More Junk DNA junk from the DI

[T.j_Runyon]

BioEssays Editor: “‘Junk’ DNA… Full of Information!” Including Genome-Sized...

Once again, no author byline.

[T_aquaticus]

From the article:

How many times have we heard it claimed that the vast majority of the human genome is “junk” and therefore could not have been designed?

We hear that from ID supporters who have argued against junk DNA because it is a problem for Intelligent Design.

Even in the face of overwhelming evidence from the ENCODE project and numerous other studies showing that most of our genome has biochemical function, most evolutionists still maintain that our genomes are largely junk. But a few brave scientists, including some rare evolutionists, have been willing to buck that trend.

What ID/creationists still don’t understand is that DNA can have “biochemical function” and still be junk. Doing something is not the same thing as functioning. Junk DNA can be transcribed at really low levels, but it is still junk DNA.

The paper finds that our DNA contains overlapping layered “’dual-function’ pieces of information,” including a “genomic code” that spans virtually the entire genome in order to “defin[e] the shape and compaction of DNA into the highly-condensed form known as ‘chromatin.’”

What we would need to see is the total number of bases needed for compaction into chromatin. How much of the non-coding DNA is needed for chromatin? The article doesn’t seem to answer this vital question.

Also, how is the bladderwort genome able to function with just 82 million bases and a gene content equal to that of other complex eukaryotes with genome sizes in the hundreds of millions or billions? The bladderwort genome lacks all of the features spoken of in the article, yet it keeps truckin’.

[evograd (Blogging Graduate Student)]

@T_aquaticus

The paper finds that our DNA contains overlapping layered “’dual-function’ pieces of information,” including a “genomic code” that spans virtually the entire genome in order to “defin[e] the shape and compaction of DNA into the highly-condensed form known as ‘chromatin.’”

What we would need to see is the total number of bases needed for compaction into chromatin. How much of the non-coding DNA is needed for chromatin? The article doesn’t seem to answer this vital question.

It’s like citing the number of pieces of junk in a great big pile of junk that are weight-bearing, technically having a function in maintaining the shape of the pile. It doesn’t surprise me in the least that large swathes of our genome would be involved in chromatin conformation, nor does it surprise me that much smaller genomes require much less.

[glipsnort (Steve Schaffner)]

@T_aquaticus

We hear that from ID supporters who have argued against junk DNA because it is a problem for Intelligent Design.

It reflects an exaggerated sense of the importance of ID. Scientists do not claim that most human DNA is junk because it provides an argument against ID; to a very good approximation, scientists do not care about ID. At all.

[scd]

@T_aquaticus

Junk DNA can be transcribed at really low levels, but it is still junk DNA.

how you explain the correlation between creature complelxity and the amount of junk?:

(image from A meta-analysis of the genomic and transcriptomic composition of complex life - PubMed)

[swamidass (S. Joshua Swamidass)]

@scd

Junk DNA can be transcribed at really low levels, but it is still junk DNA.

how you explain the correlation between creature complelxity and the amount of junk?:

How do you explain why onions have much larger genomes than us?

[evograd (Blogging Graduate Student)]

Generally speaking, more “complex” organisms (bearing in mind how broad the clades in the graphs are) can tolerate more junk.

[Art (Arthur Hunt)]

@scd

how you explain the correlation between creature complelxity and the amount of junk?

Going just by panel B of the figure, I don’t see appreciable differences between organisms with 20:and 200 cell types. Which suggests no particular connection between the relative amounts of ncDNA (or coding DNA) and complexity (as reflected in numbers of cell types).

[Rumraket (Mikkel R.)]

@scd

how you explain the correlation between creature complexity and the amount of junk?:

Oh look, it’s John Mattick again. Generally speaking, his graphs and correlations are junk.

Also you’re using the terms incorrectly. Junk DNA isn’t non-coding DNA. Junk DNA is nonfunctional DNA. Showing a graph of the proportion of non-coding DNA to number of cell types is not showing a correlation between “creature complexity” and “amount of junk”.

Is the Norway spruce tree more complex than humans, goats, and elephants? It has a roughly 20 gigabase genome, more than six times the size of the human genome. And most of it is non-coding.

[John_Harshman]

That’s known as a dog’s ass plot. It’s driven by two things: prokaryotes do indeed have smaller genomes than eukaryotes, and those data points were carefully selected to produce the desired result for eukaryotes. Anyway, who says that plants are less complex than metazoans?

[scd]

@swamidass

How do you explain why onions have much larger genomes than us?

two possibilities: in that specific case its indeed junk, or it have something to do with the plant regulation rather than with its complexity.

@Rumraket

Generally speaking, his graphs and correlations are junk

@John_Harshman

That’s known as a dog’s ass plot

@Art

Going just by panel B of the figure, I don’t see appreciable differences between organisms with 20:and 200 cell types

here is more clear figure. we can clearly see a correlation:

[davecarlson]

That plot would look radically different if the sampling of species were more thorough.

[Art (Arthur Hunt)]

@scd

here is more clear figure. we can clearly see a correlation:

@scd, perhaps you can pencil in the values for Arabidopsis (10^8, approximately), tobacco (3x10^9), and Paris japonica (>10^11) into this graph. They are all angiosperms and will have comparable numbers of cell types. (These values assume a nearly constant amount of coding DNA, a safe assumption within an order of magnitude, and are, to a first approximation both the total genome sizes and also ncDNA quantities).

You might add two lower plants (Selaginella selaginoides, 5x10^7, and Tmesipteris obliqua, >10^11) to the plot as well. They will have fewer cell types than angiosperms.

Once you do this, maybe you can comment on the usefulness of the plots you are showing, when it comes to ascertaining with any degree of certainty a relationship between complexity and genome size (ncDNA content, overall genome size, whatever).

[John_Harshman]

What does “coding or noncoding base pairs” mean, and how does it differ from “genome size”? And isn’t it time for the fugu test?

[John_Harshman]

@evograd

more “complex” organisms (bearing in mind how broad the clades in the graphs are) can tolerate more junk.

There seems no evidence of this. If there is a correlation with anything, it’s population size and generation time. Low population, high generation time species have less selection affecting genome size.

[Art (Arthur Hunt)]

@evograd

It’s like citing the number of pieces of junk in a great big pile of junk that are weight-bearing, technically having a function in maintaining the shape of the pile. It doesn’t surprise me in the least that large swathes of our genome would be involved in chromatin conformation, nor does it surprise me that much smaller genomes require much less.

This is a good analogy. It brings up something that has always confused me. These new functions, codes, and whatever that ID proponents are finding in DNA are usually non-specific when it comes to sequence (to a first approximation, at least). This means that, by the ID way of measuring things, there is really no information (CSI, in the vernacular) that corresponds to the new functions, or is hidden in these new codes.

These arguments have always struck me a sorts of own-goals. They totally undermine the informational basis of ID theory when it comes to function in biology.

[Art (Arthur Hunt)]

@John_Harshman

What does “coding or noncoding base pairs” mean, and how does it differ from “genome size”?

In the figures @scd is showing, to a first approximation, “ncDNA” and genome size are the same thing. The plots of coding DNA show this, pretty much.

[T_aquaticus]

@scd

how you explain the correlation between creature complelxity and the amount of junk?:

Hmm, let’s see how that pans out.

A single celled amoeba, Amoeba dubia: 670 billion bases
Onion: 16 billion
Human: 6 billion
Pufferfish: 0.4 billion
Bladderwort: 0.08 billion

I’m not seeing a trend. Why would equally complex plants like the onion and bladderwort differ by a factor of 200? Why would a single celled organism have a genome 100 times larger than the human genome?

[T_aquaticus]

@John_Harshman

Low population, high generation time species have less selection affecting genome size.

On rare occasions, the environment may influence genome size. This may be the case for the carnivorous bladderwort that lives in a low nitrogen and phosphorus environment that may select for reduced nucleotide synthesis.

[T_aquaticus]

@scd

here is more clear figure. we can clearly see a correlation:

I think this graph refutes yours.