Hsueh MF et al. Analysis of “old” proteins unmasks dynamic gradient of cartilage turnover in human limbs. Science Advances, October 2019.

Humans may not be able to regrow amputated limbs, but a recent study showed that damaged cartilage may regrow through a process similar to that of animals such as salamanders and zebrafish. Scientists collected 18 specimens of joint tissue from the hips, knees, or ankles of patients who underwent surgery. They then placed the tissue in a mass spectrometer and measured the age of the cartilage proteins in the sample. These analyses showed that the age of cartilage largely depended on where it resided in the body. Cartilage in ankles is young, middle-aged in the knee, and old in the hips. This correlation between the age of human cartilage and its location in the body suggests that limb repair occurs in humans in a similar fashion to certain animals in which tissue regeneration takes place at the furthest tips such as the ends of legs or tails. This finding also helps to explain why injuries to people’s knees and, especially, hips take a long time to recover and often develop into arthritis, while ankle injuries heal quicker and less often become severely arthritic. The researchers further identified the molecules that are instrumental in the regulation of this region-specific regeneration process. They are called microRNAs and, not surprisingly, are present at very high levels in animals that are known for limb, fin, or tail repair including salamanders, zebrafish, and lizards. Scientists believe that these regulator microRNAs can be utilized in the regeneration of degenerated cartilage of an arthritic joint to reverse arthritis. Regeneration of part or all of an injured human limb may even be possible by finding components salamanders have and we don’t. Finally, it is also possible that this could be a fundamental mechanism of repair that could be applied to many tissues, not just cartilage, which might open up many new avenues in the regenerative medicine.

The universe might have many Earth-like exoplanets

Doyle AE et al. Oxygen fugacities of extrasolar rocks: Evidence for an Earth-like geochemistry of exoplanets. Science, October 2019.

New astrophysical and geochemical evidence suggests that Earth may not be that unique, and Earth-like planets may be common in the universe. All of the planets in our solar system orbit around the Sun. Planets that orbit around other stars are called exoplanets.  The first exoplanets were discovered in the early 1990s. Since then, thousands of exoplanets have been revealed with over 4,000 confirmed and a further 4,495 potential candidates. There have been major efforts to narrow down the exoplanets that may have properties similar to Earth with conditions suitable for life. This includes being a rocky planet that is not too hot or cold so that liquid water can exist. When searching for exoplanets that are similar to Earth, astronomers typically look for worlds in orbit around a type of star called a red dwarf or an M-dwarf. These types of stars are somewhat similar to our sun and make up about 70% of the stars in our galaxy. However, a new study shows that rocky exoplanets in orbit around a different type of star, a white dwarf, can have interiors that are surprisingly similar to our planet. White dwarf stars are dense remains of normal stars that have exhausted their nuclear fuel. These stars are typically composed of light elements such as hydrogen and helium, but in some cases they attract heavier elements such as magnesium, iron, and oxygen in their atmospheres due to their extreme gravity. These heavy elements are thought to be introduced when a rocky exoplanet crashes into a star, which gives astronomers evidence of what the exoplanets were like before they were destroyed. In this recent study, scientists looked at six white dwarfs located 200 to 665 light-years from Earth and rocks from the planets that once orbited it. Their analyses showed that five out of the six white dwarfs had sucked up fragments whose chemical composition is similar to rocks on Earth, Venus, and Mars. While the conditions suitable for life depend upon many additional factors, this study points towards the idea that many rocky planets are likely very familiar in terms of their general composition and, therefore, structure and behavior. This study also made a substantial leap forward in being able to make inferences for bodies outside of our own solar system and indicates that it is very likely that there are truly Earth analogs out there.

Artificial leaf points to a sustainable path to carbon-neutral fuels

Andrei V et al. Bias-free solar syngas production by integrating a molecular cobalt catalyst with perovskite–BiVO4 tandems. Nature Materials, October 2019.

An artificial leaf from which a “clean” fuel alternative to petrol could be produced has been developed. Synthetic gas can be obtained from the lead by using only sunlight, carbon dioxide, and water.

Synthetic gas, also called syngas, is typically a mixture of carbon monoxide and hydrogen. It is largely produced by exposing fossil fuels such as coal or natural gas to high temperature steam and pressure, and the process releases carbon dioxide. Syngas is broadly used in a wide range of commodities including fuels, plastics, and fertilizers. While the utilization of fossil fuels has enabled large-scale industrial development in human history, the burning of fossil fuels is the largest source of emissions of carbon dioxide, which is one of the greenhouse gases that contributes to global warming. For decades scientists have been trying to discover new ways to produce syngas in order to close the global carbon cycle and to establish a sustainable chemical and fuel industry. In a recent study, researchers got inspired by leaves. These perfect little machines use sunlight to convert carbon dioxide and water into fuel for plants through photosynthesis. An artificial leaf has been designed to have two light absorbers, similar to the molecules in plants that harvest sunlight, and a catalyst made from the naturally abundant element cobalt. When the leaf is immersed in water, one light absorber uses the catalyst to produce oxygen and the other one carries out the chemical reaction that reduces carbon dioxide and water into carbon monoxide and hydrogen, thus forming the syngas mixture. The scientists are now searching for ways to use their technology to produce a sustainable liquid syngas that could serve as an alternative to petrol. Although major efforts to generate renewable energy sources are being made, the development of synthetic petrol is critical as electricity can currently fulfill about 25% of our total global energy demand. There is a huge demand for liquid fuels to power heavy transport, shipping, and aviation sustainably.

Brittlestars form a large group of sea animals that are similar to starfish. There are more than 2,000 species of brittlestars. However, this article will focus on two of them, Ophiocoma pumila (Figure 1a) and Ophiocoma wendtii (Figure 1b). In spite of their similar appearance, these two kinds of brittlestars have one main difference. While O. pumila is insensitive to light, O. wendtii is highly light sensitive. For example, the latter has different colors at day and night, as shown in Figure 1b, left and right respectively. More interestingly, O. wendtii can sense shadows of predators and quickly move into dark areas such as a cave or underneath a rock.

To understand the mechanisms behind the difference in light sensitivities of these two species, Joanna Aizenberg and her colleagues investigated1 the microstructure of both brittlestars’ outer skeletons with an electron microscope and came up with a striking result: The top surface of O. wendtii’s skeleton has very well ordered lens-like hemi spherical elements (Figure 1f). The cross section image of one of those hemispheres actually looks like a compound lens made up from two hemispheres with different diameters (Figure 1g). On the other hand, O. pumila’s skeleton had a typical stereom (sponge-like calcite) structure (Figure 1e). These images strongly suggest that the lenses in O. wendtii’s skeleton are responsible for the relatively high light sensitivity. However, understanding how that really happens require further investigation.

It is well-known that spherical lenses suffer from a problem called “spherical aberration,” which means that the light rays that are closer to the optical axis are focused at a different point than the ones that are away from the axis. A quick solution to this problem is to use two lenses, whose diameters have a certain ratio, back to back; this helps to correct the aberration originating from the first one with the second one. Interestingly, when Aizenberg et. al. calculated1 the optimum compound lens configuration for O. wendtii’s skeleton, which has the minimum aberration, their result matched the original lens structure perfectly (the orange outline in Figure 1e). They were also able to locate the focal point of these lenses (d = 4-7 um* below the lens) with the same method. Their further electron microscopy studies showed optically sensitive nerve bundles exactly at that location. All these results clearly show that O. wendtii’s skeleton has the perfect geometry to collect and focus light to improve its light sensitivity. However, there is one big question about these lenses: their material.

Calcite, a kind of calcium carbonate (CaCO3), is a common ingredient of the shell or the skeleton of marine organisms. Interestingly, the birefringence property of calcite makes it very unfavorable as a lens material. In a birefringent material the speed of the light depends on the direction it travels with respect to the crystallographic axes of the material. As a result, if one looks through it, they will observe a doubly refracted image (Figure 2). Being the most famous example of birefringent crystals, calcite’s refractive index is 1.64 parallel to one crystallographic axis and 1.49 in the perpendicular direction. Therefore a regular calcite lens cannot focus light on a single spot, unless it is oriented along a special crystallographic axis (c-axis to be specific), which would be along the diagonal of the prism in Figure 2.

At this point we are not surprised to learn that the optical axis of the O. wendtii’s lenses, and the c-axis of the calcite crystal that they are made of, indeed overlap. We are not surprised because we already had a strong feeling that these lenses should work. However, it is quite surprising that these little creatures can grow single crystals of calcite with a specific crystallographic orientation. As Kenneth Towe states in the context of a similar study, “This precise orientation of crystals is the big mystery of biomineralization. Organisms know how to do it; we do not yet know how they know.”3

Biomineralization, the controlled deposit of inorganic minerals by living organisms, is a very active research field attracting many scientists from various disciplines, including biology, physics, chemistry, and material science. In general, controlling crystal structures at small length scales is a very challenging task. Scientists spend millions of dollars to build state-of-the-art facilities for single crystal materials synthesis. They work in clean rooms, under an ultra high vacuum and at extremely high temperatures. On the other hand, from brittlestars to large whales, almost all living creatures have biominerals, such as bones and shells, manufactured in chemically dirty environments and at decent temperatures. Organisms are apparently equipped more efficiently than our laboratories are.

A. Ali Eren has a Ph.D. in Physics and lives in the USA. He studies physical chemistry of biological processes.

References

*1 um (micron) is one thousandth of a millimeter. Human hair is approximately 100 micron thick.

1. Aizenberg, Joanna, et al. “Calcitic microlenses as part of the photoreceptor system in brittlestars.” Nature 412.6849 (2001): 819-822.
2. ttp://jademellor.com/blog/2013/6/21/rainbow-rhombus, accessed 4/20/2014
3. Towe, Kenneth M. “Sea urchins as crystallographers.” Science 311.5767 (2006): 1554-1555.

Astronomers have discovered a planet with the longest known orbital period. Exoplanet Kepler-421b has been identified through the Kepler observatory, a space-based telescope. It circles its star once every 704 days. More than 1800 exoplanets have been discovered so far, but compared to Kepler-421b, those had much shorter orbital periods, like a few weeks or even a few days. The host star for Kepler-421b is much like the sun, but it is little bit smaller and relatively cooler. With an orbital distance of 177 million kilometers, Kepler-421b gets about one-fourth the light from the host star as the Earth receives from the sun, which makes the exoplanet as cold as -100 °C. The unusual orbit places Kepler-421b beyond the “snow line,” which is accepted as the dividing line between rocky and gaseous planets. Outside of the snow line, water condenses into ice grains that stick together to build planets known as “gas giants.” Since gas giant planets are very close to their stars, theorists believe that many exoplanets migrate inward early in their history. However, Kepler-421b is the first example of why such migration may not be necessary.

Sunflowers’ internal clock

Plants are known to grow toward the sun to maximize the amount of energy they absorb. Sunflowers (Helianthus annuus) show the most fascinating behavior during summer, when they follow the sun as it rises in the east every morning and sets in the west every evening. In a recent study, scientists challenged the obvious explanation for this plant’s behavior: are flowers solely responding to sunlight or are there other unknown mechanisms at work? They designed a clever yet simple experiment where they grew sunflowers in chambers with a fixed overhead light that was continuously on. Surprisingly, for several days, the sunflowers under constant light kept moving as if the sun were rising in the east and setting in the west. This unexpected result suggests that sunflowers were not responding only to the direction of the light but also to an internal biological clock. Furthermore, they discovered that sunflowers bend when one side of the stem grows faster than the other. For example, the west side of the stem seems to grow faster to bend the plant towards the east in the morning. Scientists now hope to understand how an internal biological clock in sunflowers has the opposite effects on opposite sides of the stem. Sunflowers are not the only plants performing this diurnal dance; other agriculturally important crops such as soybeans and cotton exhibit the very same behavior. Solar tracking is known to boost plant yield and discovering the mechanisms of how plants track the sunlight might have important implications for improving global agricultural yields.

Friends linked by genes

It is a common observation that close friends look alike. Even centuries ago, Plato noted the tendency that good friends usually have similar appearances. Recently, a group of geneticists took this idea even further and suggest that people on average tend to choose friends who are genetically similar. The study provided convincing evidence that we have more DNA sequences in common with the people we pick as friends than we do with strangers in the same population. Researchers performed a genome-wide analysis of approximately 1.5 million markers of gene variations from 1,932 subjects of the Framingham Heart Study, which is one of the most comprehensive genetic databases. They identified 1300 pairs of non-relative friends and compared their genetic information to each other. The analyses showed that friends share similar genetic variations (around 1% genomewide), to the degree that it is as if they have the same great-great-great-grandparent – in other words, as if they were fourth cousins. Notably, friend pairs seem to have the greatest similarity in the genes that are responsible for a sense of smell and they show the most difference in immunity-related genes. Friendship entails spending a lot of time together and looking out for each other. Odors are strong behavioral cues in human psychology and people with similar olfactory preferences might like to prefer living or hanging out in similar environments. Likewise, it is potentially a big advantage that friends don’t get infected from the same microbes at the same times, so that one of them can take care of the other. As much as these anthropological implications are merely speculations with many caveats – and despite there being many obvious social, ethnical, and cultural factors that help determine friendships – the genetic basis of friendship and other social interactions may hold answers to at least some of the mysteries of human behavior.

Indeed, the world has once again stepped into a zone of spiritual crisis—and this in itself is a historical recurrence. Before delving into the details of the topic, it would be more useful to expound on the meaning and nature of historical recurrences.

Yes, history is filled with recurrences. These recurrences are not identical to the past, but show some form of resemblance. If they had been identical, then lessons would have been learned and the same mistakes would not have been made. Thus we need to approach history not hoping to arrive at decisive conclusions, as if it would recur identically, but rather to draw wisdom from it, for we will encounter events that will resemble similar moments in the past. Let us now try and view our current crisis from this perspective.

It has often been observed that the periods in history when God burdened and pressured people the most have inspired humanity to sail towards new horizons. This is the case for individuals as well as communities. That is, just as when an individual’s burdens reaching their zenith indicates the moment of salvation is near, excessive social burdens have always refined the community and guided them in new directions. The following saintly words on the night’s darkness reflect what we are trying to say here: “Get as dark as you can. For the last phase of darkness is the moment light begins to shine forth.”

Furthermore, the macro-universe and the human being (the eminent sultan of the normo-universe) are so similar that they are almost identical. Due to this fact, let us start the discussion with the individual, by way of comparison. The relief and contentment experienced by individuals are sometimes followed by spiritual and conscientious expansions. In some other instances, the opposite may happen. Contraction, or qabdh in Islamic Sufi terminology, means being pressed or put under pressure. The handle of the sword that is interlocked with fingers and pressed is also called “qabdha.” Qabdh can also be defined as being held extremely tightly by an unknown hand. This term, indeed, has been added to Sufi terminology with this particular connotation.

The state of contraction may sometimes originate from certain individual sins, or from individual heedlessness. At first, a person unleashes himself into an effervescent climate, and lives, for some time, in a light-headed state. Immediately after, as a form of punishment, a person becomes exposed to contraction. Maybe, it is the soul that wishes to experience this state, for the redundancy of comfort and lethargy annoys the soul. Consequently, the soul often gets annoyed by the exuberance of the material world, because it wishes to be, and to stay, in a state of spiritual alertness and vibrancy regarding its longing for eternity.

In this regard, contraction results when a person lets go of himself, and is consequently cautioned by the Hand of Power. God exposes a person to contraction in order for that person to re-direct themself to Him. This is very similar to when a mother lightly slaps her child to prevent her baby from doing something wrong, or going somewhere bad, and then embraces her baby mercifully and lovingly.

In such a state, roads narrow and do not give way; causes gradually start to vanish. Here, just at this moment, one removes all causes from his memory and directs himself to the One who holds all causes in His Mighty Hand. Essentially, the aim of the Almighty is to direct a person to Himself. In these cases, if a person comprehends the real cause of what befell him, and returns to the Almighty, it means that the goal has been achieved. However, reaching this point requires an astute consciousness and perception to comprehend the fact that no single incident in the universe occurs due to blind or arbitrary coincidence. In his commentary on the Qur’an, Nursi portrays the position of two people who have fallen into a well in light of the current issue: One of the two is deprived of his ability to inquire about the hidden aspect of matters. The other person is a man of wisdom. And through the window of wisdom, this second man speaks to himself as follows (Eighth Word):

“These matters do not actually seem to be coincidental. A lion suddenly starts chasing me while I have been running in the desert; then I fall into a well and hold a tree; two mice, a black one and a white one, on the root of the tree have been gnawing at the tree; and, a dragon down below has been waiting for the moment of my fall, with a mouth wide open. Up above, the lion threatens me with his scary behavior. Standing shoulder to shoulder, these incidents can in no way take place coincidentally or by chance. Apparently, all these have been preplanned by Someone who knows me; and all these are represented through my existence.”

You see, every person who has experienced the state of contraction should view incidents in a similar way, and say to themselves: “all these incidents embracing me so tightly are directed by a superior might exceeding myself, and I am a mere extra in this play.” Of course, this should not be considered sufficient, and right away, one should take refuge in the sovereignty of the One who holds the entirety of existence in His Holy Hand.

This situation is valid for communities, too. A community is sometimes held and pressed by an iron claw, and this can be said to be that community’s contraction . Reasons for such contraction include living in idleness, being unaware of their return to Him, knocking on the wrong doors, or seeking cures in the wrong places.

Today, we can see, through the contraction of individuals and communities, that history repeats itself. This repetition has shown that troubles and turmoil can mark the beginnings of new exaltations. The crisis we are experiencing today shall become a bridge to new energy and exuberance. Indeed, is it not our mission to prepare a new era of exaltation for humanity?

Glory be to Him who created in pairs all things that the earth produces as well as their own kind (selves); and other things of which they have no knowledge. (Va Sin. 36.36)

a) The verse opens with ‘Glory to be to Him’ as if to emphasize that God Himself is beyond possessing a pair, a likeness, or an equal. It goes on to draw attention to the inner meaning of the pair-wise existence of created beings. Pair-wise existence indicates opposition simultaneously with complemantarity, the most obvious case of which is male and female. The scientific definition of pair creation also implies complementary opposites. Thus, hot and cold constitute a pair; in other words, two entities may have almost identical properties and yet be opposed to each other in the nature and effect of those properties.

b) The most interesting aspect of the verse is the examples of pairs it provides. Saying ‘We created beings in pairs’, God gives three examples:

1. ‘Pairs’ that the earth produces,

2. Pairs of selves,

3. Other things created in pairs, of which we have no knowledge.

In order to understand the hidden meaning of this verse, let us first recall the conclusions science has reached in the light of recent research.

The discovery of the positron by the physicist Anderson is regarded by some as a major turning-point in contemporary physics. It was Maurice Dirac who first postulated parity or pair-wise creation, now recognized as a basic principle of modern physics. Every particle in the universe has a certain charge and/or spin. When a particle is formed, its opposite twin or antiparticle is produced together with it, for beings are always created in pairs. The most famous of these are – electron and positron; proton and anti- proton; neutron and anti-neutron, neutrino and anti-neutrino.

It is basic principle of nuclear physics that every particle exists together with its opposite twin – we shall return to this subject in detail below.

Hence, the verse 36 informs us of a basic law of creation in the declaration: ‘We created beings in pairs’.

We may turn now to the general meaning of the verse. With the expression ‘Glory be to God’ in the opening phrase, the verse underlines the fact that God, and God alone, is without equal or likeness. The habit of analogy, of discerning a thing through its opposite, is rooted in our comprehension. But all beings that have opposites or similar partners are mortal or finite. God, on the other hand, is the Glorious: He is without likeness and beyond all. He has, however, created beings in pairs (complementary opposites).

1. Those the earth produces

This part of the verse has been interpreted by some scholars as referring to the plant kingdom. This interpretation is, however, incomplete, for had God wished, He would have specified plants. The meaning certainly includes plants but is not restricted to them.

This first category of pairs delimits the third, It would be wrong, for example, to understand the sentence to mean: ‘I have created many more pairs of which you have no knowledge’ in relation to, for example, electricity or magnetism: those belongs to the pairs produced by the earth.

Pairs produced by the earth, then, maybe listed as follows:

a) Similar pairs that differ in their physical and chemical characteristics, e.g. metals and non-metals,

b) Biologically complementary pairs: the male and female sexes of plants and animals,

c) Physically opposed pairs: e.g. positively and negatively charged ions, and hence the reversal of electric charge (polarity): the two poles of a magnet referred to as North and South, respectively.

d) Phenomena of analysis and synthesis that alter the structure of life in the soil: the vivification of plants by the action of synthesis by bacteria which fix nitrogen: the destructive and dispersive effects of bacteria that break down organic materials and cause decay, and similar complementarities.

2. Pairs ‘of their own kind (selves)’

A range meanings are inherent in this part of the verse:

a) Male and a female (opposite partners).

b) Complementary personality traits (cruel/kind, brave/cowardly, generous/miserly, etc.).

c) Traits which are similar but subject to opposed value judgements, such as recklessness/courage:hypocrisy/ courtesy: simplicity/naivete, etc. Some of these terms denote values which are very near to each other and become negative or positive according to fine judgements about circumstances and/or intentions. For example, hypocrisy is to fake goodness or consideration in order to obtain some favour or advantage unjustly:courtesy may also involve some degree of showing consideration for another individual but in that case with the good intention of winning that person over for a good cause, to become a friend etc.

3. Other pairs ‘of which they have no knowledge’

The law of parity covers all concepts of matter and energy, in the sense that quanta and the systems composed of them manifest themselves as paired or complementary opposites.

a) Processes of energy emission and absorption which physics and astrophysics have, recognized only in recent times, are an example. We have yet to fathom the secret of these processes. However, we do know of black holes where energy is drained and annihilated, and of quasars which concentrate unbelievable amounts of energy. These two regions are places which appear as twins, but exert opposing influence with respect to each other.

b) Another example is forces of attraction and repulsion: in particular, gravity counterbalanced by centrifugal force. If the opposition between these forces did not exist, all planets would either fall into their respective suns or be flung into outer space.

Gravitation and rotational motion together support a dazzling system of equilibrium in the universe. We encounter a mind-boggling harmony when we inspect this equilibrium from the standpoint of our earth and the universe. Besides forming the solar system together with the earth, the neighbouring planets also strike a similar rotational balance with their own satellites. These smaller systems then complete a further revolution around the sun. Thus, the nine planets and their many satellites all revolve around the sun in different orbits. These heavenly objects thereby avoid falling into the sun. In return, the sun balances these planets in their orbits, preventing them from escaping into space. But this is not all. A further and larger rotational motion is simultaneously taking place: the Milky Way galaxy to which the solar system belongs rotates on its axis together with our sun. This journey is completed in about 250 million years for each revolution. Our galaxy in turn is on an immense journey around the centre of the cluster of galaxies to which it belongs. Hence our earth, in the effort to sustain the balance between all these pairs of attractive and repulsive forces, rotates in four different orbits that are finally measurable by a billion years.