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Key points in plant evolution featured “fundamental genomic novelties”

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From Bowles et al., 2020, Current Biology 30, 1–7 February 3, 2020 ª 2019 Published by Elsevier Ltd. https://doi.org/10.1016/j.cub.2019.11.090

And there’s a story in that (besides the obvious one):

Dr Jordi Paps, Lecturer from Bristol’s School of Biological Sciences and lead researcher, explained: “After comparing over 200 genomes of the plant kingdom, we discovered that the origin of land plants is associated with two explosions of new genes, an unprecedented level of genomic novelty. Our findings challenge previous views of this transition being more gradual at genetic level.

“The first burst predates the origin of land plants, before they left their aquatic environments, and comprises genes that explain why plants are multicellular. The second coincides with the origin of land plants, and involved genes related to adaptations to challenges found in terrestrial environments.”

University of Bristol, “Scientists uncover how an explosion of new genes explain the origin of land plants” at ScienceDaily

Paper. (open access)

From the paper’s Summary:

Here, using an evolutionary genomics pipeline to compare 208 complete genomes, we analyze the gene content of the ancestral genomes of the last common ancestor of land plants and all other major groups of plant. This approach reveals an unprecedented level of fundamental genomic novelties in two nodes related to the origin of land plants: the first in the origin of streptophytes during the Ediacaran and another in the ancestor of land plants in the Ordovician. Our findings highlight the biological processes that evolved with the origin of land plants and emphasize the importance of conserved gene novelties in plant diversification. Comparisons to other eukaryotic studies suggest a separation of the genomic origins of multicellularity and terrestrialization in plants.

Bowles et al., 2020, Current Biology 30, 1–7 February 3, 2020 ª 2019 Published by Elsevier Ltd. https://doi.org/10.1016/j.cub.2019.11.090

Stuck for what to call this, some of us would call it creationism. But never mind. We’ll probably see more of this so hang on.

A friend writes to remind us that UC-Berkeley paleontologist Charles Marshall savaged Steve Meyer his Science review of Darwin’s Doubt because Meyer thought that something like that must have happened with animals. Marshall was sure that nothing like that could have happened; the Darwinianly evolved genes merely needed rewiring. However, the friend tells us, a 2018 study in Nature Communications (open access) confirmed Meyer’s argument: “Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty.” Jordi Paps is an author on both studies.

Either Jordi Paps needs the witness protection program or we all need to lose a bunch of Darwinian fundamentalists pronto.

Richard Dawkins doesn’t explain it all for you.

See also: World’s oldest scorpions show no change from 437 million years ago. It doesn’t sound as though the scorpions bothered with much evolution. How would we distinguish their origin from creation? At a certain point, does evolution become creation? Just wondering.

see Correcting Four Misconceptions about my 2004 Article in JMB- Doug Axe
Thank you for the link. I read it and it was interesting. I was trying to avoid a long reading bout to answer my question but it seems that no one had done what I have asked including Axe. Yesterday I went through Axe's book, "Undeniable" by searching for the word protein. There are 205 occurrences and it was interesting scrolling through each occurrence and reading the material around each. Still not sure what he actually did. jerry
Jerry- see Correcting Four Misconceptions about my 2004 Article in JMB- Doug Axe ET
Sorry if that is less than what you asked for, but it is more than other responders provided
Yes it is more than what other responders provided and I thank you for your reply. Now the question I have is how many amino acid sequences can be tested by a computer program for folding. 10^77 is a lot of sequences to test. How did he build up to that number.? He has written several articles on the Discovery site. I also bought his book a few years ago but didn’t finish it. Will see if it’s in book or any of the articles. I just thought to ask question here to get a quick answer but didn’t get one. jerry
Jerry, in my previous post i have mentioned YALE computer science professor David Gelernter who published an essay "Giving Up Darwin"... among other reasons he gave up Darwin, he also mentioned molecular biology, amino acids, proteins, etc.... i think, you might be interested in .... i think, that in that essay, Gelernter is asking the same questions as you... you may like it, it is an essay, no 15 pages paper. and, if you wish, you can jump directly to the "The Advent of Molecular Biology"-paragraph... here it is: https://claremontreviewofbooks.com/giving-up-darwin/ martin_r
The last couple of paragraphs from the paper abstract may serve as Jerry's requested "paragraph? https://www.sciencedirect.com/science/article/pii/S0022283604007624 Fasteddious
Jerry: I have not read the 15 page article, but I've read enough about Axe's findings to give a broad description. Take the size of a typical small protein, say 150 amino acids. Take the number of amino acids used in proteins, say 20 or so. Each of the 150 can be any of the 20 amino acids. That yields roughly 10^195 possible combinations of amino acids 150 units long. Next count up the number of protein folds used in nature, perhaps 10^15 protein folds that are or have been used by some lifeform on Earth at some point in the past. That yields ~10^180 times as many possible combinations as there have been useful proteins. This of course ignores the fact that there are probably many possible proteins that have never been used by any lifeform. The other approach, closer to what Axe calculated, if memory serves, was to actually produce some huge number of random amino acid sequences 150 units long, and see how many of them fold into something resembling a stable protein. I forget the details, but what Axe did was something along those lines. He then added some analysis to come up with the 10^77 number. Other attempts at that sort of analysis have yielded similar ballpark numbers as I recall. Sorry if that is less than what you asked for, but it is more than other responders provided. There are some more detailed popular accounts describing Axe's work, but I don't have any references at hand. Perhaps BA77 has something in his expansive files? If all else fails, you could indeed read the 15 page article and then you'd know for sure. Just don't use my poor excuse at an explanation as a basis for further questions or doubts. Fasteddious
Jerry @15 " Otherwise it is just a claim." Is that you ? Jerry Coyne ? Jerry, did you get the message ? ET @4 ever heard that word (CHAPERONES) ? martin_r
Read the article and write your own paragraph
Interesting response. I ask if there is a short or medium length paragraph that explains the basis of the 10^77 number and I am essentially told that there isn't one and go write my own. I am involved in technical areas as part of my business and try to provide laymen's answers to concepts that are often complicated. I was looking for a short paragraph to help convince others that Axe's calculations make sense. Otherwise it is just a claim. I can easily explain the odds of a particular protein arising and how it could happen but not the rarity of 1 in 10 ^77 for foldable let alone useable proteins. I will try the Discovery Institute. jerry
This is a 15 page technical journal article I asked for a paragraph.
Read the article and write your own paragraph ET
PW @1 "“Our findings challenge previous views… Have we heard this somewhere else lately?" sure we heard that many times before - here is another example: "Fish have evolved the ability to live on land many times, challenging the perception that this extreme lifestyle shift was likely to have been a rare occurrence in ancient times. New research shows 33 different families of fish have at least one species that demonstrates some terrestrial activity and, in many cases, these behaviors are likely to have evolved independently in the different families. A fish out of water might seem an extraordinary thing, but in fact it is quite a common phenomenon,” says study first author and UNSW evolutionary ecologist Dr Terry Ord " full article: https://www.sciencedaily.com/releases/2016/06/160622102129.htm martin_r
Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds
This is a 15 page technical journal article I asked for a paragraph. So I guess the answer is probably not. Biologic tried a layman discussion but not on the origin of the number. jerry
'But, most lay atheists 100% know, that these things WERE NOT DESIGNED / CREATED… Indeed, Martin_R @5, they evolved from a little warm puddle : As the joke goes (or something ike it) : 'First you get your little warm puddle...' Axel
Martin_r: Several years ago, I would have been just as pessimistic about Darwinists moving on to do real science as you now are. However, I'm like Darwin: we need some young people to begin seeing the deficiencies in Darwinian theory and the mounting evidence that ID principles are both explanatory and predictive. We'll see. Or, better, you'll see. I'm at an age where I cannot project too far into the future. PaV
In results of this sort I see the beginnings of a deepening theory of intelligent design. Combine the accumulating fossil data showing "explosions" at various times, with the genomic data showing the added DNA required for novel life features and functions, and stir in Michael Behe's latest demonstration of Darwinian devolution, and one begins to see the following picture. Life begins with an injection of information to generate and organize complex molecules. Added information collects these into the first simple, living cells. These "evolve" into different cells by tossing out different parts of their enhanced genome. Then there is another ID infusion of new information and metazoans arise. These too diversify by losing bits of their genome. Another big addition of ID info about 540 MYa produces the Cambrian explosion. The suddenly-appearing varied body plans then adjust, adapt and diverge by ongoing devolution. This approach continues with occasional injection of new genetic information into certain branches of life: plants, fish, molluscs, bacteria, phytoplankton, and so on arise. Each info burst allows new functions and features, which sort themselves out by natural selection and the resulting devolution, until the next info injection. Perhaps someone can begin mapping all these apparent injections of genetic info on a timeline? That would begin to reveal the "how?" of ID that materialists keep harping at us about. Evolution is thus envisaged as a sequence of ID events or processes, followed by the natural, Darwinian process of devolution and its resulting diversification. Just thinking out loud here, but this may be a way to combine Darwin with ID in a scientifically supportable theory of the history of life on Earth. Fasteddious
PaV @7 "When will they surrender? Never? Is atheism too important?" yes, to give up darwin (like YALE computer science professor David Gelernter did recently), is politically very sensitive... it could turn the world up side down. Moreover, hundred thousands of biologists worldwide would have to admit, that they were dead-wrong .... i think, this will never happen, whatever the evidence and future discoveries will be... In 2020, the evidence for CREATION is undeniable... and nothing happens... they even call us "stupid creationists" ... Like i said, this is politically too sensitive... Perhaps if Jesus will return to Earth to save us again, perhaps then... BUT EVEN IN THIS CASE, I WOULD NOT BE SO SURE !!!! martin_r
Many years ago, I posted that whole genome analysis would either prove, or disprove, Darwinism. Well, we now know that Darwinism is headed for the "ash-heap of history." Sir Fred Hoyle, even as a child, thought Darwinism to be silly. Later in life, when he took up the subject more seriously (see, e.g., his "Mathematics of Evolution"), he calculated the probability of cytochrome c coming about in random fashion. It was a huge number--and cytochrome c is a relatively small protein; however, it is 'essential' for cell division. IOW, if there is no cytochrome c, then organisms can't divide. And if they can't divide, then it's the end of the line for that organism--that is, no germ cells are possible, nor is simple fissile reproduction. This was all Hoyle needed to see to know that Darwinism was, and is, wrong. His view, however, was not enough. But now we have genome bases and computers that can compare sequences, and that means Darwinism will crumble under the new findings of new analyses. If you can't explain the rise of a relatively small protein like cytochrome c, then how do you explain, mathematically, the rise of "explosions of new genes"? When will they surrender? Never? Is atheism too important? PaV
ET @4 i doubt that Jerry ever heard of 'CHAPERONES' .... most lay people have no idea how these things work... most lay people can't tell the difference between a bacteria and a virus.... But, most lay atheists 100% know, that these things WERE NOT DESIGNED / CREATED... martin_r
PW @1 '“Our findings challenge previous views…”' yes, i have noticed that too.... Basically, this is how most mainstream scientific papers on evolution start thesedays. Don't matter whether it is from archeology, paleontology, or molecular biology.... The following might be a bit off topic, but i found it only recently and i would like to share with you guys. It is a bit older, from 2007, but it is worth to read ... Please keep in mind - this is from mainstream paper !!! Here you go: "CHALLENGING DARWIN'S THEORY OF SEXUAL SELECTION" "“May a biologist in these polarized times dare suggest that Darwin is a bit wrong about anything ? Even worse, does a biologist risk insult, ridicule, anger, and intimidation to suggest that Darwin is incorrect on a big issue ? We have a test case before us. Darwin appears completely mistaken in his theory of sex roles, a subject called the ‘theory of sexual selection’.”" https://www.jstor.org/stable/20028107?seq=1 martin_r
jerry- “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” (Axe, J Mol Biol 341, 1295-1315, 2004). And remember most proteins need a chaperone or chaperones to fold properly. They do NOT just find their proper spatial configuration on their own. ET
Can anyone in a short or medium paragraph explain why Doug Axe's thesis that operational proteins are only 1 in something like 10^77. I will try to find his exact number before time clock for changes runs out. I know it has something to do with how they fold and that how they fold is primarily a function of electromagnetism. jerry
"...an unprecedented level of fundamental genomic novelties..." "unprecedented"? pw
"Our findings challenge previous views..." Have we heard this somewhere else lately? :) pw

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