Pattern obfuscation of ocean pH

I noticed that my blog had been cited by a couple of papers, so I went to have a look.

Albert Parker has a paper in Nonlinear Engineering. I’m sure this journal wasn’t chosen for the relevant expertise of the editors and usual pool of reviewers. More likely the converse: Parker (2016) is neither good nor original, a Gish gallop of a paper, recycling bad ideas from climate denialist blogs.

The paper returns repeatedly to the Monterey Bay pH time series, contrasting this series with the Hawaii Ocean Timeseries (HOT) from the North Pacific gyre. Parker prefers the Monterey Bay series, which does not show a decline in pH to the HOT data which show significant acidification (or as Parker would probably prefer, dealkalinisation).

Whereas the HOT data were explicitly designed to test for ocean acidification and  changes to the carbon inventory, the Monterey Bay series has a more immediate goal. The Monterey Bay Aquarium measures the chemistry of the water being pumped into their tanks from an intake 17m below the sea surface in the bay. Most of the time, the water at this depth is well-oxygenated surface water, but during upwelling events, cold, hypoxic, low-pH water is drawn into the pipe. The correlation between oxygen concentration and pH is high – 0.675 according to this Masters thesis which examines the time series in detail. The upwelling events, which occur more frequently in summer, add a large amount of variability to the data, obscuring any trend in ocean surface pH. The Monterey Bay pH series is in the perfect location if you want to avoid killing your fish with hypoxic water, but an utterly useless place if you want to test for ocean acidification: pH trends could be caused by ocean acidification or changes in upwelling. A better place would have much simpler hydrography, and so a much higher signal to noise ratio, perhaps an ocean gyre north of Hawaii. Parker complains that the IPCC ignores the Monterey Bay series. Of course they do. Anyone who uses the lack of trend in the Monterey Bay series as evidence against ocean acidification is clueless.

A couple of years ago Mike Wallace produced some excitement on climate denier blogs with a compilation of all historical pH measurements into a global mean which showed variability on multidecadal time scales. The problem is that the seasonal and geographical coverage of the pH measurement varies over time. Imagine if temperature data were most abundant in summer in northern Europe in the 1920s and then more common in east Asia and in winter in the 1990s, and then back to Europe after 2000, and that climatologists simply took the mean of the raw data. Obviously this would be junk: it is no less junk when done with pH measurements. Parker is unable or unwilling to understand this point. He has even read – or at least he cites – my blog, writing that I excuse the dismissal of the historical data because of “poor sampling protocols and non-gridded data”.  I think he should read it again.

Parker is not a fan of the HOT time series. pH was measured for two periods, between these measurements, pH was estimated by a “model”. The horror, the horror.

Closing the significant gaps with computer model results or extending the time range to 1988 by computer model results is not a legitimate procedure when there is no validation for the models. No model can be trusted if not validated first against accurate measurements, and if the measurements are not available or not accurate, than the use of the model is pointless. The time series of the actually measured pH does not satisfy the minimal quality requirements to infer any trend.

Since the HOT data are archived, we can for the very first time ever, validate the “model” against the measurements.


Calculated against measured pH. The r2 is 0.85.

I think this “model” can be trusted. Nevertheless, Parker, who should not be trusted, ignores the model data, but finds a significant decline in pH of −0.00157±0.00015 pH/year even though his model ignores the strong seasonality in the data. He wants to add extra uncertainty for measurement error: I don’t think he understands how linear models work. Because of some non-linearity in the trend, Parker decides that a 60-year sine wave would be a better model. Not on statistical grounds of course. Certainly not on physical grounds. His main attraction to the model seems to be that sine waves produce oscillations and that oscillations imply natural cycles.

There’s more. Much more. But it doesn’t get any better. For example

The measured surface CO2 from the NASA OCO-2 project differ considerably from the NOAA/PMEL estimated ocean CO2 and pH as proposed by Takahashi et al (2014)

Parker (2016) spent 10 months in review and revision. And still it is dross. But Parker obviously enjoyed the experience of publishing in Nonlinear Engineering as he has since published a second paper there under his alternative name Albert Boretti.

Posted in Fake climate sceptics, Peer reviewed literature, Silliness | Tagged , , | 4 Comments

Palaeo papers can be retracted

Via Retraction Watch, I find that the conjecture, cherished by so many, that, unlike all other fields of science, there is absolutely no misconduct in palaeoecology may need revising ever so slightly as L & O have retracted Zou et al (2017).

The article by Youjia Zou, Xiangying Xi, and Chaoyang Zhang entitled “Southward migrations of the Atlantic Equatorial Currents during the Younger Dryas” (doi 10.1002/lno.10529) published in Limnology & Oceanography has been retracted by journal Editor in Chief, Robert W. Howarth, the Association for the Sciences of Limnology & Oceanography, and Wiley Periodicals, Inc. Author Zhang had no affiliation with the Georgia Institute of Technology as claimed, and the authors have been unable to provide information that would allow verification of critical aspects of how the research was conducted, leaving the journal unable to verify the intellectual integrity of the data and work.

Left pondering what “critical aspects of the research” are in question, since forgetting which institute one works for hardly seems like a hanging offence, I’ve read the paper. It is perhaps the only “high-resolution (∼ 75 yr/sample)” isotope stratigraphy with only about 20 samples in the last 14000 years. I’m sure the authors meant to write “low-resolution (∼ 750 yr/sample)”, but keyboards are such tricky things.

Zou et al report oxygen isotope, Mg/Ca and calcareous dinocyst data from two cores in the Atlantic, one either side of the thermal equator. I would have expected a sentence like ‘cores SAU1702 and SAD1006 were collected from HMS Pinafore in 2027 with a Glew corer’, but its not there. I cannot find anything about these cores via google either.

The acknowledgements should surely give some hint: who funded ship time; who gave access to cores; who paid the salaries of the palynologist and geochemists. Quick scroll to the end of the paper. No acknowledgements. Oh.

The methods section is thin and confusing, almost like the authors don’t really know what they did:

Stable isotope analyses for the cores were mainly based on foraminifers G. ruber (white variety) from the > 255 μm size fraction, using approximately 50 (80 for replicated samples) gently crushed shells, splitting into aliquots for Mg/Ca and δ18O analyses, and transferring to clean vials. Any visible coarse grains were removed prior to transfer to the vials. Samples were wet-sieved using a 75 μm mesh. Sediment from each core interval was dried overnight at ∼ 50°C, and then disaggregated in ultra clean water for 6–8 h on a shaker table.

This is to recipe to bake a loaf of bread, then knead the dough, and finally mix in water.

Some of the referencing is innovative. Take, for example,

autotrophic dinoflagellates whose distributions in geography are controlled primarily by seawater temperature and nutrient availability, more in cooler waters but less in warmer waters [Madsen et al. 2001; Barker et al. 2009])

Neither Madsen et al nor Barker et al have anything to say about dinocysts, calcareous or otherwise. This is a paper that should never have passed peer review.

But what of other papers by the authors. Zou (who, except for a coauthor, seems to be the only person using the affiliation “Department of Meteorology and Oceanography, Shanghai Maritime University”), and Xi, from the Management Faculty at Wuhan University of Technology, have many talents. A previous paper models tropical Atlantic currents during the Little Ice Age. The text on the model set-up reads thus:

an oceanic general circulation model (OGCM) proposed by Kim et al. (2004) has been employed and modified after considering the geometry of the continental shelf and bottom topography.

That is it. I can find no information in the paper about how it the model was forced. Contrast with the first paragraph of the model description in Kim et al (2004).

[7] The model used for this study is the Japan Marine Science and Technology Center (JAMSTEC) OGCM [Ishida et al., 1998], based on Modular Ocean Model version 2 [Pacanowski, 1995]. It covers a global domain except for the Arctic Ocean extending from 75°S to 75°N, and has realistic coastline and bottom topography based on the National Geophysical Data Center data set (ETOPO5). The model has a horizontal resolution of 0.25° both in longitude and latitude and has 55 levels in the vertical. The vertical grid spacing increases smoothly from 10 m at the surface to about 50 m near 500 m, about 70 m near 1000 m depth, and about 400 m at 6000 m. Data of the upper 32 levels (0–1007.29 m) are used for this study.

Zou and Xi also have papers, also lacking acknowledgements, on capsizing of bulk carriers carrying nickel ores, and the motions of anchored Capesize ships (Capesized – my new-word-of-the-day – are really big ships, too huge to fit in the Suez Canal). There are not many people can count tiny calcareous dinocysts and numerically model gigantic ships.

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The chironomid triennial

Over at the Subfossil Chironomid group on Facebook, Dr Larocque-Tobler posted a link to Zhang et al. (2017), describing it as impressive. I hadn’t seen the published version of Zhang et al, so I popped over fully prepared to be impressed.

Screenshot from facebook

Zhang et al report a transfer function for reconstructing July air temperature from chironomid assemblages using a 100-lake calibration set from the south-eastern margin of the Tibetan Plateau. The authors then apply this transfer function to a high-resolution chironomid stratigraphy from the high-elevation (3900m) Tiancai Lake. They report that the correlation between the reconstruction and the instrumental record from Lijiang (55km away and 1500m lower) is statistically significant (r = 0.45, p < 0.05,  n = 31).

This is the key figure.


Zhang et al Figure 6. (a) Chironomid-based mean July temperature (MJT) reconstruction results from Tiancai Lake based on two transfer function models: the solid black line is the reconstruction based on the weighted-average partial least squares (WA-PLS) bootstrap model with two components and the dashed black line is the reconstruction based on the weighted-average with inverse deshrinking (WAinv) bootstrap model. Red solid line is the instrumental data from Lijiang weather station, corrected applying the lapse rate and solid grey line is the three-sample moving average of the data set. Reconstruction of diagnostic statistics for the 100 lake data set where (b) displays the goodness-of-fit statistics of the fossil samples with MJT. Dashed lines are used to identify samples with “poor fit” (> 95th percentile) and “very poor fit” (> 90th percentile) with temperature [note: the percentiles are the wrong way round and should be poor fit >90th and very poor fit >95th]. (c) Nearest modern analogues for the fossil samples in the calibration data set, where the dashed line is used to show fossil samples with “no good” (5 %) modern analogues. (d) Percentage of chironomid taxa in fossil samples that are rare in the modern calibration data set (Hill’s N2< 2). (e) Comparison between the chironomid-based transfer function reconstructed trends (represented by MJT anomalies) with the instrumental data from Lijiang weather station (in red solid line, with three-sample moving average). The black solid line represents the reconstruction based on the WA-PLS bootstrapped model with two components using 100-lake calibration set.

The problem is obvious once you have found it – it helped immensely having some archived data. Compare the grey line in panel a with the red line in panel e. These are both supposed to be the three-sample moving average of the temperature data from Lijiang (a lapse-rate corrected; e anomalies) and should therefore have exactly the same shape, but the resemblance is limited. (Panel a was not shown in the Climate of the Past Discussion paper, so the reviewers at least can be absolved of any responsibility for not noticing this.)

Using the archived data from dropbox, I can confirm that panel a is correct, except that the curve should extend before 1960 as the instrumental temperature series starts in 1951. It took a while to work out what the authors had done in panel e: at least a couple of minutes.

If instead of taking the three-year moving average, you take every third year, you can get a plot that looks almost exactly like panel e. Interpolate the triennial data and the correlation with the reconstruction is very similar to what the authors report. This is obviously a very lucky error: nobody thinks that chironomids are only sensitive to July temperature every third year. This analysis implicitly assumes that the chironomids can predict temperature up to two years ahead! Now that would be impressive.


Reconstruction from Zhang et al (black) and every third year temperature data from Lijiang (red). Both series are presented as anomalies. cf panel e above

With the promised three-year moving average, the correlation is much weaker (r = 0.21, p = 0.28). I am not impressed.


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Reconstruction number 5

Climate modellers often run their models many times with slightly different initial configurations to get an ensemble of alternate realisations of climate history – parallel universes in silico. What is less well known is that certain proxies, mainly from small lakes because of their extreme sensitivity to quantum interactions with space-time substitutions, can also provide multiple realisations of climate history.

While many palaeoecologists (perhaps unwisely) attempt to reconstruct several environmental variables from one microfossil stratigraphy using transfer functions, the state-of-the-art, exemplified by the chironomid studies from Lake Silvaplana, is to reconstruct several alternative realisations of a single environmental variable.

Realisation number 1

The first realisation (fig 1) was published in the Journal of Paleolimnology. This near-annual resolution reconstruction is reported as having an excellent correlation (r = 0.65) with the instrumental data from a weather station close to the lake. This correlation would not be possible if there were substantial errors in the chronology or taxonomy, ergo, both must be at least nearly perfect.

Realisation number 2

One might expect the archived JoPL reconstruction to be exactly the same as the published reconstruction. Some parts of the curves are indeed identical (fig 1), for example near 1960 CE and near 1980 CE. Other parts have a chronological offset, for example 1860–1880 CE where the archived reconstruction lags the published figure by a few years, while yet other parts of the curves are difficult to reconcile, for example near 1900 CE.

Figure 1. _JoPL_ archived reconstruction (red) plotted on top of the published _JoPL_ figure 6a (reconstruction - open circles, instrumental - filled circles

Figure 1. JoPL archived reconstruction (red) plotted on top of the published JoPL figure 6a (reconstruction – open circles, instrumental – filled circles

The correlation between the archived JoPL reconstruction and the instrumental temperature from Segl-Maria is 0.19 (p = 0.09), far lower than that reported in the paper.

Realisation number 3

The overlapping portion of the 540-year Holocene reconstruction (Fig 2) should be identical (save for possible taxonomic and chronological revision). It is not.

Realisation number 4

The archived Holocene reconstruction is far from identical to the published Holocene reconstruction (Fig 2). Only the earliest and latest periods appear to match.

Figure 2. _Holocene_ archived reconstruction (blue) plotted on top of the published _Holocene_ figure 4a

Figure 2. Holocene archived reconstruction (blue) plotted on top of the published Holocene figure 4a

The correlation between the archived Holocene reconstruction and the instrumental air temperature since 1864 is 0.01 (p = 0.91).

Realisation number 5

The 1000-year QSR reconstruction differs in the overlapping period from all the other reconstructions. Shockingly, the published and archived reconstructions appear to be identical.

Comparison of the archived JoPL and Holocene realisations

The archived 140-yr JoPL and 540-yr Holocene reconstructions are very different in the overlapping period. The most recent value is identical, the next few values appear to have a chronological offset, thereafter any relationship is difficult to see (fig 3).

Figure 3. Reconstructions from the JoPL and Holocene papers for the last 140 years.

Figure 3. Reconstructions from the JoPL and Holocene papers for the last 140 years.

The apparent chronological offset at the end of the reconstruction suggests there might be issues with the chronology. If the chronologies are ignored and the reconstructions are instead plotted in stratigraphic order, the agreement between the reconstructions improves substantially (fig 4).

Figure 4. Reconstruction plotted in stratigraphical order. The youngest sample is sample 1.

Figure 4. Reconstruction plotted in stratigraphical order. The youngest sample is sample 1.

Of the 83 values in the 140-yr JoPL reconstruction, 69 are identical to the value in the same chronological rank as the 540-yr Holocene reconstruction. Of the 14 remaining values, which are reported to five decimal places, 11 have an integer difference ranging from -3°C to 5°C.

The chronological adjustment required to align the two reconstructions is large, up to 42 years (fig 5), far larger than can reasonably be ascribed to chronological uncertainty in the varved sediment.

Figure 5. Chronological offset required to align 140 yr _JoPL_ and 540 yr _Holocene_ reconstructions

Figure 5. Chronological offset required to align 140 yr JoPL and 540 yr Holocene reconstructions.

The jump in the offset at about 1890 reflects an overlap in the Holocene chronology which might be because of an overlap between the two cores from Lake Silvaplana used in the Holocene paper, but that is supposed to have been removed and should be older.


I am extremely excited by the hitherto unrecognised potential of chironomids to reconstruct alternative climate realisations. Regrettably, the authors did not draw our attention to this aspect of chironomid ecology and we have spent the last few years discussing whether Holocene chironomid reconstructions are reliable rather than the infinitely more important question of whether chironomids prove the existence of parallel universes.

In my next post, I will look at the archived fossil data for the Holocene reconstruction which might give some clue in the hunt for Schrödinger’s chironomid.

This document is reproducible with code archived on github. I’m sure that simultaneous reconstructions across parallel universes is the most parsimonious explanation for the different reconstructions.

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The Lake Silvaplana papers

Intrigued by the slightest of hints of rare mønsters in the Lake Żabińskie chironomid data, I decided to re-read all the papers on the chironomid stratigraphy from the varved Lake Silvaplana, Switzerland, by the same author. These papers, which reconstruct July air temperature, cover different time periods and use different reconstruction methods: here is a brief synopsis.

Journal of Paleolimnology 2009

Time period: 1850–2001 CE
Resolution: Near annual
Reconstruction method: Calibration-in-space

Key point: Good correlation of reconstruction with instrumental record (r = 0.65)

Data archived: Reconstruction

Holocene 2009

Time period: 1580–2001 CE
Resolution: Near annual
Reconstruction method: Calibration-in-space

Key point: Correlation of reconstruction with estimates of summer temperature from early instrumental and documentary data, and proxy data.

Data archived: Reconstruction and fossil data

Quaternary Science Reviews 2010a

Time period: 1032–2001 CE
Resolution: 1–20 years
Reconstruction method: Calibration-in-space

Key points: Last part of the Medieval Climate Anomaly was 1°C warmer than 1961–1990 CE. The Little Ice Age was colder by up to −1.2°C and separated into three phases. This pattern agrees with other records of the past millennium. Inferred July temperatures between ca 1900 and 2001 AD were warmer than the climate reference period (1961–1990) by 1°C, in agreement with the instrumental data.

Data archived: Smoothed reconstruction

Quaternary Science Reviews 2010b

Time period: 1177–2001 CE
Resolution: annual
Reconstruction method: Compilation of existing chironomid and new biogenic silica proxy records.

Key point: record suggests that the current decade [2000–2010 CE] is slightly warmer than the warmest decade in the previous 800 years.

Data archived: Reconstruction

Palaeogeography, Palaeoclimatology, Palaeoecology 2011

Time period: 1032–2001 CE
Resolution: 1 — ~20 years
Reconstruction method: Calibration-in-time

Key point: Inconclusive whether calibration-in-space or calibration-in-time gives better estimates.

Data archived: ?

Journal of Quaternary Science 2011

Time period: 570 BCE to 120 CE
Resolution: Annual
Reconstruction method: Calibration-in-space, combined with biogenic silica

Key points: Inter-annual to decadal temperature variability was strongly enhanced in the warm the Iron Age–Roman Period compared to the last millennium

Data archived: ?

Next steps

The most promising papers for a closer read are JoPL2009, Holocene2009, QSR2010a, PPP2011 as all present new chironomid data, they overlap in time and the reconstructions are archived for the first three. If the anticipation is too much to bare, go ahead and download the data.

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Odd ordination of the day

Your challenge is to identify half a dozen unexpected features in this Detrended Constrained Correspondence Analysis from Larocque-Tobler (2010). Bonus points if you can interpret the last two sentences of the caption.


DCCA analysis of the 101-lake training set (empty circles) constrained to temperature (July Temp), depth and DOC (arrows). The Lake Silvaplana chironomid assemblages were added passively to this analysis. A 20-point moving average was made of the axis scores of the samples (thick line). Note that the two axes were shortened to represent the changes in the fossil records.

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Air temperature, lake temperature

I’m interested in lake temperatures because I want to go swimming. I’m also interested because some palaeolimnological proxies, for example chironomids, are probably most sensitive to water temperature but are calibrated against and used to reconstruct air temperature. The stronger the relationship between air temperature and water temperature, the better the reconstructions are going to be.

I’ve found Sharma et al (2015), a global database of lake surface temperatures collected in situ and by satellite methods from 1985–2009. The database includes 286 summer lake surface time series with more 10 years.

The relationship between mean air temperature and mean water temperature is, as one might expect, strong (r = 0.91).



That’s good, but I’m more interested in the year-by-year correlations between lake and air temperature.

The median Pearson correlation is 0.69 with a wide spread. This is lower than I had expected, but the database includes metre-deep and kilometre-deep lakes; 0.03km2 ponds and the 380 thousand km2 Caspian Sea; and tropical lakes and Arctic lakes. Perhaps surface area, depth and latitude are related to the correlation.



Latitude seems to be the most important predictor of the correlation between air and water temperature. This is probably because inter-annual air temperature variability is lower in the tropics. Lake area has a slight effect, at least at mid to high latitudes (absolute latitude > 35°), with the correlation weakening in large lakes. The relationship with lake depth is unimodal, with the maximum correlation in lakes about 10m deep. Reservoirs (not shown) have a slightly lower correlation than lakes.

Taking these factors into account, the median correlation between air and water temperature for a mid to high latitude lake, less than 10km2 in area and between 5m and 50m mean depth is 0.81. This is similar to the correlation reported by Livingstone and Lotter (1998) for Lake Zurich. Livingstone and Lotter (1998) report that the correlation weakens with depth, becoming negative at 10-20m depth. Correlations reported by Livingstone and Dokuli (2001) for Austrian lakes and Rösneret al (2012) for a lake in northern Germany are also similar.

These results suggest that ~0.8 is the maximum correlation that could be expected between air temperature and an annual resolution reconstruction using an ideal transfer functions.

Real reconstructions are likely to perform less well. For example, some chironomids will live below the thermocline where the temperature will be weakly coupled to air temperature; other factors, such as oxygen concentrations will also affect the chironomid communities; and taphonomic processes will distort assemblage composition.

I suspect that on short timescales (i.e. monthly rather than whole summer), the correlations will decrease but only slightly as the thermal response time of the epilimnion in a small lake is fairly fast. On decadal to centennial scales, typical resolution for palaeolimnology, I suspect the correlations will increase slightly.

Code, as usual, on github.

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