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The internet is a seething pool of 'stuff', and one of the challenges faced by those using it is to distinguish useful information from foolish fantasy. And there surely is a lot of the latter! Thus we find that

According to a BBC news story, the Indian government's Agriculture Minister  has said that yogic farming would "empower the seeds with the help of positive thinking", and that this 'would help improve yield and soil fertility and contribute to making India prosperous.' This has been quite widely reported, with more details of the Minister's comments given in the Indian Express, including this one:

The idea is to help farmers. With the help of Rajyog [yogic practices], we should enhance fertility of the soil. It will help activity of micro-organisms in the soil too.

Somehow I can't see magical thinking having much effect on seeds, fungi, protozoa, or bacteria...

Lemons neutralise acidity. Yes, you read that right. This bit of mythinformation keeps popping up on various 'natural health' sites - here, for example. These sites all make the same claims: that the stresses of modern life put the body's pH out of whack, and that various foods can fix the problem (some even going so far as to suggest that eating the 'right' ie 'alkaline' foods will help to prevent or cure cancer). And for some weird reason lemons are listed as a food that will neutralise that pesky acidity and set the body to rights. (The site I linked to also lists pineapples, limes, oranges, tangerines, kiwifruit, and vinegar as foods that will make your tissues more alkaline.) 

The fact that lemons contain citric acid, that anything ingested must pass through the highly acidic environment of the stomach; and that the body does an excellent job of maintaining a constant pH environment around its cells - all this is happily ignored. Luckily there are science bloggers out there who do an excellent job of addressing this nonsense - Dr Kat Day's The Chronicle Flask is one of them, & you should go there now & read her great explanation of why lemons are not going to neutralise acidity and why claims to the contrary are nonsensical.

And if your DNA's been damaged by exposure to fluoride, never fear! For you can repair that damage by reprogramming water's memory, or so a commenter on the Girl Against Fluoride's FB page would have others believe. You have to distill the water first:

The forced medication [community water fluoridation] corrupts our DNA, Distilling the water clears any memory in the water, which then allows you to reprogram it.

And how does that work? Apparently you can 

reprogram the memory in it with a water proof speaker. Play the 528hz tone in the distilled water. The distilled water will absorb the vibration and change the structure of the water molecules. This water will help repair your DNA.

So here we have an example of someone who doesn't understand chemistry and also believes in homeopathy (the first is pretty much required for the second). Their thinking seems to be in line with the dangerously crazy idea, promoted by some homeopaths, that homeopathic 'remedies' can be delivered via mp3 recordings. And the idea that water's 'structure' can be modified by good or bad vibrations seems to hark back to the claims made by one Dr Emoto, who claimed that he could distinguish between ice crystals depending on whether they'd been the subject of good or bad 'intent'. Orac did a thorough dissection of these claims back in 2009, so it would appear that some woo never changes.


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This is a cross-post from Talking Teaching.

   The author of this article certainly thinks so. Under that header, he continues:

Do you really believe that watching a lecturer read hundreds of PowerPoint slides is making you smarter? I asked this of a class of 105 computer science and software engineering students last semester.

Well, first up, that's a leading (& loaded) question. And secondly, I'd be surprised if anyone really believed that. Yes, I'm sure that there are lecturers who simply read off their powerpoint slides (which really is a no-no!). And what did we use in the days Before Powerpoint (BP)? Quite likely overhead transparencies, either printed or handwritten, and yes, some of us certainly had lecturers who simply read all the information off the transparency. (I know I did!)

In other words, the header ignores the fact that Powerpoint is simply a tool. Nothing more, and nothing less. It cannot make anyone boring. That's done by the person using it; similarly, the way the tool is used will have a flow-on effect on learners. Indeed, this was the focus of a post I wrote some time ago, and if you haven't already read the 2008 paper by Yiannis Gabriel that I discussed therein, you should do so now.

A better question would be: how do we help professors to use powerpoint (& other technologies) in ways that better support student learning?

That, of course, requires that we are able to measure student learning in meaningful ways. And here I definitely agree with the author of the article: 

Any university can deploy similar testing to measure student learning. Doing so would facilitate rigorous evaluations of different teaching methods. We would be able to quantify the relationship between PowerPoint use and learning. We would be able to investigate dozens of learning correlates and eventually establish what works and what doesn't.

Perhaps we should start thinking about this.

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I've always enjoyed Nick Lane's writing1, so naturally an article he wrote for the ABC Science website caught my eye. Titled "Evolution of complex life on Earth, take 2?", it discusses an organism that appears to be neither prokaryote nor eukaryote, but something in-between.

There's a great divide between the cells that fit the description of 'prokaryote' and those that we view as eukaryotes. Both cell types have a cell membrane, which separates the cell's contents from its external environment; DNA & RNA (the nucleic acids); and ribosomes (where proteins are constructed from their constituent amino acids, in accordance with the information encoded in DNA). But beyond that, prokaryotic and eukaryotic cells are distinctly different.

Prokaryotes have a single, circular chromosome, with no nuclear membrane separating it from the cytoplasm. There are no membrane-bound organelles (as distinct from infoldings of the cell membrane, or 'plasma membrane'), and the cells are generally much, much smaller than a eukaryote cell.

In contrast, in a eukaryote the multiple, linear chromosome are separated from the cytoplasm & its contents by a nuclear membrane. In addition to ribosomes the cytoplasm contains a range of organelles, including mitochondria, golgi bodies, and (if they're photosynthetic cells) chloroplasts.

We spend quite a bit of time in class discussing the evolutionary origin of these more complex cells: for example, it's generally agreed that the mitochondria and chloroplasts are the results of endosymbiotic events. That is, each of these organelles originated from once-free-living prokaryote cells that were engulfed by some proto-eukaryote but not then digested (which is the usual fate for things that cells engulf). When this concept was first proposed by Lyn Margulis, back in the 1960s it received a fair bit of skepticism, but there's now plenty of evidence to support it. However, in class we've never really discussed what a cell in the process of becoming a eukaryote would look like, which is why I found Lane's article (& the original paper by Yamaguchi et al.) so interesting. In it, he discusses the organism pictured in the image below. It's a significant find because, as Yamaguchi & his colleagues point out,

[The] differences in cellular structure between prokaryotes and eukaryotes are so vast that the problem of how eukaryotes could have evolved from prokaryotes is one of the greatest enigmas in biology. If eukaryotes had indeed evolved from prokaryotes, then there must have been viable organisms with intermediate cellular structures.

Image credit: Fig 1 from Yamaguchi et al (2012), doi: 10.1093/jmicro/dfs062. CW: cell wall, N: nucleus, NM: nuclear membrane, PM: plasma (cell) membrane, E: endosymbionts (two of which were rod-shaped; the third resembled a spiral-shaped bacterium)

The image shows an ultra-thin section of a single-celled organism found on a polychaete worm that lived on a hydrothermal vent over a kilometre down in the ocean (Yamaguchi et al., 2012). Now, on first inspection that does look rather like a eukaryote cell, and Yamaguchi et al. point out that it has a volume about 100 times greater2 than that of a bacterium like E.coli. But as Lane notes:

It has a single nuclear membrane, with a few gaps. No nuclear pores. The DNA is composed of fine fibres as in bacteria, not thick eukaryotic chromosomes. There are ribosomes in the nucleus. Ribosomes in the nucleus! And ribosomes outside the nucleus too. The nuclear membrane is continuous with the cell membrane in several places. And some of the endosymbionts ... resemble corkscrew shaped bacteria on 3D reconstruction, making them look more like relatively recent bacterial acquisitions.

While it has internal membranes there is nothing resembling an endoplasmic reticulum, or the Golgi apparatus, or a cytoskeleton, all classic eukaryotic traits. In other words, this cell is actually nothing like a modern eukaryote. It just bears a superficial resemblance.

Unfortunately, as Lane notes, there's no genetic material available for a genome comparison that might help to place this enigmatic organism. This is because only one was found, and that was sliced into multiple ultra-thin sections for microscopic examination (which has, however, allowed a 3D reconstruction of what the original cell - and its endosymbionts - would have looked like).

One of the questions I've wondered about, in teaching about endosymbiosis as an origin for eukaryotes, is 'when did the nucleus develop? Before, or after, the endosymbiotic event that gave rise to mitochondria?' Yamaguchi et al. point out that the cell they've described doesn't have a fully-formed nucleus (only that single membrane and 'fibrous' genetic material), but does have internalised endosymbionts. From this, they suggest that

the nucleus was not necessarily formed when eubacteria started their endosymbiosis in the prokaryote host cell. Thus, the formation of the nucleus and transformation of bacteria into mitochondria might have proceeded independently

and with the host cell wall developing after the endosymbionts entered the host cell.

However, there are a lot of imponderables (& oh! how useful that genome would be here), & so the authors weren't really able to determine just where that unicellular organism sits among the domains of life. (That's assuming it's not simply an artefact of the sampling process.) Lane suggests three alternatives.

One is that it is a 'highly derived eukaryote' ie a cell adapted to a highly unusual environment that has lost many of the normal eukaryote structures. Of this, he says that

If Parakaryon myojinensis really is a highly derived eukaryote, then it's radically different in its basic plan to anything we've seen before. I don't think that's what it is.

The second option is that it's a sort of 'living fossil', surviving only in the unchanging deep-sea environment. This is the option favoured by Yamaguchi & his team. However, it's really really rare (a 12-year project has yielded just the single specimen): would such a rare organism have survived the ~2 billion years since eukaryotes evolved? Lane also comments that it

is not living in an unchanging environment: it is attached to the back of a segmented worm, a complex multicellular eukaryote that obviously did not exist in the early evolution of eukaryotes.

He suggests a third option:

it is a prokaryote, which has acquired endosymbionts, and is changing into a cell that resembles a eukaryote.

We certainly have evidence of endosymbiotic events in modern organisms, so why rule out the same thing happening among prokaryote cells? And Lane argues that when (not if) such events occur, their results are predictable - and are what we see here:

It is relatively large, with a genome that looks substantially larger than any other prokaryote, housed in a 'nucleus' continuous with internal membranes, and so on. These are all traits that we predict would evolve, from first principles, in prokaryotes with endosymbionts.

Obviously this one isn't settled yet. Yamaguchi et al.conclude by saying that

Of course, more specimens need to be collected and cultured to obtain the molecular data, including 16S rRNA genes, which will establish the evolutionary relationships between this microorganism and the prokaryotic and eukaryotic branches of life.

That's an important reminder: this is a big tale to hang on just a single cell. But it's is a fascinating story, nonetheless.


1 "Power, Sex & Suicide" has got to be on the list of the world's greatest book titles!

2 Modern eukaryotes are larger again by a factor of 100.

M.Yamaguchi, Y.Mori, Y.Kozuka, H.Okada, K.Uematsu, A.Tame, H.Furukawa, T.Maruyama, C.O'Driscoll Worman & K.Yokoyama (2012) Prokaryote or eukaryote? A unique microorganism from the deep sea. Journal of Electron Microscopy (preprint) doi: 10.1093/jmicro/dfs062


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