The FIRSTS: The cause(s) of dinosaur extinction

A few days ago, a follower of mine gave me an interesting read from The Atlantic regarding the dinosaur extinction. Like many of my generation, I was taught in school that dinosaurs died because an asteroid hit the Earth. That led to a nuclear winter (or a  few years of ‘nuclear winters’) which killed the photosynthetic organisms, and then the herbivores didn’t have anything to eat so they died and then the carnivores didn’t have anything to eat and so they died. Or, as my 4-year-old puts it, “[in a solemn voice] after the asteroid hit, big dusty clouds blocked the sun; [in an ominous voice] each day was colder than the previous one and so, without sunlight to keep them alive [sad face, head cocked sideways], the poor dinosaurs could no longer survive “. Yes, I am a proud parent. Now I have to do a sit-down with the child and explain that… What, exactly?

Well, The Atlantic article showcases the struggles of a scientist – paleontologist and geologist Gerta Keller – who doesn’t believe the mainstream asteroid hypothesis; rather she thinks there is enough evidence to point out that extreme volcano eruptions, like really extreme, thousands of times more powerful than anything we know in the recorded history, put out so much poison (soot, dust, hydrofluoric acid, sulfur, carbon dioxide, mercury, lead, and so on) in the atmosphere that, combined with the consequent dramatic climate change, killed the dinosaurs. The volcanoes were located in India and they erupted for hundreds of thousands of years, but most violent eruptions, Keller thinks, were in the last 40,000 years before the extinction. This hypothesis is called the Deccan volcanism from the region in India where these nasty volcanoes are located, first proposed by Vogt (1972) and Courtillot et al. (1986).

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So which is true? Or, rather, because this is science we’re talking about, which hypothesis is more supported by the facts: the volcanism or the impact?

The impact hypothesis was put forward in 1980 when Walter Alvarez, a geologist, noticed a thin layer of clay in rocks that were about 65 million years old, which coincided with the time when the dinosaurs disappeared. This layer is on the KT boundary (sometimes called K-T, K-Pg, or KPB, looks like the biologists are not the only ones with acronym problems) and marks the boundary between the Cretaceous and Paleogenic geological periods (T is for Triassic, yeah, I know). Walter asked his father, the famous Nobel Prize physicist Louis Alvarez, to take a look at it and see what it is. Alvarez Sr. analyzed it and decided that the clay contains a lot of iridium, dozens of times more than expected. After gathering more samples from Europe and New Zealand, they published a paper (Alvarez et al., 1980) in which the scientists reasoned that because Earth’s iridium is deeply buried in its bowels and not in its crust, this iridium at the K-Pg boundary is of extraterrestrial origin, which could be brought here only by an asteroid/comet. This is also the paper in which it was put forth for the first time the conjecture that the asteroid impact killed the dinosaurs, based on the uncanny coincidence of timing.

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The discovery of the Chicxulub crater in Mexico followed a more sinuous path because the geophysicists who first discovered it in the ’70s were working for an oil company, looking for places to drill. Once the dinosaur-died-due-to-asteroid-impact hypothesis gained popularity outside academia, the geologists and the physicists put two-and-two together, acquired more data, and published a paper (Hildebrand et al., 1991) where the Chicxulub crater was for the first time linked with the dinosaur extinction. Although the crater was not radiologically dated yet, they had enough geophysical, stratigraphic, and petrologic evidence to believe it was as old as the iridium layer and the dinosaur die-out.

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But, devil is in the details, as they say. Keller published a paper in 2007 saying the Chicxulub event predates the extinction by some 300,000 years (Keller et al., 2007). She looked at geological samples from Texas and found the glass granule layer (indicator of the Chicxhulub impact) way below the K-Pg boundary. So what’s up with the iridium then? Keller (2014) believes that is not of extraterrestrial origin and it might well have been spewed up by a particularly nasty eruption or the sediments got shifted. Schulte et al. (2010), on the other hand, found high levels of iridium in 85 samples from all over the world in the KPG layer. Keller says that some other 260 samples don’t have iridium anomalies. As a response, Esmeray-Senlet et al. (2017) used some fancy Mass Spectrometry to show that the iridium profiles could have come only from Chicxulub, at least in North America. They argue that the variability in iridium profiles around the world is due to regional geochemical processes. And so on, and so on, the controversy continues.

Actual radioisotope dating was done a bit later in 2013: date of K-Pg is 66.043 ± 0.043 MA (millions of years ago), date of the Chicxulub crater is 66.038 ±.025/0.049 MA. Which means that the researchers “established synchrony between the Cretaceous-Paleogene boundary and associated mass extinctions with the Chicxulub bolide impact to within 32,000 years” (Renne et al., 2013), which is a blink of an eye in geological times.

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Now I want you to understand that often in science, though by far not always, matters are not so simple as she is wrong, he is right. In geology, what matters most is the sample. If the sample is corrupted, so will be your conclusions. Maybe Keller’s or Renne’s samples were affected by a myriad possible variables, some as simple as shifting the dirt from here to there by who knows what event. After all, it’s been 66 million years since. Also, methods used are just as important and dating something that happened so long ago is extremely difficult due to intrinsic physical methodological limitations. Keller (2014), for example, claims that Renne couldn’t have possibly gotten such an exact estimation because he used Argon isotopes when only U-Pb isotope dilution–thermal ionization mass spectrometry (ID-TIMS) zircon geochronology could be so accurate. But yet again, it looks like he did use both, so… I dunno. As the over-used always-trite but nevertheless extremely important saying goes: more data is needed.

Even if the dating puts Chicxulub at the KPB, the volcanologists say that the asteroid, by itself, couldn’t have produced a mass extinction because there are other impacts of its size and they did not have such dire effects, but were barely noticeable at the biota scale. Besides, most of the other mass extinctions on the planet have been already associated with extreme volcanism (Archibald et al., 2010). On the other hand, the circumstances of this particular asteroid could have made it deadly: it landed in the hydrocarbon-rich areas that occupied only 13% of the Earth’s surface at the time which resulted in a lot of “stratospheric soot and sulfate aerosols and causing extreme global cooling and drought” (Kaiho & Oshima, 2017). Food for thought: this means that the chances of us, humans, to be here today are 13%!…

I hope that you do notice that these are very recent papers, so the issue is hotly debated as we speak.

It is possible, nay probable, that the Deccan volcanism, which was going on long before and after the extinction, was exacerbated by the impact. This is exactly what Renne’s team postulated in 2015 after dating the lava plains in the Deccan Traps: the eruptions intensified about 50,000 years before the KT boundary, from “high-frequency, low-volume eruptions to low-frequency, high-volume eruptions”, which is about when the asteroid hit. Also, the Deccan eruptions continued for about half a million years after KPB, “which is comparable with the time lag between the KPB and the initial stage of ecological recovery in marine ecosystems” (Renne et al., 2016, p. 78).

Since we cannot get much more accurate dating than we already have, perhaps the fossils can tell us whether the dinosaurs died abruptly or slowly. Because if they got extinct in a few years instead of over 50,000 years, that would point to a cataclysmic event. Yes, but which one, big asteroid or violent volcano? Aaaand, we’re back to square one.

Actually, the last papers on the matter points to two extinctions: the Deccan extinction and the Chicxulub extinction. Petersen et al., (2016) went all the way to Antarctica to find pristine samples. They noticed a sharp increase in global temperatures by about 7.8 ºC at the onset of Deccan volcanism. This climate change would surely lead to some extinctions, and this is exactly what they found: out of 24 species of marine animals investigated, 10 died-out at the onset of Deccan volcanism and the remaining 14 died-out when Chicxulub hit.

In conclusion, because this post is already verrrry long and is becoming a proper college review, to me, a not-a-geologist/paleontologist/physicist-but-still-a-scientist, things happened thusly: first Deccan traps erupted and that lead to a dramatic global warming coupled with spewing poison in the atmosphere. Which resulted in a massive die-out (about 200,000 years before the bolide impact, says a corroborating paper, Tobin, 2017). The surviving species (maybe half or more of the biota?) continued the best they could for the next few hundred thousand years in the hostile environment. Then the Chicxulub meteorite hit and the resulting megatsunami, the cloud of super-heated dust and soot, colossal wildfires and earthquakes, acid rain and climate cooling, not to mention the intensification of the Deccan traps eruptions, finished off the surviving species. It took Earth 300,000 to 500,000 years to recover its ecosystem. “This sequence of events may have combined into a ‘one-two punch’ that produced one of the largest mass extinctions in Earth history” (Petersen et al., 2016, p. 6).

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By Neuronicus, 25 August 2018

P. S. You, high school and college students who will use this for some class assignment or other, give credit thusly: Neuronicus (Aug. 26, 2018). The FIRSTS: The cause(s) of dinosaur extinction. Retrieved from https://scientiaportal.wordpress.com/2018/08/26/the-firsts-the-causes-of-dinosaur-extinction/ on ………. AND READ THE ORIGINAL PAPERS. Ask me for .pdfs if you don’t have access, although with sci-hub and all… not that I endorse any illegal and fraudulent use of the above mentioned server for the purpose of self-education and enlightenment in the quest for knowledge that all academics and scientists praise everywhere around the Globe!

REFERENCES:

1. Alvarez LW, Alvarez W, Asaro F, & Michel HV (6 Jun 1980). Extraterrestrial cause for the cretaceous-tertiary extinction. PMID: 17783054. DOI: 10.1126/science.208.4448.1095 Science, 208(4448):1095-1108. ABSTRACT | FULLTEXT PDF

2. Archibald JD, Clemens WA, Padian K, Rowe T, Macleod N, Barrett PM, Gale A, Holroyd P, Sues HD, Arens NC, Horner JR, Wilson GP, Goodwin MB, Brochu CA, Lofgren DL, Hurlbert SH, Hartman JH, Eberth DA, Wignall PB, Currie PJ, Weil A, Prasad GV, Dingus L, Courtillot V, Milner A, Milner A, Bajpai S, Ward DJ, Sahni A. (21 May 2010) Cretaceous extinctions: multiple causes. Science,328(5981):973; author reply 975-6. PMID: 20489004, DOI: 10.1126/science.328.5981.973-aScience. FULL REPLY

3. Courtillot V, Besse J, Vandamme D, Montigny R, Jaeger J-J, & Cappetta H (1986). Deccan flood basalts at the Cretaceous/Tertiary boundary? Earth and Planetary Science Letters, 80(3-4), 361–374. doi: 10.1016/0012-821x(86)90118-4. ABSTRACT

4. Esmeray-Senlet, S., Miller, K. G., Sherrell, R. M., Senlet, T., Vellekoop, J., & Brinkhuis, H. (2017). Iridium profiles and delivery across the Cretaceous/Paleogene boundary. Earth and Planetary Science Letters, 457, 117–126. doi:10.1016/j.epsl.2016.10.010. ABSTRACT

5. Hildebrand AR, Penfield GT, Kring DA, Pilkington M, Camargo AZ, Jacobsen SB, & Boynton WV (1 Sept. 1991). Chicxulub Crater: A possible Cretaceous/Tertiary boundary impact crater on the Yucatán Peninsula, Mexico. Geology, 19 (9): 867-871. DOI: https://doi.org/10.1130/0091-7613(1991)019<0867:CCAPCT>2.3.CO;2. ABSTRACT

6. Kaiho K & Oshima N (9 Nov 2017). Site of asteroid impact changed the history of life on Earth: the low probability of mass extinction. Scientific Reports,7(1):14855. PMID: 29123110, PMCID: PMC5680197, DOI:10.1038/s41598-017-14199-x. . ARTICLE | FREE FULLTEXT PDF

7. Keller G, Adatte T, Berner Z, Harting M, Baum G, Prauss M, Tantawy A, Stueben D (30 Mar 2007). Chicxulub impact predates K–T boundary: New evidence from Brazos, Texas, Earth and Planetary Science Letters, 255(3–4): 339-356. DOI: 10.1016/j.epsl.2006.12.026. ABSTRACT

8. Keller, G. (2014). Deccan volcanism, the Chicxulub impact, and the end-Cretaceous mass extinction: Coincidence? Cause and effect? Geological Society of America Special Papers, 505:57–89. doi:10.1130/2014.2505(03) ABSTRACT

9. Petersen SV, Dutton A, & Lohmann KC. (5 Jul 2016). End-Cretaceous extinction in Antarctica linked to both Deccan volcanism and meteorite impact via climate change. Nature Communications, 7:12079. doi: 10.1038/ncomms12079. PMID: 27377632, PMCID: PMC4935969, DOI: 10.1038/ncomms12079. ARTICLE | FREE FULLTEXT PDF 

10. Renne PR, Deino AL, Hilgen FJ, Kuiper KF, Mark DF, Mitchell WS 3rd, Morgan LE, Mundil R, & Smit J (8 Feb 2013). Time scales of critical events around the Cretaceous-Paleogene boundary. Science, 8;339(6120):684-687. doi: 10.1126/science.1230492. PMID: 23393261, DOI: 10.1126/science.1230492 ABSTRACT 

11. Renne PR, Sprain CJ, Richards MA, Self S, Vanderkluysen L, Pande K. (2 Oct 2015). State shift in Deccan volcanism at the Cretaceous-Paleogene boundary, possibly induced by impact. Science, 350(6256):76-8. PMID: 26430116. DOI: 10.1126/science.aac7549 ABSTRACT

12. Schoene B, Samperton KM, Eddy MP, Keller G, Adatte T, Bowring SA, Khadri SFR, & Gertsch B (2014). U-Pb geochronology of the Deccan Traps and relation to the end-Cretaceous mass extinction. Science, 347(6218), 182–184. doi:10.1126/science.aaa0118. ARTICLE

13. Schulte P, Alegret L, Arenillas I, Arz JA, Barton PJ, Bown PR, Bralower TJ, Christeson GL, Claeys P, Cockell CS, Collins GS, Deutsch A, Goldin TJ, Goto K, Grajales-Nishimura JM, Grieve RA, Gulick SP, Johnson KR, Kiessling W, Koeberl C, Kring DA, MacLeod KG, Matsui T, Melosh J, Montanari A, Morgan JV, Neal CR, Nichols DJ, Norris RD, Pierazzo E,Ravizza G, Rebolledo-Vieyra M, Reimold WU, Robin E, Salge T, Speijer RP, Sweet AR, Urrutia-Fucugauchi J, Vajda V, Whalen MT, Willumsen PS.(5 Mar 2010). The Chicxulub asteroid impact and mass extinction at the Cretaceous-Paleogene boundary. Science, 327(5970):1214-8. PMID: 20203042, DOI: 10.1126/science.1177265. ABSTRACT

14. Tobin TS (24 Nov 2017). Recognition of a likely two phased extinction at the K-Pg boundary in Antarctica. Scientific Reports, 7(1):16317. PMID: 29176556, PMCID: PMC5701184, DOI: 10.1038/s41598-017-16515-x. ARTICLE | FREE FULLTEXT PDF 

15. Vogt, PR (8 Dec 1972). Evidence for Global Synchronism in Mantle Plume Convection and Possible Significance for Geology. Nature, 240(5380), 338–342. doi:10.1038/240338a0 ABSTRACT

How to wash SOME pesticides off produce

While EU is moving on with legislation to curtail harmful chemicals from our food, water, and air, USA is taking a few steps backwards. The most recent de-regulation concerns chlorphyrifos (CFP), a horrible pesticide banned in EU in 2008 (and in most of the world. China also prohibited its use on produce in 2016). CFP is associated with serious neurodevelopmental defects in humans and is highly toxic to the wildlife, particularly bees.

The paper that I’m covering today wanted to see if there is anything the consumer can do about pesticides in their produce. Unfortunately, they did not look at CFP. And why would they? At the time this study was conducted they probably thought, like the rest of us, that CFP is over and done with [breathe, slowly, inhale, exhale, repeat, focus].

Yang et al. (2017) bought organic Gala apples and then exposed them to two common pesticides: thiabendazole and phosmet (an organophosphate) at doses commonly used by farmers (125 ng/cm2). Then they washed the apples in three solutions: sodium bicarbonate (baking soda, NaHCO3, with the concentration of 10 mg/mL), Clorox (germicidal bleach with the concentration of 25 mg/L available chlorine) and tap water.

Before and after the washes the researchers used surface-enhanced Raman spectroscopy (which is, basically, a special way of doing microscopy) to take a closer look at the apples.

They found out that:

1) “Surface pesticide residues were most effectively removed by sodium bicarbonate (baking soda, NaHCO3) solution when compared to either tap water or Clorox bleach” (abstract).

2) The more you wash the more pesticide you remove. If you immerse apples in backing soda for 12 minutes for thiabendazole and 15 minutes for phosmet and then rinse with water there will be no detectable residue of these pesticides on the surface.

3) “20% of applied thiabendazole and 4.4% of applied phosmet penetrated into apples” (p. 9751) which cannot be removed by washing. Thiabendazole penetrates into the apple up to 80μ, which is four times more than phosmet (which goes up top 20 μm).

4) “the standard postharvest washing method with Clorox bleach solution for 2 min did not effectively remove surface thiabendazole” (p. 9748).

5) Phosmet is completely degraded by baking soda, whereas thiabenzole appears to be only partially so.

True to my nitpicking nature, I wish that the authors washed the apples in tap water for 8 minutes, not 2, like they did for Clorox and baking soda in the internal pesticide residue removal experiment. Nevertheless, the results stand as they are robust and their detection method is ultrasensitive being able to detect thiabendazole as low as 2μg/L and phosmet as low as 10 μg/L.

Thiabendazole is a pesticide that works by interfering with a basic enzymatic reaction in anaerobic respiration. I’m an aerobe so I shouldn’t worry about this pesticide too much unless I get a huge dose of it and then it is poisonous and carcinogenic, like most things in high doses. Phosmet, on the other hand, is an acetylcholinesterase (AChE) inhibitor (AChEI), meaning its effects in humans are akin to cholinergic poisoning. Normally, acetylcholine (ACh) binds to its muscarinic and nicotinic receptors in your muscles and brain for proper functioning of same. AChE breaks down ACh when is not needed any more by said muscles and brain. Therefore, an AChEI stops AChE from breaking down ACh resulting in overall more ACh than it’s good for you. Meaning it can kill you. Phosmet’s effects, in addition to, well…, death from acute poisoning, include trouble breathing, muscle weakness or tension, convulsions, anxiety, paralysis, quite possible memory, attention, and thinking impairments. Needles to say, it’s not so great for child development either. Think nerve gas, which is also an AChEI, and you’ll get a pretty good picture. Oh, it’s also a hormone mimicker.

I guess I’m back buying organic again. Long ago I have been duped for a short while into buying organic produce for my family believing, like many others, that it is pesticide-free. And, like many others, I was wrong. Just a bit of PubMed search told me that some of the “organic” pesticides are quite unpleasant. But I’ll take copper sulfate over chlorphyrifos any day. The choice is not from healthy to unhealthy but from bad to worse. I know, I know, the paper is not about CFP. I have a lot of pet peeves, alright?

Meanwhile, I gotta go make a huge batch of baking soda solution. Thanks, Yang et al. (2017)!

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REFERENCE: Yang T, Doherty J, Zhao B, Kinchla AJ, Clark JM, & He L (8 Nov 2017, Epub 25 Oct 2017). Effectiveness of Commercial and Homemade Washing Agents in Removing Pesticide Residues on and in Apples. Journal of Agricultural and Food Chemistry, 65(44):9744-9752. PMID: 29067814, doi: 10.1021/acs.jafc.7b03118. ARTICLE

By Neuronicus, 19 May 2018

The FIRSTS: The roots of depressive realism (1979)

There is a rumor stating that depressed people see the world more realistically and the rest of us are – to put it bluntly – deluded optimists. A friend of mine asked me if this is true. It took me a while to find the origins of this claim, but after I found it and figured out that the literature has a term for the phenomenon (‘depressive realism’), I realized that there is a whole plethora of studies on the subject. So the next following posts will be centered, more or less, on the idea of self-deception.

It was 1979 when Alloy & Abramson published a paper who’s title contained the phrase ‘Sadder but Wiser’, even if it was followed by a question mark. The experiments they conducted are simple, but the theoretical implications are large.

The authors divided several dozens of male and female undergraduate students into a depressed group and a non-depressed group based on their Beck Depression Inventory scores (a widely used and validated questionnaire for self-assessing depression). Each subject “made one of two possible responses (pressing a button or not pressing a button) and received one of two possible outcomes (a green light or no green light)” (p. 447). Various conditions presented the subjects with various degrees of control over what the button does, from 0 to 100%. After the experiments, the subjects were asked to estimate their control over the green light, how many times the light came on regardless of their behavior, what’s the percentage of trials on which the green light came on when they pressed or didn’t press the button, respectively, and how did they feel. In some experiments, the subjects were wining or losing money when the green light came on.

Verbatim, the findings were that:

“Depressed students’ judgments of contingency were surprisingly accurate in all four experiments. Nondepressed students, on the other hand, overestimated the degree of contingency between their responses and outcomes when noncontingent outcomes were frequent and/or desired and underestimated the degree of contingency when contingent outcomes were undesired” (p. 441).

In plain English, it means that if you are not depressed, when you have some control and bad things are happening, you believe you have no control. And when you have no control but good things are happening, then you believe you have control. If you are depressed, it does not matter, you judge your level of control accurately, regardless of the valence of the outcome.

Such illusion of control is a defensive mechanism that surely must have adaptive value by, for example, allowing the non-depressed to bypass a sense of guilt when things don’t work out and increase self-esteem when they do. This is fascinating, particularly since it is corroborated by findings that people receiving gambling wins or life successes like landing a good job, rewards that at least in one case are demonstrably attributable to chance, believe, nonetheless, that it is due to some personal attributes that make them special, that makes them deserving of such rewards. (I don’t remember the reference of this one so don’t quote me on it. If I find it, I’ll post it, it’s something about self-entitlement, I think). That is not to say that life successes are not largely attributable to the individual; they are. But, statistically speaking, there must be some that are due to chance alone, and yet most people feel like they are the direct agents for changes in luck.

Another interesting point is that Alloy & Abramson also tried to figure out how exactly their subjects reasoned when they asserted their level of control through some clever post-experiment questioners. Long story short (the paper is 45 pages long), the illusion of control shown by nondepressed subjects in the no control condition was the result of incorrect logic, that is, faulty reasoning.

In summary, the distilled down version of depressive realism that non-depressed people see the world through rose-colored glasses is slightly incorrect. Because only in particular conditions this illusion of control applies, and that is overestimation of control only when good things are happening and underestimation of control when bad things are happening. But, by and large, it does seem that depression clears the fog a bit.

Of course, it has been over 40 years since the publication of this paper and of course it has its flaws. Many replications and replications with caveats and meta-analyses and reviews and opinions and alternative hypotheses have been confirmed and infirmed and then confirmed again with alterations, so there is still a debate out there about the causes/ functions/ ubiquity/ circumstantiality of the depressive realism effect. One thing seems to be constant though: the effect exists.

I will leave you with the ponders of Alloy & Abramson (1979):

“A crucial question is whether depression itself leads people to be “realistic” or whether realistic people are more vulnerable to depression than other people” (p. 480).

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REFERENCE: Alloy LB, & Abramson LY (Dec. 1979). Judgment of contingency in depressed and nondepressed students: sadder but wiser? Journal of Experimental Psychology: General, 108(4): 441-485. PMID: 528910. http://dx.doi.org/10.1037/0096-3445.108.4.441. ARTICLE | FULLTEXT PDF via ResearchGate

By Neuronicus, 30 November 2017

The FIRSTS: Dinosaurs and reputation (1842)

‘Dinosaur’ is a common noun in most languages of the Globe and, in its weak sense, it means “extinct huge reptile-like animal that lived a long-time ago”. The word has been in usage for so long that it can be used also for describing something “impractically large, out-of-date, or obsolete” (Merriam-Webster dictionary). “Dinosaur” is a composite of two ancient Greek words (“deinos”, “sauros”) and it means “terrible lizard”.

But, it turns out that the word hasn’t been in usage for so long, just for a mere 175 years. Sir Richard Owen, a paleontologist that dabbled in many disciplines, coined the term in 1842. Owen introduced the taxon Dinosauria as if it was always called thus, no fuss: “The present and concluding part of the Report on British Fossil Reptiles contains an account of the remains of the Crocodilian, Dinosaurian, Lacertian, Pterodactylian, Chelonian, Ophidian and Batrachian reptiles.” (p. 60). Only later in the Report does he tell us his paleontological reasons for the baptism, namely some anatomical features that distinguish dinosaurs from crocodiles and other reptiles.

“…The combination of such characters, some, as the sacral ones, altogether peculiar among Reptiles, others borrowed, as it were, from groups now distinct from each other, and all manifested by creatures far surpassing in size the largest of existing reptiles, will, it is presumed, be deemed sufficient ground for establishing a distinct tribe or sub-order of Saurian Reptiles, for which I would propose the name of Dinosauria.” (p.103)

At the time he was presenting this report to the British Association for the Advancement of Science, other giants of biology were running around the same halls, like Charles Darwin and Thomas Henry Huxley. Indisputably, Owen had a keen observational eye and a strong background in comparative anatomy that resulted in hundreds of published works, some of them excellent. That, in addition to establishing the British Museum of Natural History.

Therefore, Owen had reasons to be proud of his accomplishments and secure in his influence and legacy, and yet his contemporaries tell us that he was an absolutely vicious man, spiteful to the point of obsession, vengeful and extremely jealous of other people’s work. Apparently, he would steal the work of the younger people around him, never give credit, lie and cheat at every opportunity, and even write lengthy anonymous letters to various printed media to denigrate his contemporaries. He seemed to love his natal city of Lancaster and his family though (Wessels & Taylor, 2015).

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Sir Richard Owen (20 July 1804 – 18 December 1892). PD, courtesy of Wikipedia.

Owen had a particular hate for Darwin. They had been close friends for 20 years and then Darwin published the “Origin of Species”. The book quickly became widely read and talked about and then poof: vitriol and hate. Darwin himself said the only reason he could think of for Owen’s hatred was the popularity of the book.

Various biographies and monographers seem to agree on his unpleasant personality (see his entry in The Telegraph, Encyclopedia.com, Encylopaedia Britannica, BBC). On a side note, should you be concerned about your legacy and have the means to persuade The Times to write you an obituary, by all means, do so. In all the 8 pages of obituary written in 1896 you will not find a single blemish on the portrait of Sir Richard Owen.

This makes me ponder on the judgement of history based not on your work, but on your personality. As I said, the man contributed to science in more ways than just naming the dinosaur and having spats with Darwin. And yet it seems that his accomplishments are somewhat diminished by the way he treated others.

This reminded me of Nicolae Constantin Paulescu, a Romanian scientist who discovered insulin in 1916 (published in 1921). Yes, yes, I know all about the controversy with the Canadians that extracted and purified the insulin in 1922 and got the Nobel for it in 1923. Paulescu did the same, even if Paulescu’s “pancreatic extract” from a few years earlier was insufficiently purified; it still successfully lowered the glicemic index in dogs. He even obtained a patent for the “fabrication of pancrein” (his name for insulin, because he obtained it from the pancreas) in April 1922 from the Romanian Government (patent no. 6255). The Canadian team was aware of his work, but because it was published in French, they had a poor translation and they misunderstood his findings, so, technically, they didn’t steal anything. Or so they say. Feel free to feed the conspiracy mill. I personally don’t know, I haven’t looked at the original work to form an opinion because it is in French and my French is non-existent.

Annnywaaaay, whether or not Paulescu was the first in discovering the insulin is debatable, but few doubt that he should have shared the Nobel at least.

Rumor has it that Paulescu did not share the Nobel because he was a devout Nazi. His antisemitic writings are remarkably horrifying, even by the standards of the extreme right. That’s also why you won’t hear about him in medical textbooks or at various diabetes associations and gatherings. Yet millions of people worldwide may be alive today because of his work, at least partly.

How should we remember? Just the discoveries and accomplishments with no reference to the people behind them? Is remembering the same as honoring? “Clara cells” were lung cells discovered by the infamous Nazi anatomist Max Clara by dissecting prisoners without consent. They were renamed by the lung community “club cells” in 2013. We cannot get rid of the discovery, but we can rename the cells, so it doesn’t look like we honor him. I completely understand that. And yet I also don’t want to lose important pieces of history because of the atrocities (in the case of Nazis) or unsavory behavior (in the case of Owen) committed by our predecessors. I understand why the International Federation of Diabetes does not wish to give awards in the name of Paulescu or have a Special Paulescu lecture. Perhaps the Romanians should take down his busts and statues, too. But I don’t understand why (medical) history books should exclude him.

In other words, don’t honor the unsavories of history, but don’t forget them either. You never know what we – or the future generations – may learn by looking back at them and their actions.

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By Neuronicus, 19 October 2017

References:

1) Owen, R (1842). “Report on British Fossil Reptiles”. Part II. Report of the Eleventh Meeting of the British Association for the Advancement of Science; Held at Plymouth in July 1841. London: John Murray. p. 60–204. Google Books Fulltext 

2) “Eminent persons: Biographies reprinted from the Times, Vol V, 1891–1892 – Sir Richard Owen (Obituary)” (1896). Macmillan & Co., p. 291–299. Google Books Fulltext

3) Wessels Q & Taylor AM (28 Oct 2015). Anecdotes to the life and times of Sir Richard Owen (1804-1892) in Lancaster. Journal of Medical Biography. pii: 0967772015608053. PMID: 26512064, DOI: 10.1177/0967772015608053. ARTICLE

Play-based or academic-intensive?

preschool - CopyThe title of today’s post wouldn’t make any sense for anybody who isn’t a preschooler’s parent or teacher in the USA. You see, on the west side of the Atlantic there is a debate on whether a play-based curriculum for a preschool is more advantageous than a more academic-based one. Preschool age is 3 to 4 years;  kindergarten starts at 5.

So what does academia even looks like for someone who hasn’t mastered yet the wiping their own behind skill? I’m glad you asked. Roughly, an academic preschool program is one that emphasizes math concepts and early literacy, whereas a play-based program focuses less or not at all on these activities; instead, the children are allowed to play together in big or small groups or separately. The first kind of program has been linked with stronger cognitive benefits, while the latter with nurturing social development. The supporters of one program are accusing the other one of neglecting one or the other aspect of the child’s development, namely cognitive or social.

The paper that I am covering today says that it “does not speak to the wider debate over learning-through-play or the direct instruction of young children. We do directly test whether greater classroom time spent on academic-oriented activities yield gains in both developmental domains” (Fuller et al., 2017, p. 2). I’ll let you be the judge.

Fuller et al. (2017) assessed the cognitive and social benefits of different programs in an impressive cohort of over 6,000 preschoolers. The authors looked at many variables:

  • children who attended any form of preschool and children who stayed home;
  • children who received more (high dosage defined as >20 hours/week) and less preschool education (low dosage defined as <20 hour per week);
  • children who attended academic-oriented preschools (spent at least 3 – 4 times a week on each of the following tasks: letter names, writing, phonics and counting manipulatives) and non-academic preschools.

The authors employed a battery of tests to assess the children’s preliteracy skills, math skills and social emotional status (i.e. the independent variables). And then they conducted a lot of statistical analyses in the true spirit of well-trained psychologists.

The main findings were:

1) “Preschool exposure [of any form] has a significant positive effect on children’s math and preliteracy scores” (p. 6).school-1411719801i38 - Copy

2) The earlier the child entered preschool, the stronger the cognitive benefits.

3) Children attending high-dose academic-oriented preschools displayed greater cognitive proficiencies than all the other children (for the actual numbers, see Table 7, pg. 9).

4) “Academic-oriented preschool yields benefits that persist into the kindergarten year, and at notably higher magnitudes than previously detected” (p. 10).

5) Children attending academic-oriented preschools displayed no social development disadvantages than children that attended low or non-academic preschool programs. Nor did the non-academic oriented preschools show an improvement in social development (except for Latino children).

Now do you think that Fuller et al. (2017) gave you any more information in the debate play vs. academic, given that their “findings show that greater time spent on academic content – focused on oral language, preliteracy skills, and math concepts – contributes to the early learning of the average child at magnitudes higher than previously estimated” (p. 10)? And remember that they did not find any significant social advantages or disadvantages for any type of preschool.

I realize (or hope, rather) that most pre-k teachers are not the Draconian thou-shall-not-play-do-worksheets type, nor are they the let-kids-play-for-three-hours-while-the-adults-gossip-in-a-corner types. Most are probably combining elements of learning-through-play and directed-instruction in their programs. Nevertheless, there are (still) programs and pre-k teachers that clearly state that they employ play-based or academic-based programs, emphasizing the benefits of one while vilifying the other. But – surprise, surprise! – you can do both. And, it turns out, a little academia goes a long way.

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So, next time you choose a preschool for your kid, go with the data, not what your mommy/daddy gut instinct says and certainly be very wary of preschool officials who, when you ask them for data to support their curriculum choice, tell you that that’s their ‘philosophy’, they don’t need data. Because, boy oh boy, I know what philosophy means and it ain’t that.

By Neuronicus, 12 October 2017

Reference: Fuller B, Bein E, Bridges M, Kim, Y, & Rabe-Hesketh, S. (Sept. 2017). Do academic preschools yield stronger benefits? Cognitive emphasis, dosage, and early learning. Journal of Applied Developmental Psychology, 52: 1-11, doi: 10.1016/j.appdev.2017.05.001. ARTICLE | New York Times cover | Reading Rockets cover (offers a fulltext pdf) | Good cover and interview with the first author on qz.com

Old chimpanzees get Alzheimer’s pathology

Alzheimer’s Disease (AD) is the most common type of dementia with a progression that can span decades. Its prevalence is increasing steadily, particularly in the western countries and Australia. So some researchers speculated that this particular disease might be specific to humans. For various reasons, either genetic, social, or environmental.

A fresh e-pub brings new evidence that Alzheimer’s might plague other primates as well. Edler et al. (2017) studied the brains of 20 old chimpanzees (Pan troglodytes) for a whole slew of Alzheimer’s pathology markers. More specifically, they looked for these markers in brain regions commonly affected by AD, like the prefrontal cortex, the midtemporal gyrus, and the hippocampus.

Alzheimer’s markers, like Tau and Aβ lesions, were present in the chimpanzees in an age-dependent manner. In other words, the older the chimp, the more severe the pathology.

Interestingly, all 20 animals displayed some form of Alzheimer’s pathology. This finding points to another speculation in the field which is: dementia is just part of normal aging. Meaning we would all get it, eventually, if we would live long enough; some people age younger and some age older, as it were. This hypothesis, however, is not favored by most researchers not the least because is currently unfalsifiable. The longest living humans do not show signs of dementia so how long is long enough, exactly? But, as the authors suggest, “Aβ deposition may be part of the normal aging process in chimpanzees” (p. 24).

Unfortunately, “the chimpanzees in this study did not participate in formal behavioral or cognitive testing” (p. 6). So we cannot say if the animals had AD. They had the pathological markers, yes, but we don’t know if they exhibited the disease as is not uncommon to find these markers in humans who did not display any behavioral or cognitive symptoms (Driscoll et al., 2006). In other words, one might have tau deposits but no dementia symptoms. Hence the title of my post: “Old chimpanzees get Alzheimer’s pathology” and not “Old chimpanzees get Alzheimer’s Disease”

Good paper, good methods and stats. And very useful because “chimpanzees share 100% sequence homology and all six tau isoforms with humans” (p. 4), meaning we have now a closer to us model of the disease so we can study it more, even if primate research has taken significant blows these days due to some highly vocal but thoroughly misguided groups. Anyway, the more we know about AD the closer we are of getting rid of it, hopefully. And, soon enough, the aforementioned misguided groups shall have to face old age too with all its indignities and my guess is that in a couple of decades or so there will be fresh money poured into aging diseases research, primates be damned.

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REFERENCE: Edler MK, Sherwood CC, Meindl RS, Hopkins WD, Ely JJ, Erwin JM, Mufson EJ, Hof PR, & Raghanti MA. (EPUB July 31, 2017). Aged chimpanzees exhibit pathologic hallmarks of Alzheimer’s disease. Neurobiology of Aging, PII: S0197-4580(17)30239-7, DOI: http://dx.doi.org/10.1016/j.neurobiolaging.2017.07.006. ABSTRACT  | Kent State University press release

By Neuronicus, 23 August 2017

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Midichlorians, midichloria, and mitochondria

Nathan Lo is an evolutionary biologist interested in creepy crawlies, i.e. arthropods. Well, he’s Australian, so I guess that comes with the territory (see what I did there?). While postdoc’ing, he and his colleagues published a paper (Sassera et al., 2006) that would seem boring for anybody without an interest in taxonomy, a truly under-appreciated field.

The paper describes a bacterium that is a parasite for the mitochondria of a tick species called Ixodes ricinus, the nasty bugger responsible for Lyme disease. The authors obtained a female tick from Berlin, Germany and let it feed on a hamster until it laid eggs. By using genetic sequencing (you can use kits these days to extract the DNA, do PCR, gels and cloning, pretty much everything), electron microscopy (real powerful microscopes) and phylogenetic analysis (using computer softwares to see how closely related some species are) the authors came to the conclusion that this parasite they were working on is a new species. So they named it. And below is the full account of the naming, from the horse’s mouth, as it were:

“In accordance with the guidelines of the International Committee of Systematic Bacteriology, unculturable bacteria should be classified as Candidatus (Murray & Stackebrandt, 1995). Thus we propose the name ‘Candidatus Midichloria mitochondrii’ for the novel bacterium. The genus name Midichloria (mi.di.chlo′ria. N.L. fem. n.) is derived from the midichlorians, organisms within the fictional Star Wars universe. Midichlorians are microscopic symbionts that reside within the cells of living things and ‘‘communicate with the Force’’. Star Wars creator George Lucas stated that the idea of the midichlorians is based on endosymbiotic theory. The word ‘midichlorian’ appears to be a blend of the words mitochondrion and chloroplast. The specific epithet, mitochondrii (mi.to′chon.drii. N.L. n. mitochondrium -i a mitochondrion; N.L. gen. n. mitochondrii of a mitochondrion), refers to the unique intramitochondrial lifestyle of this bacterium. ‘Candidatus M. mitochondrii’ belongs to the phylum Proteobacteria, to the class Alphaproteobacteria and to the order Rickettsiales. ‘Candidatus M. mitochondrii’ is assigned on the basis of the 16S rRNA (AJ566640) and gyrB gene sequences (AM159536)” (p. 2539).

George Lucas gave his blessing to the Christening (of course he did).

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Acknowledgements: Thanks go to Ms. BBD who prevented me from making a fool of myself (this time!) on the social media by pointing out to me that midichloria are real and that they are a mitochondrial parasite.

REFERENCE: Sassera D, Beninati T, Bandi C, Bouman EA, Sacchi L, Fabbi M, Lo N. (Nov. 2006). ‘Candidatus Midichloria mitochondrii’, an endosymbiont of the tick Ixodes ricinus with a unique intramitochondrial lifestyle. International Journal of Systematic and Evolutionary Microbiology, 56(Pt 11): 2535-2540. PMID: 17082386, DOI: 10.1099/ijs.0.64386-0. ABSTRACT | FREE FULLTEXT PDF 

By Neuronicus, 29 July 2017

Pic of the day: Skunky beer

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REFERENCE: Burns CS, Heyerick A, De Keukeleire D, Forbes MD. (5 Nov 2001). Mechanism for formation of the lightstruck flavor in beer revealed by time-resolved electron paramagnetic resonance. Chemistry – The European Journal, 7(21): 4553-4561. PMID: 11757646, DOI: 10.1002/1521-3765(20011105)7:21<4553::AID-CHEM4553>3.0.CO;2-0. ABSTRACT

By Neuronicus, 12 July 2017

The FIRSTS: Increase in CO2 levels in the atmosphere results in global warming (1896)

Few people seem to know that although global warming and climate change are hotly debated topics right now (at least on the left side of the Atlantic) the effect of CO2 levels on the planet’s surface temperature was investigated and calculated more than a century ago. CO2 is one of the greenhouse gases responsible for the greenhouse effect, which was discovered by Joseph Fourier in 1824 (the effect, that is).

Let’s start with a terminology clarification. Whereas the term ‘global warming’ was coined by Wallace S. Broecker in 1975, the term ‘climate change’ underwent a more fluidic transformation in the ’70s from ‘inadvertent climate modification’ to ‘climatic change’ to a more consistent use of ‘climate change’ by Jule Charney in 1979, according to NASA. The same source tells us:

“Global warming refers to surface temperature increases, while climate change includes global warming and everything else that increasing greenhouse gas amounts will affect”.

But before NASA there was one Svante August Arrhenius (1859–1927). Dr. Arrhenius was a Swedish physical chemist who received the Nobel Prize in 1903 for uncovering the role of ions in how electrical current is conducted in chemical solutions.

S.A. Arrhenius was the first to quantify the variations of our planet’s surface temperature as a direct result of the amount of CO2 (which he calls carbonic acid, long story) present in the atmosphere. For those – admittedly few – nitpickers that say his views on the greenhouse effect were somewhat simplistic and his calculations were incorrect I’d say cut him a break: he didn’t have the incredible amount of data provided by the satellites or computers, nor the work of thousands of scientists over a century to back him up. Which they do. Kind of. Well, the idea, anyway, not the math. Well, some of the math. Let me explain.

First, let me tell you that I haven’t managed to pass past page 3 of the 39 pages of creative mathematics, densely packed tables, parameter assignments, and convoluted assumptions of Arrhenius (1896). Luckily, I convinced a spectroscopist to take a crack at the original paper since there is a lot of spectroscopy in it and then enlighten me.

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The photo was taken in 1887 and shows (standing, from the left): Walther Nernst (Nobel in Chemistry), Heinrich Streintz, Svante Arrhenius, Richard Hiecke; (sitting, from the left): Eduard Aulinger, Albert von Ettingshausen, Ludwig Boltzmann, Ignaz Klemenčič, Victor Hausmanninger. Source: Universität Graz. License: PD via Wikimedia Commons.

Second, despite his many accomplishments, including being credited with laying the foundations of a new field (physical chemistry), Arrhenius was first and foremost a mathematician. So he employed a lot of tedious mathematics (by hand!) together with some hefty guessing along with what was known at the time about Earth’s infrared radiation, solar radiation, water vapor and CO2 absorption, temperature of the Moon,  greenhouse effect, and some uncalibrated spectra taken by his predecessors to figure out if “the mean temperature of the ground [was] in any way influenced by the presence of the heat-absorbing gases in the atmosphere” (p. 237). Why was he interested in this? We find out only at page 267 after a lot of aforesaid dreary mathematics where he finally shares this with us:

“I certainly not have undertaken these tedious calculations if an extraordinary interest had not been connected with them. In the Physical Society of Stockholm there have been occasionally very lively discussions on the probable causes of the Ice Age”.

So Arrhenius was interested to find out if the fluctuations of CO2 levels could have caused the Ice Ages. And yes, he thinks that could have happened. I don’t know enough about climate science to tell you if this particular conclusion of his is correct today. But what he managed to accomplish though was to provide for the first time a way to mathematically calculate the amount of rise in temperature due the rise of CO2 levels. In other words, he found a direct relationship between the variations of CO2 and temperature.

Today, it turns out that his math was incorrect because he left out some other variables that influence the global temperature that were discovered and/or understood later (like the thickness of the atmosphere, the rate of ocean absorption  of CO2 and others which I won’t pretend I understand). Nevertheless, Arrhenius was the first to point out to the following relationship, which, by and large, is still relevant today:

“Thus if the quantity of carbonic acid increased in geometric progression, the augmentation of the temperature will increase nearly in arithmetic progression” (p. 267).

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P.S. Technically, Joseph Fourier should be credited with the discovery of global warming by means of increasing the levels of greenhouse gases in the atmosphere in 1824, but Arrhenius quantified it so I credited him. Feel fee to debate :).

REFERENCE: Arrhenius, S. (April 1896). XXXI. On the Influence of Carbonic Acid in the Air upon the Temperature of the Ground, The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science (Fifth Series), 49 (251): 237-276. General Reference P.P.1433. doi: http://dx.doi.org/10.1080/14786449608620846. FREE FULLTEXT PDF

By Neuronicus, 24 June 2017