The Western Geologist

According to this article, from China's Xinhua news agency, the Earth's core is officially "really, really hot." Apparently, it was previously only "really hot." Yes, those are in fact technical terms.

One of the people I referred to in my earlier post about the internal review policy of the USGS has left a comment on that thread. It's reprodced below:

Hi All:
In my earlier post to the obscure ACG listserve, which was reproduced in this more public forum, I wrote, "...However, there have been instances of BRD people not having appropriate peer review when publishing things. There was one BRD pub that clearly had a biased slant toward caribou-pipeline interactions."
I was recently made aware that the said report (A) DID have full internal review, and (B) was NOT biased. I based my comments on the media representation of the report, and I was not fully informed. I apologize for misleading readers in this way and for mischaracterizing the report.

Regards, Peter

I'd like to thank Peter for his comment, although I doubt that the ACG listserv is any more obscure than this blog. We get about 35 visitors per day, and most don't stick around all that long. I'd like to thank the ones that do.

Here's what I wrote about the 2002 study:

In 2002 a group headed by a USGS scientist published a report that dealt in part with the potential impact of the development of ANWR. This group had studied the caribou herds in that part of Alaska for 12 years and one of their findings was that female caribou who were either close to giving birth or had young calves tended to avoid roads and pipelines (they apparently preferred to be at least 4 km away from those features). That study reported that full development of 1002 area of ANWR (the area where the proposed drilling would occur) was likely to cause mortality rates of calves in the local caribou herd to decrease by 8.2%, and that a reduction of 4.6% was sufficient to cause growth of the herd to cease (Figure 3.28 in their report shows their data). The reason this caused a problem is that the scenario they used to arrive at their 8.2% calculation wasn't necessarily realistic since it was based on all of the 1002 area being developed and that wasn't necessarily realistic. Some development scenarios had plans with a much smaller footprint (you can see a map of all the plans in the follow up memo). The authors of the original study were taken to task for not including these plans in their report. The follow up memo included the predicted mortalities based on 2 more realistic drilling plans (the mortalities were estimated using exactly the same procedures as in the original report). The predicted mortalities for those two models were 0.7 and 1.2 %. The authors of the original report had in fact included models that didn't required full development (again you can see a map of their scenarios in the follow up memo), but they just focused on the 8.2 % figure (the worst case scenario). The USGS is not supposed to set or advocate policy although USGS authors can evaluate proposed scenarios, but they can't pick a favorite. The 2002 report crossed that line.

In addition both the original 2002 report and the follow up memo are available on line so I think it's difficult to claim that the authors were censored.

I wonder if Peter would consider that a fair characterization of the events surrounding the 2002 report and the follow up memo. Since their report was properly internally reviewed, I do agree that there wasn't any impropriety on the part of the report's authors (I apologize for stating that there was). However, it still seems to me to be difficult to support the claim that the 2002 report was censored since that report is still available. Moreover, the mortality rates in the follow up memo were calculated using the same models as in the original report, and the conclusion of 2002 report does seem to be based on an unrealistic drilling scenario.

This post is going to be a somewhat random dump of the thoughts that are currently spinning around in my head. I apologize in advance. I haven't posted in a while so I feel obligated to post something.

I'm currently in my first year in a teaching position. Prior to this I was in a pure research position. I'm currently striving to find some balance between the two. This semester I'm directly teaching three classes and overseeing 5 labs (my teaching load was similar last semester). I'm also trying to get a decent amount of research done too, which is proving difficult. I did recently get ahold of a seriously cool portable X-ray fluorescence (XRF) machine, which I've wanted for some time now and have very ambitious plans for. I've got 1300 samples waiting to be scanned in my lab (plus another 1200 from a friend). I'm also just drooling at the chance to take this thing out into the field and start using it on outcrops. I've got a couple in mind, but they'll probably have to wait until summer 2008. Our department is also fortunate enough to have several motivated, bright, curious, undergrads who are interested in working on independent research projects with me. I'm grateful for them. I hope that I don't squash their interest in geology.

My most recent publication was highlighted by the editor of the journal I submitted it to, and I also just found out that it appeared in the 'Research Highlights' section of Nature. That's not nearly as good as having a publication in Nature, but I'll take it.

Our puppy was recently spayed and she REALLY wants to wrestle with our other dog instead of taking it easy in her crate. She's not the convalescent type. She's supposed to be on the equivalent of bed rest, but she'd much rather chase her brother around the house and go outside and chase birds. I'm especially looking forward to the time when we can give her a bath (she's not supposed to get wet for a couple of weeks). Luckily she's really fond of standing in the shower, so we don't have to struggle with her when it's bath time. Our other dog howls like he's being killed when we try to give him a bath (although he's much better behaved if we take him to a groomer). I'm very anxiously looking forward to the time when our pup loses interest in our shoes. Fortunately she likes my wife's shoes more than she does mine.

I think I may have found the Texas equivalent of Chris Buttars. See this link. I wait with bated breath to see what comes of this. (ht Pharyngula).

I recently started reading Francis Collins' book 'The Language of God'. My mom sent it to me. I'm thinking of posting my thoughts after each chapter. I've finished a chapter and a half now, and I'm generally feeling frustrated/annoyed. Collins is a fairly engaging writer, but his arguments in favor of theism haven't been stellar as of yet (maybe they get better).

I'm thinking of trying to brew mead. I've been homebrewing off and on for a few years, and I'd really like to branch out. When I was in grad school one of the profs gave me a bottle of a great, dry pear-flavored mead that he'd made. I don't know how to describe the taste, but it was wonderful. I'd like to see if I could make something like that. I'm also considering making a Grand Cru or something similar. Just before I left California I went to a microbrewery in Sacramento that made one of the best Belgian-style ales I've ever had. It was, by itself, almost enough to make me want to live in Sacramento. This part of Texas doesn't have a lot of microbreweries (St. Arnold's in Houston is the closest).

OK, that's all I have for now. I ought to get back to work.

I'm going to start the new year by revisiting some posts I uploaded last year.

The first is on the occurrence of anomalous fossils in the geologic record.

The fossil record


The second is on ice cores:

The GISP2 ice core and the age of the earth

The Living Waters Store has this gem of a game for sale: Intelligent Design vs. Evolution Board Game.

Evangelistic, educational, entertaining.

At last, a board game that reveals the insanity of perhaps the greatest hoax of our times -- the unscientific "theory of evolution."

"Intelligent Design vs Evolution" is unique in that the playing pieces are small rubber brains and each team plays for "brain" cards. Each player uses his or her brains to get more brains, and the team with the most brains wins. It has been designed to make people think . . . and that's exactly what it does.

"Ray Comfort and Kirk Cameron are doing much more than revealing the bankruptcy of molecules-to-man evolution. They have a greater purpose: proclaiming biblical authority and reaching the lost with the precious gospel message. Enjoy this wonderful family game as you also become better equipped to defend our precious Christian faith." -- Ken Ham, President, Answers in Genesis.

I've said it before, your "precious Christian faith" does not necessarily preclude a belief in evolution. What precludes a belief in evolution is the unnecessarily literal word-for-word interpretation of the creation account in Genesis.

Hat tip to Fark for this one. I love the headline submitted:

"Intelligent Design: The Board Game." Because "Evolution: The Board Game" takes far to long to play and you can't make up the rules as you go along.

Appointees of the Bush Administration have been accused of censoring and distorting data that was incompatible with their ideological views. George Deutsch a press officer at NASA who wanted the word 'theory' inserted after The Big Bang (insisting it was a religious view) and tried to keep reporters away from NASA scientist Jim Hansen is an example.

I'm a little late with this but earlier this week I read a post at Red State Rabble about the internal review policy of the U.S. Geological Survey (see here and here). The articles I linked to suggest that the USGS is instituting a policy to censor data that aren't compatible with Bush Administration policies. While I don't think the present administration has behaved very responsibly when it comes to handling data I don't think the USGS internal review policy is being installed to stifle scientists.

There has been a very interesting discussion of this policy on the listserv of the Affiliation of Christian Geologists (you'll need to set up an account in order to access the archive). Several current USGS employees have contributed to that discussion. I've reproduced one of the responses, by Peter Haeussler, who works for the USGS in Anchorage, Alaska below:

First, a history lesson on the different divisions of the USGS. There's the NMD - national mapping division (makes maps), the WRD - Water Resources Division (does water stuff), the GD - Geologic division (geologic mapping, energy, minerals, earthquakes, volcanos, climate change, etc), and now the BRD - Biological Resources Division (the biology folks pulled out of Fish and Wildlife Service, NPS, and perhaps BLM in the early days of the Clinton administration under Bruce Babbit as Secretary of the Interior. Babbit wanted to start an organization equivalent to the USGS for biology folks, but Newt Gingrich and the contract on America didn't give the new organization the organic act, so it never started. In the meantime, these scientists had no home, so, once it was clear the USGS was not to be eliminated under Newt's scheme, the director of the USGS offered to make a new division of the USGS for the biology folks. and thus was born the BRD part of the USGS.)

Here's how GD scientists publish in non USGS publications. Perhaps unbeknownst to most non-USGS folks, the GD geologists have always had to get two "internal" reviews of their publications before publishing in any outside journal. (these days, this includes abstracts. Also, neither reviewer has to be from the USGS) After you respond to those reviews, you make your corrections, and give the whole package to your immediate supervisor. (If you use geologic names in the paper, then there is an additional review that makes sure that geologic names are used properly) The supervisor should look it over, see that appropriate responses are made, then 'sign off' on the manuscript. Then it gets sent to a publications group chief, who then says it gets 'directors approval'. Then, you are officially given permission to submit the manuscript wherever. It does slow down the publication process, but invariably these interval reviews improve the manuscript and the content. The goal is to make sure the USGS is not publishing crap. You might be surprised to learn that there are a manuscripts that die after these reviews. It's a big no no to publish without internal review. You'd get spanked. The internal reviewers are chosen by the author of the paper and not by a supervisor or some political appointee. In a smaller office like the one I'm in, you can end up using your same friend to review manuscripts too many times. And avoiding certain people who have terminal indigestion. And you can end up having rubber stamp reviews. But it's OK.

I think the 'new' policy (I've not read it, but have been told) basically implements the GD internal review policy across all divisions of the USGS. I've heard the BRD scientists in my office (actually they are all located across town and we don't interact with them much) complain about this new policy. They see this as interfering. GD folks don't think this is an unnecessary burden. However, there have been instances of BRD people not having appropriate peer review when publishing things. There was one BRD pub that clearly had a biased slant toward caribou-pipeline interactions. The USGS really gets spanked in Washington when stuff like this happens. It's bad for everyone.

It's funny Charles mentioned this. I saw Al Gore speak at lunch today at AGU. Gore actually mentioned this press report and the quote from James Estes, and Gore said he was horrified of the censorship. He mentioned the climate guy at NASA (Ames??) who had felt he had been censored as well. Gore's main point of the talk was that scientists need to tell the truth on what they know, even if it may be "an inconvenient truth." He pointed out that Galielo's conclusions about our solar system were also an inconvenient truth and that he published on it. It was important to get the truth out.

I think partly in response to the NASA guy (I saw him on 60 minutes), we at the USGS were recently given more guidance about how to express personal opinions in the course of conveying our scientific results to the public. I think this is excellent, and I think it makes it much easier to give a personal opinion (often with policy implications). I do a fair amount of earthquake hazards work, and I get these questions all the time. I appreciate more freedom to speak on policy. I just need to be clear to the audience what is my USGS science versus what is my opinion as a citizen.

I tried to find which division of the USGS that Estes is in from USGS internal web sites, but I can't find it easily. His research is all about charismatic megafauna, so I think it's likely he's in BRD and not GD. Nonetheless, Estes has published in Science and received meritorious service awards, so I doubt he would be slowed down much by the new rules.

Regarding the last couple of things mentioned: is this high visibility science? or is this policy sensitive? I've seen those checkboxes on our manuscript routing sheets. The high visibility question is merely for the press people in the USGS to play up the science. NASA does so well in part because they have such a good press machine. The USGS tries to emulate that. I do find the question about 'policy sensitive' more troubling. But I'm not aware of that impacting anything.

Regards, Peter

I spent a couple years working with the Earthquake Hazards Team at the USGS (the team I was part of was in the GD). I actually thought that the internal review process was USGS-wide and not just for GD (although commenter mark on the RSR thread says the same procedure is used in WRD). I've been through the internal review process both as an author and as a reviewer, and I've found it very helpful. Its main purpose is to make sure that publications by USGS authors are of a high quality, not to hinder or censor data. The process is pretty straightforward. The author picks two reviewers (Haeussler says that they don't have to be USGS employees, which is news to me – all of the internal reviewers in the team I worked on were either USGS employees or volunteers, although we did hit up visiting scientists too). The interval review is just like standard peer review for a journal. The reviewer goes over the document and makes sure the data support the conclusions, that the format of the paper is decent, etc. The author then revises the manuscript and submits it to the Team Chief Scientist, who signs off on it. The TCS looks at the reviewers comments and the revised manuscript and if the reviewers' comments have been addressed the manuscript is approved (although the review by the TCS can be cursory).

This process applies not only to papers but also to abstracts and newspaper articles. The review is pretty quick for abstracts, it usually doesn't take more than a day. As you can probably imagine, the days leading up to the AGU Fall Meeting abstract submission deadline are usually pretty busy. The review process for a paper is longer. It usually took a week or two, but it did take me a couple of months to get a paper back from a reviewer in one case (I expected that going in since he was really busy).

The USGS internal review policy is available online here and here (I should note that the date on these links is May 2006, so they might not be the final version). I've reproduced the section that deals with sensitive information below. From the second link:

4. Policy. All information products (see SM 1100.1) must be reviewed and approved for official release and dissemination, whether they are published by the USGS or an outside entity, if the work has been funded, whole or in part, by the USGS or if USGS affiliation is identified with the authorship. Processes for review and approval may differ for different kinds of information products (print, digital, or audiovisual) but must be consistently applied throughout the USGS.

If during preparation, review, or approval, an information product is determined to be of a particularly sensitive nature, the appropriate Bureau and Departmental officials should be consulted. Issues or concerns of a sensitive nature include those that have current or future policy implications (such as land and resource management decisions) or that involve matters of national interest, security, or potential commercial gain. Additionally, coordination and review should include the appropriate Office of Communications representative in instances of policy-sensitive products or those that may be of such a level of visibility that a communication strategy is warranted to handle their release.

Information products should not recommend or appear to advocate or prescribe a particular public policy or course of action. Information products carry no disclaimer that could suggest that the product does not meet USGS standards of scientific excellence, integrity, and objectivity.

I don't see anything particularly ominous in this policy. I can understand why people would be concerned since scientists have been censored in the past, but I don't feel threatened by this policy. I hope I'm right.

I'm going to end this post by looking in a case that was mentioned by both Peter Haeussler by CANOE. Here's the relevant quote from the CANOE article:

President George W. Bush's administration has been criticized for scientific integrity issues. In 2002, the USGS was forced to reverse course after warning oil and gas drilling in Alaska's Arctic National Wildlife Refuge would harm the Porcupine caribou herd. One week later a new report followed, this time saying the caribou would not be affected.

I think it's hard to characterize that paragraph as anything other than misleading. Here's a really nice article from the Washington Post from 2002.

Here is a link to the original report (section 3 is the relevant section) and here is a link to the follow up memo.

In 2002 a group headed by a USGS scientist published a report that dealt in part with the potential impact of the development of ANWR. This group had studied the caribou herds in that part of Alaska for 12 years and one of their findings was that female caribou who were either close to giving birth or had young calves tended to avoid roads and pipelines (they apparently preferred to be at least 4 km away from those features). That study reported that full development of 1002 area of ANWR (the area where the proposed drilling would occur) was likely to cause mortality rates of calves in the local caribou herd to decrease by 8.2%, and that a reduction of 4.6% was sufficient to cause growth of the herd to cease (Figure 3.28 in their report shows their data). The reason this caused a problem is that the scenario they used to arrive at their 8.2% calculation wasn't necessarily realistic since it was based on all of the 1002 area being developed and that wasn't necessarily realistic. Some development scenarios had plans with a much smaller footprint (you can see a map of all the plans in the follow up memo). The authors of the original study were taken to task for not including these plans in their report. The follow up memo included the predicted mortalities based on 2 more realistic drilling plans (the mortalities were estimated using exactly the same procedures as in the original report). The predicted mortalities for those two models were 0.7 and 1.2 %. The authors of the original report had in fact included models that didn't required full development (again you can see a map of their scenarios in the follow up memo), but they just focused on the 8.2 % figure (the worst case scenario). The USGS is not supposed to set or advocate policy although USGS authors can evaluate proposed scenarios, but they can't pick a favorite. The 2002 report crossed that line.

In addition both the original 2002 report and the follow up memo are available on line so I think it's difficult to claim that the authors were censored.

One of the things about teaching that I'm coming to appreciate is the amount of time it takes to put a lecture together. I've put a fair number of talks together during my short career, but that's different than putting together three 50 minute lectures per week. I've been posting my lectures online so my students can download them and hopefully treasure and reread them for years to come (who knows, it could happen). I'm also trying to be respectful of copyrights. I've come across a few photo collections that have been very helpful:

USGS Photo LIbrary

BLM Abandoned Mine Lands (ALM)

Earth Science World Image Bank

USGS Fact Sheets

Photos by Bruce Railsback

The Geo-Images Project

NOAA Photo Library

If any readers know of other good collections I'd appreciate it if you'd let me know.

I got the chance to catch up with a friend who works for the USGS today. Since he's far more knowledgeable about stresses in the crust than I am I asked if he'd comment on my posts about the earthquake in Hawaii. He was willing, but apparently the DOI wasn't. When he tried to visit this blog he was redirected to a page that notified him that visiting blogs wasn't allowed (I suspect any URL with blogspot in it is flagged). He was kind enough to submit a request that The Western Geologist be added to an approved list of websites. We'll see what happens.