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
   • Sound, Fury, and Mutant Squirrels
   • Biotech 'Chassis?'
2. Oops: UK DNA Database Deletion
   • Fingerprints, DNA Profiles: From Hammurabi to Scotland Yard
   • Using Knowledge Wisely and Well
   • 'It Seemed Like a Good Idea at the Time'

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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:

• "Early Hands, Mutant Mice"
  (August 28, 2015)
  Particularly
  • "Super-Intelligent Mice" — Imagined and Real
    • From Laban's Sheep to Mutant Safflowers
    • Rules, Principles - - -
    • - - - and Speculation

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.

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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

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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:

• "Hate People? Not an Option"
  (September 6, 2015)
• "Morality isn't Just About 'Morality' "
  (September 7, 2014)
• "Caesar, Civilization, Dealing With Change — and Building a Better World"
  (August 31, 2014)

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:

• "Pig Organs, Ancient Immigrants"
  (October 16, 2015)
  Particularly
  • Tech, Old and New
  • Think!
  • CRISPR Genetic Tech: Pigs as Organ Transplant Donors?
    • Synthetic Organisms, like Chickens
    • Remembering Who We Are
• "Kidneys, Experiments, and Ethics"
  (September 25, 2015)
  Particularly
  • Love, Science, and Being Human
  • Kidneys and Stem Cells
    • Stem Cells, Organ Transplants, and Ethics
• "DNA Test Hype; and Studying Life's Origins"
  (December 5, 2014)
  Particularly
  • Applied Genetics: Technology is Technology
  • Being Human
  • DNA Test: Science, Technology, Marketing, and the FDA
    • Looking Ahead
• "Ebola: Scary, and Beatable"
  (October 17, 2014)
  Particularly
  • Getting a Grip About Health
  • Leviticus, Dubrovnik, and Typhoid Mary
  • Nurses, Torches, and Pitchforks
• "Regeneration: Getting Closer to Growing Lost Organs"
  (August 29, 2014)
  Particularly
  • Growing a Thymus from Scratch
    • Technical Issues
    • Ethics
  • Brand-New Tech, Same Old Challenges

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¹More about:

• Design and synthesis of a minimal bacterial genome"
  Clyde A. Hutchison III, Ray-Yuan Chuang, Vladimir N. Noskov, Nacyra Assad-Garcia, Thomas J. Deerinck, Mark H. Ellisman, John Gill, Krishna Kannan, Bogumi, J. Karas, Li Ma, James F. Pelletier, Zhi-Qing Q, R. Alexander Richter, Elizabeth A. Strychalsk, Lijie Sun, Yo Suzuki, Billyana Tsvetanova, Kim S. Wise, Hamilton O. Smith, John I. Glass, Chuck Merryman, Daniel G. Gibson, J. Craig Venter; Science Vol 351, Issue 6280 (March 25, 2016)
• "Multiplex Genome Engineering Using CRISPR/Cas Systems"
  Le Cong, F. Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D. Hsu1, Xuebing Wu, Wenyan Jiang, Luciano A. Marraffini, Feng Zhang; Science, Vol 339, Issue 6121 (February 15, 2013)
• J. Craig Venter Institute
  www.jcvi.org
• Wikipedia
  • Genetic redundancy
  • Genome engineering
  • J. Craig Venter Institute
  • Mycoplasma genitalium
  • Mycoplasma laboratorium
    • Minimal genome project
    • Concerns and controversy
    • JCVI-syn3.0
  • Synthetic biology

² Going home with your baby:

• " Identification of Newborn Infants"
  The American Journal of Nursing; Vol. 28, No. 1, pp. 33-36 (January 1928)

³ Genetics, medicine, law, and society:

• Wikipedia
  • DNA profiling
    • DNA databases
    • Considerations when evaluating DNA evidence
  • Genetic testing
    • Ethics
• "Criminal Genes and Criminal Brains"
  "Are we there yet?"
  Patricia Smith Churchland, Psychology Today (May 7, 2013)