Pages

Friday, June 23, 2023

The Third Pole Water Line - 2

The Boss Determines Water Level
In the first post of this series we focused on Pakistan in the context of "The Third Pole Water Line".

But there is more to it than that:

"Unprecedented and largely irreversible changes to the Hindu Kush Himalayan cryosphere, driven by global temperature rises, threaten two billion people and are accelerating species extinction.

ICIMOD’s new report – Water, Ice, Society, Ecosystems in the Hindu Kush Himalaya – is the most accurate assessment of changes to the Asia high mountain cryosphere to date. It is also the first time their impacts on water, biodiversity and society have been properly mapped.

The report urges policymakers to prepare for the cascading impacts of climate change in this critical mountain biome, which provides freshwater services to a quarter of the world’s population.

It calls for urgent international support and regional cooperation for inevitable, near-term loss and damage, and to help communities adapt."

(Snow and ice in the Hindu Kush Himalaya are fast disappearing, with grave implications for people and nature, emphasis added). Wow, everyone must be really into avoiding such a catastrophe eh?, and must be doing everything required to avoid it eh?:

"The world is falling well short of the progress needed to meet the United Nations’ sustainable development goals by 2030 in areas ranging from poverty to clean energy to biodiversity, with a growing gap between wealthy and developing nations, according to a report Tuesday from the nonprofit tracking the goals.

Ocean Heat

The coronavirus pandemic stalled the limited progress made in the years after United Nations member states adopted the goals in 2015. Now, halfway through the 15-year time frame, not a single one of the goals is on target to be met.

'We’re at the risk of a lost decade for sustainable development,' said Guillaume Lafortune, a lead author of the report and vice president and head of the Paris office of the Sustainable Development Solutions Network, the nonprofit launched by the UN to foster and track sustainable development. “And there’s actually a risk that the gap between rich and poor countries on sustainable development might be bigger in 2030 than it was in 2015.'"

(World well short of pace needed to meet UN’s 2030 sustainable development goals). Yikes ...

Meanwhile:

"On the heels of a new annual heat record set in 2022 — the latest in a string of record-setting years — average ocean surface temperatures around the globe have spiked since early March. Excluding polar regions, they are about two-tenths of a degree Celsius warmer than scientists have ever observed at this time of year via satellite data.

Translation: What might seem like a small uptick in temperature can have profound effects.

“Averaged over the planet, that’s a really big anomaly,” said Alex Sen Gupta, a research scientist at the Climate Change Research Center at the University of New South Wales in Australia."

...

"'You’ve got this relentless rise of greenhouse gases in the atmosphere,' said Michael McPhaden, a senior scientist at the National Oceanic and Atmospheric Administration. 'We just know unless that turns around in some way, we will continue to set records.'"

(What an ominous surge in ocean temperatures means for the planet). It is called "doing the same thing over and over while expecting a different result each time" (On The Origin of Genieology).

Yeah, that's the ticket (The Authoritarianism of Climate Change, Ice sheets can collapse at 600 metres a day, far faster than feared, study finds).

The previous post in this series is here.


"It wouldn't do to say ..."




Thursday, June 22, 2023

It's In The GenBank - 8

Fort Knox Mythology
I. Background

Previous to this post (It's In The GenBank - 7) Dredd Blog took a look at a small percentage of genome record errors involving a mismatch between the amino acids said to be associated with codons in the CDS segments in .GBFF files.

In other words, if in a range of nucleotides a codon therein was supposed to "code for" a particular amino acid, did the GenBank record have the correct amino acid listed in the "/translation=" section of that .gbff file?

Small percentages of errors have been discovered in public databases for many a year:

"Overall, we conclude that, as a conservative estimate, 1 in every 20 public database records is likelyto be corrupt. Our results support concerns recently expressed over the quality of the public repositories. With16S rRNA sequence data increasingly playing a dominant role in bacterial systematics and environmental biodiversity studies, it is vital that steps be taken to improve screening of sequences prior to submission." 

(At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies, 2005, emphasis added). Got 'science' (If science was perfect, it wouldn’t be science)?

The errors in that cited paper took an incredible amount of work to discover (ibid), however, the errors Dredd Blog is pointing are very easy to detect, and are not related to sample collection errors as was the case in the cited paper.

Anyway, the appendices in the previous version (A-K) are supplemented with Appendix L in today's post.

These translation errors are based solely on the data in GenBank sequence files, where a particular codon is not the codon that codes for the specified amino acid specified.

The errors could be a word processor user's typo, or any of several other causes.

The purpose of this post and the previous one in this series is not to determine the cause of the error, the purpose is simply to point out that some errors do exist in the public database arena.

Users should know how to detect and correct them prior to using them in any number of pursuits.

II. Closing Comments

The GenBank is a wonderful public database, and a wonderful public service.

Links have now been provided (HTTP, FTP, etc.) to that rich source of information concerning many microbial genomes found on our planet.

I hope it provides some benefits to Dredd Blog users. 

The previous post in this series is here.

Appendix L Genbank 8

This is an appendix to: It's In The GenBank - 8



GBFF '.seq' File Analysis
of Translation | CDS Data
and Amino Acid - Codon
Mismatches

GenBank File
and/or Version
Translation|
CDS Counts
AA - Codon
Mismatches
'gbvrl522'
OP626104.1
83|83 4
OP626105.1 83|83 8
OP626106.1 83|83 15
OP626108.1 83|83 7
OP626109.1 83|83 16
OP626110.1 83|83 20
OP626112.1 83|83 5
OP626113.1 83|83 8
OP626114.1 83|83 5
OP626115.1 83|83 3
OP626116.1 83|83 6
OP626117.1 83|83 10
OP626118.1 83|83 19
OP626121.1 83|83 10
OP626122.1 83|83 7
OP626123.1 83|83 4
OP626124.1 83|83 11
OP626125.1 83|83 12
OP626126.1 83|83 24
OP626127.1 83|83 6
OP626128.1 83|83 35
OP626130.1 82|82 18
OP626132.1 83|83 19
OP626133.1 83|83 55
OP626134.1 83|83 19
OP626135.1 83|83 24
OP626136.1 82|82 7
OP626137.1 83|83 7
OP626138.1 83|83 7
OP626139.1 83|83 19
'gbvrl559'
OQ261707.1
83|83 37
'gbvrl521'
OP612151.1
79|79 1
'gbvrl494'
OP263627.1
83|83 6
OP263629.1 83|83 8
OP263633.1 83|83 2
OP263634.1 83|83 1
'gbvrt51'
KM273123.1
13|13 208
KP164983.1 13|13 208
'gbvrt264'
MT554046.1
11|11 232
'gbvrt262'
MN248535.1
12|12 251
MN869009.1 11|11 219
'gbvrl503'
OP373388.1
83|83 23
OP373392.1 83|83 14
OP378697.1 82|82 1
'gbvrl512'
OP484340.1
82|82 2
OP484341.1 83|83 8
OP484666.1 83|83 56
OP484667.1 83|83 1
OP484669.1 83|83 9
OP484670.1 83|83 12
OP484676.1 82|82 25
OP484677.1 83|83 7
OP484679.1 81|81 12
OP484684.1 83|83 59
OP484687.1 83|83 6
OP484691.1 83|83 8
OP484694.1 83|83 1
OP484695.1 83|83 14
OP484696.1 82|82 18
'gbvrl511'
OP459202.1
82|82 1
'gbvrl538'
OP881941.1
82|82 1
'gbvrl526'
OP687940.1
82|82 4
OP687941.1 82|82 1
OP687942.1 82|82 1
OP687949.1 82|82 1
OP689666.1 83|83 4
OP689667.1 83|83 57
OP689668.1 83|83 11
OP689669.1 83|83 5
OP689670.1 83|83 5
OP689674.1 83|83 11
OP689675.1 83|83 20
OP689677.1 83|83 30
OP689678.1 83|83 20
OP689681.1 83|83 6
OP689685.1 83|83 4
OP696840.1 72|72 17
'gbvrt266'
ON920705.1
12|12 213
OP326280.1 11|11 94
'gbvrl584'
OQ721925.1
82|82 1
OQ721929.1 81|81 1
OQ721930.1 82|82 1
OQ725698.1 12|12 4279
'gbvrl565'
OQ349200.1
6|6 4475
OQ349202.1 6|6 4476
'gbvrl515'
OP523979.1
83|83 17
OP523983.1 83|83 27
OP523989.1 83|83 20
OP523993.1 83|83 26
OP523995.1 83|83 26
OP523998.1 83|83 2
OP523999.1 83|83 12
OP524001.1 83|83 7
OP524007.1 83|83 1
OP526855.1 82|82 86
OP526861.1 79|79 1
OP536686.2 83|83 3
OP536688.2 83|83 3
OP536697.2 83|83 3
OP536702.2 83|83 4
OP536704.2 83|83 7
OP536709.2 83|83 2
OP536711.2 83|83 4
OP536712.2 83|83 1
OP536713.2 83|83 5
OP536718.2 83|83 19
OP536731.2 83|83 2
OP536732.2 83|83 3
OP536737.2 83|83 3
OP536738.2 83|83 1
OP536740.2 83|83 2
OP536742.2 83|83 5
OP536745.2 83|83 4
'gbvrt55'
KX644918.1
12|12 253
'gbvrt261'
MH481133.1
12|12 255
MK460224.1 14|14 230
MK483118.1 11|11 165
'gbvrl531'
OP776338.1
10|10 4404
OP776339.1 10|10 4393
OP776340.1 10|10 4392
'gbvrt47'
JX181763.1
13|13 185
'gbvrt53'
KU237286.1
11|11 232
'gbvrl528'
OP715818.1
83|83 8
OP715819.1 83|83 12
OP715820.1 82|82 21
OP715821.1 83|83 13
OP715822.1 83|83 13
OP715823.1 83|83 20
OP715825.1 83|83 7
OP715829.1 82|82 8
OP715831.1 83|83 16
OP715833.1 83|83 26
OP715834.1 83|83 5
OP715835.1 83|83 7
OP727820.1 83|83 3
OP727823.1 83|83 24
'gbvrt265'
MZ043820.1
12|12 199
OK587334.1 12|12 224
OK638184.1 12|12 254
'gbvrl583'
OQ702766.1
81|81 1
'gbvrl524'
OP650029.1
82|82 7
'gbvrt57'
LC648429.1
12|12 281
LC648431.1 12|12 303
LC648432.1 12|12 311
LC706451.1 12|12 216
'gbvrl500'
OP339848.1
83|83 1
OP339850.1 82|82 27
OP339855.1 82|82 19
'gbvrl546'
OQ054223.1
82|82 3
OQ054225.1 82|82 1
OQ054241.1 82|82 1
'gbvrl490'
OP205067.1
83|83 2
OP205072.1 83|83 1
OP205074.1 83|83 1
OP205083.1 83|83 6
OP205084.1 83|83 47
OP205087.1 83|83 15
OP205088.1 83|83 43
OP205090.1 83|83 1
OP205093.1 83|83 1
OP205098.1 83|83 3
OP205105.1 83|83 1
OP205106.1 83|83 5
OP205110.1 83|83 1
OP205112.1 83|83 1
OP205118.1 83|83 1
OP205125.1 83|83 1
OP205133.1 83|83 1
OP205134.1 83|83 1
OP205135.1 83|83 3
OP205136.1 83|83 1
OP205137.1 83|83 1
OP215280.1 82|82 26
OP215287.1 83|83 2
'gbvrl535'
OP837334.1
83|83 7
OP837335.1 83|83 9
OP837336.1 83|83 22
OP837337.1 83|83 8
OP837338.1 83|83 24
OP837339.1 83|83 1
OP837341.1 83|83 27
OP837342.1 83|83 64
OP837345.1 83|83 14
OP837349.1 83|83 10
OP837350.1 83|83 13
OP837351.1 83|83 13
OP837352.1 83|83 16
'gbvrt50'
KF482070.1
12|12 244
KF840516.1 12|12 210
KJ190949.1 11|11 225
KJ190955.1 11|11 236
'gbvrl551'
OQ117368.1
10|10 1562
'gbvrl550'
OQ102159.1
9|9 3582
'gbvrt40'
EF626812.1
12|12 268
EF626813.1 13|13 293
EF626814.1 13|13 290
EF626815.1 13|13 296
EF626816.1 13|13 294
EF626817.1 12|12 269
'gbvrl570'
OQ419006.1
83|83 49
OQ419053.1 83|83 51
OQ419091.1 83|83 19
OQ427114.1 82|82 1
OQ427117.1 82|82 1
OQ427132.1 82|82 2
OQ427140.1 82|82 2
OQ427152.1 82|82 2
'gbvrl497'
OP296992.1
10|10 5341
OP303783.1 82|82 1
OP303795.1 81|81 1
'gbvrl572'
OQ451894.1
83|83 1
OQ451896.1 83|83 12
OQ451897.1 83|83 1
'gbvrl520'
OP594192.1
83|83 21
OP594193.1 83|83 27
OP594195.1 83|83 47
OP594203.1 83|83 1
OP594207.1 83|83 13
OP603002.1 82|82 9
OP603003.1 82|82 2
OP603008.1 82|82 1
OP603014.1 82|82 3
'gbvrl575'
OQ541850.1
9|9 5408
OQ547740.1 7|7 3609
OQ551110.1 6|6 1271
'gbvrt56'
LC498571.1
12|12 250
LC498572.1 12|12 221
LC565708.1 12|12 242
'gbvrl530'
OP764614.1
83|83 3
OP764615.1 82|82 28
OP764616.1 83|83 7
OP764617.1 83|83 35
OP764618.1 83|83 5
OP764619.1 83|83 11
OP764621.1 83|83 1
OP764622.1 83|83 5
OP764623.1 83|83 6
OP764624.1 83|83 20
OP764625.1 83|83 4
OP764627.1 83|83 12
OP764628.1 83|83 19
OP764629.1 82|82 11
'gbvrt260'
MF370348.1
12|12 194
MH141597.1 12|12 245
'gbvrl543'
OP972835.1
6|6 4471
'gbvrt9'
AY728214.1
12|12 334
AY728216.1 12|12 329
AY728219.1 12|12 360
AY728226.1 12|12 314
AY728232.1 12|12 304
AY728235.1 12|12 292
'gbvrt44'
HM147138.1
12|12 264
HM147139.1 12|12 248
HM147141.1 12|12 231
HQ834450.1 11|11 206
HQ834451.1 11|11 217
'gbvrt3'
AP010869.1
12|12 266
AP011543.1 12|12 199
AP011544.1 12|12 188
'gbvrl518'
OP566509.1
7|7 3581
'gbvrl507'
OP413713.1
83|83 1
OP413715.1 83|83 1
OP413716.1 83|83 1
OP415180.1 83|83 2
OP415189.1 83|83 2
OP415190.1 83|83 1
OP415193.1 83|83 1
OP415194.1 83|83 2
OP415196.1 83|83 1
OP415199.1 83|83 2
OP415203.1 83|83 26
OP415204.1 83|83 2
OP415206.1 83|83 6
OP415213.1 79|79 208
OP415222.1 83|83 1
OP415224.1 83|83 92
OP415230.1 83|83 41
OP415232.1 83|83 46
OP415234.1 83|83 46
OP415237.1 83|83 1
OP415240.1 82|82 49
OP415242.1 83|83 12
OP415246.1 83|83 4
OP415247.1 83|83 3
OP415249.1 83|83 3
OP415255.1 83|83 24
OP415258.1 81|81 32
OP415264.1 82|82 84
OP415272.1 83|83 1
OP415278.1 83|83 1
OP415281.1 83|83 4
'gbvrl563'
OQ320441.1
82|82 1
OQ320444.1 82|82 7
OQ320455.1 82|82 1
OQ320457.1 82|82 1
OQ320468.1 82|82 1
OQ320511.1 82|82 1
OQ320513.1 81|81 3
OQ320520.1 82|82 3
OQ320523.1 82|82 4
'gbvrl886'
U00735.2
9|9 2133
'gbvrl540'
OP924545.1
9|9 5291
'gbvrl576'
OQ557940.1
81|81 1
OQ557950.1 82|82 8
OQ566226.1 7|7 3600
OQ566227.1 7|7 3600
OQ566228.1 7|7 3600
'gbvrl499'
OP331334.1
83|83 2
'gbvrt1'
AB202078.1
12|12 233
AB212225.1 12|12 219
AB511282.1 12|12 202
AB661661.1 13|13 266
AB777216.1 12|12 233
AB777217.1 12|12 196
AB777218.1 11|11 450
AB777219.1 12|12 339