NCSE and the Nature of Science

The National Center for Science Education (NCSE, United States) is an organisaton devoted to defending evolution and climate change. It has a long and admirable history of defending evolution from creationist attacks and of keeping creationism out of American public schools. Part of that defense involves keeping religious teachers and scientists as allies by suppporting the view that there is no necessary conflict between religion and science. NCSE has been a strong supporter of methodological naturalism—the view that science is restricted to investigating the natural world. I'll refer to this view as accommodationism.

Can NATO defend itself without the United States?

American Secretary of State Marco Rubio thinks that the United States of America has been subsidizing the defense of Europe and it's time for European nations (and Canada) to start paying more to defend Europe against Russia. According to Rubio, the other NATO countries have been taking advantage of the United States by cutting back on defense spending and using the money to fund social programs. (Gasp!)

Yeah, but our like-minded partners have to have capability and that's been part of the problem is the erosion in European defense capabilities because they've taken vast amount of the monies that these are rich countries and because of the NATO umbrella they it gave them the flexibility to spend a tremendous amount of their revenues on social programs and not on defense. Now maybe that trend line will begin to change.

First, let's be very clear about the huge US military budget. Only a fraction of that money is being used in the direct defense of Europe from Russian aggression. Canada, Poland, and France do not need to spend billions on B2 bombers that spend most of their time sitting on airfields and only occasionally are used to bomb targets in Iran. They do not need to spend billions on nuclear powered aircraft carriers positioned in the Caribbean or the South China Sea. They do not need to pay for troops in Iraq and Syria. They do not need to give Israel almost four billion dollars a year in military aid. And they do not need to spend huge amounts of money to fund a National Guard that can be used to police their cities.

Second, the Russian invasion of Ukraine has shown us that the threat from Russia is not that serious. Russia can't even conquer a medium-sized country right on its border. (Although it can do a lot of serious damage.) The idea that Russia poses a serious military threat to the main NATO countries is ludicrous.

Third, for all its posturing about defending Europe, the United States has failed to provide Ukraine with the supplies and equipment needed to prevent a gradual Russian takeover of Ukrainian territory. I guess the Americans decided to use the money to fund social programs instead.

Fourth, Canada and the European NATO countries are pretty much done with the constant bullying and insults from American leaders. We may be on the verge of finding out whether the United States needs allies.

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American Secretary of State Marco Rubio explains the Venezuelan protection racket

I was watching Marco Rubio testify before a Congressional committee this morning. I'm interested because I live in Canada and we are one of the countries in the Western Hemisphere that are now supposed to be under the thumb of the United States.

So I paid attention when Rubio explained how the protection racket works with Venezuela because Canada will soon be next on the list. I'll quote directly form his testimony below but here's how I think it works.

America is using its military power to blockade Venezuelan ports and prevent any oil from being shipped except under special circumstances. The sale of oil to foreign countries must be approved by the United States and the United States will determine the price—usually the current market price. The payment won't go to Venezuela, instead it will be deposited into special accounts, for example in Qatar, that will be controlled by members of the Trump administration.

Venezuela can apply to use this money but only for the benefit of the Venezuelan people. For example, Venezuela could use it to fund the police or purchase medicine and equipment from the United States. They can also use it to buy light crude oil that can be used to dilute their heavy crude. They used to buy this from Russia but now they are buying it all from the United States.

Members of the Trump administration will decide which projects to fund. Unused money from the sale of Venezuelan oil might become the property of the USA (or its leaders).

Marc Rubio forgot to mention the legal and ethical justification of such a scheme but I'm sure he'll explain it later on. Other countries in the Western Hemisphere are interested.

From The United States Department of State.

And one of the tools that’s available to us is the fact that we have sanctions on oil. There is oil that is sanctioned that cannot move from Venezuela because of our quarantine. And so what we did is we entered into an arrangement with them, and the arrangement is this. On the oil that is sanctioned and quarantined, we will allow you to move it to market. We will allow you to move it to market at market prices – not at the discount China was getting. In return, the funds from that will be deposited into an account that we will have oversight over, and you will spend that money for the benefit of the Venezuelan people.

Why was that important? Venezuela was running out of storage capacity, okay. They were producing oil. They were drilling oil. They had nowhere to put it. They had nowhere to move it. And they were facing a fiscal crunch; they needed money in the immediacy to fund the police officer, the sanitation workers, the daily operations of government.

And so we’ve been able to create a short-term mechanism. This is not going to be the permanent mechanism, but this is a short-term mechanism in which the needs of the Venezuelan people can be met through a process that we’ve created, where they will submit every month a budget of this is what we need funded. We will provide for them at the front end what that money cannot be used for. And they have been very cooperative in this regard. In fact, they have pledged to use a substantial amount of those funds to purchase medicine and equipment directly from the United States. In fact, one of the things they need is diluent*, or diluent* depending how you want to pronounce it. And that basically is the light crude that you need to mix with their heavy crude in order for the oil to be able to be mixed and moved. They’re getting – they used to get 100 percent of that from Russia. They are now getting 100 percent of that from the United States.

So we’re using that short-term mechanism both to stabilize the country but also to make sure that the oil proceeds that are currently being generated through the licenses we’ll now begin to issue on the sanctioned oil goes to the benefit of the Venezuelan people, not to fund the system that existed in the past.

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The Third Way Evolution Conference

The Third Way of Evolution is a strange organization composed of mavericks who think they're not getting enough attention. Here's how they describe their movement.

The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon intervention by a divine Creator. That is clearly unscientific because it brings an arbitrary supernatural force into the evolution process. The commonly accepted alternative is Neo-Darwinism, which is clearly naturalistic science but ignores much contemporary molecular evidence and invokes a set of unsupported assumptions about the accidental nature of hereditary variation. Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis. Many scientists today see the need for a deeper and more complete exploration of all aspects of the evolutionary process.

Why it's necessary to be intelligent in order to explain function in the human genome

I follow the posts of Intelligent Design Creationists in order to see whether they have finally begun to understand science. Imagine my excitement when this post appeared on the Science and Culture website!

Why Intelligence Is Necessary to Explain Nature’s Functional Information

Alas, my excitement was short-lived. The post is actually about a podcast interview with William Dembski and not somebody intelligent.

• On the Meaning of the Word "Function"
• The Function Wars: Part I
• The Function Wars: Part II
• The Function Wars: Part III
• The Function Wars: Part IV
• Restarting the function wars (The Function Wars Part V)
• The Function Wars Part VI: The problem with selected effect function
• The Function Wars Part VII: Function monism vs function pluralism
• The Function Wars Part VIII: Selected effect function and de novo genes
• The Function Wars Part IX: Stefan Linquist on Causal Role vs Selected Effect
• The Function Wars Part X: "Spam DNA"?
• The Function Wars Part XI: Stefan Linquist responds to my critique
• The Function Wars Part XII: Revising history and defending ENCODE
• The Function Wars Part XIII: Ford Doolittle writes about transposons and levels of selection
• The function wars are over

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These AI predictions are becoming ridiculous!

The first issue of Nature in 2026 has an article by science writer David Adam.

The Science of 2050
Nature explores the future breakthroughs that could shape our world.

The online version has a different title and subtitle but the text is the same. It begins with a quote from "futurologist" Nick Bostrum.

“There’s a good likelihood that by 2050, all scientific research will be done by superintelligent AI rather than human researchers. Some humans might do science as a hobby, but they wouldn’t be making any useful contributions.”

There's no attempt in the article to apply critical thinking to such a ridiculous prediction and the author doesn't consider the implications. If Bostrum (whoever that is) is right then that's the end of graduate studies and after 2050 nobody will be getting a Ph.D. in physics, biology, geology, or chemistry.

I hope I live long enough to see AI collecting and analyzing fossils in Greenland or studying volcanoes in Hawaii. Maybe I'll still be around when AI figures out how memories are stored or which transcription factor binding sites are functional in the human genome. And if I'm very, very lucky I'll see live to see all of my colleagues in the Department of Biochemistry abandon their labs and take up some scientific hobby like alchemy or intelligent design.

David Adam and the editors of Nature should be ashamed of themselves for publishing such nonsense.

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Teaching the nature of science vs the scientific method

There's been a lot of talk about how to teach science literacy. The discussion in the USA centers around STEM (science, engineering, technology, mathematics) and this acronym has also spread to other countries. It's an unfortunate development since there's a big difference between teaching science and teaching those other three topics.

Most studies suggest that we focus on teaching The Nature of Science (NOS). There's no definition of this topic that everyone agrees to but the essence is that students need to understand how our society generates knowledge. In the context of the natural sciences, this means understanding the process of discovery. There's general agreement that what this means is critical thinking that's evidence-based. It's another way of saying that we need to teach critical thinking and the importance of using evidence to back up and test your claims of knowledge. "Appreciating the scientific process can be even more important than knowing scientific facts. People often encounter claims that something is scientifically known. If they understand how science generates and assesses evidence bearing on these claims, they possess analytical methods and critical thinking skills that are relevant to a wide variety of facts and concepts and can be used in a wide variety of contexts.”

National Science Foundation, Science and Technology Indicators, 2008

The reasoning behind this emphasis is based on two pedagogical facts. The first is that it's impossible to teach all the facts and theories of a typical scientific discipline like astronomy or geology. It's pointless to make students memorize information that they will forget as soon as the class is over, Instead, as the argument goes, we need to teach students to understand how evidence is gathered and how it becomes fact. Teach students how to appreciate science and its power to create knowledge. That's something that will stick with them all their lives.

What are American primaries?

I'm a Canadian who's always been puzzled about American primaries. It seems to me that the purpose of these primaries is to help a political party choose its candidates for the next election. It seems like two of the parties, the Republican party and the Democratic Party, have managed to get state governments to fund their primary elections for reasons that are not very clear to those of us who live in other countries.

Today I was watching Michael Smerconish on CNN. He always has a poll question that provides a deep (and troubling) insight into his way of thinking. Today he announced that he is part of a class action lawsuit demanding that independent voters be allowed to vote in primary elections. That sounds weird to me because I'm used to a system where only members of a party get to choose who their candidates will be.

I was aware of the fact that many Americans see this differently and I knew that some states allow non-party members to pick the party candidate. Nevertheless, I was curious to see how CNN listeners would respond to his poll question.

Here are the results.

I find that result astonishing. 86% of respondents think they should be able to choose the candidate of the Republican or Democrat party even if they don't belong to one of those parties. What do they (you?) think is the purpose of primaries in the United States?

Here's a list of states and who they allow to vote in one of the primaries. It seems like the states actually have laws governing how political parties are able to choose their candidates.

I don't know of any other democracy that has such a bizarre system. I'm a member of one of the political parties in Canada and I participated in selecting our party leader. I would be outraged if my government passed a law allowing members of another party (or nonmembers) to help select my party leader or candidate. Why are such laws acceptable in the United States?

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Answers in Genesis uses the latest DNA research to destroy evolutionary proof (not!)

There's been so much bad news this week that I though you might enjoy a little humor to lighten your day. Here are some devout Young Earth Creationists making fun of some stupid comments they've found on the internet and calling on some professor to "destroy" evolutionists who believe in junk DNA [Latest in DNA Research Destroys Evolutionary “Proof”].

Even more regulatory elements?

The expression of genes is regulated at many levels but one of the most important is regulation at the level of transcription. Transcription initiation is controlled by transcription factors that bind to sequences near the promoter and either activate or repress transcription.

A lot of work has been done on transcription regulation in mammals over the past 40 years. The general impression from these detailed studies of individual genes is that regulation usually involves a relatively small number of transcription factors that bind to sequences within 1000 bp or so of the transcription start site.

This model was challenged by the ENCODE studies in 2012. ENCODE researchers claimed to have discovered hundreds of thousands of cis-regulatory elements (CRE's) covering a substantial percentage of the genome. If they are correct, then this means that there are dozens of transcription factors controlling the expression of every gene.

Will AlphaGenome from Google DeepMind help us understand the human genome?

I recently reported that Google's AI program does a horrible job of summarizing the junk DNA controversy. [The scary future of AI is revealed by how it deals with junk DNA] That led to a discussion about the "intelligence" in artificial intelligence and whether AI was capable of distinguishing between accurate and inaccurate data.

Google DeepMind is an artificial intelligence research laboratory headquartered in London, UK. Two of its programmers, Demis Hassabis and John Jumper, were awarded the 2024 Nobel Prize in Chemistry for developing AlphaFold, a program that predicts the tertiary structure of proteins.

Intelligent Design Creationists post their #1 story of 2025

Here's the post on Science & Culture (sic) by Casey Luskin: Happy New Year! No. 1 Story for 2025: Bombshell Overturns Myth of 1 Percent Difference.

How many times have you heard it said that the human and chimpanzee genomes are so similar that they are only “1 percent different” at the level of their DNA? This shows, we were told, not only that humans and chimps share common ancestry, but that humans aren’t all that special, which is a common talking point in science journalism and other public discussions. After all, we’re just slightly modified chimps! This “fact” has been discussed so much that it has become what the late biologist Jonathan Wells famously called an “icon of evolution.”

But now, new data reported in a recently published Nature paper by Yoo et al. has overturned this previous claim. The new findings reveal that human DNA is far more different from chimp DNA than previously thought.

That should be major news in the science world, yet those involved don’t seem interested in highlighting their discovery.

The activity of "random" DNA supports the junk DNA model

I complain a lot about the quality of science writing but today's post is very different. I want to highlight an article by Michael Le Page that he just published in New Scientist. It's one of the best articles on junk DNA that I've ever seen in popular science magazines and newspapers [Human-plant hybrid cells reveal truth about dark DNA in our genome].

I've admired Michael Le Page for many years because of his articles on climate change and evolution. It doesn't surprise me that he's right about junk DNA.

The scary future of AI is revealed by how it deals with junk DNA

Today I did a Google search for the term "JUNK DNA" and, as usual, the first thing I saw was the Google AI description of junk DNA. It's wrong, but that's not the scary part. The most frightening thing about the AI description is that it promotes three videos that misrepresent science and two of them are from well known kooks.

What does this tell you about current versions of AI? It tells you that it is not intelligent in any meaningful sense of the word. It tells you that Google AI is incapable of distinguishing between scientific facts and ignorance. It tilts toward the loudest voices on the internet and, as we all know, those voices are frequently wrong.

How many lncRNA genes in the human genome? (2025)

There is considerable controversy over the total number of genes in the human genome. The number of protein-coding genes is pretty well established at somewhere between 19,500 and 20,000. It's the number of non-coding genes that's disputed.

There's general agreement on the number of well-defined small RNA genes such as snRNAs, snoRNA, microRNAs etc. Similarly, the number of ribosomal RNA and tRNA genes is known. The problem is with identifying genuine long non-coding RNA genes (lncRNA genes). Estimates vary from less than 20,000 to more than 200,000 but most of these estimates fail to define what they mean by "gene." Many scientists seem to think that any detectable transcript must come from a gene.

This doesn't make any sense since we know that spurious transcripts exist and they don't come from genes by any meaningful definition of gene. The only reasonable definition of a molecular gene is a DNA sequence that's transcribed to produce a functional product.¹

The idea that spurious, non-functional, transcripts exist has been described in the scientific literature for many decades. One of my favorites is in a paper by Ponting and Haerty (2022) quoting another paper from thirteen years ago by Ulitsky and Bartel.

The cellular transcriptional machinery does not perfectly discriminate cryptic promoters from functional gene promoters. This machinery is abundant and so can engage sites momentarily depleted of nucleosomes and rapidly initiate transcription. The chance occurrence of splice sites can then facilitate the capping, splicing, and polyadenylation of long transcripts. A very large number of such rare RNA species are detectable in RNA-sequencing experiments whose properties are virtually indistinguishable from those of bona fide lncRNAs. Consequently, “a sensible [null] hypothesis is that most of the currently annotated long (typically >200 nt) noncoding RNAs are not functional, i.e., most impart no fitness advantage, however slight” (Ulitsky and Bartel, 2013: p. 26).

The important point here is that the correct null hypothesis is that these transcripts don't have a biologically relevant function and the burden of proof is on researchers to demonstrate function before assigning them to a genuine gene. My colleagues at the University of Toronto made the same point in a paper published in 2015.

In the absence of sufficient evidence, a given ncRNA should be provisionally labeled as non-functional. Subsequently, if the ncRNA displays features/activities beyond what one would expect for the null hypothesis, then we can reclassify the ncRNA in question as being functional. (Palazzo and Lee, 2015)

There are a number of well-defined lncRNAs that have been shown to have distinct reproducible functions. The key question is how many of these biologically relevant lncRNA genes exist in the human genome. I struggled with the answer to this question when I was writing my book. I finally decided to make a generous estimate of 5000 non-coding genes and that implies several thousand lncRNA genes (p. 127). I now think that estimate was far too generous and there are probably fewer than 1000 genuine lncRNA genes.

I have not scoured the literature for all the examples of human lncRNAs having good evidence of function but my impression is that there are only a few hundred. This post was incited by a recent publication by researchers from the Hospital for Sick Children and the University of Toronto (Toronto, Canada) who characterized another functional lncRNA called CISTR-ACT that plays a role in regulating cell size (Kiriakopulos et al., 2025).

I was prompted to revisit this controversy by the accompanying press release that said ...

Unlike genes that encode for proteins, CISTR-ACT is a long non-coding RNA (or lncRNA) and is part of the non-coding genome, the largely unexplored part that makes up 98 per cent of our DNA. This research helps show that the non-coding genome, often dismissed as ‘junk DNA’, plays an important role in how cells function.

We're used to this kind of misinformation² in press releases but I thought it would be a good idea to read the paper. As I expected, there's nothing in the paper about junk DNA but here's the first sentence of the introduction.

The human genome contains more long non-coding RNAs (lncRNAs) than protein-coding genes (GENCODE v49) which regulate genes and chromatin scaffolding.

The latest version of GENCODE Release 49 claims that there are 35,899 lncRNA genes. This is the only reference in the Kiriakopulos et al. paper to the number of lncRNA genes. There's no mention of the controversy and none of the papers that discuss the controversy are referenced.

The GENCODE number is close to the latest version of Ensembl, which lists 35,042 lncRNA genes. I couldn't find any good explanation for these numbers or for the definition of "gene" that they are using but what's interesting is how these numbers are climbing every year; for example, a paper from two years ago listed a number of sources and you can see that the RefSeq and GENCODE numbers are much smaller than today's numbers (Amaral et al., 2023).³

We intend to provoke alternative interpretation of questionable evidence and thorough inquiry into unsubstantiated claims.

Ponting and Haerty (2022)

It's perfectly acceptable to state your preferred view on lncRNAs when you publish a paper. The authors of the recent paper may want to believe that there are more lncRNA genes than protein-coding genes but I think it's important for them to define what they mean by "gene" when they make such a claim. What's not acceptable, in my opinion, is to ignore a genuine scientific controversy by not mentioning in the introduction that there are other legitimate views.

It's a shame that they didn't do that because their paper is a good example of the hard work that needs to be done in order to demonstrate that a particular lncRNA has a biologically relevant function.

In closing, I want to emphasize the recent review by Ponting and Haerty (2022)⁴ that points out the importance of the problem and the kinds of experiments that need to be done in order to establish that a given RNA comes from a real gene. This is how a scientific controversy should be addressed. Here's the abstract of that paper ...

Do long noncoding RNAs (lncRNAs) contribute little or substantively to human biology? To address how lncRNA loci and their transcripts, structures, interactions, and functions contribute to human traits and disease, we adopt a genome-wide perspective. We intend to provoke alternative interpretation of questionable evidence and thorough inquiry into unsubstantiated claims. We discuss pitfalls of lncRNA experimental and computational methods as well as opposing interpretations of their results. The majority of evidence, we argue, indicates that most lncRNA transcript models reflect transcriptional noise or provide minor regulatory roles, leaving relatively few human lncRNAs that contribute centrally to human development, physiology, or behavior. These important few tend to be spliced and better conserved but lack a simple syntax relating sequence to structure and mechanism, and so resist simple categorization. This genome-wide view should help investigators prioritize individual lncRNAs based on their likely contribution to human biology.

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1. See Wikipedia: Gene; What Is a Gene?; Definition of a gene (again); Must a Gene Have a Function?.

2. No knowledgeable scientist ever said that all non-coding DNA was junk. We've known about non-coding genes for more than half-a-century.

3. See How many genes in the human genome (2023)?

4. See Most lncRNAs are junk

Amaral, P., Carbonell-Sala, S., De La Vega, F.M., Faial, T., Frankish, A., Gingeras, T., Guigo, R., Harrow, J.L., Hatzigeorgiou, A.G., Johnson, R. et al. (2023) The status of the human gene catalogue. Nature 622:41-47. [doi: 10.1038/s41586-023-06490-x]

Kiriakopulos et al. (2025) LncRNA CISTR-ACT regulates cell size in human and mouse by guiding FOSL2. Nature communications: (in press). [doi: 10.1038/s41467-025-67591-x]

Palazzo, A.F. and Lee, E.S. (2015) Non-coding RNA: what is functional and what is junk? Frontiers in genetics 6:2(1-11). [doi: 10.3389/fgene.2015.00002]

Ponting, C.P. and Haerty, W. (2022) Genome-Wide Analysis of Human Long Noncoding RNAs: A Provocative Review. Annual review of genomics and human genetics 23. [doi: 10.1146/annurev-genom-112921-123710

Ulitsky, I. and Bartel, D.P. (2013) lincRNAs: genomics, evolution, and mechanisms. Cell 154:26-46. [doi: 10.1016/j.cell.2013.06.020]