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Real Time rtPCR Test to Detect Covid 19 Disease

Covid 19 disease is caused by a virus named SARS-COV-2. The test to detect it is called Real Time Reverse Transcriptase Polymerase Chain Reaction(Real time rtPCR}. PCR was concieved by a California surfer named Kary Mullis and he was awarded the nobel prize for that. PCR is a way of making copies of DNA. If a double standed helix of DNA is heated it will separate into two single strands. After cooling, and if there are complementary bases in solution, a enzyme called  DNA polymerase rebuilds the strands into the double strands. So,each cycle in PCR doubles the amount of DNA. 10 cycles will create about 1000 copies and 20 cycles will make over 1,000,000 copies. Heating the copies destroys the original polymerase so each cooling cycle had to have fresh enzyme added. Then, it was discovered that the polymerase in a hot spring bacteria called Thermophilus aquatica did not denature. Using that meant the test could be done faster because it did not have to be paused to add the polymerase enzyme in each cycle.
The virus that causes covid 19 is not DNA based.  Rather,  it is single stranded RNA. To run it on a PCR machine it must be converted into DNA. So another enzyme called reverse transcriptase must be used used to covert it into DNA.
PCR only copies DNA. The test was called rtPCR.  To ID the DNA, another test must be done and that test was called gel electrophoresis.   In gel electrophoresis the amplified  DNA is placed in a gel cell and an electric current is applied.  This causes sections of the DNA to migrate.  Then, it can be compared to a known DNA.  It took much longer to do these tests and had more errors.
A new technique was developed that was faster and more accurate, It could also not only ID the virus early on, it could quantify it. This test is called Real Time rtPCR, It is a sophisticated test using probes and fluorescent markers to look for sections on the RNA strand that are unique to the virus.  Early in the test,  the virus can be identified and even quantified.  It can tell how many copies of RNA were in the sample taken from the patient.  It can not only ID the virus, it can give an idea of the load of virus the patient has and how much the patient is putting into the environment.  Real time means that one can look at the ongoing test in real time rather than waiting for the PCR and electrophoresis to be completed.

On December 31st, the Chinese government reported to the World Health Organization that there was a pneumonia in patients in Wuhan China of unknown origin.  A few days later it had been sequenced and identified as a novel(new) corona virus.  The virus and it’s disease quickly spread in  China.   A Real Time rtPCR test was developed to ID the virus.

In the US,  the CDC developed it’s own test for the virus but used different sections on the viral strand to ID the virus.  The test kits the CDC sent out for running the tests were faulty and that was a problem that had to be corrected.  Also,  there were few labs approved that could do the tests.  Another problem was  that  the CDC requirements for who could be tested was too narrow.  The patient had to show symptoms and a history of contact  to someone from China.

Since then,  more labs can do the test and there are fewer restrictions on who gets tested.  A company called Roche has a machine and test procedure that is very fast and can run many  tests and that has been approved.  Because the US is behind on testing there could be many  more cases out there and  the virus could be more widespread.  Catching up on testing is imperative.  It needs to be done along with all the other things being done in a situation that is getting worse here and much of the rest of the world.

by Paul Snoey

 

Ribbon Cutting for North Main Avenue

On Friday the 14th, Officials and interested citizens gathered at Overlook Park.  They were there to begin a one mile walk to the entrance of the Carty Unit of the refuge.  There were about sixty people who made the walk.  The purpose was to celebrate the completion of the improvements to North Main Avenue with a ribbon cutting.

At the entrance to the refuge, The Mayor of Ridgefield, The refuge project leader, and a spokesperson from the Federal Highway Administration made comments about the project.  Then, several children were each given a pair of scissors and the ribbon was cut.  This project was to improve access to the refuge, especially for pedestrians.  There is also a new entrance to the refuge through the port and a trail from there will take hikers along the west side of Carty Lake and join the Oaks to Wetlands trail near the Cathlapotle plank house. This will make for a loop  of a little more than five miles.  The trail by Carty Lake is closed now but may be open in a few weeks.

By Paul Snoey

Building The Arched Culvert on N Main Avenue

The rebuilding of North Main Avenue brought many improvements to the city’s northern arterial street.  Adding two new culverts and raising the street to over 10 feet higher will  put the road and  at least one driveway  above the floods for both Gee Creek and the Columbia River.  There is a wide sidewalk that will get pedestrians and joggers out of the street.  New guard rails on both sides  should prevent vehicles from going off the road.  Of all the events, putting the arched culvert together was the most interesting

The arched culvert pieces were assembled on August 22nd of last year.  There were 24 pieces that made for 12 arches.  Since the arches had to support each other, the two halves had to be placed in the footings simultaneously.  To do that, two giant mobile  cranes were used.  Each half culvert section weighed 77 tons.  The work had to be carefully coordinated to protect the machinery, the concrete arches, and the workers.  It was fun to watch.  It was Legos, Tinker Toys, and Tonka Toys for big boys and girls.  Below are some of the photos I took on that day.

The heavy pieces of culvert had to be picked off the truck bed, attached to cable rigging, and swung into place. There was a queue of trucks entering and leaving from opposite sides all day long.  It meant 24 trucks each carrying one half section of culvert.

To move the sections into position, each piece had  several points of connection using cables, chains, and pulleys.  At the top of each section, facing the camera, are holes into which rebar will be placed.

Even though the pieces were quite large, they needed to be placed in exactly the right place in the footings.  It meant careful coordination with the two crane operators with the men in the lift helping to guide the process.  Since the two pieces would come to rest on each other, they had to be placed at the same time.

As the day progressed, the final pieces of the culvert were placed.  Note the array of chains, pulleys, and cables.   Looking at the back of the crane, there can be seen a stack of very heavy weights which counterbalanced the cranes.  It was easy  to see how skillfully the assembly was done.

The sections of the culvert were all put in place on August 22, but there still  was much work to be done.

Paul Snoey

Paving on N Main Avenue

 

Paving was done on N Main Avenue today and appears to be almost complete. On the west side, forms have been placed for the sidewalk, which has yet to be poured.  There still remains guard rails to be placed on both sides.  There has been an 8″ water main installed in the street ending with a hydrant at the entrance to the refuge.  Under the future sidewalk, there is a two inch sewer force-main that will carry sewage from the refuge into town.  The completion date is still scheduled for December 31st.

Looking to the north behind the two workers, the end of a new 10′ culvert can be seen.  This culvert carries a tributary of Gee Creek that used to drain into Gee Creek on the east side.  The improvement created an opportunity for a salmon incubator and I asked the state to consider it.  Yesterday, the state granted permission for a remote site incubator to be installed on property owned by Raul and Claudia Moreno.  The Lewis River Hatchery has committed 5,000 Coho eggs for early January.  This incubator will be part of an educational program with the State Department of Fish and Wildlife and likely students from Union Ridge will be visiting.

Wednesday afternoon update:  Crews were installing a guard rail on the east side today and finishing paving on the North end.  There was a lot of crew members on site today working in several different places along the project.  Heavy rain is predicted beginning tomorrow and the National Weather Service has issued a flood watch for Thursday evening through Sunday morning.  The original culvert under N Main was only 10 feet in diameter and tended to back up during a heavy rain event.  If we do have heavy rain, it will be interesting to see the difference the new culvert makes.

Contributed by Paul Snoey

PAUL’S POWER WAGON

I have a DR Field and Brush Mower that I use to cut brush along the creek to make room to plant trees.  Planting trees requires moving tools,  sand and dirt, and the trees themselves.  Trees in pots can be heavy as are all the tools for planting them.  Wheelbarrows are hard work, especially carrying a load up and down a steep hill or over rough terrain.  My machine can take several attachments such as a snow blower or a wood chipper.  They don’t make a wagon attachment but will sell you one with the power unit built in for as much as $2500 or more.

So, I asked Tevis Laspa for help in making a wagon that could be attached to the power unit, and he responded that it sounded like a fun project.  I found a pair of wheels on casters and that a 1.25″ steel pipe would connect the wagon to the power unit.  After making a prototype out of a piece of siding, Tevis and I discussed how to make the unit.  It was made of welded rectangular steel tube stock with the casters and pipe welded to the frame.  When I came home this morning I saw Tevis had delivered it.  I took it for a test drive down the trail at Union Ridge and back home via N 5th Ave.     Tevis showed ingenuity in  putting the connecting pipe though the steel stock.  It makes for a very sturdy connection.

Thank you so much Tevis.  It’s just in time as trees can be planted soon.

Contributed by Paul Snoey

Old Town Storm Water to Get Treatment Facility

Most of the blocks from Pioneer Street to Division Street and from North 5th Avenue to North Main Avenue discharge directly into Gee Creek by the Heron Ridge Street Bridge. It is the largest source of storm water pollution in old town Ridgefield.. The City of Ridgefield applied for a Clark County Clean Water Fund Grant administered by the Lower Columbia Fish Recovery Board. It was ranked number one for funding. The engineering was completed earlier this year, went out to bid, and the City Council awarded the contract to Odyssey Construction.

The project is between Maple Street and Heron Ridge Drive just east of North 3rd Avenue. The project is well into construction with a construction completion date at the end of October. It will provide treatment for low storm water flows with an overflow provision for high level flows.  This project will improve water quality of storm water into Gee Creek, especially during times of low summer flows.

The city of Ridgefield is to be commended for this improvement.  It will make a difference.

Contributed by Paul Snoey

North Main Avenue Project

This afternoon I went to the site to see the progress of the culvert  project. The sections of the wing-wall are sitting on the road on the south side. The wing-wall on the Northeast corner of the culvert has been partially done but nothing on the other corners. There is a tributary that came into the creek on the east side and the project will switch it to the west side. To do that, another culvert needs to be installed. It will be a ten foot  wide corrugated metal culvert and there are six twenty-foot sections by the staging area. The new road and pedestrian trail must be built and paved. No doubt this project will not be built by BirdFest on October 5th. It may be several weeks before this project is complete. The project website has no information about a change in scheduling and has not been updated since September 13th.

(Monday morning update:  The completion date is now Friday, November 29th.)

contributed by Paul Snoey

Allen Canyon Creek Flow Restored

A couple of weeks ago I showed a photo of this area  on Allen Canyon Creek.  The creek had stopped flowing and there was just a small pool with some Coho fry that were trapped.  We’ve had about 4 inches of rain since  September 8th.  I’ve never seen this high a flow so early in the year.  We have not had enough rain to saturate the ground enough to create runoff so the creek will drop pretty fast but probably will have some flow through the end of the year.  It’s interesting that the Coho fry stay in the pool just below the fern on the right bank.   They are free to go anywhere but seem to like their home pool.  This morning I dropped some gold fish food and let it float downstream.  With in  a few seconds the fry eagerly ate it. It is a good way to know if they are still there.  Notice how clear the flow is after such a heavy rain.  Water quality is excellent on Allen Canyon Creek.  However, for much of the summer, there is no flow.  The water is there but trapped behind dams to hold water for stock ponds and in storm water detention ponds.

The Lower Columbia Estuary Partnership is accepting grant applications  for stream rehabilitation projects that facilitate fish recovery.  Private individuals  can’t apply but the City of Ridgefield can. If there was a study that looked at those places on Allen Canyon Creek where water is held it may be possible to modify them to release water in times of need.   Allen Canyon Creek could become a stream that could carry a much better population of Coho Salmon and possibly cutthroat trout as well.  How about it City?  Could you consider applying for a grant to improve stream flow on Allen Canyon Creek?

Contributed by Paul Snoey

More on North Main Avenue Construction

The photo above was taken last Thursday.  The reflection of the arched dome has created an illusion that the culvert is a complete circle.  Because the worksite was flooded all week,the contractors were unable to work.  Later on Thursday, a larger pump was brought in and it began pumping down the area on Friday.  By Saturday morning, the level of water had dropped about 3 feet or more.  Another large pump was brought in Saturday morning.  Sunday was a day of heavy rain and by tonight my rain gauge had 1.18 inches of rain.  The watershed for Gee Creek is 8.7 square miles.  A one inch rain on the watershed dumps 150 million gallons or more.  Some of this water is soaked into the ground  or stored in ponds and wetlands or storm water facilities.  The water that makes it to the creek can only go through the North Main Avenue crossing.  With the extra pumping today, the water level stayed about the same.  The National Weather Service is predicting another round of heavy rain early Tuesday.  This could be a real problem:  The high flows on the creek today will not have much time to drain the watershed before the next storm and the ground is beginning to be soaked increasing the amount of runoff.   September is a month of transition from summer into fall.  Occasionally, early autumn storms can arrive.  This year has been unusually stormy so far and is making things difficult for the project.  It is a little ironic that this project should prevent any future flooding on North  Main Avenue but is being delayed by a flooded worksite.

~ Contributed by Paul Snoey

The End of The Drought

A couple of years ago I had mentioned to Kathy Winters that I had seen a garter snake chasing some fish in a pond that had almost gone dry.  With the long summer drought, the same pond has only a few inches of water left again this year.  In driving by a few days ago, there was another snake in the pond and I could see lots of movement from what I  thought were fish.  I was curious and came back with a bucket of water and a net.  A couple of scoops and these creatures were in the net.  I took a few home and put them in an aquarium.  I took the above photo and grabbed a field guide.  These are larval long toed salamanders.  These are what the garter snake was after.  They are very fast swimmers and could avoid a garter snake.  But as the pond got drier they were becoming more vulnerable.

The photo above is of Allen Canyon creek.  This creek had stopped flowing several weeks ago.  There are a few pools like this and the Coho fry released from the incubator are stranded.  This afternoon, we had two heavy rain showers and they dropped almost an inch of rain.  It may be enough to get the creek flowing again and save these fish.   I may be able to stop watering trees along Gee Creek if it rains just a little more.  Perhaps Autumn is a little early this year.

 

 

N Main Ave Reconstruction

 

North Main Avenue has been closed from Depot Street to the entrance of the Carty Unit of the refuge since  the July  4th  week-end.  The old 10 foot  diameter corrugated  metal culvert has been removed, much material excavated, and a great deal of rock and sand imported.  There  has been  a steady stream of trucks going in and out for several weeks.  By midweek the area for the new culvert had been prepared and trucks began delivering the components to build the footings.  There are 8  pieces, each weighing  55,000 lbs.
The footing pieces for the South side were placed Wednesday and the pieces for the North side were to be placed as well.  However, there  is a problem with the crane and as of Friday evening the crane is sitting quietly and the pieces of the footing are still uninstalled.  The groove running down the middle of the footing will be where the precast arched dome will be set.  The interior pieces of the footing have rebar sticking out of them.  Forms have been built and will be filled with concrete.  This will make for a solid footing.  One of the workers stated the plan is to lower the arched dome next week.  However, this was before the problem with the crane happened.  At 3:30 PM today there were no workers on site.  It’s likely the crane must be repaired before work can be resumed. Since each piece of footing weighs more than 27 tons, it is easy to see why.

Climate Change Revisited

 

The graph above is the latest Monthly graph (May) for 2019.  The peaks for each year are always  in May. As growth begins in the northern hemisphere, it begins to take CO2 out of the atmosphere thus  the dip seen each year.  The increase each year from month to month is due to the burning of fossil fuels.  The difference between May 2019 and May 2018 is 3.6 PPM.  All the months so far in 2019, are above 3.0 PPM, a large increase.  The three biggest carbon emitters in the world are the US, China, and India.  The US increased it’s CO2 emissions in 2018 by 2.5%,  China by 4.7 %, and India by 6.3%.   The world as a whole increased it’s CO2 emissions by 2.7% compared to 2017.  So, the world is increasing emissions of CO2 instead of reducing emissions, reversing a trend the last few years.  The reason is economic growth of all three countries.  China is relying on coal for producing electricity, as is India, even though both are making strides in alternative energy sources.

 

The graph above is of the increase each year of CO2  from 1960 through 2018.  The black bars represent the average for the decade.  It is notable that the first decade averaged less than 1.0 ppm, while the decade beginning in 2000 averaged almost 2.0ppm. As mentioned above, so far in 2019, the monthly averages are over 3 ppm higher than last year.  If that trend continues, then 2019 could be the highest yearly average ever.  2019 will be the last year of the decade.  If the average is 3 ppm, then the decade will average about 2.5 ppm.  So, it’s clear that we are increasing emissions of CO2 rather than decreasing.

GLOBAL AVERAGE TEMPERATURE BY YEAR:  1850 TO 2018

The colorful stripes above represent the temperature of the earth over the past 168years.  Each stripe is one year and the colors from blue to red represent cooler to warmer.   This graph was obtained from a “Show your Stripes” website.  It shows in an elegant manner the rise in temperature of our planet in the last few decades.  The last few decades have been notable for record heat, cold, rain,  drought, hurricanes, and typhoons.  The signature of  a warming world due to an ever increasing amount of CO2 into the atmosphere is strong.

I recently read about the winter that Lewis and Clark and company spent at Fort Clatsop.   They were miserable.  They were tired of eating mostly elk meat.  They must have been dirty and stinky.  They were wet because it rained all the time.  They were happy to break camp in the spring and head up the Columbia River and home.  It was the beginning of the modern age that began with the industrial revolution in England.  The age we’re in now is largely fueled by fossil fuels.  I could think about our explorers in the modern age.  After a day in the field they could come back to, let’s say, a hotel, take a hot shower,  and put on clean clothes.  Then, while drinking a cold beer, Meriwether Lewis could write up a report and e-mail it to Thomas Jefferson.    Then, they could fly back home.  The point is that the modern world is wonderful.  However, we are not paying the social and environmental cost associated with it.  The climate scientists are telling us that we must stop putting CO2 into the atmosphere.  To do that we must stop burning fossil fuels.  Some climate scientists are saying that not only must we stop emitting CO2, but we must begin removing it.   That would be tough.  It will be tough enough just to slow emissions.  CO2 has a long residence time in the atmosphere and the level of CO2 in the atmosphere now will have consequences that last hundreds if not a thousand years.  It is unlikely that we can change our minds in the future and undo the ongoing changes.  The best we can do is to slow the changes down.   However, there is great resistance to doing that and I’m doubtful that we will but there is always hope.  Many people are working  hard to make a difference.

contributed by Paul Snoey

Union Ridge Giants

 

If you walk to Union Ridge School on N 8th Avenue, you will be greeted by some giant Douglas Fir trees at the end of the street.  The largest, to the left in the photo, is 145 feet  tall and is 19 feet in circumference at chest height.  It is the largest of some very big trees here and being among them is a pleasure.  Myrna Mills, a former deputy city clerk for the City of Ridgefield, said that when she was a student at Union Ridge, she and other students planted some of these trees.

The Carnegie Institute of Ecology at Stanford University did a study of carbon uptake in forests.  Their conclusion was that 25% of man made carbon dioxide emissions  are taken up by the world’s forests.  It makes sense to preserve and protect forests and trees.   In the United States, Pacific Northwest forests are the best at removing carbon from the atmosphere.  Douglas firs can live over a thousand years and can rival redwoods and giant Sequoias in size.  In addition to their beauty, trees clean the air, provide cooling, and remove carbon dioxide from the air.

Ridgefield has a lot of trees.  When I am in the Carty Unit near Lake River and look  back into town, there are so many trees I can barely make out the houses.  There are many places in Ridgefield  where more trees can be planted so let’s  do that.

Contributed by Paul Snoey

 

Salmon Incubator Set Up

Contributed by Paul Snoey

The Remote Site Incubator was set up on Riemann Road early last week and on Jan 3rd, 10,000 Coho eggs were placed in a basket on top of the incubator.  As can be seen in the photo below,  the embryos have developed eyes.  They will need a few more weeks before hatching.  After hatching,  they will stay in the incubator for a month or so and when ready, will swim out of the overflow.  They will disperse downstream and spread themselves out along the creek as far as the refuge.  They will stay in Gee Creek for about one year and then head down the Columbia River and into the Pacific Ocean.  Of course, the odds of coming back are very small.

 

 

 

 

 

A little More on Shiny Geranium

The photos  below were  taken in early June of 2017 at the  South bound Gee Creek Rest Stop on I-5.  It is of an area taken over by shiny geranium.  The plants are about 18″ high and  loaded with flowers and seed pods.  It’s incredible ability to produce seeds sets it apart from other geraniums and  other weed species.   Each flower can produce a seed pod containing five spring loaded seeds that can be thrown several yards.  This ability is why it can be such  a problem.  It is on Pioneer street now and North Main Avenue and a few other places around town.  There were six acres on a property north of town that were taken over and I have  worked with the property owner for two years now to eliminate it.  I visited that property today as well as Pioneer Street and a couple of other places and can see that trying to eliminate it has not worked.