Mail from A Creationist (2nd Update)

Finally! After writing my blog for over 3 months, I’ve received my 1st email challenge – from a creationist, named Chris Sanford. Let’s see what he has to say:

1a. Chris Sanford (Copied Directly)

Hey there,
    I stumbled across your blog and found it interesting to say the least. My name is Chris and I am from a different perspective than your own. So I was just wondering many evolutionist claim that evolution is a done deal, a settled fact. Yet Look at DNA for example, 1 strand of DNA contains the same amount of information that would fill 500 volumes of books, 1000 pages each. Where did this information come from? Look at the almost unspeakable intricate organelles that are contained within a single cell. This all came about by chance and luck, and blind guidance via natural selection? Evolution simply cannot answer these arguments. As I said to another contact of mine, evolution is big on philosophy but short on evidence. You see most evolutionist will say this had to happen first, and then this had to happen, yet when it comes to evidence which science is really all about, they are lacking to say the least. I would love to hear you on these issues, also I have a blogspot check it out and let me know what you think...

http://designedbymeansofintelligence.blogspot.com/

until we go to the ends of the earth...

Acts 1:8

商宣中

Chris Sanford
louisvchr@aol.com

1b. My 1st Reply

Hi, Chris,

First of all, thanks for emailing me, and I appreciate it. So let’s start talking.

Scientific Theories are Always Updating – So is Evolution

Firstly, you said that

…evolutionists claim that evolution is a done deal, a settled fact.

That's not an accurate claim. Nothing in science is ever a “settled fact”, since science is just a method of acquiring knowledge about the universe through the scientific method (see my post on), and thus scientific theories, and even laws are updated to become even more reliable and accurate. Thus, any evolutionist that understands science correctly will never say that evolution is absolute truth.

What we mean instead is that the process of evolution is a model that fits the current evidence, be it fossils, genes, or morphology. Until a better model is found, we’ll have to stick with evolution.

Stop Arguing from Irreducible Complexity, Really

You claimed that

1 strand of DNA contains the same amount of information that would fill 500 volumes of books, 1000 pages each. Where did this information come from?

and asked me to

Look at the almost unspeakable intricate organelles that are contained within a single cell.

This is known as the irreducible complexity argument – one stating that something in an organism is too complex to have evolved naturally. That' has been refuted for so much times that’s it’s old. But I’ll explain it again here.

Let’s start with DNA. According to the Oxford Compact Dictionary, information means

1 facts or knowledge provided or learned.
2 what is conveyed or represented by a particular sequence of symbols, impulses, etc.

Now, the information in dictionaries fit both the definition of 1 and 2, while the genetic code only fits definition 2. Plus, DNA isn’t something that is read and interpreted by a mind, it’s just a chemical that’s a major player in the synthesis of amino acids, so I don’t think you can compare it directly to the information in books.

Anyway, it does seem taunting. How is it possible that these 3 billion genes can create a such a complex organism, if it wasn’t designed intelligently? But do note that we didn’t start off as complex organisms – the Theory of Evolution predicts that we evolved first from extremely simple, self-replicating chemical structures. These organisms had a poorly functioning and extremely simple genetic code compared to what we have now, and thus they would be extremely simple in their structure as well.

But natural selection is the one that makes the difference. When the organisms replicate, there will be genetic mutations inevitably, and thus there will be variation between the organisms. Some organisms will thus be better suited to the environment, and survive long enough to replicate, while those with inferior functioning genetic code will get eliminated from the gene pool quickly. Repeat this process of weeding out “bad” genes and retaining the “good” ones for 4 billion years, and it isn’t hard to see why we have such a nicely functioning body, with such complex cells.

Look at My Answering Creationist Claims Series

Lastly, you said that evolution is

…big on philosophy but short on evidence.

So do me a favour and look at my Answering Creationist Claims series – you can find them through the blog archive. And while you’re at it, why not present some evidence for creationism/intelligent design? ;-)

I hope this has been sufficient to answer your questions, and I’ll wait for your reply.

Sincerely,
Darren Wong

2a. Chris Sanford

Hey there, first of all thank you for responding to my email. I love an intelligent conversation. So let's address your comments one by one. You say that no scientist would say that evolution is would never say that evolution is a fact?

"Evolution is a fact: as much a fact as plate tectonics or the heliocentric solar system."  Barbara C Forrest and Paul R Gross, Oxford University Press, 2003 http://www.guardian.co.uk/science/2005/sep/01/schools.research

"Evolution is a fact. Beyond reasonable doubt, beyond serious doubt, beyond sane, informed, intelligent doubt, beyond doubt evolution is a fact. The evidence for evolution is at least as strong as the evidence for the holocaust. Richard Dawkins "the Greatest show on earth.

http://www.associatedcontent.com/article/2486574/richard_dawkins_says_evolution_is_a.html

So are you saying that Richard Dawkins who is the top evoutionist in the world, who also claims that evolution is a fact does not understand science correctly. Let me rephrase that, that is exactly what you are saying with your own words. So there seems to be some disagreement with you in your own scientific community.

Secondly you say that we started off as simple celled organisms, that were in your own words "extremely simple". While this is a good idea, where is the evidence to prove this? When have we ever in life, ever seen a single cell that is simple? Also you mention mutations must have occurred. Do you have evidence to prove that they occurred, or again is this where evolution is big on philosophy and short on the evidence. Can you name one, not 10, or even 100, simply one mutation that has added information to the genome. You see here is the thing, mutations are harmful to the organism and never helpful. I know of not one mutation that has added information to the genome. Yet I am not the only one who cannot come up with one instance of a mutation adding information to the genome. Here is another man whom you surely know who cannot come up with one instance of a mutation adding information to the genome.

http://www.youtube.com/watch?v=zaKryi3605g&feature=related

I would love to present you with some evidence for Creation.

The 2nd law of thermodynamics or entropy is definitely not an evolutionists’ best friend. Entropy affects everything in our universe, from you car to your body (as the Bible says our body is wearing out) to the planet and the sun and every aspect of our universe. Entropy is simply the law that everything is moving from a state of order to a state of chaos. In other words everything is breaking down on a cosmic scale. We are running out of gas, we are running out of energy. If you break a branch off a tree and throw it on the ground, entropy is going to take place, the stick is not going to become a tree, but it is going to break down and rot. It is going to move from a state of order ( a stick) to a state of disorder (mulch). And here you thought this was going to be difficult to understand. Now I think the point definitely needs to be emphasized that this is a law of science! The 2nd law of thermodynamics. For anything to become a law of science it must be proven without any contradictory evidence. There are only about 6 laws of science that exist. I have a list of them and most of them I cannot understand. This one I can. The Bible again and again says that the world is growing old like a garment, and wearing out. Guess what God is telling us about the 2nd law of thermodynamics long before it ever discovered by man. Oh the wisdom and intelligence of God. Who can measure the depths of His understanding??!! Now this is a law of science. Everything is getting worse. Do you see where the contradiction lies now? Evolution teaches that everything is getting better, that our world started out a barren wasteland with poisonous gases and all these things and it is getting better. Yet a law of science proves the very opposite is true. The Bible says the very same thing, so the only place that contradiction lies, is the theory of evolution and a law of science. So this law of science says that in the beginning everything was as good as it was ever going to be. Guess what?? God’s Word compliments this law of science and does not contradict it. Genesis 1:31 “and God saw all that He had made and behold it was very good”. So at the very beginning the Word of God says that it was very good. This agrees with the 2nd law of thermodynamics. Then everything began to move to a state of chaos. When did this happen? I believe when man sinned and God cursed the earth. Theologians call this the cosmic curse, that God not only cursed the earth but the whole universe itself is under the curse. At this point entropy began to take place and continues to this day. I have created a chart that will help you better realize this concept, it is an extremely vital concept for us to understand. It is not a hard one to grasp at all. Everything in our universe is breaking down. I went and played basketball on Saturday, now this year I am going to be 30 years old. Now this is Saturday I went and played basketball, and today is Monday and I am still feeling the pain. My body is wearing down, because I live in the universe, I am subject to entropy. My car is in this universe, my family, friends, computer, television, everything that exists in our universe is subject to the law of science called entropy. Keep in mind this is a law of science.

Also you said that Irreducible complexity has been refuted so many times, but all you did was offer the definition of information. You failed to offer any proof to refute this. If you mean by refuting this that organisms started out as simple, where is the evidence for this? Hope to hear from you soon...

until we go to the ends of the earth...

Acts 1:8 
商宣中
Chris Sanford
louisvchr@aol.com

2b. My Reply

Dear Chris,

Here are my answers:

Fact – But Only Because It’s The Best Model Currently

When I said that “any evolutionist that understands science correctly will never say that evolution is absolute truth”, I actually meant that he/she wouldn’t say that the Theory of Evolution is completely accurate, and doesn’t need to be updated anymore. That’s why I used the words “absolute truth” and “settled fact”, not simply “fact”.

As for the scientists who say that evolution is a fact, they only mean that evolution is a fact as far as the evidence goes. Look at what Barbara C. Forrest and Paul R. Gross said:

Evolution is a fact: as much a fact as plate tectonics or the heliocentric solar system.

What they were saying is that evolution is just as factual as plate tectonics and the heliocentric solar system. Why are these theories considered as a fact? Because the current empirical evidence supports them strongly.

And look at what Richard Dawkins said in The Greatest Show on Earth:

Even the undisputed theory that the moon is smaller than the sun cannot, to the satisfaction of a certain kind of philosopher, be proved in the way that, for example, the Pythagorean Theorem can be proved. But massive accretions of evidence support it so strongly that to deny it the status of ‘'fact’ seems ridiculous to all but pedants. The same is true of evolution. Evolution is a fact in the same sense as it is a fact that Paris is in the Northern Hemisphere. Though logic-choppers rule the town, some theories are beyond sensible doubt, and we call them facts. The more energetically and thoroughly you try to disprove a theory, if it survives the assault, the closer it approaches what common sense happily calls a fact.

Source: The Greatest Show on Earth, page 10

By saying that “evolution is a fact”, he didn’t mean that evolution was 100% accurate and undisputed, but that the evidence supports it strongly enough that it’s currently the closest model to the “fact”. Of course, if we really want to take semantics and logic so seriously, only mathematics can prove something to be a fact.

Of course, once a fossil rabbit shows up in the Precambrian Period, then the Theory of Evolution is rendered false right away. And I do admit that Dawkins can get overzealous at times.

Beneficial Mutations – Here They Are

Richard Lenski’s Long Term E.coli experiment

One of the 12 flasks containing suddenly housed E.coli that were able to utilize citrate as a source of energy at generation 31,127, when a defining feature of Escheria coli is that it can’t use citrate.

Nylon-eating Bacteria

Nylon-eating bacteria are a strain of Flavobacterium that is capable of digesting certain by-products of nylon 6 manufacture, found in 1975 by Japanese scientists in ponds containing waste water from a nylon-producing factory. The bacteria were able to digest certain by-products of nylon 6 manufacture, such as the linear dimer of 6-aminohexanoate. Since nylon never existed before February 28, 1935, this is certainly a case a mutation adding beneficial “information”, and the 3 enzymes used in the digestion of nylon by-products were not found in other strains of Flavobacterium.

The 2nd Law: Compatible with Evolution

The Law of Entropy is frequently raised by creationists in an attempt to discredit evolution, but it doesn’t work. I’ve already written about the topic here: Answering Creationist Claims (Part 7 – The 2nd Law of Thermodynamics Truthfully Explained), so I won’t be repeating them.

On a side note, if the Law of Entropy shows that evolution is false, then the same holds for “microevolution”, a term creationists love to use. Microevolution is still guided by exactly the same processes as “macroevolution” aka genetic mutations and natural selection. Thus, if you’re to insist that the 2nd Law renders evolution false, you’re also saying that organisms are unable to adapt at all, which is certainly contradictory to what’s observed.

In Science, We Can Make Reasonable Predictions

Sometimes, you’ve just can’t prove something. However, we can make rational predictions based on what’s most probable.

Let’s say that my blog’s hits is at 3000. Now, I can’t prove that I really had that much visits, since I can’t trace every single hit to the respective readers. Plus, it could be that Sitemeter is buggy and thus gave me a wrong count. But what's the most probable cause of my hit counter reaching 3000? Yes, that would be 3000 unique visits, because that’s how it works normally.

So I’m going to admit this: no, biologists don’t have concrete fossil evidence for the existence of the earliest self-replicating chemicals. However, the earliest possible fossils were found in the form of stromatolites, which date back to to the Lower Archaean eon. Within the stromatolites are possibly fossilized cyanobacteria, which are extremely simple in structure and look like small rods. From that point on, fossils keep on increasing in complexity, and the first multicellular fossil was found to be dated at around 600 million years ago. The trend has kept on ever since (of course, unicellular organisms still exist alongside).

Based on common sense, it would be most probable that the increase in complexity of organisms has always been the trend since evolution begun. So if we reverse the process, what do we get? Yes, organisms get even more simple as we go back in time. But even I’m wrong about the simplicity of the earliest self-replicating molecules, at least the 3.5 byr old cyanobacteria would count?

What About Other Religions?

I would also like to note that even that even if evolution is deemed false, that doesn’t mean that Biblical creation is true. We still have other religions, remember? According to Hinduism, Brahma is responsible for creation, Buddhism states that thoughts and desire are the reason we’re in this universe, the Romans, Greeks, Egyptians all have their own hypotheses for explaining the presence of life. To determine which hypothesis is true, and which isn’t, we need to provide scientific evidence.

So you say that God created entropy after men sinned? Well, show evidence that the Garden of Eden is true. Plus, evidence that God created birds before mammals and reptiles.

Sincerely,
Darren Wong

PS: Would you separate your passages into smaller chunks? Thanks. :-)

3a. Chris Sanford

Hey thank you again for another very interesting email. When you are talking about theory, you wrote "Why are these theories considered as a fact?" A Theory is not a fact, that is why it is called a theory. The only "facts" in science are the scientific laws which about only 7 exist in the scientific world. I really think that we need to get our ducks in a row when it comes to this issue. Also as far as the best theory that is possible, that is a pretty sad testimony for the theory of evolution. When it comes to the evidence concerning Intelligent Design, the evidence for a Creator is overwhelming. Have you ever looked at the evidence for a Creator Darren?

As far as the 2nd Law of thermodynamics is concerned. Basically this law states that everything is moving from a state of order to a state of chaos. Basically we are running out of usable energy. The problem is simply this, it cannot be compatible with evolution because if our solar system were billions of years old, entropy would be at such a degree that there would not be life sustainable. As far as micro-evolution is concerned. It also affected by entropy. Yet these organisms did not start out simple as the evolutionist claim, but were complex at the very beginning. The fossil record shows this. Can you name one "simple organism" that has ever been found within the fossil record. What about the oldest fossils of fish we have? They are almost a picture perfect image of fish today, and the same is true with birds, etc.

As far as other religions are concerned Darren thank you for bringing this up. If there is a God, who did create the world. That would render Him pretty powerful, being powerful He would also be Intelligent. Intelligent on a scale that no one has ever seen. His intelligence would even go as far as knowing the future. So if you can find one religious book that accurately predicts the future then that would be safe to say, this is the Word of God. There is one book Darren that accurately predicts events hundreds even thousands of years in advance, and there is only 1. The Bible. The Bible is the only religious book with prophetic writing, The Biblical prophecies have come about 100% of the time. Not one Darren, not one single prophecy in the Bible has ever failed.

Let me give you some examples. Isaiah 45:1 says Thus says the Lord to King Cyrus His anointed. Here the prophet Isaiah names a king 200 years before the king was ever born. How do we know that Isaiah did not write this down after Cyrus came to power and claim to have written it down before?? The Dead Sea Scrolls that were found in 1947 prove that this Scripture was written down before Cyrus came to power! Jeremiah accurately predicted that Israel would be in captivity 70 years. Jeremiah 25:11 'This whole land will be a desolation and a horror, and these nations will serve the king of Babylon seventy years. Daniel accurately predicted Alexander the Great, the Roman Empire, The Greek Empire, and many other things. Daniel 2:31-43 Out of all the religious books in the world, there is one and only one that has prophetic writing. The Bible is that book. In fact 1/4 of the Bible is prophetic writing. Many of these prophecies have been fulfilled, some are yet to be fulfilled, but not one has failed, God’s Word has a 100% track record, so it is safe to say we can put our trust in the Word of God. Many of the prophecies of God’s Word have to do with the 1st coming of the Lord Jesus Christ. It is prophesied something like 200 times that Jesus was to come the 1st time. We know from history that this indeed did happen.  Micah 5:2 which was written about 750 years before Christ came predicted that He would be born in Bethlehem.  Zechariah 11:12 predicted that He would be sold for 30 pieces of silver.

Now earlier you mentioned mathematics can prove something to be a fact. Lee Strobel in his book “the Case for Christ” tells the mathematical odds for Christ to have fulfilled 7 prophecies. Now keep in mind when you read this that Jesus fulfilled hundreds of prophecies. The Mathematical odds for Jesus to fulfil 7 prophecies would be the same odds as someone covering the entire earth in 4 inch by 4 inch white tiles. Hiding a gold star under only one of those tiles. And you walking up on the very 1st try and finding this gold star!! By the way you are blindfolded. That one of many tiles may be hidden in the Sahara desert, it might be hidden in Italy, it might be hidden in the country of China, or even Russia. Remember you only get one shot to try and find this star and you are blindfolded...Now you may say impossible!! Yet this mathematically is the same odds for Jesus to fulfill 7 prophecies, can you imagine what the mathematical odds are of Him fulfilling all the prophecies that He did!! Impossible right? Yet with God Darren nothing is impossible. Looking forward to hearing from you...

until we go to the ends of the earth...

Acts 1:8

商宣中

Chris Sanford
louisvchr@aol.com

3b. My Reply

Dear Chris,

Pardon me for my late reply, as I’ve been quite busy lately. Anyway, here’s my answer to your arguments:

Hypotheses, Theories, Laws, and Facts

First of all, I would to address how the 4 terms above are used in more detail.

Let’s start with facts. In science, facts are described as verifiable and objective observations, which means that its existence can be verified using the scientific method. For example, it is a fact that the Sun rises everyday, since it can verified using the scientific method and has overwhelming evidence for it.

A hypothesis is a rational and educated guess about the explanation for an observed phenomenon, but lacks evidence to support it.

A scientific theory, on the other hand, is a well-substantiated explanation of some aspect of the natural world, based on a body of hypotheses and laws that have been repeatedly confirmed through the scientific method. A theory explains a large set of related phenomena, and its details are subject to constant tweaking, but its core principle still remains. For example, the Theory of Evolution is described briefly as “descent with modification”, and while much of its details has been modified over time, its predictions still hold. Only when the core tenets of the theory is found out to be wrong is the theory considered as being false.

A scientific law is a descriptive principle of nature that manages to holds in all circumstances covered by the wording of the law. Plus, it implies a casual relationship between elements involved, is only able to describe an extremely finite set of observations, and doesn’t provide an explanation of how a phenomenon occurred; it only describes how it should work.

A common mistake to to assume that a scientific theory can become a scientific law, as there are several fundamental differences between the two. Firstly, as stated above, a scientific law only describes a phenomenon, while a theory explains one.

Plus, once it is found out that a law fails to describe even a single phenomenon that it covers, then it has to be overhauled or simply thrown out of the window; but if theory is found out to inaccurate, it’s simply modified, but rarely gets replaced entirely. A good analogy I found on Wilstar.com is this:

An analogy can be made using a slingshot and an automobile.

A scientific law is like a slingshot. A slingshot has but one moving part--the rubber band. If you put a rock in it and draw it back, the rock will fly out at a predictable speed, depending upon the distance the band is drawn back.

An automobile has many moving parts, all working in unison to perform the chore of transporting someone from one point to another point. An automobile is a complex piece of machinery. Sometimes, improvements are made to one or more component parts. A new set of spark plugs that are composed of a better alloy that can withstand heat better, for example, might replace the existing set. But the function of the automobile as a whole remains unchanged.

A theory is like the automobile. Components of it can be changed or improved upon, without changing the overall truth of the theory as a whole.

Thus, just because something is a theory instead of a law doesn't mean it lacks evidence; in fact, it's quite the contrary. However, both scientific theories and laws have one thing in common: they're just attempts to describe/explain scientific facts, through the most reliable method possible. Thus, it’s wrong to say that scientific laws are scientific facts.

Creationism Has No Backing Evidence

You said:

Also as far as the best theory that is possible, that is a pretty sad testimony for the theory of evolution. When it comes to the evidence concerning Intelligent Design, the evidence for a Creator is overwhelming. Have you ever looked at the evidence for a Creator Darren?

Let me make it clear: evolution is a theory well-supported by the evidence. Evidence for it from includes genetics, fossils, which are laid out exactly as evolution predicts, comparative anatomy, embryology and has been observed in real life. While I did not elaborate much on the evidence for evolution in my blog, I’ve already answered quite some attempts to “disprove” evolution in my Answering Creationist Claims series, and in my previous email to you on beneficial mutations. These include the no-transitional fossils argument, the irreducible complexity argument, the bird argument, the fixity of species argument, the entropy argument (read this again), the young-earth argument etc. So take a look at them, and have those replies considered deeply.

Now let’s consider creationism. For Biblical creation to be true, there needs to be a large amount of empirical evidence available for the Garden of Eden, creation of the universe within 6 days (or periods), birds coming before insects, and most importantly, that the Judeo-Christian God did it. Yet so far, there’s not even one peer-reviewed literature that presents any form of empirical evidence for creation.

The High Failure Rate of Biblical Prophecies

Before you say that the Bible has fulfilled every prophecies, here’s a list of those that it didn’t (there are also rebuttals on the prophecies you told me about) – Skeptic’s Annotated Bible: Prophecies in the Bible . Look at all these prophecies and refute everyone of them, or your statement that the Bible’s prophecies are 100% accurate is simply wrong.

Plus, some of the prophecies you stated were made true in the Bible (and the Dead Sea Scrolls), and since they aren’t independent sources, they’re unreliable – who knows, perhaps someone was modified the Bible for political reasons?

But let me tell you directly about one notable prophecy that failed. It is stated in the Bible (KJV) on the end of the world:

Matthew 24:34 - Verily I say unto you, This generation shall not pass, till all these things be fulfilled.

Mark 13:30 - Verily I say unto you, that this generation shall not pass, till all these things be done.

Luke 21:32 - Verily I say unto you, This generation shall not pass away, till all be fulfilled.

All these 3 passages have one thing in common – they state that Jesus predicted that the end would come within the lifespan of the listeners. The same statement is also reconfirmed in these passages:

Matthew 16:28 – Verily I say unto you, There be some standing here, which shall not taste of death, till they see the Son of man coming in his kingdom.

Mark 9:1 – And he said unto them, Verily I say unto you, That there be some of them that stand here, which shall not taste of death, till they have seen the kingdom of God come with power.

Luke 9:27 – But I tell you of a truth, there be some standing here, which shall not taste of death, till they see the kingdom of God.

So tell me, has the end of the world come yet? Has the kingdom of the Judeo-Christian God come to power? If not, then the Bible’s inerrancy is seriously doubted.

Yours sincerely,
Darren Wong

On a Side Note…

Chris is so much better than this fundamentalist from Bible Life Ministries.

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.

Jebbus, save me from your followers (if you exist).

I sent an email to Bible Life Ministries in hope that they would take a look at my blog, and have an intelligent conversation. Guess what I got? Insults. You would’ve thought that god-loving people will do better. Anyway, here’s the exchange:

1. Rebuttal of "Top Ten Scientific Facts Proving Charles Darwin's,Theory of Evolution is Wrong, False, and Impossible" – Me

Hi, Mr. Rieske. I'm Darren Wong, an evolutionist. I've took a look at your claims that the evolution is impossible, and I definitely do not agree with it. I have thus given rebuttals to it in my blog: http://warforscience.blogpsot.com. In my Answering Creationist Claims series, I gave evidence for evolution, and cleared up misconceptions about it. I hope sincerely that you would take a look at it, and see for yourself that evolution is scientifically established. Thanks.

PS: You can accept evolution and still be saved, right?
Romans 10:9 If you confess with your mouth the Lord Jesus and believe in your heart that God has raised Him from the dead, you will be saved. For with the heart one believes to righteousness, and with the mouth confession is made to salvation.

2. Re: Rebuttal of "Top Ten Scientific Facts Proving Charles Darwin's,Theory of Evolution is Wrong, False, and Impossible" – Kent Rieske

Hi Darren,
I nearly click the "X" on your email, and I certainly will without opening it if you write back.

First, I don't debate or bother with brainwashed people on blogs. Bible Life Ministries is NOT a debate forum.

Second, no you cannot accept evolution and be saved because you do not believe in your heart the very first verse in the Bible. You are lost and destined to spend eternity in HELL (which was also created by God).

Genesis 1: 1 In the beginning God created the heavens and the Earth.

Don't bother reading beyond Genesis 1:1 until you believe and accept it in your heart. You are simply brainwashed, and I have MORE BAD NEWS. You have no way to correct it. This page explains why.

Brainwashing, Psychiatry, Psychology, Psychotic, Sociology, Sociopath, Schizop

Kent

3. Ever Heard of Theistic Evolution? (Whether you bother to open it or not) – My Reply.

Whatever, Mr. Rieske, but have you ever heard of Theistic Evolution? It's the believe the Genesis and evolution are mutually compatible. See Answers in Creation. That's a good Christian website.

And when did evolution had anything to do with the beginning of the Universe and the Earth, anyway? It addresses the change of life over time (not the origin of life). And who is to say that god did not put this process into motion. For the Bible itself are full of parables, isn't it?

And you just contradicted yourself. You said that I'm going to hell (whatever that is) because I don't believe in Genesis 1:1, but isn't it said in Roman 10:9 that you only have to believe that Jesus was resurrected to be saved? Hey, even you said that on the website.

Lastly, before you call me brainwashed, I accepted evolution through myself. No one forced it upon me. My school hasn't taught it yet.

A Piece of My Mind

Oh yeah, Mr. Rieske, it does seem that I’m going to a non-existent hell that a “sky fairy” created, because he loves me, but I believe in evolution. Seriously, man, what’s this bullshit? I sent the email in hope of an intelligent debate. It seems I should’ve thought better.

Not only did Kent not even try and take a look at my points, he just outright insulted me, and cursed me to go to hell. Now, has Jesus not said that you should love your enemy? But such reactions are only to be expected from a fundamentalist. I doubt that a response will be given, but anyway, I’ll wait. For now, my friends, you may take a good laugh at the hypocritical and hard-headed mindset of this creationist.

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

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

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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)