Monthly Archives: October 2014

We Just Had The Warmest September on Record

We have been having a run of very warm months, and according to the GISS database, updated yesterday, September was the warmest on record, and the records go back to the late 19th century. This is global average temperature of the surface.

I’ll have more about this later, as other databases are updated. Sometimes one data set shows slightly different results than others, so it is good to look at them all as a group. Also, NOAA has not updated its climate watcher thingie yet.

If October, November and December turn out to be very warm as well, 2014 will end up being one of the top three or four warmest years on record, despite a somewhat cold start.

One liner to turn a column of text into a comma separated list

You have the following list:

Firstline
Secondline
Thirdline
Fourthline
Fifthline
Sixthline

You want to turn it into something that looks like this:

Firstline,Secondline,Thirdline,Fourthline,Fifthline,Sixthline

All you have is a stick of bubble gum, a broken lightbulb, and a bash shell with the usual tools installed. How would you do it?

Here are a few suggestions.

perl -pi.bak -e 'unless(eof){s/\n/,/g}' textfile

This will produce a backup called textfile.bak and modify the original file.

A rather involved sed one liner could do it:

sed -n 's/.*/&,/;H;$x;$s/,\n/,/g;$s/\n\(.*\)/\1/;$s/\(.*\),/\1/;$p'

Using tr:

cat textfile | tr '\n' ','

There are numerous other possibilities. Free to make suggestions. Also, how would you reverse the process?

Science Online Died. Why?

Science Online was an amazing annual unconference that started a few years back and grew and became part of the reshaping of public communication about science. This year, the people running the conference started out with the plan to move the conference to a new venue, Atlanta, and last week abruptly announced that the conference would not happen and the ScienceOnline organization would be shut down. Those who paid the registration fee would be refunded.

A few science writers and bloggers are writing about how great ScienceOnline was and how much it will be missed, and some are providing a few comments about why it had ended. I won’t bore you extensive thoughts about how great the conference was (a little at the end). I’ve written about that before, and since I did not attend the last two, I’m not really in a position to extol its wonderfulness at this point. Besides if you are reading this you surely already know what ScieneOnline was and how great it was.

I would like to know, however, why the project shut down. This is not morbid curiosity. ScienceOnline was a big, vibrant, powerful, a meaningful thing in my profession, and its sudden and unexpected (to me, anyway) demise can’t pass without some analysis. If All the Scientists one Friday morning got an email saying the American Association for the Advancement of Science would stop publishing Science Magazine and shut down all operations by Saturday, they wouldn’t just say “Oh, that was nice while it lasted. Oh well.” They would be compelled to discover why an organization central to their profession would shut down. Well, the demise of ScienceOnline is like that, but a couple of orders of magnitude smaller. Frankly I find the lack of serious consideration as to why ScienceOnline shut down in the few posts that mention it to be odd. Spooky even. Happy Halloween.

Here are my random thoughts on the matter.

ScienceOnline was growing, and there was no significant event or change in the nature of the science communication community that would suggest that such a successful project would not be able to continue. I think it is reasonable to say that it should have continued and it should not have shut down.

There have been suggestions that ScienceOnline was ruined by Bora Zivkovic, the former principle of the operation. Bora was accused, tried, and convicted of inappropriate behavior and forced to resign. The nature of that inappropriate behavior is up in the air, in the sense that people have labeled it with various legally meaningful terms that don’t actually apply, questions have been raised in the same venue as some of the accusations about the veracity of those accusations, and the entire exercise was riddled with posturing, hard feelings, look-at-me-too antics, and a certain amount of bullying, variously coming from some of the dramatic protagonists working from many different angles. There is a Standard Line that goes with the Bora Saga, and within a few weeks of the breaking of that story (almost one year ago, I believe) every one knew the Standard Line. At that point you eitherr towed it faithfully, objected to it anonymously, because questioning it openly felt like it would lead to your own trial and conviction. That was a mess, but I don’t think it had anything directly to do with ScienceOnline closing, because one entire conference happened AFTER that event, and after all, despite the always entertaining ability for so many professionals who operate on the internet to act like middle school students, in the end, most people eventually pull on their big kid pants and get real. Two years after a person involved in a conference leaves the process, the conference can move on.

There have also been suggestions that ScienceOnline was ruined by so-called “Feminazis” who had gone after Bora or used that problem as a means to do their evil work. This suggestion has been made to my knowledge only sarcastically, with the indication that “oh, any minute now the MRA’s (Mens Rights Activists) will be accusing the feminazis of bla bla bla….” I mention this here only so I don’t have to insert it later in an Updated version of this post, because I am perfectly confident the accusation will be made if it hasn’t been already. This possibility is just as absurd of an explanation as the aforementioned “Bora Ruined It” hypothesis. It requires no more consideration. It has been brought to my attention that some have read this paragraph as a suggestion by me that “feminazis” ruined the conference. Clearly, I am saying a) that didn’t happen, b) the idea is out there and c) the idea is stupid. Which is what I said. But now I said it again. AND DON’T USE THAT WORD FEMINAZI

There are two material differences between ScienceOnline 2015 and the previous conferences. One is the venue. The conference has always been held in the Research Triangle, and Scio 2015 would be held in Atlanta. Maybe everybody hates Atlanta. Maybe the Triangle offered a unique palatial charm not to be found many other places. I’m sure that latter aspect is true, but I find it hard to believe that this would cause ScienceOnline to tranmogrify form the “Un Conference” to the “NoWay Conference.”

The second material difference is the registration fee, which I think had gone up to something like $400 (it may have been less than $200 a few years ago). Also, the student price was something like 20 dollars off that, which I regarded as cynical when I first saw it. This could be a real effect.

I have heard that most of the sponsorship dropped out. Some have said this is because they were mad at Bora, but that seems incredibly unlikely for a number of reasons, including his total lack of involvement in the conference. I would like to know why so many sponsors dropped out and what the impact of that was. It may have contributed to the very high registration fee. These two things together may have been a problem.

I also heard that while in previous years there was typically a long waiting list to get into the conference to begin with, this years the number of attendees was way down, far lower than the expected amount (in the 200’s range instead of over 400?). I’d like to see the exact numbers on this. This could be a cause of the failure of the organization and conference; if 200 people fail to give you $200, that’s a lot of moola you didn’t get. Or it could be an effect. All those people who don’t like Atlanta, didn’t want to miss the Charm of the Triangle, and didn’t want to spend twice what they spent in a previous year opted out. Or maybe they were just still mad a Bora and needed to be in a snit, or maybe they were mad at the Bora Haters and needed to be in a snit. Hard to say. My guess is that the price drove a lot of people away.

Added: I’m being told that last year’s conference sucked. I had also heard t was great. But the fact that some people think it sucked matters.

There is one major effect which feels to me like the most likely reason. I may get the following bit a bit wrong in detail, simply because I don’t know all the details, but my understanding is that Karyn Traphagen, Anton Zuiker, an Bora Zivkovic were the three driving elements in prior versions of Science Online (not counting last year) along with a few others. Bora was the most visible face, having been a community organizer de facto or professionally on the Science Internet for years. The three of them made Science Online out of nothing, crafted it, expanded it, made it an incredible success. Then they were no longer involved. Then it shut down. One could hypothesize that the new organizers, and I have no idea who they ended up being, simply killed ScienceOnline because they didn’t know what they were doing. I suppose that question should be asked, but I have no reason to think it. But I do know that a rather amazing, perhaps even unlikely, kind of event was generated by a handful of people, most visible Bora, with Karyn and Anton very much engaged, and it may be that the magic worked only for them. What that magic was I can’t say. Maybe this moment in time … the moment when ScienceOnline 2015 was cancelled, happened every year but Bora, Anton and Karyn simply trudged past that and made it happen anyway. Maybe at this point in time there was always a shortage of interest by the online community but then the Three Conferenceoteers got in every body’s face and made them excited about the upcoming event. Maybe the project always lost its sponsors at this point, but then Bora, Anton and Karyn would show up on their doorsteps, begging or dressed in funny kitten suites or doing whatever they needed to do to bring them back in the fold. This does not imply a lack of will or ability on the part of the organizers that shut down the conference, but rather, an amazing ability that probably grew and developed every year as the project projected, on the part of the original organizers, that was lost when they were lost.

Keep in mind that the transition wasn’t smooth, as I remember. Last year’s conference was still going to happen on the grounds of momentum alone, Bora left, and pretty quickly his compatriots did as well, staying involved for various lengths of time. A smooth transition over a few years of the major players is quite doable. A wholesale housecleaning is dangerous.

For my part, I appreciated ScienceOnline and I’d like to retroactively thank Bora, Anton and Karyn, and others who may have been involved, for making that amazing thing happen. It was inclusive across several dimensions (gender, age, ethnocultural identity, professional level, nature of field). It included art and science. It was unconferencey (though for me that was less of a draw, I’ve been attending unconference style conferences for some time). It had the Charm of the Triangle. It was not in Atlanta! It was a good conference. Thank you three for making that happen. It is a shame to see the project end.

(Quick note added: I now see Karyn is still very much involved but Anton as an advisor. Perhaps it was more Bora originally if my theory of losing the founders as having been important is correct.)

See this discussion.

Added: This is a good run down of possible reasons for the demise of Science Online. I haven’t seen anyone looking for “the cause” (I think most people in this community are beyond thinking so simplistically, we are science communicators and scientists after all) but most of the other points are worth checking out.

Solve the Climate Crisis – Reelect Scott Peters in California's 52nd

This is an endorsement by Climate Hawks Vote, which I support.

Climate Hawks Vote is delighted to endorse Scott Peters in California’s 52d Congressional District of San Diego for his strong climate leadership and for taking first place in our August 2014 survey. And his approach just may break partisan gridlock in Congress.

Scott Peters has a reputation as a problem solver. Climate hawks tend to fly on the left wing of the Democratic Party, but Peters has demonstrated that climate transcends political partisanship. He’s spoken out onsuper-pollutants, national security, and resiliency, all issues that should not be bogged down in partisan bickering.

Peters eked out a victory in 2012 in a swing district, and he’s facing a very tough reelection fight – DC pundits consider his race one of the few true tossups of 2014. He could have ducked the thorny climate issue. Instead, he stepped up to the plate in a big way once in office, taking on a leadership role in the House Sustainable Energy & Environment Coalition, authoring bills, and speaking out in the national and local press. That took political courage.

His courage is reflected in our scorecard, which measures leadership – not just votes – on climate. In the short time he’s been in Congress, he’s in fifth place among all Democrats in the House of Representatives, above stalwart climate hawks in Oregon, Vermont, and deep blue parts of California; the scorecard is cumulative since 2011.

Peters has also been endorsed by the US Chamber of Commerce – the first time we’ve ever agreed with the Chamber! but that fact gives us hope: perhaps climate can transcend politics. We need to return Scott Peters and his problem solving approach to Congress.

Peters joins our list of fall 2014 endorsees including Shenna Bellows (Maine-Senate), Paul Clements (Michigan-06), and Gary Peters (Michigan-Senate). We’re backing up our endorsement with organization on the ground in this swing district. Our on-the-ground organizers helped Brian Schatz close the deal in the Hawaii Senate primary and helped Ruben Gallego defeat a coal-funded opponent in Arizona’s 7th Congressional District.

First person in US to catch Ebola: The Meaning of Ebola Patient Two (updated)

The first person ever to catch Ebola in the United States is now in isolation at Texas Health Presbyterian Hospital.

Don’t panic, even if you live in Dallas. But also, don’t fall into the hyperskeptical trap of assuming that because scientific authorities tell you everything is fine that concern is irrational. There are very rational reasons to be concerned. But you need to be smart about what to be concerned about.

A couple of weeks ago, as you know, a man came to Dallas with pre-symptomatic Ebola, and became symptomatic there. This was the first case of a person being diagnosed with Ebola in the US. The case was botched. The hospital sent home a man with pre-Ebola symptoms who had come from West Africa. He was later admitted after he got a bit sicker and tried a second time to get treatment. There were other ways in which the case was not handled too well, mainly from a public relations and messaging standpoint, but the CDC and the hospital involved seemed to be doing a good job and getting their acts together.

Now, the situation has developed in a rather disturbing way. A health worker that had been caring for Patient 0 has now been diagnosed with Ebola. This happened overnight. The patient was under self monitoring, had a mild fever, went to the hospital, was tested, and the reasonably reliable preliminary test indicated Ebola. A second much more reliable test is being done now but it is expected to be positive.

I just watched the news conference and from this I gathered the following important bits about the new patient.

<li>The patient was in the low risk pool.  Among Patient 0's contacts, there were higher risk and lower risk.  Higher risk individuals were being isolated and/or monitored very closely, lower risk individuals were self monitoring. This patient was self monitoring.</li>

<li>The person cared for Patient 0 during his treatment prior to his death at Texas Presbyterian; there was no contact during the initial botched visit. </li>

<li>The new Ebola patient used protective procedures (gown, mask, gloves) in that care.  The exact nature of the care beyond that is being kept secret at the moment owing to HIPAA rules.  (But see below to see how absurd the HIPAA rules are in this case.)</li>

<li>The new patient seems to have lived with a second person who is now also in isolation.</li>

Hazmat suit wearing teams arrived during the night at the apartment complex of the new patient, and decontaminated public areas such as the lobby of the apartment building, and the interior of the patient’s car. It is thought that there is a pet inside the person’s apartment, but teams, as of this writing have not entered the apartment. They plan to do that soon. Local police doorknocked everyone in the “immediate area” to explain to them that they should not panic, did a “reverse 911” call for the area, and are re-door knocking this morning. So, the identity of the patient will be known any moment now because you can’t really do all that without that happening. (Which, frankly isn’t too relevant. I’m not sure if HIPAA rules should protect health care workers in quite the same way as patients, though they may in fact do so.)

So, what is the meaning of this all?

First it means that when hundreds of administrators, police, government officials, hospital employees, health workers, etc. are tasked with the job in the US of making sure no one gets Ebola from a person who has Ebola, and also tasked with the care of that person, a) one person gets Ebola anyway, and b) the first patient dies.

I very quickly add that this is a TINY SAMPLE SIZE OF N=1 and I’m being a bit cynical here. But it is still true that all these resources failed to prevent what every one feared, and what the authorities said would not likely happen.

Second, note that this new patient did not get Ebola from Patient 0 prior to his first visit to the hospital, or after that first botched visit. Again, small sample size, but it points out something important. When we say that a human with Ebola can spread the disease only when they are symptomatic, that probably doesn’t even count the initial fever period. Infectiousness is probably correlated to the severity of the symptoms. The family members or heath workers who deal with the bodily fluids randomly coming out of a person who is dying of Ebola, bed ridden and very sick, are at the highest risk, even those in the lower risk pool like this new patient. (This is why the HIPAA rules need to be set aside. We actually need to know what this person’s role in the process was, what this person did exactly. That is important information that the public has a right to know. If this reveals the name of the worker by deduction, then so be it. The person’s name has already been effectively revealed by deduction form the activities at the person’s home.) But, importantly, once a person is really infectious, they are really, really, infectious. See my quick note below on spread of Ebola.

Third, note that the medical authorities have said all along that following proper procedures minimizes risk. Note that even when following proper procedures one person was infected anyway. Note that at this morning’s press conferences, the authorities have not changed their story. This is partly your fault, members of the public, because collectively you seem unable to understand that Ebola is both very dangerous and manageable. Your collective insistence that your fear being ramped up is somehow proof that Ebola has gone airborne is an example of that. If you collectively stop being unmitigated morons about this, then the authorities can stop being alarmingly Orwellian about it. Maybe.

Fourth, think about this. A huge effort is made to avert a possible Ebola outbreak. The effort fails in a couple of ways, but we get lucky, those failures don’t cause too many problems other than, possibly, the death of the patient because care was not timely and proper drugs were not administered. But as far as the concern over an outbreak goes, the early screw ups did not cause one. So, proper and resource intensive procedures are in place and everything is going as well as it can be. Then somebody gets ebola anyway. This explains West Africa. Here, in the US, we have 200 people for every Ebola patient. In West Africa, you might have 1 person for every 100 (possible) patients out there. Those numbers are made up, but you get the point. In order to limit Ebola in West Africa we’d have to do what we can do here, and that proves to be of limited utility. Prior outbreaks were stopped because of the high ratio of health workers AND the disease burning out by killing almost everyone in some families or small villages so spread was stopped. So now we have a better sense of what is going on there. Imagine that every person in the US isn’t just someone who heard about Ebola in some other city. Imagine, instead, that everybody in the US lives in an apartment building in which one or two other people in the building have Ebola. And there are no hospitals.

So, collectively, that is all good news and bad news. One more piece of good news: We are near the end of the period during which someone who may have been infected might show up.

On the spread of Ebola

I’ve written about how Ebola is spread before and about the unlikelihood of it “becoming airborne” (see links below). But I keep hearing, again and again, that this or that vague observation someone has made proves that it has already gone airborne. Well, I’ve got a bit more to add to that discussion to help people put it in perspective. The truth is, pretty much every one who is saying it is already airborne or that it is likely to go airborne or that eventually it is inevitable that it will go airborne is an airhead. Sorry for the strong language, but at this point it is simply true that with so much information out there about this being utterly wrong is not acceptable.

Consider Norovirus. It is roughly as infectious as Ebola. Two years ago, for example, we had an outbreak of it here in the Twin Cities. Someone at my son’s daycare had it. Then my son, then everyone else at his daycare, and everyone in our family, and everybody. Had it been fatal, the entire region would be dead. It is not airborne, but it is a disease that there is a good chance all the people crowing about Ebola needing to be airborne have had, have seen in action. Next time you feel the need to insist that Ebola is airborne remember the last time everybody in your family, one by one, got the “stomach virus” (as it is often called). It wasn’t airborne. You got it because germs form someones’ poop or vomit got into your mouth. Perhaps you should not have been licking people’s anuses or drinking their vomit with a straw during that time. Oh, you claim you did neither of these things? OK, fine, you weren’t doing that. But you still got kooties that came from vomit or poop. The way bodily fluids get around, and the opportunities for contact, are much greater with Ebola. With the stomach flu, most of the time most people can make their own way to the bathroom to have diarrhea and vomiting. With Ebola, the sicker patients are lying in bed doing this in a closed room. Everything gets kooties on it. Maybe they were soiling themselves and puking for a few hours in a “taxi” waiting to get into a hospital. Touch touches stuff that touches stuff and bits of Ebola rich feces or Ebola laced vomitus are now on your hands.

Even the flu is only barely spread airborne, but mainly through direct or indirect contact. Ebola is more infectious because it does better with indirect contact.

UPDATE: Major Media is reporting, based on a Sunday AM show interview, that there was a “breach” in protocol in Dallas. But the doctor interviewed did not say that. He said, essentially, that there must have been a breach but they do not know what happened. This is important for media to get right, and it is the media’s job to get these things right. If there was no breach in protocol, then the existing protocol allows for Ebola to cross the boundary. If there was in fact a breach, and we know what it was and can confirm it, that is a very different situation. To be clear: The fact that protocol was in place and used and Ebola got across does NOT mean that Ebola is being transmitted by air or in some other unknown way. It could mean that protocol was breached, but without specific evidence we don’t know that to be true, and we don’t know what went wrong. In between these two is the very high probability that standard protocol has a weakness or two that could be shored up. Personally, based on my own experience (not with Ebola) and based on some reports from the field, I would suggest this has to do with how gowns, masks, and esp. gloves are handled. You have to use the same kind of protocol to remove these things as when you are using these things. Perhaps care workers should be demasked, degloved, and degowned by a masked/gloved/gowned coworker who has just suited up in a space away from the patient. (I don’t think that is done now.)

More on Ebola:

Pterosaurs by Mark Witton

Pterosaurs: Natural History, Evolution, Anatomy by Mark P. Witton is a coffee-table size book rich in detail and lavishly illustrated. Witton is a pterosaur expert at the School of Earh and Environmental Sciences at the University of Portsmouth. He is famous for his illustrations and his work in popular media such as the film “Walking With Dinosaurs 3D.”

The first pterosaur fossil was found in the late 18th century in the Jurassic Solnhofen Limestones, in Germany, the same excellent preservational environment that would later yield Archaeopteryx. They person who first studied it thought the elongated finger bones that we now know supported a wing served as a flipper in an amphibious creature. Not long after, the famous paleontologist George Cuvier recognized the winged nature of the beast. Witton notes that at the time, and through a good part of the 19th century, it was possible to believe that many of the odd fossils being unearthed were of species that still existed but were unknown to science. This is because most of the fossils were aquatic, and who knew what mysterious forms lurked beneath the sea? But a very large flying thing like this first pterosaur was very unlikely to still exist, unseen by European and American investigators. It had to be something major that was truly extinct. So in a way the history of extinction (the study of it, that is) was significantly shaped by this find. By the early 20th century there had been enough publication and study of pterosaurs to give them a place in paleontology, but not a lot else happened until the 1970s, when a combination of factors, including advanced technology that allowed more detailed and sophisticated study of fossils, led to much more intensive study of pterosaur anatomy and behavior.

Pterosaurs are part of the large taxonomic group that includes the lizards, dinosaurs, and birds, but they branched off within that group prior to the rise of the latter two. So, they are not dinosaurs, but cousins of dinosaurs. You can call them flying lizards, but not flying dinosaurs.

Witton explores this interesting history in some detail, and then proceeds to explore various aspects of pterosaur biology, starting with the skeleton, the soft parts (of which there is some direct but mostly indirect evidence), their flight, how they got around on the ground, and their reproductive biology. These explorations into pterosaurs in general is followed by several chapters devoted to the various groups, with a treatment of the evidence for each group, reconstructions of anatomy, locomotion in the air and on the ground, and ecology.

The resemblance of this layout to a detailed field guide for birds (or some other group) is enhanced by the use of color-coded bleeds at the top of each page, separating the book’s major sections or groups of chapters. The book ends with a consideration of the origins and endings of the “Pterosaur Empire.” It turns out that we don’t actually know why they went extinct. They lasted to the end of the Cretaceous, so going extinct along with their dinosaur cousins is a reasonable hypothesis, but they had already become somewhat rare by that time.

Pterosaurs are cool. Pterosaurs: Natural History, Evolution, Anatomy is a cool book.

Of related interest:

  • LOL Pterosaurs ….
  • Reconsidering the Reconstruction of the Pterosaur
  • Flying Dinosaurs: A New Book on the Dinosaur Bird Link
  • Giant Semiaquatic Predatory Dinosaur
  • Titanic Fearless Dinosaur Unearthed
  • Honey, I Shrunk The Dinosaurs …
  • NewLink Genetics, of Ames Iowa, Implicated in African Ebola Genocide?

    According to those intimately involved in the response to the West African Ebola outbreak, NewLink Genetics owns the rights to a piece of the puzzle needed to quickly test and deploy one of two likely Ebola vaccines and they are holding up the entire process because they are not entirely sure they are going to get rich on it. Other suggest it is incompetence. NewLink seems to be claiming it is just a lot of paperwork. In the end, tough, none of these excuses is convincing. This is one of those cases that gives Big Pharm a bad reputation.

    From as story in Science:

    Stephan Becker is tired of waiting. The virologist at the University of Marburg in Germany is part of a consortium of scientists that is ready to do a safety trial of one of the candidate vaccines for Ebola. But the vaccine doses he’s supposed to test on 20 German volunteers are still in Canada. Negotiations with the U.S. company that holds the license for commercialization of the vaccine…have needlessly delayed the start of the trial… “It’s making me mad, that we are sitting here and could be doing something, but things are not moving forward,” Becker says.

    … it’s inexplicable that one of the candidate vaccines, developed at the Public Health Agency of Canada (PHAC) in Winnipeg, has yet to go in the first volunteer’s arm, says virologist Heinz Feldmann, who helped develop the vaccine while at PHAC. “It’s a farce; these doses are lying around there while people are dying in Africa,” says Feldmann,…

    At the center of the controversy is NewLink Genetics, a small company in Ames, Iowa, that bought a license to the vaccine’s commercialization from the Canadian government in 2010… Becker and others say the company has been dragging its feet the past 2 months because it is worried about losing control over the development of the vaccine. But Brian Wiley, vice president of business development at NewLink Genetics, says the company is doing all it can. “Our program has moved forward at an unprecedented pace,” he says. Even if it took another few months, “we would still be breaking a record in terms of getting this into patients.” Wiley says the holdup is “the administrative process”: agreeing on a protocol, getting collaborators to sign the right contracts, securing insurance in case something goes wrong.

    Marie-Paule Kieny, a vaccine expert and WHO assistant director-general, disputes that NewLink is dragging its feet. “We have so far been able to resolve issues along the way, to get moving as fast as possible,” she says.

    A stock of the Canadian-developed VSV vaccine is stored at PHAC in Winnipeg. The Canadian government owned 1500 doses, 800 to 1000 of which it has donated to WHO; the rest are owned by NewLink Genetics.

    Scientists say WHO’s vials could have already been shipped to the research centers planning to do phase I trials. One such trial is scheduled at the Walter Reed Army Institute of Research in Silver Spring, Maryland; other studies, by a consortium that includes WHO and Becker, are on the drawing boards in Hamburg, Germany, in Geneva, and at sites in Kenya and Gabon. PHAC is ready to ship the doses “at a moment’s notice,” a representative says.

    But for a clinical trial to start, regulators require information about how the vaccine was manufactured, and that resides with NewLink Genetics, which has been slow to release it, people familiar with the negotiations say. …

    Part of the problem may be that NewLink is a small company, with about 100 employees, that has concentrated on immunotherapies to fight cancer in recent years. The Biomedical Advanced Research and Development Authority—a U.S. government agency tasked with speeding up the development of emergency drugs and vaccines—recently sent two staffers to Ames to help NewLink file documents needed by the U.S. Food and Drug Administration, a U.S. government representative says. “Our engagement of outside help has nothing to do with our competence, but with the urgency around this matter,” Wiley says.

    Those who are taken ill and die of Ebola are the victims of a natural disaster, until paperwork, incompetence, greed, or some combination of those delays an international response by weeks time. After that, it is something else.

    Humans being loud under water, Cuttlefish

    Last June (and May and July and part of August) we had a lot of precipitation in Minnesota. This caused lake levels to rise modestly. One lake, which is large enough to have meaningful waves, has older settlement along it so lots of cabins, boat houses, and such are right on the shoreline. With the lake level up, waves threatened the material possessions of rich white people, so naturally something had to be done. A No-Wake Rule was put into effect.

    A No-Wake Rule means the oversized fishing boats and smallish cabin cruisers that normally ply this large exurban lake need to all go at 5 m.p.h. or less, and forget about wake boarding, water skiing, and all those other fast, wake churning activities. The result? A lot of butt hurt, a near First World depression setting in in the Twin Cities wester suburbs. Somebody took away our boy toys!

    But then, somebody went fishing. It isn’t a great fishing lake. It is mainly a go-fast lake. In fact, it is on this particular lake, I believe (with no evidence I quickly add) the method of fast-trolling for muskies was invented. This is a way to “go fishing” and go fast at the same time. You drag the lure behind you as fast as your boat will go. It is said you can catch muskies this way. To my knowledge it has never happened. Just more boy toy.

    Anyway, somebody went fishing on the No Wake Lake, and guess what happened? They caught a boat load of fish! Literally! Then their friends went out fishing, and they caught a boat load of fish too! Pretty soon all the fisherpersons who had access discovered that when you don’t drive giant boats back and froth across the lake at high speed all day, the fish feed. When you do, they hunker down, feed infrequently, and grow slowly.

    Now, I’m not going to vouch for this relationship just yet, but it makes intuitive sense. In my own experience, quiet places are where you catch fish. If I’m fishing up at the lake, once the boats start driving around skiing (say on a fourth of july weekend) I might as well reel it in and go get a beer, because that’s the end of the fishing. I’m pretty sure my best fishing has been on Wednesday and Thursday, before the startup of the loud and noisy weekend. And that’s on a quietish part of a relatively quiet lake.

    The only reason I’m mentioning this now is because I came across this story from my Science News Roundup:

    The blare of human noise causes birds to pipe down and frogs to breed less frequently. Now, scientists have found a humanmade sound that has a far more colorful effect: The boom of a ship’s engine makes common cuttlefish (Sepia officinalis) change the complex swirls of skin hues, stripes, and spots that they use for camouflage and communication. …when researchers placed a loudspeaker near cuttlefish tanks and played the sound of an underwater engine, the animals swam more and changed colors more often. They also raised their first pair of arms, which are used to sense water movements, more frequently…The sounds of crashing surf had no effect, providing the first evidence that engine noise may stress the animals out.

    The original story is here, in American Naturalist.

    I would love to see a large number of large lakes shut down for boating. No motors. Eventually, of course, there will be no gas powered motors, with the shut down of fossil fuels. I promise you, when we start using quiet electric boats for fishing, the fishing will get better.

    Paul Clements and Gary Peters for Congress in Michigan

    This is an endorsement by Climate Hawks Vote, which I support.

    Climate Hawks Vote announces endorsements of two Michigan Democrats: Paul Clements for Congress in Michigan’s Sixth District, and Gary Peters for Senate, because the Koch brothers and Big Oil need to stop using Michigan’s shores as a dumping ground for their pollution and Michigan’s politicians for their agenda.

    Paul Clements is challenging none other than Fred Upton, chair of the House Energy & Commerce Committee – these days, the House Big Oil Lackey Committee. As the face of Big Oil, Upton was named the number one enemy of the earth. It’s into his pockets that Big Oil money goes – he’s among the top recipients of money from the oil, gas, and coal-fired electric utility industry. And when Big Oil spilled into the Kalamazoo River, Upton demanded answers for about a week, then went back to business as usual, pushing bills to gut the EPA.

    Voting out Fred Upton piqued our interest… but Climate Hawks Vote won’t get involved in a race between a horrible Republican and a mediocre Democrat (we won’t name names, but our scorecard will). Luckily for the voters of southwestern Michigan, Paul Clements is a true climate champion. “Climate change is the greatest threat to Michigan and to the world in the 21st century,” he says. His new ad – watch it here – touts clean energy solutions.

    We wouldn’t be endorsing if we didn’t think Clements has a chance; he’s considered to be Upton’s toughest challenger in years, and anything can happen to entrenched incumbents in a year in which Eric Cantor lost. The district begins as R+1, i.e. a very slight Republican edge that can be beaten by smart Democratic campaigning. Climate Hawks Vote aims to defeat Upton to send a clear message: Big Oil and Michigan waters don’t mix.

    We’re also endorsing Gary Peters, running against Terri Lynn Land in an open seat for Senate. Like Clements, Peters is explicitly running on climate change and the effect it’s having on the Great Lakes. Peters fought the Koch Industries-created piles of petcoke in Detroit, and he’s been carrying a bill to boost electric vehicles – a classic made-in-Michigan solution to climate change.

    As before, we’re backing up our endorsement with talons, er, boots on the ground for Peters + Clements voters. Our on-the-ground organizers helped Brian Schatz close the deal in the Hawaii Senate primary, and we helped Ruben Gallego defeat a coal-funded opponent in Arizona’s 7th Congressional District. We aim to win in Michigan.

    Antarctic Sea Ice and Global Warming

    Did you ever leave your freezer door slightly open on a humid day only to find chunks of new ice formed at the gap? When that happens, did you conclude “Oh, my freezer is colder than usual, I wonder how that happened?” No. You concluded that you had left the door slightly open, some cold got out, and vapor froze on your gasket.

    Sea ice is hard to make. The sea is salt water, so it has a lower freezing point than fresh water. The sea has potentially large waves and lots of currents. This is just not a situation where ice can easily form. Yet, it does form on the oceans near the Earth’s poles because it is really cold there. But even within that context, more or less ice can form because of important details like how much fresh water is mixing in with the cold salt water, and exactly where currents of warmer or colder water are going. The formation of sea ice at the ends of the Earth is probably somewhat more complicated than the formation of frost and rind on your refrigerator.

    (A quick note: Sea ice is ice that sits on, and therefore, essentially, in the sea. It is not glacial ice. Those are two very different things. I’m sure you knew that but just in case this is a good moment to point it out.)

    In recent years, the amount of sea ice forming around Antarctica has bee going up. Global warming causes local warming but it also causes local cooling (like when the Arctic Vortex got knocked off center last winter and visited the middle of North America, an event that still causes a sense of fear and loathing among those of us who experienced it). So when we hear about expanding sea ice in the Antarctic, knowing that anthropogenic global warming is a real thing, we might assume that this is just one of those phenomena that runs counter to expectations but that is still part of the overall process of warming-driving climate change resulting from the addition of greenhouse gasses to the atmosphere.

    And that is essentially correct, though the reasons may be a bit unclear and require further study.

    So, thinking about our freezer, and the overall problem of making sea ice, there seem to be three things that can cause more of this ice. One might be the addition of fresh water to the system. That seems likely if the Antarctic glaciers are melting (which they are). Depending on where the fresh water goes, that could allow the formation of sea ice. Also, if precipitation increased in the area, that would add fresh water.

    Second, the area where the sea ice is forming could be colder. That seems backwards in on a warming planet, but actually, that can happen too. Antarctica is, to a larger extent than the Arctic, a semi-closed system of air and sea currents, because it is a roundish continent surrounded by sea at one end of the planet. This means that cold air might be retained over the continent rather coherently. At the North Pole, “Winter (January) temperatures … can range from about ?43 °C (?45 °F) to ?26 °C (?15 °F), perhaps averaging around ?34 °C (?29 °F),” while at the South Pole, “In winter, the average temperature remains steady at around ?58 °C (?72 °F).” (source: Google). The north pole is sea, the south pole is land, and the south pole is at a higher elevation, but those differences are partly why the south pole is colder. Anyway, with all this cold air on the Southern Continent, perhaps one only needs to have air currents change a little to move that cold air over the sea a bit more to add to the chances of freezing water and making sea ice.

    Third is the possibility that the disruptive effects of storms, waves, or surface currents could change, making for a calmer environment, allowing more ice formation.

    Have any of these things happened?

    Yes. Yes, they have.

    Joe Romm has a writeup on some recent research that helps to explain the increase in Antarctic Sea ice (NOAA: Record Antarctic Sea Ice Growth Linked To Its Staggering Loss Of Land Ice).

    The National Snow and Ice Data Center notes:

    …sea ice surrounding the Antarctic continent reached its maximum extent on September 22 at 20.11 million square kilometers (7.76 million square miles). This is 1.54 million square kilometers (595,000 square miles) above the 1981 to 2010 average extent, which is nearly four standard deviations above average. Antarctic sea ice averaged 20.0 million square kilometers (7.72 million square miles) for the month of September. This new record extent follows consecutive record winter maximum extents in 2012 and 2013. The reasons for this recent rapid growth are not clear. Sea ice in Antarctica has remained at satellite-era record high daily levels for most of 2014.

    “What we’re learning is, we have more to learn,” said Ted Scambos, lead scientist at NSIDC.

    The unusual sea ice growth in Antarctica might be caused by changing wind patterns or recent ice sheet melt from warmer, deep ocean water reaching the coastline, according to scientists at NSIDC. The melt water freshens and cools the deep ocean layer, and it contributes to a cold surface layer surrounding Antarctica, creating conditions that favor ice growth.

    From Skeptical Science:

    The most common misconception regarding Antarctic sea ice is that sea ice is increasing because it’s cooling around Antarctica. The reality is the Southern Ocean surrounding Antarctica has shown strong warming over the same period that sea ice has been increasing. Globally from 1955 to 1995, oceans have been warming at 0.1°C per decade. In contrast, the Southern Ocean (specifically the region where Antarctic sea ice forms) has been warming at 0.17°C per decade. Not only is the Southern Ocean warming, it’s warming faster than the global trend. This warming trend is apparent in satellite measurements of temperature trends over Antarctica…

    And, from NOAA:

    Much of this year’s sea ice growth occurred late in the winter season, and weather records indicate that strong southerly winds blew over the Weddell Sea in mid-September 2014. Antarctica is a continent surrounded by open ocean. So unlike the Arctic, where surrounding landmasses constrain how much sea ice can expand, Antarctic sea ice can spread out over a bigger area. Winds blowing from the land toward the ocean encourage ice growth in the waters north of the continent.

    Winds probably did not act alone to spur so much sea ice growth; melting land ice may have played a role. Most of Antarctica’s ice lies in the ice sheets that cover the continent, and in recent decades, that ice has been melting. Along the coastline, ice shelves float on the ocean surface, and much of the recent melt may be driven by warm water from the deep ocean rising and making contact with ice shelf undersides.

    How does the melting of land ice matter to sea ice formation? The resulting meltwater is fresher than the seawater. As it mixes with the seawater, the meltwater makes the nearby seawater slightly less dense, and slightly closer to the freezing point than the ocean water below. This less dense seawater spreads out across the ocean surface surrounding the continent, forming a stable pool of surface water that is close to the freezing point, and close to the ice onto which it could freeze.

    Added cold seems to be a factor. Added fresh water seems to be a factor. Changes in where cold air and relatively fresh water goes seems to be a factor. I don’t know about storminess and currents at the outer edge of ice formation.

    The dramatic and steady increase in Antarctic Sea Ice is yet another example of the effects of climate change.

    Vote For Jeanne Shaheen, New Hampshire Senate

    This is an endorsement by Climate Hawks Vote, which I support.

    We’re working our way through scoring Senate Democrats on climate leadership, using the same lodestar that we’ve used on House Democrats: who’s leading on climate by engaging the public? It’s slow going – results might not be final until mid-October or later. However, given the intense interest in certain races, we’re releasing a few scores early. Jeanne Shaheen has earned a high score, and thus our endorsement, for her deep commitment to energy efficiency.

    Jeanne Shaheen, New Hampshire Senator, has earned a very high score on our scorecard, and thus our endorsement. She’s carrying one bill, the Energy Savings & Industrial Competitiveness Act, so we knew she had an interest in energy efficiency. What surprised us in scoring her actions was the depth of her commitment to the issue. She’s stumped for energy efficiency up and down her home state. She’s visited manufacturers, Portsmouth Naval Shipyard, Ivy League classes, an island historic hotel, and, it seems just about every business in the state to send a message with broad appeal: the energy that is both the cheapest and the cleanest is the energy that isn’t used in the first place. She’s been speaking out on energy efficiency, frequently and consistently, for years. And in doing so, she’s educated and engaged the public on a critical issue with bipartisan appeal.

    If Shaheen were in the House of Representatives, she’d rank among the top half-dozen House Democrats on our tough scorecard. Again, we’re scoring leadership to separate climate hawks from those who might vote the right way but who duck the issue in engaging with the public.

    Shaheen is being challenged by a joke of a Republican who’s flip-flopped as much on climate science as his residency. However, Climate Hawks Vote doesn’t endorse mediocre Democrats who’ll put the climate crisis on the back burner just because they’re fighting bad Republicans. Rather, we selectively endorse only those who demonstrate leadership. Here, Jeanne Shaheen understands the moral imperative of the climate crisis. She’s working with a Republican, Rob Portman (R-OH), to pass a solid bill. She’s earned our endorsement, and she deserves another term in the Senate.

    Shenna Bellows of Maine for Senate

    This is an endorsement by Climate Hawks Vote, which I support.

    We’re endorsing climate hawk Shenna Bellows to be the next Senator from Maine because business as usual is no longer good enough in the face of a local and worldwide crisis. Long-time incumbent Susan Collins admits the existence of a problem, to her credit; but far from proposing credible solutions, her actions range from policy homeopathy to delay to active hindrance.

    While working on our sophisticated scorecard measuring leadership – not just votes – on climate for Senate Democrats, we are also tracking four Senate Republicans in advance of the 2014 election. We’re measuring Susan Collins’ record of public engagement, bills authored and cosponsored, press releases, website, and internal Senate groups joined, beginning January 2011, using the same yardsticks we’re applying to Democrats. And, to be blunt, her record of leadership is worse than her mediocre voting record.

    We weight public engagement far more than any other factor. Leaders need to be interacting with citizens on this immense issue, whether it’s speeches on the Senate floor or town halls with local fishermen or keynoting business conferences. Collins hasn’t done any of that. Instead, she had one moment in the spotlight in September 2011 delivering the GOP’s rebuttal to President Obama’s weekly address, in which she demanded a time-out for EPA regulations.

    The bills she’s authored have been, mostly, to track, curb, and delay “major regulations,” DC-speak for EPA rules. She’s cosponsored a pro-Keystone XL bill and bills to “rein in the EPA.”

    Her press releases likewise sound a similar theme: the only acceptable response to climate change is to sit down and do nothing for a year. Or two. Or until Congress thinks of a plan to repeal and replace Obamacare, ooops, we mean, EPA regulations.

    Collins’ appeal to some national environmental groups is obvious: she accepts the science, unlike most Republicans of the climate zombie era, and bipartisanship sounds nice. But her delay-and-dither approach is flat out wrong. Maine, faced with ocean acidification and warming seas affecting its iconic lobster harvest, deserves better. Support for business-as-usual politicians like Collins, and her many counterparts on the Democratic Party side, is tantamount to acceptance of a business-as-usual carbon emissions trajectory.

    We founded Climate Hawks Vote to elevate the voices of those few leaders who see the climate crisis as a priority. Shenna Bellows has earned our endorsement. She will seek limits on carbon emissions. She opposes the Keystone XL pipeline. And – unlike Collins – she’s taken a firm stand on an issue important to Maine voters and the larger climate community: she’s opposed the proposed Portland Montreal Pipeline Reversal, a plan to re-engineer an existing pipeline to carry carbon-intensive tarsands from Canada to Portland, Maine and then to the global marketplace. Maine needs to elect Shenna Bellows to the Senate.

    As with prior races, we’re backing up our endorsement with organizing on the ground. Past successes include winning nominations for Brian Schatz, Hawaii-Senate, and Ruben Gallego, Arizona-07.

    Can Dogs Transmit Ebola? And, should Excalibur be put down? they put down Excalibur.

    UPDATE: They killed the dog.

    UPDATE: I’m adding this here because it is my current post on Ebola. Thomas Eric Duncan, the person who became symptomatic with Ebola in Dallas, had died at the Texas Health Presbyterian Hospital (according to news alerts).

    A nurse’s assistant in Spain caring for Spanish nationals returned with Ebola from West Africa contracted the disease, gaining the dubious distinction of being the first person to be infected with Ebola outside of that disease’s normal range in West Africa, Central Africa and western East Africa. There is speculation that she contracted the disease by contacting the outside surfaces of her own protective gear, which is exactly what I’ve speculated to be a likely cause of infection in health care workers. This is not certain, however.

    Members of her family and others, including additional health care workers, are in quarantine. There is evidence that the hospital procedures were inadequate to keep a lid on Ebola in this context, and nurse’s unions and others are protesting and demanding change.

    Meanwhile, the Spanish government has claimed that there is “scientific evidence” that dogs can transmit Ebola, so Excalibur, the nurse’s family dog, will be euthanized and incinerated. People have gone to the streets to safe the dog.

    So, can dogs get, or transmit if they get it, Ebola? Short answer: Yes, and probably not. Here’s my thinking on this, and some information.

    1) Pick a random species, or to make it easier, pick a random mammal, and test to see if it can transmit a disease known in humans. It is unlikely to be the case because diseases are to some degree adapted to exist in certain hosts, and host vary, well, by species. So it seems unlikely.

    2) On the other hand, Ebola seems to be able to infect a very wide range of mammals. Ebola resides in multiple species of fruit bats (though maybe not uniformly or equally well). A range of mammals seen to be suitable intermediates between fruit bats and humans. The mammals known to be able to harbor Ebola are diverse. It isn’t like only primates can be infected. So, it seems quite possible.

    3) On the third hand, I’ve never heard of dogs being addressed as an issue in the current crisis in West Africa or during prior outbreaks. One would think that if dogs were a concern this would have been mentioned by someone some time.

    4) On the fourth hand, dogs in Central Africa are less likely to be house dogs, hanging around with the family on the couch, and more likely to be working dogs that spend all their time outdoors. A Spanish family pet may have hung around on the sick bed with an ill individual. I don’t know about dogs in West African cities. By the way, you have to go look to see what the story with dogs there is, and it may within that context. I’ve noticed that westerners tend to have a rather monolithic view of how humans “elsewhere” (especially the “third world”) relate to their dogs, based on a concept we hold of them, not based on actual knowledge. How dogs fit in with humans from place to place and time to time varies.

    5) I’ve read a good amount of the peer reviewed literature on Ebola and I can not recall anything about dogs.

    5) But … A quick check of Google Scholar did come up with one study. From the abstract:

    During the 2001–2002 outbreak in Gabon, we observed that several dogs were highly exposed to Ebola virus by eating infected dead animals. To examine whether these animals became infected with Ebola virus, we sampled 439 dogs and screened them by Ebola virus–specific immunoglobulin (Ig) G assay, antigen detection, and viral polymerase chain reaction amplification. Seven (8.9%) of 79 samples from the 2 main towns, 15 (15.2%) of 14 the 99 samples from Mekambo, and 40 (25.2%) of 159 samples from villages in the Ebola virus–epidemic area had detectable Ebola virus–IgG, compared to only 2 (2%) of 102 samples from France. Among dogs from villages with both infected animal carcasses and human cases, seroprevalence was 31.8%. A significant positive direct association existed between seroprevalence and the distances to the Ebola virus–epidemic area. This study suggests that dogs can be infected by Ebola virus and that the putative infection is asymptomatic.

    I’ve not looked further at the literature. This study suggests, unsurprisingly (see point 2 above) that dogs can harbor the virus. However, they don’t seem to be symptomatic. Therefore, spread from a dog seems unlikely. I would think the dog could be kenneled for a few weeks, rather than being put down.