply. The most important standard is that when you are challenging other experts you'd better be an expert yourself.

First off, what is junk DNA?
About two percent of our genome carries out functions we know about, things like building our bones or keeping the heart beating. What the rest of our DNA does is still a mystery. Twenty years ago, for want of a better term, some scientists decided to call it junk DNA.

Dan has already addressed this response but let me throw in my own two cents.

There was never, ever, a time when knowledgeable scientists said that all 98% of the DNA that wasn't part of a gene was junk. Not today, not twenty years ago (1996), and not 45 years ago.

There has never been at time since the 1960s when all non-gene DNA was a mystery. It certainly isn't a mystery today. If you don't know this then you better do some reading ... quickly. Google could be your friend, Prof. Lau, it will save you from further embarrassment. Search on "junk DNA" and read everything ... not just the entries that you agree with.

I added a bunch of links at the bottom of this post to help you out.

Is it really junk?
There’s two camps in the scientific community, one that believes it doesn’t do anything and another that believes it’s there for a purpose.

And you’re in the second camp?
Yes. It's true that sometimes organisms carry around excess DNA, but usually it is there for a purpose. Perhaps junk DNA has been coopted for a deeper purpose that we have yet to fully unravel.

It is possible that the extra DNA in our genome has an unknown deeper purpose but right now we have more than enough information to be confident that it's junk. You have to refute or discredit all the work that's been done in the past 40 years in order to be in the second camp.

I strongly suspect that Prof. Lau has not done his homework and he doesn't know the Five Things You Should Know if You Want to Participate in the Junk DNA Debate.

What possible "deep purpose" could this DNA have?

Maybe when junk DNA moves to the right place in our DNA, this could cause better or faster evolution. Maybe when junk genes interacts with the non-junk ones, it causes a mutation to occur so humans can better adapt to changes in the environment.

Most of the undergraduates who took my course could easily refute that argument. I'm guessing that undergraduates in biology at Brandeis aren't as smart. Or maybe they're just too complacent to challenge a professor?

We've got a serious problem here folks. There are scientists being hired at respectable universities who aren't keeping up with the scientific literature in their own field. How does this happen? Are there newly hired biology professors who don't understand evolution?

Eddy, S.R. (2012) The C-value paradox, junk DNA and ENCODE. Current Biology, 22:R898. [doi: 10.1016/j.cub.2012.10.002]

Niu, D. K., and Jiang, L. (2012) Can ENCODE tell us how much junk DNA we carry in our genome?. Biochemical and biophysical research communications 430:1340-1343. [doi: 10.1016/j.bbrc.2012.12.074]

Doolittle, W.F. (2013) Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. (USA) published online March 11, 2013. [PubMed] [doi: 10.1073/pnas.1221376110]

Graur, D., Zheng, Y., Price, N., Azevedo, R. B., Zufall, R. A., and Elhaik, E. (2013) On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution published online: February 20, 2013 [doi: 10.1093/gbe/evt028

Eddy, S.R. (2013) The ENCODE project: missteps overshadowing a success. Current Biology, 23:R259-R261. [10.1016/j.cub.2013.03.023]

Hurst, L.D. (2013) Open questions: A logic (or lack thereof) of genome organization. BMC biology, 11:58. [doi:10.1186/1741-7007-11-58]

Kellis, M., Wold, B., Snyder, M.P., Bernstein, B.E., Kundaje, A., Marinov, G.K., Ward, L.D., Birney, E., Crawford, G. E., and Dekker, J. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. (USA) 111:6131-6138. [doi: 10.1073/pnas.1318948111]

Morange, M. (2014) Genome as a Multipurpose Structure Built by Evolution. Perspectives in biology and medicine, 57:162-171. [doi: 10.1353/pbm.2014.000]

Palazzo, A.F., and Gregory, T.R. (2014) The Case for Junk DNA. PLoS Genetics, 10:e1004351. [doi: 10.1371/journal.pgen.1004351]

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Joe Hanson tells us about evolution

Joe Hanson Ph.D. (Biology) of It's Okay To Be Smart is posting a series of videos on evolution. They're called The 12 Days of Evolution.

The first one is "What Is Evolution Anyway?" You won't surprised to learn that Joe Hanson conflates "evolution" with "natural selection" and fails to mention the most important features of evolution [see What Is Evolution]. You WILL be surprised to learn that Jerry Coyne has the same objections I do! [Twelve Days of Evolution: #1: What’s evolution?]

We need to do a much better job of educating the general public about the meaning of evolution but first we need to educate the teachers. It's okay to be smart but it's not okay to just pretend to be smart.

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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.

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

Who's to blame for bad science communication?

Most of us agree that there's a problem. A lot of what passes as science isn't being correctly communicated to the general public.

Lot's of people share the blame but I tend to focus on those people whose job is science communication. It must be true that science journalists aren't doing as good a job as they should.

A few years ago I attended a meeting on "The Two Cultures" in New York City. E.O. Wilson gave the plenary talk and he explained why everyone likes scenery that resembles the African savannah. It's because that's where humans originated [E.O. Wilson in New York]. The science journalists who were there applauded enthusiastically. I didn't.

Later on there was a session on science communication featuring a panel of science journalists. They insisted that the problems were not their fault. They can only rely on what scientists are telling them and that's what they report. Elizabeth Pennisi would be proud.

Carl Zimmer pointed out that it is important for science journalists to have a good source of scientists they can call on for advice whenever they are working on a new story. The other journalists didn't get it.

Richard Lenksi wonders who's to blame and he has created a poll [Science Communication: Where Does the Problem Lie?]. Go and vote.

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The null hypothesis of Darwinian evolution, again

I've read the paper by Schopf et al. (2015). Here's the entire section on Darwinian evolution.

How could the seemingly identical sulfur-cycling anoxic sediment-inhabiting biotas of the ∼1.8-Ga Duck Creek and ∼2.3-Ga Turee Creek cherts, like those of Proterozoic stromatolitic cyanobacteria (6, 8), have evidently remained fundamentally unchanged over billions of years?

We suggest differing answers for these two early-evolved hypobradytelic lifestyles:

i) For cyanobacteria, the answer evidently lies in a genetically encoded ecological flexibility derived from their early adaptation to geologically exceedingly slow changes of the photiczone environment (e.g., of solar luminosity, UV flux, day length, and CO₂, O₂, and usable sulfur and nitrogen). Because of their large population sizes, global dispersal by ocean currents and hurricanes, and capability to generate oxygen toxic to anaerobic competitors for photosynthetic space, these ecologic generalists adapted to and survived in a wide range of habitats (6).

ii) Once subseafloor sulfur-cycling microbial communities had become established, however, there appears to have been little or no stimulus for them to adapt to changing conditions. In their morphology and community structure, such colorless sulfur bacteria—inhabitants of relatively cold physically quiescent anoxic sediments devoid of light-derived diel signals and a setting that has persisted since early in Earth history—have exhibited an exceedingly long-term lack of discernable change consistent with their asexual reproduction (6).

Given these observations, it might be tempting to interpret such sulfur-cycling communities as evidencing the “negative” null hypothesis of Darwinian evolution—if there is no change in the physical biological environment of a well-adapted ecosystem, there should be no speciation, no evolution of the form, function, or metabolic requirements of its biotic components—a confirmation of Darwin’s theory that seems likely to be provided only by ecosystems fossilized in an environment that has remained essentially unaltered over many hundreds of millions of years.

Although logically required, this aspect of evolutionary theory has yet to be established.

Nature criticizes science hyperbole and bad science writing

There's a very interesting editorial in the Oct 14, 2014 issues of Nature [see here]. It's about a scientific paper that turned out to be misleading and the role of science writers and journals in promoting that story.

The editors of Nature remind us that ...

Extraordinary claims, as the saying almost goes, demand more scrutiny than usual to make sure they stand up. That is how science works. Claim and counter-claim: intellectual thrust and experimental parry.

They report on an upcoming meeting meeting of the Council for the Advancement of Science Writing in Columbus Ohio. Apparently, this council is composed of scientists and journalists and the goal of the meeting is to search for "lessons learned by scientists and science writers" in light of their publicity campaign promoting the flawed paper.

The Nature editors note that ...

The first thing to highlight is that such a thing as the Council for the Advancement of Science Writing even exists. Too many scientists dismiss the media and journalists as sloppy and unwilling to engage in both detail and ambiguity. In fact, there can be no branch of journalism as self-scrutinizing and anxious about its performance as that which covers science. It is hard to imagine political and sports reporters taking the time to discuss so thoroughly what (if anything) they did wrong after one of their stories went belly-up.

Indeed, that's admirable, but it's another example of journalistic hyperbole. I do not believe that this branch of journalism (science writing) is as "self-scrutinizing" as they would have us believe. I do not believe that science writers usually debate and discuss what they did wrong when a story goes belly-up.

But it may be true that science writers are increasingly "anxious" about their performance. Why are they so "anxious"? It's because they are doing a very sloppy job characterized by parroting press releases written by amateurs whose main goal is to promote their institution or by science journals that want publicity.

Science writers (and journals) used to get away with this but now ...

The (welcome) rise of the science blogger has fuelled this navel-gazing. Some bloggers seem to spend most of their time criticizing other science writers, or at least debunking examples of what they regard as inferior science writing. But they do lots of good stuff too. Although traditionalists lament the decline of science coverage in the mainstream press, a terrific amount of analysis and comment, much of it very technical, is happening online under their noses.

There's an interesting slip of the tongue in that paragraph. If science writers are really interested in self-scrutiny then they should welcome the arrival of a group of bloggers who point out their errors. This should be a "good" thing but the Nature editors clearly contrast this role (criticizing science writers) with other "good stuff" that bloggers do. Apparently the criticism of science writing doesn't count as "good stuff." It just makes science writers anxious—which they weren't before science bloggers came on the scene and pointed out what a bad job they were doing.

Nature then admits its complicity in hyping the event and not doing a proper skeptical analysis of the findings. The editors then get to an important issue.

Some may question the timing of the announcement, made when the paper was released on the Internet, not accepted or published by a journal, but at least the evidence was there to examine. If the scientists and the media both largely acted properly, then what should be discussed at next week’s meeting? It could do worse than start by screening the celebratory online video produced by ... and released to accompany the announcement. Scientists and journalists can include as many academic caveats as they like, but the sounds and images of champagne corks popping tend to render such statements of caution just that — academic.

There is a deeper issue here: science not by press conference but presented as an event. What in reality is a long, messy and convoluted process of three steps forward and two steps back is too easily presented as giant leaps between states of confusion and blinding revelation. At the heart of this theatre is the artificial landmark of a peer-reviewed paper. Fixed print schedules and releases to journalists under embargo (with or without champagne videos) help to lend the impression that the publication of a paper is the final word on a question — the end-of-term report on a scientific project that details all that was achieved.

I bet you're thinking that this is all about the ENCODE publicity campaign and how Nature was totally at fault for misrepresenting the data and hyping the false claims of the ENCODE Consortium.

Nope. It's about the discovery of gravitational waves—a paper that turns out to have been wrong because scientists didn't do the proper controls.

Meanwhile, Nature, and science writers in general, have yet to admit that they failed massively in September 2012 and they have done little to convince us "bad" bloggers that they are capable of self-scrutiny. This is serious because in this case Nature and its editors were very active participants in the making of videos and holding press releases [see How does Nature deal with the ENCODE publicity hype that it created?]. Let me remind you of the video PRODUCED BY NATURE featuring Senior Editor Magdalena Skipper in which she promotes the idea that most of the human genome is functional. [Note: I'm getting error messages when I try to run this video.]


Maybe there are other things that the Council for the Advancement of Science Writing could be talking about? Maybe there are other examples of bad science journalism that the editors of Nature should be addressing?

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On choosing a new university president

At many (most?) universities in North America the selection of a new President is a very secret affair. Students and faculty are not consulted during the process and the candidates are not known. In fact, the process is so secret that the search committee can't even ask for outside advice about the candidates because that would reveal that they have applied for the job.

This is a very dangerous way to hire a university President because there's a great danger that the members of the search committee will, out of ignorance, choose someone that the university community doesn't respect. I've seen it happen at my own university and it happened at the University of Saskatchewan leading to the President being dismissed [The Board of Governors at the University of Saskatchewan fires President Ilene Busch-Vishniac].

Fortunately, Florida State University doesn't operate like that. The leading candidates for the job of President were vetted at an open forum with students and faculty members. One of the leading candidates was Republican State Senator, John Thrasher. One of the things that students and faculty learned was that Thrasher doesn't believe in evolution and doesn't believe that humans are responsible for climate change [A Creationist May Become Florida State University’s Next President].

As you might imagine, the students and faculty were opposed to hiring him as President. That didn't seem to matter to the Board of Governors who voted 12-1 to hire John Thrasher [A Creationist Just Became Florida State University’s New President] [Thrasher is choice for FSU, despite loud opposition].

From the Tallahassee Democrat ...

Storbeck/Pimentel, the search firm helping FSU select its next leader, conducted surveys following each candidate's campus forums last week. Thrasher received favorable ratings from only 11 percent of the responders, while 87 percent said he was not fit to be FSU's president. By comparison, the other three candidates had favorable scores between 78 and 91 percent.

The FSU Faculty Senate, which represents all 16 colleges at the university, passed a unanimous resolution Friday calling for the trustees to hire one of the three academics among the four finalists.

"We deserve a president who plays on the national stage, one who walks the walk, one who won't put off potential donors in the other party," Michael Buchler, a music professor and faculty senator, said during the public comment period. "FSU has never hired a president who didn't have experience in the classroom."

Apparently the Board of Governors don't care what the students and faculty think. What could possibly go wrong?

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The filter problem

Drugmonkey (@drugmonkeyblog) doesn't think there's a filter problem [There is no "filter problem" in science].

He writes,

Seriously.

It is your job as a scientist to read the literature, keep abreast of findings of interest and integrate this knowledge with your own work.

We have amazing tools for doing so that were not available in times past, everything gets fantastically better all the time.

If you are a PI you even have minions to help you! And colleagues! And manuscripts and grants to review which catch you up.

So I ask you, people who spout off about the "filter" problem.....

What IS the nature of this problem? How does it affect your working day?

I'm trying to keep up with a number of very broad and diverse fields. For example, as a textbook author, I need to keep abreast of just about everything that might be covered in an introductory biochemistry course. I'm also trying to keep informed about evolutionary biology; especially molecular evolution because I teach a course on that topic and I blog about it. I don't want to miss exciting developments in pedagogy (teaching) and the philosophy of science. Finally, I like to be up-to-date on the latest advances in other disciplines.

Here's the problem. There's a lot of junk out there. It's a waste of time to scan all of the science journals that might possibly have something of interest to me and it's a waste of time to get any "tools" to do it for me. Most of the time I wouldn't even know what to ask for. For example, I don't want to see all the papers on photosynthesis but I need to see the one that's going to change my textbook. I don't want to see all the papers on mutation rates but I do want to see the ones that are worth blogging about.

There were times when I could sit down for a few hours every week and scan the tables of contents of the leading journals in my field. Those days are long gone and my "field" has expanded enormously. I need to filter but I'm pretty sure I'm missing some important papers. In fact, I know this because just about every month I hear from others about things that I've missed months, or even years, ago.

I have a filter problem. I'm filtering out some important things and reading far too much junk. My filter problem can't be solved. If it wasn't for blogs, I'd be in bigger trouble.

We're in the middle of a discussion about the function wars. It's obvious to me that members of the ENCODE Consortium also have a filter problem. They've filtered out all kinds of information about the organization of the human genome. They don't understand the evidence for junk DNA, for example, and they don't have a good grasp of evolution. On the other hand, they've probably read every recent paper on the methodology of RNA-Seq, ChIP, and data analysis algorithms.

I'm glad that drugmonkey doesn't have a filter problem. Or, should I say, I'm glad that he THINKS he doesn't have a filter problem. It must be comforting to believe that he's keeping abreast of everything relating to his interests. I've never felt like that.

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How does Nature deal with the ENCODE publicity hype that it created?

Let's briefly review what happened in September 2012 when the ENCODE Consortium published their results (mostly in Nature).

Here's the abstract of the original paper published in Nature in September 2012 (Birney et al. 2012). Manolis Kellis (see below) is listed as a principle investigator and member of the steering committee.

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

Most people reading this picked up on the idea that 80% of the genome had a function.