Discussing Junk DNA with an Adaptationist, Again

Nils Reinton is a molecular biologist working in the field of medical diagnostics and he has been challenging the concept of junk DNA in the comment section of a recent posting. The title of that posting, Everything Is There for a Reason?, was direct response to an earlier posting from Nils where he claimed that we shouldn't label DNA as "junk" because it's a science stopper.

During the discussion in the comment to my posting, I challenged Nils to answer a number of questions. He has responded on his blog SciPhu with Hey junk people, I accept your challenge (part I). I resonded to his answers in Discussing Junk DNA with an Adaptationist.

Now Nils has weighed in with Hey junk people, I accept your challenge (part II).

Q: Why is the Fugu genome so much smaller than that of other fish?

and

Q: When two similar species differ in genome size by a factor of two—probably due to an ancient polyploidization—is the majority of DNA in both species functional?

A: His argument is that since the genome size differs between species, much of it must be junk. But, you could easily use the same argument towards a function, by saying that the difference in genome size is a defining (functional) difference between species. We just do not know do we ! And, why does the difference in size not give you reason to speculate on function at least in parts of these regions ? Others have however, speculated far better than me on this topic, and a thorough introduction to such research can be found at junkdna.com and following this link to “The Principle of Recursive Genome Function“.

No, my argument was not that the extra DNA has to be junk just because there are two similar species that differ in the sizes of their genomes.

The question was directed at adaptationists who postulate a function for everything. I wanted to know the adaptationist explanation for those observations. What is it? Following a polyploidization is it possible that most of the DNA in the larger genome becomes non-junk right away?

Incidentally, by linking to the HoloGenomics website (junk.dna), Nils does not enhance his credibility.

Q: In the human lineage there are over one million Alu sequences. They all look like degenerate versions of 7SL RNA. Are all of these sequences functional? If so, what function could they be doing? And why do the human Alus look so different from the mouse ones?

A: I am not saying all Alu-elements are functional. On the “what is junk” scale, one extreme is that everything that hasn’t been ascribed a function is junk (Larry Moran’s position !?) and on the other end is “nothing is junk”. My position is somewhere in the middle: Some of the DNA in our genome is possibly junk. A number of individual Alu-elements will undoubtedly end up in the “junk”-category when more is known about our genome. That said, it has been shown that Alu-elements can constitute (parts of) regulatory and functional elements. It’s rather hard to tell which ones are functional by just looking at them. I therefore refuse to call them “junk” by default, - I strongly feel that the “junk”-label is a dismissal of any possible function(s) and should be used with caution if at all, - even for Alu-elements.

My position is that a huge amount of the DNA in our genomes is junk. That position is based on many different lines of evidence as well as on rational extrapolation from what we know and don't know about molecular biology and evolution.

Nobody is arguing that every single Alu element is junk. That would be stupid because we know for a fact that some of them have secondarily acquired a function. The point is whether most of this repetitive sequence can be reasonably assumed to be functional, and if so, what kind of function does the adaptationist imagine for most of these sequences?

In the absence of any reasonable functional explanation, and in the face of evidence that most Alu elements are degenerate retrotransposons, it is reasonable to adopt the working hypothesis that they are junk. That's not a science stopper. It's just common sense.

Q: Most intron sequences do not seem to have a function. Why does the size of introns in the same gene vary so much in related species and why isn’t the sequence conserved in most cases?

A: This argument is similar to the genome size argument above, and the answers for bullet 5 and 6 are equally valid here. Thus, there may be many reasons for a variation in intron size and this variation is not a very good argument to support the “junk” hypothesis. Also, the intron can contain regulatory elements and the c-gamma example above goes to show that introns can even contain functional (as in transcribed) genetic elements.

The fact that we have a few examples of functional intron sequences is no reason to assume that most of them are functional in the face of abundant evidence that they are not. That's a position that only a confirmed adaptationist would take.

This is a case where the exceptions tend to prove the rule not that the exceptions make a new rule.

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Two Heidelberg graduate students reject junk DNA

Science in School is a magazine for European science teachers. Two graduate students¹ have just published an article in the November issue: Not junk after all: the importance of non-coding RNAs.

Note: The article has been edited to remove some of the references to junk DNA and the editor has added the following disclaimer to the end of the article: Editor’s note: Some parts of the introduction and conclusion were rephrased to avoid any misunderstanding concerning the nature of ‘junk DNA’, which is not the focus of this article. Here's a link to the revised article: Not junk after all: the importance of non-coding RNAs. More changes are expected.

Not junk after all: the importance of non-coding RNAs

Originally assumed to be useless ‘junk DNA’, sections of the genome that don’t encode proteins have been revealed as a source of many important non-coding RNA structures.

The central dogma of molecular biology is that DNA is used as a template to create messenger RNA (mRNA), which in turn is translated into proteins that build the tissues in our bodies and carry out the main functions of our cells and organs. In other words, DNA → mRNA → proteins. Interestingly, though, only 2% of the DNA in our whole genome codes for proteins! So, what does the other 98% of the human genome do? In the mid-1900s, it was widely believed that a great part of our genome was useless, repetitive ‘junk DNA’. However, this belief goes against the evolution theory, which suggests that useless sequences would be eliminated from the genome since their maintenance requires energy. In the late 20th century and the early 21st century, this junk DNA has been shown to not only contain important regulatory elements for transcription, but also sequences that encode various non-coding RNAs that have functions in many cellular mechanisms.

I just finshed a podcast interview with Kat Arney and one of the questions she asked was what is the most important thing I'd like scientists to know about this topic. I picked evolution—I'd like modern researchers to understand that there's more to evolution than natural selection. You can see the problem in this example where two students who are working toward a Ph.D. at a top lab in Europe think that junk DNA "goes against the evolution theory."

That's sad. It's also sad that these two students think that 98% of our genome might be devoted to regulation and non-coding genes.

We need to focus on educating the next generation of scientists and that starts with educating science teachers. This is not the way to do it.

Here's the contact information for Science in School. I've written the editor at editor@scienceinschool.org. Please send a message if you are as concerned about the spread of scientific misinformation as I am.

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Zuzana Koskova at the European Molecular Biology Laboratory in Heidelberg (Germany) and Miguel Hernandez at the University Hospital, Heidelberg. I tried sending an email message to Zuzana Koskova but got no reply. I was unable to find contact information for Miguel Hernandez.

Jonathan Wells (1942 - 2024)

Johnathan Wells died recently. He was a well-known Intelligent Design Creationist and that's why Evolution News (sic) is eulogizing him by posting multiple tributes and excerpts from his books and essays.

I think it's only fair to post links to my efforts to demonstrate the serious flaws in his arguments. I'm particularly proud of the series of articles I wrote when he published his book The Myth of Junk DNA. I went through every chapter and analyzed his arguments against junk DNA. It won't surprise anyone to learn that I found those arguments lacking in substance and in some cases I discovered that Wells had misrepresented the science.

Here are my posts.

• Jonathan, Moonies, and Junk DNA
• Junk & Jonathan: Part I—Getting the History Correct
• Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?
• Junk & Jonathan: Part 3—The Preface
• Junk & Jonathan: Part 4—Chapter 1
• Junk & Jonathan: Part 5—Chapter 2
• Junk & Jonathan: Part 6—Chapter 3
• Junk & Jonathan: Part 7—Chapter 4
• Junk & Jonathan: Part 8—Chapter 5
• Junk & Jonathan: Part 9—Chapter 6
• Junk & Jonathan: Part 10—Chapter 7
• Junk & Jonathan: Part 11—Chapter 8
• Junk & Jonathan: Part 12—Chapter 9
• Junk & Jonathan: Part 13—Chapter 10

Jonathan Wells never responded directly to my criticism but he did respond to a comment that Paul McBride made on one of his blog posts. Paul asked him why he didn't respond to my post and here's what Wells said,

Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.

This is typical of the attitude of most Intelligent Design Creationists. They are happy to publish lengthy books denegrating science and scientists but couldn't be bothered responding to criticism.

Here's are some other post of mine where I demonstrate the flawed thinking of Jonathan Wells.

• Jonathan Wells talks about junk DNA
• Jonathan Wells illustrates zombie science by revisiting junk DNA
• Brace yourselves, a new "Icons" is coming
• Jonathan Wells proves that life must have been created by gods
• Answering ten questions from the IDiots
• John Mattick vs. Jonathan Wells
• Some Questions for IDiots
• American Loons: #409 Jonathan Wells and #411 John West
• A Dishonest Intelligent Design Proponent?
• We Called Out IDiot Jonathan Wells, and He Folded
• Jonathan Wells Sends His Regrets
• Watch Jonathan Wells Screw Up
• Jonathan Wells Talks About Sequence Conservation
• Ohmygod! These photographs are faked!
• Fossil Horses and Directed Evolution
• Peppered Moths and the Confused IDiots
• Jonathan Wells reviews the Christiane Nüsslein-Volhard and Wieschaus Experiment

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Society for Molecular Biology and Evolution (SMBE) spreads misinformation about junk DNA

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. SMBE sponsors several journals incucluding Genome Biology and Evolution (GBE), which is published by Oxford Academic Press.

The latest issue of GBE has a paper by Stitz et al. (2021) that describes some repetitive elements in the platyhelminth Schistosoma mansoni. The authors conlcude that some of these elements might have a function and this prompts them to begin their discussion with the following sentences.

The days of “junk DNA” are over. When the senior authors of this article studied genetics at their respective universities, the common doctrine was that the nonprotein coding part of eukaryotic genomes consists of interspersed, “useless” sequences, often organized in repetitive elements such as satDNA. The latter might have accumulated during evolution, for example, as a consequence of gene duplication events to separate and individualize gene function (Britten and Kohne 1968; Comings 1972; Ohno 1999). This view has fundamentally changed (Biscotti, Canapa, et al. 2015), and our study is the first one addressing this issue with structural, functional, and evolutionary aspects for the genome of a multicellular parasite.

It is unfortunate that the senior authors didn't receive a good undergraduate education but one might think that they would rectify that problem by learning about genomes and junk DNA before publishing in a good journal devoted to genomes and evolution. Alas, they didn't and, even worse, the journal published their paper with those sentences intact.

As you might imagine, these statements were seized upon by Intelligent Design Creationists who wasted no time in posting on their creationist blog [Oxford Journal: “The Days of ‘Junk DNA’ Are Over ”].

But that's not the worst of it. The same issue contains an editorial written by Casey McGrath who self identifies as a employee of the Society for Molecular Biology and Evolution in Lawrence Kansus (USA). She is the Social Media Editor for Genome Biology and Evolution. The title of her editorial is "Highlight—“Junk DNA” No More: Repetitive Elements as Vital Sources of Flatworm Variation" (McGrath, 2021). She starts off by repeating and expanding upon the words of the senior authors of the study that I referred to above.

“The days of ‘junk DNA’ are over,” according to Christoph Grunau and Christoph Grevelding, the senior authors of a new research article in Genome Biology and Evolution. Their study provides an in-depth look at an enigmatic superfamily of repetitive DNA sequences known as W elements in the genome of the human parasite Schistosoma mansoni (Stitz et al. 2021). Titled “Satellite-like W elements: repetitive, transcribed, and putative mobile genetic factors with potential roles for biology and evolution of Schistosoma mansoni,” the analysis reveals structural, functional, and evolutionary aspects of these elements and shows that, far from being “junk,” they may exert an enduring influence on the biology of S. mansoni.

“When we studied genetics at university in the 1980s, the common doctrine was that the non-protein coding parts of eukaryotic genomes consisted of interspersed, ‘useless’ sequences, often organized in repetitive elements like satellite DNA,” note Grunau and Grevelding. Since then, however, the common understanding of such sequences has fundamentally changed, revealing a plethora of regulatory sequences, noncoding RNAs, and sequences that play a role in chromosomal and nuclear structure. With their article, Grunau and Grevelding, along with their coauthors from Justus Liebig University Giessen, University of Montpellier, and Leipzig University, contribute further evidence to a growing consensus that such sequences play critical roles in evolution.

There's no rational excuse for publishing the Stitz et al. paper with those ridiculous statements and there's no rational excuse for compounding the error by highlighting them in an editorial comment. The Society for Molecular Biology and Evolution should be ashamed and embarrassed and they should issue a retraction and a clarification. They should state clearly that junk DNA is alive and well and supported by so much evidence that it would be perverse to deny it.

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McGrath,C. (2012) Highlight—“Junk DNA” No More: Repetitive Elements as Vital Sources of Flatworm Variation. Genome Biology and Evolution 13: evab217 [doi: 10.1093/gbe/evab217]

Stitz, M., Chaparro, C., Lu, Z., Olzog, V.J., Weinberg, C.E., Blom, J., Goesmann, A., Grunau, C. and Grevelding, C.G. (2021) Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni. Genome Biology and Evolution 13:evab204. [doi: 10.1093/gbe/evab204]

ENCODE/Junk DNA Fiasco: The IDiots Don't Like Me

Casey Luskin has devoted an entire post to discussing my views on junk DNA. I'm flattered. Read it at: What an Evolution Advocate's Response to the ENCODE Project Tells Us about the Evolution Debate.

Let's look at how the IDiots are responding to this publicity fiasco. Casey Luskin begins with ...

University of Toronto biochemistry professor Larry Moran is not happy with the results of the ENCODE project, which report evidence of "biochemical functions for 80% of the genome." Other evolution-defenders are trying to dismiss this paper as mere "hype".

Yes that's right -- we're supposed to ignore the intentionally unambiguous abstract of an 18-page Nature paper, the lead out of 30 other simultaneous papers from this project, co-authored by literally hundreds of leading scientists worldwide, because it's "hype." (Read the last two or so pages of the main Nature paper to see the uncommonly long list of international scientists who were involved with this project, and co-authored this paper.) Larry Moran and other vocal Internet evolution-activists are welcome to disagree and protest these conclusions, but it's clear that the consensus of molecular biologists -- people who actually study how the genome works -- now believe that the idea of "junk DNA" is essentially wrong.

The biggest mistake in the history of molecular biology (not!)

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 evidence that supports junk DNA and they vehemently reject the notion that 90% of our genome is junk.

I was recently alerted to a video on junk DNA produced by Creation Ministries International in which they quote John Mattick.

A leading figure in genetics, Prof. John Mattick said ...'the failure to recognize the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology'.

The creationists are making the common mistake of equating noncoding DNA and junk DNA but the quotation sounded accurate to me since John Mattick makes similar mistakes in his publications. I decided to try and find the exact quotation and reference and the closest I could come to a direct quote was in a paper by Mattick from 2007 (Mattick, 2007). He's referring to introns—here's the exact quotation.

It should be noted that the power and precision of digital communication and control systems has only been broadly established in the human intellectual and technological experience during the past 20–30 years, well after the central tenets of molecular biology were developed and after introns had been discovered. The latter was undoubtedly the biggest surprise (Williamson, 1977), and its misinterpretation possibly the biggest mistake, in the history of molecular biology. Although introns are transcribed, since they did not encode proteins and it was inconceivable that so much non-coding RNA could be functional, especially in an unexpected way, it was immediately and almost universally assumed that introns are non-functional and that the intronic RNA is degraded (rather than further processed) after splicing. The presence of introns in eukaryotic genomes was then rationalized as the residue of the early assembly of genes that had not yet been removed and that had utility in the evolution of proteins by facilitating domain shuffling and alternative splicing (Crick, 1979; Gilbert, 1978; Padgett et al., 1986). Interestingly, while it has been widely appreciated for many years that DNA itself is a digital storage medium, it was not generally considered that some of its outputs may themselves be digital signals, communicated viaRNA.

However, the idea of the biggest mistake in molecular biology predates that reference. Mattick is quoted in a Scientific American article by W. Wayt Gibbs where Gibbs is discssing the "suprising" fact that regulatory sequences are conserved and that some genes are noncoding genes (Gibbs, 2003).

“I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.”

The discovery of introns in the mid-1970s was definitely a surprise but it's not true, as Mattick implies, that they were immediately assumed to be junk. In fact, as he points out, there was a lot of debate over the possible role of introns in the evolution of protein-coding genes where they could stimulate exon shuffling. Later on, the presence of introns was recognized to be an essential component of alternative splicing.

Once more and more sequences were published it became apparent that neither their size nor their sequences were conserved except for the spliceosome recognition sequences. It soon became obvious that their sequences were evolving at the neutral rate demonstrating that they were mostly junk. Mattick assumes that this conclusion—that introns are mostly junk—is one of the biggest mistakes in molecular biology. I think the opposite is true. I think that the failure of most molecular biologists to understand junk DNA is a huge mistake.

The creationists are misquoting Mattick when they say that the classification of all noncoding as junk is the biggest mistake in molecular biology. In the quotations above, Mattick is specifically referrring to introns but I'm sure he won't be upset to be misquoted in that manner since he firmly believes that most noncoding DNA is functional.

There's a bit of an ironic twist here. If it were true that knowledgeable scientists in the 1970s actually believed that all noncoding DNA was junk then I'd have to agree that this would have been a big (biggest?) mistake. But they didn't and it wasn't a big mistake. As I've said many times, no knowledgeable scientist ever said that all noncoding DNA was junk since they (we) all knew about noncoding genes, regulatory sequences, centromeres, and origins of replication, all of which are functional noncoding DNA. We now know that about 1% of our genome is coding sequences and about 9% is functional noncoding DNA. The other 90% is junk.

[Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means]

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Mattick, J.S. (2007) A new paradigm for developmental biology. Journal of Experimental Biology 210:1526-1547. [doi: 10.1242/jeb.005017]

Gibbs, W.W. (2003) The unseen genome: gems among the junk. Scientific American 289:46-53.

James Shapiro doesn't like junk DNA

Shapiro doubles down on his claim that junk DNA doesn't exist.

It's been a while since we've heard from James Shaprio. You might recall that James A. Shapiro is a biochemistry/microbiology professor at the University of Chicago and the author of a book promoting natural genetic engineering. I reviewed his book and didn't like it very much—Shapiro didn't like my review [James Shapiro Never Learns] [James Shapiro Responds to My Review of His Book].

John Parrington and the C-value paradox

We are discussing John Parrington's book The Deeper Genome: Why there is more to the human genome than meets the eye. This is the second of five posts on: Five Things You Should Know if You Want to Participate in the Junk DNA Debate

1. Genetic load

John Parrington and the genetic load argument

2. C-Value paradox (this post)

John Parrington and the c-value paradox

3. Modern evolutionary theory

John Parrington and modern evolutionary theory

4. Pseudogenes and broken genes are junk

John Parrington discusses pseudogenes and broken genes

5. Most of the genome is not conserved

John Parrington discusses genome sequence conservation

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2. C-Value paradox

Parrington addresses this issue on page 63 by describing experiments from the late 1960s showing that there was a great deal of noncoding DNA in our genome and that only a few percent of the genome was devoted to encoding proteins. He also notes that the differences in genome sizes of similar species gave rise to the possibility that most of our genome was junk. Five pages later (page 69) he reports that scientists were surprised to find only 30,000 protein-coding genes when the sequence of the human genome was published—"... the other big surprise was how little of our genomes are devoted to protein-coding sequence."

Contradictory stuff like that makes it every hard to follow his argument. On the one hand, he recognizes that scientists have known for 50 years that only 2% of our genome encodes proteins but, on the other hand, they were "surprised" to find this confirmed when the human genome sequence was published.

He spends a great deal of Chapter 4 explaining the existence of introns and claims that "over 90 per cent of our genes are alternatively spliced" (page 66). This seems to be offered as an explanation for all the excess noncoding DNA but he isn't explicit.

In spite of the fact that genome comparisons are a very important part of this debate, Parrington doesn't return to this point until Chapter 10 ("Code, Non-code, Garbage, and Junk").

We know that the C-Value Paradox isn't really a paradox because most of the excess DNA in various genomes is junk. There isn't any other explanation that makes sense of the data. I don't think Parrington appreciates the significance of this explanation.

The examples quoted in Chapter 10 are the lungfish, with a huge genome, and the pufferfish (Fugu), with a genome much smaller than ours. This requires an explanation if you are going to argue that most of the human genome is functional. Here's Parrington's explanation ...

Yet, despite having a genome only one eighth the size of ours, Fugu possesses a similar number of genes. This disparity raises questions about the wisdom of assigning functionality to the vast majority of the human genome, since, by the same token, this could imply that lungfish are far more complex than us from a genomic perspective, while the smaller amount of non-protein-coding DNA in the Fugu genome suggests the loss of such DNA is perfectly compatible with life in a multicellular organism.

Not everyone is convinced about the value of these examples though, John Mattick, for instance, believes that organisms with a much greater amount of DNA than humans can be dismissed as exceptions because they are 'polyploid', that is, their cells have far more than the normal two copies of each gene, or their genomes contain an unusually high proportion of inactive transposons.

In other words, organisms with larger genomes seem to be perfectly happy carrying around a lot of junk DNA! What kind of an argument is that?

Mattick is also not convinced that Fugu provides a good example of a complex organism with no non-coding DNA. Instead, he points out that 89% of this pufferfish's DNA is still non-protein-coding, so the often-made claim that this is an example of a multicellular organism without such DNA is misleading.

[Mattick has been] a true visionary in his field; he has demonstrated an extraordinary degree of perseverance and ingenuity in gradually proving his hypothesis over the course of 18 years.

Hugo Award Committee Seriously? That's the best argument he has? He and Mattick misrepresent what scientists say about the pufferfish genome—nobody claims that the entire genome encodes proteins—then they ignore the main point; namely, why do humans need so much more DNA? Is it because we are polyploid?

It's safe to say that John Parrington doesn't understand the C-value argument. We already know that Mattick doesn't understand it and neither does Jonathan Wells, who also wrote a book on junk DNA [John Mattick vs. Jonathan Wells]. I suppose John Parrington prefers to quote Mattick instead of Jonathan Wells—even though they use the same arguments—because Mattick has received an award from the Human Genome Organization (HUGO) for his ideas and Wells hasn't [John Mattick Wins Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research].

For further proof that Parrington has not done his homework, I note that the Onion Test [The Case for Junk DNA: The onion test ] isn't mentioned anywhere in his book. When people dismiss or ignore the Onion Test, it usually means they don't understand it. (For a spectacular example of such misunderstanding, see: Why the "Onion Test" Fails as an Argument for "Junk DNA").

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When philosophers talk about genomes

Postgenomics is a compendium of twelve scholarly articles by philosophers and sociologists who write about the implication of the human genome sequence and subsequent work on interpreting the results. The volume is edited by Sarah Richardson, a professor in Social Sciences (History of Science) at Harvard University (Boston, Massachusetts, USA), and by Hallam Stevens, a professor of History at Nanyang Technology University in Singapore (Singapore).


The first essay is by Stevens and Richardson and it outlines the goal of the book.

Ed Yong Updates His Post on the ENCODE Papers

For decades we've known that less than 2% of the human genome consists of exons and that protein encoding genes represent more than 20% of the genome. (Introns account for the difference between exons and genes.) [What's in Your Genome?]. There are about 20,500 protein-encoding genes in our genome and about 4,000 genes that encode functional RNAs for a total of about 25,000 genes [Humans Have Only 20,500 Protein-Encoding Genes]. That's a little less than the number predicted by knowledgeable scientists over four decades ago [False History and the Number of Genes]. The definition of "gene" is somewhat open-ended but, at the very least, a gene has to have a function [Must a Gene Have a Function?].

We've known about all kinds of noncoding DNA that's functional, including origins of replication, centromeres, genes for functional RNAs, telomeres, and regulatory DNA. Together these functional parts of the genome make up almost 10% of the total. (Most of the DNA giving rise to introns is junk in the sense that it is not serving any function.) The idea that all noncoding DNA is junk is a myth propagated by scientists (and journalists) who don't know their history.

We've known about the genetic load argument since 1968 and we've known about the C-Value "Paradox" and it's consequences since the early 1970's. We've known about pseudogenes and we've known that almost 50% of our genome is littered with dead transposons and bits of transposons. We've known that about 3% of our genome consists of highly repetitive DNA that is not transcribed or expressed in any way. Most of this DNA is functional and a lot of it is not included in the sequenced human genome [How Much of Our Genome Is Sequenced?]. All of this evidence indicates that most of our genome is junk. This conclusion is consistent with what we know about evolution and it's consistent with what we know about genome sizes and the C-Value "Paradox." It also helps us understand why there's no correlation between genome size and complexity.

Do plants have junk DNA?

Current Opinion in Plant Biology has a special edition devoted to Genome studies and molecular genetics 2024. The only paper (so far) that discusses plant genomes is one devoted to RNAs. Here's the abstract ...

Anyatama, A., Datta, T., Dwivedi, S. and Trivedi, P.K. (2024) Transcriptional junk: Waste or a key regulator in diverse biological processes? Current Opinion in Plant Biology 82:102639. [doi: 10.1016/j.pbi.2024.102639]

Plant genomes, through their evolutionary journey, have developed a complex composition that includes not only protein-coding sequences but also a significant amount of non-coding DNA, repetitive sequences, and transposable elements, traditionally labeled as “junk DNA”. RNA molecules from these regions, labeled as “transcriptional junk,” include non-coding RNAs, alternatively spliced transcripts, untranslated regions (UTRs), and short open reading frames (sORFs). However, recent research shows that this genetic material plays crucial roles in gene regulation, affecting plant growth, development, hormonal balance, and responses to stresses. Additionally, some of these regulatory regions encode small proteins, such as miRNA-encoded peptides (miPEPs) and microProteins (miPs), which interact with DNA or nuclear proteins, leading to chromatin remodeling and modulation of gene expression. This review aims to consolidate our understanding of the diverse roles that these so-called “transcriptional junk” regions play in regulating various physiological processes in plants.

Restarting the function wars (The Function Wars Part V)

The term "function wars" refers to debates over the meaning of the word "function" in biology. It refers specifically to the discussion about junk DNA because junk DNA is defined as DNA that does not have a biological function. The wars were (re-)started when the ENCODE Consortium decided to use a stupid definition of function in order to prove that most of our genome was functional. This prompted a number of papers attempting to create a more meaningful definition.

None of them succeeded, in my opinion, because biology is messy and doesn't lend itself to precise definitions. Look how difficult it is to define a "gene," for example. Or "evolution."

Nevertheless, some progress was made. Dan Graur has recently posted a summary of the two most important definitions of function [What does “function” mean in the context of evolution & what absurd situations may arise by using the wrong definition?]. The two definitions are "selected-effect" and "causal-role" (there are synonyms).

Evelyn Fox Keller (1936 - 2023) and junk DNA

Evelyn Fox Keller died a few days ago (Sept. 22, 2023). She was a professor of History and Philosopher of Science at the Massachusetts Institute of Technology (Boston, MA, USA). Most of the obituaries praise her for her promotion of women scientists and her critiques of science as a male-dominated discipline. More recently, she turned her attention to molecular biology and genomics and many philosophers (and others) seem to think that she made notable contributions in that area as well.

Minimum Centromere Size in Plants

In an earlier posting we examined the structure and organization of centromere DNA. In mammals, the centromere consists of multiple tandem repeats of a 180 bp sequence. There are usually thousands of these repeats at each of the 23 centromeres giving an average size of about 3 Mb (3000 Kb) per centromere. The total amount of centromeric DNA amounts to about 2% of the entire human genome [Centromere DNA].

We assumed that all of this DNA was essential and none of it is junk DNA. However, we know that's not a correct assumption since there are many variants at each centromere. If we were to take the minimum size for each functional centromere, the total amount of essential DNA would be much less (probably <1% of the genome). Many workers are trying to figure out how much DNA is required in order to have a functional centromere. One approach is to identify abnormal chromosomes that segregate normally at mitosis with only a small number of repeats at their centromeres. THEME

Genomes & Junk DNA

Total Junk so far

    54%
In the latest issue of PNAS, Murata et al. (2008) looked at small minichromosomes in the plant Arabidposis thaliana. The minichromosomes were produced as a by-product of a transformation experiment that inserted T-DNA into the centromere of chromosome 2.

The five standard chromosomes of Arabidopsis each have centromeres consisting of about 1600 copies of a 180 bp repeat (avergae size 2.7 Mb - 3.0 Mb. The four minichromosomes, α, β, γ, and δ, have centromeres ranging in size from 0.5 Mb to 2.3 Mb. The δ minichromosome appears to segregate normally with only 500 Kb of centromere DNA (about 2800 repeats). This may be close to the minimum size required to assemble a kinetochore.

If this minimum size is true in mammals well—a reasonable assumption—then perhaps only 15-20% of centromere DNA is actually essential and the rest is excess junk DNA produced by unequal cross-overs and DNA replication slippage. Because expansion and contraction of repetitive DNA is unavoidable, there will be considerable variation within a population. Individuals that have close to the minimum amount of DNA at any one centromere will be underrepresented in the population because many of their offspring will have died. Individuals with a large excess of centromere DNA will be overrepresented because their lineages are less likely to encounter lethal deletions. (Provided that there is no fitness penalty for carrying excess DNA.)

Thus, in a certain sense, some of the "excess" centromeric DNA is required as a buffer against the possibility of future deletions. The extra DNA does not contribute to the viability of the individual carrying it but it does contribute to the survival of that individual's offspring. At some point, the potential advantage in terms of offspring survival will become too small to have any influence on the lineage of an individual. This will define the maximum amount of "excess" DNA at the centromere. I wonder if it is possible to model the effect of having extra centromeric DNA?

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Murata, M., Yokota, E., Shibata, F. and Kashihara, K. (2008) Functional analysis of the Arabidopsis centromere by T-DNA insertion-induced centromere breakage. Proc. Natl. Acad. Sci. (USA) 105:7511-7516. [PubMed] [doi:10.1073/pnas.0802828105]

Junk DNA in New Scientist

I just got my copy of the July 14th issue of New Scientist so I can comment on the article Why 'junk DNA' may be useful after all by Aria Pearson. RPM at evolvgen thinks it's pretty good [Junk on Junk] and so does Ryan Gregory at Genomicron [New Scientist gets it right]. I agree. It's one of the best articles on the subject that I've seen in a long time.

First off, Aria Pearson does not make the common mistake of assuming that junk DNA is equivalent to non-coding DNA. The article makes this very clear by pointing out that we've known about regulatory sequences since the 1970's. The main point of the article is to discuss recent results that reveal new functions for some of the previously unidentified non-coding DNA that was classified as junk.

One such result is that reported Pennacchio et al. (2006) in Nature last year. They analyzed sequences in the human genome that showed a high degree of identity to sequences in the pufferfish genome. The idea is that these presumably conserved sequences must have a function. Pennacchio et al. (2006) tested them to see it they would help regulate gene expression and they found that 45% of the ones they tested functioned as enhancers. In other words, they stimulated the expression of adjacent genes in a tissue specific manner. The authors estimate that about half of the "conserved" elements play a role in regulating gene expression.

There are a total of 3,124 conserved elements and their average length is 1,270 bp. This accounts for 3.9 × 10⁶ bp out of a total genome size of 3.2 × 10⁹ bp or about 0.1% of the genome. The New Scientist article acknowledges, correctly, that more than 95% of the genome could still be junk.

Is this all junk DNA? Unlike most other science journalists, Pearson addresses this question with a certain amount of skepticism and she makes an effort to quote conflicting opinions. For example, Pearson mentions experiments claiming that ~90% of the genome is transcribed. Rather than just repeating the hype of the researchers making this claim, Pearson quotes skeptics who argue that this RNA might be just "noise."

Most articles on junk DNA eventually get around to mentioning John Mattick who has been very vocal about his claim that the Central Dogma has been overturned and most of the genome consists of genes that encode regulatory RNAs (Mattick, 2004; Mattick, 2007). This article quotes a skeptic to provide some sense of balance and demonstrate that the scientific community is not overly supportive of Mattick.

Others are less convinced. Ewan Birney of the European Bioinformatics Institute in Cambridge, UK, has bet Mattick that of the processed RNAs yet to be assigned a function - representing 14 per cent of the entire genome - less than 20 per cent will turn out to be useful. "I'll get a case of vintage champagne if I win," Birney says.

Under the subtitle "Mostly Useless," Pearson correctly summarizes the scientific consensus. (I wish she had used this as the title of the article. The actual title is somewhat misleading. Editors?)

Whatever the answer turns out to be, no one is saying that most of our genome is vital after all. "You could chuck three-quarters of it," Birney speculates. "If you put a gun to my head, I'd say 10 per cent has a function, maybe," says Lunter. "It's very unlikely to be higher than 50 per cent."

Most researchers agree that 50 per cent is the top limit because half of our genome consists of endless copies of parasitic DNA or "transposons", which do nothing except copy and paste themselves all over the genome until they are inactivated by random mutations. A handful are still active in our genome and can cause diseases such as breast cancer if they land in or near vital genes.

The ENCODE project made a big splash in the blogosphere last month (ENCODE Project Consortium, 2007). This study purported to show that much of the human genome was transcribed, leading to the suggestion that most of what we think is junk actually has some function. Aria Pearson interviewed Ewan Birney (see above) who is involved in the ENCODE project.

The real surprise is that ENCODE has identified many non-coding sequences in humans that seem to have a function, yet are not conserved in rats and mice. There seem to be just as many of these non-conserved functional sequences as there are conserved ones. One explanation is that these are the crucial sequences that make humans different from mice. However, Birney thinks this is likely to be true of only a tiny proportion of these non-conserved yet functional sequences. Instead, he thinks most are neutral. "They have appeared by chance and neither hinder nor help the organism."

Put another way, just because a certain piece of DNA can do something doesn't mean we really need it to do whatever it does. Such DNA may be very like computer bloatware: functional in one sense yet useless as far as users are concerned.

This is a perspective you don't often see in popular articles about junk DNA and Pearson is to be commended for taking the time and effort to find the right scientific perspective.

The article concludes by reporting the efforts to delete large amounts of mouse DNA in order to test whether they are junk or not. The results show that much of the conserved bits of DNA can be removed without any harmful effects. Some researchers urge caution by pointing out that very small effects may not be observed in laboratory mice but may be important for evolution in the long term.

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ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816. [PubMed Abstract]

Mattick, J.S. (2004) The hidden genetic program of complex organisms. Sci. Am. 291:60-7.

Mattick, J.S. (2007) A new paradigm for developmental biology. J. Exp. Biol. 210:1526-47. [PubMed Abstract].

Pennacchio, L.A., Ahituv, N., Moses, A.M., Prabhakar, S., Nobrega, M.A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K.D., Plajzer-Frick, I., Akiyama, J., De Val, S., Afzal, V., Black, B.L., Couronne, O., Eisen, M.B., Visel, A., Rubin, E.M. (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature 444(7118):499-502.

Junk & Jonathan: Part 4—Chapter 1

I received a copy of the book a few days ago and this is my first posting on its contents. For a list of other postings on this topic see the link to Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

This is a very small book. There's only 114 pages of text—it's more like a large pamphlet than a book. If I'd read it from front to back in one sitting it would only have taken an hour or so. But I couldn't read it in one go because nobody can put up with IDiot rhetoric for that long!

Chapter 1 is The Controversy over Darwinian Evolution. It has nothing to do with junk DNA.

Wells begins by telling his readers that evolution is a fact. By that he means "microevolution." Wells doesn't believe in macroevolution or common descent and he even challenges the evidence for speciation. As usual, he supports his claims with selected quotations from scientists.

Sixty year after Dobzansky wrote this, biologists had still not observed the origin of a new species ("speciation") by natural selection. In 1997, evolutionary biologist Keith Stewart Thomson wrote: "A matter of unfinished business for biologists is the identification of evolution's smoking gun," and "the smoking gun of evolution is speciation, not local adaptation and differentiation of populations."

Wells is telling his readers that as long as biologists have not directly observed a new species forming then speciation has not been demonstrated. This rules out all evidence from the fossil record and all evidence from molecular phylogeny. Nice trick.

Problem is, there's lots of lots of evidence for speciation, including some examples where speciation has been caught in the act. Wells, like most IDiots, doesn't understand how evolution works. He seems to think that new species will form overnight and that all biologist have to do is keep their eyes open and record the examples.

I don't know for sure whether Wells intends to emphasize speciation by natural selection when he claims that, "biologists had still not observed the origin of a new species ("speciation") by natural selection." If that's his intent then it's true that there are very few examples of true speciation (biological species concept) that can be attributed directly to natural selection. As Jerry Coyne points out, reproductive isolation is mostly due to accident (random genetic drift) and not natural selection [The Cause of Speciation]. That's in line with modern evolutionary theory and Coyne should know because he's one of the world's leading experts on speciation. [UPDATE: Coyne and some commenters have corrected me. Coyne actually does think that most speciation is due to natural selection. I'll stick with Futuyma as my authority. He's much more open to the idea of speciation by random genetic drift (Evolution 2nd ed. p. 447)]

There are two possibilities here. Either Wells is deliberately misleading his readers by emphasizing that speciation must occur by natural selection or he's ignorant of modern evolutionary theory. Since most IDiots have a concept of evolution that dates back to the nineteenth century, I'll go with the second explanation. However, there's almost certainly an element of deception in his remarks since Jonathan Wells has a long history of deliberately misrepresenting evolution.

Theme

Genomes
& Junk DNASo, Wells is dead wrong about the first point in his book. There's abundant evidence of speciation (and macroevolution) and, furthermore, modern evolutionary theory does not attribute speciation exclusively to adaptation (i.e. there's more to evolution than Darwinism).

The importance of Wells' rejection of macroevolution will become obvious later on in the book when he argues that Intelligent Design Creationism does not rule out common ancestry. He agrees that someone like Michael Behe can believe in common descent and still be a card-carrying IDiot.

By the way, Wells is clever enough to cover his bases in case speciation is ever observed.

Of course, even if scientists eventually observe the origin of a new species by natural selection, the observation would not mean that natural selection can also explain the origin of significantly new organs or body plans. But the fact that scientists have not observed even the first step in macroevolution means that "evolution's smoking gun" is still missing.

The rest of the chapter (three pages) is a re-hash of arguments Wells made in Icons of Evolution and elsewhere.

• The Cambrian Explosion "contradicts Darwin's theory that major differences should arise only after millions of years of evolution ...."
• Molecular evolution isn't accurate: "molecular evidence is plagued with inconsistencies." The rejection of molecular evidence as unreliable is going to cause problems for Wells later on since he relies on it for some of his arguments about junk DNA. As usual, the IDiots want to have their cake and eat it too.
• Homology is a circular argument, according to Wells, so you can't use homology as evidence for evolution. That's correct. Similarity is the evidence and homology is the conclusion. This flaw in Wells' reasoning has been pointed out to him repeatedly over the past decade but he ignores all criticism and continues to use arguments that have been refuted.
• The Haeckel drawings were fakes and, "The truth is that vertebrate embryos start out looking very different from each other, then they converge somewhat in appearance midway through development before diverging as they mature." This has nothing to do with junk DNA so I won't discuss the massive amount of embryological evidence for evolution.

Wells closes with,

So microevolution is a fact, supported by overwhelming evidence, but macroevolution remains an assumption, illustrated with icons that misrepresent the evidence or rely on circular reasoning. The icons are not science, but myth.

This sets the tone for the rest of the book. Even though it is filled with references to the scientific literature there's never any discussion of alternative hypotheses or conflicting data. This is not a book where the author wants to inform his readers about the exciting controversies and conflicts within science. This is a book where the author wants to promote creationism by attacking and misrepresenting evolution using faulty logic and untruths.

The next paragraph is quite interesting. He invokes the beliefs of Americans as support for his claims. Apparently they're much more perceptive that the typical evolutionary biologist. (I wonder what he thinks of Australians and Europeans?)

This may be one reason why—despite the Darwinists' near-monopoly over science education—most Americans still reject the doctrine that human beings evolved from ape-like ancestors by unguided processes such as random variation and survival of the fittest.

I think this means that Wells also rejects common ancestry. If so, it will mean that he can't use it to support any of his arguments later on in the book, right?

Finally, at the very end of the chapter we get to the point,

In the 1950s, neo-Darwinists equated genes with DNA sequences and assumed that their biological significance lay in the proteins the encoded. But when molecular biologists discovered in the 1970s that most of our DNA does not code for proteins, neo-Darwinists called non-protein-coding DNA "junk" and attributed it to molecular accidents that have accumulated in the course of evolution. Like peppered moths, Galapagos finches, Darwin's Tree of Life, homology in vertebrate limbs, and Haeckel's embryos, "junk DNA" has become an icon of evolution. But is it science of myth?

I've discussed Wells' ignorance of history in previous postings but, for the record, here are the facts.

• By the 1970s molecular biologist were well aware of the fact that non-protein coding genes existed (e.g. ribosomal RNA genes, tRNA genes etc.)
• By the 1970s molecular biologists knew of several functions of DNA sequences that weren't genes. Origins of replication and regulatory sequences were well-known but there were others.
• Even in the 1970s no knowledgeable molecular biologist could ever defend the idea that all non-coding DNA was junk. (It's true that there were some stupid scientists who weren't aware of tRNA genes and regulatory sequences and made silly statement because of their ignorance but they don't count.)
• By the 1970s junk DNA was a fact. The scientific controversy was over how much of our genome is junk. Is it the majority or only a small percentage?
• By the 1970s knowledgeable evolutionary biologists were well aware of the fact that most of our genome was mutating and evolving as though most changes were neutral (genetic load arguments). This didn't mean that most of our genome was junk but it did mean that the sequence couldn't be important or we would never be able to tolerate the genetic load. This was not common knowledge among biologists—still isn't.
• By the 1970s most molecular biologists were aware of the so-called "C-value paradox" where very closely related species have very different genome sizes. They correctly interpreted this to mean that the species with the large genomes probably didn't need all that extra DNA. (Up until now, Intelligent Design Creationists have not offered a reasonable answer to The Onion Test. Wells tries on Chapter 8.)
• The proponents of large amounts of junk DNA in our genome would hardly ever have referred to themselves as "Darwinist" or "neo-Darwinists." In fact, they tended to be among those evolutionary biologists who opposed adaptationism and favored Neutral Theory and random genetic drift. Pluralist concepts were much more compatible with the idea of significant amounts of junk DNA than strict "Darwinist" interpretations of genome evolution.

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Do the IDiots Understand Biochemistry and Molecular Biology?

 

We've been discussing whether Intelligent Design Creationists understand enough about biochemistry, molecular biology, and evolution to warrant their criticisms of these fields. The answer is clearly "no" as they demonstrate time and time again.

This time it's an anonymous posting on the premier IDC website, Evolution News & Views [Long Non-coding RNA Punches Another Hole in "Junk Genome" Myth]. The anonymous poster links to a recent paper in Genes & Development that shows a function for a particular long non-coding (lnc) RNA. The paper implies that many of these lncRNAs (up to 400) are expressed in mouse erythroid cells.

Regulatory RNA have been known and studied for at least four decades and various lncRNAs have been characterized over the past twenty years. The IDiot at Evolution News & Views seems to think that this is a new discovery proving that there's no junk in our genome. The facts are quite different.

As I pointed out in my review of The Myth of Junk DNA, the amount of the genome devoted to producing lncRNAs is about 0.1% [Junk & Jonathan: Part 6—Chapter 3]. So, not only have we known about regulatory RNAs for many years, we also know that their genes don't account for very much of the genome, I figure it can't be more than 2% even when you include all of the most optimistic estimates of regulatory RNAs [see What's in Your Genome?].

But the ignorance of the IDiots is much more profound than just being incapable of calculating percentages. The latest posting reveals the depth of their ignorance.

These findings have two important implications. First, non-coding regions of the genome were assumed to be leftover evolutionary relics that no longer play a functional role. The assumption was not due to extensive studies of non-coding regions of the genome, but rather to a commitment to what is known as the central dogma of molecular biology: DNA is transcribed into RNA and RNA is translated into amino acids to make proteins. This was considered the primary purpose of DNA. The non-coding regions were assumed to have no function, and were dismissed as the natural consequence of genetic "junk" accumulating over time. This paper is one among an accumulating corpus of papers discussing new and interesting functions of the non-coding regions of the genome. (See The Myth of Junk DNA by Jonathan Wells for a history of "junk" DNA and additional references describing the function of so-called "junk" DNA. See here for a discussion on the regulatory role of introns.)

There was never a time in the past fifty years when knowledgeable biochemists and molecular biologists thought that all non-coding DNA was nonfunctional junk. This was never an assumption of the Central Dogma of Molecular Biology which states that "... once (sequential) information has passed into protein it cannot get out again" [Basic Concepts: The Central Dogma of Molecular Biology]. There are many scientists who have misconceptions about the Central Dogma [The Central Dogma Strawman] but the IDiots go one step farther by misunderstanding the misconception!

We've known about functions in non-coding DNA since the early 1960s as anyone who has ever glanced at a textbook would know. It's hard to tell whether the IDiots are just butt-ignorant of basic science or whether they are lying. This is an especially tricky problem when the silly strawman argument is popularized by Jonathan Wells because he's supposed to know the science [Junk & Jonathan: Part 1—Getting the History Correct] [Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?].

We know that most of our genome is junk because we know a great deal about genomes, genes, biochemistry, molecular biology, and evolution. We know which parts are likely to be functional and which parts are likely to be broken genes and other kinds of junk. We know this because we understand the subject, not because we are covering up our ignorance.

The IDiots are ignorant of the science and they assume that everyone else is as well. That's a very bad assumption.

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Educating an Intelligent Design Creationist: Evidence for Junk

I'm replying to a post by andyjones (More and more) Function, the evolution-free gospel of ENCODE. That was the fourth post in an exchange between me and him. In response to his latest post, I'm working my way through five issues that Intelligent Design Creationists need to understand. So far, we've covered four of them.

Educating an Intelligent Design Creationist: Introduction
Educating an Intelligent Design Creationist: Pervasive Transcription
Educating an Intelligent Design Creationist: Rare Transcripts
Educating an Intelligent Design Creationist: The Specificity of DNA Binding Proteins
Educating an Intelligent Design Creationist: The Meaning of Darwinism

Intelligent Design Creationists have difficulty understanding the arguments for junk DNA and the evidence that supports those arguments. We try to explain the genetic load argument but it doesn't seem to penetrate. We try to explain that half of our genome is composed of defective transposons and viruses—often fragments of the intact genes. This doesn't phase them. And no matter how many times we describe the "C-value Paradox" and why junk DNA resolves the paradox, that evidence is ignored. We patiently describe the megabase pair deletions of the mouse genome and why this is evidence of junk. We teach them about copy number variation in the human genome and why DNA fingerprinting works. We show them examples of deletions and insertions in the genomes of different individuals telling them that these seem to have no effect as far as we know. We take time to explain modern evolutionary theory and why it is consistent with junk DNA. Finally, we describe our detailed textbook understanding of transcription and DNA binding proteins and they don't listen.

Andyjones says,

The fact that some very good scientists have not found functions for all of the genome does not negate the many functions they have found so far, for many classes of genetic element, including those commonly classed as ‘junk’. And they are still working. Part of the problem is this: if a layperson were to take apart a microchip, would he be able to discern the function of all the parts at the first attempt? Probably not. The problem is not lack of intelligence, but an early lack of understanding of the principles by which the thing is built. As soon as he understands a particular design principle, suddenly huge areas of the chip will be comprehensible to him. I humbly suggest that we have a number of such minor revolutions ahead of us in molecular biology. We are making great strides, but we do not yet understand all the principles of the transcriptome never mind the whole interactome. Perhaps there is more to learn about binding sites for RNAP? Or take pseudogenes: they have already been found to function in some cases as regulators, through their RNA transcripts interacting with real gene RNA transcripts. Then, alternative splicing is only partly understood. Who knows what other mechanisms operate at the RNA level? If you can’t imagine the function yet, it can be pretty hard to find it. But if one asserts there is no function (for example for rare transcripts) like Larry does, it will be even harder to find it.

This is a common theme among the Intelligent Design Creationists and, in fairness, among many molecular biologists. They think that junk DNA is simply an expression of ignorance. They ignore everything we tell them. They think that just because they don't understand something then nobody else does either.

In spite of what our opponents say, we actually have a pretty good understanding of the principles behind how a genome is built. Population genetics tells us that it ain't designed.

When I assert that rare transcripts probably have no function I'm not just talking through my hat and I'm not the only biochemist who says that. When I say that one million little bits and pieces of Alu SINES are very unlikely to have a function, that's not just idle speculation. When the ENCODE workers try to tell me that most of the genome is a huge web of 636,336 regulatory sequences, I can test this claim against the vast amount of information that we already know about genomes and transcriptional regulation and declare that this makes no sense. These are not arguments from ignorance.

Opponents of junk DNA are never going to be credible unless they tell us why the genetic load argument is invalid. They need to explain how their ideas comport with the data on genome size (The Onion Test). They need to explain why the average gene needs 5000 regulatory sites. They need to come up with a reasonable explanation for lack of sequence conservation. They need to tell us why the vast majority of defective transposons evolved a function.

Opponents of junk DNA need to address the arguments and evidence for junk DNA and stop pretending that those arguments don't exist.

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What's in Your Genome?

The total size of the human genome is estimated to be 3.2 × 10⁹ bp [How Big Is the Human Genome?]. Here are the major components.

Transposable Elements: (44% junk)

   DNA transposons:

• active (functional): <0.1%


• defective (nonfunctional): 3%

   retrotransposons:

• active (functional):<0.1%


• defective transposons
              (full-length, nonfunctional): 8%
              L1 LINES (fragments, nonfunctional): 16%
              other LINES: 4%
              SINES (small pseudogene fragments): 13%


• co-opted transposons/fragments: <0.1% ^a

  ^aCo-opted transposons and transposon fragments are those that have secondarily acquired a new function.

Viruses (9% junk)

   DNA viruses

• active (functional): <0.1%


• defective DNA viruses: ~1%

   RNA viruses

• active (functional): <0.1%


• defective (nonfunctional): 8%


• co-opted RNA viruses: <0.1% ^b

  ^bCo-opted RNA viruses are defective integrated virus genomes that have secondarily acquired a new function.

Pseudogenes (1.2% junk)

• (from protein-encoding genes): 1.2% junk
• co-opted pseudogenes: <0.1% ^c

  ^cCo-opted pseudogenes are formerly defective pseudogenes those that have secondarily acquired a new function.

Ribosomal RNA genes:

• essential 0.22%
• junk 0.19%

Other RNA encoding genes

• tRNA genes: <0.1% (essential)


• known small RNA genes: <0.1% (essential)


• putative regulatory RNAs: ~2% (essential)

Protein-encoding genes: (9.6% junk)

• transcribed region:
              essential 1.8%
              intron junk (not included above) 9.6% ^d

  ^dIntrons sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.

Regulatory sequences:

• essential 0.6%

Origins of DNA replication

• <0.1% (essential)

Scaffold attachment regions (SARS)

• <0.1% (essential)

Highly Repetitive DNA (2% junk)

• α-satellite DNA (centromeres)
• essential 1.0%
• non-essential 2.0%
• telomeres
• essential (less than 1000 kb, insignificant)

Intergenic DNA (not included above)

• conserved 2% (essential)
• non-conserved 26.3% (unknown but probably junk)

Theme Genomes & Junk DNATotal Essential/Functional (so far) = 7.7% Total Junk (so far) = 65% Unknown (probably mostly junk) = 27.3%

For references and further information click on the "Genomes & Junk DNA" link in the box

LAST UPDATES: May 10, 2011 (fixed totals, and ribosomal RNA calculations)
June 3, 2011 (added total genome size)
February 5, 2013 (reformatted)

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The IDiots Don't Understand Junk DNA

So what else is new?

The chief IDiot (Casey Luskin) over at Discovery Institute claims that junk DNA is a science-stopper. This is such old news.

Every time scientists find a function for some non-coding DNA we are treated to another diatribe against junk DNA. In fairness, it's not just the IDiots who do this. Some so-called scientists are just as guilty. They don't understand junk DNA.

Here's a clue. Junk DNA is DNA that has no function. It is not non-coding DNA. Lots of non-coding DNA has a function (regulatory sequences, origins of replication, centromeres, telomeres, SARs, etc. etc). But, in mammals, most of it doesn't. Most of the human genome is junk.

Just because we discover a function for some little bit of non-coding DNA does not mean that all of it has a function. Use your head. This is elementary rationalism. Oops, I almost forgot, that's not their strong point.

Think of pseudogenes or degenerative alu sequences, for example. They will always be junk DNA.