Influencing our destiny - and then it gets destroyed so it has to reshape itself - Part 1

Determining our destiny by changing our DNA

An interesting article in New Scientist (12 October 2013, "Life's purpose", p32-35) describes how organisms can drive their own evolution. It describes how living organisms can affect their own DNA to direct their destiny to some extend, and thus not only random changes in our DNA (mutations) direct the evolution of organisms. Indeed, living organisms need to adjust to their environment (e.g. certain animals become white during winter and thus in winter other genes are expressed than in summer) and if this only happens via random mutations then probably our ability to adapt to a changing environment is too slow. This doesn't mean animals and plants change knowingly their DNA but changes in appearance and behaviour (phenotype) may cause more likely changes in certain parts of the DNA (genotype), and the way how this may work is probably via epigenetics whereby the changes may follow some set rules that we still need to discover and which may be identical in most (all?) living organisms (as I described before, one very interesting new field in science but I think also very close to the ultimate knowledge because how much more can you discover than studying the role of genes and the "junk" DNA (including promoters and enhancers) between them and the molecules attached to them? Maybe how the building blocks of molecules play a role in this?).

For instance, changes in food during pregnancy can change the DNA of the child by changing the acetylation and methylation of the DNA, making certain parts of the DNA active (i.e. more open, Euchromatin) and others inactive (i.e. more closed, Heterochromatin) and thus certain proteins will be more, respectively less expressed than normal (that is also why I think mothers should listen to their unborn babies who tell them what they need for their correct development (indeed, often the eating behaviour of women changes during pregnancy) while this may also explains why certain drugs affect the embryo). In addition, it is more likely changes (mutations) happen in active (open) DNA than in inactive (closed) parts. Thus, even when someone has normal genes (i.e. without a mutation), it is still possible that genes become active while others are silenced and don't work because of the presence of molecules attached to genes or promoters. In the first case, more proteins are formed while in the latter fewer or no proteins are produced and these changes can have dramatic effects on our health. I can imagine that certainly an increased or reduced activity of promoters may influence a number of genes. In addition, if more mutations can occur in a more active region, then this may be difficult to notice because: 1) is the change in activity the result of a mutation or 2) is the mutation the result of increased gene activity? Certainly during our embryonic development, it is very important that genes become active or inactive at the right moment so the correct amount of proteins are produced at the right time; otherwise there can be serious consequences. And thus, maybe in future we may be able to test in petri dishes whether certain food or drugs are potentially dangerous for the unborn child by testing whether they change the epigenetics of certain essential genes during the embryonic development (although well-meaning advise can sometimes be wrong advise if we misinterpret data and thus I think women should mainly listen to their unborn baby). If, in addition, it is known whether the drug can pass the placenta and thus can reach the embryo, it can be decided whether or not the drug should be given to a pregnant women. We may be able to decide whether a drug should be tested on a larger or smaller (if any) number of animals, certainly when the test method becomes reliable. But not yet, because probably not all differences in DNA result in changed (negative) activity and some changes may even be beneficial. Similarly for adults, so we may one day be able to predict the activity of a drug in an individual, not only because mutations in genes change the effect of the drug in the body but also changes in epigenetics may result in changed activity of drugs (e.g. the metabolisation of the drug changes or a drug doesn't bind to receptors). As a result, the drug may have a different effect in certain persons compared to most people so that they need different amount or even other drugs to be effective. The article "Our genomic future" (New Scientist, 7 September 2013, p. 10-12) describes how some laboratories already screen people's genome to find genetic mutations that are responsible for diseases. However, I think we need to be careful interpreting these data that shows differences in genes between people: maybe a difference may not affect the action of the protein; maybe there are other (yet unknown) pathways that take over; maybe a gene without a mutation may not function because it is located in an inactive region (e.g. a drugs may silence a gene); ... . Therefore, some drugs that work for one persons may not for others or they need different doses; thus the more drugs on the markets the more chances there is something for everyone. Still many years to go before we know it all. But already kits and apps are being developed to help diagnose people for instance whether they are diabetic (and this may fly-start in developing countries while Westerners may mistrust these tools).

Thus, when animals behave in a specific way, then this may result in more activity in certain regions of the DNA (and maybe even in more mutations in that region) and less in others and changes in these parts of the DNA can result in an imprinting of the activity. The changed activity will result in changed amounts of proteins (including enzymes) and thus changed behaviour and even appearance (e.g. alcohol abuse during pregnancy can result in disabled children as alcohol may affect the DNA of the unborn child via epigenetics; therefore pregnant women should not listen to their body if it wants alcohol although one glass may not harm (while a sudden stop may also harm?)). These changes may be past from generation to generation if the reproductive cells are involved to ensure organisms continue to adjust to their environment to guarantee maximal survival. This article describes how external changes can indeed affect sperm cells so the changes are passed on to the next generations. E.g. a dislike for certain food when that food is associated with something negative may result in epigenetic changes so the next generations don't need to experience something negative, they "know" from previous generations; this also demonstrates animals are born with fear for their enemies and don't need to learn this fear (and thus nightmares about wolves may indicate we still fear wolves because they hunted us long ago). Indeed, a very frightening event can sometimes be felt even in the underbelly.

Thus, evidence is growing that organisms can indeed ((un)knowingly) change the way they look and behave but more research is needed to understand this better. Still, there are already some clues: the article "How gene tweaks reach descendants" (New Scientist, 19 April 2014, p. 14-15) describes how miRNA (microRNA) that are produced in response to stress or long-standing lifestyle, can enter the testicles and influence the DNA of sperm cells by causing epigenetic changes that, as described above (paragraph 2), result in changed gene activity. This effect can be seen up to the third generation, partly because the miRNA influence the sperm cell's DNA directly but maybe also because they can be transferred to the next generation via the cytoplasm of sperm cells. After a number of generations the effect can disappear. However, I can imagine that when stress is caused to many animals (including females although if an essential gene is silenced or activated in both males and females it may have a disadvantage) and the stress remains present during a few generations (thus becomes permanent), the effect of changed epigenetics will last much longer and even becomes permanent; DNA may even mutate so the animal can adapt permanently to the stressful stimulus to increase its survival chances in the new situation and a new species may emerge. (I also wonder: what may be the effect of the release of stress hormones (such as adrenaline) during stressful periods on the imprinting in reproductive cells? Maybe these hormones help the miRNA?). But of course, not only epigenetics needs to be involved, also spontaneous mutations or proteins that affect DNA may be involved. Still lots of work to discover all of it.

That animals may be able to influence their destiny was already suggested by Jean-Baptiste Lamarck but neglected afterwards although of course Charles Darwin and many others were also correct. An example are the giraffe versus okapi. They are closely related, still the giraffe has a much longer neck and other camouflage than the okapi; they don't even mate. As okapis live in forest while giraffes on the Savannah, their appearance is adjusted to their environment. Equally, elephants on the Savannah are able to grow taller than those living in forests but also have a different body shape.

Thus, looking at the evolution from dinosaurs to mammals (see Figure 2), animals need to adjust actively to their environment although random mutations also influence evolution (for instance, an animal has already a positive adjustment before the environment changes). In the beginning, dinosaurs were quite small but herbivores grew larger over time as plants grew large while species diversity increased as the surface of the earth changed (continental drift) and species needed to adjust. When some animals decided to eat meat, their teeth, digestive system and even appearance changed so they could kill and thus the choice of food resulted in changes in the DNA that could be past onto the next generations. The carnivores too became larger to be able to kill larger prey but also because killing one animal resulted in plenty of food. Thus, there was selection towards carnivores who adapted their body to kill while herbivores further adapted by developing defence mechanisms such as horns and living in groups. Becoming taller also means changes to the body. At the same time, smaller animals (including mammals) probably became almost invisible for larger carnivores as they were insufficient to feed them and thus it was in their advantage to remain small (e.g. how many people notice mice and rats?). Smaller carnivores may have developed to become scavengers, eating leftovers. And thus a diversity of animal species emerged according to their needs. Finally, herbivorous and carnivorous dinosaurs may have become too big to remain sustainable, eating too much and reducing their own food supply while changing their environment, giving chances to other species. A meteor and volcanic eruptions further reduced the amount of food as mainly larger plants died and dinosaurs couldn't recover and disappeared. Smaller surviving plants were eaten by small surviving animals (amongst them mammals) although also here many disappeared. Small dinosaurs also disappeared, maybe because their DNA was 'too old' to be able to adjust as imprints in their DNA were too strong, i.e. they were too specialised to be able to eat and digest the new food. Birds were the exception amongst the dinosaurs because, as they can fly and thus move to different areas, their DNA remained flexible and thus they were able to adjust and survive up to our days.

Figure 1: T. Rex on real scale next to another dinosaurs and humans in the background for comparison. But dinosaurs could be nice, looking after their eggs. Photo's taken at the Dinoworld exhibition, a great exhibition for everyone.

Then the story repeated itself for the small mammals who could become taller as they no longer needed to hide and vegetation (= food) became abundant again, although they never reached the same size as dinosaurs (whales are the exception), partly because their bone structure is different (too heavy) but also because they use more energy to keep their body temperature high (during the time of the mammals, temperature on Earth is lower than during the time of the dinosaurs, and thus keeping our body temperature constant is an advantage while being small may have been an advantage in a warm climate to prevent overheating; large may have been an advantage in a warm climate to prevent bodies became too hot (large body needs lots of heat to warm after cool night) or too cold (large body keeps heat long enough during the night)). Also plants changed by having flowers and fruit and thus many animals adjusted to reach the food. Thus, changes in the environment resulted in plants and animals that needed to adjust, resulting in changes in the epigenetics of DNA regions, opening and closing certain regions to change the expression of proteins while also mutations in active regions could occur that may also have affected other parts of the animal. For instance, when food becomes mainly available in trees, it will force many animals to climb or find other ways to get food. But certain DNA regions can't change too much as they contain essential genes. Indeed, evolution repeats itself although with different outcomes according to the situation.

Figure 2: Evolution of the dinosaurs until mammals replaced them after the dark period when T. Rex and other monsters lived. Photo's taken at the Dinoworld exhibition.

Other examples are whales who developed breathing holes at the top of their head that can close when they dive as this is more practical than a nose at the front of their head. Flatfish changed the shape of their body but also head so they are able to see with both eyes above the seafloor where they hide. Snakes even seem to adapt very fast as their DNA changed in such a way that it promotes mutations to adjust to the environment. More examples in Figure 3. Many of these changes happen after animals change their diet or behaviour (e.g. living in cages) that affect the epigenetics of their DNA. As a result, the shape of head and/or body may change so they are better able to reach and eat the food they prefer or survive a nutrient-poor diet. I think the biggest contributor to changes in DNA are chemicals taken in by animals and plants via food as each food has another composition.

Figure 3: A large diversity of plants, fish and many more animals exist all over the world, each as much as possible adopted to their surroundings in order to survive such as carnivorous plants (first photo) get sufficient nutrients in poor ground from eating insects or clownfish (remember Nemo, last picture) that are able to hid in poisonous anemone.

Indeed, animals and plants may not only direct their own DNA, but maybe plants (and bacteria living on and in animals) even influence the DNA of animals so both animals and plants benefit. Or animals prefer some food so much that they try to influence their own DNA so that the animal's shape changes in order to reach the food easier. E.g. orchids seem to be very depending for their reproduction on some insects who adjusted to take the nectar of those plants. And although only few insects will be able to fertilise the plants, the orchids can almost be sure they will be fertilised as those few insects prefer the orchids above other plants. As a result, the species can remain unchanged over a long period but changing environment (e.g. the insects disappear) may also lead to the disappearance of the orchids because the connection between plant and insect became so strong that adjustments are no longer possible in a changing environment. Today, many fear that the possible disappearance of bees (due to pesticides and parasitic infections?) may result in the collapse of many plant species that rely on bees for their reproduction. Another example: many animals seem to rebuild themselves to blend in with the environment in which they are living to become invisible for predators while others resemble flowers so they attract their prey. It is difficult to believe that only random mutations direct living species to adapt to the environment as these adaptations often require a number of changes in the DNA and thus a change in one part may result in changes elsewhere while random mutations are probably too slow and may even have a negative effect if they occur at the wrong place.

In addition, animals favour those that resembles them, and thus an animal born with a specific phenotype will often prefer an animal with a similar phenotype, and thus if a phenotype has an advantage, the animal will survive and mate with someone that resembles it, giving birth to off-spring that looks like the parents and thus a new (sub)species may arise. If, for instance, miRNA are present that affect the epigenetics, the the off-spring will more likely mate with someone like it and thus the effect can pass to the next generation.

"Aliens VS predators" (New Scientist, 26 April 2014, p. 40-43) describes the fast-track evolution well whereby random mutations probably are insufficient although may help in the survival of species. Because the invasion of a very poisonous toad that migrates very fast in Australia, many animals die after eating them. But those surviving evolve: they learn to avoid the toads. Other animals go further: e.g. it is observed that certain snakes have now a smaller head so they can no longer eat the toads (probably those that had bigger heads eat the toads and died and thus here probably the changes are not the result of changes in the DNA (always when the numbers of killers are too big, animals become smaller) while others are no longer interested. Here changes in the environment force animals to adjust so they can survive. The toads advancing fastest are in such a hurry their immune system can't even develop properly so they may one day collapse while the slower toads may settle. Already some people start to like them while some native species that survived eating them may start developing immunity against their poison and thus survive eating them, maybe one day even start preferring them (the collapse of the ecosystem after their arrival may force some species to eat them as other food becomes sparse). It is the same with humans: wherever we appeared, systems collapsed and animals had to adjust in order to survive. Nevertheless, the invasion may be too big and the whole system may continue to get destroyed.

Maybe B immune cells act in a similar way to remember a certain illness. During maturation, B cells are formed with mutations in their DNA that result in the expression of proteins that recognise specific antigens. When such an antigen is present in the body, a certain B cell that recognises the illness will remain in the body as memory B cells and thus there is an imprinting of the mutation in the DNA so next time the response to the illness can be faster. How is it possible that during an infection the correct B cells emerge if it only depends on random mutations, even when many B cells are formed each day? Maybe the invading pathogens forces certain mutations in the DNA of immune cells as the B cells are exposed to the pathogens; this contact may trigger certain signals in the B cells that affect the DNA of the B cells (I am only hypothesising)? In many bacteria it is known that infections can result in a kind of immunity as parts of the DNA of viruses are built in the genome of bacteria so they have a faster response after a new invasion (known as CRISPRs); therefore the bacteria are actively changing their own DNA by incorporating foreign DNA for their advantage. Thus, maybe pieces of pathogens can also influence B cells?

Humans

Concerning humans, changes in walking (i.e. upwards) resulted in many changes in other parts of our body. Our decision to start walking on our legs may have resulted in changed activity in certain parts of our genome and thus imprinting of our walking behaviour but maybe also on how we use our arms and hands as these could now be used even when walking. Changes to our diet such as using fire to warm our food but also cultivation of animals (e.g. drinking milk resulted in being able to drink milk as an adult but also to eat cheese that can be stored longer for moments of food shortages) resulted in more energy for our brain and thus they were able to grow larger, making us smarter and we became able to dominate our environment and the whole planet. A large brain is now typical for humans and thus large brains are the result of imprinting while they also required changes to our head. Fire gave us warmth in winter but also allowed long-distance messages that together with our speech allowed us to warn others of dangers or to inform about sources of food. All these changes in our behaviour resulted in changes to our genes so the first hominids prepared our path to become who we are while changes continue to happen. And one change probably triggered many others (e.g. walking upwards changed the position of our head and thus our neck so that we became able to speak). Even today, it seems that studying helps to slowdown the development of Alzheimer while also changes in our food patterns (more healthy) and medicines (we study thus we can fight diseases) result in people living longer. We even start changing our DNA very consciously by correcting malfunctioning genes. Thus, because we think, we change our behaviour and thus our appearance (although our heads can't continue to become bigger but then changes may happen so we get a more efficient brain or we use tools such as tablets that help us memorise). Still, some humans continue having the soul of T. Rex and can only think about destruction: they see an elephant and want to kill it. But in contrast to T. Rex that was a meat-eater and could only think about killing, humans can see nature and relax and can fight the "T. Rex" inside themselves.

Whoever thinks I made mistakes or has suggestions to improve this article can leave a comment. Indeed, scientists discuss science to correct each other so our knowledge increases and humanity can advance towards a better society. For instance, you may be better in describing what I mean and suggest how I can explain something better.