Showing posts with label genetics. Show all posts
Showing posts with label genetics. Show all posts

Friday, April 1, 2016

Synthetic Life, DNA Profiles

Syn 3.0, developed by the Venter Institute, has fewer genes than any 'wild' bacteria. The 'artificial' microcritter is another important step in understanding how life works.

On the other side of the Atlantic, folks in the United Kingdom will be deciding what to do about a bureaucratic SNAFU and their national DNA database.
  1. New (Semi-) Synthetic Bacterium
  2. Oops: UK DNA Database Deletion

Ethics Matter


We're a long way from Čapek's fictional factory mass-producing synthetic people.

I've talked about robots, real and imagined, Rotwang's ersatz girlfriend in "Metropolis" — that chap had issues — and I'm getting off-topic. (May 22, 2015; August 15, 2014)

Or maybe not so much.

I've seen attitudes toward science and technology shift from silly optimism to equally-silly pessimism.

I am reasonably certainly that mutant safflowers won't destroy civilization. On the other hand, ethics matter as much now as they ever did.

Deciding to Act Like Humans



(From Carolyn A. McKeone/Science Photo Library, via BBC News, used w/o permission.)

Studying this universe, bacteria included, and using what we learn, is part of our job. Ethics apply, as they do with everything we do. (Catechism of the Catholic Church, 2292-2296, 2402-2405, 2456)

The world's resources are meant for our reasoned use, but our "dominion" is not absolute. Inflicting needless suffering on critters is a bad idea and we shouldn't do it: and we certainly should take our neighbor's needs into account. (Catechism, 2415-2418)

I don't see a problem with editing a bacterium's genes: although I suppose someone, somewhere, worries about 'bacteria rights.' I've discussed synthetic organisms, like cows and chickens; Laban's sheep; and Romans 11:19-24, before:
An easy way to approach new ideas is to assume that they're good because they're new: or bad for the same reason. "Easy" isn't necessarily "right," we've got brains and should use them, and I've been over that before, too: a lot. (March 13, 2016; August 30, 2015)

Basically, humans are animals "...endowed with reason, capable of understanding and discernment...." (Catechism, 1951)

But we're not just animals. We're made in the image of God, with free will. We can think about our behavior, and decide what we do: or don't do. (Genesis 1:26-27: Catechism, 1700-1706, 1730)

Or we can decide that thinking's too much work, and follow whatever impulse pops into our head. My experience has been that I'm better off if I think before I act. (Catechism, 1730, 1778, 1804, 2339)

And now, Syn 3.0: the latest thing in genetically edited critters.

1. New (Semi-) Synthetic Bacterium



(From AAAS/SCIENCE, via BBC News, used w/o permission.)
("The set of essential genes is specific to Syn 3.0; other bacteria, living under different conditions, will posses their own must-have minimal " genetic software' "
(BBC News))
"Synthetic bug given 'fewest genes' "
Jonathan Amos, BBC News (March 25, 2016)

"Scientists have taken another step in their quest to understand the bare genetic essentials of life.

"A team led by US research entrepreneur Craig Venter has created a semi-synthetic, functioning bacterium in the lab that has fewer than 500 genes.

"This minimal number is lower than in any known free-living bug in nature.

"The group says its investigations aim to push the boundaries of fundamental knowledge and could lead to novel means to make new drugs and other chemicals.

" 'Our long-term vision has been to design and build synthetic organisms on demand where you can add in specific functions and predict what the outcome is going to be,' said Daniel Gibson, who is a co-author on a paper describing the latest work in Science Magazine...."
I wrote about Venter's project a few years back. I still think research at the J. Craig Venter Institute is a basically good idea. (November 22, 2013)

That's not how everybody sees it, though.

As a Wikipedia page said, "the main controversy from the project is the undue amount of publicity it received from the press due to Venter's showmanship...." I don't see that as a problem: but I worked in marketing for two decades, and that's another topic.

Sound, Fury, and Mutant Squirrels


There's a juicy conspiracy theory or three lurking in details of the J. Craig Venter Institute's research.

I enjoy conspiracy theories: in fiction.

Which reminds me: my warning that mutant squirrels and corrupt pet store owners are plotting against humanity is a joke. I made it up. We need not fear being enslaved in the squirrels' nougat mines. (November 23, 2014)

Back to the Venter Institute.

This genetic engineering research project started with Mycoplasma genitalium, a parasitic bacteria identified in the early 1980s.

The good news is that the 'wild' variety can be killed with antibiotics. The bad news is that anyone infected with M. genitalium will need antibiotics: badly.

The bug may or may not be transmitted through sexual intercourse — which means that rational discussion of treatment quite likely will get drowned out by emotion-drenched rants. Me? I prefer rational discourse to sound and fury. (May 1, 2015; July 6, 2014)

Where was I? Genetic research, conspiracy theories, antibiotics, sound and fury. Right.

This "synthetic" bacterium, Syn 3.0, is what scientists got after editing out "unnecessary" genes from M. genitalium. And no, I do not think the J. Craig Venter Institute is plotting with [bogeyman] to enslave ['good guys']: although that might make a nifty tale.

Researchers edited Syn 3.0 — much easier to say than Mycoplasma laboratorium, it's 'scientific' moniker — down to 473 "necessary" genes. They know what 324 do: the remaining 149 probably do something, but the scientists don't know what: yet. They're running experiments to find out.

Biotech 'Chassis?'


What's "necessary" and what's not varies. As Jonathan Amos points out:
"...Context is everything. Other microbes will live in different types of environment, with different ways of operating.

"A bug that powers itself via sunlight and photosynthesis will not have the same essential set of genes, for example, as an organism that processes methane to derive its chemical energy...."
(Jonathan Amos, BBC News)
Another point: we've been learning that some genetic code is redundant. That's a good thing, since we need most biochemical functions. If something goes wrong with the coding on one part of the genome, it's better if the broken code's function has a backup elsewhere.

It's sort of like a four-engine airplane, as Dr. Venter said: if one engine on the right side goes out, the plane can still fly. If both starboard engines fail: the pilot will be looking for someplace where "a survivable crash landing" is an option. (FAA)

So: why do I think this 'tampering with things man was not supposed to know' is a good idea?

For starters, we're learning more about how life works by tweaking this bacterium's code. We've also been learning how much we don't know about genetics, and started learning how to make life better with what we do know. And like I said, ethics apply. (January 23, 2015)

A synthetic 'life lite' organism could serve as a chassis for biotech microcritters producing pharmaceuticals, biochemicals, and other substances. Whether it'll be safer and more economical than tweaking 'wild' organisms is something we'll be learning.

I put a short resource link list near the end of this post.1

2. Oops: UK DNA Database Deletion



(From Science Photo Library, via BBC News, used w/o permission.)
"Wiping of DNA and fingerprint records 'puts public safety at risk' "
BBC News (March 11, 2016)

"Hundreds of DNA and fingerprint records that could have been held for national security reasons in England and Wales have been deleted, a report reveals.

"Biometrics Commissioner Alastair MacGregor said police were 'risking public safety' by failing to apply for extensions to hold DNA profiles of suspects who have not been convicted.

"He also said some records which were still stored should have been removed.

"The Home Office said the system worked well 'in the vast majority of cases'...."
My fingerprints are on file somewhere, and for all I know my driver's license photo is in a database.

That doesn't upset me, partly because I'm not engaged in criminal enterprises: partly because I try to limit my angst to things that matter, or can control to some extent.

As Job 5:7 says, "man himself begets mischief, as sparks fly upward" — so I'm quite sure that corrupt officials could misuse fingerprint data, or pretty much anything else. So could I, for that matter, and that's another topic.

Or maybe not so much.

I keep saying this. Technology isn't bad, by itself. Neither is science. Both are tools which we can use to help, or hurt, our neighbors. How we use them is up to us. (August 29, 2014)

Studying this wonder-filled creation and using what we learn to make new tools is part of being human. There's more is to life, and that's yet another topic. (Catechism, 1723, 2292-2296)

Fingerprints, DNA Profiles: From Hammurabi to Scotland Yard



(From PA, Science Photo Library; via BBC News; used w/o permission.)
"...A new system limiting DNA record storage was introduced in October 2013.

"Previously, DNA profiles and fingerprints could be stored indefinitely, regardless of whether someone had been charged or convicted.

"The anomalies were revealed in the commissioner's second annual report since the new rules were introduced...."
(BBC News)
The United Kingdom's rules about DNA evidence are an example of positive law: rules we make up that define how folks may act, and what rights we have.

When positive law isn't too far from natural law, unchanging ethical principles, societies work smoothly. When positive law isn't, it's time to change the rules. (August 31, 2014; August 29, 2014)

That's been happening quite a bit lately. I was among the Americans who thought we could do better, a half-century back, and that's almost another topic:
Folks in Babylon used fingerprints as an anti-counterfeiting measure on clay tablets, some three millennia back. Law officials in Hammurabi's day took fingerprints of folks who had been arrested.

More recently, collecting fingerprint evidence was police procedure during the Qin Dynasty — not to be confused with the Qing dynasty. I've mentioned the latter's meltdown, about a century back now, before. Not in any detail, though. (July 3, 2015; March 6, 2015)

It took the current iteration of Western civilization quite a while to rediscover fingerprinting as a useful identification technique.

Jan Evangelista Purkyně's 1823 publication may have encouraged Robert Blake Overton to write Scotland Yard in 1840. A mess of unsolved crimes later, Juan Vucetich developed a system for collecting and cataloging individual fingerprints, using Alphonse Bertillon's research. (Wikipedia)

That was in the late 19th century. Many folks have gotten used to using fingerprint identification, although some probably associate fingerprints with crime.

And that brings me back to DNA as a forensic tool. Here's what the BBC News article says about the UK's DNA database:
  • Police take a DNA sample from every individual they arrest, and since 1995 profiles have been added to an electronic database
  • Two types of DNA profile - a string of numbers and two letters (indicating gender) - are held; individuals and crime scenes
  • An individual sample is taken through a cheek swab and contains the entirety of a person's genetic information
  • The profile contains very limited information - but it is sufficient to identify a person, for example from samples taken at a crime scene
  • The database held 5.7m DNA profiles from individuals and 486,691 from crime scenes, as of 31 March 2015
  • The Home Office, which operates and maintains the database, says in 2014/15, it provided 30,330 matches, including to 438 offences of homicide and 635 rapes
  • Since 1998 more than 300,000 crimes have been detected with its help, it says
    (From Biometrics Commissioner's annual report, 2015, Home Office, National DNA database annual report; via BBC News)
Particularly since DNA identification is a new technology, I'm quite certain that rules about its use will be changing fairly often.

Using Knowledge Wisely and Well



(From Science Photo Library, via BBC News, used w/o permission.)
"...The report also revealed that DNA profiles and fingerprints of 7,800 people were held on a separate police counter-terrorism database as of October last year.

"The database holds biometric records of those convicted in relation to terror investigations and others who have not been convicted but where retention is deemed necessary for national security purposes.

"It also allows for the extended retention of material taken from an individual who has not been convicted when a senior officer makes a national security determination (NSD).

"Of the 7,800 individuals, 4,350 - or around 55% - had never been convicted of a recordable offence...."
(BBC News)
I am quite sure that DNA databases can be abused: like any other technology.

Tech isn't the problem. How we use it can be. I do not think we should stop collecting genetic information, outlaw fingerprint identification, or ban all tech invented since 1804, 1769, 2800 BC, or some other arbitrary date.

I think that any tech, new or old, is dangerous if we don't use the brains God gave us. As I've said before, we've used fire almost as long as we've made stone tools: and folks mishandle it on occasion. (January 29, 2016)

I think that eventually collecting DNA samples will be as routine — probably filed as part of whatever we'll be calling birth certificates — and as unremarkable as today's neonatal heel prick.

Infants in my part of the world get their footprints taken — after the heel prick, oddly enough, so there's a little blood spot on our kids' prints — before they leave the delivery room.

Footprinting goes back at least to 1928,2 when a New York hospital footprinted/fingerprinted babies and mothers at birth: apparently to reassure nervous parents as much as any other reason.

I see no problem with establishing someone's identity at birth, or before: provided that the information isn't misused.

Early genetic screening could save lives, or get used to 'purify' the gene pool.

The former seems like a good idea. The latter — I can hardly be enthusiastic about efforts to prevent people like me, and that's yet again another topic. Topics. (February 13, 2015; January 23, 2015)

'It Seemed Like a Good Idea at the Time'


Another idea that almost looks good at first glance is using genetic data to spot "criminals" before a crime is committed.

There's a bit of science behind that notion. Some traits, like low frontal lobe activity, may be more common among folks with particular genes. Trouble in the frontal lobe can be associated with emotional and behavioral problems.

Let's say that's all true — and the last I heard, having 'bad' genes only means that a person is more likely to have problems.

I think locking up or euthanizing everyone with 'bad' genes might keep a few folks from committing their first crime. I also think I'd probably be behind bars or dead: neither of which are attractive options.

Since I act quite a bit like my father, and two of my kids act a lot like me, I'm pretty sure that there's a genetic component to my neurological glitches. My version's been called a few different things. The current label is autism spectrum disorder.

That, and depression, were diagnosed a few years back. I'll be taking powerful antidepressants and other prescribed pharmaceuticals for the rest of my life: but I'm okay with that, since I can now think without 'fighting the machinery.'

Like I keep saying, I'm expected to keep myself healthy: within reason. (Catechism, 2288-2289)

A few relatively-minor traffic offenses aside, I don't have a criminal record: partly because I'm sharp enough to realize that crime doesn't pay — enough.

I try to do what is right because I think ethics matter: but let's face it, the benefit/risk ratio for criminal activity is unacceptable; at the low end, anyway. Even more topics.

I put another link list of resources at the end of this post, focusing on genetics and bioethics.3

And, inevitably, here's more of why I think science and technology don't solve — or cause — all our problems:
1More about:
2 Going home with your baby:
3 Genetics, medicine, law, and society:
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Friday, January 22, 2016

DNA, Headless Skeletons of York

We've been learning quite a bit about humanity's family history recently: thanks partly to our increasingly-detailed knowledge of DNA and the human genome.

I'll be taking a look at what scientists are learning about Roman Britain, Anglo-Saxons, and headless skeletons.
  1. English: Anglo-Saxon, and a Whole Lot More
  2. Immigrants in Roman Times
I'll also indulge in an uncharacteristically-terse (for me) explanation of what science is doing in a 'religious' blog.

Using Our Brains: Or Not


I think the universe is billions, not thousands, of years old; Earth isn't flat; Adam and Eve weren't German; poetry isn't science; and thinking is not a sin.

That's because I'm a Catholic.

I think the universe follows knowable rules: which means we can learn how it works — and THIS IS OKAY. We're supposed to study this universe, and use what we learn. (Catechism of the Catholic Church, 32; 339, 2292, 2295)

Scientific discoveries invite us "to even greater admiration for the greatness of the Creator."(Catechism, 283)

I've got free will, so I could decide that I'd rather ignore this wonder-filled creation: or indulge in whatever whims grabbed me. I'm better off if I think about what I do, though, and that's another topic. (Catechism, 1730-1738, 1762-1770)

The folks whose bones were disinterred for this research have been dead for a millennium or two, but the bones are still human remains. I hope what's left of their bodies were "treated with respect and charity." (Catechism, 2300-2301)

I'm not worried about 'Revenge of the Mummy Returns' spooks wreaking hideous vengeance on the Godless scientists. That might make a nifty movie ‐ it has, actually, quite often. And that's yet another topic.

I had a point, lurking somewhere in that verbiage. Got it! Superstition is a bad idea, and against the rules. (Catechism, 2110-2111, 2138)

Respect for the dead doesn't mean that autopsies are wrong. (Catechism, 2301)

I've nattered on about the faith, science, autopsies, and Mr. Squibbs, before. A lot. (August 28, 2015; January 9, 2015; August 15, 2014)

1. English: Anglo-Saxon, and a Whole Lot More



(From Duncan Sayer, via BBC News, used w/o permission.)
("This triple burial from Oakington, Cambridgeshire, includes metal and amber grave goods"
(BBC News))
"English DNA 'one-third' Anglo-Saxon"
Paul Rincon, BBC News (January 19, 2016)

"The present-day English owe about a third of their ancestry to the Anglo-Saxons, according to a new study.

"Scientists sequenced genomes from 10 skeletons unearthed in eastern England and dating from the Iron Age through to the Anglo-Saxon period.

"Many of the Anglo-Saxon samples appeared closer to modern Dutch and Danish people than the Iron Age Britons did...."
Anglo-Saxons almost certainly didn't call themselves Anglo-Saxons, or didn't until recently.

They spoke Old English for the most part, "Angul-Seaxan" is Old English for Latin "Angli-Saxones," the Venerable Bede called at least some of them Anglorum, and Gildas called them Saxones. They're folks who lived along the western European coast when the Roman Empire broke up.

We're still sorting out exactly what happened. Detailed records from that era of Western history are, understandably, a tad spotty. Apparently British rulers like Vortigern may or may not have invited Germanic troops as reinforcements in conflicts with Picts and Scots.

Either way, the Germanic warriors decided that eastern England looked better than where they'd been living — brought their families over, and were 'allowed' to stay.

Centuries later, Charles the Simple of West Francia struck a similar deal with Göngu Hrólfr.

Folks speaking my language call him Rollo these days: Göngu Hrólfr, I mean. It's what happened when Hrólfr got Latinized, and then spoken by folks speaking post-Elizabethan English. Hrólfr is still a not-uncommon name, but it's spelled and pronounced Rolf now.

Where was I? Anglorum and Saxones, the Venerable Bede, Gildas, Vortigern. Right.

'Anglo Saxons' started moving to England something like 15 centuries back now.

Assorted Germanic folks kept coming, and then from 1016 to 1066 another bunch invaded England: the Danes and Normans. Normans are still running the place, and I've said that before. (December 11, 2015)

Folks from various spots in northwestern Europe aren't nearly as different from each other as some of us imagine.

These scientists focused on a few rare mutations that show up about twice as often in the old Celtic-British population as they do in these upstart Angli-Saxones.

And I am not going to get started on the Verden incident and what happened after folks on part of my family tree started invading folks on another part. (August 9, 2015)

More:

2. Immigrants in Roman Times



(From York Archaeological Trust, via National Geographic, used w/o permission.)
("Geneticists sampled the dense inner-ear bone to extract ancient DNA from the skulls of several Roman-age skeletons discovered at Driffield Terrace in York"
(National Geographic))
"DNA Reveals Far-Off Origins of Ancient 'Gladiators' "
DNA testing is telling scientists more about the origins of a group of headless Romans.
Andrew Curry, National Geographic (January 19, 2016)

"People in the Roman Empire really got around.

"Evidence from a Roman-era cemetery in York, England shows that the city—once a major outpost on Rome’s distant frontier—was home to both locals and to immigrants from thousands of miles away.

"In a paper published Tuesday in the journal Nature Communications, Trinity College Dublin geneticist Dan Bradley and his colleagues analyze DNA preserved in the dense inner ear bones of seven skulls found in the cemetery. They report that six of the skeletons have DNA matching people living in modern-day Wales. But to researchers' surprise, one of the men came from a long way away—the other end of the Roman Empire, in fact.

" 'The nearest genetic matches were from Palestine or Saudi Arabia,' Bradley says. 'He definitely didn't come from Europe.'..."
The University of Reading's Gundula Müldner analyzed chemical signatures in the subject's teeth — discovering that he was from somewhere "arid and hot," as she told National Geographic. She says the best fit is the Nile Valley, or a very similar environment: certainly somewhere in the Near East.

This isn't the first time someone from elsewhere in the Empire ended up in where England is now. A woman from Africa, wearing an ivory bracelet, was buried in York during the Roman occupation.

Ebocarum, Jórvík, York, and Headless Skeletons



(From York Archaeological Trust, via National Geographic, used w/o permission.)

The decapitated skeletons are from a cemetery on the outskirts of Eboracum, a provincial capital which became Jórvík, ruled by folks with names like Halfdan Ragnarsson, Guthred, and Ragnall ua Ímair. The locals call it York these days.

Two Roman emperors died there while it was still called Eboracum: Septimius Severus and Constantius Chlorus

The fellows headlined by National Geographic weren't emperors.

The odds are pretty good that they were soldiers or gladiators. They were all above average height, more muscular than usual, and under age 45 when they died. Many showed signs of healed injuries, including one who had been bitten by something along the lines of a lion or bear.

They weren't all from the Near East. Earlier analysis of bones and teeth showed that some grew up in colder climates: maybe where Germany and Poland are now. Some of them had eaten millet as children: a grain we think wasn't available in Britain at the time.

This research is a big deal, since it helps us understand how folks who weren't emperors or senators lived during Roman times. One thing we've learned is that folks moved around: a lot, in some cases.

More:
stuff:
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Friday, November 27, 2015

Mutant Medflies, GMO Mosquitoes

First, the good news: releasing genetically-modified medflies and mosquitoes may mean fewer crop failures; and fewer deaths from malaria.

Now, the not-so-good news: I'm pretty sure some folks won't think it's good news.
  1. Mutant Medflies
  2. Malaria-Resistant Mosquitoes

Learning — Sometimes the Hard Way


I suspect that Hubris, self-confidence above and beyond the call of reason, helps account for the occasional real-life analogs to fictional "mad scientists." (December 12, 2014)

As I've said before, often, I think folks whose attitude toward science resembles the ardent Mr. Squibbs — the bald chap in that cartoon — are sincere. I'm also quite sure they're wrong. (December 12, 2014; October 31, 2014)

I do not think the lesson of Auschwitz, Dachau, Tuskegee, and Willowbrook is that science is Satanic. It's that ethics apply to science, just like anything else we do. (Catechism of the Catholic Church, 2292-2295, 2415-2418)

We've been learning — sometimes the hard way — how to be careful with new science and technology.

In 1753, for example, Georg Wilhelm Richmann decided to see how an insulated rod interacts with a thunderstorm. Scientists still experiment with lightning: but from a safe distance, or inside something like a Faraday cage.

Radium, Thalidomide, and Using our Brains


In 1900, Otto Walkhoff learned why carrying a tube of radium in one's pocket is a bad idea. That led to effective radiation treatments: and, from 1913 to 1935, freewheeling research and quackery.

Meanwhile, folks were painting glow-in-the-dark watch faces: some 4,000 in the U.S. and Canada. The most famous — or infamous — case was when women working at a United States Radium Corporation factory had been told the radium paint was harmless.

The owners and scientists at U.S. Radium obviously knew the hazards of working with radium. Nearly a century later, America has different problems, and that's another topic. Topics.

Starting in the mid-1950s, thalidomide was sold as a "wonder drug" for insomnia, coughs, colds and headaches. About 2,000 dead children later, scientists were starting to do the sort of research that's now part of testing before new drugs are sold.

The lesson from these experiences isn't that science and new technology are bad. Learning about the universe, and using that knowledge to develop new technology, is part of being human. It's what we're supposed to do.

God gave us brains. Using them sensibly is up to us. (Wisdom 7:17; Catechism, 154-159, 307, 1730, 2292-2295, 2415-2418)

Famines, Sumerians, and Making Sense


I remember the first Earth Day, back in 1970. Four decades and many fizzled doomsday predictions later, I still think environmental awareness makes sense — within reason. (July 5, 2015; June 15, 2014)

But I think remembering why we developed new technologies also makes sense.

Famine is a problem in some areas — not, I think, because we lack the technology to grow enough food for everyone; but because we don't get resources to folks who need them. Correcting this injustice is one of many unfinished tasks. (August 9, 2015; July 5, 2015; May 3, 2015)

One reason folks in Western civilization produce so much food is that we've developed and used increasingly effective pesticides.

Traditional pesticides like arsenic, mercury, and lead were being replaced by nicotine sulfate from tobacco leaves in the 17th century. In the 19th century we added pyrethrum from chrysanthemums, and rotenone from the roots of tropical vegetables; and more exotic compounds in the 20th.

We also learned why we need to be careful about what we dump into an ecosystem.

My guess is that we've used pesticides of some sort ever since someone started growing crops.

The first written record of pesticide use we've found so far is from Sumer, about 4,500 years ago. Documentation of any sort is a bit spotty that far back. The earliest cuneiform we know of is from sites like Jemdet Nasr, our name for a place near Kish, and that's yet another topic.

Sumerians dusted crops with sulfur, and some folks still do. Sulfur is a "green" pesticide, in the sense that it's an element with a long history: but so is arsenic. Neither is particularly good for humans: which is why it's a good pesticide.

The whole point of pest control is to keep other living critters from eating or spoiling food we're planning to eat. I don't see a problem with that, and I'll get back to the ethics of being human.

The Rig Veda, written a few centuries after the earliest Sumerian documents, mentions biopesticide: a new word for an old idea, controlling pests with plants or animals that prey on, or are poisonous for, the pests.

More:
The last I heard, we still aren't sure exactly what biopesticide the Rig Veda mentioned. It might be a fungus: or something else. Whatever it was, a big problem with traditional biological pest controls is the scale of today's food needs.

We could, in principle, use agricultural tech from the 'good old days:' put up with the occasional famines; and either kill off the billions of 'extra' folks, or let them die of starvation.

That's not acceptable, on ethical1 grounds: and I'm pretty sure that the 'extra' people would object. Strenuously.

1. Mutant Medflies



(From Oxitec, via BBC News, used w/o permission.)
"Australia trial for GM fruit fly"
Paul Rincon, BBC News (November 24, 2015)

"Australia will carry out trials of a genetically modified insect to see if it can control a destructive crop pest.

"The engineered Mediterranean fruit flies possess a gene that prevents female flies from reaching adulthood.

"When released into the environment, they mate with wild members of the same species and pass on the gene to their offspring, which die before they can cause damage to crops.

"The flies have been produced by the British-based company Oxitec...."
I remember the 1981 'medfly crisis' in California. Being 'environmentally conscious' was a big deal then, too, so the California governor okayed ground-level malathion spraying. That didn't work. Medflies breed and move faster than spray crews could work.

Then helicopters sprayed nine counties with malathion: which didn't work, either.

After losing crops worth millions of dollars, with crops worth billions threatened, fleets of helicopters started nighttime spraying: and the California governor drank a glass of malathion to show it doesn't hurt humans.

Meanwhile, entomologists released sterile male medflies. Millions of them. That may have been what finally stopped the 1981 medfly outbreak.

Malathion: For External Use Only


Malathion is an organophosphate parasympathomimetic, which means that it's an ester of phosphoric acid that affect the parasympathomimetic nervous system: part of the autonomic nervous system.

That's the part of a critter's nervous system that handles involuntary functions: those critters that have nervous systems, that is.

Humans are opportunistic omnivores and large as animals go:2 so the California governor probably didn't suffer terribly serious ill effects from drinking malathion.

We're not as spectacularly unkillable as some critters, but I strongly suspect that we'll prove as durable as rats, cockroaches, and scorpions.3

That said, I wouldn't willingly drink malathion. It's not particularly toxic to humans, but our bodies metabolize it into malaoxon, which in a large enough dose gives us headaches, nausea, and several other unpleasant sensations.

A big enough dose of malathion will kill us. So would a whole lot of small doses, if we kept drinking the stuff: but that doesn't happen often. Folks can be daft, but we're generally not that daft.

Medfly Origins and Gene Splicing


Adult Mediterranean fruit flies, Ceratitis capitata, are about two-thirds the size of a housefly: 4 to 5 five millimeters, 1/6 to 1/5 inch, long. (Global Invasive Species Database)

Depending on where you read it, these critters started out in the Mediterranean area or Sub-Saharan Africa: which isn't quite the same place. Either way, they're one of the reasons countries have rules about importing and inspecting fruit.

Insecticides have come a long way since folks started using Flit, back in the 1920s. So has our understanding of why we have to be very careful about how we use them.

The big problem with pesticides is what I keep saying about life on Earth: our molecular machinery is highly modular. For example: Drosophilidae, a family of flies; zebrafish; and humans; all use the PAX6 gene to grow retinas. (March 6, 2015)

The good news is that we can patch code from bacteria into tobacco plants and potatoes: letting the plants produce their own pesticides. (February 6, 2015; January 9, 2015; December 26, 2014)

The not-so-good news is that chemicals that will kill insects aren't particularly good for us, either. That's why I think modifying medfly genes may be a good idea. I also think it's likely that some folks will see that the critters are "genetically modified," and jump on the nearest 'down with GMOs' bandwagon.
"...Oxitec male flies are released to mate with wild female flies. When they do, they pass on a 'self-limiting' gene which prevents female offspring from reaching adulthood.

"This prevents the females from stinging fruit crops, or reproducing, thus shrinking populations of the fly in the release area...."
(Paul Rincon, BBC News)
On the other hand, I'm quite certain that gene splicing isn't "safe," in the sense that bad things won't happen if we don't use our brains. Even some of our most basic tech, like fire, still gets troublesome on occasion. (December 5, 2014)

2. Malaria-Resistant Mosquitoes



(From Jim Gathany/CDC, via Reuters, used w/o permission.)
("An Anopheles stephensi mosquito obtains a blood meal from a human host through its pointed proboscis...."
(Reuters))
"Scientists create mosquito strain with malaria-blocking genes"
Will Dunham, Reuters (November 23, 2015)

"Scientists aiming to take the bite out of malaria have produced a strain of mosquitoes carrying genes that block its transmission, with the idea that they could breed with other members of their species in the wild and produce offspring that cannot spread the disease.

"The researchers said on Monday they used gene-editing, a genetic engineering technique in which DNA can be inserted, replaced or deleted from a genome, on a species called Anopheles stephensi that spreads malaria in urban India.

"They inserted DNA into the germ line, cells that pass on genes from generation to generation, of the species, creating mosquitoes with genes that prevent malaria transmission by producing malaria-blocking antibodies that are passed on to 99.5 percent of offspring...."
Malaria isn't always fatal, but it's a serious disease: affecting the lungs, brain, liver, and other major systems.

We get malaria when one of the four or five species of Plasmodium that cause malaria in humans gets past our body's outer defenses. Artemisinin-resistant malaria microbes showed up in southeast Asia. I talked about that in January. (January 23, 2015)

Scientists will probably find replacements for artemisinin: but malaria treatments wouldn't be needed if mosquitoes didn't carry the critters to new hosts. That's the goal of this research: malaria-resistant mosquitoes.

That makes more sense than it might seem. If malaria microbes can't survive in mosquitoes, mosquitoes can't carry the microbes to new hosts: and fewer folks get sick.

University of California-San Diego's Valentino Gantz said that genetically modified mosquitoes, released to mate with wild skeeters, would pass their tweaked genes on to the next generation.
"...'It can spread through a population with great efficiency, increasing from 1 percent to more than 99 percent in 10 generations, or about one season for mosquitoes,' University of California-San Diego biologist Valentino Gantz said...."
(Will Dunham, Reuters)
I put links to more resources about malaria and mosquitoes at the end of this post.4

Fear, Ethics, and Getting a Grip


Is ending the mosquito's role in spreading malaria ethical? Taking a broader view, should we be trying to cure disease at all?

Edmund Massey's views on disease, fear, and God, are among the reasons I am profoundly glad that the 'good old days' are behind us. (January 23, 2015)
"...The fear of disease is a happy restraint to men. If men were more healthy, 'tis a great chance they would be less righteous. Let the Atheist and the Scoffer inoculate. Their hope is in and for only this life. Let us bless God for the Afflictions He sends upon us, and grant us patience under them...."
("Against the Dangerous and Sinful Practice of Inoculation," Edmund Massey (1722))
In sharp contrast, there's Pope Pius VII's 1814 statement that vaccination is "a precious discovery which ought to be a new motive for human gratitude to Omnipotence." (February 12, 2014)

I'm a Catholic, so I think life and health are "precious gifts." Keeping ourselves healthy is, within reason, a good idea. So is healing folks who are ill, and caring for folks who are dying. (Catechism, 2278-2279, 2288-2289)

I also think that humans are animals: but we're not just animals. We're made "in the divine image:" with dominion over this world. (Genesis 1:27)

Our dominion isn't ownership. We're stewards, responsible for the creatures and resources of this world: for our reasoned use, and for future generations. (Catechism, 1951, 2415-2418, 2456)

I don't think 'interfering' with mosquito genes is wrong. We might discover practical issues: although I'm nowhere near as concerned about these mildly-modified mosquitoes as I was about 'mutant eucalyptus' trees, back in 2010.

ArborGen tweaked eucalyptus genes so the trees could endure freezing temperatures. The idea was to provide hardwood fiber for high-quality pulp and paper, from trees grown in the northern United States.

So far, that sounds like a good idea: but so did introducing rabbits to Australia, and that's yet again another topic. (Apathetic Lemming of the North (June 13, 2010))

More of my views on health, technology, and being human:
1 Pre-industrial agricultural technology came close to feeding everybody, except during famines: but that was when there weren't nearly as many folks around as there are now. I do not think there are "too many" people. I certainly do not think non-European countries should be "helped" by trimming their populations down to match the preferences of "civilized" folks.

I'm more concerned about countries like Japan, where folks aren't raising quite enough kids to take over as older generations die.

I've harangued about this, but not recently:
As a Catholic, I must think that human life is sacred: which means that I can't approve of genocide, among other things. (Catechism, 2258-2317)

As I keep saying, I'm expected to love God, love my neighbors, see everyone as my neighbor, and treat others as I'd like to be treated. (Matthew 5:43-44, 7:12, 22:36-40, Mark 12:28-31; Luke 6:31 10:25-27, 29-37; Catechism of the Catholic Church, 1789)

2 We can get by without meat, but by nature we're omnivorous: along with badgers, bears, coatis, hedgehogs, and chimps:
Although some animals, like elephants and whales, are bigger than we are; we're among the larger critters on Earth. (June 19, 2015)

3 We do get sick, and avoiding disease is a good idea. However, I think it's noteworthy that plagues like the Black Death didn't do more than slow us down. More of my take on being human:
4 Mosquitoes, malaria, and more:
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Friday, November 20, 2015

Europe's Complex Heritage

I stopped using the term "Caucasian" several years ago. I've discussed the "Anglo-Teutonic" race, Neanderthals, and getting a grip, before. (September 25, 2015; October 31, 2014)

Turns out, folks from the Caucasus moved into Europe at least once — along with many other folks.
  1. Georgian DNA, Homebodies, and Wanderers
  2. Basque Background
We're still learning more about humanity's family history. It's a lot more complicated than we thought. (July 11, 2014)

Thinking is Not a Sin


If you've read my 'science' posts before, you know why I think the universe is billions, not thousands, of years old; Earth isn't flat; Adam and Eve weren't German; poetry isn't science; and thinking is not a sin.

Briefly, I think the universe follows knowable rules: which means we can learn how it works. This is okay. We're supposed to study this universe, and use what we learn. (Catechism of the Catholic Church, 32; 339, 2292, 2295)

Scientific discoveries invite us "to even greater admiration for the greatness of the Creator."(Catechism, 283)

I also think that this world is changing, in a state of journeying — in statu viae — toward an ultimate perfection. (Catechism, 302-305)

Humility is accepting reality — including scientific discoveries — also remembering that God's God, I'm not.1 (Catechism, 283, 2540, 2559)

1. Georgian DNA, Homebodies, and Wanderers



(From Eppie Jones, via BBC News, used w/o permission.)
("DNA was retrieved from this 10,000-year-old skeleton in Western Georgia"
(BBC News))
"Europe's fourth ancestral 'tribe' uncovered"
(November 16, 2015)

"Geneticists have detected a fourth ancestral 'tribe' which contributed to the modern European gene pool.

"Research shows Europeans are a mixture of three major ancestral populations - indigenous hunters, Middle Eastern farmers and a population that arrived from the east in the Bronze Age.

"DNA from ancient remains in the Caucasus has now revealed a fourth population that fed into the mix...."
The photo's caption says "Western Georgia," which could mean somewhere near the Apalachicola River — but doesn't.

This Georgia is on the east side of the Black Sea, north of where Urartu used to be. "Georgia" is my culture's name for the country. Folks who live there call their land საქართველო, Sakartvelo — I think.

Greeks and Romans called the folks living there Colchians and Iberians, depending on whether they were in the western or eastern part. I'll stick with "Georgia," and figure that you know what area I'm talking about.

Anyway, Eppie Jones and other scientists have been studying DNA from two men who lived in western Georgia 13,300 and 9,700 years back, three centuries shy of "10,000 years;" and another man who died about 13,700 years ago, where Switzerland is now.

Comparing their DNA with folks living in western Eurasia, the scientists found that today's Georgian DNA is a lot like the samples they have from a dozen millennia back.

They also discovered that folks living throughout Europe — particularly northern Europe — are genetically similar to the early Georgians.

My fairly-recent ancestors are from southern Norway and the northern British Isles: so it looks like I'm related to the Georgian subjects of this study.

DNA: Still Learning



(From Eppie Jones, via BBC News, used w/o permission.)
("A view from the Satsurblia cave in Western Georgia, where a human bone dating from over 13,000 years ago was discovered."
(BBC News))

We've learned a lot since 1928, when Frederick Griffith's experiment suggested that DNA carried genetic information; and 1944, when the Avery-MacLeod-McCarty experiment showed that DNA, not proteins, carries genetic information in bacteria.

More recently, research like the Human Genome Project has mapped the human genome. We've mapped the billions of DNA base pairs in our chromosomes — but we don't know what many of them do.

Not yet.

Scientists have developed new ways to recover DNA from increasingly old burials. Back in the 1990s, it looked like we could extract DNA from insects caught in amber: and an 80,000,000-year-old dinosaur.

Scientists double-check results: with disappointing results in this case. Early research hadn't taken environmental contamination and DNA's chemical stability into account. The "dinosaur DNA," for example, was from a human Y chromosome.

These days, it's rare for researchers to identify DNA that's more than several hundred thousand years old. (Wikipedia)

Quite a bit's happened in the last 200,000 years, though. That's when anatomically modern humans showed up. That's what scientists call folks who look pretty much like us.

For one thing, we're learning that today's genetic patterns aren't much like they were in the past. That's hardly surprising. As I've said before, humans travel. (July 11, 2014)

In a way, I'm a bit surprised that so many of the folks who lived in the Caucasus a dozen millennia back stayed where they were.

More recently, about 5,000 years ago, another group — herders we call the Yamna or Yamnaya — formed when hunter-gatherers from the Caucasus and eastern Europe moved into land north of the Caucasus: joining folks from the Mal'ta-Buret' culture.

Genes, Norwegians, and Steppe Pastoralists



(From Joostik, via Wikimedia Commons, used w/o permission.)
"...The Yamnaya transformed the gene pools of northern and central Europe, such that some populations, like Norwegians, owe around 50% of their ancestry to these Steppe pastoralists.

"But the Yamnaya were themselves a mixed population. Around half of their ancestry came from a sister group to the hunter-gatherers who inhabited Europe before farming, while the other half appears to be from a population related to - but noticeably different from - the Middle Eastern migrants who introduced farming.

"Researchers have now analysed genomes from two hunter-gatherers from Georgia that are 13,300 and 9,700 years old. The results show that these Caucasus hunters were probably the source of the farmer-like DNA in the Yamnaya...."
(BBC News)
It looks like Yamnaya brought the early version of most European languages with them when they moved west into my ancestral homelands, about 5,000 years ago. Wikipedia has a pretty good write-up on Proto-Indo-European language.

They also brought horses, metal-working tech, and plague. We've found plague DNA in Yamnaya burials: and Europe's population dropped after they arrived. (BBC News (October 23, 2015))

We recovered, though.

People may be "allergic to change," but for the last 2,000,000 or so years, humans have been coping with a changing world. And that's another topic. (February 20, 2015; July 11, 2014)

Humanity on the Move



(From Wikimedia Commons, used w/o permission.)
(Map of Georgia, Abkhazia, Ajara, and South Ossetia; showing Dmanisi, a townlet and archaeological site in the Kvemo Kartli region.)

Folks have been living in cities like Faiyum and Jericho for millennia. Sorting out exactly how long isn't easy, since inhabited cities keep getting rebuilt. Excavations for an embassy in Londinium, for example, unearthed 10,000-year-old tools. (June 6, 2014; April 4, 2014)

Getting back to the Caucasus region, the Homo erectus version of humanity was living there 1,800,000 years ago. We look different now, but folks still move around.

I'm an anatomically modern human, descended from folks who left Africa more than six dozen millennia back. My ancestors reached central North America recently.

I'm prone to sunburn, thanks to an ancestral stopover in northwestern Europe, I'm related by marriage to folks who came here after heading east across Asia — and that's yet more topics.

Maybe you've seen enough about Dmanisi, Upper Palaeolithic genomes, and all that. if not, there's more at the end of this post.2

2. Basque Background



(From AFP/Getty Images, via BBC News, used w/o permission.)
("Two men saw a tree trunk with a 'tronza' (traditional Basque saw) during a rural sports championship"
(BBC News))
"Ancient DNA cracks puzzle of Basque origins"
(September 7, 2015)

"DNA from ancient remains seems to have solved the puzzle of one of Europe's most enigmatic people: the Basques.

"The distinct language and genetic make-up of the Basque people in northern Spain and southern France has puzzled anthropologists for decades.

"One theory proposed that they were an unmixed pocket of indigenous hunters...."
Basque Country is between Spain, France, and Andorra.2 It's a mountainous place, tucked into the southeast corner of Europe's Bay of Biscay. Quite a bit of traffic goes through the Port of Bilbao, but Basque valleys aren't particularly on the way to anywhere.

Folks have been living there for at least 32,000 years. Today's Basques have a unique language, Euskera, and unique customs.

The BBC News article says Euskera "is unrelated to any other spoken in Europe, or indeed the world."

That's possible, although Basques may have picked up bits and pieces of Iberian and other Indo-European languages as the millennia rolled by.2

Torsten Günther and other scientists filled in a few pages of the Basque story recently: showing that ancestors of today's Basques were local hunters, plus farmers who moved in between 3,500 and 5,500 back. The farmers had been living in around the Atapuerca Mountains.2

Folks have been living in the Atapuerca region for 430,000 years, give or take. We haven't changed much, sadly. (June 5, 2015)

More from me, accepting reality:
1 More about humility and thinking:
"CONSCIENCE: The interior voice of a human being, within whose heart the inner law of God is inscribed. Moral conscience is a judgment of practical reason about the moral quality of a human action. It moves a person at the appropriate moment to do good and to avoid evil (1777–1778). An examination of conscience is recommended as a preparation for the reception of the Sacrament of Penance (1454)."
(Catechism of the Catholic Church, Glossary, C)

"HUMILITY: The virtue by which a Christian acknowledges that God is the author of all good. Humility avoids inordinate ambition or pride, and provides the foundation for turning to God in prayer (2559). Voluntary humility can be described as 'poverty of spirit' (2546)."
(Catechism of the Catholic Church, Glossary, H)

"SIN: An offense against God as well as a fault against reason, truth, and right conscience. Sin is a deliberate thought, word, deed, or omission contrary to the eternal law of God. In judging the gravity of sin, it is customary to distinguish between mortal and venial sins (1849, 1853, 1854)."
(Catechism of the Catholic Church, Glossary, S)
2 More than you may wan to know about:
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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.