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Back in the early days of this blog, I wrote a piece entitled ‘You Should All Be Ashamed of Yourself’, in which I slammed the anti-vaccination movement for their promotion of pseudoscience, exposing children and other members of the public to preventable infectious disease, and generally being douchebags. Well, several years have passed since then, but the antivaxxers haven’t gone away. Their claims about the dangers of vaccines have been thoroughly discredited, but still they persist, as arrogant, ignorant, and dangerously wrong-headed as ever.

I do not pretend to be an expert in any field of science, but my final year degree research has led me to spend the past six months or so working in the field of immunology, so I feel at least able to communicate the science and the research on the benefits and risks of vaccines.

On the other side of the divide, we have discredited doctors, airhead celebrities, and naturopathic pseudoscience-peddlers, and I hope to shed some light on the antivaxxers, and hopefully have a few laughs along the way.

More soon.
Lee

The Return of Letters from an Island Mind and a Response to Creation Ministries International’s ‘15 (Not Very Good) Questions for ‘Evolutionists”

Hello!

It’s been a long while since I lasted posted here. There’s no specific reason for the long hiatus. I have been busy with my degree (Biochemistry & Genetics), but I’ve also not been particularly active in arguing against Young Earthers and other peddlers of silly religious stories and pseudoscientific ideas. Recently though, I’ve found myself drawn increasingly back into the fight, and remembered just how much I used to enjoy the argument.

So, by way of getting back into the swing of things, I thought I’d take a shot at Creation Ministries International’s ‘15 Questions for Evolutionists’. I’m by no means the first ‘evolutionist’ to respond to this, but I intend to demonstrate to you, the reader, that CMI’s questions are based on dishonest and unrepresentative straw-men and arguments from ignorance and personal incredulity. Here’s a link to the article on CMI’s website, so you can judge for yourself what kind of opposition we’re up against. 

http://creation.com/15-questions

Okey dokey, let’s crack on, and respond to each of these questions in order…

1. How did life originate? 

Oh dear, we’re off to a good start aren’t we? This is a straw-man. The theory of evolution can be broadly defined as the scientific model which seeks to explain the diversity of life on Earth. It does not deal with the origin of the first life-forms, nor does the origin of life really have any major bearing upon the evolutionary processes which shaped the diversification of that first organism into the myriad forms we see today.


There is a field of scientific study which seeks to explain the origin of the first organisms, but this falls into the theory of abiogenesis rather than evolution. This is a large area of interest, and many working within the field of biochemistry are seeking satisfactory answers for the origin of life on Earth. It has been demonstrated under both laboratory and field conditions that many if not all of the basic building blocks of life can be formed by simply by chemical processes (and even the most hard-headed of creationists probably wouldn’t argue the all chemistry is magical). Amino acids, nucleotides, carbohydrates, and fatty acids have all been shown to be produced from inorganic precursors, in experiments which mirror conditions similar to those thought to have existed on the prebiotic Earth. I may return to blog on this topic at a later date, but it’s scarcely relevant here, as even if one wishes to attribute the existence of the first organism to a divine intervention, that does NOTHING to challenge the validity of the concept of speciation proceeding through evolutionary processes.

2. How did the DNA code originate?

Once again, this question speaks more to abiogenesis than evolution, and so is again kind of dishonest, but I am nothing if not stubborn in my refusal to be outfoxed by a creationist. 

The ‘genetic code’ refers to the specific relationship between DNA base and protein amino acid sequences, and several slightly different versions of the code are actually observed in living and near-living organisms, indicating that there has been some variation in the process through evolution. 

DNA uses a triplet code, in which each amino acid is encoded by a sequence of three bases. Since DNA consists of four bases, this allows for 64 codon combinations to code for the 20 amino acids used in proteins. 

Wikipedia has this to say on the origin of the genetic code:
http://en.wikipedia.org/wiki/Genetic_code#Origin

The comparison of DNA to man-made coding systems is a dishonest one, as DNA has many other features that written languages do not, including self-replication. 

3. What? You said 15 questions - you’ve lumped a bunch of questions together here! Do I have to respond to all of these? I did’t sign up for this.

How could mutations create the huge volumes of information in the DNA of living things?

Ah, a reworded version of the old creationist staple ‘what process can create new genetic information?’

Genetic mutations are indeed an important part of evolutionary process, as they create the variation upon which selective processes can act (more on this later). Apart from point mutations (substitutions, additions or deletions of individual bases) which can produce new alleles of existing genes, there are actually several processes which can lead to the addition of ‘new information’ and increase the overall length of the genome. An entire gene can be duplicated, creating two copies of the same gene. As there is now an additional copy of the gene, one copy is now able to freely mutate without adversely affecting the host. The presence of ‘pseudogenes’ (gene-like sequences of DNA which have lost their function due to mutation) and the existence of families of closely-related proteins are testimony to this process. Additionally, transposons are DNA sequences which are able to integrate themselves into the DNA of another organism through a process known as ‘homologous recombination’, which can add genetic material from another species (mostly in prokaryotes such as bacteria and simple unicellular eukaryotes). Finally, polyploidy (common in plants) involves an increase in the overall number of chromosomes in an organism. In animals chromosomes are generally arranged in n pairs, giving an overall chromosome number in most cells of 2n (in humans n = 23). Germ cells (spermatozoa and ova) have one chromosome from each pair, so germ cells have a chromosome number of n, and the fusion of the two germ cells creates a zygote (fertilised cell) with 2n chromosomes. In plants, the production of diploid (2n) germ cells can occur, with the result that various combinations can produce fertilised cells with 2n, 3n, 4n and even 6n chromosomes. These polyploid forms are represented in many familiar cultivated plants. 

How could such errors create 3 billion letters of DNA information to change a microbe into a microbiologist?

While mutations are the result of errors in DNA replication, this does not imply that all mutations cause harm. In fact, many mutations at the molecular level are simply neutral. Harmful mutations (for example, missense and nonsense mutations in essential genes) will reduce the fitness of an organism, and reduce the odds of these mutations being passed on, but it is estimated that every human being has approximately 100 new mutations that were not present in either of their parents, and for the most part these mutations cause no harm. As outlined before, gene duplication coupled with mutation is able to produce novel forms of a protein. 
It is true that information for controlling the use of proteins is encoded in DNA, but this control usually occurs through the action of DNA binding proteins which inhibit or promote the transcription of the DNA sequence into mRNA (this is complex, and again deserves separate discussion) but if the implication here is that any mutation will create a non-functional gene, then this is simply false.

How can scrambling existing DNA information create a new biochemical pathway or nano-machines with many components, to make ‘goo-to-you’ evolution possible?

Oh good, the old ‘irreducible complexity’ argument.

Creationists often like to argue that the complexity of biochemical systems is evidence against evolution, and that the inability of ‘evolutionists’ to explain the evolution of every single step of every single biochemical pathway proves their position. In fact, we often find simpler versions of biochemical pathways in other organisms, but increased complexity often provides a selective advantage by allowing more precise control of metabolic pathways. No-one is suggesting that complex biochemical pathways just happened by random chance - all that is necessary is that a successive series of alterations can exist with each serving some purpose. It’s actually a version of the old Darwin quote-mine about the evolution of the eye, re-branded for the age of molecular biology.

Okay, this is getting a bit long now, so I will be back with the second part of this response on Friday.

4. Why is natural selection, a principle recognized by creationists, taught as ‘evolution’, as if it explains the origin of the diversity of life?

I can’t decide whether this is a straw man, or an argument from ignorance. Either way, it’s certainly a little dishonest. Natural selection is taught as one element of the selective processes involved in evolution (along with sexual selection and genetic drift).

No-one who understands evolution would make the argument that natural selection accounts for the development of new traits. New traits arise as a product of mutations. In each generation, we see a natural degree of genetic variation between members of a population. In some cases, this will result in the appearance of an entirely new allele (for instance, colour morphs arising within one species), but often the differences are more subtle than this. Depending on the selective pressures operating within the environment, a variation that confers even a slight advantage will result in the individuals possessing those traits potentially having greater reproductive success.

To use the example of Darwin’s finches, slight variations in beak morphology enable certain individuals to be more capable of utilising certain food sources, and therefore having a better chance of surviving to produce greater numbers of progeny. Over successive generations, those with beak morphology best suited to their niche will also have greater reproductive success, gradually shaping the beaks from the basal form to the multiple forms we see in the extant species of Galapagos finch. The variations are not in fact ‘back-and-forth’ but driven in a certain direction by the finches’ environment.

5. How did new biochemical pathways, which involve multiple enzymes working together in sequence, originate?

This is a re-tread of the earlier question about ‘irreducibly complex’ systems. Looking at other species, we do see simpler forms of similar biochemical pathways that make use a smaller number of enzymes. A mutation in enzyme that catalyses one reaction, may enable it to perform a similar function in another substrate, as enzymes merely increase the thermodynamic favourability of reactions by stabilising their intermediates, or coupling an unfavourable process to one which produces an excess of free energy. Richard Lenski’s work with Escherischia coli observed the evolution of the ability to use citric acid as an energy source arising independently in three of the twelve initial populations.

http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment

Arguments to irreducible complexity do not take into account the exaptation of reactions that initially operated in a simpler pathway to use in stages of other, novel biochemical processes.

The evolution of many pathways is still not full understood, but to suggest that no work has been done in this field is simply laughable. 

6. Living things look like they were designed, so how do evolutionists know that they were not designed?

Living things may possess the superficial appearance of design (although this attribution of complex biological system to design may say more about human psychology than it does about anything else) but we often find such staggering examples of what, if these systems were truly designed, would be considered examples of shoddy workmanship. An example is (no joke intended) camel’s toes. Camels are artiodactyls (even-toed ungulates) belonging to the family Camelidae, which also includes the South American camelids (the llama, alpaca, guanaco, and vicuna). All other ungulates are notable for walking on the tips of their phalanges, which have thickened into hooves. This mode of locomotion is highly effective on firm surfaces such as the pampas of South America, but on the loose desert sands of the Sahara and Arabian and Gobi deserts, hooves are a hindrance. Since the ancestors of camels were hooved, evolution is unable to simply ‘throw away’ the hoof and replace it with a foot more suited to walking on sand, such as a wide, flat paw. Instead, a large fleshy pad has formed around the hoof, acting as a sort of ‘sand-shoe’. The appearance of design in living things can be readily attributed to natural selective processes acting within their environment.

Why should science be restricted to naturalistic causes rather than logical causes?

Science, by definition seeks empirical evidence for its hypotheses. It looks for naturalistic causes rather than supernatural ones. Since no suspension of the laws of nature has ever been observed, any explanation invoking the supernatural would be vastly more unlikely than a naturalistic one. Extraordinary claims require extraordinary evidence. To quote David Hume ‘“No testimony is sufficient to establish a miracle, unless the testimony be of such a kind, that its falsehood would be more miraculous than the fact which it endeavors to establish”

7. How did multi-cellular life originate?

To answer this question, it is possible to look at multi-cellular organisms today. Not all multi-cellular life-forms are as complex as say, a tetrapod or athropod. Sponges are nothing more than a collection of essentially undifferentiated cells held together by a secreted collagen matrix. If such a congregation of cells produced a selective advantage in a certain environment, then it makes sense that multi-cellular organisms could become established, and over time the complexity of such cell colonies could increase. There are many examples of multi-cellular organisms that are in fact colonies of discrete single-celled ones. 

8. How did sex originate?

The origin of sexual reproduction is a fascinating development in the evolutionary history of life (possible future blog). Here the assertion is made that asexual reproduction provides twice as much ‘reproductive success’ for the same investment of resources, and equates this with evolutionary fitness.

This may seem a little difficult to understand at first, so let’s examine precisely what this means. For an asexually reproducing organism such as a bacterium or archaeon, the primary reproductive process is binary fission. The cell replicates its DNA, and then splits in half to produce a pair of near genetically identical daughter cells. So for each parent cell, two offspring are produced, and where the availability of resources is not a limiting factor, the population size can double with each generation. Using the example of a single-celled, sexually reproducing protist, sexual reproduction will involve two cells each undergoing a meiotic division to produce haploid gametes, which then fuse to produce two diploid daughter cells. Therefore, two parent cells produce two daughter cells. In the case of protists, population growth occurs because the adult cells are able to undergo binary fission. So, we have double the number of daughter cells for each parent cell. However, this is to ignore two major advantages conferred by sexual reproduction.

Due to the meiotic production of haploid gametes, sexual reproduction promotes genetic variation. This is in sharp contrast to asexual reproduction, in which the population of offspring is near identical to the parents. Population with low genetic diversity are certainly more vulnerable to certain catastrophic events. Therefore natural selection can strongly act in the favour of organisms that are able to produce a greater degree of variation within their offspring. Competition between individuals may favour certain genotypes over others, so the ability of parents to create a range of genotypes within their offspring is clearly a desirable state.

http://en.wikipedia.org/wiki/Evolution_of_sexual_reproduction#Promotion_of_genetic_variation

Sexual reproduction also assists in the production of novel and advantageous combinations of genes. Let’s imagine that a set of new metabolic traits arise in a population of bacteria. Let us use the example of amino acid synthesis. Certain strains of E. coli are auxotrophic for certain amino acids, meaning that they are unable to synthesise those amino acids, and are only able to grow on culture media containing these. For example, our parent strain may be auxotrophic for tryptophan, phenylalanine, and leucine. These bacteria will be able to grow well only on media containing tryptophan, phenylalanine and leucine. If mutations arise which fix these broken pathways occur in certain individuals within the population, then those individuals may be able to grow on media containing only two of three and will pass this ability onto their progeny. However, the chance of all three, or even two of these mutations occurring in the same cells will be reduced. However, if sexual reproduction were to occur, the advantageous genes could rapidly be transmitted through the population. This example is somewhat simplistic, but demonstrates how sexual reproduction allows novel positive genotypes to become ‘grouped together’ in individuals.

 So, all that is necessary for sexual reproduction, is the existence of distinct parental germ cells that undergo fusion to form a fertilised cell which is genetically distinct from, but shares genetic material with, both parents. 

As for the other question, the origin of gender, well this begins with the origin of anisogamy. Anisogamy is the existence of distinct ‘male’ and ‘female’ germ cells. As an example, in many animals, the male gametes (spermatozoa) are small and highly motile, whereas female gametes (ova) are large and non-motile. Anisogamy is not a requirement of sexual reproduction, but it has become fairly well established. Sperm competition is one possible explanation for this phenomenon. Sperm competition states that in polygamous species, competition arises between the sperm of two or more males. This may have driven sperm to become smaller and develop motility, as males which produced smaller and faster spermatozoa would have a selective advantage over those without. The production of numerous sperm also creates and advantage, and the smaller the sperm, the more that can be produced for the same investment of resources. 

As for distinct biological gender in the sense of ‘complementary genitalia’ these are not universal. For instance, fish and many invertebrates lack external genitalia. Females lay eggs, males produce sperm, and the gametes fuse outside of the body. The evolution of genitalia is not evidence of intent, but rather of a LONG period of co-evolution.

9. Why are the (expected) countless millions of transitional fossils missing?

Simple. They aren’t. It is indeed true that Darwin acknowledged the lack of fossil evidence for biological evolution but he also rightly surmised that this was likely due to the rarity of fossilisation, and the relative infancy of paleontology at the time. In any case, Darwin was a long time ago, and many more fossils have been discovered since this time. The problem mainly lies in creationist ignorance or dishonesty about what constitues a transitional or ancestral form (a subtle, but important distinction), and what we should expect to see. Risible creationist double-act Ray Comfort and Kirk Cameron propose the absurd ‘crocoduck’ as a ‘missing’ transitional form, but the existence of such a creature is simply not a prediction of the theory of evolution. This is where the study of cladistics becomes invaluable to evolutionary biology. 

Cladistics is the modern approach to the classification of living organisms, and relies upon the ability of scientists in a variety of fields to place organisms into groups known as ‘clades’. Simply put, a clade is a group which consists of all the species which are derived from a common ancestor. Clades can be the set of subspecies within a single species, or the set of species within a genus, or the set of genera within a family, or any gradation above or inbetween. 

I have previously written a series of blogs on transitional fossils, and these can be found in my archive, but let’s look at the crocoduck as an example and see why this is so fucktarded.

Crocodilians and anatids (ducks, geese, and swans) are both modern extant clades, and while it is true that they share a relatively recent common ancestor, no-one with an understanding of cladistics would ever suggest that we should find a species that is halfway between a crocodile and a duck, because crocodiles did not evolve from ducks, nor ducks from crocodiles. You share a common ancestor with your second cousin (a great-grandparent) but you wouldn’t expect to find a ‘transitional’ relative between you and them who looks like a chimeric blending of you. Rather, if you were to look at the two lines which lead back to the common ancestor, you would see them becoming more and more similar. So, let us apply the same logic to the crocodile (I will choose the Nile crocodile (Crocodylus niloticus) and the mallard (Anas platyrhynchos) and trace these back through the nesting of clades to find the common group that they both belong to:


Crocodylus niloticus > Crocodylus > Crocodylinae > Crocodylidae > Crocodylia > Crocodylomorpha > Loricata > Pseudosuchia > Archosauria

Anas platyrhynchos > Anas > Anatidae > Anatoidea > Anseres > Anseriformes > Aves > Avialae > Paraves > Maniraptora > Theropoda > Saurischia > Dinosauria > Dinosauriformes > Dinosauromorpha > Avemetatarsalia > Archosauria

So, as we can see, although the ancestry between crocodiles and ducks is fairly recent in terms of the total age of life on Earth, you have to go some way up in the hierarchy of relatedness before you find a clade to which both crocodiles and ducks belong. This clade is the archosaurs, which includes crocodilians, dinosaurs, pterosaurs, and modern birds. The last common ancestor of crocodiles and ducks would therefore be a species that represents the branching point between the clades Pseudosuchia, and Avemetatarsalia. Although it is never possible to say with absolute certainty whether an individual species is that exact species, the known species that best fits the bill is the basal archosaur, Euparkeria

http://upload.wikimedia.org/wikipedia/commons/thumb/2/22/Euparkeria_BW.jpg/220px-Euparkeria_BW.jpg


Doesn’t really look like a crocoduck, does it? What it does look like is what evolution predicts it would look like - an animal that shares features of both Pseudosuchia and Avemetatarsalia, or in more colloquial terms crocodiles, and dinosaurs. But, you can hear them cry, that looks NOTHING like a duck! Well no. It wouldn’t. Birds are generally classified as maniraptoran dinosaurs using the current classification, but they are a highly-derived form. However, there are clear transitionals (one cannot say whether or not they are truly direct ancestors) around the branching point of modern birds, and feathered dinosaurs, of which the most well known is Archaeopteryx but also remarkable examples like Anchiornis

http://en.wikipedia.org/wiki/File:Anchiornis_martyniuk.png

10. How do ‘living fossils’ remain unchanged over supposed hundreds of millions of years?

What’s being implied here is the idea that evolution says that species must be continuously undergoing large-scale macroscopic change. This is simply untrue. A species may undergo rapid phenotypic change or remain relatively stable for long periods of time. It’s largely a question of the selective pressures acting upon the lineage. Additionally, an organism’s outward appearance may remain relatively stable, but this may belie a much greater degree of underlying genetic change. There’s simply no way of knowing.

In any case, there are actually relatively few species that have remained unchanged for tens or even hundreds of millions of years. The coelocanth, Latimeria spp is often cited as an example, as coelocanths were thought to have been extinct for millions of years before the two extant species were rediscovered in the Indian Ocean. However, although the modern coelocanths have been placed in the same order as the prehistoric species, they are actually noticeably different animals. Coelocanths are interesting in that they are somewhat similar to the ancient lobe-finned fish which gave rise to tetrapods, but to call them living fossils may be misleading. Similarly, the tadpole shrimps, Triops and Lepidurus (primitive crustaceans which have achieved some popularity as unusual pets due to their unusual, and rather cute, appearance) are superficially similar to fossil species, but genetic analysis of these genera actually demonstrates a much greater deal of diversification than was initially suspected. Africa Gomez, who lead the study of tadpole shrimps argued against the use of the term ‘living fossils’ in scientific discussion, arguing that it was misleading. In actual fact, a living fossil is simply an organism that retains many of the ancestral characteristics of its lineage. 

http://en.wikipedia.org/wiki/Living_fossil

11. How did blind chemistry create mind/ intelligence, meaning, altruism and morality? If everything evolved, and we invented God, as per evolutionary teaching, what purpose or meaning is there to human life?

Woah, okay. This is another two for the price of one question. First of, we’re looking at evolutionary psychology and the origin of mind, then veering off sharply into philosophy.

The real answer is, we don’t understand the mind very well. Cognitive science is a relatively young field. Does that mean we need to invoke god? Can mind/intelligence not emerge from the  complex electrochemical reactions that occur in our brains? As for altruism and morality, it’s my belief that these things have arisen due to our evolution as social primates. We see evidence of these behaviours in other social species. Morality, which seems to be a fairly innate thing in most individuals, can actually be seen as a product of a relatively small number of concepts, such as empathy and justice, and there are compelling cases to be made for these having been traits selected for by evolution. 

As for ‘purpose’ and ‘meaning’? Do you really need god to give your life that? That’s kind of sad. Do I believe my life has purpose or meaning on the scale of the entire cosmos? I’m not so vain. Do I believe my life has purpose or meaning as judged by the world I live in and to the people whose lives my actions affect? Of course. If this is all there is (and you needn’t believe that to accept evolution) than what we do here is ALL that matters. Don’t get so hung up on the next life that you forget that you have one already.

Also, that second bit is nothing to do with evolution. AGAIN.

12. Why is evolutionary ‘just-so’ story-telling tolerated?

Okay, now you’re just being childish, CMI. We can never really know precisely what happened at every step of our evolution, and what precise selective pressures shaped us or other species from the origin of the first self-replicating system to now, but the natural sciences don’t deal in firm proof. The sciences use inductive reasoning to infer possible explanations based on observations, and use predictions based upon those explanations to validate them. Scientific explanations, unlike those of religion, are flexible, and we modify them based on what we observe. Like your mum. Sorry. That was childish.

13. Where are the scientific breakthroughs due to evolution? 

This is a rhetorical question, right? As biologist and devout Orthodox Christian, Theodosius Dobzhansky once observed, “nothing in biology makes sense except in the light of evolution.”
It is the grand unifying theory that underpins the biological science. To argue that a theory that has so enhanced our understanding ‘hinders scientific discovery’ is dishonest. Dick move, CMI, dick move.

http://www.rationalskepticism.org/evolution/advances-to-society-because-of-the-theory-of-evolution-t21306.html

T
he OP in this thread lists a few for starters, but as I said, underpinning principle of the biological sciences. Almost every published scientist working in the biological sciences is what CMI would ludicrously call an ‘evolutionist’ and if you think that no breakthroughs are being made in some of the fastest moving fields in science then you’re being wilfully ignorant. I’m starting to really despise you, CMI…

 

14. Science involves experimenting to figure out how things work; how they operate. Why is evolution, a theory about history, taught as if it is the same as this operational science?

Because, again, you don’t know how science works. Much of our understanding of the natural sciences is based on observation and the application of inductive reasoning and inference to develop explanation which have predictive power. If we are able to generate hypotheses whose predictions closely reflect reality, we can be fairly sure that our explanation is a good one. It’s odd that you should pick on biosciences, as the earth sciences and astronomy operate in a similar way, but then you Young Eathers have a problem with those too don’t you?

As for experimental evolution, there is actually a lot of work. Richard Lenski’s E. coli experiment, as well as all the selective breeding that’s ever been done, provide experimental evidence of evolutionary theory. Seriously. Look Lenski up. That shit is fascinating.

15. Why is a fundamentally religious idea, a dogmatic belief system that fails to explain the evidence, taught in scienceclasses? Karl Popper, famous philosopher of science, said “Darwinism is not a testable scientific theory, but a metaphysical [religious] research programme ….” Michael Ruse, evolutionist science philosopher admitted, “Evolution is a religion. This was true of evolution in the beginning, and it is true of evolution still today.” If “you can’t teach religion in science classes”, why is evolution taught?

Unlike CMI, which seems intent on quote-mining Karl Popper (after all, he’s been dead for 20 years, so he can’t sue you), I’m going to present what Karl Popper actually said, so you can judge for yourself

http://en.wikipedia.org/wiki/Karl_Popper#Origin_and_evolution_of_life

As for Michael Ruse, well lo and behold, another quote-mine! Jesus doesn’t like liars, CMI.

Here’s what Michael Ruse actually has to say. I’m not sure I fully agree with his personal philosophy, but that’s okay. We don’t all have to see things in exactly the same way. The point is, Michael Ruse never called evolution a religion in the sense that it’s distinct from science.

Fuck you very much, CMI.

 

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