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GENES; DNA; MLM; IMPRINTED GENES

Duke scientists map imprinted genes in human genome

http://www.eurekalert.org/pub_releases/2007-11/dumc-dsm112607.php


The article under this link deals with so called imprinted genes. I myself prefer the word silencing when necessary, but most of all I like different idea of explaining the fact that some genes sometimes work and sometimes do not. As it is put in the above mentioned article they turn on and off over time.

My idea is that the whole problem is a problem of coding, reasonable coding of information so that it can be passed over to the next generation and this generation can make use of such inherited information. There must be a system of information that does not change remarkably, e.g. that fact that humans have two legs and two arms, two eyes, etc. But it can differ in size, color etc. Then there must be also information about different traits that are helpful for survival. Some snakes e.g. when just half out of their egg and when attacked by predator can pretend to be dead, and give a stinking odor out of their mouth to pretend decaying. This is really helpful as the predator leaves. This behavioral information must be stored as well in DNA, not in genes most probably but aside of genes, in epigenome.

As the complexity of organism increases so must also increase the complexity of information storing. This must include the volume, size and number of information as well as the system of storing. The more information is stored the more the organism is in bad need to organize this storing in a more developed and complex way.

As a simple example, just imagine your home book shelf and huge senate library, for sure they are organized differently. The same system applies for comparing storage of spare parts in a small one man pc repair shop and the system of storing parts at DELL Company. One might think of many more such examples. All of them show one thing: the more information must be stored the more sophisticated system of storing is necessary.

The “imprinted genes” express maybe only one level of such storing of information. That level that permits for turning some genes on or off according to some other information, maybe even information perceived from the outside world. Like the agouti mouse or experiments with some flies that when exposed to ether developed four wings instead of two as usual.

This basic principle of storing information and passing it over to the next generation is relatively easy to understand, what will be a major problem is how to find out when what genes are active under what outside conditions and in what organisms.

I predict several-level memory, that I call MLM, multi-level memory, where certain information is stored at its level depending on its value for organism. The first question is how organism can recognize that certain information is or is not important. The only correct answer must be the number of repetitions of a certain event. Actually the development of eye, so often used by many scientists to show the development, is a good example for this many fold repetition principle. If there was some light, and it was, and it changed with darkness, which it did too, then there might be some importance in using this light signal. It may have been linked to the feel of warmth too. It also may have helped the organism to orient better in the surroundings.

The first stage was only a part of a cell that got light sensitive; it could recognize light on light off only. But as this information got repeated many times, there may have developed the second stage of it, soft recognizing of shapes, maybe recognizing of size etc. In order to get more precise information based on light, the light sensitive part had to further specialize and get better and be able to make the difference from what direction the light or shadow is coming form. In order to do that the light sensitive part had to become concave not flat.

The complete development of eye can be found in scientific literature and also in internet, so I see no need to repeat it here. What is important here is the fact of multi-level memory organization of DNA, and how it came to being.

In humans we have further much more sophisticated systems of storing information, cultural information as well. Many scientists speak about the inborn ability of a human child to learn a language. Well, this again might be due to MLM, multi-level memory, because the ability to communicate in words is so important and it has happened many times in last about 20 to 30 000 years, where scientists suppose the real beginning of human language communication. So this experience has been repeated maybe over one or more thousand generations which in turn can be enough for storing this information in DNA. Then it appears to us as a inborn ability of a child to grasp language of her/his parents. Actually, the first attempts to communicate may be much older, maybe sever hundred thousands years, in some animals, say sharks, that are told to live and look like today as they did some 200 million years ago.

I was inspired to write this short article by this work from internet where there are findings that I can support and some I must disagree with.

Gossip and human evolution

Many scientists write about gossip as necessary social habit. The tendency to gossip is at the heart of the social life of many people, and most casual conversations are concerned with matters of social importance (Dunbar, 1996).

I think that many scientists dealing with humans and humanity have the problem of language. They take some word from normal language and implement this into their studies, and get mislead by this word or by some others. Language is very often a barrier to understanding. Therefore I believe it is absolutely necessary to give phenomena correct names. Gossip for sure is not a proper scientific description of that what people call gossip. One must get the idea how gossiping may have developed.

I prefer to call the environment of any organism its Informational Environment. I call it informational as everything, all the signals that organism perceives from its environment is information for this organism, and it plays absolutely no role whether we speak ok bees, bears, sharks, apes or humans. This is of course also valid for much smaller organisms as viruses or bacteria. It is always information from the outside world that reaches organism and organism processes this information.

There are thousand of thousands of examples one might use to illustrate this idea. One of these examples, well-known to basically everyone is car driving. I have described this example already many times in my other short works. Just imagine yourself or some other young person in the situation of learning driving. Mostly these people sit unrelaxed, their eyes wide open, their hands holding the steering wheel firmly and the speed is usually not higher than some 30kmh.. A skill car driver offers a completely different picture, he is relaxed, leaned back in his seat, his hands are loosely on the steering wheel and there is no sign of fear of unease in his eyes and he drives 160kmh on German autobahn.. The reason is the ability of coping with the amount of information approaching the driver. The brain of the skilled driver is used to deal with the speed with which the information is approaching his eyes. He has learned that by mere repetition of driving. The more one drives and the higher the seed at which he drives the faster one learns to drive.

Of course, it is not the only example. We can speak of all games like basketball, ice-hockey, soccer, football, volleyball, tennis or table tennis; all these games are illustration of how human brain can learn to cope with the speed at which it must make decisions.

Most probably gossip has developed from originally useful passing information to somebody else, or even requiring the passing of such information by questions. It can be viewed as reasonable to ask your neighbor whether he knows a good plumber if some tubes went broken in your house. It saves time, you do not have to test all the plumbers form your neighborhood. The same logic goes with car repairs, doctors, teachers, hairdressers and all others who offer some service.

It may have happened that one of such craftsmen was not too god and people from his neighborhood kept saying that and this information got even to his own ears. Most probably he felt abused but he learned his lecture and started the same saying about the other craftsmen so increasing his chances to get jobs form other people by gossiping about the others.

I believe it is necessary to make a precise definition of gossip. There might be two of them right now. One saying that gossip is passing over false information, the other that gossip is passing over whatever information. In such a case teacher would have to be gossiping gall the time. The second definition could be refined to get rid of teachers, and it may say this: gossip is passing over some socially important information. Well, did we get rid of teachers? No, we did not. Teachers pass over only socially necessary information, if it were not so, some of that they say would be absolutely unnecessary and would be deleted from the teaching plans,

So I believe that the real definition of gossip is passing over the untrue information. There might be many reasons for doing so. It does not have to necessarily be only telling that some craftsman is not good enough in order to get him out of job and get all his customers. It can also be used for supporting one’s own position in the hierarchy of the group one is living in as well as decreasing the position of somebody else which in turn again increases one’s own position.

So gossiping was most probably at first only passing over of useful and helpful information. But soon it was discovered that this can be used for other purposes also. Gossiping is a sort of cheating; it is passing over false information. In the studies of chimpanzees it was found out that even chimpanzees do cheat when the want to get some advantage. They pretend danger, everybody runs away, and the get really easy access to the thrown away food. This might be taken as evidence that it is not only people who cheat, cheating is everywhere in the nature, only the means of cheating are different, humans can use language and pass over deliberately false information. And that is gossip.

Steven Pinker lecture on violence

Some time ago Steven Pinker had his lecture on violence in the internet as video. He showed that when violence is measured by number of death, number of wars and these is put in relation to historical development, then, we have less violation today, spite wars being waged at present time.

I do not want to analyze if Steven Pinker was or was not correct. I am just completely satisfied that somebody sees what I believe to see as well. The change in violence through humanization, or socialization of humans can really be easily seen. I have already written a small article on this topic using the development, or change in violence that has been used in dealing with different opinions.

Typically two knights would star a God judgment, a fight where only one remained alive. Some centuries later not knights and swords were used but cords. At these times it started to happen that not only the death was the decisive factor that showed who won, but it usually was enough that one of the rivals was hurt in such a way that everybody could see him bleeding.

Even a bit later instead of cords pistols were used. At this time it was also getting more common that rivals were satisfied either when the other one was injured or even that he was afraid, and they sometimes deliberately shot aside, their purpose was not to kill.

Today when we have disputes in developed societies we usually do not kill, though it still sometimes happens, but we have “word fight”. The problem is how can be recognized who won, when there is no blood seen. The answer is easy: the one wins who says the last word. The logic of this fight rule is that the other person is not smart enough to give any answer. When this was recognized as a rule, many persons have developed sayings that do not say anything to the problem but make it difficult for the other rival in word-fight to give answers. These “last words” or “last sentences” are very often absolutely stupid, there is no logic except the logic of the rule of the last word in a human word fight.

Typically, males do complain about women having always the last word, one such funny thought goes like this: In any dispute between a male and a female the female has always the last word. If a male says something afterwards it is to be considered as the beginning of the next dispute.

These two interesting topics have arrived me this morning

Today I would like to write about two articles published in the internet, both of them trying to describe and explain some human behavioral phenomenon. One on the articles deals with cheating, why we cheat, how much and who cheats more. The other article deals with the finding that there is or might be a relation between the way of upbringing and sexual maturity in girls.

By the study described in this article called Do-gooders can become the worst cheats there are only few people who really do not cheat. It seems that cheating is one weapon in the arm races for survival and is used as excuse or explanation for achieving “higher” goals.

The second article, called Early Puberty in Girls May Reflect Home Life, deals with the possible link between the way how good or how poor girls are cared for in their families and their sexual development. The basic idea is that the worse the parental care the faster sexual development. The proposed explanation for this idea might be that the child must get adjusted to its environment that means if the environment is unpleasant it is necessary to be able to reproduce faster, and vice versa.

There are other findings that support this idea. The age of the first sexual encounter in girls usually differs according to achieved schooling and anticipated further schooling. So girls who attend schooling to become hairdresser usually have their first sexual experience one or two years earlier than girls going for university career.

This in turn supports the idea of adaptation of organisms, in this case young human females, to their environment. This also includes the anticipation of further schooling for those who want and are able to pursue this path.

If there really is such adaptation, then, of course, the puristic idea of mutation is a sheer nonsense. Most probably there are many different ways of influencing the next generation, and mutation is only one of them, and most probably even not too much important. The most important way of influencing the next generation is the ability to adapt to environment and store this information about this adaptation in DNA, so that the next generation does not have to go through the same adaptation process again and can use its energy for further development. Mutation can actually be a very primitive way of adaptation in low level organism, and it can be an obsolete way of adaptation in higher level organisms, in which it actually does more harm.

The question of race, intelligence, evolution and equality

This blog came to me this morning; it deals with the idea of race, IQ and development suggested by some other blogger. This is strange how simple some people are. The idea is completely different. Humans are only one biological species, like dogs, fish, sharks, bats, rabbits, etc. The fact that we differ depends mostly upon environment and the ability of all organisms to get adapted to its environments.

We are equal in the sense that we are not hens or dogs or frogs. This makes us one group. But because this group is rather large, at resent time some 6 billion “units” it cries for next differentiation into smaller groups because no human brain can remember all 6 billion people, it is too much information. So we differentiate. The next reason for making this differentiation is that we do not lie to by too low in the human hierarchy. In order not to be the last one we need somebody to be under us and we always find someone who is under us, and we meet plenty of such people and we group them by some easily noticeable features. It used to be color of skin, color of hair, language, size of body or body shape, or shapes of parts of body like shape of eyes, ears, cheeks, nose, and just such features we can easily see and compare.

I prefer to give example with dogs. Dogs are one group and all dogs are equal in the sense that they are dogs and not elephants or snakes. But inside of the group of dogs suddenly this equality ceases to exist, just consider how equal is the biggest dog in the world with the smallest dog in the world. If the big one would be a female and the small one a male they even cannot copulate. So there are differences, they have always been and they will always be.

We behave like lions, we kill other animals to have food, and we kill each other for mating or for hierarchy, regardless whether inside one group or between groups.. We can always make smaller and smaller group having the same traits different from the other groups. It means we are different, and we even differ in IQ. If it were not so, everybody would have to be awarded Nobel price, everybody would have to be chess world champion.

There is another example showing that we differ. It is sports. If we were supposedly totally equal everybody would have to be able to run 100 meters sprint in the world best time, everybody would have to be the best basketball player in the world and so on. This all is apparently not the case. So we really differ. But, now it comes, we are all humans and that is where we are totally equal.

So we have two sides of the problem. We are equal at the level of being humans but inside of this human group we are not equal. What people do not understand is that the fact that we differ does not constitute any fact that might discriminate others who are not the same as we are.

We should respect each other just only because of being humans and regardless the differences.

People do not want to understand this because of a deep seeded notion of hierarchy. I have written plenty of short papers explaining what hierarchy is and how it works. The above mention blogger just does not understand and cannot grasp the sentence I wrote here in bold italics. The blogger thinks only in categories of hierarchy, who is under me and who is above me. He forgets that the one who is higher should and must use his abilities to help the others who are below him in the hierarchy and so help the total human race develop faster. Actually, he is rather primitive as so many of us.

Some time ago there was a poll made in many countries of the world, the poll concerned the question whether people do more accept the belief of God as creator of everything or if they prefer to believe in evolution. Extremely high percentage of people was found by this poll to believe in God as creator of everything, or at least of humans.

On the other hand we have people like Dawkins, extremely smart and knowledgeable man, scientists who published m any books, e.g. “The selfish Gene” or “The extended Phenotype”. Man who holds many lectures on origin of species, and is overall respected scientist.

Here I would like to quote a part from his book “The extended Phenotype” to show the way of thinking of Dawkins with which I really strongly disagree.

Complex adaptations to an environment may arise in individual organisms through instruction from that environment. In many cases this certainly happens. But, given the assumption of epigenetic, not preformationistic, embryology, to expect such complex adaptation to be translated into the medium of the genetic code, by some other means than the selection undirected variation, is a gross violation of all I hold rational.

I will try to explain why this idea here so beautifully presented by Dawkins is at least partially wrong. It must be wrong. If it were correct we would have really a problem in explaining evolution without any kind of creator, whatever form he might appear.

If genes do not change due to environment, then there must be a question “how did they come to being?” a pretty difficult one to explain. To only expect that genes did create themselves just by undirected variation denies Dawkins himself by his example of evolution of eye.

He correctly describes, in one of his lectures, the evolution of eye as follows. There was a simple organism with light sensitive surface. The organism could not see in our sense of speaking about what we see, but it could recognize whether there is light or not. Like day and night or direct exposition to sun radiation or shade behind some stone. It took then many years until the organism developed a concave part of its surface to specialize in recognizing light. The concave form enables the organism to recognize from what direction the light is coming, compared to the even surface that does not offer this possibility. Later some specific tissue will develop that concentrates the light more precisely, the lens. And so Dawkins actually perfectly describes how environment broadcasts signals, facts to organism and how organism takes these signals and adapts to them. And it makes even more than only that, it can store this information in genetic code and pass this information, in our case the information how to create an eye to next generations, by which it saves energy and time to all offspring of all next generations.

If Dawkins were right with his idea of organisms not reacting, not adapting to their environment, and we would have to accept his idea of undirected variation, we would have to ask many other questions. One of the questions could be “why do we have eyes at all?” Basically we cannot expect that by really stupid undirected variation in genes one possible outcome would be an eye. There are animals that have an eye with similar abilities as our human eye but they also have other means of orientation in their environment. “Why can we see only in the light spectrum we are sensitive to and not also in infrared or ultraviolet parts of light spectrum? “ Some animals do. If there were no influence whatsoever executed by environment upon the organism then we would have to have eyes capable of seeing in the entire spectrum of light. What we certainly do not do.

In order to support this idea I am going to express my idea here about our senses. If we were born on the Moon, we would not have ears at all. Why? Because there is no need for ears in environment where there is no medium carrying sound waves, no atmosphere. We might draw a link to elephants; these animals are believed to have sound receptors in their feet, being able to “hear” somebody walking miles away. Actually they are believed to have developed a system of using their feet to produce sound as well as receipt the sound and so they created a way of communication using their feet for “listening” to sound.

Sound is nothing else than just waves spreading in some environment, some medium. Everybody or nearly everybody knows that water and other materials denser than air can also carry sound and actually these materials do this better than air. So the reason for developing whatever type of hearing, be it with our ears of with feet in elephants, is that there is necessity for such development. As I have said before it would be useless for an organism developing on the Moon to have our ears. It could not hear anything either, as there is no medium carrying these sound waves. On the other hand such organism might develop good receptors for receiving waves from the material The Moon is made of, like elephants.

I would here suggest my idea of evolution as a constant interaction of organism with its environment. All senses that we know, and it really does not matter whether we take our ears or the navigational systems of bats, all such senses are always tuned to receive signals from the environment in which the organism live.

I return here once more to Dawkins. If there were really only undirected variation, then I would suppose we would have to find somewhere some animal having human nose, a fish for example, or mouse with wings. Statistically seen there must have been such cases if Dawkins were right.

On the contrary to Dawkins and many other genetic hard liners I think that the only explanation for life an evolution is to realize how the genetic code as well as epigenetic code came to being. In order to show some other examples I just name two. One is old and known and describes the attempt of cutting the tail of a cat off and expecting that her offspring will be born without the tail. Well, this experiment did not work at all, and is still used as evidence for the fact that environment does not have any influence upon evolution. The second example is much newer. It describes laboratory experiment in which some two wing flies were treated by ether and the started to develop four wings. This was repeated over many generations and after twenty generations they developed four wings without being treated with ether. This shows the perfect influence of environment upon evolution of organism and in this way it supports my ideas and not the ideas of Dawkins.

In order to be careful I would like to say that my ideas are not primitive Lamarckanian ones. It is the question of creating a code in which some information can be passed over to next generations, and also what everything can be coded in such a code and how many levels are there in such a this code. Just recall my example with the Morse code being used by a Czech and a German. If only two Czechs or only two Germans do use Morse code they have no problems to understand each other. If a Czech tries to use Morse code and communicate with a German, well, it will not function, because the second level of coding is not the same, once the message was coded in the Czech language and cannot be therefore decoded by somebody who is capable of using only German language as the next code. In DNA this seems to be the case too, there is level of genes and level of epigenome. I suppose that there are even more levels than only these two. One of them might be the way of storing information by shape of a par of DNA which also seems to be the case according to some scientific works.

Driving and Texting

Driver distraction plays a role in nearly 80 percent of auto accidents. Polls show that Americans overwhelmingly think that text-messaging while driving ought to be outlawed. But more than half of those same Americans say they do, in fact, text-message while driving."Sociologists call it pluralistic ignorance," Kevin Wehr, an assistant professor of sociology at California State University-Sacramento told McClatchy Newspapers recently. "It's this concept where reality applies to everybody but me. We justify things because we think we're better or different from other people. But, of course, we are not better than others. We are just as bad as the next folk.

''The American credo: Do as we say, not as we do.

This text is fully republished from this blog.

As it is said here scientists called this phenomenon PLURALISTIC IGNORANCE. That means that we suppose to be better than the other people. This is no fully true. The problem is that we do our text messaging basically always when we feel the need, and mostly nothing happens. Let’s out of 100 messages we have problems only in one single case, and mostly we can master the problem of distraction. The problem is that the police, journalist, doctors, judges only see the cases when it really went wrong, when really some car accident was caused by the distraction of writing some text message. So it would be like saying that it must be prohibited to fly with an airplane because there are possibilities of a crash and death. Well, as we all well-know, such accidents in air traffic do happen, they do happen in any human activity, the problem are the results, and the simple statistics.

In order to be able to say ho really dangerous the text messaging while driving is we would have to know the total number of all such messages written while driving and compare this number with the number of accidents really caused by this phenomenon, which means we would have to be able to exclude all car accidents where the driver tries only to make an excuse of his distraction by writing such message in a hope he will be excused or not handled so severely. And exactly this might be quite a problem, not that it would not be possible, but in any case of car accident where the driver explains his false driving by typing a message while driving this would have to be checked upon. Police officers would have to try to set up a time framework of accident and try to prove that it really happened due to writing the text message.

If a person has text-messaged say 500 times and nothing happened, not even the slightest distraction, then such a person receives 500 times appositive signal that this is ok and that this activity can be done because it is absolutely not dangerous. This is the problem of repetition of signals. I deal with these in my idea of MLM, multi-level memory. It is actually a training, like basketball, football or whatever other training needed for some human activity, as music playing, bicycle riding, horse riding , swimming, painting, speaking and studying foreign languages etc.

My basic idea of this notion is that what matters is just only the number of repetitions of some activity, which means statistics, to learn some activity properly and gain positive feedback on doing so. The more you do it and the more times it went ok, the more secure you will be and in car you are running the danger of making a mistake, a mistake that sometimes causes only heart beat, but sometimes heart still stand.

Second this is really a good example for sociology, a science that deals with the systems of interactions of humans among other humans, in their informational environment. The same is valid for ethology that is a science dealing with the same task in animals and not in humans.

How we do express what we see, feel or hear or experience in some other way

In this study, the researchers constructed a computer program where one group of dots on a computer screen seemed to follow a single dot across the screen. They asked study participants to describe what they were seeing. Most responded with something like, "That swarm of dots is chasing this other dot, attempting to capture it." The researchers interpreted this to mean that the participants had assigned agency to an inanimate object, the dots, and that this was empirical verification of an agency-detection mechanism that was set so high that it would produce false-positives.


This quotation is taken from here.

Whoever was the scientist expressing this idea, well, he has got the right to say so, but most probably he or they are completely wrong. The proper view at what the tested persons said would be a different one. People try to describe what they experience as short as possible, mostly, and if they must describe something they have never seen before, they try to find similarities, and if the easiest similarity is ascribing some inanimate thing animate traits so they do it, but the purpose of it is the ease of explanation. It would cost them too much energy to think how to describe that phenomenon and not ascribing the animate traits.

This is a typical task, teachers face everyday, how to explain something what students have never heard of before. Usually, teacher uses some kind of example that pictures similar principle and is commonly known to students. Just take the typical model of money and goods flow, so called circular flow in economics. It was first described by a doctor who noticed the similarity of blood circulation and circulation of money and goods in society.

Of course no one in economics would come up with the idea that this doctor is stupid because he ascribes animate traits to inanimate things like money and goods and services.

Funny, that these so called scientists do not know something as easy as this explanation. People just choose explanation that is fast at hand, and it will be supposed that the other person knows this picture. If the other person would not know the picture / model, such description would make no sense, and the first person would try to find other ways of describing the experienced phenomenon.

A good thing to do in order to understand this is to read and listen to works and lectures of Steven Pinker, one of the best psychologists based on linguistic point of view that is how words, grammar and language as such influence evolution of humans