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Beyond immediate death count: Long Covid and blood clots: Covid-19 as a blood clot disease

Coronavirus disease 2019 (COVID-19 ) is caused by a virus. Its name is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2.)  This is one of a number of respiratory viruses.

Myth: Covid only affects the lungs. And only about 0.5% of infected people get sick and die, so the rest of us will be okay.

Fact: Covid-19 is an endothelial blood clot disease as well as a pulmonary disease. Blood clots travel to all other organs in the body, including the brain, and can cause serious damage even in survivors. People are at least ten times more likely to get blood clots issues and neurological issues,than dying.

Many covid-19 survivors report painful and debilitating symptoms. Some report feeling like they were being suffocated.  During these episodes their blood oxygen levels drop, which causes biochemical stress in many organs.

The death rate alone is staggeringly higher than what we normally see from influenza.

A death rate of .5% is higher than any other viral pandemic that has hit the United States since the Spanish flu, the 1918 flu pandemic. The United States of America has a population of over three hundred million people. Over eight hundred thousand Americans have already died due to this disease. If left unchecked, Covid-19 would kill millions Americans.

Deaths are just a small part of the coronavirus story: Covid-19 is an endothelial blood clot disease.

Many covid-19 patients have blood clots in the legs, lungs, and cerebral arteries leading to the brain. Likely in other locations as well.

Above image: formation of an occlusive thrombus in a vein.

Take blood clots seriously

Blood clots are no joke. They may lead to.

* strokes

* encephalitis (swelling of the brain)

* heart attacks

* inflammation of the heart

* deep vein thromboses in the legs

* clots in the lungs

* stroke-causing clots in cerebral arteries.

* pain, shortness of breath

* fatigue, dizziness due to lack of oxygen to the brain

* kidney failure

* degradation of kidney dialysis: clots can clog kidney dialysis machines.

Doctors have documented short term neurological damage in covid patients, even in some otherwise asymptomatic people.

It is likely that there is long-term neurological damage as well.

“If you start to put all of the data together that’s emerging, it turns out that this virus is probably a vasculotropic virus, meaning that it affects the [blood vessels],”

In a paper published in April in the scientific journal The Lancet, Mehra and a team of scientists discovered that the SARS-CoV-2 virus can infect the endothelial cells that line the inside of blood vessels.

Endothelial cells protect the cardiovascular system, and they release proteins that influence everything from blood clotting to the immune response. In the paper, the scientists showed damage to endothelial cells in the lungs, heart, kidneys, liver, and intestines in people with Covid-19.

– Covid-19 May Be a Blood Vessel Disease, Dana G. Smith

How covid-19 attacks the brain

John Hamilton writes

Many patients who are hospitalized for COVID-19 are discharged with symptoms such as those associated with a brain injury….

COVID-19 also appears to produce many other brain-related symptoms ranging from seizures to psychosis, a team reports in the Jan. 5 issue of the journal Alzheimer’s & Dementia…. it may even increase a person’s risk of developing Alzheimer’s disease.

For many affected patients, brain function improves as they recover. But some are likely to face long-term disability, de Erausquin says.

… “What we found was that the very small blood vessels in the brain were leaking,” Nath says. “And it wasn’t evenly — you would find a small blood vessel here and a small blood vessel there.” The injuries resembled those from a series of tiny strokes occurring in many different areas of the brain, Nath says.

How COVID-19 Attacks The Brain And May Cause Lasting Damage, Jon Hamilton

Conclusions

Many covid-19 survivors may die many years or decades earlier than they otherwise would have, due to the blood clots and endothelial damage.

The full death toll of Covid-19 will likely be many times higher than the current toll. As 1/2022 over 839,000 Americans have died. It is certain that that over the coming years and decades many more people will die from their covid-19 damage. As such, we should be diligent in protecting ourselves, our loved ones, and everyone in our communities.

How to protect ourselves

Gather knowledge, e.g. Covid 19 is an airborne virus

Wearing masks in certain situations – Unmasking mask myths

Note that vaccinated people can be protected yet still transmit covid-19.

Social distancing

Washing hands

Zinc supplements and coronaviruses, rhinoviruses, common cold

Getting a covid-19 vaccination

Covid-19 Vaccine Tracker, Bloomberg

High effectiveness of covid-19 vaccines, breakthrough cases and the base rate fallacy

References

High effectiveness of covid-19 vaccines, breakthrough cases and the base rate fallacy

What Does COVID Do to Your Blood? John Hopkins Medicine, Panagis Galiatsatos, M.D., M.H.S. and Robert Brodsky, M.D.

Covid-19 May Be a Blood Vessel Disease, Which Explains Everything, Dana G. Smith, Elemental, 5/29/2020

How COVID-19 Attacks The Brain And May Cause Lasting Damage, Jon Hamilton, Shots: NPR Health News, 1/5/2021

Microvascular Injury in the Brains of Patients with Covid-19 Letters, New England Journal of Medicine, Myoung-Hwa Lee et al, DOI: 10.1056/NEJMc2033369

The chronic neuropsychiatric sequelae of COVID‐19: The need for a prospective study of viral impact on brain functioning, Gabriel A. de Erausquin et al, Alzheimer’s & Dementia [journal,] 1/5/2021,  https://doi.org/10.1002/alz.12255

Our Covid-19 articles

Respiratory viruses (influenza, rhinoviruses, coronaviruses etc)

How do viruses spread? Airborne vs non-airborne

Beyond immediate death count: Long Covid and blood clots: Covid-19 as a blood clot disease

High effectiveness of covid-19 vaccines, breakthrough cases and the base rate fallacy

How vaccinated people can be protected yet still transmit covid-19

Vaccines – what does 95% efficacy actually mean?

Simple DIY masks could help flatten the curve. We should all wear them in public.

Unmasking mask myths

How does the Schrodinger equation create orbitals?

How does the Schrödinger equation (from quantum mechanics) create atomic orbitals and molecular orbitals that?

Where do these beautiful three dimensional shapes come from?

Why do they have the shapes that they do?

This lesson assumes that you have already learned about –

waves and superposition

constructive and destructive interference

the classical models of the atom

Neils Bohr and his semi-quantum mechanical model of the atom

the Schrödinger model of the atom

Physicists use the Schrödinger equation to model an e- around a nucleus.

Hence, e- = electron

Let’s first review the idea of superposition: Notice what happens here when two waves pass through the same space, at the same time.

The waves are not bouncing off of each other – they pass through each other.

Waves can add together – constructive interference. That’s what we see here.

Below we see two waves that add together to create a region where they cancel out. This is destructive interference.

Can we make waves appear to stand still? Consider what happens when two waves come at each other, at just the right speed and height:

A standing wave is produced!

We see this in music all the time. Pluck a string on a guitar or violin.

Musicians call the first standing wave the fundamental, or first harmonic.

Higher frequency standing waves are called overtones.

This violin string isn’t quite showing a standing wave, but it gets close.

We can get standing wave on any physical object, like on a cymbal, or on any flat round disk.

Your loudspeakers, on a stereo system or in earbuds, move like this.

Well, in the Schrödinger equation:

  Constructive interference leads to regions where we’re more likely to find the e-.

  Destructive interference leads to regions where we’re less likely to find the e-.

Here we model an electron as a standing wave around the nucleus of an atom. Compare the left and right side.

On the left a standing wave is produced, when the wavelength is of such a length that it creates constructive interference. On the right the wavelength has a different length, and no constructive behavior develops.

Allowed                                             Not allowed

This is what happens in atoms – e- aren’t solid objects.

Instead, e- are understood to be quantum phenomenon that follow a wave equation!

When the wavelength of the e- allows for constructive interference, that is where it has an effect.

Of course, that model for e- around an atom is too simple. It is flat.

So let’s show a standing wave in three dimensions.

How do these equations lead to the spherical “s” orbitals?

This next image is from 6.3 Development of quantum theory

Here scientists use the Schrödinger equation to model an e- as standing waves in three dimensions.

from Opentextbc.ca, Chapter 6. Electronic Structure and Periodic Properties of Elements

What would it look like inside these spheres?

Below is a “traveling wave resulting from a point source emitting symmetrically in 3 dimensions producing spherical wavefronts.”

One of the upper quadrants of the region has been removed in order to expose the internal structure of the wave”

from intothecontinuum.tumblr.com

Just like the 2D case we can also create a ‘”standing wave resulting from an outward and inward traveling wave”

from intothecontinuum.tumblr.com

Now that we have made it here, here is a chapter on electron orbitals from ChemPRIME (Moore et al.)

This chapter is great for honors or AP physics or chemistry students.

Creating d and f orbitals

The same general idea is true for how d orbitals and f orbitals appear.

There are many possibilities for the wave function of an e- with a higher amount of energy.

We add all of them together – this is superposition.

Most of those waves cancel each other out (destructive interference.)

Whatever remains is there and assumes a certain shape (constructive interference.)

Here is a simplified version – different wave possibilities adding together to create a d orbital.

Molecular orbitals

Hybrid orbitals, what we see in molecules, are more complex examples of the same idea:

We see wave functions interfering with each other.

When two orbitals overlap we get more complex forms of interference, leading to new shapes.

https://chem.libretexts.org/Bookshelves/General_Chemistry/Book%3A_General_Chemistry_Supplement_(Eames)/Valence_Bond_Theory/Hybrid_Orbitals

Here, a hydrogen atom 1s orbital bonds with another Hydrogen atom 1s orbital.

This creates a H2 molecule with a sigma orbital (σ).

https://www.grandinetti.org/molecular-orbital-theory

This is a representation of two oxygen atoms merging into an O2 molecule in the singlet state.

This shows the most accurate representation for the actual shape of the molecule.

The original 2s and 2p atomic orbitals can be seen merging to create Sigma and Pi orbitals, which bind the atoms together.

The 1s orbitals do not combine and still show the individual atoms.

This GIF is from Wikimedia Commons, O2 MolecularOrbitals Anim.gif

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Teaching quantum mechanics in high school

I would love to hear how science teachers are teaching quantum mechanics in high school. Many of us plan to have a week long sequence in Honors Physics, or AP Physics, or perhaps in a science elective.

This could even be done in regular college-prep level physics classes if the students are so motivated. Having discussions like these – even done totally qualitatively, without math, are hallmarks of an inspiring science classroom.

I’m putting together here my resources on teaching various aspects of quantum mechanics, in what seems to be a reasonable order. Please understand that this is not an online textbook. These articles were each developed separately, so there is a lot of overlap.

Also, there is no mathematics, calculus, or differential equations required.

The nature of reality itself! The allegory of the cave

The wave nature of matter

Why did we have to develop modern physics? What is wrong with just keeping classical physics?

Early quantum theory

Schrodinger model of the atom

Schrodingers cat

Articles about the consequences of quantum mechanics

What are covalent bonds between atoms?

The normal force: So, objects really never touch?

How time and space could be a quantum error correcting code

The origins of space and time

Quantum teleportation (and it isn’t what you think)

Time’s arrow may be traced to quantum source

The quantum thermodynamics revolution

The four possible types of multiverses

Parallel universes in quantum mechanics

How do batteries work?

How do batteries work?

Let’s start by looking inside one, and seeing the flow of electrical charges.

Chemical reactions occur within battery.

e- are stripped away from the carbon electrode.

e- try to flow from – terminal to + terminal, if a conducting circuit exists.

Here’s an amazing explanation: How A Battery Works by John Denker at Av8n.com

Relationship between battery and voltage

Voltage sources

Water doesn’t flow by itself unless going downhill

Hills create a drop.

Charge doesn’t flow by itself unless going “down voltage”, i.e. down a change in “potential difference”.

Batteries or generators create a potential difference.

.

Oxymoron alert! Batteries do not provide “charge”

Batteries may run out of something, sure but they certainly don’t run out of electrical charges.

Technically speaking, they can’t be charged or re-charged?!

The total amount of charged particles in a battery is always the same.

Let’s think this through: The charges in batteries (and wires!) are electrons. We’ll abbreviate them as e-.

e- are already in the battery, wire, etc.

Batteries merely provide the voltage (“pressure”)  to move the e-

When e- flow out of one end, new e- come into the other end.

So what is it that batteries lose over time? They lose ENERGY.

Batteries are powered by chemical reactions.

So over time batteries lose chemical potential energy.

When you “recharge” a battery, you’re using electricity to alter the battery’s chemistry.

You’re taking electrical energy and storing that in chemical bonds in molecules, within the battery.

So you don’t give batteries more charge: you give it more energy.

Apps

Students use that wheel at the bottom to control the animation playback. It lets them play it at the speed they want and reverse it anywhere they need to to understand what is happening.

How does a lithium battery work in an electric car?

PhET battery voltage app

PhET battery resistor circuit

HONORS

What is going on with electromagnetic fields inside a battery?

In Physics forums we find these details.

Contributor leright writes:

Inside the battery, the negative charges flow IN THE DIRECTION OF THE E-FIELD, which means the negative charges are going AGAINST the electrostatic force set up inside the battery.

The electrons are able to flow against the electrostatic force because of an opposing chemical potential.

Normally, a battery which is not shorted out or connected to a load is under equilibrium conditions, meaning the chemical potential inside the battery exactly equals the electrical potential. Under these conditions, no charge carriers flow.

If you connect the positive terminal of the battery to the negative terminal, through some load, the electrons at the negative terminal of the battery flow through the wire to the positive terminal by the electric field set up by the E-field external to the battery.

When these electrons reach the positive terminal, the E-field inside the battery is momentarily reduced which in turn upsets the equilibrium between the chemical and electrical potential.

The chemical potential then dominates and allows the negative charge to continue flowing from positive terminal to negative terminal until equilibrium is once again established.

Notice that the electrons flow AGAINST the coulomb force inside the battery. They are able to do this because of the chemical potential, which is slightly greater than the electrical potential when equilibrium is disturbed.

Contributor Vanesch adds:

The whole point is that the flow of electrons (and ions) is not controlled by the electrostatic potential, but by the ELECTROCHEMICAL potential.

That electrochemical potential is also function of the concentrations of chemicals and a battery is exactly such a structure, where the gradient in electrochemical potential and the gradient in electrostatic potential are in opposite directions.

Hence, it is the electrochemical potential which drives electrons and ions against the electrostatic force.

Of course, the electrostatic potential is a PART of the electrochemical potential. So it is true that the electrostatic force tends to diminish the tendency to flow against the E-field, but if the concentration gradients can overcome this, then nevertheless, the charges flow against the electrostatic force.

The price to pay is that this flow will change the concentrations of chemicals in exactly the way which is necessary to “drop” the gradient of the electrochemical potential.

The system reaches a static condition when the electrochemical potential is equal everywhere: in that case, charges are not “motivated” to move anymore.

This situation can STILL contain both a gradient in electrostatic potential and a gradient in concentrations.

This is BTW, what happens in a PN junction in a semiconductor. There, you DO have an E-field, and NO charges flowing (because they are pushed exactly the same amount in the opposite direction by the concentration gradient, and both cancel).

E-field-inside-of-a-battery: Physics Forums

Learning Standards

Massachusetts 2016 Science and Technology/Engineering (STE) Standards

HS-PS2-9(MA). Evaluate simple series and parallel circuits to predict changes to voltage, current, or resistance when simple changes are made to a circuit
HS-PS3-1. Use algebraic expressions and the principle of energy conservation to calculate the change in energy of one component of a system… Identify any transformations from one form of energy to another, including thermal, kinetic, gravitational, magnetic, or electrical energy. {voltage drops shown as an analogy to water pressure drops.}
HS-PS3-2. Develop and use a model to illustrate that energy at the macroscopic scale can be accounted for as either motions of particles and objects or energy stored in fields [e.g. electric fields.]
HS-PS3-3. Design and evaluate a device that works within given constraints to convert one form of energy into another form of energy.{e.g. chemical energy in battery used to create KE of electrons flowing in a circuit, used to create light and heat from a bulb, or charging a capacitor.}

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Helium cycle

On Earth, the production of new helium is result of radioactive decay.

Helium is found in large amounts in minerals of uranium and thorium.

About 3,000 metric tons of helium are generated per year throughout the lithosphere.

Earth’s crust [He] =8 parts per billion

Seawater [He] = 4 parts per trillion.

Earth may gain He atoms from outer space, from cosmic rays

Most He in Earth’s atmosphere escapes into space by several processes.

Near Earth’s surface, the average KE of He atoms is not enough for them to escape Earth’s gravitational field.

In the exosphere, He atoms have a greater KE, so some do escape.

Much 3He leaves Earth in this way. Some 4He leaves in this way.

Some He undergoes photoionization by the polar wind. This then escapes along open lines of the Earth’s magnetic field.

Some He goes into space due to direct interaction of the solar wind with the upper atmosphere.

This occurs during the short periods of lower magnetic-field intensity while the Earth’s magnetic field is reversing.

talkorigins.org Helium gas discussion

Learning Standards

Next Generation Science Standards

HS-LS2-4. Use mathematical representations to support claims for the cycling of matter and flow of energy among organisms in an ecosystem.

A Framework for K-12 Science Education Practices, Crosscutting Concepts, and Core Ideas (2012)

LS2.B: Cycles of Matter and Energy Transfer in Ecosystems

College Board Standards for College Success: Science

Standard ES.4 – Cycles of Matter and Energy: Matter on Earth is finite and moves through various cycles that are driven by the transformation of energy

LS.4.1 Matter Cycling – Students understand that matter is continuously recycled within the biological system and between the biological (biotic) and physical (abiotic) components of an ecosystem.

ESH-PE.4.2.2 Construct a graphical representation of the global carbon cycle (or the cycle of some other element or molecule), and use this representation to predict the effects of some environmental change (e.g., evolution of life, tectonic change, human activity) on carbon cycling (or the cycling of some other element or molecule).

Enduring Understanding 3A – Biogeochemical cycles are representations of the transport, transformation and storage of elements on a local, regional or global scale.

___________________________________________

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Hydrogen cycle

Like carbon, nitrogen, and phosphorus, there is also a cycle of hydrogen here on Earth.  Hydrogen atoms move between biotic (living) and abiotic (non-living) sources.

Hydrogen (H) is the most abundant element in the universe.

On Earth, common H-containing inorganic molecules include water (H2O), hydrogen gas (H2), methane (CH4), hydrogen sulfide (H2S), and ammonia (NH3).

Organic compounds contain H atoms (as well as C.)

The chemistry of the Hydrogen cycle is highly relevant to the development of life on Earth and mostly likely elsewhere in space.

Hydrogen fuels rockets, but what about power for daily life? We’re getting closer. Phys.OrgHydrogen cycle

Image from, Development and testing of new materials for high temperature PEM water electrolysis, Antonio Luis Tomas-Garcia

Where does our H2 come from? (sources)

biological processes in the oceans

biological (microbial) processes in soils

photochemical production in the troposphere via CH2O also written as H−CHO, formaldehyde.

Where does the H2 go? (sinks)

soil uptake

photochemical destruction in the troposphere by OH radicals

Free H2 can then be consumed by other microbes, oxidized photochemically in the atmosphere, or lost to space.

Cycling: H2 molecules usually exist within the atmosphere for 4 to 7 years before they get taken up in a soil sink.

Hydrogen production and leakage

As we develop hydrogen based industries, in what ways will we be producing, distributing, and using hydrogen? In what ways will hydrogen leak out into the atmosphere?

In the left column we see H2 production.

In the middle column we take into account the fact that once H2 gas is made, it needs to be distributed by trucks, ships, cargo trains, etc.

In the third column we see H2 being used by end-use customers.

Notice that in every step some H2 gas leaks out. Leaks are unintended, and unavoidable. We can minimize them but they will never be zero.

 

image from, Emission scenarios for a global hydrogen economy

Possible effect on ozone layer

“Increased atmospheric emissions of hydrogen will therefore inevitably lead to increased levels of water vapour in the stratosphere which will in turn lead to increased stratospheric cooling. This cooling may change the distribution of polar stratospheric clouds which play an important role in the formation of ozone holes and hence may delay the recovery of the ozone layer.”

A mitigating factor is that “The potential environmental risks from the hydrogen economy were found to be small in comparison with the environmental benefits. ” …. “the few available studies all point to the impact of large potential hydrogen leakages on the stratospheric ozone layer as being small”

– Hydrogen for Heating: Atmospheric Impacts – A literature review

Possible effect on global warming

Hydrogen gas indirectly acts as a greenhouse gas because it interferes with the global chemical reactions which control the methane levels and the formation of ozone.

Methane and ozone are the second and third most important greenhouse gases after carbon dioxide.

There is still much uncertainty about how much H2 gas would affect global warming, although the effect is currently considered to be very small.

– Hydrogen for Heating: Atmospheric Impacts – A literature review,

Possible effect on air quality 

H2 is relatively inert. It offers almost no chemical reactivity with urban pollutants such as NOx, O3, SO2, CO, VOCs and suspended particulate matter. Thus it has no direct influence on urban air quality.

However, because of its reaction with hydroxyl radicals: OH + H2 → H2O + H it plays a weak role in the long-range transport of photochemical ozone. This may affect ozone levels in the lower atmosphere, although the effect is currently estimated to be very small.

Caution in relying on Hydrogen power

Using hydrogen as a source of power for vehicles certainly has its drawbacks—among them the cost and the inefficient use of energy—but researchers are now warning against hydrogen for another reason, The Guardian reports: scarcity and a subsequent dependence on fossil fuels….

“Hydrogen-based fuels can be a great clean energy carrier, yet their costs and associated risks are also great,” said Falko Ueckerdt, at the Potsdam Institute for Climate Impact Research (PIK) in Germany, who led the research.

“If we cling to combustion technologies and hope to feed them with hydrogen-based fuels, and these turn out to be too costly and scarce, then we will end up burning further oil and gas,” he said. “We should therefore prioritise those precious hydrogen-based fuels for applications for which they are indispensable: long-distance aviation, feedstocks in chemical production and steel production.”

The research, published in the journal Nature Climate Change, calculated that producing and burning hydrogen-based fuels in home gas boilers required six to 14 times more electricity than heat pumps providing the same warmth. This is because energy is wasted in creating the hydrogen, then the e-fuel, then in burning it. For cars, using e-fuels requires five times more electricity than is needed than for battery-powered cars.

text above from Researchers Warn Against Becoming Too Dependent On Hydrogen To Power Cars Elizabeth Blackstock, May 2021, Jalopnik 

Using hydrogen fuel risks locking in reliance on fossil fuels, researchers warn Damian Carrington, 5/6/2021, The Guardian (UK) 

Potential and risks of hydrogen-based e-fuels in climate change mitigation Falko Ueckerdt et al., Nature Climate Change volume 11, pages384–393(2021)

Hydrogen Production and Distribution Alternative Fuels Data Center, US Dept. of Energy, 

Some critics of Hydrogen power

The government’s embrace of ‘clean hydrogen’ helps no one but the fossil fuel industry, Richard Denniss, The Guardian , 5/2/2021

 

External articles

Atmospheric researchers present new findingson the natural hydrogen cycle. CalTech

Assessing Leaks in a Global Hydrogen Infrastructure: Can it Perturb the Natural Hydrogen Cycle?

The Hydrogen Grand Challenge

Leaked hydrogen fuel could have small negative effects on atmosphere

Hydrogen fuel could widen ozone hole

Global Environmental Impacts of the Hydrogen Economy

Hydrogen Effects on Climate, Stratospheric Ozone, and Air Pollution

Impact of a possible future global hydrogen economy on Arctic stratospheric ozone loss, with graphic

What Are The Pros And Cons Of Using Hydrogen To Generate Electricity?

The Hydrogen Hoax , The New Atlantis, by Robert Zubrin

 

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References

Bas van Ruijven et al., Emission scenarios for a global hydrogen economy and the consequences for global air pollution, Global Environmental Change, Volume 21, Issue 3, 2011, Pages 983-994,

Hydrogen for Heating: Atmospheric Impacts – A literature review, BEIS Research Paper Number 2018: no. 21, Dept. for Business, Energy and Industrial Strategy, UK

Learning Standards

Next Generation Science Standards

HS-LS2-4. Use mathematical representations to support claims for the cycling of matter and flow of energy among organisms in an ecosystem.

A Framework for K-12 Science Education Practices, Crosscutting Concepts, and Core Ideas (2012)

LS2.B: Cycles of Matter and Energy Transfer in Ecosystems

College Board Standards for College Success: Science

Standard ES.4 – Cycles of Matter and Energy: Matter on Earth is finite and moves through various cycles that are driven by the transformation of energy

LS.4.1 Matter Cycling – Students understand that matter is continuously recycled within the biological system and between the biological (biotic) and physical (abiotic) components of an ecosystem.

ESH-PE.4.2.2 Construct a graphical representation of the global carbon cycle (or the cycle of some other element or molecule), and use this representation to predict the effects of some environmental change (e.g., evolution of life, tectonic change, human activity) on carbon cycling (or the cycling of some other element or molecule).

Enduring Understanding 3A – Biogeochemical cycles are representations of the transport, transformation and storage of elements on a local, regional or global scale.

 

 

Birds

Definition of birds

Birds are a group of warm-blooded vertebrates

They are characterized by the presence of feathers, toothless beaked jaws, the laying of hard-shelled eggs, a high metabolic rate, a four-chambered heart, and a strong yet lightweight skeleton.

Birds live worldwide; range in size from the 5 cm (2 in) bee hummingbird to the 2.75 m (9 ft) ostrich. There are about ten thousand living species.

Evolution of birds

Almost all dinosaurs went extinct about 65 million years ago (at the end of the Cretaceous Period), after living on Earth for about 165 million years.

Almost all branches of the dinosaur family tree died out, except for the branch with small feathered dinosaurs. That branch proliferated and developed into the birds that we know today.

Zina Deretsky, National Science Foundation. Air sac system of birds and of Majungasaurus.

This infographic is one way to show the relationship between various forms of dinosaurs.

It illustrates that today’s birds are the last remaining branch of the dinosaur family tree.

Image by Shawn Gould and Jen Christiansen, from How Dinosaurs Grew So Large—And So Small, John R. Horner, Kevin Padian and Armand de RicqlèS
Scientific American 293, 56 – 63 (2005)

Groups of birds

Raptors, also known as birds of prey, are birds that primarily hunt and feed on vertebrates, and that are large relative to the hunter.

Raptors have keen eyesight for detecting food at a distance or during flight, strong feet equipped with talons for grasping or killing prey, and powerful, curved beaks for tearing flesh.

The term raptor is derived from the Latin word rapio, meaning to seize or take by force.

In addition to hunting live prey, many birds, such as fish eagles, vultures and condors, eat carrion.

Condors are under vultures, in the order of Cathartiformes.

Notice that raptors, like reptiles, are not a true clade.

“There’s No Such Thing As Reptiles Any More – And Here’s Why”

Phylogeny of core landbirds modified from Mindell et al. (2018). The shaded box encompasses the raptorial grade (see text), within which we propose that all orders are considered raptors. Raptors as a group is paraphyletic and mostly share the raptorial lifestyle passed down from their single common ancestor.

Such grouping assumes then that the raptorial lifestyle was lost twice independently with the ancestors of both the Coraciimorphae and Passeriformes/ Psittaciformes clades.

Commentary: Defining Raptors and Birds of Prey

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Learning Standards

Benchmarks for Science Literacy, American Association for the Advancement of Science

Students should begin to extend their attention from external anatomy to internal structures and functions. Patterns of development may be brought in to further illustrate similarities and differences among organisms. Also, they should move from their invented classification systems to those used in modern biology… A classification system is a framework created by scientists for describing the vast diversity of organisms, indicating the degree of relatedness between organisms, and framing research questions.

SAT Biology Subject Area Test

Evolution and diversity: Origin of life, evidence of evolution, patterns of evolution, natural selection, speciation, classification and diversity of organisms.

Teaching About Evolution and the Nature of Science, National Academy Press (1998)

Biological classifications are based on how organisms are related. Organisms are classified into a hierarchy of groups and subgroups based on similarities which reflect their evolutionary relationships. Species is the most fundamental unit of classification.

Zeroth law of thermodynamics

People normally think of the three laws of thermodynamics. But there is one idea that they all depend on, so basic that it often gets overlooked: the zeroth law. 

This idea works like the transitive rule of algebra:

If A = B  and B = C  then A = C

If the temp of object A = temp of object B,

and the temp of object B = temp of object C,

then the temp of object A = temp of object C

Therefore all three systems would be in thermal equilibrium.

thermal-equilibrium Tim Sharp Zeroth Law
http://www.livescience.com/50833-zeroth-law-thermodynamics.html

Let’s watch three different materials fulfill this law, by coming into thermal equilibrium.

Animation by Charles Xie

Thermal equilibrium (in this example) is reached when the temp of all pieces = 13.4 degrees C.

zerothlawthemo

http://weelookang.blogspot.sg/2012/09/the-zeroth-law-of-thermodynamics.html

Also see https://www.grc.nasa.gov/www/k-12/airplane/thermo0.html

Another way to view this:

“When body A is placed in thermal contact with body B, there will be a flow of thermal energy between the two bodies. Thermal energy will flow from the body at a higher temperature, to the one at a lower temperature, until thermal equilibrium between the two bodies is reached.”

– Loo Kang Lawrence

Charles Xie Thermal Equilibrium

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Measuring mass in the metric system

In science and engineering we often have to make measurements of mass. Now, I understand that a lot of American students have affinity for the traditional English system of measurements.

But we can’t make much progress in any field of science or engineering without first becoming conversant with the metric system. It is used worldwide. 

How do we measure mass? To learn practical, hands-on skills, see our lesson here.

Measuring mass with a triple beam balance

But in this lesson we’re going to get a feel what various masses would actually look like in real life.

Kilograms

A kilogram is 1,000 grams. It is abbreviated as kg.

Can we convert between kilograms and pounds…. not quite [TBA]

But if all measurements are done here on Earth then 1 kg of mass has a weight of about 2.2 pounds.

Here’s a 1 kg steak dinner

image from TripAdvisor, Outback Steakhouse, Las Vegas Blvd

How can we visualize this? About the mass of a liter bottle of water or soda. 

About the mass of good size hardcover book. About the mass of a quart of Gatorade.

Or about the mass of an adult Black-Footed Ferret.

 

Grams

A metric unit of mass is the gram abbreviated as g.

What kind of things are about a gram in mass?

Centigrams

Centi means 1/100th    0.01   10-2

A smaller metric unit of mass is the centigram abbreviated as cg.

It is one one-hundredth of a gram.

What kind of things are about a cg in mass? Many medications come in 1 cg size, although they more often are measured as 100 mg. Here are magnesium supplement pills.

When a pencil tip breaks, a bigger piece could be about 1 cg.

(We could name something that has a mass of gram and divide it in ten pieces)

 

milligrams

milli means 1/1000th    0.001   10-3

This is 1/1000th of a gram.

What kind of things are commonly measured in milligrams? 

Many doses of medications are measured in milligrams:

Amitriptyline (Elavil) treats chronic pain and depression.

Atorvastatin (Lipitor) treats high cholesterol.

Amlodipine (Norvasc) treats high blood pressure and angina.

Here is crushed powder of a medication shown next to a penny for comparison.

Penny, 1 mg, 10 mg, 25 mg

 

Micrograms

Yet even smaller is the microgram abbreviated as μg

micro means 1/1,000,000th    0.000001   10-6

Just one one-millionth of a gram

What kind of things are commonly measured in micrograms?

Grains of sand are around 30 to 50 micrograms.

Mass of a grain of sand

 

Nanograms

Abbreviated as ng.

nano means 1/1,000,000,000 th    0.000000001   10-9

Imagine cutting a raisin into a billion pieces. Each of those tiny pieces has a mass of about one ng.

What kind of things are about a nanogram in mass?

A human cell or a grain of birch pollen. Note that in this picture, each dot that you can see is likely dozens of pollen grains stuck together.

Each individual grain by itself is so small that you’d need a microscope to clearly see it.

Nanograms are very small compared to anything we see in our daily lives, but they are large compared to a single atom

Chemistry math & mass problem

How many atoms of iron (Fe) are in 1 ng (1.0 x 10-9 g) of iron?

This problem from xaktly – Chemistry – The Mole.

We start by finding the molar mass of iron from the periodic table. It’s 55.85 g/mol.

We use the molar mass to convert to moles.

Then multiply by 6.022 x 1023 atoms per mole to get the number of atoms.

1 ng of iron atoms is about 1 x 10 ^ 13 atoms!

That’s 10,000,000,000,000 atoms.

 

Videos

Powers of Ten and the Relative Size of Things in the Universe

Thanks for reading. While you’re here see our other articles on astronomybiologychemistryEarth sciencemathematicsphysicsthe scientific method, and making science connections through books, TV and movies.

 

Computer apps

Powers of Ten (JAVA) For Windows and Macs.  Check to see if this runs on Android phones or Chromebooks.

Secret Worlds: The Universe Within: Molecular Expressions

The size and scale of the universe

htwins.net – scale of the universe

Smartphone and tablet apps

Cosmic Zoom app by Tokata. For Android and iPad

Google Play Store link

About cozmic zoom

Powers of Minus Ten, by Dynamoid Apps. iPad app

thepartnershipineducation.com Powers-of-minus-ten

Link for the Apple app store

Learning Standards

Massachusetts Science and Technology/Engineering Curriculum Framework

Science and Engineering Practices: 5. Using Mathematics and Computational Thinking: Apply ratios, rates, percentages, and unit conversions in the context of complicated measurement problems involving quantities with derived or compound units (such as mg/mL, kg/m 3, acre-feet, etc.).

National Council of Teachers of Mathematics

Students need to develop an understanding of metric units and their relationships, as well as fluency in applying the metric system to real-world situations. Because some non-metric units of measure are common in particular contexts, students need to develop familiarity with multiple systems of measure, including metric and customary systems and their relationships.

National Science Teachers Association

The efficiency and effectiveness of the metric system has long been evident to scientists, engineers, and educators. Because the metric system is used in all industrial nations except the United States, it is the position of the National Science Teachers Association that the International System of Units (SI) and its language be incorporated as an integral part of the education of children at all levels of their schooling.

Busting myths: No Virginia, some sugars aren’t better than others

Myth “Some sugars are better for our bodies than others.”

Myth “Natural, raw or unrefined sugars are better.”

Myth “It is better to use honey, maple syrup, agave syrup, or coconut sugar.”

Myth “Corn syrup is worse for us than other sugars”

Myth “Natural sugar is better than processed sugar.”

Reality: None of those claims are really true. In reality our metabolism breaks down all sugars the same way.

Agave syrup, maple syrup, coconut sugar – none of these are sugar alternatives – they are just sources of sugar.

Sucrose, a common sugar, is a disaccharide. That means it is a two-part molecule, made of glucose and fructose.

And get this – sucrose is not absorbed by the human GI tract. Instead, our intestines secrete an enzyme, sucrase-isomaltase.

This breaks down any sucrose into glucose and fructose, and it is those smaller sugars which are absorbed. So our body doesn’t care which kind of sugar we eat; the result is the same.

Image from sucraid.com/about-csid

Myth “Natural sugar is better than processed sugar.”

All sugars are processed.  The so-called “processed” white sugar that people are afraid of is just sugar from a natural source, sugar cane or beets.  Brown sugar? The same as white sugar, except that the molasses hasn’t been removed. Not healthier whatsoever.

“Raw honey” may be unprocessed, but it isn’t any healthier. It is just sugar mixed with water, pollen and a few other organic molecules. You’re not going to be helped by the microscopic amount of nutrients in raw honey unless you ate pounds of it a day.

Myth “High fructose corn syrup is worse for you than other sugar.”

Reality? Nope. It’s literally the same thing.

image from Examine.com, difference between HFCS and sugar

More details on this bit here – What is the difference between high fructose corn syrup (HFCS) and sugar?

Myth “Sugars higher on the glycemic index are worse for you.”

Nope. Such claims come from flawed studies, see below for details.

So, are we saying that sugar is good for you? No, we aren’t saying that either. Mainstream science already knows the answer, and people just refuse to hear it: For most people, having some sugar in our diet has always been fine. The problem comes from diets which have huge amounts of sugar, and not enough of other foods that actually are good for us.

While no one, single diet is best for everyone, science points to the same direction: Eat a balanced diet with whole grains, beans, legumes, vegetables and fruit. Have less meat, and certainly less processed meat. Eat far less fried foods. Watch your total calorie intake. Keep daily sugar and fat intake lower. There you go.

 

What’s wrong with those glucose versus sucrose studies?

In those studies, researchers did the following: They fed huge amounts of only one type of sugar molecule to one group of rats, and huge amounts of a different type of sugar molecule to another group of rats. Then they looked at how the health of the rats were affected over time.

Problem 1: These studies don’t resemble real world eating. Humans don’t spend entire days eating nothing but fructose or nothing but sucrose.  The way that our metabolism would handle that is different from how it would handle normal eating, in which sugar is only a small part of the diet. In real life, even in poor diets, sugar is still only a fraction of the total: there are also proteins, complex carbohydrates, fats, oils, vitamins, minerals, etc.

Problem 2: Some studies attempted to see how consuming different sugars affects one’s resulting blood sugar level. Sugar molecules which create a higher result are said to be higher on a glycemic index; sugar molecules which create a lower result are said to be lower on the glycemic index.  Yet these are unnatural diets in which rats ate only pure sugars. When we study the results of normal diets, with actual food, there’s almost no difference between sugars. A meal’s impact on resulting blood sugar levels depends on the amount of sugar and how fast it gets absorbed, not on the type of sugar molecule.

Problem 3: Rats do not metabolize sugars in the same ways that humans do. Hence, any inaccuracies due to the above problems become magnified, making the results non applicable to humans.

Result: The data from those studies are essentially useless.

Honors biology details
Glucose enters the glycolysis metabolic pathway at the top.

Here it is phosphorylated by Hexokinase.

Fructose enters glycolysis pathway two steps later, where it meets phosphofructokinase.

Thus, eating pure fructose allows the energy to be metabolized a bit faster than eating pure glucose.

But people don’t consume huge chunks of pure sugars. When eating anything resembling real life meals, the difference is very little.

Studies on High-fructose corn syrup (HFCS)

High-fructose corn syrup (HFCS) is also known as glucose-fructose, isoglucose and glucose-fructose syrup. There is no scientific evidence that HFCS itself causes obesity or metabolic syndrome, but rather overconsumption and excessive caloric intake of any sweetened food or beverage may contribute to these diseases.

Epidemiological research has shown that the increase in metabolic disorders, such as obesity and non-alcoholic fatty liver disease, is linked to increased consumption of sugars and calories in general.

A 2012 review found that fructose did not appear to cause weight gain when it replaced other carbohydrates in diets with similar calories.

A 2014 systematic review found little evidence for an association between HFCS consumption and liver diseases, enzyme levels or fat content.

The American Heart Association recommended that people limit added sugar (such as maltose, sucrose, high fructose corn syrup, molasses or cane sugar) in their diets.

High fructose corn syrup article

Is Sugar Really Toxic? Sifting through the Evidence

Scientific American Staff and Ferris Jabr, Scientific American, July 15, 2013

https://blogs.scientificamerican.com/brainwaves/is-sugar-really-toxic-sifting-through-the-evidence/

By consuming so much sugar we are not just demonstrating weak willpower and indulging our sweet tooth – we are in fact poisoning ourselves according to a group of doctors, nutritionists and biologists, one of the most prominent members of which is Robert Lustig of the University of California, San Francisco…

A few journalists, such as Gary Taubes and Mark Bittman, have reached similar conclusions. Sugar, they argue, poses far greater dangers than cavities and love handles; it is a toxin that harms our organs and disrupts the body’s usual hormonal cycles.

Excessive consumption of sugar, they say, is one of the primary causes of the obesity epidemic and metabolic disorders like diabetes, as well as a culprit of cardiovascular disease. More than one-third of American adults and approximately 12.5 million children and adolescents in the U.S. are obese. In 1980, 5.6 million Americans were diagnosed with diabetes; in 2011 more than 20 million Americans had the illness.

…. Because fructose metabolism seems to kick off a chain reaction of potentially harmful chemical changes inside the body, Lustig, Taubes and others have singled out fructose as the rotten apple of the sugar family. When they talk about sugar as a toxin, they mean fructose specifically.

In the last few years, however, prominent biochemists and nutrition experts have challenged the idea that fructose is a threat to our health and have argued that replacing fructose with glucose or other sugars would solve nothing.

First, as fructose expert John White points out, fructose consumption has been declining for more than a decade, but rates of obesity continued to rise during the same period. Of course, coinciding trends alone do not definitively demonstrate anything.

A more compelling criticism is that concern about fructose is based primarily on studies in which rodents and people consumed huge amounts of the molecule – up to 300 grams of fructose each day, which is nearly equivalent to the total sugar in eight cans of Coke – or a diet in which the vast majority of sugars were pure fructose. The reality is that most people consume far less fructose than used in such studies and rarely eat fructose without glucose.

…. Not only do many worrying fructose studies use unrealistic doses of the sugar unaccompanied by glucose, it also turns out that the rodents researchers have studied metabolize fructose in a very different way than people do—far more different than originally anticipated.

… Even if Lustig is wrong to call fructose poisonous and saddle it with all the blame for obesity and diabetes, his most fundamental directive is sound: eat less sugar. Why? Because super sugary, energy-dense foods with little nutritional value are one of the main ways we consume more calories than we need, albeit not the only way.

Glycemic index and obesity

Janette C Brand-Miller, Susanna HA Holt, Dorota B Pawlak, Joanna McMillan

Glycemic index and obesity, The American Journal of Clinical Nutrition

Volume 76, Issue 1, July 2002, Pages 281S–285S

https://doi.org/10.1093/ajcn/76.1.281S

Although weight loss can be achieved by any means of energy restriction, current dietary guidelines have not prevented weight regain or population-level increases in obesity and overweight. Many high-carbohydrate, low-fat diets may be counterproductive to weight control because they markedly increase postprandial hyperglycemia and hyperinsulinemia.

Many high-carbohydrate foods common to Western diets produce a high glycemic response [high-glycemic-index (GI) foods], promoting postprandial carbohydrate oxidation at the expense of fat oxidation, thus altering fuel partitioning in a way that may be conducive to body fat gain.

In contrast, diets based on low-fat foods that produce a low glycemic response (low-GI foods) may enhance weight control because they promote satiety, minimize postprandial insulin secretion, and maintain insulin sensitivity.

This hypothesis is supported by several intervention studies in humans in which energy-restricted diets based on low-GI foods produced greater weight loss than did equivalent diets based on high-GI foods.

Long-term studies in animal models have also shown that diets based on high-GI starches promote weight gain, visceral adiposity, and higher concentrations of lipogenic enzymes than do isoenergetic, macronutrient controlled, low-GI-starch diets.

In a study of healthy pregnant women, a high-GI diet was associated with greater weight at term than was a nutrient-balanced, low-GI diet.

In a study of diet and complications of type 1 diabetes, the GI of the overall diet was an independent predictor of waist circumference in men.

These findings provide the scientific rationale to justify randomized, controlled, multicenter intervention studies comparing the effects of conventional and low-GI diets on weight control.

Straight talk about high-fructose corn syrup: what it is and what it ain’t,

Straight talk about high-fructose corn syrup: what it is and what it ain’t,

John S. White, The American Journal of Clinical Nutrition

Volume 88, Issue 6, December 2008, Pages 1716S–1721S, https://doi.org/10.3945/ajcn.2008.25825B

High-fructose corn syrup (HFCS) is a fructose-glucose liquid sweetener alternative to sucrose (common table sugar) first introduced to the food and beverage industry in the 1970s. It is not meaningfully different in composition or metabolism from other fructose-glucose sweeteners like sucrose, honey, and fruit juice concentrates.

HFCS was widely embraced by food formulators, and its use grew between the mid-1970s and mid-1990s, principally as a replacement for sucrose. This was primarily because of its sweetness comparable with that of sucrose, improved stability and functionality, and ease of use.

Although HFCS use today is nearly equivalent to sucrose use in the United States, we live in a decidedly sucrose-sweetened world: >90% of the nutritive sweetener used worldwide is sucrose. Here I review the history, composition, availability, and characteristics of HFCS in a factual manner to clarify common misunderstandings that have been a source of confusion to health professionals and the general public alike.

In particular, I evaluate the strength of the popular hypothesis that HFCS is uniquely responsible for obesity. Although examples of pure fructose causing metabolic upset at high concentrations abound, especially when fed as the sole carbohydrate source, there is no evidence that the common fructose-glucose sweeteners do the same.

Thus, studies using extreme carbohydrate diets may be useful for probing biochemical pathways, but they have no relevance to the human diet or to current consumption. I conclude that the HFCS-obesity hypothesis is supported neither in the United States nor worldwide.

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