Pseudogenes: functional or non-functional


(Chris) #1

Agreed. Today various insects and spiders are eaten around the world. Re pseudogenes, we will probably find, as with other pseudogenes, that they actually are functional.


How much did God affect evolution?
(Matthew Pevarnik) #2

I’m sorry. What are you referring to? You don’t just get to come around and say all pseudogenes are functional (where’s your evidence?) and even if they were, that’s not even the point. Taken from the end of the particular blog post:

Why would the Creator design humans, rhinos, tigers and other mammals that never or almost never eat insects with remnants of insect-digesting genes? Is it just a coincidence that the earliest mammal fossils, found alongside dinosaurs, appear to have been insect eaters, and modern herbivores and carnivores have remnants of insect-digesting genes? For those that believe that all animals were plant-eaters in the Garden of Eden, why do so many herbivores have remnants of insect-eating genes? If mammals were created in the last 10,000–6,000 years, how could they evolve from insect-eaters to herbivores and carnivores so quickly, modifying their teeth, jaws, intestinal tracts, etc. to be optimized for their new diets?

Furthermore the shared mutations are what is most important. There are lots of ways to deactivate a gene and to have the exact same deactivation’s across a wide number of genes is best explained only by a once shared common ancestry.


(Chris Falter) #3

At least 80% of pseudogenes in the human genome are not even transcribed. (Source.) If they are not transcribed, how can they possibly be functional?

Blessings,
Chris


(Chris Falter) #4

Hi Chris,

I was able to research the matter a little bit more. A later/better study–by the same team that published the ENCODE study–shows that the human genome has 14,112 pseudogenes. Of these, only 876 (6.2%) are transcribed.

93.8% of pseudogenes in the human genome are not even transcribed. If they are not transcribed, how can they possibly be functional?

Now let’s examine those few pseudogenes that are transcribed. Xu and Zhang examined 34 such pseudogenes in the human genome and determined that only 5 (14.7%) have any functionality as evidenced by selection pressure.

Assuming that all of the 876 transcribed pseudogenes in the human genome have the same ratio of functionality (14.7%) as those examined by Xu and Zhang, we can infer that 129 of them are functional.

Based on this analysis, what proportion of human pseudogenes are actually functional? 129 / 14112 = 0.0091 – less than 1%.

Certainly there is some imprecision in this analysis. The proportion might be a little lower, or it might even be two or three times as large. There is no particular reason to think so, but scientific analysis being what it is, I would be willing to admit that possibility.

In any case, it is impossible for the percentage of functional pseudogenes to exceed 6.2% because that is the limit imposed by their transcription rate.

Thanks,
Chris Falter


(Chris) #5

… and neither do you just get to come around and say they’re non functional. At best you can say that neither functionality nor non-functionality has been established in most cases.

"Pseudogenes have not received much attention in the scientific literature because they are assumed to be “junk.” But that is changing rapidly. Where pseudogenes have been carefully studied, they are often found to be functional, and in some nonstandard ways. Part of the problem … [cont]https://evolutionnews.org/2018/06/on-hominid-fossils-and-universal-common-ancestry-denis-lamo


(Matthew Pevarnik) #6

As @Chris_Falter literally just said over 90% of pseudogenes are not even transcribed. Please stop propagating silliness that they are all functional.


#7

Here’s another relevant paper:

In this study, they found that about 15% of human pseudogenes are transcribed, and that 88 out of 11,216 had strong evidence for function. Almost 80% of the pseudogenes had at least 1 function-associated biochemical association, such as the presence of active transcription factor binding sites upstream. That being said, the vast majority of those 80% of pseudogenes (~85%) were associated with active chromatin only, which isn’t compelling evidence of functionality at all, given that processed pseudogenes preferentially insert themselves in active chromatin. There is no good evidence that a substantial fraction of human pseudogenes are functional.

It’s important to note that even those pseudogenes that are found to be functional don’t stop being pseudogenes as a result. Pseudogenes can be adapted for new functions and still retain their obvious appearance of originally being a pseudogene.


(Chris Falter) #8

Let’s think carefully here. Logically, these two statements are 100% consistent:

  • “Pseudogenes … are often found to be functional”
  • The vast majority of the pseudogenes in the human genome cannot possibly be functional, because they are not transcribed.

Yes, many pseudogenes in the human genome are transcribed, representing a potential for many future research papers describing the functionality of a pseudogene previously thought to be non-functional.

But no: The remainder–the vast majority–are inert, full stop.

I don’t have the entire text of what Ann Gauger, et al. wrote in the Theistic Evolution book that Klinghoffer quoted. Consequently I don’t want to accuse her and her collaborators of bad faith. But I will say this: The passage she/they quoted from Wen, et al. (2012) can in no way be construed, in its original context, as supporting the notion that more than a slim minority of pseudogenes will ever be found to be functional. Here’s why: Wen, et al, cited early, preliminary studies suggesting that anywhere from 3% to 20% of human pseudogenes are transcribed. The point of Wen’s paper was to encourage fellow researchers not to ignore the potential for function in the slim minority of pseudogenes that are transcribed. Wen was not suggesting that researchers beat their heads against the wall in a vain attempt to find functionality where DNA is not even transcribed.

Thus it is scientific malpractice to cite Wen’s paper as support for the potential of functionality in every pseudogene. Klinghoffer gets the story of pseudogenes really, really wrong. Whether that’s because he misread his sources or because his sources misread the literature, I cannot say.

@aarceng I am not blaming you personally; I am quite sure you quoted Klinghoffer in good faith. I would just recommend that you not rely on Klinghoffer as a source of knowledge about biology. This is not the first time he has gotten things backwards.

Warm regards,
Chris

P.S. @evograd - I am not surprised that you are better versed in the literature than I and found a better/more recent study. Thanks for bringing us the latest/greatest. If you think I have misunderstood anything, please do not hesitate to correct it. Thanks!


(Stephen Matheson) #9

The notion that everything in a genome is “functional” has profound implications for biology. It means that Christmas trees require at least 6 times as much genetic information as humans do. This must mean that Christmas trees are 6 times as complex as humans are. Maybe think twice before cutting one down for some Christianized pagan ritual?

https://www.nature.com/articles/nature12211


#10

LOL!  


(Chris) #11

@pevaquark, if you’d read the linked article you would have found " Part of the problem is that a pseudogene may be active in specific tissues only during particular stages of development, making identification of their functions difficult. "
Please read the article before making further comments.

It was initially assumed on evolutionary grounds that pseudogenes were non-functional. Since then many have been found to have function.

The current situation is that some have been found to be functional, most have not had functionality determined one way or the other. Has no function actually been confirmed; as opposed to not observed; in any pseudogene?


(Stephen Matheson) #12

That’s false in a few different ways, which is an impressive achievement.

Pseudogenes are defined by their structure primarily and by their capacity for expression secondarily. In other words, some sequences are classified as pseudogenes because they resemble a fully functional gene (one that can be expressed as mRNA and can code for a protein) but are mutated such that no functional protein can be made, and some are classified as pseudogenes because they cannot be expressed (an apparent coding sequence but without a promoter; these are so-called processed pseudogenes). Evolutionary reasoning plays no role in defining them.

Moreover, neither evolution nor molecular biology makes broad assumptions about whether a particular pseudogene has “function.” A pseudogene can’t make a protein but looks like a sequence that can. That’s all a pseudogene is. In fact, we do know that some pseudogenes perform functions, and this is not surprising or weird, since lots of DNA sequences that aren’t genes can perform functions. Typically these are rudimentary “functions” that involve binding of regulatory proteins. Sometimes the “function” is to serve as a decoy for other processes. None of these “functions” invalidates any evolutionary explanation for the presence or formation of a pseudogene.

Evolution certainly does not assume anything about pseudogene “function.” What evolution does is more dramatic: it explains their existence and their presence in particular genomic locations in particular lineages. Without common descent, processed pseudogenes make no sense. Hundreds of olfactory receptor pseudogenes in the human genome make no sense. When you combine common descent with molecular biology (which explains how retroelements work and how promoters work and how frameshifts work and why wrecked genes don’t get spliced out of genomes), you have a simple, clear, explanation for pseudogenes and for millions of retroelements that comprise vast proportions of animal genomes.


(Chris Falter) #13

He read it. I read it. We both understand it.

By all appearances, what seems to have happened is that you found a quote or two that you like in the article, and you keep citing those quotes. However, based on what you keep saying in this thread, you do not understand the biology. For that matter, you do not appear to have understood what @pevaquark and I are saying to you.

I will give it one more shot.

These two statements are logically consistent:

  1. “many [pseudogenes] have been found to have function.”
  2. The vast majority of human pseudogenes cannot possibly have function (assuming no further evolution) because they are not transcribed.

You keep repeating #1 in the vain belief that it will disprove #2. No matter how often you do so, however, you cannot possibly disprove #2 by this repetition because the two statements are not logically exclusive. Both can be (and are) simultaneously true.

This is false. The vast majority are not transcribed, so they do not have functionality.

Yes–in those (the vast majority) which are not even transcribed.

I do not understand why this has been so hard for you, Chris. Several people besides me have explained this to you, and they are far more qualified than I.

Blessings,
Chris


#14

This discussion illustrates the glaring integrity problem that the YEC position has when it tries to engage science. Why should interpretation of the evidence require such intellectual acrobatics?


#15

Adding the problem of a lack of transcription, if these are functional genes then why is there a lack of sequence conservation?

False. Scientists concluded that pseudogenes were non-functional based on the evidence. That evidence includes a lack of a transcript, lack of sequence conservation, and lack of open reading frames. They didn’t assume anything.

The lack of conservation, lack of a transcript, and lack of open reading frames for the full protein are all strong observations that you need to address.


(Curtis Henderson) #16

This is not a new argument from the YEC or ID camps. It seems like a field that would be ripe for exploration. Can you imagine the Discovery Institute cranking out papers showing how sequences thought to be “pseudogenes” actually have critical functions? It would be some very compelling evidence to support their narrative. Yet, I haven’t actually seen anything close to attempting this. I wonder why that is…


(Stephen Matheson) #17

A biologist who really believed that all stuff in genomes has “function” could turn to fungi to do experiments. The evolutionary account, in which variations in genome size (specifically in numbers of transposable elements) arise during bursts of transposon activity, could be challenged by showing that these are actually intelligently-designed components with biological “functions.” In this age of CRISPR, and building on decades of research on yeasts in the lab, the research program could be straightforward. And some real scientists have already kicked things off:


#18

Functional pseudogenes are a problem for many other ID arguments. As we have seen in other threads, many ID supporters argue that even the smallest changes to genes will destroy their function. With pseudogenes, you have DNA sequence that is accumulating mutations at a rate consistent with neutral drift which is strong evidence that very few, if any, mutation are deleterious within the gene. This would also mean that there is function found throughout sequence space, yet another contradiction of one of their main arguments.


#19

Another interesting example is the bladderwort. It has about the same number of what we would consider classical functional genes as that found in other animals and plants. The difference is that the bladderwort genome is just 0.082 billion bases compared to 3 billion bases for the (haploid) human genome and 56 billion for the onion genome. Nearly the entire bladderwort genome is made up of what we call functional genes, and it lacks the hundreds of thousands of pseudogenes found in other species.

Someone in the ID camp needs to explain how the bladderwort can survive without all of this functional DNA, and how it can be as complex as an onion with a genome that is just 0.1% of the size of the onion genome.


(Phil) #20

If tomatoes evolved from bladderworts, why do we still have bladderworts? :frowning_man:t4:

Just kidding of course. Goggled bladderworts and learned they and tomatoes have a common ancestor, as well as a bit about how they cleaned up their genome. Interesting stuff.