Pseudogenes: functional or non-functional

[cwhenderson (Curtis Henderson)]

@jpm

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

Oh Phil, thank you for that good laugh!

[T_aquaticus]

@jpm

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

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.

You missed the low hanging fruit!!

Bladderworts are carnivorous plants. If they share a common ancestor with tomatoes then we already have examples of the transitional forms:

[aarceng (Chris)]

@cwhenderson

Can you imagine the Discovery Institute cranking out papers showing how sequences thought to be “pseudogenes” actually have critical functions?

If you search their site you will find several articles on pseudogenes but I don’t see that they’re "cranking them out ". E.g.
As Research Advances, Debunking “Junk DNA” Is Almost Trendy
…transcript numbers, and working like switches to turn other genes on or off. We’ve seen “ pseudogenes ” (still assumed to be decaying remnants of evolutionary duplication events) acting as regulators. Even…

[cwhenderson (Curtis Henderson)]

@aarceng

If you search their site you will find several articles on pseudogenes

It’s been a few months since I perused Bio-complexity, but I don’t recall seeing any research done on potential functions of pseudogenes. A report on the discoveries of other groups is not the research I was envisioning. Obviously, there would be hurdles to such research in humans, but analysis of psuedogenes in human cell lines should be feasible and would be a great way to actually support what they claim based on the ENCODE project.

[T_aquaticus]

@aarceng

…transcript numbers, and working like switches to turn other genes on or off. We’ve seen “ pseudogenes ” (still assumed to be decaying remnants of evolutionary duplication events) acting as regulators. Even…

Finding a handful of pseudogenes that act as gene regulators does not mean the other 100,000 also have function.

[aarceng (Chris)]

@T_aquaticus

Finding a handful of pseudogenes that act as gene regulators does not mean the other 100,000 also have function.

Correct, however since some pseudogenes that formerly were believed to be non-functional have now been shown to have function it casts doubt on the assumption that pseudogenes are non-functional. Remember that very few have at this stage have been examined in detail.

From a YEC perspective we would not be surprised that some pseudogenes have lost their function since creation since everything has been affected by the fall.

[pevaquark (Matthew Pevarnik)]

@aarceng

From a YEC perspective we would not be surprised that some pseudogenes have lost their function since creation since everything has been affected by the fall.

Like the pseudogenes (even with shared deactivations in closely related species) for digesting insects that all mammals have or the pseudogenes for making teeth in birds and turtles or the pseudogenes for making enamel in baleen whales or the over 50%+ deactivated genes out of 1200 for smelling that are gone but have remnants in cetaceans. Does YEC have any specific pseudogenes that we should expect to find or just simply come in after the data and claim some happened after the fall and the others are all functional?

[T_aquaticus]

@aarceng

Correct, however since some pseudogenes that formerly were believed to be non-functional have now been shown to have function it casts doubt on the assumption that pseudogenes are non-functional.

You would first have to show that those specific pseudogenes were once thought to be non-functional.

@aarceng

Remember that very few have at this stage have been examined in detail.

They have all been examined for sequence conservation. A lack of sequence conservation is very strong evidence for a lack of function.

[Chris_Falter]

@aarceng

since some pseudogenes that formerly were believed to be non-functional have now been shown to have function it casts doubt on the assumption that pseudogenes are non-functional. Remember that very few have at this stage have been examined in detail.

Hi Chris,

I’m tempted to think you’re playing a game with us on the thread. No matter what evidence and logic is presented to you, you keep repeating the exact same two-sentence thought. Let’s review:

It all started with this post, from which you have not deviated:

@aarceng

Re pseudogenes, we will probably find, as with other pseudogenes, that they actually are functional.

The refutations have taken three basic directions:

(1) Shared DNA sequences in pseudogenes point to common ancestry.

@pevaquark

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.

(2) The theory of evolution does not assume that every pseudogene does not have function.

@sfmatheson

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.

@sfmatheson

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.

@sfmatheson

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.

(3) The vast majority of pseudogenes in the human genome have already been investigated and shown to have no possibility of function.

@Chris_Falter

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?

@Chris_Falter

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?

@evograd

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.

@Chris_Falter

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.

@Chris_Falter

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.

@Chris_Falter

aarceng: most [pseudogenes] have not had functionality determined one way or the other.

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

@Chris_Falter

aarceng: Has no function [i.e., lack of function] actually been confirmed; as opposed to not observed; in any pseudogene?

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

@T_aquaticus

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

@T_aquaticus

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

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.

Yet, here we are 28 posts later, and you still have not addressed a single one of the logical and evidential points that strongly refute your assertion. You just keep repeating the same two-sentence thought, as if repetition will somehow magically make the enormous amounts of scientific evidence and logic just disappear without a trace:

@aarceng

since some pseudogenes that formerly were believed to be non-functional …

False. See point #2 above: The theory of evolution does not assume that every pseudogene does not have function.

@aarceng

… have now been shown to have function it casts doubt on the assumption that pseudogenes are non-functional…

False. See point #3 above: The vast majority of pseudogenes in the human genome have already been investigated and shown to have no possibility of function.

@aarceng

…Remember that very few have at this stage have been examined in detail.

False. See point #3 above: The vast majority of pseudogenes in the human genome have already been investigated and shown to have no possibility of function.

So your statement has been strongly refuted by the evidence presented by many people. Yet you keep repeating it without bothering to address that evidence.

This is a serious problem. Your repetition of the same inaccuracies casts doubt on the assumption that you are willing to engage with us in good faith discussions.

If you want to keep receiving credibility and respect in this discussion forum, Chris, I suggest that you start giving respect to the people who are interacting with you by actually thinking about the logic and the evidence they are presenting to you.

Assuming no change in behavior on your part, at some point in the near future I will probably conclude that trying to interact with you on issues of scientific evidence is a waste of time and effort. Others may do the same.

Of course, as followers of Christ we have many important things in common. If you make it impossible for us to talk constructively about scientific evidence, then we’ll just have to move on to other topics.

Best regards,
Chris Falter

[aarceng (Chris)]

I think it may be best to let this topic rest for now.