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Messages - A-Team

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1
Consequences / Re: COVID-19
« on: March 14, 2020, 12:58:43 AM »
Quote
Who wants to know?
In other words, your educational level is low, you like it that way, you don't read English too well, fly off the handle misunderstanding simple sentences, then dive into slander because prospects of this disease have gotten you hysteric and challenging your ignorance just doubles down on that.

Last chance before permanent blocking: 

2
Consequences / Re: COVID-19
« on: March 14, 2020, 12:40:48 AM »
pietkuip, I'm calling your bluff: how do you know so much with such authority?

Third time: are you a MD/ Ph.D with an extensive publication record in coronavirus research and clinical treatment of infectious disease? Look up Robb on Pubmed if you even know what that is. As someone explained, he is talking about survival of a lipid-bilayer viroid at ambient temperature.

Second time: look at the picture below. Mol bio 101. What are they specifically predicting for the evolving threat scenarios for this virus? Put up or shut up.

3
Consequences / Re: COVID-19
« on: March 14, 2020, 12:37:29 AM »
pietkuip, how do you know so much with such authority?

Please answer the question: are you a MD/ Ph.D with an extensive publication record in coronavirus research and clinical treatment of infectious disease? Or just another nervous nelly with zero scientific background in anything halfway relevant?

Can you take a moment away from your vital research to establish some minimal competency? Look at the picture below. What are they specifically predicting for the evolving threat scenarios for the covid-19 corona virus?

4
Consequences / Re: COVID-19
« on: March 14, 2020, 12:12:27 AM »
As made perfectly clear in the post, it's not my list nor my advice. There are some items in there worth considering and others that are harmless. Primum non nocere ... Dr. Robb seems in compliance.

pietkuip ... I gather you are a MD/ Ph.D with an extensive publication record in coronavirus research and clinical treatment of infectious disease? Or just another anxious / panicked internet denizen with zero scientific background in anything halfway relevant?

Perhaps you found it really scary to read that in his opinion "there will be NO drugs or vaccines available this year to protect us or limit the infection. Only symptomatic support is available."

I am not looking for advice myself as we live out in a remote desert on a gated and patrolled 60,000 hectare property that came with a 1950's concrete underground bomb shelter complete with a steel hatch and ceramic air filter, not that there's a need to go inside.

5
Consequences / Re: COVID-19
« on: March 13, 2020, 10:04:25 PM »
Quote
set the mask aside for a couple weeks before re-use. washed my hands and changed clothes. bagged clothes also.
Smart. From earlier research on these masks, it seems the effective pore size of the mask (0.8 micron) is considerably larger than the diameter of the virus (0.1 micron) but much smaller than the diameter of a typical air droplet in which the virus is suspended after a cough. So what happens is the mask catches the air droplet which quickly evaporates leaving the virus on the outer surface of the mask where it is viable for 9 days or so.

Below, passing along 'as is' very detailed recommendations from an MD who began studying the molecular biology of coronaviruses beginning in the 1970's and has kept up. The steps he personally takes just during regular flu season are quite interesting.

"Coronavirus Health Advice - James Robb, MD FCAP
Retired professor of pathology at UC San Diego
05 March 2020-20

1. If you have a runny nose and sputum, you have a common cold

2. Coronavirus pneumonia is a dry cough with no runny nose.

3. This new virus is not heat-resistant and will be killed by a temperature of just 26/27C (78-80F) degrees. It hates the sun.

4. If someone sneezes with it, it takes about 10 feet before it drops to the ground and is no longer airborne.

5. If it drops on a metal surface it will live for at least 12 hours - so if you come into contact with any metal surface - wash your hands as soon as you can with a bacterial soap.

6. On fabric it can survive for 6-12 hours. Normal laundry detergent will kill it.

7. Drinking warm water is effective for all viruses. Try not to drink liquids with ice.

8. Wash your hands frequently as the virus can only live on your hands for 5-10 minutes, but - a lot can happen during that time - you can rub your eyes, pick your nose unwittingly and so on.

9. You should also gargle as a prevention. A simple solution of salt in warm water will suffice.

10. Can't emphasize enough - drink plenty of water!

THE SYMPTOMS

1. It will first infect the throat, so you'll have a sore throat lasting
3/4 days.

2. The virus then blends into a nasal fluid that enters the trachea and then the lungs, causing pneumonia. This takes about 5/6 days further.

3. With the pneumonia comes high fever and difficulty in breathing.

4. The nasal congestion is not like the normal kind. You feel like you're drowning. It's imperative you then seek immediate attention.
 
These are the same precautions I currently use during our influenza seasons, except for the mask and gloves:

1) NO HANDSHAKING! Use a fist bump, slight bow, elbow bump, etc.

2) Use ONLY your knuckle to touch light switches. elevator buttons, etc.. Lift the gasoline dispenser with a paper towel or use a disposable glove.

3) Open doors with your closed fist or hip - do not grasp the handle with your hand, unless there is no other way to open the door.

Especially important on bathroom and post office/commercial doors.

4) Use disinfectant wipes at the stores when they are available, including wiping the handle and child seat in grocery carts.

5) Wash your hands with soap for 10-20 seconds and/or use a greater than 60% alcohol-based hand sanitizer whenever you return home from ANY activity that involves locations where other people have been.

6) Keep a bottle of sanitizer available at each of your home's entrances. AND in your car for use after getting gas or touching other contaminated objects when you can't immediately wash your hands.

7) If possible, cough or sneeze into a disposable tissue and discard.
Use your elbow only if you have to. The clothing on your elbow will contain infectious virus that can be passed on for up to a week or more!

What I have stocked in preparation for the pandemic spread to the US:

1) Latex or nitrile latex disposable gloves for use when going shopping, using the gasoline pump, and all other outside activity when you come in contact with contaminated areas.
Note: This virus is spread in large droplets by coughing and sneezing.
This means that the air will not infect you! BUT all the surfaces where these droplets land are infectious for about a week on average - everything that is associated with infected people will be contaminated and potentially infectious.

2) Stock up now with disposable surgical masks and use them to prevent you from touching your nose and/or mouth (We touch our nose/mouth 90X/day without knowing it!). This is the only way this virus can infect you - it is lung-specific. The mask will not prevent the virus in a direct sneeze from getting into your nose or mouth - it is only to keep you from touching your nose or mouth.

3) Stock up now with hand sanitizers and latex/nitrile gloves (get the appropriate sizes for your family). The hand sanitizers must be alcohol-based and greater than 60% alcohol to be effective.

4) Stock up now with zinc lozenges. These lozenges have been proven to be effective in blocking coronavirus (and most other viruses) from multiplying in your throat and nasopharynx. Use as directed several times each day when you begin to feel ANY "cold-like" symptoms beginning. It is best to lie down and let the lozenge dissolve in the back of your throat and nasopharynx. Cold-Eeze lozenges is one brand available, but there are other brands available.

I hope that this pandemic will be reasonably contained, BUT I personally do not think it will be. Humans have never seen this virus before and have no internal defense against it.

Tremendous worldwide efforts are being made to understand the molecular and clinical virology of this virus. Unbelievable molecular knowledge about the genomics, structure, and virulence of this virus has already been achieved. BUT, there will be NO drugs or vaccines available this year to protect us or limit the infection within us. Only symptomatic support is available.

6
Consequences / Re: COVID-19
« on: March 13, 2020, 05:16:39 PM »
Quote
The myth of “China originally hid the outbreak” is irrational, vicious and false.
It's time to move on from vapid virtue-signaling and everyone singing kumbaya to read the wrenching full account -- and censorship / reprimands that continue to this day -- written by the ER head doctor Ai Fen 艾芬 who provided the whistle that the first whistleblower drs used.

The govt knew they had a new type of coronavirus outbreak in mid-November. The disease had been raging in Wuhan for some time with the earliest hospital admissions in mid November. ER and respiratory doctors suspected immediately the "unresponsive atypical pneumonia" was related to SARS.

Metagenomic DNA sequencing from alveolar lavage just takes overnight; tBlastn at GenBank another five minutes to kick out beta Coronaviridae as the best hit (indeed SARS would be at the top of the stack at 97% identity).

So they knew because China has perhaps a million molecular biologists at the Ph.D level and beyond; the instruments are all made there as are many key bioinformatic algorithms. Some idiot at CDC offered assistance to China from US virological know-how -- it's the other way around.

This patient additionally had a bacterial infection with Ps aeruginosa, a common intractable opportunistic pathogen along with 46 other bacterial species of unknown relevance. Anti-virals alone wouldn't affect outcome in this situation.
 
"A 55 year-old from Hubei province contracted Covid-19 on November 17 [ie had become so ill that he went to the hospital]. From that date onwards, one to five new cases were reported each day...."

https://scienceintegritydigest.com/2020/03/11/dr-ai-fen-the-wuhan-whistle/
https://twitter.com/r_h_ebright?lang=en
https://www.scmp.com/news/china/society/article/3074991/coronavirus-chinas-first-confirmed-covid-19-case-traced-back

There are new 'insider' epidemiology numbers in the above links; perhaps someone else here can do the comparisons with official releases. Divergences may be continuing up to the present date.

The lead scientist Shi Zhengli 石正丽 spent a decade collecting bat coronaviruses all over China.  Back at the Wuhan Institute of Virology, her large lab had been experimentally modifying the spike protein S from 2006 on to study for example how a 12 bp insertion engineered furin site interacting with human ACE2 receptor changes infectivity, species barriers and vaccine design (common and valid pursuits, prompt open access articles, funded in part by grants from the US).

She immediately suspected but couldn't confirm the virus escaped from her lab, not from a dropped test tube or infected lab tech but from flawed disposal.

https://www.scientificamerican.com/article/how-chinas-bat-woman-hunted-down-viruses-from-sars-to-the-new-coronavirus1/?amp

Labs generate quite a volume of daily waste, quite a bit biological. For example, to ramp up production of a viral spike protein by growing live virus on multiple human cell lines, where does the 100 liters of left-over media go after centrifuging?

Some waste gets autoclaved, a lot gets flushed down the drain, lesser amounts go to an expensive secure incinerator, and the rest is trucked to the town dump in plastic bags to be compacted by a large bulldozer. In the US, I've seen voluminous hospital waste (syringes, bedding, bandaging etc) escaping our local landfill into the creek so this is hardly an issue just for China. The recent BSL-4 upgrade at WIV (and nationwide directives) likely addressed this.

The problem Chinese authorities have  in controlling the narrative is that 'the internet never forgets'. There's really no way to delete peer-reviewed articles from PubMed. Even if you get the journal to retract the article, PubMed will just add a note to that effect to the top of the abstract. The full text remains mirrored on PubMedCentral in multiple countries, clouds and personal computers.

It's astonishing shocking to read the research that went on with coronaviruses over the last 15 years both in China and the US. Early on, the danger wasn't recognized; it was about flu remedies. It's no crazier though than what went on with Salk and Sabin polio virus vaccines. (PV is another single stranded positive sense RNA virus but unrelated.)

http://www.virology.ws/2015/09/10/why-do-we-still-use-sabin-poliovirus-vaccine/

Right now the research community is very divided, given an estimated 5000 additional bat coronaviruses, over whether ever more isolates should be collected, propagated and genetically engineered to prevent the next outbreak through early study.

Others say this is a terrible idea, leave the bats alone, we need fewer BSL-3 and -4 facilities, not more, that this approach all but guarantees lab accidents will happen whereas as natural transmission wouldn't have. Indeed, a long list of pathogen escapes and staff transmission from secure labs have been documented in the modern era.

7
Consequences / Re: COVID-19
« on: March 12, 2020, 05:24:19 PM »
Really bad idea, Steve. It's completely illegal in the US because it has had horrific outcomes in the past (thalidomide, hgh-CJD from pooled cadaver pituitaries, and a thousand others). In the US, we could care less if some obscure pharma gets an obscure product approved by a foreign country. That goes back to 1975, Japan approving tainted dura mater from Germany. That didn't work out too well.

An internet forum of anxious innocents is no place to knock clinical medicine, promote self-medication, herbal medicine, New Age nuttery, widespread known carcinogenic antivirals, anecdotal medicine of miraculous recoveries, goat testicle injections, homeopathy, aromatherapy, folk medicine, power of prayer, snake oil, Silver Solution coronavirus cures sold by televangelist Jim Bakker (newly out of prison), non-stop tv drug ads from ("ask your dr if ldsfjedfmdskfdol is right for YOU").

The last thing we need right now is hospital corridors filled with family members who read  something on twitter or pharma reps (attractive young women with marketing backgrounds) urging providers to use a company product (free ticket to Hawaii for enough Rx, not joking). 

Informed consent from the patient for an experimental treatment -- how exactly is that obtained from a desperately ill patient on CPAP?

The current loophole, 'compassionate use' of products never vetted for safety or efficacy is bad enough. This is already being turned around to threaten drs with google search results such as dr so-and-so isn't compassionate (wouldn't prescribe ldsfjedfmdskfdol for grandpa).

The US has already started clinical trials of remdesivir in coordination with ongoing Chinese clinical trials. What they are looking for is proof of efficacy: a measurable gain in clinical outcome. It is completely irrelevant whether it knocks down viral reproduction in lab cell lines or not.

Powerful drug cocktails on top of the 25-30 different prescription medicines (not joking) some of patients are already taking for co-morbidities? Not going to happen. Contra-indicated.

This compound, as explained earlier, is promising in terms of targeting viral RdRP genes rather than a viral gene with human homolog cross-targeting. However remdesivir is all-purpose (any RNA virus), not at all particularized to the covid-19 RdRP. It could very likely be improved by combinatorial chemistry (which has now gone virtual and structure-guided).

Remdesivir is not seen by the viral enzyme.  It is a pro-drug metabolized in the body to myriad other chemicals. Do any of those been have unintended consequences? Viruses have already developed drug resistance to the active form of remdesivir -- it's an easy point mutation followed by strong reproductive selection.

Normally this drug category (base analog, eg 5-fluorouracil) has many dangerous side effects. In fact they are often used in microbiology labs as intentional mutagens. In HIV, they can kick the cancer can down the road which can buy the patient some time. Maybe there'll be a cure later (Nixon's war on cancer began in 1971 but it's worse than ever).

"NIH clinical trial of remdesivir to treat COVID-19 begins
https://www.nih.gov/news-events/news-releases/nih-clinical-trial-remdesivir-treat-covid-19-begins

Study enrolling hospitalized adults with COVID-19 in Nebraska.

Novel Coronavirus SARS-CoV-2 This scanning electron microscope image shows SARS-CoV-2 (round magenta objects) emerging from the surface of cells cultured in the lab. SARS-CoV-2, also known as 2019-nCoV, is the virus that causes COVID-19. The virus shown was isolated from a patient in the U.S. NIAID-RML

A randomized, controlled clinical trial to evaluate the safety and efficacy of the investigational antiviral remdesivir in hospitalized adults diagnosed with coronavirus disease 2019 (COVID-19) has begun at the University of Nebraska Medical Center (UNMC) in Omaha. The trial regulatory sponsor is the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health. This is the first clinical trial in the United States to evaluate an experimental treatment for COVID-19, the respiratory disease first detected in December 2019 in Wuhan, Hubei Province, China.

The first trial participant is an American who was repatriated after being quarantined on the Diamond Princess cruise ship that docked in Yokohama, Japan and volunteered to participate in the study. The study can be adapted to evaluate additional investigative treatments and to enroll participants at other sites in the U.S. and worldwide.

There are no specific therapeutics approved by the Food and Drug Administration (FDA) to treat people with COVID-19, the disease caused by the newly emergent SARS-CoV-2 virus (formerly known as 2019-nCoV).

Remdesivir, developed by Gilead Sciences Inc., is an investigational broad-spectrum antiviral treatment. It was previously tested in humans with Ebola virus disease and has shown promise in animal models for treating Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS), which are caused by other coronaviruses.

“We urgently need a safe and effective treatment for COVID-19. Although remdesivir has been administered to some patients with COVID-19, we do not have solid data to indicate it can improve clinical outcomes,” said NIAID Director and U.S. Coronavirus Task Force member Anthony S. Fauci, M.D. “A randomized, placebo-controlled trial is the gold standard for determining if an experimental treatment can benefit patients.”

Clinical trials of remdesivir are also ongoing in China. NIAID developed the current study taking those designs into account, and in accordance with consultations convened by the WHO on the development of a therapeutic trial for patients with COVID-19.

Participants in the NIH-sponsored trial must have laboratory-confirmed SARS-CoV-2 infection and evidence of lung involvement, including rattling sounds when breathing (rales) with a need for supplemental oxygen or abnormal chest X-rays, or illness requiring mechanical ventilation. Individuals with confirmed infection who have mild, cold-like symptoms or no apparent symptoms will not be included in the study. In accordance with standard clinical research protocols, eligible patients will provide informed consent to participate in the trial.

Quote
"Pharmaceutical giant Gilead, in its a rush to begin clinical trials on a potential treatment, may have violated federal law instead of waiting for slow-to-come federal approvals on drug exports."
https://www.axios.com/trump-coronavirus-drug-china-gilead-f3afd89a-c66e-4ace-b546-53fb416ae34d.html

8
Consequences / Re: COVID-19
« on: March 09, 2020, 12:15:36 PM »
For people here following the science side of this virus, the best two resources are biorxive (hasty preprints) and pubmed (final peer-reviewed), not so much press releases from know-nothing campus publicists or pharma marketing promotions of pre-existing repurposed miracle drugs (possibly with rush-rush clinical trials and carcinogenic side effects).

https://www.biorxiv.org/search/
https://pubmed.ncbi.nlm.nih.gov/

While PubMed is a known quantity familiar to anyone in biomedical research, Biorxive's specialty is serving early-release manuscripts that may or may not ever be submitted to a journal. It's well-suited to fast-breaking events like covid-19; researchers get a permanent dol and a priority claim in exchange for open collaboration. Quality varies; it's strictly caveat emptor but then so is peer-reviewed.

https://www.statnews.com/2020/02/03/retraction-faulty-coronavirus-paper-good-moment-for-science/

The search portal at biorxiv is quite clever but short on explanation. The rules (wild cards? caps? hyphens?) can be worked out though by simply searching repeatedly. This virus is nasty in that its nomenclature is poorly conceived, isn't informative, doesn't scale and hasn't stabilized. In contrast, human genes are assigned unique names (no aliases) with homologs numbering, enforced by journals and strict rules on acronym formatting (eg all caps, no superscripts, no italic, no greek or latin).

420 results for term "coronavirus"
114 results for term "2019-nCoV"
054 results for term "SARS-CoV-2"
001 results for term "HCoV-19"
050 results for term "COVID-19" or "covid-19"
170 results for term "coronavirus AND spike"
028 results or term "coronavirus AND TMPRSS2”
027 results for term "coronavirus AND furin"
009 results for term "remdesivir"

The clever bit is that you can combine search results adding/removing checkboxes on the promising items and biorxiv remembers this through multiple searches as long at the tab stays open. After refining your list via zooming down titles -> abstracts -> free full text or pdf, biorxiv will save it out to any of the common journal citation standards.

These can be sorted in reverse chronological order so if someone later fault-finds on an earlier article, you don't have to read it. Biorxiv can't search forward in the manner of GoogScholar to find all articles citing a given article. It does however provide a twitter search for comments on a given article. These are highly repetitive, usually self-promoting or otherwise annoying but sometimes kick out a useful resource.

The bottom line after all this is a level playing field: if there was any time left to actually read the filtered articles, you have a good idea of what's known and what's not and can pursue a research angle being fairly sure it's of community interest, a known unknown.

To summarize search results, almost all current research is looking at preventing the coronavirus from entering the cell via vaccines targeting the activation and fusion domains of the spike protein.

This decidedly won't work in the short term (first round of pandemic) and may never work as the spike protein is massively shielded by glycans ubiquitous in host proteins and exposed parts of it are rapidly evolving in many directions.

The reason for spike protein emphasis is two-fold: targeting say a human protease co-opted into helping the virus complete its life cycle could have a kazillion normal functions of its own all over the body, often only partly known. Knocking down virus production in this way then results in serious side effects.

Secondly, the patient has to be at a fairly advanced stage of diagnosed covid-19 disease before the drug can be administered whereas the vaccine protection can be cheaply done in advance on a population-level scale suppressing even emergence of the disease.

Of the couple hundred articles I looked at, the most useful was this slow-moving meander of 10 Feb 2020 that gets to the good stuff around page 26, doing well a lot of what needed to be done in terms of feeding supercomputer bioinformatic tools, leaving me with ideas for the next step, and providing all the start-up resources to do that. This virus is evolving very unevenly along its length and even within individual proteins. Adding to the 240 micro-variant genomes available today isn't going to address this.

Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop.. André, JK Millet, GR Whittaker
https://www.biorxiv.org/content/10.1101/2020.02.10.942185v1.full

9
Consequences / Re: COVID-19
« on: March 07, 2020, 10:55:04 AM »
Continuing on from #1993 and #2020, covid-19 viral activation and invasion of lung pneumatocytes has unusual and undesirable features that reflect rapid recent evolution of its genome.

The research action centers on the spike protein because it seems to have acquired aggressive new properties from a specific upstream 12-base insertion (creating a 4 amino acid furin-like cleavage site motif) that greatly facilitates adhesion to the ACE2 receptor which facilitates fusion (mediated by a downstream spike domain) with the host cytoplasmic membrane, the entry point of viral RNA into the cell interior where it reproduces.

There are 182 complete covid-19 genomes as of today being studied with both wet lab and dry lab (bioinformatic) approaches. NextStrain collects all these and presents them as a branching phylogenetic tree that grows every day and sometimes gets rearranged.

This tree clusters closely related covid-19 genomes the same way that your desktop organizes related files into a nested folder hierarchy but using advanced statistical methods such as maximal likelihood models that have been under intense algorithmic development for half a century. However these trees can be made under many different assumptions and parameter sets. A tree that aligns amino acids (rather than nucleotides), eg those from the upstream half of the spike protein, might give a rather different topology from a whole genome nucleotide tree.

On the data side, the 182 genomes are mostly not the ones we want: the early ones. Many are just chains of descendants: A in Wuhan gave it to B in Milan and C in Vatican City, B gave it to D in Austria and E in Spain, C gave it to F, G and H in Dubai with 0-2 mutations at each step along the way. The real information lies in more covid-19 genomes from Wuhan but not descended from A.

This is useful early on in a pandemic for the tracebacks and self-quarantining that buy some (mostly squandered) preparedness time but as Sam documents above, that train left the station a month ago.

Molecular biologists want the genomes from the very earliest stages of viral spread in late Nov 2019 for five principal reasons:

-1- to work out the ancestral genome that first crossed the species barrier.
-2- to determine the carrier species because it may harbor many other coronavirus strains.
-3- to determine what adaptive changes took place that caused covid-19 to spread so virulently.
-4- to better understand mutational processes in covid-19 and future properties may evolve.
-4- to resolve whether mutational gain/loss of nucleotides represents an insertion or deletion.

However the epicenter of spread, which is not necessarily the epicenter of origin, has been bulldozed to the ground, its entire stock of wildlife incinerated and its infected denizens cremated without any genetic sampling. Under the circumstances, the focus was eradication; public health mandarins would hardly be bowing to requests for viral agent preservation from scientists.

Prior to the outbreak, Wuhan had two institutes (not one) collecting coronavirus genomes from wild bat populations and requesting isolates from other virology labs around the world, for example the Manitoba, Canada BSL-4 facility.

Assembling such a resource makes research sense in a country like China with strong science and a costly history of viral outbreaks in both livestock and humans. For its part, the US maintained a massive collection of anthrax strains until the FBI autoclaved the entire set after a rogue worker mailed a weaponized one around.

In summary, only a few of the 182 genomes originated early on in Wuhan but because of privacy considerations neither preprints, GenBank annotations or GISAID metadata make clear if any of the people were affiliated with the two corona virus laboratories.There is very little specific clinical information about the eight original ICU patients that triggered the ophthalmologist's alert. We don't know if any of the covid-19 genomes represents the transmitting patient with acute angle glaucoma.

Regardless, the genomes at NextStrain fall into two early-diverging clades (strains) that split early on and never later hybridized (through RNA recombination). These were noticed back in February and denoted L and S clades (for distinguishing mutations that affected leucine and serine codons). The topology of that branch of the tree has been stable ever since.

The original authors were careful to say of the two strains, the L type “MIGHT be more aggressive and spread more quickly”. However nobody since has honored that cautionary statement. Because of transmission chains, subsequent internal mutational divergences in both clades, and lack of healthy human volunteers, this idea is very difficult to pursue. Note that every node on the tree defines, through its descendants, its own clade or strain.

The NextStrain tree is unrooted, meaning that deep ancestry is not indicated by outgroups (closely related corona and other viruses). This is so bizarre that other researchers immediately added a variety of outgroups and recomputed the tree to see which of L and S is closer in genomic sequence to the first covid-19 to escape its initial animal host. And that the 'more ancestral' sequence is said to be the smaller clade, S. That needs to be revisited now that the data set is so much larger.

The phylogenetic tree unambiguously resolves the upstream spike protein mutation as an insertion. This was correctly inferred in the ‘uncanny’ preprint where it is called the 4th ‘HIV’ region. That’s not entirely off the mark but it’s better called the putative gain-of-function furin-like cleavage site resulting from the new four basic amino acid motif.

This preprint was withdrawn by author request; it was not retracted (shame on you FAS) and could conceivably resurface after massive revisions. It never mentions weaponization. The pdf is still offered at biorxiv; there’s a good discussion of its myriad problems too by others in the field:

https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf
https://www.tandfonline.com/doi/full/10.1080/22221751.2020.1727299

To date, there’s still no good explanation for how the furin-friendly insertion arose in the spike protein. Some of the better spike protein analysis is provided in the links and images below.

https://tinyurl.com/th8zpq3 21 Jan 2020 discovery of furin site (in Chinese)
https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1 images and structural analysis AC Walls et al
https://www.sciencedirect.com/science/article/pii/S0166354220300528?via%3Dihub French paper on furin site
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281273/ real furin motifs are longer
http://virological.org/t/evolutionary-epidemiological-analysis-of-93-genomes/405 GISAIS metadata for 93 genomes
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324781/ RNA recombination
https://tinyurl.com/r9fm3zw remdesivir
https://tinyurl.com/uopplv2 L and S clades
https://www.sciencedirect.com/science/article/pii/S193131282030072X?via%3Dihub early paper

10
Consequences / Re: COVID-19
« on: March 05, 2020, 11:24:01 PM »
Bruce, your follow-up question to #1993 is a good one. A lot of scientists are concerned covid-19 already had, for whatever reason, multiple routes of entry into the human cell (ie beyond ACE2) at the time of release or that it can or will quickly evolve by point mutation the common additional mechanisms that other ssRNA viruses use to get into mammalian cells, either because of replicative advantage or selective pressure from partially effective drugs and immunological approaches.

The viral load in one NEJM German patient was reported as ~100,000,000 mature viroids per single ml of phlegm. At those titers, rare events happen all the time.

It is not plausible that a de novo (innovative) route will evolve by point mutation over a time span relevant to the current pandemic. There is no mechanistic counterpart in RNA viruses to MDR in hospital bacteria which arises from shared plasmids. However single point mutations in, say the spike protein, could provide resistance to multiple unrelated drugs targeting the same site.

Multiple routes of entry will vastly complicate the current Hail Mary approach of tossing already-approved or compassionate-use experimental drugs that target binding sites on either the infecting viroid or receptor proteins external to the cell surface. For example, chase through the thirty million biomedical abstracts at PubMed to see about lisinopril (200 million US Rx per year) which is known to target ACE1 so maybe perturbs the homolog ACE2; it’s been considered before but it doesn’t even bind ACE2 much less block covid-19.

https://www.ncbi.nlm.nih.gov/pubmed/

But who knows, maybe something will work out. Pro-drugs like remdesivir don’t act on surface receptors; they have to be taken up and partly metabolized (not CYP450 here); remdesivir is a ribosyl adenylate analog that reversibly inhibits the RdRp replicase while evading proof-reading  excision. It is not specific to covid-19 or even coronaviruses; resistance has evolved previously in related RNA viruses.

Talk about rush-rush clinical trials and long-shot vaccines is primarily panic mitigation. The last thing the hospitals want right now is an ER full of worried well. The last thing FDA wants is another thalidomide. The last thing govt wants is rebuttal of the official narrative.

The current information environment is largely a mix of inapplicable older journal articles on other viruses, rushed preprints, hurry-up peer-review publications, unsupervised manuscript archives including Chinese-language only, and expert opinion from twitter blowhards..

Fortunately Bruce is asking about something we can easily check for ourselves without outside assumptions other than accuracy of posted genome sequences.

The covid-19 protease story is involved overall but not difficult, lots come into play during the life cycle. Furin is a known quantity, a human serine proprotein convertase encoded on human chr 15 whose catalytic activity may have been co-opted by covid-19 for its own activation agenda.

It’s mainly about the furin binding site on a target protein, wrongly described at wikipedia as the four residue, basic amino acid motif RXR/KR of arginines and lysine in the primary amino acid sequence. However that motif alone gives rise to numerous false positives and false negatives, so we’ll be needing to feed the covid-19 sequence to a 20-residue motif bioinformatic tool called PiTou that uses a hybrid experimental / hidden Markov chain to find furin sites much more accurately.

It's not possible to get from RXR/KR to a twenty residue motif by incremental point mutations unless the rest was already very close (as 4 to the 16th is too large with intermediate stage utility).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281273/

Cleavage though is just downstream of the core tetrapeptide which has to be exposed for the furin enzyme to get at a valid substrate. This motif almost always will be on the surface because the 3-4 positive electric charges are about impossible to bury from entropic considerations. The exceptions are internal salt bridges (eg opsins) or an oligomeric binding partner that offsets the positive charges with negatives. However the 20 amino acid requirement really raises the ante.

In the case of the covid-19 spike protein, it is a homomeric trimer with known atomic level structure in both the inactive and activated configurations so we can check whether the RXR/KR etc is exposed. Even so, there could be steric hindrance in the intact virion. This has to be studied with cryoEM as few viruses beyond tobacco mosaic virus are crystallizable for xray structure elucidation. Proteolytic cleavage (unlike drug binding) is always irreversible because of energetics (55M water).

11
Consequences / Re: COVID-19
« on: March 05, 2020, 07:18:03 PM »
Bruce and others asked about how genomes of different isolates of covid-19 differ in their RNA sequence after mutations during multiple rounds of replication in humans.

Recall the viral genome here is a single stranded, single segment, positive sense 28 kb RNA complete with host-provided 5' cap and 3' poly-A, in effect a messenger RNA ready for ribosomal translation to viral proteins (and poly-proteins) in an affected host cell.

That's all compiled for us daily at a genome browser called NextStrain, a project of the Trevor Bedford lab in Seattle which today shows an unrooted phylogenetic tree for the 166 different genomes currently posted at GenBank (or GISAID). It's interactive, stable, easy to use and provides all the mol bio basics as you mouse-over the display.

https://nextstrain.org
https://twitter.com/trvrb

To date, all have been point mutations (single nucleotide changes). These may or may not change an amino acid in its encoded protein (non-synonomous vs synonymous or silent). It's difficult to determine from sparse clinical data or bioinformatics alone or together what the practical effect if any that a mutational change brings about, even a change in the much-studied spike protein homotrimer central to the ACE2-based entry into the cell.

Taking the next step in evaluating spike mutations involves the stalwart online bioinformatic tools tBlastn at NCBI GenBank nucleotides and xray crystallographic structure modelling at PDB and SwissProt

https://blast.ncbi.nlm.nih.gov/Blast.cgi
https://www.rcsb.org/

No indels (insertions or deletions) have been reported to date relative to the oldest Wuhan sequence though these are fairly common in covid-19 counterparts in other species, in the coronovirus family overall, indeed in vertebrate viruses in general.

No recombination events as been observed yet either. Coronaviruses don't pass through DNA via a reverse transcriptase as part of their life cycle so what does this even mean? It means when someone like a health care worker is simultaneously infected by two or more strains of covid-19, the RNA-dependent RNA polymerase (RdRp) that replicates the viral genome may switch templates ('copy choice') part way through the transcription cycle creating a hybrid genome from the two strains. In short, this is not recombination as defined for diploid DNA genomes but similar to it in its gene shuffling effect (after several rounds).

12
Arctic sea ice / Re: MOSAiC news
« on: February 22, 2020, 06:20:13 PM »
A steady tailwind bearing for 56 hours produced the incredible straight drift of the proxy buoys for the Polarstern seen in Uniq's #635 animation above. Chasing down the stats, the ice pack moved at 2.1% the speed of the 1000 hPa wind (confirming what 'they' have been saying for years).

This wouldn't be possible without unresisting exits for the ice such as Fram, Nares and SV-FJL gap because the ice pack cannot compress further against land. (Over-rafting pressure ridges provide too much pushback when the ice is thick.)

Data from awiMet should someone wish to refine the estimate by providing the std error:
wind m/s,bearing 12,110 12,110 12,110 11,110 11,110 12,110 12,120 13,110 12,110 12,110 11,110 12,100 12,100 12,110 13,110 14,110 14,110 13,110 13,100 13,100 14,100 14,100 14,100 15,110 16,110 16,110 16,110 16,110 16,100 14,110 15,100 14,100 12,100 12,110 12,110 12,110 12,110 12,110 13,110 11,110 11,110 9,110 10,110 10,100 10,110 11,100 10,90 9,90 9,90 8,90 9,90 8,90 

Both ImageJ and Gimp offer image enhancement by convolution kernels, both canned (Process -> shadows) and roll-your-own DIY. They have a very beneficial effect on the Kaleschke SIC lead product (and downstream overlays), enhancing lead visualization without blowing up the grayish white interstitial background like linear contrast change, local adaptive (clahe) or histogram equalization.

To the extend the leads are anisotropic -- and they will be from TPD or during passage of a cyclone -- the choice of convolution 'direction' matters. The mp4 below used 'northeast'. No rocket science is involved automating out from the canned convolution to converge onto a quasi-optimal element of GL(3,R) wrt to frame average and that extends to a rolling window of GFS winds.

While some people are twittering from the KD, others are not. Kaleschke did not have time to describe productions methods but it is clear from Uniq's remarkable match-up in#635 of microwave leads with WorldView infrared that SIC leads just takes a longer radar wavelength approach to heat escaping through the ice. The images can't help but agree.

In other words, low Ghz radar meets up with long wavelength infrared in the electromagnetic spectrum, the difference being WV infrared is at the mercy of cloud cover while low Ghz sees through them better (in winter). It benefits from processing to darken warmer regions (ie the leads). We don't know what processing steps were taken but clearly they can be improved for the purpose of overlays on GFS weather,  Ascat scatterometry etc etc which don't see the leads but have other, complementary strengths.

The tripods have proven a planning and operational fiasco. Just drill through the ice, freeze in some 5 m fiberglass poles with no guy wires, hang slack electric and data cables off them, your pressure ridge problems are over. And where did Mosaic get their no-go snowmobiles, out of a museum?

13
Arctic sea ice / Re: MOSAiC news
« on: February 15, 2020, 01:32:16 PM »
Quote
KD yellow circle, PS magenta circle
Looks about right. The KD may be aiming east of the PS in order to catch the transpolar drift (instead of fighting it). If the ships are drifting in opposite directions, the KD could struggle all day with the ice but end up farther away from the Polarstern than when it started.

14
Arctic sea ice / Re: MOSAiC news
« on: February 13, 2020, 10:31:21 PM »
Decent offering today at FoMo -- a top and bottom DEM of the Mosaic floe and surroundings on youtube which is converted to mp4 below (because the the youtube controller is so annoying in not looping and moving on to unwanted material ... take the spaces out of https://youtu.be   /KJf5XOkB5m0 to see).

Nothing is labelled; no distance or height scale or Ice Camp locations are shown. The Polarstern is the dark squiggle. This is not expert use of display software by any means but it is a good start and a breakthrough for FoMo in terms of an interesting post.

It would have been better simply to have done an annotated slide show of the best views rather than the clumsy fly-through. That could include a plan view grayscale of the two DEM data layers. Every frame is angled though. Two screenshots are shown below.

Question is, if the floe is in hydrostatic equilibrium shouldn't the bottom be predictable from the top (apart from density altering inclusions). That is, with a free-floating ice berg, 10% is above the water and 90% below. Here though the overall contiguity of the ice pack and resultant mechanical strength over-ride the buoyant tendencies of individual pieces.

15
Arctic sea ice / Re: MOSAiC news
« on: February 11, 2020, 09:24:59 PM »
Quote
PS flew west & north yesterday 
Another 48 hours of that coming. The Polarstern reached new lat and lon records of 87.8 89.2 at 19:00Z which is 245 km from the pole and 919 km from the entrance to the Fram Strait. The weather pattern is pushing the whole Euro side of the icepack in that same direction.

That is shown in a 62-day Ascat below. The darker areas are thick MYI ice; significant pieces of it (though not the Lincoln Sea and west) will irreversibly enter the export staging area if the GFS winds keep up as expected. Not unrelated: the Arctic Oscillation index just hit a new high.

The bow radar we've been looking at is a ~10.0ghz product called a sigma S6 Ice Navigator system made by Rutter Inc of St Johns NL (https://rutter.ca/ice-navigation/). It's also been installed on the Healy and RV Lance.

The radar is operated by bridge command only and never before have scientists requested it for Polarstern research. The 1.5m wide X-band antenna is mounted on starboard side of platform B in crow's nest.

https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2016JC012387

It does not seem to have been configured properly (to compensate for motion using feedback from gyros) resulting in images not nearly as sharp as they could be. The whole control panel has been cropped out in the meereis archive.

The basic purpose when the Polarstern is underway is distinguishing between open water, ice pans, open water leads in ice fields and ice ridges that can trap icebreakers. In open water the ice radar detects small bergy bits and growlers (large and small glacier calving pieces) that can significantly damage a vessel.

16
Arctic sea ice / Re: MOSAiC news
« on: February 10, 2020, 03:04:08 PM »
Quote
still headed north and west, picking up speed
This Polarstern drift will continue strongly in this direction for several more days due to a persistent anti-cyclone to the north of Wrangel Island. Tailwinds will reach 10-12 m/s which are sub-gale strength.

The ship was at lat lon 87.8 91.7 at 1200Z today and will reach 88.1 86 later in the week, putting them in peak transpolar drift position. The concern has gone from them milling about for months in the Central Arctic to reaching the Fram four months ahead of schedule.

Fram export has really picked up under these wind conditions though it has been steady since mooring. It's very unusual to see the Fram  'intake funnel' of curved concentric leads extend up and past the north pole. This development will become even more extreme this week; the significance is the last of the very oldest and thickest MYI is being drawn down towards export.

The Fram situation seems completely uncoupled to the Nares-Banks Island ice above the CAA. Nares export has ceased for the time being.

An unusual collision of a very large ice plate with the Mosaic floe happened yesterday a couple of km off the bow over just six hours. A small pressure ridge much closer to the Polarstern has also developed off the port bow in the vicinity of the proposed airstrip.

If L Kaleschke is able to add a few earlier years to the lead visualization archive, it might be possible to test the proposition that ice motion has really gotten worse this year. These leads add a large number of trackable features allowing much higher resolution to description of motion.

17
Arctic sea ice / Re: MOSAiC news
« on: February 07, 2020, 05:10:51 PM »
Quote
lol
The circle, arrow and text overlay tools are confusing in ImageJ. Set the palette color, draw the overlay on the ROI, then Edit --> Draw to flatten your overlays into the base image. Otherwise the overlay will disappear with no undo! Maybe try RAMMB to locate the KD, rotate that by 105º CW and rescale to overlay on the jp2 version of PolarView which has mouse-over lat lon.

The prospects for the KD not being able to reach the Polarstern at all or getting permanently stuck on the return trip (with all the leg2 scientists aboard) are a definite concern.

Continuing the analysis from #578, the Polarstern's floe is being squeezed between two shear plates that hit at oblique angles with a delay of six hours or less, first from the left (port bow) and then from the right (port quarter). This is one of the few sequences where the coupling between events can be seen cascading throughout the bow radar view as the ice accommodates the squeeze by over-rafting into pressure ridges and keels. The mp4 is rotated 90º CW; the b/w scale bar is in multiples of the 118m ship length. The Polarstern's bow is at the b/w hemispheres, the stern is at the end of the first black bar.

The Ascat pair supplements the AMSRE leads pair above but shows the active and inactive zones more clearly in the two difference frames. The GFS anti-cyclone is above the active zone; the thick and resistant central MYI is more or less immobile. The Polarstern was on the boundary between the two zones.

Band 15 etc at WorldView are partly obscured by clouds and has confusing radial swathing so an ice motion pair there is not feasible.

The gangplank and Ice Camp area are abaft the starboard beam...

18
Arctic sea ice / Re: MOSAiC news
« on: February 06, 2020, 08:59:38 PM »
Quote
not a bad route.
The temptation is to sneak along the lee polynya north of FJI. However the Kapitan isn't going to do that as it could easily slam shut, pushing the ship onto the rocks as the wind changes over to forming a lee polynya on the other side or below.

I don't expect the Barents to freeze over: too warm, too shallow, too windy, too mixed, too unstratified, too much Atlantic Water coming in below Bear Island. Every year people get fooled into thinking new ice is forming when the satellite mp4 show the wind has merely blown the ice pack through the island gaps. Again. St Anna trough is more nuanced.

The slide show below shows a couple of ways using Uniq's triple of buoys for patching the database of 196 S1AB images for an additional 34 missing Polarstern locations, a situation that has gotten much worse with the ship in the pole hole.

Basically, the close-in buoys move in parallel curved tracks, more or less keeping their distance and defining a stable triangle. Adding in a known high precision of a nearby date with PS location establishes a fiducial quadrilateral that can be moved and re-located at three buoy points on a frame timestamps that lack a PS location. The lat lon can then be read from the graticule or pixel coordinates.

Mosaic_mult has quit; they were privy to the ship's precision GPS and plotted it even when the Polarstern was off the latest S1AB. Since their images came with high resolution graticules, the earlier lat lon could be read off that (or interpolated from flanking locations on slow dates).

Once a complete set of once-a-day 06:00 locations are known, the track can be drawn in GoogEarth with pop-up links at each point along the path to the radar image, GFS nullschool of that hour, local buoy radar of ice motion, and global AMSRE leads.

Update 1: added a png showing how Polarstern lat lon can be measured directly off S1AB radar scenes: (1) find the ship which is a bright radar reflector with a stable pattern of floes around it, (2) zoom in 1600% with the BAS IWS viewer provided at PolarView, (3) capture the lat lon at the middle of the ship, (4) transcribe the data (5) check to see if consistent with approximate lat lon at sailwx and MET, (6) check on PolarView jpg graticule, (7) repeat on a later date for reproducibility.

Each of the steps can go wrong! Rechecking everything for the date with the biggest longitude anomaly at Reply #427 for 27 Jan 2020 shows the S1AB method seems to have produced an accurate reading of the PS location.

Update 2: added a distance scale to the graticule. Here a 0.1º difference in latitude corresponds to 11.1 km and a 1.0º difference in longitude amounts (at 87.5º latitude) to 4.85 km. These are the dimensions of full graticule grid cells. The buoy graticule may need adjustment;it is added manually after the tracks are calculated.

Here buoys and Polarstern are being plotted to a tenth (1110m x 485) or maybe even a hundredth of a grid cell 110m x 49m). With FoMo reporting a 1000m shear off the port side disrupting the ROV site and bow radar showing multi-km disruptions almost every day, the scale of ice motion distinct from joint passive drift is commensurate with these sub-grid scales.

Note too that GPS readings at extreme latitudes can be disrupted by solar flare, meaning a perfectly functioning buoy GPS will not really be reporting to the accuracy of what it says on the box.

All this means buoy and Polarstern locations need to be taken with a grain of salt. Accuracy depends on the precise timing with respect to leads opening and closing and shearing forward and back.

19
Arctic sea ice / Re: MOSAiC news
« on: January 31, 2020, 01:37:47 PM »
Quote
image processing in Java?
Yes, ImageJ freeware was built by and for scientists doing advanced imaging analysis in cell biology and astronomy. It is extremely stable and fast with a large tool overlap with Photoshop and Gimp but many powerful ones of its own. It has a common code base with great updating but grows by independent contributed modules (.jars) that don't trip over each other as you add them. Most of these are implemented algos from mathematics-based IP journals. It is very convenient for complex manipulations of stacks (ie time series). One weakness is very limited 'undo'; another is alpha channel masking.

C Katlein, the ROV operator on leg 2, has been posting interesting photos almost every day (despite FoMo publicists repeatedly insisting the Polarstern's 100 mbps internet connection doesn't allow for this.) 

https://twitter.com/CKatlein

Other people are tweeting about bear visits; these have been far more frequent than FoMo has acknowledged. These are not always seen by the bear guards; some visits alongside the ship are inferred from tracks. Both polar bears and foxes associate ships with food; people on the AF even fed them over the rails. 

The first image below shows the view from below: the ROV mapping the depths of pressure ridge keels. Only the z axis is provided so the xy scale relative to the Ice Camp and the five ridges being drilled isn't provided but probably is 500 m or so. Some of the keels go quite deep, perhaps 5 m; it's hard to say as palette colors don't match depth colors.

The ROV is also pictured measuring an ablation stake sticking out the bottom of the icepack. Ice, especially on keels, is lost frictionally from drift relative to stationary ocean water; deeper keels melt because they're situated in water above the freezing point. The sub-freeboard ice pictured is 0.9 m.

FoMo is reporting extreme bounces in ship weather today that are in mild contradiction to the weather data they send out to awiMet, sailwx, DWD (Germany's NWS), and ECMWF. This might result from using instantaneous data vs hourly means or from stations at different heights above the ice.

Oddly, Mosaic does not seem aware of GFS nullschool providing frequently re-initialized and so far quite accurate 3-hour views of wind direction and strength forming the basin-wide cyclonic weather pattern, despite having a full-time staffer on board from Deutscher Wetterdienst. All the comments to date take a purely point perspective whereas a synoptic view is essential to understanding where the warm and cold air are coming from, why the ice is fracturing and where the Polarstern will drift next.

Attached also is an edited list of 56 recent papers by leg 2 leader C Haas. His background is geophysics and main current interest observation-based sea ice thickness. Free full texts are easily located online by searching on the full titles; he also maintains a ResearchGate page. His most recent paper, moored sonars in the Laptev, has just gone into review at open source/open review Cryosphere Today (where he is an editor!).

Compare this statement from Haas to the data hoarding during leg 1:

Quote
One of the objectives of the CryoVEx campaign was to observe how snow and sea-ice thickness varies along a CryoSat track from the coast of Canada across the multiyear ice zone into the first-year ice further north.

A week after this part of the CryoVEx campaign was completed, data processing has progressed and we can present some first results. These will be invaluable for CryoSat and IceBridge data processing by the various groups, for assessment of the state of Arctic sea ice after an exceptionally warm winter, and for initializing predictions of summer ice conditions.

https://www.the-cryosphere-discuss.net/tc-2019-307/
http://blogs.esa.int/campaignearth/2017/05/01/cryovex-first-results-show-sea-ice-continues-to-thin/

20
Arctic sea ice / Re: MOSAiC news
« on: January 28, 2020, 07:26:25 PM »
Nice interview, psymmo7. Haas is not correct about ten minute intervals between bow radar scenes. For example, the Nov 11 has two scenes three minutes apart, 12:00 and 12:03.

This is important for determining operational safety. That is, can massive rifts open in seconds or is the time scale minutes, hours or days, conveniently preceded by ample warning noise? They have already had one scientist fall in up to her waist, another to the top of his boot.

On leg 1, they ran out of connectors and could not replace critical cabling buried under yet another overnight pressure ridge until the relief icebreaker arrived. Some of the cracks grew very slowly and could be monitored for days, like the one that eventually toppled and broke the Met tower.

FoMo posted a great graphic yesterday showing open water many meters wide associated with an overnight 5 m pressure ridge that buried their snowmobile track.

Looking through the totality of bow radar image pairs to date, the worst case scenario was the Jan 26th pair 09:57/11:59 (see above mp4), with massive km-scale leads and ridges forming within 2hrs 02min of separation. Quite a wide area was affected over days so it wouldn't take bad luck to be in the wrong spot at the wrong time.

In past years, we have seen cracks propagate from Banks Island to western Siberia overnight, minimally 40 km/hr. The Norwegian airboat camps were hit twice with serious loss of equipment.
Quote
Added a close up from 27th onwards of the nearest Obuoy (to the north east)
Here is the mega track of buoy 201904 back to Day One. The display is generated by the 16,142 points at 10-minute intervals. The attached kml file allows unlimited zoom, rotation, and co-display with other types of tracks such as S1AB availability, bow radar availability, wind direction from sailwx and so on.

The Polarstern's track would be virtually indistinguishable at this scale, with a constant offset from this buoy. The velocity of buoy 201904 is easily computed within its csv and assigned a color palette, as is any scalar quanity (such as salinity or temperature at a given depth) measured by the buoy.

The buoy overview graphic at Meereis Portal is done well; the palette allows selection of individual buoy types and color changes. There do not appear to be any 'snow buoys' or 'other' displayed. Again, this is best done in GoogEarthPro with a folder containing a folder of each buoys class because this allows disentangling the complexity via checkboxes and visitor download of the data generating the image.
Quote
testing the brakes before a hairpin bend
The proximity to the cyclone center could have unprecedented effects on ice disruption.

21
Arctic sea ice / Re: MOSAiC news
« on: January 26, 2020, 03:25:53 PM »
The Polarstern got caught up in strong winds to the southeast at about 06:00 this morning as GFS foresaw a few days back. The winds are not quite gale force but will peak in the 10-12 m/s range and stay brisk for a couple of days.

Under these conditions, longitude will be gained at about a tenth of a degree per hour; in 3 days the ship could plausibly be at 87.2 100.0.

A very dramatic lead opened off the port side, preceded by a possibly enabling large scale shift two km off the bow. The event is still ongoing so we await the next day of bow radar (which unfortunately has become erratic again). In part, an old prominent slipline reopened, not entirely but with new leads taking off at the ends.

Looking at the regional wind stress picture over this time frame, it appears that the problem is not high wind speed per se at the ship but rather its rapid fall-off nearby, ie the stress gradient. How far out that matters is a big unknown, perhaps ice basinwide contiguously adjoined to the Polarstern floe (ie rigid body motion).

I added streaming awiMet ship weather to the ice radar since that wasn't happening at their end. It's a doable nuisance to go back to the Nov 1st start because of almost daily gaps in hourly awiMet weather and unsynchronized missing or unusual radar timestamps. There is enough black space to include a small thumbnail of GFS winds at each of the 320 bow radar frames to date. The  bow to stern length of the ship (9.4 pixels) could also be depicted.

22
Arctic sea ice / Re: MOSAiC news
« on: January 22, 2020, 01:21:45 PM »
Quote
Obuoy temperature ani's for reference, 10-75m
Tech note: scales are different
The buoy sets are slightly different too? It looks like as many as 3 could be run without entanglement. The animation of the final frames and side-by-side are shown below.

Looking at 'Mosaic_multisensor' to see if the Mosaic expedition had access to other radar satellites in addition to what PolarView shows for Sentinel, it appears the answer is no. M_m is still poorly done with no mid-course improvements, with satellite images lacking critical access numbers, provided dates erroneous, 48 hour applicability falsely claimed, too small choice of scale, gratuitous rotations that make comparison of successive images difficult, lat/lon of position not synched with  S1AB and obliteration of the Polarstern region with the red circle. However a precise lat/lon for 0600Z can be read off the images on days no S1AB was taken. A poorly implemented scientific product inevitably raises questions about the rest.

The Polarstern is currently drifting west and more south 'on top' of a meandering anti-cyclone. Actual drift is generally 'to the right' of near-surface wind direction. Accurate latitudes are not disclosed so sailwx will sit at "87.5" even as it declines; longitude is decreasing by 1º per 22 hrs. The inset shows "87.4" is due at about 1800Z (except that wind direction and speed vary by the hour).

Very minor shearing is showing on the most recent day of bow radar. 'Follow' offered a possible explanation yesterday for varying image exposure and orientation: the radar is not gimbaled and so changes its incident angle if the stern swings around or the bow rises/falls (as ice anchors fail). This data could be used to uniformize the imagery but it is not disclosed, The PS also has strain gauges welded along its hull. That data is not disclosed either.

'Despite being solidly frozen into the ice, the forces of wind and currents* affect the ship. Depending on their directions, the Polarstern is pushed against the MOSAIC floe or pulled away from it. The latter strains the six ice anchors, which therefore need to be need to be monitored regularly. Today's check showed that five anchors were properly fixed - however one needed some additional care: Steffen and Andreas found a gap next to the 1.20 meters long metal I-beam. They filled it up with snow and poured water inside. The mix freezes solid almost immediately at the current temperatures of -28 °C.'

* No significant independent near-surface currents are known under ice in the central Arctic Ocean. A paper from N-ICE2015 describes the acoustic doppler measurement process and results; the four floes were located near the tip of the Yermak Plateau, meaning measured small currents were affected by tides, rising Atlantic Water boundary currents, adjacent ice edge, and passing storms; thus it is inapplicable to the Polarstern's situation.

https://agupubs.onlinelibrary.wiley.com/doi/10.1002/2016JC012391 see 2.2.5, 3.5 and Fig 10

23
Arctic sea ice / Re: MOSAiC news
« on: January 12, 2020, 08:04:22 PM »
Below, all 252 bow ice radar frames are concatenated into a single image running from Nov 1st to Jan 9th at 36 fps (50% faster than movie film). The frames are about 6 hours apart. Thus the 70 days (1680 hrs or 100,800 min or 6048000 seconds of actual elapsed time have been collapsed to 7 seconds of mp4 video, which is a speed-up of 864,000-fold relative to a person standing on the bow watching the ice move. Glacial motion of Jakobshavn and Petermann have been depicted many times at similar rates on their respective forums.

The timestamp has been lowered to wasted space next to the bow-stern axis scale. Blurred areas on the periphery have been cropped away for a better fit of file dimensions to forum constraints. Dim areas have been preferentially brightened with linear, gamma and adaptive local contrast correction and focus sharpened with slight unsharp mask.  The initial size of 90MB reduces after conversion of ImageJ to 18 MB avi to a final very reasonable 4.3MB mp4, thanks to free online cloudconvert.com by Munich’s Lunaweb GmbH).

Ice movement can sometimes be seen more easily in a fast inverted image; that is provided at 48 fps with more periphery removed. Be sure to set the controller to loop and move the mouse off the mp4.

One surprising aspect throughout this imagery is that leads close up before they can freeze over, even at very low air temperatures (-30ºC). Open leads historically have been viewed as important direct conduits between ocean heat and its loss in winter to the atmosphere, with refreezing reducing but not totally blocking the effect until an insulating snow cover can build up.

Here none of the leads have stayed open more than a day or two before slamming shut, with refreezing and heat loss having minimal time frames in which to operate. However we don't know how representative the bow radar area is relative to the overall ice pack. Notably, giant lead fields in the Beaufort can stay open for weeks before freezing over.

24
Arctic sea ice / Re: MOSAiC news
« on: January 04, 2020, 10:24:45 PM »
This is the Mosaic forum. If you can find an application for RAMMB, great. Otherwise perhaps start a separate forum for it?

The aurora borealis is off-topic and done vastly better on nullschool; on the Polarstern, people report spending two months at sea without seeing even a single star because the ship has to be so bright. Your image lacks corroborative evidence yet that should have been easily available because the AB view (from OVATION / SWPC / NCEP / NWS / NOAA) updates every 10 minutes or 5x the frequency of RAMMB.

Lightning flashes? Rare in the central Arctic but done infinitely better by a Finnish company detecting weak radio waves. They recently compiled a surprisingly number of AO events out of their vast global archive. RAMMB, can't go back in time. That's a big problem for PolarView too.

Snow vs rain? Yes, with interpretation but that is somewhat a false dichotomy. The Polarstern has lots of snow buoys set out and much fancier ice camp equipment measuring density, internal melt, flooding history, salinity, impurities and so forth. Not going to get at those with RAMMB.

Better time resolution of lead opening and closing than S1AB? Possibly, though RAMMB resolution is not a good match to intrinsic dimensions of ice features. Six-hour bow radar shows how much S1AB itself misses, despite its 30x better resolution than RAMMB.

Even recreational bow radar is digitized once a minute so meereis could be providing 3600x the time resolution or 51x better than RAMMB resolution. Once an hour is probably the sweet spot in terms of file size and correlating with hourly wx data and 3-hourly GFS. However for abruptness of kinematics, a bit of once a minute or continuous analog would be interesting.

Storms? That seems to have been the motivation underpinning RAMMB. For the Polarstern, what we most need are surface wind forecasts and surface roughness. The top priority would be getting ECMWF again; windy dropped the Arctic because there weren't enough clicks.

Transit of relief icebreakers? Yes if only we knew why their progress varied: were they encountering thick ice, stopping for polar bear photos, or putting out buoys? So far none of the ships have made their logbooks or ice thickness data available. Here 51 minutes is better than S1AB burst mode but still not great for velocity estimation. Then there are is the issue of no one digitizing location off RAMMB frames and estimating error with that.

As explained here many times, Lambert azimuthal is used is for its equal area pixels, not because it represents the AO with "less distortion" than conformal polar stereographic (angle preserving). PS, Greenland down, is standard in almost all direct satellite products we use. With netCDF we can interconvert in Panoply.

Lambert thus seems a bad idea because each round of interconversion degrades already blurry data, ie initial PS to RAMMB to PS for overlay say with WorldView night bands or S1AB leads loses detail we cannot afford to lose, the roundtrip is appalling.

The bow radar products above exceeded 150 MB as gifs; 20 MB gifs are a nothing-burger. Maybe RAMMB could offer mp4 and ditch the horrific download code too. A 10 terabyte external drive is very affordable (skip starbucks, make your own coffee and avocado toast).

You might also consider basic contrast adjustments before posting -- two or three clicks can vastly improve clarity of RAMMB animations. For leads and ridges, wavelength matters. If day'n'night is looking at escaping heat in infrared and active radar is looking at roughness backscatter, the two won't correlate that well.

The RAMMB project deserves our applause for putting a lot of opaque satellite channels within practical nrt reach. I am open to it having an application to Mosaic but just don't see what that is. It's hard to find an angle where it is 'best in category'.

25
Arctic sea ice / Re: MOSAiC news
« on: January 04, 2020, 06:45:25 PM »
Quote
if we all clap our hands, Tinker Bell can fly again (?)
Nothing to cheer about here, the Polarstern is drifting into a a long-stagnant zone (per Ascat), getting ever farther behind the eight-ball in terms of hitting their target next October.

Random drift north is not to be conflated with systemic transpolar drift -- the weather pattern for the latter is specific, very different, and yet to kick in.

RAMMB is cool but what is it good for? Not aurora borealis (via reflection on clouds); nullschool has a great tool for that already under its ‘Space’ setting.

Real time Polarstern position? The ship already posts its lat lon online once an hour in real time, that's 2000 times since mooring. It's easy to heuristically predict the ship's position 3-4 days ahead using GFS-ns winds as on Dec 31st in #460.

https://www.awi.de/fileadmin/user_upload/MET/PolarsternCoursePlot/psobsedat.html

Some of the buoys post much more frequently than the 51 minute JPSS satellite and some have 5 dp of positional data. However the public has been denied access to the really high accuracy/high frequency ship and floe buoy data.

We also have four dp precision lat lon posted 2-3x a day at 41 m S1AB resolution attached here back to Oct 4th, 175 scenes to date. RAMMB can’t be used to patch gaps in S1AB coverage (eg Nov 16th) because its archive only goes back two weeks.

2020 01 04 0538  8  86.9848 115.4547
2020 01 04 0400  8  86.9780 115.4551

Determining the maximal resolution setting of RAMMB requires a scale screenshot that includes both the 85º and 87.5º parallels. Those are separated by 698 pixels along the 115º meridian which has length 278.0 km between those two latitudes. Thus the maximal resolution of RAMMB is 398 m/pxl.

However clouds and atmospheric turbulence lead to a 5x5 pixel blur/wobble in the Polarstern's dot. Picking the central pixel gives a 3x3 uncertainty so the actual ability to determine ship latitude is 1200 m, so about 30x worse than the resolution of S1AB which in turn is 2x worse than bow radar.

On 20-01-04 08:00, the PS was at 87.0,115.4 which means 37 pixels between 115 and 117.5, the next graticule line over on RAMMB maximal resolution. That distance is 14.55 km. This means that that the longitudinal resolution is about 0.1º, perhaps a slight improvement on the censored location at AWIwx.

Quote
Ship radar images of the last 14 days. Actual radar-image sequence of RV Polarstern from the last 14 days. More videos can be found here. From January, these videos will be available here by a drop down menu.

Live stream from on board: The latest radar images of the ship’s surroundings. Every day, here at meereisportal.de we show from now on a video sequence of ship radar images. The RV Polarstern’s marine radar systems will continue to operate throughout the drift phase and images produced by the system are transmitted to Bremerhaven several times a day.

The imaging system, which shows Polarstern in the centre of the screen, offers vital information on floe movements, deformation and formation of cracks in the ship’s immediate vicinity.
Well, that is a decent plan but higher-ups may have killed that initiative already. It's only a matter of time (days?) before the above text and two month archive are deleted from the Meereis Portal server.

My guess: some antique boomer at AWI is obsessed with putting all Mosaic reports into a thick special-issue journal in 2023. However there are hardly any print journals left now and there won't be any by then.

Like open source buoy data, bow radar can be processed as it comes in, published in a timely way, and contribute to our understanding of icepack deterioration in the Arctic Ocean. In 2023, no one will have the slightest interest in 2019-20 sea ice motion.

Alternatively, all is well and the delay in posting is due to the lead scientist on bow radar only returning to port Wednesday on the KD and just back at work on Monday. I looked at their bow 2017 bowradar paper from the N-ICE2015 five month drift in the very different marginal ice zone (https://doi.org/10.1002/2016JC012387), earlier work cited there, and the 19 forward citations.

They could readily clone this paper for leg 1-2 and then again for legs 3-4 and 5-6. However it's not clear whether ice motion metrics really describe what is going on (see below), nor whether seasonal or year-to-year comparisons can be made, mostly because no previous data exists for the Polarstern's location.

SHEBA, an earlier year frozen into the ice, took place 22 years ago; did the Des Groseilliers even have bow radar then, was it strictly analog, was it filmed, is it archived somewhere online? SHEBA and N-ICE2015 both experienced severe ice motion but more? less? about the same? as the Polarstern is seeing now.

We have a great opportunity to add value to Polarstern bow radar because  it is optimized for the bridge when the ship is underway, not for later perusal. Right now it is over-exposed close to the ship where the return signal is strongest (radial contrast mask?), blurry on the periphery (radial unsharp mask?), higher resolution close in (better detail in 2-3x scale enlargement), offered in grayscale (more interpretable in indexed palette?) and so on.

Still, making a 2x-invert pair below for the tight cyclone of 16 Nov 2019. I don't see a path forward to really describing the complexity of sea ice motion, especially the repeated openings and closings of the same floe line, causing multiple collisions in the same pressure ridge. The extent of ridge venation is just astonishing at the resolution and incident angle of bow radar.

Polarstern helicopters could be imaging the bow radar surface elevations every week with lidar. This is imperative for determining ridge elevation and change. The ROV could be measuring keels from below (though it has scarcely been operable). Lidar data is apparently taken but not disclosed, other than leaked, unscaled, undated, ungraticuled images such as in Rembler's October 23 blog. The blue may just be over-tint on grayscale DEM but with the noxious overlays and scale again not provided(!), it isn't too useful.

The Jan 2020 lidar (airborne lidar scanner ALS) came back with some new cracks and ice dynamics in the heavily instrumented L-site. We have no idea where the site is or where new/old cracks map; no lidar has been released. The L-site is off-limits to bow radar. Its past and current locations have not been released.

Were buoys deployed within the bow radar viewing fame, can we overlay tracks on the Nov-Dec footage, what became of buoys during the storm chaos, is the turmoil seen representative of a larger area?

26
Arctic sea ice / Re: MOSAiC news
« on: January 03, 2020, 07:00:30 PM »
There's been a good series of Leg 1 blogs up at UA Fairbanks by R Rembler that supplement those of M Shupe and BBC. These represent all that we really know -- or will ever know -- about how sea ice motion is affecting operations on the Mosaic floe.

AWI has censored and silenced all other sources in favor of relentless, uninformative :). The Carl Zeiss culture of quality is long gone; Germany today is VW diesel, AWI information management, and 21 of 103 buoys dead within days including 8 set out by AWI and 2 of 6 placed en route by the Kapitan Dranitsyn. An additional 24 floe buoys have been silenced and do not report to the international buoy tracking service.

These buoys aren't AWI's property as they seem to think; the buoys, the ship, all the equipment and the data itself are owned by taxpayers who funded Mosaic. AWI itself does not have one pfennig of its own.

As an aside, note the KD's exit swath is still quite visible today on S1AB. Scientists from Leg 1 just disembarked in Tromsø on Jan 1st; no information is available on what they observed in transit (ice thickness is always measured).

Big plans for daily bow radar release have seemingly foundered: still no coverage of Oct 4th to Oct 31, all coverage stopping on Dec 31, no response at all to polite inquiries from the designated on-shore scientific contacts, web page promises have been shelved, and annoyance expressed by the Meereis Portal communication leader that the (non-forum) public dares question map quality and delays.

Apparently quite a few outside scientists are unhappy with the kindergarten-level portal; they may not be aware Germany invented kindergarten back in 1837.

In other words, download a complete bow radar set now before it disappears forever (or gets locked down in a threatened proprietary format). It takes five to make a complete non-overlapping set: 20191101_20191114.avi, 20191115_20191128.avi, 20191201_20191214).avi, 20191215_20191228).avi and the largely redundant 20191218_20191231).avi. These are small files found at https://data.meereisportal.de/maps/animations/Iceradar/

Open each as grayscale with the free Imagej frame reader. Do not check 'virtual stack'. Under Images --> Stack --> Tools --> Concatenate, join the avi in temporal order, save as avi or gif. In ImageJ, Command-Shift-D pauses to let you to duplicate any subset of frames, for example ones flanking a certain date or all those showing major ice action.

Quote
18 Nov 2019 - A big storm By Rob Rember
https://uaf-iarc.org/author/rob-rember/

… On Friday 15 Nov 19, we were notified that the weather was going to get substantially worse over the weekend and that by Sunday winds would exceed gale force (14 m/s). On Saturday the 16th, we quickly went out to sample the first- and second-year ice sites in case our Monday coring was cancelled.

The storm came on Saturday night and continued all day Sunday the 17th as predicted. Winds consistently exceeded gale force for most of the day. The ice opened and closed in front and to the side of the ship several times. At one point from the bridge there was 50 m of open water with waves beginning to form, while on the [starboard] side the ship continued to be moored to the ice floe.

There were large cracks that opened all over our local area (ocean city, remote sensing, ROV site etc.) that stayed open for many hours. We had substantial damage to several power lines as the flow separated and came back together.

This morning the wind is still up around 15 m/s and the damage assessment has begun. We surveyed our coring sites, they are completely intact and can be reached with minimal detours. UAF science has luckily fared well. Other sites will require some major rebuilding with 700 kg power nodes tipped over as ice drifted/sheared and pulled on cables that were fixed to the power distribution hubs.

In the next 30 minutes we will have a meeting to discuss the new steps. The ice is still moving and we are not in a stable situation to begin rebuilding. Even so, the UAF team will head out this afternoon to continue the sea ice coring times series we started approximately a month ago.

I looked at GFS winds, sailwx, ship weather, Rammb, bow radar and seven enveloping S1AB images for confirmation, first noting a 2º longitude lurch in Polarstern position overnight. The big ice radar action came later, on the 19th-20th under continuing strong and strongly shifted winds.

The explanation: ship weather is measured on high and provided as hourly averages so ground level gale force gusts are depracated; GFS 'surface' winds are non-observational so the 1000hPa may be better. Both are in good agreement with Rembler's blog.

Bow radar captures 360º but 80º has been blacked out, notably the entire Mosaic floe and near-ship instrument area observed by Rember whose times, dates and wind speeds may be off because the Polarstern does not use UTC and he does not use the metric system.

I've observed a puzzling non-grasp of causality at Mosaic. Arctic winds and ice motion stress are basin-wide, not local; nothing can be predicted from ship wx point forecasts alone. One glance at the GFS forecast -- a strong, sharply curved cyclone passing repeatedly over the Polarstern at different bearings should have warned them (indeed we called it out here well in advance). It is not homogenous high winds that cause destructive ice motion but high curvature and rapid temporal change in streamlines and their bearings.

Available S1AB: note imagery from the key date of Nov 16th is missing
S1B   2019 11 22 0546   85.7341   120.8084
S1B   2019 11 22 0408   85.7353   120.8119
S1B   2019 11 22 0230   85.7352   120.8192
S1B   2019 11 21 0643   85.7429   120.9425
S1B   2019 11 21 0327   85.7446   120.9824
S1B   2019 11 20 0602   85.7656   121.6001
S1B   2019 11 20 0424   85.7643   121.5311
S1B   2019 11 19 0700   85.8011   120.5766
S1B   2019 11 19 0521   85.8020   120.4943
S1B   2019 11 19 0343   85.8009   120.4512
S1B   2019 11 18 0619   85.8510   120.7805
S1A   2019 11 18 0530   85.8556   120.8340
S1B   2019 11 18 0441   85.8609   120.9092
S1B   2019 11 17 0538   86.0462   122.4998
S1A   2019 11 17 0449   86.0532   122.4685
S1B   2019 11 17 0400   86.0595   122.4405
-+-   2019 11 16 0600   86.1243   120.4086
S1B   2019 11 15 0554   86.1891   118.3766
S1B   2019 11 15 0416   86.1897   118.3522
S1A   2019 11 15 0327   86.1897   118.3386

Hourly ship weather: 60 straight hours of >10 m/s (last column)
86.1   122.4   17 11 19   0000   15
86.1   122.4   16 11 19   2300   16
86.1   122.4   16 11 19   2200   13
86.1   122.3   16 11 19   2100   14
86.1   122.2   16 11 19   2000   16
86.1   122.1   16 11 19   1900   16
86.1   122.0   16 11 19   1800   19
86.1   121.8   16 11 19   1700   19
86.2   121.6   16 11 19   1600   20
86.2   121.5   16 11 19   1500   21
86.2   121.3   16 11 19   1400   20
86.2   120.9   16 11 19   1200   19
86.2   120.8   16 11 19   1100   18
86.2   120.6   16 11 19   1000   17
86.2   120.4   16 11 19   0900   17
86.2   120.3   16 11 19   0800   17
86.2   120.1   16 11 19   0700   16
86.2   120.0   16 11 19   0600   15
86.2   119.9   16 11 19   0500   14
86.2   119.7   16 11 19   0400   12
86.2   119.6   16 11 19   0300   12
86.2   119.5   16 11 19   0200   12
86.2   119.4   16 11 19   0100   13
86.2   119.3   16 11 19   0000   13

GFS nullschool cyclonic winds:
245° @ 11.2  m/s  2019/11/16/0000Z
250° @ 12.9  m/s  2019/11/16/0300Z 
250° @ 14.3  m/s  2019/11/16/0600Z
250° @ 13.5  m/s  2019/11/16/0900Z
255° @ 15.8  m/s  2019/11/16/1200Z
260° @ 14.1  m/s  2019/11/16/1500Z
275° @ 15.0  m/s  2019/11/16/1800Z
290° @ 11.1  m/s  2019/11/16/2100Z 
320° @ 13.4  m/s  2019/11/17/0000Z 
310° @ 10.7  m/s  2019/11/17/0300Z
315° @ 11.5  m/s  2019/11/17/0600Z 
325° @ 11.6  m/s  2019/11/17/0900Z 
355° @ 10.1  m/s  2019/11/17/1200Z 
350° @ 13.3  m/s  2019/11/17/1800Z 
360° @ 14.7  m/s  2019/11/17/2100Z 
360° @ 14.9  m/s  2019/11/18/0000Z
005° @ 16.4  m/s  2019/11/18/0300Z 
005° @ 13.9  m/s  2019/11/18/0600Z 
010° @ 14.4  m/s  2019/11/18/1500Z 
010° @ 10.2  m/s  2019/11/18/0900Z

27
Arctic sea ice / Re: MOSAiC news
« on: January 01, 2020, 05:56:32 PM »
Below, another version of the Polarstern's drift so far based on once-a-day precise S1AB positions from the csv attached above. We are seeing a great many wheel reinventions but few improvements on what Google Earth freeware has long provided in web browser form from a quick template paste and click. The kml file has to be attached as txt for the forum.

The ascat mp4 shows the Polarstern's position within plastically deforming ice. Actually the ice is quite strong and brittle at sustained -30ºC temperatures but appears almost liquid on ascat because over-rafting, ridging and lead opening take up any slack.

The Polarstern's drift has been contained so far within the small rectangular overlay; the last frame shows daily drift positions. While the resolution is much less than S1AB or bow radar, ice motion still appears quite dramatic at the ship's location even at ascat's scale.

Cryo2Smos ice thickness has progressed up to what Mosaic thought it would be back on Oct 1st, three full months ago. The regional buoy array could provide more accurate pointwise data on growth; thickness depends on where and how the buoy was initially installed. Snow depth, if any, slows transmission of cold from the air into the ice.

Boundary conditions, in this instance Greenland, can very much constrain ice response to wind stress.  Right now, with 15 straight hours of 8-10 m/s wind from a ship wx station bearing of 120º, the Polarstern should be (and is) moving poleward and to the west.

However there is a lot of thick ice ahead of it and that ice is pressing up against solid land. This means less actual displacement than if the wind were still at 240º. The wind field is not homogenous however and has been moving ice rapidly along north Greenland towards the Fram Strait (above) which may ease the push-back..

Folding in forecast uncertainty, it isn't feasible to predict ice motion more than 3-4 days out. Broad-brush seasonal weather forecasting may be on the horizon but halfway reliable predictions of trans- or circumpolar drift are lacking, even as hindcasts. Buoy trajectories are largely inapplicable to Mosaic drift because only 0-1 are launched per year in the central Arctic Ocean and those mainly in early August.

Sea ice motion will be a major driver of the 'end game' for Arctic sea ice; our lack of understanding effectively derails all attempts at predicting this from trend lines.

28
Arctic sea ice / Re: MOSAiC news
« on: December 29, 2019, 11:55:48 PM »
Two significant new offerings at Meereis Portal: the interactive buoy GIS display discussed earlier in #437 and release of sea ice motion radar cam scenes looking out from the Polarstern bridge  (link in #454).

Note the comparable radar on the antique RV Lance digitized an image a minute with a 360º view and range of 9 km during N-ICE2015 whereas with Mosaic the 280º field of view excludes the Ice Cam, reports every six hours (ie at 1/360 the frame rate) with only 5.2 km of range.

Note the 06:00 daily nadir S1AB coincides with the 06:00 oblique ship radar, meaning the two cannot be color-composited though the Sentinel at 200% can fill in the missing ice camp (2nd image).

We looked at marginal ice zone action and a radar cam article back in #83: https://doi.org/10.1002/2016JC012387

Presumably the PS has more sophisticated radar than they're letting out because you can buy better recreational boating radar for a few $k on ebay. The blackout on the Ice Camp could plausibly be attributed to rfi with all the other equipment out there. Dedicated instruments and strain panels monitor conditions there but that data has not been shared except anecdotally (and via S1AB analysis here). 

The full dataset is sent daily over the Polarstern's fast internet (still being denied on Dec 27th) to Bremerhaven where it is bundled into rolling windows of two weeks extent (14 days x 4x = 56 frames served as slow avi movies). The archive goes back to Nov 1st but increments daily. No explanation has been offered for the delayed upload on Dec 15th and first mention on "Follow Mosaic" on Dec 28th.

It's not clear if the Oct 4-31 floe motion is being held back or just delayed. The ice would have been in total chaos back then going by the chaos of the last two months in strengthened thickened ice, below. The minute-by-minute research grade terabyte dataset is not available which is appropriate.

The archive began duplicating the avi with identical and fully interchangeable m4v formatted videos on Dec 15th, reminiscent of the head-scratching duplication of 'mosaic_multisensor' with all-purple sea ice concentration overlays.

The file sizes are kept to a few MB using avi even though they are really just gif slide shows. ImageJ is very unusual in having an avi reader. This opens them as image stacks, with helpful options for grayscale and 180º rotation (to better align with S1AB and other 'greenland down' satellite imagery).

ImageJ is also very good at sharpening the periphery, reducing the overly bright returns from ice near the bow, changing palette, and concatenating bimonthly bites into a single image. Surprisingly converting the avi to forum-friendly mp4 at https://cloudconvert.com give as very helpful further reduction in file size.

The smaller gif at the bottom features the dramatic lead that opened a few km south of the Polarstern on 15 Dec 2019. Moderate benefit can come from contrast enhancement, sharpening and an indexed palette.

The bridge radar is confusing on first view, so set it on loop and (after download) click repeatedly on the double arrow to speed it up. The white scale bar is intrusive. Its central tip is the center of the fixed polar coordinate frame in which the bridge radar is stationary. It isn't clear if the bow-stern axis is also fixed nor if it points north-south. (The integrated navigation system records this information but it is not provided.)

The timestamp would be better with seconds and minutes rounded away, repositioned lower into vacant black space. The stern may wag about causing the view to shift when little is actually happening; the ship is also drifts and rotates quite a bit over the 60-day time frame of the video.

Overall, it is astonishing that scientists have been able to keep equipment deployed on the ice running at all. Actually, we have no idea how Leg 1 data collection went as little can be gleaned from short :) reports.

Expeditions like this were already being squeezed out of the picture by advanced calibrated satellites, massive buoy arrays and long range autonomous gliders. The ice seems too far gone for the floe platform concept to work.

Just because the ship will be drifting aimlessly until early January (when winds sweeping up from Siberia will finally send it Fram-ward) doesn't mean the ice will be quiescent. Worse, record lows have arrived with -34.7ºC recorded on 19-12-28 at 23:00 utc, making damaged equipment that much harder to repair.

And it seems that we are far short of the 8-10 extreme weather events expected in winter at the Polarstern's location (below or see #368). It's been quite stormy in the North Atlantic but so far extreme weather has not moved up past Svalbard to any extent.

29
Arctic sea ice / Re: MOSAiC news
« on: December 20, 2019, 01:04:25 PM »
M Nicolaus has a strong background in sea ice physics with a special interest in autonomous buoy arrays and underwater ROVs and took part in N-ICE 2015. Some of his 2018-19 publications are attached below. Like C Haas, he supports open research and better communications with the public. (We shall see.)

The ROV site had to be taken out of action yet again due to new shearing, floe leads and pressure ridges that they are blaming the KD track for. We don't have a close-in map of KD movements because S1AB is spotty and barely has enough resolution to catch ephemeral tracks.

No maps of the revised Mosaic ice camp or summary of instrument status during leg 1 have been provided for months; only the vaguest text indications have been provided so far (eg, MET shifted 0.6 km past the bow).

The Dec 19th photo at 'follow mosaic' shows the KD leaving. The condition of the ice is shocking -- the full-size picture is worth a close look.

One horrific mistake I see over and over at Meereis  and Mosaic sites is confusion between data and information. It is completely irrelevant that they collected 26 terabytes of data (enough to fill a $175 external drive for an iMac). The web cam at my birdfeeder provides much more than that yet very little information (sparrows like sunflower seeds). What information is in those 26 TB ... soot from the PS smokestacks makes aerosol monitoring unworkable? And how is the short shelf life of Arctic information accounted for if publications are put off to 2023 as planned?

Ice-tethered platforms & ROV, Progress report
M Hoppmann, B Rabe, M Nicolaus, F Wenzhöfer, P Anhaus, D Scholz, ...

Sea-ice Properties derived from Ice Mass-balance Buoys using Machine Learning
L Tiemann, M Nicolaus, M Hoppmann, M Huntemann, C Haas

Seasonal evolution of snow depth on Arctic and Antarctic sea ice from Snow Buoy measurements
M Nicolaus, S Arndt, M Hoppmann, C Katlein, N Maaß, L Rossmann, ...
EGU General Assembly Conference Abstracts 20, 7666

The Sea Ice Drift Forecast Experiment
H Goessling, A Schweiger, E Blanchard-Wrigglesworth, T Krumpen, ...
EGU General Assembly Conference Abstracts 20, 16546

The Arctic Cloud Puzzle: Using ACLOUD/PASCAL Multiplatform Observations to Unravel the Role of Clouds and Aerosol Particles in Arctic Amplification
M Wendisch, A Macke, A Ehrlich, C Lüpkes, M Mech, D Chechin, ...
Bulletin of the American Meteorological Society 100 (5), 841-871
 
Arctic warming interrupts the Transpolar Drift and affects long-range transport of sea ice and ice-rafted matter
T Krumpen, HJ Belter, A Boetius, E Damm, C Haas, S Hendricks, ...
Scientific reports 9 (1), 5459

30
Arctic sea ice / Re: MOSAiC news
« on: December 17, 2019, 12:24:03 AM »
Quote
Oh what tangled webs we weave, when first we practice to deceive (W Scott, 1808)
Here the wind power density during leg 1 is shown once a day for days that have have S1AB images, with a few gaps filled in by interpolation so all 78 days are represented. The four storm events show up fairly clearly on the slides though here the GFS needs to have its 3-hour resolution shown that brackets each event.

These unfortunately run into file size problems at decent resolution, even compressed as mp4 (which works better at faster displays than for slide shows; nullschool images have very complex color and compress poorly). I don't really see a way forward for a year long expedition other than breaking into months or legs.

31
Arctic sea ice / Re: MOSAiC news
« on: December 15, 2019, 09:11:52 PM »
Here are recent paper titles from the highly qualified Mosaic leg 2 leader, AWI's Christian Haas. His interests are much more remote sensing and ice-related than leg 1 atmospheric physicists. Let's hope that there will be a much more open science focus to Polarstern communications in coming months.

Winter rain, as Haas notes, would really be a game-changer for snow thermal properties and spring albedo. The recent polar lightning, detected by a Finnish company specializing in remote detection and employing my neighbor, also came as quite a surprise. The Polarstern is not set up to detect it unless it is right overhead. Rain? The PS may have doppler radar but not one dedicated to rare events.

Some strong winds are expected this week but nothing approaching gale force. The GFS outlook has changed so much from yesterday that it is hard to predict coming Polarstern drift, though it will be almost entirely to the west (smaller longitudes) with a small component north, so maybe 86.7, 114.0 by Dec 20th from where it is now, 86.6, 117.7.

-- Arctic warming interrupts the Transpolar Drift and affects long-range transport of sea ice and ice-rafted matter

-- Ice and snow thickness variability and change in the high Arctic Ocean observed by in situ measurements

-- Helicopter-borne measurements of sea ice thickness, using a small and lightweight, digital EM system

-- Arctic warming interrupts the Transpolar Drift and affects long-range transport of sea ice and ice-rafted matter

-- 13-years of sea ice draft observations in the Laptev Sea from moored ADCPS and ULSs

-- The timing and intensity of snowmelt processes on sea ice are key drivers

-- Seasonal changes in snow properties from passive and active microwave satellite observations: 

-- Vertical snow structures from in-situ and remote sensing measurements

-- The Arctic Permafrost Geospatial Center-a portal for high-quality open access scientific data related to permafrost

-- Snow depth on Arctic sea ice derived from airborne radar measurements

-- Large-scale ice thickness distribution of first-year sea ice in spring and summer north of Svalbard

-- Contrasting ice algae and snow dependent irradiance relationships between first year and multiyear sea ice

-- Snow-related variability of spectral light transmittance of Arctic First-Year-Ice in the Lincoln Sea

-- Seasonal changes in snow properties from passive and active microwave satellite observations

-- Snow depth on Arctic sea ice derived from airborne radar measurements

-- 13-years of sea ice draft observations in the Laptev Sea from moored ADCPS and ULSs

-- Contrasting ice algae and snow dependent irradiance relationships between landfast firstyear and multi year sea ice

-- The 2018 North Greenland polynya observed by a newly merged optical and passive microwave sea-ice concentration

-- Snow-related variability of spectral light transmittance of Arctic First-Year-Ice in the Lincoln Sea

-- Contrasting ice algae and snow dependent irradiance relationships between landf-ast first year and multi-year sea ice

-- Ice and snow thickness variability and change in the high Arctic Ocean observed by in situ measurements

32
Arctic sea ice / Re: MOSAiC news
« on: December 15, 2019, 05:52:40 PM »
Right, this is all about getting to the right scale as constrained by forum image widths. Previously we've determined that a degree of latitude as marked on S1AB jpg with lines is 2712.26 pixels for what we know is 111.111 km on WGS84 (which we have to use here as all GPS data refers to the earth ellipsoid).

Thus image distances can be measured in pixels (often fractional if points are diagonal) and converted to meters by multiplying by 41.0 for both S1AB jpg and S1AB.8bit.jp2 (at 100% zoom in the polar viewer plugin).

Doing this, it emerges that the Polarstern was 3703 m north of the shear line. The 79 km long open lead created in this area ranged from 730 m in width to a more typical 487 m to 159 m at narrows. A lead of this width cannot be bridged by wooden palettes and a sled, nor is it feasible to kayak across regularly carrying staff, bear guards and fuel for instruments (as Mosaic was doing earlier).

The dramatic regional shear animation of post #412 that compared Dec 12 06:19 to Dec 13 03:43, repeated below, was done in Polarstern-stationary coordinates (lagrangian) which removes background ice pack movement (secular drift).

The rifting took place as the pack as a whole moved almost due westward by 4301 m but with a 410 m north component. Relative to the Polarstern, the shear area moved an additional 4146 m southeastward.



It's worth walking through GPS decimal points which have quite different associated measures for lon than lat.

At 86.6º, a tenth of a latitude degree increment represents 11.111 km, a hundredth 1111 m, a thousandth 111 m, a ten-thousandth 11.1 m and a hundred-thousandth 1.1 m.  The first is what we are looking at with sailwx and AWImet; the second what GFS-nullschool can discriminate at maximal scale, the third enough to show a buoy lurch and the last the nominal resolution claimed by typical Mosaic buoys (4th GPS decimal point).

Note the buoys are in motion during whatever time it takes for them to measure their position. Those speeds, given as the color scale on uniq's animations rarely exceed 1 km/hr which is 1000 m per 3600 seconds or 0.27 m/s. So if it took them 5 seconds, that would be 1.4 m which might amount to a correction to their last decimal.

2019 12 13 0343  86.6  119.5  86.5918  119.4764  rough and refined PS locations post shear
2019 12 12 0619  86.6  120.1  86.5982  120.1285  rough and refined PS locations pre shear

So what needs to be done -- and I am leaving this to Tor B -- is download the data files for 2-3 buoys above the shear and 2-3 below using the map below (or as provided by uniq), delete the irrelevant columns, combine into a single spreadsheet with times of reported synchronized by row. Then add a new column and fill with the subtraction of above/below longitude columns.

The graph should show a big lurch at the hour of rifting.

As a control, go back a week or so to establish the big lurch is way out of the ordinary, not 'normal variation'. Going forward, the winds have hardly been enough to stress the ice, meaning delaunay buoy triangulations across the shear line will have stable edges.

Nonetheless, this morning's pair of S1AB 3 hrs 16 min apart don't show a quiescent situation on the Mosaic ice pack (lower animation). Indeed a small rift seems to be closing at the later time. This does not necessarily affected deployed instruments as only a small flat area near the ship is currently used.

The Kapitan Dranitsyn can be seen crossing the shear line within hours of its formation. It's not clear what would happen to an icebreaker caught in a sudden shear event. The Polarstern, being frozen in for a year, is more at risk.

Shear events with km scale displacements are multi-daily events even at the scale of a single S1AB frame, but one crossing a 118 m object amidship would not be expected unless the ship, like Los Angeles, is sitting on an inactive fault line predisposed to re-awakening.

While the Polarstern has not disclosed the data that would allow analysis (it being below the resolution of S1AB), they have had slabs of ice sliding back and forth in front of the bow, micro-shear events. In addition, the undocumented Dec 6th event saw a larger faulting event come right through Mosaic ice camp.

In summary, the ice has been shifting around a lot already this winter at various scales with only 2 months down and 4-5 months to go. It's tempting to say 'more than usual' but hard to go beyond anecdotal impressions. This has been a very odd winter in terms of no coherent ice pack drift (as visualized above in Ascat whole-Arctic mp4).

33
Arctic sea ice / Re: MOSAiC news
« on: December 14, 2019, 08:46:17 PM »
Quote
one showing a spurious lat lon and a couple who think it's 15 dec already. Will make a manual correction at some point.
Somebody not doing a proper job of curation and posting in ingestible format at the upper end makes pipeline science all but impossible for everyone downstream. Buoys and AWI wx present new problems every day. (Despite that, the latter is ingested directly by ECMWF for Arctic forecasting.)

Even if you made manual corrections all the way back to Oct 4th (and posted them prominently), there is no mechanism to correct the source (ie fix shabby or non-existent QA tools there). Tomorrow, instead of rolling your animation forward on auto-pilot to the next day, the add-ons will have to be manually corrected. For 95 buoys? For 95 pipelines feeding large scale climate prediction?

Following up on the near-catastrophic shear on Dec 13, the buoy system should show a lurch to the right (west) on the more southerly buoys above the shear line relative to the buoys on the Polarstern side of the line (north is below).

However that is not immediately apparent, probably because we need to run the buoy data much closer to its intrinsic positional resolution. That is, it would suffice to limit the graticule to 86.50-86.65 and 117-121 or about a tenth of the area in uniq's animation above. This would allow more of the 4-5 decimal points in the buoys's GPS to come into play, not just one.

Alternatively, if the rupture was not abrupt but spread out over a few hours, we might have to dig into select buoy db numerical analysis rather than rely on graphics to date the event.

In terms of weather contribution to causality, 3-hour GFS shows a complete reversal of wind direction accompanied by an up down up cycle of wind strength with sharp wind curvature in between though not right at the Polarstern's location. Note this wx depiction would not be identical to the GFS forecast on Dec 12th because it re-initializes each day; the time series was made well after the fact.

Until the buoy reanalysis is finalized, it is not feasible to assign a time of shear rupture to a pair of bracketing GFS frames; even then we don't know the offset between cause and effect.

34
Arctic sea ice / Re: MOSAiC news
« on: December 13, 2019, 10:04:11 PM »
Quote
24-hr shear gif is jaw-dropping
Early morning, just absent-mindedly updating the S1AB collection, not seeing any drama on the ingest of the three Dec 13's, not expecting much by way of drift at low wind, at best thinking about the KD cutting a swath pre-conditioning the ice camp to future lead and ridge problems, then wondering when that meaningless lead came about, checking with the 24 hr, making the overlay pair, running it real fast in ImageJ, then my jaw-dropping moment seeing the long shear boundary, to pondering what an event-driven diesel spill during refueling the PS would mean for Arctic research, to asking whether risk to researchers is maybe higher than anticipated (indeed higher than acceptable, this being the 4th major incident in 69 days), to looking at historical stats on expected major cyclones of winter still ahead.

We have the tools to do a lot more analysis on the Friday The 13th fracture (FT13). It does seem fairly easy to recognize conditions conducive to disruptive events a couple days out on GFS, though it seems we don't know enough about ice pack strength to differentiate between deformation and shear, much less predict location of shear lines relative to the Mosaic ice camp. The surprise is, we do know enough to make those predictions.

The attachments below are just two plain text documents giving active urls to all Sentinel Viewer back to mooring and their accompanying PS position- and S1AB-aware GFS nullschools. The buoy position repositories and ship weather are at their respective archives

Sure, we could post a swinging risk needle like the Forest Service does for fire hazard but would it really be actionable down at the ship, would someone not go out to tend a deployed instrument when the needle was on yellow or red?

The buoy swarm animation provides a very sensitive nrt tool that can detect and report occurrences of not-too-remote rifting, though their current distribution was not thought out and is sub-optimal. However an after-the-fact announcement is not a warning, unless the shearing is taking place in abrupt stages (like earthquake after-shocks).

Here Uniq will be looking for an upper zone of plastic buoy position deformation in conjunction with a lower zone of rigidity that preceded the rupture at the interface. Would that give hours of warning or minutes? Would that give warnings of all events or just some?

Here we need a whole lot less mickey mouse from the inhabitants of the Mosaic buoy deploying academic silos, like delays in posting, lack of Iridium redials, lack of time synchronization, irregular GPS reads, lack of gap repair, lack of QA, and worst of all, dumbing down the decimal points (AWI, I'm talking to you).

In other words, changing inter-buoy distances provide an interferometric mesh from which a tensiometer is built. GPS is not up to lasers but still very capable today since Every Decimal Point Matters even if the last is not quite as good as the first. Right now, buoy runs take too long for the desktop but there are ultra-fast migration options for anything in R.

Given eight years of planning, why are we scrambling today to put together risk mitigation software?

35
Arctic sea ice / Re: MOSAiC news
« on: December 13, 2019, 11:49:02 AM »
Round-about route the last day as the going got toughter but docking as expected to the east of the Polarstern on the 05:31 on Dec 13th. The Kapitan Dranitsyn is still moving into position between 03:43 and 05:21. The 07:00 S1B just misses in its coverage.

The tracks have to be captured within 24 hrs on a S1AB or they become all but impossible to follow.

The large extended black lead to the south (up) is an unexpected overnight development but so far seems to have no effect on fueling or Mosaic ice camp equipment. It is not notably active between 03:43 and 07:00. There is no sign of it yesterday on the 05:30 S1A.

Regionally, there is quite a bit of ice dynamics, mostly shearing. The PS and KD are perhaps 10 km north (down) of a massive block shear zone. The overnight pair of images below are being viewed in a coordinate system in which the Polarstern is fixed.

This would have been a full-on disaster had the shear line come through Ice Camp while the Polarstern was refueling or exchanging out equipment and scientists. It didn't and people on the ground may have been oblivious to it.

The explanation of the event is the passing of mild wind shear from southeast to northwest across the Polarstern's position. At no time were winds extreme; instead the delta of wind (6 km/hr to 31 km/hr) caused the ice to move differentially across the gradient.

The ice is still too mechanically weak this winter to distort south of the PS's position so brittle-fractured along a line parallel to wind stress where it is thicker. The event is largely over per GFS though ice movement is foreseen to somewhat reverse in coming days. Again, this was not a winter cyclone, just uneven regional wind stress.

On uniq's upcoming (we hope!) mega buoy animation, we can expect some sharp zigzags distinguishing buoy sets above and below the event. This will greatly improve time resolution of the main fracture over what 24-hr S1AB can do, in this instance 24 less 2:36 hrs compared to half-hourly or even ten minutes.

2019 12 13 0343
2019 12 12 0619


Start at the location below and step back in 3-hr steps (keyboard 'j').

https://earth.nullschool.net/#2019/12/13/0300Z/wind/isobaric/1000hPa/orthographic=-45.00,90.00,1100/loc=119.5,86.6

36
Arctic sea ice / Re: MOSAiC news
« on: December 08, 2019, 08:50:43 PM »
This :) was written on Nov 27th but dated Dec 6th and does not address the most damaging storm of the trip on 03-06 Dec 2019. Pulks are sleds being used along with wooden palettes to bridge small leads. Presseisrücken are pressure ridges.

Co-leader Shupe is now over two weeks overdue on his weekly blog. Cires is not blogging the storm, Helmholtz quit in mid-October. Not substantive use is being made of twitter.

No news is a variant on fake news and historical revisionism: if they don't report the Dec 6th storm, it didn't happen. (Those satellites are sooooo annoying: 4 S1AB scenes today + clear Terra Modis.)

Quote
we will have an emergency runaway very soon. In the spring we will build it so that even bigger planes like an Antonov can land normally and not only with skis.
I sincerely doubt this looking at increasingly disheveled Mosaic floe which has not stabilized since the Dec 6th storm. Rex doesn't indicate where this runway will be located nor how thick the ice is; in the original plans, this was to be bladed by Piston Bullies in the flat dark areas (former melt ponds). However Mother Nature got there first.

If he is looking for volunteers to drive the bulldozers out on thin ice, like at Borneo, i am opting out. Surely Rex knows how slowly and unevenly ice thickens in the autumn; if not, a quick look over the ship's 100 mbps internet at the nearby Simb3 ice buoy graphs suffices. Those show 1.254 m snow + ice today -- the ice thickness they expected at mooring on Oct 5th some 66 days ago.

https://www.cryosphereinnovation.com/387850

The Polarstern is looking at five days of inconsequential wind not strong enough to do any more damage. The ship will drift a bit north from its present record of 85.3º N but also a bit east from 121.2º E. We don't know at this point whether the weather will be calm or windy when the relief icebreaker arrives.

The Kapitan Dranitsyn's call sign is UCJP; the other numbers are IMO 7824405 and MMSI 273138300. We will be following the ship closely to see how much unavoidable damage and ridge/lead preconditioning it does in approaching the Polarstern. However it last reported on Dec-03 at 11:30 UTC, meaning it turned off its new state-of-the art navigation beacon after heading up from Murmansk.

This accomplishes nothing for Mosaic because we can still see the ship's stacks and tracks on Sentinel and RAMMB infra-red.

https://www.sailwx.info/shiptrack/shipposition.phtml?call=UCJP

Contrary to their inept static drift model, this is not favorable for reaching wind fields that would bring them towards the Fram Strait. At high latitude, the ship will never get past that gigantic immobile block of MYI documented in the previous post.

The Polarstern is currently 1477 km from Svalbard whereas at mooring on Oct 4th the ship was 1646 km away on Oct 4th. If this rate keeps up (it won't), it would take 579 days drifting on a WGS geodesic (won't happen) to reach Longyearbyen (won't happen in 2020-22).

I've attached the updated archive of S1AB images of the Mosaic floe. In addition to timestamp, rough and precise lat,lon, wind speed, wind direction and ship temperature each entry has direct links to both GFS nullschool and the jp2 image at bslmagb.nerc-bas.ac.uk/iwsviewer/. The former is built out of the preceding variables; the only technical tricks involve nullschool using lon, lat order and rounding odd times down (eg 02:59 to 00:00) which is easily fixed with modular round-off relative to the 3-hour spacings (eg 01:31 to 03:00). That's MROUND(RIGHT(timestamp,4),300) in your spreadsheet.

It's quite feasible to add thumbnails of the Mosaic floe, P-buoy tracks and regional wind the Polarstern is experiencing to each timestamp row in the S1AB database without growing file size too badly. A better alternative might be to make a mp4 at various scales out of every 3-hour nullschool GFS since mooring and flash those that have associated imagery.

37
Arctic sea ice / Re: MOSAiC news
« on: December 07, 2019, 01:05:22 PM »
Quote
makes sense to have a picture of the site
That one is a mirror image, an old conceptual layout. We do have the original site plan from the 126 page planning document up-forum as well as a later as-built map in radial coordinates centered on the ship. We also have the modified site plan they just released up-forum; it is no longer radial and quite blurry at all the places it has been posted.

None of these maps are at all appropriate to the pending redeployment of the Ice Camp -- if there is one -- after yesterday's big rearrangement.

38
Arctic sea ice / Re: MOSAiC news
« on: December 05, 2019, 08:23:00 PM »
The whole ending strikes me as highly contrived, all about filming a meet-up with two buddies and later them eating ribs and french chocolate. The Lance has a helicopter pad but they are not using it so the adventurers will be able to say they went boat to boat per the original plan.

The tent camp is also well within reach and capabilities of the Svalbard helicopter service that extracted the crew from the grounding in the Hinlopen Strait last December.

The Lance does not really have to chops for this job and keeps getting frozen in the 30 cm ice but they are scripted to moor along an ice edge so the two do not have to be seen being picked up from a zodiac even though they are having to be rescued as they don't have the food or fuel to continue under current ice conditions and more weeks of unfavorable floe drift.

There is a Norwegian icebreaker at the scene but they are not using it. The Polerstern's relief icebreaker is not likely to be headed towards Svalbard -- way out their way and through more ice than necessary. These ships have all turned off their GPS beacons; sailwx is only receiving the Polerstern's.

Updates -- and some pointed questions about an actual purpose for the trip -- can be found in the comment section at this Norwegian site which updates almost hourly:

https://direkte.vg.no/nordpolen_ousland/news/5de62459d45a8b0011b1677f

Quote
Just before Lance left Longyearbyen, a research ship also left north. I see on Marine traffic that this ship is on standby on the ice (on starboard side of Lance), probably be the new state-of-the-art icebreaker for the Norwegian Polar Institute, "Crown Prince Haakon" a research assignment in the area and can contribute if necessary. The name may be icebreaker Haakon Magnus "is located just to the east of you, can't they break a real trap for you?

How much does it mean for the expedition to go "unsupported", which is not possible with post-supplies? And how do they manage to meet in the icy, dark and snowstorm. Even with GPS and satellite phones, this must be a major challenge. The two teams of polar explorers have agreed on a common point on GPS that they both are heading towards.

Bengt Rotmo and Aleksander Gamme, friends coming on foot to the tent camp, have emergency rockets and a signal gun too, so they can use it to show where they are. There is a doctor on board the Lance though no issues are expected.

39
Arctic sea ice / Re: MOSAiC news
« on: December 03, 2019, 03:34:04 PM »
Quote
Is there some way to indicate how much (if any) the distance between buoys changes over time?
Yes. Put the three buoy lat lon columns in a spreadsheet, making sure their half-hour time stamps are in register. Add the haversine formula (http://mathworld.wolfram.com/Haversine.html) as 7th-9th columns to calculate sides. Add a 10th column that sums these to a triangle perimeter. Use the SSS formula sqRT (s(s-a)(s-b)(s-c) with s the semi-perimeter for the area. Draw each triangle using an online triangle tool, capture, bin-color in proportion to area, float as otherwise transparent layers and animate. YES YOU CAN

date   hour   lat-P201   lon-P201   lat-P204   lon-P204   lat-P207   lon-P207
01 12 19   03:00   85.9394   113.4152   85.9400   112.7791   86.0074   112.4806
01 12 19   02:30   85.9413   113.3999   85.9420   112.7633   86.0093   112.4640
01 12 19   02:00   85.9432   113.3855   85.9438   112.7479   86.0111   112.4486
01 12 19   01:30   85.9450   113.3719   85.9457   112.7335   86.0128   112.4341
01 12 19   01:00   85.9467   113.3608   85.9474   112.7194   86.0146   112.4214
01 12 19   24:30   85.9485   113.3505   85.9491   112.7078   86.0163   112.4103
01 12 19   24:00   85.9503   113.3405   85.9509   112.6973   86.0180   112.3994

The tool below will put your choice of inter-buoy distance along the bottom rescaled to a constant length. Then you can see the relative shape change in the other two sides.

https://www.triangle-calculator.com/?q=a%3D3+b%3D4+c%3D5&submit=Solve

Quote
average the ice motion arrows over a month somehow
In the past we have tried loading the month as grayscale in gimp and using the 'average layers' command on a duplicated stack (image menu). That gives a so-so wind rose at each grid point that could be compared year on year by image subtraction to give a 2015-19 animation.

It may be that OsiSaf ill-advisedly puts the center of the arrow over the grid point (as mosaic_multi does) instead of the tail. So we need to first redraw the arrows with no heads using the OsiSaf netCDF than no one can get to work. Alternatively Panoply (or command line) dumpNC would give numeric x,y values at grid points or regions of interest that could be passed on to Excel which has a good wind rose chart.

The next three days or so on GFS look like more of the same: moderately strong winds at a fixed bearing. Below, the png assumes a mid-range coriolis angle of 25º of ice movement CW to the direction of the wind. Zonal and meridional components r,θ = lat lon are shown for the 05:00Z nullschool of today roughly scaled to the cube of 100 hPa wind speed from comparing response at periods of constancy.

In three days time, my expectation is the Polarstern will drift to 86.2  121.9 (ie on 09:00 on 06 Dec 2019 according to sailwx tables). Thus 1/6th of the trip will be over without any real indication of Fram-ward transpolar drift.

Sentinel coverage of the Mosaic floe has resumed. Daily instability suggests very little of it is fit for purpose.

S1B  2019 12 03 T 0643  17  210  -17.1  86.0017  115.6685   

http://bslmagb.nerc-bas.ac.uk/iwsviewer/?image=DataPolarview/111_S1jpeg2000_201912/S1B_EW_GRDM_1SDH_20191203T064336_4414_N_1.8bit.jp2


Technical note: nullschool provides a clean 1º graticule over land if wind is set to none. AwiMet provides the green location circle. Setting the scale parameter to 3000 maximizes resolution. Longitude has been increasing by 0.05 deg/day over the last 24 hours but latitude by only 0.005, setting the wind scaling. (Mean recent change or tangent to the PS position curve could be determined more accurately with high resolution S1Ab or buoy data.)

The tangent vector is set by rotating to vertical using the Polarstern's current longitude, drawing a perfect horizontal, then rotating back. The wind direction is drawn as the tangent vector to the radial vector of the osculating circle to the curving wind sprite at the PS. Dropping the perpendiculars then gives the desired breakdown of motion in terms of lat,lon. Here taking the ratio of r,θ component vectors causes the wind scaling factor to drop out.

40
Arctic sea ice / Re: MOSAiC news
« on: December 02, 2019, 05:15:02 PM »
Co-leader M Shupe has an excellent new on-site blog out; note that despite the Nov 27th tag the storm event being discussed only covers the 18-23 Nov 2019. More has happened since then

We could see the damage just looking at S1AB time series but it is great to have confirmation and  specific details beyond satellite resolutioon. Note buoys are not on the Mosaic floe and may be affected differently or not at all.

I don't think things would have gone better had they selected another floe; the ice was garbage everywhere at their latitude on Oct 5th and still is. Had they gone closer to the pole, transpolar drift would have become even more problematic than it is now: the GFS wind forecast translates heuristically to more south and east backtracking of their trajectory.

85.9  113.8 19-12-02 09:00    8  250    -27.1
85.9  113.4 19-12-01 21:00    8  300    -24.1
86.0  113.1 19-12-01 09:00   10  310    -21.8
86.0  112.8 19-11-30 21:00    8  340    -27.0
86.1  112.9 19-11-30 09:00    9   20    -28.0
86.1  113.5 19-11-29 21:00   10   30    -25.8

Quote
Postcards from a frozen icebreaker – Part 14
By Matthew Shupe 11/18/19
https://blogs.agu.org/thefield/2019/11/27/postcards-from-a-frozen-icebreaker-part-14/

I was startled by the phone call shortly after midnight. Trouble at Met City. Felix had just arrived on the bridge for his night watch from 12-4am. He always takes a look around camp when arriving for his duties. And there was no 30m mast. Simply gone.

We had seen the crack before, and apparently it got active and pulled on some of the guy lines, ultimately pulling the mast down. The sonic anemometer failed right away, possibly from just being unplugged. Upon later inspection it is bent, can likely be straightened, re-calibrated, and put back into operation.

Our met sensor remained operational the whole time, including [while lying on the ground] after the fall. We will test both of these instruments against others, but it is looking like they will both live to see another field measurement.

The mast itself might also be salvageable. Some bent legs the ship can likely fix and a few damaged sections that will just be taken out of service. Thus, it may become a 25m mast but that would be better than nothing. Now we just need the ice to settle down so we can think about a redeployment.

The chaos has contributed to this feeling. Major ice dynamics running from the northwest to the southeast of us, across the bow of the ship. They have sheared our camp, and the Fortress, in half. This was part of a regional event with lots of ice motion, likely driven by a strong storm with very high winds.

Initially the lead opened many meters across, followed by some shear with the far side of camp moving towards the ship, then away again. In the last days it all moved again perhaps 500m.

Met City is almost directly in front of Polarstern while Ocean City remains approximately where it was (after a slight move to stay away from the ridge). A much longer daily voyage for us to get to Met City, and now it means bringing fuel cans to run generators. Met City is now very dark.

“Continuity” is a very important concept for MOSAiC. But it’s also a huge challenge in the current Arctic conditions. In the last week we’ve had so much ice movement, right out in front of the ship. We watched Met City move back and forth across the view from the bridge.

Intermittently we are able to reach it, going from floe to floe. While at other times there is no access possible. And this limited access impacts the continuity of our measurement on the ice. We are running Met City on a couple of generators but the runtime is such that we must refuel twice per day.

Last night the ice movement left us no route to Met City so the generator fan went out at 4:30 am local time. This limited access is leaving its mark on the Met City data stream but others experiments are also impacted.

Sampling sites have move further away or broken up entirely; the Ocean City hut had to be moved; the whole Remote Sensing installation will need to be relocated, and more. Continuity of the observations has definitely been compromised.
An outdated map of the Ice Camp layout was included, not attached below because it is one we have seen before, now presented at a blurrier resolution. It does not show the layout of the cracks and ridges discussed in the post.

Once again there is nothing but 404's in trying to locate the original full resolution file. Neither the new lidar elevation map nor ice bottom ROV imagery have been released in any form.

Last time I wrote the help desk, they got back to me saying the ship could only be contacted intermittently, even though we know today it had a 100 mbps internet connection ever since leaving Tromsø.

41
Arctic sea ice / Re: MOSAiC news
« on: December 02, 2019, 04:46:56 PM »
Quote
coordinates taken from polarview images in red and collated
Coordinates  were shared earlier from the 106 Sentinel-1AB images available since the Polarstern moored on Oct 4th. These were hand-digitized using the fast and accurate new PolarView plugin.

No new S1AB images have appeared during the last 48 hours, very unusual. It means during all 16 orbital passes over the Polarstern, the sensors were either shut down, malfunctioning, taking scenes in interferometric mode, or taking images but suspending distribution. This happens every time the Mosaic floe is encountering disintegration issues. Coincidence?

The P-buoys give the ship's position 2-3 times a day, always in the early morning UTC hours. The accuracy is about a third of the ship's length. The timestamps refer to nadir or satellite passage over the center of the scene. While these are more accurate than we need (to the second), the minutes can be anywhere between hours.

Like most buoys, the three close-in P-buoys call in their GPS coordinates 24 times a day, every half hour on the half hour. Since 4 dp accuracy is important to measure ice pack deformation, the issue arises of how to best collate them with the erratic timestamps of Polarstern S1AB images.

The Polarstern's lat lon is seldom co-temporal with the buoys, only 15 times out of 106. However the other 91 can be linearly interpolated back to the nearest half hour using the rate of change of lat lon. The ones below are already synched to the buoys and do not need interpolation:

S1B   2019 11 29 T 0400   86.1220   115.0394
S1B   2019 11 22 T 0230   85.7352   120.8192
S1B   2019 11 19 T 0700   85.8011   120.5766
S1A   2019 11 18 T 0530   85.8556   120.8340
S1B   2019 11 17 T 0400   86.0595   122.4405
S1B   2019 11 10 T 0230   85.8219   115.9915
S1B   2019 11 07 T 0700   85.9198   116.7922
S1A   2019 11 06 T 0530   85.9191   117.7247
S1B   2019 11 05 T 0400   85.9509   118.8770
S1B   2019 10 26 T 0700   85.4533   127.4991
S1B   2019 10 19 T 0530   84.9215   133.1910
S1B   2019 10 14 T 0700   84.7783   134.5386
S1A   2019 10 13 T 0530   84.8574   135.0090
S1B   2019 10 07 T 0530   85.0846   134.3174

The Pbuoy dataset has various repairable glitches (shown below) not repaired by the buoy owner; the month-old errors are simply passed on 'as is' to the Meereis and sailwx portals to be ingested into Uniq's animation algorithm.

Since 94 - 12 - 3 = 79 other Mosaic buoys are currently reporting -- and some of these will have glitches of their own -- there is a need to repair the damage and regularize the data.

The best way to go is set up a master clock, say on the half hour back to the beginning, then hang all the data off it to synchronize analysis. Although Mosaic experiments often produce complex data types that don't fit in (below), they still be indexed in if that serves some purpose.

For example, a source like GFS nullschool only reports at 3 hr intervals so has gaps at 5 out of 6 positions, whereas sailwx and awiMet shipboard weather report hourly. Ascat reports 3 times a day but swath timestamps are hard to come by for the concurrent PS location. OsiSaf reports a rolling window of ice movement every two days between 12:00Z. Most satellite products (such as Amsr2 ice concentration or cryo2smos ice thickness) report every 24 hours.

On these forums, we are looking for scalability, transparency, regularization and portability:

Scalability: Any number of buoys or images can be tied to the master clock's indexing field; indeed all put into a single common file. The issue is keeping file size manageable over the course of the Mosaic year. If not, the latency on common operations like 'sort' or 'fill down' becomes unworkable. The key here is keep image collections such GFS weather pictures elsewhere, still indexed though by the master clock.

Transparency: This means suppling the data in human-readable data or image format such as plain txt, comma separated variables, netCDF, kml, gif, png, jpg or mp4 visible in the post itself or as an attachment anyone with an old cheap computer can download, open in free software and process for themselves. More and more climate change sources are using arcane binary formats the average person cannot work with.

Regularization: Errors, gaps and glitches should be repaired just once, rather than 50 people making the same tedious repairs 50 times over. To a certain extent, this is enforced by keying to the master clock. I will post repaired P-buoys, synched S1AB and reconciled sailwx/awiMet in a bit.

Correction and collation of databases can be done very rapidly if you still have a 25 year old Mac running MS Works 1.0; it has gotten much harder since.

Portability: The data should be immediately importable into other open software for specialized projects, such as Excel, Gimp, ImageJ or R for statistical analysis, charting, slide shows, animations and movies.

42
Arctic sea ice / Re: MOSAiC news
« on: November 29, 2019, 09:12:38 PM »
Quote
Rammb down, line of dots?
IT will be back in Monday after a long weekend.

'Follow Mosaic' was better today but long is the transect, on what floe is it located, what is its history and initial thickness, what have they found so far -- none of your business apparently.

Hippocrates once said, you cannot walk the same Arctic sea ice transect twice ... was this floe representative, what commotion has the site undergone in the last 60 days?

The location and date (but not the time, the exif was stripped) are given as 86.08 113.73 on the 29th. That would be well south of anywhere the Polarstern has been recently. However if the Polarstern persists in using "ship time" and changing that every Saturday (they say to better party with the incoming icebreaker at its meal times), the date itself becomes problematic.

The last few days have seen a brisk sub-gale force wind (2nd column, m/s) from a consistent direction pushing the ship steadily east with a touch of south. The ship is at a record easterly position at 113.8 but at an unexceptional latitude. Again, this is a great opportunity to study ice pack movement at a constant stress vector.

Assuming the work party photo was taken at the same time as the last of the four Sentinel-1AB this morning, the work site can be located approximately using the fabulous new PolarView plug-in from bslmagb.nerc-bas.ac.uk. The exact study floe cannot be determined because of the lack of timestamp on the photo.

http://bslmagb.nerc-bas.ac.uk/iwsviewer/?image=DataPolarview/111_S1jpeg2000_201911/S1B_EW_GRDM_1SDH_20191129T053813_F681_N_1.8bit.jp2

86.1   113.8   29   17:00   09   40
86.1   113.9   29   16:00   10   40
86.1   114.0   29   15:00   11   40
86.1   114.0   29   14:00   11   40
86.1   114.1   29   13:00   12   50
86.1   114.2   29   12:00   11   50
86.1   114.3   29   11:00   12   60
86.1   114.4   29   10:00   12   50
86.1   114.5   29   09:00   13   60
86.1   114.6   29   08:00   13   50
86.1   114.8   29   06:00   12   40  05:38   86.0079   114.8607
86.1   114.9   29   05:00   14   40  04:49   86.1120   114.9497
86.1   115.0   29   04:00   13   50  04:00   86.1220   115.0394
86.1   115.1   29   03:00   12   50
86.1   115.3   29   02:00   13   50  02:22   86.1262   115.2108
86.1   115.4   29   01:00   10   40
86.1   115.5   29   00:00   11   50
86.1   115.6   28   23:00   12   50
86.1   115.7   28   22:00   12   50
86.1   115.8   28   21:00   13   50
86.1   115.9   28   20:00   12   40
86.1   116.0   28   19:00   13   50
86.1   116.1   28   18:00   12   50
86.1   116.2   28   17:00   11   40
86.2   116.3   28   16:00   10   40
86.2   116.4   28   15:00   11   40
86.2   116.5   28   14:00   9   50
86.2   116.5   28   13:00   9   40
86.2   116.6   28   12:00   8   30
86.2   116.7   28   11:00   8   30
86.2   116.8   28   10:00   9   30
86.2   116.8   28   09:00   9   30
86.2   116.9   28   08:00   8   20
86.2   117.0   28   06:00   6   30  0635   86.1642   116.9532
86.2   117.0   28   05:00   6   40
86.2   117.1   28   04:00   7   50  0408   86.1665   117.0933
86.2   117.2   28   03:00   7   50
86.2   117.2   28   02:00   8   60
86.2   117.3   28   01:00   7   50
86.2   117.3   28   00:00   7   60
86.2   117.4   27   23:00   7   60
86.2   117.4   27   22:00   8   70
86.2   117.5   27   21:00   7   70
86.2   117.5   27   20:00   7   60
86.2   117.6   27   18:00   7   70
86.2   117.7   27   17:00   7   70

43
Arctic sea ice / Re: MOSAiC news
« on: November 26, 2019, 05:29:54 PM »
There is a golden opportunity to study how ice drift correlates with wind direction during an unusual period of steady wind speed and direction in in late October. As Nansen observed during the voyage of the Fram, motion of the ice was almost always offset from the direction of the wind. However he lacked the big picture that we have today (eg basin-wide cyclone).

The response of the Polarstern is shown in the two-frame animation and the csv of its variables below. Note both the zonal and meridional drift components were linear, with moderate drift to the north but a strong component to the east, forming a large angle to the wind direction (which is counter-intuitive but expected).

The ship presents a very large target to the wind but is of a negligible mass compared to the larger ice pack. Mosaic has declined to make public the ship's bearing (ie alignment with wind) over time, presumably to reserve for themselves (in 2023) the capability of using the GFS forecast to make a few days of ice motion forecast.

Attached also are the wind roses for wind direction and wind speed during the 229 hours of this low variability event.

44
Arctic sea ice / Re: MOSAiC news
« on: November 23, 2019, 05:20:01 PM »
Right. At first it looks like one of those pen machines putting a personal touch on a massive junk mail campaign. But the trails actually differ quite a bit in their details upon trying to overlay them by a simple translational move. The question is, how to distinguish deformation from shear and discontinuities such as a lead opening.

The long PolarView weekend continues. I wrote them, they are off somewhere not responding. The pink square masking goes away if all but S1 are de-checked; problem is now in the feed. No new images have been ingested since the 22nd.

Mosaic is going to new extremes to keep the world uninformed.

45
Arctic sea ice / Re: MOSAiC news
« on: November 23, 2019, 10:30:06 AM »
Here is a stomach-churning zoom centered at the Polarstern to go with that very effective hangover blur above. The last S1B of Nov 22nd has been rotated so that the pole is to the bottom left.

The second image shows a cyclone forming in the upper Fram and wandering up to the Polarstern's location before drifting off to the Kara Sea. The effects on leads and ridging would be fairly minor except for pre-conditioned fissures. Whatever the drift induced in the ship, even if it mimics transpolar drift, has nothing to do with transpolar drift.

The mp4, adapted from Uniq above with the Mosaic floe circled, shows the very unfortunate situation the Polarstern is in relative to large scale failures in the ice pack. Be sure to set on loop so it will rocks back and forth.

The 3x enlargement shows extreme disruption of the Mosaic ice camp over this time frame. Black lines are open water of new leads; white lines are pressure ridges. The Polarview portal to Sentinel imagery is currently badly broken and no files of any kind are available yet for today, the 23rd.

Mp4 are now easy to make in forum-acceptable form by saving ImageJ stacks to avi and then applying cloudconvert. It requires dimensions be even.

https://cloudconvert.com/avi-to-mp4

46
Arctic sea ice / Re: MOSAiC news
« on: November 22, 2019, 11:47:17 AM »
The situation has gotten increasingly dire in the immediate vicinity of the Mosaic ice camp as extensional forces have opened multiple km-wide bands. A second Sentinel image of 05:46 has just come in that provides a snapshot of ongoing motion -- the situation has worsened considerably in the last three hours. PolarView has just now posted a third intermediate time, the 04:08, but we won't be able to follow events further until tomorrow morning other than hourly weather and drift which are unremarkable (there's no storm) since the last S1AB:

   Lat  Long  YY-MM-DD  UTC     Wind       T(C)  hPa
  85.7  120.7 19-11-22 10:00    5   50    -16.3 1016.0
  85.7  120.8 19-11-22 09:00    4   40    -17.0 1015.5
  85.7  120.8 19-11-22 08:00    5   10    -16.1  1015.0
  85.7  120.8 19-11-22 07:00    4  340    -16.1  1014.5

This event will be extremely disruptive to all deployed experimental equipment and effectively destroys the floe for purposes of studying its evolution over a year. Let's hope the Polarstern and all the people aboard stay safe as the event continues to unfold today.

This is a very unfortunate situation ultimately attributable to climate change, its amplification in the Arctic Ocean and the long-term trend to thinner, more mobile ice that cannot resist wind stresses.

The upper two images follow Mosaic convention with north up, the first needs a click to display full size; the lower animation has S1AB orientation of the Pole down the 120º meridian with inverted insets in coordinates attached to the ship at 2x enlargement.  The 4x enlargement is also north down after contrast leveling and light unsharp mask.

Some of the 87 surviving autonomous buoys out of the 100 deployed in the Mosaic project will likely succumb to the same ice pack deformations affecting the Polarstern. So far, they all reported on the 22nd or 23rd with the exceptions below. All but the last two are Chinese buoys that have previously had reporting delays.

300234068118580   SVP    PRIC   MOSAiC   15 11 19   86.19   118.51   
300234010077180   GPS    TUT    MOSAiC   19 11 19   86.08   117.27   
300234065091830   GPS    TUT    MOSAiC   19 11 19   86.01   123.00   
300234065090840   GPS    TUT    MOSAiC   21 11 19   85.51   120.54   
300234065980590   GPS    TUT    MOSAiC   21 11 19   85.73   123.98   
300234065981590   GPS    TUT    MOSAiC   21 11 19   85.61   118.57   
300234065984580   GPS    TUT    MOSAiC   21 11 19   85.95   121.98   
300234065985570   GPS    TUT    MOSAiC   21 11 19   85.92   121.06   
300234067705700   IT      AWI    MOSAiC   21 11 19   85.75   121.63   
.................90094   ITP   WHOI   MOSAiC   21 11 19   85.68   121.98   

47
Arctic sea ice / Re: MOSAiC news
« on: November 21, 2019, 04:27:57 PM »
Quote
A lot of movement overnight
This was the worst ice dynamics yet ... and just after they got done laying a bridge over a recurrent lead with scrap palettes and a wooden sled. It is unfortunate that the remote experimental stations have to be tethered to the ship with power, data and fuel lines because these are subject to breakage and burial.

The massive rift chain to the Polarstern's southeast (fresh leads are black on S1AB) shows the response of the ice to to divergent wind stress: extensional faulting resembling NW trending Nevada basin and ranges as the Pacific Plate scrapes past the N American -- and about on the same distance scale. Both play out slowly in time; here the ice failed a couple days after the "84º" wind divergence event pictured in the GFS post above.

A parallel fault zone runs above, below and so far around the Mosaic floe. So far, it has mostly been around because the Fortress is not the path of least resistance for fractures (being thicker). The two Sentinels for the day are in and 'follow-mosaic' :) seems to run a couple days behind events, so unless skies are infrared-clear we won't know until 03:30 utc on Friday what is currently going on.

No question though that the Mosaic floe has experienced some strong ice dynamics even though the wind has been and will be mild short-term. The shifting ice we can see between Sentinel orbits only 3.25 hrs apart may or may not translate to significant damage to remote towers and lines.

The Polarstern itself, forming a barrier much higher than ice, seems to attract ridging, which on the stern side would seem to require daily resetting of slack lines mooring the ship to ice anchors. This recurrent lead/ridge may have originated from the icebreakers maneuvering early on.

Between onboard pollution from the ship's stacks and daily repairs to deployed sensors, scientists may not be getting the steady data streams expected. It would be no better on another floe. Trip leaders said early on that this was probably the last possible year for such an expedition. Maybe it was last year.

It's always been clear that Sentinel radar images, like Ascat scatterometery, arrives at sub-optimal visual contrast but it's never been clear how to best fix a given image, much less make a matching stack for a time series given variations between different orbital angles and nadirs.

Sentinel currently provides 82 images back to mooring on Oct 5th with only five days of missing coverage. The attached S1AB csv database has been merged with sailwx, AwiMet and nullschool GFS to bring in location, wind speed, wind direction, air temperature and links.

The easiest thing to do in terms of small file sizes, convenient format, quick turn-around and pioneering a pipeline for the the ultimate unattended objective fix of the jp2 is use the jpg for now and its intrusive graticule, followed by the Level tool in gimp, as shown in the mini-tutorial attached.

Sentinel images on ice are inherently speckled and while 'there's a app for that'  a slight unsharp mask can bring further small benefits. One size does not fit all however: improving a 100x100 km scene is not optimal for smaller sub-scenes like the Mosaic floe. There we would like to maximally improve the resolution or clarity of the image right around the Polarstern and the Mosaic floe.

48
Arctic sea ice / Re: MOSAiC news
« on: November 20, 2019, 09:01:12 PM »
Well put, Archi.

I say lay on the amenities, whatever it takes for creature comforts. They have been worried about sustaining Leg 2 morale since the get-go. They'll be beyond the reach of planes, helicopters and even support icebreakers over that time frame.

Mosaic has not released a ship's roster so we don't even know whom to thank. There's crew of 44 and capacity for 80 scientific and technical staff at any given time according to wiki. Most of the people are there to maintain complex instruments at remote sites (no easy job) though scientific team leaders are alongside working too. The breakthrough on internet bandwidth has made a big difference on who needs to be present.

Esther Horvath, photographer and communications manager of the MOSAiC expedition "wants to document the unknown faces on the front lines of climate science. "Who are the scientists? This is what I'm extremely interested in; to show climate change stories through the eyes of scientists, showing how they live in such an extreme remote location."

Chief scientist:
Markus Rex PS122/1: 20 Sep 2019 – 15 Dec 2019
Christian Haas PS122/2: 15 Dec 2019 – 15 Feb 2020
Torsten Kanzow PS122/3: 15 Feb 2020 – 15 Apr 2020
Markus Rex PS122/4: 15 Apr 2020 – 15 Jun 2020
Dieter Wolf-Gladrow PS122/5: 15 Jun 2020 – 15 Aug 2020
Markus Rex PS122/6: 15 Aug 2020 – 14 Oct 2020

The photo today shows some of the damage from recent ice dynamics. We've seen this already on Sentinel but don't know the specifics. However Mosaic has been very cagey about providing a revised map of Ice Camp as-built (and re-built and re-built again) or shareing measured ice elevations above and below.

For example, the open lead necessitating the bridge has itself been cropped out of the photo. We have no idea where the Ocean City and Remote Sensing Site are located today nor how serious the fracture is nor how to follow it on remote sensing.

I don't think this secrecy serves them. The damage control and data hoarding is pure paranoia. No ship radar with 100 Mbps internet? Dumbing down GPS position -- do they fear a cruise missile? What is someone going to do with bearing data beyond a scarcely publishable fourier analysis?

What it boils down to is somebody on the grant committee -- Mosaic dipped deeply into a pot shared with Antarctica and Greenland -- said 'this is never going to work plus it's been done before by N-ICE2015 and SHEBA'. And if they had access to minute by minute floe motion, would now be saying 'I told you so, no way time evolution of a single floe can be followed for a whole year'.

So it seems to be about embarrassment. They are making zero headway on the drift, have no prospects of drifting over the Pole, and the floe is rearranging itself daily if not disintegrating, undercutting the  key talking point about research novelty. This is why Shupe chose the name 'Fortress' for a crummy ice jumble and put it on Mosaic maps.

Today saw the usual turmoil on the Mosaic floe and also some puzzling (since winds have abated) regional torque with the ice no longer moving coherently over the short time frame between two S1AB. Divergent wind stress from yesterday cannot be the attribution because there's not even short term conservation of linear or angular ice momentum because of way too much frictional dissipation.

The two Sentinels are co-registered on the Polarstern (red dot); the faux interferometry that shows complex regional motion in this coordinate frame used the S1AB grayscale average for the 3rd luminance channel of the HSL 'RGB'.

49
Arctic sea ice / Re: MOSAiC news
« on: November 20, 2019, 11:44:36 AM »
Hefaistos calls our attention to another excellent BBC piece on the Akademic Fedorov trying to get home by Martha Henriques. It is best read in its entirety but a few highlights are being posted below:

How not to get stuck in the Arctic sea ice
https://www.bbc.com/future/article/20191114-how-mosaic-expedition-avoids-getting-stuck-in-arctic-sea-ice

Quote
News reaches us that boxes of kit and the Polarstern’s large gangway fell into a widening stretch of water.

Odd, no mention of this :( event at 'Follow_Mosaic' :). Possible allusion to it in Shupe's AGU blog. I struggled with 'boxes of kit'. Did the reporter mean boxes of clothes, unloaded scientific equipment or just stuff/things in general? Did they sink to the bottom of the sea or were they retrieved? Ditto the large gangway, loss of that leaves them stranded on or off ship, other than the mummy box chair unloaded by crane.

The Polarstern  is looking at a week of total blah weather ahead according to GFS. I don't expect any significant net drift; there's no indication of when or if the transpolar drift wind pattern will set up. Ice deformation can act from afar but I don't expect that this week because the millions of sq km of weak ice acts as a sponge that limits long range teleconnection of compression and extension.

However the Mosaic floe is looking very beat up after the storms and wind divergence on the two S1AB available for Nov 20th:

S1B   2019 11 20 T 06:02
S1B   2019 11 20 T 04:24

Quote
The AK rams the same piece of ice back and forth, maybe 70 times. The drift of the ice meanwhile carries the ship north. During those hours of ramming, the ship drifted so far   that it got back almost to its starting latitude to the north before we finally broke through.

Then the ship gets stuck a second time a few hours later and begins a second period of ramming. That’s when the captain decides to turn on the ship’s reserve engine. The Fedorov has four engines, but rarely uses all at once because this ramps up the ship’s fuel consumption. The fourth engine does the trick, helping the Fedorov break free again.
The captain really really did not want to get stuck for the winter in the ice. The ship is sitting unusually high in the water after the crew shifted scientific cargo onto the Polarstern plus 700 tons of diesel. The loss of weight left the Fedorov sitting so high in the water that the hull reinforcement area is now floating above the ice pack. The Fedorov is not a true icebreaker to begin with.

If the Fedorov were to get stuck, we would have two options: help from the Polarstern or hailing a nuclear-powered icebreaker such as the Yamal. "They are all busy and you don’t know when you will get one. And of course they are very, very expensive.”

The photo below shows how the 25 m wake sealed up almost immediately. The ship was in a compressive regime so ridging was almost immediate.

50
Arctic sea ice / Re: MOSAiC news
« on: November 20, 2019, 10:59:02 AM »
Quote
That's disturbing: not really seeing ice thickening at PS location on Cryo2Smos
Here the time series are using 26 rolling weekly averages according to the Cryosat2 freeboard  / Smos thinness merger of observational ice thickness. There is some thickening over this period in the 0.8 to 1.2 m range. Oddly the ice is thicker to the southeast of the Polarstern's position.

It's hard to say whether that is notably fast or slow relative to past years because there's no long term consistent data set using these satellites and the refined merger algorithm.

Mosaic, in their floe planning, expected to find 1.2m ice here back on October 5th. That is 17 days before the first data frame here and 43 days before the final frame (which has finally attained that thickness). So it's probably fair to say that 1.2 m thickness is quite late.

20191111_20191117
...
20191016_20191022

Technical note: after setting the rectangle bounding the Polarstern's drift over these dates (using locations in the S1AB database from sailwx), set the color picker in Gimp to radius 5 which will fill the bounding box and take the average. Then fill a small overlaid rectangle with this color and pick the whole image with the non-contiguous color selector, capturing the local selection on the palette bar after adding 0.05 m subdivisions from the grid tool. The desired product (ice thickness growth in the Polarstern's vicinity) is then the animation of the palette bar. This could be done on the original png file without the -45º rotation to 'Greenland down' or better still by utilizing the nicely done netCDF file in Panoply which includes error estimates etc and has the option of exporting and analyzing numeric values of the equal area projection pixels. However this won't change bottom-line talking points obtained from much faster image analysis.

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