Beta-Globin Pseudogene Is Functional After All

[ChetSinger]

This is a recent article posted by ICR that is of particular interest to me.

One of the key arguments of human evolution has now suffered the same fate as many other debunked icons of the errant paradigm of "junk DNA." In this case, it is new research related to the beta-globin pseudogene—which now shows it to be functional and important to hemoglobin gene regulation.

Hemoglobin is a protein in human red blood cells that transports oxygen throughout the body's circulatory system. The human hemoglobin protein is actually a cluster of two chains of different sub proteins. One of these chains is called the "alpha-globin" which remains the same from embryo development to adulthood. The second set is called the "beta-hemoglobin" chain which specifically changes at the embryo-to-fetal transition and again at the fetal-to-adult transition. This amazing bio-engineering allows the developing embryo-baby to receive oxygen at the correct levels throughout its critical growth processes.

The human beta-globin proteins are encoded in a cluster of six genes that extends over 80,000 bases on chromosome 11. The embryo-to-adult growth stage expression of each gene in the cluster depends on that specific gene's interaction with a control region preceding the whole cluster called the "locus control region" or LCR.

While five out of the six genes in the beta-globin cluster encode functional proteins, one of the genes called HBBP1 does not, because of several stop sequences in its code that were once thought to be mutations. This gene was classified as a pseudogene (a broken defunct remnant) because of its assumed non-functionality. Because the gene, along with its presumed errors, is also found in chimpanzees, evolutionists claimed it as proof that humans inherited their version of the gene from a common ancestor with chimps...

This is of personal interest to me because I was confronted with this once during an online debate (not on CF) and had no answer. So today I'm pleased as punch. This particular argument has been a big deal to evolutionists: it was used as evidence in the Dover trial: Here's a portion of the transcript (search for beta-globin).

There's more to the ICR article, and I'm not going to paste the entire thing. But one thing I've taken from it is that we creationists shouldn't be easily intimidated by evolutionary arguments from genetics. After all, we're only just beginning to understand what's really going on in our genome. And the more we learn, the more elegant our genetic code is revealed to be. And the more praise the Lord is due.

 

[sfs]

This is a recent article posted by ICR that is of particular interest to me.



This is of personal interest to me because I was confronted with this once during an online debate (not on CF) and had no answer. So today I'm pleased as punch. This particular argument has been a big deal to evolutionists: it was used as evidence in the Dover trial: Here's a portion of the transcript (search for beta-globin).

There's more to the ICR article, and I'm not going to paste the entire thing.

The evidence that HBBP1 is functional is that it appears that mutations do not accumulate in it; indeed, the fact that it's functional is worth an entire scientific paper. Since mutations do accumulate in most pseudogenes, this would also seem to be evidence that most pseudogenes are not functional.

But one thing I've taken from it is that we creationists shouldn't be easily intimidated by evolutionary arguments from genetics. After all, we're only just beginning to understand what's really going on in our genome. And the more we learn, the more elegant our genetic code is revealed to be. And the more praise the Lord is due.

You seem to be looking at a different genome than geneticists are. The more we look at the genome, the more it looks like a crazy-quilt of patches layered on top of gibberish on top of function.

 

[ChetSinger]

You seem to be looking at a different genome than geneticists are. The more we look at the genome, the more it looks like a crazy-quilt of patches layered on top of gibberish on top of function.

Really? Your opinion surprises me, because what I've been reading is exactly the opposite: we're discovering more and more functionality among the "gibberish" each year. I know you're a geneticist, but I hear other geneticists saying different things.

Here's an example. It's an extract from a TIME article that I bought, which I've been able to find on the web.

Junk DNA — Not So Useless After All

Junk. Barren. Non-functioning. Dark matter. That’s how scientists had described the 98% of human genome that lies between our 21,000 genes, ever since our DNA was first sequenced about a decade ago. The disappointment in those descriptors was intentional and palpable.

It had been believed that the human genome — the underpinnings of the blueprint for the talking, empire-building, socially evolved species that we are — would be stuffed with sophisticated genes, coding for critical proteins of unparalleled complexity. But when all was said and done, and the Human Genome Project finally determined the entire sequence of our DNA in 2001, researchers found that the 3 billion base pairs that comprised our mere 21,000 genes made up a paltry 2% of the entire genome. The rest, geneticists acknowledged with unconcealed embarrassment, was an apparent biological wasteland.

But it turns out they were wrong. In an impressive series of more than 30 papers published in several journals, including Nature, Genome Research, Genome Biology, Science and Cell, scientists now report that these vast stretches of seeming “junk” DNA are actually the seat of crucial gene-controlling activity — changes that contribute to hundreds of common diseases. The new data come from the Encyclopedia of DNA Elements project, or ENCODE, a $123 million endeavor begun by the National Human Genome Research Institute (NHGRI) in 2003, which includes 442 scientists in 32 labs around the world.

ENCODE has revealed that some 80% of the human genome is biochemically active. “What is remarkable is how much of [the genome] is doing at least something. It has changed my perception of the genome,” says Ewan Birney, ENCODE’s lead analysis coordinator from the European Bioinformatics Institute.

Rather than being inert, the portions of DNA that do not code for genes contain about 4 million so-called gene switches, transcription factors that control when our genes turn on and off and how much protein they make, not only affecting all the cells and organs in our body, but doing so at different points in our lifetime. Somewhere amidst that 80% of DNA, for example, lie the instructions that coax an uncommitted cell in a growing embryo to form a brain neuron, or direct a cell in the pancreas to churn out insulin after a meal, or guide a skin cell to bud off and replace a predecessor that has sloughed off.

“What we learned from ENCODE is how complicated the human genome is, and the incredible choreography that is going on with the immense number of switches that are choreographing how genes are used,” Eric Green, director of NHGRI, told reporters during a teleconference discussing the findings. “We are starting to answer fundamental questions like what are the working parts of the human genome, the parts list of the human genome and what those parts do.”...

It goes on and on, describing how the results of Project ENCODE are being used to learn more about the switches involved in various genetic diseases. It's becoming clear to me that the amount of "gibberish" is decreasing, not increasing, as we dig deeper.

Shouldn't we be rejoicing at these kinds of discoveries? Atheists have been beating us up for years, denying God by claiming that more than 90% of our genome is leftover evolutionary junk. But it's turning out to be a denial based on ignorance: the more we learn, the less junk we see.

I think this is an evangelizing opportunity for us: while atheists used to point at our genome and crow about evolutionary junk, we can now point to our genome and crow about the Author of Life.

 

[Fascinated With God]

You didn't address his point that true "junk DNA" accumulates mutations. There is such a thing as defunct genes that are no longer expressed in modern man, for which any number of mutations to those gene produce no effect.

 

[metherion]

Forgive me, but I still don't see exactly how this falsifies any evolutionary arguments.

Okay, instead of a set of conserved mutations in a nonfunctional psuedogene in three species (Assuming I'm reading the transcript correctly, without seeing the referenced slides I could be mistaken, but the transcript references chimpanzees, gorillas, and humans), we have a conserved gene that has the same form and function and is built the exact same way across three different species since they diverged. The quote that makes me think 3 species is here:

And if you go on to the next slide, what I'd like to show you are three organisms, the gorilla, the chimpanzee, and the human being that share the exact same set of molecular mistakes.

I got that from the transcript link in the OP.

I don't see how going "Ah ha, that code isn't junk!" negates the "shared without change across two or three related species that diverged millions of years ago but is still identical, which is what we'd expect to see according to evolution" part. Okay, so the code was classified wrong because we didn't know what it did, but that doesn't change the code sequence, nor does it mean that the chimpanzee no longer shares that code sequence built in the exact same way.

Something just seems off about the premise of the article. Wouldn't it be more the prediction of geneticists that that particular psuedogene was non-functional, and then more work in geneticists which fixed that assumption, with the evolution part just standing off to the side going "Yep, those codes are conserved across these species, regardless of what they mean."?

Metherion

 

[ChetSinger]

Forgive me, but I still don't see exactly how this falsifies any evolutionary arguments.

Okay, instead of a set of conserved mutations in a nonfunctional psuedogene in three species (Assuming I'm reading the transcript correctly, without seeing the referenced slides I could be mistaken, but the transcript references chimpanzees, gorillas, and humans), we have a conserved gene that has the same form and function and is built the exact same way across three different species since they diverged. The quote that makes me think 3 species is here:



I got that from the transcript link in the OP.

I don't see how going "Ah ha, that code isn't junk!" negates the "shared without change across two or three related species that diverged millions of years ago but is still identical, which is what we'd expect to see according to evolution" part. Okay, so the code was classified wrong because we didn't know what it did, but that doesn't change the code sequence, nor does it mean that the chimpanzee no longer shares that code sequence built in the exact same way.

Something just seems off about the premise of the article. Wouldn't it be more the prediction of geneticists that that particular psuedogene was non-functional, and then more work in geneticists which fixed that assumption, with the evolution part just standing off to the side going "Yep, those codes are conserved across these species, regardless of what they mean."?

Metherion

Hello. The evolutionary argument was that God wouldn't make the same mistake three separate times. It's presence and "brokenness" was considered evidence that the mistake occurred once in the past and was passed on.

Since it's functional that argument now fails. It can now be considered a design decision.

 

[Fascinated With God]

It still proves that humans are genetically linked to gorillas and chimpanzees, which is not consistent with any YEC interpretation.

 

[sfs]

Really? Your opinion surprises me, because what I've been reading is exactly the opposite: we're discovering more and more functionality among the "gibberish" each year. I know you're a geneticist, but I hear other geneticists saying different things.

Here's an example. It's an extract from a TIME article that I bought, which I've been able to find on the web.

The Time article is, to be blunt, rubbish -- not uncommon in popular articles about science, unfortunately. At no point in the last several decades have geneticists thought that all noncoding DNA was junk. Multiple kinds of non-coding, functional DNA have long been known; what wasn't known was how much there was of it.

When the concept of junk DNA was first proposed, the original guess as to how much of the human genome was functional was 20%. That was several decades ago. The Human Genome Project showed that only ~1.5% of the genome coded for proteins, but the researchers never suggested that only coding DNA was functional. The first decent estimate of the fraction of the genome that was functional came with the publication of the mouse genome in 2002, which identified 5% of DNA as being conserved between humans and mice, and therefore likely functional. The paper explicitly stated that further functional DNA might be found, in particular functional DNA that was specific to one lineage or the other. With the findings of the ENCODE project (assuming Manolis Kellis's arguments are correct), the minimum fraction that's functional is now around 9%; it could be as high as 20%.

It goes on and on, describing how the results of Project ENCODE are being used to learn more about the switches involved in various genetic diseases. It's becoming clear to me that the amount of "gibberish" is decreasing, not increasing, as we dig deeper.

Over ~40 years, the amount of junk in the genome has gone from 80% to somewhere between 80% and 90%. That really doesn't look like a decrease to me.

Shouldn't we be rejoicing at these kinds of discoveries? Atheists have been beating us up for years, denying God by claiming that more than 90% of our genome is leftover evolutionary junk. But it's turning out to be a denial based on ignorance: the more we learn, the less junk we see.

I've never seen an atheist argue that God doesn't exist because our genomes are littered with junk; the only people who've seemed to care have been creationists, who for some reason have insisted that God couldn't have created creatures with useless DNA. That strikes me as a bizarre argument (have they noticed how much of the universe is wasted space?), but the main point is that it's wrong: most of the human genome really is junk.

I think this is an evangelizing opportunity for us: while atheists used to point at our genome and crow about evolutionary junk, we can now point to our genome and crow about the Author of Life.

I prefer to stick to the truth. God, the author of life, created us by means of evolution, and our genomes have a great deal of DNA whose sequence does not matter.

 

[SkyWriting]

The evidence that HBBP1 is functional is that it appears that mutations do not accumulate in it; indeed, the fact that it's functional is worth an entire scientific paper. Since mutations do accumulate in most pseudogenes, this would also seem to be evidence that most pseudogenes are not functional. You seem to be looking at a different genome than geneticists are. The more we look at the genome, the more it looks like a crazy-quilt of patches layered on top of gibberish on top of function.

That is true. It still looks like gibberish at this time.
I would never be proud of such thoughts though
and I'd keep them to myself.

 

[SkyWriting]

Hello. The evolutionary argument was that God wouldn't make the same mistake three separate times. It's presence and "brokenness" was considered evidence that the mistake occurred once in the past and was passed on. Since it's functional that argument now fails. It can now be considered a design decision.

It was an ungrounded argument to start with.
Everyone knows that there is value in failure.
Every time you set your foot down on the floor
your brain makes a judgment call.
Your mostly wrong every step.

If God controlled this world there would
be no need for evolution to run this hell.

 

[SkyWriting]

It still proves that humans are genetically linked to gorillas and chimpanzees, which is not consistent with any YEC interpretation.

DNA is a construction set, like Leggo's.
Similar construction pieces don't create family ties.

 

[sfs]

DNA is a construction set, like Leggo's.
Similar construction pieces don't create family ties.

DNA is nothing like LEGOs. Different versions of a gene can function exactly alike, but have different sequences. Comparing functionally equivalent versions across species, you can easily trace the family tree of that gene as various mutations have accumulated. And you can do again for another gene, and again, and again. If you do, you will find that they tell a consistent story of descent from a common ancestor.