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Time is the Enemy. See? November 20, 2018

Posted by stuffilikenet in Toys, Uncategorizable.
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Needs No Title November 20, 2018

Posted by stuffilikenet in Photography, Uncategorizable.
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Manufactured Human Organs November 20, 2018

Posted by stuffilikenet in 3D Printing, Awesome, Brain, Science, Star Trek Technology.
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Scientists at Tel Aviv University have created human organs (little ones but, hey) from a bit of biopsied tissues.  They separated the cells from the rest, induced pluripotency and built up organs in differentiated cell layers on a gel scaffolding.  They were able to grow cardiac, spinal and cortical cells from the biopsy sample.

This is critical to success: the cells are the patient’s own cells, with little chance of immune system rejection.  These guys (Tal Dvir, Reuven Edri, NAdav Noor, Idan Gal, Dan Peer and Irit Gat Viks) are currently engaged in regenerating an injured spinal cord and an infarcted heart with spinal cord and cardiac implants. They have also begun to investigate the potential of human dopaminergic implants to treat Parkinson’s disease in animal models.

They have big plans for this technology: “We believe that the technology of engineering fully personalized tissue implants of any type will allow us to regenerate any organ with a minimal risk of immune response,” Prof. Dvir concludes.

Homework: Reuven Edri et al, Personalized Hydrogels for Engineering Diverse Fully Autologous Tissue Implants, Advanced Materials (2018). DOI: 10.1002/adma.201803895

Diagnosing Alzheimer’s with AI November 12, 2018

Posted by stuffilikenet in Applications, Awesome, Brain, Science.
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This is pretty good news if you think Alzheimer’s can be slowed or halted in some way (unproven, but a good idea): researchers funded by NIH have developed a (so far) 100% accurate method of diagnosing Alzheimer’s before any clinical symptoms appear.  The study seems pretty bullet-proof, too: Prospective 18F-FDG PET brain images from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) (2109 imaging studies from 2005 to 2017, 1002 patients) and retrospective independent test set (40 imaging studies from 2006 to 2016, 40 patients) were collected. 90% of the images were used as training data and the rest used as test data.  The learning algorithm developed for early prediction of Alzheimer disease achieving 82% specificity at 100% sensitivity, an average of 75.8 months prior to the final diagnosis.

Figure 2:

Example of fluorine 18 fluorodeoxyglucose PET images from Alzheimer’s Disease Neuroimaging Initiative set preprocessed with the grid method for patients with Alzheimer disease (AD). One representative zoomed-in section was provided for each of three example patients: A, 76-year-old man with AD, B, 83-year-old woman with mild cognitive impairment (MCI), and, C, 80-year-old man with non-AD/MCI. In this example, the patient with AD presented slightly less gray matter than did the patient with non-AD/MCI. The difference between the patient with MCI and the patient with non-AD/MCI appeared minimal to the naked eye.

I do recommend doing your homework (below), since the paper is pretty digestible for the alert layman, and the study itself well structured.

Homework:

  1. Yiming Ding, Jae Ho Sohn, Michael G. Kawczynski, Hari Trivedi, Roy Harnish, Nathaniel W. Jenkins, Dmytro Lituiev, Timothy P. Copeland, Mariam S. Aboian, Carina Mari Aparici, Spencer C. Behr, Robert R. Flavell, Shih-Ying Huang, Kelly A. Zalocusky, Lorenzo Nardo, Youngho Seo, Randall A. Hawkins, Miguel Hernandez Pampaloni, Dexter Hadley, Benjamin L. Franc. A Deep Learning Model to Predict a Diagnosis of Alzheimer Disease by Using 18F-FDG PET of the BrainRadiology, 2018; 180958 DOI: 10.1148/radiol.2018180958

 

Crisis Management Down Under November 8, 2018

Posted by stuffilikenet in Brilliant words, Geek Stuff, Science.
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"Where have all the bloody teaspoons gone?" is an age old question in the workplace. In an article in the BMJ [not concerned with scatology, but British Medicine] from 2005, researchers at the Burnet Institute in Australia attempt to measure the phenomenon of teaspoon loss and its effect on office life. They purchased and discreetly numbered 70 stainless steel teaspoons (54 of standard quality and 16 of higher quality). The teaspoons were placed in tearooms around the institute and were counted weekly over five months. After five months, staff were told about the research project and asked to complete a brief anonymous questionnaire about their attitudes towards and knowledge of teaspoons and teaspoon theft.

During the study, 56 (80%) of the 70 teaspoons disappeared. The half life of the teaspoons was 81 days (that is, half had disappeared permanently after that time). The half life of teaspoons in communal tearooms (42 days) was significantly shorter than those in rooms linked to particular research groups (77 days). The rate of loss was not influenced by the teaspoons’ value and the overall incidence of teaspoon loss was 360.62 per 100 teaspoon years. At this rate, an estimated 250 teaspoons would need to be purchased annually to maintain a workable population of 70 teaspoons, say the authors.

The questionnaire showed that most employees (73%) were dissatisfied with teaspoon coverage in the institute, suggesting that teaspoons are an essential part of office life. The rapid rate of teaspoon loss shows that their availability (and therefore office life) is under constant assault.

One possible explanation for the phenomenon is resistentialism (the theory that inanimate objects have a natural aversion to humans), they write. This is supported by the fact that people have little or no control over teaspoon migration.

Given the widely applicable nature of these results, they suggest that the development of effective control measures against the loss of teaspoons should be a research priority

Hilarious. But wait; there’s more.

Exasperated by the disappearance, the scientists decided they would measure the phenomenon. Do the teaspoons really disappear over time? The answer was a resounding yes: spoons in research institute tearooms seem to have legs. While good fun, the research is a good example of a study design referred to as "longitudinal".

A longitudinal study uses continuous or repeated measures to follow particular individuals – in this case, teaspoons – over prolonged periods of time. The studies are generally observational in nature: the scientists simply watch and collect data over time. Typically, no external influence is applied during the course of the study. Beyond just working out where all the teaspoons have gone, this study type is also useful for evaluating the relationship between risk factors and the development of disease (for example, heart disease), and the outcomes of treatments over different lengths of time. In this study, the main questions posed by our researchers were to determine the overall rate of loss of teaspoons, and to work out how long it took for teaspoons to go missing.

They purchased 70 teaspoons (16 of which were of higher quality), each one discretely numbered and then distributed throughout the institute. Counts of the teaspoons were carried out weekly for two months, then fortnightly for a further three months. Desktops and other immediately visible surfaces were also scanned for "misplaced" spoons. After five months of covert research, the study was revealed to the institute, and staff were asked to return or anonymously report any marked teaspoons which may have found their way into desk draws or homes.

Good study design

This type of data collection provides a simple example of what makes a good longitudinal study. If we break it down, a longitudinal study needs to:

  • take place over a prolonged period (this study was done over 5 months)
  • be observational in nature (teaspoons were observed and counted, there was no intervention)
  • conducted without external influences (teaspoon users/thieves were not aware they were being studied until the conclusion of the study itself).

Results

 

The results show that 56 (80%) of the 70 teaspoons disappeared during the study, and that the half life of the teaspoons was 81 days (that is, half had disappeared permanently after that time). The study also showed the half life of teaspoons in communal tearooms (42 days) was significantly shorter than for those in research group specific tearooms (77 days). The rate of loss was not influenced by the teaspoons’ value. All of these pieces of information directly answer the main question posed by the researchers.

Conclusions

A longitudinal study is terrific at following individuals or teaspoons over a period of time and observing outcomes. But, by definition, the design means there can be no intervention (as we are just observing a phenomenon). The researchers could not employ a tool or an intervention to prevent spoons from being "misplaced", and the researchers could only report a spoon missing. As the study is observational only, there is no way of finding out what has happened to the spoon, just that it is lost. The authors were able to conclude that the loss of workplace teaspoons was rapid, and their availability in the tearoom was constantly under threat.

Homework: Megan S C Lim et al. The case of the disappearing teaspoons: longitudinal cohort study of the displacement of teaspoons in an Australian research institute, BMJ (2005). DOI: 10.1136/bmj.331.7531.1498

Package Installers for Windows and MacOS November 6, 2018

Posted by stuffilikenet in Applications, Geek Stuff, Publishing Tools, Video.
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I have been forced at gunpoint to use a Mac for the last six weeks at my newest place of employment, and not without a few tears. I had to learn to install IntelliJ, NetBeans and Eclipse (already had that one) for MacOS. The company which enslaves me uses MacOS’ Self Service app, from which I installed Homebrew. Homebrew does every installation you could possibly desire (well, nearly) and I installed in short order git, gradle, Java and IntelliJ–all correctly and findably by each other, managing the pathname (or whatever they are called in MacOS). I must say, this makes first-day setup for the engineers much quicker, and much simpler. Good thing too, since the poor sods are going to be working with a bewildering variety of the manifold technologies which enable the hydra-headed beast which is my employer.

It turns out that Homebrew is a MacOS-only product; but there are several package installers which can work with Windows, such as Scoop,

 

Chocolatey and Npackd,  I quite liked Scoop (hence the Youtubery), but you may wish to try the others.  Good luck; for your more complex setups this can be a real timesaver.

Arizona Exposure October 30, 2018

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Arizona is pretty much paradise in the winter months.  We spent the winter of 2017-8 there and had an interesting time staring at Nature’s landscapes. It  was a  bit of a shock for me to realize how much I like desert landscapes. I really didn’t expect it.

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Someday I will learn how to stack images, and then I will show you only one photo.  Until then, however…

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Please bear in mind that all sunsets are much redder than my camera will capture,or my eyes are really going (could be).

I’m Pretty Sure Nobody Reading This Watches Music Videos, But… October 30, 2018

Posted by stuffilikenet in Brilliant words, Video.
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Fit Any Scatter Plot June 7, 2018

Posted by stuffilikenet in Brilliant words, Geek Stuff, Science.
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A wonderful paper in the archives of the University of Rochester  shows how any random scatter plot can be fit to a curve with enough parameters, and thence a lower number of same is often thought to be a good measure of an expression’s fitness for use…until now. “The mathematician John von Neumann famously admonished that with four free parameters he could make an elephant, and with five he could make it wiggle its trunk…The aim of this short note is to show that, in fact, very simple, elementary models exist that are capable of fitting arbitrarily many points to an arbitrary precision using only a single real-valued parameter θ. This is not always due to severe pathologies—one such model, studied here, is infinitely continuously differentiable as a function of θ. The existence of this model has implications for statistical model comparison, and shows that great care must be taken in machine learning efforts to discover equations from data since some simple models can fit any data set arbitrarily well.”

Tall claim?  Nope.  The author, Steven T. Piantadosi, shows two examples of data points fitted with a simple equation

 

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can be fit to any arbitrary set of data plots……like these:

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Mind you, the parameter θ needs to be calculated precisely: ”Both use r = 8 and require hundreds to thousands of digits of precision in θ.”.

Gee whiz (and hilarity) aside, the paper demonstrates the fallacy of using unreasonable models for this sort of algorithmic from-data derivation to create meaning from what might be noise, or Joan Miro’s signature.

Sore Loser June 5, 2018

Posted by stuffilikenet in Hello Kitty, RV and camping, Uncategorizable.
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Lily wants a drink before the next hand

The Delight of Propane Chicken June 5, 2018

Posted by stuffilikenet in RV and camping, Toys.
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EXCITING UPDATE:

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Yellow Creek Campground May 29, 2018

Posted by stuffilikenet in Mushrooms, Photography, RV and camping.
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in Plumas County is a delightful PG&E-owned small campground with nearly no amenities. It has eleven campsites, two without raccoon boxes, two vault toilets and at least running water.

It is, however, beautiful beyond compare.  Located on a meadow with a stream

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passing one-third of the campsites and with a canopy of pines and firs to shade the campers, it’s a little garden spot all its own…and then there are the mushrooms.  Oh my goodness, the mushrooms.

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I fear I have left out a few.  Don’t worry; it’s raining right now so I should have new ones for you soon.

I relaxed after a hard day of squatting to photograph mushrooms (that weren’t there when I left camp this afternoon) by photographing their newer brethren, freshly emerged into my camera’s eye while being serenaded by at least six different kinds of birds (a red hawk among them) at sunset.  After dark there are frogs to keep the gentle susurration going, so that my sleep is as peaceful as can be…except knowing there are black bears about (my first day here there was a mound of bear evidence1).

Also, there are cute ice flowers to be admired, if you look carefully for them.

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1. I may continue to use “evidence” as an euphemism for all things scatological in future.

Synchro de Mayo May 21, 2018

Posted by stuffilikenet in RV and camping, Toys, Uncategorizable, Uncategorized.
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is not really what it’s called, it is just when it happens.  A congregation of some of the 2600-odd Volkswagen Vanagon Synchros in the United States, it’s really a long camping party in Hollister State Recreation Area and the best place to see immaculately kept and/or innovatively modified Synchros:

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There’s one in every crowd, I guess.

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Why four wheel drive?

 

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Vanagon owner doing what they do most.

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The newest Volkswagen four-wheel drive: not for sale in California (or maybe the USA)

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Typical Vanagon in its native habitat.

There were other VW vans there, of course:

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Dimensional Analysis of a Dometic Toilet April 22, 2018

Posted by stuffilikenet in RV and camping.
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is the least satisfactory way of finding out which model is being examined.  The paperwork for Dometic toilets only goes back so far.  Dometic dimensional analysis What happens if your Lazy Daze is twelve years old? You can’t find the proper part numbers online, that’s what.  I speak as a tireless expert geek; you can’t get it off the net. And so, you make do with toilet seals that do not match perfectly, and slide around until they are no longer seals, but volcanoes of an odiferous bent…I mean vent.

Well, since I am a tireless geek (and since I live near the stinking thing), I kept looking.  Finally ran into Philip at Morro Dunes RV Park, who carefully asked me about the configuration of my toilet.  Stumped, he asked me to text him pictures of the thing disassembled, which I did…and then he found the right seals.  IMG_20180325_191531924_HDRIt It helps that Phil has been fixing RVs for the better part of fifteen years.

But wait!  there’s more. Removing the toilet from the base to change the seal started a leak at the back of the thing, which was difficult to trace, but eventually fixed with Teflon tape (zip ties, Teflon tape, Velcro, Sugru and duct tape are my favorite things), blood, sweat and swearing.

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Glories March 4, 2018

Posted by stuffilikenet in Photography, Publishing Tools, Toys.
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I grew up in a devoutly Methodist household, and we had paintings  of Our Lord  which often featured the suggestion of God’s presence through rays of light streaming through clouds.  In fact, I don’t usually see these rays which I call Glories all that often; apparently the particles necessary for such diffraction are rare enough that glories don’t come standard with every sunset.

Then, too, when I see them I don’t have a nice camera with me…just my cell phone.  The current default camera app in Android 6.0.1 does not feature exposure control, making it very difficult to catch the rays (usually sunsets present as a bright band of yellow in my camera).  Thankfully, the Google Play store offers other camera apps, such as CameraZOOM. I have been able to finally capture a good enough sample to share (cropped in The GIMP):

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Glories near Lake Havasu

EXCITING UPDATE:  Glories viewed from ISS

Image: A rare optical phenomenon spotted from orbit

Busses By The Bridge February 8, 2018

Posted by stuffilikenet in RV and camping, Toys.
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BBTB is a celebration of all things VW, but most especially busses.  My missus does not miss a chance to celebrate her particular misguided passion, despite the huge cost and compete unreliability of a thirty year-old, poorly designed, cheaply built invention of Adolph Hitler.

Just sayin’.

Now, lest you think me bitter or this subject, I point out that there were 600 better implementations of the Vanagon in this show alone, many of them fully functional and not at all plagued with the sorts of things which indicate the van in question was never restored, reconditioned or renovated.  At all.  Check the few photos below for pointed examples:

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Joshua Tree National Park February 8, 2018

Posted by stuffilikenet in Awesome, Mutants, Photography, RV and camping, Uncategorizable.
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Warning: foul language

JTNP is a dangerous place for the unwary naturalist or hiker.  Forget about scampering naked through the desert during a full moon; this place is populated by a truly bewildering variety of spiked, barbed,pointed and sharp plants guaranteed to impale an incautious passerby on the briefest hike, or trip to the restroom.

Take, for example, this beautiful specimen of Darwinian selection:

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This is known as the Spanish Bayonet, the Pointy Bastard or the Unwary Thighstabber. My wife says this is her least favorite plant, possibly due to unfortunate personal experience.  Spanish Bayonet is very stiff and the point is very hard.  I do not doubt this pointy bastard could be used as a bayonet.

Next a more delicate, elegant stiletto of a plant:

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Note the barbed thorns and tips. This herd-culling flora is known as the Lacerating Motherfucker, for good reason. Sometimes called the Wait a Minute, it grabs anything organic which brushes it and drags it towards itself in a series of painful spasms.  One presumes the plant benefits passively from the organic matter of its victims decaying around it, thus enriching the local soil. It is perhaps worth noting that many desert species secrete chemicals which inhibit the germination of other plants.  This helps explain why there are small bare patches surrounding most plants in Joshua Tree National Park.  Worth noting, too, is that the space is just large enough for small critters to pass, but not humans.

Ouch.

Then there are the more obvious instruments of torture, the standard cacti, some of which are exceptionally well defended1, such as the Malevolent Spiny Fucker:

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Closely related in terms of armament and disposition is That Dangerous Spiked Fucker:

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Not lastly (because I’m typing this in a very cramped camping chair and I need to go have a beer) is the Psychotic Rapier Clusterfuck.  Do not trip near this plant.

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As usual, the wonders of Nature make me sit back and admire her ingenuity from safely inside a locked room with air conditioning, a stereo system playing Vivaldi and powerful adult beverages to celebrate my narrow escapes.2

I would not have you finish reading this little note without understanding that the grandeur of the place is unparalleled in my experience. The Flintstonesesque scenery will make any visitor think they have landed on another planet designed by Irwin Allen, or maybe Ray Harryhausen.3:

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1.  The best defense is a good offense.

2.  I haven’t even talked about the night hikes through the Stabby Wastelands following an experienced madman to “my spot”, nor the boulder scrambling urges that demand to be addressed by the Flintstones’ rock formations here. Honestly, I don’t know what I was thinking.

3.   Seriously. Maybe Luc Besson?

Patrick’s Point, Postage-stamp Park January 12, 2018

Posted by stuffilikenet in Mushrooms, Photography, RV and camping.
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In December I had the most delightful visit to Patrick’s Point Park, a 1.5 mile by about 1.0 mile-wide campground and park. Being pretty darned cold, it was mostly empty, the way I prefer my natural surroundings. It was peak mushroom season and shrooms were found about every five feet on the nature trails.  Only one hallucinogenic (amanita mascara), so don’t rush there to pick’em; their are signs all over the place admonishing visitors to leave the shrooms and flowers untouched.  And since nobody is around, violators will be easy to spot.

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This set of photos is just me on a maybe one-mile hike. For comparison, that is a size 11 men’s foot you see in the images. Also; there is ample scenic beauty besides my unnatural interest in mushrooms.

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Leavis Flat Campground January 5, 2018

Posted by stuffilikenet in Photography, RV and camping.
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Leavis Flat campground is a charming little side-of-the-road spot, with no pavement, no water (except the creek; see photos, below) and nobody else here, at least in January.  The ranger did come by (with a gun and a bullet-proof vest—I wonder what’s going on here usually?) to determine we were not bums, transients, bindlestiffs nor other kinds of ne’er-do-wells and that we had, in fact, paid to get in.  Leavis Flat is perhaps too close to Los Angeles for comfort.

Regardless, our little campsite had lovely views of the nearby creek, beautiful scrub oaks, chestnuts and mulberry treeIMG_20180104_091720819s  and, except for the very occasional car, just the sound of the creek to lull us to sleep. It’s a welcome change from having to spend several days in the SF bay area.

The creek is surrounded on all sides by the kinds of rocks you expect in the California foothills; bring your boots if you like to scamper up a creek bouldering.

Nice.  There are also lovely little bare areas with just leaves that look like floors

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freshly strewn with flower petals:

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Very relaxing, with nobody around at all.The real reason we camped here is (besides the low cost of entry) is proximity to California Hot Springs, which we intend to visit before departing for Joshua Trees.

IMG_20180104_160902217 EXCITING UPDATE:  California Hot Springs is closed for the nonce, so we charged up the hill to see the 100 Giants,a redwood grove here in Sequoia National Park.  A nice little ride (11 miles from Leavis Flat campground up to about 6700 feet)in the missus’ Vanagon, the show and ice hardly mattered.

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…or…

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I have left out the devastation of certain pine species along the way; apparently beetles ran rampant (or drought killed just this one species among other trees such as sequoia and cedar), as most of the long-needled pines are dead, dead, dead. Very sad and kind of spooky, seeing these dead trees among the live ones.

The Best Things in Life January 1, 2018

Posted by stuffilikenet in Awesome, Mutants, Photography, RV and camping.
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The momentous stuff in my life pales in comparison with a good camping trip…like this one. At our favorite local (abandoned) campground:

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Within walking distance of here we found, well, this:

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All found within twenty minutes, each cluster was part of a greater whole.

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This is the view across the pond…reflected in the water, then rotated and cropped in GIMP, the poor man’s Photoshop.