Human Evolution as a Function of the RNA World
by MikeGeneFrom here:
The human and chimpanzee genomes vary by just 1.2 percent, yet there is a considerable difference in the mental and linguistic capabilities between the two species. A new study showed that a certain form of neuropsin, a protein that plays a role in learning and memory, is expressed only in the central nervous systems of humans and that it originated less than 5 million years ago. The study, which also demonstrated the molecular mechanism that creates this novel protein, will be published online in Human Mutation, the official journal of the Human Genome Variation Society. [..]
Led by Dr. Bing Su of the Chinese Academy of Sciences in Kunming, China, researchers analyzed the DNA of humans and several species of apes and monkeys. Their previous work had shown that type II neuropsin, a longer form of the protein, is not expressed in the prefrontal cortex (PFC) of lesser apes and Old World monkeys. In the current study, they tested the expression of type II in the PFC of two great ape species, chimpanzees and orangutans, and found that it was not present. Since these two species diverged most recently from human ancestors (about 5 and 14 million years ago respectively), this finding demonstrates that type II is a human-specific form that originated relatively recently, less than 5 million years ago.
Gene sequencing revealed a mutation specific to humans that triggers a change in the splicing pattern of the neuropsin gene, creating a new splicing site and a longer protein. Introducing this mutation into chimpanzee DNA resulted in the creation of type II neuropsin. "Hence, the human-specific mutation is not only necessary but also sufficient in creating the novel splice form," the authors state.
The results also showed a weakening effect of a different, type I-specific splicing site and a significant reduction in type I neuropsin expression in human and chimpanzee when compared with the rhesus macaque, an Old World monkey. This pattern suggests that before the emergence of the type II splice form in human, the weakening of the type I splicing site already existed in the common ancestor of humans and chimpanzees, implying a multi-step process that led to the dramatic change of splicing pattern in humans, the authors note. They identified a region of the chimpanzee sequence that has a weakening effect on the splicing site that also probably applies to humans. "It is likely that both the creation of novel splice form and the weakening of the constitutive splicing contribute to the splicing pattern changes during primate evolution, suggesting a multi-step process eventually leading to the origin of the type II form in human," the authors state.
May 8th, 2007 at 9:26 am
What does this have to do with the RNA world hypothesis, or even with RNA in general?
Comment by grendelkhan — May 8, 2007 @ 9:26 am
May 8th, 2007 at 9:48 am
Probably the emphasis on splicing (processing of RNA)
Comment by Raevmo — May 8, 2007 @ 9:48 am
May 8th, 2007 at 10:38 am
But the RNA world hypothesis is supposed to pre-date bacteria–the events it describes are roughly a thousand times older than the events described in the article. You might as well call the post "Human Evolution as a Function of the Carbon Cycle", because after all, there's carbon in DNA.
Comment by grendelkhan — May 8, 2007 @ 10:38 am
May 8th, 2007 at 10:49 am
Hi Grendelkhan,
You wrote…
I have hinted (an understatement) to MikeGene that he often puts his bias into his posts to Telic Thoughts. In this one, the only hint of bias is in the title. He provided no other arguments. Just a thought provoking article I happen to find very interesting.
Would you rather Mike offer up another post of about how Dawkins is using science to unfairly push an Athiest agenda?
I hope not, I would rather talk about science. Wouldn't you?
I will respond on-topic after I have had a chance to digest the article.
Thanks Mike.
Regards,
TP
Comment by Thought Provoker — May 8, 2007 @ 10:49 am
May 8th, 2007 at 1:25 pm
Hi All,
Even though I may be just an obtuse, stupid, low-life Atheist, I will offer my take on the significance of this.
Recently (2004), scientists "…sequenced the type II"“spliced region of neuropsin gene in humans and representative nonhuman primate species. [The] comparative sequence analysis showed that only the hominoid species (humans and apes) have the intact open reading frame of the type II splice form, indicating that the type II neuropsin originated recently in the primate lineage…" link.
This provides evidence of a real distinction between common animals and near-human apes.
The abstract that MikeGene referenced portends evidence that makes that distinction closer to modern humans (5 million years). It further identifies a switch "…that triggers a change in the splicing pattern of the neuropsin gene, creating a new splicing site and a longer protein…" that is potentially one of the things that makes humans unique.
Some people, especially in Telic Thoughts, might suggest this switch was prewired "…as a Function of the RNA World."
Provoking Thought
Comment by Thought Provoker — May 8, 2007 @ 1:25 pm
May 8th, 2007 at 1:27 pm
I understand that Mike has a habit of smearing his bias all over the articles he posts, but in this case, he didn't even bother writing anything other than a headline and "From here".
Is that supposed to be some kind of threat? I should shut up if I don't want to get the hose, I mean boring atheism post, again?
It's not one or the other. I can complain about Mike's incredible laziness in posting this and still prefer that he post science articles. It's not like Mike's posting-science mechanism is irrevocably bound to his lazy-and-misleading-headline mechanism. Or maybe it is; I don't know him.
Comment by grendelkhan — May 8, 2007 @ 1:27 pm
May 8th, 2007 at 1:29 pm
That's weak. That's incredibly weak. There's not the least evidence that this is the case, and it's nothing but abstract handwaving to bring the RNA world hypothesis into play here. I'm not saying that folks here wouldn't think that, but they'd be fools for doing so.
Comment by grendelkhan — May 8, 2007 @ 1:29 pm
May 8th, 2007 at 1:33 pm
Hi Grendelkhan,
If you really want me to start arguing the ID side I will.
What would it take to convince you of the possibility of front-loading?
How drastic of a change would it take?
Here we have a switch that might change Chimpanzees into humans. Not a gradual change, and instant one.
Provoking Thought
Comment by Thought Provoker — May 8, 2007 @ 1:33 pm
May 8th, 2007 at 2:23 pm
That wasn't my point, but okay. My point was that Mike is posting nonsense.
How did we get to front-loading? I'm pretty fuzzy on the concept, but I think you'd have to show that primitive organisms had a lot of unused genetic information that was weirdly preserved over long periods of time; if you think junk DNA proves front-loading, you'd have to show how useful information could be extracted from it. But all of this is beside the point; to get from "single-gene mutation an important difference between chimps and human" to "this mutation–not the roots, but this actual mutation–was contained in simple RNA from billions of years past" is a staggering leap. For one thing, it assumes some kind of predestination for which there's, again, no evidence. The idea also seems prone to the sort of false-positive that the specified complexity is prone to–rendering it a meaningless idea. I suppose if you could show the future course of one species or another, based on the front-loaded information you'd divined, you might have something. But it would contradict pretty much everything we know about genetics, so I'd be very interested in any positive results coming from this quarter. Start with yeast or something else that breeds quickly, perhaps.
No, we don't. If you took a chimp germ line, made this change and grew a new chimp, you wouldn't have a human; you'd have… well, I have no way of knowing, but I can hypothesize that you might have a smarter chimp; it would be an interesting experiment to try. (Uplift, anyone?) It's a single-gene variant which looks to have important and far-reaching effects, but they're not that far-reaching.
Comment by grendelkhan — May 8, 2007 @ 2:23 pm
May 8th, 2007 at 2:29 pm
Hi Grendelkhan,
Thank you for this latest comment. And while I agree with most of what you said, I do have an ID argument that I would like to explore. It involves "retrocausality". I'm supposed to be working now, so I will explain more details later.
Provoking Thought
Comment by Thought Provoker — May 8, 2007 @ 2:29 pm
May 8th, 2007 at 5:43 pm
Can't you guys recognize a pop quiz when you see it?
I'll take a stab at it.[chunkdz raises hand]
An RNA world determined that life could be protein based, thus carrying the potential for cellular life.
RNA also carried the potential for multicellular life in single celled eukaryotes by encoding for proteins like 'G-Protein coupled receptors'…like neuropsin I.
GPCR's like neuropsin are integral in the signal transduction pathways of eukaryotes, which provides a mechanism for external stimuli to alter gene splicing patterns. For instance, forcing mice to swim, or subjecting them to pavlovian fear-memory training can alter the splicing patterns of their pre mRNA's.
So we come full circle and find that RNA is both the medium and the mechanism that, when triggered by environmental stimuli, can alter it's own production of novel proteins, like neuropsin II.
This potential was present in the RNA world, and was simply waiting to be exploited by environmental influences that would potentially produce humans. This supports the optimality of RNA as a coding mechanism, and supports the "designed to evolve" paradigm.
Am I even close?
Comment by chunkdz — May 8, 2007 @ 5:43 pm
May 8th, 2007 at 7:28 pm
Hi Grendelkhan,
You write:
It is ironic that you accuse me of laziness when you are the one who has had the time to post comments to a blog throughout the day. I posted this thought provoking bit of science news to update the blog right before running off to work.
That's the hypothetical, geological RNA world. I'm focused on the actual, biotic RNA world "“ the world that is studied when scientists explore the cell. It is clear that the biotic RNA world is an integral part of the cell, interfaced at many levels with the protein world. As such, some from a non-telic perspective view this RNA world as a fossil or frozen accident, left-overs from the hypothetical, geological RNA world. If so, all I'm pointing out here is that it is unlikely that the human brain would have evolved without this "fossil/frozen accident." It's not that surprising, given that most genes expressed in the human brain undergo alternative splicing or RNA editing.
Grendelkhan, instead of complaining about me, why didn't you simply and politely ask me to clarify the meaning of the title?
Comment by MikeGene — May 8, 2007 @ 7:28 pm
May 8th, 2007 at 7:28 pm
Hi TP,
You wrote:
Who doesn't? I have long noted that there is a mountain of data out there ripe for re-interpretation from a teleological perspective. Is there something wrong with that?
Comment by MikeGene — May 8, 2007 @ 7:28 pm
May 8th, 2007 at 7:37 pm
Hi Mike,
I wrote…"I have hinted (an understatement) to MikeGene that he often puts his bias into his posts to Telic Thoughts."
You asked…
Nobody, especially not me.
Welcome back from the dark side.
You wrote…
Absolutely nothing. Let's do science!
Regards,
TP
Comment by Thought Provoker — May 8, 2007 @ 7:37 pm
May 8th, 2007 at 10:28 pm
Mike, take that target off your shirt.
Comment by Bradford — May 8, 2007 @ 10:28 pm
May 9th, 2007 at 2:02 pm
chunkdz:
RNA also carried the potential for multicellular life in single celled eukaryotes by encoding for proteins like 'G-Protein coupled receptors'"¦like neuropsin I.
GPCR's like neuropsin are integral in the signal transduction pathways of eukaryotes, which provides a mechanism for external stimuli to alter gene splicing patterns.
Wrong gene. There are two that were named neuropsin by their discoverers. That shouldn't have happened — someone wasn't paying attention– but the nomenclature has since been cleaned up. One "neuropsin", aka Opsin 5, is a GPCR. However, the "neuropsin" in the research that MikeGene referenced is KLK8, a serine protease.
So, nice try but you fail the pop quiz!
Comment by Nick — May 9, 2007 @ 2:02 pm
May 9th, 2007 at 2:47 pm
Hi Mike,
You wrote…
So, do I get a passing grade on the pop quiz for at least coming close to what you were thinking? (my first comment, not the Chimpanzee to Human hyperbole)
(sticks tongue out at Chunkdz)
Regards,
TP
Comment by Thought Provoker — May 9, 2007 @ 2:47 pm
May 9th, 2007 at 4:49 pm
Are you calling all of your commenters lazy and (presumably) unemployed, or just the ones who ask questions you don't like answering?
So, because the alternative-splicing process takes place at the pre-mRNA stage of translation, you mentioned RNA. I see. But alternative splicing shows up in a variety of places; the new discovery isn't that the splicing took place, but rather the changes that it made. It's like being amazed that DNA is eventually translated into protein–it's not really the point of the article. Hence my confusion.
The idea that features, at whatever scale, turn out to be useful later, isn't a new one. RNA is clearly not a fossil; it's used, as you pointed out, in a myriad of fashions in the cell. Because a DNA mutation can have its effect mediated by RNA, that's no reason to call the whole RNA system a "fossil/frozen accident", and I don't think anyone actually does, any more than we consider tetrapod limbs to be a "fossil/frozen accident" left over from lobe-fins on fish.
Did you not notice the first comment on the post? Here, I'll repeat it.
What does this have to do with the RNA world hypothesis, or even with RNA in general?
You've answered this now, and I appreciate it.
Comment by grendelkhan — May 9, 2007 @ 4:49 pm
May 9th, 2007 at 4:55 pm
I wasn't going to post anything other than to say what Mike Gene already said: The RNA World is now.
I assume press releases are mostly fiction (judging by what I observe on the cable news networks and read on the Web), so I tried to find if the research was published on the Web.
No luck. Neither the publisher's site nor two of the authors personal websites list the research.
I suspect its real. No problem. But I really don't like "science" by press release. No proper citation to begin with, almost never in any press releases I've ever read! Journalists (publicists, and popularizers_ don't know the first thing about reporting science!
But why even bother to publish research when one can issue a press release?
Seems a bit redundant to me! LOL
I did find many very interesting related links however, including the one linked to by Thought_Provoker.
From the paper linked to by TP: The difference between being "intellectually" a human or a mouse is in the RNA splicing.
Then the scientists hybridized human brain material with the brain material of insects to see what they'd get!
Science is so FNCOOOL!
If you test higher on an IQ test it could be because your RNA is spliced differently than a mouse's.
And if a mouse RNA was spliced differently, the mouse would be as smart as you!
How does that figure in the whole "front-loading" thing?
(And don't tell me I gotta read your book, GDit! WHAT book?! LOL)
Comment by Rock — May 9, 2007 @ 4:55 pm
May 10th, 2007 at 6:38 am
Hi Grendelkhan,
What in the world makes you think I didn't like answering your question?
Don't you know that the term "RNA World" is commonly used to refer to the RNA biochemistry inside a cell? Here is just one representative example:
New perspectives on neoplasia and the RNA world.
Hall PA, Russell SH.
Hematol Oncol. 2005 Jun;23(2):49-53.
Key tenets of modern biology are the central place of protein in cell regulation and the flow of genetic information from DNA to RNA to protein. However, it is becoming increasingly apparent that genomes are much more complex than hitherto thought with remarkably complex regulatory systems. The notion that the fraction of the genome involved in coding protein is all that matters is increasingly being questioned as the roles of non-coding RNA (ncRNA) in cellular systems becomes recognised. The RNA world, including microRNA (miRNA), small inhibitory RNA (siRNA) and other RNA species, are now recognised as being crucial for the regulation of chromatin structure, gene expression, mRNA processing and splicing, mRNA stability and translational control. Furthermore such ncRNA systems may be perturbed in disease states and most notably in neoplasia, including in haematological malignancies. Here the burgeoning evidence for a role of miRNA in neoplasia is reviewed and the importance of understanding the RNA world emphasised.
If we agree that RNA is not a fossil or frozen accident, we're left with our agreement.
It would have been nice if you had given me a chance to answer the question before launching ad hominems.
Comment by MikeGene — May 10, 2007 @ 6:38 am
May 10th, 2007 at 6:44 am
Hi Rock,
It's the RNA world that confers great adaptability into cells, enhancing their evolvability. As for brains, what is learning if not a certain form of adaptability and evolvability?
Once again, evolution is encapsulated.
Comment by MikeGene — May 10, 2007 @ 6:44 am