New Scientist published an interesting article recently in its January 2009 issue. It can be found online here: http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html?full=true

The front cover of the issue stated in headline form ‘Darwin Was Wrong’. The article went on to discuss how Darwin’s tree of life was actually incorrect, and how some assumptions underlying relationships between organisms weren’t quite as simple as they seemed. Let us discuss the article itself, but before doing so, I would like to point out that New Scientist have, after the publication of its controversial front cover, acted irresponsibly with the unfair statement made, purely to sensationalise its story and attract more readers. The magazine is read by many anti-evolutionist religious fundamentalists, and an unfair headline which hasn’t been more accurate will stick in the minds of these individuals, rather than the content of the article itself.  These people will assume that the whole theory of evolution is in fact wrong, which of course has already been stated by many creationist and intelligent design websites following the publication of this issue. New Scientist themselves acknowledged this in an editorial post:

“None of this should give succour to creationists, whose blinkered universe is doubtless already buzzing with the news that “New Scientist has announced Darwin was wrong”. Expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse.”

A better title would have been ‘What Darwin didn’t know about the tree of life’. Coming onto the article and it’s points. Darwin thought the relationships between all species, living and extinct, fitted onto a tree-like pattern. He assumed that all species descended by a branching process from earlier ancestors, which themselves had descended by a branching process, until you reached the very first ancestor of all life forms that have ever lived. He described this tree-like idea as the tree of life. However, Darwin based this idea upon the forms of life that he had studied and could observe at the time. These consisted of animals and plants, which are multicellular forms of life. And since nothing at the time was known about the inheritance of traits, he also postulated that traits were passed down from previous generations to the next, in one, vertical direction.

Those assumptions are now known to be incorrect, however one must sympathise with Darwin, as he lived at a time where methods for detecting and analysing genes were far from being available. The article itself points out why these assumptions were incorrect. Firstly, it has been shown in prokaryotes (which are cells without nuclei, e.g. bacteria) that genes can be transferred between organisms which are not ancestors/descendants of one another, or between different species (a process known as horizontal gene transfer, HGT), in addition to the usual transmission via cell division, from parent to daughter cells. This occurs fairly regularly in prokaryotes, so genes can be ‘shuffled’ within a population. Thus, trees constructed based on DNA sequences may be different to trees constructed using other data based on vertical inheritance. There is also evidence supporting this phenomenon occuring in eukaryotes (cells with nuclei), including plants and animals (some genes have even been found to be a result of HGT in humans and elephants).

Secondly, the assumption that speciation occurs exclusively in branches has also been shown to have many exceptions. For instance, rather than one entity branching out to form two or more entitities, there are examples in nature where two lineages can breed together to form a hybrid species. This is true for many prokaryotic lineages, as well as many eukaryotes; for example, it is thought that a eukaryote once engulfed a prokaryotic bacterial species, and this lead to the lineage of cells containing mitochondria (the energy producing machinery in cells), which are ancient remnants of those bacteria. Also, it is accepted that eukaryotes themselves were formed by a fusion of two prokaryotes. Thus, this merging of two lineages to give one is the opposite to the branching process.

Finally, Darwin’s assumption of all life forms being descended from one single cell may also be incorrect, due to the nature of of the processes described above; it is more likely that there was an ancestral population of cells rather than a single ancestral cell. However, the individual ancestor to all of life may be a single replicating entity that gave rise to other replicating entities, of which only DNA and RNA survive today, as currently known. The carriers of these replicators are therefore all related, and thus Darwin’s idea of a universal common ancestor for all of life may still hold.

To conclude, Darwin made certain assumptions about the tree of life (i.e. it’s applicability to all living organisms) which have shown to be incorrect, however we know that it still pretty much applies to most animals, and so it is unfair to have labelled him bluntly as ‘wrong’, since animals were what he dealt with mainly. The relationships between all forms of life will look different to a universal tree; more like a web network. But this web too will provide the roots of a tree that is applicable to individual lineages of eukaryotes, including animals.

  • Microevolution occurs; Macroevolution doesn’t. This is a fallacious claim. Microevolution is evolution which occurs below the species level, i.e. variation within a population. Macroevolution occurs at and above the species level, i.e. the formation of new species and clades. Although most Biologists regard the distinction between the two to be non-existent, the mechanisms which lead to both are one and the same; gradual, cumulative selection. Macroevolution is simply an accumulation of microevolution. If a macroevolutionary change can be described as going from the bottom to the top of a staircase, then the microevolutionary steps constitute the individual stairs. However, it is also possible for macroevolution to occur in larger ‘spurts’, through mutations which occur in the genes involved in the development of an organism (e.g. Hox genes, which are involved in patterning the body axes, giving rise to morphology); for example, by changing the sequence of a transcription factor (a switch for turning genes on or off) for these genes, the body morphology can be radically changed. Speciation of many organisms has also been directly observed, ranging from bacteria to drosophila. Macroevolution is a gradual accumulation of microevolutionary steps, but may also occur in larger rare bursts, for example through changes in the sequence or expression of genes involved in the development of an organism (e.g. Hox genes).
  • Evolution is pure chance. This statement shows a huge misunderstanding of evolution. At its most basic fundamental level, evolution has two basic components: genetic mutation, and natural selection. Genetic mutations are random, and occur due to errors during DNA replication, chemical mutagens, radiation, and other factors and processes. These mutations give rise to the diversity that we see amongst genotypes, through to species variability. However, what decides whether mutations are beneficial or harmful is natural selection.

    Natural selection is the passive process by which any allele that confers an advantage on an individual’s reproductive fitness will increase in frequency within a population, whereas any allele that has a detrimental effect will decrease in frequency. Therefore, since reproductive fitness involves competing against all other individuals, where only the most reproductively fit ones pass on their genes, natural selection is a non-random process. This is where the idea of chance disappears. Natural selection is the complete opposite to chance. Any slight modification that impacts upon an individual’s reproductive fitness will be under selection. Evolution is not pure chance. Only genetic mutations are random; natural selection is a gradual, cumulative, nonrandom process.

  • Evolution does not produce new ‘information’. This could not be further from the truth. Information here is defined as new DNA sequences which code for new traits. There are many ways in which new information is created, the main being through genetic mutation, whereby the DNA sequence of a gene is changed, which can produce a new variant of the gene (allele). Also, the ‘amount of information’ within the genome can be increased (i.e. increasing the number of genes and variants of those genes). The most common way for this to occur is via gene duplication and divergence.
    This illustration shows a gene that has duplicated. (Figure taken from https://i1.wp.com/www.wikidoc.org/images/7/72/Gene-duplication.png).

    This illustration shows a gene that has duplicated. (Figure taken from http://www.wikidoc.org/images/7/72/Gene-duplication.png).

    Genes can duplicate through errors in the replication of chromosomes, or even whole genomes, or during sexual reproduction when homologous recombinational events are uneven, giving rise to extra DNA sequences which may contain the whole of an extra copy of a gene. The organism which inherits this extra copy will now have two copies of the same gene with the same function. Thus, one copy is available to freely mutate and diverge, whilst the other retains its original function, without affecting the fitness of the individuals who carry it. Over time, it may form a new allele (variant of the same gene), which will provide a new function. If this allele is beneficial to the individual’s survival and reproduction, then it will be inherited by future generations and will spread through the population. Thus, this new piece of ‘information’ will be incorporated into the genomes of the population. New traits however do not come exclusively through increasing number of genes or mutations in genes themselves; the changes in interactions of the gene products themselves, and the expression patterns of genes, all give rise to new combinations of traits which can be utilised by the organism. Genetic mutations can produce ‘new information’, which can be subject to selection. gene duplications and divergence can increase the ‘amount of information’ in a genome. However, there are other processes that also create new ‘information’ in the genome.

  • Modern day animals evolving into other modern day animals. Species do not evolve into other species. In some circumstances, integration of two species can occur if there are no reproductive barriers, but this is different to one species becoming exactly like another. However, organisms can evolve structures and morphological characteristics that are similar to those found in other organisms residing in similar environments (a process known as convergent evolution). The eye is an example of this, and has evolved many times independantly. All the animals that we observe around us are at the end of the branches of the tree of life. These end branches do not evolve into one another. Just like anybody who has a sibling will share a common ancestor with them (father or mother), and also with cousins (grandparents). Modern day animals do not evolve into other modern day animals. All modern day animals are terminal branches of the tree of life, and do not evolve into each other.

  • Species never evolve into other ‘kinds’; dogs remain dogs, cats remain cats. This misconception originates from the fallacy of classifications of organisms. Humans, more specifically, taxonomists, classify organisms according to certain criteria. As observers of modern day life, we can name individual species according to our own standards, i.e. a dog as a dog, and a cat as a cat. The same goes for naming groups of animals. A whale is a modern day animal which lives in the sea. We classify it as a mammal, because we can trace its evolutionary history back to a land mammal. However, we can also point out that we are all descendants of fish, because the first land dwelling creatures originated in the sea. Some fish gained the ability to spend time on land as well as continue living in the sea, and these fish were known as amphibians. Those amphibians gave rise to modern day amphibians, and reptiles, which eventually gave rise to modern day reptiles, and mammals. So technically, we could classify all mammals as reptiles, and all reptiles as amphibians, and so on, until we classify everything as fish. But we don’t, as this would not help us one bit in describing groups of species, hence we use a system which allows us to do so.  It can take millions of years for many species to evolve into new species, and since we are not around to directly observe all events of speciation, we have to infer them from the fossil record and phylogenetic analyses. After inferences have been made, we may name each separate individual species that forms part of a lineage leading up to a modern day animal for our own purposes. Each individual species is a branch which branches off from another branch, and so on, until you reach a terminal branch, which would either represent an extinct species, or a modern day animal. However, taking the evolutionary lineage of the dog as an example, a dog can be called a wolf,  since it evolved from the gray wolf; it is taxonomists who give names to members of species from different places in time of a specific lineage, which have descended with modification. Speciation is like a rainbow spectrum; you can observe different individual colours, but when you examine them closely, they are all a smooth continuation of one another, with no distinct boundary; humans classify individual colours according to our own criteria, however in reality, violet is just a continuation of indigo, which is just a continuation of blue, which is just a continuation of green, etc. All species are related, and share common ancestors, ultimately sharing a single ancestor or population from which all species are descended. Species are named according to criteria used by Taxonomists, however, all species are really just a branch of the tree of life. A species may be named by branch or lineage, but we name modern day animals according to our standards, and also to help identify and describe particular species.

  • If humans evolved from monkeys, why are there still monkeys around? A very common misconception which shows two errors of misunderstanding. The first is simple; humans did not evolve from monkeys, we simply share a common ancestor with them. This can be confusing when the term ape is used, as the layperson usually uses the term interchangeably with monkey; since we evolved from, and are apes, the layperson wrongly assumes that this must mean we evolved from monkeys. This is of course incorrect, as ape is the name given to the clade, or group of related organisms, which includes the ancestors, and living members of gorillas, chimpanzees, orangutans, and of course, us humans too. We four form a clade known as the Great Apes; another clade, known as the lesser apes, includes gibbons. These clades are part of a bigger group, known as an order, called primates. Primates also include monkeys, and our relationship to them can be traced to a common ancestor around 40 million years ago.
    This tree shows the relationships between apes and other primates, including monkeys, and also the relationships between the apes themselves.

    This tree shows the relationships between apes and other primates, including monkeys, and also the relationships between the apes themselves (Figure taken from http://www.greatapetrust.org/images/primates/primates_tree.gif).

    Monkeys are often confused with chimpanzees, and thus a double misconception arises when people mistakingly assume humans evolved from chimpanzees, and then slip up again to assume that chimpanzees and monkeys are one and the same. A second fallacy assumes that if one species evolves from another, it should somehow replace the original species. This is false. Species are broadly defined as separate populations which cannot successfully interbreed with one another to produce reproductively viable offspring. Speciation, the process of the development of new species, can occur in many ways, but one key stipulation is that there is reproductive isolation between the two populations that are eventually going to become separate species. This means that no interbreeding can take place between the two, so that over time, an accumulation of many individual differences will no longer support viable reproduction. The most common way for reproductive isolation to occur is if there are geographical barriers separating two populations, or if some members of the original population migrate away, to form a separate population. When this occurs, these separated populations may have different ecological requirements, so replacement of the older species does not necessarily happen. Of course, replacements can occur if both species are reunited in the same niche (environment); if there is a competition for the same resources between both species, and one successfully outcompetes the other, then the unsuccessful species will become extinct. But in the case of humans and other apes, this was not the case, and since each species coexisted with each other successfully, there was no reason for any ‘replacement’ to occur. Humans did not evolve from monkeys; we share a common ancestor with them. We are apes and have evolved from earlier lineages of apes. When speciation occurs, a new species does not necessarily replace the species from which it is descended.

Welcome!

January 25, 2009

Hello. Thank you for visiting my blog. I am a Scientist and a Medical Student, and I care passionately about the truth, be it regarding the nature of our Universe, or about claims that are made by individuals within other fields outside of Science. Reaching truths requires making observations, attempting to explain them, gathering evidence to support those explanations, and finally, constantly questioning and modifying explanations to incorporate new findings.

The nature of this methodology is central to the Scientific Method, which is the best and only way to provide explanations for the workings of our Universe. There have of course been other attempts to explain how our Universe works, but Science has been the only field of enquiry which does justice to the elegance and grandeur that this Universe possesses, and it is for this reason that I as a Scientist feel so priviliged to be able to ask important questions and obtain awe-inspiring answers. The Scientific Method is what I would call Rational Thinking, and can be applied to anything. Thus, we can use this method to analyse the truth value of practices such as Religion, Astrology, Paranormal activities, etc. Equally, we may use the method to revisit older ideas and modify them according to new evidences, or debunk myths which may have no truth value whatsoever. In this blog, I hope to be able to use Rational Thinking to discuss ideas both in and out of science.

My main field of interest is Evolutionary Biology; I study Evolution at a molecular and genomic level, and am also interested in Ethology. Evolution provides the grand explanation for the complexity and nature of life, and allows us to correctly infer events from the past, as well as make many predictions for future discoveries. Through this blog, I also seek to discuss and explore Evolutionary Biology in more detail.

Evolution was first formally and correctly described by Charles Darwin, in 1859, in his ingenious book, On The Origin Of Species By Natural Selection. Evolution is supported by evidence from many fields, both inside and outside of Biology, and it is these massive amounts of mutually supporting evidence which have established Evolution the be a fact. Independent enquiries and investigations in different fields all point towards the same conclusions, and these include studies of Genetics, Morphology, Biochemistry, Phylogenetics, Geology, Geography, Paleontology, Comparative Anatomy, Physiology, Physics, Mathematics, and many more.

The Theory of Evolution describes how Evolution occurs. The Modern Evolutionary Synthesis is currently accepted by most Evolutionary Biologists to be the best explanation for the mechanism of Evolution, which incorporates Darwinian Natural Selection with Mendelian Genetics.

Darwinian Natural Selection describes how organisms change over time through a process of descent with modification, by a passive process in which those individuals who survive and reproduce will pass down to their offspring the traits which helped them to do so, whilst individuals with traits that did not help them to survive and reproduce would die out without passing them down. Charles Darwin described Natural Selection in On The Origin Of Species By Natural Selection:

“The preservation of favourable variations and the rejection of injurious variations, I call natural selection.”

Mendelian Genetics is the study of heredity and variation of traits, and was first observed and described by Gregor Mendel. Traits are inherited as discrete units rather than in a continuous form, and we now call these inherited units Genes. Genes are segments of DNA, and are the instructions that build and regulate our bodies, as well as those of every other living organism on Earth.

Thus, the Modern Evolutionary Synthesis states that Evolution occurs by Natural Selection acting on variations produced by Genes, and forms the basis for the study of Evolutionary Biology. In future blogs, I will discuss some of the evidence itself for Evolution and it’s mechanisms. I will also discuss evidence which discredits the arguments made by Intelligent Design and Creationism advocates, who refuse to accept the fact of Evolution, based on misunderstood and misconceived arguments, as well as personal incredulity’s.