applied science xcience

Making Mice Miss Memorable Moments Minutely Modifiable Maybe

It took a few minutes to make that title so I hope you appreciate it 🙂

A lot of research has gone into memory and how it works in our brains. As a result we know an awful lot about how the processes involved form the biochemical structures that are memories. Where they are located and how they are formed or not.

What we don’t understand as clearly is how forgetting happens.

We can do experiments with people and animals to learn things about how this all works but to do experiments where the object is to interfere in a manner that might cause permanent alterations / damage we can’t use humans.

But how do you know if an animal has learned something or not? If they have forgotten something or just didn’t learn it in the first place. Testing to see if they remember something can be complicated by not knowing this difference.

Researchers in Japan and Toronto have worked out how to test that with mice. And they’ve found that the time of day that the testing happens affects the outcome.

Something about the time of day just before they normally wake up, when BMAL1 levels are normally low, causes mice to not recall something they definitely learned and know.

BMAL1 is a protein that regulates the expression of other proteins. For those not well steeped in how DNA/RNA works you can think of it this way: If the DNA is a book of instructions on how to build proteins that build and operate the cells that build us then regulatory substances are like filter glasses that alter how the lines of instruction in that book are read and carried out.

Mice with less BMAL1 were more strongly affected with recall problems than those with normal amounts of BMAL1. So of course researchers will be looking further in how this works with an eye on how it might help develop treatments for diseases such as alzheimers. Modifying how much BMAL1 is present to try and modify memory recall is likely being planned next.

Why the body’s own internal clock, the circadian rhythm, would moderate recall in this way has them scratching their heads for now.

One more thing I learned from the Science Daily article is the term ‘zeitgeber’.

A zeitgeber is a measurement of time, the environmental cue of light turning on.

applied science xcience

SENOLYTICS could be it.

(Update at end)

Always have to take a skeptical view whenever the phrase Fountain Of Youth comes into the text but it is an interesting idea: get rid of the senescent cells and rejuvenate the system.

What does that? This class of materials called SENOLYTICS.

Plus the news that senescent cells can have two nuclei was a bit of a head scratching jaw dropper.

New cause of cell aging discovered: Findings have huge implications for cancer and age-related health conditions — ScienceDaily


Mayo researchers have had success with humans given Senolytics.

demonstrated for the first time that senescent cells can be removed from the body using drugs termed “senolytics”

Now that we’re up to scenescent cell count reduction it shouldn’t be long before they start to work out metrics for changes in bio-function and overall health. Yahoo!

applied science social commentary xcience

Revivification News During Easter Week

An interesting collision of science news and religious holy days took place this past week.

While the Christian world got ready to observe Easter, remembering how Jesus was executed and then resurrected, the world of Science was announcing the cellular reanimation of hours-dead pig brains. (Nature, MedicalExpress)

Nothing divine was going on with the reanimated pig brains – the researchers were just checking a hunch. They have been working with tissue taken from brains, dead ones of course. The fact that the tissue is from dead animals and is isolated in 2D sheets instead of in a 3D matrix of neural tissue, like it normally is, presents problems. Such as: How do you know the results aren’t being affected in some way by these limitations? Are the results from studies applicable to living specimens?

To further complicate studies dead tissue has biochemical processes happening that change the very things being studied in a short time. It was inevitable that compounds would be developed to perfuse the tissue to try to maintain some semblance of the chemical environment that the tissue was in while still in a living creature. The blood replacement they used in this particular lab they call BrainEx (for Ex Vivo).

What they noticed was that even after hours of being ‘dead’ the tissue showed signs of cellular viability. So they devised a simple test – through a hog processing company they got access to a few heads from recently killed pigs. After extracting the brains they perfused them with the Brainex solution. And what they found has many many people wondering . . . neural cellular integrity was preserved, some neuronal, glial, and vascular cellular functionality was restored.

They didn’t see any evidence of global, coordinated neural activity so while the parts might have limited restored functionality the brain itself wasn’t switched back on in any real sense. But this is just a first step . . . who knows where it might lead? Just like in the old Brer Rabbit story I’m guessing it will become a tarbaby that will lead us into a philosophical and ethical thorny briar patch. (and I just mentioned the issues around using that term in a recent post)

Some of the easy ones to predict are: when can we say the creature is really dead? Or a human? For those jurisdictions that use brain death as a determining factor – will they revised ‘when’ that can be said to take place with finality? What about the stock in cryogenic-suspension companies that only preserve the head – will that go up? What does Dead really mean? I’m sure others will come up with more.

So while all the wannabe Doctor Frankensteins of the world have some hope . . . I’m wondering if next Easter some people will be replacing that Bunny with a Piggy. After all this aspect has nothing seriously connecting it with the religious event (and is likely pagan inspired) and neither animal lays eggs.


After we lock it up, what can we do with the locker?

Another lost draft being published late . . .

Researchers have found a way to dramatically speed up the formation of the mineral magnesite. Magnasite formation removes carbon dioxide from the atmosphere. Normally this process takes many, many years but they say they can shorten that to days . . .

So if all goes well we’ll be producing magnesite as fast as we can . . . which brings me to the question: What is Magnesite good for?

The Wikipedia article on its uses lists many. But a lot of them involve burning it and release the Carbon. What else could mega-tons of magnasite be used for?

applied science social commentary xcience

It was a Fact Of Life until it wasn’t

My whole life the thinking on mitochondria was that the DNA for that was passed only from the Mother. Our own DNA comes from both parents but not that of the symbiotic bacteria that power all of our cells.

That has led many people down the path of searching for an original Eve. The single female from which all of us are descended. Maybe.

Well it turns out that mDNA can be inherited from the Father as well. As discussed in this article in TheConversation new research has shown, conclusively, that this happens.

So what will happen to all the research already done that assumed otherwise? Guess it will all have to be reconsidered at a minimum.

An aside to this: as I was discussing this with the only other person in the room at the time a side-track of thought had me asking if the mDNA is really yours in a legal sense.

Your nuclear DNA, the stuff that makes you uniquely you and me me is definitely your own in a sense that could be legal.

But that mDNA . . . that’s a bacteria that lives within your cells. Is that ‘yours’ from a legal point of view?

Try this mental exercise:

IF I could exchange the mDNA in the cells in your body with mDNA from cells in some other (mine for instance) human body (essentially replacing your mitochondria with mine) then I have three questions:

1 – would that work? Would the replacement mitochondria carry on supplying energy for the host cells in a way that doesn’t create problems?

2 – if the answer to Question 1 is Yes then would that mean that ‘you’ are any different from the ‘you’ you were before the switch?

3 – IF Q1 has a Yes and Q2 has a Yes then can we really say mitochondria are specific and ‘ownable’?

applied science xcience

Hacking Information Processing Problems In Human Brains

A long while ago I remember being introduced to the idea that we do not sense the world directly because we actually experience the results of sensory data being turned into information.

The cells in the ear that turn mechanical vibration into electrical signals are just the beginning of a chain of circuits of neurological processing steps that turn those signals into what we perceive as stereophonic sounds. Sounds are what those neuro circuits create for us.

Similarly the signals from cells in your eyes’ retina that turn light and colour into  electricity and chemistry aren’t vision – there is more processing going on before we get the ‘visuals’ that we think we see with our eyes.

And when something goes wrong with that processing we get strange effects. Dyslexics see some things, letter shapes, differently from the rest of us. Synesthesia  causes people to taste colours and see sounds.

Recent research shows that tinnitus may be a product of altered processing that might be amenable to repair. Now I read about how chronic pain may also be approached in the same way.

“researchers at the UNC School of Medicine showed they could target one brain region with a weak alternating current of electricity, enhance the naturally occurring brain rhythms of that region, and significantly decrease symptoms associated with chronic lower back pain”

Makes me wonder what other processing alterations could be done to repair or even enhance the basic human brain / mind system. That it can have an effect is pretty much recognized by now as this Reuters article “Do-it-yourself brain stimulation has hidden risks” shows.



Predictive Powers Built Into The Basic Mammalian Model?

I was reading this article on how researchers have analysed the neural circuits of mice as they walk and figured out how they ignore the sound of their own steps while retaining the ability to hear other things at the same time. Like the sound of a cat sneaking up on them.

It’s really quite neat and it relies on the brain being able to generate predictive information that the brain’s listening circuit then uses as a filter to filter out that sound with good accuracy.

And they think it will lead to a better way into understanding how people do this same thing while refining activities like speaking and playing an instrument.

In the last paragraph I read something that resonated with a favourite theory of mind of mind.

“By figuring out how the brain normally makes predictions about self-generated sounds, we open the opportunity for understanding a fascinating ability — predicting the future — and for deepening our understanding of how the brain breaks during disease.”

To me, and my theory, the ability to predict the future in the behaviour of another creature is a milestone in our development. One which we would not exist without our ancestors evolving it.

Think of it: until that moment the thinking processes in a creature are relatively confined to a model of self within a model of the world outside the self. (that is a very simplified version)

The moment you evolve the functionality to predict some future event, process, action, or reaction the brain has expanded it’s capability in a stupendous way. Then the extension of that power to being able to predict what some other creature might do leads to a mind being able to imagine another mind within it. And have that captive model mind work well enough that it’s behaviour correctly predicts the actual creature’s behaviour. That sounds like a simple thing but step back for a moment and let it sink in. A mind is an open-ended, near infinite, thing. Moving from biology to mind is one step. moving from one mind to more than one mind within the same ‘mind’ is a qualitatively different thing.

A predator that cannot do this goes hungry, starves and dies. One that can eats, reproduces and passes on this capability.

Could this neural circuitry found in the research the article is about be part of the basis at the root of predictivity?





applied science xcience

Bio-Hacking is a Thing Now

kisspng-scientist-science-fair-clip-art-science-kids-clipartIt’s been coming for a while now. Bio-Hacking.

When I was barely out of my teen years Intel came up with the 8008 and the 8080. I got a 6800 development kit. Like many others I wanted to tinker with this new technology and see what I could make computers do. Previous to this a computer was something that lived behind glass walls in specially designed environments and processed your utility bills and spit out punch cards or paper in large continuous streams. But now anyone could have one and who knew what might come of that.

Well it’s 40 years later and the human world has completely changed because every thing that the computer became part of has gone into ‘evolutionary overdrive’. We now carry one or more computers in our pockets that are so far advanced compared to even the large machines of that age that it’s almost ludicrous.

Genetics is going through that same change right now.

Bright, young, eager students (hackers and hobbyists) can now engage in activities that only expensive labs could a decade ago. Activities like gene splicing. Bright kids like Keoni Gandall who literally assembled a gene factory / lab in his home.

This New York Times article will likely be a bit of an eye-opener for many. In it you’ll find out that researchers at the University of Alberta recreated an extinct version of Horsepox (a relative of Small Pox) from mail-order parts they reassembled. Without any authorities knowing or getting involved.

It’s really just beginning, this revolution. CRISPR-CAS9 is the 8008 of this nascent tech explosion. What may come is only limited by the imaginations and machinations of a lot of people who aren’t even in the field . . . yet. Some of them are still wearing diapers . . .



social commentary xcience

Could an AI be the keeper of extinguishing languages?

Watching a news item about a movie being made in an indigenous setting using indigenous actors speaking the language of their past ancestors. The actors all had to get a language boot camp and still learn how to pronounce the words from the script because none of them speak it. Only about 12 people in the world still speak it – they are all elders and those factors make resurrecting the language extra complicated.

I’ve seen this with other languages at other times – once the speakers are dead and gone the language is likely gone as well.

Even if some lingual genius were to learn these languages that would stave off extinction by one lifetime.

But what if an Artificial Intelligence were to take on the role of learning and using a dying language?

An AI might be able to acquire a new spoken language faster than the average human. And, potentially, it is more easily deploy-able to different places in the world at the same time.

If the AI was able to converse in the new language then that would mean that even after the last native speaker of that language had died there would still be ‘some-one/thing’ that researchers, teachers, students and the curious could converse with. And being able to hold conversations with someone is much better than the instead. Instead of just consuming media and mimicking content.

If this doesn’t already exist it will be possible anytime now. I’m writing this in the fall of 2017 and in the not so distant past a change took place that accelerated machine learning of human language (deep learning and sequence-to-sequence learning). You can read more about that in this article in a series over at

That article is about languages that have a written form – not all do. I am not a linguist but I suspect that many human languages have been spoken only. So an easily used interface that an elderly, computer agnostic / illiterate, individual could operate would be ideal. Possibly a human-like robot designed  styled to be non-threatening, say with a child-like size and appearance. That would help create the right psychological (and possibly emotional) mental state in the elderly person ‘teaching’ the bot their language. It leads them into a parental or grand parent role which might help get their emotional ‘buy in’ of the process. One could say that the little bot is standing in for all the children in the future who might learn the language being passed down.

It’s a shame when a culture or language disappears from the world of man. It’s as if the efforts of all those who contributed to its development over the decades and centuries were ultimately lost to time. And the real shame is it doesn’t have to be that way.



Tinnitus detectable as structural changes in how the brain processes thought and emotion

I’m a person with Tinnitus.

When I was a child I thought it meant you had a tin ear – that it meant you couldn’t hear or differentiate musical tones the way most people could. I’ve since learned that’s not what it means.

What it means to me is that there is a background noise to my life that never goes away completely. Right now as I sit here there’s an air cleaner running quietly in the room, a TV going in the other room, the occasional car or truck passing by outside and every now and then the air conditioner turns on.. But mixed in with that is a hiss; it has a slight;y high pitched edge dancing on top but most of the time it’s a hiss.

The way I describe it most of the time is to say ‘It’s like there’s a water tap running in a bathroom elsewhere in the house.’ Sometimes it gets louder and becomes a ringing in my ears. Most of the time I forget it’s there – the real world is too noisily busy to notice it. But it never ever goes away completely.

When I first moved out on my own I found myself always listening to either the radio or music when I went to sleep (all night TV wasn’t a thing back then and VHS hadn’t been invented let alone DVDs or steaming media). I later learned that nearly all people with tinnitus do the same. It’s because when the real world gets really quiet the internal noise becomes all that much more noticeable.

People with severe symptoms can find their ability to carry on a normal life badly disrupted. Effects can range from simply being debilitating to driving people insane. Thankfully mine is not that bad – I can carry on a fairly normal life and it doesn’t prevent me from enjoying it for the most part.

I wasn’t born with it, I think.
I’m pretty sure mine comes from noise-induced hearing loss. And I know exactly how it happened because I did it to myself – at the time I was only 8 and had no idea I was destroying my hearing and setting off structural changes in my head. I was just doing what 8 year olds do, exploring the limits of my world.

Long story short: I subjected my ears to an extremely loud horn pushed up nice and tight because there was a slight tickling sensation at the loudest point. For two days all I could hear was a loud screaming ringing in my ears – I bluffed my way through those days and didn’t let on I couldn’t hear a thing. Eventually the ringing died off and the hearing came back. The ringing sound never completely went away though . . . and the hearing probably never completely came back either. C’est la vie . . . enough about me.

Medical science knows that tinnitus comes from damage to the hearing system but beyond that little is known. There has been no external way to verify someone has it for instance. Other than their own testimonials there was no test that could be done to differentiate those with the condition from those without it.

Until now that is.

A team headed by Fatima Husain, University of Illinois speech and hearing science and neuroscience professor, has been conducting research using Functional MRI imaging and has shown changes in how the brains of tinnitus patients work when compared to those without it.

In the first I’ll mention she was “trying to understand how the brain adapts to having tinnitus for a very long time”. I’ve had it for over 50 years so I think I’d be in that cohort.

What did her team do? “Using fMRI, Husain’s team previously compared how the brain processes emotion in patients with mild tinnitus and people without the condition”

What did it find? ” … in contrast to those without tinnitus, patients with mild tinnitus showed greater engagement of different areas in the brain when processing emotional sounds.”
Okay, what about patients with not so mild tinnitus? “To further understand this altered brain activation, Husain conducted a new fMRI study to see if there were any differences among tinnitus patients. Because some patients adjust to the ringing in the ears while others do not, the severity of the condition can vary greatly.” I think I’ve been able to have a life not greatly affected by the condition.

What does that mean? “Patients with lower tinnitus distress used an altered pathway to process emotional information. The path did not rely on the amygdala, commonly believed to play an important role in emotion processing in the brain. Instead, patients who had adapted to their tinnitus symptoms used more of the brain’s frontal lobe, a region critical for attention, planning and impulse control. The researchers suggested that the greater activation of the frontal lobe might be helping to control emotional responses and reduce tinnitus distress.”

So does that mean that the brains of most of you (readers without this condition) use the one of the oldest parts of your brains’  architecture, the amygdala , to process the emotional content of stimulae but I do not? That my condition has disrupted the utility of that resource and forced my brain to enlist capacity in the most recently developed part of the brain, the frontal lobes?

Hmm . . . all kinds of questions arise here.
What is causing this break in the connection to, or usability of , the amygdala?
How does this drafting of portions of the frontal lobe for this task affect the other activities of the frontal lobe?
In what way do I, and other low stress tinnitus patients, process emotional content differently from you who do not have the condition?
The Amygdala is also central to memory. If tinnitus affected using it for one function how has it altered use of this aspect of it’s function? Do I remember things in a mechanistically different way than you?

The second item (also from is by the same researcher.

This is more of what she has learned using that great new tool fMRI.

“Using functional MRI to look for patterns across brain function and structure, the new study found that tinnitus is, in fact, in the hearers’ heads — in a region of the brain called the precuneus, to be precise.
The precuneus is connected to two inversely related networks in the brain: the dorsal attention network, which is active when something holds a person’s attention; and the default mode network, which are the “background” functions of the brain when the person is at rest and not thinking of anything in particular.
. . . The researchers found that, in patients with chronic tinnitus, the precuneus is more connected to the dorsal attention network and less connected to the default mode network. Additionally, as severity of the tinnitus increased, so did the observed effects on the neural networks.
. . . It also implies that tinnitus patients are not truly at rest, even when resting. This could explain why many report being tired more often. Additionally, their attention may be engaged more with their tinnitus than necessary, and that may lessen their attention to other things. If you have bothersome tinnitus, this may be why you have concentration issues”

I just learned of the Default Mode Network this past year and the ramifications of it are still percolating through my mind. And now I find that it’s maybe not being used as much (or in the same way) as it is in ‘normal’ people. Well geeee whiz – now I’m more curious than ever about it.

For those who haven’t heard about the Default Mode Network it’s another thing that was suspected for a long time but actual verification was discovered after researchers began using fMRI to peek inside operating brains.

Ever since Hans Berger invented the EEG and noticed constant electrical activity there has been a suspicion that the brain is always working no matter how rested or inactive the person appears. Later research showed that some areas of the frontal lobe became less active during focused thought. And that there was only a 5% difference in metabolic activity between resting and fully engaged brains. But it took fMRI to actually see the various parts of the brain firing in bouts of interrelated activity while a person wasn’t actually consciously thinking of anything at all.

All in all my first take-away from all of this news if I sure am happy that brain function is so dam plastic. If it wasn’t then the mal-connect with my amygdala caused by my tinnitus might have left me seriously damaged in some fundamental and debilitating way. The fact that another part of the brain can be repurposed to perform the job the system cannot use the amygdala for is part of that plasticity. That it’s affect on the normal functioning of that part of the brain is not noticeable to myself or others in any way can also be credited to that same plasticity.

Another title for this could have been ‘Brain Plasticity Protects Against Dumb Choices’