Friday, November 22, 2013

Spears, Dogs, and Artificial Organisms

We've depended on "artificial" organisms for millennia. What's new is how we make them.
  1. Synthetic Biology, 21st Century Style
  2. Dogs, DNA, and New Data
  3. Very Old Spears and Slightly Old News

Intelligence and Assumptions

We have increasingly objective intelligence tests, but it's easy to be very subjective about who's smart and who's not. Maybe you've run into this attitude:
  • I am brilliant
  • You work very hard
  • He makes lucky guesses
Ever since we started learning that people didn't always look the way we do now, some folks assumed that people who look like contemporary Europeans are smart, and those who don't - aren't.

As for "cavemen," Africans, and the Irish: regarding them as human at all was a step up.

Our brains have gotten quite a bit bigger over the last million years, and folks living today are probably smarter than our very distant ancestors. If we're not, all that extra space for neural circuitry was a huge waste of time and resources.

I think it's important to remember, though, that the folks who learned to use fire without killing themselves, developed string, and turned sharp sticks into effective hunting tools couldn't have been all that stupid.

If anything, the size of our brains sets the bar higher for how much we can improve today's tech.

Knowledge, Tools, and Decisions

Learning about the world and making tools is part of being human. Over the generations, we learn more, and develop new sorts of tools. It's what we're designed to do.

Whether we use our knowledge and tools to help or hurt other folks depends on decisions each of us make. 'Because I can' doesn't excuse bad behavior. (Catechism of the Catholic Church, 356-358, 373, 2293-2296)

Maize, Fire, and Getting a Grip

Some technology is so old that it seems "natural:" like cooking fires, string, and maize. We may never know who first wove plant or animal fibers into the all-purpose material we call string. It may or may not predate our habit of cooking over an open fire.

More recently, we started modifying organisms. That's "recently" in a paleontological sense.

About 10,000 years ago, someone turned a wild grass, probably something like teosinte, into maize. On the other hand, maybe the wild grass 'just happened' to start growing unusually large kernels.

Since folks in prehistoric Mesoamerica are as human as I am, I vote for maize being an early example of genetic engineering. When folks who share my hereditary melanin deficiency reached Mesoamerica, they thought maize looked useful: and modified it some more. We're still at it, which upsets a few folks and feeds millions.

Getting a Grip About Laban's Sheep

That some folks understand genetics better than others is nothing new.

I'm pretty sure that Laban, son of Nahor, wouldn't have agreed to Jacob's suggested wages if he'd known more about sheep. (Genesis 30:31-34)

Today, most Americans probably don't fear the evil eye, but a remarkable number of us are scared silly of genetically modified organisms. Sure, we're developing some new technology: but people have been using 'synthetic' organisms like chickens and macaroni wheat for a very long time.

I think technology, old or new, can be dangerous: if folks aren't careful. But we've learned how to live with fire, maize, and telephones. I think we'll keep learning.

More of my take on tech:

1. Synthetic Biology, 21st Century Style

(J. Craig Venter Institute, via LiveScience, used w/o permission.)
"Researchers transplanted the genomes of Mycoplasma capricolum bacterium into Mycoplasma mycoides bacterium in 2007. They later accomplished the same trick with a synthetic genome in 2010."
"Incredible Tech: How to Engineer Life in the Lab"
Tanya Lewis, Incredible Technology, LiveScience (November 18, 2013)

"The year was 2003, the place MIT. A handful of engineers, computer scientists and a molecular biologist convened, intent on answering a simple question: What if biology were faster, cheaper and more predictable to engineer?

"The molecular biologist was Pamela Silver, of Harvard Medical School. Along with biological engineers Drew Endy and Randy Rettberg, then at MIT, Silver taught an elective course in which students built cellular circuits using genetic parts, just as one might build a computer chip out of transistors. The approach would form the foundation of the field known as synthetic biology....

"...Thanks largely to increases in speed and reductions in cost, DNA tech can now create standardized genetic parts that can be combined inside simple cells such as bacteria or yeast...."
This article discusses applied genetics more clearly and less flamboyantly than many I've read. It's a refreshing change of pace from the sort of SCIENTISTS CREATE LIFE!!!! headlines of decades past.

However, without minimizing the importance of what folks at the J. Craig Venter Institute and other places are doing: that last paragraph is a trifle misleading.

Yes, we've recently been able to work directly with genetic information encoded inside individual cells. This is a remarkable achievement: and, I think, one that is a basically good idea.

In the movies, a "synthetic organism" might terrorize Tokyo, pollute Portland, or generally make a nuisance of itself until being killed in a confrontation with excessive collateral damage.

In reality, one synthetic organism detects arsenic and releases chemicals that neutralize the toxin. Another, Berkeley's Bactoblood, pinch-hits for blood. I see these functions as threats to 'business as usual,' but I don't have a problem with that.

Electronics Techs have Breadboards; Now Biotechs have Chassis Organisms, Almost

A team of biologists headed by Craig Venter made the first synthetic cell from parts they got from assorted bacteria and yeast. That was about three years ago.

Today, we're closer to having working models of a minimal organism that can serve as a sort of organic breadboard for biotechs, or biological technologists, or BTs, or whatever we'll call the folks. My native language has words that didn't exist when I grew up, which makes it easier for us to talk about tech that used to be 'science fiction.'

I love it, but my fascination with language and ideas is probably stronger than my interest in tech and science. And that's another topic.

The reason we "can now create standardized genetic parts" is that the parts were essentially modular to begin with. The cells in my body use the same basic 'machinery' as cells in dogs, geraniums, and matsutake.

This knowledge doesn't bother me, but even if it did: — God decided to design life that way, and my opinion won't change reality.

2. Dogs, DNA, and New Data

"DNA hint of European origin for dogs"
Jonathan Amos, BBC News (November 14, 2013)

"The results of a DNA study suggest that dogs were domesticated in Europe.

"No-one doubts that 'man's best friend' is an evolutionary off-shoot of the grey wolf, but scientists have long argued over the precise timing and location for their emergence.

"The new research, based on a genetic analysis of ancient and modern dog and wolf samples, points to a European origin at least 18,000 years ago.

"Olaf Thalmann and colleagues report the investigation in Science magazine.

"It adds a further layer of complexity to the story...."
Maybe nobody at BBC News doubts that today's dogs descended from wolves: but the last I heard, some folks were still having conniptions over anything involving evolution; and I suspect that some scientists may still be hedging their bets about wolves, dogs, and origins.

That said, Jonathan Amos does a pretty good job of discussing a complicated topic. My opinion.

Where dogs came from, how old the first ones are, and how they've developed, is very hard to sort out. People and dogs have lived together for since long before written records. When we move we're likely to take our dogs with us. After more than ten thousand years, that's a lot of travel.

Getting back to dogs, finding DNA from one particular sort of dog in local dogs shows that at folks with that sort of dog were there. And, as I said, we move around. A lot.

One more complication: dogs and wolves still get along well enough to produce the occasional litter of wolf-dogs and dog-wolves. I've wondered if calling wolves and dogs two different species really makes sense, and that's yet another topic.

Looking at Dogs

Scientists have been studying dog DNA for several years, and figured that today's dogs all come from wolves that started living with humans. That was about 15,000 or so years back; probably in the Middle East or maybe East Asia.

So far, so good. Folks lived in the Middle East and East Asia 15,000 years back, and they had dogs. Or wolves. Or dogs that looked a lot like wolves, or wolves that acted a lot like dogs - - - seriously, as anyone looked at German Shepherds and gray wolves and not noticed a few similarities?

As Jonathan Amos wrote:
"...The problem with these claims is that palaeontologists have found fossils of distinctly dog-looking animals that are 30,000 years old or more...."
(Jonathan Amos, BBC News)
That's a rather large problem.

Ancient Wolves: 'Gone to the Dogs'

"...Dr Thalmann, from Finland's University of Turku, and his team, have had another go at trying to sort through the conflicting DNA evidence.

"They compared genetic sequences from a wide range of ancient animals - both dogs and wolves - with material taken from living canines - again, from both dogs and wolves.

"This analysis reveals modern dogs to be most closely related to ancient European wolves or dogs - not to any of the wolf groups from outside Europe, nor even to modern European wolves (suggesting the link is with old European wolves that are now extinct). And because the dog remains used in the research are dated to be more than 18,000 years old, it indicates a timing for domestication that is much older than some researchers have previously argued.

"If correct, it means dogs started to diverge from wolf populations when humans had yet to settle into fixed, agricultural communities and were still hunting and gathering...."
(Jonathan Amos, BBC News)
If wolves were people, they might think that the ones we started working with have 'gone to the dogs.' I gather that today's dogs are not as smart as wolves: and, given half a chance, will be slavishly devoted to humans who don't actively abuse them. That's one reason I like cats a bit better, and that's still another topic.

My guess is that we've got a great deal more to learn about our dogs: and everything else in this wonder-filled universe.

Folks with dogs having a longer history, or prehistory, than we thought doesn't surprise me at all. Dogs can be wonderful hunting assistants, so folks who depended on hunting for their food having dogs makes sense.

Folks who don't look British, or American, or whatever, being smart doesn't surprise me, either, and that's part of the next topic.

3. Very Old Spears and Slightly Old News

(PLOS ONE, via, used w/o permission.)
"A sample of Gademotta pointed artifacts exhibiting micro- and macrofracture features indicative of projectile weaponry."
(Yonatan Sahle and others, via PLOS ONE)
"Stone-tipped spears predate existence of humans by 85,000 years"
Jennifer Viegas, Discovery News via (November 14, 2013)

"Remains of the world's oldest known stone-tipped throwing spears, described in a new paper, and so ancient that they actually predate the earliest known fossils for our species by 85,000 years.

"There are a few possible implications, and both are mind-blowing. The first is that our species could be much older than previously thought, which would forever change the existing human family tree.

"The second, and more likely at this point, is that a predecessor species to ours was extremely crafty and clever, making sophisticated tools long before Homo sapiens emerged.

"Homo heidelbergensis, aka Heidelberg Man, lived in Africa, Europe and western Asia from at least 600,000 years ago. He clearly got around, and many think this species was the direct ancestor of Homo sapiens in Africa and Neanderthals in Europe and Asia...."
I'll get back to the recently-published research by Yonatan Sahle and others, which this article should have been focusing on: my opinion. The research is important, and probably significant: but nowhere near as potentially "mind blowing" as this sort of coverage suggests.

For example, we've known that the Schöningen spears are more than a third of a million years old since 1997. That's when radiocarbon dating confirmed their age. Folks made and used them roughly 380,000 to 400,000 ago.

What we've learned so far about our family's history is that 380,000 years back we simply didn't look British. The Neanderthal and current highbrow model probably didn't show up until maybe 200,000 years before we invented writing, pocket watches, and the Internet.

Being Human

Jennifer Viegas defines "our species" as Homo Sapiens. That's accurate enough, although as I said before: I'm not convinced that "species" have sharply-defined limits. Not outside useful lists like the one Linnaeus developed.

If "our species" is limited to folks who look a great deal like people living in some part of the world today, these tools were made by folks who 'weren't human.'

I'll agree that folks who don't look like me can be "crafty and clever," but I'd probably express the idea differently. About a half-century back, when America was getting around to several long-overdue reforms, some of us noticed that 'Americans' often described 'foreigners' in regrettable ways.

For example, the new family in town might include someone who was "sly," not like the "shrewd" American next door.

I'm part Irish, myself, and so am a bit biased about bias. I wouldn't be here if a "smooth-talking" young Irishman hadn't won the heart of a decent American girl, a few generations back.

Now, back to those old spear points.

Spears, Shoulders, and Speculation

(Yonatan Sahle, W. Karl Hutchings, David R. Braun, Judith C. Sealy, Leah E. Morgan, Agazi Negash, Balemwal Atnafu, via PLOS ONE, used w/o permission.)
"A sample of Gademotta pointed artifacts exhibiting micro- and macrofracture features indicative of projectile weaponry."
(Yonatan Sahle and others, via PLOS ONE)
"Earliest Stone-Tipped Projectiles from the Ethiopian Rift Date to >279,000 Years Ago "
Yonatan Sahle, W. Karl Hutchings, David R. Braun, Judith C. Sealy, Leah E. Morgan, Agazi Negash, Balemwal Atnafu, PLOS ONE (November 13, 2013)


"Projectile weapons (i.e. those delivered from a distance) enhanced prehistoric hunting efficiency by enabling higher impact delivery and hunting of a broader range of animals while reducing confrontations with dangerous prey species. Projectiles therefore provided a significant advantage over thrusting spears. Composite projectile technologies are considered indicative of complex behavior and pivotal to the successful spread of Homo sapiens. Direct evidence for such projectiles is thus far unknown from >80,000 years ago. Data from velocity-dependent microfracture features, diagnostic damage patterns, and artifact shape reported here indicate that pointed stone artifacts from Ethiopia were used as projectile weapons (in the form of hafted javelin tips) as early as >279,000 years ago. In combination with the existing archaeological, fossil and genetic evidence, these data isolate eastern Africa as a source of modern cultures and biology...."
I don't recommend this article, unless you enjoy long paragraphs and technical text. I'm not sure why academics write that way.

Until we started relying on the agricultural technology, about a dozen millennia back, folks ate what they caught or gathered. Harvesting the edible parts of plants is easier with tools, but using our hands and teeth works, too. Hunting without tools is possible: but our built-in equipment isn't designed for that.

That's probably why we invented spears. These more-or-less sophisticated pointed sticks can be thrown, or pushed into a target. When you're hunting for the day's meat, you're more likely to come back with enough if you don't have to run up to critters with a spear.

We're faster than critters like sloths and banana slugs, but even someone who is "swift as a deer" - isn't: and I'm drifting off-topic. Again. The point is that throwing a spear doesn't require a hunter to run down the day's meat: or sneak right up to it. We don't move as quietly as cats: more topics.

For a while, scientists assumed that spears designed and used for throwing were developed by humans: Homo Sapiens. Being able to throw a spear takes shoulders pretty close to the current model: but the design for that part of our chassis is about 2,000,000 years old. The neural circuits needed for throwing accurately may be even older, but proving that might be difficult. (July 5, 2013)

Tools, Africa, and a Changing Universe

There will be discussion of what Yonatan Sahle and others found, and the conclusions they published: probably quite a bit. My guess is that we'll keep learning that tools were developed earlier than previous research suggested.

Happily, paleontologists and anthropologists seem to have gotten over the notion that folks who aren't European aren't very smart: and that folks from Africa are "degenerate and feeble-minded."

I won't argue that folks have always been pretty much just like we are today. We've tracked some changes in the last few centuries. All the evidence we've found says that we've changed quite a bit in the last few dozen millennia: and even more since our earliest generations.

I'm okay with that. This is a changing universe, and it'd be odd if we didn't change, too.

I've got more to say about dealing with:

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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.