Science Blogs

Epigenome links nature and nurture

Sciencebase - 10 March, 2015 - 17:41

“Cells use their DNA code in different ways, depending on their jobs [heart, brain, lung, skin cell etc] — just as the [chamber] orchestra in this video can perform one piece of music in many different ways. The combination of changes in gene expression in a cell is called its epigenome.”

Epigenomic changes are chemical changes, ‘tweaks’, to DNA and to the protein packaging the DNA. They don’t directly affect genes themselves but affect regions of the genetic code that turns genes on or off. Methylation is one such tweak that primes a gene to be switched off. Environment, diet, exercise and activity, whether you smoke or drink, and many other external factors can alter your epigenome, thus providing a link between nature and nurture, your behaviour, health, longevity, and even those characteristics of your offspring and grandchildren. More on the symphony playing in your cells here.

KEYWORDS: Epigenome, epigenomic, epigenetics, genetics, genome, genomics, gene, genes, DNA, methylation, health, disease, cancer, Alzheimer’s disease (AD)

Epigenome links nature and nurture is a post from the science blog of science journalist, photographer and musician David Bradley
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Are you a tetrachromat?

Sciencebase - 2 March, 2015 - 17:51

Riding in on the train of *that* dress – is it gold/white or blue/black a lot of colour vision questions have emerged. Despite people becoming quickly bored after the initial couture virality and now that it’s been around the world’s media 50 times in all its shades, there is still plenty to say. Wired pretty much wrapped up the threads, so I won’t go into that and you can Google it if you really want to see their article.

But, there’s a “spectrum” looking chart of different colourful shades, hues doing the rounds now. If you see fewer than 20 different hues, the article accompanying it says, you’re probably a dichromat, two cones in the retina of your eye or one of the three not functioning in the way it should. If you see between 20 and 32 you’re a trichromat, three fully functioning cones. But, if you see 32-39 different colours you have a fourth type of cone in your retina making you a tetrachromat; colours are much more distinguished apparently, but they’re not so keen on yellow. If you can see more than 39 colours, you’re not a pentachromat, you’re a little fibber.

When I looked at the chart, I thought I could see 36 hues, well definitely more than 32…it seemed to depend on what angle I was looking at my laptop screen and whether my eyes were scanning across the width of the spectrum rather than staring as to whether distinct bands appeared. I couldn’t get a consistent count, definitely at least 32, but possibly just 32. So, I scouted around for an alternative test for tetrachromicity, which looks a bit like the standard test for so-called “colour blindness” (dichromaticity). If you can see anything other than the three obvious colours seen by trichromats, then you’re obviously a tetrachromat…except that…hmmm…

tetrachromat-test

It got me thinking. How can these tests be valid? Computer screens only use red-green-pixels, they cannot display all the hues a tetrachromat would be able to see. I checked around and found another blogger who agrees, an online test cannot demonstrate tetrachromicity. As she says: “computer screens do not provide enough colour information to be able to ‘tap into’ the extra dimension that tetrachromats may possess”. Vision expert, Mark Changizi confirmed this point.

So, if you were counting almost 50 shades hues of colour in that chart and imagining that you somehow have a superpower, well, the odds are against you.

Are you a tetrachromat? is a post from the science blog of science journalist, photographer and musician David Bradley
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Silent Spring master notes

Sciencebase - 27 February, 2015 - 12:10

UPDATE: I cranked up the bass a little on the latest mix, check it out, it’ll get your blood pumping…

I posted my song, The Silent Spring from critique on one of the songwriter forums and got a few listens and some nice positive comments, in particular with regard to the mastering I did…an area in which I’m really just a novice.

But, here are a few notes about what I did, just for my own personal notekeeping to be honest, but others might find them interesting if they’ve listened to the song. I suppose I could share the pre-mastered version, but there’s little point suffice to say it sounds quite dull and lifeless tonally compared to the mastered version, which is bright, sparkly and fills the stereo field with crisp and clear resolution between the different instruments and voices, thanks to my tweaking a preset in the iZotope Ozone mastering software, not because of any skill of mine (other than listening and feeling that it sounded right).

From my reply to the forum:

Mastering…I really ain’t an expert. But it seems to boil down to getting all the parts to sound as good as you can individually and making them work together at that level first (getting a good mix, in other words) and then working at the master track level to do EQ (equalisation), stereo imaging/widening, compression (to dampen down any too loud bits) then maximising/limiting to bump up the sound without it distorting in that order on the whole thing as a whole. Oh, some reverb in there too, to bring it all together and give it an ambience as if you’re hearing it in a hall or something.

You can do all that with the basic plugins, the VSTs, in my DAW (digital audio workstation, it’s Mixcraft, which is like Garage Band but for Windows). But for this song, I used a demo version of iZotope Ozone 5 and started from one of its presets called “Excitation and widening” and moved the various sliders or which there are many until it sounded as good as I could get it to sound to my ears in my headphones…

In future productions, I will try and emulate what Ozone does using VSTs for those four/five components mentioned above (thanks to MonoStone for spelling them out for me via email, he’s the real expert). I should also namecheck James Z, who gave me some early EQ lessons but also pointed out what mastering can do.

mixcraft-screenshot

I think in the old days mastering was more about making a tune work for the pressing technology of vinyl records. These days it’s really just about adding sparkle and width to the song and improving the clarity (and boosting it for radio), so that each track you scooped and FXed sounds as good as possible sitting in with all the others.

This song has quite a few tracks – lead vocal, three sets of backing vocals (with the female doubled), lead guitar, lead guitar for solo (doubled), electric rhythm guitar, acoustic rhythm guitar (doubled), arpeggio acoustic guitar (doubled), bass guitar, percussion, I think that’s it…

I reckon I’ve spent about 10-15 hours on it in total from writing the first chord progression and ad libbing the lyrics to recruiting Emmazen and mastering it…and not counting the 37 years of playing guitar before getting to that point, hahahah.

You can hear the song via the Sciencebase Dave Bradley BandCamp page or on Soundcloud.

Silent Spring master notes is a post from the science blog of science journalist, photographer and musician David Bradley
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The Silent Spring

Sciencebase - 26 February, 2015 - 16:45

A song of hope with an allusion to both the book of the eponymous title and recent revolutionary springs…

The Silent Spring by Dave Bradley

The Silent Spring

They tell us history is a lesson to learn
Too many times we ignore it
They say the danger is a stranger to burn
Through the seasons they implore it

It doesn’t matter how near or how far
The border lands we deplore them
They feed us lies that just won’t settle the score
Fail to see that we abhor them

Across the desert a healing wind blows
Now the promise of a silent spring
Though lines were drawn and the borders were closed
Above the cloud the eagle spreads her wings
Above the cloud the eagle spreads her wings

They say that fear is the enemy within
Too many times that we have sworn it
From East to West their lies begin to wear thin
The oath I swore I could ignore it

Across the desert a healing wind blows
Now’s the promise of a silent spring
Though lines were drawn and the borders were closed
Above the cloud the eagle spreads her wings

And through the valleys a healing wind blows
With the promise of a silent spring
The lines were cut but no borders are closed
Above the cloud the eagle spreads her wings
Above the cloud the eagle spreads her wings

And in the cities a healing wind blows
With the culture of a vital sting
The ties once cut and all borders exposed
Above the cloud the eagle spreads her wings

And through the desert a healing wind blows
With the promise of a silent spring
The lines once cut and our feelings deposed
Above the cloud the eagle spreads her wings
Above the cloud the eagle spreads her wings

Words & Music by Dave Bradley
Vocals, acoustic and electric guitars, bass dB
Backing vocals @Emmazen
Arranged and produced by dB

The amazing @Emmazen joined me on backing vocals and her voice soars like an eagle on this one. This version is the high-res remixed and remastered song available for download from BandCamp. You can also have a listen via the Sciencebase SoundCloud page.

silent-spring-pinterest

The photo was taken from Stiffkey Marshes in North Norfolk looking across to distant coastal pine trees embedded in sand dunes under a glowering evening sky.

The Silent Spring is a post from the science blog of science journalist, photographer and musician David Bradley
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How to calculate wind chill

Sciencebase - 24 February, 2015 - 10:18

Wind-chill, windchill, wind chill factor, wind chill index is an estimate of how cold you will feel at a given air temperature when there is a wind blowing. It is a popular tool used by weather presenters to make you feel worse about going outside when it’s cold and windy! Seriously, if, for example, the reported air temperature (as measured by a thermometer housed in one of those white boxes with the grills, a Stevenson screen, or shelter) is -7 Celsius and the wind is blowing at a steady 8 km/h, then it will “feel” like it’s -11 Celsius. But why and how does one get from -7 to -11, 4 degress C cooler?

wind-chill-index

Here’s the physics and formula courtesy of Wikipedia: “A surface loses heat through conduction, convection, and radiation. The rate of convection depends on the difference in temperature between the surface and its surroundings. As convection from a warm surface heats the air around it, an insulating boundary layer of warm air forms against the surface. Moving air disrupts this boundary layer, or epiclimate, allowing for cooler air to replace the warm air against the surface. The faster the wind speed, the more readily the surface cools.” Additionally, skin sweats so air blowing on exposed sweaty skin will cause cooling by evaporation, but the likelihood of you sweating and then exposing your skin when you’re outside and it’s -7 Celsius is quite low…

The calculation used by the US and UK weather forecasters and meteoroligists for wind chill is quite complicated looking but relatively easy to implement with a modern calculator, although different regions use different units F vs C, mph vs kmh, so you have to make sure you’re using the appropriate formula. A neat chart (by RicHard-59 on Wiki) saves you the trouble of doing the calculations yourself, if you’re a common or garden weather presenter.

And, here’s a nice video description of wind chill that I first saw mentioned on the Free Technology for Teachers blog:

For pedants in Australia, it’s rare that a wind chill is observed, you might want to try “heat index” instead… ;-)

How to calculate wind chill is a post from the science blog of science journalist, photographer and musician David Bradley
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Is it okay to kick a robot?

Sciencebase - 12 February, 2015 - 15:34

By now, you’ve probably seen the astounding quadruped robots that have been built and demonstrated by Boston Dynamics. These machines run like four-legged animals and don’t seem to mind when their human companions give them a kick…hold on…give them a kick? Is that really the best example to set impressionable people watching the videos?

One could argue that it’s a machine, it doesn’t “mind” being kicked, if that demonstrates just how robust the software and servos are to disturbances in the forces around them. But, it is still quite a disconcerting thing to see. The next generation might be togged up with heads and fur, for instance, to make them look even more like animals, that would make for even more uncomfortable viewing, I reckon. And, then, of course, ultimately, such a robot might be endowed with artificial intelligence, sentience, even. Would kicking a bot that knows what you’re doing be moral?

This also raises another question. If we build sentient robots, would it be sensible to give them pain receptors? Would we want them to know to avoid things that might hurt. And, Asimov aside, might a robot in pain having been kicked feel that retaliation was the ethical thing to do from its perspective?

Is it okay to kick a robot? is a post from the science blog of science journalist, photographer and musician David Bradley
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Follow me, follow them

Sciencebase - 5 February, 2015 - 09:07

Not quite in the words of the 1978 Genesis hit “Follow you, follow me”, I took a look at Twitter dashboard and found that there is a neat Top 9 (don’t ask) of twitter users who a lot of people who follow @sciencebase also follow

sciencebase-followers@NASA · @NatGeo · @wiredscience · @TEDTalks · @Discovery · @ScienceNews · @neiltyson · @NatureNews · @guardianscience

Follow me, follow them is a post from the science blog of science journalist, photographer and musician David Bradley
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My first chemistry experiment #UnRealTimeChem

Sciencebase - 2 February, 2015 - 17:06

My choral friend Jo mentioned making “poisonous” orange juice when she was a nipper and giving it to a boy she and her friends didn’t like. Apparently, they crushed up some bits of plants, including foxgloves, which of course contain digitalin, the heart drug. Add enough of that to his OJ and they could’ve been in serious trouble. Just as well there was no belladonna (deadly nighshade) or monkshood (Devil’s Helmet or wolfsbane).

boy-telescope

Anyway talking of serious trouble…as a kid I was always messing around with magnets and motors, batteries and bulbs, iron filings, little circuits, broken radios (well they were broken after I’d messed around with them), watches, telescopes, magnifying glasses and stuff. But, by aged 9 or 10 I’d taken my first foray into chemistry. I’d got hold of a little stoppered plastic vial and mixed up some washing-up liquid and water and added some of the 3-in-1 oil I usually drizzled on to the chain and into the little holes on the underside of my bike. I don’t remember what I was trying to do with this, my first chemistry experiment. Obviously, the mixture would have formed some kind of mucky emulsion. Hashtag #JuvenileAlchemy.

Anyway, I remember some snitch reported me to my teacher when they saw me shaking my vial behind the bike sheds (no, that is not a euphemism!). I got hauled in to see the headmaster, I think my parents were dragged in too. Of course, the vial with its gloopy contents was confiscated but not before the headmaster had a good sniff. I’m not sure what any of the adults thought I had been up to. I was just naively doing chemistry. Maybe they thought I was abusing solvents or sniffing glue or something, but at age 9 I didn’t even know that was a thing…

I almost certainly had an idea from a science library book, I used to read three or four each evening at that age. Anyway, the experience put me off chemistry for years and so I went back to messing with magnets (again, not a euphemism) and I seem to remember trying to make an electromagnet from a chunk of steel from my Dad’s toolbox and a bit of insulated wire that I jabbed into the wall socket…oh dear…did I mention I was a bit naive, almost electrocuted myself, needless to say. Still, at least I didn’t try to give anyone a heart attack with poisonous orange juice, eh?

*The photo isn’t me, by the way…

My first chemistry experiment #UnRealTimeChem is a post from the science blog of science journalist, photographer and musician David Bradley
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Reactive Sabbatical

Reactive Reports - 6 May, 2014 - 17:16

As you may have noticed, Reactive Reports has been somewhat less active than it was during its golden years, 1999 to 2009. I am still writing lots about chemistry and science in general, but updating the various blogs and websites where there is no longer a commissioning editor, as it were, has had to take a backseat in preference to the writing that pays the bills in order to allow me to indulge my other creative passions – music and photography.

I’ve always used some of my own photos where I could to illustrate blogs, news and features and websites, you can see some of my recent albums via my flickr pages. During the last year or so I have been fine-tuning (hahah) my songwriting and production skills to put together an eclectic collection of originals, some acoustic and folky, some electric and indie, a few funky, and one a bit long and proggy. Anyway, the fruits of that musical labour are now available from the usual online musical outlets including BandCamp.

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