About Orphan Genes — What’s the Big Problem for Evolution?
Just for clarification, the article was written by @Agauger. It would be great if she could clear up any confusion or questions we may have about the article.
I could be completely wrong, but I think Ann Gauger does not accept common descent (in the narrow sense), at least between large species groups (e.g. between humans and other mammals). This makes for some interesting internal conflict within the letter. Here are two sections from the letter next to each other:
This is an example of the strange back and forth I have often seen in the writings by ID supporters. At one moment a writer will be completely open to common descent, explaining how it is entirely compatible with Intelligent Design. Sometimes in the very next paragraph that same writer will be arguing against common descent, and arguing that the only reason common descent is accepted is a rigid and dogmatic adherence to the theory of evolution.
That’s a good article. I am happy that Patrick posted it.
Now, I would add that in my opinion, there is solid evidence that the designer probably used guided common descent and intelligent design.
My question for @Agauger is about the Theistic Evolution book. Is there a chapter in the book that argues for intelligently guided common descent? It seemed to me that all the chapters that were about common descent argued against it. I’d be more than happy to revisit it.
My question for @Agauger is about the Theistic Evolution book. Is there a chapter in the book that argues for intelligently guided common descent?
`There is no chapter that argues for common descent that I know of. It’s an interesting question because there are arguments on both sides. If I had the time it would be worth the time to do a deep study of the arguments on both sides. Perhaps a really good book could be made of it.
Any time there is a situation where two sides hold extremely adamant views it is worth examining all views from an agnostic point of view. But no prior commitments allowed. That’s not easy for most people to do.
Hope all is well. I’d like to break down this portion from your letter:
“Now, I would add that in my opinion, there is solid evidence that the designer probably used guided common descent and intelligent design. However, I don’t have time to write about all the science surrounding the issue of common descent (or common ancestry).”
When you use Guided common descent (though wouldn’t this be intelligent design? Confused as to why you included “and intelligent design”) do you mean UCA? Or some form of separate ancestry? Also I noticed you said common descent but then included or common ancestry in parentheses. Do these two terms mean different things to you?
Hi, TJ. Common descent and common ancestry our equivalent in my mind. I included the parenthesis to indicate that.
Yes, I think of guided common descent as due to intelligent design. I guess I was being redundant here also. Do I mean universal common descent? I don’t know. Probably not. There are differences between Phyla or Classes that need explanation.There are orphan genes as well. For evidence for common descent there are sequence similarities, the existence of pseudogenes, and endogenous retroviruses in identical locations. Intelligent design advocate have arguments to explain these things, but demonstrating their argument will be very hard. Yet the different features between groups require explanation also, in particular the ubiquitous and surprising existence of group-specific orphan genes.
Ok, thanks for clearing things up! Judging from your past work like in “Science and Human Origins” and your most recent work on Adam and Eve I get the feeling you think Humam evolution took place at the level of genus. Is this an accurate assessment?
PS I find the requirement for at least 5 characters a waste of time when a simple yes would do.
I know your time here is very limited, but I would be very interested in a discussion on orphan genes and how the ID community views them. Obviously, it is beyond the limits of this thread so a separate discussion would be needed. I guess I don’t see why mutations that cause previously non-coding DNA to suddenly be transcribed poses a problem for the theory of evolution and was wondering why the ID community has suddenly clung on to this argument.
The simpler the better!
The answer to your question ties in with a number of differences between the evolutionary point of view and ID. Evolutionists tend to think that function is easy to get from random sequence. The nylonase gene was a poster child for this attitude.They disagree with Doug Axe’s estimate for the rarity of functional protein folds in sequence space. This is the issue of exaptation or pre-adaptation. Evolutionists think that is such a thing happens commonly. ID proponents think that it’s very difficult to get function from random sequence, or to put it another way, to acquire a new function by accident, if you will, leading to a new structure or chemical activity or new gene as in the case of orphan genes.
There is a basic difference in assumption between evolutionary biologist and intelligent design proponent as to the ease of acquiring function. If nonfunctional non-coding DNA acquires function readily when expressed, then orphan genes are trivial to acquire. If nonfunctional non-coding DNA is nonfunctional when expressed then orphan genes arising from non-coding DNA requires some sort of pre-adaptation or design.
Ironically, until the widespread sequencing of genomes, biologists expected to find similar coding sequences in every genome, precisely because they assumed getting completely new genes was going to be extremely difficult. Read the old literature and you will see this. The appearance of orphan genes has changed scientists‘s point of view to accommodate the presence of orphan genes. The idea has become that it is easy to get new function from random sequence. By necessity.
I believe your response was meant for @T_aquaticus.
I also think it’s important to mention de novo genes, which you seem to be focusing on, aren’t the only explanation for orphan genes.
Feel free TJ. I’d like to hear more.
Well I think first things first some really aren’t orphans and this is due to sampling. We just haven’t sequenced enough genomes yet. I recall reading that when H. influenzae was first sequenced, 64% of its ORF’s were orphans. Now it’s like 5 percent (I will track this down.) So some are just singleton genes (I believe this is the right term) so they may seem to not be related to any other genes but over time that could change as it has for other possible orphans. Then I think there could be technological reasons why we can’t detect their relatives. Then I also think horizontal gene transfer and gene loss could also explain them. Doug Axe used gene loss as an explanation for a de novo protein that Venema referenced in a review of Doug’s book. Though the paper’s author did rule out gene loss. So I think there are other reasons for the appearance of orphans or at least what seem to be orphans besides de novo gene origination.
So even if we were able to show a mutation occurring in real time that did produce a new gene with function it would still be argued that it is not evidence for evolution, but for Intelligent Design?
Design if it does, design if it doesn’t. Seems rather circular to me.
Go figure. Scientists are incorporating new information into the theory of evolution. Most of us thinks this is how science and theories should work.
Orphan genes are identified by RNA, not by DNA. For many human orphan genes there is known orthologous DNA in the chimp genome with the difference being a lack of transcription of the chimp DNA.
All genes are made of DNA, but not all DNA is made up of genes.
That seems to be the case here as well:
It isn’t circular. It is just a catch-22:
I’m starting to see the evolutionary process as much like a Sierpinski triangle and a round of the chaos game, which is of course designed. I got chills playing. Beauty and elegance.
In order to test universal common descent we would first need to know what it is that determines final developed form. What determines the destiny of the developing embryo?
Is it determined by the genome? If so how can we test that especially in the face of researchers who say genomes do not determine what develops. Genes influence and control development but do not determine what develops. Much like an assembly line doesn’t determine what they are assembling but each step controls and influences what will be assembled.
If it is the genome and there is only a less than 2% genetic difference between humans and chimps, one would think we should be able to link the genetic differences to all of the observed anatomical and physiological differences. If we can’t then clearly genetic change is not the mechanism for diversification.