The Onion Test was created by Ryan Gregory in 2007 [The Onion Test] and published in the scientific literature by Palazzo and Gregory in 2014. It goes like this. Take your favorite hypothesis suggesting that most of the DNA in the human genome is functional and use it to explain why the onion, Allium cepa, needs a genome that is five times larger than the human genome. Then explain why closely related species of onion need twenty times more DNA than humans.
Rob Sheldon has an intriguing answer that can only be created by someone with a lot of biases and very little knowledge of biology. He claims that the human genome is chock full of information and it is packaged and condensed in a way that is the best possible code. Humans have the machinery to decode this sophisticated packaging algorithm but other species are more primitive so they have much less efficient compression algorithms. Here's how he describes it ...
There may be some very good reasons for onions to have large genomes....I think that's his main argument—something to do with fractal dimensionality.
The DNA is software. The proteins are the video feed. The nucleus is the CPU. Humans have highly complex coding/decoding machinery in the nucleus. When mathematical analysis is performed on human DNA, it is found to have a fractal information dimension greater than 3 (papers available upon request)–indicating that at least 3 different codes are simultaneously present. This is a number bigger than chimpanzees, whose DNA is not so compressed, and if I recall correctly, come in around 2.5 or so in fractal dimensions. The paper did not analyze onions, but I think it is safe bet that the fractal dimension is < 2.0. What does this changing dimension mean for DNA size? Well the information in DNA is proportional to the volume of phase space, so if humans have dimension 3.0, then the volume ~ (3.2GBytes)^3 ==> 27 GBytes. This dwarfs the 15GBytes of the onion, but then I don’t know the fractal dimensionality of onions.
Now admittedly, the papers don’t do the entire genome, they look at little subsets, so I may be generalizing too much to say that I know the dimension of information packing. But if the genome had junk DNA in it, it would drive the number lower, not higher, because junk DNA is uncorrelated to everything else.
This is categorically what is NOT found, and so even without the ENCODE results, it is manifestly obvious that human DNA is not mostly junk.
But, not content with that, he enters another dimension ....
But if DNA is compressed and packed so efficiently in humans, why is it not packed that way in onions?Most undergraduates could destroy this argument in a few seconds so I'll leave it to them in the comments.2 It's a classic example of why a physicist should not try to understand biology without consulting a basic introductory textbook.
One paper that was published 3 years ago or so, suggested that embryonic development from ovum to embryo was driven by a clock. As the transcriptase zipped along the DNA, proteins were made successively by the cell, and the ordering and timing of the proteins were such as to drive the embryogenesis and development. In other words, the spatial location of the DNA was converted into temporal development of the organism. Then if an organism needed to prolong a stage of embryogenesis, the most direct way would involve adding more DNA. No extra machinery is needed, no added complications and regulators, just another 1GByte of DNA to transcribe and the necessary 30 minutes will be added to the development.
There's more ...
Crude, but why do that at such a high cost to the genome of every cell?We are gradually making some progress in educating Intelligent Design Creationists but it is a slow and painful process. Some of them actually begin to understand modern evolutionary theory and population genetics and there's a brief glimmer of hope, from time to time, suggesting that they know the difference between Darwinism and modern evolutionary theory. Some of them even admit that natural selection isn't all there is to evolution.
Well, perhaps there is a plant virus that hijacks the "clock" to crank out tumors. This onion solution would then be impervious to such a virus. It might even give it an "evolutionary advantage".
Then the "Onion Test" is not a Darwinian challenge to ID, but an ID challenge to Darwinian imagination. Why don’t they take their own medicine: if the junk isn’t functional why doesn’t it get selected out?
All this learning seems to disappear in the junk DNA debate. They still insist that advocates of natural selection (Darwinists) are the ones who invented the idea of junk DNA. That's just dead wrong but we may never be able to convince the IDiots.
1. Google "Sheldon physics" and look at the images. It gets you lots and lots of cool photos that I would love to incorporate into my blog.
2. Hint: how many regulatory genes would have to be regulated in this manner by inserting extra long introns and how much DNA would have to be added to delay production of the first transcript by 30 minutes?
Palazzo, A. and Gregory T.R. (2014) The Case for Junk DNA. PLoS Genetics (published May 8, 2014) [doi: 10.1371/journal.pgen.1004351]
217 comments :
«Oldest ‹Older 201 – 217 of 217ERV insertions are exactly like any other mutation - rarely good, often irrelevant, and sometime bad. Exactly like the more run-of-the-mill invasive virus' that insert into your genome (Hepatitis and liver cancer.)
http://www.ncbi.nlm.nih.gov/pubmed/24511094
http://www.ncbi.nlm.nih.gov/pubmed/18818873
http://www.ncbi.nlm.nih.gov/pubmed/25033295
As most of you probably know, the term “junk DNA” (jDNA) was introduced half a century ago as jargon for presumably non-functional genomic DNA sequences in organisms with high C-value, such as humans.
When referring to this part of the genome, particularly in informal settings such as blogging, it is unpractical to constantly refer to it as “the so called junk DNA”; so, I usually call it jDNA. Obviously, it would be nonsensical to consider this genomic DNA as non-functional, just because it was labeled “junk DNA”.
In my comments above, I asked the following 3 questions, in an effort to address potential biological functions for the so called “junk DNA”, hoping that some of the people who have blasted the ENCODE leaders for their refusal to address inconvenient questions will be very happy to address them.
My first question was in context of the null hypothesis that jDNA has accumulated simply because its rate of deletion has been lower than that of origin (please see the comments above to see exactly the context in which they were asked):
1. Can genomic DNA that exists simply because of a mutational imbalance (that is, no selection) have a biological function or not?
Then, after I reemphasized again the null hypothesis that jDNA has accumulated because of a mutational imbalance, which has been promoted by many people here at Sandwalk, I asked again:
2. Can this jDNA have a biological function or not?
Finally, after John Harshman brought up my old hypothesis that jDNA provides a protective mechanism against deleterious insertional mutagenesis by endogenous and exogenous insertional elements, I asked the question in the context of this specific biological function:
3. Can this jDNA provide a protective mechanism against deleterious insertional mutagenesis by endogenous and exogenous insertional elements or not?
I hope that some of the readers will answer these questions, so I’ll continue to ask them.
The general consensus has been that if a feature is not under selection we can't call it functional. Do you disagree? If so, what is your definition of "function"? If jDNA provides "a protective mechanism against deleterious insertional mutagenesis", and yet organisms with more or less jDNA do not differ in their fitnesses, can that mechanism be considered to be a function? Most of us, including me, would say not. You?
We can probably agree that if the number of insertions is independent of genome size and if the insertion locations are random, an organism with lots of jDNA will have fewer insertions in functional regions than one with little jDNA. And this would decrease that component of the deleterious mutation rate that depends on insertions. Two notes: 1) If; 2) How is that a function?
Peer, you did not answer any of Ace's questions about ERVs. You wrote some things that appear to be answers to some other questions you're substituting.
For example:
- Why do they all have genes for ENV which is essential for viruses but not so much for ERVs?
They don't have all ENV genes. They are characterized by gag and pol genes and the envelope genes are picked up from the genome.
YOU DID NOT ANSWER THE QUESTION. Why do they have Env? You then go on to discuss your shit hypothesis that the info God front-loaded into our genome turned into HIV etc. by just randomly picking up an Env. Extraordinary claim not backed up by extraordinary evidence; and you did not answer the question: why do ERVs have Env?
Moreover, quite a few of your statements are extraordinary claims not backed up by extraordinary evidence. Example:
- Why do the older ERVs that we share with most other primate species have the most mutated LTRs?
These might be the originally frontloaded VIGEs and be subject to a non-random mutational mechanism, although it my also be due to an analysis-bias.
At first glance, it seems like you're conceding that humans share a common ancestor with apes and you're pushing the "front-loading" back tens of millions of years to that common ancestor. But that can't be, because you're a Flintstones! Meet the Flintstones! creationist who thinks the ancestors of all today's land animals stepped off Noah's Ark 4,300 years ago during the Fifth Dynasty of the Old Kingdom of Egypt.
No, here you're hypothesizing "subject to a non-random mutational mechanism, although it my also be due to an analysis-bias".
I interpret "analysis-bias" to be the usual creationist accusation of a conspiracy of scientific fraud.
As for your "non-random mutational mechanism", you're saying that an unknown mechanism supported by no evidence made the SAME mutational mistakes in the exact same places in the ERVs of humans and of chimps, gorillas, etc., arranged in a unique nested hierarchy which just happens to match the tree formed from anatomical considerations.
Extraordinary. It's like going in a library, seeing a book labelled "William Shakespeare's Othello", and hypothesizing that it started as "Cather in the Rye" and then a non-random mistake mechanism just happened to make it identical to Othello.
John Harshman says: ”If jDNA provides "a protective mechanism against deleterious insertional mutagenesis", and yet organisms with more or less jDNA do not differ in their fitnesses, can that mechanism be considered to be a function? Most of us, including me, would say not. You?”
If jDNA does not increase the fitness of the organisms carrying it, then obviously it does not have a biological function. Specifically, in the case of my theory, jDNA must provide protection against deleterious insertional mutagenesis in order to be considered functional; and, according to my theory, it does (BTW, you need to read the paper in order to fully understand the model and the supportive evidence and arguments ( http://biorxiv.org/content/early/2013/11/18/000588).
“The general consensus has been that if a feature is not under selection we can't call it functional. Do you disagree?”
So, if a feature is not under selection, then the consensus is that it cannot have a biological function. So, the features that are not under selection, but the result of genetic drift and neutral evolution, are not functional and therefore useless and irrelevant for evolution. Well, I have to think more about this, but in the meantime, I’ll not be surprised if you get banned from Sandwalk .
Claudiu,
You seem to be conflating two things: the reason a trait arose and the reason a trait is maintained (if it is). An adaptive trait might arise through drift, but if it's adaptive it's maintained through selection. I don't think you have a good understanding of Larry's opinions.
Forget about Larry’s opinions, that was just a secondary comment to which I forgot to add a ‘smile’ (still, parenthetically, can you explain us how “An adaptive trait might *arise* through drift” and neutral evolution?)
Back to the main subject of our conversation, are you OK with the definition of ‘biological function’ as I explained it above?
Can genomic DNA that exists simply because of a mutational imbalance (if you prefer, you can consider this DNA the result of drift and neutral evolution) have a biological function or not?
A second, more specific question:
Can jDNA, which in humans occupy mare than 90% of the genome, provide a protective mechanism against deleterious insertional mutagenesis by endogenous and exogenous insertional elements, or not?
Claudiu: Does the term "exaptation" strike a familiar note? And you don't seem to have explained a definition of "biological function".
And you seem to be using terms that avoid the question of selection. I still don't understand what you mean by "biological function", nor do I know what "protective mechanism" means unless it has something to do with selection.
"can you provide refernces for your claims: 1. A few organisms nearly lacking junk DNA exist naturally, e.g. many bladderworts (small carnivorous plants such as Utricularia gibba), and they seem to be evolving as well as everything else."
Yes. See below for examples.
Maybe they lost it? Did you check for that?
Of course. These plants lost lots of DNA. They function fine without it. Therefore, they didn't need that DNA, and it is reasonable to think that what they lost of "junk" DNA.
Carretero-Paulet, Lorenzo, Pablo Librado, Tien-Hao Chang, Enrique Ibarra-Laclette, Luis Herrera-Estrella, Julio Rozas, and Victor A. Albert. 2015. High gene family turnover rates and gene space adaptation in the compact genome of the carnivorous plant Utricularia gibba. Molecular Biology and Evolution. doi: 10.1093/molbev/msv020 http://mbe.oxfordjournals.org/content/early/2015/01/31/molbev.msv020.abstract
Carretero-Paulet, Lorenzo, Tien-Hao Chang, Pablo Librado, Enrique Ibarra-Laclette, Luis Herrera-Estrella, Julio Rozas, and Victor A. Albert. 2015. Genome-Wide Analysis of Adaptive Molecular Evolution in the Carnivorous Plant Utricularia gibba. Genome Biol. Evol. 7(2):444–456. doi:10.1093/gbe/evu288
Greilhuber, J., T. Borsch, K. Müller, A. Worberg, S. Porembski, W. Barthlot. 2006. Smallest Angiosperm Genomes Found in Lentibulariaceae, with Chromosomes of Bacterial Size. Plant biol (Stuttg); 8(6): 770-777. DOI: 10.1055/s-2006-924101
Ibarra-Laclette, Enrique, Eric Lyons, Gustavo Herna´ndez-Guzma´n, Claudia Anahı´ Pe´rez-Torres, Lorenzo Carretero-Paulet, Tien-Hao Chang, Tianying Lan, Andreanna J. Welch, Marı´a Jazmı´n Abraham Jua´rez, June Simpson, Araceli Ferna´ndez-Corte´s, Mario Arteaga-Va´zquez, Elsa Go´ngora-Castillo, Gustavo Acevedo-Herna´ndez, Stephan C. Schuster1, Heinz Himmelbauer, Andre´ E. Minoche4, Sen Xu, Michael Lynch, Araceli Oropeza-Aburto, Sergio Alan Cervantes-Pe´rez, Marı´a de Jesu´s Ortega-Estrada, Jacob Israel Cervantes-Luevano, Todd P. Michael, Todd Mockler, Douglas Bryant, Alfredo Herrera-Estrella, Victor A. Albert4 & Luis Herrera-Estrella. 2012. Architecture and evolution of a minute plant genome. Nature 498, 94–98. doi:10.1038/nature12132
Peer, you wrote: “You were indeed parotting the wiki-bigmouths. A quick search reveals that the evolution of bladderworts is non-observed, but assumed from DNA sequences. Do some homework yourself, please.” and “I have the advanatge of real knowledge on biology over your parotting the bigmouths.”
I try to “parrot” people who demonstrate evidence of “real knowledge on biology”. You should try it.
Evolution of bladderworts is unobserved but inferred from differences in DNA sequences, in accordance with what is known of chemistry, DNA, and evolution. Your “front-loaded DNA” is unobserved but inferred from the incompatibility of “junk DNA” with a recent origin of life on earth. That recent origin is incompatible with what is known of geology, astronomy, chemistry, biology, and nuclear physics. Which is more probable?
But of course you don’t know. And it would take doing a lot of homework for you to figure it out.
Peer says: "2. Biologists have gone to the lab and constructed mice that lack many of the DNA sequences thought to be junk. The mice did just fine.
No, you mix this up with the observation of conserved junk DNA that could be removed from the mouse genome without any measurable consequences."
"Removed from the mouse genome without any measurable consequences" is the definition of "did just fine" you flipping IDiot. You IDiots always want to redefine words and play word games.
"This is not a problem for ID."
Of course it crushes ID. IDiots all said that all mutations are catastrophic. I proved that with a list of quotes from IDiots recopied by Rumraket where ID proponents said all mutations are catastrophic, you accused me of being a liar, either because because I know more about ID than you do, or because you KNOW what IDiots teach and you were lying about it. But aw, every human baby has 100-200 more mutations than its parents and twice that number relative to its grandparents, etc.
You IDiots said all mutations were catastrophic. CATASTROPHIC. Bye-bye ID!
"It poses a huge threat to selectionism, however, and the long ages (how do you prseserve conserved regions without selection...)"
You don't, DUH! Since ENCODE, there have been several papers on non-conservation between humans and related species and also within the human species and there is too much variation for it all to be functional, if it were all functional the mutations would KILL YOU or the other individuals. Because there is so much variation, the upper limit on functional DNA is repeatedably shown to be 7-8%, maybe 9 if you're an optimist.
The non-selected regions have accumulated mutations and the mutational pattern forms a unique nested hiearchy, aka tree of life.
If you IDiots were right, bladderworts would have more non-coding DNA than coding DNA. You were proven wrong. End of story.
You didn't know shit about bladderworts or any species with big or small genomes. You learned every bit of science you know from creationist websites run by pathological liars. If you were any dumber you'd be Gomer Pyle. Ha ha, we get to laugh at your ignorance and credulity.
https://www.youtube.com/watch?v=MTlqBYuShAU
John,
Most people with reasonable understanding of biology and common sense, and with no hidden agenda, know what a biological function is, but, apparently, that’s not enough for you.
As you know, there are multiple recent articles trying to define “biological function’ (amusingly, even one by ENCODE). Why don’t you select a definition of ‘biological function’ that you like and post it here, so we all can use it as a reference definition?
Regarding your apparent difficulty in understanding what ‘protective mechanism’ means in context of my hypothesis, let’s try to keep it as clear as possible with following example.
Two organisms or lineages, A and B, have the same number of genes and regulatory elements. However, organism/lineage A has a large amount of extra genomic DNA, let’s call it jDNA, which has not been selected for, but has accumulated because of an imbalance between the rate of its origin and deletion.
These two organisms/lineages are exposed to inserting elements that integrate randomly in the genome, and we observe that there are fewer deleterious insertional mutations in A than in B. I think it is reasonable to regard the molecular immune protection conferred by jDNA against insertional mutagenesis a biological function. Weather, you consider this a case of exaptation or not, it is clear that this jDNA has a significant biological function that can be critical for evolutionary survival.
it is clear that this jDNA has a significant biological function that can be critical for evolutionary survival
No, it isn't clear. It might be, but that all depends on how strong the selection is. And I note that your example seems plausible (to the degree that it's plausible) only if we're talking about separate species. Do you agree that you're talking about species selection?
The example above is clearly about “two organisms/lineages”, but if you insist, I guess, it can also apply to “species,” although I’m not sure how you define a “species” (as you know, the definition of “species” has been a highly controversial issue) (BTW, do you have a definition of "biological function" that you think is reasonable and we can use as a reference definition?).
Now, about the “selection”, Natural Selection that is, which you insist must be essential for anything that is deemed to be biologically functional.
Weather strong or weak, Natural Selection is a pervasive force in evolution, and indeed Natural Selection is continuously acting on the so called “junk DNA” (jDNA). For example, when jDNA is exapted as a molecular immune protective mechanism against deleterious insertional mutagenesis in organism/lineage/species A, then this functional DNA enters positive selection.
When this exposure ceases, and there is no need for a protective mechanism, then this DNA enters negative or purifying selection; obviously, if this selection is weak, as is the case of species with high C value, such as humans, then it cannot overcame the mutational imbalance favoring the new addition of DNA and, therefore this DNA persist.
In light of all these facts, I think it is reasonable to replace the term “junk DNA” with the concept of symbiotic DNA (sDNA).
Peer wrote: “I have the advanatge of real knowledge on biology over your parotting the bigmouths. . . . A quick search reveals that the evolution of bladderworts is non-observed, but assumed from DNA sequences. Do some homework yourself, please.”
I try hard to “parrot” people who demonstrate “real knowledge on biology”. You should try it.
The evolution of bladderworts is non-obserted but inferred from patterns of DNA sequences in light of what is know about chemistry and biology. Your hypothesis of front-loaded DNA is non-observed but inferred from the conflict between observed of DNA variation and your assumption that the world and all living things were created in the past few thousand years, an assumption in coflict with what is known about geology, astronomy, nuclear physics, and biology.
Which idea is more likely to be true? Oh, right, you wouldn’t know, without doing a lot more homework yourself.
Peer wrote: “can you provide refernces for your claims: ‘1. A few organisms nearly lacking junk DNA exist naturally, e.g. many bladderworts (small carnivorous plants such as Utricularia gibba), and they seem to be evolving as well as everything else.’ Maybe they lost it? Did you check for that?”
Yes, I can provide reference. See below.
And yes, of course bladderworts lost a lot of DNA their ancestors had. That is evidence that the lost DNA was not necessary. It can reasonably be called “junk.” And despite the near lack of junk DNA, bladderworts continue to evolve. More evidence suggesting that such DNA is not needed for evolution.
Carretero-Paulet, Lorenzo, Pablo Librado, Tien-Hao Chang, Enrique Ibarra-Laclette, Luis Herrera-Estrella, Julio Rozas, and Victor A. Albert. 2015. High gene family turnover rates and gene space adaptation in the compact genome of the carnivorous plant Utricularia gibba. Molecular Biology and Evolution.
Carretero-Paulet, Lorenzo, Tien-Hao Chang, Pablo Librado, Enrique Ibarra-Laclette, Luis Herrera-Estrella, Julio Rozas, and Victor A. Albert. 2015. Genome-Wide Analysis of Adaptive Molecular Evolution in the Carnivorous Plant Utricularia gibba. Genome Biol. Evol. 7(2):444–456.
Greilhuber, J., T. Borsch, K. Müller, A. Worberg, S. Porembski, W. Barthlot. 2006. Smallest Angiosperm Genomes Found in Lentibulariaceae, with Chromosomes of Bacterial Size. Plant biol (Stuttg); 8(6): 770-777.
Ibarra-Laclette, Enrique, et al., et al. 2012. Architecture and evolution of a minute plant genome. Nature 498, 94–98.
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