Gene Duplication Puns

Why does gene duplication occurs while performing gene annotation?

Usually Creationists attempt to dismiss Gene Duplication as a source of additional genetic information because as they argue, the duplicated version of a gene is just a copy of the same information [6]. Now what puzzles me about this argument is that even though Creationists don't accept Gene Duplication or an increase in CN of a gene as being "Additional Information"... they'd turn around and argue that a loss or reduction in the CN of a Gene counts as a "Loss of Information" [4,5].

For example, Creationists would not accept that duplicating multiple copies of the AMY2B Gene in Dogs as being "Additional Information" [1], yet they'd argue that Polar Bears losing several copies of the AMY1B Gene is a "Loss of Information" [3].

To help clear up this appearant contradiction in logic, I want to ask Creationists a question and I'd appreciate if they explain themselves when giving the answer.

Question: If Gene duplication or an increase in Gene copy number doesn't count as "Additional Information", why then does a loss or a decrease in Gene copy number count as a "Loss of Information"??

REFERENCES:

1. The genomic signature of dog domestication reveals adaptation to a starch-rich diet; Erik Axelsson et al, 2013. [PDF]: https://www.researchgate.net/publication/235375792_The_genomic_signature_of_dog_domestication_reveals_adaptation_to_a_starch-rich_diet

2. Diet shaped Dog domestication; Science Daily, 2013: https://www.sciencemag.org/news/2013/01/diet-shaped-dog-domestication

3. Polar bear evolution is marked by rapid changes in gene copy number in response to dietary shift; David. C. Rinker et al, 2019: https://www.pnas.org/content/116/27/13446#F1

4. Study reveals new genomic roots of ecological adaptation in polar bear evolution; Science Daily, 2019: https://www.sciencedaily.com/releases/2019/06/190617164624.htm

5. Behe Vindicated Again: Goldfish Are Broken Carp; Evolutionnews, 2019: https://evolutionnews.org/2019/07/behe-vindicated-again-goldfish-are-broken-carp/

6. Evidence of New Genetic Information?; Dr. Georgia Purdom, 2008: https://answersingenesis.org/genetics/mutations/evidence-of-new-genetic-information/

this article claims gene duplication is not viable for evolution https://creation.com/do-new-functions-arise-by-gene-duplication

thoughts? I've fallen for things like this before, this one seems like he has somewhat of a case although im ignorant. thoughts?

In an article from Evolutionnews.org [2], Casey Luskin of the Discovery Institute attempted to critique a 2010 paper on the evolution of Antifreeze in Antarctic Eelpouts [1]. Although numerous claims were made throughout the article, I'll be focusing on Casey's calculations on gene duplication rates, since that seems to be the most significant argument he's making.

Casey goes on to calculate the time it should have taken for the Antarctic Eelpout to evolve 30 copies of the AFPIII gene in the following quote.

Quote: "In his 2005 textbook Evolution, Douglas Futuyma states that a high estimate of the gene duplication rate is “about 0.01 duplication per gene per million years". A given gene will thus be duplicated about once every 100 million years...What are we to make, then, of the fact that Antarctic eelpouts have over 30 AFPIII genes, all of which are said to have resulted from a duplication of a single AFPIII gene which evolved at some point in the past 50 million years in response to changing ocean temperatures?...It should have taken some 3 billion years just to accomplish..." [2] - Casey Luskin 2011

Basically he's arguing that because genes duplicate at a rate of 0.01 per gene per million years, then it should take about 3 Billion years to get 30 copies of a gene.

And here's where my concerns with Casey's calculations begin. Casey failed to take into account that organisms can have thousands of genes, so even at a rate of 0.01 duplications per gene per million years can result in hundreds of duplicates in just a few million years.

Quote: "Gene duplication gives rise to paralogs and is considered the major mechanism to generate genetic diversity and new functions (Lynch, 2002). The general rate of gene duplication is ∼1% (0.01) per gene per million years, while 50% of duplicated genes are lost every 4 million years (Lynch, 2002). In a species with ∼20,000 genes (such as ticks), ∼1,000 genes will become fixed over 10 million years." [4]

In addition to Casey's failures to properly calculate the rates of gene duplication, he also fails to take into account that not all genes evolve at the same rate. the rate of "0.01 duplicates per gene per million years" is only an average gene duplication rate for an entire genome. Furthermore, a duplication is not always limited to a single gene; entire segments of DNA, containing many genes, can be duplicated. For example, a single copy of gene could theoretically become 32 copies of that gene in only 5 duplicati

Not a denier just very curious to know :)

1. I'm currently reading Kenneth Miller's book, "Only a Theory". In the book, he talks about about bacteria digesting nylon evolved. I didn't quite understand how the length of the gene was added with new base pairs. Would someone explain?

2. He talks about how fishes quickly evolved to survive on way colder conditions. He says a digestive enzyme gene rapidly changed by experimenting with a copy of the gene and then modifying the duplicated gene to produce the desired outcome. How does the gene have duplicate copies of itself? How does it know if a particular mutation is "working"?

3. He points out this particular evolutionary change was very rapid. When does rapid evolutionary changes happen and when does it take a long time for another change to appear.

If you guys would take the time to explain, I'd be extremely grateful!

"In the read depth (RD) approach mostly a non-overlapping sliding window is used to count the number of short reads that are mapped to a genomic region overlapped with the window. Then these read count values are used to identify CNV regions."

• https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1705-x

Just curious. I would think not if it is a sliding window and thus CNVs would be relative to the depth of the flanking regions.

Greetings! I am currently interested in molecular evolution and programming. I want to detect all gene duplications for a certain group of mammals. What are the best methods and algorithms to use?

Evolutionists love to cite gene duplications as a source of new information. I've argued vociferously that ID proponents don't serve themselves well by framing the ID argument in terms of information (software) vs. chemistry (hardware).

Gene duplications don't explain very well the origins of the Topoisomerase paralogs (duplicates) in humans. Topoisomerase 2-alpha and 2-beta are an example. If one of the duplicates (paralogs) is missing, sickness and death results. Evolutionists don't have a good explanation why these specialized complementary topoisomerases should evolve to exist from an ancestral form -- except via the usual handwaving.

They never think how life critical paralogs (such as the Topoisomerases paralogs) could evolve without having to admit it must evolve free of strong selection. If one paralog (duplicate) is so strongly selected for that it is life critical, do evolutionists realize that without the paralog the creature is already dead? End of story. No evolution. The gene duplication story is worthless.

[Sure yeasts don't have these paralogs, but then how did humans evolve them such that they are life critical.]

In comparable manner is the evolution microtubule tubulin paralogs (duplicates) by gene duplication. Without at a bare minimum the alpha,beta, and gamma paralogs (duplicates), microtubule polarity (as in street signs for a one-way highway), the microtubule is functionless and hence the creature is dead. Gene duplication is pointless, since the creature would already be dead. End of story. No evolution.

Do evolutionists examine these issues? Well, they claim to solve microtubule evolution by simulataneous gene fusions for no good reason. Do they work out the a priori probabilities of such events? Nope, they suggests it's natural, but when in fact it would require miracles almost indistinguishable from miracles of special creation. "Co-evolution" or "parallel evolution" are the new buzzwords. But they are euphemisms for events that would have to be miraculous as a matter of principle -- except they refuse to say so.

BTW, I describe some of the wonders of TopoIsomerase 2 enzymes here:

https://crev.info/2019/06/creationist-topoisomerase-research/