More Junk DNA junk from the DI

as i said above, of course that there are some deviations (onion, fugu etc, in these cases it might be indeed junk or their “junk” part have nothing to do with their complexity), but we need to look at the rule rather than the exceptional, and this plot indeed prove that there is a general correlation between junk\non-coding DNA and complexity.

IOW, you are now confirming that there is no “correlation between creature complelxity and the amount of junk”, despite your earlier claim. Or are you saying an onion is more “complex” than you are?

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I don’t mean to imply that there’s necessarily a causal link between “complexity” and “ability of the genome to tolerate more junk”. As you say, it’s down to things like generation times, population sizes, and arguably available metabolic energy, and these are things that correlate with “complexity” (again bearing in mind the broad clades in the graphs).

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How does it “prove” this? Please be specific?

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They correlate with organismal size, perhaps, in terms of sheer numbers of cells. And size may be weakly correlated with complexity. Organismal complexity is however hard to measure objectively. Number of cell types, for example, depends greatly on how closely you look. The more important thing about the graph is that the data points are cherry-picked in order to put humans at the top, and all the points that don’t fit the story have been left out.

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For reference, see here.

image

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And no one who knows what s/he is talking about conflates “noncoding” with “junk,” @scd. We’ve known for a very, very long time that some noncoding sequence has function.

Promoters are a good example. When was the first promoter discovered?

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According to the Supplemental Table 1, they state that Chlamydomonas reinhardtii has 12.5 different cell types. I would love to know how they got this value.

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IMO, if the plot is properly populated and the different species correctly annotated, then this general correlation will become so weak as to be non-existent.

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You haven’t shown that it is a rule. You have extremely cherry-picked data.

According to that paper, genome size has more to do with the mechanisms an organism has for purging bloated genomes. It says nothing about genome size being necessary for complexity.

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Point five eh? I’m fascinated by the idea of half a cell type.

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Chlamydomonas is a single-celled alga. I think that when it forms haploid gametes it divides symmetrically. That might be half a cell type, but where are the other 11?

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In the paper from the Mattick group, they assert that all bacteria, being single celled, have but one cell type. But this is not true. B. subtilis, which is on their list, has at least two. Heck, E. coli may have four or more.

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Caulobacter crescentus, for example.

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Plus there are cyanobacteria with terminal differentiation.

To be honest, I don’t understand the source of the values in Supplemental Table #1 column: ‘Complexity (mean number of different cell types)’, in the last tab of the Excel workbook. For the Archaea & Bacteria plus many of the other organisms, they reference the Joint Genome Institute’s Integrated Microbial Genomes (IMG) system. Perhaps I’m missing something but I can’t see where the ‘Complexity’ figures are derived from those references.

I believe they simply assert that all bacteria have only one cell type - no reference, just “single-celled, thus one cell type”.

I could trace some of this back to a couple of books that I don’t have access to. One was coauthored by Margulis and probably has a lot of creative license. The other seemed to be an introductory biology text, which probably isn’t the best source for metrics that would go into a study like this.

I can’t seem to get to any of those numbers from the references cited. “12.5”, “4.3”?

Myxococcus xanthus is a really interesting bug. It can form specialized cells (i.e. tissue formation) within fruiting bodies:

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from the abstract: “Here we extend on that work and, using data from a total of 1,627 prokaryotic and 153 eukaryotic complete and annotated genomes, show that the proportion of ncDNA per haploid genome is significantly positively correlated with a previously published proxy of biological complexity, the number of distinct cell types”

where do you see that they pick up the data? we are talking about huge number here. not just few species here and there.

there is a correlation between the number of cell-types and the amount of non-coding/junk DNA.

i have no problem with that. call it anything you want. after all many scientists used that term:

https://www.nature.com/articles/443521a

https://www.nature.com/articles/news040503-9

I believe their correlations with complexity are done using a small number of species (the last sheet in Supplemental Table 1), not with all 1627 prokaryotic and 153 eukaryotic species.

There is no doubt that, if one added to their analysis 50 plant species that more properly reflect the breadth of genomes in the plant kingdom, then the alleged correlation noted in the paper under discussion would evaporate.

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