Floral colour schemes in the garden pond

UPDATE: Two bio friends on Facebook came back with two different answers when I posed this question there. Grace Baynes pointed to a paper about genetic changes in stems from the same specimen of Mimulus (monkeyflower) plants here. The keyphrase in the paper “monkeyflowers mutate as they grow”.

Julie Webb posted: tranposable elements and pointed to a paper suggesting that this can occur because of viral infection, here.

I planted up some aquatic plants in #PondLife as regular readers will know. Among them a few Mimulus in a pot. They’re in full bloom right now. Big, buttery yellow horn-shaped flowers with patches of burgundy red and ruddy spots leading into the flower.

Mimulus flower pond
Original mimulus bloom

Now, at some point early in Covid lockdown, I plucked some of the shoots protruding from the basket of Mimulus and planted them in another basket-pot in the pond with some nutrient-depleted aquatic compost (as I had with the initial bunch).

The new shoots took well and one of them bloomed a week or so ago. Same horn-shaped flowers, same colours, but a lot smaller than the make crop.

However, this morning more of the offshoots have bloomed and they have produced similar small flowers but with a very different pattern and colour scheme. Now, if these had been grown from seeds from the original plant I’d have invoked Mendelian genetics to explain the colour variation. But, these offshoots are as the name would suggest shoots off the original plant. They’re genetically identical, they’re not even clones, they’re simply bits of the original plant…

How emerging viruses jump from species to species

David Bradley reporting from the Royal Society, January 2004

The list of emergent viruses continues to grow. In the early 1990s, there was HIV, ebola, lassa, and others, almost all having jumped from their natural host species to humans. More recently, hepatitis C, Sin Nombre, West Nile, and of course SARS emerged. The common factor, said Dr Eddie Holmes of the University of Oxford, is that they use RNA rather than DNA to carry their genetic code.

Holmes believes that the genetics of our immune systems and viral genetics should be an equally important research focus. To infect a new species, an emerging virus has to overcome the new host’s immune system and to replicate in its cells, the success of which depends on both viral and host genetics and other factors.

But, Holmes asked, why do such pathogens emerge and what controls the emergence? Ecological change, as emphasized in Tony McMichael’s talk, is the governing factor – change in human proximity and change in host-species population density. The key to understanding lies in the fact that RNA viruses mutate a million times more rapidly than organisms with DNA. This endows them with great adaptability. On the other hand, a high mutation rate constrains viral evolution by capping the viral genome’s size, which limits adaptability. Higher mutation rates, after all, mean more chance of error in the viral genes. This “error-threshold”, explained Holmes, means that if a virus has to evolve a lot to jump between species then it is more likely to fail. We eat a multitude of plant viruses every day but no one has yet fallen prey to turnip mosaic virus.

The coronaviruses such as SARS, are different. They have a much bigger genome than other RNA viruses, which means that SARS and its relatives should evolve more slowly but their larger genome gives them greater adaptability. A better understanding of the constraints to RNA virus evolution will allow us to make better predictions about the emergence of new viruses and help us find improved therapeutic procedures. Rather than thinking about what RNA viruses can do, we should concentrate on their limitations.

Read on… Influenza and emerging viruses

What use are moths?

Steve on one of the mothing Facebook groups told us he gave a talk about moths and was asked if we had any use for them. Other than making silk from silk worms (the larvae, or caterpillars, of the domestic silkmoth, Bombyx morihe) was at a loss to suggest any purpose to moths other than their role in the wider concept of life on earth and diversity and all that. He posed the question on the group and was offered quite a few reasons to be cheerful when it comes to moths.

Hebrew Character moth

Shaun suggested that people have an odd relationship with moths as they are used as symbols and in myths in a variety of cultures, as food – some people eat the larvae and they’re an important protein source packed with essential minerals, they can be used as invasive plant controls and for the study of genetics etc. As decoration in jewellery, clothing, tattooing etc. Paul pointed out the traditional food of Aboriginal Australia, the witchetty grub, which is the larva of several moths, most notably the Cossid Moth Endoxyla leucomochla. There are a food source in Europe too and a form of tea that is brewed with moth and other insect faeces in China.

Martin’s take was that we make use of moths for interest, study, research, and in hobbies. They “brighten our lives,” he says. They also act as a gateway into other activities and interests, such as flowers, trees, walking, travel, and friendship.

Common Quaker moth

Antony pointed out that pollination is probably the main use.

Matthew, somewhat tongue-in-cheek asked what do we use blue tits for? Or shrews? It’s not all about utility!

Roly asserted that moths have an important position in nature’s foodchain. Many birds wouldn’t exist without caterpillars for their chicks. He also added ever so slightly flippantly, I think, that his wife reckons she finds moths very handy for making her clothes look moth-eaten, proof that she needs continually to shop, though I’ve never seen a clothes moth in our closets, Roly emphasises.

Pale Brindled Beauty moth

Stewart had a research example of moth usage: Spodoptera frugiperda and Trichoplusia ni cell lines are used in the recombinant baculovirus expression system to produce proteins. The baculovirus most studied for this is Autographa californica multicapsid nucleopolyhedrovirus.

Are great tit beaks really getting greater?

Heard a news snippet on BBC Radio 4 this morning reporting on how Brits using bird feeders has apparently led to great tits (Parus major) evolving longer beaks. I read an article or two (National Geographic and The Guardian) to check out how the science was being reported elsewhere and then took a look at the original research paper itself.

The researchers talk of 26-year data set from live birds in Wytham and estimate a 4 micrometre ± 1 micrometre per year lengthening in this species. That seems like quite a small change, despite that their analysis of avian genetics in this species allows them to suggest some kind of correlation with bird feeder use compared to Dutch counterparts where no lengthening was observed. Could bird feeders really have had sufficient impact on brood size rates they discuss for great tits? For a start, is 4 micrometres actually significant at all in 2500 birds measured…that’s some pretty mean measuring but with a 25% error bar…?

Research paper is here: http://science.sciencemag.org/content/358/6361/365

They found the Twitter gene

If just one of the genes that helps build the language areas of the brain doesn’t work for whatever reason, then the whole system fails. There would be no gossip, no chit-chat, no watercooler wit, no bar-room banter. The lesson learned by scientists studying the gene FOXP2 in members of a family who have inherited a problem. A case study in writing the right headline for your science blog post…one commenter on the original article even asked if the twitter gene was one and the same as the search engine optimisation (SEO) gene. Of course, it isn’t another commenter pointed out that’s BLSHT2. And in an article with such a well-honed link bait title, one must assume it is highly up-regulated.

The Twitter gene by Anna Perman on Genetic Spaghetti

One of the later comments offers a nice allegory on genetics and genetic modification. It’s from someone going by the name of “BillyBobLiar”:

“There are two cars, one faster than the other. I remove a screw from the engine of the fast car. It now goes the same speed as the other car. I show the screw to my friend and say ‘ this piece is what makes the fast car go faster’. ‘You think?’ says my friend. He goes to the slow car and returns with a similar screw. ‘How do you explain this then?’ he asks, ‘the slow car has the same piece’. I say ‘aha! If you looks closely, you will see that they are different at the top. One has a cross and the other just has a line’. ‘I see’ he says, ‘so this piece is what makes the fast car fast, and it can do so because it has a cross on the top and not a line’. ‘Yes’ I say.

Later that evening my friend calls me. ‘I’ve had a great idea’ he says. ‘What?’ I say. ‘Well, if we put the piece with the cross into slow car, it should also become fast’ he says. ‘That sounds about right’ I say, ‘we’ll try it in the morning’. ‘I can’t wait’ he says.”

Genetics at a SNP

Genetics at a SNP – There are genetic variants, SNPs, associated with a tendency to have almost any physical trait such as baldness, athleticisim, green eyes, red hair, obesity, alcohol dependence, type 2 diabetes and many other diseases, even the amount of earwax one produces. There are also SNPs associated with the presence of metabolic enzymes or the lack thereof that mean an individual is more or less responsive to a given pharmaceutical or other therapeutic agent. There are often variations between human populations, so a SNP that is common in one geographical or ethnic group may be much rarer in another. Now, UK researchers have developed a very simple technique for finding SNPs that could revolutionise testing for genetic disease markers and more…

Five feisty science books on David’s desk

Five super science books landed on my desk during the last week or two, everything from a Haynes manual for the Space Shuttle to hacking life and from astrobiology to the discovery of Lucy by way of the fact of evolution.

  • The Fact of Evolution – Opponents of evolution are wont to say it's "just" a theory, as if that somehow implies it's a fiction or not proven. Scientists often dislike talking in plain or making absolute, definitive statements. But, science writers and some scientists really don't mind telling it like it is. Forget the wishy-washy word "theory" with its non-scientific baggage, this is the Fact of Evolution. The onus is on opponents to prove otherwise by coming up with evidence for their own "theory".
  • Biopunk: DIY Scientists Hack the Software of Life – Biopunks, as defined by science writer Marcus Wohlsen, are part of a loosely knit, multifaceted movement to find ways to permit people to engage in DNA research without the restrictions and costs imposed by the scientific and medical establishment. Practitioners, some self-taught, set up shop in their kitchens or garages, believing that significant biological advances are more likely to occur as more people get involved in the enterprise. DNA for DIY GM, in other words.
  • The Lucy Man – Biography of the man who discovered 'Lucy' – perhaps the most well-known fossil ever. Scientists dream of making a discovery that changes the way we think. That dream came true for Donald Johanson when he found 'Lucy' (Australopithecus afarensis); Lucy changed everything we know about human evolution.
  • From Dying Stars to the Birth of Life – Personally, I'm with Fermi when it comes to intelligent ET – if they're out there, where are they? Nevertheless, there could very well be less than technological life on other worlds, indeed it is almost inevitable. This is the incredible story of the birth of an entirely new field of science called astrobiology – a field that is now investigating whether life might exist on other worlds. From the discovery that other stars in our galaxy are circled by planets to the detection of single-cell organisms found living on Earth in extremely hostile environments, this account details the recent breakthroughs made by astronomers and earth scientists over the last few decades. Based on these findings, it argues that scientists now have the technology they need to move from speculating or fantasizing about extraterrestrials to possibly providing humanity with the first definitive proof that we are not alone.
  • Space Shuttle Haynes Manual – The NASA Space Shuttle Manual: An Insight into the Design, Construction and Operation of the NASA Space Shuttle (Owner's Workshop Manual). Sounds like a spoof but an astrogeek's insider dream. Shame they're all heading for museums rather than flying more missions…

The latest five science books to land on the desk of David Bradley Science Writer @sciencebase.

Smoking cadmium and benchtop X-rays

Latest science news including this week’s round up from my SpectroscopyNOW column:

  • Smoking out cadmium problem – A statistical analysis of spectroscopic data is helping scientists home in on the problem of decreased fruit and vegetable consumption being associated with an elevated concentration of cadmium in the blood of male smokers.
  • Short, sharp outburst – A new approach to generating ultra-short, high-density electron pulses for the production of advanced X-ray sources has been developed. The approach could lead to a bench-top X-ray synchrotron for materials science, pharmaceutical research and nanotechnology research.
  • Metabolic obesity – Evidence from NMR spectroscopic studies of individual metabolic profiles would suggest that the way our bodies digest and process nutrients in the food we eat is different for every person and could ultimately affect overweight and obesity problems.
  • Heavy metal and hardened arteries – The way in which arterial plaques form, atherogenesis, is not yet completely understood despite a significant number of research studies in this area. Now, a study using rabbits on a high-fat diet (HFD) has investigated the effects of changes in the concentrations of heavy metalsin several tissues using spectroscopy.
  • Electronic ‘nose’ can predict pleasantness of novel odours – Our sense of smell may not be as subjective as we thought, as scientists develop an electronic nose that can distinguish between pleasant and unpleasant odours.
  • Scientists embrace openness – "Everybody makes mistakes. And if you don't expose your raw data, nobody will find your mistakes." –Jean-Claude Bradley [no relation]

Top Ten Mutants

dna-testIf you ever thought genetics was only about disease, then check out the popular SNPs list on SNPedia. A SNP (pronounced “snip”) is a single nucleotide polymorphism, which in BradSpeak(TM) is basically a difference in a bit of your DNA that makes you different from the rest.

Anyway, here’s the Top Five SNPs that might be described as having no obvious direct medical importance.

  • rs1815739 sprinters vs endurance athletes (I reckon I lack both)
  • rs7495174 green eye color and rs12913832 for blue eye color
  • rs6152 can prevent baldness (this was discovered far too late for me)
  • rs1805009 determines red hair (some “comedians” might suggest this be swapped to the second list below)
  • rs17822931 determines earwax (and presumably how well your ears stay clear of insect infestation)

And, here’s the more sober list of SNPs that could have serious medical implications should you happen to discover you have one of these when you have your genome read by the likes of 23andMe.

  • rs9939609 triggers obesity (not a genetic excuse for eating too much)
  • rs662799 prevents weight gain from high fat diets (ditto)
  • rs4420638 and rs429358 can raise the risk of Alzheimer’s disease by tenfold or more
  • rs7903146 and rs12255372 linked to type-2 diabetes, the latter also to breast cancer
  • rs324650 influences alcohol dependence, rs1799971 makes alcohol cravings stronger (it would not be funny to say, “Mine’s a pint, with a whisky chaser”, right now)

It was a twitter discussion between SNP experts mza and attilacsordas that led me to the SNP list.

Blog Action Day on Poverty

Kwazulu Natal, South Africa
We are, the media tells us, either on the verge or diving head first into a global recession the likes of which we have never seen. Countless financial headlines have screamed Credit Crunch, which sadly isn’t a wholegrain breakfast cereal for day-traders, for a year now. Banks are borrowing billions from taxpayers to allow them to lend even more money to each other.

There has almost been not a thought for the millions of people out of work and out of a home the ruins of whose lives the apparent collapse of capitalism is built. Anyone who thought Freddie Mac and Fanny Mae were porn star names, or the Lehmann Brothers were a support act for Marx (as in Groucho and gang) surely now knows better. Stocks and share prices yo-yo between lower highs and increasingly depressing lows.

But, away from the cold-sweating of traders, the pinging of stripy braces, and the red screens of death, on the market floors of the so-called developed world, the old-school third world, the allegedly developing world continues in its grinding abject poverty. However, providing the developed world does not collapse into utter chaos, Jenifer Piesse of the Department of Management, at King’s College London and the University of Stellenbosch, RSA working with Colin Thirtle of the Centre for Environmental Policy, at Imperial College London, and the University of Pretoria, RSA, suggest in a recent issue of the IJBT that at least one product of modern capitalism, genetically modified (GM), herbicide tolerant (HT) white maize, developed in the USA to save labour might help ease poverty in the developing world too.

They report how HT white maize is now being grown by smallholders in KwaZulu Natal, South Africa, and elsewhere and use panel data for Africa, Asia and Latin America to investigate the effects of factor endowments and biased technological change on productivity growth, labour incomes and poverty reduction. Can GM produce a Green Revolution (GR) in Africa and would it be poverty
reducing, as it has been in Asia, they ask.

Their preliminary findings demonstrate that a simple absence of population pressure on the land slows yield growth, which itself largely explains labour productivity growth in agriculture. Labour productivity growth is the key determinant of wages, growth in GDP per capita and poverty reduction.

“Africa seems to have fared poorly in poverty reduction because many countries have abundant poor quality land,” the researchers explain, “There has been yield growth, but it has not led to growth in labour productivity, as it did during the Asian green revolution.” This finding suggests that GM technology that raises labour productivity could be enormously beneficial, so long as employment is maintained.

Their analysis reports that yield growth in Asia was about 2.6% per year, but that Africa was not far behind at 2.0%. However, labour productivity in Asia grew at 1.5% per annum, whereas Africa managed only 0.4%. Yields in Asia grew at 1.1% faster than labour productivity and there was substantial progress in poverty alleviation. In contrast, in Africa, yields grew 1.6% faster than labour productivity, but the impact on poverty has been less.

They explain that yield growth is in fact a main cause of labour productivity growth in both continents, but in Africa the impact is far weaker. The most obvious cause is that both yields and labour productivity grow less where land to labour ratios are low, which is particularly true in the countries of sub-saharan Africa, the researchers say.

Jenifer Piesse, Colin Thirtle (2008). Genetically modified crops, factor endowments, biased technological change, wages and poverty reduction International Journal of Biotechnology, 10 (2/3) DOI: 10.1504/IJBT.2008.018354

This post was published as part of the Sciencebase contribution to Blog Action Day.