Friday, December 26, 2014

Found: Genes for Fins, Paws, and Hands

Scientists found the genetic code mice use for growing paws — in spotted gar, after they thought about what happened to fish 300,000,000 years back.

An amateur fossil hunter found a complete ichthyosaur skeleton in Wales, professional fossil hunters found parts of a critter that isn't quite an ichthyosaur in China, and other paleontologists described a cat-size dinosaur that lived in what's now Montana.

Still other scientists named a Cambrian — thing — after an esteemed colleague. Quite a few Cambrian critters are just like nothing that lives on today's Earth.
  1. Fins, Paws, and Hands: the Genetic Connection
  2. The Penarth Ichthyosaur
  3. Not Quite an Ichthyosaur
  4. Cat-Size Montana Dinosaur
  5. Another Cambrian Whatsit

Being an Animal

I've got a physical form, one with characteristics of an animal; so when I look in a mirror, I see eyes, nostrils, and a mouth. The hair tells me I'm looking at a mammal, other characteristics peg me as a primate.

I'm not just an animal, though. I'm a human, so I'm an animal that can use reason: a person, able to decide what I will or won't do. (Catechism of the Catholic Church, 1951, 1730)

There's more along those lines, in Catechism, 1700-1706.

Since I'm a Catholic, I believe that God is making the universe: and that scientific discoveries are an invitation "to even greater admiration for the greatness of the Creator." (Catechism, 279, 283, 301-308)

I go over this sort of thing pretty regularly:

Knowledge and Being Rational

Before I became a Catholic, I thought the universe was beautiful and orderly: that it worked according to knowable principles.

When I became a Catholic, that was no longer an option. Now I must think that the universe is beautiful and ordered. (Catechism, 32)

I also must believe that fire, gravity, all natural processes, exist and change in knowable ways. These are secondary causes: which we can observe and study.

Since natural processes are created by God, reflecting some facet of the Creator's truth, according to their nature, we can learn something about God by studying them. (Catechism, 282-289, 306-308)

More accurately, we may observe, study, and learn from, natural processes. We have free will, and may decide to ignore anything. (Catechism, 1730)

Responsibility comes with that freedom: and that's another topic. (Catechism, 1731-1738)

I've been over this before. (July 15, 2014)

Fearing knowledge is irrational. As Leo XIII wrote, "truth cannot contradict truth." (Catechism, 159, 214-217; "Providentissimus Deus") (July 15, 2014)

And now, something really interesting: bat wings, dolphin flippers, and homology.

Bats, Birds, and Pterosaurs

(From Jerry Crimson Mann, via Wikimedia Commons, used w/o permission.)
("The principle of homology illustrated by the adaptive radiation of the forelimb of mammals. All conform to the basic pentadactyl pattern but are modified for different usages. The third metacarpal is shaded throughout; the shoulder is crossed-hatched."

I've talked about convergent evolution, "the independent evolution of similar features in species of different lineages," before. (June 6, 2014)

That's why birds, bats, and pterosaurs have wings that look an awful lot alike.

They're alike in more than general appearance, though. They've each got pretty much the same sort of bones inside. What varies is the size and shape of each bone, and how many show up at the far end of the wing.

Several possible explanations come to mind.

Maybe it's sheer coincidence: three times? When the rest of the skeleton in these critters also follows the same basic plan??

Maybe God exists: and either doesn't have much of an imagination; or made critters this way so that He could throw folks into the everlasting fires of Hell for using our brains. That sounds crazy to me. I've discussed God, faith, and getting a grip, before. (May 7, 2012; January 16, 2010)

What makes more sense, to me anyway, is that bat, bird, and pterosaur wings are evidence of common descent: that they're built the same way, because the critters have a common ancestor.

The "common descent" explanation doesn't involve wildly unlikely coincidences, or belief in a deity with severe personality disorders. It's also supported by a growing body of evidence.
I don't "believe in" evolution, not in the sense that I think that studying life's story on this planet will tell us everything about — everything. But I think we're learning more about what happened before we showed up: and it's a fascinating story.

Besides, as a Catholic I must believe that this universe is in a "state of journeying" toward an ultimate perfection. It's in the rules. (Catechism, 302)

1. Fins, Paws, and Hands: the Genetic Connection

"Modern genetics confirm ancient relationship between fins and hands"
University of Chicago Medical Center, via ScienceDaily (December 22, 2014)

"Efforts to connect the evolutionary transition from fish fins to wrist and fingers with the genetic machinery for this adaptation have fallen short because they focused on the wrong fish. Now, researchers describe the genetic machinery for autopod assembly in a non-model fish, the spotted gar.

"Paleontologists have documented the evolutionary adaptations necessary for ancient lobe-finned fish to transform pectoral fins used underwater into strong, bony structures, such as those of Tiktaalik roseae. This enabled these emerging tetrapods, animals with limbs, to crawl in shallow water or on land. But evolutionary biologists have wondered why the modern structure called the autopod--comprising wrists and fingers or ankles and toes--has no obvious morphological counterpart in the fins of living fishes.

"In the Dec. 22, 2014, issue of the Proceedings of the National Academy of Sciences, researchers argue previous efforts to connect fin and fingers fell short because they focused on the wrong fish. Instead, they found the rudimentary genetic machinery for mammalian autopod assembly in a non-model fish, the spotted gar, whose genome was recently sequenced.

" 'Fossils show that the wrist and digits clearly have an aquatic origin,' said Neil Shubin, PhD, the Robert R. Bensley Professor of organismal biology and anatomy at the University of Chicago and a leader of the team that discovered Tiktaalik in 2004. 'But fins and limbs have different purposes. They have evolved in different directions since they diverged. We wanted to explore, and better understand, their connections by adding genetic and molecular data to what we already know from the fossil record.'

"Initial attempts to confirm the link based on shape comparisons of fin and limb bones were unsuccessful. The autopod differs from most fins. The wrist is composed of a series of small nodular bones, followed by longer thin bones that make up the digits. The bones of living fish fins look much different, with a set of longer bones ending in small circular bones called radials...."
There will not be a test on this, but I figured it wouldn't hurt to go over some words in this article, starting with "autopod:" which has nothing to do with automated personal vehicles.

Looking for a good-enough description of "autopod," I ran into this:
"The limb is organized into three regions: stylopod, zeugopod, and autopod (in order from proximal to distal). The two distal regions of the skeleton contain a number of periodic and quasi-periodic pattern motifs. The zeugopod consists of two parallel elements along the anteroposterior (AP) axis and the autopod contains 3-5 (in most cases) elements along the same axis...."
(Limb development/Periodicities of the limb pattern, Wikipedia)
Mercifully, there's an illustration to go with all that verbiage. (March 28, 2014)

If the illustration looks familiar, it should. It's a diagram of the bones in a human arm: one bone from shoulder to elbow, two from elbow to wrist, a whole lot of bones in the wrist, then five lines of bones going out from the wrist.

For that matter, that's the arrangement of bones in our legs, and the basic plan for all tetrapod limbs. What changes is the size and shape of the bones: and how many show up at the far end. (March 28, 2014)

Ungualtes like horses, cattle, and pigs, may have only one or two 'toes:' although tapirs have four on their back feet. Whales, porpoises, and dolphins, oddly enough, started out with hooves: about 50,000,000 years back. (Evolution of cetaceans, Wikipedia)

Then there's polydactyly and polydactyl cats, and that's yet another topic. Topics.

Where was I? Autopods, bones at the end of tetrapod limbs; tetrapods, vertebrates with four limbs; critters with hooves, and critters whose ancestors had hooves; cats with extra toes. Right.

Spotted Gar and Mutant Mice

Scientists had tried inserting genes that control limb development from teleosts, the most common sort of bony ray-finned fish — which are called Actinopterygii, and I am not going to wander off-topic again.

The molecular machinery in the cells of fish, mice, geraniums — all life on Earth — is very modular. (November 22, 2013)

But the fish genes didn't work in mice. Then the researchers realized that ancestors of today's teleosts went through Whole Genome Duplication (WGD), a sort of reshuffling of the genetic deck, about 300,000,000 years back.

Ancestors of today's teleosts and tetrapods had parted ways by that time: which probably explained why the gene swap didn't work.

Ancestors of the spotted gar, however, split off from teleost fish before the WGD. These scientists tried putting the 'autopod' genes from spotted gar in mice: and this time the fish genes worked.

It looks like mice and spotted gar use the same snippets of genetic code to tell the ends of their limbs how to grow. That could be a whacking great coincidence: or evidence that mice and spotted gar had a common ancestor: a very long time ago.

2. The Penarth Ichthyosaur

"7ft ichthyosaur fossil found on beach near Penarth"
BBC News (December 19, 2014)

From Jonathon Bow, via BBC News, used w/o permission"An amateur fossil hunter has unearthed a 7ft skeleton of a carnivorous marine reptile on a beach in south Wales.

"Jonathan Bow, 34, discovered the ichthyosaur while walking the shoreline in the Penarth area.

"A palaeontologist at the National Museum Wales said the discovery is important as it appears to be complete.v 'Something this large and complete is a once in a lifetime find,' said Mr Bow, a computer programmer in Swansea.

"Other fossils from the Jurassic period have been unearthed in the area, dating back 200 million years.

"He said anyone walking the dog on the beach could have found it, adding that an inch-long piece of rock took his eye after being exposed on a changing tide in September...."
"Anyone" might have found that ichthyosaur fossil before Mr. Bow did: but not recognized it as part of a Jurassic predator.

We've learned a great deal about ichthyosaurs since the mid-19th century: but finding a complete skeleton is still a remarkable event.

Scientists found part of an amphibious ichthyosaur in 2011, which should tell us how these marine reptiles returned to the ocean. (November 21, 2014)

3. Not Quite an Ichthyosaur

(From Chen X-h et al., via, used w/o permission.)
(Eohupehsuchus brevicollis.)
"Eohupehsuchus brevicollis: Paleontologists Discover Short-Necked Triassic Marine Reptile" (December 18, 2014)

"Paleontologists led by Dr Xiao-hong Chen of the China Geological Survey’s Wuhan Center have discovered a new species of marine reptile that lived in what is now China during the Lower Triassic, about 245 million years ago.

"The newly-discovered creature belonged to Hupehsuchia, a group of enigmatic Triassic marine reptiles that is known exclusively from two counties in Hubei Province, China.

"One of the common features of the group was a modestly long neck with 9-10 cervical vertebrae.

"The new fossil, named Eohupehsuchus brevicollis, for the first time shows a short neck in this group, with six cervicals...."
Hupehsuchia look like ichthyosaurs, but weren't around nearly as long: a few million years, to the 160,000,000-year run of the ichthyosaurs. Or would be that "swim?"

Ichthyosaurs and Hupehsuchians may be related: or we may be looking at another example of convergent evolution, critters looking alike because they're suited to the same sort of life in similar environments. (June 6, 2014)

They're called Hupehsuchians because quite a few of their fossils are from Hubei Province, China. The Hupmobile, on the other hand, was made by the Hupp Motor Company, 345 Bellevue Avenue, Detroit, Michigan: and that's yet again another topic.

4. Cat-Size Montana Dinosaur

(From Brian Engh/RaymondM. Alf Museum of Paleontology, via, used w/o permission.)
("Life restoration of Aquilops americanus."
"Aquilops americanus: Small Cat-Sized Dinosaur Discovered in Montana" (December 11, 2014)

"A group of paleontologists led by Dr Andrew Farke from Raymond M. Alf Museum of Paleontology has described a new genus and species of ceratopsian dinosaur that lived in what is now southern Montana during the Early Cretaceous epoch, about 108 million years ago.

"The new dinosaur belongs to a group of herbivorous, beaked dinosaurs called Ceratopsia, better known as horned dinosaurs. Unlike its famous relatives, such as Triceratops, it lacked horns and a bony neck frill.

"It is named Aquilops americanus, meaning American eagle face.

"The genus name refers to the hook-like beak at the front of the skull, used to snip plants during feeding.

"Aquilops americanus was about the size of a small cat, weighing around 1.6 kg and measuring around 60 cm in total length.

"It is the oldest species of horned dinosaur known from North America, about 40 million years older than the iconic horned dinsoaur Triceratops, which weighed up to 4,000 times more.

" 'This dinosaur lived nearly 20 million years before the North America’s oldest previously known horned dinosaur,' said Dr Farke, who is the lead author of the paper published in the journal PLoS ONE...."
Aquilops americanus may not have looked quite as cute as that illustration implies. The tip of its snout probably wasn't as blade-like, either.

Scientists have found only one specimen of Aquilops americanus so far, so we can't be all that sure about how this little dinosaur lived.

It's important, though, at least for folks piecing together the story of life in the Cretaceous, some 146,000,00 to 66,000,00 years ago.

As the PLoS ONE article's abstract says, Asia and North America seem to have an on-again/off-again relationship. Sort of.

It looks like Asia and North America were connected at least occasionally during the early Late Cretaceous — followed by a time when the continents were separated, before connecting again in the Late Cretaceous.

(From Ron Blakey, NAU Geology; via Wikimedia Commons; used w/o permission.)
(Earth in the Early Cretaceous, about 105,000,000 years ago.)

(From Ron Blakey, NAU Geology; via Wikimedia Commons; used w/o permission.)
(Earth in the Late Cretaceous, about 90,000,000 years ago.)

That sort of thing's important to paleontologists, and fascinates me. Your experience may vary.

5. Another Cambrian Whatsit

"Nidelric pugio: 520-Million-Year-Old Fossil of Spiny Marine Animal Found in China" (December 10, 2014)

(Nidelric pugio) From Derek Siveter, Oxford University; used w/o permission."A multinational team of paleontologists headed by Dr Thomas Harvey from the University of Leicester, UK, has described a strange balloon-shaped animal that swam in the Cambrian seas about 520 million years ago.

"The new fossil belongs to a now-extinct family of bizarre, balloon-shaped animals known as Chancelloriidae.

"It was uncovered from the Cambrian Series 2 Heilinpu Formation near Chengjiang, Yunnan Province, China.

" 'There is only one fossil of this enigmatic animal after thirty years of collecting by our Chinese colleagues at Chengjiang. It is exceptionally rare, but it shows us just how strange and varied the shapes of early animals could be,' said Dr Harvey, who is a co-author of the paper describing the discovery in the journal Scientific Reports....

[Dr. Harvey said:] "...'Amongst the fossils are many animals that can be related to modern forms, including distant relatives of arthropods such as crabs and lobsters, and a wide variety of worms.'

"'There are also several enigmatic fossils that don’t seem to fit in with anything living today, and amongst these are the chancelloriids. These fossils provide an unprecedented view of life in Earth’s ancient seas.' "
Nidelric pugio is named after Richard Aldridge, the Bennett Professor of geology at the University of Leicester, who died this year. Professor Aldridge helped piece together Earth's story, and whether conodonts were pieces of clams, sponges, vertebrates, or worms.

This bag-shaped animal wasn't large by today's standards: about 9 centimeters long. It might be a Chancelloriid, which are also extinct: or something else.

Chancelloriids are probably sponges; or Halkieriids — critters that looked like armored slugs — or something else.

"Or something else" seems to describe quite a few critters that lived during the Cambrian, 541,000,000 to 485,000,000 years back — give or take a few million.

Just about all life was in the ocean then, apart from the occasional microbial mats and molluscs that came ashore to eat the mats.

Earth was heating up then: literally and figuratively. Our planet had been really cold earlier. The last I heard, scientists think there were a few ice-free patches near the equator: or not.

Either way: this was more than our usual ice age, where continental glaciers only get about halfway down from the poles. (August 30, 2013)

Earth's average temperature was rising when the Cambrian explosion happened.

That was a short period, geologically speaking, when just about every body plan we see in today's animals showed up: and some we don't.

Some critters preserved in the Burgess Shale looked a bit like today's worms and arthropods.

Others, like Hallucigenia and Yohoia — don't.

Maybe there's are only so many ways a creature can swim, walk, crawl, or fly effectively: and that's why today's animals look the way they do.

Or maybe we'll meet folks whose ancestors developed on another planet — who think we have too few eyes, and too many arms. And that's still another topic. (July 18, 2014; April 18, 2014)

Finally, maps of our world in the days of Chancelloriids: give or take ten million years.

(From Ron Blakey, NAU Geology; via Wikimedia Commons; used w/o permission.)
(Earth in the Early Cambrian, about 540,000,000 years ago.)

(From Ron Blakey, NAU Geology; via Wikimedia Commons; used w/o permission.)
(Earth in the Late Cambrian, about 500,000,000 years ago.)

More, mostly about Earth's backstory:

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Marian Apparition: Champion, Wisconsin

Background:Posts in this blog: In the news:

What's That Doing in a Nice Catholic Blog?

From time to time, a service that I use will display links to - odd - services and retailers.

I block a few of the more obvious dubious advertisers.

For example: psychic anything, numerology, mediums, and related practices are on the no-no list for Catholics. It has to do with the Church's stand on divination. I try to block those ads.

Sometime regrettable advertisements get through, anyway.

Bottom line? What that service displays reflects the local culture's norms, - not Catholic teaching.