In last chapter of my book I try to convince readers that biochemistry, molecular biology, and evolution are sloppy processes and the idea of a sloppy genome is a logical consequence of evolution. The chapter contains Chautauguas on genomics, the function wars, intelligent design creationists, and scientific controversies.
Click on this link to see more. Chapter 11: Zen and the Art of Coping with a Sloppy Genome
19 comments :
Good morning,
One common refrain I hear from other biologists is that evolution would select against junk DNA because of energy wasted to maintain/carry it. My impression would be that this would be trivial compared to something like maintaining ion gradients across membranes, but I can not find numbers to back this up. Do you have any references that you could point me to, or have you made estimates on the fraction of total energy it would require to carry junk DNA? It does not seem like a straight forward calculation, as it would have to include (a lot of) additional histone synthesis, background transcription, etc.
Anonymous, one problem with this calculation is that junk DNA isn't gained or lost as a single piece, so the relevant part isn't the total energy (or other) cost of having it vs. not having it. It's the incremental cost of one more transposon, or the differences in genome size among the current population. There's never a situation in which individuals with zero junk are competing against individuals with lots of junk. You might resort to species selection, but even that would seem to fail the onion test.
Do all people who are new to posting start with “Good morning”? Good point John. Selection can only act on the deleterious effect of adding a single transposon at a time. If one takes the average size of a transposon to be 1000 bp, just for the sake of putting a number on it, then a single transposon would represent an increase of 3.3E-7 relative to the human genome- clearly trivial. As such, I agree that selection would not affect the outcome. Likewise, if one developed the magical ability to selectively remove a single transposon, the advantage would be trivial. I guess I phrased my question poorly. How about this: what is the metabolic cost of junk DNA as a percentage of total metabolic activity, using humans as an example (naturally, as we represent the pinnacle of evolution). If we assume, as I think many readers of this site should, that ~90% of the genome is junk, then we can rough out the answer by just asking what is the metabolic cost of our current genome size, which seems like something that someone, somewhere might have calculated, but I cannot find it. That being said, there is a fair amount of work in that calculation- one would need to input the cost of histone synthesis and histone turnover rates, the cost of histone modifications (whatever those do), the cost of background transcription of that junk DNA, maybe even a smidgeon of junk protein synthesis. I suppose the cost of a larger nucleus too, with more lipids, nuclear pores, etc. The more I think about it, maybe no one has tried to figure this out. In my imagining, the metabolic cost of “the genome” is trivial compared to other metabolic costs, but I have only intuition to back up that thought.
@anonymous
Michael Lynch and Georgi Marinov addressed this issue in 2015 by trying to calculate the cost of a new gene. Here's a blog post on the topic where I discuss the cost of junk DNA.
Georgi may want to comment.
The cost of a new gene
Slightly off topic, but I just bought and then returned a digital copy of your book from Amazon because as I was browsing through the chapter on why we aren’t all dead, I found that pages were out of order. As the author you might want to tell them this.
I will eventually buy the book, but want a copy that isn’t defective.
@Donald
I hope you're not referring to the positioning of the Boxes. Is there no way to view the digital copy so that you can see the Boxes as separate from the normal text pages?
I returned it so I can’t say. But there was a statement that was cut off, a box, and then a full page of text , and then a page that completed the sentence. If it was supposed to be that way it was very confusing.
I prefer since I live in an apartment to buy digital books, but I think I will break down and get the dead tree version.
I just ordered the hard copy and being a prime member it will be here in a day or two. I’ll check and see if it was just a box of text that confused me in the digital format and let you know.
I bought the KOBO e-book version, I finished reading it and reviewed it on my blog:
https://korthof.blogspot.com/2023/06/scientists-say-90-of-your-genome-is.html
Larry, thanks for writing the book!
In my Kindle version there is a sentence beginning at p86,location 1574, as "That’s exactly what you would expect if most of their genomes ", and completes on p88, location 1596.
On p9,location 335, there is a line containing "has the sequence AGTC and not CTGA even", that should be "ATGC and not CGTA".
The book was great! How do non-coding genes (tRNA, rRNA, etc) avoid being translated to protein?
@Steve
The print version has a box on page 86 ("TICK, TOCK, THE MOLECULAR CLOCK"). The box is shaded and printed in a different font so it's clear that it's an insert. Does the Kindle version not show this in the original file that you received? Did you alter the font and background?
The mistake on page 9 will be corrected.
Eukaryotic mRNAs have 5' caps and ribosome binding sites with initiation codons. Some of the other noncoding RNAs are never exported to the cytoplasm.
My version has a heading on p87, location 1574, but no box, of "TICK, TOCK, THE MOLECULAR CLOCK". The next Kindle page has a quotation by Masatoshi Nei (p87, location 1581). Next K-page (p87, location 1584) is the start of a paragraph that begins "Modern evolutionary theory explains a puzzling result....". The next paragraph (same K-page) rolls over to onto the next K-page (p87, location 1592). The next K-page is the remainder of the broken sentence, as above, at p88, location 1596. I have not altered anything.
I have just finished reading your book. Very enjoyable.
p18. "10 trillion cells". I guess this number comes from https://pubmed.ncbi.nlm.nih.gov/23829164/ but there is a better estimate in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991899/. 30 trillion cells, of which 3 trillion are nucleated. The junk DNA may stretch far beyond Pluto, but it only weighs 20g.
p121. I was confused by Fig 5.4. I didn't know a precise definition, but I basically thought that exons inside protein coding genes were coding regions. I wasn't helped by the way some black boxes were labelled 'Exons' and other, apparently identical ones, were labelled 'Coding region'. All became clear when I read note 6.41, but it was some time before I came across that.
Some typos. I like the first one which made me think of coriander.
p163. spice variants
p193. Yeilds
p352, note 6.41. There is no Figure 1.13.
@Graham
Estimates of the number of cells in a typical human body are all over the map. I picked what I though was a reasonable number. I assume there's a great deal of variation because some people are bigger than others and that can't just be due to cell size.
Thanks for reporting the typos. It's amazing how many we missed in spite of some serious editing. I think we're doing better than most books, though.
I don't understand the last one (p352, note 6.41). Could you be more specific?
@Steve
So, the only way of recognizing that page 87 is a box is that the title is in all caps. Is that correct?
What about pages 92-93? Do you recognize that as a box or does it look like the paragraph on page 94 follows the last one on page 93?
What about pages 60-61 ("DNA FINGERPRINTS")?
Larry said: "I don't understand the last one (p352, note 6.41). Could you be more specific?"
Sorry, that's my typo, in fact two of them! p325, note 6.31 refers to Fig 1.13.
@Graham
I explained the gene icons in chapter 1 where I pointed out that the coding regions were colored black and there's noncoding RNA at each end (p. 29). Exons are the parts of the gene that are included in the mature transcript. I don't mention UTRs until chapter 5 where they are labeled in Figure 5.4.
I realize that it's a common misconception to assume that all exons are coding DNA and that's why showed those gene icons in chapter 1.
Correct about the box on p87. Similarly with 92-93 and 60-61. There is nothing in my Kindle edition that is immediately recognizable as a box. I was initially slightly confused by references to them.
I’m a bit late getting back to you, but I now have the dead tree version and yes, I was confused by what turns out to have been a box.
Donald
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