New genes and special traits

Faith & Science Conversation
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I got all excited about a recent paper about an apparently human-specific gene that is likely to be involved in brain development. The story involves several interesting questions:

  • What does it mean for a gene to be “human-specific”? Are there any human genes that don’t exist at all in other lineages?
  • Do we know whether any of these human-specific genes contribute to (or explain) human-specific traits?
  • How do human-specific genes arise?
  • How do new genes arise?
    So I’m writing a little blog series on the topic. The first post is up, and feedback (comments, questions, error corrections, requests for improvements in the next post) is welcome.
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Or on the flip side, what proportion of the genetic differences between chimps and humans merely allelic? The answer may surprise you…

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Quick note to the moderators and others:
It seems that my post is close to the edge of the forum’s guidelines for “spam.” If I read those guidelines correctly, they are meant to discourage (or ban) new posts that simply link readers to another site containing the author’s own work or writing. That’s a smart and reasonable policy, and I will gladly avoid the edge in any future contributions. Sorry about that!

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Moderator note: The mods are aware that there has been some inconsistency in how this policy has been understood and enforced. We are working on clarifying that policy and enforcing it more consistently in the future.

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I like your scientific contributions. I hope you will be allowed to continue.

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:slight_smile: Thanks! @BradKramer and the other moderators are right to limit spam-like posting here. I admit I was a little grumpy when I saw the word ‘spam’ associated with my post, but it’s Monday and 36 hours ago I was driving all night back from the DC march so I plead “sleep debt.” :slight_smile:

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You have no idea what goes on here when there are no rules or rules that aren’t enforced!

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Looks good Steve - I touch on this fascinating story a wee bit in my next post as well - though don’t worry, for the full details folks will need to read your series. I just use it as a nice example of new information being produced in a way that ID folks claim is impossible.

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Our friend Joshua @Swamidass has opened a thread or two by writing a four paragraph summary of findings, and providing a link to an article for those who want the background details. Because the four paragraphs stand on their own, the opening post conforms with forum guidelines.

Or so it seems to me as a non-moderator.

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One of the questions worth considering is:
What does it mean to say that a gene is ‘human-specific’? Or more broadly, what does it mean to say that any gene is unique to any particular species or lineage?

Here are two extremes.

The FoxP2 gene is a huge story because it seems to control language ability. Mutations in the gene create language impairments. Perhaps more interestingly, the human version of the gene seems to have been subjected to strong selection. If we grant the prominence of language as a human-specific specialization, then we have a gene that looks like a candidate for membership in a “gene that makes us human” collection.

But the human version of the gene is almost completely identical to non-human versions. It differs from other mammalian versions by just two amino acids. We know that even a single such change can radically alter a protein’s functions and roles, so my point is not that the two-amino-acid difference is biologically unimportant or uninteresting. My point is that the human FoxP2 gene, structurally speaking, is just a slightly tweaked version of a gene that is found in (as far as I know) all vertebrates. I don’t think we should call it a ‘human-specific gene.’

A gene that is utterly unique to a species would be a coding sequence (meaning a DNA sequence that encodes a protein sequence) that existed in that species but not in any form in its closest relatives. I don’t know of any examples of this in humans yet. The best way to get such an utterly unique gene is to have it hop into the genome from somewhere else. This is known to happen, but I don’t think it is known to underlie the formation of any specific unique human coding sequence. That would be the other extreme.

But between those two extremes are some genes found in humans that are very different, structurally, from similar genes in our closest relatives. The gene may exist in some form in our fellow primates, but the human form is much bigger, or much smaller, or perhaps the protein that it makes is a lot different due to changes in splicing or processing.

So while we don’t yet know (as far as I know) of radically new genes in the human genome, we do have some very interesting examples of that last type of new gene. And very intriguingly, the best examples so far are all genes that are involved in brain development. The confluence of “new genes” with the most notable human specialization that there is (cognitive prowess and bloated brains) is pretty darned interesting.

One final comment: I was focused on protein-coding genes in this post, but there are other kinds of genes (depending on how one uses the word), and there are some important genomic elements in humans that may fall into that “utterly unique” category I created above. Here is a somewhat recent review of those (open access). I haven’t looked to see if there are unique lncRNAs or other similar ‘genes’ in humans but it would be really interesting to do that.

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Isn’t the FoxP2 gene in Neandertals identical to ours?

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Yep!
http://www.nature.com/news/2007/071018/full/news.2007.177.html

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I think that FoxP2 was also found to be important in the songs of Finches. That’s one busy gene.

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I believe the key word here is “traits”. From the standpoint of either religion or philosophy, (i.e. for BioLogos’ purposes) I would think that the focus should be on traits (if there are any) that distinguish US (modern humankind) from all other animal life. The well-known early examples of human specific genes do not fit this requirement; i.e., the lactase enzyme that allows milk to be nutritious to human adults, and the amylase enzyme that allows starchy foods to constitute such a major component of our diets. It is very likely that both of these developed from evolutionary pressure AFTER our species became truly human. At first the FoxP2 enzyme which affects the language centers of the brain seemed a good candidate, since language use is perhaps the most solid human-specific trait. But since FoxP2 seems to be present even in birds (to help them learn the calls proper to their species), there must be some subtle structural difference which has not yet been discovered.

But perhaps we are missing the most important lesson to be learned from this search: We should not be looking for human-specific genes that affect how the human brain is __first constructed. As a problem solving organ, much like a computer, it was already over-designed in our Homo ergaster ancestors (an Ex-aptation), Until recently it just was not programmed effectively; it had no efficient operating system. Out of the trillions of neural circuits possible, a pruning system was needed to keep only those circuits that proved useful by experience and to remove those that didn’t. "Use it or lose it" became the watchword that produced Adam, and separated him from his Neanderthal cousins. Further studies along the lines of Evo-Devo may soon gives us better ideas of how this came about, but it will in no important way change the need for us to worship our Creator.
Al Leo

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"The FOXP2 gene provides instructions for making a protein called forkhead box P2. This protein is a transcription factor, which means that it controls the activity of other genes. It attaches (binds) to the DNA of these genes through a region known as a forkhead domain. . . "

"Researchers suspect that the forkhead box P2 protein may regulate hundreds of genes, although only some of its targets have been identified.

“The forkhead box P2 protein is active in several tissues, including the brain, both before and after birth. Studies suggest that it plays important roles in brain development, including the growth of nerve cells (neurons) and the transmission of signals between them. It is also involved in synaptic plasticity, which is the ability of connections between neurons (synapses) to change and adapt to experience over time. Synaptic plasticity is necessary for learning and memory.”

“The forkhead box P2 protein appears to be essential for the normal development of speech and language. Researchers are working to identify the genes regulated by forkhead box P2 that are critical for learning these skills.”

FOXP2 gene - Genetics Home Reference

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That’s a very good point, and I agree with you in principle, especially because wiring is critical for cognitive function and is a lifelong process. But it’s still the case that a few of the most “human-specific” genes we know about are involved in brain development.[quote=“aleo, post:16, topic:34294”]
Until recently it just was not programmed effectively; it had no efficient operating system. Out of the trillions of neural circuits possible, a pruning system was needed to keep only those circuits that proved useful by experience and to remove those that didn’t. “Use it or lose it” became the watchword that produced Adam, and separated him from his Neanderthal cousins.
[/quote]

I’m not sure I understand you here. But mechanisms of pruning and plasticity are very ancient, and I know of none that is different between humans and mice, much less between humans and other primates. But I do agree with you that we should be looking hard for human-specific wiring systems.

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The FoxP genes seem to be an example of deep homology. Fox genes in general are ancient in animals.

Evo-devo, deep homology and FoxP2: implications for the evolution of speech and language

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The basic mechanisms of pruning & plasticity may be known, but how they interact with the growth of new neurons that appear only later in life is not well known. Indeed, it is only recently that neuron growth into adulthood was generally accepted. As @gbrooks9 points out, the role of forehead box P2 protein in brain development (new growth & synaptic plasticity) is a hot topic of current research. I await an explanation of how a Frenchman, who had severe hydrocephalus as a child, could operate as an adult in today’s society when over 90% of his brain cells had been destroyed by the pressure. Somehow, as his original brain cells were being destroyed, the remainder (probably with the aid of new cells) managed to compensate. Even when (not just IF) science uncovers the mechanisms, the brain seems to be a ‘miraculous’ organ.
Al Leo

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There is certainly a lot that we don’t know, but there is no indication that mechanisms of human neural plasticity (referring to rewiring of synapses and/or pruning of axons/dendrites) are even slightly different than in other animals. Adult neurogenesis is common throughout the vertebrates, and there is no indication that plasticity and remodeling are any different in newly-born adult neurons of humans than in the same neurons in any other mammal. And I guess I disagree that adult neurogenesis is a recently accepted thing; it’s been undisputed in the rodent olfactory system and hippocampus for decades. In humans, adult neurogenesis in the hippocampus has been known for nearly 20 years, and was strongly suspected long before that. (I guess this is the right time to disclose that I have a PhD in neuroscience and my specialty is developmental neurobiology.) An excellent review article is linked below.

What does seem to be different in humans is the extent of adult neurogenesis in the striatum. No one knows yet what this means. And that’s certainly very interesting.

In short, we have very little reason to suspect that human synaptic plasticity or wiring, in embryos or adults, is unique. We have the apparently primate-specific neurogenesis in the adult striatum. And we have evidence that genetic regulatory systems show human-specific patterns in the brain. But I don’t think you can make a scientific case for humans being different from other mammals in their pruning or their “use it or lose it” systems. And, for my part, I don’t quite understand why you would want to.

Adult Neurogenesis in Humans- Common and Unique Traits in Mammals

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I really do appreciate your responses, Stephan. You are filling in some pretty large gaps in my education. And you are correct in an observation about my motivation being “non-scientific” in nature.[quote=“sfmatheson, post:21, topic:34294”]
But I don’t think you can make a scientific case for humans being different from other mammals in their pruning or their “use it or lose it” systems. And, for my part, I don’t quite understand why you would want to.
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Deep inside me, I believe that in some ways we are created in God’s Image–that we are truly a different form of life that can have unique value. I know it is foolish to think that this can be supported scientifically, but it can’t help motivate the research in that direction.
Al Leo

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