A new book on CRISPR, gene editing, and their ethical implications

May 7, 2017 • 10:15 am

Word on the street is that the book shown below, by Jennifer Doudna and Samuel Sternberg, is very good (it’s out on June 13; click on screenshot to go to Amazon link). You may have heard of Berkeley professor Jennifer Doudna, one of the pioneers in using the new CRISPR technique to genetically edit cells—”genome editing”; co-author Samuel Sternberg studied with Doudna as a postdoc and now works for a biotechnology company.

And I hope you’ve heard of CRISPR (“clustered regularly interspaced short palindromic repeats”), which is a method of genome editing that grew out of pure science: the discovery that bacteria have immune systems in which they incorporate into their own DNA short bits of DNA from invading viruses, and then use those bits, along with an enzyme called Cas9, to cut up and destroy the genomes of those viruses when they invade again. This is analogous to our own immune system, which has a memory that can inactivate harmful proteins the body has experienced before. (This is the basis of vaccination.) That pure science grew, through the work and ingenuity of many scientists, into a method that now enables us to cut DNA at any given sequence in nearly any species (including our own), and then insert new DNA of our own making, or DNA taken from other cells. We could cure sickle-cell anemia by editing into sufferers the “normal” hemoglobin gene, and do likewise with many other genetic diseases. We could get rid of the AIDS virus that hides in the human genome. We could genetically engineer crops to make them resistant to insects and herbicides. We can study gene function by selectively inactivating genes or visualizing their expression using proteins that fluoresce. We already have some ability to do these things, but the CRISPR-Cas9 system makes this dead easy.

But there’s also the possibility of editing not just the genes in bodies, but the genes in sperm and eggs, giving rise to the possibility of genetically changing our own and other species, permanently—or directing our own evolution. (It’s not just humans, either; we could alter disease-carrying insects to render them harmless.) The possibility of germline editing carries with it severe ethical problems: how much can we and should we change our own genetic legacy? Both the methodology and ethics are discussed in Doudna and Sternberg’s book, as this Amazon summary shows:

A trailblazing biologist grapples with her role in the biggest scientific discovery of our era: a cheap, easy way of rewriting genetic code, with nearly limitless promise and peril.

Not since the atomic bomb has a technology so alarmed its inventors that they warned the world about its use. Not, that is, until the spring of 2015, when biologist Jennifer Doudna called for a worldwide moratorium on the use of the new gene-editing tool CRISPR—a revolutionary new technology that she helped create—to make heritable changes in human embryos. The cheapest, simplest, most effective way of manipulating DNA ever known, CRISPR may well give us the cure to HIV, genetic diseases, and some cancers, and will help address the world’s hunger crisis. Yet even the tiniest changes to DNA could have myriad, unforeseeable consequences—to say nothing of the ethical and societal repercussions of intentionally mutating embryos to create “better” humans.

Writing with fellow researcher Samuel Sternberg, Doudna shares the thrilling story of her discovery, and passionately argues that enormous responsibility comes with the ability to rewrite the code of life. With CRISPR, she shows, we have effectively taken control of evolution. What will we do with this unfathomable power?

(There’s some nastiness in the field about who gets priority for this discovery, as it’s sure to garner a Nobel Prize (getting CRISPR to this point is the work of dozens of people, but certain scientists—not Doudna or Sternberg—are trying to establish hegemony. There’s also a big patent battle over the use of the system, but I won’t get into that. Go here if you want to read the dirty details.)
Now you could read about the CRISPR-Cas9 system on Wikipedia, or you could read a good but technical paper by Doudna and Emmanuelle Charpentier (another pioneer in this area) published in Science (free at the link).  But if you have any interest in science, or in bioethics, I’d strongly urge you to learn about the new methods of gene editing, how they work, what they can do, and their ethical implications. You might order the book above, and I’d also direct you to two explanations by our own Matthew Cobb.

The first is a BBC show he did about gene editing, (“Editing life”), whose description and link I’ve given before.

And now Matthew’s just published a short primer on the issue called “The brave new world of CRISPR”, which appeared in the new Biological Sciences Review. That piece will bring every reader up to speed. Sadly, it’s not online free, but if you email me I’ll send you a pdf.

The CRISPR system is the most important innovation in biotechnology since the advent of DNA sequencing methods; its development is a fascinating story and its ethical implications are profound. You need to learn about it if you have any interest in science. I’ve given you at least five resources to do so.

Here are Doudna and Sternberg:

 

NYT’s piece on a Muslim comedian evades some important issues

May 7, 2017 • 9:15 am

Yesterday’s New York Times had an article written by a Muslim comedian, Zahra Noorbakhsh (you can see part of her act here). Her piece, “It’s not this Muslim comedian’s job to open your mind,” recounts the dilemma of a woman expected to have a comedic mission: to show Americans that Muslims are just like everyone else. This is a task that she doesn’t like, and doesn’t think she should have to take on. (This task, by the way, is also something that many atheists are urged to do by humanizing heathenism, and I think it’s a good strategy for nonbelievers. There’s no better way to dispel bigotry than by seeing and associating with those you were taught to dislike—one theme of the wonderful South Pacific song “You’ve got to be carefully taught.”)

Noorbakhsh chafes under this burden, and thinks it’s useless to try:

This ambivalence has followed me as I’ve fielded similar requests during a time when the Trump administration has attempted to defend its “Muslim ban” campaign promise in the courts, Islamophobic attacks have been reported throughout the country, and fears of a “Muslim registry” still swirl throughout my community.

The idea that jokes will stop the tide of fear, hate and misunderstanding about people who practice Islam is seductive. As a comedian, though, I’m not convinced. We have tried this before.

After Sept. 11, Muslim comics went on what I call “We’re not that scary, we’re funny and just like you!” tours, in desperate attempts to push back against bigotry. In 2005, the “Axis of Evil” tour fought stereotypes with jokes by Muslim comedians in shows throughout the country. In 2013, the docu-comedy “The Muslims Are Coming” aimed to introduce Middle America to normal, huggable, everyday Muslims.

I played this game, too. I tried to humanize Muslim families, with my one-woman show, “All Atheists Are Muslim,” sharing the story of moving in with my white atheist college boyfriend, and telling my parents about it. It’s a typical boy meets girl story, up against thousands of years of cultural tradition and religious doctrine. The message the audience was meant to be left with was that if total nonbelievers and Muslims can find common ground, then everyone in between should be able to.

Unsurprisingly, none of this worked. I saw firsthand that the fairy tale, mind-opening reaction that producers imagined was nowhere to be found. While mixed-race and interfaith couples often thanked me after my shows, many others let me know that I was one of the “good Muslims” whom they didn’t have a problem with. I hadn’t made them more empathetic to Muslims as a whole.

Her solution is just to expose tensions; the underlying theme (see below) is that the tensions, and worry about Muslims, is simply a manifestation of bigotry against Muslims, “Islamophobia” (I prefer to call that bigotry “Muslimophobia”):

. . . Television producers, publishers and those booking events for college campuses all seem to want something similar: a representative of an “everyday” Muslim (I still don’t really know what that means) with an outlook relatable enough to get audiences to forget their bigotry. These pleas don’t make me as sad as the ones that come from Muslim activists, who seem to be begging: Use your jokes to make us human; make us likable; let us prove to people that we’re just like them.

I do understand that comedy has some potential to open people’s minds. But I’ve become convinced that the primary role of political humor today shouldn’t be to alleviate tensions or smooth out differences. It should be to heighten them and illuminate for everyone what is a moment of crisis.

I sympathize with Noorbakhsh: why should the burden of solving the “Muslim problem” rest on her shoulders. She’s a comedian, for crying out loud! But still, she attributes all the tension she’s supposed to relieve as “bigotry” (she uses the word). And there’s the rub, because for many the Muslim problem does not simply come down to “othering”.  (It does, of course, for Trump and his Ban, as well as attacks on Muslims.) Rather, it also reflects a suspicion toward and fear of Islam’s religious dictates, and the attendant fear that they’ll cause harm not just to America, but to the world as a whole. Islam is the most misogynistic, the most violent, and the most intolerant of the world’s great faiths, and its pefidy hasn’t yet been tamed by Enlightenment values. All religions are useless and sometimes harmful reflections of human delusion and irrationality, but Islam is, at present, the most harmful.

Should a comedian deal with those issues in her act? I don’t think so. But at least Noorbakhsh and the Times might recognize that there’s more to the issue than bigotry. As the correspondent who sent me this article commented,

The author of the Times piece elides all the reasons why Muslims are “not just like the rest of us,” ignoring the ideology of Islam, and casting negative reactions to Islam as racism and ignorance.  No editor at the Times thought to point out any of this to her.  There’s an undercurrent of hostility to the piece: it’s not her fault (or Islam’s) if we have negative reactions to the religion; it’s our fault.
You’ll see that as soon as you read it.  We just cannot advance the conversation if major news outlets like the time won’t publish pieces asking the questions that need to be asked…”
Judge for yourself.

Spot the snipe!

May 7, 2017 • 8:15 am

Speaking of snipe (see previous post), can you see this one? Yes, this is a real snipe hunt, not a bogus one inflicted on young campers. The photos come from Stephen Barnard in Idaho, with his notes indented. Click photos to enlarge; reveal at 11 a.m. Chicago time.

1. Extremely difficult. Nearly impossible in my opinion, although the bird is clearly visible, if not visually identifiable. I knew it was there because I heard it calling.

2. Much easier.

Readers’ wildlife photos

May 7, 2017 • 7:30 am

Roger Latour sent what he describes as “a couple of pictures showing the spring flora on mount Royal in Montreal. A must-see when in Montreal!”  Roger’s notes are indented.

On the left: Erythronium americanum (yellow trout lily) and on the right Acer saccharum (sugar maple):

Podophyllum peltatum, a sequence showing emergence of the very rare (here anyway…) May-apple. The plant was most likely introduced by Amerindian natives as medicinal plant well before the arrival of the French. A few fenced off colonies here and there on the mountain, all doing fine!


Sanguinaria canadensis (bloodroot, in the Poppy family Papaveraceae):

And a token animal—one hard to photograph—by Stephen Barnard. It’s a Wilson’s snipe (Gallinago delicata). As he says,

This is craziness. The bird was no more than 20 ft. from me. My Idaho birding friends are telling me it’s my totem, but I was thinking more along the lines of a wolf, or a bear, or an eagle. 🙂

Sunday: Hili dialogue

May 7, 2017 • 6:30 am

UPDATE: Okay, everything historical listed happened on May 8, so just reread this tomorrow! Blame it on my writing it at 4:30 am

_________

Good morning on Ceiling Cat’s Day: Sunday, May 7, 2017. It’s a beautiful day in Chicago, though chilly, with a predicted high of only 50° F (10° C).

Although Holi—the Indian spring festival of colors during which people pelt each other with powdered and liquid dyes—was on March 13, for some reason Indian-American students at my university celebrated it yesterday, sending up clouds of color across the street from my building:

Today, though, really is National Lamb Day, and by that I mean lamb meat: the ideal meal with a good Bordeaux—or most reds. really. And Helston, Cornwall, England, sees a strange holiday today: Furry Dance, described in Wikipedia as “one of the oldest British customs still practised today.”  (I can’t find out how old it is.) It’s an all-day combination of dances and pageants celebrating the advent of Spring, and there’s a video below that shows the Children’s Dance and the Midday Dance:

The children’s dance involves over 1,000 children aged from 7 to 18, all dressed in white, the boys with Lily of the Valley buttonholes and the girls wearing flowers in their hair, the flower determined by the school they attend. They come from St Michael’s School, Nansloe School, Parc Eglos School, and Helston Community College: each year a different school leads the dance.

. . . the midday dance is perhaps the best known: it was traditionally the dance of the gentry in the town, and today the men weartop hats and tails while the women dance in their finest frocks.[5]

Traditionally, the dancers wear Lily of the Valley, which is Helston’s symbolic flower. The gentlemen wear it on the left, with the flowers pointing upwards, and the ladies wear it upside down on the right. Lily of the Valley is worn on Flora Day by dancers, bandsmen, Flora Day stewards and by those who are “Helston-born”.

On this day in 1794, a famous scientist was executed: in Paris, French chemist Antoine Lavoisier was tried, convicted and guillotined in a single day. On May 7, 1886, the first glass of Coca Cola was sold—as a patent medicine—at Jacob’s Pharmacy in Atlanta, Georgia. On this day in 1902, Mount Pelée erupted on Martinique, wiping out the entire town of Saint-Pierre and nearly all of its residents; over 30,000 people perished. On May 7, 1978, Reinhold Messner and Peter Habeler became the first people to summit Mount Everest without supplemental oxygen. Here’s the great Messner on top:

Exactly two years after that climb, the World Health Organization officially declared smallpox eradicated from our species: a great triumph for science, field work, and epidemiology—and Homo sapiens. 

Notable people born on this day include Edward Gibbon (1737), Harry S. Truman (1884; the buck stopped there), Edmund Wilson (1895), David Attenborough and Don Rickles (both 1926), Thomas Pynchon (1937), Ricky Nelson (1940), and Pat Barker (1943, read her Ghost Road trilogy). Those who died on this day include nobody I think worthy to list, and this is a first. Meanwhile in Dobrzyn, today’s Hili dialogue has both a title and an explanation by Malgorzata:

THE NEST

Hili: You are disapproving of me again, aren’t you?
A: And I know why.
In Polish:
Gniazdo
Hili: Znowu masz do mnie pretensje!
Ja: I wiem o co.
Explanation: ​The trellis Hili is on goes almost to the roof— and is dangerously close to a nest of starlings.​
Lagniappe: some mimicry from David Bygott via Ziya Tong via Matthew Cobb: a moth whose ancestors evolved to resemble thorns:

Finally:  Ssshhhh . . . Gus is sleeping:

When eating trumps breathing

May 6, 2017 • 3:00 pm

My excuse for linking to HuffPo UK: I found the video on another site and, looking for information about it, found a description on the Regressive Rag:

A man named Joel Rosenthal discovered a family of raccoons living under his house, so he did the logical thing and made them internet stars.

His first genius step was to give them a bowl of cereal, which they didn’t really understand. Rather than skimming the yummy cereal off the top of the milk, they just plunged their faces in.

The entire ordeal was really cute, but the funniest part of the video is easily Joel’s commentary.

Ireland investigates Stephen Fry for blasphemy

May 6, 2017 • 12:30 pm

Blasphemy is a crime in Ireland; the Constitution of 1937 (see here) says the following:

ARTICLE 40

6. 1° The State guarantees liberty for the exercise of the following rights, subject to public order and morality:  i. The right of the citizens to express freely their convictions and opinions. The education of public opinion being, however, a matter of such grave import to the common good, the State shall endeavour to ensure that organs of public opinion, such as the radio, the press, the cinema, while preserving their rightful liberty of expression, including criticism of Government policy, shall not be used to undermine public order or morality or the authority of the State. The publication or utterance of blasphemous, seditious, or indecent matter is an offence which shall be punishable in accordance with law.

Wikipedia has a good article on the blasphemy law, its history, and its implementation in Ireland. The upshot is that it’s been contested, especially by the organization Atheist Ireland, and a referendum on the issue of blasphemy was proposed in 2014 but has yet to take place. No offenses have been prosecuted since 2009, but the law remains on the books.

In the meantime, according to both the BBC and the Independent in Ireland, Stephen Fry is being investigated by the Gardaí, the Irish police, for blasphemy in a part of a television interview with Gay Byrne that I’ve put up previously (here and here)/ Here’s the offending segment:

This is reasonable doubt and in no way should be subject to prosecution. But the investigation proceeds:

From the BBC:

Appearing on The Meaning of Life, hosted by Gay Byrne, in February 2015, Fry had been asked what he might say to God at the gates of heaven.

Fry said: “How dare you create a world in which there is such misery? It’s not our fault? It’s not right. It’s utterly, utterly evil. Why should I respect a capricious, mean-minded, stupid god who creates a world which is so full of injustice and pain?”

He went on to say that Greek gods “didn’t present themselves as being all seeing, all wise, all beneficent”, adding “the god who created this universe, if it was created by god, is quite clearly a maniac, an utter maniac, totally selfish”.

The Irish Independent reported a member of the public made a complaint to police in Ennis in the same month the programme was broadcast. He was recently contacted by a detective to say they were looking into his complaint.

The viewer was not said to be offended himself but believed Fry’s comments qualified as blasphemy under the law, which was passed in 2009 and carries a maximum penalty of a fine of 25,000 euros (£22,000).

The law prohibits people from publishing or uttering “matter that is grossly abusive or insulting in relation to matters held sacred by any religion, thereby causing outrage among a substantial number of the adherents of that religion”.

The Independent adds this:

A garda source said the matter is being investigated.

“A complaint has been received and it is currently being investigated. Detectives will speak to those involved if they are available and a file will be sent to the Director of Public Prosecutions (DPP).”

A well-placed source said it was “highly unlikely” that a prosecution would take place.

Ireland is the only country in the developed world to have introduced a blasphemy law this century.

It is not seemly for a non-theocratic nation to have a blasphemy law. Ireland should dump it.

 

Addendum by Grania Spingies

Nothing will happen to Stephen Fry. Ireland’s idiotic and ill-conceived blasphemy law was deliberately written to be unenforceable.

This isn’t the first time an interfering busybody has tried to cause trouble for an actor or comedian by using this law. Irish comedians Dara Ó Briain and Tommy Tiernan have fallen foul of thin-skinned offense-takers. However the law clearly states:

“A defence is permitted for work of “genuine literary, artistic, political, scientific, or academic value”.

That doesn’t mean that this is much ado about nothing.

The true danger of this modern version of an archaic law in Ireland is that it is frequently promoted by Muslim majority countries at United Nations level (Organization of Islamic Conference) as an endorsement of their own blasphemy laws and for the creation of more of these laws all over the globe. The CFI points out here:

Pakistan’s submission urges that UN member states prohibit by law “the uttering of matters that are grossly abusive or insulting in relation to matter held sacred by any religion, thereby causing outrage to a substantial number of adherents to that religion.”  Clearly, the Irish blasphemy legislation is being used to legitimize the “defamation of religions” movement, a dangerous threat to international freedom of expression. (Emphasis my own.)

Blasphemy laws in countries where they are taken seriously are in fact highly dangerous things. Ken White over at Popehat has for some years written multiple posts detailing the passing of such laws and their effect around the world. If anyone is in doubt as to why all blasphemy crimes should be abolished immediately and have no place in a fair and just society, you should take a look at his collection of articles on the subject.

He sums it up succinctly here:

“anti-blasphemy laws are a tool for religious majorities to suppress religious minorities, and a mechanism for the more powerful to oppress the relatively powerless, and tend to be used in a lawless manner resembling modern witch hunts. That is the norm we are asked to embrace.”

h/t: Charleen