How do creationists explain applications of common descent in modern comparative genomics?

[pitabread]

Long story short: Understanding the genome and in particular identifying genes and their functions involves comparisons across various species. Modern comparative methodologies use evolutionary relationships as part of that comparative analysis (see this paper as an example).

edited to add: Here are a couple additional resources on the use of phylogenetic (evolutionary) trees in conjunction with comparative genomics:

Comparative Genomics: Methods and Applications
Phylogenetic Footprinting (slideshow presentation)

In turn, this knowledge of genes and the genomes is applied in various fields including agriculture (both livestock and crops), medical research, forestry and conservation biology.

Have creationists ever bothered to even attempt to address this or does this remain a large branch of applied evolution that they continue to ignore?

(The closet I've found is this article on Answers in Genesis where the author basically complains about evolutionary bias in comparative genomics and suggests an unbiased approach is needed. Naturally, they don't actually say what that approach should be nor suggest what advantage there would be to other methods. All they seem to care about is making us less related to chimps because reasons.)

 

[~Anastasia~]

Hi, by the way I'll say up front that I'm NOT interested in arguing this ... just up late and browsing, and this caught my attention.

(And by the way, I do have a background in science, believe in special creation, but much of what passes for "creation science" makes me cringe, if any of that tells you where I'm coming from.)

But in a way, it doesn't really have to be explained? If God created man, animals, plants, and obviously He used genes to direct development and procreation, just as He uses internal organs to carry out normal life functions, why should it be surprising that there are great similarities? Especially when things "work"? Each creature when it reproduces, reproduces in kind. So what does it matter if there are great similarities, as long as you don't have dogs inadvertently giving birth to kittens. Likewise, should it matter if man, elephants, tigers, and mice all breathe with lungs, since lungs "work"? Would it be more "proof" of creation if every creature had its own kind of breathing organs? I suppose it would, but apparently that wasn't the way God chose to make things happen.

Anyway, just a bit of a supposition. Like I said, I am NOT into arguing this, and my faith doesn't rest upon particular interpretations of creation. Those are not the important details, IMO. But just offering a friendly thought.

Have a good evening/day (whichever the case may be).

And welcome to the forums.

 

[mark kennedy]

Long story short: Understanding the genome and in particular identifying genes and their functions involves comparisons across various species. Modern comparative methodologies use evolutionary relationships as part of that comparative analysis (see this paper as an example). In turn, this knowledge of genes and the genomes is applied in various fields including agriculture (both livestock and crops), medical research, forestry and conservation biology.

I've actually spent some time on the HAR (Human Accelerated Regions), it's not exactly a strong area for Darwinian evolution.

Have creationists ever bothered to even attempt to address this or does this remain a large branch of applied evolution that they continue to ignore?

Ignore it? Are you kidding me, the accelerated evolution of brain related genes is one of the great unanswered questions of Darwinian evolution:

In one of the areas of the human genome that would have had to change the most, Human Accelerated Region (HAR), we find a gene that has changed the least over just under 400 million years HAR1F. Just after the Cambrian is would have had to emerge de novo, fully formed, fully functional and permanently fixed along broad taxonomic categories. In all the time since it would allow only two substitutions, then, while the DNA around it is being completely overhauled it allows 18 substitutions in a regulatory gene only 118 nucleotides long. The vital function of this gene cannot be overstated:

The most dramatic of these ‘human accelerated regions’, HAR1, is part of a novel RNA gene (HAR1F) that is expressed specifically in Cajal– Retzius neurons in the developing human neocortex from 7 to 19 gestational weeks, a crucial period for cortical neuron specification and migration. HAR1F is co-expressed with reelin, a product of Cajal–Retzius neurons that is of fundamental importance in specifying the six-layer structure of the human cortex. (An RNA gene expressed during cortical development evolved rapidly in humans, Nature 16 August 2006)​

This all has to occur after the chimpanzee human split, while our ancestors were contemporaries in equatorial Africa, with none of the selective pressures effecting our ancestral cousins. This is in addition to no less then 60 de novo (brand new) brain related genes with no known molecular mechanism to produce them. Selection can explain the survival of the fittest but the arrival of the fittest requires a cause:

The de novo origin of a new protein-coding gene from non-coding DNA is considered to be a very rare occurrence in genomes. Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee. The functionality of these genes is supported by both transcriptional and proteomic evidence. RNA– seq data indicate that these genes have their highest expression levels in the cerebral cortex and testes, which might suggest that these genes contribute to phenotypic traits that are unique to humans, such as improved cognitive ability. Our results are inconsistent with the traditional view that the de novo origin of new genes is very rare, thus there should be greater appreciation of the importance of the de novo origination of genes…(De Novo Origin of Human Protein-Coding Genes Plod 2011)​

Whatever you think happened one thing is for sure, random mutations are the worst explanation possible. They cannot produce de novo genes and invariably disrupt functional genes. You can forget about gradual accumulation of, 'slow and gradual accumulation of numerous, slight, yet profitable, variations' (Darwin). That would require virtually no cost and extreme benefit with the molecular cause fabricated from vain imagination and suspended by pure faith.

(The closet I've found is this article on Answers in Genesis where the author basically complains about evolutionary bias in comparative genomics and suggests an unbiased approach is needed. Naturally, they don't actually say what that approach should be nor suggest what advantage there would be to other methods. All they seem to care about is making us less related to chimps because reasons.)

Look harder:

Often scientific reports or mainstream media claim 99% identical comparisons between human and chimp genomes. The number has been dropping in some circles recently, but is still on the order of 95+%.(A Fresh Look at Human-Chimp DNA Similarity, Answers in Genesis)
​

If you want to get into comparative genomics let's do this.

May the truth prevail,
Mark

 

[pitabread]

If you want to get into comparative genomics let's do this.

It's a simple question: how do creationists reconcile the application of evolutionary biology (specifically phylogenetic relationships of organisms) utilized in modern comparative genomics methods. And especially with respect to industry application.

I'm not really interested in discussing human/chimp comparisons specifically, because quite frankly, that's not the question. I just linked to the AiG article since it was an admission by that author that yes, evolutionary biology (or "evolutionary bias" as they keep calling it) is applied in the world of genomics. Unfortunately, they do little else but complain about that fact.

If you have something to offer in this regard, then please do so. If you just want to talk about human evolution, that's not the topic.

 

[pitabread]

But in a way, it doesn't really have to be explained? If God created man, animals, plants, and obviously He used genes to direct development and procreation, just as He uses internal organs to carry out normal life functions, why should it be surprising that there are great similarities? Especially when things "work"? Each creature when it reproduces, reproduces in kind. So what does it matter if there are great similarities, as long as you don't have dogs inadvertently giving birth to kittens. Likewise, should it matter if man, elephants, tigers, and mice all breathe with lungs, since lungs "work"? Would it be more "proof" of creation if every creature had its own kind of breathing organs? I suppose it would, but apparently that wasn't the way God chose to make things happen.

We're talking specifically about methodologies which are used in comparing genomes of organisms. Modern comparative genomics uses phylogenies (i.e. evolutionary relationships) of organisms, specifically the relative divergence times of species with respect to each other. It is by doing this (and assuming background mutation rates) that regions of the genomes can be identified undergoing neutral (i.e. non-selective) evolution versus regions under different types of selective pressure. In the latter case, those regions can be identified as being functionally significant to the organism.

So all this begs the question: if life was specially created, then it was created to look like it evolved.

And welcome to the forums.

Thank you, although I'm actually an old member who used to frequent this place a decade ago. Just back under a different account.

 

[~Anastasia~]

We're talking specifically about methodologies which are used in comparing genomes of organisms. Modern comparative genomics uses phylogenies (i.e. evolutionary relationships) of organisms, specifically the relative divergence times of species with respect to each other. It is by doing this (and assuming background mutation rates) that regions of the genomes can be identified undergoing neutral (i.e. non-selective) evolution versus regions under different types of selective pressure. In the latter case, those regions can be identified as being functionally significant to the organism.

So all this begs the question: if life was specially created, then it was created to look like it evolved.

I do understand your point. But you see, what is, IS. And that is observed and tested with a bias already predisposed to understand in a particular way. So unless glaring exceptions are found, everything is acceptable and appears as evidence. But my point is simply that, why must God start with new building blocks each time? If one were to begin with a different bias, the observations will often make just as much sense as evidence for that position. (I must say, the creation/evolution debate is unique in this regard.)

And I would also say that it makes more sense from a creation perspective, IMO, to allow for some basic evolution - i.e. that different species of leopard all evolved from a leopard prototype rather than God specifically creating different species of leopards. How far "down the tree" this ought to rightly go, I have not really investigated, but I believe there are limits.

I should also say that I changed directions professionally in a slight sense about 25 years ago, and in a very divergent sense about 19 years ago, so research since that time hasn't really made it into my concerns. That's a small part of the reason I don't want to argue this, but the larger reason is that I have rarely found it profitable, even when I was at the height of what was going on academically.

Like I said, just interested in friendly discussion and pointing that out. At the end of the day, most of these conversations turn up with no way to conclusively prove either way.

There is something to your point that life was created in such a way that it appears to have evolved. But if you like, ask yourself how it could be created NOT to appear that way? The answer might make no sense at all. The only possible answers I can think of would mean introducing something AS proof that there was no evolution, and God really doesn't seem to be interested in proving Himself. Indeed, that would remove one of our most precious gifts from Him ... free will.

 

[mark kennedy]

It's a simple question: how do creationists reconcile the application of evolutionary biology (specifically phylogenetic relationships of organisms) utilized in modern comparative genomics methods. And especially with respect to industry application.

I discuss comparative genomics by seeing what the actual comparisons are. You not asking a question, at least not about comparative genomics.

I'm not really interested in discussing human/chimp comparisons specifically, because quite frankly, that's not the question. I just linked to the AiG article since it was an admission by that author that yes, evolutionary biology (or "evolutionary bias" as they keep calling it) is applied in the world of genomics. Unfortunately, they do little else but complain about that fact.

There are two issues here, the overall genetic divergence and direct comparisons of protein coding and regulatory genes. You haven't a clue about either.

If you have something to offer in this regard, then please do so. If you just want to talk about human evolution, that's not the topic.

You apparently don't have a topic

 

[pitabread]

I discuss comparative genomics by seeing what the actual comparisons are. You not asking a question, at least not about comparative genomics.

I'm not talking about the actual comparisons. I'm talking about the methodologies utilized in making those comparative analyses. Specifically the linkage of phylogenetic relationships of species (i.e. common descent) utilized in conjunction with the analysis of genomes to identify regions undergoing varying types of selection (included conservation). I linked this paper (A high-resolution map of human evolutionary constraint using 29 mammals) as an example of such usage. I'd refer you to the section under "Sequencing, assembly and alignment".

In turn, modern comparative genomics has various industry application (Google comparative genomics in agriculture, for example, and you'll find umpteen examples). Which is where I find there is a disconnect between what creationists believe and what we are seeing in terms of applied evolutionary biology.

Now, do you have anything to comment on this?

There are two issues here, the overall genetic divergence and direct comparisons of protein coding and regulatory genes. You haven't a clue about either.

Before you start flinging baseless accusations, perhaps you may want to take a real stab at addressing what I posed in the OP.

 

[pitabread]

I do understand your point. But you see, what is, IS. And that is observed and tested with a bias already predisposed to understand in a particular way. So unless glaring exceptions are found, everything is acceptable and appears as evidence. But my point is simply that, why must God start with new building blocks each time? If one were to begin with a different bias, the observations will often make just as much sense as evidence for that position. (I must say, the creation/evolution debate is unique in this regard.)

I'm not talking about evidence though. Evolutionary science has been well established to the point that we're well past that point. Rather this is about application of that science, including of common descent itself.

There is something to your point that life was created in such a way that it appears to have evolved. But if you like, ask yourself how it could be created NOT to appear that way?

Of course. Genetic chimeras would be a perfect example of this. We (humans) are already capable to doing this via genetic engineering. There is no reason that genetically speaking, life on Earth would need to fit into a nest hierarchy of evolutionary relationships. But when we examine life at the genetic level, that's exactly what we find. Which in turn is evidence that life evolved over billions of years and was not spontaneously created as individual species.

Conversely if we did find genetic chimeras in nature that would turn evolutionary biology on its head. But to the best of my knowledge, that's never been the case.

 

[The Stamp]

I do understand your point. But you see, what is, IS. And that is observed and tested with a bias already predisposed to understand in a particular way. So unless glaring exceptions are found, everything is acceptable and appears as evidence. But my point is simply that, why must God start with new building blocks each time? If one were to begin with a different bias, the observations will often make just as much sense as evidence for that position. (I must say, the creation/evolution debate is unique in this regard.)

OK lets run with that idea, what is this God, where is this God and how does it do what you think it does?

 

[pitabread]

Here is another paper that discusses comparative genomics based on differing phylogenetic distances: Comparative Genomics (2003). It provides a bit more insight into the relationship between phylogenies (evolutionary relationships) and how genomes are compared.

 

[pitabread]

OK lets run with that idea, what is this God, where is this God and how does he it do what you think it does?

Please, let's not. I'd rather not have this thread go spiraling off topic. Start a new thread for that.

 

[The Stamp]

Please, let's not. I'd rather not have this thread go spiraling off topic. Start a new thread for that.

OK sorry but creationist will soon take it into fantasy land.

 

[pitabread]

OK sorry but creationist will soon take it into fantasy land.

My experience is that this topic is most often ignored, but sometimes deflected with hand waving or otherwise off-topic rebuttals.

Regardless, I think it's a bit of a perplexing issue for creationists. That's why I found it amusing that Answers in Genesis is acknowledging it (or at least that author is), but only suggests finding new methodologies because they don't like that the current ones utilize evolutionary relationships. Meanwhile, scientists utilizing this stuff in the real world don't care. They use what works.

That said, I still hold out hope that one day a creationist will not only acknowledge this but offer up a proper, reasoned rebuttal based on actual methodologies. But that day has yet to come.

 

[The Stamp]

My experience is that this topic is most often ignored, but sometimes deflected with hand waving rebuttals.

Regardless, I think it's a bit of a perplexing issue for creationists. That's why I found it amusing that Answers in Genesis is acknowledging it (or at least that author is), but offer up nothing much except suggesting finding new methodologies because they don't like that the current ones utilize evolutionary relationships. Meanwhile, scientists utilizing this stuff in the real world don't care. They use what works.

That said, I still hold out hope that one day a creationist will not only acknowledge this but offer up a proper, reasoned rebuttal based on actual methodologies. But that day has yet to come.

I just thank my lucky stars I don't have to do what they do, imagine what it must be like to be knocked back every time they try to defend their beliefs, you've got to give them 10 out of 10 for perseverance.

 

[~Anastasia~]

Please, let's not. I'd rather not have this thread go spiraling off topic. Start a new thread for that.

Being that you have asked, I won't reply. Not out of ignoring. But as I said, I'm not interested in debate. ALWAYS happy to answer questions and discuss, but arguing isn't my thing. Like I said though, much of "creation science" makes me cringe, as does a good bit of "modern Christianity". If that's all you folks ever come in contact with, I don't blame you for your positions.

Have a good day.

 

[mark kennedy]

I'm not talking about the actual comparisons. I'm talking about the methodologies utilized in making those comparative analyses. Specifically the linkage of phylogenetic relationships of species (i.e. common descent) utilized in conjunction with the analysis of genomes to identify regions undergoing varying types of selection (included conservation). I linked this paper (A high-resolution map of human evolutionary constraint using 29 mammals) as an example of such usage. I'd refer you to the section under "Sequencing, assembly and alignment".

You interested in comparative genomics but not actual comparisons. I don't seriously you have a clue what that paper is about after making a statement like that. Notice the abstract starts with the word 'comparison':

"Comparison of related genomes has emerged as a powerful lens for genome interpretation." (NCBI)
​

They are finding commonality across broad taxa, that's a comparison.

In turn, modern comparative genomics has various industry application (Google comparative genomics in agriculture, for example, and you'll find umpteen examples). Which is where I find there is a disconnect between what creationists believe and what we are seeing in terms of applied evolutionary biology.

You say that without any reference to creationist or scientific literature. This is not applied evolutionary biology, although there might be some interesting inference for homology.

Now, do you have anything to comment on this?

Comment on what, your interest in comparative genomics or your disinterest with anything actually being compared.

Before you start flinging baseless accusations, perhaps you may want to take a real stab at addressing what I posed in the OP.

I'll buy baseless but there isn't enough here to warrant an accusation either way.

 

[pitabread]

You interested in comparative genomics but not actual comparisons. I don't seriously you have a clue what that paper is about after making a statement like that.

I thought I was pretty clear; I'm interested in the methodology of the comparison. Namely, the fact that methodologies in comparative genomics often rely on phylogenetic relationships of the species being compared. The paper I linked was an example of such a methodology.

Is there something not clear about this?

You say that without any reference to creationist or scientific literature. This is not applied evolutionary biology, although there might be some interesting inference for homology.

Uh, yeah it is applied evolutionary biology. In effect, it's applied common descent.

It's also not really a point of argument. The reason I linked to the AiG article in the opening post was the fact was simply pointing out that they also acknowledge it. I mean, we're talking real world applied science here. There's no debate about this.

Comment on what, your interest in comparative genomics or your disinterest with anything actually being compared.

Again, I'm referring to the methodology used, not the outcomes (although certain there is a lot of that in the literature; hence why it's an applied science).

Do you have any comments about the methodology?

 

[mark kennedy]

I do understand your point. But you see, what is, IS. And that is observed and tested with a bias already predisposed to understand in a particular way. So unless glaring exceptions are found, everything is acceptable and appears as evidence. But my point is simply that, why must God start with new building blocks each time? If one were to begin with a different bias, the observations will often make just as much sense as evidence for that position. (I must say, the creation/evolution debate is unique in this regard.)

And I would also say that it makes more sense from a creation perspective, IMO, to allow for some basic evolution - i.e. that different species of leopard all evolved from a leopard prototype rather than God specifically creating different species of leopards. How far "down the tree" this ought to rightly go, I have not really investigated, but I believe there are limits.

I should also say that I changed directions professionally in a slight sense about 25 years ago, and in a very divergent sense about 19 years ago, so research since that time hasn't really made it into my concerns. That's a small part of the reason I don't want to argue this, but the larger reason is that I have rarely found it profitable, even when I was at the height of what was going on academically.

Like I said, just interested in friendly discussion and pointing that out. At the end of the day, most of these conversations turn up with no way to conclusively prove either way.

There is something to your point that life was created in such a way that it appears to have evolved. But if you like, ask yourself how it could be created NOT to appear that way? The answer might make no sense at all. The only possible answers I can think of would mean introducing something AS proof that there was no evolution, and God really doesn't seem to be interested in proving Himself. Indeed, that would remove one of our most precious gifts from Him ... free will.

Some of the commonality is kind of interesting, there are genes that are called household genes, they are very much the same across broad taxa. For a long time they were saying chimps and humans were so much alike that the differences had to be accounted for by regulatory genes. Come to find out with whole genome sequences the differences to over 120 mbp (million base pairs) because of indels (insertions/deletions). There is at least one codon difference in 70% of the protein coding genes, in 20% of the protein products they found gross structural differences.

Comparative genomics is a fascinating study, I'm constantly learning more. Recently I heard about the Krispur gene that can actually cut and splice genes anywhere on the genome. I'm often astonished at the people who pursue these discussions for years and never bother to learn anything about the life sciences. There are some truly amazing things going on.

 

[USincognito]

OK lets run with that idea, what is this God, where is this God and how does it do what you think it does?

Apologetics are off topic for this thread and this subforum. If you want to discuss that subject, start a thread in Apologetics.