Boxes about science - "grey boxes" in the book

Adolf Portmann (1897–1982)

Portmann was a Swiss biologist who studied the biological meanings of the external appearance of organisms in the first half of the 20th century. He showed that there are a large number of conspicuous structures, patterns and colours on the surfaces of the bodies of animals, which were very frequently formed as a means of communication within the species and between species (called address phenomena). However, in addition to address phenomena, nonaddress phenomena occur in nature, which Portmann considered to be manifestations of a general tendency of all organisms towards self-presentation. In my opinion, a great many of these structures were formed as a consequence of autoelection and, in organisms that are not equipped with sight, as a form of warning or masking coloration. From the standpoint of spreading any newly formed alleles, it is certainly advantageous if they increase the viability of their bearers. However, it is even more advantageous if there is an external indication of their presence in the genome (such as a red spot on the tail), which opens the possibility of very rapid spreading through autoelection. After the Second World War, German biology (and all works written in German) were completely pushed aside by American biology, as a consequence of which the aspects introduced, e.g., by Portmann, remained practically unknown to modern biologists who are thus not greatly affected by these works.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Cumulative citation index

The cumulative citation index is the total number of cases in which the results of a certain author published in one of his articles were cited in the scientific articles of his colleagues. In practice, mostly only citations in journals included in the Web of Knowledge database (the new form of the original Science Citation Index database) are included and auto-citations are also included – i.e. cases, where the author or one of the co-authors of an article cited this article. Both are substantively incorrect, but technically readily feasible. The older an author is, the larger the value of his cumulative citation index becomes. Thus, it is usual to assess the quality of a scientific worker or scientific team according to the number of citations achieved over a certain shorter period of time, for example, over the past 5 years. In this case, older authors with a greater number of formerly published works are, of course, also at an advantage, because their older works can also be cited in this period of time. However, in fields where works age rapidly, for example, in molecular biology, this advantage is not great. It is a matter of speculation whether this sufficiently compensates older workers for the disadvantages entailed in the obligation to sit in various commissions and councils.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Exceptions from rules

Rules (laws) are generally not one hundred percent valid in science and there are frequently a number of exceptions. This is caused primarily by the fact that, as they are formulated, they are excessively simplified and thus imprecise. Take, for example, the rule that females generally select males is valid only assuming that females invest more valuable resources into reproduction than males. However, this is not true for a number of species. For example, it does not hold for giant water bugs of the Belostomatidae subfamily, where the female lays her eggs on the back of the male and he then carries them, defends them and ensures that they get enough oxygen for three weeks. The total weight of the eggs is twice that of the male and care for them is a great burden on him. Females can copulate with a number of males, but a male decides whether he will accept eggs from a female or not. As the area of the backs of males is a factor limiting reproduction, fierce competition occurs amongst females for males willing to accept batches of eggs. The adage “the exception proves the rule” should properly be “the exception tests (or allows testing of) the rule”. In this form, it is a profound truth – when we study the individual exceptions from rules, we should always discover their cause (in the above case, the cause of the deviation from the rule is the fact that the males, and not females, invest the more valuable resources into offspring). If we can find the reason for the individual exceptions, we confirm that we have understood the nature of the rule properly.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Grants and grant reports

A large proportion of funds for science are obtained by scientists, not from their employers, a research institution or university, but rather from specialized national or international grant agencies. A scientist thinks up an interesting and feasible grant project, describes it in detail and exactly calculates the funds required to resolve it. Then he or she submits the proposal in a grant competition, announced by the individual agencies, usually once annually. The officials first exclude all the proposals that did not meet the relevant formal requirements (form B-6 was not accompanied by a confirmation from the Vice-Dean for public relations that the animal facilities do not currently keep duck-billed platypuses infected either with foot and mouth disease or bird flu) and then send them to a number of scientists (usually applicants from previous years – whose addresses they have in their databases) for expert evaluation. On the basis of the expert reports obtained, a commission of experts of the particular grant agency (consisting of scientific workers who keep an eye on one another) establishes an order of the submitted proposals and a few percent of the best projects are then financed. Projects usually last three years and each year the responsible worker submits a report on the results obtained and the manner of managing the funds. The present system has the great advantage that it tends to favour the capable and hard-working rather than the incapable and lazy, that it promotes cooperation amongst the employees of a single institution (who are not competing for a joint package of institutional funds) and that it limits the potential for intervention by easily corruptible officials and politicians. It has the disadvantage that it tends to favour short-term projects with predictable outputs, that chance plays a considerable role in the allocation or non-allocation of funds, specifically in the reviewers that receive the project for evaluation and their momentary moods, and also that creative scientific workers are buried under mountains of paperwork. It is said, but this will most probably be only a rumour, that experienced scientists write grant proposals for projects that they already have more than 75% completed. They then use the allocated funds for work on new projects that, if they turn out well, can become the subject of the next grant application. And worst – some of us even insist that there is no other reasonable approach as it is a well known fact that scientific discoveries can, in actual fact, not be planned in advance.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Is it possible to write in a biological text that alleles learned to do something in order to achieve something else?

Of course, but only in the case that you are not a student who is writing a thesis work and expects to encounter an unfriendly or especially dense reviewer. It is usually completely clear from the context that you are not suggesting that alleles have the ability to plan their future behaviour in relation to achieving some future goal. It is, of course, possible to state quite correctly that plants form attractive flowers because the members of this species who accidentally gained this ability by mutation in the past better attracted pollinators than their competitors and thus had a greater number of progeny, who inherited this ability. However, it will be far easier to understand if we simply state that plants form flowers so that they can attract pollinators.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Journal with impact factor

A journal with impact factor is a journal that was included in a certain bibliographical data base (Science Citation Index) some years ago on the basis of a combination of coincidences, and since then has been considered to be more prestigious than some possibly better non-impacted journals. Each year, the database operators calculate an impact factor for particular journals included in this database; this is the average number of references to one article in journals included in the database within the first two years after the publication of the article. Half of the journals had an impact factor of less than 1 in 2004; however, there were about 10 journals with an impact factor of greater than 30. The higher the impact factor of the journal, the better the articles published in it are considered to be when evaluating the performance of a scientific worker or scientific institution. Simultaneously, a substantial number of evaluators (and evaluated persons) apparently do not realize that the order of the journals would be completely different if the impact factors were calculated from the number of references, not within two years, but within four or even ten or fifty years after the publication of the relevant articles and that it is frequently not possible to statistically demonstrate a connection between the impact factor of a journal and the number of references to the individual articles published in it. (This apparent paradox is caused by the fact that the differences in average citation are mainly caused by differences in the probability of the occurrence of a few highly cited articles; most articles that are published in any journal are cited to roughly the same degree. To be more specific, 20% of biochemical or molecular biological works are apparently not cited even once even five years after publication, approximately 75% of articles in the social sciences are not cited and 95% of articles in the humanities, where there is a tendency to write and refer to books, are never cited. The main contribution of the existence of a database of impacted journals thus does not consist in its usefulness for evaluation of the quality and quantity of scientific work, but in the fact that it reduces to a certain degree the scope for establishing an increasing number of scientific journals and thus permits concentration of the sources of scientific information in the already existing journals. After a certain period of time, a new journal can be included in the database of impacted journals; but its articles must be sufficiently cited beforehand. And who would send his good article to an “unimpacted journal”?

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Negative and positive results

A scientific study is performed in an attempt to support or negate the validity of a certain hypothesis. In the optimum case, the study has the character of a cross experiment – a certain result would support the studied hypothesis while the opposite result would throw it into doubt. In this case, the study provides only one of the answers, yes or no. However, very frequently, our studies have an asymmetric output. For example, one result supports our theory, but the opposite result does not mean anything at all. In this case, the study can yield the answer yes (no) or do not know. In the second case, this is called a negative result. You would probably like a specific example; here is one: If we do not manage to find a transition link in the palaeontological record, then this can mean that that link never existed, but it can also mean that a fossil has not been preserved, or that we have simply not found it yet. However, if we find the intermediate link, our hypothesis will be supported.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

References

It is not possible to simply assert something in a scientific text; all our statements must have a basis. Either a reason must be given for our statement or we must demonstrate that someone made (and thus somehow justified) this statement before us. References are used for this second purpose – the name or names of the authors of the relevant source and the year of the publication are written directly in the text and a list of references is placed at the end of the text, giving the name of the relevant article and journal or book where it was published. Understandably, it would be best to give the author who discovered the fact or was the first to give a basis for it. However, in practice this is usually far from the case. Authors of articles usually cite the sources from which they themselves learned the given fact. Of course, at least theoretically it should be possible to follow the chain of references in older and older journals back to the original source. Scientific workers are glad when they are cited in the works of other authors. The purpose of a number of citations in scientific articles is thus to please (or corrupt) the relevant colleagues, who could well be amongst the reviewers of the particular article and thus decide on its acceptance for publication (see Review process in a scientific journal) or, at the very least, in the future can, in return, cite our articles in their works.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Review process in a scientific journal

If a scientific worker makes a discovery (and, in fact, also if he doesn’t make a discovery), he must write an article about his results for a scientific journal. He sends the manuscript of the article to the editor of the journal and he then usually sends it to two or three reviewers, i.e. scientists who work in the same field and, where possible, in the same or a similar area. These are frequently members of the editorial board of the particular journal, whose results or theories are mentioned in the article (especially if they are mentioned in a negative context) or authors who have published an article on a similar subject in the particular journal in the past. These reviewers (unless they happen to be your acquaintances who support you or who will require your favour in the future) attempt to find mistakes in the article that would form a basis for rejecting it. If no important mistakes are found in the article but they still don’t like something about the results (for example, that they didn’t discover them themselves), they think up some inadequacies (the author doesn’t sufficiently discuss the possibility that …, instead of method xy it would have been better to use method yx) and suggest to the editor that the article be rejected or at least be fundamentally rewritten (which, under current conditions with an excess of manuscripts of articles, is generally the same thing in the last analysis). On the other hand, if they like the article, find you empathetic or if it is useful for them if your article is published (for example, because they can refer to it in their works or because you cite their article in it in a favourable context), they recommend to the editor that your article be published. In any case, the final decision on the fate of the article lies with the editor who can, but need not, follow the recommendations of reviewers. Reviewers should be unknown to you; in actual fact, in at least half of cases, it is possible to guess who was involved. Especially in the case of favourable reviews, their authors usually take care that you will be able to guess their identities. In some journals, the reviewers do not obtain information from the editor on who is the author of the particular article; in others, the reviewer must sign his review. Studies that have been performed have, however, shown that this has minimal impact on the quality of reviews. It has been found that young reviewers and reviewers who are conversant with statistics write somewhat better reviews.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Scientific article

At the present time, scientific results are usually published in the form of a brief article in one of the many thousands of scientific journals. A scientific article usually consists of a brief Abstract summarizing the most important results, of an Introduction chapter, which is intended to describe the purpose of the study and place it in the broader context of the field, of a Results chapter, containing the uncommented results of the study (we measured this and that, the difference was/was not statistically significant), a Discussion chapter, stating what we think our results mean, how they agree or do not agree with knowledge to date and what follows from them. The article is usually ended with acknowledgement of people who contributed to completion of the study (but not enough to be included amongst the authors of the study) and of grant agencies that financed our research work, see Grants and grand reports, and also a list of references cited in the article, see Box References. Overall, an article (in the fields of biology) usually has 2000–6000 words and 3–6 graphs and tables, i.e. takes 4–12 pages in the journal.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Scientists and research workers

Although the general public has probably not even noticed it, the “scientist” as a special species has been forced out of practically his entire original biotopes in the natural sciences and has been replaced by the much more successful species “research worker”. The differences between scientists and research workers are not obvious at first glance. However, research workers do not usually ask “Why?”, but rather “How?” and can use complicated and expensive methods to determine which enzyme, which sequence, which molecular weight, which redox potential, or how many molecules of substrate per minute. Average research workers have incomparably greater scientific performance (number of publications and number of citations of these publications) and thus gain higher professional positions than the average scientist. This would be even truer if below-average research workers were compared with below-average scientists. To the contrary, the differences will not be so great between top research workers and top scientists. However, because the highly above-average are a negligible minority in the population, for tactical reasons a great many scientists act as if they were research workers and state this profession in their curriculum vitae. For this reason, it is difficult at the present time to determine the exact numbers of scientists and research workers in the scientific community and the first impression that scientists no longer exist in nature could, in fact, be erroneous.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Sir Karl Raimund Popper (1902–1994)

Popper was probably the most important philosopher of science of the 20th century. For example, he was concerned with the aspect of confirmability (verifiability) and refutability (falsifiability) of scientific theories (see also Theories and hypotheses). It is interesting for evolutionary biology that he basically never understood it and simultaneously spoke about it very authoritatively.

Czech people will find it of interest that he died almost immediately after ancient and famous Charles University awarded him an honorary doctorate. In fact, it seems that an honorary doctorate or award from my alma mater is one of the most dangerous events that a person can encounter. It is surprising that the right to award prizes and honorary doctorates of Charles University has not yet become the subject of strict international control. Purely at random, the political map of the Near East could look entirely differently if someone had warned Shah Mohammad Reza Pahlavi against the danger of accepting an honorary doctorate from Charles University.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Supernatural forces and science

Science cannot decide on whether supernatural forces exist or not. If there were a God who did not have to obey the natural laws of our world, then he could arrange for the experiments of scientists to have any results whatsoever and they could thus never either discover or exclude his existence. The explanation of a certain natural phenomenon based on the assumption of the action of supernatural forces is thus not scientific and is bad because it is necessarily erroneous or because science does not recognize the existence of God. Science cannot decide whether this is erroneous or not. It is unscientific because no consequences follow from it that scientists could test and thus potentially falsify. It is simply not possible to test the lack of correctness of a supernatural explanation and thus, in science, we must always attempt to explain the observed phenomenon by natural means – by processes not including the action of supernatural forces. It is quite possible that we will never be able to explain some phenomena by natural means; but this does not change matters. If evolution or God gave us reasoning, we must try as honestly as possible to use it to understand our world.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

The financial inaccessibility and unread nature of professional journals

The publishing of most professional journals has been taken over by commercial publishing houses and their prices have been cranked up to absolutely impossible heights. It has been calculated that, while publication costs for one article work out at approximately $ 500, libraries around the world pay a total of $ 16°000 for one article (costs estimates in 1999). This sum is comparable with the average costs for the research itself, which correspond to approximately $ 20°000 per published article. The greater part of this sum ends up in the pockets of commercial publishers of professional literature. A few years ago, scientists attempted to rise up against the dictate of commercial publishers and began to massively sign a petition exhorting other scientists to boycott journals that do not publish an electronic version of articles that is freely accessible to the public on the Internet within six months of publishing the printed version. Of course, the boycott was unsuccessful and most authors continued to send their manuscripts to the relevant journals. When someone organizes the next boycott, I would like to suggest a “minor” adjustment – so that the boycott doesn’t hurt the boycotter more than the boycotted, it should not consist in not sending manuscripts to expensive journals that do not publish an electronic version, but in not citing works “published” in these journals. The decrease in the impact factor of the journal will certainly make the publisher see sense very quickly.

And to explain the fact that professional articles do not get read: with the present system of managing science, we don’t read other people’s articles: we have to save time somewhere so that we can write our own articles. The approach proposed by colleague Zrzavý, that we read only articles in which our own name appears (I hope that I understood him correctly and that he didn’t mean articles in which his name appears) so far seems to me to be too radical.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

The relationship between a hypothesis and a model and a theory

There is not usually any difference between a hypothesis and a model in science. A model is basically our hypothesis of the nature of a phenomenon. (However, not every hypothesis need be a model; some hypotheses are not related to the nature of things, but only to the existence or nonexistence of a certain phenomenon.) In technical fields, models are intended so that study of their behaviour in cases where this is advantageous or even necessary can replace study of the behaviour of the actual, modelled object. Models are created in science so that we can test their validity and thus reject the relevant hypothesis. A theory is actually a more complicated hypothesis, to be more exact, it is a system of several or a great many interconnected hypotheses. The usual concept of lay persons that a hypothesis is an insufficiently verified theory certainly does not hold true.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Theories and hypotheses

The destiny (or rather, the fate) of a theory is to be developed, i.e. altered over time in such a manner that it is gradually capable of encompassing and explaining more and more phenomena. In this, it differs fundamentally from a hypothesis. The destiny (or rather, the unavoidable fate) of most hypotheses, is to be falsified, i.e. to be rejected as invalid. Understandably, scientists would prefer to be able to verify their own hypotheses, to confirm their validity. I would like to emphasize the word “own” in the previous sentence. We very happily demonstrate the falseness of other peoples’ hypotheses (and these are in the majority around us). Unfortunately, we must accept the unpleasant fact that scientific hypotheses (at least outside the field of mathematics) cannot be verified. For example, the hypothesis “all mammals give birth to live young” can be shown to be false if we encounter at least one mammal, for example, a duck-billed platypus, that hatches from an egg. However, if we did not discover a mammal hatched from an egg in books or nature, this would certainly not mean that we have confirmed our hypothesis. Until we study the reproduction of all mammals, extant and extinct, there still remains the possibility that such a mammal exists or existed (and that we have simply not found it) and that our hypothesis is thus invalid. As was convincingly explained by Karl Raimund Popper, hypotheses are thus divided into only two groups in science, the invalid, i.e. falsified, and the conditionally valid, i.e. those that have so far resisted attempts at falsification.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Thomas Samuel Kuhn

A historian of science (1922–1996) who was concerned with the laws governing development and scientific progress. He demonstrated that the concept of science as a regularly progressing process refining our knowledge is basically erroneous. He showed that three phases alternate in science. The phase of normal science is usually longest; here, slow development and refinement and elaboration of existing theories actually occur. This is followed by the phase of crisis science, when it is found that an ever increasing number of facts don’t fit into the existing theory. The third phase is a scientific revolution, when the old theory is rejected and replaced by a new theory. The previous period and the previous theory are then forced out of the textbooks and subsequently from the consciousness of the relevant scientific community and, after some time, the history chapters of textbooks are rewritten as if the new theory had existed throughout all time. A new comfortable period of normal science begins. According to Kuhn, the main reason for this discontinuous development of science is the existence of paradigms – assumptions on which the accuracy of the theory stands or falls. However, during the period of normal science, scientists are not even aware of the existence of the paradigm and thus do not think about or test its validity.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more

Trofim Denisovich Lysenko (1898–1976)

A capable or rather capable-of-anything demagogue and absolutely incapable plant physiologist who, in the 1930s and 1940s, got on Stalin’s good side and, shielded by his absolute political power, for a great many years and in the name of Marxism-Leninism, practically destroyed first genetics and later other fields of biology in the Soviet Union and partly in its political satellites. The era of Lysenkoism in the Soviet Union finally ended in the 1960s. He declared that genetics at that time was a bourgeois quasi-science serving the interests of the governing capitalist class and initiated its replacement by progressive, Soviet genetics. Lysenkoists stated that there are no genes, that the hereditary properties of organisms change under the influence of natural conditions, that one known species can change into a different known species, e.g. as a consequence of lack of nutrition, or that living cells can be formed in a test tube from a mixture of simple substances. In the Soviet Union and other communist countries, they found a great many willing helpers who, partly from fear, partly from stupidity and partly from calculation, massively falsified scientific data and liquidated any scientific opponents through political means. In their campaign against official genetics, they brought a number of interesting phenomena to light that were known by older breeders and that seemed to be contrary to accepted genetic knowledge of the time. In this way, they discredited them for a long time and prevented them from becoming the subject of serious study.

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The classical Darwinian theory of evolution can explain the evolution of adaptive traits only in asexual organisms. The frozen plasticity theory is much more general: It can also explain the origin and evolution of adaptive traits in both asexual and sexual organisms Read more