Biological Information and Intelligent Design: de novo or ex nihilo?


(system) #1
Do some DNA sequences emerge from nowhere, without a natural origin?
This is a companion discussion topic for the original entry at https://biologos.org/blogs/dennis-venema-letters-to-the-duchess/biological-information-and-intelligent-design-de-novo-or-ex-nihilo

(Dennis Venema) #2

Thank you for reading, and I am available to answer questions. A Merry Christmas to you as well. :slight_smile:


(Richard Wright) #3

Hi Dennis,

I struck me when reading this that it must take a lot of time and energy to do what you so admirably do, find the exact quotes from the IDer(s) doubting the process in question, then carefully and clearly showing how their arguments are off base.

As usual I loved your post, you make the biology so easy to understand. Thanks for the hard work and look forward to your next article. And Merry Christmas!


(Dennis Venema) #4

Thanks for your kind words, Richard. A Merry Christmas to you & yours as well.

Reading this section of Darwin’s Doubt was another moment of “he can’t seriously be arguing this, can he?” Yes, it really does seem that Meyer thinks de novo genes come out of nowhere by some unexplained mechanism. If this is what he really thinks - and I’ve done my best to read his argument in its entirety and in context - then he simply doesn’t know enough about what he is writing about, sadly.


(Peaceful Science) #5

Excellent article on ORFans and de novo genes. Very clear and understandable too.

I’m curious @Paul_Nelson’s thoughts, as he has been making that argument for a while.


(Peaceful Science) #6

@DennisVenema, in the next post you look at protein folding. Looking forward to it.

This article might be helpful for teaching. I found it pretty good and understandable. https://peerj.com/articles/cs-100/


#7

Hello Dennis,
Thank you for all the work you do to translate biological knowledge into a form that nonspecialists can comprehend. I have made use of your work in some of my blogging on evolution (e.g. https://letterstocreationists.wordpress.com/2014/04/02/realistic-expectations-for-transitional-fossils/ ).

I know this issue was discussed a bit in the comments on your earlier article on nylonase, but the treatment in Wikipedia indicates strongly no frameshift mutation was involved in the evolutionary development of the gene. The Wikipedia entry “Nylon-eating Bacteria” states:
”… Further study revealed that the three enzymes the bacteria were using to digest the byproducts were significantly different from any other enzymes produced by other Flavobacterium strains (or, for that matter, any other bacteria), and not effective on any material other than the manmade nylon byproducts…This discovery led geneticist Susumu Ohno in a paper published in April 1984 to speculate that the gene for one of the enzymes, 6-aminohexanoic acid hydrolase, had come about from the combination of a gene duplication event with a frameshift mutation. Ohno suggested that many unique new genes have evolved this way. A 2007 paper that described a series of studies by a team led by Seiji Negoro of the University of Hyogo, Japan, suggested that in fact no frameshift mutation was involved in the evolution of the 6-aminohexanoic acid hydrolase.”

The 2007 paper they cite here is Seiji Negoro, et al., Nylon-oligomer Degrading Enzyme/Substrate Complex: Catalytic Mechanism of 6-Aminohexanoate-dimer Hydrolase, Journal of Molecular Biology Volume 370, Issue 1, 29 June 2007, Pages 142–156. That 2007 Negoro paper seems to discuss mainly the mechanism of the hydrolase.

The 2005 Negoro paper you cited [Journal of Molecular Biology Volume 370, Issue 1, 29 June 2007, Pages 142–156] talks more about the genesis of the active EII gene from the barely-active EII’ gene. The abstract concludes, “…Here, we propose that amino acid replacements in the catalytic cleft of a preexisting esterase with the beta-lactamase fold resulted in the evolution of the nylon oligomer hydrolase.” That seems to be the basis of Wikipedia indicating in this “Nylon-eating Bacteria” article that no frameshift was involved.

The Wikipedia article “Frameshift Mutations” likewise claims that the frameshift concept is likely wrong:
“Frameshift mutations have been proposed as a source of biological novelty, as with the alleged creation of nylonase, however, this interpretation is controversial. A study by Negoro et al (2006) found that a frameshift mutation was unlikely to have been the cause and that rather a two amino acid substitution in the active site of an ancestral esterase resulted in nylonase.”
In this case the Wikipedia article cites the 2005 (not 2006) J. Molecular Biology article that I mentioned above.

In the comments on your earlier article, you stated that “As I understand it, confusion arises that there are duplications of the enzyme after the initial frameshift mutation that creates the first nylonase. These duplications undergo mutations that improve their specificity (recall that the first nylonase is a pretty poor nylonase). “ This implies that the Wikipedia interpretation is incorrect.

Would you mind elaborating more on what exactly the ancestral gene was and where the frameshift-causing mutation took place, how that affected the gene in terms of its original function, how Wikipedia erred, etc.? Hopefully you can address this in some detail in a separate article, with some of your nice illustrative figures. This nylonase gene is one of the clearer evidences for evolution, but the Wikipedia treatment can be used to dismiss it as just a trivial matter of a couple of point mutations. Thanks…

Scott Buchanan


(Dennis Venema) #8

Hi Scott - the wiki article is incorrect. They are misunderstanding the papers (not surprising, since they are not guaranteed to be biologists).

The “pre-existing ancestral esterase with the beta-lactamase fold” is the one that was produced by the frameshift in the unrelated gene. The amino acid substitutions later make it a better nylonase.


(George Brooks) #9

I think it’s worth reading the VERY brief question in the OP (also in the thread’s title)!
See below:

Naturally, it would be oh-so-wonderful if scientists were able to see - - not just an occasional mystery - - but a Pattern of all new DNA sequences having such “novelty” that it would be impossible to think that a base pair here or there was incorrectly replicated.

Wouldn’t that make EVERYONE’s life easier? But no. What we find is a crazy quilt of all
sorts of ways that DNA sequences get altered:

  1. copied into other DNA sequences [the other side of the coin is described in (5) and (7) below];
  2. perfectly copied except for one molecule;
  3. copied with multiple errors;
  4. in the middle of an existing sequence, receiving a foreign strand of DNA sequence from
    out of the blue (with no known purpose or purpose still unknown);
  5. in the middle of an existing sequence, receiving a foreign strand of DNA sequence from
    out of the blue (but known to exist elsewhere in the same version) [see (1) above];
  6. Same as (4) above, but “In Between” existing DNA sequences;
  7. Same as (5) above, but “In Between” existing DNA sequences [see (1) above].
  8. And scenarios I haven’t even imagined so far.

As one might see, only the “mystery” of either (4) or (6) evades easy explanation.

Some readers might remember my answer to a frequent question to me: How does God guide evolution?

My answer, received as humor but intended quite seriously: “God uses cosmic rays” to interfere with the perfect replication of DNA strands.

But as I have studied, I have read that surprisingly little energy - - at just the wrong time - - can interfere with the perfect replication of DNA strands:

a) the presence of water molecules;
b) the over-abundance or lack of a cellular enzyme or some other factor that contributes to correct replication;
c) the presence of other radiation far weaker than Cosmic rays… and so on.


#10

Dennis,
Thanks for clarifying where Wikipedia went wrong.
I still think it would be useful to know more on what exactly the ancestral gene was (its function, and its name if it has one) and where the frameshift-causing mutation took place in that gene, and how that affected the gene in terms of its original function. Your prior article on nylonase indicates the new gene makes a radically different protein with different folds and all, so presumably that killed off the original function of this gene. Did that harm the organism, or was the original gene fairly redundant?

If this is more than you want to address in a comment, I understand; if so, I would look forward to a more detailed treatment in an article whenever you can get to it.
Thanks,
Scott


(Dennis Venema) #11

As far as I know the function of the original gene is unknown - but its sequence is reported in the original Ohno paper. Whatever it was could not have been essential for survival in that context, since the mutation did destroy it, yes.