The platypus and the Komodo dragon


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The platypus (Ornithorhynchus anatinus) has 26 pairs of chromosomes in total, compared with the 23 pairs present in humans. But researchers had long been confused about which ones are autosomal (inherited equally by males and females), and which ones determine sex. Most of the time for humans two full copies (XX) of the arbitrarily numbered chromosome 23 is a female and one full and one partial copy (XY) is a male. One serious consequence for males of this arrangement is that any genes with challenges on the the unmatched regions of the X chromosome cannot be compensated for – there’s nothing there. This can be a very big deal – the X chromosome contains about 155 million base pairs (5% of the human genome), while the Y chromosome contains about 59 million base pairs. In addition there are what are called pseudo-autosomal regions on both the X and the Y. Most of the time in females one X chromosome in each cell is randomly deactivated so what’s available might either be DNA from the father or the mother. The current best guess is that the human Y chromosome contains between 50 and 60 protein-coding genes, and the human X chromosome contains between 800 and 900 protein-coding genes.

Most birds, some fish, some crustaceans (notably the very complicated Macrobrachium rosenbergii, known as the giant river prawn), some insects (butterflies and moths) and some reptiles (the Komodo dragon – Varanus komodoensis) use a ZW system. ZZ is a male and ZW is a female so the female’s contribution determines the sex of the offspring. In our present context the Komodo dragon is interesting because, while it can see objects as far away as 300 meters, its retinas only contain cones, so it is thought to have poor night vision, reasonable ability to distinguish colors, and poor visual discrimination of stationary objects. A tough laboratory subject.

The platypus and its relatives (monotremes) do not possess the OPN1SW gene so they would be unable to see blues and purples – for example, the sky would always appear overcast.



Three Genes for Human Beings


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With apologies to J.R.R. Tolkien …

Achromatopsia is a disorder characterized by a partial or total lack of color vision sometimes occurring with other vision problems such as sensitivity to light (photophobia), involuntary back-and-forth eye movements (nystagmus), and nearsightedness (myopia). Three genes of special interest in achromatopsia are OPN1LW, OPN1MW and OPN1SW where the fifth characters stand for long, medium and short. Most people have one copy of the OPN1LW gene and one or more copies of the OPN1MW gene on each X chromosome. A nearby region of DNA, known as the locus control region (LCR), regulates the activity of these genes. Only the two opsin pigment genes nearest the LCR, generally the OPN1LW gene and the first copy of the OPN1MW gene, are active in the retina and contribute to color vision. Usually, the OPN1LW gene’s location is described as Xq28 [q being the long arm of the X chromosome] at about  base pairs 154,144,224 to 154,159,032 while the OPN1MW gene’s location is at base pairs 154,182,596 to 154,196,861. Things never are simple: the OPN1SW gene is located at 7q32.1 base pairs 128,772,489 to 128,775,790. This remoteness is not necessarily a bad thing – as we shall see, translocations of parts of OPN1LW and OPN1MW cause all sorts of trouble.

Opsins are a collection of proteins that are light sensitive – when struck by a photon they can emit an electron so that a useful signal can be processed. The earlier prokaryotic life-forms such as Archaea (the so-called simple single celled organisms) and Bacteria have type I opsins as do some eukaryotic forms like green algae. Type I opsins react to light faster and more reliably than type II opsins like those used by eukaryotes like us.

Most animals with eyes have retinas, which are the light-sensitive tissue at the back of the eye. The retina contains two types of light receptor cells, called rods and cones, that transmit visual signals from the eye to the brain. Rods provide vision in low light. Cones provide vision in bright light, including color vision. Most of the time there are three types of cones, each containing a specific opsin that is most sensitive to particular wavelengths of light. The brain combines input from all three types of cones to produce normal color vision. The opsin made from the OPN1LW gene is more sensitive to light in the yellow/orange part of the visible spectrum (long-wavelength light), and cones with this pigment are called long-wavelength-sensitive or L cones. The opsin made from the OPN1MW gene is more sensitive to light in the middle of the visible spectrum (yellow/green light), and cones with this pigment are called middle-wavelength-sensitive or M cones. The opsin made from the OPN1SW gene is more sensitive to light in the blue/violet part of the visible spectrum (short-wavelength light), and cones with this pigment are called short-wavelength-sensitive or S cones.

Blocking the Blues


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As is well-known, sensory hypersensitivity is common in the autism spectrum. For visual or optical challenges there are two aspects – control of the lights used to illuminate classrooms and living spaces AND protective eyewear. One of the older and frequently cited papers is D.M. Fenton & R. Penney (1985) The Effects of Fluorescent and Incandescent Lighting on the Repetitive Behaviours of Autistic and Intellectually Handicapped Children, Australia and New Zealand Journal of Developmental Disabilities, 11:3, 137-141, DOI: 10.3109/13668258508998632

As it happens, there are a number of causes of visual hypersensitivity: (1) medications like tetracycline and digitalis; migraine headaches; some types of dyslexia; meningitis and lupus; as well as some types of macular degeneration and cataracts. There are certainly night blindnesses that are caused by vitamin shortages – typically of vitamin A, C, E, lutein and beta-carotene.

So I asked the grapevine for genes implicated in photophobia. So far, the count is 43.


A student wearing glasses that block some blue and white light

Lombok – some updates


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Three minor events (R4.5 and R5.1 on 8/21 and the R4.9 on 8/22) in the last couple of days. That’s not worthy of inclusion in the news cycle. But geological time is different than news time. Each circle represents an earthquake in the last 4 weeks – 90 events is a lot in such a small area (perhaps 1000 square miles) in less than one month. Without a major event like a Richter 8.5, for example, there should never be two Richter 6.9s so close in time and space.  The Richter 6.3 and 6.4 are too strong to be classical prime aftershocks, and the two Richter 5.9s are out of profile as well. Currently, the spread of events to Sumbawa island is not worrying many people as western Sumbawa is not target-rich. Likewise, a tsunami rumbling through either the strait to the west or the strait to the east is unlikely to cause major damage – neither strait hosts a major city, and neither strait is used to transport valuable commodities. Cynically, very few people not on Lombok would care  much if a major earthquake, with or without tsunami, struck Lombok.  Even a somewhat impressive VEI=4 eruption [between 0.1 and 1.0 cubic kilometers of ejecta; plume heights between 10 and 25 kilometers; happens about once every 25 years world-wide; probably pyroclastic flows, lava, hot ash) from Rinjani (on Lombok) or Tambora (on Sumbawa) or Agung, Batur or Bratan (on Bali) or perhaps some new volcano would only cause local damage. The eruption of Mount Saint Helens in Washington State in 1980 was a VEI=5 event, while Pinatubo 1991 is now commonly described as a VEI=6. Tambora (on Subawa) 1815 and Samalas (on Lombok; now known as Rinjani)  in 1257 were VEI=-7 events that impacted the climate of the our planet.

Lombok – history


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There are two problems if one seeks a large, statistically useful sample of seismic events on or around Lombok: (1) there does not seem to be any contemporary data for Richter 4.2 or weaker events and (2) not much history before 1975. The use for weak events today that I doubt anyone can feel is that they would be a good signal for magma movement. Most of the time no one cares about events below Richter 5.0 – the exception is when there is a volcano nearby. Then hundreds or even thousands of Richter 1s and 2s in a short time are a clear warning of an imminent eruption. For example, if there were hundreds of Richter 3s shaking Lombok today that is a profoundly different situation than just a few Richter 3s. The second problem is there are about 40 years of seismic history available. Unfortunately, the quality of most data more than 20 years ago is doubtful. The equations and sensors have not changed much, although Indonesia has improved its hardware in the last 12 years or so. For intermediate strength earthquakes (Richter 5.5 to Richter 7.4) the date, time, Richter and epicenter are useful. The measure of depth was a problem. To be fair, it may be that depth to the nearest 10 kilometers is close enough. For powerful earthquakes (Richter 7.5 or greater) what is really needed besides the epicenter is the geographical extent of major damage. That still is not available today. For weaker earthquakes Richter 4.0 to Richter 5.4 it is not clear that these were always recorded. That is something of a pragmatic measure – they rarely cause significant damage. Below we have Lombok earthquakes 1950-1999 – one Richter 5.8 in 1995 (cayn circle at the top; and that was well offshore) and 8 other Richter 5.0 to Richter 5.4s. That’s just about earthquake-free,  especially by Indonesian standardsLombok_Earthquakes_1950_1999

Then three Richter 5 or greater events – three of which were offshore – in 16 years


Five Richter 4s (zero Richter 5s) in the last three and one half years.Lombok_Earthquakes_2015_2018

Lombok (continued)


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Lombok_20180809the orange dot with the orange line and text is a very recent R5.9 whose epicenter was about 30 km from the earlier R6.4 and R6.9 (bigger yellow and white dots to the right).

We’ll see what Planet Earth has in store for Lombok and Indonesia. I certainly hope the Indonesian government is devoting a great deal of thought and energy. I would think, especially after the anomalous R5.9, that serious thought should be given to

1. how to get aid to Lombok (and probably Bali) if there is a major earthquake there – with or without tsunami. As far as I know, Lombok International (IATA: LOP) is the only airport on the island. You can check in on things at – there is an EN at the top for the English language version

As readers may recall, airport construction (an upgrade) was delayed and the opening date re-scheduled several times. Many issues contributed to the delays including problems with site security; thefts of construction materials and equipment from the site; issues of land use; tensions with some of the local community over compensation; and employment on the site. Other issues involved the quality of construction of the main runway and taxiways and problems with the control tower. So we may see a quality assurance audit by our planet if there is a major geological event. I would be concerned what can be done for evacuation and reconstruction both if the airport remains intact and if the airport is damaged.
2. There would be something of a domino effect – suppose the airport is working
and the air is clear of ash. Evacuating tourists by air is technically possible. But
if the resident population has to be moved – where do they go and how do they get there? Even if the Indonesian military can heroically shuttle 3 million people by helicopter to Bali so what? There’s no room there.
3. Similarly, it should be considered what to do if ferries and their docks are damaged.
4. This all gets much more complicated if there is a volcano blasting ash 10,000 feet into the air. There has, alas, not been much work on classifying volcanic eruptions by duration. The problem for modern airliners is simply the threat of an imminent eruption will effectively stop flights in – and will accelerate flights out to avoid ash damage to engines, wings and bodies. A volcanic threat could last months as was shown by events in Iceland not so long ago (Eyjafjallajokull 2010). The real challenge with all of this is the Earth has not announced a schedule, so the Indonesian government and its military would be making decisions on the fly, so as to speak, if things go badly wrong. I would think NOW is a really good time to look ahead and think what might be needed.
Perhaps this will all just end quietly. The recent R5.9 suggests otherwise



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Here’s an eagle’s eye view of some recent earthquakes on the island of Lombok in Indonesia. As noted, the four off-island but nearby quakes (in cyan) were all under Richter 5.0. Indonesia has thousands of these Richter 5 and Richter 6 events per year and they rarely get any attention.

Indonesia is made up of over 17,500 islands: 17,504 according to the Indonesian Coordinating Ministry for Maritime Affairs; 17,508 according to the CIA; and 18,307 according to the Indonesian National Institute of Aeronautics and Space (usually abbreviated as LAPAN). I would say it is fair to claim that just over 900 are permanently inhabited. Politically, Lombok is part of West Nusa Tenggara, and the Sumbawa peninsula on the right (= east) belongs to that province as well. Bali with some nearby islands is a province grouped with the Lesser Sunda Islands. For purposes of comparison, Bali has an area of about 5800 square kilometers (2200 square miles – slightly smaller than the state of Delaware) and a population of 4.2 million, while Lombok has an area of 4500 square kilometers (1700 square miles – a little bigger than the state of Rhode Island) and a population of 3.3 million. Bali and Lombok are the 15th and 17th largest Indonesian islands, respectively.

Government Spending in Western Africa


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Generally, Western African governments earn revenue from taxes, mining concessions and fishing rights. The percentages belong reflect the deficit (expenses being larger than revenues) as a percentage of revenues. Sao Tome and Principe has a balanced budget and the Democratic Republic of the Congo and Mauritania came close.