Here is a question about orphan genes and bees.
I heard a Discovery Institute podcast and I think they found a high level of orphan genes in E Coli and bees. I think they said the orphan genes in bees were directly related to their ability to communicate with each other. It’s hard to think of more important species than bees and e coli. I’m wondering if there’s a correlation between orphan genes and their importance to humans.
It is a nice testable hypothesis. What do you think?
I haven’t heard the podcast, but there more than 10,000 species of bees. Is the claim regarding orphan genes specific to the Western Honey Bee Apis mellifera, or bee genomes in general?
Maybe @pnelson knows? Or perhaps a literature search will reveal something?
Probably this paper:
Breathlessly reported on by Jeffrey Tomkins of ICR here:
This question comes from @Eric_Johnson. Welcome!
@evograd and @davecarlson are PhD students in evolutionary biology, and quite good at what they do. You are really fortunate to have their engagement on this. 
Seems like there is a conflation here between taxonomically restricted and orphan genes. These two things are not the same.
According to the ICR article above there are multiple bee “kinds”.
ICR: While there are obvious differences between bees and other types of insects that clearly defy evolution on a grand scale, understanding orphan genes may prove to be a valuable tool in sorting out the created diversity among bee kinds and understanding patterns of design in genomes.
I wonder how they determined there are multiple “kinds” of bees, and how many bee “kinds” there are?
Indeed. I once got called out by a reviewer for that because I was using pairs of species from the same genus to identify “orphans”, but they lineage (genus) specific genus, not orphans.
The paper that @evograd found looks at genes at a variety of levels of taxonomic restriction–from actual orphan genes to genes specific to arthropods (which includes > a million species).
Here’s the podcast in question.
Only listened once in August. I listened to it again. The claim was that an orphan gene in bees permits bees to engage in social behavior. It’s probably hard to overestimate how many on the planet would starve w/o the gene.
There are several issues with this claim.
First of all, these are not orphan genes. They are Taxonomically Restricted Genes. That a big difference. By definition, TRGs are not orphan!
Neither orphan genes nor taxonomically restricted genes are a challenge to evolutionary science. There are several mechanisms for evolution to make new proteins.
In fact, taxonomically restricted genes are taxonomically restricted at several different levels, and this is therefore a confirmed prediction of common descent.
Neo-Darwinism is not the current understanding of evolutionary science. In a sense @Paul_Nelson is right. These genes are a problem for neo-Darwinism, but who cares? Neo-Darwinism has not been the prevailing theory in evolutionary science for over 60 years.
@Zachary_Ardern might have some additional thoughts to add. He is very thoughtful scientist working in this area.
First, I fully realize I didn’t belong at the adult table, or the little kids table. Maybe I belong in the basement with the colored blocks with letters. According to Wikipedia, TRG’s are a subset of orphan genes. More importantly however, I don’t think your objections are relevant to my initial testable hypothesis.
Hmm. Interesting. Maybe I made a mistake. However, if there is analogues in other species, then it isn’t orphan…so…
You are right~!
How do we go about determining which species are associated with humans or not? One possibility is looking at domesticated bees versus wild bees. Would that work? Or are you getting at something else?
Misread. Per wiki ‘Orphans are a subset of taxonomically-restricted genes (TRGs)’ sorry.
That makes more sense. Orphans are the TRG that are restricted to a single species. So there is some overlap, but this is a technicality/boundary case. Normally TRGs are found in many species. If there found in only one, we would call them orphans.
The article makes the point that the truly orphan genes they identified were biased towards being secreted proteins that function more-or-less independently. That makes them easier to evolve de novo as they’re not mixed up with with other pathways leading to negative pleiotropic effects.
What does common descent predict will come first? The primordial bee population or the TRG? Or are both possible? I would think that a population of bees without their social behavior would be utterly worthless.
Common descent predicts there will be TRGs at several levels of the taxonomy. “Primordial bees” is poorly defined, so you can’t make clear predictions about it. We expect TRGs before and after the first “bees,” however we define them.
Why would they be worthless?
Something like 90% of bee species are solitary, and responsible for pollinating most of the food we eat: https://www.greenandblue.co.uk/blogs/news/5-things-you-need-to-know-about-solitary-bees
So whatever is TRG to bees as a whole is not likely the cause of the social behavior you are envisioning.
Nice choice of adverb. 
How do we go about determining which species are associated with humans or not? One possibility is looking at domesticated bees versus wild bees. Would that work? Or are you getting at something else?
This list is a start.
I disagree with primates because that would only apply to an advanced technological society. My intuition which admittedly accounts for nothing would think whales and bats are good candidates for orphan or restricted genes. I’ll admit I didn’t understand what Nelson was talking about with e coli. Presumably as long as you have humans, you have e coli, so it isn’t necessary vital to preserve. @AJRoberts has talked a lot about how important e coli is. I wish the podcast was more specific with the social behavior of bees but Nelson was making a different point than me.
This Wikipedia quote on orphan genes is interesting considering Fungi round out the top 5 most important organisms in my article above.
De novo genes were once thought to be a near impossibility due to the complex and potentially fragile intricacies of creating and maintaining functional polypeptides,[10] but research from the past 10 years or so has found multiple examples of de novo genes, some of which are associated with important biological processes, particularly testes function in animals. De novo genes were also found in fungi and plants.