Category Archives: science & natural history

The philosophical spider

Oliver Sacks, talking about his recent autobiography:
http://www.csicop.org/si/show/oliver_sacks_on_hallucinations/
“Yes, well, I was living then down on Venice Beach in the early 1960s, and there were a lot of drugs around. And people said to me, if you really want something striking take Artane. Artane is a belladonna-like drug which is used in treating Parkinson’s. And they said just take twenty, you’ll still be in partial control. Anyhow, I took these tablets. At first I noticed nothing. I had a rather dry mouth, difficulty accommodating, my pupils were dilated. Nothing else. Then I heard a car door slam and footsteps, and I thought it was my friends Jim and Kathy. They often visited me on Sunday. I shouted “Come in!” and we chatted. I was in the kitchen.

“There was a swinging door between the kitchen and the sitting room. I said, “How do you like your eggs done?” And we chatted in the four or five minutes while I prepared their ham and eggs. Then I walked out with the breakfast on a tray and . . . there was no one there. I was so shocked I almost dropped the tray. It hadn’t occurred to me for a moment that all this was hallucinated, at least that their part of the conversation was hallucinated. I thought I’d better watch myself. But this was followed by some even stranger things, including having a conversation with a spider. I think the spider was real enough; there weren’t any visual elements.

“But then the spider said, “Hello,” with a voice like Bertrand Russell. And for some reason it didn’t surprise me any more than Alice was surprised by the White Rabbit. I said, “Hello yourself.” And we had a conversation. Actually, an abstract conversation about some points in analytic philosophy.

“Many years later, I mentioned this philosophical spider to a friend of mine, an entomologist. He nodded his head and said, “Yes, I know the species.”

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River dipping again: messing about on the river 2014

A joyful sunny day down by the River Tale near Escot House, with youngsters and adults
engaged in all sorts of fun. My fun lies in looking in nets and buckets.

I like to try and identify what I see: I’m better with the big obvious stuff, to be honest, but I can tell the difference between a fox and a badger at least nine times out of ten…

There is a temptation on the part of youngsters to pull up a net and, if it hasn’t got any fish in it, to dismiss the net as empty. But if you look closer, and see what comes out of the debris at the bottom, you will find another layer of adventure and discovery. (And another one again, if you have some magnification to hand.)

The most spectacular insect we saw last year was also the first and last species I saw yesterday: a golden-ringed dragonfly (Cordulegaster boltonii) came to inspect me as I stood on the bank at the start of the day, and escorted me off the premises when I left.

Other dragonfly varieties were spotted during Sunday, but I couldn’t identify them with any confidence: I would guess they were from the genus _Libellula_, the chasers. With a decent photo I might have visited http://www.british-dragonflies.org.uk/ or
http://www.surfbirds.com/dragonfly-guide.html which I am sure would have sorted out the species.

We didn’t see much by way of butterflies: some small whites and a tortoiseshell passed through during the day. I expect more butterflies were up at the main gardens.

Lots of bees: the white-tailed bumble bee Bombus terrestris and carder bees Bombus pascuorum(?), as well as honey bees and a sprinkle of small solitary bees. A plant I didn’t know was absolutely covered in common wasps (Vespula vulgaris), and a couple of their kin were chewing at the wooden posts to make their carton nests.

I know little about flies but was attracted by a little blond sepsid abundant on the burdock: they have spots on their wings and wave them slowly, in a manner that irresistably reminds me of ground crew signalling to aircraft taxiing on a runway.
http://moving-wildlife.blogspot.co.uk/2010/07/insight-into-new-world. html

Neither
https://www.flickr.com/search/groups/?w=413853@N21&m=pool&q=sepsid nor http://www.ispotnature.org/search/node/sepsid were hugely useful in tracking it down and I couldn’t find a free key from
http://www.royensoc.co.uk/content/out-print-handbooks but a flick through the latest books by Chinery
http://www.amazon.co.uk/dp/0002199181/ and
http://www.amazon.co.uk/dp/0007298994/ turned up
a grass or cereal fly of the genus Geomyza as a likely ID, and they are Opomyziids, not Sepsids at all.

There were several specimens of the showy Banded and Beautiful damselfly species Agrion virgo & A. splendens – sometimes called demoiselles or jewelwings. I discover these days they are properly referred to as in the genus Calopteryx, meaning beautiful-winged. They mingled all day with the raft-builders and dam-makers and gold-panners. Other species were around too, maybe the Blue-tailed or Variable Damselflies.

The damselflies were also a group which were found in the river itself, as larvae: we found three vaguely different-looking examples, but this time I expect we would need not just a photo but a lens or microscope to identify them properly. Some nice clues are to be found at
http://www.dragonfly-images.co.uk/

The star turns of the day for me were two juveniles of the water scorpion, Nepa cinerea. I hadn’t seen one for 30 years or more, so finding one was a joy, then someone turned up another. We didn’t catch any, but there were many pond skaters of around; there are nine species I believe, although http://www.britishbugs.org.uk/systematic_het.html lists only seven. Gerris lacustris is literally the Common Pond Skater, but others are common too.

Several whirligig beetles were brought in, fun to watch whizzing around like dodgem cars on the surface of the water. Joke of the Day: “Oh, that’s a whirligig beetle. I’ve no idea why they are called that”. (The Latin is as good: Gyrinus natator =”swims in circles” – yes, they do.)

We turned up another fine water beetle, which I think now might have been Agabus didymus as being the species of Agabus that is most often found in running water.
(H/T Watford Coleopterists Group http://www.thewcg.org.uk/ )

Snails were pretty abundant: the only ones big enough for me to risk a ‘spot’ were I believe _Lymnaea stagnalis_, the UK’s biggest snail, but the ones we found were hardly that.

Among the rest were a number of fly larvae: worms swimming with twisting movements, and maggots weaving through the detritus. With a hand lens I might have had a better go at the two water mites I spotted, but I would have needed a microscope to do anything with the ostracods. And creating a bit of a stir were two leeches: I believe many leeches are vegetarian, but I chose not to put our specimens to the test.

The greatest excitement, of course, was created by any find of fish.

I was first off the mark with a couple of bullheads (Cottus gobio), which as a boy I would have called a Miller’s Thumb, a flat-spread fish of stones and gravel, which is pressed to the river bed by the flow of water over its body and fins. Also, a bit of a British speciality, I’m told.

We also turned up a couple of stone loach (Barbatula barbatula).

Small three-spined sticklebacks (Gasterosteus aculeatus) were found in in abundance, their little pectoral fins going nineteen to the dozen. We also pulled up a male and female of breeding size: a colourful red-bellied blue-eyed male and a grey pregnant female.

Other joke of the day: a young man proudly invited me to look in the bottom of his net, in which he had captured… a bubble. I explained that bubbles were quite rare in the river, but you could find them at this time of year as they migrate upstream to breed.

D

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An assassin bug killed a cow!

I couldn’t find that story online. I don’t think it’s true.

Here are some British assassin bugs:
http://www.britishbugs.org.uk/gallery/heteroptera/Reduviidae/reduviidae.html

They are not poisonous – that is, a cow wouldn’t die from eating one.

But they are venomous – that is, they inject deadly digestive saliva
into their prey – but their prey is other insects, and even if they can kill an insect bigger than themselves, a cow wouldn’t die if it was bitten by one.

Few insects are venomous, and those that are, won’t kill a cow, at least, not on their own. [A big swarm of bees could kill just about anything that didn’t run away, I think, and the same with a colony of army ants.]

Some spiders are deadly, like the Black Widow spider:
http://en.wikipedia.org/wiki/Black_widow_spider

Some scorpions are deadly, like the Fat-tailed Scorpion:
http://www.orkin.com/stinging-pests/scorpions/deadly-scorpions/

One octopus is deadly:
http://www.pbs.org/wnet/nature/interactives-extras/animal-guides/animal-guide-blue-ringed-octopus/2177/

Some jelly fish are deadly:
http://en.wikipedia.org/wiki/Box_jellyfish

I don’t think any insects are deadly.

What insect stings are, is painful. How painful? You measure the pain of an insect sting according the Schmidt Index, named after a man who having been stung hundreds of times in his career as an entomologist decided to write some notes on it.

http://scienceblogs.com/zooillogix/2008/01/29/the-schmidt-sting-pain-index/

According to his scale, the very worst stings of all are the stings of the bullet ant. Also very painful is being stung by a velvet ant (a type of wasp). The sting of a velvet ant is so painful that it is nicknamed the ‘cow killer’, as the sting is so painful that it was supposed it would kill a cow. It didn’t kill Schmidt and I don’t think one has ever killed a cow, but that might be where the assassin bug story got started.

http://lancaster.unl.edu/pest/resources/cowkiller.shtml

But there is one way an assassin bug bite could kill a cow. Insects that carry diseases can be deadly. I think the Anopheles mosquitos that carry malaria have killed more people than died in all the wars since recorded history. Still do, millions every year. And so tsetse flies and other insects that carry diseases of cattle, can kill a cow that way.

I mentioned Sir Vincent B Wigglesworth:
http://en.wikipedia.org/wiki/Vincent_Wigglesworth
who studied a bug called Rhodnius. Rhodnius is an assassin bug http://en.wikipedia.org/wiki/Rhodnius_prolixus
It feeds mostly on armidillos, but it can bite humans, and when it does, it can give them Chagas’ Disease, and you can die of it. In fact, these bugs can give Chagas’ Disease to about 150 different animals. So if a Rhodnius bit a cow and the cow later died of Chagas’ Disease, then maybe you could say that a cow died because it was bitten by an assassin bug. But it can take 10-20 years to get Chagas’ Disease…

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Playing chess with pigeons

“Debating creationists on the topic of evolution is rather like trying to play chess with a pigeon; it knocks the pieces over, craps on the board, and flies back to its flock to claim victory.” — Scott D. Weitzenhoffer

D

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Four comments on DNA and evolution, with references

As usual on Twitter, it’s possible to gallop through many claims which take a wretchedly long while to unpick, if they are not referenced.

Here’s an unpicking of some Tweets from @JamesPlaskett to @ergrieve :

@JamesPlaskett 11 August

a) similarity greets the eye reflected in blueprint. Why should that tell u anything new?

b) Some simple organisms have more DNA …than humans, e.g snails + goldfish. That confounds the argument for common descent

c) Some animals look + behave very similarly whilst showing enormously differing DNA, e.g. frogs. There are some 3,000 types, all v. froggy but DNA differs more than that between bats + blue whales.

d) If the genomic similarity did show common ancestry it would of itself say nothing of how they split.

Seatbelts on, everyone:

a) similarity greets the eye reflected in blueprint. Why should that tell u anything new?

DNA & other genetic evidence shows similar DNA in similar creatures, and the greater the bodily (phenotypic) similarity, the greater the genetic similarity. This is certainly what you would expect from evolutionary standpoint, but it’s not clear what you would expect from other standpoints.

Yet, sequencing studies also show a branching tree in non-functional elements, the parts of the genome that are not part of the blueprint, and shows the same tree in those bits of DNA which contribute to the less vital parts of proteins, all of which can wander apart by genetic drift. The new DNA story of the evolution of the cytochrome c protein matches entirely the old amino-acid-sequence story:
http://www.ncbi.nlm.nih.gov/pubmed/181584

If rRNA is at all relevant, we have had the most detailed tree yet produced using base sequences:
http://www.zo.utexas.edu/faculty/antisense/downloadfilestol.html

I think that is just stunning.  This evidence of molecular drift is very highly supportive of the branching tree of evolution, and is impossible to account for by any process involving design/creation (which can’t explain why there are non-functional parts of DNA at all, let alone why tiny differences are found in them in similar species).

Summary: http://phylointelligence.com/genetics.html

b) Some simple organisms have more DNA …than humans, e.g snails + goldfish. That confounds the argument for common descent

“More DNA”: does that mean the number of chromosomes? We don’t understand everything about why different organisms have different numbers of chromosomes (the karyotype), but what we do understand I think is completely consistent with common descent.

Carp typically have 50 chromosomes. Goldfish have 100. This seems a straightforward instance of polyploidy (genome duplication), of no great significance. [Polypoidy seems important in speciation events, and may confer selective advantages, like greater body size.] There is certainly no significance in comparing the goldfish number of 100 to the human number of 46.

‘Snails’ are a big group, and not all of them have more chromosomes than 46. Numbers I have found range from 14 to 56; one garden snail, Helix aspersa, has 56, while another, Cepaea nemoralis, has 44. Molluscs in general seem to have started with 13, and polyploidy and other rearrangements have produced the range we now see. Again, I’m not sure what significance is being read into these findings.

Karyotypes, far from contradicting common descent, are often helpful in confirming relatedness inferred from other evidence (e.g. most great apes have the same chromosome number, 48; most carp have 50). The exceptions also support common descent: the goldfish karyotype is clearly derived from the basic carp karyotype; they don’t have 50 new and original chromosomes.

The best example of karyotype analysis supporting common descent is, why do humans have 46 chromosomes, while chimps have 48, if we are supposed to be so closely related? Yet human chromosome 2 bears all the hallmarks of being made out of two other ape chromosomes, including having an ‘endpiece’ (telomere) in the middle. The simplest explanation is that our set of 46 comes from a common ancestor with apes which had 48. There’s a detailed discussion here:

http://blogs.discovermagazine.com/loom/2012/07/19/the-mystery-of-the-missing-chromosome-with-a-special-guest-appearance-from-facebook-creationists/

Analysis has been done, reconstructing family trees based on chromosome arrangement, similar to those done with cytochrome c and rRNA sequences. Here’s one for molluscs:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194838/

So, chromosome numbers very much support the evolutionary story about common descent.

c) Some animals look + behave very similarly whilst showing enormously differing DNA, e.g. frogs. There are some 3,000 types, all v. froggy but DNA differs more than that between bats + blue whales.

This point I find puzzling: I haven’t been able to find it made and explained elsewhere (is it original to HJP?), despite spending some time searching online, so I’m going to have to do some reconstruction.

This point is based on some sort of quantificition of the range of ‘differing DNA’, but I’m not sure if that’s a claim about karyotypes or genomes.

If it’s a claim about the genome, I can’t find any statistics about the ranges among frogs and mammals. Frankly, not that many species have had their whole genome sequenced. The genome sequence commented on here:

http://newscenter.berkeley.edu/2010/04/29/xenopus_genome/

shows that frogs fit in family tree of evolution, and have many commonalities with other classes of organism, in support of the idea of common descent.

If it’s a claim about karyotypes: the range of diploid chromosome counts among bats is between 16 and 50; the number for whales is generally 44 with a few 42s. The range for frogs is something like 14-54, as far as I can tell. The claim that frog karyotypes are importantly more diverse than are those of mammals is not supported.

http://bentley.tosm.ttu.edu/personnel/RJBaker/Publications/112-Karyotypic%20evolution%20in%20bats-Baker%20and%20Bickham-1980.pdf

http://www.tandfonline.com/doi/abs/10.1080/03749444.1981.10736629#.UhHo1W07yP8

But let’s assume that it’s true, that karyotypes are more different among frogs than among mammals. Evolution of chromosome arrangements takes time; we might expect this process to have produced a greater range in frogs for that reason alone (last common ancestor of all frogs was maybe 200 million years ago, LCA of bat/whale=?60mya).

Also, from what we can see, “evolutionary changes in chromosome numbers have taken place about twenty times faster in mammals than in frogs”, so we’re catching up! That also fits your intuitions based on the overall differences in body form of mammals and frogs.

http://en.wikipedia.org/wiki/Frog#Evolution http://www.pnas.org/content/71/8/3028.full.pdf

Just counting chromosomes tells you nothing about how different the actual genes are, of course. Polyploidy does not necessarily result in any differences in form or behaviour. Frogs which differ in their chromosome number can be very difficult to tell apart.

http://munews.missouri.edu/news-releases/2011/1227-frogs-use-calls-to-find-mates-with-matching-chromosomes-university-of-missouri-researchers-find/

So, if I’ve understood the point being made, I suggest this isn’t a line of argument helpful to the anti-Darwinian camp. If I’ve misunderstood, explanations and/or references to any and all of the original data are invited.

[By the way, the original claim said “800 types of frog”, now we’re up to 3,000, but the best estimate for the number of species of tail-less amphibian (‘frogs and toads’) I still think is 5,000.]

d) If the genomic similarity did show common ancestry it would of itself say nothing of how they split.

In case of chromosomal arrangements, it tells us a lot about how they might have split. Species with different chromosome arrangements will likely not be interfertile. Agreed, it’s hard to demonstrate natural selection using DNA, but observed mutation rates in DNA fit entirely what we need to provide the raw material of natural selection (e.g. Nilssen and Pelger 1994 see earlier post: https://minorityattack.wordpress.com/2013/08/03/jamesplaskett-dialogue-of-the-deaf-pt-2-points-of-difference/).

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@JamesPlaskett Protesting too much: no spontaneous beneficial mutations?

James Plaskett has been directing us to the anti-Darwinian writings of Richard Milton in support of the claim that there are no spontaneous beneficial mutations.

The go-to experiment for beneficial mutations is undoubtedly the very long and painstaking work led by Richard Lenski, which showed the spontaneous appearance of bacterial lines able to metabolise citrate. These are generations raised in over twenty years of research in which samples are frozen, where the appearance of a mutation can be demonstrated to arise and arise repeatedly, and these mutations are not merely the ready re-expression of a formerly dormant capacity.
http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment#Evolution_of_aerobic_citrate_usage_in_one_population
But I don’t think Milton was aware of that instance when he wrote.  Then, the classic case was antibiotic resistance in bacteria:

“For instance, from a single bacterium one can grow a population in the presence of an antibiotic, and demonstrate that organisms surviving this culture have mutations in genes that confer antibiotic resistance. In this case (in contrast to the situation with the peppered moth populations described above) origin of the population from a single bacterium allows comparisons of the mutated genes with the corresponding genes from the original bacterium, verifying that the variant sequences were not present before the culture with antibiotics and therefore arose as de novo beneficial mutations.”

Edward Max, http://www.talkorigins.org/faqs/fitness/ 1.2.1

Let’s turn to Milton’s objections  (which have fallen off the web, but I presume Milton still stands by them):

“This claim can never be strictly true. In order to do what Dr Max describes here, the experimenter would necessarily have to both culture the new population from his single experimental bacterium AND fully sequence the DNA in that same single bacterium for later comparison. But, of course, analysing the DNA of the experimental bacterium must necessarily destroy it, making it impossible to culture from.
“Instead the experimenters do the next best thing: they select a number of individuals from the same culture, which they assume to be genetically identical and they analyse the genes of one (or more) and use the others to culture the new colony. If the bacterium they select to analyse appears not to have any genes for antibiotic resistance then they assume that the same must be true for its close relative they are using to breed.”

http://web.archive.org/web/20041012235607/http://www.alternativescience.com/talk.origins-antibiotic.htm

I think that ‘genetically identical’ assumption is a good one, and can also be shown to be true. Because these are bacteria arising from asexual reproduction of a single cell (a routine microbiological technique), they are all necessarily genetically identical ‘twins’ and will remain so until the appearance of any mutations. You can sample from the population to show that whatever it takes to be resistant to an antibiotic is not there at one point and is there at a later point.

You can even see this in real time. A bacterial population with a single founder will spread across a plate up a gradient of increasing antibiotic concentration until they are brought to a halt by the antibiotic. After a pause, suddenly and spontaneously, they break through to the neighbouring area of the plate which was previously uninhabitable.  (I seem to remember seeing that on Bang Goes The Theory earlier this year.)

“Despite Dr Max’s denials, the case of antibiotic resistance in microorganisms is exactly the same in principle as that of so called ‘industrial melanism’ in the peppered moth. It is simply a case of one variety of the species flourishing while another variety dies off, because of changed environmental conditions.”

I think that shows that Milton hasn’t understood the power of the single-founder experiments. There is only one variety to start with.

Elsewhere:

“…It is perfectly feasible that many bacteria possess genes that can provide resistance — whether or not those genes are currently expressed, and whether or not they have even been identified by geneticists as genes for providing antibiotic protection. Such unexpressed genes are known to be sometimes ‘switched on’ by environmental pressures of just the life-threatening kind that are applied to bacteria in the lab. So, even if antibiotic resistance were genuinely arising during the experiment, it is not necessarily arising de novo, as Dr Max claims, but may merely be a genetic throwback.”

It may be the work hasn’t been done to exclude this possibility in every case, but certainly there are many examples of single changes in DNA sequences that produce antibiotic resistance.  These cases are not due to the turning on of an unexpressed pre-existing capacity, these are spontaneous beneficial mutations in a gene expressed throughout (http://aac.asm.org/content/44/7/1771.full).

The Lenski team has also nailed what is going on in their experiments, and it too is certainly not the recovery of a previously unexpressed capacity.

Milton also offers:

“Perhaps Dr Max and other convinced Darwinists might say that choosing one bacterium for genetic analysis and a very close relative for culturing is as close as one can get to experimental certainty, and is almost scientific proof. But the whole point of science is that ‘almost’ isn’t good enough.”

Although I think the lab work is immune to the criticisms Milton offers, I think this statement is also worth challenging: it is a misconception about the nature of science.   As close as you can get to certainty is as close as you can get, and if you demand a higher standard, you are demanding, not just proof beyond reasonable doubt, but proof beyond unreasonable doubt. And that’s Milton’s problem, not a problem with the neo-Darwinian synthesis.

Reflection: It’s actually enough for only one element of the neo-Darwinian synthesis to fail: for mutations to be too uncommon or never beneficial, or for natural selection never to be observed in or out of the lab., nor mating barriers; or for the molecular tree to contradict the morphological tree, or for some other prediction to be disproved… And yet it seems Milton wishes to dispute every little bit of it. He protests too much.

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Oak Eggar Moth

http://www.westmidlandbirdclub.com/images/spbf/OakEggar.jpg
Just chased one of these out of the study
D

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