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Saturday, February 17, 2024

How to end the war in Ukraine according to a Canadian Conservative "diplomat"

In my opinion, the war in Ukraine is much more complicated than most people realize. We are constantly bombarded with propaganda from all sides and it inhibits rational thinking. One of the few reliable facts is that Vladimir Putin is a very smart bad person.

Lots of people think they have the answer to ending the war in Ukraine. One of the latest pundits is Chris Alexander who has published his thoughts in the Feb. 16, 2024 edition of Canada's Globe and Mail: Ukraine is paying the price for our nonchalance toward Russia’s leadership. Alexander spent years in Canada's Foreign Service, including many years in Moscow and a stint as Canada's ambassador to Afghanistan. In 2011 he was elected to Parliament as a Conservative MP and served as Minister of Citizenship and Immigration in Stephen Harper's cabinet. His reputation as a politician was very different than his previous, mostly admirable, reputation as a diplomat. Here's a excerpt from his Wikipedia article.

Wednesday, February 14, 2024

Copilot answers the question, "What is junk DNA?"

The Microsoft browser (Edge) has a built in function called Copilot. It's an AI assistant based on ChatGPT-4.

I decided to test it byt asking "What is junk DNA?" and here's the answer it gave me.

Sunday, February 11, 2024

Older but wiser?

With age comes wisdom, but sometimes age comes alone.

Oscar Wilde

Like many baby boomers, I sometimes forget people's names and other important bits of information. Sometimes I can't find a word that's been in my vocabulary for decades. These lapses are often temporary but very annoying. It's a sign of age. (I am 77 years old.)

We often make fun of these incidents and consol ourselves with the knowledge that we may be old but we are much wiser than we were in our younger days. We have years and years of experience behind us and over the years we've learned a thing or two that we never understood when we were listening to the Beatles on the radio. We've lived through the Cuban Missile crisis, the war in Viet Nam, the assassination of two Kennedys and Martin Luther King, and a host of cultural changes. We've lived in several different countries and we've raised children. All of these experiences have made us wiser, or so we think.

Friday, February 09, 2024

Open and closed chromatin domains (and epigenetics)

Gene expression in eukaryotes is influenced by the state of chromatin. Tightly packed nucleosomes inhibit the binding of transcription factors and RNA polymerase so that genes in these regions are "repressed." From time to time these regions loosen up a bit allowing access to transcription complexes and subsequent transcription.

The tightly packed regions are known as closed domains and the accessible regions are open domains. Some authors add an intermediate domain called a permissive domain. This model of eukaryotic gene expression has been around for 50 years and the important mechanisms controlling the switch were worked out in the 1980s. I found a recent review that covers this issue in the context of epigenetics and the image below comes from that paper (Klemm et al., 2019).

Wednesday, February 07, 2024

Philip Ball's new book: "How Life Works"

Philip Ball has just published a new book "How Life Works." The subtitle is "A User’s Guide to the New Biology" and that should tell you all you need to know. This is going to be a book about how human genomics has changed everything.

Monday, January 29, 2024

"People also ask" about junk DNA

I'm interested in the spread of science misinformation on the internet. The misinformation about the human genome is a good example that illustrates the problem. There are many other examples but I happen to know a lot about this particular one.

Anyone trying to find out about junk DNA will find it impossible to get a correct answer by searching the internet. The correct answer is that the amount of junk DNA in the human genome is controversial: some scientists think that most of our genome is functional while others think that as much as 90% is junk. The scientific evidence strongly favors the junk side of the controvesy and that's very well explained in the Wikipedia articles on Junk DNA and Non-coding DNA.

Wednesday, January 10, 2024

Benjamin Lewin's new book and his view of the human genome

I was a big fan of Benjamin Lewin. Back in the 1970's he published the first volumes of what was to become Genes, the authoritative textbook of molecular biology. I admired his ability to understand the latest experiments and put the results in the appropriate context.

Later on, when he founded the journal Cell, his editorials and other writings were always insightful. His editorial judgement was impeccable—he always published the very best papers in molecular biology.1

Saturday, January 06, 2024

Why do Intelligent Design Creationists lie about junk DNA?

A recent post on Evolution News (sic) promotes a a new podcast: Casey Luskin on Junk DNA’s “Kuhnian Paradigm Shift”. You can listen to the podcast here but most Sandwalk readers won't bother because they've heard it all before. [see Paradigm shifting.]

Luskin repeats the now familiar refrain of claiming that scientists used to think that all non-coding DNA was junk. Then he goes on to list recent discoveries showing that some of this non-coding DNA is functional. The truth is that no knowledgeable scientist ever claimed that all non-coding DNA was junk. The original idea of junk DNA was based on evidence that only 10% of the genome is functional and these scientists knew that coding regions occupied only a few percent. Thus, right from the beginning, the experts on genome evolution knew about all sorts of functional non-coding DNA such as regulatory sequences, non-coding genes, and other things.