Dark DNA and the New Mechanism of Evolution?

Here is an article on the issue of Dark DNA.

Dark DNA got its name from the cosmological phenomenon called Dark Matter – the undetectable 25% of the mass of the universe that scientists know exists because they can detect its effects…

Similarly Dark DNA has eluded the sequencing of the genomes and yet scientists know it must exist because they see its effects, such as in case of the sand rat…

“My colleagues and I first encountered this phenomenon when sequencing the genome of the sand rat (Psammomys obesus), a species of gerbil that lives in deserts. In particular we wanted to study the gerbil’s genes related to the production of insulin, to understand why this animal is particularly susceptible to type 2 diabetes.

But when we looked for a gene called Pdx1 that controls the secretion of insulin, we found it was missing, as were 87 other genes surrounding it. Some of these missing genes, including Pdx1, are essential and without them an animal cannot survive. So where are they?

The first clue was that, in several of the sand rat’s body tissues, we found the chemical products that the instructions from the “missing” genes would create. This would only be possible if the genes were present somewhere in the genome, indicating that they weren’t really missing but just hidden…”

This is something John Harshman and other bird lovers should like:

“…This kind of dark DNA has previously been found in birds. Scientists have found that 274 genes are “missing” from currently sequenced bird genomes. These include the gene for leptin (a hormone that regulates energy balance), which scientists have been unable to find for many years. Once again, these genes have a very high GC content and their products are found in the birds’ body tissues, even though the genes appear to be missing from the genome sequences…”

It seems that the so-called  “junk DNA” and evolution itself with its mechanism need a major rethink due to new things like dark DNA…

Is it going to happen? I doubt that very much…

19 Replies to “Dark DNA and the New Mechanism of Evolution?”

  1. J-Mac
    Ignored
    says:

    This is an old issue…but it keeps coming up in the many different science mags…
    Junk DNA is the issue that drove a wedge between ENCODE and hard-core Darwinists… Dark DNA is just another step towards the reconciliation, I think, provided PZ. Myers, Dan Grour, Larry Moran, John Harshman, Joe Felsenstein and many others are willing to accept the reality of scientific evidence over their religious dogma…

    The question remains though…Will they?

  2. Entropy Entropy
    Ignored
    says:

    The fact that some DNA strands are hard to sequence, because they’re too rich in GC for example, is not surprising. This has been known for eons. Why should we change the way we think about evolution? How does it follow that evolution and junk-DNA have to be rethought from “these sequences are very hard to obtain”?

    P.S. That’s an interesting article. Thanks for linking to it.

  3. John Harshman John Harshman
    Ignored
    says:

    This is just silly. Genes with a high GC content are hard to amplify and hard to sequence, but “dark DNA” is a silly name that implies (though vaguely) something much more mysterious and important. The mystery and importance are not actually there.

    This has nothing at all to do with junk DNA either, just protein-coding genes with unusually high GC content.

  4. J-Mac
    Ignored
    says:

    John Harshman:
    This is just silly. Genes with a high GC content are hard to amplify and hard to sequence, but “dark DNA” is a silly name that implies (though vaguely) something much more mysterious and important. The mystery and importance are not actually there.

    This has nothing at all to do with junk DNA either, just protein-coding genes with unusually high GC content.

    Thanks John.
    If it happens that the so-called “junk DNA” has something to do with this issue, can I count on your support?
    I’m sure that an open-minded scientists like yourself would mind, would you?

  5. Neil Rickert
    Ignored
    says:

    John Harshman: The mystery and importance are not actually there.

    And that why it’s a mystery — what could be more mysterious than not being there!

    Mystery = gap = evidence for god of the gaps.

    Just what the ID people need (while denying that they are for a god of the gaps)

  6. John Harshman John Harshman
    Ignored
    says:

    J-Mac: If it happens that the so-called “junk DNA” has something to do with this issue, can I count on your support?

    What do you mean by “your support”? If it turns out that junk DNA has something to do with “dark DNA”, I will certainly agree that it does.

  7. John Harshman John Harshman
    Ignored
    says:

    Neil Rickert: Mystery = gap = evidence for god of the gaps.

    Sure, but my point is that there is no mystery and no gap.

  8. Neil Rickert
    Ignored
    says:

    John Harshman: Sure, but my point is that there is no mystery and no gap.

    But you are referring to real gaps and real mysteries. The trouble with real gaps, is that they can be disproved.

    The imagined gaps and imagined mysteries are far more persuasive, because they are impossible to disprove.

  9. Entropy Entropy
    Ignored
    says:

    I insist: what kind of logic connects: “this DNA is very hard to sequence” to “therefore junk-DNA and evolution should be revised”?

  10. John Harshman John Harshman
    Ignored
    says:

    Neil Rickert: But you are referring to real gaps and real mysteries.The trouble with real gaps, is that they can be disproved.

    No, I’m not. Why would you think so? Also, it makes no sense to say that real gaps can be disproved; if they’re real, any supposed disproof is false. Or did you mean to say something else?

  11. DNA_Jock
    Ignored
    says:

    Holy shit, people will grasp at anything.
    Your first link (Hron et al. 2015) demonstrates that the “missing genes” of your second link (Lovell et al. 2014) are an artefact of whole genome sequencing techniques: by and large, they are not “missing” at all, merely absent from the alignment, due to a combination of high CG-content (which leads to fewer reads in the dataset) and being surrounded by low complexity repetitive and palindromic repeats (which causes them to be excluded from the final alignment in error (as Seroussi et al. 2016, your third link, explains)).
    Specifically, if your whole genome alignment lacks some supposedly essential gene, say leptin or EPO, yet you find the effing gene product in the organism, it’s a pretty good bet that your alignment dropped the sequence in error. Sure enough, if you go looking for the “missing” gene, you find it.
    Learn about whole genome sequencing and contig alignment techniques.

  12. Rumraket Rumraket
    Ignored
    says:

    J-Mac: This is an old issue…but it keeps coming up in the many different science mags…

    Stop reading science mags and read publications from the primary literature instead. Get enough education to be able to understand the methods, then read the results, then read the discussion and conclusion, then form your own conclusion.

    Simply don’t read popular press articles that report on scientific results, they are often sensationalistic, overdramatized, blow up discussion and disagreement into epic international controversies, and mostly wrong.

    They do this to get your attention, in effect by being clickbait. It’s really just a reflection of how news that doesn’t involve someone being stabbed, or sex-scandals, has a hard time being seen in the marketplace. For those reasons alone you should stay away from reporting on science in the popular press.

  13. Rumraket Rumraket
    Ignored
    says:

    Entropy:
    I insist: what kind of logic connects: “this DNA is very hard to sequence” to “therefore junk-DNA and evolution should be revised”?

    The logic of a total lack of education in the relevant fields.

  14. GlenDavidson
    Ignored
    says:

    Once again evolution seems more capable of mutation over a relatively short time than was thought possible, and of course the creationist misses the point and tries to make it about “junk DNA.” True, it might carve out a small amount of “junk,” nothing new or generally unexpected, but barely relevant to “junk DNA” at all.

    Excessive mutation will often stop a gene from working, yet somehow the sand rat’s genes manage to still fulfil their roles despite radical change to the DNA sequence. This is a very difficult task for genes. It’s like winning Countdown using only vowels.

    This is what is interesting. Your typical creationist dullard claims that evolution can’t occur because there is very little functionality, while in at least this case the mutations have been frequent enough to allow genes that are readily sequenced in relatives to “hide” because of their high GC content. The lesson is that genes can change a great deal and still function in at least some cases.

    That evolution can be even more tolerant of change than is typically thought predictably is ignored by the creationists, who just blather on about junk DNA, and project their religious dogma onto others. Well, we didn’t expect insight from them, and of course we didn’t get it.

    Glen Davidson

  15. J-Mac
    Ignored
    says:

    Rumraket:

    Is Nature also a bad science mag?

    “‘Dark matter’ DNA influences brain development

    Researchers are finally figuring out the purpose behind some genome sequences that are nearly identical across vertebrates.

    A puzzle posed by segments of ‘dark matter’ in genomes — long, winding strands of DNA with no obvious functions — has teased scientists for more than a decade. Now, a team has finally solved the riddle.

    The conundrum has centred on DNA sequences that do not encode proteins, and yet remain identical across a broad range of animals. By deleting some of these ‘ultraconserved elements’, researchers have found that these sequences guide brain development by fine-tuning the expression of protein-coding genes.

    The results1, published on 18 January in Cell, might help researchers to better understand neurological diseases such as Alzheimer’s. They also validate the hypotheses of scientists who have speculated that all ultraconserved elements are vital to life — despite the fact that researchers knew very little about their functions.

    “People told us we should have waited to publish until we knew what they did. Now I’m like, dude, it took 14 years to figure this out,” says Gill Bejerano, a genomicist at Stanford University in California, who described ultraconserved elements in 20042.

    When nothing happens

    Bejerano and his colleagues originally noticed ultraconserved elements when they compared the human genome to those of mice, rats and chickens, and found 481 stretches of DNA that were incredibly similar across the species. That was surprising, because DNA mutates from generation to generation — and these animal lineages have been evolving independently for up to 200 million years.

    Genes that encode proteins tend to have relatively few mutations because if those changes disrupt the corresponding protein and the animal dies before reproducing, the mutated gene isn’t passed down to offspring. On the basis of this logic, some genomicists suspected that natural selection had similarly weeded out mutations in ultraconserved regions. Even though the sequences do not encode proteins, they thought, their functions must be so vital that they cannot tolerate imperfection.

    But this hypothesis hit a road block in 2007, when a team reported knocking out four ultraconserved elements in mice — and found that the animals looked fine and reproduced normally3. “That was shocking — those mice should have been dead,” says Diane Dickel, a genomicist at Lawrence Berkeley National Laboratory in California, and first author of the study in Cell1.

    A closer look

    Dickel and her colleagues revisited the problem using the gene-editing tool CRISPR–Cas9. In mice, they deleted four ultraconserved elements — individually and in various combinations — that lie within regions of DNA that also contain genes important in brain development. Again, the mice looked okay. But when the investigators dissected the rodents’ brains, they discovered abnormalities.

    Mice lacking certain sequences had abnormally low numbers of brain cells that have been implicated in the progression of Alzheimer’s disease. And those with another ultraconserved element edited out had abnormalities in a part of the forebrain that’s involved in memory formation, as well as epilepsy. “Normally it looks like a blade, but in these mice, the blade was squiggly,” says Dickel.

    Figure 6A from Cell paper.

    A normal part of the mouse forebrain (left) versus a mutated form (right).Credit: D. Dickel et al., Cell 172, 1-9 Jan. 25, 2018. Elsevier Inc. 2017.

    She suggests that the resulting cognitive defects would endanger mice in the wild. Therefore, variations in these ultraconserved regions would not spread through a population, because afflicted individuals would be less successful at reproducing than those who were unaffected.

    Future studies might explore whether people with Alzheimer’s disease, dementia, epilepsy or other neurological disorders have mutations in these overlooked non-coding sequences. Although the functions of many other ultraconserved sequences remain unknown, Bejerano feels confident that they, too, will prove essential. But he remains perplexed by the level of conservation — up to 100% — in some of the sequences because biology often tolerates minor variations. “Mysteries are still on the table,” Bejerano says.

    https://www.nature.com/articles/d41586-018-00920-x

    John Harshman,

    Do you remember a while back Larry Moran using the example of knockout mice as proof for junk DNA?

  16. DNA_Jock
    Ignored
    says:

    Rumraket: Stop reading science mags and read publications from the primary literature instead. Get enough education to be able to understand the methods, then read the results, then read the discussion and conclusion, then form your own conclusion.
    Simply don’t read popular press articles that report on scientific results, they are often sensationalistic, overdramatized, blow up discussion and disagreement into epic international controversies, and mostly wrong.

    J-Mac: Is Nature also a bad science mag?
    [quotes from Nature]

    Oooh-errr, J-Mac burned Rumraket, but good!
    But wait a sec — J-Mac’s quote reads like it is a news item.
    And sure enough, it is!
    ROFL
    Here’s the deal J-Mac: when Rumraket (or any other scientist) encourages you to read the primary literature, they are referring to the scientific articles (written by research scientists), and not the news items that accompany them (written by journalists, some good, some not so much, but none of them primary literature).
    So when you attempt to refute Rumraket by quoting something that a journalist, Amy Maxman, wrote in Nature, you are making his point for him.

  17. John Harshman John Harshman
    Ignored
    says:

    J-Mac: Is Nature also a bad science mag?

    “‘Dark matter’ DNA influences brain development

    You will note that the definition of “dark matter” in that article (which, as has been mentioned, is not primary literature) is completely different from the definition in the OP. It’s just a buzz-phrase connoting mystery, behind which you can hide.

    UCEs are not junk DNA. Larry Moran never claimed they were junk DNA. Nobody ever claimed they were junk DNA. In fact, their conservation is definitive evidence that they aren’t junk DNA.

  18. Entropy Entropy
    Ignored
    says:

    J-Mac,

    Do you seriously think that ultraconserved DNA elements are the very same thing as high-GC content-difficult-to-sequence DNA segments just because two journalists used the word “dark” when talking about them?

    Are you authentically that illiterate? I suggest you get one of your children to read those and help you understand the difference. Coming from them you might be a bit more inclined to try and understand.

  19. Entropy Entropy
    Ignored
    says:

    Rumraket: The logic of a total lack of education in the relevant fields.

    It looks like the logic of a total lack of education in any field. J-Mac doesn’t have a clue.

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