Answering Creationist Claims – Morality in Evolution

A common claim of creationists would be that evolution promotes immorality. Such claims can arise from nothing less than ignorance, and here I shall explain why evolution does promote morality and altruism, instead of challenging it.

Scientific Theories are Descriptive

Science is a method to understand the world around us, and it does so through the scientific method, which is tried-and-true. Now, as science observes and make conclusions, that means it is descriptive – it simply tries to give us a better understanding of the world. To blame immorality on scientific theories is simply absurd, as science is not an instruction manual - it is up to us to determine what actions should we take.

This is very unlike religion, which explicitly and repeatedly requests that we follow its teachings, making it instructive. Moreover, it does so through blind faith, not through reason and evidence.

Social Darwinism – Natural Selection Misunderstood

Creationists also frequently claim that the teachings of natural selection leads to Social Darwinism, which is political ideology in which only the “fittest” survive, and the weak are left to die, and Adolf Hitler implemented this system. His rationale was that based on the misunderstanding that natural selection meant “survival of the fittest”, and the Catholics are superior to Jews, thus Jews must be exterminated. Creationists frequently refer to his actions as evidence that evolution leads to immorality.

Yet, this is not the case. Natural selection doesn’t necessarily means that a particular individual must kill as many other organisms as possible; nor does it mean that an individual must be vastly superior to other individuals to survive. It simply means that the phenotypes that are better adapted to the habitat would have a greater chance of reproducing and passing on their genes (or more specifically, alleles). The phenotypes do not need to be competing with each other to survive – they can be helping each other directly or indirectly, increasing both individual’s fitness. Such interaction between 2 different species is known as mutualism (between sea anemone and hermit crabs, bees and flowers, ungulates and digestive bacteria etc); within the same species, it is known as co-operation (ants, bees, and of course, Homo sapiens).

Altruism – An Evolutionary Explanation

We have already mentioned that natural selection doesn’t need to be competitive, but also collaborative. However, how does evolution explain the appearance of morality and altruism? There’re many possible mechanisms suggested, some of them may be right, some of them may be wrong – it is even possible that all are true. Let’s take a look at the proposed mechanisms. But before that, let me note that the problem of morality is much greater for creationism than evolution. After all, as stated in Plato’s Euthyphro:

Is the pious loved by the gods because it is pious, or is it pious because it is loved by the gods? – the Euthyphro dilemma

or in modern-day words:

Is what is moral commanded by God because it is moral, or is it moral because it is commanded by God?

Answer that, theists.

Kin Selection

Kin selection refers to the theory that organisms may display caring towards their relatives, thus increasing their relatives reproductive fitness but at a cost of their own fitness. If viewed from a purely competitive and individualistic perspective, natural selection would’ve got rid of individuals that exhibit such behaviour, and thus genes that promote such behaviour would rarely (if ever) reach fixation. However, such behaviour is found in many organisms, the most famous example be the infertile worker ants and bees, who are unable to reproduce and yet decide the fate of the entire hive.

Hamilton's Rule

Altruism with have superior to a particular genes survival when Hamilton’s rule as put forward by W.D. Hamilton is met:

rB > C

where r = coefficient of relatedness between the individuals, B = the benefits in fitness received by the recipient, and C = the cost in fitness imposed on the actor.

The value of r can be calculated pretty easily. In a diploid organism, an offspring gets exactly half of its genes from one its parents. Thus their relatedness is 0.5. For the cousin and grand offspring, they get 1/4 of their genes from one their last common parent, and thus their relatedness with that parent is 0.25. Based on this equation, we know that r=n⁵.

Hamilton proposed 2 ways in which altruism would be favoured. The first is when kin recognition is high enough, which means that an organism favours those that are more genetically similar to it. However, as organisms are most certainly unable to measure the genetic relatedness of a relative, kin recognition only occurs if the particular genes can have externally visible phenotypical effects. This is known as the “Green-beard effect”, and it serves as a valid explanation for the evolution of morality.

Kin selection can also happen even if kin recognition is not present in viscous populations – a population in which the movement of organisms from their birthplace is relatively slow. In viscous populations, individuals will frequently breed with close genealogical relatives, and thus Hamilton’s rule can be met. This doesn’t explain altruism, though.

Reciprocity

Reciprocal altruism refers to the behaviour that an individual would help another individual in the hope of mutual interaction with the recipient in the future. In social terms, it’s: “I helped you, and thus I expect you to help me back.”. This is a very possible explanation for the evolution of morality (and revenge), as this behaviour is see in cleaner fish, vampire bats (possibly), chimps, orang-utans, and of course, human society. It’s also used to explain why humans help strangers, which are hard to explain using kin selection.

Direct Reciprocity

Robert Trivers presented direct reciprocity as a model for the evolution of cooperation. This form of reciprocity requires that the 2 individuals meet again, recognize each other, and remember their last encounter to predict what would happen in the future. Direct reciprocity is highly similar to the Prisoner’s Dilemma (PD). In this dilemma, there are 2 individuals. If both cooperate (C), both will gain rewards (R); while if both defect (D), both will get penalties (P). However, if one individual cooperates while the other defects, the co-operator will be penalized, while the defector will be rewarded handsomely.

Direct reciprocity can only promote altruism if:

w > c / b

where w = the probability of another encounter between the same two individuals, c = cost, b  = benefit. Thus, it is required that the probability of another encounter between the same two individuals exceeds the cost-to-benefit ratio of the act.

Indirect Reciprocity

Indirect reciprocity doesn’t require repeated encounter between the same individuals. In indirect reciprocity, one individual is the donor while the other is the recipient. The donor can decide whether to cooperate and help the recipient.

Indirect reciprocity has 2 models:

The "Upstream" Model

The “upstream” model states that when the donor helps the recipient, the recipient will be motivated to help another individual, perhaps because he/she got a positive feeling about it. This may create a domino effect which spreads through the community. While this model is harder to understand in detail, it has been observed in economic experiments.

The "Downstream" Model

This model is based on reputation. If an the donor helps the recipient (and someone knows of it), his/her reputation will be enhanced. Such a system is all too common within human society, and studies have shown that an individual of good reputation is more likely to be helped by others in the animal kingdom as well.

Indirect reciprocity can only promote altruism if:

q > c / b

where q = probability of knowing someone’s reputation, c = cost, b = benefit. In other words, it only works when the probability of knowing someone’s reputation exceeds the cost-to-benefit ration exceeds those of the altruistic act.

Diagram (a) shows direct reciprocity, in which A helps B, and B helps A, or they may defect. Diagram (b) shows the “upstream” model, which is based on motivation; and the "downstream" model, which focuses on reputation.

Sexual Selection

In many animal societies, the female are responsible for taking care of their children. This is very detrimental to the survival of the mother – it requires time, energy, and resources. Now, if both parents are responsible for caring the children, the load would be ultimately be decreased for the mother. However, that doesn’t work if the father (biological or not) doesn’t even think of the children, much less care for them. Thus, it is proposed that females may have preferred loyal, caring partners over individualistic partners, and thus the “moral” gene is the one had a great probability of being inherited.

Conclusion

In this post, I not only debunked the creationist’s claim that evolution leads to immorality, but also gave an explanation on how evolution is perfectly able to explain altruism as well. I’ll wait for creationists to refute what I just said.

As a side note, though, all the explanations above have one thing in common: they all imply that altruism succeeds because of selfishness. Kin selection is not “true” morality, one only helps those that are closely related genetically, and that doesn’t fit with how our society thinks morality should be.

As for reciprocity, it happens because the individual expects something in return. In direct reciprocity and perhaps the “upstream” model of indirect reciprocity, you help someone because you want to get help from them in the future. Hell, they’ve got this Chinese saying that “Good deeds shall be rewarded in return”, and I simply hate it when charities used this saying to urge us to donate – that’s actually an act of selfishness.

In the “downstream” model of direct reciprocity, you help someone, and you get reputation for it. Who doesn’t want it? Some may protest that this is caused by the willingness of the spectator – the donor didn’t explicitly want better reputation. I doubt that. I’ve seen a lot of cases (including mine) when an individual helps someone because he thinks that’s politically correct, because people may look down upon him if he/she doesn’t lend a helping hand, because by doing he feels “good” etc. Self-centeredness under the guise of helpful acts, that’s what we all (or at least me) see in most cases.

However, despite my cynical view of morality, I don’t think that it should be removed from society or ignored altogether. At least, it still maintains harmony and peace much better than a purely competitive mindset.

Answering Creationist Claims (Part 9a – Deny The Age of the Earth and You Deny Science Itself)

The sudden expansion of space-time from a singularity of infinite mass + temperature around 13.73 billion years ago marked the beginning of the universe. Soon, it would cool down, and allow the formation of galaxies. Around 4.56 billion years ago, a part of a massive molecular cloud, giving to the Sun and planets of the Solar System, including Earth itself. Then, a Mars-sized planet called Theia smashed into the Earth, and the part of the enormous amount of debris collapsed and formed the Moon. Finally, around 4 billion years ago, the first life appeared on Earth, most likely through abiogenesis, and life have evolved and came into their present form now.

No, I take that back. In order to foster “religious tolerance”, I propose the theory that a sky daddy created us around 6000 years ago (or any other time), and that he done in about 6 days (or ages). Alright, that was complete sarcasm, but when people believe in such bullshit instead of science, we have a thing to worry about. Creationists keep on spending their time convincing children and the uninformed that the {add any religion here} view is literally true to undermine science education, and so is Bible Life Ministries. Proving them wrong is absolutely necessary.

Radiometric Dating

The most famous dating method is obviously radiometric dating, and since it shows that the Earth is billions of years old, it has been the target of creationist attacks. However, radiometric dating is one of the most established dating methods ever. Let me explain how it works.

Radioactive Decay

As we all know, all atoms consist of protons and neutrons as the nucleus, with electrons in orbit around the nucleus. Quite some elements has their own isotopes, which means same atomic number, different neutron count. A nuclide is an atom characterized by its atomic and neutron number. The difference is that an isotope is a member of an element of same atomic number with differing neutron count; while a nuclide refers to only one type of atom (not a member of any element group). It’s just a difference in semantics, anyway.

There are many types of decay, including alpha decay, which ejects an alpha particle (2 protons and 2 neutrons bound together) from the nucleus; Beta-Negative (β⁻) decay, in which the weak nuclear force causes a neutron to be converted into a proton, and ejects an electron and an antineutrino; gamma decay, which happens when the nucleus is still left in an excited state after alpha/beta particles have been emitted, and by emitting a gamma ray, it can turn back to its ground state.

Alpha Decay - Nucleus Emits Alpha Particle

Beta Negative Decay - One neutron turns into a proton, while a electron(e⁻) and antineutrino(ν_e) is ejected.

Gamma Decay

Cause

Some nuclides are unstable. That is, they decay spontaneously into a different atom over time. We call that atom a daughter nuclide. How does this happen? Well, at subatomic levels, the interactions between matter are governed by the strong nuclear force, which is the most powerful force over subatomic distances; electrostatic force, which plays a big role as well; and in the case of beta decay, the weak nuclear force is involved.

These forces create many interactions which can alter the state of particles, and cause them to release energy. While excited particles can maintain their form when undisturbed, this is never the case. As the Second Law of Thermodynamics states, overall entropy is always increasing, and thus when certain excited particles are disturbed (by quantum vacuum fluctuations), their arrangement are changed, and they release energy and become a less-excited particle (aka their ground state).

The Half-life

Radioactive decay is a stochastic process, as it is virtually impossible to predict when a particular nuclide will decay. Nevertheless, we are able to predict general trends when a certain number of the same nuclide are present. We call this trend as the half-life, which is the time taken for half of the nuclides in a group of atoms to decay.

Let’s take a piece of wood as an example. To date the wood, we use Carbon-14, which decays into Nitrogen-14. Carbon-14 has a half-life of 5730 years, which means that within 5730 years, about half of the Carbon-14 nuclides would’ve decayed into Nitrogen-14. So that’s 1:1 ratio of nuclides. In another 5730 years, half of the remaining 50% Carbon-14 nuclides will decay again, leaving 25% of the atoms in the wood as Carbon-14, and 75% as Nitrogen-14. And so on, until we reach a point when there is virtually no Carbon-14 left, and we are unable to determine its age any further. For Carbon-14, that’s about 60,000 years.

There many other nuclides that can be used, such as Potassium-40, which decays into Argon-40, and has a half-life of 1.3 billion years. Because of this, we are able to use it determine the age of the oldest rocks. Then we have the Uranium-Lead dating method, which one of the most refined dating methods ever, with an error margin of 2-5%. As the time taken for Uranium-235 to decay into Lead-207 is 700 million years, while Uranium-238’s decay into Lead-206 is 4.3 billion years, we can collaborate the data taken from both sources, and thus get an very accurate example.

Preconditions

Radiometric dating requires that no nuclide may enter or leave the object for its whole lifetime. As it is possible that a particular object may be contaminated, it is absolutely necessary that checks be made to ensure that it is not altered.

For radiometric dating to be accurate, the object being dated should have enough numbers of parent nuclides. There must be a measurable ratio between parent and daughter nuclides. This is highly dependent on the half-life of the nuclide being measured. For example, Carbon-14 is useless beyond 60,000 years, as there would be to little Carbon-14 left to make accurate measurements. Potassium-40, on the other hand, will still be accurate even after billions of years.

Closure temperature

The closure temperature of a system is the temperature in which the system have cooled down enough to form a state where exchange of nuclides with the environment is impossible. Radiometric dating can only be used to start dating from the point the system reaches its closure temperature, as contamination would be highly unlikely after that. The closure temperature varies from mineral to mineral. In the case of of Carbon-14 though, renewal of the nuclide stops when the organism dies, instead of when reaching a closure temperature.

How Reliable is Radiometric Dating?

Couple of experiments have shown that radioactive decay is virtually unaffected by environmental factors: chemical reactions, heat, pressure, electromagnetic & gravitational fields, etc. These experiments include those done in the lab, studies of the Oklo natural nuclear reactor, and astrophysical observations of the luminosity decays of distant supernovae (which occurred long ago as the light has taken a great deal of time to reach us). All of them strongly point to the fact that decay rates have been constant throughout history (ignoring human errors and variation, that is).

But what about the so-called errors in of radiometric dating as claimed by creationists? Most of their claims are usually about instances when radiometric dating gave unexpected results, and they hail it as proof that it is not valid. Yet the problem is that even if radiometric dating fails in one instance because of some problem, it doesn’t invalidate radiometric as a whole. In fact, multiple radiometric dating methods and even non-radiometric dating methods can be used in conjunction to get the best answer, and so far, it works virtually every single time.

The last creationist method would be contamination. Yes, it is admitted that Carbon-14 is susceptible to contamination, and thus shouldn’t be treated too confidently. However, most other nuclides can be checked for contamination and they are extremely accurate. So far, contamination or not, all of the results points to a billion years old Earth. There literally 0 cases in which a different result was obtained. Don’t ignore that, creationists.

Conclusion

In my post, I have explained that the age of the Earth is an established fact, and is confirmed through radiometric dating, which is the best dating method ever. All of them point to a 4.54 billion year old Earth, and none contradicts that. However, we have yet to see a scientific paper that shows that the Earth is only 6000 or millions of years old. Let’s wait.

Previous: Answering Creationist Claims (Part 8 - The Fluid Nature of Chromosomal Count)

Next: Answering Creationist Claims (Part 9b - Evidence for a 4.54 billion year old Earth through Radiometric Dating)

Answering Creationist Claims (Part 8 - The Fluid Nature of Chromosomal Count)

Our genes lie within our chromosomes , which plays an extremely important part in heredity. A common creationist claim would be the “fixity of species”, and from this comes Bible Life Ministries’ and the Creation-Evolution Encyclopaedia's claim that the chromosomes counts are fixed (or if it changes, it’s deleterious). Such a claim can only come from ignorance on the topic of genetics, and it shall be my topic today.

What’s a Chromosome? (Brief)

A chromosome is a structure in our cells that is made up of DNA and proteins. It contains almost all of our genetic information, and comes with gene regulation proteins. Depending on the species, the chromosome can contain from 10,000 to 10,000,000 base pairs.

Chromosomes of Eukaryotes

Eukaryotes are organisms which cells contain nuclei (plants, animals, etc.). The nucleus of the eukaryotic cells houses the chromosomes, which are linear and rod shaped. Near the centre of the chromosome is the centromere, which is the point where 2 homologous chromatids and microtubules fuse. At the the tips of the chromosome are the telomeres, which contain repetitive DNA (with 2 chromatids present, that makes it 4 telomeres). It is shown that these repetitive DNA are responsible for maintaining the integrity of our genes, as they protect our genes by “capping” them. Eukaryotic chromosomes replicate through cell division, either by mitosis; and meiosis (in which the chromosomal count of the cell is halved), which is responsible for producing gametes.

(1) Chromatid. One of the two identical parts of the chromosome after S phase. (2) Centromere. (3) Short arm (4) Long arm.

Chromosomes of Prokaryotes

Prokaryotes (bacteria & archaea) chromosomes are single and circular, and vary greatly in size, from 160,000 to 12,200,000 base pairs in the bacterium Candidatus Carsonella ruddii and Sorangium cellulosum, respectively. Prokaryotic chromosomes are less sequential than those of eukaryotes, and replicate from a (or multiple) point(s) of origin. As they do not have a nucleus, prokaryotic chromosomes are organised into a structure known as the nucleoid instead.

Best Case of Chromosome Number Change – Chromosome 2

Most members of the family Hominidae have 48 chromosomes. Humans have 46. Huh? How could this be? After all, if evolution was true, we should have same chromosome counts, right? Well, at least that’s what claimed by creationists. To find the answer to this, let’s take a look at Chromosome 2 of humans.

Chromosome 2: Strong Evidence for Common Ancestry of Humans and Modern Apes

What’s so special about Chromosome 2? Because it’s damn similar (near-identical) to Chromsome 2a and 2b of chimps combined. Moreover, it’s a telomere-telomere fusion at region 2q13. And we have scientific evidence for that.

Firstly, there is is a inverted head-head arrangment of the TTAGGG array and the adjacent sequences at the predicted fusion site, which are surprisingly similar to the telomere points found in human (and ape) chromosomes. In other words, after the repeated TTAGGG sequence, the sequence inverts, becoming CCCTAA (it’s not GGGATT as CCCTAA is the reverse sequence that TTAGG maps to {A <> T, G <> C}).

Secondly, since Chromosome 2 is said to be a fusion of Chromosome 2a and 2b, there must be 2 vestigial centromeres, right? Well, that’s exactly the case. When scanning with DNA probes, signals for the presence of a centromere was detected somewhere around q21.3-q22.1, in the long arm of Chromosome 2. The other centromere is actually used (so it's not vestigial after all), and it lines up with 2p chromosome of chimps.

These 2 chromosomes strongly point to the fact that after diverging from chimps around 6-7 million years ago, Chromosome 2a and 2b underwent a telomere-telomere fusion, and thus is evidence for evolution.

Other Cases in Which Individuals of a “Kind” Have Different Chromosome Counts

Since chromosomes counts are supposedly “fixed” and all chromosomal changes are deleterious, let’s see the diploid chromosome count of “kinds”.

Fox “Kinds”

Arctic Fox	Alopex lagopus	50
Bat-eared Fox	Otocyon megalotis	72
Bengal Fox	Vulpes bengalensis	60
Fennec Fox	Vulpes zerda	64
Gray Fox	Urocyon cinereoargenteus	66
Kit Fox	Vulpes macrotis	50
Red Fox	Vulpes vulpes	34
Tibetan fox	Vulpes ferrilata	36

Horse “Kinds”

Horse	Equus ferus caballus	64
Przewalski's Horse	Equus przewalski poliakov	66
Donkey	Equus africanus asinus	62
Moutain Zebra	Equus zebra	32
Plains Zebra	Equus quagga	44
Grévy's Zebra	Equus grevyi	46
Burchell's Zebra	Equus quagga burchellii	44

On a side note, a normal horse (64 chromosomes) can breed with a Przewalski's Horse (66 chromosomes) and produce a completely fertile hybrid offspring (65 chromosomes).

Conclusion

Thus, as it have been shown, the chromosome count is in fact variable. Not only can we see evidence for it in Chromosome 2, but even different species of the same "kind" (which means nothing in science) have different chromosome counts. Thus the creationist claim that all chromosome changes are harmful and that there is a "fixity of species" is completely wrong.

And since the most of Bible Life Ministries following claims are completely unrelated to evolution, I will only address the one that is. (Tip: something to do with the age of the Earth).

References

IJdo et al. (1991). "Origin of human chromosome 2: an ancestral telomere-telomere fusion". Proceedings of the National Academy of Sciences 88: 9051–5. doi:10.1073/pnas.88.20.9051. PMID 1924367

Previous: Answering Creationist Claims (Part 7 – The 2nd Law of Thermodynamics Truthfully Explained)

Next: Answering Creationist Claims (Part 8 – Deny The Age of the Earth and You Deny Science Itself)

Answering Creationist Claims (Part 7 – The 2nd Law of Thermodynamics Truthfully Explained)

One of the most common creationist claims is that evolution is in conflict with the 2nd Law of Thermodynamics – and yet it is one of the most thoroughly refuted claim. Yet ignorance is still widespread about this claim, and I will give a thorough explanation on this law.

Definition of Thermodynamics

Thermodynamics is study of the laws that govern:

• the conversion of energy from one form to another;
  
• the direction in which heat flows;
  
• and the availability of energy to do work.

Thermodynamics is based on the concept that there is a measurable quantity of energy in any closed system, known as the in the internal energy (U). This only takes into account the total kinetic and potential energy in the matter of the system that can be transferred as heat, and thus doesn’t involve chemical and nuclear energy.

The 2nd Law of Thermodynamics Explained

The 1st Law of Thermodynamics states that energy in an isolated system must be constant. Thus, for the the internal energy (U) of the system to change, it must be open. In a system of constant mass, the internal energy is equal to the heat present (Q) plus the amount of work done (W). Hence the equation: U = Q + W.

This is exactly the same as the principle of the conservation of energy, which states that energy can only be converted, but never created or destroyed. All natural processes strictly conform to this law, and this brings us to the 2nd Law.

While energy can transform from one form to another, in all cases, the process is irreversible to a certain extent. The direction of flow of energy and the principle of entropy is the subject of the 2nd Law of thermodynamics.

Rudolf Clausius, founder of the concept of entropy, stated that:

heat cannot be transferred from body to a second body at a higher temperature without producing some other effect

and

the entropy of a closed system increases with time

These 2 statements gave rise to the concept of temperature (T) and entropy (S). Temperature determines whether heat will flow into or out from the system; entropy is the measure of the unavailability of energy in a system to do work.

Lord Kelvin explains the Law further:

It is impossible to convert heat completely into work in a cyclic process.

What can we infer from their statements? Firstly, heat will tend towards flowing from a system of higher temperature to one of lower temperature. And when this process occurs, usable energy is irreversibly lost, and thus the overall entropy of the system increases. For the entropy of one system to decrease (aka increase of usable energy), energy must be transferred from a second system of higher temperature, and at cost of increased entropy of the second system. Based on this Law, Lord Kelvin put forward the idea of the “Heat Death of the Universe” as a possible way in which the Universe may come to an end.

In short, the definition for the 2nd Law of Thermodynamics is: the law that states the direction of heat flow and dictates that overall entropy in a closed environment increases over time.

Carnot's Heat Engine diagram (modern) - where heat flows from a high temperature T_H furnace through the fluid of the "working body" (working substance) and into the cold sink T_C, thus forcing the working substance to do mechanical work W on the surroundings, via cycles of contractions and expansions.

The Sun as the One and Only Source of Energy

Creationists claim that the Second Law of Thermodynamics is true, and thus evolution cannot occur. This claim however, is based on a misunderstanding of the Law. Let’s take a look at Bible Life Ministries version of the claim:

The second law of thermodynamics proves that organization cannot flow from chaos. Complex live organisms cannot rearrange themselves into an organism of a higher form as claimed by evolutionists. This is scientifically backwards according to the second law of thermodynamics, which has never been proven wrong. Scientists cannot have it both ways. The second law of thermodynamics is proven to be correct. Evolution lacks any scientific proof. The Theory of Evolution is contrary to proven scientific truth.

The problem with their claim is that the 2nd Law of Thermodynamics works only with in closed system, and the Earth (or more specifically, the Earth’s surface) is not isolated. Meet the Sun.

The Sun, a massive ball of hydrogen plus helium is constantly undergoing nuclear fusion, a process that gives out massive amounts of energy to the Solar System. This is can only be expected as heat always flow from a place of higher temperature to one of lower temperature, as stated in the 2nd Law. Because of this, the Earth’s entropy is maintained, and thus is able to support evolution, and life itself for that matter. Without a source of energy, both creationism and evolution is not possible, as life would never have appeared. Of course, maintaining the Earth’s entropy requires an increase in the Sun’s entropy.

Another point is that evolution would still be possible even if the entropy of the Earth’s surface is increasing (given that it is slow enough). The mechanisms of evolution is largely based on genetic mutations + natural selection. Genetic mutations will surely occur, regardless of entropy levels. An increase in usable heat/energy will not prevent mutations. Natural selection is also quite unrelated to the Laws of Thermodynamics. It is simply the process in which individuals which are better adapted to the environment and are fertile get to to pass their genes on. These processes aren’t directly related to thermodynamics (see Definition of Thermodynamics). If I am wrong on this, please tell me :-). Thanks.

Conclusion

In this post, I have given the truthful explanation of the 2nd Law of Thermodynamics. Thermodynamics is shown to be unrelated to the processes that drive evolution, but even if it did, evolution would be possible, as the Sun is still there. So no, creationists, stop using that refuted-a-thousand-times tactic.

The next post will address Bible Life Ministries claim that the chromosome count is unchangeable, and that species are “fixed”. Stay tuned.

References

(2005). Oxford Dictionary of Science Fifth Edition. Oxford University Press Inc. pp 812-813. ISBN 978-0-19-280641-3

Previous: Answering Creationist Claims (Part 6 – DNA Repair is Natural)

Next: Answering Creationist Claims (Part 8 - The Fluid Nature of Chromosomal Count)

Answering Creationist Claims (Part 6 – DNA Repair is Natural)

Bible Life Ministries, with their ignorance on the topic of genetics, now goes on to claim that DNA repair proves the existence of an intelligent designer. Let’s take a look at their claim:

The scientific fact that DNA replication, including a built-in error checking method and a DNA repair process, proves the evolutionary theory is wrong. The fact is, any attempt by the DNA to change is stopped and reversed...

…Evolutionists, even doctors of biology, believe the mutation nonsense, but they have a hissy fit at the thought that nuclear radiation could possibly cause a mutation. They start nutty, false rumours that three-eyed frogs are being found near a nuclear power plant. If the mutation theory were true they should be overjoyed at the thought that nuclear radiation could possibly create a three-eyed frog by mutation. They should go around radiating everything in sight in order to speed up the evolution of a new species. Evolutionists should irradiate themselves. Perhaps they would grow a brain by mutation.

From this claim, Bible Life Ministries has shown its blatant ignorance and their apparent liking for insults. Typical creationist mindset. Anyway, let’s see why DNA repair can be a product of evolution as well.

What is DNA repair?

DNA repair is a set of mechanisms in which our cells identify and correct damages made to our genes. Everyday, environmental factors cause great damage upon our DNA, mainly through ionised radiation (including ultraviolet rays, beta/gamma rays. There is little evidence that hand phone radiation harms us, though.), and also through normal metabolic activities. This relentless assault from so many factors creates an average of 1 million molecular lesions per day. Accumulated, these damages cause cancer, diseases and aging. Despite that, we still survive into 70s on average, and that’s to thank our body’s DNA repair mechanisms.

Breif Summary of DNA Repair Mechanisms

Direct Reversal of Base Damage

Direct reversal of lesion is obviously the simplest way to repair it, but is rarely possible, as most lesions are irreversible. However, in some cases, it works. On of these cases would be the formation of thymine dimers (a common type of cyclobutyl dimer) upon irradiation with UV light. Through the photoreactivation process, the enzyme DNA photolyase repairs the DNA lesion. Photoreactivation is present in most bacteria and also in quite a few eukaryotes, including some vertebrates, but is absent in humans and other placental mammals.

Repair of a UV-induced pyrimidine photodimer by a photoreactivating enzyme, or photolyase. The enzyme recognizes the photodimer (here, a thymine dimer) and binds to it. When light (wavelength between 300 and 500 nm) is present, the photolyase uses its energy to split the dimer into the original monomers. (After J. D. Watson, Molecular Biology of the Gene, 3d ed. Copyright © 1976 by W. A. Benjamin).

Alkylating agents are also one group of chemicals that can lead to DNA damage. These agents are quite common in the environment, are used as anticancer compounds in the clinical setting, and exist inside cells. Such agents can cause damage to the DNA backbone. These are a the proteins that is responsible for the repairing of such damages: the N-terminal domain of the E. coli Ada protein, the O⁶-alkylguanine-DNA alkyltransferase family, and the AlkB family.

Nicks can be repaired by a DNA ligase if all that has happened is that a phosphodiester bond has been broken, without damage to the 5′-phosphate and 3′-hydroxyl groups of the nucleotides either side of the nick This is often the case with nicks resulting from the effects of ionizing radiation. (DNA ligase is the same enzyme used to bond DNA strands together)

Repair of a nick by DNA ligase.

Base Excision Repair (BER)

The single base lesion is the most common form of DNA damage occurring in the human genome. A DNA base can be lost through spontaneous hydrolysis, oxidized and/or alkylated during physiologic metabolism and can be modified by exogenous DNA damaging agents.

Base excision repair is the pathway most commonly used to repair small, non-helix distorting base lesions, such as incorrect bases (like uracil) or damaged bases (like 3-methyladenine)from the genome.

Base Excision Repair in Action.

Nucleotide Excision Repair (NER)

Nucleotide excision repair is an versatile repair pathway that is capable of able to deal with more extreme forms of damage such as intra-strand crosslinks and bases that have become modified by attachment of large chemical groups. It is also able to correct cyclobutyl dimers by a dark repair process, providing those organisms that do not have the photoreactivation system (such as humans) with a means of repairing this type of damage.

Nucleotide-excision Repair in Action

Mismatch Repair (MMR)

DNA mismatch repair is a highly conserved pathway in which our cells repair base-base mismatches and insertion/deletion mispairs generated during DNA replication and recombination. Mismatch repair systems maintain the integrity of our genomes by suppressing non-homologous recombination and was recently shown to play a role in DNA damage signalling in eukaryotic cells. Defects in MMR increase the spontaneous mutation rate, and have been associated both hereditary and sporadic cancers.

The proteins unique to MMR were first identified in prokaryotes, in which the loss of such proteins resulted in increased mutations and a mutated phenotype. These proteins are known as the “Mut” proteins. Of all the “Mut” proteins, MutS, MutL, MutH are essential in detecting the mismatch and directing repair machinery to it.

Brief View of MMR Steps

The first step in the MMR system involves efficient recognition of helical distortions (mismatches) resulting from nucleotide misincorporation or DNA polymerase slippage. After that, the newly synthesized DNA strand containing the incorrect information must be selectively removed and re-synthesized. Strand discrimination is an essential feature of all MMR systems; in its absence, a replication error is just as likely to be used as a template for repair as it is to be repaired. Whereas the latter steps in MMR require proteins involved in general DNA metabolic processes, the initial mismatch recognition and removal steps require specialized Mut proteins, which are highly conserved evolutionarily.

Double-Strand Breaks (DSBs) Repairing

There are 3 methods to repair double-strand breaks. These are: homologous recombination (HR), non-homologous end joining (NHEJ), and microhomology-mediated end joining (MMEJ).

What does those chemical reactions have to do with an “Intelligent Designer?”

At first glance, such a system may look too complex too have evolved. However, there is a simpler explanation for DNA repair than to invoke a designer. Its called evolution through natural selection. As any system that has an repairing system, no matter how primitive, gives the phenotype a much greater survival advantage, and over the years, continued improvement of the DNA repairing system evolved it to the complex system it is today. The creationist seems to miss the point that the first DNA repair system need not be as effective nor as complex before.

Secondly, the DNA repair system is far from perfect. In fact, this system is unable to handle all types of molecular, and repair damages much slower than the occurring of lesions themselves. In fact, this is the cause of aging and the obvious increase in diseases as we grow older. Sometimes, the repair systems even cause greater damage than the lesions it’s supposed to repair. Surely an omniscient designer wouldn’t create such a error-prone repair system?

Conclusion

While there isn’t much scientific papers on the evolution on DNA repair systems, the Theory of Evolution is still able to explain this system. The absence of evidence is not evidence of absence. I found a paper that seems to be related to the evolution of DNA repair systems, but I can’t access it - Catalytic Promiscuity and the Divergent Evolution of DNA Repair Enzymes. If anyone has access to the paper, I would be glad to know its details. :-)

However, the creationist may say that this systems fits the Bible/Quran better, as our body is constantly going downhill, just as stated in their “holy text” and the Second Law of Thermodynamics. This claim however, isn’t true at all, and I shall show in my next post that evolution fits nicely with the Second Law of Thermodynamics.

References

Yukiko Mishina, Erica M. Duguid, and Chuan He. (2006) Direct Reversal of DNA Alkylation Damage. Chem Rev. 2006 February ; 106(2): 215–232.

Yuan Liu, Rajendra Prasad, William A. Beard, Padmini S. Kedar, Esther W. Hou, David D. Shock, and Samuel H. Wilson. (2007) Coordination of Steps in Single-nucleotide Base Excision Repair Mediated by Apurinic/Apyrimidinic Endonuclease 1 and DNA Polymerase. THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 282, NO. 18, pp. 13532–13541

Brian D Harfe and Sue Jinks-Robertson. (2000). DNA MISMATCH REPAIR AND GENETIC INSTABILITY. Annu. Rev. Genet. 2000. 34:359–99

Guo-Min Li. (2007). Mechanisms and functions of DNA mismatch repair. Cell Research (2008) 18:85-98. doi: 10.1038/cr.2007.115

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Answering Creationist Claims (Part 5 – The Egg and the Sperm Disprove… What?!)

This time, Bible Life Ministries claim that the “Human Egg and Sperm Prove Evolution is Wrong”. I cannot understand what do the reproductive cells have to do with disproving evolution, but since they put it up, I’ll have to refute their funny claim.

Where in the Universe did you learn about sexual reproduction?

The human female like other mammals has XX sex chromosomes, and the male has XY sex chromosomes. The female egg contains the X-chromosome, and the male sperm contains either an X-chromosome for the reproduction of a female or a Y-chromosome for the reproduction of a male. The female eggs all develop within the ovaries while she is a baby (foetus) within her mother's womb.

So, the female has XX sex chromosomes like other mammals, while the males do not? It seems they think that all mammals have XX chromosomes except human males! Guess I’ll need to give them an elementary crash course on sex chromosomes (if you already understand it, just skip this section).

Sex-determination Systems

XX/XY System

In this system, females have XX chromosomes, and are known as the homogametic sex; males have XY chromosomes, and are called the heterogametic sex. This system is found in most mammals (including humans), some insects of the genus Drosophila, and some plants of the genus Gingko.

Drosophila XY sex-chromosomes.

XX/X0 System

This system is similar to the XX/XY system above. Females have XX chromosomes, while males have X0 chromosomes (the 0 indicates none). This system is observed in a number of insects, including the grasshoppers and crickets of order Orthoptera and in cockroaches (order Blattodea).

ZZ/ZW System

In this system, it is the ovum that determines the sex of the offspring, instead of the sperm as the XX/XY and the XX/X0 system. In this system, males are the homogametic sex with ZZ chromosomes; while females are heterogametic with ZW chromosomes. This is the system used in birds, some fish, and some insects (including butterflies and moths), and some reptiles, including Komodo dragons.

Haplodiploid System

This system is special in the sense that an offspring that is formed from the union of a sperm and an egg (fertilised) becomes a female; an unfertilised offspring becomes a male. Males have have only half the chromosome count of females, and are haploid; females are diploids. This system determines the sex of the offspring of many hymenopterans (bees, ants, and wasps), spider mites, coleopterans (bark beetles) and rotifers.

Haplodiploid diagram.

Temperature-dependent sex determination

The sex of the offspring of this system is determined by the temperature of the eggs. Instead of chromosomal sex determination systems, this is a environmental sex determination system. The eggs are affected by the temperature at which they are incubated during the middle one-third of embryonic development. This critical period of incubation is known as the thermo-sensitive period (TSP).

Temperature-dependent Sex Determination

Polyphenic System

A sex-determining polyphenism allows a species to reproduce normally while permitting different sex ratios. In tropical clown fish, the dominant individual in a group becomes female while the other ones are male, and blue wrasse fish are the reverse. If the dominant individual dies, another individuals will change its sex and replace it. This system ensures that there will always be a mating couple when two individuals of the same species are present.

Other Systems

Some species, such as some snails, practice sex change: adults start out male, then become female. In Bonellia viridis, larvae become males if they make physical contact with the female, and females if they end up on soil. In some arthropods, sex is determined by infection, as when bacteria of the genus Wolbachia alter their sexuality; some species consist entirely of ZZ individuals, with sex determined by the presence of Wolbachia.

So there you go. These are the main sex determination systems found. None of these systems pose any threat to evolution, and instead support it strongly.

Phenotypes Cannot Affect Genotypes

Evolutionists claim environmental factors cause small changes in the offspring in the evolutionary chain. However, the environmental experience of the female cannot change the chromosomes within her eggs and cannot have any effect upon her offspring. Her body cannot go into the eggs contained within her ovaries at her birth to make an intelligent genetic change. Females cannot be a part of the evolutionary theory for these reasons.

They got half of it right. The last sentence is just plain ignorance, though (the same thing is repeated for the male sperm). They foolishly think evolutionists say that evolution can be driven by direct effects of the environment on the genes! Perhaps they meant natural selection + genetic mutation. Here’s a short description of how it works:

Firstly, every time gene duplication/replication occurs, something goes wrong. The gene mutates. Most mutations are neutral as over 90% of our genes are useless. Of the mutations that have an effect on the phenotype, most are harmful. Those individuals with mutations that decrease their survivability will be eliminated from the gene pool. In some cases, though, the mutation is beneficial to the individual, and the individual will be better adapted to the environment, and thus pass on its genes.

It’s just that simple. Can’t Bible Life Ministries even understand this? In contrast to what Bible Life Ministries claim, chromosomal sex determination systems have been studied, and they do support the Theory of Evolution.

Multiple Independent Origins of Sex Chromosomes in Amniotes

The general consensus in the scientific community is that amniotes were sexually determined by environmental factors originally, and chromosomal sex determination systems appeared late on the scene.

Birds evolved the ZZ/ZW sex determination system, and snakes also evolved this system independently. On the other hand, mammals evolved the XX/XY system independently. The split of the mammals from the rest of the amniotes occurred around 315 million years ago, whereas the archosaurs (birds, crocs, dinosaurs, possibly turtles) diverged from the lepidosaurs (snakes, lizards) around 260 million years ago.

There are 2 ways to explain the presence of the ZZ/ZW system in both birds and snakes. The first model is that the ZZ/ZW system appeared before archosaurs and lepidosaurs diverged, and some of the archosaurs/lepidosaurs reversed to temperature-dependent sex determination later. This model has serious problems, as the regaining of a feature is considered extremely unlikely in the Theory of Evolution.

The second model predicts that snakes and birds developed the ZZ:ZW system independently. This system fits the Theory of Evolution nicely, and has been proven genetically. After all, the autosome being converted to sex chromosomes in birds is different from that in snakes.

Independent origins of sex chromosomes in birds, snakes, and mammals. In ancestral amniotes, which presumably used temperature-dependent sex determination, there were no sex chromosomes. Sex chromosomes then evolved from autosomes on three independent occasions in birds, snakes, and mammals. A different autosome was converted to sex chromosomes in each of these three lineages. The ZZ:ZW system emerged twice (once in birds and once in snakes), whereas the XX:XY system emerged once in mammals.

Conclusion

We have now established that Bible Life Ministries claim that the reproductive cells disprove evolution is nothing more but ignorance. You would’ve hoped they would at least do more research if they want to challenge the Theory of Evolution.

Their claim shows an even worse understanding of evolution, which I would take great pleasure in refuting. After all, DNA doesn’t have a mind, does it?

References

Eric J. Vallender, Bruce T. Lahn. (2006) Multiple independent origins of sex chromosomes in amniotes. PNAS vol. 103 no. 48 18031-18032.

Previous: Answering Creationist Claims (Part 4 – Irreducible Ignorance)

Next: Answering Creationist Claims (Part 6 – DNA Repair is Natural)

Answering Creationist Claims (Part 4 - Irreducible Ignorance)

Behold, for what you are going to see is an argument popularised by Michael Behe’s “Darwin’s Black Box” – Irreducible Complexity. Yes, for if a truly irreducibly complex organism is to be found, evolution is utterly crushed. The definition for irreducible complexity is as follows: “A single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning.” Despite being refuted by scientists repeatedly, creationists still love to use this tactic, and Bible Life Ministries is no different.

Single Cell Complexity Doesn’t Threaten Evolution

Their claim starts with the saying that scientists believe “that lightning struck a pond of water, causing several molecules to combine in a random way, which by chance resulted in a living cell”. That is certainly oversimplifying and misrepresenting abiogenesis, but I will not tackle it. Instead, I shall tackle the claim that a living cell is so complex that it couldn’t have evolved.

Creationists claim that a cell is too complex to have evolved, but actually it can. The first organism did not have to be as complex as the organisms nowadays. It simply needed to be able to self-replicate. In such a case, even a simple combination of RNA and proteins would’ve been sufficient. Over time, it would evolve into being more and more complex, with new functions rising. This fits the model of evolution nicely.

This may have been the first living organism.

Bible Life Ministries also claimed that the cell is too complex to have evolved by chance. Duh. Evolutionists never claimed that evolution is a fully-random process. While the process of genetic mutation may be random, natural selection is not, even the interaction of chemicals are governed by certain laws.

The Bacterial Flagellum is Reducibly Complex

E. coli cells use long, thin structures called flagella to propel themselves. These flagella form bundles that rotate counter-clockwise, creating a torque that causes the bacterium to rotate clockwise.

The flagellum is arguably the most interesting organelle ever, as it is powered by a rotary motor. This design is almost never found in any other organelle/living organism, and is quite an evolutionary puzzle. Because of this, the flagellum is touted by creationists worldwide as evidence for “Intelligent Design”. How wrong they are.

The flagellum of Gram-negative Bacteria moves using a rotary motor. One cannot help but compare it to the motors in our cars.

The Type -III Secretion Apparatus

The Type-III Secretion Apparatus (often written Type III secretion system and abbreviated TTSS or T3SS) is a protein structure and an organelle, found in several Gram-negative bacteria. T3SS is used by pathogenic bacteria as a method infect other microorganisms. Current evidence suggests that the bacterial flagella and T3SS evolved from a simpler secretion system and share at least nine homologous constituents.

Flagella assembly ATPases - the FliI proteins (Protein flightless-1 homolog) is also homologous to T3SS ATPases. Because ATPases energize numerous biological processes, FliI may have evolved independently of flagella function, having later been recruited to energize flagella assembly.

The T3SS secretes proteins directly from the cytoplasm through the membrane of the bacteria into the cytoplasm of the host cell or into an external medium. It does so by using thin, rigid, hypodermic needle-like protein complexes anchored to the envelope by basal structures resembling those of the flagella. In fact, in some cases, both the flagella and T3SS export same or similar proteins through the cell membrane, thus showing both organelles are highly similar in function and structure.

The T3SS has shown that the flagella can be evolved, and is thus further evidence against irreducible complexity.

Conclusion

I have now debunked the claim that irreducible complexity debunks evolution. Bible Life Ministries used 2 of the most famous structures associated with irreducible complexity, and yet both of the structures could’ve evolved through evolution. (See Part 1 – Birds Support Evolution for my answer to the evolution of flight, another commonly touted example of irreducible complexity).

In the next post, Bible Life Ministries funny claim that “Human Egg and Sperm Prove Evolution is Wrong” will be answered in detail.

References

Wong, Tim; Amidi, Arezou; Dodds, Alexandra; Siddiqi, Sara; Wang, Jing; Yep, Tracy; Tamang, Dorjee G.; Saier, Milton H. (2007). "Evolution of the Bacterial Flagellum: Cumulative evidence indicates that flagella developed as modular systems, with many components deriving from other systems". Microbe 2 (7): 335–40.

Previous: Answering Creationist Claims (Part 3 – What’s a Missing Inferior Branch?)

Next: Answering Creationist Claims (Part 5 – The Egg and the Sperm Disprove… What?!)

Answering Creationist Claims (Part 3 – What’s a Missing Inferior Branch?)

For some reason, after denying that the phylogenetic tree of life exists, Bible Life Ministries goes on to claim that so-called “Missing Evolutionary Inferior Branches” prove evolution wrong (Why do they try do disprove branches of a tree which they claim doesn’t exist is beyond my understanding). This isn’t even an argument, but another ignorance of the Theory of Evolution.

Do You Even Know How Evolution Works?

Their claim is that some individuals will branch off and create new evolutionary pathways. Those which are superior would create succeed in surviving and the branch would progress until this day. The less adaptable individuals would create new branches as well, but would eventually die out.

Well, here’s one thing I need to admit: They got this right. Those that survived and reproduced successfully would have their genes passed down, but not those who didn’t. But they get it wrong straight after this.

They claim that scientists have been searching so much for superior evolutionary branches that they missed all those branches that didn’t survive until this day. Well here’s the truth: Every fossil found almost certainly did not had its lineage until this day. No scientist would ever claim that a fossil represents our direct ancestor. Instead, every fossil is a great-great-great-great…… grand uncle/aunt. Archaeopteryx did not evolve into modern day birds; we did not evolve from Tiktaalik, but from a similar tetrapod. There is no way to confirm whether a fossil is our direct ancestor, and the odds are much higher that it is on a similar, but separate branch.

As you can see, there's quite a big number dead branches on the Tree of Evolution. So yes, the fossil record is consistent with the Theory of Evolution after all.

No scientist ever claimed that we directly descended from this fishes/tetrapods, nor do they say that this set of fossils represent a perfect, linear evolution. Instead, they are more like cousins.

Conclusion

Thus, as I have shown, the "missing inferior branches" are in great abundance. So maybe (almost certainly) the fact is that Bible Life Ministries is completely ignorant of evolution.

Bible Life Ministries next claim involves a old creationist tactic: Irreducible Complexity. Let me shred this claim in the next post.

Previous: Answering Creationist Claims (Part 2b - No Intermediates? Wake Up, Please.)

Next: Answering Creationist Claims (Part 4 - Irreducible Ignorance)

Answering Creationist Claims - (Part 2b - No Intermediates? Wake Up, Please.)

Ignorant of the theory of evolution, Bible Life Ministries goes on to claim that all fossils doesn’t represent intermediates; those that do are frauds. Funny how creationists would refuse to consider all those verified fossils and instead claim that the Paluxy River footprints are proof of creation. Without wasting time, let’s take a look at their claims.

Ardipithecus ramidus

Probable life appearance in anterior view of Ardipithecus ramidus.

The find for “Ardi” began in 1994, in the Middle Awash region of Ethiopia. Dated at 4.4 million years ago. Ardi further completes our understanding of human evolution. Such a fossil would certainly be picked apart by creationists with the “greatest” claim ever: “It’s just an ape.” Not an average ape, mind you.

By bringing us closer to the 6,000,000 BC point in which humans-to-be and chimpanzees-to-be diverged, Ardipithecus revolutionised the way we think of our ancestry. It weakened the theory that protohumans were savannah apes that diverged from a quadrupedal ape. Instead, Ardi was a fully bipedal, woodland ape.

What Makes "Ardi" a Great Fossil?

Feet Unlike Chimp's and Human’s

Ardi’s feet is quite intermediate between those of humans and those of chimps. Just like chimps, the toes are opposable, but they’re shorter. Plus, the feet aren’t flexible enough to from climbing trees and grasping veins, and they’re more human-like from that point of view.

Human-like Hands

The fingers of Ardipithecus ramidus are long and dexterous, much like human’s. Its wrists are also more flexible than those of contemporary apes.

Small Canines

Canines are used by apes as a sign of male superiority. In a monogamous society, male apes have large canines, and they’re used in conflict with other males when fighting over females. However, Ardipithecus ramidus fossils showed that males did not have large canines, and certainly not larger than those of females. This feature shows that our ancestors did not have much conflict between males and males, and is great evidence that our ape ancestors had more pair-bonding and parental investment than previously thought.

Pelvis Suited for Walking

Ardi’s pelvis, although crushed and needed to be reconstructed by advanced digital technology plus anatomy experts, it nevertheless points to the fact that Ardi’s pelvis are wider than quadrupedal chimps and narrower than bipedal Australopithecines aka intermediate. This is greater evidence that our ancestors became bipeds before geniuses (Ardi’s brain volume is estimated to be 300 and 350 cm³, which is about the size of a modern bonobo’s/female chimp’s brain, but smaller than Lucy's 400 to 550 cm³ brain).

Archaeopteryx

Archaeopteryx Fossil (Berlin)

Archaeopteryx – arguably the most famous fossil ever. Found in a limestone quarry in Southern Germany in 1861, the bird is now widely recognised as the best example of the reptile-bird transition. And guess what, Bible Life Ministries call it a fraud. They claim that it is a dinosaur fossil with fake feathers, and thus shows how dishonest evolutionists are.

OK, so the source came from In the Beginning: Compelling Evidence for Creation and the Flood, written by Dr. Walt Brown, who isn’t a scientist. Here’s the quote: “Allegedly, thin layers of cement were spread on two fossils of a chicken-size dinosaur, called Compsognathus. Bird feathers were then imprinted into the wet cement”. It’s on page 148.

Unfortunately, the case doesn’t hold strong for Bible Life Ministries. Palaeontologists that examined the London Archaeopteryx arrived at a quite different conclusion - “Proof of authenticity is provided by exactly matching hairline cracks and dendrites on the feathered areas of the opposing slabs, which show the absence of the artificial cement layer into which modern feathers could have been pressed by a forger.”. This is featured here: Archaeopteryx is not a forgery..

To add to the point, Compsognathus’s skeleton is much more different from those of Archaeopteryx – there are too much differences between the 2 species. In fact, there could not have been a better reptile-bird intermediate. I shall not reinvent the wheel, as there is already a good source here: Archaeopteryx's Relationship With Modern Birds

Titaalik roseae

One the most beautiful discoveries in the early 21st century would be Titaalik. Found in 2004 by Neil Shubin and his team in the Arctic Circle, it is now in the Hall of Fame as one of the most important fossils, well alongside Archaeopteryx and Australopithecus. Tiktaalik is the perfect example of the fish-tetrapod transition. Once again, Bible Life Ministries claim it is a fraud.

Tiktaalik Model with Fossil Cast

Here’s their funny argument: “Since Archaeopteryx is a fraud (of course it’s not), therefore Tiktaalik is a fraud!” Don’t understand their logic? Me too. Unlike Piltdown Man, Archaeoraptor, and other frauds, Tiktaalik was certainly not found by “amateurs”, and the process of finding and excavating it is quite well documented. Bible Life Ministries, perhaps you would be kind enough to read “Your Inner Fish” by Neil Shubin?

Yet in a twist, Bible Life Ministries suddenly change their mind and acknowledge that Tiktaalik is true, just not an intermediate - it is nothing more than another species of fish. Notwithstanding the confusion, let us show the poor (wilfully ignorant) creationists why is Tiktaalik so exciting, and how it contributes to a better understanding of evolution.

What Features of Tiktaalik Make It a Fish-Tetrapod Intermediate?

Loss of the Operculum

The operculum is a plate of bone that forms a flap that covers the gills in most bony fishes. The operculum’s primary function is to assist the fish in moving water across the gills. Losing the operculum allows the neck to move freely. All tetrapods don’t have the operculum, while primitives ones still retain the gill but have lost their operculum nevertheless. Tiktaalik lost its operculum but retained the gill, which is only expected from a fish-tetrapod intermediate. By losing the operculum, Tiktaalik was able to move its head independent of its body, and had a true neck. Also, without the operculum, Tiktaalik should’ve breath mainly using its mouth.

Dwarfing of the Hyomandibula

The stapes is a piece of bone in our middle ear. It was originally a gill arch bone known as the hyomandibula. In Eusthenopteron, the hyomandibula large and boomerang like, in Acanthostega it's a small piece of bone, and in Tiktaalik it's exactly between.

Comparison between the operculum and hyomandibula of fish and tetrapods.

The Skull

The main difference between fishes and tetrapods is the shape of their skull. Fishes have round, conical skulls with their eyes on the sides; tetrapods have flat skulls with their eyes on top. Tiktaalik has a flat skull, yet with some leftover characteristics from fish skulls.

Dorsal view of Tiktaalik skull. Scale bar equals 5 cm.

Primitive Wrist Bones and Fingers

Fishes have fins, tetrapods have limbs. This is one of the main differences between them. To crawl on land, the fins are expected to evolve into limbs. And that’s what seen in Tiktaalik.

The difference between fins and limbs lie mainly in their skeletal layout, The base of a typical fin contains 4 or more pieces of bones; limbs have a single bone known as the humerus that connects to the shoulder, which are connected to 2 forearm bones, then to pieces of bones, and finally to digits.

So let’s take a look at Tiktaalik’s fin/limb. One can only awe at what a great finding it is indeed – to have found such a perfect intermediate between swimming fins and walking limbs. Read the description, and see for yourself.

a, Dorsal view; b, ventral view. Elements with stipple shading were preserved in articulation in NUFV 109 and prepared in the round. Elements with a dashed outline are reconstructed based on their presence in the articulated distal fin of NUFV 110. It is not known how many radials lie distal to the first, second and fourth in the proximal series. Note the dorsal expansion of the distal articular facets on the ulnae and third distal radial/mesomere. The dorsal expansion of these facets would have facilitated extension of the distal fin.

Other Claims

Here’s a list of species which are obviously unrelated to transitional fossils, yet somehow included by Bible Life Ministries in their unfounded claims.

The Coelacanth

A living fossil.

Once thought extinct since 70 million years ago, the coelacanth was found in December, 1938 off the eastern coast of South Africa. Quite a startling discovery indeed, as it is such a great “living fossil”. That is, not counting the opportunity that the coelacanth provided for creationists to annoy us.

So it basically boils down to the same old question: “Since the coelacanth has remained unchanged for 350 million years, evolution is false.” This assumption is so wrong on many levels.

Firstly, this thought wrongly assumes that evolution is linear, continuously progressing towards humans as an end product. Instead, evolution is continuously branching, a process known as speciation. A fish can keep on evolving into a better fish while another fish may evolve to survive on the land. The coelacanth is one that stayed in water.

It is also wrong to think that evolution is working towards a goal with an end product in mind. It is driven by the force of natural selection, that is the continuous interaction between individuals in a struggle to survive and reproduce. Our ancestors did not have a great plan to live on land, it was just natural instinct for survival that led them to venture out of water, perhaps to escape larger, predatory fishes. The coelacanth is a fish that managed to survive in its current form, and thus did not need to change.

Lastly, the living coelacanths represents the genus Latimeria, not a species, and has changed from its ancestors. It is just that the changes were minor.

The Platypus

Evolution: Results may vary.

I’m not very sure what exactly is Bible Life Ministries is trying to prove by using the platypus, but I’ll address it nevertheless.The platypus and the echidna are monotremes, the only mammals that lay eggs, and the platypus sure seems to have quite mix of mammalian and reptilian features (At least Bible Life Ministries is right on this one). What I find funny comes next.

Bible Life Ministries then goes on to claim that the platypus has the characteristics of many creatures but is not a link to any of them. Duh!!! No one ever said that the platypus was a link to any species! Mammals diverged into 2 different branches about 140 million years ago, one of them which would later diverge into placentals and marsupials; the other branch consists of the monotremes. Get your facts straight.

But what about the supposed “mix” of the characteristics in the platypus? Well the platypus is halfway between mammals and reptiles, so no surprise that it moves quite awkwardly. It lays eggs because it works, so no reason to change it. The males have poison as a result of sexual selection, and it doesn’t kill, just create great pain. Its famous bill is simply convergent evolution, and works quite differently from a duckbill. No problem for evolution whatsoever.

An Atavistic Dolphin

An atavistic dolphin was caught in November 2006.

It seems here that Bible Life Ministries thought that we actually labelled the dolphin with rear flippers as evidence that dolphins evolved from dogs. Please, creationists, the article itself stated that it was a dog-like ancestor, not dogs. Sheesh. Moreover, Bible Life Ministries last sentence stated that the dolphin was just another odd species that “god” created. That shows their complete misunderstanding of what the fuss was all about.

What we find fascinating here is not that we found a vestigial flipper. It is long known that cetaceans’ hind limbs are hidden within their body (See my previous post for more details). Instead, what we are dealing with here is an atavism, which is the appearance of a structure that was present it the individual’s ancestor, but not anymore in the present. In other words, it means that hind limbs of mammals were once present, but have since been reduced to pieces of bone in the dolphins body; this bottleneck dolphin however has hind limbs, and thus is a case of atavism. Another example is the growth of toes in atavistic horses. Atavisms are caused by a abnormal reading of genes, in which pseudogenes are accidently transcribed.

Conclusion

It certainly looks as if Bible Life Ministries did not do any research on the transitional fossils listed. They're just repeating the mantra: "There're no transitional fossils... Just show me one, just one...". It it shown in this post that there are quite a large number of transitional fossils, despite the fact that this is just a tip of the iceberg. No more excuses, creationists. Face the fossil record.

Bible Life Ministries 3rd claim focuses on missing evolutionary branches. However, this claim isn’t even an argument, but simply a gross misunderstanding of the Theory of Evolution. I’ll explain it in the next post.

References

Shubin, N.H. (2009) Your Inner Fish. Penguin Books. ISBN 978-0-141-02758-6

Daeschler, E.B. et al. 2006. A Devonian tetrapod-like fish and the evolution of the tetrapod body plan. Nature 440: 757-763.

Charig et al, Archaeopteryx is not a forgery., Science, 1986, v.232, p.622-626.

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Next: Answering Creationist Claims (Part 3 – What’s a Missing Inferior Branch?)

Answering Creationist Claims (Part 2a - We Don't Jumble Fossils Together)

In this post, I shall refute “Bible Life Ministries” claim that “Species Without a Link Proves Evolution is Wrong.” Let’s start with their claim:

The evolutionist will claim that the presence of many individual species proves evolution. This shallow statement is devoid of reason, logic and scientific proof. Evolutionists line up pictures of similar-looking species and claim they evolved one from another. The human "family tree" is an example of this flawed theory. Petrified skulls and bones exist from hundreds of species of extinct monkeys and apes. Evolutionists line up the most promising choices to present a gradual progression from monkey to modern man. They simply fill in the big gaps with make-believe creatures to fit the picture. This procedure can be done with humans only because there are many extinct monkey and ape species. They never do this with giraffes, elephants or the Platypus. The pictures are placed in all of the textbooks that evolutionists use to teach kids this nonsense. The pictures are simply a grouping of individual species that does not prove evolution.

They’re trying to claim that scientists simply jumble similar looking fossils together and call it evolution. As usual, this claim is full of false statements and ignorance. You would’ve thought that if they really wanted to refute evolution, they should at least do a little research. Let us see how easy it is to refute them.

How To Determine a Fossil’s Place on the Tree

Scientists most certainly do not simply pick out similar-looking fossils and say: “Well this fills the missing link.” There are a few things to consider when analysing fossils:

Geology

The Geologic Time Scale

The Earth’s crust is divided into many layers known as strata(singular: stratum). Every stratum can be distinguished from each other through its own unique characteristics. A few examples are the Devonian, Carboniferous, Permian, Triassic strata. The Law of Superposition states that sedimentary layers are deposited in a time sequence, with the oldest on the bottom and the youngest on the top. However, sometimes the sequence is changed as a result of thrust faults. There are multiple methods to determine the age of strata, namely: radiometric dating  thermoluminescence dating  and incremental dating. Through the combination of these theories, we can create the geologic time scale for the Earth.

The theory of evolution predicts that we evolved from earlier, simpler life forms into later, complex life forms, and this is exactly the case. The current fossil evidence shows an increase in complexity from the first microorganisms which were found to be 3.5 billion years old straight up to today. Older strata usually contains less diverse and smaller number of fossils, while older strata houses complex and more abundant fossils, save for the multiple mass extinctions that occurred.  This is known as the Principle of Faunal Succession and strongly supports the theory of evolution. In other words, a species below the stratum of another species couldn’t have evolved from it.

Human history is too short to be visible on this timescale.

Continental Drift

Why do we find whales in the deserts? Why was Tiktaalik found in the Arctic Circle? And why are similar species distributed unevenly all over the world? The answer is continental drift. This theory states that the Earth’s continents were once joined together in a super-continent called Pangaea in the Permian period. Pangaea later broke off in the Jurassic period to form Laurasia to the north and Gondwana at the south. Both of these continents would later separate off again and finally arrive at the places they are today.

The movement of continents are explained in plate tectonics. The surface of the Earth consists of lithospheric plates that moved through geological time, resulting in the modern-day position of the continents. The continents as we know it are only elevated areas of the the lithospheric plates. The lithospheric plates consist of the continental and oceanic crust plus the upper mantle. The plates lie upon a fluid layer of lava known as the asthenosphere, which is responsible for the movement of the plates.

By collaborating the our knowledge of continental drift with molecular biology, we can determine where fossils belong in the phylogenetic tree, but let’s postpone this matter.

Tectonic Plates with Their Movement Vectors

Comparative Anatomy

Homologous Structures

We can find a lot of anatomical similarities between groups of living things. For example, all vertebrates share a backbone, all flowers have petals, stigma, anthers etc. The difference is that they vary in form and look, but the overall pattern remains the same.

The adaptation of groups of animals that share homologous structures (same form, different function) to fit their environment is known as adaptive radiation. The gradual spreading of organisms with adaptive radiation is known as divergent evolution.

As individuals or groups which share more features in common are supposed to have diverged earlier from a common ancestor, comparative anatomists look for homologous structures in animals to determine how closely related are they. The comparison of homologous structures allowed scientists to show that bats evolved from shrew-like creatures, instead of birds (Leviticus 11:13-19).

The concept of homologous structures is presented here. All mammals share the same pentadactyl pattern for their limbs, yet have adapted it for different uses.

Vestigial Structures

Vestigial structures are one of the strongest evidence for evolution. A vestigial structure is a homologous structure that is underdeveloped and useless or adapted for different uses. There are plenty of vestigial structures found in organisms, be it extinct or alive. A vestigial structure suggests that the environment the species lived in no longer had selection pressures on that structure, and could focus on other parts.

A lot of skeletons show traits of vestigiality, such as wings on flightless birds, the coccyx of apes etc.  The best example is the hind limbs of whales and other cetaceans. The appearance of vestigial pentadactyl limbs in cetaceans is strong evidence that whales were not simply created, but evolved from a earlier tetrapod that lost functionality for its legs. As Douglas Futuyma said, vestigial structures do not make sense without evolution. Why would a creator create such structures cannot be explained by creationists.

One of the ways to determine whale evolution is the vestigiality of its hind limbs.

Molecular Biology

Molecular Clock

Differences between homologous molecules can be quantified and expressed as, for example, the number of nucleotides and amino acids that have changed. We can use the differences between homologous molecules to determine the rate of evolutionary change much more precisely than we can simply through the phenotypes of the genes.

In the 1960s, it was discovered that the the number of differences between amino acid sequences of the proteins of different species was proportional to the time they were predicted to diverge from a common ancestor. The more differences in the amino acid sequences, the longer the divergence. Since the rate of change was identical for every species, we can use not only update the sequence of branching events in a phylogenetic tree, but the time when it occurred.

But how reliable is this method, you ask? Of course, the molecular clock is not expected to work like our watches do, which measures time accurately based on standard units. Instead, a similar analogy can be found in radiometric dating. Radiometric dating is founded on the observation that the half-life of same types of elements are same, while the molecular clock is based upon the observation that the difference between homologous molecules increase proportionally to the time since divergence.

Although scientists have found out that the molecular clock is more erratic than other clocks, such as radiometric dating, it is not too large. To increase accuracy, a large number of proteins are compared to determine the average rate of evolutionary change. The more differences, the more accurate the clock. This clock is later collaborated with outside sources (the fossil record, continental drift) and to determine its accuracy. Yet even with such efforts to minimize error, the clock is still found to be estimate dates older when compared with other methods. Nevertheless, the molecular clock still provides very compelling evidence for evolution, and so far it has been very consistent with other methods.

So how does this contribute to classification of fossils, anyway? Well, we can determine whether a fossil is truly a member of a specific genus(or class, species, etc.) So if we find a humanoid that is 25 million years old in Australia, we can safely conclude that it must be unrelated to the Homo genus, since the molecular clock puts the divergence of the Homo genus from chimps at around 6 million years ago, and continental drift also says otherwise.

Conclusion

In this post, it has been made very clear that we do have a lot of methods to determine where a fossil belongs, and whether it really represents a transition between earlier and older species. It is certainly not just, “Well I think this is the best guess”. I may have missed other methods of determining a fossil’s place in the phylogenetic tree, and if that is so, any comments would be greatly appreciated.

By the way, you have shown your ignorance again, creationists. And yes, in my next post, your alleged claims that all those beautiful fossils such as Australopithecus, Tiktaalik, Archaeopteryx etc. cannot support evolution will be utterly destroyed. At the meantime, take your time and do a little research, please.

References

Futuyma, D. J. (1995). Science on Trial: The Case for Evolution. Sunderland, MA: Sinauer Associates Inc.. pp. 49. ISBN 0878931848.

Anne Waddingham. (2009). The Britannica Guide to Genetics. Encyclopaedia Britannica Inc. pp 209-211. ISBN 970-0-7624-3620-0

(2005). Oxford Dictionary of Science Fifth Edition. Oxford University Press Inc. ISBN 978-0-19-280641-3

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