A Ten-Year Check-Up Shows Gene Therapy Patients are Alive and Well | 80beats

genes

What’s the News: Medicine in the age of genes overflows with daring new techniques and treatments, from personalized chemotherapy to prenatal genetic testing, each heralded as a game-changer. But rarely do we get an assessment of a treatment’s long-term good, which is why recent papers following up on one of the most controversial genetic treatments, gene therapy, are making waves: though one patient developed leukemia from the treatment, 13 of 16 kids treated with gene therapy for a severe immune disorder at least 9 years ago have been cured, adding to the sense that the field is on its way to recovery from early setbacks.

The Backstory:

Gene therapy involves correcting errors in cells’ genetic code. In the case of some of these children, who had no functioning immune system due to X-linked SCID—severe combined immunodeficiency, or “bubble boy” syndrome—bone marrow transplants had been the only way to effectively treat the disease (for kids with ADA-SCID, caused by a missing enzyme, weekly enzyme injections are also possible, but bone marrow transplants are the only way to eliminate it). But marrow transplants require a matching donor, like a sibling, and when one isn’t available, the odds of ...


Did sex with Neanderthals and Denisovans shape our immune systems? The jury’s still out | Not Exactly Rocket Science

The Neanderthals may be extinct, but they live on inside us. Last year, two landmark studies from Svante Paabo and David Reich showed that everyone outside of Africa can trace 1-4 percent of their genomes to Neanderthal ancestors. On top of that, people from the Pacific Islands of Melanesia owe 5-7 percent of their genomes to another group of extinct humans – the Denisovans, known only from a finger bone and a tooth. These ancient groups stand among our ancestors, their legacy embedded in our DNA.

Paabo and Reich’s studies clearly showed that early modern humans must have bred with other ancient groups as they left Africa and swept around the world. But while they proved that Neanderthal and Denisovan genes are still around, they said little about what these genes are doing. Are they random stowaways or did they bestow important adaptations?

When I spoke to Reich about this earlier this year, he was starting to sift through the data. “To a first approximation, they are random,” he said. “It’s possible that modern humans could have used the Neanderthal or Denisovan material to adapt to their environment, but we ...

Moon over Afghanistan | Bad Astronomy

Posted without comment: the waning third quarter Moon over Afghanistan, as seen by astronaut Ron Garan on board the International Space Station:

[Click to embiggen.]

You can follow Ron on Twitter and see these amazing pictures as he posts them.

Image credit: NASA. Technically, I saw this on Nancy_A’s Twitter stream before I saw it on Ron’s, so tip o’ the spacesuit visor to her.

Related posts:

- Squishy moonrise seen from space!
- What a falling star looks like… from space!
- Crescent Moonset from space
- A puzzling planet picture from the ISS
- Followup: City lights from space


Questioning the Candidates on Dominionism | The Intersection

By Jon Winsor

Questions about Dominionism and national politics are now moving out of the muckraking exposés and the religion pages and into elite journalism. Yesterday, NPR’s Fresh Air devoted most of its air time to journalist Rachel Tabachnick on the topic of Dominionism. Now, NY Times Chief Editor Bill Keller is going there as well:

This year’s Republican primary season offers us an important opportunity to confront our scruples about the privacy of faith in public life — and to get over them. We have an unusually large number of candidates, including putative front-runners, who belong to churches that are mysterious or suspect to many Americans. Mitt Romney and Jon Huntsman are Mormons, a faith that many conservative Christians have been taught is a “cult” and that many others think is just weird. (Huntsman says he is not “overly religious.”) Rick Perry, Michele Bachmann and Rick Santorum are all affiliated with fervid subsets of evangelical Christianity, which has raised concerns about their respect for the separation of church and state, not to mention the separation of fact and fiction.

I honestly don’t care if Mitt Romney wears Mormon undergarments beneath his Gap skinny jeans, or if he believes that the stories of ancient American prophets were engraved on gold tablets and buried in upstate New York… Every faith has its baggage, and every faith holds beliefs that will seem bizarre to outsiders. I grew up believing that a priest could turn a bread wafer into the actual flesh of Christ…

In the last presidential campaign, Candidate Obama was pressed to distance himself from his pastor, who carried racial bitterness to extremes… I don’t see why Perry and Bachmann should be exempt from similar questioning…

To get things rolling, I sent the aforementioned candidates a little questionnaire.

Keller lists some of his questions in his op-ed (which you can read here).

Tuesday, conservative columnist Michael Gerson defended the conservative field from the criticisms on Dominionism, saying (sarcastically):

The Dominionist goal is the imposition of a Christian version of Shariah law in which adulterers, homosexuals and perhaps recalcitrant children would be subject to capital punishment. It is enough to spoil the sleep of any subscriber to The New Yorker. But there is a problem: Dominionism, though possessing cosmic ambitions, is a movement that could fit in a phone booth…

Many have become unhinged by the interpretive power of a simple idea. In the case of Dominionism, paranoia is fed by a certain view of church-state relations — a deep discomfort with any religious influence in politics: Even if most evangelicals are not plotting the reconstruction of Cromwell’s Commonwealth, they nevertheless want to impose their sectarian views on secular institutions. It is a common argument among secular liberals that the application of any religiously informed moral reasoning in politics is a kind of soft theocracy. Dominionism is merely its local extension. [My emphasis.]

But Bill Keller and others have been rightly asking what kind of reasoning? There shouldn’t be anything wrong with asking common sense questions about what someone’s “religiously informed moral reasoning” is:

Asking candidates, respectfully, about their faith should not be an excuse for bigotry or paranoia. I still remember, as a Catholic boy, being mystified and hurt by the speculation about John Kennedy’s Catholicism — whether he would be taking orders from the Vatican… And of course issues of faith should not distract attention from issues of economics and war. But it is worth knowing whether a candidate has a mind open to intelligence that does not fit neatly into his preconceptions.

This echoes what some of the exposé writers have been saying about Dominionism as a political phenomenon. Here is an excerpt from Sarah Posner’s piece at Slate:

The commenters who have jumped on the [New Apostolic Reformation] frequently overstate the size of its following… Most chilling, though, is the willingness to engage in what’s known in the Word of Faith world as “revelation knowledge,” or believing, as Copeland exhorted his audience to do, that you learn nothing from journalism or academia, but rather just from the Bible and its modern “prophets.” It is in this way that the self-styled prophets have had their greatest impact on our political culture: by producing a political class, and its foot soldiers, who believe that God has imparted them with divine knowledge that supersedes what all the evil secularists would have you believe.

In this way, Dominionism may be a prominent example of a certain dangerously Manichaen way of thinking. And you may not even need Francis Schaeffer or Dominionism to think that way–or even participate in a movement with Dominionist roots.  For instance, you could subscribe to Cleon Skousen’s strain of Mormonism. (See this article on the “Tea Party’s artist” John McNaughton, who was influenced by Skousen, and this one on Cleon Skousen and Glenn Beck).

Gerson is right that the public could seize on a “simple idea” about Dominionism, but that misses a critical point. In a complex, modern nation such as ours, it’s crucial for us to know how a candidate thinks–as Keller implies, whether they can think open-mindedly and empirically about important questions. If they’re trapped in dogma, or they toe the line for a certain passionate constituency trapped in dogma, voters need to know that before they cast their ballots.


Why the Most Active Seismic Zone East of the Rockies Gets Ignored | 80beats

quake

The magnitude 5.8 quake that struck central Virginia on Tuesday was felt from Florida to Maine to Missouri. “This is probably the most widely felt quake in American history, even though it was less than a 6.0,” says Michael Blanpied, a USGS seismologist DISCOVER contacted after the event. The reason for this intensity is that the East Coast, like the controversial New Madrid Seismic Zone in the central U.S., is located amidst old faults and cold rocks in the middle of the North American tectonic plate, and seismic waves travel disturbingly far in such stiff, cold rock.

We would do well to take a hint from Tuesday’s expansive shake-up. It’s lucky that it struck in rural America. But a similar tremblor in the crowded cities of the central U.S. above the New Madrid zone is a matter of when, not if. And the region is woefully unprepared to mitigate the damage, as Amy Barth explores in a piece from an upcoming issue of DISCOVER:

The disastrous winter of 1811–12 is the stuff of legend in the Midwest. In the span of a few months, three major earthquakes rocked ...


Putting the eye in Irene | Bad Astronomy

Over the past few days, hurricane Irene has grown as it approaches the United States. The NASA/NOAA Earth-observing GOES 13 satellite has been keeping an eye on the storm, and images it has taken have been put together into this dramatic video showing Irene from August 23 at 10:40 UTC to 48 hours later… just a few hours ago as I write this:

Pay attention about 20 seconds into the video (August 23 at about 20:00 according to the clock at the top of the video). You can see the eye wall region burst into existence, and a few seconds later the eye itself suddenly appears. Also, a surge of white clouds appears to the right of the eye and wraps around the hurricane. That’s where warm air has risen strongly, overshooting the cloud tops, and producing intense rainfall (5 cm/hour according to TRMM!). Overshooting tops, as they’re called, happen frequently in tropical storms as they intensify. For what it’s worth, something like that happens in stars as well as hot plasma rises rapidly from under the surface, though astronomers tend to call it "convective overshoot".

Irene is currently a strong Category 3 hurricane (with ...


Scientific American interviews me about evolution in the city (and more to come) | The Loom

Steve Mirsky, host of the excellent Science Talk, a podcast at Scientific American, talked to me the other day about all sorts of things. Part one of our talk is now online. We talk about my recent story about evolution in New York City. (Scientific American has a special issue dedicated to cities this month.) Listen to the podcast here.

Steve will be posting the second part of the talk soon.


Ann Coulter Nostalgia: Behold, For *I* Am The Giant Flatulent Raccoon | The Loom

It’s been a while since we’ve treated to the spectacle of Ann Coulter lecturing about evolution, but she’s at it again. She’s just written an op-ed in the wake of Rick Perry’s recent statement that Texas teaches evolution and creationism [his word] because evolution is “just a theory out there.”

Coulter takes this opportunity to remind us that she dedicated a third of her 2006 book Godless to demolishing evolutionary biology. Apparently the scientists who have published over 59,000 papers on the topic of evolution since she published her book didn’t get the memo.

To rectify that situation, Coulter now informs us that “it is a mathematical impossibility, for example, that all 30 to 40 parts of the cell’s flagellum — forget the 200 parts of the cilium! — could all arise at once by random mutation.”

Of course, nobody is saying they evolved all at once by random mutation. Nobody except for Ann Coulter. To see what scientists are actually saying, you can start by reading this review that presents a detailed hypothesis about the incremental evolution of the flagellum and the cilium, based on actual experiments. In a ...


An Earthquake Of Another Sort Rocks My House. | The Intersection

This is a guest post by Jamie L. Vernon, Ph.D., a research scientist, policy analyst and science communications strategist, who encourages the scientific community to get engaged in the policy-making process

I woke up this morning to an unexpected jolt, and I don’t mean another earthquake shake.  Nope, this was a little more invigorating. It seems PZ Myers didn’t like my post about Richard Dawkins and he has decided to turn me into a pinata.  I rather enjoyed his piece. He makes some interesting and entertaining points (some well-founded, some…not so much). I don’t mind taking some heat for my opinions. We all know it’s part of being a blogger, right?

I’ve always been amazed by the mob that he unleashes on unsuspecting religious fanatics.  They are quite effective at taking down their prey.  I wish I had been given more notice, I would have at least done my hair and makeup before the party.  I sincerely welcome all the new commenters to The Intersection.  I hope Chris doesn’t mind that I’m wrecking his house while he’s away.

If you don’t know Mr. Myers, he’s an atheist blogger who takes a zero tolerance stance against religion.  Personally, I think he’s an entertaining character, sort of like Bill O’Reilly and Sean Hannity…Ed Schulz, even.  To me, what he does is entertainment, not science communication, but that’s another story.  It’s a story I’ll try to come back to later. Today, I have to do some science and I really don’t have time for a cage match with the Pharyngulites. But, don’t worry folks, I’m here and I’m listening. If you get unruly, though, I’ll have to put you in time out.

What?! It works for my 2 year old.

If we all step back and take a deep breath, we might be able to have a conversation. We might actually learn something from one another.  After all, we speak the same language.  Yelling is not a more effective way to make your point. After I do some work, perhaps I’ll have some time to share my thoughts and I’ll listen to yours, Mr. Myers and Pharyngulites. Even with our differences, I know we’re on the same team.

In the meantime, take a look at this video, and I think you’ll get my point:

Follow Jamie Vernon on Twitter, Google+ or read his occasional blog posts at “American SciCo.”


Ostriches sleep like platypuses (and look wide awake when they do) | Not Exactly Rocket Science

How does an ostrich sleep? Almost imperceptibly, it seems. Even though an ostrich might be sound asleep, it can look wide awake or, at most, a little drowsy. John Lesku from the Max Planck Institute of Ornithology discovered this by fitting six ostrichers with “Neurologgers”, electrode-laden helmets that measures their temperature, brain activity, eye movements and neck muscle contractions.

The video above shows three of the birds cycling through two different types of sleep. The first is called ‘slow wave sleep’ or SWS, where the ostriches’ brain waves are slow and strong. Even though this is typically known as deep sleep, the birds look alert. They stay still, but their eyes are open and their necks upright. Nonetheless, the readings from the Neurologgers clearly showed that they were asleep.

In the second phase, known as ‘rapid eye movement’ or REM sleep, the ostriches’ brain waves are fast and weaker. Now, the birds shut their eyes, which move rapidly behind closed eyelids. They necks also start to droop and sway, righting themselves with awkward jerks like people falling asleep at a talk. Biologists have previously interpreted this as a sign of a tired ostrich. That’s partly right, although the animal ...

Tim Minchin in Boulder! | Bad Astronomy

I’m really excited: the flippin’ brilliant musician Tim Minchin is playing in Boulder on October 9th!

Tim is a skeptic, and a very, um, outspoken one. He is an amazing piano player, and his songs are a combination of devilish music and even more diabolic lyrics. His song Storm (embedded below) became an instant skeptic classic. When he performed at TAM London the audience practically carried him away on their shoulders.

So yeah, I’m pretty happy he’s coming here. As I write this tickets are still available at the Boulder Theater. I’ll be there! I hope to see lots of BABloggees there too. NOTE: his lyrics are NSFW, and I mean that really and truly. But they’re awesome.

Come to think of it, it’ll be interesting to see how Storm will play here in Boulder, where you can’t throw a crystal without hitting a place to get your chakras aligned. Hmmm.

Related posts:

- A Storm has arrived
- TAM London in review


The liberal religious and astrology | Gene Expression

In the comments below a weird fact came to light: it does not seem that liberal/Democrat reduced skepticism toward astrology vs. conservatives/Republicans can be explained just by a secularization, and therefore diminished Christian orthodoxy. There are two reasons for this. First, on a priori grounds most people are religious, liberals and conservatives. The difference between the religious and irreligious on this issue would have to be rather large, and the different apportionment across ideology to be striking, for it to drive the division which seems so robust. Second, within the results it seems rather clear that the gap between liberals and conservatives is most evident amongst the religious of both! In other words, secular liberals and conservatives tend to agree (and be skeptical) in relation to astrology. While religious conservatives are skeptical of astrology, as one would expect from orthodox conservative Christians, religious liberals are not. The table below shows some results.

Astrology is….

Very scientific
Sort of scientific
Not at all scientific

Protestant
Liberal
5
31
64

Conservative
5
18
77

Catholic
Liberal
3
35
62

Conservative
6
25
69

No religion
Liberal
6
22
72

Conservative
9
31
60

Atheist & agnostic
Liberal
7
19
74

Conservative
3
22
75

Believe in higher power
Liberal
3
26
71

Conservative
3
31
66

Believe in god sometimes
Liberal
1
28
71

Conservative
19
18
63

Believe in god with doubts
Liberal
3
29
68

Conservative
3
20
77

Know god exists
Liberal
6
35
59

Conservative
6
21
73

Southern Baptist
Liberal
11
33
56

Conservative
7
16
77

United Methodist
Liberal
4
13
83

Conservative
4
23
73

Episcopal
Liberal
4
23
72

Conservative
5
16
80

Bible is Word of God
Liberal
8
41
51

Conservative
6
22
72

Bible is Inspired Word of God
Liberal
5
28
67

Conservative
5
21
74

Bible is Book of Fables
Liberal
3
23
73

Conservative
8
21
71

Humans developed from animals
Liberal
4
25
71

Conservative
8
25
67

Humans did not develop from animals
Liberal
7
37
56

Conservative
5
16
79

Observe the huge ...

Beware of scientific revolutions! | Gene Expression

Above is the Ngram result for paradigm shift, a ubiquitous descriptive concept which can be quite slippery when applied to contemporary science. For example, every few years there is always a new “revolution” which is going to overturn “Darwinism.” Be it punctuated equilibrium, symbiogenesis, or epigenetics. But over time revolutionary fervor abates, and the orthodoxy remains standing, albeit with modifications and alterations, making it all the more robust.

I thought of this when I saw Andrea Cantor’s comment below in relation to twin studies:

Twin studies underestimate heritability only if you subscribe to the crude notion that the effect of genes is additive, i.e., keeping “environments” the same, the more similar two people are genetically the more alike they will be. This ignores everything we now know about the way genes work.

Genes are not self-activating: they do not turn themselves on and produce traits. Genes do not, in fact, produce anything. Genes are turned on and off by the epigenome in response to environmental inputs. If you are inclined to doubt this, then consider: If all the cells in our body are supposed to contain identical ...

Landfall | Bad Astronomy

I’m on travel with a dodgy internet connection, so I can’t update the blog with news as much as I’d like. But as most of you must know — and some are experiencing — hurricane Irene made landfall, and is now thrashing the U.S. east coast. NASA has GOES 13 satellite video of the event from space:

You can find out more about this video and what it means at NASA’s page on Irene.

I grew up in Virginia and spent a summer in Houston, so I’ve seen my share of hurricanes. This one looks pretty nasty, so I’m hoping everyone stays safe. If authorities tell you to get out, get out. If you guess wrong and stay, it’s not just your life at stake, it’s those who have to rescue you as well.

Credit: NASA/NOAA GOES Project, Dennis Chesters


Riddle Time!

UPDATE:  Solved by Kristian at 12:49 CDT

Welcome!   I see you made it back for another adventure in riddling.

We’re still in reality, but “reality” can encompass a lot of territory.  So, whenever you’re ready, jump right on in to the deep end of reality:

Ljubljana Dragon, Ljubljana, Slovenia

This is a modern discovery.

It would not have been known to our ancestors.

There’s something unusual about today’s answer.

Santa Claus might leave this in your stocking, if you’re anything like me.

In fact, it defines one whole side of normal.

Nobody is exactly sure why, either.

You could say this child is from a two-parent family.

We don’t know if there are any other sibs in the group.

We do know that every 2.5 days, this does something noteworthy.

NASA – Kepler FOV against Milky Way

Alright, chew on that for a while.  You know where to find me when you get an answer, but don’t delay.  I doubt this riddle stays open for very long.

Awwwww! A baby…

I’ve got your missing links right here (27 August 2011) | Not Exactly Rocket Science

Top picks

Anonymous blog written by a Fukushima robot operator, reveals the inner workings of the clean-up effort. He’s probably a Syrian lesbian though.

How do you freak out lampreys? Give them a whiff of death. With TERRIFYING video of deranged, leaping lampreys

The Neuroskeptic is killing it at the moment. He discusses whether sleep give us a chance to defragment out brains and your third parent – random chance – in the context of eugenics.

The illusion of asymmetric insight & how it affects perceptions of others and turns summer camps into Lord of the Flies

A *beautiful* post on resonance, by Ann Finkbeiner.

“Having a restless planet is a consequence of having a habitable one.” Phil Plait on what’s with all the quakes.

I am mightily irritated at this count of “8.7 million species“. Without bacteria and archaea? Nonsense. John Wilkins has the right idea: “It’s hardly an objective fact about the world. We may as well be cataloguing toys.”

Susan Dominus tells the story behind her NYT mag story on remarkable twins joined at the head

Tiny rainmakers: Bacteria, fungal spores & algae in the stratosphere, changing weather

I love that Nature News is the type ...

My Moon hoax | Bad Astronomy

In February 2011 I did a live web video interview with Andrew Shaner of the Lunar and Planetary Institute where we talked about the Moon Hoax. It was a lot of fun!

Andrew just did something great for kids: he took some of the better moments of the interview, along with those from Paul Spudis, a lunar expert, and created a web page called Conspiracy Showdown. It takes some of the more widely-known claims of hoaxery and sets up short clips debunking them. Here’s an example with me, talking about why the Soviets didn’t blow the whistle:

Yes, for some reason he has a guy in a squirrel costume introducing the clips. It’s for kids, so don’t ask. If a quadrilateral sponge can live in a pineapple under the sea, a squirrel can wonder about the Moon Hoax.

Anyway, I think this is a fun thing for schoolkids, if the question of the reality of Apollo ever comes up in the classroom. And who knows? You might like it too.

Related posts:

- My Moon webcast is now online
- Moon Hoax: why not use telescopes to look at the landers?
-

Measure rainfall, help scientists learn more about Hurricane Irene | The Intersection

This is a guest post from Darlene Cavalier, founder of Science Cheerleader and Science For Citizens and contributing editor at Discover Magazine.

Scientists want you to record and share rain measurements and other on-the-ground observations in part to help pinpoint hurricane Irene’s actions, determine her next steps, and better predict and react to future storms. In addition to your help recording on-the-ground rain precipitation, scientists rely on watershed volunteers to provide important clues about the effects of storm-water runoff, carbon cycles of waterways, etc. Here’s a list of opportunities to get involved in local watershed monitoring efforts.

To help scientists record on-the-ground rain measurements, you will need a high capacity rain gauge.

Don’t have a rain gauge? Enter here to win a free one so you can join in next time! Through the Changing Planet series, a partnership with National Science Foundation, NBC Learn, and DISCOVER Magazine, we’re offering up to 20 of these gauges to our members, free of charge ($25 value).

(Note: Safety first. Please heed all evacuation recommendations issued in your area.)

Not able to collect and measure rainfall? Anyone with a computer can also get into the act. The Philadelphia Inquirer published sites where you can find real-time information from ocean buoys, bridges, area stream gauges, and even satellites. [Find list of links, below.]

Here are some opportunities for you to measure rainfall:

CoCoRaHS: Community Collaborative Rain, Hail, and Snow Network The Community Collaborative Rain, Hail, and Snow Network (CoCoRaHS) is a volunteer network of backyard weather observers. People of all ages measure and map precipitation (rain, hail and snow) in communities across the United States. The data is used by a wide range of agencies and programs.Volunteers are needed for two programs.
SKYWARNSKYWARN spotters are essential information sources for the National Weather Service with the responsibility to identify and describe severe local storms. Observations by spotters helps the National Weather Service issue more timely and accurate warnings for tornadoes, severe thunderstorms, and flash floods and thus save lives.
RainlogNot on the east coast? Here’s one for south westerners. Join RainLog‘s network of over 1,000 volunteers that use backyard rain gauges to monitor precipitation across Arizona and in neighboring states. Data collected through this network will be used for a variety of applications, from watershed management activities to drought planning at local, county, and state levels.
Tracking Climate in Your BackyardKids: Tracking Climate in Your Backyard seeks to engage youth in real science through the collection, recording, and understanding of precipitation data in the forms of rain, hail, and snow.

Here are some websites, originally published by the Philadelphia Inquirer, that post data and images to answer the following questions:

How fast is the nearest stream rising?
A U.S. Geological Survey site logs data from stream gauges. http://pa.water.usgs.gov/

Is there a storm-surge tracking map?
Developing, by the U.S. Geological Survey. http://water.usgs.gov/osw/floods/2011_HIrene/index.html

How hard is it blowing in your neighborhood?
Greg Heavener, National Weather Service meteorologist in Mount Holly, recommends this site, where people with personal stations upload their data. Searchable by zip code. http://www.wunderground.com/

What are Delaware River observations?
Includes data from water-level sensors installed on bridges after past floods. http://www.water.weather.gov

What’s happening offshore?
The National Oceanic and Atmospheric Association logs ocean-buoy data, including wind speed and wave heights. http://www.ndbc.noaa.gov/
Rutgers University is part of the Mid-Atlantic Regional Association Coastal Ocean Observing System, which posts data on satellites and the underwater “gliders.” Has an Irene science blog. http://www.maracoos.org/

What does Irene look like?
The National Weather Service’s Hurricane Center has the most recent forecasts, including radar images and wind-speed probabilities. http://www.nhc.noaa.gov/

How about from space?
NASA images and video. http://www.nasa.gov/ mission_pages/hurricanes/main/index.html