Overheard on NPR....there's a new "campaign" button floating around.

"At least Clinton's lies didn't get anyone killed"

they would be kings

I read somewhere that our current administration doesn't want to govern so much as they want to rule. Our foreign policy and the domestic agenda of the administration surely seems to point this out. It makes following the national news as depressing as the international news.

triplets

I've decided to try to enforce a little self discipline here and only try to write when I have something somewhat intelligent to say. One way to facilitate this is to call this page "Home" that will include anything general (state of the state, politics, general bullshit), along with two side blogs for science or computer-related thougts. Their links will be located at the upper right of the page.

And someday I'll think of a better title for all of this...it's so hard to not make it too generic yet so simple to make it sound totally banal.

Speaking of blogs, an essay on NPR by Scott Simons the other day kind of put blogs into perspective. Inane, sad, whatever. The take home message is that most ordinary days in someone's life does not make great literature. The other is that good writing is really a profession, and not an easy one at that.

So true.

Google--anything it can't find?

In my "private" blog, I noted the very funny story in the Onion written by a guy that said his mom had found his blog...and there are things in people's blogs that you wouldn't want your mother to read. Anyway, mentions of Google searches by nosy moms everywhere made me search my name. Besides the usual links to many work pages (and many for that other Mark Strom that appears to write and lecture about religion), there it was...a link to this very blog.

It really makes me wonder how this search engine even found the page in the first place. After publishing, it's up what, like all of 30 seconds on the Blogger Home page? Amazing technology involved in the search algorithm as well as the server implementation for this search service. I haven't used a different search engine in months.

More Mac OS X 10.3 installs

We've installed 10.3 on two additional computers this week. One, an older iMac DV 400 Mhz G3 and my wife's iBook (800 Mhz G3). The installs went fairly smoothly. No problems really on the older iMac. I'm surprised that it runs as well as it does, considering this computer only has 256 Mb of RAM. I set it up with three users (myself and the two kids), and the fast user switching seems to work fine. The only "disappointing" part of the latter is that the video card doesn't support Quartz Extreme so you don't get to see the cool cube rotation. The only thing that slowed down the installation was having to change permissions on many of their files once they were moved into their own home folders.

On the iBook install, initially every Microsoft application crashed shortly after starting up. I fixed permissions and rebooted and immediately had the flashing finder--which reminded me that I hadn't removed that old Haxie for font smoothing. Zapped that and everything was back to normal. The next morning, MS Entourage wouldn't open any email, but a quick rebuild of the database took care of that problem.

Panther and Safari

I've had a chance to play with Safari 1.1 the past couple of days, and it's definitely become my everyday browser of choice. Besides speed, compatibility, and stability improvements, I noticed the improved downloads ability where it cleans up after itself (i.e., you only see the unpacked or uncompressed file in your download location). Very nice.

The only thing I stil miss is having the option to include the URL on printed pages. Since the Apple developer Dave Hyatt is looking for feedback on Safari 1.1 on his Surfin' Safari Weblog, this is it.

Panther Installation stories

We've now installed Panther (Mac OS X 10.3) on three computers. My two work computers (Powerbook and PowerMac G4 DP450) and our home iMac (1 GHz, flatscreen). The installs were straight upgrades instead of the more laborious archive and install or clean install. The upgrades of the Powerbook and iMac went without a hitch. The only customization was to make sure the older Epson print drivers that included the 740 were installed (not default), and to leave out all of the language translations (at least on my Powerbook). Both were installed with zero problems and all applications appear to work as advertised.

The only one I was concerned about was the PowerMac, and rightly so--this has been my work computer since it came with OS 9, and I've been upgrading it with new OS's and have never done a clean install of any of them. I've also installed a ton of 3rd party software (and deleted much of it too), Fink for Unix style programs, developers tools, preference panes, and so on. In other words, there's probably a lot of junk floating around on it, some of which may not work right under 10.3. So, to cover my bases, I did all the disk maintenance I could think of, including rebuilding the volume with DiskWarrrior, optimizing the drive with Tech Tools Pro 3.9, and repairing disk permissions. After unplugging the external Firewire drive and CD burner (as recommended), I started the installation. Again, loading the disks and clicking OK when prompted went without a hitch. The problems started on reboot after the final steps of installation. The login window displayed correctly, but then after logging in, there was a longer than usual pause while the Finder launched. Then when it did, the first app crashed almost immediately after opening followed by the Finder blinking on and off--using the force-quit command to relaunch the Finder had no effect, and the system looked dead in the water.

After searching around and trying basic stuff (like booting into single user mode and running fsck -f [-y didn't work because of "journaling"], or booting from the install CD and running disk utility to repair the drive and fix file permissions), I found similar instances on the Apple OS 10.3 support forum. It turns out that programs or pref panes that load on start up that are incompatible with the OS might do this. One specifically mentioned the Haxies, small programs that add functionality to the Finder. It turns out that way back before better font smoothing was added to the OS, I had installed such a Haxie (Silk) to turn on smoothing in MS Word. Luckily the System Preferences could still be launched from the Dock--after disabling this, the system rebooted normally, and all looks well.

Next time--more on the performance and enhancements found in Mac OS X 10.3 Panther.

Panther...

I installed Mac OS X 10.3 (Panther) on my Powerbook tonight. So far, so good and everything I use seems to run without any updating. The whole computer seems definitely faster. Expose is a cool and useful tool. If you haven't heard, with a simple touch of a key or movement of the mouse to a hot corner, all open windows on the desktop shrink so that all are visible. When the mouse cursor is dragged over the windows, the name of the file or application is displayed. Clicking on a window brings that window to the front and everything back to normal size.

Contrary to the problems some users are experiencing, the install process went smoothly. The only think I did prior to installation was to "repair all priveleges" using Disk Utility. Except for leaving out the language packs and making sure all older Epson print drivers were installed (we have an older Epson 740), I just had it do the simple update installation, rather than the archive or clean install methods.

Anyway, more later as I try the new features.

Hell Has Frozen Over

This week Apple released a version of iTunes and the iTunes Music Store for Windows, with the tag line above (which reflects their previous attitude about selling anything for Windows). Gotta love their sense of humor, but this also represents a pragmatic approach they're taking with there business. They're selling iPods like crazy to users of both Mac and the PC platform, so the release of iTunes will give Windows users the same easy interface to transfer their music. I wish my son would hurry up and buy the one he's been saving his money for. Anyway, what's more is that Apple has worked out a deal with AOL to prominently place a link for one-click registration and integration with the ITMS on the AOL Music site. And finally, they announced a deal with Pepsi to give away 100,000,000 songs via a promotional give away. Given that to date they've sold around 14 million songs, this is quite the give away.

Yes, they are getting serious about this. There form of DRM seems to be acceptable to most and just might be the way that finally works. I am planning to buy a few songs/albums soon to try it out myself.

But I'm still waiting for my genome grant to start in order to get that G5.

Ahhhnold!!!

The California recall election. What better way to demonstrate that we're the best democracy in the world? California, the world's 6th largest GNP, now to be governed by a former weight lifting, body building, woman groping, action movie acting….simple family man. It'll be interesting to see his new economic stimulus plan to get California out from under that 38 billion dollar debt. I don't suppose he'll get much help from the Kennedy family, Maria not withstanding. On TV I just saw how Jay Leno introduced him. It's fitting. Just glad I don't live there.


The reformatted and rebudgeted genome grant went back to the USDA. Hopefully the money will be transferred soon and I start the process of getting it allocated to the four other organizations. Time to start advertising for a post-doc as well.

Apple Stores

This has got to be one of the most mixed up blogs around. I still can't on a consistent theme.

Anyway, today I'll focus on things Macintosh. The new Apple Store opened in University Village last night. I decide to drive down to check it out and maybe get the free T-shirt that was given to the first 1000 visitors. I just missed getting one--if I'd only been there 5 minutes earlier. There were several people coming out with more than one, but I'm sure they went in with someone! Anyway, it's good looking store--I had thought it might be two floors since the sport store that occupied the space previously had one. But it's on a single floor, displays of all the models, components of the digital lifestyle, and so on. The new 15 inch Powerbook looks great--it now has the same aluminum case that the 12 and 17 inch models have. All ports for plugging in USB, Firewire 400 and 800, video adapters and so on are located on the sides instead of the back. This part is not as clean looking as my Titanium but it does look easier to plug things into it.

But what I'm really "lusting" after is the new dual 2 GHz Power Mac G5. I'm thinking that I might get this with the genome grant. Hey, I'll need something fast for all that annotation and my dual 450 G4 is getting on in years (well, 2 anyway). Of course I could just upgrade the G4 to a dual 1.2 GHz G4 with an after market processor. These are pretty fast too. We'll see!

Oh, one more thing. It looks like the lamotrigine is working in controlling my focal seizures. They stopped a week ago after the dosage was increased to a new level. So far so good!

Government and trust...

I work for a government agency and I'm proud of what I do. The majority of people that I work with and around are bright, thoughtful, and motivated. We believe in the mission of the agency, and work hard to solve the problems we know are important to our constituents and for the preservation of our natural resources.

So why do I now feel a sense of depression with government, our government, in general? It's actually an easy question to answer, although it's been hard to admit it, until now. This week President Bush and other members of the administration are now acknowledging that no evidence has been found to link al-Qaeda and Saddam Hussein. They're saying this is what they meant all along. Yet, for almost 2 years members of the administration continuously linked Iraq with 9/11. This was the mantra used over and over again to justify our invasion. That and the fact that Iraq had WMD and wanted to use them, but that's for another discussion.

The backpedaling is so rapid that you have to worry that one of them might trip over themselves and get hurt. Is the change politically motivated? Of course. There's an election to campaign for!

Five months ago I was among the majority who felt there was sufficient justification for our invasion of Iraq. It now appears that I'm among the growing majority that feels the exact opposite. The loss of trust is beginning to run deep. The campaigns for 2004 have begun.

A mixed bag

There's an interesting series of notes in Macintouch on how to justify the use of Macintoshes in mixed computer environments and the rationale given by many network administrators to standardize on a Wintel platform. It seems ludicrous, particularly when such an attempt occurs in an educational institution, where choice and free thought is promoted, and in fact is supposed to be a fundamental tenet of our society. To paraphrase one post, it's time to turn the arguments around. When IT discusses the need to standardize, ask them for their cost-benefit analysis for the Windows platform. Make sure they don't forget to include the cost of installing security patches, cleaning computers of viruses, updating virus dats, etc. One university euphemistically calls this "remediation." Oh, good. Today Microsoft reported that they expect another worm/virus attack this week.

I've spent the last several days working out the last few details on the genome grant. For the sequencing phase we're down to working with my favorite university genome center (one of several built for the human genome sequencing project) or to continue to work with a commercial sequencing outfit. There are significant advantages and disadvantages to both.

The genome center is considerably cheaper which will allow my collaborators and I to carry out our original , have considerable experience in completing genomic sequence of high quality, they are close to me physically, and it will be easier to set up a collaborative agreement with them (instead of having to work on a huge contract. The genome center will also be slower (other concurrent projects), and at the quoted dollar amount, once they get to the hard part (gap closure), there may not be enough funds to cover it.

The commercial outfit will be faster, more integrated with our bioinformatics partner, and will give a high quality sequence. However, they will be considerably more expensive which will not allow us to complete some of the educational and annotation objectives, and at the budgeted amount, may not be able to actually complete the entire genome (no or few gaps) without additional money (contract is fixed for a certain number of base pairs).

Interesting process, and I'm learning a lot.

Budget disasters

I was in in Portland the past couple of days for a meeting of regional fish health pathologists and managers. The group is a committee that has been together for over 20 years, with bi-annual meetings to share notes, discuss individual problems, discuss policy, etc. What's been different and saddening is to see how deep various state and federal budget cuts are, cuts that impact a lot of good environmental science in the region. Because of the California budget crisis, state workers have been forced to absorb draconian budget cuts, furloughed employees, and a major reduction in the number of pathologists to cover the state. There's basically 3 left for the entire state, who must routinely travel to hatcheries all over the state in order to even carry out rudimentary inspections of fish hatcheries all over the state, some which raise Endangered Species Act-listed stocks. Sounds like a disaster in the making, not just for the loss of important services, but also because of the potential for a vehicle accident involving these hard-working and stretched to the limit people.

The entire situation makes our budget problems pale (although we may end up laying off many of our contract workers this fiscal year). More on this later.

IT departments and Macs

Personally, I'm sick and tired of the constant security problems that computer worms and viruses cause. Well, yeah, who isn't? What I mean is I'm sick and tired of the fact that MS seems to leave so many security holes open for hackers to exploit. Because of this, I'm inclined to write the following.

It's obvious from the things i've written or links on this page that I use Macintosh computers, at work and at home. I'm a molecular biologist/microbiologist, and besides regular use of common software of science and business (MS Office, web browsers), much of the specialized software I use for molecular biology is either available only for the Mac or runs better on the Mac. (OK, this has change some over the past few years, but it's my argument and I'm sticking to it.) Seriously, it's been easier to run my lab with the Mac platform...I and members of my group can more easily troubleshoot problems, there are fewer problems to troubleshoot, and the actual computers have a much longer time of life (making them much easier to afford in a lab environment where every dollar counts). I think Mac OS X (and in particular the latest Jaguar 10.2.x) is an absolutely stellar OS, and for me has been a rock solid and extensible OS. I can run software written for Mac OS X, I can still run older Mac software under OS 9 (Classic), I can run programs written for UNIX with GUIs under X-Windows, and I can compile and run programs with command line interfaces. More importantly, it's secure!! Besides the several computers I use daily (PowerMac G4 dual 450 Mhz, a 1 Ghz Powerbook, and a 1 Ghz flat screen iMac (the latter two both recently upgraded from their G3 400 Mhz counterparts), I also administer a 1 Ghz G4 XServe server (running naturally Mac OS X Server) at work. This computer runs a forums web site, as well as serves many Filemaker Pro databases for two groups, and is a file server for about 20 users.

So why am I writing this?

Mostly because of an interesting take on corporate IT groups recently published by Robert X. Cringely under the title "May the Source Be With You: IT Productivity Doesn't Have to Be an Oxymoron, but Outsourcing Isn't the Way to Achieve It". The topic was also touched on by John Gruber on his Daring Fireball blog. The part from Cringley's column that strikes a chord is where he discusses the Mac and wonders why IT doesn't employ it more instead of Linux if an alternative to MS products is desired. First he uses the argument that many IT departments deploy MS servers and clients because that's what they know, yet still fail at keeping those servers and clients secure. The true "geek" IT members migrate to Linux--it's cheaper, fast, and extensible. Yet it takes the same number of IT staff to keep them deployed (the geek factor?). Why not instead set up Mac XServes. They're relatively cheap, powerful, fast, and reliable. All important services (web, file sharing for all platforms, print serving, DNS, DHCP server, etc) can be set up through easy to configure GUI interfaces (the geeks can still use the command line). They are easy to configure and once set up just run. So why doesn't the generic IT use them more? Simple--it can threaten people's jobs. An entire network, support for hundreds to to thousands of users, will literally take fewer support staff than similarly configured network/servers running other OSs.

I've become convinced that this is the "culture" that is pervasive at my own institute. I've been staying out of it lately but we've had some major IT decisions made recently that to me don't make much sense from a financial or intellectual sense. Instead it's "standards" and "requirements" and what headquarters "wants". "We're going to run MS products and why would you want to use a Mac?" What I don't see is someone taking a stand and saying, "you know there is a better, cheaper, and more productive way." I'm fed up enough with this last worm dustup (and watching our IT scramble to install the patches on all the windows machines--a patch availabe for over a month), that I'm going to start making some noise. I've just got to figure a way to not make it sound like the old Mac evangelism. That doesn't seem to work with them.

Today's health report

The seizures pretty much continue as they have been. Last Thursday I started a medication called lamotrigine, which is an anti-seizure (and anti-depressant) medication. Can't tell if anything is happening with it. I think I'm having a few headaches from it, and sometimes the seizures seem to be not as intense. But the frequency stays the same, 4-6 per day. This Friday I have another MRI scheduled, this time with a galladium dye injected first. This is supposed to give better contrast to blood vessels on the scan. Can't wait.

Tonight I had planned to talk about an article I read in Scientific American regarding the lack of public access to on-line science journals--but I'll save that for another time. Instead, I decided to post something I've been entering in a private blog--mostly because I've been able (or better, had to) avail myself of some pretty amazing medical diagnostic technology due to an usual problem I've been experiencing.

Sunday, Aug. 17
I started experiencing periodic episodes of numbness combined with a weakness and muscle spasm in my right arm this week. It's a hard feeling to describe but it stops me in my tracks until it passes. A few times it was so severe that I couldn't even move my arm--it felt paralyzed for a few seconds. Finally it alarmed my wife (and me) enough to go to my doc about it. X-rays (looking for some skeletal abnormality in my neck that might pinch a nerve) were inconclusive. However, there's enough worry that I have to get a CT scan tomorrow--and we are supposed to leave on our vacation to Chelan. It's going to turn out to be nothing (I hope) and we can get out of here for a week's relaxation with my family. I've had fewer "spells" today so I'm hopeful I just inflamed or pinched a nerve. Maybe I shouldn't be typing!

Monday, Aug. 18
A somewhat disappointing day. We are unable to go on our planned vacation because I need more tests. The CT scan I had today was inconclusive as to the cause of these muscle "siezures" in my arm. The initial read by the radiologist had him suggesting I had had a mild stroke-like event in the left capsular lobe of my brain. I then had a followup appointment with a neurologist who showed us the CT scan and and told us he was not convinced that the spot pointed to by the radiologist was anything. However, he insisted we postpone our trip and tomorrow I go in for an EEG (electroencephalogram) and an MRI (magnetic resonance imaging) on my head. He is thinking these may be a type of seizure. While writing this I had another one, only my third of the day, but it seemed a little more intense than the ones I've been having the last couple of days and this time I felt it on my side below my arm. Time to put away the laptop and get some rest.

Tueday, Aug. 19
Tonight I was finally able to talk with my neurologist (never thought I'd have one of my own) about the results of the EEG and MRI tests I had today. The EEG is the test where you have 20 electrodes stuck to your scalp (the tech was appreciative of the fact that I had thinned my hair for the test); 8 on each side, 3 down the middle and a ground. In all things electrical, the ground is always important! The EEG results were normal (I have brain waves!!), with no evidence of stroke or major seizure disorders. The CT scan from Monday (which is like entering a small Stargate on "Stargate") and the MRI today do not reveal anything major, no tumors, no evidence of stroke, etc. However the MRI did appear to show that I have what's called a "venous angioma" on the left side of my brain, which is a disordered clump of veins that drain the blood supply there. It's possible I've always had this but just now focal seizures have started because of it, possibly because of some scar tissue there (and my seizures just happen to be localize to my right arm, which is better than headaches, blurred vision, etc). Evidently venous angiomas are fairly common, and in general do not represent an increased risk of bleeding, aneurysms, etc., nor is surgery indicated. The radiologist and neurologist want to schedule another MRI, this time with a dye to get better contrast in those blood vessels. MRIs of your head are not that much fun--there's a reason why they ask you if you're at all claustrophobic or jackhammerophobic. But in the meantime, I meet with my neurologist (I'm sounding a bit possessive about him aren't I?) on Thursday to discuss some possible mild antiseizure medications.

In the meantime the incidence of these "spells" or focal seizures has decreased from ~6 a day for three days down to 2 yesterday and today. While the diagnosis of the cause appears to be somewhat benign, with a fairly good prognosis, overall the episode does make one think about the other possibilities. I was a bit thrown today when the EEG specialist asked me if I was related to someone he had seen 12 years earlier with the same last name. When I replied the person was my uncle, he stopped and said he remembered him well and the fact that my uncle had died of an aggressive glioblastoma (very malignant brain tumor). He quickly went on to say that my test results so far did not indicate any tumor of any kind but it was something one can't help but think about. Just a year ago a neighbor friend of ours died of the same thing, less than 6 months after the initial diagnosis. Our mortality becomes more and more real as we get older, that's for sure.

Where has IT been?

Is the MSBlast worm slowing down? CNet reports it is but that it may not be done [CNET News.com]. I can understand home users not necessarily keeping up to date on all the patches their systems might need to prevent problems like this. But I was floored by the fact that it wasn't until Friday that my parent organization (at the national as well as local level) didn't act to ensure all Windows computers were patched until late Friday (Aug. 15). When I checked work voice and email Saturday morning, there was a flood of messages regarding this--basically all machines had to be pulled from the network until the patches were applied. Come on! This patch was available for over a month. Where has the NOT GOOD ENOUGH FOR GOVERNMENT IT team been?

Oh, and how did MS protect itself from the SYN flood scheduled for Saturday by the worm? They pulled the server (windowsupdate.com) off the network! Now that's a patch.

Pods Unite

This has been out for awhile, but there's a great television commercial out that I wanted to mention here. Volkswagen and Apple have announced a joint product pairing with the VW Beetle and the Apple iPod. I love our Passat, but this would be a fun combo.

I just finished reading a series of BusinessWeek articles that discusses Apple and their changng business strategy towards becoming more of a consumer electronics and services company. The articles talk about the success of the iPod, iTunes and the iTunes on-line music store, Apple's ability to innovate, the XServe server, and so on. All in all, fairly positive, with few really glaring mistakes. The one semi-whopper that stands out was the statement (in "Picking Apple as a Server Solution") that the XServe would suffer in competition with Linux because it uses proprietary software. Gee, it seems pretty open to me--the XServe/Mac OS X Server 10.2.x I run at work (Apache/MySql/PHP, file sharing services, etc) is certainly based on the open source model with GUI OS X interfaces slapped on top.

W32/Blaster update

I paid a bit more attention to various news articles about the W32/Blaster worm. It turns out that besides trying to infect other computers in the local network, it also initiates a CP SYN flood denial-of-service attack against windowsupdate.com. Like I referenced earlier, although I may be using a computer/OS that only has a small share of the market, I can get my work done while remaining fairly confident that computer and internet security are taken seriously.

The Apple site has a wonderful tribute to the late Gregory Hines today. It probably won't stay up for long but it features Hines tap dancing in a white tux, black background, with a small Apple logo and the slogan "Think Different" in the upper right hand corner.

LooooveSan!

This is funny but not funny. As I sit here doing a little work, on the local TV news comes a story about local businesses who's computers cannot boot because of this new LovSan or Blaster worm that exploits weaknesses in the RPC (remote procedure call) service in Windows NT, 2000, and XP. I didn't follow it completely but evidently the worm is somehow preventing many people from even booting their computers that they need to do to download the patch. CNET has a complete story here.

I'm not trying to be smug, but it is nice to sit here working on my TiBook, and simply reflect on these problems without having to scramble to download all those patches!!

new iMac

We sort of bit the bullet today and purchased a new 17 in flat screen iMac. The old iMac was getting a bit slow, particularly with the digital video and in its ability to display large collections of digital still photos. We put an Airport card in the old one and put it up in S's room, with the new one down in the office. Sweet computer. Even the little HK round speakers sound great for their size. More later.

For kicks I've added a couple of things to the molecular biology forums site that make it more fun. First was a couple of different ways to get an RSS feed from the site that allows newsreaders (like NetNewsWire for Mac OS X). Check out the molbio forums RSS info at this link

The second was a way to create a portable list of recent posts from the same forums. This used a PHP add-on from the phpbb forums web site called Topics Anywhere. It generates a javascript that calls the info from the server forum database using PHP scripting commands. It's what I'm using in the right hand menu of this blog.

Gotta like this. Comcast is testing 3 Mbps service in various parts of the country, as "the cable giant plans to expand consumer trials for a high-speed Internet service, the latest step in the Comcast's effort to double the speed of its standard cable-modem product" [CNET News.com]. Tonight I got 1.6 Mbps, not bad and better than what we were getting for awhile with attbi. Of course, I think the neighbor kid who's really into p2p music downloading is on vacation!

Just when I start to try to get my head around all the various blogging tools and the use of RSS, there's this report about a coming fight about the RSS specs. Evidently, a power struggle over RSS technology has developed, which "pits blog pioneer Dave Winer against opponents at IBM, Google and others clamoring for a different format" [CNET News.com].

I'm still working on understanding the simple parts of blogging and RSS. For example, I'd love to be able to include a list of my favorite news sites in the right side column, and have the current top 3-5 stories on those sites automatically listed every time this page is opened. More importantly (depending on whether I ever develop this particular blog into something interesting for others and not just myself), I'd like to syndicate this particular blog. This is not something that's available with the free version of Blogger that I'm using. Moveable Type looks like a great blogging tool, but the requirements are such that I'm not in the position to use it. I did read last week that the group who puts this out is starting a blogging hosting service, called TypePad, ranging in price from $4.95 to $14.95 per month. I'll keep an eye on this.

ARS Technica has a pretty decent article on the state of the Mac, Mac OS X, and the upcoming Panther release (OS X 10.3). It's the initial column of Mac.Ars, written by Eric Bangeman. It's a balanced, well thought out article on Apple's software and hardware directions, third party software developers for the Mac, and the future for Panther Server.

In a CNet report today, federal government says there is new evidence that an attack is being planned on computers using Microsoft's Windows. [CNET News.com]. Yep, it's another in a long series of vulnerabilities in Windows. It was handled on our network by blocking TCP and UDP ports 135, 139, and 445 for all inbound connections at the firewall. Easier I guess than trying to patch all the desktop machines. At least this time we weren't completely shut down--the last time something like this happened, there was this very knee-jerk reaction. It didn't matter that almost half the computers on our network are Macs.

Sequencing quest....

To follow up on our quest to settle once and for all our choice for contractor for our genome sequencing project, today we found out that it's official that our first choice is getting out of the sequencing business but staying in the bioinformatics business. This means we either allow the company to subcontract out our sequencing or we split the job as I alluded to in a previous post. I'd like to keep it close at hand, but I want to be fair with my collaborator. Of course, with the internet, neither of us is more than a few seconds away from the data.

A poll released Monday in Spacetoday.net suggests that the American public continues to support NASA and the space shuttle program [spacetoday.net]. 68% agree that the shuttle should continue to fly with a higher number yet agreeing that we should continue to send humans into space. Yes, there have been two horrific accidents in the shuttle's history, but most people realize that there will always be risks in space flight. We're a long ways from Star Trek. The investigation into the Columbia accident will result in significant safety changes, and indeed it will be safer. But even if NASA and all the top engineers and scientists in the world think they've carefully assessed every risk, there's always the chance that something, the unexpected, will be missed. We're not where we are by not taking risks.

I've always been a sucker for space flight in general, ever since the Mercury days. The Right Stuff is one of my all time favorite books and movies. I still remember where I was when Armstrong and Aldrin set down on the moon. I've been to the Smithsonian Air and Space Museum in Washington DC three times--and it's the same exhibit!

I'm trying out NetNewsWire as an RSS newsreader, blogging tool, etc. This should contain my first link from it.

There's a blog at MacDevCenter regarding the success of Apple's iTunes. You can read about it here: [MacDevCenter]. What's interesting to me is how so many other would-be providers of on-line music are now jumping in to the fray with their versions, once they saw the success of the iTunes music store. However, for a while anyway, I think they'll continue to screw it up [iTunes Bandwagon, CNET].

Today I met with the Scientific Coordinator of the UW Center for Genome Sciences. They're interested in entering into a collaboration with us, but it would be strictly on the sequencing side of the project. They haven't built the kind of automated annotation tools that IG has been offering. Yet, because they are a not-for-profit University cost center, this part of the proposal might end up quite a bit cheaper. We'd then have to either complete the annotation manually, (a lot of BLAST searches!), or subcontract this part out, again with a company like IG. I'm very interested in getting a budget proposal from them.

A few hours later, a bid came from the former IG associates that are now part of what they call the FIG (I won't write what that stands for as I'm not sure they're public yet). Good solid proposal, but higher than what IG came in at. All in all, while I would like the idea of the sequencing taking place a 15 minute walk away from work, IG with its one-stop shopping (we think) may still be the best way to go. In a long conversaton with G today, one thing we wish is to visit the company to be convinced that they are not going to close up shop. We have one shot to get this right!

Another thing that's been going on the past few days. My collaborator on the genome grant and I have just enough of a funny feeling about our potential industry partner to think about looking around for an alternative. There's something about being responsible for that much money, but to also realize that it is a finite number. On this subcontract there can be no cost overruns!

After contacting my former grad school mentor, I've got a few leads on companies and organizations that might be interested in tackling such a project and be able to meet the goals we've set out in the original grant proposal (and in the two year time frame). Next week should be interesting as I meet or talk with some of these other groups.

Last week I listened in on an agency conference call, watched the streaming web feed, and followed along using the powerpoint presentation, on the new agency planning and budgeting process. Fascinating stuff :) and it goes along with the matrix team management style.

We will comply.

Then today my DD told me that starting in FY04, all of our base budgeting will be compared to our annual spending plan...monthly! This includes all categories, including travel and training. In other words, we will need to match our spending plans with our programs (so far so good), but the difficulty arises in trying to come up with and then match monthly spending plans. Come on, this is research and it's so difficult to project the myriad of things that can go right, as well as go wrong, in any project that involves uncertainty (after all, if we knew the answers, it wouldn't be called research!). So, what do we do? Take a deep breath and just do it. Oh, by the way...this is due by COB next Tuesday!!!

So, will I have time to think about anything else? Is this now going to be the life of a program manager? As usual, we'll see how it all pans out.

Somebody made a comment to me this morning regarding US AG John Ashcroft's visit to Seattle, to which I flippantly responded,

"It's funny how important and powerful he's become even after he lost a Senate seat to a dead guy."

My colleague laughed, so I guess this struck him as funny. But really, when you look back at the last couple of years, there's been some profound changes in our country. And most of us, me included, don't always pay attention when we should. And it's often not very funny.

Over the next few weeks, I'll be working with my collaborators to prepare the final budget for our genome sequencing grant. It's amazing how much the cost has come down in the past few years. The original submitted proposal was at ~$0.10 / base pair. Since the funding is actually about 17% less than what was requested (somewhat typical and I'm not complaining), I was able to get the company who'll actually perform the sequencing to cut that about 15%. This will include training in house (Chicago) on their gene annotation software, which in itself will be interesting to write about here. It's time to start exploring how many of the genetic analysis tools have been ported to Mac OS X, besides BLAST.

This is a new blog where I'll try to come up with something thoughtful once in awhile related to my work as a long-time scientist (molecular biologist/microbiologist), a beginning manager in government, my experiences with technology and computers, and whatever else comes to mind.

Just like the millions of other blogs out there.

if you've come here looking for that other blog, I've moved it. You'll have to ask where...