Snake segmentation

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Blogging on Peer-Reviewed Research

Life has two contradictory properties that any theory explaining its origin must encompass: similarities everywhere, and differences separating species. So far, the only theory that covers both beautifully and explains how one is the consequence of the other is evolution. Common descent unites all life on earth, while evolution itself is about constant change; similarities are rooted in our shared ancestry, while differences arise as lineages diverge.

Now here's a new example of both phenomena: the development of segmentation in snakes. We humans have 33 vertebrae, zebrafish have 30-33, chickens have 55, mice have 65, and snakes have up to 300 — there's about a ten-fold range right there. There are big obvious morphological and functional differences, too: snakes are sinuous slitherers notable for their flexibility, fish use their spines as springs for side-to-side motion, chickens fuse the skeleton into a bony box, and humans are upright bipeds with backaches. Yet underlying all that diversity is a common thread, that segmented vertebral column.

snakeseg.jpg
(Click for larger image)

Vertebral formula and somitogenesis in the corn snake. a, Alizarin staining of a corn snake showing 296 vertebrae, including 3 cervical, 219 thoracic, 4 cloacal (distinguishable by their forked lymphapophyses) and 70 caudal. b, Time course of corn snake development after egg laying (118-somite embryo on the far left) until the end of somitogenesis (~315 somites).

The similarities are a result of common descent. The differences, it turns out, arise from subtle changes in developmental timing.

Similarities

Let's consider the similarities first. We know how segments form in many vertebrates: it's a process of progressive partitioning of an unsegmented, relatively undifferentiated mass of cells called the presomitic mesoderm. This mass extends the length of the body and tail of the early embryo. If you just watch the developing embryo, you can actually see the cells self-organize serially, from front to back, with little knots of cells pinching off to form each segment. It's very cool to see, and I've often witnessed it in my zebrafish embryos.

Looking deeper at the molecules involved, there is an elegant clockwork mechanism ticking away. There is a slowly receding gradient of Wnt/FGF molecules that travels down the presomitic mesoderm, and at the same time, there is a faster oscillation of Notch-related molecules that has the same cycle as the timing of segment formation. Each tick of the Notch clock sets aside the most anterior cells expressing Wnt/FGF, and the go on to form a segment. Wnt/FGF recedes back a little further, and at the next cycle of Notch, the next segment is pinched off, and so on, until the gradient runs out of presomitic mesoderm, and the array of segments is complete.

This latest work is an extensive analysis of the molecular basis of segment formation in the zebrafish (Danio rerio), chicken (Gallus gallus), mouse (Mus musculus), and the new player in this game, the corn snake (Pantherophis guttatus), with its impressive roster of 315 total segments. They examined many genes, including FGF and Wnt3a of course, but also many of their downstream targets, as well as components of the retinoic acid counter gradient, and molecules involved in the oscillator, like Lunatic fringe.

No one should be surprised to learn that snakes have the very same segmental clock that fish and mammals and birds have already been shown to have — the same molecules are observed, operating in the same compartments, with roughly the same relationships. They all use a conserved developmental mechanism.

Differences

So what causes the obvious difference of 300 segments vs. 30? There are two simple hypotheses that would fit within the clock and wavefront model. One would be that the wavefront recedes more slowly, or at the same speed but over a longer mass of presomitic mesoderm, allowing more ticks of the oscillator to occur before the wavefront ends at the tailtip. The other is that the wavefront is operating at roughly the same rate, but the oscillator is operating at a much faster rate, partitioning off many more smaller segments.

The answer is the latter. The snake clock is running at a much higher speed than the clock in a chicken or mouse, so that over the same relative span of time for segment formation, it counts off many more pulses and triggers many more segments to assemble. The estimates are a little bit complex, because these species all have very different overall times of development, with the snake being slowest overall, so rates had to be normalized to specific developmental events. Among the standard metrics was the number of cell generations during the period of segment formation; about 21 cell generations to make 300 segments in the snake, about 17 generations to make 65 segments in the mouse.

There were other subtle differences that hint at some changes in gene regulation, for instance, in that Lunatic fringe expression shows more simultaneous stripes in the corn snake than in other species, but this may also simply be a side effect of the more rapid cycling of the somitic clock.

This is a demonstration of the real power of evo-devo. When we talk about major evolutionary changes in phenotype, like the increase in segment numbers in snakes, the way to track down and figure out the specific molecular details is to study the developmental processes behind the morphology, and look for the small differences that lead to the differing outcomes. In this case, we see a direction for further research: it looks like a quantitative change in the regulation of a developmental regulator, the somitic clock, is responsible for the variation. Now the next big question is to identify the specific adjustments to the clock — what small shifts in the sequence of various genes lead to the clock running faster or slower?

At any rate, it's another case where we don't need a watchmaker, just blind, tiny, incremental changes to the machinery of development.


Gomez C, Ozbudak EM, Wunderlich J, Baumann D, Lewis J, Pourquie O (2008) Control of segment number in vertebrate embryos. Nature 454:335-339.

272 Comments

Hi PZ,

‘Tis a great post which demonstrates once more the evo-devo implications of homology, with respect to vertebrae segmentation.

Regards,

John

Hi PZ,

‘Tis a great post of yours which demonstrates the evo-devo implications of homology, with this elegant study of vertebral segmentation in snakes.

Regards,

John

You realize, of course, that while you may have explained the 300 vertabrae, you’ve completely failed to address the 299 obvious gaps.

John Kwok said:

Hi PZ,

‘Tis a great post of yours which demonstrates the evo-devo implications of homology, with this elegant study of vertebral segmentation in snakes.

Regards,

John

You can say that again. Oh, you did!

stevaroni said:

You realize, of course, that while you may have explained the 300 vertabrae, you’ve completely failed to address the 299 obvious gaps.

It also doesn’t explain how life began, how the universe got here, why the planets rotate [sic] around the sun and why dark ale is better than pale ale.

The theory falls short.

Was the snake in the garden a corn snake?

Do we associate faster clocks with Satan??

Thanks PZ for a very interesting article. Scientists solving mysteries, it’s great.

stevaroni said:

You realize, of course, that while you may have explained the 300 vertabrae, you’ve completely failed to address the 299 obvious gaps.

Reed Braden said:

It also doesn’t explain how life began, how the universe got here, why the planets rotate [sic] around the sun and why dark ale is better than pale ale.

The theory falls short.

301 gaps. Seems there is one at either end also.

Beautiful. I envy your life of constant discovery, PZ.

Reed Braden said:

stevaroni said:

You realize, of course, that while you may have explained the 300 vertabrae, you’ve completely failed to address the 299 obvious gaps.

It also doesn’t explain how life began, how the universe got here, why the planets rotate [sic] around the sun and why dark ale is better than pale ale.

The theory falls short.

But of course it explains what it claims to explain (and better with each new discovery), and explains what no other “theory” can. Which is why the “creationist” alternatives keep retreaing into “don’t ask, don’t tell.”

So I guess the only thing wrong with evolution is that it “expels” people and leads to Nazism. ;-)

FRANK J Said: So I guess the only thing wrong with evolution is that it “expels” people and leads to Nazism.

It is so ironic that racism was in the Bible a millennium and a half before a single Nazi talked about Social Darwinism.

PZ’s article is part of the amazing current adventure of bringing evolutionary theory down to the molecular level.

That adventure could easily have failed. Snakes could, for instance, have had a genetic makeup that was completely different from other reptiles– which would have made creationist terms like macro-evolution and “kinds” into terminology at the forefront of science. It just didn’t work out that way. Radically different phenotypes have been shown to have similar genetics, with minor mutations in the genetic switches causing most of the differences between them.

PZ’s research was a direct test of evolutionary theory, and could have come up with results that falisified a big chunk of that theory. It just didn’t, because the data didn’t turn out that way.

Frank B,

I guess you know that my comment was sarcasm, but for the benefit of lurkers who might miss it, I do find one “design” argument convincing. Which is that it was not “by accident” that “Expelled” said nothing about what better explains the evidence than evolution, regardless of deserved or undeserved social implications. That IDers chose to avoid one of the best opportunities for them to promote their “theory” speaks volumes. As did the “expulsion” of PZ Myers.

So much of the ID/Creationist propaganda is simply “ATTACK”. So “Expelled” attacked. The producers didn’t want to talk above their target audience’s heads (or above their own heads for that matter), so it made sense not to talk about irreducible complexity. The molecular basis for the development of the vertebrae is way above their heads, so they will stick to probabilities and other standard talking points. Who needs evidence or a science degree or other such sophistries?

Frank B said: The molecular basis for the development of the vertebrae is way above their heads, so they will stick to probabilities and other standard talking points. Who needs evidence or a science degree or other such sophistries?

The sophistries show who is winning, and which side is in crisis. Evolution or creationism and its siblings.

On a recent trip to a butterfly sanctuary in St Marten, I saw a large moth ( Atlas moth) with wing marking remarkably similar to an eagle’s head seen in profile. The eagle has earned the reputation as a fearsome predator and some of the reputation is rubbing off on that moth, giving it some protection from other birds.

Similarly, science has earned a good reputation is largely seen as the font of medicine, food, progress and advancement. So the creationist moths are painting themselves with the terminology of science, and desperately want in, to be seen and respected like scientists. Despite all the slander Ben Stein heaped upon science in general and biology in particular, how many scientists pretend to be priests, and use religious language hoping to impress other “evilutionists”? Count how many creationists dress up in lab coats and routinely use terms like, “specified complexity”, “probability of biotic reality” and such terms to impress fellow creationists.

The hawks and mynahs that mistake the atlas moth for a real eagle, are at a relative disadvantage compared to the birds that can tell an atlas moth from an eagle. Likewise people who can tell pseudo scientists from the real ones too will be at a relative advantage.

At any rate, it’s another case where we don’t need a watchmaker, just blind, tiny, incremental changes to the machinery of development.

It amazes me that a human, who has no control over the next breath he or she will or will not take, assumes they have no need for the “Watchmaker”, when what they are really saying is they have no need for God.

I believe Matthew 10:29 Are not two sparrows sold for a farthing? And one of them shall not fall on the ground without your Father. 30 But the very hairs of your head are all numbered. 31 Fear ye not therefore, ye are of more value than many sparrows. 32 Whosoever therefore shall confess me before men, him will I confess also before my Father which is in heaven.

There is none so blind as he who will not see.

The eagle has earned the reputation as a fearsome predator and some of the reputation is rubbing off on that moth, giving it some protection from other birds.

If eagles and moths were placed together in an enclosed space for a lifetime, and indeed for centuries, there would be no “rubbing” off of defense systems one to the other. That is wishful thinking on the part of a pseudo scientist.

This constant vocalizing of evolutionist stating that they are scientist, while creationist and those believing Intelligent Design are not, is totally absurd. Science is science. It is the interpretation of scientific findings and facts that differ, not the process!

For too long, evolutionist have gotten by with this. It is time for the public to be educated concerning this ridculous claim.

An Observer said: If eagles and moths were placed together in an enclosed space for a lifetime, and indeed for centuries, there would be no “rubbing” off of defense systems one to the other. That is wishful thinking on the part of a pseudo scientist.

That’s not what was meant. Mimicry is a natural phenomenon readily explained through evolutionary mechanisms, but those mechanisms are not as simple as ‘leaving the two together.’ I wonder if you’re familiar with the general process by which evolution says such mimicry would take place. Would you mind explaining it?

For too long, evolutionist have gotten by with this. It is time for the public to be educated concerning this ridculous claim.

Perhaps when there is some scientific output which validly supports either Creationism or Intelligent Design, you may have your point. If you know of some already, please share it with us.

Nor none so dense as those who refuse to learn.

Cleary a literalist. Doesn’t understand metaphors.

An Observer said:

The eagle has earned the reputation as a fearsome predator and some of the reputation is rubbing off on that moth, giving it some protection from other birds.

If eagles and moths were placed together in an enclosed space for a lifetime, and indeed for centuries, there would be no “rubbing” off of defense systems one to the other. That is wishful thinking on the part of a pseudo scientist. … For too long, evolutionist have gotten by with this. It is time for the public to be educated concerning this ridculous claim.

Hi Mr Troll, I am willing to bite today. The observation is quite simple,the wing markings of the atlas moth looks remarkably like an eagle’s head and beak in profile. I even gave a link for you to see. Please educate us on how this remarkable markings developed as explained by your version of science.

BTW thank you for accepting and providing corroboration to my central claim. Science has a better and greater reputation among the public than religion. Creationists like you clamor to be called scientist. You guys wish, nay dream, your musings be accepted as science.

On the other hand, the number of scientists sounding like theologians and clamoring to be accepted as wise gurus of spirituality are very very few. Shows very clearly theology has lost the race for reputation in the public perception.

An Observer said: I believe Matthew 10:29 Are not two sparrows sold for a farthing?

Thank you Observer, I learned something new today. Someday it will come in handy.

[RS slips into a day dream of appearing in Jeopardy (link for the benefit of our European friends]

RS: I will have Money and Matters for 2000$ Alex.

Alex Trbek: This is the currency used in ancient Judea.

RS: [buzz]

Alex: RS!

RS: What is a farthing?

Alex: Correct!

Maybe the observer would like to know a good example of mimicry concerning butterflies, the Viceroy and the Monarch. The Monarch tastes bad so birds learn to avoid it. The Viceroy, which looks similar, benefits from this. The relative population sizes are important for both species (kinds). Viceroys need a smaller population size to the Monarch, or else the birds will learn the wrong lesson and kill Viceroys and Monarchs. Now this is a probability exercise that Dempski should practise with.

Great post!

Snakes are fascinating creatures. And useful to have around if you don’t want lots of rodents.

The mutation for this 10x segmentation must be a simple one, considering that long-bodied leglessness seems to have evolved multiple times in lizards (see glass lizards and slowworms, and keeping in mind that snakes are now classed as a subgroup of lizards). Granted, both slowworms and glass lizards are in the same family (Anguidae), but it begs the question: how many times has this trait evolved?

Ravilyn Sanders said:

Thank you Observer, I learned something new today. Someday it will come in handy.

[RS slips into a day dream of appearing in Jeopardy (link for the benefit of our European friends]

RS: I will have Money and Matters for 2000$ Alex.

Alex Trbek: This is the currency used in ancient Judea.

RS: [buzz]

Alex: RS!

RS: What is a farthing?

Alex: Correct!

Actually, a farthing is a Rennaissance England coin (4 farthings = 1 penny). King James didn’t know his Judaean currency. (Admittedly, neither do I. But I do know some Rennaissance English currency)

Ravilyn Sanders said: Alex Trbek: This is the currency used in ancient Judea. … RS: What is a farthing? … Alex: Correct!

Incorrect: In another mis-translation from the King James Bible, the old British quarter-penny dating back to the 13th century (in Britain - not Judea) was used, as it was familiar to the readers. See http://en.wikipedia.org/wiki/Britis[…]arthing_coin - see http://bible.somd.com/nave/nave1796.shtml for a more detailed explanation.

An Observer said:

This constant vocalizing of evolutionist stating that they are scientist, while creationist and those believing Intelligent Design are not, is totally absurd.

Facts do not become absurd merely because you don’t like them.

Science is science. It is the interpretation of scientific findings and facts that differ, not the process!

Wrong, it is the process that differs. Scientists make predictions based on their interpretation of theories and then go see if the facts confirm them, ie, tiktaalik. Creationists get facts and then interpret them according to their preconceptions. Your lying Jedi tricks will not work here.

Observer is back, this time to observe…

“It amazes me that a human, who has no control over the next breath he or she will or will not take, assumes they have no need for the “Watchmaker”, when what they are really saying is they have no need for God.”

Heck, it amazes me too that nature has no demonstrable need for a watchmaker.

More is the wonder.

Nontheless, aside from your personal incredulity, there is simply no evidence whatsoever that there is any watchmaker anywhere to be found. After 30 centuries of searching, that’s a damning statistic, there, O.

Am I wrong? Go ahead, put some evidence on the table.

Oh, that’s right, you don’t actually doevidence, do you? You just “observe”.

More is the pity.

Okay, it is obvious that either clock can be used to establish a phase difference driving the number of segments. But I wonder if the absence of legs makes this easier? IIRC snakes have a lot more freedom in the number of segments (possibly of various kinds) than some other vertebrates, which suggests that perhaps some constraints are lifted.

In another mis-translation from the King James Bible, the old British quarter-penny dating back to the 13th century (in Britain - not Judea) was used, as it was familiar to the readers.

So those facts aren’t even worth a farthing, there are several mutual exclusive creationist scenarios presented there, yet creationists persist in claiming that “The Truth Is In There”? Curious.

Incorrect: In another mis-translation from the King James Bible, the old British quarter-penny dating back to the 13th century (in Britain - not Judea) was used, as it was familiar to the readers. See http://en.wikipedia.org/wiki/Britis[…]arthing_coin - see http://bible.somd.com/nave/nave1796.shtml for a more detailed explanation.

[Putting on my best imitation of a literalist, blame my lack of experience if it sounds anyway coherent or logical]

What you are gonna believe? Something stated so clearly and so explicitly in the only true authenticated Word of God ™ or some historians, numismatists and wikipedia? If the Holy Bible says sparrows are sold at the rate of 0.5 per farthing, that must be true.

Hitler did not believe farthings existed as a coin before the 13th century. What a personification of evil he was! Why do you numismatists and etymologists and historians insist on believing the same thing Hitler did?

I demand all references to farthings coming into existence in the 13th century stricken from the history books. No, sir, you are not going to teach that kind of evil in our school district!

What? Courts struck it down? OK we demand equal time for Biblical numismatism to counter balance the blasphemous thesis. You are not against balanced teaching of both sides of the issue are you? All we want is fair time to be given to our view of Intelligent Numismatism.

What that is also ruled illegal? God, please, please pretty please, I beseech you to send a couple of tornados to Dover PA area. That will teach them. OK OK how about critical analysis of the history of coinage and currencies? This should not be construed as promoting Biblical Numismatism in any way, (wink wink)!

You guys are all bunch of evil atheists out to get us! Wait till we get couple of more our guys in the Supreme Court. First thing we are going to do in the next Inquisition is to get the iron maiden embrace all of you PT posters. Lukers too.

Ravilyn Sanders said:

An Observer said: I believe Matthew 10:29 Are not two sparrows sold for a farthing?

Thank you Observer, I learned something new today. Someday it will come in handy.

[RS slips into a day dream of appearing in Jeopardy (link for the benefit of our European friends]

RS: I will have Money and Matters for 2000$ Alex.

Alex Trbek: This is the currency used in ancient Judea.

RS: [buzz]

Alex: RS!

RS: What is a farthing?

Alex: Correct!

Incorrect!

A farthing is a British coin “a British coin worth one quarter of a penny and 1/960 of a pound sterling”

They used shekels in Ancient Judea

Just a quick question.

Now the next big question is to identify the specific adjustments to the clock — what small shifts in the sequence of various genes lead to the clock running faster or slower? (emphasis mine)

Wouldn’t it be “small shifts in the squence of various regulatory regions”? If the mutations in question were in the actual genes, the actual proteins would differ, but since the difference appears to be in the regulation of the genes, the mutations must lie outside of the actual “genes”.

Do I have this correct?

stevaroni Wrote:

But, you’ll notice the one thing the “evil Darwinists” don’t seem to do is censor HR.

Well, that is not cruel enough. “Evil Darwinists” come up with diabolical threats like the, … like the, … (Oh horrors, I can’t say it) … like the BATHROOM WALL! Shudder!

The “Terrified Christian” is a term coined by Thom Hartmann to describe the fearful Christian who is presently the target of the thinly veiled attacks by McCain and the religious right on Obama, portraying him as the ‘Prince of Darkness’. Sad really that some Christians are so succeptible to such foolishness.

Mike Elzinga said:

Wow, it looks like PuffOnStuff has a lot to be afraid of. Doesn’t he know that some of the Liberal Darwinist moderators on this board know from whence he is posting and can track him down, despite his disguise, and do evil to him? You know they will.

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This page contains a single entry by PZ Myers published on July 23, 2008 11:33 AM.

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