How Many Stars Are There?

October 9, 2017 at 11:28 am | Posted in Science, Space, uncategorized | 2 Comments

I’ve always enjoyed things that bring perspective on our place in the universe and the nature of space around us. I’ve posted on The Ultra Deep Field, How Our Solar System Actually Moves, Lanikea: Our Home Supercluster, Across the Universe, Quite Enough (on scale), and more.

A new treat: The European Southern Observatory is hosting a Gigapixel image of the Milky Way. You can shift it to full screen if you like. As you zoom and zoom, more and more stars show at every point. You can click and drag the image or use the tools across the bottom. Consider this a photo of our galactic neighborhood. It gives you more of a sense of just how large it is. Many of those points of light have planets.
David

 

DNA testing – Part 3 – Follow-up

June 5, 2017 at 10:27 pm | Posted in Health, History, Online services, Science | 1 Comment
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I’ve written before on DNA testing. In the first article in 2015, I compared the 4 prominent services for personal DNA testing. I chose 23andme. I then reported the broader results. Now I have some updates to that discussion.

It’s turned out the Y chromosome has had a lot more mutation than the maternal line so they had to update the haplogroup naming conventions last year. The original paternal haplogroup name is no longer current and the tree more complex. In my case, the guys wandered further too.

A few terms for the major testing:
Autosomal is the 22 pairs of chromosomes in the cells nucleus, excluding the pair of sex chromosomes. It’s the broad overview and allows you to match to other family members, etc.

Y-DNA is the Y or male sex chromosome. It traces your male line back: fathers, fathers, father, etc. You need to be a male or have a male member of the family tested for this one.

mtDNA – mitochondrial DNA comes from the mitochondria. It is passed down from mothers to both sons and daughters. It traces the mothers line back: mothers, mothers, mothers, etc.

Haplogroup – those that share a common ancestor based on haplotypes, groups of genes inherited from a single parent. We all have a paternal and maternal haplogroup. Haplogroups can be viewed in a tree structure of sequential mutations.

They can trace these 2 lines back roughly 100,000 years now for well-tested populations.

23andMe
Skip forward 2 years and 23andMe has finally upgraded my data to their new site format as promised. For a while, they were offering health results only to Canada and the UK due to US restrictions on “diagnosis.” With the site redesign, they’ve removed a lot of the more detailed health analysis and focus now on general markers like lactose intolerance, sleep depth, and so forth. Gone are more diagnostic things like Celiac and Parkinson’s markers.

Reporting is more centralized and distributed to tabs to support smaller screens. It surprised me to discover printing the reports (for me to PDF) gave a more complete view.

A new report on the Maternal line (haplogroups) goes back as far as the National Geographic’s “Deep Ancestry” report (below) although the second has slightly more detail.

The paternal haplogroup name was updated but there’s a gap between the tree map in the paternal section and the specific haplogroup named. As I discovered on FTDNA below, it’s also less specific.

Genographic
Meantime, I had also decided to take advantage of a sale on National Geographic’s Genographic Project. I wanted to support their work, and it offers more of a deep ancestry approach.

Here a deviation has taken place. Family Tree DNA used to do all their testing, allowing you to load your DNA test results into FTDNA (below) afterwards for free. However, for US customers, Helix is now doing their testing. They’re using a newer system that is not compatible with FTDNA. If you get the Helix test (white box, spit not swab), you can’t download the genome after either.

But as I’m Canadian, I still got the black, cheek swab kit to send to FTDNA in Texas.

My first impression of the Genographic results wasn’t positive – they didn’t notify me when the results were up. And the first presented report is “Genius” matches. It displayed famous people (not geniuses) who had some unmentioned genetic match. Essentially a pointless report.

The Regional Ancestry report had quite different percents from 23andMe but I suspect was less accurate due to the much smaller testing population.

What I did enjoy was the Deep Ancestry reports. This showed the maternal and paternal lines over thousands of years, migrating across vast distances as the ages changed.

There is also a Hominin report for the percent of Neanderthal DNA. This varied substantially from the 23andMe result as well.

Another disappointment was printing. The reports didn’t print well and the official printable report that summarized much of the above was missing all the maps even though the reports refer to them. I had to use screen captures for the maps and assemble them with the reports myself.

Given that 23andMe now includes very similar reports and has a great deal more other ones, it’s certainly preferable. It’s possible the Helix testing for Americans offers more reports or detail but that’s unclear. I suspect 23andMe would still be superior.

Family Tree DNA
Because I got the old Genographic kit, I could transfer the results to Family Tree DNA for free. This allowed downloading the Genome file and offered a few basic reports.

One of note though was the Y-DNA haplotree. This went much further than 23andMe, offering a Haplogroup that was 15 steps more detailed. And there they offered a further test (at a cost) to take it a few steps further.

From this, I discovered the links between the 23andMe paternal map and their designation of my haplogroup plus further steps that FTDNA named.

One of the bigger differences with FTDNA is their a la carte approach to ordering tests. You send in or transfer one sample and then pay just for the tests you want when you want them. Where the others above include autosomal, mtDNA, and Y-DNA, FTDNA lets you choose. Y-DNA is of no use for women, for example, as they don’t have the Y chromosome.

You can also choose the degree of testing for the mt and Y reports. If you’re a male and test all 3 at the basic level, it will cost you more than these others. But for serious researchers, there is a level of detail available you don’t see in the one-size services.

The site has many “projects” where members discuss details of their research. The one’s I looked at required the Y67 test to join as they were specific to certain haplogroups.

FTDNA offered me a significant autosomal discount, so I ordered the Family Finder test to connect with a few relatives on the system. This gave me the Matches section and Chromosome browser, similar to what 23andMe has. The Origins reports where too general to be of much use. They did not match known family regions either.

Also note they’re using the oldest technology now.

Conclusions
I’d still recommend 23andMe for the overview. Their reports are broader and bring a more complete perspective. They use newer tech and have a larger customer base which increases accuracy and matches.

Family Tree DNA is superior if you want to explore genealogy in greater detail. They have more detailed test options but use older tech and are more expensive. Just understanding the value of their options requires a serious exploration.

National Geographic Genographic Project loses much of it’s advantage as others begin to include deep ancestry reporting. With their migration to the newer tech, it can’t be uploaded to FTDNA nor the genome downloaded for other services.

Ancestry also includes a DNA testing service but this would only be helpful if you use their services already. The family tree building software is sophisticated but is an ongoing expense.

From some of the commentary I’ve read on-line, serious researchers use several of the services for different features and to connect with different populations. As the number tested grows, the detail levels will increase. Added features will make going back in and taking a look around again useful, even for the casually curious.
David

Our Seed Heritage is Our Food Supply

March 8, 2017 at 6:13 pm | Posted in Economoney, Health, Justice, Movies, Science | Leave a comment
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Recently I saw the film Seed: The Untold Story. While I was familiar with the presented issues, I wasn’t aware of just how extensive they were.

For example, did you know that 94% of seed diversity was lost in the last century? Some countries have made it illegal to collect heritage seeds, saying they need to “maintain the quality” (monopoly) of commercial stocks. And yet history has repeatedly shown us the hazards of widespread use of the same crop. Mono-crops can be compromised or wiped out by easily spread disease.

A more recent development is seed patents. Make a few small changes and you can own the seed stock. Farmers are not allowed to collect seeds or the seeds produce only one crop, obliging them to buy seeds again every year. Those seeds are often dependent on chemical sprays and again encourage mono-crops.

Thousands of farmers in India were convinced to borrow to buy seed they formerly harvested themselves. They got a crop they couldn’t renew and often failed, bankrupting them and causing over 250,000 suicides.

Thousands of small seed companies have been bought up by chemical companies which now control 2/3 of the global market. In other words, our food supply has become very dependent on international chemical corporations. The same ones who are patenting seeds.

The “small changes” that allow patenting seeds often take the form of genetic modification. Unlike our long history of culturing plant qualities through selective breeding, Genetically Modified (GMO) foods have directly altered DNA, often by adding features from other species. They’ve added fish DNA into tomatoes, for example. Those foods are then put on the market, untested. Some crops like corn and soy are almost all GMO, both of which are widely used in packaged food.

Scientific research is beginning to show correlations between GMO food consumption, cancer, and other health issues. Our dinner tables have become a laboratory for testing GMO. Unlike the also present pesticide residues, GMO cannot be washed off.

As pollination doesn’t recognize farm boundaries, nearby fields get contaminated. The seed owners can successfully sue farmers for using patented plants they didn’t plant. And the supply of non-GMO seeds gets further compromised, again moving towards mono-crops.

Yet the film is not dominated by a doomsday message. They also cover solutions and highlight people who are saving seed diversity for future generations. And happily, governments are slowly legislating GMO labeling so consumers can make informed choices.

Western Canada has a well-developed seed-sharing community.
David

The Hidden Life of Trees

November 21, 2016 at 10:55 pm | Posted in Media, Nature, Science | 3 Comments
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My father was a forest scientist, professor, and conservationist with an expertise in tree disease. While I didn’t follow in his footsteps, I’ve maintained a love of the forest.

Forest science has evolved considerably in recent years in ways that many people are unaware of.

The Hidden Life of Trees is the best-selling book by forester Peter Wohlleben. Here, the author, Dr. Suzanne Simard, and Dr Teresa Smhayetsk talk about how trees support each other, including other species, but know friends and family.
(from a longer DVD Intelligent Trees)

On YouTube

Dr. Suzanne Simard is a western Canadian forest scientist who explains in a TED talk how trees communicate. This includes an underground network for transporting signals and sharing nutrients.

On YouTube

And here the author Wohlleben is interviewed, also mentioning the “wood wide web” and wheat “talking” at about 220 Hz.

On YouTube

And if you’ve not seen it, The Man Who Planted Trees. An old favorite.

On YouTube
Enjoy!
David

The Connected Universe

November 11, 2016 at 4:46 pm | Posted in Media, Movies, Science, Space, Technology | Leave a comment
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For some years, I’ve been watching the work of self-taught physicist Nassim Haramein. He’s given many seminars on his ideas and released video of them, including the 6-hour Beyond the Event Horizon. Many people have studied how to explain his ideas and more recently they’ve launched an on-line “academy” to take it further. He’s also shown up in various works like the film Thrive.

Some of his ideas have been wildly speculative, like the grave of Jesus or the meaning of a comet. But the unfolding physics has been quite fascinating. As with Einstein and Buckminster Fuller, the physics is driven by his experiences.

While my physics isn’t strong enough to test his work, he has been working with several traditional physicists and has had his work published – peer-review is the key screening for  science.

His model proposes a solution for Unified Field Theory but it comes out of left field, dropping the standard model of 4 forces into 2 and placing a black hole inside every proton. Key also is reintroducing spin into Einstein’s Field equations (also related to that black hole) and a universal scaling law. The results of his formulas are more accurate than the Standard model.

Meanwhile, he’s been working on a film to bring the ideas to a larger audience. In the summer of 2014, I saw clips at the Vancouver production studio of the in-progress work. Some of the film was also shot in Vancouver and Whistler. The project ended up being the most successful Indigogo fund-raising campaign and first into a new Vimeo distribution product.

The film is called The Connected Universe and has now been released. It can be watched on-line for about $7. The trailer.

While the film talks about his work and how it developed, Nassim stays very general on science, focusing more on the broader ideas and the potential impact they could have on our world-view.

He talks about how we’ve been looking at matter to define space but it’s actually space that defines matter. At about the halfway point, he explores how important an information feedback mechanism is for the universe. This is the source of the self-organizing systems that surround us. Without it, form would never have arisen in the first place let alone evolved over billions of years. However, he goes on to suggest that the feedback mechanism is what makes space conscious and able to learn about itself. This is a subtle form of materialism.

I would suggest space arises in self-referral consciousness, so consciousness defines space. Awareness automatically creates a feedback mechanism by being aware of what arises in space (itself). In other words, consciousness provides a built-in feedback mechanism that is present in space and in matter.

As we mature as people, we notice progressively more subtle layers of our own nature. That awareness brings a more alert feedback mechanism which is self-enhancing.

But I fully agree that the universe is one massive feedback mechanism.

The film is full of gorgeous graphics although much of it is artist expression rather than an accurate illustration of the dynamics.

At several points, they come back to the importance of our attention.

Nothing would be the same if we weren’t there. We’re actually participating in this incredible, complex, will-works of nature. [the] communication of all the things in it is occurring through this imprint that we leave on the structure of space-time as we go along, as we interpret what we see and how we feel. So we have a responsibility in our interpretations, in our feelings, in our behaviors, in what we are feeding the universe.
— Nassim Haramein

The film does touch on the importance of spin, forces, and the universality of black holes as I mentioned prior. But I was disappointed they skimmed over it and didn’t display a model of the dual torus and the inner dynamics that create the 2 fundamental forces – attractive and repulsive. It’s also absent any test results.

By comparison, here’s a TEDx talk he did with a little more of the science.

Many people think technology alone holds the key to creating a better future for humanity. But there is more to it than that. It is the consciousness with which we create and wield that technology that will significantly impact our world.
— Patrick Stewart, narrator

Primarily, the film talks about the broader ideas and possible consequences of vacuum energy devices and a new world-view of being intimately connected. We could say a film of vision rather than application.
David

Gut Health

October 26, 2016 at 7:28 pm | Posted in Health, Science | 8 Comments
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All disease begins in the gut.
–- Hippocrates

An average-sized human body comprises over 37 trillion cells. Most of them specialize and work in groups, like as skin, muscle or organ, for the common good. Our digestive system breaks food down into proteins and nutrients that cells need to function and communicate. However, good digestion requires the support of a wide range of microbes that live in our gut. They estimate there is 10x more microbes living in our gut than cells in the body.

‘Gut health’ is a term increasingly used in the medical literature and by the food industry. It covers multiple positive aspects of the gastrointestinal (GI) tract, such as the effective digestion and absorption of food, the absence of GI illness, normal and stable intestinal microbiota, effective immune status and a state of well-being.
research paper

Our gut has turned out to have more neurons that our brain, leading to the term “gut brain”. The gut is also a central part of our immune system.

The microbes help us and we support them. But if some of them get carried away and overpopulate, we need to bring them back into balance.

For example, if we have too much sugar (including low quality carbs) in our diet, microbes like yeast (candida) become excessive. The yeast signals a demand for more sugar and we crave it. But anything in excess overwhelms the other microbes and throws the gut balance off. What we need to properly digest other foods is reduced.

This is chronic for some people. Too far out of balance and GI issues migrate to other parts of the body causing skin problems (thrush, age spots, rashes, adult acne), yeast infections, bloating, food and chemical sensitivities, bad breath, chronic fatigue, allergies, reduced immune function, stubborn gut fat, reduced serotonin (happiness), and so forth. Every piece of research I looked at had still more that could be added to this list.

This process can lead to the gut barrier being compromised, leaking particles into the blood stream and on into places they don’t belong. Known as “leaky gut”, this leads to increased infections, inflammatory problems, metabolic disorders and intestinal diseases. Research suggests gut imbalance can have a key role in autoimmune diseases.

Our modern diet has a few foods said to cause the most trouble with gut health.

1 – azodicarbonamide – an additive to whiten flour that is banned in the EU and other places but legal in N. America. It’s widely used in fast food buns.
2 – diet soda – the artificial sweeteners. Yeast loves all sweeteners.
3 – coffee – due to its acidity. Even worse with added sugar, especially found in fancy coffees.
4 – alcohol – kills friendly microbes

You may recognize some of these from the cancer risk list too.

A lean chicken burger and diet soda isn’t as healthy as you might think. More so if this is your regular diet.

Another thing to mess with gut health is antibiotics. They are very useful for bringing problem microbes under control but do this by cutting a wide swath. It’s thus important to restore our microbiome after taking antibiotics. NSAIDs like aspirin and Advil can also cause trouble.

The effect of ciprofloxacin [an antibiotic] on the gut microbiota was profound and rapid, with a loss of diversity and a shift in community composition occurring within 3–4 d[oses] of drug initiation. By 1 wk after the end of each course, communities began to return to their initial state, but the return was often incomplete.
research paper

If we restore gut balance, the many symptoms subside. However, starving the sugar-loving yeast can take several months. Even if we fast for a few days and break the sugar craving, until gut balance is restored, there will be a much greater tendency to “fall off the wagon” on diets, etc.

To restore gut health, you need sources of healthy microbes like:
1) Kefir
2) fermented veggies like Sauerkraut or Kimchi
3) probiotic supplements

Probiotic yogurt is a popular solution these days but commercial yogurt is usually pasteurized for longevity, killing the microbes. Most also have added sugar.

Ironically, if you have a yeast issue, fermented foods like sauerkraut may cause more bloating. They become more suitable after some balance is restored for maintaining balance.

Thus, a supplement is a good idea to restore gut health. You want one with billions of microbes and a number of strains. Somewhat like a good multivitamin.

(Unless you have a specific issue like Crohn’s that is better served by very specific strains.)

My local health food store recommended a more expensive one with more strains and numbers for post-antibiotics but a regular one for general restoration.

These probiotic supplements don’t last for more than a couple of weeks in the gut but they “elbow out” the bad guys and give the chance for beneficial microbes to get reestablished.

When you begin a supplement, it’s common to notice quick changes with digestion and elimination. Even with a colicky baby for a supplementing nursing mother.

Foods recommended to feed your gut flora (called prebiotic) included whole oranges, bananas, artichokes, yams, lentils and garlic. Overall, you want a diet emphasizing whole foods with a plant base for optimum health.
David

The Great Bear Rainforest – Coastal Revival

May 3, 2016 at 9:41 pm | Posted in Nature, Science | 2 Comments
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The Great Bear Rainforest is a temperate rain forest along the NW coast of North America on the Pacific Ocean. It runs from the Discovery Islands (across from Campbell River*, BC) up to the Alaskan panhandle border. Much of it is mountainous and intersected by fiords. (a map)

First named by environmental groups, a large section became protected earlier this year (years after an agreement was reached) with other areas under some protection. Most old growth forest within is now protected.

A ban on the trophy hunting of bears was also negotiated, but a changed government brought the hunt back. Ironic they allow bear hunting in a place with this name.

A rather creative solution has been to buy area hunting rights and manage them as if they were being used for hunting. But instead, they’re used for eco-tourism – the bears are shot with cameras instead of guns. They even have to go through all the motions and procedures to behave like hunters: firearms handling, hunting licenses, and so forth. It’s rather ridiculous they have to go to such lengths to protect a single species of wildlife. The first videos below describe more.

The area is also highlighted due to an attempt to build an oil pipeline from the tar sands of Alberta to the coast, dramatically increasing tanker traffic on a stormy, complex coast. Many remember the Exxon Valdez spill in the area. But tar sands oil is worse and much harder to clean up.

It’s a remarkable area, rich with wildlife. But it’s also remote. The most likely way you’d see it is on a cruise ship to Alaska while it travels up the coast. The area includes the world’s largest population of Spirit bears, also called kermode. A series of short videos have been produced speaking about the area and some healthy approaches to sustaining it.

1 – Raincoast’s Fight

https://www.youtube.com/watch?v=DcfTqQL9Ias

2 – Banning The Trophy Hunt

https://www.youtube.com/watch?v=cZVLR6RFeVM

3 – The Spirit Bear (Kermode or white)

https://www.youtube.com/watch?v=cbX-4T_5Z9A

4 – Revival of the Humpback Whales

https://www.youtube.com/watch?v=4Yq62sdmpcg

5 – The Marine Detective

https://www.youtube.com/watch?v=HCarB7ige44

David
* about a half hours drive north of me. I live on the more moderate and populated SW coast on sheltered waters.

Stargazing

March 25, 2016 at 2:14 pm | Posted in Online services, Science, Space | 1 Comment
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We’ve developed the bad habit of leaving the lights on all night. On streets, on porches and in yards, on stores and in offices. A world that never sleeps and never sees the Milky Way.

“Stargazing is extinct in cities like New York City and London, but it’s also endangered in places all over the world because of urbanization. We rounded up the most incredible places to see the night sky, and a few places that need to be preserved.”

The Weather Channel has set up images from various low light locations around the world that are ideal for watching the night sky. Does the night sky above you look like this? Best is on New Moon nights, so they offer a calendar too.

Light pollution ruins star gazing but also restful sleep, natural rhythms and thus health. Blackout curtains can help but then you can’t wake with the sun. Motion detectors can make a big difference on your property.
David

Gravity Waves, Part 2

March 9, 2016 at 8:39 pm | Posted in Science, Space | 2 Comments
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A couple of years ago, I wrote a short bit about gravity waves. It’s the last prediction of Einstein’s General Relativity that hadn’t been directly experimentally verified – after 100 years. Last fall, a major 3 year upgrade was completed on the Ligo detectors in Louisiana and in Washington state. Just after they where turned back on, they detected a merger of 2 black holes that happened long ago and far away.

That event released more energy than 1 billion, trillion suns – that’s more than we have in the known universe. So the event made waves in space-time. Such an event is expected about once every 10,000 years, so it was fortuitous timing.

After rigorous verification, that discovery has been officially announced and the last prediction is experimentally verified.

The upgraded equipment can also detect other sources of gravity waves. This opens a new window on the universe. We can now explore the universe not just with light waves (electromagnetic spectrum) but with gravity waves.

Here Brian Greene reviews the discovery:

https://www.youtube.com/watch?v=s06_jRK939I

For more background, you may enjoy these:
Rumour of the discovery and more detail on gravity waves.

The follow-up on the discovery

David

Eating for Life

December 10, 2015 at 4:27 pm | Posted in Economoney, Health, Science | 1 Comment
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Eating based on beliefs or special diets that are not designed for your specific body can have unintended consequences. Variety is what makes food interesting and ensures we get the diversity of nutrients required.

Readers of this blog know I did a series on the CHIP program. This included some of the science for shifting to a more plant-based diet, minimizing cancer risk, and overall self care. The program was originally designed for heart patients but was expanded to the whole population.

I quite liked the approach as it looked at how and what we eat, fitness, emotional health, and more. CHIP recommends a primarily plant-based diet but suggests you move in that direction rather than mandating anything.

The weakness however is not differentiating recommendations by body type. For myself I’ve found Ayurveda adds some useful extras. For a start, they begin with your body type and make dietary recommendations accordingly. They recognize that not all of us will respond to the same vegetables or other foods in the same way. Each of us needs a certain emphasis or balance of food types.

Ayurveda favours a vegetarian diet that includes dairy, but they allow for the full range and can recommend some occasional fish or white meat. They have a food as medicine approach. Dairy is also prepared in specific ways. Clarified butter, soft cheeses, and boiled milk, for example.

Ideally, we begin with initial recommendations and then experiment. Pay attention to how foods make you feel afterwards. But be very careful where sugar is involved. Sugar confuses the bodies intelligence so it messes up the signals and creates craving. Also, you may find dietary needs change with age and life, so we may need to tune up choices periodically.

But if we can learn to take the bodies lead in our eating choices rather than some dietary rules or beliefs, we’ll do much better and enjoy life more.

Science is beginning to catch on to this. Programs are being developed (as yet far too expensive) that make science-based diet and exercise recommendations that are specific to your body. By combining DNA, blood, and other tests, we’ll soon be offered more personalized recommendations.

Meantime, enjoy the experiment.
David

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