Friday, February 10, 2006

The Truth About Logging In This Universe

Maybe, in a parallel universe, I became a naturalist and ended up studying forest ecology.  As it happens, I live in this Universe, and I did not think I could get anyone to pay me to study forest ecology.  Maybe, in a parallel universe, I became a politician.  But I live in this Universe, and in this Universe, I dislike politics.  But I never realized just how much poolitics there is in forest ecology.  So if there is a parallel universe,  with a j7uy5 studying forest ecology, I sure hope there isn't so much politics in that one, too, because that j7uy5 would be pulling his hair out right now.

This all started last year, when a graduate student at Oregon State University (OSU) submitted a short paper to the journal, Science.  
Post-Wildfire Logging Hinders Regeneration and Increases Fire Risk
D. C. Donato,1* J. B. Fontaine,2 J. L. Campbell,1 W. D. Robinson,2 J. B. Kauffman,3 B. E. Law1

We present data from a study of early conifer regeneration and fuel loads after the 2002 Biscuit Fire, Oregon, USA, with and without postfire logging. Natural conifer regeneration was abundant after the high-severity fire. Postfire logging reduced median regeneration density by 71%, significantly increased downed woody fuels, and thus increased short-term fire risk. Additional reduction of fuels is necessary for effective mitigation of fire risk. Postfire logging can be counterproductive to the goals of forest regenration and fuel reduction.

1 Department of Forest Science, Oregon State University, Corvallis, OR 97331, USA.
2 Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331, USA.
3 Institute of Pacific Islands Forestry, U.S. Department of Agriculture Forest Service, Pacific Southwest Research Station, 60 Nowelo Street, Hilo, HI 96720, USA.

* To whom correspondence should be addressed. E-mail: dan.donato{at}oregonstate.edu

Originally published in Science Express on 5 January 2006
Science 20 January 2006:
Vol. 311. no. 5759, p. 352
DOI: 10.1126/science.1122855
When the study was published, it genrated some interest in the mainstream media, and some among bloggers:
(Note that the fifth item there was picked up on Tangled Bank.)

But the intrigue actually started before the paper was even published.  As outlined in an article published on The Scientist, in turns out that some scientists -- including some faculty at OSU -- tried to get the publication supressed.  This was highly unusual, according to a senior editor at Science:
Wildfire logging debate heats up
Controversial Science paper lacked appropriate caveats, some forestry scientists say

[Published 27th January 2006 06:21 PM GMT]

Nine scientists wrote a letter to Science asking the journal to withhold a one-page article on the potential risks of post-wildfire logging, arguing the article was short on qualifiers and context. But some forestry scientists say they support the conclusions, and last week, the journal published the paper.  [...]

Science editors have never considered delaying publication of an article after it has passed peer review and been accepted, Science editor-in-chief Donald Kennedy told The Scientist in an E-mail. Kennedy said that he can recall only one other case where someone has requested publication delay of another group's paper and that "it is an unusual way for senior faculty members to behave, especially with respect to a graduate student."  [...]
"Unusual" way to behave, indeed.  Most faculty advisors would be thrilled if one of their students got a paper published in Science.  

Unfortunately, that is not the end of the story.  After the paper was published, the federal funding for the folks doing the research was pulled.  A Congressman was irritated by this, and asked for an investigation:
Lawmaker Seeks Probe of Logging Study
By JEFF BARNARD , 02.07.2006, 06:12 PM

Questioning whether the Bush administration is manipulating science for political ends, Rep. Jay Inslee, D-Wash., called Tuesday for an inspector general's investigation into why federal funding was suspended for a study that goes against White House-supported legislation to speed up logging after wildfires on national forests.

In a letter and a speech on the floor of the U.S. House of Representatives, Inslee called for an investigation by the inspector general of the U.S. Department of Interior into whether the U.S. Bureau of Land Management was punishing researchers from Oregon State University for coming up with findings that don't fit with White House policy goals.

"Unfortunately, it's very apparent to most neutral observers that under this administration in a variety of ways that the scientific process has been corrupted by political influence," Inslee said in a telephone interview. "We saw that when the administration and their political forces tried to shackle distribution of information by the chief climate scientist in the United States, Dr. James Hansen, two weeks ago." [...]
Mr. Inslee must have been on to something.  In fact, just one day after he asked for an investigation, the funding was restored.
Agency Restores Funding for Logging Study
Associated Press Writer

February 8, 2006, 11:09 PM EST

GRANTS PASS, Ore. -- A federal agency restored funding Wednesday for a study that has provided evidence for conservationists opposing the Bush administration's policy of logging after wildfires.

The U.S. Bureau of Land Management's decision to lift its suspension of the final year of a three-year grant to Oregon State University came a day after a congressman called for an investigation of the funding cutoff.

Rep. Jay Inslee, D-Wash., had asked the Interior Department's inspector general to examine whether the bureau was punishing the researchers for their findings. [...]

"The key to effective censorship is to make sure no one's looking, and this time everyone was watching," said Andy Stahl, director of the Forest Service Employees for Environmental Ethics, an environmental group in Eugene.
So all's well that ends well?  Not exactly.  This is not over, and will not be over until there is a sensible occupant in the White House.  Personally, I hope that Inslee continues to press for an investigation.  The whole thing stinks of cronyism and corruption.  We need to find out who was pulling strings to get the funding cut, and why.  If this turns out to be the way it appears to be, it would mean that someone in the Administration was yielding to pressure from industry groups, in a manner inconsistent with the public interest.  That is corruption, and if that is what happened, we need to stop it from happening again.  The culture of corruption has gone too far.  The only way to put an end to it is to find the individuals who are responsible for each instance, and put them out of government service.

I would like to think that graduate students doing innocent research would not have to be bothered by this kind of thing.  But we have a government that knows no boundaries when it comes to meddling in other people's business for the sake of industry profits.  

Although, to be fair and balanced, I have learned that there is no career that is insulated from political influence, and none ever has been.  Imagine, I once thought that going into medicine would keep me safe from meddling politicians.  Now, I laugh at that quaint notion.  And now, I wonder if I could get some federal funding to go looking for one of those parallel universes.

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Sunday, February 05, 2006

RR4 Experience

I decided to take a break from the usual political and science/medicine fare.  Greg, from the Information is Free blog, asked some questions about RR4/64, which I will answer here, along with some unsolicited information.  

The computer I am using now has three operating systems on it, and two hard drives.  Windows XP was installed first, on the first drive.  Second, Suse 9.3 was installed, by resizing the NTFS partition to make room for the new operating system.  All of the critical data were backed up to the second drive before doing the repartitioning.  Suse automatically installed a boot loader with a menu that made it easy to choose an OS at startup.   I installed Suse 10.0 later, in the same space that 9.3 had been (on the first drive.)

On the second drive, I left some space to use specifically for trying out different types of Linux.  About 20GB is available for that purpose.  I won't bore you with my "life list" of distros I've tried.

More recently, I installed RR4 on the second drive.  That worked OK, but when I installed the boot loader, it only included items for booting Windows and RR4; it did not include Suse on the menu.  I fixed that using the Suse installation disk, which has a "repair" option.  The Suse repair reconfigured the boot loader, and appropriately included items for Windows, Suse, and RR4.

Over the last couple of days, a new version of RR4 came out.  I deleted the partition for the old one, and installed the new one.  This time, I did not have the RR4 installation program install a boot loader.  After the installation, I merely edited the menu item in GRUB to reflect the new boot files in RR4.  That worked fine, although I found that some of the aspects of the boot menu are counterintuitive (at least using my brand of intuition).  

RR4 offers several options.  The easiest is to simply boot from the live DVD.  I think that most fairly recent computers will do this by default.  That is, you do not have to change any esoteric settings.  If there is a bootable DVD in the drive when the system is started, it will boot from the DVD, rather than from the hard drive.  

Booting from the DVD is slower than booting from the hard drive, and launching programs is slower, but it is very simple to do.  The DVD includes programs for email, web browsing, and typical office functions such as wordprocessing and spreadsheets.  Therefore, a user can do almost anything one ordinarily would do with a computer, even if the hard drive does not work.  I think that the live DVD option is what the author of RR4 was referring to with the mention of getting up and running in 5 minutes.  

Another option for using RR4 involves installing it to the hard drive.  That requires making two partitions, at least; one for the OS, and another for swap space.  This has advantages and disadvantages.  The big advantage is that the system starts and runs more faster than it does if running a live DVD.  The disadvantage is that it takes up space on the hard drive.  Also, since (almost) no computer that is operational has extra unpartitioned space on a hard drive, it is necessary to resize an old partition and make new partitions before the new OS can be installed.  This is not something one does casually, since it is easy to really mess things up and lose data in the process.  It requires an intermediate level of knowledge and a bit of confidence to do.

Actually, the partition took in the installation program is not difficult to use, and I think a beginner could do it, but I would not recommend it unless you are using an old computer that you don't care much about, or have a really good friend who can bail you out if you mess up.  In any case, a backup of all important data is a really really good idea.  It helps to have two hard drives, because if you mess up during the partitioning process, and have a fully operational operating system on the other drive, it is pretty easy to recover from an error.  It also makes it easy to back up a lot of data.

Installing RR4 to the hard drive can be done using different methods.  The easiest is to use precompiled binaries.  Note that you do not have to actually understand what that means in order to do it.  Just pick that option.   The Gentoo installer then creates all the necessary directories and puts the necessary files in the correct places.  With that option, there are very few choices to make in order to prepare for the installation.  You choose some things like your time zone, language, and whether or not to install a boot loader.  Unless you are very familiar with configuring boot loaders (GRUB -- grand unified boot loader -- in this case) you will want to let the installer set up the boot loader for you.  It will recognize a Windows installation automatically, if one exists.  Then, when you reboot, you first see a menu that lets you choose whether to boot Windows or RR4.  Unfortunately, if you have another kind of Linux, you will have to add that to the menu somehow.  (note: this was true for my setup, but I did not experiment to see if it always is true.)  This is not much of an issue, since presumably anyone who is going to run three or more OSs is prepared to manually edit a boot menu.  

Using precompiled binaries, the installation takes some time, I would estimate about 20 minutes, but frankly I did not keep track, and could be off by quite a bit.  The time is spent unpacking the binaries from archive files.  The installation does not download or compile anything.

The reason that Greg asked about the details of the installation, is that RR4 and RR64 are based on Gentoo.  Gentoo is a type of Linux that has a (well-deserved) reputation for being the most versatile Linux, but also is the most technically demanding for the user.  Prior to the development of the Gentoo graphical interface for installation, most people would install Gentoo using scripts that download the source code and compile everything.  That is a very time-consuming process, and requires a great deal of technical knowledge.  However, it enables the user to customize the operating system in ways that sometimes are highly desirable.  A full discussion of that is not something I want to get into right now.  The point is that RR4 allows a user to do that, if desired, but also allows a user to sidestep the most difficult and time-consuming aspects of the installation.  

What some people want to get from reading a post like this, is advice on whether or not they should try a new version of Linux.  I will address that now.

RR4 is good for beginners, since it is easy to set up.  Although the easiest installation does not give you all the advantages, it works fine and would be adequate for the majority of casual computer users.  RR4 is also good for advanced users who want the convenience of a graphical installer, but who could do the installation using a command line if they wanted to.  RR4 is also good for anyone who wants to mess around with a highly configurable system, regardless of skill level.  I am using it specifically to acquire a greater skill level, but since I probably will make mistakes, I am not planning to use it as my primary operating system...at least for now.  

I would not recommend that someone switch from a different, functioning version of Linux, to RR4.  Greg mentioned that he uses Fedora, and presumably he is pretty happy with that.  I doubt that there would be any pragmatic reason for him to switch.  Likewise, I am happy with Suse, and don't have a specific reason to stop using it.  But RR4 gives me more options to play around with, so it is fun to have.  It is sort of like a automobile hobbyist  who has one car that he or she takes to work every day, and another that he or she tinkers with in the garage.  It is the same kind of thing, only a lot cheaper.  In fact, it doesn't cost anything.

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