Kondrashov's Paradox: Why We Haven't Died 100 Times Over

Conversation
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Once again you are shown to reject the clear statements of the experts in the field. It is firmly and widely acknowledged that the vast majority of mutations are deleterious. Not just the tiny minority of mutations that affect the protein-coding region. This was also confirmed by the work of Racimo and Schraiber on the genome-wide DFE.

“In summary, the vast majority of mutations are deleterious. This is one of the most well-established principles of evolutionary genetics, supported by both molecular and quantitative-genetic data.”

Keightley P.D., and Lynch, M., Toward a realistic model of mutations affecting fitness, Evolution, 57(3):683–5, 2003.

It is very interesting to note, however, that the scientists here, at least, seem to be betting the farm on junk DNA, despite the mounting evidence that the term is completely inappropriate and it does in fact have function. The concept is just one more in a long line of scientific embarrassments brought on by the dogma of evolution.

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Let me quote a bit more from the paper so you come to understand that your view of “junk DNA” is contrary to science:

The exome makes up less than two percent of the human genome and the rest, formerly known as “junk DNA,” is largely comprised of elements that regulate the timing, cell type, and levels of gene expression. Until recently, limitations in technology and a lack of knowledge about the specific locations of regulatory elements in DNA caused the field to focus on coding regions of the genome, where 85% of known disease-causing variants have been described [18]. With projects like ENCODE [19] and the Epigenomics Roadmap [16] coupled with advances in next generation sequencing, we now have epigenomic reference maps that have helped to delineate the genome-wide locations of regulatory elements in hundreds of human cell types. These maps allow the interrogation of the other 98% of the genome, which is as essential to gene function as coding regions.

When the authors say “non-coding”, they are definitely referring to what you are erroneously calling “junk”.

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Will the answer to Roy’s earlier comment be "I’m shocked, shocked, to see that ABCDEFGHIJKLMNOPQRSTUVWXYZ is going on in this place!”?

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All the experts in the subject matter here are convinced it’s junk DNA.

Hmmm. Maybe this is a clue.

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Agreed. So would some onions.

I’m not saying its a significant factor, just that it’s technically (mathematically rather than practically) non-zero.

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And there it is, exactly as described, and even using the reference I mentioned.

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True, and in this they’re unfortunately ignorant of the topic. A lot of molecular biologists seem to suffer from this ignorance, including many on the ENCODE team. Nobody every thought that all non-coding DNA was junk. About 10% of the genome is functional, and 80% of the functional part is non-coding. Most of what ENCODE found are not regulatory elements. I suggest you (and the authors you cite) read Larry Moran’s book What’s In Your Genome to correct your misperception.

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Yes, and that is exactly wrong. Directly, unambiguously wrong. It is simply a historical falsehood, a myth, that non-coding was ever taken to be equal to junk DNA.

You really should read Larry Moran’s book https://whatsinyourgenome.blogspot.com/

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So, you have far less function than an onion, which has far more DNA?

Palazzo and Gregory - The Case for Junk DNA

This is not to say that none of the nonprotein-coding majority of the genome is functional—examples of functional noncoding sequences have been known for more than half a century, and even the earliest proponents of “junk DNA” and “selfish DNA” predicted that further examples would be found. Nevertheless, they also pointed out that evolutionary considerations, information regarding genome size diversity, and knowledge about the origins and features of genomic components do not support the notion that all of the DNA must have a function by virtue of its mere existence. Nothing in the recent research or commentary on the subject has challenged these observations.

Doolittle and Brunet - On causal roles and selected effects: our genome is mostly junk

The idea that much of our genome is irrelevant to fitness—is not the product of positive natural selection at the organismal level—remains viable. Claims to the contrary, and specifically that the notion of “junk DNA” should be abandoned, are based on conflating meanings of the word “function”. Recent estimates suggest that perhaps 90% of our DNA, though biochemically active, does not contribute to fitness in any sequence-dependent way, and possibly in no way at all.

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Hmmm. Maybe it’s not.

And finally, here is a piece about the view of Thomas Cech, a Nobel price winner that devoted it’s entire career on RNA, regarding «junk RNA ».

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Which is how many people, exactly? Even for arguments from authority/popularity, you’re making an extremely weak one with this.

I’ll go with the evidence presented by the scientists who more recently have actually undertaken to study this so-called “junk” and have begun uncovering function after function. If you want to remain deliberately ignorant, that’s of course an option available to you.

Could it be that they are convinced it’s junk precisely because they realize that evolution falls apart the moment we lose the ability to sweep most mutations under the rug? Surely it couldn’t be that!

The DFE I used from Racimo and Schraiber takes the full human genome into account, not just the regions previously deemed “functional”. Clearly they did not think you can just write off all those regions of the genome as if they have no effects at all when mutated.

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Your misconceptions are innumerable. First of all the junk conclusion was arrived at by people who originally believed the entire genome to be functional (ironically, for evolutionary reasons they thought natural selection would get rid of everything that didn’t serve a function).

So by even presenting this issue as if junk has only recently begun being studied you’re literally reversing the history. It was through it being studied that they discovered it was junk.

T. Ryan Gregory documents many examples on his blog here: The junk DNA quotes of interest series. | Genomicron

Quotes upon quotes upon quotes from papers, conferences, Nobel-prize speeches etc. by scientists discussing possible functions of the loci they studied, despite their innumerable hypotheses again and again coming up short.

With respect to how a lot of these claimed functions are found, typically they don’t actually discover any functions experimentally. They extrapolate them from data. They discover something like transcriptional activity, find it varies by tissue or cell type, and mistakenly conclude on this basis alone that this implies it’s functional. They typically don’t have a null hypothesis or even negative controls (how would nonfunctional DNA behave using the same assays?).

For the latter part, I’m not even kidding. They did science without negative controls. Some authors reproduced the ENCODE results with random nonfunctional DNA. Using the same sorts of assays, showed that they could get reproducible gene-expression from just scrambled DNA intentionally created to not have any functions.

In other cases, where actual functions are discovered, it’s then used to make grandiose and basic fallacious extrapolations (one therefore all transposons are inferred functional, for example).
They invariably misrepresent the history by claiming the locus of interest was “previously dismissed as junk” but never give any citation for the claim (there is no citation they can give because it’s simply false).

Correct. It couldn’t because they haven’t studied the history of the subject or the reasons why the junk hypothesis was alighted upon in the first place. But you’d have to know something about this subject to even begin to discuss it, and you don’t.

Which regions are those? Citations please. Give me a “previous” citation that says explicitly which portions are functional and which are not. Then a new one that overturns the old one.

Good luck.

No proponent of junk-DNA thinks that. Your comment just proved you know nothing about this subject.

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Why are you linking me the propaganda institute essentially all posts of which are brimming with mistakes and basic errors in reasoning? Seriously after all this time on this forum and having discussed junk DNA so many times you should be able to anticipate the criticisms of this trash yourself.

But no, you just copy-paste links to these worthless articles having all the same flaws discussed here a hundred times before.

Why do you ID-creationists never show any sign of being able to learn something new?

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And by the way, one last thing: the whole concept of junk DNA is a complete red herring with respect to GE. I went ahead and tested a SLiM sim with 1% of the genome size I used previously (10 mil bp for coding only), and then I used the DFE for amino-acid changing mutations that Eyre-Walker and Woolfit published. Then I used the mutation rate of 7.2 per individual that Felsenstein suggested. Can you perhaps take a guess at what happened? The population crashed much faster than before. Junk DNA is not an escape route here.

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LMAO. Paul, Eyre-Walker and Woolfit et al. 2006 is a DFE for deleterious mutations only. What DFE did you use for beneficials?

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Treating this non-rhetorically, I think that psychological need for closure (NFC, i.e. aversion to uncertainty) explains at least some of this. It’s both a factor in the need for religious beliefs to satisfy existential uncertainty, especially fear of death, but is also a trait that it makes it more difficult to learn new things. When new knowledge creates uncertainty resulting in anxiety, that creates resistance to adopting that knowledge.

I do think a lot of creationists and ID proponents are the way they are in part because of traits like high NFC.

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Did you even read what Felsenstein posted here? He suggested an effective mutation rate per individual of 7.2, which is 10x less than the actual mutation rate. The only reasonable implication I can get out of his statement would be that he thinks mutations in the “junk” can be ignored with respect to mutation accumulation. His problem is that I tested his theory and it still produces fitness decline.

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It seems to me that you are the one that shows no sign of being able to learn something new. The posts I linked to point to new scientific publications that provide evidence that large chunks of so-called junk DNA or RNA are in fact functional. Have you at least taken a look at these recent publications ? For example, this one below, arguing that « rather than a gene-centric landscape dotted with repetitive “junk,” mammalian DNA is a TE-rich ecosystem in which TEs drive gene regulatory networks and evolution ».

https://www.cell.com/cell/abstract/S0092-8674(26)00520-9

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Not quite sure what you did there, but you seem to equate “non-coding” with “junk” and “functional” with “coding”, and you seem to equate “mutation” with “amino-acid changing”. GIGO.

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Fits the standard form already mentioned: find a few elements in a class with clear functions, assume that every element has a function, declare that junk DNA is falsified.

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