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Deletions of ~510 regulatory genes in humans versus chimpanzees cause humans to lose some traits -- like "bony" penises -- and gain others -- like big brains.  (Source: Gary Wales)

Most primates have spine-filled penises to allow a male to penetrate through dried penis secretions of other males to increase the chance of fertilization when mating with females with multiple partners.  (Source: Philip Reno, Stanford University (left) Bonobos at (right))

The idea that removed regulatory sequences led to increased brain growth in humans was confirmed using testing in transgenic mice (the left embryo has the regulatory sequence removed -- note the blue dye in the brain cortex noting growth).  (Source: Nature/HHMI)
Mankind may have lost spiny penises and whiskers, but it gained far more -- large brains and intelligence

When you look at mankind, for better or worse, we're pretty special.  Arguably no single species has been able to reshape the planet in its image as fully as humans.  So what happened during the course of evolution to make humans so dramatically different in intelligence and abilities from even our closest relatives, say chimpanzees?

That's what a multi-school team set out to answer [press release], with advanced genetic analysis.  The team was led by David Kingsley [profile], a top geneticist at the non-profit Howard Hughes Medical Institute, and included a number of researchers from Stanford University, which is located in Palo Alto, California.

I. The Hunt for Missing Genes

While some find it hard to fathom how a set of small genetic changes could result in dramatically different anatomies -- say growing fins versus arms -- Professor Kingsley has shown in stickleback fish changes to regulatory DNA could have dramatic impact on anatomy and appearance.

Similarly some of the crucial differences between humans and chimps were found to be not actual gene additions or deletions, but rather changes to regulatory DNA.

In total 510 gene sequences can be found in chimps and a variety of other mammal species, but are "surprisingly missing" from humans.  Computer analysis showed that many of these sequence deletions were clustered around steroid hormone genes (which influence sex and anatomy) and neural development genes.

These regulatory changes were thought to grant humans unique traits like bigger brains and erect spines, and cause them to lose other traits such as whiskers and bony penises (more on that later).

But locating potentially important deletions only took the team so far.  They then needed to analyze the deletions.  Describes Professor Kingsley, "We had a team of interested graduate students, postdocs, and developmental biologists poring through this list. It was a fun detective hunt that led to lots of interesting discussions."

II. Penis "Bones" and More -- Intriguing Findings

One inactivation that produced a critical impact in humans was the removal of regulators of the gene GADD45g around neural-specific sequences.  GADD45g triggers cell growth.  So by disabling this regulatory sequence human brains were able to grow larger and more dense, allowing the rich cortex and connecting layers that give rise to intelligence, complex personality, and advanced motor learning.

Other changes revolved around a special sex-specific receptor.

Did you ever stop to wonder why cats and dogs have whiskers and we don't?  Critics of evolutionary theory have long posed such examples.  Well it turns out humans have the genes to potentially grow whisker-like features, but one of the deletions inactivates the growth.

Specifically the deletion is the removal of a regulatory sequence for the androgen receptor, which causes the protein androgen to be produced in that vicinity.  Androgen is responsible for "turning on" male-specific traits.  In this case, knocking out the regulatory sequences knocked out the "on" switch, leaving the genes for whiskers permanently inactivated (barring a rare insertion of an androgen regulatory sequence via future evolution).

A similar male-specific inactivation occurs with the androgen receptor and genes coding for penis bones.

While whiskers may be familiar material, most don't know that chimps and some other mammals actually have "bony" barbs in their penises.  These barbs aren't true bones.  Rather they are made of keratin, the hard material found in human fingernails.

The penis "bones" act as a form of natural male enhancement -- though humans seem to be getting along fine without them.  Gill Bejerano [profile], a developmental biologist at Stanford University in California was responsible for tracking down exactly how humans lost their penile "bones".

Professor Bejerano says we lost our spiny penises approximately 700,000 years ago, around the time humans split from Neanderthals.  A deletion of an androgen receptor regulatory sequence was, once again, to blame.

Increased neural development may have given rise, in part to monogamy, which in turn may have allowed the gene to become non-critical.

Why do chimps and other mammals need bony penises?  In nature, competition is always fierce.  Frequently multiple males try to fertilize the same female over the course of a couple days.  The dried secretions from the first males block entrance to latecomers, in an attempt to increase their chances of being the one to achieve fertilization.

But with a bony penis in hand, such secretory barriers pose little obstacle.  The bony penis is able to break through such obstructions with virtually no damage to the precious male member.

In humans such situations are rare, so sex organs have become simpler.  In other words, because of monogamy we don't need our penises to be spiny any more.

The paper on the changes, including the loss of the penis bones is published [abstract] in the journal Nature, arguably science's most prestigious peer-reviewed journal.

III. The Tip of the Iceberg

Even with a wealth of clues in hand, delving into these mysteries is daunting says Professor Bejerano.  At time the human genome "can be a huge, impenetrable mystery" he says, but, "[Researchers are] beginning to tease out some of the molecular differences that make us human."

A lot more "teasing"/working the data will be necessary if we hope to fully crack that puzzle, though.  The investigation into whiskers, brain development, and penis bones was only the tip of the iceberg.  

Armed with the knowledge of where deleted sequences lie in the human genome, investigators can now perform additional research (one potential target of interest: removed female evolutionary mechanisms dealing with spiny penises) to discover more regulatory differences and how they changed humans and make us look and act far different from our distant monkey relatives.

Outside of scientific interest, learning about how are brains got big and our penises less bony doesn't seem to have a lot of practical applications, but Professor Kingsley explains the methods developed will play a critical role in "solving" the puzzles of genetic-related diseases such as arthritis, cancer, malaria, HIV, Alzheimer's, and Parkinson's (some of which are caused by viruses, but in which genetic dispositions play a major role).

He states, "It's now possible to begin identifying some of the particular molecular changes that contribute to the evolution of human traits. We think that the same sorts of lists and approaches will eventually help illuminate human disease susceptibilities as well. It's a great time to be studying not only where we came from, but also how our genetic history shapes many aspects of current human biology."

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"Surprisingly missing"
By kingius on 3/10/2011 9:44:43 AM , Rating: -1
This seems to be surprising only if you consider that we are of the same stock as the other species of mammal being examined; if we never were, then it would be no surprise.

Furthermore, the idea that these are somehow deletions is another assumption; that they were there in the first place. The only way to say that with any certainty is to add them in and see what happens to the resulting offspring; if the features reappear then that would be proved. (Cause and effect).

Lastly, if we are descended from the same ancestor, isn't it equally likely that the missing pieces of DNA relate to how we behave differently from other animals; such as our inability to fit into our environment properly, as instead we behave more like insects (ants, who also destroy large swathes of their surrounding environment in service to a queen).

RE: "Surprisingly missing"
By PaterPelligrino on 3/10/2011 10:40:44 PM , Rating: 3
I hear you babe. I get your meaning. I catch your drift.

From the article:

Did you ever stop to wonder why cats and dogs have whiskers and we don't? Critics of evolutionary theory have long posed such examples. Well it turns out humans have the genes to potentially grow whisker-like features, but one of the deletions inactivates the growth.

At first glance, it might appear difficult to understand why Yahwei would give us the genes to grow cat-like whiskers and then not activate them. What's that all about you ask.

Well to those godless heathens who will see this as yet more proof that we share a common evolutionary ancestry with other creatures, let me just say right up front that Yahwei has written this inactivated DNA into our genetic code to test our faith. Like what he does with fossils, he deliberately leaves misleading info lying around so that only those of faith will make the difficult effort to overcome doubt and prove themselves worthy of His love. After all, if the fossil and DNA evidence didn't openly contradict the biblical narrative, it wouldn't be necessary to have faith. The test that He demands of each of us is that we chose Him in spite of the evidence.

So rather than threaten my unshakable faith in the literal truth of the biblical narrative, this latest scientific discovery only serves to confirm my belief in our Sacred Text. In fact, with each additional bit of contrary evidence, my belief is only strengthened!

Oh glory hallelujah can you feel the buzz!

RE: "Surprisingly missing"
By kingius on 3/11/2011 10:05:51 AM , Rating: 2
The point that you seem to have missed is that the sequences are not there, so they are assumed to be deleted. That sort of logic would not stand up in court. 'I couldn't find the loot, so he must have destroyed it! It was him, he's the robber, obviously!'

As an aside, here's a quick request, can we have less Biblical references please. Your solitary god has no place in this conversation.

RE: "Surprisingly missing"
By PaterPelligrino on 3/11/2011 7:51:20 PM , Rating: 2
The evolutionary significance of the above study lies in the fact that there exists in the human genome the same DNA found in other species for producing such non-human traits as cat-like whiskers. What distinguishes us from those whiskered species is that we lack the genetic switch to activate those genes and actually grow the whiskers. Obviously the control DNA has been deleted/inactivated; what else could possibly explain the existence of the whisker gene in the human genome - why would we even possess that gene?

Darwin's elegant theory works perfectly here: the existence of the whisker gene proves our kinship to other species; the lack of the on-switch explains how we came to differ from those species. No doubt, more such non-expressed genetic material linking us to other species will be found in the fullness of time; after all, the referenced study is just the first to explore this approach.

If evolution functions as claimed (tho you and I both know - wink, wink, nudge, nudge - it's all bollocks), this makes perfectly good sense. Evolution is driven by random genetic mutation. A chance mutation in the regulatory DNA would have drastic consequences. Most of these simple mutations would prove deadly, but very occasionally, a non-expressed gene would have benefits that would increase the chances of survival. Accordingly, the disappeared regulatory DNA would deactivate/disappear and the stranded (whisker) gene would be left behind as a kind of genetic smoking gun.

The team found 510 segments that are present in chimps and other animals but missing from the human genome. Only one of the missing segments would actually disrupt a gene; the remaining 509 affect the DNA that surrounds genes, where regulatory sequences lie

The article states that the researchers knew the precise location of the deleted regulatory DNA, so I suspect there were other methods not mentioned in the above summary that were used to identify the deleted info. Most likely the full Nature article has more to say on that topic.

But, as I said in my prior post, all this counter-evidence is just Yahwei fk'g with our heads and testing our faith - the True Believer will not be swayed. (Give me the secret creationist handshake.)

RE: "Surprisingly missing"
By kingius on 3/14/2011 11:44:56 AM , Rating: 2
Basing your argument on a supposition is not a good idea. Unless the researchers can demonstrate what they are saying (read - prove it) then it's just words, ideas and empty air.

It's high time we demanded proof of these claims, as big as they are. If this were aliens being discussed, many would be saying 'extraordinary claims require extraordinary proof'. I don't agree with that sentiment - all facts should be equal - but I do want some semblance of proof from those who make grand claims and want them to be taken as being true.

I see nothing in your post to say that you are equally diligent, just a lot of biblical jokes that probably passes for playground humour these days. If nothing else, consider this; the fool takes what others state at face value.

RE: "Surprisingly missing"
By PaterPelligrino on 3/14/2011 11:14:49 PM , Rating: 4
Unless the researchers can demonstrate what they are saying (read - prove it) then it's just words, ideas and empty air.

Ah yes, proof. We all know how important proof is to the creationist. So remind me again, where exactly is the proof for all the "words, ideas and empty air" that is the Bible?

It's high time we demanded proof of these claims, as big as they are. If this were aliens being discussed, many would be saying 'extraordinary claims require extraordinary proof'. I don't agree with that sentiment - all facts should be equal - but I do want some semblance of proof from those who make grand claims and want them to be taken as being true.

Bushes that burn and talk, that a supernatural being no one has ever seen created the world and us in his image, that Yahwei even exists at all, those are certainly the kinds of claims that would require convincing proof - so how about you give us some of that proof you creationists value so highly. Maybe the believers in Christianity's many competing religions would change sides if presented with a little of that proof. A world not divided by waring religions would be nice don't you think? So convince us.

If nothing else, consider this; the fool takes what others state at face value.

Absolutely priceless. A creationist - someone who thinks that everything written in a 3000 yr-old collection of tribal creation myths is word for word true - telling us that "the fool takes what others state at face value." You're only a Christian because of when and where you were born. If you were Saudi you'd be a Muslim, Tibetan a Buddhist, sub-continent Indian most likely a Hindu, etc., etc. The religion that is so central to your very idea of yourself is something you've been spoon-fed by the society in which you happened to be born.

The genetic material for cat-like whiskers is there in our genome - that's a fact. Even tho it's there, we don't have whiskers because the genetic material is not activated. It's not activated because the regulatory DNA, the on-switch that activates that info, is not there. If it weren't missing, we would grow the whiskers. The only possible explanation for the existence of whisker DNA in our genome is that we are descended from creatures who did grow those whiskers. Now that I've shown you how to think, anything else I can help you out with?

You're an idiot kingus, and like all creationists, a hypocrite as well. You demand absolute proof from the scientists, demand that every tiny detail be accounted for with mathematical certainty, pigheadedly refuse to see all the proof that you are given, yet naively swallow all the superstitious, self-important drivel from the creation myths of a tribe of bronze-age goat herders. You blindly accept all that biblical nonsense, and demand respect for your creed to boot, while you yourself deny the equally dumb gods of all the competition. You live in a airtight, bubble-world of circular reasoning and haven't the smarts to realize how dumb you look when you pontificate that "the fool takes what others state at face value".

"Intel is investing heavily (think gazillions of dollars and bazillions of engineering man hours) in resources to create an Intel host controllers spec in order to speed time to market of the USB 3.0 technology." -- Intel blogger Nick Knupffer

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