Popular science books aren't fact-checked

Michael Marshall is a science journalist. He published a short essay in New Scientist where he laments the fact that popular science books may contain lots of errors. The title of the original article was Getting the facts right but the online version is Readers deserve beter from popular science books. The blurb is the same for both versions.

"There is a dirty secret in publishing: most popular science books aren't fact-checked. This needs to change, says Michael Marshall."

Most of you won't be able to read the article because it's behind a paywall but here's a few paragraphs that should stimulate discussion.

No, the problem is much simpler, and it is a dirty secret of non-fiction publishing: most books aren’t fact-checked. If an author makes a mistake or misinterprets a study, nobody stops them.

In journalism, fact-checking practices vary widely. New Scientist has two layers of editors, who each ensure readability and accuracy. Others are even stricter: fact-checkers at The New Yorker re-report entire stories. Non-fiction publishing is far more relaxed. Often, there is no fact-checking at all: editors offer guidance on readability, but take factual claims on trust. The UK publishers of my book The Genesis Quest did this (though my US publishers, a university press, recruited anonymous peer reviewers).

It is easy to see why this has happened. Nuance is difficult to sell. If your book has a counterintuitive thesis, or simply promotes a moral panic, it is easier to market. Non-fiction authors who are rigorous and careful can’t compete. That’s why shops are flooded with books about one neat trick for a better life or how everything you know is wrong. But without fact-checking, these books might as well be scrawled in crayon. Publishers must do better.

For the record, my book was sent out to reviewers and I got back some very helpful comments that caused me to make some serious changes. I also sent it to some of my colleagues and they corrected quite a few errors.

The last part of Marshall's essay is something that I've been worried about for many years, "Non-fiction authors who are rigorous and careful can’t compete."

Note: I inserted an image of Philip Ball's latest book because it's a recently published popular science book. I have no idea whether it was fact-checked or not. (But I have my suspicions.)

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Science journal tries to understand misinformation

The November 1, 2024 issue of Science contains three articles on misinformation in science. The articles tend to concentrate on the standard examples such as vaccine misinformation but there's another kind of misinformation that's just as important. I'm talking about scientific misinformation that's spread by journals like Science and Nature.

Do any of you remember the arsenic affair? That's when science accepted a paper by Felisa Wolfe-Simon and her collaborators claiming that they isolated a bacterium that substituted arsenic for phosphorus in its DNA. The paper was published online and was severely criticized after a ridiculous NASA press conference. It was eventually refuted when Rosie Redfield and others looked closely at the bacterial DNA and showed that it did not contain arsenic. The paper has still not been retracted. [See Reviewing the "Arseniclife" Paper.]

And let's not forget the massive misinformation campaign associated with the publication of ENCODE results in 2012.

Some transcription factors can be both activators and repressors! Textbooks have been saying this for decades

This is another post about a bad press release based on a lack of knowledge of the history of the field.

Here's the press release from Washington State University as reported in SciTechDaily

Scientists Discover “Spatial Grammar” in DNA: Breakthrough Could Rewrite Genetics Textbooks

“Contrary to what you will find in textbooks, transcription factors that act as true activators or repressors are surprisingly rare,” said WSU assistant professor Sascha Duttke, who led much of the research at WSU’s School of Molecular Biosciences in the College of Veterinary Medicine.

Rather, the scientists found that most activators can also function as repressors.

“If you remove an activator, your hypothesis is you lose activation,” said Bayley McDonald, a WSU graduate student who was part of the research team. “But that was true in only 50% to 60% of the cases, so we knew something was off.”

Looking closer, researchers found the function of many transcription factors was highly position-dependent.

They discovered that the spacing between transcription factors and their position relative to where a gene’s transcription began determined the level of gene activity. For example, transcription factors might activate gene expression when positioned upstream or ahead of where a gene’s transcription begins but inhibit its activity when located downstream, or after a gene’s transcription start site.

... By integrating this newly discovered ‘spatial grammar,’ Christopher Benner, associate professor at UC San Diego, anticipates scientists can gain a deeper understanding of how mutations or genetic variations can affect gene expression and contribute to disease.

”The potential applications are vast,” Benner said. “At the very least, it will change the way scientists study gene expression.”

"Cancer Virus Hunters" by Gregory J. Morgan

That seven Nobel Prizes were awarded directly or indirectly for work in tumor virology illustrates the impact of the field on biomedical understanding. (p. 273)

We've entered a new era in the field of molecular biology. Almost all of the emphasis and excitement these days is based on studies of mammals, especially humans. Most of the big bucks are for studying some aspect of medicine so that even if you are interested in basic science you have to slant it toward curing some disease.

Anti-science New York Times doubles down on the lab leak conspiracy theory

On June 3, 2024,the New York Times published an opinion piece by Alina Chan in which she promoted the lab leak conspiracy theory about the origin of COVID-19. Her views are not shared by the scientific community and the newspaper was criticized by many who pointed out the many flaws in Chan's arguments and her lack of objectivity.¹

I suspect that some people at the NYT might have been somewhat embarrassed by the response to their reckless behavior so they prepared a response. It was written by David Leonhardt who identifies himself as "a senior writer at the New York Times who runs "The Morning", our flagship daily newsletter." He published his article on the website that he runs and the title sounds like it might be an objective appraisal of the evidence in favor of a natural origin of COVID-19 originating in the Wuhan market: Two Covid Theories.

Don't be fooled by the title. Leonhardt makes no attempt to summarize the massive amount of evidence in favor of a natural origin. Instead, he treats the scientific view and the lab leak conspiracy theory as equally probable.

Do you find both explanations plausible? I do.

As I’ve followed this debate over the past few years, I have gone back and forth about which is more likely. Today, I’m close to 50-50. I have heard similar sentiments from some experts.

“No one has proof,” Julian Barnes, who covers intelligence agencies for The Times, told me. “Everyone is using logic.” Julian’s advice to the rest of us: “Be wary, keep an open mind, rule nothing out.”

Let's be clear about what's necessary in order for the lab leak conspiracy theory to be probable.

1. There has to be evidence that SARS-CoV-2 was present in the Wuhan Institute of Virology (WIV) before the pandemic started. There is none.
2. The graduate students, post-docs, scientists, and research technicians at WIV all deny that they were working with SARS-CoV-2 or any closely-related virus before the pandemic started. In order for the lab leak conspiracy theory to be true they must be lying and engaging in a massive coverup. This is totally inconsistent with their behavior over the past two decades. (The woman in the photo is Shi Zhengli, an internationally renowned scientist who Alina Chan accuses of lying—a claim that David Leonhardt thinks is quite possible.)

The latest opinion piece looks to me like an attempt to defend the NYT against accusations that it is anti-science. You would think that in such a defense, the author would be able to present good scientific evidence for the lab leak conspiracy theory, right? Here's the three arguments advanced by David Leonhardt in support of this massive conspiracy.

1. COVID-19 was first detected near the market in Wuhan and the Wuhan Virolgy Institute is in Wuhan.
2. Leaks happen.
3. China controls the evidence (i.e. conspiracy).

I think we are fully justified in claiming that the NYT is anti-science. I think the newspaper owes the scientific community an apology for ignoring the evidence of a natural origin and disparaging the reputations of reputable scientists who reject the lab leak conspiracy theory in favor of a natural origin.

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1. [The New York Times promotes the lab leak conspiracy theory] [Real scientists destroy the Alina Chan lab leak conspiracy theory] [The New York Times goes all in on “lab leak”] [No, gain of function research did not cause COVID-19]

Publishing a science book - Lesson #1: The publisher is always right about everything

Don't bother trying to reason with a publisher. All of them have different views on proper style and every single one of them is absolutely certain that their style is the only correct one.

I'm in the middle of the copyedit stage of my book. This is the stage where a copyeditor goes through your manuscript and makes any corrections to spelling and grammar. This is a lot of work for any copyeditor having to deal with one of my manuscripts and I greatly appreciate the effort. My book is a lot better now than it was a few weeks ago. (Who knew that there was only one l in canceled?)

It's also the stage where the publisher imposes their particular style on the manusript and that can be a problem. I'll document some of the issues in subsequent posts but to give you an example, consider the titles of books in the reference list. I wrote it like this: The Selfish Gene and Molecular and Genome Evolution. This is not in line with my publisher's handbook of style so the titles were converted to lowercase as in: The selfish gene and Molecular and genome evolution. I objected, pointing to numerous other science books that used the same titles that are on the covers of the books and suggesting that my readers were more familiar with The Selfish Gene than with The selfish gene.

I was overruled by my publisher who noted that they make their style choices for good reasons—it's for "consistency, clarity, and ease of reading." I assume that publishers, such as Oxford, would make the same argument while insisting that the title should be The Selfish Gene.

In case you ever find yourself in this position, you should keep in mind that your contract will almost certainly say that the publisher has complete control of your book and they can make any changes they want as long as it doesn't affect the meaning of what you wrote.

Here's what it says in my contract, "The Publisher shall publish the Author's work in whatever style and format it thinks most suitable ... While the Publisher may, in its sole discretion, consult the Author with respect to said style and format, the Publisher retains the right to make all final decisions on matters of format, design, selling price and marketing."

I was aware of some issues with inappropriate covers and tiles in the past so I had an extra sentence added to the contract that said, "The Publisher and Author will discuss and agree upon the title and cover design." It's a good thing I put that in because the publisher was pressuring me to change the title of the book and I was able to resist.

Authors can't win most fights over style and format. I've been discussing the publishing of science books with a number of other authors over the past few months and several of them told me not to bother trying to argue with a publisher because they will never give in. They have a set style for all books and they won't make an exception for an individual author no matter how good an argument you make.

I didn't listen to those other authors. Silly me.

I'm thinking of trying to write a standard set of guidelines that scientists could put into their contracts to cover the most egregious style restrictions. It might be helpful if all science writers would insist on inserting these guidelines into their contracts.

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University press releases are a major source of science misinformation

Here's an example of a press release that distorts science by promoting incorrect information that is not found in the actual publication.

The problems with press releases are well-known but nobody is doing anything about it. I really like the discussion in Stuart Ritchie's recent (2020) book where he begins with the famous "arsenic affair" in 2010. Sandwalk readers will recall that this started with a press conference by NASA announcing that arsenic replaces phosphorus in the DNA of some bacteria. The announcement was treated with contempt by the blogosphere and eventually the claim was discproved by Rosie Redfield who showed that the experiment was flawed [The Arsenic Affair: No Arsenic in DNA!].

This was a case where the science was wrong and NASA should have known before it called a press conference. Ritchie goes on to document many cases where press releases have distorted the science in the actual publication. He doesn't mention the most egregious example, the ENCODE publicity campaign that successfully convinced most scientists that junk DNA was dead [The 10th anniversary of the ENCODE publicity campaign fiasco].

I like what he says about "churnalism" ...

In an age of 'churnalism', where time-pressed journalists often simply repeat the content of press releases in their articles (science news reports are often worded vitrually identically to a press release), scientists have a great deal of power—and a great deal of responsibility. The constraints of peer review, lax as they might be, aren't present at all when engaging with the media, and scientists' biases about the importance of their results can emerge unchecked. Frustratingly, once the hype bubble has been inflated by a press release, it's difficult to burst.

Press releases of all sorts are failing us but university press releases are the most disappointing because we expect universities to be credible sources of information. It's obvious that scientists have to accept the blame for deliberately distorting their findings but surely the information offices at universities are also at fault? I once suggested that every press release has to include a statement, signed by the scientists, saying that the press release accurately reports the results and conclusions that are in the published article and does not contain any additional information or speculation that has not passed peer review.

Let's look at a recent example where the scientists would not have been able to truthfully sign such a statement.

A group of scientists based largely at The University of Sheffield in Sheffield (UK) recently published a paper in Nature on DNA damage in the human genome. They noted that such damage occurs preferentially at promoters and enhancers and is associated with demethylation and transcription activation. They presented evidence that the genome can be partially protected by a protein called "NuMA." I'll show you the abstract below but for now that's all you need to know.

The University of Sheffield decided to promote itself by issuing a press release: Breaks in ‘junk’ DNA give scientists new insight into neurological disorders. This title is a bit of a surprise since the paper only talks about breaks in enhancers and promoters and the word "junk" doesn't appear anywhere in the published report in Nature.

The first paragraph of the press release isn' very helpful.

‘Junk’ DNA could unlock new treatments for neurological disorders as scientists discover how its breaks and repairs affect our protection against neurological disease.

What could this mean? Surely they don't mean to imply that enhancers and promoters are "junk DNA"? That would be really, really, stupid. The rest of the press release should explain what they mean.

The groundbreaking research from the University of Sheffield’s Neuroscience Institute and Healthy Lifespan Institute gives important new insights into so-called junk DNA—or DNA previously thought to be non-essential to the coding of our genome—and how it impacts on neurological disorders such as Motor Neurone Disease (MND) and Alzheimer’s.

Until now, the body’s repair of junk DNA, which can make up 98 per cent of DNA, has been largely overlooked by scientists, but the new study published in Nature found it is much more vulnerable to breaks from oxidative genomic damage than previously thought. This has vital implications on the development of neurological disorders.

Oops! Apparently, they really are that stupid. The scientists who did this work seem to think that 98% of our genome is junk and that includes all the regulatory sequences. It seems like they are completely unaware of decades of work on discovering the function of these regulatory sequences. According The University of Sheffield, these regulatory sequences have been "largely overlooked by scientists." That will come as a big surprise to many of my colleagues who worked on gene regulation in the 1980s and in all the decades since then. It will probably also be a surprise to biochemistry and molecular biology undergraduates at Sheffield—at least I hope it will be a surprise.

Professor Sherif El-Khamisy, Chair in Molecular Medicine at the University of Sheffield, Co-founder and Deputy Director of the Healthy Lifespan Institute, said: “Until now the repair of what people thought is junk DNA has been mostly overlooked, but our study has shown it may have vital implications on the onset and progression of neurological disease."

I wonder if Professor Sherif El-Khamisy can name a single credible scientist who thinks that regulatory sequences are junk DNA?

There's no excuse for propagating this kind of misinformation about junk DNA. It's completely unnecessary and serves only to discredit the university and its scientists.

Ray, S., Abugable, A.A., Parker, J., Liversidge, K., Palminha, N.M., Liao, C., Acosta-Martin, A.E., Souza, C.D.S., Jurga, M., Sudbery, I. and El-Khamisy, S.F. (2022) A mechanism for oxidative damage repair at gene regulatory elements. Nature, 609:1038-1047. doi:[doi: 10.1038/s41586-022-05217-8]

Oxidative genome damage is an unavoidable consequence of cellular metabolism. It arises at gene regulatory elements by epigenetic demethylation during transcriptional activation1,2. Here we show that promoters are protected from oxidative damage via a process mediated by the nuclear mitotic apparatus protein NuMA (also known as NUMA1). NuMA exhibits genomic occupancy approximately 100 bp around transcription start sites. It binds the initiating form of RNA polymerase II, pause-release factors and single-strand break repair (SSBR) components such as TDP1. The binding is increased on chromatin following oxidative damage, and TDP1 enrichment at damaged chromatin is facilitated by NuMA. Depletion of NuMA increases oxidative damage at promoters. NuMA promotes transcription by limiting the polyADP-ribosylation of RNA polymerase II, increasing its availability and release from pausing at promoters. Metabolic labelling of nascent RNA identifies genes that depend on NuMA for transcription including immediate–early response genes. Complementation of NuMA-deficient cells with a mutant that mediates binding to SSBR, or a mitotic separation-of-function mutant, restores SSBR defects. These findings underscore the importance of oxidative DNA damage repair at gene regulatory elements and describe a process that fulfils this function.

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The 10th anniversary of the ENCODE publicity campaign fiasco

On Sept. 5, 2012 ENCODE researchers, in collaboration with the science journal Nature, launched a massive publicity campaign to convince the world that junk DNA was dead. We are still dealing with the fallout from that disaster.

The Encyclopedia of DNA Elements (ENCODE) was originally set up to discover all of the functional elements in the human genome. They carried out a massive number of experiments involving a huge group of researchers from many different countries. The results of this work were published in a series of papers in the September 6th, 2012 issue of Nature. (The papers appeared on Sept. 5th.)

Science communication in the modern world

Science editors asked young scientists to imagine what kind of course they would have created if they could go back to a time before the pandemic [A pandemic education]. Three of the courses were about science communication.

COM 145: Identification, analysis, and communication of scientific evidence

This course focuses on developing the skills required to translate scientific evidence into accessible information for the general public, especially under circumstances that lead to the intensification of fear and misinformation. Discussions will cover the principles of the scientific method, as well as its theoretical and practical relevance in counteracting the dissemination of pseudoscience, particularly on social media. This course discusses chapters from Carl Sagan’s book The Demon-Haunted World, certain peer-reviewed and retracted papers, and materials related to key science issues, such as the anti-vaccine movement. For the final project, students will comprehensibly communicate a scientific topic to the public.

Camila Fonseca Amorim da Silva University of Sao Paulo, Sao Paulo, Brazil

COM 198: Everyday science communication

As scientific discoveries become increasingly specialized, the lack of understanding by the general public undermines trust in scientists and causes the spread of misinformation. This course will be taught by scientists and communication specialists who will provide students with a toolset to explain scientific concepts, as well as their own research projects, to the general public. Upon completion of this course, students will be able to explain to their grandparents that viruses exist even though they can’t see them, convince their neighbors that vaccines don’t contain tracking devices, and explain the concept of exponential growth to governmental officials.

Anna Uzonyi Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

COM 232: Introduction to talking to regular people

Communicating science is difficult. Many scientists, having immersed themselves in the language of their field, have completely forgotten how to talk to regular people. This course hones introductory science communication skills, such as how to talk about scary things without generating mass panic, how to calmly discourage the hoarding of paper hygiene products, and how to explain why scientific knowledge changes over time. The final project will include cross examination from law school faculty, who are otherwise completely uninvolved with the course and possess minimal scientific training. Recommended for science majors who are unable to discuss impactful scientific findings without citing a P value.

Joseph Michael Cusimano Bernard J. Dunn School of Pharmacy, Shenandoah University, Winchester, VA, USA.

They sound like interesting courses but my own take on science communication is somewhat different. I think it's very difficult for practicing scientists to communicate effectively with the general public so I tend to view science communication at several different levels. My goal is to communicate with an audience of scientists, science journalists, and people who are already familiar with science. The idea is to make sure that this intermediate group understands the scientific facts in my field and to make sure they are familiar with the major controversies.

My hope is that this intermediate group will disseminate this information to their less-informed friends and relatives and, more importantly, stop the spread of misinformation whenever they hear it.

Take junk DNA for example. It's very difficult to convince the average person that 90% of our genome is junk because the idea is so counter-intuitive and contrary to the popular counter-narratives. However, I have a chance of convincing the intermediate group, including science journalists and other scientists, who can follow the scientific arguments. If I succeed, they will at least stop spreading misinformation and false narratives and start presenting alternatives to their sudiences.

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Science writing in the age of denial

Here's an interesting presentation by Sean B. Carroll, the evolutionary biologist and author of several books on evolution. He's also written a fascinating book on Jacques Monod and he gave a talk at the University of Toronto a few years ago on the role of chance in evolution—I have a signed copy of his book (see the photo and my blog post: Biologist Sean Carroll in Toronto).

Sean likes to emphasize the importance of storytelling in science communication and education. By this he sometimes means stories about individual scientists and sometimes stories about the history of a subject. As Vice President for Science Education at the Howard Hughes Medical Institute in Washington DC (USA) he has helped craft some short videos for high school students and the presentation contains an example of one on evolution. I'm not sure I fully agree with his emphasis on storytelling—as least not to the extent that he promotes it—but some version of it can be useful as long as it doesn't get in the way of understanding important concepts.

I leave it to you to decide whether the short HHMI video is the best way to teach high school students about evolution. I personally don't like the undue emphasis on natural selection and natural history.

The reason for drawing your attention to an old 2012 presentation is to remind you about the charactieristics of science denial. Sean explains the six rules of denialism.

1. Doubt the Science
2. Question Scientist's Motives and Integrity
3. Magnify Disagreements among Scientists and Cite Gadflies as Authorities
4. Exaggerate Potential Harm
5. Appeal to Personal Freedom
6. Acceptance Would Repudiate Key Philosophy

His examples are the denial of evolution by creationists and the rejection of vaccinations by chiropractors. Today, we see how the same rules apply to those who reject COVID-19 vaccinations and to the Lab Leak Conspiracy Theory.

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Style vs substance in science communication: The role of science writers in major science journals

Science writers have always had articles published in the leading science journals such as Science and Nature but over the past few decades their role seems to have increased so that now even lesser journals employ them to write articles, commentary, and press releases. I recently posted an example of where this can go horribly wrong [Society for Molecular Biology and Evolution (SMBE) spreads misinformation about junk DNA].

The role of science writers has come to dominate the pages of Science and Nature so that we now have a situation where only two thirds of the pages in a typical issue are devoted to actual science publications and most readers are concentrating on the news and opinons in the front part of the journal. In some cases, the science writers control the image of these journals as happened at Nature during the ENCODE publicity campaign in 2012. Over at Science, Elisabeth Pennisi has done more to spread misinformation than any scientist in the field of molecular biology.

These are cases where science writers have sacrificed sustance for style. They write nice readable articles that promote the image of their journal but are scientifcally incorrect.

Let's look at a specific example. Back in 2005 Science celebrated its 125th anniversary by publishing "125 Questions: What We Don't Know." One of those questions was "Why Do Humans Have So Few Genes?"—a question that scientists had adequately answered in 2005 but you wouldn't know that from the short article written by Elizabeth Pennisi [SCIENCE Questions: Why Do Humans Have So Few Genes?]. The article was full of untruths and misinformation. There were lots of other questions in that issue that were just as ridiculous if you knew the topics.

Now, you might imagine that these questions were posed by the leading researchers in their fields but you would be wrong. The list of questions was drawn up by editors and science writers as described in the anniversary issue [SCIENCE Questions: Asking the Right Question].

We began by asking Science’s Senior Editorial Board, our Board of Reviewing Editors, and our own editors and writers to suggest questions that point to critical knowledge gaps. The ground rules: Scientists should have a good shot at answering the questions over the next 25 years, or they should at least know how to go about answering them. We intended simply to choose 25 of these suggestions and turn them into a survey of the big questions facing science. But when a group of editors and writers sat down to select those big questions, we quickly realized that 25 simply wouldn’t convey the grand sweep of cutting-edge research that lies behind the responses we received. So we have ended up with 125 questions, a fitting number for Science’s 125th anniversary.

Isn't it remrkable that editors and writers are being asked to evaluate science (substance) as if their opinions were more important than those of the scientists?

Has Science learned from these mistakes? No, because a few months ago they published a new list of 125 questions in collaboration with the 125th anniversary of Shanghai Jiao Tong University: 125 Questions: Exploration and Discovery. The list of questions hasn't gotten any better; it includes questions like, "How do organisms evolve?"; "What genes make us uniquely human?"; and "How are biomolecules organized in cells to function orderly and effectively?" Many of you can imagine what the short accompanying explanation looks like and you would be right.

Pennisi's original question has disappeared but there's a very similar question in the 2021 list.

Why are some genomes so big and others very small?

Genome size, which is the amount of DNA in a cell nucleus, is extremely diverse across animals and plants, and varies more than 64,000-fold. The smallest genome recorded exists in the microsporidian Encephalitozoon intestinalis (a parasite in certain mammals), and the largest genome belongs to a flowering plant known as Paris japonica, which has 150 billion base pairs of DNA per cell (50 times larger than that of a human). Plants are interesting in that their genome size plays an important role in their biology and evolution. But as the authors of a 2017 paper in Trends in Plant Sciences wrote: “Although we now know the major contributors to genome size diversity are non-protein coding, often highly repetitive DNA sequences, why their amounts vary so much still remains enigmatic.”

Sandwalk readers know that knowledgeable scientists came up with good answers to that question about 50 years ago. One answer is that different species have different amounts of junk DNA because some species don't have large enough populations to eliminate it by natural selection. In other cases, the differences are due to polyploidization.

You would think that after all the criticism of Science over their past coverage of genomes and junk DNA that the writers and editors would know this. But they don't, and that's because science writers and editors seem to be remarkably immune to scientific criticism. (The topic probably doesn't come up when they get together at their science writers' conventions.) I'm making the case that they are so focused on style (science writing) that they just don't care about substance (scientific accuracy).

The major journals have a serious problem that they don't recognize. A lot of the stuff that appears in their journals is not scientifically accurate or, at the very least, is misleading. They're not going to fix this problem if their editorial staff is dominated by science journalists.

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Style vs substance in science communication: The science writer perspective

I want to address a recent article on science writing: When editors and scientists meet: communicating science without dumbing it down. The author is Alex Ip and the article is a commentary on a panel session about science writing at the ScienceWriters2021 conference held in early October [Editing experts: How to help scientists meet journalism standards].

Off to the publisher!

The first draft of my book is ready to be sent to my publisher.

Text by Laurence A. Moran

Cover art and figures by Gordon L. Moran

• 11 chapters
• 112,000 words (+ preface and glossary)
• about 370 pages (estimated)
• 26 figures
• 305 notes
• 400 references

©Laurence A. Moran

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Scientists say "sloppy science" more serious than fraud

An article on Nature: INDEX reports on a recent survey of scientists: Cutting corners a bigger problem than research fraud. The subtitle says it all: Scientists are more concerned about the impact of sloppy science than outright scientific fraud.

The survey was published on BioMed Central.

Cafe Scientific Mississauga

We had a great time last night discussing Can You Tell Real Science News from Fake News?

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"The Perils of Public Outreach"

Julia Shaw is a forensic psychologist. She is currently a senior lecturer in criminology at the London South Bank University (London, UK). Shaw is concerned that we are creating a culture where public outreach is being unfairly attacked. Read her Scientific American post at: The Perils of Public Outreach.

Shaw's point is rather interesting. She believes that scientists who participate in public outreach are being unfairly criticized. Let's look closely at her argument.

What scientists write in academic publications is generally intended for a scientific community, full of nuance and precise language. Instead, what scientists say and write in public forums is intended for lay audiences, almost invariably losing nuance but gaining impact and social relevance. This makes statements made in public forums particularly ripe for attack.

What's in Your Genome? Chapter 4: Pervasive Transcription

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! The first chapter is an introduction to genomes and DNA [What's in Your Genome? Chapter 1: Introducing Genomes ]. Chapter 2 is an overview of the human genome. It's a summary of known functional sequences and known junk DNA [What's in Your Genome? Chapter 2: The Big Picture]. Chapter 3 defines "genes" and describes protein-coding genes and alternative splicing [What's in Your Genome? Chapter 3: What Is a Gene?].

Chapter 4 is all about pervasive transcription and genes for functional noncoding RNAs.

Chapter 4: Pervasive Transcription

• How much of the genome is transcribed?
• How do we know about pervasive transcription?
• Different kinds of noncoding RNAs
•         Box 4-1: Long noncoding RNAs (lncRNAs)
• Understanding transcription
•         Box 4-2: Revisiting the Central Dogma
• What the scientific papers don’t tell you
•         Box 4-3: John Mattick proves his hypothesis?
• On the origin of new genes
• The biggest blow to junk?
•         Box 4-4: How do you tell if it’s functional?
• Biochemistry is messy
• Evolution as a tinkerer
•         Box 4-5: Dealing with junk RNA
• Change your worldview

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What's in Your Genome? Chapter 3: What Is a Gene?

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! The first chapter is an introduction to genomes and DNA [What's in Your Genome? Chapter 1: Introducing Genomes ]. Chapter 2 is an overview of the human genome. It's a summary of known functional sequences and known junk DNA [What's in Your Genome? Chapter 2: The Big Picture]. Here's the TOC entry for Chapter 3: What Is a Gene?. The goal is to define "gene" and determine how many protein-coding genes are in the human genome. (Noncoding genes are described in the next chapter.)

Chapter 3: What Is a Gene?

• Defining a gene
•         Box 3-1: Philosophers and genes
• Counting Genes
• Misleading statements about the number of genes
• Introns and the evolution of split genes
• Introns are mostly junk
•         Box 3-2: Yeast loses its introns
• Alternative splicing
•         Box 3-2: Competing databases
• Alternative splicing and disease
•         Box 3-3: The false logic of the argument from         complexity
• Gene families
• The birth & death of genes
•         Box 3-4: Real orphans in the human genome
• Different kinds of pseudogenes
•         Box 3-5: Conserved pseudogenes and Ken Miller’s         argument against intelligent design
• Are they really pseudogenes?
• How accurate is the genome sequence?
• The Central Dogma of Molecular Biology
• ENCODE proposes a “new” definition of “gene”
• What is noncoding DNA?
• Dark matter

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What's in Your Genome? Chapter 2: The Big Picture

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! I thought I'd post the TOC for each chapter as I finish the first drafts. Here's chapter 2.

Chapter 2: The Big Picture

• How much of the genome has been sequenced?
• Whose genome was sequenced?
• How many genes?
• Pseudogenes
• Regulatory sequences
• Origins of replication
• Centromeres
• Telomeres
• Scaffold Attachment regions (SARs)
• Transposons
• Viruses
• Mitochondrial DNA (NumtS)
• How much of our genome is functional?

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What's in Your Genome? Chapter 1: Introducing Genomes

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! I thought I'd post the TOC for each chapter as I finish the first drafts. Here's chapter 1.

Chapter 1: Introducing Genomes

• The genome war
• What is DNA?
• Chromatin
• How big is your genome?
• Active genes?
• What do you need to know?

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