Friday, January 31, 2014

Cave Men, Sea Monsters, Dead Scorpions, and Theoretical Physics

There's probably a bit of Neanderthal in me, since my ancestors were their neighbors: and that heritage could affect my health.
  1. Neanderthal Heritage
  2. Event Horizons, Revisited
  3. A Swarthy Swede, Sort of
  4. Scorpions, Venom, and a Repurposed Protein
  5. Funnysaurus and the Middle Triassic
Before getting into ancestry, sea monsters, theoretical physics, and dead scorpions; why thinking and learning aren't sins:

Faith and Reason

Mawkish posts, drenched with emotional appeals to faith, aren't at all uncommon. Neither, sadly, are screeds about the evils of science: or the dangers of taking religion seriously.

That's why I think my blatant faith and interest in science may need an explanation.

I'm interested in science, by the way, not "Bible science." I don't see value in struggling to fit what we've learned during the last three and a half centuries into a 17th century Calvinist's timetable.

I'm a Christian and a Catholic. My faith doesn't demand an interest in science, but it's not threatened by knowledge.

Because I'm a Catholic, I don't have to stop thinking to follow my faith.

Faith, belief in God and trusting the Almighty, comes from the Holy Spirit: but it's something I do, using my will and reason. (Catechism of the Catholic Church, 154-158)

Science, methodical study of this world, is okay. That's because:
"...God cannot deny himself, nor can truth ever contradict truth.... the things of the world and the things of faith derive from the same God...."
(Catechism, 159)

Living With Reality

The argument that orderly change means an orderly God cannot exist has about a 150-year head start, as I said on Google Plus a few days ago. (January 28, 2014)

Someone had mentioned the claim that bombardier beetles couldn't have survived if evolution happened. Being the sort of person I am, my answer started with other weird critters and God.

Short version: bombardier beetles exist. So do platypuses and cephalopods. I'm quite sure that they're all the result of orderly change: and that God made it happen.

That is emphatically not the same as emoting that evolution is the religion of the antichrist. (January 2, 2014)

You've probably already read that I take reality "as is." I do not expect God to conform to what folks in Mesopotamia thought several thousand years back, or to what a Calvinist bishop thought, a few centuries ago.

I think that this universe is not static. Things change. (Catechism, 302)

Because I am Christian and a Catholic, I also believe that God:
  • Exists
  • Created everything
  • Is constantly sustaining everything
  • Uses secondary causes
This is not inconsistent with my belief that God does, on rare occasions, get obviously involved. We call those incidents "miracles." (Catechism, 279-308, Glossary)

Hammers and Architects

I don't see how an immense, ordered creation can show that an infinite, orderly Creator does not exist.

I also do not see how learning about the processes by which this creation continues to exist can threaten a reasoned belief in God.

That would be as silly, I think, as studying how buildings are made and coming up with this conclusion (September 7, 2010):
  • Hammers are involved in the creation of buildings
  • Hammers are not architects
  • Hammers exist
  • Therefore there are no architects
Enough about the big-picture stuff. Now, about beetles - - -

Bombardier Beetles

These remarkable creatures can produce a boiling-hot mix of water and other chemicals in a specialized chamber at their rear end.

It's an effective defense mechanism, and as wildly improbable as the electroreceptors in the bill of a platypus, or the photoreceptors in a cephalopod's eyes.

Although I would not expect to convince a creationist that a bombardier beetle's design came about through the process we call evolution, or a born-again atheist that God sustains existence: this critter isn't as inexplicable as it seems.

Modular Design and the Bombardier Beetle's Butt

Animals in general have mechanisms inside their cells which produce chemicals used in the bombardier beetle's specialized glands. As I've said before, life is remarkably modular at the cellular level.

All insects have some of the bombardier beetle's mechanisms, and some beetles have everything except the bombardier beetle's unique defense mechanism.

We haven't found fossils which show the intermediate steps, yet: but I'm pretty sure that this critter evolved.

Insects, beetles included, have hard shells we call exoskeletons. The critters produce chemicals which, when combined, form a brownish substance that helps harden that exoskeleton. Their bodies also produce foul-smelling substances from the same sort of chemicals, storing them in small sacs below their 'skin.'

Basically, their bodies keep little stink bombs under the skin.

Living cells produce hydrogen peroxide. In the bodies of some beetles, hydrogen peroxide gets mixed with catalysts — producing heat and pressure which forces the stink bomb contents out of the beetle.

Beetles with these stink bombs have muscles that keep the bombs from leaking. In the bombardier beetle, these muscles also work a valve that controls the discharge.

The process that changed stink bombs into the bombardier beetles' pepper spray gun only happened once: far enough back for 500 species of the critters to develop, and spread to every continent except Antarctica. My guess is that eventually we'll find enough fossilized beetle parts to work out when and where it happened.

Interestingly, bombardier beetles are unique: unlike tetrapods with wings. That happened three times that we know of so far: bats, birds and pterosaurs; and that's almost another topic.

1. Neanderthal Heritage

(From Bence Viola, via ScienceDaily, used w/o permission.)
"View of the cave in Siberia where the Neanderthal was found whose DNA was analyzed in the current study."
"Neanderthals' genetic legacy: Humans inherited variants affecting disease risk, infertility, skin and hair characteristics"
Harvard Medical School, ScienceDaily (January 29, 2014)

"Remnants of Neanderthal DNA in modern humans are associated with genes affecting type 2 diabetes, Crohn's disease, lupus, biliary cirrhosis and smoking behavior. They also concentrate in genes that influence skin and hair characteristics. At the same time, Neanderthal DNA is conspicuously low in regions of the X chromosome and testes-specific genes....

"...'Now that we can estimate the probability that a particular genetic variant arose from Neanderthals, we can begin to understand how that inherited DNA affects us,' said David Reich, professor of genetics at HMS and senior author of the paper. 'We may also learn more about what Neanderthals themselves were like.'

"In the past few years, studies by groups including Reich's have revealed that present-day people of non-African ancestry trace an average of about 2 percent of their genomes to Neanderthals...."
Remains of this particular Neanderthal were in a cave, quite a few of us lived in caves in the 'good old days,' and I've opined about "cave men" before. (December 20, 2013)

Maybe I'm a bit sensitive about the "cave man" stereotype because I'm descended from folks who lacked the good sense to stay where humanity didn't have to take shelter in caves, and that's another topic. Topics.

Folks whose ancestors stayed in Africa missed out on the Neanderthal heritage, since Neanderthals stayed in Europe and Eurasia.

Scientists have studied Neanderthal DNA at particular spots on the human genome, but this is the first time that all of our genetic code was searched for Neanderthal ancestry. Reich and the others also started looking at how our Neanderthal heritage affects us.

"Most Exciting:" What's Not There

"...Reich and colleagues -- including Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Germany -- analyzed genetic variants in 846 people of non-African heritage, 176 people from sub-Saharan Africa, and a 50,000-year-old Neanderthal whose high-quality genome sequence the team published in 2013.

"The most powerful information the researchers used to determine whether a gene variant came from a Neanderthal was if the variant appeared in some non-Africans and the Neanderthal but not in the sub-Saharan Africans.

"Using this and other types of information, the team found that some areas of the modern non-African human genome were rich in Neanderthal DNA, which may have been helpful for human survival, while other areas were more like "deserts" with far less Neanderthal ancestry than average.

"The barren areas were the 'most exciting' finding, said first author Sriram Sankararaman of HMS and the Broad Institute. 'It suggests the introduction of some of these Neanderthal mutations was harmful to the ancestors of non-Africans and that these mutations were later removed by the action of natural selection.'..."
(Harvard Medical School, ScienceDaily)
Two parts of today's human genome are particularly lacking in Neanderthal genes: the X chromosome, and parts involved in male fertility. The pattern suggests that many children with Neanderthal and non-Neanderthal parents may have been infertile.

That's really odd, since even the most unrelated groups today have no trouble having healthy children when we get together. Neanderthals were different from today's average human: but not that different, and they hadn't been a distinct group for more than about 500,000 years. That's a very short time, on the evolutionary scale.

Possible fertility issues aside, Neanderthals may have passed along some useful traits.

Neanderthal DNA shows up in genes affecting keratin filaments: fibrous protein that strengthens skin, hair, and nails. That may have come in handy as my ancestors moved into some of Earth's less hospitable climates.

Trying to Quit Smoking? Thank — or Blame — the Neanderthals

"...The researchers also showed that nine previously identified human genetic variants known to be associated with specific traits likely came from Neanderthals. These variants affect diseases related to immune function and also some behaviors, such as the ability to stop smoking. The team expects that more variants will be found to have Neanderthal origins...."
(Harvard Medical School, ScienceDaily)
Human behavior isn't hardwired, but some of us find particular activities easier than most: or harder. For example, folks with particular genes are more likely to get hooked on smoking. (ScienceDaily (March 27, 2013))

I noticed that this Harvard Medical School article was curiously vague about whether Neanderthal genes made it easier for folks to stop smoking: or harder. A hundred years ago I could have assumed that since the Ivy League boys weren't specific, they'd discovered that non-Africans had inherited a weakness from folks who were most sincerely not British.

I'd like to think that folks at Harvard were less tense about that sort of purity. After all, they let an African-American and a Jew graduate in the 1870s. They even allowed Catholic students, and that's yet another topic.

If Neanderthal genes make it harder to stop smoking, we may have another 'why the Neanderthals died out' explanation coming. I doubt that our cousins chain smoked themselves to extinction, but impaired ability to control bad habits could have been lethal in ice age Europe and Eurasia.

2. Event Horizons, Revisited

(From ESO/S. Gillessen/MPE/Marc Schartmann, via, used w/o permission.)
"This fascinating space wallpaper shows a simulation of a gas cloud passing close to the supermassive black hole at the center of the galaxy in mid-2013."
"Black Holes Get Even Weirder with New Stephen Hawking Theory"
Tia Ghose, LiveScience (January 27, 2014)

" Black holes may be even weirder than scientists had thought, according to a new paper by famed astrophysicist Stephen Hawking.

"The paper, which attempts to resolve a paradox between the theories of general relativity and quantum mechanics, was published Jan. 22 in the preprint journal, and has not gone through peer review.

"In the article, Hawking contends that the notion that even light cannot escape a black hole's gravitational pull once it passes a certain point — known as the event horizon — may not be true...."
I don't blame physicists for being a bit dubious about Steven Hawking's latest paper. They finally got used to event horizons and Hawking radiation: and now this. More to the point, Hawking's new paper introduces a new idea that needs to be carefully considered.

Hawking may be right this time, too: or not. Either way, scientists will be discussing this new wrinkle in black hole physics for quite while.

Steven Hawking is a lifetime member of the Pontifical Academy of Sciences, by the way, which doesn't make him a Catholic. As far as I know, his beliefs are still agnostic. I'll get back to that.

The Firewall Paradox

"...Einstein's theory of general relativity predicts the existence of black holes — objects so incredibly massive and dense they pull everything nearby into themselves, and past a point known as the event horizon, not even light cannot escape them. [The Strangest Black Holes in the Universe]

But two years ago, theoretical physicist Joseph Polchinski of the Kavli Institute for Theoretical Physics at the University of California, Santa Barbara and colleagues discovered a wrinkle in the theory, dubbed the Firewall Paradox....
(Tia Ghose, LiveScience)
The next excerpt is long, but please bear with me. How reality works near black holes is one of today's more intriguing puzzles, and this article does a pretty good job of explaining what physicists are trying to learn.
"...The paradox relies on a thought experiment involving an astronaut drifting into a black hole. According to Einstein's theory of general relativity, the astronaut would approach the event horizon and then pass it, blissfully unaware of impending doom. That's because the astronaut would be in free fall, and should therefore feel the laws of physics the same as if he were anywhere else in the universe, Nature News reported....

"...But quantum mechanics ... dictates that black holes are not perfect cosmic vacuum cleaners. In 1974, Hawking theorized that black holes leak particles at their edges — a phenomenon known as Hawking Radiation.

"Given that these particles represent a type of 'information' that can escape the event horizon, Polchinski and colleagues predicted that a fiery, energetic ring should exist just inside the event horizon — at least if quantum theory holds true.

"The firewall would incinerate the astronaut before the dense core compressed the astronaut to a tiny speck....

"...The firewall messes up the notion of smooth, unwrinkled space-time at the event horizon....

"...To resolve the paradox, Hawking's new paper proposes that there is no fixed boundary of an event horizon....

"...Rather than being fixed, these apparent horizons shift wildly with the behavior of quantum particles inside the black hole. Energy and matter trying to escape the black hole's death grip would be stuck for a time, before eventually being released...."
(Tia Ghose, LiveScience)
Polchinski's firewall, if it exists, is a very definite feature in what physicists thought was a smooth, unwrinkled tract of spacetime at the event horizon. Hawking's new paper suggests that an event horizon isn't a fixed boundary, that it shifts back and forth depending on what's happening inside the black hole.

That means that information could escape from a black hole. If the new model of black holes is accurate, we still wouldn't know much about what happens inside. A physicist at the University of Alberta in Edmonton said that it would be like trying to reconstruct a burned book from its ashes.

Belief, Science, and Free Will

Wikipedia's page on Steven Hawking says that he's agnostic, so I assume that he thinks we can't know whether or not God exists. For his sake, I hope he changes his mind, but I don't assume that his agnosticism means I can't believe what he says about physics.

That would be silly. So would claiming than my faith makes me an expert on quantum mechanics: or auto mechanics, for that matter. (August 19, 2010)

It's possible to infer God's existence from the physical world. (Catechism, 282-289) But it's also possible for someone to look at this vast and ancient cosmos and assume that God isn't there.

I've run into folks who can't or won't believe that this creation implies a Creator, and others who can't or won't believe that God works on a colossal scale.

If what we observe made us believe, whether we wanted to or not, we wouldn't have free will. God could have hardwired us to go through the motions of worship and praise, like clockwork toys: but didn't.

As it is, we're free to make up our own minds. Free will makes virtue possible, but it also allows sin: and that's yet again another topic. (May 23, 2012)

3. A Swarthy Swede, Sort of

(CSIC, via BBC News, used w/o permission.)
"The team was surprised by the hunter gatherer's unusual colouring"
"Hunter-gatherer European had blue eyes and dark skin"
Rebecca Morelle, BBC News (January 27, 2014)
"Scientists have shed light on what ancient Europeans looked like.

"Genetic tests reveal that a hunter-gatherer who lived 7,000 years ago had the unusual combination of dark skin and hair and blue eyes.

"It has surprised scientists, who thought that the early inhabitants of Europe were fair.

"The research, led by the Institute of Evolutionary Biology in Barcelona, Spain, is published in the journal Nature.

"The lead author, Dr Carles Lalueza-Fox, said: 'One explanation is that the lighter skin colour evolved much later than was previously assumed.'..."
I think it's too early to say that my ancestors' melanin deficiency is a recent development. This is one individual, who lived in what's now Spain. Folks living in that part of the world today aren't as pale as your stereotype Swede, which may have more to do with events of the last thousand years than this hunter-gatherer's appearance.

"This ... was Unexpected"

(J M Vidal Encina, via BBC News, used w/o permission.)
"The bones of the 7,000-year-old man were discovered in a cave in Spain"
"...Two hunter-gatherer skeletons were discovered in a cave in the mountains of north-west Spain in 2006....

"...Scientists were able to extract DNA from a tooth of one of the ancient men and sequence his genome.

"The team found that the early European was most closely genetically related to people in Sweden and Finland.

"But while his eyes were blue, his genes reveal that his hair was black or brown and his skin was dark.

" 'This was a result that was unexpected,' said Dr Lalueza-Fox...."
(Rebecca Morelle, BBC News)
I've said it before: it's nice when observation confirms what scientists thought; but when new facts don't fit established theories, that's exciting.

Up to now, scientists figured that when folks moved from Africa to Europe, about 45,000 years back, they quickly paled. It made sense: Europe didn't get as much sunlight as Africa, and still doesn't; humans synthesize vitamin D in our skin; and pale skin would let us get by with less light.

It made sense, and may prove to be the best explanation.

But this individual's ancestors had almost certainly been in Europe for roughly 40,000 years, and he had dark skin. Since he's related to today's Swedes, we need to take another look at skin tone, vitamin D, and Europeans.

We can get vitamin D from our skin, or from what we eat. This individual's diet would have been mostly protein, since agriculture hadn't caught on in his part of the world yet. In principle, at least, he could have gotten enough vitamin D that way.

If that's the case, Europeans didn't lose their tan until they started growing crops: adding quite a bit of starch to their diet, at the expense of the nutrients in meat.

We'll know more, as scientists find more DNA from Europe's oldest inhabitants.

4. Scorpions, Venom, and a Repurposed Protein

(From robertpaulyoung via Flickr, Inside Science; used w/o permission.)
"How The Scorpion Got Its Venom"
Joel N. Shurkin, Inside Science News Service (January 24, 2014)

"A single mutation may account for lethal animal's toxin.

"Hundreds of millions of years ago, when the ancestors of land animals crawled out of the seas and flopped on a primordial beach they learned quickly that to survive they were going to have to develop new tools for catching prey. Venom became one of these tools.

"Scientists have found that in most cases all that is required to turn a protein vital for life into a substance that can kill is a mutation in one gene.

"A group of scientists have discovered that is true of scorpions. A team led by Shunyi Zhu of the Institute of Zoology at the Chinese Academy of Sciences found that a common protein used as part of the scorpion's immune system was the origin of the scorpion's venom...."
Zhu and others looked at proteins called defensins. Many plants and animals use defensins to fight bacterial infections. Changing one gene that's involved in making defensins changes the protein into a venom-ready protein.

Venom would have been good for scorpions when they re-emerged from the ocean. It looks like these critters started out on comparatively dry land. Then as now, floods happened, washing some scorpions into the sea.

Living in water would have allowed scorpions to grow larger, for the same reasons that whales are bigger than elephants.

More than you probably want to know about dead scorpions:

Shrinking Scorpions and Evolution

"...Scientists think that scorpions originated on land and were eventually swept into the ocean, evolved during the time they spent there and then reemerged, perhaps 400 million years ago.

" 'I guess the emergence of toxins from defensins is a consequence of adaptation of scorpions to their decreased size that increases difficulty in capturing prey when they emerged from the seas,' Zhu said. They were larger in the water but had to shrink physically over the course of their evolution on dry land, and it became harder to kill and catch some prey. So they developed venom...."
Not that Silurian scorpions decided that they'd start producing venom. Those with venom lived longer and had more little scorpions than those without. That's the idea, anyway.

I see no problem with the idea that change happens; that natural processes happen in an orderly, knowable way: and that God has the patience and power to work on a cosmic scale.

For me, that makes more sense than believing that ancient Mesopotamians knew everything; or that evidence of mountain building and erosion, from the Hadean eon to the Holocene epoch, is a sort of intellectual booby trap.

I might as well try to believe that God looks like the dude on the Sistine Chapel ceiling.

Michelangelo Buonarroti's Creation of Adam fresco, detail
(From Michelangelo Buonarroti, via Wikipedia, used w/o permission)

5. Funnysaurus and the Middle Triassic

(Brian Choo, via, used w/o permission.)
"This is an artist's impression of a shallow reef in the latest Middle Triassic of China. The newly discovered Fuyuansaurus acutirostris was similar to another protorosaur, Tanystropheus longobardicus (long-necked reptile in the center). © Brian Choo, 2013"
"Fuyuansaurus acutirostris: Long-Snouted Protorosaur Discovered in China"
Sergio Prostak, (January 16, 2014)

"Paleontologists from the National Museums Scotland, the Field Museum of Natural History in Chicago and the Institute of Vertebrate Palaeontology and Palaeoanthropology in Beijing, have described a new genus and species of aquatic reptile that lived in the middle Triassic seas (247-235 million years ago) of the eastern Tethys Ocean.

"Protorosaurs were a diverse group of predatory reptiles that flourished from the latest Permian to the early Late Triassic in what are now Asia, Europe and North America.

They were characterized by their long necks and elongated neck vertebrae. The most bizarre of these reptiles was the long-necked Tanystropheus longobardicus, which had a neck up to 3 m
[eters] long.

Unusual among protorosaurs, the newly discovered reptile, Fuyuansaurus acutirostris, had a very elongate snout....
There's nothing particularly funny about "Fuyuansaurus acutirostris" but I keep hearing it as "funnysaurus" in my mind's ear.

Another funny thing: we talk about the "mind's eye," but not the mind's ear or nose; or tongue, now that I think about it: and that's still another topic.

There haven't been living protorosaurs for more than 200,000,000 years. Fuyuansaurus acutirostris' needle-like teeth tell us that the critters probably ate fish or crustaceans, which helps paleontologists fit them into the Triassic food chain.

Related posts:


Brigid said...

POV change: "Animals in general have mechanisms inside our cells which produce"

Number agreement: "that natural process happen in an orderly, knowable way"

Missing end quote: "about the "mind's eye, but not the"

The Friendly Neighborhood Proofreader

P.S. Some agnostics are fairly sure there is a God, but aren't sure which version is the real deal and aren't convinced it's possible to find out.

Brian Gill said...


About POV change: not so much, since humans are animals and people; but it's an awkward sentence, so it's changed.

Number agreement: agreed, changed.

Agnostics? Right. I'm leaving that one alone, since there's only so much I want to get into one post. The "is there a God? What is the nature of God?" set of questions deal in part with the nature of reality, categories of certainty, and metacognition that's - again - more than I want to cram into one post. Or book, if it came to that. ;)

Thanks again.

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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.