TL:DR – Brief spot of garden birding with friends in Teesdale and some sightseeing.
We spent a lovely couple of days with wonderful friends at their place in Teesdale…unfortunately I’ve been struggling to walk with an ankle injury so the usual long country walks and sightseeing were off the agenda, but we did get to toddle around the fabulous Bowes Museum in Barnard Castle and to sample some local ale at the local pub for local people (and their friends).
Our friends had also arranged a fabulous selection of birds to use their garden bird feeders while we were there: Brambling, Nuthatch, Coal Tit, Great Spotted Woodpecker (M+F), Redpoll, Goldfinch, Long-tailed Tit, Great Tit, Blue Tit, Dunnock, Robin, Chaffinch, Jackdaw, Rook (either or both of which repeatedly knocked the feeders on to the lawn), Blackbird, House Sparrow, Starling (mainly in the trees not on the feeders); also Chiff Chaff calling from one of their trees. Didn’t see Tawny Owl on this visit.
The Tees at Barnard Castle was too rough and high within my walking range to catch sight of Dippers or wagtails fishing this time, but there were Mallard ducklings on the foamy banks and a solitary Whooper Swan looking rather out of place below the castle ruins.
TL:DR – Recent experience with asking ChatGPT chemistry questions reveals the limitations of this language model, despite the claims and hype of an ignorant US politician speaking in March 2023.
There was lots of talk of ChatGPT apparently deciding to teach itself organic chemistry…now…ChatGPT is language model, it’s not really an artificial intelligence (AI) in the strict sense, all it really is is a sophisticated autocomplete that analyses your prompts and weighs up the most likely combination of words with which to reply. I wondered whether the only chemistry in all that hype was the chemistry between olfactory receptor and odourant molecules in bovine ordure. So, I set it a challenge, giving it the following prompt:
You are to act as an expert organic chemist. You need to devise a reaction scheme using retrosynthetic analysis for the drug molecule Taxol.
This is how it responded:
Taxol is a complex natural product that has antitumor activity and is used in the treatment of various cancers. The molecule contains a complex array of functional groups, including multiple stereocenters, which make its synthesis a significant challenge.
Here is a possible retrosynthetic analysis of taxol:
Step 1: The first step involves disconnection of the C13 side chain from the taxane core. This can be achieved using a standard acid-catalyzed esterification reaction between a carboxylic acid and an alcohol. This disconnection leads to the formation of the intermediate 10-deacetylbaccatin III.
Step 2: The second step involves disconnection of the A and B rings from the taxane core. This can be achieved using a retro-Diels-Alder reaction. The retro-Diels-Alder reaction involves breaking the six-membered ring formed in the Diels-Alder reaction between the A and B rings. This leads to the formation of the intermediate 9-dihydro-13-acetylbaccatin III.
Step 3: The third step involves disconnection of the C ring from the taxane core. This can be achieved using a ring-opening reaction. The ring-opening reaction involves breaking the bond between C9 and C10, leading to the formation of the intermediate 7,8-didehydro-10-deacetylbaccatin III.
Step 4: The fourth step involves disconnection of the D ring from the taxane core. This can be achieved using a ring-closing reaction. The ring-closing reaction involves forming a new bond between C1 and C14, leading to the formation of the intermediate 5-deoxy-4-O-methyltaxol.
Step 5: The final step involves disconnection of the C2 side chain from the taxane core. This can be achieved using a standard nucleophilic substitution reaction. This leads to the formation of the final product, taxol.
Overall, the retrosynthetic analysis of taxol involves a series of complex reactions, including esterification, retro-Diels-Alder reaction, ring-opening reaction, ring-closing reaction, and nucleophilic substitution reaction. These reactions can be challenging to carry out in practice, and developing efficient and practical synthetic routes to taxol remains an active area of research in organic chemistry.
Now, it’s a long time since I did any retrosynthetic analyses for organic chemistry and I was never any good at them when I was meant to be. So, I’ll put this to social media and see what some proper chemists think.
First comment in was from ChemJobber, who said “the first disconnection to start with 10-deacetylbaccatin is reasonable”
I wrote about the first total synthesis of Taxol back in the 90s, and recall that the overall reaction scheme had well over 20 steps…
Nessa Carson dissected it and found the ChatGPT scheme rather lacking – here. She also pointed out that in Step 5 it completes the retrosynthesis of Taxol by disconnecting it all the way back to… Taxol (lol)
TL:DR – It’s spring and at least one hibernating moth, the Red-green Carpet, has arrived in our garden so far this year
Lit up with my Heath trap again last night and despite the rain, but perhaps because it didn’t drop below 9 Celsius there was a small clutch of moths to ID and record this morning. Specifically, 2x Clouded Drab (new for the year), Common Quaker, Early Grey, 2x Hebrew Character, and a Red-green Carpet, also NFY.
The Red-green Carpet is usually on the wing in the Autumn, the males die, but the females can hibernate to lay eggs in the spring. To my eye, they generally look green with some spots and patches at this time of year, but the autumnal ones are more obviously green and red…ish.
The “carpet” part of its name refers not to the notion that its larvae eat carpets, rather than in the 1700s when species were first being classified and named, the early entomologists and indeed the Lepidopterists perceived the beauty of these creatures and equated their colourful patterns and markings as being like the luxury items carpets were at the time.
The Red-green Carpet moth is a beautiful and fascinating species of moth that belongs to the family Geometridae, which includes many other species commonly known as “carpet moths”. This moth is found throughout Europe, including the United Kingdom, where it is one of the most common species of carpet moth.
Like all Lepidoptera, the species undergoes a complete metamorphosis, with four distinct life stages: egg, larva, pupa, and adult. The eggs are laid on the leaves of the host plant, which can include a wide variety of deciduous trees, most commonly oak and rowan. The larvae, which are often called “inchworms” (US usage) because of their distinctive way of moving, measuring the earth…hence geometers undergo several moults before pupating. The pupa is a non-feeding, transformative stage in which the larva transforms into the adult moth. Finally, the adult emerges from the pupa and begins the cycle anew by finding a mate and the females laying eggs.
TL:DR – The Northern Lights, Aurora Borealis and their antipodean equivalent, the Southern Lights, Aurora Australis, are a visible phenomenon seen in the polar skies as particles from the solar wind interact with particles in the earth’s upper atmosphere.
Lots of lucky locals, by which I mean people a bit further north in Norfolk saw the northern lights, the Aurora Borealis, in Norfolk and elsewhere. There is a slight possibility of seeing them in Cambridgeshire although finding somewhere with little light pollution around here is a tough call, but more to the point it’s been cloudy and wet when other places have had their lightshow these last couple of nights. In recent years they have been observed from Devon and Cornwall.
So, what are the northern lights?
The northern lights are a natural phenomenon generally occurring close to the poles, in the high or low latitude regions of the Arctic and Antarctic. The phenomenon is caused by the interaction between charged particles from the Sun and the Earth’s protective magnetic field.
The Sun constantly emits a stream of charged particles, called the solar wind, which travels through space and interacts with the Earth’s magnetic field. When these charged particles collide with the oxygen and nitrogen in the Earth’s atmosphere, they gain energy, they are excited, when the excitement passes, the particles release energy in the form of light. This produces the glowing, coloerful display that we see as the Northern Lights, or the Southern Lights, the Aurora Australis.
The colours of the Northern Lights depend on the type of gas particles that are colliding with the charged particles and the altitude at which the excitement occurs. Oxygen at higher altitude will glow red and at lower altitude will grown green. Nitrogen produces blue and purple hues.
Usually, seeing the Aurora Borealis involves heading to the colder regions Iceland, Norway, Sweden, Finland, or Canada during the winter months and hoping for a strong solar wind, caused by lots of activity on the surface of the sun. Occasionally, activity and conditions are just right for people to see them farther from the poles as has happened in recent days.
Aurora comes from the name of the Roman goddess of the dawn. It’s related to the name of the Indo-European goddess of the dawn and ultimately the root is from ancient Greek “to shine” with particular reference to the dawn sky.
Borealis comes from the Latin Boreas meaning the “north wind” and from the Greek Boreas, also the name of the god of the north wind.
Australis derives from the Latin word auster meaning “south wind” and hence relates to the southern part of the world.
I haven’t ever managed to see nor photograph the Northern nor the Southern Lights hence the allusion to the lyrics of a 1978 song by progressive rock band Renaissance. The singer with the band, Annie Haslam, was renowned for her operatic training and her five-octave vocal range. I recently updated an article you might like on how to sing.
The photo above was taken by Simaron at Vestrahorn, Southern Iceland in September 2022.
TL:DR – Pheromones are a useful tool for discovering what day-flying moths are in your neighbourhood.
As regular readers know, I do a bit of mothing…I have had a FUN lure, a pheromone lure aimed at attracting Grapholita funebrana. It’s been sighted in the garden for a couple of weeks with nothing appearing until 21st March 2023 at which point I was lucky enough to catch a couple of micro moths, Pammene giganteana (known to some unofficially as the Early Oak Piercer) not the target species but nice to see, nevertheless.
The larvae of the Early Oak Piercer feed inside oak-apple galls, which are themselves formed by parasitic wasps.
According to Anglian Lepidopterist Supplies from whom I bought this and other pheromone lures, the FUN lure has a long list of non-target species that might be drawn to it at different times of year, there may be others yet to be reported:
TL:DR – The bird report pages noted what seemed to be quite an unusual number of Alpine Swifts across the UK during March 2023.
Back in 2019, we took a trip to Greece, the first in many years, we saw lots of wildlife, including Alpine Swift, Tachymarptis melba, careening way above our heads in Athens.
The alpine swift is a medium-sized bird with a wingspan of around 540-600 mm. It has a dark-brown body with a slightly paler throat and underbelly. In flight, it is easily identified by its long, narrow wings and its distinctive white belly patch, which contrasts sharply with the dark body. It is a skilled and agile flier, capable of catching insects on the wing with great precision. Indeed, it rarely touches down, spending almost its whole life, once fledged on the wing, except perhaps when incubating eggs in their nests. It will only very rarely land on the ground.
During the breeding season, which typically runs from May to August, Alpine Swifts build their nests in crevices and holes in the rocky cliffs and mountainsides of southern Europe to the Himalaya. They use their saliva to glue together small twigs and feathers, forming a shallow, cup-shaped nest. The female lays a clutch of 2-3 eggs, both parents take turns to incubate the eggs for around three weeks.
After the breeding season, the Alpine Swift migrates south to spend the winter in sub-Saharan Africa. They are known for their long-distance flights and are capable of covering up to 1000 km in a 24-hour period. They will return to the same nest sites year after year.
As I was writing this, yet another “ping” came in on my rare bird sightings app to alert me to another Alpine Swift having been spotted in the UK. It’s March 2023. Quite early for the Common Swift, which we always see in the UK each summer. Alpine Swifts though? Very unusual. They have been sighted in numerous places in the UK and Ireland this spring.
Sightings have been reported since mid-March this year in the following counties: Antrim, Armagh, Cheshire, Cork, Cornwall, Devon, Dorset, Down, Dublin, Dumfries & Galloway, East Sussex, Essex, Forth, Glamorgan, Gloucestershire, Isle of Man, Isle of Wight, Kent, Leitrim, Lincolnshire, London, Lothian, Mayo, Norfolk, Northumberland, Pembrokeshire, Somerset, Waterford, Wicklow, Yorkshire.
The early reports were marked as “notable” rather than “mega”. In 2022, there was just one noted in March, although later in the year a few others were sighted. Similarly for previous years. So, while I admit, I’d not known about their habits this far north and west of southern Europe, it does seem that a large number have appeared in British and Irish skies very early in the spring this year.
One cannot make generalisations about animal behaviour based on data from a single year, of course. However, the appearance of Alpine Swifts in numbers, this early in the year, suggests something may have changed for them this period. It could simply be changes in weather patterns and wind currents, whether or not those are due to climate change is a different matter. It is known that Alpine Swifts to range quite widely during their migration so maybe this is not an aberration at all and just a reversion to a pattern they followed some time in the distant past.
Stephen Moss discussed the recent irruption of Alpine Swifts in The Guardian some time after my original post and alluded to the fact that because of climate change, this species may well begin breeding in the UK at some point in the next few years, if it hasn’t already done so.
TL:DR – Is it possible to get career advice from a language model? I prompted ChatGPT to help me out.
I’ve been in science communication for more than 30 years, you could say I’m in the late stages of my career, so I am seriously thinking about the next few years of my working life, but not entirely sure in what direction to go or indeed whether I shouldn’t just retire at this point (if only!). So, I gave ChatGPT the following prompt to see what it would come up with:
You are to act as a careers guidance counsellor with many years experience.
I added some personal career history and hobbies and asked it to come up with some advice for what I should do in the latter part of my career. This is what it had to say:
It sounds like you have had a very successful and diverse career as a freelance science journalist over the past 30+ years. Given your current situation and interests, there are a few different options you could consider.
Diversify your writing topics: Since you are already a skilled writer and journalist, you could try expanding your repertoire and writing about new topics. Perhaps there are areas of science that you haven’t explored before, or you could branch out into other areas of journalism such as arts or culture. This could help keep your work fresh and engaging, and could also potentially lead to new clients and opportunities.
Combine your interests: You mention that you are also a singer-songwriter and photographer. Perhaps there are opportunities to combine these interests with your writing. For example, you could write articles about music or wildlife photography, or even use your writing skills to promote your own music or photography. You could also consider exploring other creative outlets, such as podcasting or video production.
Explore new career paths: If you are feeling like you want a bigger change, there are many other career paths that could be a good fit for someone with your skills and experience. For example, you could explore teaching or mentoring, either in science or journalism, or even in music or photography. You could also consider starting your own business or consulting firm, using your expertise to help others in your field.
Prioritize your well-being: It’s clear that you have been through a lot in recent years, and it’s important to prioritize your well-being as you consider your next steps. This might mean taking some time off to recharge, or finding ways to work that allow for a better work-life balance.
It’s not really anything I hadn’t thought of myself, but if I hadn’t it would be nice to see it spelled out. The final suggestion is perhaps the most important for me though. I’ve never really taken much time off over the years. I do feel like I could do with a proper break. Just need to get my passport renewed, fix this Achilles’ tendon injury and get my walking boots packed for a butterflying trip to Greece, ASAP…
TL:DR – A new study has demonstrated the ability of red flour beetles (Tribolium castaneum) to recycle water in their rectums. This feat allows the beetles to survive in some of the driest environments on Earth.
The research team of Kenneth Halberg and colleagues built a transcriptomic atlas of the beetles’ life stages, which allowed them to systematically compare gene expression across tissues and stages. By searching the atlas for genes with enriched expression in the rectum, the researchers were able to identify a specific gene associated with this phenomenon, Nha1.
Electrophysiological experiments confirmed that Nha1 plays a crucial role in ion transport in rectal cells and water uptake by the rectum. In fact, silencing the expression of Nha1 led to water loss, emphasizing the importance of this gene in the beetle’s survival.
Red flour beetles have a large surface-to-volume ratio that makes them particularly vulnerable to environmental water loss. However, the beetles’ rectal complex enables them to recycle water from their faeces and even harvest water from moist air. This remarkable ability is key to the beetle’s survival in arid settings.
The findings of this study shed light on the evolution of water recycling and conservation mechanisms in insects. Furthermore, the transcriptomic atlas of red flour beetles, known as BeetleAtlas, can be used to address a range of unresolved questions on Tribolium biology. Overall, this research highlights an intriguing adaptation that allows insects to thrive in challenging environments.
“NHA1 is a cation/proton antiporter essential for the water-conserving functions of the rectal complex in Tribolium castaneum,” by Muhammad T. Naseem et al. Proc Natl Acad Sci
TL:DR – If you’re online, you cannot ensure complete privacy. But, here are some tips on keeping at least some of your private life private.
Often those in power declare that we shouldn’t worry about privacy, they often say “If you’ve got nothing to hide, then you’ve got nothing to worry about”. So let them all have clear bathroom windows and no shower curtains, shall we? Isn’t that a good idea? No? Didn’t think so!
Wanting privacy isn’t about hiding something it is about being in control of what other people can see, whether that’s your bathroom or bedroom habits, your browser medical search history, the niche sites you peruse, the hobbies and habits you have.
Unfortunately, the powers that be, marketers, and many others do not necessarily care about your privacy and in the worst case scenarios can peep through your bathroom window and lift the shower curtain for a good look at your privacy, as it were.
There are various ways in which websites and companies can track users. Some of these tools persist from site to site even if you are not logged in, even if you use an incognito browser tabe, and sometimes even if you’re using a virtual private network (VPN), perhaps even the hyper-private browser Tor. It is likely that many of the methods used break privacy laws and regulations such as GDPR, but the companies and the regulators do not seem to care about this, on the whole.
Here are some of the most common methods:
Cookies: Cookies are small files stored on a user’s device that contain information about the user’s activity on a website. Websites use cookies to remember user preferences, track user behavior, and personalize content.
Fingerprinting: Fingerprinting is a method of tracking users by collecting information about their device, such as the browser type, screen resolution, and operating system. This information is used to create a unique “fingerprint” that can be used to identify the user across websites. There is an excellent and detailed explanation of device fingerprinting here and more on how to test and combat.
Tracking pixels: Tracking pixels are small, invisible images embedded in a website or email that can be used to track user behaviour. When a user loads a page or opens an email, the tracking pixel sends information back to the website or company about the user’s activity.
Web beacons: Web beacons are similar to tracking pixels, but they can also collect information about the user’s location and device.
HMTL5 tracking: HTML5 Web Storage API allows websites to store information on a user’s device, similar to cookies. This information can be used to track user behaviour and preferences across multiple sessions.
WebRTC: An HTML5 feature, can be used for real-time communication between browsers, but it can also be used to obtain a user’s IP address, which can be used to track their location.
Canvas element – Can be used for browser fingerprinting to uniquely identify a user’s device, and the Geolocation API, which can be used to track a user’s location.
Web browser and extension tracking – Some browser extensions and plugins can track user activity and send data back to their servers. Similarly, some browsers themselves may have tracking features or send user data back to the browser developer or other third parties.
Behavioural tracking: Behavioural tracking involves analyzing a user’s activity on a website or across multiple websites to build a profile of their interests and preferences.
Location tracking: Websites and apps can track a user’s location through GPS, Wi-Fi, or IP address.
Social media tracking: Social media platforms track user activity on their sites and across the web.
Mouse tracking: It is possible to identify a user based on the way in which they move their mouse or trackpad when browsing. It is even possible to fingerprint a user from the way they type.
It’s important to note that while these tracking methods are used for various reasons, including personalization and advertising, they can also be used for nefarious purposes such as identity theft or stalking. Therefore, it’s important for users to understand how they are being tracked and take steps to protect their privacy online.
Unfortunately, while you can block and delete cookies and use a VPN to mask your real internet address (IP) it is very difficult to fake your device fingerprint. there are so many factors associated with your device that make it unique, even among millions of other devices (this has been known about since the 90s, if not earlier, I wrote about it on my old Tech Talk website sciencetext.com back then.
If you imagine that you’re protected from device fingerprinting, give this site a click and run some tests. Even if you have do-not-track enabled, cookies blocked, IP obfuscated behind a VPN, and clear all history and data between sessions, your browser version, operating system, screen resolution, plugins, fonts, and many other features of your device setup, will betray you.
Now, there might be a few other people out there who have a similar setup and this would make it hard for trackers to identify you uniquely even with detailed fingerprinting. However, there will always be a few snippets of info that are leaked from your system. Combining the various methods mentioned above and perhaps even using machine learning (AI) will guarantee that a third party, if they so wish, can open your bathroom window and with a little more effort lift the shower curtain, revealing all!
I asked ChatGPT to offer me some guidance:
Here are five steps that users can take to protect their privacy and combat online tracking:
Use privacy-enhancing browser extensions: There are several browser extensions available, such as uBlock Origin, Privacy Badger, and HTTPS Everywhere, that can block tracking scripts, ads, and other invasive web technologies. These extensions can help protect your privacy and improve your browsing experience.
Opt-out of tracking where possible: Many websites and advertising networks allow users to opt-out of tracking. Look for the “Do Not Track” setting in your web browser and consider installing an ad blocker that can block tracking scripts and cookies.
Use a VPN: A virtual private network (VPN) encrypts your internet traffic and hides your IP address, making it more difficult for websites and companies to track your online activity. A VPN can also help protect your data from snooping and other forms of surveillance.
Be cautious about sharing personal information online: Avoid sharing sensitive personal information, such as your full name, date of birth, and address, on social media and other websites. Be wary of phishing scams and other attempts to trick you into revealing personal information.
Keep your software up-to-date: Software updates often include security patches that can help protect your device from malware and other security threats. Make sure to install updates for your operating system, web browser, and other software as soon as they become available.
Device fingerprinting is the most insidious form of tracking and is very difficult to circumvent. One has to assume that governments, law enforcement, as well as corporations, and other entities are well aware of its power and have in many cases been using it for decades.
Here are some tips on reducing your risk of being tracked by device fingerprinting. None of it is foolproof even if you combine all of them diligently.
Use a privacy-focused browser: Some web browsers, such as Tor Browser and Brave, are designed with privacy in mind and include features that can help reduce device fingerprinting. These browsers may use anti-fingerprinting techniques, such as blocking or spoofing browser APIs that can be used to uniquely identify a user’s device.
Disable browser extensions: Browser extensions can add functionality to your browser, but they can also be used to track your activity and collect data. Disable or remove any extensions that you don’t need, and be cautious when installing new ones.
Use a Virtual Private Network: A VPN can help mask your IP address and make it more difficult to track your activity online. Some VPNs also include anti-fingerprinting features that can help make your device less unique.
Change browser settings: Some browser settings, such as blocking third-party cookies and disabling JavaScript, can help reduce the amount of data that can be used to uniquely identify your device. Be aware that some websites may not function properly with these settings enabled, so you may need to experiment with different settings.
Use a different device: If possible, consider using a different device for sensitive activities or for accessing websites that are known to use fingerprinting. Using a device that is less frequently used or that has been reset to factory settings can help reduce the amount of data that can be used to identify your device.
TL:DR – Mothing is a simple, but educational and fascinating hobby. The data it accumulates can be useful scientifically.
I have lit up with a couple of different traps through the winter, but with generally disappointing results. There are not a lot of trees in our neighbourhood, which I suspect is the reason we don’t get a huge number of moths. That said, very few moth-ers see lots of moths in the gardens during the winter months.
15Watt Heath type, portable moth trap in place and ready for lighting up time
I put out my “spare” Heath trap last night. It is basically an ultraviolet fluorescent tube supported above funnel on top of a plastic box. The UV tube attracts nocturnal moths. They flap about a bit around the tube, perhaps bash into the vertical plastic vanes, and drop into the box. The box contains a load of cardboard egg cartons and the moths will generally secrete themselves among the hollows once they’re bored with chasing the light.
Come the morning, the diligent moth-er will be up at dawn to identify and count the moths trapped overnight, record the data ready to send off to the county moth recorder for scientific analysis along with records from others. The moths themselves are released off-site into bushes and undergrowth, preferably near dusk, and safely carry on with their lives.
The haul from the moth trap, if you could call it a haul, was the biggest and most diverse of the year so far. Four moths of three different species. A micro moth known as Diurnea fagella, which arrived about three weeks earlier than this in 2022, a second Hebrew Character, and the first Early Grey, two of them. At the height of summer, I expect to see a couple of hundred moths of 60 differents species on a lighting up night. But, it was just 7 Celsius overnight, that and other factors at play can keep numbers down until well into the spring it seems.
Now, you are perhaps wondering whether this is ethical or even worse cruel and there are definitely arguments for and against. But, what is definitely known is that we need to monitor the natural world to know anything about it with the aim of helping protect it, conserve, and restore. The moths are just one indicator of whether a location is environmentally healthy. They are often expert pollinators. They and their larvae also provide food for birds, frogs, and various other animals. They are themselves beautiful and fascinating creatures and deserve their place in the world just as any other living creature. I wrote on this issue about a year after I started mothing.
Oh, and if you were worrying about your woolen carpet and your three-piece suit, there are actually something like 1500 different species of moth in the UK, and only one or two species have larvae that eat textiles.
Incidentally, it was some of the names that first drew me to mothing. The one I mentioned above, Hebrew Character is fascinating and closely related etymologically to the Setaceous Hebrew Character.