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Messages - A-Team

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Consequences / Re: COVID-19
« on: March 14, 2020, 12:58:43 AM »
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: 

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.

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?

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.

Consequences / Re: COVID-19
« on: March 13, 2020, 10:04:25 PM »
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!


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.

Consequences / Re: COVID-19
« on: March 13, 2020, 05:16:39 PM »
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...."

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.

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.)

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.

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

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.

"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."

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).

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.

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

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:

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. 21 Jan 2020 discovery of furin site (in Chinese) images and structural analysis AC Walls et al French paper on furin site real furin motifs are longer GISAIS metadata for 93 genomes RNA recombination remdesivir L and S clades early paper

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.

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).

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).

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.

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

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).

Arctic sea ice / Re: MOSAiC news
« on: February 26, 2020, 04:52:04 PM »
Is the Polarstern close to the North Pole?
No. It was at 88.5044  41.20 this morning which is as close to the pole as it will ever get, 166.3 km away. To see what happens next, load grid-on nullschool with the lat lon for Polarstern from awiMet and draw radial latitudinal and tangential longitudinal components of wind stress as shown below. The PS will be moving south and west at 3:1 proportions, with longitude losing 0.2º per hour (1.450 km/hr).
A quick look at overall buoy drift for feb1-24. Quite a lot of dropouts recently.
Using the IABP buoy archive, there appear to be 79 working buoys (reporting on 25-27 Feb) and 31 that have failed (not reported in a  week or more).

The ones closest to the Polarstern can be found by first sorting the attached database for those closest to the ship in longitude, then sorting that subset by latitude which is more important to closeness.

300434063387850   SIMB3       Dart     MOSAiC   88.51   43.31   6.1 km
300234068225020   IT          OSU      MOSAiC   88.51   43.32   6.2 km
300234066081140   Snow_Buoy   AWI      MOSAiC   88.51   43.32   5.8 km
       -+-          -+-       -+-        PS     88.50   41.20
300234068705730   SIMBA       PRIC     MOSAiC   88.50   43.20   5.8 km
300234066081170   Snow_Buoy   AWI      MOSAiC   88.49   33.28  23.1 km
300234068917830   IT          OSU      MOSAiC   88.49   35.43  16.9 km

Arctic sea ice / Re: MOSAiC news
« on: February 26, 2020, 12:50:44 PM »
Indeed, the variable rate of KD closing on the Polarstern in this morning can be measured (in units of pxls/51 min in the 34 frames of uniq's #651), 72 km to go. Question is, does the KD have enough fuel to get back to Norway a week from now?

If the KD can maintain a speed of 1 knot above the ice pack drift, that would be two days for a rendezvous on Feb 28/Mar 01 to the south and west of the PS's current location at 88.50 41.2 at 07:42 this morning.

Winds are fairly strong right now at 12 m/s. That will complicate or even delay crane unloading for a few days though not personnel swapping. The Polarstern is currently a bit to the right and below the pole hole of Sic-Leads but is drifting into the currently active fracture zone.

Arctic sea ice / Re: MOSAiC news
« on: February 25, 2020, 05:48:55 PM »
We're getting mixed signals at the moment: is the KD stuck or just proceeding slowly, has it already exhausted so much fuel it cannot get back to Norway, is another icebreaker passing by in the vicinity capable of refueling it? Both bloggers onboard have gone silent.

The Rammb frames on which both ships are visible do not show the KD closing on the PS. That is consistent with either the KD being stuck or just making very slow progress.

The "Kapitan Dranitsyn" supply icebreaker is barely making any progress. "The mood on board the Polarstern is very tense," said Chief Scientist Professor Christian Haas. "There is uncertainty as to how to proceed. The colleagues are disappointed that there is no foreseeable return soon.

But since mid-December the sea ice in the winter arctic has grown steadily, it is up to 160 centimeters thick and provided with many dense press ice ridges by stormy winds. Open and thin jobs are rare. And so the KD is struggling slowly - with such high energy consumption that the fuel will not be enough to return to Norway. 

Ideally the KD will reach PS in the next few days, the expedition blog led by the Bremerhaven Alfred Wegener Institute (AWI) says: "However, the weather and ice conditions are still adverse."

Markus Rex expects the KD to reach Polarstern in the next few days. It is only 50 nautical miles away.  She had made good progress in the past 24 hours. Rex says planes are also available in Canada. But better weather is also needed for their use.

Chief Christian Haas says  it was presumptuous to believe that in mid-February a conventionally operated ship would get to the central Arctic. There is no experience with it, not even with the "Kapitan Dranitsyn".

Haas believes that the winter journey should have been planned for a longer period than the two months planned. "Of course we have a luxury problem," he admits. Researchers today did not want to be away from home for longer than two or three months. "We are happy and excited to be here," emphasizes Haas. The food is also good. But the team is now very exhausted from work and is longing for a more relaxed time.
Will the PS reach the North Pole?
No. Forget the spaghetti models, just look at GFS wind. The ship is already below the pole and proceeding west and south where the transpolar drift will take over. Nothing in the recent past is relevant to the ice thinness and wind patterns this year. The circumpolar drift from the Laptev to Fram has been going on for many millennia.

Is it surprising the Mosaic floe contains sediment from the Siberian shelf?
No. Where else could the ice have formed, given its posted track from Ascat? If there is no dueling hypothesis, there is no information content.

On WorldView, the Laptev Sea can be seen to be awash in algal bloom and fine sediment (from between islands, from melting coastal and submerged yedoma, from Lena Delta) in late August (see early locked posts on this forum). The only surprise would be coarse sediment too dense to have been suspended long, indicating a role for land-fast ice.

As explained some years back by Pink Floyd, we don't need no education to answer such questions ("Another Brick in the Wall").

Arctic sea ice / Re: MOSAiC news
« on: February 24, 2020, 11:22:41 PM »
On Rammb, the 60 frame time series is needed, color the dot pairs you're sure of. The PS also responded to a change in wind bearing around the same time. The longitude of the KD can be estimated easily enough but latitude retrieval depends on including the outer 85º circle in the time series (on the extremely flighty Rammb display) so that the number of pixels to 87.5º can be measured to proportion the KD's location.

Since GFS nullschool gives the same wind speed and direction wherever you click (within reason), the KD and PS will have the same drift as long as neither is under steam. The short cut is just to count pixels between the two Rammb dots over time: if constant, the KD is still stuck.

It's interesting to read people onboard the PS are hoping the KD can get closer, needn't actually get to the PS. Presumably that makes multiple round trips a lot easier for the helicopters. The PS has two and the KD a larger one. Closer though means more problematic for the KD crew and leg2 scientists in terms of returning home, though possibly the outbound broken swath could be re-used.

Update: persistent strong winds over the last 36 hours are pushing the local icepack rapidly west, taking the Polarstern with it at a record clip of 0.4º lon/hr. More of the same is forecast for the  next 72 hours with an increasing southerly component.  The KD is no longer on a streamline to the PS but rather on a parallel one heading to the the FJL gap.
This will leave the PS at perhaps 88.3 20.0 by the first of March, leaving the ship 857 km from its 15 Oct 2020 final destination in near-prime transpolar drift position that could end the mission by the first of June some 4 1/2 months early.

Arctic sea ice / Re: MOSAiC news
« on: February 24, 2020, 09:08:20 PM »
The KD has gotten itself stuck and unstuck multiple times before. The question here is if they could, would they continue north to the Polarstern without enough fuel for the return trip in thick ice? They could perfectly well moor alongside the Polarstern and await the melt season.

This would be better for the scientific program. The KD itself does not carry the Pistenbullys necessary to plow an 1800 m wheeled airplane runway but an opportunity might arise for staff and crew exchanges.

If the KD cannot get itself unstuck, it might take several months to lease a heavy duty nuclear icebreaker that could escort the KD to the Polarstern or more likely back home. Most capable icebreakers are contracted out months or even years in advance; the KD is not in an emergency situation.

In the last few years the Kapitan Dranitsyn has been modified as a passenger vessel, with 49 outside cabins for 100 passengers. Public accommodation includes spacious lounges, bars, a heated swimming pool, gym, sauna, library and a small hospital. wiki
Air drops for both the KD and PS could bring in lighter essentials; these are a whole lot safer than multiple landings on ungroomed airstrips which could bring on emergencies for which there is no response.

One option not yet mentioned is for the more capable icebreaker Polarstern to fire up its engines, go free up the KD and perhaps escort it south a bit, do the exchanges, and return to wherever its current position has drifted. This would leave the power (and data collection) off for a prolonged period at deployment sites so more likely the many tons of irreplaceable scientific equipment would have to pulled in first.

This would entail an enormous amount of de-installation and re-installation work in high wind chill (but not dark) and seriously undermine the scientific mission. Alternatively a skeleton crew and generator could be left in a lifeboat equipped as shelter to keep things repaired and going.

Arctic sea ice / Re: MOSAiC news
« on: February 24, 2020, 05:18:18 PM »
Although RAMMB has been showing the Kapitan Dranitsin closing in on the rapidly drifting Polarstern by the end of February, visibility from above is often obscured by clouds. It now appears that the KD is stuck in the thicker colder ice nearer the pole (as predicted above), still 100 km from the PS.

That is not an impossible distance for helicopter exchange of leg2/leg3 scientists and for transfer of experimental matériel but flight conditions are currently far from acceptable: gale-force 15m/s at 15:00 at 88.6 53.3 on Feb 24th. The KD was able to un-stick itself returning last time by shifting fuel from port to starboard tanks.

Follow-Mosaic speaks of multiple Twin Otter landings maybe being feasible on unprepared airstrips at both the KD and PS sites but that potentially doubles down on catastrophic risks without resolving the underlying issues.

The KD was supposed to bring extra fuel to the PS but now it seems if the KD does that, it won't have enough fuel of its own to get back to Tromsø, so a relief icebreaker for the relief icebreaker has to be considered.

Both ships are provisioned for up to a year so scientific work can continue at least at the PS. Despite conditions, the ROV has been able to log over 80 km of undersea ice mapping, even photographing that ringed seal investigating another misaligned thermistor cable. (Because they couldn't find a suitable 'thermodynamic' floe back in October, the PS moored on a pressure ridge jumble.)

Something has gone wrong at the ice radar archive. The heavy white scale bar is now lying over the image, causing loss of data. This bar should never have been placed here as ample black space was available in the masked region. It has never been clear whether this represented compass NS; better had digital lat, lon and ship axis bearing been placed above a km length scale bar. All that was provided on the device screen but cropped out. The ice pack (and the embedded PS) may be rotating more than anticipated.

Meanwhile the PS is moving west at an extraordinary rate of 0.4 ºlon/hr, bringing it into an extreme fracturing zone caused by cyclones barreling in through the SV-FJL gap instead of the usual winter path up the Fram. This pattern has greatly enlarged the Fram intake funnel out beyond the north pole (as noted here last week), with even the Lincoln Sea ice being drawn in. The Polarstern will be located just to the right of the pole hole (ie 50º at nullschool) later this afternoon.

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?

Arctic sea ice / Re: MOSAiC news
« on: February 21, 2020, 01:03:21 PM »
leads and apparent wave structures move through the ice rather than with it
OsiSaf gives another view, more along the lines of wind-induced. Ascat over 81 days gives yet another perspective, of smooth flow.

The Polarstern will continue to move rapidly poleward and towards the Fram this week under the influence of cyclones passing over Greenland. If it does reach the pole, it may be stuck in that area for quite a while as that ice is off the transpolar drift in most years.

The ship is currently at record lat lon of 88.5 66.2 on 20-02-21 at 15:00 with warm persistent winds in the 13 m/s range which are borderline for outdoor work. The Kapitan Dranitsyn is 184.1 km (still a week away) as of noon today at 87.06 89.1, with progress reported slowed by the same storm. Neither ship will be visible on Sentinel over the next weeks though the wavy KD track is available at 04:50 this morning.

Arctic sea ice / Re: MOSAiC news
« on: February 20, 2020, 08:28:08 PM »
The Polarstern continues to drift rapidly north and west in high winds and driving snow associated with the warm wet cyclone moving slowly across the Arctic Basin from FJL. Staff is confined to the ship under these conditions which will persist for the next couple of days.

FoMo is reporting hazardous ice motion (creating snow-covered open water) but these leads are not yet showing on the PS bow radar. These will worsen because of the ice pack cannot follow the sharp curvature of the wind. Meanwhile on-ice instruments may need repair but cannot be serviced. On Feb 13th, the whole Central Observatory experienced a brief (unexplained) power blackout.

The KD is not showing on RAMMB because of cloud cover though the PS has been visible at times. Its location is not known because it does not post a weather report nor turn on its beacon. It is seeing similar weather to the PS and drifting along the same streamline. It may be possible to pick up on its Sentinel track from yesterday and find a current position.

Uniq provides the AMSR2 view on the freeze forum today #929:

The Polarstern continues to fly north and west under the cyclone. It is visible on RAMMB but the KD is not (nor does it provide its location).

Iain provides a WorldView visible animation of the CAA Perry ice bridge and compared to earlier years #925. That area has been monitored with an observatory of moorings for years.

The Barrow Strait Real Time Observatory: Under-ice Monitoring in the Canadian High Arctic Nov 2017

These can also be visualized using the new SIC lead product from L Kaleschke, the last 60 days below. Unfortunately it does not going any farther west than shown. He is on the KD and seemingly unreachable.

Arctic sea ice / Re: MOSAiC news
« on: February 19, 2020, 12:40:27 PM »
@CKatlein 6h Finally our resupply icebreaker is so much delayed, that Polarstern has reopened the bar! #MOSAiC
That storm coming up from the Caribbean has morphed into a strong cyclone that is now predicted to drift across the FJL line into the Arctic basin and past close to the Polarstern as it gradually dissipates, even as a new system comes in.

This will significantly complicate the rendezvous of the KD and Polarstern as their drifts will be affected differently. At these stronger wind stress gradients, the Ice Camp experimental area may have more problems with pressure ridges, opening leads and shear lines. So far ice motion has been limited to shears on the periphery. (Much higher winds occurred earlier on the drift: 20-02-01 20 m/s.)

The KD appears to be at 86.4771  89.8613 at 05:55 this morning though the track on Sentinel is ambiguous and Rammb is cloudy. If so, with the Polarstern at 88.25  74.4 and moving rapidly west, the two ships are separated by 211 km with a rendezvous maybe ten days off.

Temperatures have already risen by 15º and winds are quite a bit stronger than GFS had foreseen yesterday (or rather, the discrepancy between observed shipboard winds and GFS winds has widened). These temperatures per se are still too cold and transient to melt ice but the Kara/Barents/FJL ice will be greatly dispersed and disrupted.

   Lat  Long  YY-MM-DD  UTC     Wind       T(C)   hPa      GFS
  88.3   71.6 20-02-19 19:00   14  110    -13.1  978.3
  88.3   71.8 20-02-19 18:00   13  110    -13.3  978.8  10.5  120
  88.3   72.0 20-02-19 17:00   13  100    -13.6  979.1
  88.3   72.2 20-02-19 16:00   13  100    -14.0  979.5
  88.3   72.4 20-02-19 15:00   14  100    -14.3  979.9  11.0  115
  88.3   72.6 20-02-19 14:00   14  100    -14.6  980.3
  88.3   72.8 20-02-19 13:00   14  100    -14.7  980.6
  88.3   73.0 20-02-19 12:00   15  110    -14.8  980.8  12.7  115
  88.2   73.5 20-02-19 10:00   16  110    -14.3  981.4
  88.2   73.7 20-02-19 09:00   16  110    -13.6  981.5  12.8  115
  88.2   73.9 20-02-19 08:00   16  110    -13.2  982.1
  88.2   74.4 20-02-19 06:00   16  100    -12.7  982.5  13.9  115
  88.2   74.6 20-02-19 05:00   14  110    -12.9  983.4
  88.2   74.8 20-02-19 04:00   15  100    -13.4  983.7
  88.2   75.0 20-02-19 03:00   14  100    -13.7  984.6  12.1  100
  88.2   75.2 20-02-19 02:00   12  100    -13.9  985.2
  88.2   75.4 20-02-19 01:00   12  110    -13.9  985.6
  88.2   75.5 20-02-19 00:00   12  110    -13.6  986.0  10.1  125 most recent bow radar
  88.2   75.7 20-02-18 23:00   12  110    -12.9  986.3
  88.2   75.8 20-02-18 22:00   12  110    -13.2  986.5
  88.2   75.9 20-02-18 21:00   12  110    -13.4  986.7  10.3  115
  88.2   76.1 20-02-18 20:00   13  110    -13.4  986.7
  88.1   76.3 20-02-18 18:00   11  110    -14.3  986.9  10.1  115
  88.1   76.4 20-02-18 17:00   11  110    -15.4  987.2

Arctic sea ice / Re: MOSAiC news
« on: February 18, 2020, 09:45:29 PM »
FoMo released a new map of the area around the ship today! It is reproduced below as their enlarged view 1696 x 1620 pixels (at which text is readable) so needs a click and large device screen. A dozen or two acronyms are not explained in the Legend.

No map scale is provided; however the PS measures 118 m, indicating the large squares are 500 m and the dotted smaller squares 100m.

There is no labelled lat lon graticule and north is not indicated as it varies with drift but is more or less at the top, going by recent S1AB with graticules. A near-vertical line of the grid system runs through something called nav(0,0) but the horizontal lines have no special relationship to nav(0,0). The grid appears set to be parallel / perpendicular to the Polarstern's bow-stern axis, which makes some sense the ice camp is accessed off the starboard side.

The map only includes 1000 pixels of the area mapped daily by the ice radar which points out 1310 pixels (2.5 km) from the bridge. Oddly an overlay of the bow radar does not have any features matching the runway.

The bluish-white base map appears to be heights determined by the laser altimeter patched together from helicopter overflights on different days. No scale (z axis) is provided but generally white indicates pressure ridges and surface ice jumbles. Some of these represent summer floe-building collisions and were already present at mooring back on Oct 4th; others are newer (not indicated despite symbols for leads and ridges in the legend).

Starting at the top left, the text overlays can be assigned png mouse-over x,y pixel coordinates and analyzed in a sortable database, sampler below and full csv attached.

The Remote Sensing site (RS on the map) acknowledged the loss of three instruments yesterday: KuKa, X-Scat and Elbara (a passive L-band 1.4 GHz smos-type radiometer). No spare parts are available on board, none are coming with the KD and implausibly by air on leg 4. (L Kaleschke's research involves Elbara; he is on the KD.)

No explanation has been given for three devices all failing (unsuitable connectors? power supply is from the PS). UWBRAD, an ultra-wideband 0.5–2GHz radiometer, is still working as is the SSMI radiometer (19, 37, 89 GHz) and the GNSS-R.

This is a major loss for remote sensing improvement. No summary of total trip up-time been provided. J Stroeve wrote about problems back on Dec 1st, tweeting "Our radar is once again connected to the power while some instruments are still awaiting connection."

The map term GNSS occurs in three places. Probably GNSS-R was intended for reflected GNSS signals from snow/ice  which relate to ice thickness, altimetry and scatterometry of various types of satellite GPS-like signals. pg 87

Technical inspection of the new map establish it as a disturbingly amateurish product given its importance to operation planning and communications. Surely a shipload of scientists on a $150,000,000 budget stuck on board for days at a time by weather could muster up someone onboard or ashore with basic graphics skills (such as editable layer compositing). They will need a journal-quality map later ... and this is not it.

Arctic sea ice / Re: MOSAiC news
« on: February 18, 2020, 08:52:21 PM »
Earthquake M 5.2 - North of Svalbard  2020-02-18   85.740°N 22.699°
This site is called the Sparsely Magmatic Zone (SMZ) of the Gakkel Ridge. Only one large volcanic center at 19° E has been noted over the entire extent of this segment.

JD calculated years ago on another forum that even when the volcano field erupted a bit east in the Eastern Volcanic Zone (EVZ), the amount of heat released was utterly inconsequential as far as melting Arctic Ocean ice or even for turbulent disruption of the salinity and thermal layers.

Did the 1999 earthquake swarm on Gakkel Ridge open a volcanic conduit?

In 1999, a seismic swarm of 237 teleseismically recorded events marked a submarine eruption along the Arctic Gakkel Ridge, later on also analyzed by sonar, bathymetric, hydrothermal, and local seismic studies... We find event locations scattered around 85°35′ N and 85° E at the southern rift wall and inside the rift valley of the Gakkel Ridge. seismic station on FJL 35 year earthquake record

Arctic sea ice / Re: MOSAiC news
« on: February 18, 2020, 03:09:25 PM »
New snowbuoy 2020S99. A touch south east of p207.
"This buoy replaces 2019S92, which was crashed during a ridging event." Does that mean inactive 82, 83, 85, 88-91, 95, 97, 98 met similar fates?

On the inactive snowbuoy setting, they only show 2019S95 which was operative for 6 days at the M7 site co-deployed with 2019O7 and 2019T71:

2019S79   86.00   119.17   07.10.19-28.11.19 (52)    
2019S80   85.96   122.71   08.10.19-02.11.19 (26)
2019S92   86.04   117.73   07.10.19-26.11.19 (50)
2019S95   84.62   133.29   11.10.19-17.10.19 (6)

2019S81   88.25   85.17   07.10.19
2019S84   86.49   109.32   07.10.19
2019S86   88.16   69.44   10.10.19       
2019S87   88.40   81.98   09.10.19       
2019S93   88.04   80.39   07.10.19       
2019S94   88.20   74.00   10.10.19    
2019S96   88.08   77.50   29.10.19
2020S99   87.96   75.37   10.02.20

"2019S92 was at the L1 site, co-deployed with 2019R9, 2019W4, 2019I1, 2019F1, 2019T67, one ASFS, one MARC" so we could determine from S92 where the mysterious L1 site is relative to the Polarstern.

Ditto 2019S93 which was co-deployed at L2 with 2019R8, 2019W2, 2019I2, 2019T63, 2019T65, 2019F2, ASFS, MARC

The ASFS (Shure's sonic atmo sled, see above) that "got eaten by a pressure ridge" was at L3. They got that unburied on 15 Feb 2020 according to FoMo but it is not yet functioning. At the L1-3 sites, they are trying to do air, ice, ocean in coordination so it hurts to have a major component down.

2019S94 was co-deployed at L3 with 2019M30, 2019W3, 2019T70, 2019I3, 2019F3, ASFS, UNMANNED-ICE-PRIC

Today at 03:00 the L2 site was at lat lon 88.0420  80.3936 whereas the PS was at 88.1  77.9 per awiMET which is 11.4 km away. The PS can be located slightly better using RAMMB (at 03:27 at 88.074  77.85) which is 10.21 km away but the last known precise location for the PS from S1AB was on 2020 02 02 at 05:46 87.3446   95.4993.

Given a similar calculation for L1 and L3, the three lines could be visualized on GoogEarth where they would not quite radiate out consistently from the PS location because of error but be very close to displaying the overall configuration. Following the L123 triangle over time would show rotation.

Although difficult to see on Sentinel, the KD is still 263 km away from the Polarstern but winds remain moderate (despite the nearby 953 hPa low) and ice pack motion is favorable for trajectory convergence. It's not unusual for ships and explorers get caught on a treadmill where despite a whole day's effort, they make no progress towards their goal. That's not happening here (to the extent the KD can make headway).

Arctic sea ice / Re: MOSAiC news
« on: February 17, 2020, 05:05:42 PM »
The KD has been making better progress north, aided by ice pack drift. A long section of track is outlined in yellow in the gif below, needs click. Meanwhile the Polarstern is drifting west. The extreme low pressure system coming to the Barents will have little effect on winds which will remain sub-gale force.

Arctic sea ice / Re: MOSAiC news
« on: February 16, 2020, 08:37:59 PM »
publish diary as text
The concept: a hardy explorer pecking out a diary on a courier typewriter like in days of olde? Nansen had electric lights already on the Fram. The PS has two bars, a sauna and a swimming pool.

Meanwhile, the Kapitan Dranitsyn has advanced 34.7 km in the last 21 hours. Not all of it was in the direction of the Polarstern,  only about 14 km. The zigzag route yields an effective linear approach speed of 16 km/day which means 18 more days till docking with the Polarstern, say early March. And delays will be similar or worse for those returning to Tromsø.

Because the ice is drifting, getting to the Polarstern is like crossing a river: start quite a ways upstream, not right across. That's not an easy calculation though, a lot of imponderables:

If the KD is moving at x(t) m/s at bearing a(t) under steam but the ice around it is drifting y(t) m/s at bearing b(t), how many days does it take, given the GFS wind forecast f(t) to reach the PS which is not under steam but has been drifting at z(t) m/s at bearing c(t)? Nansen's rule of thumb was the icepack drifts at 2% of the wind speed at an angle of 20-40% to it from the Coriolis effect.

The KD is probably not doing the math here but instead just seeking a pragmatic route that avoids thickest pressure ridges. Those could be more prevalent than in the past because ice pack motion has gotten measurably worse.

Meanwhile, the current Polarstern scientific team is still deploying equipment 4.5 months after mooring. These instruments have to installed far from the lights of the ship which would disturb what they are trying to measure. The location has not been disclosed. The acronyms ITBOB, ENVI-POPE and AZFP stand for:

-- Ice-tethered bio-optical properties and radiation
-- Platform  cluster for Optical,  Physical and Ecological sensors
-- Acoustic Zooplankton Fish Profiler

Arctic sea ice / Re: MOSAiC news
« on: February 16, 2020, 11:30:02 AM »
If anyone is good in Danish
So bizarre: providing routine blog text only as a png image. It just takes a second though to run it through free online Danish OCR ( and then google-translate.

"Tomorrow there is a general clean-up and a single trip out on the ice to drill cores in the EMIRAD measurement area near the ship.

The other morning, when I was with the chemistry team at the "dark site" and taking samples, I saw a slight light to the south on the horizon. "Dark site" is so far from the ship that there is no light pollution, and therefore you can see even the faintest shades of light.

I took a picture of the horizon with my mobile camera, but when I got home and looked at the picture, it looked like I had turned off the phone. It was completely black and there was no hint of light. The sun is still far below the horizon, and it's not even twilight, but we've got the moon back and it gives some light when we're out.

Last weekend we had a strong low pressure with strong winds and temperature fluctuations. Saturday morning started with blizzard and 20 m / s and temperature of about -12 degrees.
During the day the wind subsided while the temperature dropped to -38 degrees towards evening.

The captain had forbidden going out on the ice in the morning, and I spent most of the day in the "cold lab" working with ice samples from our measuring range. "Cold lab" is a container on the back deck which is designed for laboratory. The laboratory has -15 degrees, so you can work with your snow and ice samples without melting. Compared to the outside temperature, it feels warm in the lab.

I am working on mapping the composition of the ice cream; the size and distribution of air bubbles and the distribution of salt in the ice. It affects what we measure with our satellite instruments, which is why it is important to be able to develop computer models.

There is still some wind, but the temperature was only -15 degrees when we were out digging our instruments out of the drivers."

R Tonboe has an English language twitter site but has not posted anything since 27 Nov 19. His interests with Mosaics are remote sensing, ice team and ESA radiometer. His 2019-20 papers:

Version 2 of the EUMETSAT OSI SAF and ESA CCI sea-ice concentration climate data records

In situ observed relationships between snow and ice surface skin temperatures and 2 m air temperatures in the Arctic

Estimating the snow depth, the snow–ice interface temperature, and the effective temperature of Arctic sea ice using Advanced Microwave Scanning

Will low primary production rates in the Amundsen Basin (Arctic Ocean) remain low in a future ice-free setting, and what governs this production?

Estimating sea ice parameters

Satellite passive microwave sea-ice concentration data set intercomparison: closed ice and ship-based observations

SMOS-HR: A high resolution L-band passive radiometer for Earth science and applications
The Kapitan Dranitsyn is not making much forward motion today. It is visible on the animation up to about 06:00 on Feb 16th. It is a challenge to meet up not only because of the ice but because the  two ships experience different (and changing) drift trajectories.

Arctic sea ice / Re: MOSAiC news
« on: February 15, 2020, 01:32:16 PM »
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.

Arctic sea ice / Re: MOSAiC news
« on: February 14, 2020, 08:48:09 PM »
cancelled procurement of a new polar research vessel, Polarstern II  for legal reasons
Perhaps the language was such that only a German firm could win the contract?

@CKatlein 5h  [20-02-14 13:00 UTC]
Exchange between #MOSAiC leg 2 and 3 was planned for tomorrow (15 Feb).
However the supply icebreaker is still 168 miles away [270 km] and in the last
hour moved less than 1000m
. #naturewins

In other words, the KD is practically stuck with 270 km of much thicker ice to cross (though pressure ridges may be the problem this year, not the thermodynamically thickened). At this rate, the KD is 270 hours away (15.4 days) except that's optimistic since the Polarstern drifted 20.4 km away in the last 29 hours.

S1AB today should show the KD's track, except there may not be one if the previous track has sealed over and they are not making a new one. We know more or less where to look from S Arnd's post the other day about crossing 85ºN. Believe that's it's track below 85.1461 80.6331 at 05:47 on 14 Feb 2020. The Polarstern was at 88.0 80.9 at that hour.

If abrupt wind stress gradients matter for disruption of the ice pack, the PS bow radar tomorrow could be interesting in terms of shear.

Technical note: despite the PS not disclosing its position and no S1AB coverage, when there is a break from in the latitude decimal, it means the ship crossed 87.9000 and 88.0000 parallels, though in the latter instance, the PS didn't transmit its weather for 3 hours.

88.0   84.8 20-02-13 08:00   13  110    -28.9
87.9   85.3 20-02-13 05:00   13  110    -28.8

87.9   88.3 20-02-12 03:00    9  110    -31.9
87.8   88.4 20-02-12 02:00    9  110    -31.7

Arctic sea ice / Re: MOSAiC news
« on: February 14, 2020, 03:45:37 PM »
Given the lack of scales, it is very difficult to make out what is what on the surface and undersides of the Mosaic floe from the youtube provided. In particular, the top priority area is really in front of the bow radar, covered every six hours since 01 Nov 19 but not yet interpreted. Met City etc aren't located; the sensor area is already illuminated by nautical twilight.

This would have been better done as side by side hill-shaded digital elevation models or as user-controlled joy stick as done for surface and basement rocks of some Greenland glaciers. One issue is the very different scales -- the surface heights being about a ninth of underwater keel depths. This alone is a good reason for just providing unadorned grayscale DEMs and letting users take it from there. The attached mp4 reverses colors as the blue is harder to follow than its orange.

The Polarstern, after a prolonged episode of high winds and rapid motion, is now becalmed at 88.0 80.3 at noon on 20-02-14 UTC. The passage across the outer arm of the Chukchi anti-cyclone at about midnight on Feb 14th may have resulted in shearing but that won't show until tomorrow. The bow radar is swinging wildly suggesting that one or more sea ice anchors have come undone in the prolonged 14-15 m/s winds.

Looking ahead to the extreme low pressure in FJL, that is not foreseen to result in extreme winds at the Polarstern's position. A sharp gradient to nearby high pressure is needed for strong winds.

showing most Mosaic IABP buoys
The overlay of 14 days of Sic_Leads to Feb 13th  shows the sea ice motion over the buoy triangulation...

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   /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.

Arctic sea ice / Re: MOSAiC news
« on: February 13, 2020, 09:00:10 PM »
If so, the KD is still 3º of latitude away from the PS so 330 km plus some longitude; going will be slower in thicker ice and 15 m/s wind so maybe 1 km/hr or ~336 hrs which is 14 days, a lot later than planned. The KD was held up by Barents waves for a week or more. Leads cannot be assumed to stay open under conditions of compressive stress and pressure ridges are everywhere this year. Both ships will be in the pole hole of most satellites for weeks.

2h @CKatlein
Today we had a short power blackout in the Central Observatory of
MOSAiC, anyways all heaters are running and all systems are warm and
cozy again. Strong winds mostly kept us inside the vessel for the day.
Feb 12
While our supply icebreaker is still 200 miles away making 1-2 knots [2.8 km
hr], we get to experience the first twilight at 87.8° N. The  icedrift takes us
further north with a speed of 0.3 knots [0.6 km/hr]

The buoy array data is already being used, as it should, to study error in various sea ice motion products. Is TL is aware of or using the Sic-Leads product yet?

What we have discovered so far, which is something really new, is how salt from ice gets into snow. We knew that snow can be very salty, but now we have pictures of pockets of brine water in snow. This is important for how snow looks from space. It means that it looks more similar to sea ice.We might think that the ice is getting thicker where, in reality, there's just more (salty) snow on it. Then we have an error in estimates.
Please. This was known and published long ago, just google upward extrusion of brine pockets in maturing sea ice. Yes, this could improve satellite interpretation if only we knew where and how much.

Arctic sea ice / Re: MOSAiC news
« on: February 13, 2020, 04:57:28 PM »
MOSAIC_AUDI :) L :) G B :) :) K
Weird that they don't provide the date of the interview. A couple of weeks old?
Furious winds in seven days according to ECMWF
That gradient would give rise to a strong CCW cyclonic push towards the Fram. The last of the CW circulation right now is sending the Polarstern that way at a rapid clip. GFS foresees another 18 hours of this before the ship is becalmed and even moves back the other way. Bow radar has been uneventful so far during this run towards Svalbard.

The new SIC-Leads product gives a considerably more nuanced picture of ice pack motion than gridded OsiSaf. The lead images are difficult to adjust though 'equalize' the grayscale histogram gives a quick over-exposed look that doesn't overlook the small cracks.

Arctic sea ice / Re: MOSAiC news
« on: February 12, 2020, 04:41:41 PM »
Polar coord directions are confusing! Winds from the south? Not terribly descriptive at Pole. Being straightened out on the earth ellipsoid would be quite uncomfortable.
One way to remember is the "Far East" (in the eurocentric view) is Asia. Western Europe is west of that though east of the US East Coast which is west of the UK.

It all revolves around the Greenwich meridian. That runs through the center of the Fram Strait west of Svalbard. Going CCW from there is east; CW is west. The Polarstern is steadily losing east longitude (0.1º per hour) because it is going west towards the 0º meridian. Our maps use 'Greenland down' which is 45º west rather than a 0º vertical.

The leg 1 Polarstern staff voted to have all their maps point north. Maybe we could vote, though the world would take little note, to make east west and west east and move the 0º meridian to Greenland? How would that work for the South Pole? Let's not go there.

The mp4 follows ultra-local bow ice motion during the time the Polarstern has been under steady tail winds straight from 110º (time frame of Uniq's #596). These winds will perhaps continue another 81 hours to 02/15/0000Z (it's 20-02-12 15:00 now).

The question is, where will the PS track be by then? 88.05 79ºE. Will there be extreme motion in the bow radar and if so, why then and not the last two days?

Arctic sea ice / Re: MOSAiC news
« on: February 12, 2020, 01:16:30 PM »
That is a surprisingly large westward component. And increasing, despite a steady wind bearing. Seems like is it 'should' have been more northerly with less of an eastward component.

Arctic sea ice / Re: MOSAiC news
« on: February 11, 2020, 09:24:59 PM »
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 ( 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.

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.

Arctic sea ice / Re: MOSAiC news
« on: February 10, 2020, 05:45:04 PM »
This seal is a very long ways from the nearest open water. No photo of it on FoMo today. Seals don't just dive and take their chances on finding the next open lead when they need to breathe -- so presumably a maintained breathing hole is near the Polarstern. Ringed seals will also use cracks and gaps in the ice cover (such as tracks from relief icebreakers?).

Ringed seals have 2.5 cm long claws on their fore-flippers and can dig holes through 2m ice. The ice at the ROV hole is just over a meter thick; maybe the seal will do a better job of keeping it open.

But how can they catch fish underwater in mid-winter when it is dark already on the ice surface  and much darker below? They hunt under the ice for schooling fishes (particularly polar cod) and pelagic invertebrates but possibly also copepods etc living on the underside of the ice probably using whiskers.

Six seal species live in the Arctic: harp, hooded, spotted, ribbon, ringed, bearded. The latter two use breathing holes in the ice. Most of the ringed seals' time is spent near shore ice, but their ability to maintain cone-shaped breathing holes—which the animals excavate in the ice using the claws of their front flippers—allows them to occupy areas much farther from the ice edge than other seals can reach. Physiological adaptations help them make deep, sustained dives, reaching depths of 300 feet and remaining submerged for up to 45 minutes. But before surfacing, they sometimes blow bubbles up their breathing hole to check for polar bears, their main predator.

Feb 4
Today we had a #seal in the #ROV hole, and a fish in the zooplankton net.
Almost the entire ecosystem, except the top predator... yet #icedrift
Feb 3: so was it strong or weak?
Today we measured #seaice strength with a Borehole Jack from #NTNU #icedrift

See: Engineering Properties of Sea Ice
Journal of Glaciology 19(81):499-531 1976
DOI: 10.1017/S0022143000029476

Feb 2: more gear sank:
After moving operations from yesterday to today due to windchills down
to -59°C, we were deploying sediment traps with the #ROV again.
Unfortunately one had to be sacrificed to Neptune.

126 buoys deployed, 87 time series available:

Während der MOSAiC Expedition wurden bereits 126 Bojen ausgebracht. Die Daten und Messzeitreihen [time series] von insgesamt 87 Bojen können jetzt schon über abgerufen werden. 

Arctic sea ice / Re: MOSAiC news
« on: February 10, 2020, 03:04:08 PM »
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.

Arctic sea ice / Re: MOSAiC news
« on: February 09, 2020, 02:16:08 PM »
KD is making good progress two hours later. It measures ice thickness, not by the silly system of people comparing a painted yardstick to overturned ice but by a EM induction instrument projected from the bow.

This totals thousands of km of swath data by now that would have helped in comparing various observational and model approaches to this key parameter. However the thickness will not be divulged until 2023 when no one will have the slightest interest. [We call this 'dog in the manger' science after an Aesop fable.]

The KD is in a dense coverage area of S1AB; however we won't see the PS and KD join up because the PS is going ever deeper in the pole hole this week to 88.0º.  We can expect the KD to use its previous track coming in so as not to create yet another damaging swath near the study area.

At the three L-sites within the MOSAiC Distributed Network (~15 km distant from Polarstern at the beginning), the project will install Atmospheric Surface Flux Stations (ASFS) that include measurements at 0-3m height of pressure, temperature, relative humidity, high-frequency three-dimensional winds, high-frequency water vapor and carbon dioxide concentrations, surface height (snow depth), surface infrared temperature, surface heat flux, and up- and down-welling longwave and shortwave radiation.

Adjacent to these atmospheric surface flux measurements at each of the four locations will be an ice mass balance buoy for measuring ice thickness and thermodynamic structure, and an Autonomous Ocean Flux Buoy for measuring ocean fluxes of heat, momentum, and salt. Jointly these measurements allow for a full documentation of the thermodynamic state of the sea ice.

Additionally, an array of GPS position buoys will be installed across the full MOSAiC Distributed Network to provide detailed information on ice dynamics.  page 36
The Polarstern lost an important piece of remotely deployed atmospheric flux equipment yesterday; unfortunately the Kapitan Dranitsyn is not bringing a replacement as it had already left before the pressure ridge occurred. Mosaic did not share the previous loss of function of this device, its earlier repairs, nor even its approximate current location.

This used up quite a bit of helicopter fuel; the KD will be bringing more. However between legs 3/4, only planes can reach the PS. The 1500m runway is very much in doubt currently due to constant development of pressure ridges, leads and offset shears. Planes are primarily for staff exchange; they cannot bring in fuel.

This hole by the gangplank ... what were they thinking? It freezes over from cold ice on the sides (so use 4x8 marine plywood insulated with foam) and from the cold air (use 8" foam board cover, not a complex flimsy tent that cannot be set up in wind). Any lumber yard in the US would have these. Immersion heaters? -- the hole is not even hot tub-sized and just a few meters from ship power supply. $29.95 per 3000W @ ebay.

We have seen so many times that gear testing back home (Bay of Bothnia? ice-fishing in Minnesota?) would have greatly reduced data downtime at Arctic drift sites. No record of downtime has been disclosed and never will be.

Arctic sea ice / Re: MOSAiC news
« on: February 08, 2020, 03:47:54 PM »
82.25N 68.77E, barely visible on the jpg
not sure how long this link to the jp2 viewer will last.
A lat lon time for KD on sailwx or cruise locators to remove white dot ambiguity and identify interlopers? Not seeing a swath, maybe seals up too fast or takes thicker ice or they've been in a lead.

Links last many months, unlike at the PolarView portal which only stores the jpg for 30 days. The url preserves the all-important auto-generated hexadecimal, here 46F8_N_1, which is essential to finding the big package on the awkward Copernicus Sentinel portal. The is a huge breakthrough for the end user.

I've safely archived all the jpgs and lossy jp2 links containing the Polarstern back to Oct 4th mooring. The attached cvs contains direct viewer links to all the jp2 scenes as well as to GFS weather of their date and hour.

Below all 373 scenes to date of Polarstern bow radar are collected in two mp4. The second of these (3x) examines the history of the peculiar area just in front of the bow that has seen bad shearing but has since been stable for months. These are uniformly brightened and sharpened with mild local contrast (CLAHE 63 1.75 in the montage).

Arctic sea ice / Re: MOSAiC news
« on: February 07, 2020, 05:10:51 PM »
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...

Arctic sea ice / Re: MOSAiC news
« on: February 07, 2020, 02:27:31 PM »
how are lat lon of Polarstern calculated from buoys and/or S1AB?
See update in #575. Buoy and ship positions dependnot only on ice pack drift but also on the timing of position reports relative to shears and other displacements which are of comparable scale.

The latest bow radar is showing significant ice pack motion at numerous sites within its viewing window that presumably are representative of a much broader area including the Mosaic experimental sites and beyond.

The 6-hour bow radar imagery is shown together with 6-hour GFS winds but understanding causation requires looking at large-scale two day ice movement on the Siberian side induced by the stationary anti-cyclone between Wrangel and NSI, as displayed well by the ANSRE leads resource.

The Polarstern's floe is being squeezed between two shear plates, the ice accommodates the stress on it by over-rafting into pressure ridges and keels. Analysis continued in #581...

Arctic sea ice / Re: MOSAiC news
« on: February 06, 2020, 08:59:38 PM »
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.

Arctic sea ice / Re: MOSAiC news
« on: February 05, 2020, 01:53:22 PM »
photo credit: Lukas Piotrowski
Here are 127 days of Ascat and AMSRE leads from Oct 1st to today. The Polarstern is currently about a third of the way from the pole to Severnaya Zemlya (87.5 95.0 20-02-05 09:00). It is feasible to overlay the leads and still see how the MYI ice on Ascat is drifting. Note the multiple origins of ice exiting the Fram.

The overlay of sea ice concentration derived leads on cry2smos derived thickness works well though thickness doesn't change much over the mid-Oct early-Feb time span. (Note only 103 days are available compared to 127 for Ascat and SIC leads because of a delayed start to cry2smos and delayed archiving necessity.) This new product AMSRE lead archive from L Kaleschke has enabled some important new visualizations.

No action today on the bow radar and none expected for the next few days as the ship drifts farther north and then east. The Polarstern will be within the pole hole of S1AB so no images will be available.

It would be instructive to make a one-day three-way comparison of infrared (#557 250m VIIRS brightness temperature, band I5 night), SIC leads and S1B. It is a little trickier to synchronize an overlay 24-hour leads on GFS nullschool winds which is 3-hour without file size getting out of hand.

Arctic sea ice / Re: MOSAiC news
« on: February 04, 2020, 08:52:04 PM »
The Polarstern has been on the job for 39 years. Its hull is designed to lift up when experiencing compressive forces from the sides. It's not clear what happens if the ship is torqued by forces at shearing angles. It has strain gauges welded on the lower hull but when frozen in, options are limited. Would the ship roll on its side or suffer structural damage?

In olden days, ships had  stout oak beams running abeam, seemingly crushproof. That design didn't end well for the Jeanette: 

On 7 Sep 1879, the ship became frozen in the ice at 71°N 175°E. For the next 21 months, Jeannette drifted in an erratic fashion, frequently doubling back on herself. On 12 June of 1881, the pressure of the ice crushed the Jeannette. De Long and his men unloaded provisions onto the ice and watched as the ship sank at 77°N 155°E [well south and east of the Polarstern).

Wreckage eventually came ashore on the central east coast of Greenland where it was discovered by Nansen on a field trip there. This inspired his theory idea of Transpolar Drift. It is evidence, along with carbon-dated beached logs at Morris Jesup, that the TPD (and Fram export) have been operative a very long time, even when the ice was much thicker and extensive than today.

Note the distinction: Transpolar Drift refers to surface ice blown by the wind; Fram export is return flow of Atlantic Water inflows that are ~300 m below the surface. The two often work together at the intake funnel of the Fram Strait at ~82º (East Greenland Current). Mosaic is tracking this double-diffusing Atlantic Water and its turbulent eddies at depth for the entire expedition.

However it's not immediately apparent from the buoy array tracks that the cw TPD -- which is air pressure pattern-dependent and ultimately driven by ccw earth rotation -- is operative this year.

The Beaufort Gyre, the other textbook staple, is still going around and around in the minds of True Believers despite irrefutable satellite evidence to the contrary. A Beaufort arm of floes derived from MYI ice off the CAA reaches up the AK coast to the Chukchi in most years but never completes a gyre. Today Beaufort winds are circulating in a nice gyre but in the wrong direction!

Arctic sea ice / Re: MOSAiC news
« on: February 04, 2020, 01:08:29 PM »
art of moving without moving
Art of back and forth on Feb 4th: The three bow radar scenes are best processed individually because of contrast variability extremes within the master frames. They are all from the same date, Feb 3rd. Some of the leads, shears and ridging may extend into the Mosaic ice camp experimental areas or impinge on the planned port side airstrip.

The new archive of Arctic-wide leads extracted daily from AMSR-E by L Kaleschke are shown with exaggerated contrast under land and graticule masks from AMSR2. The red star at 87.5 95.0 shows the approximate position of the Polarstern.

It is not currently possible to definitively relate new leads seen on the basin-wide scale with much smaller features that can be seen at bow radar resolution.

T Lavergne's OsiSaf shows ice motion at a similar scale as AMSR-E. The two aren't readily compared because OsiSaf needs two days of data to get one picture of motion; further the data is gridded meaning the features used in AI are not retained or displayed.

T Krumpen is on different legs of the Polarstern (1a AF + leg 4 vs leg 3) than Kaleschke but both work at AWI so it reasonable to expect sea ice motion products to be improved soon. (Not in summer though.)

No S1AB today. The Polarstern will soon be in its pole hole again (but not that of AMSRE leads), followed by a full day of Fram-ward drift, followed by becalmed. What might be called aTPD (accidental Transpolar Drift).

87.5   95.3 20-02-04 14:00    8  180    -27.4 latest SIC review of over-estimates

Arctic sea ice / Re: MOSAiC news
« on: February 03, 2020, 09:25:37 PM »
Drift may appear faster when hourly reports are missing
Slower? If the drift is A --> B  --> C  and the hourly is missing for position B, then the A --> C speed will be slower to the extent ABC are not co-linear (triangle inequality).

FoMo gave a dramatic example of this on Jan 14th (while omitting the key parameter, sampling interval). At a buoy track crossing, the difference in position (distance covered) is zero as is the speed but not the elapsed time.

The triangle inequality also holds on the surface of a sphere (or any Riemannian manifold) but lines have to be geodesics. The buoys are not constrained to move on geodesics (which become complicated in a hurry on the WGS ellipsoid).

Distances between two lat lon points are typically approximated with the sphere's haversine even if that geodesic doesn't follow along the actual buoy track. When the points are close (ten minute sample times, slow speeds, no jogs), the difference is utterly negligible and in fact ordinary lines on the euclidean tangent plane suffice.

The issue here is not the ice speed per se but how it got there, what keeps it there and what alters direction. In a situation like the central Arctic with negligible near-surface currents and tidal influences, this is mainly wind pushing on ridges but retarded by keels and drag with sea water.

Because of friction, there's no conservation of momentum: a floe in motion doesn't stay in motion. Kinetic energy is quickly being dissipated as (unnoticeable) heat.

Is there is such a thing as terminal velocity for ice (as for skydivers) and have we approached it during the Mosaic expedition. Yes, wind can't keep up with subsurface drag which goes up like the cube. No, because the 10-12 storms expected haven't happened; extreme winds so far have been south of Svalbard and east in the Barents.

Arctic sea ice / Re: MOSAiC news
« on: February 03, 2020, 04:44:37 PM »
arriving very close to last week's location
Very effective visually to have tracks speed up as the drift speeds up. The km/hr scale has tripled to accommodate actual data (next post); scales are not the same in different buoy animations. Km/hr is the appropriate unit here; it's hard to picture a floe moving even one meter per second (SI extremism?). For glaciers, m/d makes more sense (Jakobshavn got up to 51 m/d).

The question is, do the buoys show this behavior every year but we just don't notice because their motion is commonly dumbed down to weekly resolution? I would say no, the wind pattern has been very peculiar this year -- and that's about to continue with strong poleward motion turning east.

Been there, done that, doing it again:

  87.4   94.0 20-02-03 18:00
     87.4   93.9 20-02-03 17:00
         87.4   93.8 20-02-03 16:00
             87.4   93.7 20-02-03 14:00
                87.4   93.6 20-02-03 13:00
                   87.4   93.5 20-02-03 12:00
                      87.4   93.3 20-02-03 10:00
                          87.4   93.2 20-02-03 08:00
                          87.4   93.2 20-02-03 05:00
                      87.4   93.3 20-02-03 03:00
                   87.4   93.5 20-02-03 01:00
                 87.4   93.6 20-02-03 00:00
             87.4   93.7 20-02-02 23:00
         87.4   93.8 20-02-02 22:00
     87.4   93.9 20-02-02 21:00
  87.4   94.0 20-02-02 20:00

The lead openings and closings are very active on a day by day basis though not much of that shows up on the Polarstern bow radar. The new scale bars are multiples of the 118m ship's length as almost all activity is nearby.

The Polarstern was in range this morning for a 06:00 Sentinel at 87.4 93.2. PolarView is just now back from its near-daily breakdown; nothing north of 86.9 is showing.

Arctic sea ice / Re: MOSAiC news
« on: February 02, 2020, 04:43:43 PM »
A late S1AB surfaced for 06:02 on Jan 31st. The PS is at 87.4365 96.4841 on that image; the floe is quite altered in appearance. Some rifts are nearby that may have absorbed some of the wind stress.

The Polarstern (red asterisk) barely made it onto Sentinel coverage. The image is rotated 180º from PolarView to correspond better with Mosaic orientation. The blue arrow runs along the ship axis with starboard and port sides indicated. The bow radar points along this axis but is imaged as vertical. An extended rift (yellow arrows) possibly corresponds to a local shear line seen active above. The exit track of the KD is still visible as a white streak.

The second image is a composite of two consecutive Sentinel orbital scenes derived from the jp2 rather than the jpg. The blue ellipse shows a rift zone a ways from the Polarstern. This rift is difficult to date because coverage by Sentinel has been spotty with the ship dodging in and out of the pole hole in recent weeks.

Another S1AB just surfaced, for 02 Feb 2020. A remarkable rotation and translational drift of the Polarstern region took place during these 48 hours.

Arctic sea ice / Re: MOSAiC news
« on: February 02, 2020, 04:03:22 PM »
Some rapid drift south yesterday. PS has spent over 16 days in this area. Verify those leads!
It may not work that well to compare infrared (heat leaks) to radar (salinity, SIC). Leads freeze over within hours at the prevailing winter temperatures; that will affect the two images differently. The infrared image has much better resolution during cloud-free days.

A lot can be done with this AMSRE time series from L Kaleschke, including visualization of whole icepack drift about as well as Ascat. Both suffer somewhat from incoming weather systems.

The major cyclone is affecting the ice around the Polarstern at quite a few locations but so far not as severely as the Nov 19th storm. That didn't really give rise to major chaos until the 22nd.

On the bow radar, the Polarstern at 118 m in length scales to just 12 pixels in length. A few multiples of that radius would pick up most of the instrument sites, the test runway, CTD and ROV  holes and other observation sites. The 3x enlargement is about all the image quality allows after enhancement. Almost all of the starboard side gets masked out in the archive for unknown reasons (the radars can provide 360º coverage as seen in N-ICE2015 data).

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