A friend recently posted a figure on Facebook that instructs authors in the correct way to prepare a summary paragraph (abstract) for publication in Nature. It uses a specific example and th… Read More

So many books ... so little time Read More

In spite of what you might have read, the human genome does not contain one million functional enhancers. The Sept. 15, 2022 issue of Nature contains a news article on "Gene regulation"… Read More

Graduate students, postdocs, and other "academic workers" are on strike for higher wages and better working conditions at University of California schools but it's very difficult to understa… Read More

I discuss a recent editorial in Science that advocates expanding university education in order to prepare students for jobs. I believe that the primary goal of a university education is to… Read More

I just read an annoying article in Boston Review: The Inflated Promise of Science Education. It was written by Catarina Dutilh Novaes, a Professor of Philosophy, and Silvia Ivani, a teaching… Read More

Nature Methods is one of the journals in Nature Portfolio published by Springer Nature. Its focus is novel methods in the life sciences. The latest issue (October, 2022) highlights the… Read More

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… Read More

(This is a copy of an essay that I published in 2006. I made some minor revisions to remove outdated context.) Overheard at breakfast on the final day of a recent scientific meeting: "D… Read More

I've been trying to reason with creationists for more than 30 years, beginning with debates on talk.origins back in the early 1990s. Sometimes we make a little progress but most of the time… Read More

Can natural selection occur by chance or accident? No, with qualifications. Can evolution occur by chance or accident? Yes, definitely. While tidying up my office I came across an antho… Read More

Wikipedia has a way of assessing the quality of articles that have been posted and edited. The rankings are somewhat confusing and it’s hard to find the complete list of quality catego… Read More

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 dealin… Read More

The ENCODE article on Wikipedia is a pretty good example of how to write a science article. Unfortunately, there are a few issues that will be very difficult to fix. When Wikipedia was forme… Read More

Here's a recent video podcast (Aug. 23, 1022) from the Institute for Creation Research (sic). It features an interview with Dr. Jeff Tomkins of the ICR where he explains the history of junk… Read More

ENCODE has mostly abandoned it's definition of function based on biochemical activity and replaced it with "candidate" function or "likely" function, but the message isn't getting out. B… Read More

The Wikipedia article on the Human genome contained a reference that I had not seen before. "Finally DNA that is deleterious to the organism and is under negative selective pressure is cal… Read More

A recent paper in Nature claims that 75% of synonymous mutations reduce fitness in yeast. The results were challenged (refuted?) ten weeks later in a manuscript posted on a preprint server… Read More

NPR tweeted out a summary of the new CDC (United States) guidelines on COVID-19. The figure was posted under the name of Dr. Marcus Plescia, chief medical officer for the Association of Stat… Read More

There has been an enormous expansion of papers on cancer and many of them make a connection with a particular human gene. A recent note in Trends in Genetics revealed that 15,233 human genes… Read More

The most important issue in alternative splicing, in my opinion, is whether splice variants are due to splicing errors (= junk RNA) or whether they reflect real biologically relevant alterna… Read More

Just before getting banned from Wikipedia, I was about to deal with a claim on the Intergenic region article. I had already fixed most of the other problems but there is still this statement… Read More

My account on Wikipedia has been blocked by some editor named Bbb23 after receiving a complaint from another editor named Praxidicae. Praxidicae has been blocking my attempts to edit article… Read More

I used to think that Wikipedia was a pretty good source of information even for scientific subjects. It wasn't perfect, but most of the articles could be fixed. I was wrong. It took me m… Read More

We've known for more than half-a-century that a lot of noncoding DNA is functional. Why are some people still surprised? It's a puzzlement. A paper in Trends in Genetics caught my eye as… Read More

Functional DNA is best defined as DNA that is currently under purifying selection. In other words, it can't be deleted without affecting the fitness of the individual. This is the "maintenan… Read More

This is a story about misleading press releases. The spread of misinformation by press offices is a serious issue that needs to be addressed. The Institute of Cancer Research in London (… Read More

Wikipedia has an article on the Human genome. The introduction includes the following statement, Human genomes include both protein-coding DNA genes and various types of DNA that does no… Read More

I'm a big fan of Kat Arney and I loved her 2016 book Herding Hemingway's Cats where she interviews a number of prominent scientists. If you haven't read it you should try and get a copy even… Read More

It's theoretically possible that the presence of abundant transposon fragments in a genome could provide a clade with a selective advantage at the level of species sorting. Is this an import… Read More

The important issue is whether alternative splicing is ubiquitous or rare. What are the evolutionary implications? I believe that almost all of the splice variants that are routinely d… Read More

The classic Modern Synthesis is effectively dead. It was replaced by a more modern version that includes Neutral Theory, Nearly-Neutral Theory, and the importance of random genetic drift. Pr… Read More

I'm very disappointed in scientists and philosophers who try to defend ENCODE's behavior on the grounds that they were using a legitimate definition of function. I'm even more annoyed when t… Read More

Stefan Linquist is a philosopher at the University of Guelph (Guelph, Ontario, Canada). He recently published a paper on function that I discussed [The Function Wars Part IX: Stefan Linquist… Read More

The authors of a recent paper think we need a new term "spam DNA" to describe some features of the human genome. Fagundes, N.J., Bisso-Machado, R., Figueiredo, P.I., Varal, M. and Zani, A.L… Read More

How much of the human genome is functional? This a problem that will be solved by biochemists not epistemologists. What is junk DNA? What is functional DNA? Defining your terms is a key pa… Read More

I just stumbled upon an opinion piece published in EMBO Reports on May 22, 2022. The author is Frank Gannon who is identified as the former Director of the QIMR Berghofer Medical Research In… Read More

Manolis Kellis is a professor of computer science at the Massachusetts Institute of Technology (MIT). Sandwalk readers will remember him as one of the ENCODE leaders who participated in the… Read More

Today is the 78th anniversary of D-Day—the day British, Canadian, and American troops landed on the beaches of Normandy in World War II.1For us baby boomers it always meant a day of sp… Read More

I've been trying to fix the Wikipedia artilce on Noncoding DNA but it's quite a challenge because the page is controlled by editors who are opposed to junk DNA and I am accused of starting a… Read More

Here's a link to a short podcast on non-coding DNA narrated by Shurjo K. Sen, Program Director, Divison of Genome Sciences. This is the complete text. Non-coding DNA. So I could talk abo… Read More

I decided to edit the Wikipedia article on non-coding DNA by adding new sections on "Noncoding genes," "Promoters and regulatory sequences," "Centromeres," and "Origins of replication." That… Read More

A hard-hitting review will be published in Annual Review of Genomics and Human Genetics. It shows that the case for large numbers of functional lncRNAs is grossly exaggerated. A long-tim… Read More

The new complete human genome sequence gives us a first-time look at the structures of human centromeres. This is my sixth post on the complete telomere-to-telomere sequence of the human g… Read More

The new complete human genome sequence adds an extra 8% of DNA sequence that's a source of variation in the human population. The sequence also corrects some errors in the current standard r… Read More

How can different molecular biologists have such opposite views of the history of their field? I'm posting links to two papers without comment. One of them is from my friend and colleagu… Read More

A detailed examination of the new complete human genome reveals that 54% of it consists of various repetitive elements. Some of them are transcribed and some aren't. This is my fourth post… Read More

Check out this freshperson seminar course on Parts Unknown: The Dark Matter of the Genome at Harvard. It is offfered by Amanda J. Whipple of the Department of Molecular and Cellular Biology… Read More

Karen Miga deserves a lot of the credit for the complete human genome sequence. Karen Miga is a professor at the University of California, Santa Cruz, and she's been working for several… Read More

It's going to be extremely difficult, perhaps impossible, to merge the new complete human genome sequence with the current standard reference genome. The source DNA for the new telomere… Read More

The newly sequenced part of the human genome contains the same chromatin regions as the rest of the genome and they don't tell us very much about which regions are functional and which ones… Read More

The new completed human genome sequence contains some previously unknown large duplicatons (segmental duplications). This is my third post on the complete telomere-to-telomere sequence… Read More

The first complete human genome sequence has finally been published. This is my first post on the complete telomere-to-telomere sequence of the human genome in cell line CHM13 (T2T-CHM13)… Read More

A few months ago, the press office of the University of California at San Diego issued a press release with a provocative title ... Illuminating Dark Matter in Human DNA - Unprecedented Atl… Read More

John Mattick and Paulo Amaral have written a book that promotes their views on the content of the human genome. It will be available next August. Their main thesis is that the human genome i… Read More

John Mattick has a new book coming out in August where he defends the notion that most of our genome is full of genes for functonal noncoding RNAs. We have a pretty good idea what he's going… Read More

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… Read More

My book manuscript has been reviewed by some outside experts and they seem to have convinced my editor that my book is worth publishing. I hope we can get it finished soon. It would be nice… Read More

Jacques Fresco died last December. I am kind of a scientific grandson of Jacques Fresco since he mentored my Ph.D. supervisor, Bruce Alberts when he (Bruce) was an undergraduate at Harvard.W… Read More

Akiko Iwasaki is a Professor of Immunology at Yale and a former student in my department (Dept. of Biochemistry, University of Toronto). She got her undergraduate degree in biochemistry in t… Read More

Take any vaccine you can get whenever you can. Moderna is the probably the very best vaccine and Pfizer-BioNTech is a close second. AstraZenica is very good but Johnson & Johnson not so… Read More

The Omicron wave is surpassing all records for the number of cases in Ontario. The province has given up on testing for most people so the actual case counts are far higher than the reported… Read More

The Omicron variant of SARS-CoV-2 contains a large number of novel mutations in the spike protein. How did these mutations occur and what is their effect on the properties of the variant?… Read More

Danish scientists have looked at the first 785 cases of Omicron variant in Denmark. The most important lesson is that 83% of the cases were fully vaccinated. (Mostly two doses of an mRNA vac… Read More

Scientists are very interested in the omicron variant and why it is so dangerous. Since vaccinated people are getting infected, it must mean that the omicron variant isn't effectively neutra… Read More

I've learned a bit of immunology from hanging out with immunologists so I'm going to try and explain how vaccines protect you from the worst consequences of an infection and why booster shot… Read More

This is a debate sponsored by the Royal Institute of Philosophy on the question "Has science killed philosophy?" It suffers from one of the main problems of the philosphy of science and that… Read More

Michael Hiltzik is first off the mark writing for the Los Angeles Times: These authors wanted to push the COVID-19 lab-leak theory. Instead they exposed its weaknesses. Hiltzik is one of… Read More

Harper is set to publish Viral: The Search for the Origin of COVID-19 in just a few days. The authors are Alina Chan, a postdoc at the Broad Institute of MIT and Harvard, and Matt Ridley, a… Read More

I'm currently discussing the meaning of "function" with a small group of scientists and philosophers and it's not easy to come up with an acceptable definition. Imagine how much more difficu… Read More

This is an updated version of what's in your genome based on the latest data. The simple version is ... about 90% of your genome is junk The more sophisticated version is… Read More

I'm on the editorial board of an education journal so I've been following the pedagogical literature for many years. The idea of active learning, or student-centered learning, has been aroun… Read More

COVID-19 vaccinations are soon going to be available for children in Ontario, Canada. Will parents vaccinate their children? The Toronto Star recently published a poll where parents of a… Read More

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… Read More

I just read a review in Science of Douglas Futuyma’s new book How Birds Evolve: What Science Reveals About Their Origin, Lives, and Diversity. [Contextualizing avian origins and evolut… Read More

You can't get much more anti-science than a book about Adam and Eve. Nevertheless, Stephen Schaffner—a computational biologist at the Broad Institute of MIT in Boston—decided tha… Read More

Lots of people seem to be confused about the origin of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. The investigating committee ot the World Health Organization (WHO) conclud… Read More

Dogs can be trained to detect fresh cadavers but can they detect bodies that have been buried for months or years? Can they detect places where a dead body has rested for a short period of t… Read More

The generation of ATP in mitochodrial membranes is driven by the energy from a protonmotive force caused by the movement of protons from a high concentration in the space between the inner a… Read More

An interesting paper on COVID-19 infections in the USA during 2020 was recently published in Nature. The take-home lessons are: about 78% of infections were probably undocumented so th… Read More

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 eve… Read More

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… Read More

The Society for Molecular Biology and Evolution (SMBE) is a pretigious society of workers in the field of molecular evolution. I am a member and I have attended many of their conferences. SM… Read More

The creationists are committed to proving that most of our genome is functional because otherwise the idea of an intelligent designer doesn't make a lot of sense. They reject all of the evid… Read More

A recent review in Science has the following subtitle, "Why most scientists say it's unlikely that SARS-CoV-2 originated from a lab leak." The title of that article was Call of the Wild but… Read More

Here's a link to a recent review on the origins of SARS-CoV-2 written by 21 scientists from seven different countries. They are all recognized experts on the subject. Holmes, E.C., Golds… Read More

I would like to think that the media will eventually wake up and recognize the science behind the origin of SARS-CoV-2. It overhelmingly supports a natural origin and does not support the la… Read More

This is really worth one hour of your time. You will learn about knowledge and abduction and lots of other things Read More

I just received my copy of a book by Arlin Stoltzfus on mutation. I haven't finished reading it but I thought Sandwalk readers should know about it so they can order their own copy. This… Read More

This is a video published a few weeks ago where Jon Perry interviews Richard Dawkins. Jon Perry is the author of animations posted on his website Stated Clearly. He (Perry) has a very adapta… Read More

The Modern Synthesis is the version of evolutionary theory popularized by Julian Huxley and supported by the leading evolutionary biologists of the 1930s, 40s, and 50s. The general idea… Read More

Lots of people have been sucked in to the lab leak conspiracy theory based on reporting in newspapers and magazines. One of the widely-cited sources is an article published in Newsweek on Ju… Read More

Here's an interesting video where the hosts of "This Week in Virology" (Vincent Racaniello, Rich Condit, and Kathy Spindler) discuss the origin of COVID-19 with three scientists who were on… Read More

Nessa Carey wrote a horribe book about junk DNA where she completely misunderstood the science. It's one of many examples of bad science journalism [Nessa Carey doesn't understand junk DNA]… Read More

Here's a paper that has recently been posted on the preprint server bioRxiv. Nurk et al. (2021) The complete sequence of a human genome. [doi: 10.1101/2021.05.26.445798] I usually don't… Read More

Chinese scientists isolated virus particles from a patient admitted to hospital on December 26, 2019 in Wuhan, China. The RNA genome was sequenced and the sequence was immediately distribute… Read More

Richard ("Rick") Young is a Professor of Biology at the Massachusetts Institute of Technology and a member of the Whitehead Institute. His area of expertise is the regulation of gene express… Read More

The origin of SARS-Cov-2 is a hot topic these days. As far as I can tell, the consensus view among the experts is that the ancestor is from bats but it evolved in an intermediate host before… Read More

Emily Mortola and Manyuan Long have just published an article in American Scientist about Turning Junk into Us: How Genes Are Born. The article contains a lot of misinformaton about junk DNA… Read More

There's been a lot of talk about the possibility that SAR-CoV-2 originated in the Wuhan Institute of Virology and accidentally escaped, causing the COVID-19 pandemic. There's no evidence tha… Read More