Creationism, ID Thriving on Lies, Ignorance and Fallacies


Expelled:  No Intelligence Allowed

Expelling Expelled

I think this section will be the last post where I will discuss matters pertaining Intelligent Design (ID). I think that enough people have written enough about this movie, but I wish to illustrate Ben Stein as the sort of dishonesty that I frequently find in both Creationism and ID. Before continuing, again, I don’t think that Steve Fuller, Michael Behe, Stephen Meyer, William Dembski, and some other ID thinkers are dishonest people. I know that they are sincere in their belief and wish the advancement of science. But again, that doesn’t make them correct regarding their views on science, needless to say that it won’t excuse Stein from being so incredibly dishonest in this movie. This movie is propaganda in the worst sense of the word.

Supposed Expelled People from Academia

One of the things that Ben Stein wants to defend is "academic freedom". In U.S. jurisprudence, academic freedom involves two things: (1) the protection of a college teacher from undue pressures by the administration; (2) freedom of teachers to speak their mind. This is precisely derived from the First Amendment of the U.S. Constitution and protects education, even unpopular views, from antagonistic forces against academia. However, contrary to the impression given by Stein in the movie, this freedom also implies several responsibilities: among them, not being arbitrary, and respecting meritocracy (each teacher should earn his or her position according to his o her merit). Just as freedom of speech does not allow you to yell "fire!" in a theater, so academic freedom does not allow you to teach something unscientific as science in a science class. A science teacher who encourages a college or university to display a Creationist museum to "scientifically educate" people about the origin of the world should be expelled.

Having said that, maybe you will have the slight impression that I will be extremely happy that university, colleges and other institutions expelled certain people portrayed in … Expelled … for favoring ID. See … it is a bit more complicated than that. Let’s see each of these people who were allegedly "expelled":

  • Richard von Sternberg: The allegation is that Sternberg was fired from the Smithsonian Institute because he dared publish an article by Steven Meyer on "how life began". ( ~ Sad face ~ ) Yet, as it turns out, the paper in question was not about "how life began", but it was about the Cambrian Explosion. And he was not fired from the Smithsonian as he claims in Expelled. Congressmembers Mark Souder and Rick Santorum alleged that there was a "massive conspiracy" in the Smithsonian against Dr. Sternberg, and Soulder wrote a report on the incident whose original URL addy has been removed ( Fortunately, we do have access to certain online posts about it (the next best thing given the circumstances), like Ed Brayton’s article on the subject. As it turns out, contrary to what Stein claims in the movie, Mr. Sternberg did not follow the peer review process which is indispensable in all academic journals. To all of us academics, we know from the outset that this is highly irregular. He was not employed by the Smithsonian at the time, he was working for the National Institutes of Health. He was appointed by the Smithsonian for an unpaid position, and had access to the National Museum of Natural History for research. By the time Meyer’s paper was published, he had resigned from his position as journal editor six months earlier. Some firing! By the way, did I say that the Smithsonian renewed his status as Research Collaborator for three more years in 2006? Wow! His life is ruined indeed! ( ~ sniff!!! tears ~ ) Poor martyr! And I know that Stein was sooooooo concerned! It seems, though, that Sternberg is lying through his teeth.
  • Caroline Crocker: She claims that she was fired (or according to Ben Stein, beheaded) for just "mentioning" ID in slides she was showing he cell-biology students. According to her, for that reason alone she was expelled from George Mason University. First, she did not just mention ID, she was teaching Creationism and scientifically discredited Creationist statements (she even shows some of the slides), and her science students were outraged. She was not immediately expelled from teaching, she was able to finish the semester. She was under contract at the time, and the university was not obliged to renew it. She was not fired. Now she is employed at the Intelligent Design and Evolution Awareness (IDEA), a pro-ID organization.
  • Michael Egnor: He supposedly enraged Darwinists to the point of their wish to "exterminate" his career by … saying foul things about him in his blog! Why is that? Because he dared to say in his blog that doctors did not need to study evolution in order to practice medicine. Well, he was not fired from his job, he was not expelled, nothing has been made to his career. If you say something controversial in your blog (as I am doing now) and people respond in a nasty way, and then whine … all I have to tell you is: "Welcome to the Internet!" Lucky for me, I regulate comments in my blog! It is the advantage of being a blog administrator! I can’t control what others say about me in other blogs, though.
  • Robert Marks II: According to Stein, he was "forced" to return grant money because he said something about ID in his website. As it turns out, the reason why his website was shut down temporarily was because it was hosted by Baylor University. The administration was concerned that ID would be linked to Baylor, and it did not want to be associated with it. Baylor granted Marks his wish for Baylor to host his website, as long as he didn’t use the term "laboratory" to describe what he was doing there. The website in question was totally unrelated to his research in Baylor, hence it served no academic purpose. By the way, he was never expelled from anywhere. He is still holds his position as full professor of the School of Engineering and Computer Science (see?! … his website has NOTHING to do with his academic research).
  • Guillermo González: Supposedly he had problems in Iowa State University because of his book on ID, despite, according to Stein, a "stellar research record" which included the discovery of several planets! Wow! How could you fire someone like that?! Unless … that’s false. He has never been credited with the discovery of any extra-solar planets at all during his stay in Iowa University. He claims that he was denied tenure, which placed his career in jeopardy. In the academic world we know that such denials happen all the time. During his stay in Iowa State University, he had made absolutely no valuable research at the time, no articles, no nothing. He only supervised one graduate student for dissertation, and that’s it. Doing almost nothing about what makes you have tenure usually will lead to … no tenure. Why would he be given tenure? And yes, he published his book on ID, and that may have influenced … why? Usually if you publish a book describing your perspectives, but is not based on any actual research … guess what? … it won’t count for tenure!
  • Pamela R. Winnick: According to Stein, Winnick, as a reporter, was pressured to take sides in favor of evolution, but that she preferred to remain neutral. This is completely untrue. Her articles are completely in favor of ID since 2000. In 2001, she interviewed Michael Behe, and refused to make any hard questions to him. Then she heavily criticized PBS’ Evolution series (I highly recommend them), because they did not cover ID, falsely claiming that ID had been favored by prestigious universities on scientific grounds. Later, in 2005, she wrote another article which was completely anti-evolution. She has done the same in the Weekly Standard and the Wall Street Journal. Is this being "neutral"? And what is interesting … she was never fired from her job. She still write articles in the Post-Gazette. Figure that!

The Pseudo-Conflict: Science v. God

The movie is set up so that it appears that there is actual conflict between evolution and a belief in God, and we can see that structure all the way in the movie. All of the pro-evolution people interviewed in the movie are professed atheists. And even when there are atheists in the movie who are friendly to religion (D. Eugenie Scott and Michael Ruse), the movie focused on religion’s foes: Richard Dawkins, Daniel Dennett, and P. Z. Myers.

Why didn’t Stein interview Kenneth Miller, or Francis Collins (the head of the Human Genome Project), or Francisco Ayala, or many other renowned scientists who have made very significant contributions to science, are Neo-Darwinists, and also believe in God? The editors of Scientific America asked Mark Mathis (the film’s co-producer) why didn’t they include these pro-evolution religious scientists to the discussion. His answer was that: "Ken Miller would have confused the film unnecessarily." What?! I think that by not including these scientists, the film purposely confuses the public.

This is confirmed by the fact that Stein interviewed Dawkins’ foe, Alister McGrath. Stein shows that McGrath effectively argues against Dawkins’ book, The God Delusion, but for some reason he forgets to say that McGrath is pro-Neo-Darwinian evolution and that he is a deep admirer of Dawkins’ books where he discusses evolution. He even loves Dawkins’ first masterpiece The Selfish Gene. Where he does not agree with Dawkins is in the way he deals with the subject of God and theology in general, and criticizes (rightfully) Dawkins’ concepts of "memes" and "virus of the mind".

The same thing happens when he interviews John Polkinghorne. He is one big promoter of process theology, which is an evolution-embracing theology. Why doesn’t he ask Polkinghorne about his views on evolution? Why does he only ask him about the so-called "warfare" between science and religion?

As a Christian, and Roman Catholic, this makes me furious. This is a complete distortion of the states-of-affairs of present-day relationship between science and religion.

Weird Interviews

I was intrigued by the fact that Stein believed that it was appropriate and very, very wise to interview Jonathan Wells regarding the validity of ID. Isn’t he one of those scientists who deny that HIV causes AIDS, despite all of the evidence for it? Interesting!

Oh, and by the way, he is a Unificationist, and he says that it was in the Unification Theological Seminary, and reflecting on the teachings of Sun Myung Moon, that he discovered that it was his mission in life to destroy Darwinism. Wow! There is a scientific motive! (?!) He’s soooo very objective regarding his statement that Darwinists distort evidence purposely. Do you want to count on this guy to do science?!

Later, Wells says in the movie that he does favor the idea that some species change over time, but his objection to Darwin was that his book was called The Origin of Species. Yet, apparently he never even read the book, because he says that Darwin wrote a book about the origin of species, implying that somehow Darwin dealt with the question of abiogenesis, the matter of how life began. News-Flash: Darwin never dealt with the problem of abiogenesis. When he was talking about the origin of species, he was talking about speciation, the way new species appear from earlier ones. Ah! And by Stein assenting to Wells’ statement, he reveals he never read Darwin at all. A little piece of advice: when you do a great enterprise, such as … I don’t know … making a documentary … be sure to read and know your stuff before doing the documentary.

He also interviews David Berlinski …. considering that he is also an AIDS denialist, global-warming skeptic, I wonder if such an interview was wise too. Among his many "brilliant" statements we find that he mis-characterized Jon von Neumann as being an evolution skeptic, while in reality he was all for Darwinian evolution. He also disputed whale evolution and made all sorts of interesting calculations about it, but he admitted that he did not have any evidence to back that up (he never looked at the genetic evidence, for instance). Too bad! Oh, and Ann Coulter, that despicable person who shows her face many times on so-called "TV-news" (FOX News is not a news network), says she was tutored by Berlinski (and Dembski). Wow! That will certainly add his scientific credibility on the matter!

Much later in the movie, Stein interviews Dr. Marciej Giertych, a population geneticist, who claims that Darwin says that "information" (genetic information?) increased over time, but that such thing was not possible, because nothing in genetics shows increase on information. Wow! That is some claim, except that it is not true. (I’m sorry that me … a philosopher … have to correct a population geneticist). First, Darwin never talked about information. Secondly, increased genetic information has been observed empirically. For example, some years ago (1975), some scientists discovered something they considered highly improbable: bacteria growing on nylon. The problem was that nylon is a purely synthetic substance and bacteria won’t grow on it … yet, there it was! What happened? Through genetic study of the bacteria they realized that what happened was that through mistakes in DNA replication of a certain sequence led to increase DNA information. This mutation made bacteria produce a substance called nylonase, which is an enzyme that lets bacteria digest nylon. In other words, increase in DNA information has been empirically tested (see Prijambada, et al. (1995) and Yomo, et al. (1992)). This is not the only case this occurs.

I love the fact that to counter-argue with Richard Dawkins, Stein says that Dawkins misleads the public when he says that no one sane or knowledgeable person would doubt evolution if they look at the evidence. Well, I would have to side with Dawkins this time in such a claim if the best Stein has is all the pro-ID people he interviewed.

Constant Caricaturing of Informed Scientists

I hate the fact that Stein prefers to make fun of knowledgeable people. When he says that Stanley Miller did his experiment and failed, he said that "many" abandoned his line of research. Who are the "many" people he’s talking about? Stanley Miller and many other labs do continue making an abiogenesis research, some in more or less the same line as Miller’s.

He interviews Michael Ruse, one of the world experts on Darwin and evolution, formed biologist, today philosopher of biology. Ruse says that a popular theory of abiogenesis is that life probably began with crystals. Stein mockingly showed a magician with a crystal ball to make fun of the theory. For those who don’t know chemistry: a crystal is a substance whose molecules align or form a regular pattern. For example, graphite (which is used commonly in pencils) is a crystal because the Carbon molecules form a consistent hexagonal shape, diamonds are crystals, ice-water is crystal too (the water molecules align when they are below zero), and so on. By mocking Ruse regarding crystals, Stein is confessing his own ignorance on the subject, and further he kept showing such overwhelming foolish ignorance by insisting that he didn’t see how do you get from "mud" to "living being". "Mud" has never been discussed in abiogenesis.

Further, he purposely distorts the theory of panspermia to mean that life was seeded by aliens. Such a statement is blatantly false! The panspermia theory says that probably a meteorite carrying life came from space. This is one of the best expressions of Stein’s dishonesty.

He also questions Eugenie Scott when she says that one of the best kept secrets is that many religious people are OK with evolution. Despite Stein’s comments in this respect, this statement is true. However, he paints this as if it is a conservative v. liberal sort of debate. Yet, for instance, in Dover, Pennsylvania, the vast majority of Christians who defended evolution there were not liberal. Some of them were hard-core conservatives. In one of Ken Miller’s speeches on evolution and ID in Ohio, the hostess of the activity said that a great number of people supporting evolution were conservatives, and liberals in that state were not as active in defending teaching evolution.

Finally, I wish to state that despite the positions expressed by P. Z. Myers, Dawkins and Dennett in their interviews with Stein, the fact is that they stopped believing in God as the result of their acquaintance with evolutionary theory, this is just their experience. Other people have responded to Neo-Darwinian evolution differently. Kenneth Miller has stated that he believes in God in part because of evolution, Darrel Falk says that evolution has enriched his religious convictions and spiritual life, Alister McGrath sees evolution as a product of the Creator God, and so on. In my personal case, evolution has enriched my relationship and understanding of God, as well as to understand our own humanity and ways to look for solidarity, not only with the rest of humanity, but with every living being on this planet.

Misrepresenting the Law

Stein questions the tendency to address the issues regarding Creationism and ID in court. Well, he is very intelligent, and should know that the U.S. Constitution says that there is a separation of Church and State. Public schools cannot teach anything religious, because that would mean that the state is teaching a particular religion as being true. If ID turns out to be religious and not a scientific theory, then its teaching in science school is a violation of the First Amendment of the Constitution, since the state is injuring children who have the right to freedom of religion.

ID claims it is not religious, yet it still has to show that it is science. It has not shown that under any stretch of the imagination. Buckingham and Bonsel were religiously motivated when they promoted ID in school. Teachers and students’ parents were injured when the School Board decided that ID should be taught, it was a violation of the First Amendment. Case closed!

Unquestioning Devotion to Darwinism: Nazi Germany???!!!

Stein proceeds to make this reasoning, which is nothing but a chain of non-sequiturs: evolution leads to atheism, atheism leads to no ethics, no ethics leads to fascism (Nazi Germany and the extermination of Jews). There is absolutely no sociological or historical basis for this.

He uses Berlinski’s "wisdom" to brighten his mind, when he says that Darwinism is not sufficient for being a Hitler, but it is "necessary". How does he know? Because he read Hitler’s Mein Kampf and "Darwinism is there" (whatever that means). This view is promoted by Richard Weikart with his book From Darwin to Hitler. He is a known member of the Discovery Institute, as is Berlinski. I’m not going to say that each member of the Discovery Institute holds this view (I have no evidence for it), but it is highly suggestive.

Before blaming Darwin for gross anti-Semitism and fascism, I wonder if we should first follow Our Lord’s advice. Christians should look first at our log in our own eye (remember my previous post?). For instance, how did this whole anti-Semitism thing begin in Europe? Romans were anti-Semitic, and Christians did not do much to make it go away. Quite the contrary, we Christians embraced it! Remember the Crusades? When Pope Urban II called for a Crusade to fight against the "enemies of Christ and every race on this Earth" (he referred to the Moslems), this had an effect over all of Europe. One of the reactions was to kill Jews. Why Jews? German warlords reasoned the following way: why do we need to travel all the way to the Holy Land, if we have the "enemies of Christ" right here with us? What was the result? The first Holocaust ever! In 1096, the Jews in Spier, Worms, Manz, Cologne, Trier, Metz, and other towns were simply assassinated by people going to the Crusades. The Pope didn’t intend for Jews to be killed, and yet, Christians took the initiative of killing them without mercy. So, each time that the Pope called for a new Crusade, Jews would be killed. The Crusades were the ones which led to institutionalize anti-Semitism in Europe, an attitude which reached the twentieth century.

Forgive my pedantry, but I wish to point out that the Crusaders had no knowledge of Darwin or evolution by then. The Crusades began in the eleventh century, while Darwin lived in the nineteenth century. So, Berlinski’s assertions are simply false.

In fact, if we want to be honest, the vast majority of people who read Darwin would never create a Nazi government, nor would they kill Jews or condemn them to concentration camps. They would never favor someone like Hitler in power. Neo-Darwinism does not imply fascism, nor Nazi ideology.

In the cyberworld there is a term for this: Godwin’s Law. The law says the following: "As an online discussion grows longer, the probability of comparison involving Nazis or Hitler approaches 100%." Ben Stein’s movie is nothing more than a glorified instance of Godwin’s Law. It is a reductio ad Hitlerium by excellence.


Expelled is nothing more than propaganda by Ben Stein. I’m deeply sorry, because I consider Stein to be intelligent, but he did show he is willing to mislead, lie and deceive in this movie. With this article, I close the subject of evolution v. ID.

I’m going to continue talking about the brain, human nature and culture in our next posts.


Prijambada, I. D., Negoro, S., Yomo T., Urabe, I. (1995, May). Emergence of nylon oligomer degradation enzymes in pseudomonas aeruginosa PAO through experimental evolution. Applied Environmental Microbiology, 61, 5, 2020-2022.

Yomo, T., Urabe, I., Okada, H. (1992, May). No stop codons in the antisense strands on the genes for nylon oligomer degradation. Procedures of the National Academy of Science of the United States of America, 89, 9, 3780-3784. doi: 10.1073/pnas.89.9.3780

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Intelligent Design Thriving on Lies and Ignorance

Do not judge, and you will not be judged; because the judgments you give
are the judgments you will get, and the standard you use will be the
standard used for you. Why do you observe the splinter in your brother’s eye
and never notice the great log in your own? . . . Hypocrite!

~ Jesus of Nazareth (Matthew 7:1-3,5a)

From Part IX on, we will focus on culture, morals and ethics in full, leaving gradually biological discussions behind. However, these series would be incomplete without a final note on Creationism and Intelligent Design (ID) movement in general. Unlike other articles, this one is explicitly made to condemn much of their views and accusations to those scientists, philosophers, religious people and even Charles Darwin himself.

If there are people who wish to believe as a matter of faith that the world was created in six days, or that humanity came from wet dirt, and so on, it is definitely their right to do so. However, they have no right to two things:

  1. Say that an opinion or group of statements which clearly do not constitute a proper scientific theory is science;
  2. Try to teach such opinion or group of statements as science

Religious thinking can be good if it moves people to search for the truth in honesty. Contrary to the views held by the so-called four "horsemen" of New Atheism (Richard Dawkins, Daniel Dennett, Sam Harris and Christopher Hitchens), religion can move people to search for the truth, but this will only do if it is done under a specific framework, where religion can invite rational discussions about a variety of subjects, and does not interpret its Sacred texts as being literally true (i.e. literalism). Our Lord explicitly condemned the approach of placing the letter of the Law over other people’s dignity and the truth. As Hans Küng rightfully points out, He relativized Sacred Scripture in order to follow what is objectively good for individuals and society (Matthew 5:17-48; 19:1-30; 23:1-36; Mark 2:23-27). This is an example followed by St. Paul later when he converted from a zealous Jew to become the sort of Christian who opened the door to much tolerance (not completely) for the benefit of gentility, women, slaves, and others (see my articles about this specific subject: part 1, part 2, part 3).

A religion or spiritual path which leads to our own growth must have a component of what Scott Peck called "dedication to reality". In the religious arena, this translates to the practice of putting our faith to the test. If you suppose that every single word in the Bible is true verbatim, then you must subject it to be tested through both logic and empirical evidence. Literalist views of the Bible fail altogether in both aspects, because the Bible is a book that contradicts itself very much, and at the same time some of its claims (not everything) have been shown to be archaeologically or historically false.

The approach made by many Christians since Christianity’s infancy and even earlier (with Judaism) is to not treat Genesis literally. We have a very nice tradition that dates back as early as the beginning of the first century A.D. with the Jewish philosopher Philo of Alexandria, who stated clearly that the nature of the stories in Genesis should lead any thinking mind to recognize that the story of creation cannot be taken literally. This is a tradition followed by many Christian thinkers, especially the most eminent cases of Saint Augustine of Hippo and Saint Thomas Aquinas. Even Pope John Paul II treated both stories of creation (Gen. 1:1-2:4a; Gen. 2:4b ff.) as being myths, which were directed to people who had no scientific framework to understand what we are able to comprehend today. And he is not the only one to have this opinion, because in many Christian denominations there are people who have completely embraced this idea. There are many theologians and scientists who have proposed viable alternatives to understand creation from an evolutionary standpoint: Kenneth Miller, Michael Dowd, John Haught, Francis Collins, Alister McGrath, Darrel R. Falk, Karl W. Giberson, Hans Küng, Denis Edwards, and John Polkinghorne, just to mention a few. There are many Christian organizations made up of scientists around the world who clearly embrace evolution and reconcile it with Christian faith, such as the BioLogos Foundation, the American Scientific Affiliation, and Chistians in Science. Even atheists such as Michael Ruse reject the assertion made by the so-called "new-atheists" that a Christian cannot be an honest Neo-Darwinian. Even when he identifies several problems with Christian theology, Ruse’s conclusion is that Neo-Darwinians can be Christians and vice-versa. Chris Mooney and Sheril Kirshenbaum, who are openly atheists or agnostics, also attack the so called "new-atheists" for their statement that an honest Darwinist should reject any faith in God, or any form of theological understanding of evolution. Other evolutionists like Douglas J. Futuyma and Charles Susanne have pointed out that the acceptance of evolution does not imply much about the belief in God, and we cannot state that such a belief is incompatible with many religious views. The literal refutation of Genesis, along with scientific discoveries and spiritual insight help us grow spiritually in any religious tradition. To adopt literalism is to cripple our spirit. Like Michael Dowd says, evolution will lead religious and spiritual traditions to their glory if they accept the "Gospel according to St. Charles [Darwin]".

Dedication to reality implies dedication to the truth. Reality and truth are correlates, since truths tell us many aspects about reality. To abandon dedication to reality, and all commitment to reason in order to embrace Biblical literalism inevitably leads to three things: lies, ignorance and fallacies. Unfortunately, these are what we see in Creationism and the Intelligent Design movements.

Hoaxes and Mistakes in Science

Before judging Creationism and ID, let us look first at "the log in our own eye" before looking at the splinter in both of these movements.

Certainly there have been many frauds hoaxes in science since it started existence. Creationists and ID advocates love to throw them at the face of us who favor evolution. For instance, the Piltdown Man fraud, where supposedly fragments of an "unknown early human" skull and jawbone were discovered in 1915. Supposedly this was a "missing link" between man and earlier forms of primates. For many years it was used as evidence of evolution, but in 1953 it was discovered to be a hoax: they were the lower jawbone of an orangutan placed as pieces of a fully developed modern human bone.

There have been many similar forgeries, hoaxes and cases of misidentification. Here are some of them:

  • Piltdown Man: forgery created in 1915, discovered as forgery in 1953
  • Nebraska Man: discovered in 1917, it was a case of misidentification demystified in 1925.
  • Rhodesian Man: discovered in 1921 is another case of misidentification where the human jaw, sacrum, tibia and bones were wrongly used for a skull of a Neanderthal (Homo neanderthalensis); demystified in 1974.

This is not limited to frauds regarding the so-called "missing link" between "apes and humans". As I have said in Part IV of this series, there cannot be any missing link between apes and humans, because we didn’t come from apes, nor monkeys, nor chimpanzees. Neither Darwin nor any other evolutionist ever talked about apes being ancestors of humans. Secondly, we have enough substantial evidence that there are no missing links between earlier forms of primates and humans. We could discover additional fossils which can help us establish a more complete picture of the jigsaw puzzle of evolutionary ancestry, but as far as it goes there are next to no gaps left to fill.

However, there have been other cases of misidentification, for example, in the case of the Burgess Shale:

  • The Anomalocaris saron was mistaken for an odd species of shrimp.
  • The mouth of an Anomalocaris was mistaken for a jellyfish.

The fraud and mistaken-identity arena is not limited to fossil discoveries either. It can extend to embryos. For example, Ernst Haeckel is famous for having drawn embryos he said he studied and used them as a proof of evolution. Today, even some biology books point to him as the real discoverer of the structure of embryos as evidence for evolution. Unfortunately, much of these drawings have been shown to be evident fraud, and that some of the embryos he drew were not the ones he claimed to have studied (see Richardson (1998)).

There are other experiments whose importance have been completely overblown, especially when it comes to the subject of abiogenesis. This is a separate question in relation to Neo-Darwinian evolution, since the evolution only explains how organisms change and evolve, while abiogenesis is merely concerned about how life began. For example, Alexander Oparin formulated the theory of the primeval organic soup from which life is supposed to have come to be. Many years later, Stanley Miller used Oparin’s theory, included energy (in the form of electricity), and this organic soup generated aminoacids, which are the building blocks of life. This experiment had strong implications regarding life’s origins. However, a careful scientific analysis did show that the combination of substances of the primeval soup were wrong, because apparently it did not agree with what has been found archaeologically, and seem not to correspond with the original environment of more than three billion years ago.

Mistakes happen in science! Sometimes intentional, sometimes not! However, we must be careful before condemning all of science as a faulty enterprise, and all its knowledge as invalid. Contrary to claims being made by many religious people, science is a humble discipline in general. Science does assume that mistakes and frauds are going to happen from time to time. Mistakes, whether intentional or not, are part of human nature, is part of what we are. However, science has created self-correcting mechanisms which enable it to discover in the end some set of "evidence" as fraud, hoax, forgery, misidentification, mistake or error. The people who discovered that the Piltdown Man was a hoax were scientists, and in fact evolutionists: especially Gerrit Smith Miller, Jr. and Franz Weidenreich. The same thing happened with the Burgess Shale discoveries, and many other cases. Why? Because natural science is based on logic and evidence.

Despite these hoaxes and mistakes, there is a vast amount of evidence … genuine, solid, corroborated, no-fooling evidence … of the evolution of our species. Most, if not all, of the intermediaries between Austhralopitecus afarensis and Homo sapiens sapiens have been accounted for in the fossil record. There are vast amounts of discoveries that show how amphibians developed limbs from fins (I discussed some of that in Part IV of our series), we even have enough fossil record that shows how whales evolved from land mammals (see Prothero (2007) and Coyne (2009)). We have SO much more that paleontology has discovered which is completely ignored by the media and, needless to say, people.

Even when Haeckel’s drawings were hoaxes, the rest of embryonic research has been genuine and true, and is a strong evidence for evolution. It is not as Answers in Genesis says, that if evolution were true then the embryos of millions of years ago should be significantly different from ours. Quite the contrary! Evolutionists say that if we have fish as the ancestors of all vertebrates, then the initial stages of amphybians’, reptiles’, birds’, and mammals’ embryonic development should look like fish, with much of the same fish structures (similar but not identical). As the embryo keeps developing, then the marked differences between animals begin to emerge. As it turns out, embryological research have spectacularly confirmed this hypothesis. The study of embryos have confirmed that due to this fish-like embryological process, we have hiccups, we have hernia (if males make too much effort), we have limbs, and many other features which have been shown to evolve from fish. The statement made by Answers in Genesis is nothing more than a misrepresentation by conservative and fundamentalist Christian groups. This is strange case where despite the forgery, Haeckel’s proposal was indeed correct.

Unfortunately, the public is completely ignorant about the continued research on abiogenesis, making many important discoveries regarding the possibilities of the origin of life. Stanley Miller’s team has considered not only the aminoacids being made in their lab (a total of 13 of 25 that are necessary for life), but also those that come from meteors. During the Earth’s formation, there was some heavy pounding of meteors for billions of years. Miller’s team and other groups have continued to experiment with other compounds in order to discover which combination of substances led to the origins of life.

What is mainstream’s Christianity (especially the conservative and fundamentalist sectors) contribution to science? Answer: Nothing. Their contribution has been limited to yelling: "Hooray! Hooray! The Piltdown Man is a forgery! Haeckel was a hoaxer! Hooray!" However, they have not made any research nor made any experiment to show that their statements are true.

In fact, the problem with much of the elite within the Creationist and ID movements is that they deceive, ignore evidence (and even hide it from the public), and worse … convince a whole lot of people that what they say is true. This is not humility, it is arrogance.

Back to the Dover Case …

(I Give the Background of the Dover Case in Part III of These Series)

Judge Jones III was FURIOUS! He never expected this from Christians who are supposed to not lie under oath. However, there they were. Both of the most vocal proponents of Creationism in the Dover School Board of Education were caught lying. When he wrote down his decision, Judge Jones called them liars four times (see pp. 46, 105, 115, 137). We could quote one of those times:

The citizens of the Dover area were poorly served by the members of the Board who voted for the ID Policy. It is ironic that several of these individuals, who so staunchly and proudly touted their religious convictions in public, would time and again lie to cover their tracks and disguise the real purpose behind the ID Policy (p. 137).

Now, if a Federal judge uses such strong language to refer to these very "good" Christian people, we have to look at what they did.

For instance, Bill Buckingham, former police man, and member of the Dover School Board, is Creationist by conviction, and he was vocal about it. However, in the Dover case, he conceded the teaching of ID as an alternative to Neo-Darwinism, in order to at least show that Darwin’s theory of evolution is not the only valid theory in science.

Judge Jones wanted to examine the motivations behind the Dover School Board for accepting On Pandas and People as an acceptable biology text book. He was asked in court by the Plaintiff’s lawyer if his motivation was religious. Buckingham claimed it was not, because ID (as taught in Pandas) was not conventional Creationism, but another "valid" scientific theory which happens to consider the existence of an intelligent designer. The attorney asked him to look at a video of his statements on the news, and this is what he saw:

He claimed that he made a human mistake, because he was nervous about the camera being in front of him. Ah! Let’s give him the benefit of the doubt. But …

… there was still another problem. Both Buckingham and another member of the Board, Alan Bonsel, in their sworn depositions, made a statement that they had absolutely no idea who donated the books of Pandas which appeared in the Dover school to be handed to science students. Later, on trial, Buckingham changed his story, and said that he asked the members of the church he belonged to about $1,100 to buy Pandas. He received some money through donation, he deposited the money and made a check ($860) and gave it to whoever wanted to buy the books. He claims now that he was told in his church that the check was going to be given to a "businessman" to buy the books for the school … but that he had absolutely no idea who that person was. However, in the trial he admitted he gave that check to Alan Bonsel, and it was Bonsel’s father who bought the books.

When Alan Bonsel went to testify, he stood by his deposition stating that he had absolutely no idea where the money came from. The Plaintiff’s attorney showed him a canceled $860 check endorsed by Bonsel himself. After showing him the check, and making him admit that Buckingham gave him the check, the attorney asked him: "Do you wish to reconsider your deposition statement that you had no idea where the check came from?" Then Bonsel tried to make the statement that what he meant in his deposition was that he did not know who exactly were the Church donors who placed the cash in the basket, therefore "he did not know where the money came from".

Judge Jones’ face was red with righteous rage and interrupted him saying something like this: "Stop! Hang on a minute! Don’t insult the intelligence of this court by pretending that by saying that you had no idea where the money came from it means that Buckingham and you solicited it, collected it, bundled it, and transmitted it!"

Ignoring Evidence

But this was not the only questionable aspect of ID defenders. As we said in Part III, one of the leading advocates for ID, Michael Behe, testified in court in order to defend his "irreducible complexity" proposal. As we saw in Part III of these series, he used the three icons of ID: the bacterial flagellum, the blood clot cascade, and the immune system. We showed the refutation of the claim of irreducible complexity in the cases of the bacterial flagellum and the blood clot cascade, but … what happened with the refutation of irreducible complexity in the case of the immune system?

In his book, Darwin’s Black Box, Behe argues that there is simply no scientific research published regarding the evolution of the immune system. The Plaintiff’s attorney asked precisely Behe about this fact. He placed in front of Dr. Behe a journal with an article on the evolution of the immune system and asked him if he read it before. He said no. Then he reached for another journal with another article about the same subject, he said no. Then he reached for another journal with another article, he said yes. Then he reached for other journals and academic books about the subject, until it piled up in front of Behe. The attorney said that it seemed incredible that he could claim that there has been no research published regarding the evolution of the immune system, yet, there they were! Behe’s response left Judge Jones perplexed. Behe said: "Yes! They are here! But they are still not enough!" The judge rightfully was surprised at the degree, not only of the complete lack of research he made in his book regarding his claim that science cannot account for the evolution of the immune system, but also that he was willing to ignore evidence to that effect. Today, much of the studies are focused on the way the immune system self-assembles as key to understand how it evolved. This self-assembly process is explained online by Kathryn Applegate, who has a PhD in computational biology: Part 1, Part 2, Part 3.

Behe’s move is not exlusive to him alone. For all practical purposes it permeates all of Creationism and ID. They usually project their own defect on those who favor Neo-Darwinian evolution. Projection is nothing but the evidence of their own lack of scientific standards.

One of the most eminent examples can be seen in On Pandas and People. If you read the book, you notice that it compares two animals: the Eusthenopteron, which is considered a fish, and the Ichthyostega, which is considered an amphibian (p. 103). Then it falsely states that, between both, there are no intermediary species, and that there are evolutionary gaps between them, inferring that the Ichthyostega could have not evolved from fish, especially if you compare their the fins of the Eusthenopteron to Ichthyostega’s limb. Yet, by the time this book was published, there were already two transitional forms between them such as the Panderichthys and the Acanthostega (see Part IV of these series for an illustration on the evolution of these limbs). As a matter of fact, many years after Pandas was published, and during the Dover trial, Neil Shubin discovered the Tiktaalkik which is an intermediary between the Panderichthys and the Acanthostega (see Part IV of these series).

Evolution from Fins to Limbs

(From Boisvert, et al., 2008
a. Euthenopteron, b. Panderichthys, c. Tiktaalik, d. Acanthostega)

Hiding information from students is not good science, nor does it do any service to the truth. And this was not the only misleading statement. Pandas uses the concept of irreducible complexity, and showed the examples of the blood-clot cascade as evidence for it. It also used the same definition of Creationism used in earlier versions of the book. Pandas was removed from school curriculum as a biology textbook precisely because it purposely misled students. Too bad, so sad, but Pandas and other ID books should never be taught in schools as part of a science curriculum. It should be forbidden from science class by all means.

The same can be said about other claims, such as the one that says that no speciation a la Darwin has ever been observed. Of course, the grossest and caricaturish sort of this statement (a strawman) is when they say that you have never seen a duck begetting an alligator, nor a chimpanzee begetting humans. This is an invalid response, because no one who favors evolution has ever made such a claim, not even Darwin.

Regarding speciation though, we have been able to observe instances where this clearly happens or is in the process of happening. Since we don’t have millions of years for our disposal (due to our relatively short lifetimes), we cannot see how a giraffe, for instance, will evolve into something else. However, we can observe bacteria evolving into new species in lab. This is due to the fact that bacteria reproduce pretty fast. This has been done successfully with E. coli, as it has been worked out by Richard Lenski and his student Zachary Blount, who have been able to observe how bacteria evolve different ways to "solve" a problem of lack of food. These solutions are genetic mutations which, through natural selection, are able to succeed over others which didn’t have those specific mutations. Since these bacteria evolve in such a way in which parts of their genetic code interchanged between them leads to no reproduction (i.e. sexual reproduction), they can be considered new species. What is more amazing is that this was done using a procedure to isolate bacteria, and sometimes some isolated colonies of bacteria would evolve "finding" the same solution (see Blount et al. (2008), see also Dawkins (2009) for a less technical exposition and explanation of this experiment).

We have also seen speciation in some species of insects. Dianne Dodd has carried out experiments with fruit flies, isolating their populations through many generations, and when they are mixed, these populations can no longer reproduce with each other … hence speciation (see Dodd (1989)). There are other experiments which have been carried out with similar results: see Rice & Hostert (1993), Rice & Hostert (1993), Kikpatrick & Ravigné (2002), just to mention a few.

In nature, we even observe this process happening. For example, we have seen this in the case of walking-sticks in southern California which speciate due to their adaptation to new environments (See Nosil & Sandoval (2008), and here is the link to the article). It has even been seen in the case of salamanders (Niemiller (2008)) and mice (Britton-Davidian, et al. (2000))!

So the assertion that no speciation has ever been observed in nature or in lab is simply false. Why do Creationists and ID advocates keep saying that there is no evidence?! As Our Lord would say: "There is no worst blind person than he who doesn’t want to see. If you have ears to listen, then listen."

Being a True Follower of Christ and Being Honest

Despite everything I have shown, I don’t want to claim that all Creationists or ID advocates are dishonest people. I would say that the vast majority of those who follow these movements are honest people who have been misled. Their biology education is usually lousy, or they have been misled mostly by Church pastors, priests or other religious authorities.

I also want to point out that not even many of the people leading the ID movement are dishonest. For instance, it is hard for me to claim that Stephen Meyer, Michael Behe and William Dembski are dishonest. However, I do claim that their reasoning is full of philosophical and scientific gaps. None of their proposals have been accepted by mainstream science, precisely because the introduction of a supernatural force or entity into biological process lacks any explanatory value from a scientific standpoint. Dembski’s "no-free lunch" and the so-called "Fourth Law of Thermodynamics" have no scientific value or use whatsoever. Behe continues to promote irreducible complexity even when it has been completely refuted by science. Meyer still cannot grasp the concept of non-sequitur when he states that if something living seems designed, most probably it is because it has been intelligently designed. By doing this, they find sympathy in substantial amount of people whose agenda has nothing to do with their ID views. Bill Buckingham and Alan Bonsel are strict Creationists, they really believe that the Earth was created in six days. This is not a belief shared by Meyer, or Behe, or Dembski. On the other hand, Buckingham and Bonsel used ID precisely to further their agenda.

The lack of scientific standards of the ID think-tank, especially the Discovery Institute, opens a can of worms for science. In Dover, Behe asserted again and again that he favored a very loose definition of science that would admit astrology. The same reasoning could apply to magic, or Crowleian witchcraft, New Age spiritualism, etc. as being science. Once you let the supernatural in scientific explanations, you are destroying what makes science valuable: providing natural explanations for natural phenomena. Even Philip Johnson, the founder of the Discovery Institute and the founder of the ID movement recognizes this fact:

I . . . don’t think that there is really a theory of intelligent design at the present time to propose as a comparable alternative to Darwinian theory, which is, whatever errors it might contain, a fully worked out scheme. There is no intelligent design theory that is comparable. Working out a positive theory is the job of the scientific people that we have affiliated with the movement. Some of them are quite convinced that it is doable, but that is for them to prove. . . . No product is ready for competition in the educational world. ~ Berkeley Science Review (Spring 2006), my bold.

FollowingChrist means to follow the Way, the Truth and the Life. When Bill Buckingham addressed his Church, explicitly told its members to donate funds to buy Pandas, and said that Jesus Christ was crucified two thousand years ago, and that they should show they follow Christ by donating to buy these books. Not only it is a direct violation of the second commandment (thou shalt not take God’s name in vain), but also distorts the purpose of the Cross to mean that we serve Christ by buying books which purposely ignore facts, lying under oath, and misunderstanding what finding truth through science is all about. I wonder how Our Lord would say if He saw His followers acting like that.

But they are not the only liars. Despite that a lot of Creationists and people in the ID movement are honest people, others purposely keep lying to the public, even hiding evidence. One of them, I’m sad to say, is Ben Stein … and his movie Expelled! This will be the subject of my next post.

I only wanted to finish this first blog post of Part VIII by answering one question Dan Dennett asked theologian John Haught one time: shouldn’t ministers, priests, and religious authorities be held accountable each time they mislead people by saying that Creationism and ID are science, and evolution is not? The answer is "yes", they should be accountable.


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Why do We Have Hiccups?

Being human has its annoyances. For instance, don’t hiccups drive you crazy?! Many times they are brief. Other times, they can be a pain in the … neck … literally! Do you know that the longest uninterrupted hiccup lasted from 1922 to 1990? No kidding! The unfortunate guy who had this incredibly long problem was called Charles Osborne, look for it in the Guinness World of Records. According to one source, he hiccuped a total of 430 million times over that 68-year period.

Like the appendix, hiccups have absolutely no function, and no survival value whatsoever. They simply consist of involuntary contractions of the diaphragm which bring abrupt rushes of air into the lungs. Why do we have them? Neo-Darwinism has an answer to this problem.

Neil Shubin reminds us that we came from fish! Some of those fish evolved into amphibians, many of them which had gills, much like the Acanthostega. Our ancestors, fish and amphibians, had a very small brain which basically controlled all aspects of their body: breathing, digesting, heart beats, and so on. Basically, the brain consisted in what we now call the brain stem, the place where all of these processes took place. This means that the nerves that controlled breathing connect the stem of the brain directly to the gills, both which were located almost next to each other. This worked pretty well for our ancestors, as well as for fish today, but this arrangement sucks for mammals, especially humans.

As our ancestors kept evolving, we stopped breathing through those gills close to our brains. We now breathe with our lungs, which are located aaaallll the way down our chest, very far from our brain stem. If our bodies were "intelligently designed" such as Creationists and intelligent design (ID) advocates suggest, these nerves should connect the diaphragm with the spinal cord at the same level each to prevent all sorts of problems … such as hiccups. The nerves that control the diaphragm, the vangus and phrenic nerves, come from the brain stem and extend all the way to the chest cavity to reach the diaphragm. The longer these nerves, the more the chances that anything that affects them interrupts their activity, and when this happens … well .. hiccups!

Notice that hiccups show a rhythm, a pattern of sudden inhalation of air which Neil Shubin has noticed in amphibians such as tadpoles, they use both lungs and gills to breathe. The whole physical process between both is so similar, that biologists have proposed that they are one and the same process. They are so similar, that Shubin thinks about many of the ways we stop hiccups:

Gill breathing in tadpoles can be blocked by carbon dioxide, just like our hiccups. We can also block gill breathing by stretching the wall of the chest, just as we can stop hiccups by inhaling deeply and holding our breath. Perhaps we could even block gill breathing in tadpoles by having them drink a glass of water upside down (Shubin, 2009, p. 192).

The Brain is a Mess!

This whole deal about hiccups reveal that our nervous system is not so well designed. If this is so, what does this imply for our brain? It is one very amazing composite organ (or system of organs), but, as we have said in Part V, it is a mess. The professor of neuroscience at John Hopkins University, David Linden, says that he is impressed by the brain, but he is not amazed at how it is organized. He describes it as a "cobbled-together mess". We cannot understand the brain from an ID perspective, precisely because the brain does not seem to be "intelligently designed". According to Linden, the brain is "quirky, inefficient and bizarre … a weird agglomeration of ad hoc solutions that have accumulated throughout millions of years of evolutionary history" (Begley, 2007).

An analogy with the computer world will make you understand what he is talking about. In 1984, Richard Stallman wanted to create a new operative system he could call GNU (a recursive acronym which stands for "GNU’s Not Unix"). Every operative system has a kernel, which is the part of the program that actually allocates hardware resources to the programs it is running. He wanted to use the microkernel model, which he considered to be extremely powerful, and he would call the GNU Hurd ("Hurd" stands for "Hird of Unix-replacing daemons"; and what is a "Hird"? It stands for "Hurd of interfaces representing depth" … See? A mutually recursive acronym!) Why did he choose the microkernel model? Mostly because the kernel is divided into different servers, each carrying out a different job. This is the equivalent to the theory of division of labor in the software arena. The more servers carry out different jobs, the end result would be great, cheap but efficient. Having servers run together, but performing different complex tasks will make things a lot simpler.

Another programmer called Linus Torvalds begged to differ. He wanted to create his own kernel, which today is called Linux, which was built using another philosophy: the monolithic kernel. Why did he consider it better? In the case of the monolithic kernel you have a kernel that is one entity, indivisible, which carries out all the jobs. This would be far, far better in terms of efficiency and debugging than any microkernel.

Of course, we may ask why would microkernels be more inefficient to develop, operate and debug? It may well be that separating the kernel into servers to do different jobs would sound like a good idea, but then you have to coordinate among servers so that they run efficiently! As a result, you have a living nightmare. The GNU Hurd logo will give you an idea of why this is so complicated:

GNU Hurd Logo

To debug it is a living hell, because if the bug occurs in the connection between servers, then you’ll have to try to find out if the bug happened between server A and server B, or server A and server C, or if it does involve many servers simultaneously, or if it occurred before or after server A sent a signal to server B, and so on. As Linus states very clearly, the supposed simplicity of micokernels is a false simplicity.

It is not surprising that ever since 1990 the GNU Hurd is still in development phase and is not ready for public use. Linux, on the other hand, is widely used along with the rest of the GNU components, forming a GNU/Linux operative system. Today this operative system is being modified by corporations and user-communities everywhere in the form of distributions.

The problem with our brain is that it resembles a microkernel of hundreds of servers. There are too many parts of the brain carrying out so many different functions, and at the same time establishing the most implausible connections you can imagine, like, for instance, when the part of the brain that has to do with vision is in the very back of the brain, and it is divided into many different organs each carrying a different function for vision. There are twenty areas of the brain dedicated to just vision. As I have stated in Part V, the extreme degree of complexity in the brain is not and argument for Creationism or ID, because an intelligent designer would have made our brain far more efficiently an much less messy. Of course, you may claim that God is a wild and crazy guy, and that’s why He made our brains that way. I feel, though, that this is not a theology many people are willing to accept.

If we look at our from an evolutionary standpoint, the way our brain is organized makes perfect sense. At least the GNU Hurd is being intelligently designed, but our brain was not even designed by the GNU Project. It was designed through a series of legacies our ancestors left us within our own skull. We can see in it signs of exaptation: different organs performing different functions, and then together assuming another higher-level function.

Our Reptilian Brain … Again!

No one should be surprised at this fact. We have hiccups because our brain is organized according to our evolutionary ancestry. Hiccups are the result of our reptilian brain! As we have said in Part V, our brain is a set of organs, and is organized according to the way it evolved. Remember these illustrations inspired by Paul MacLean’s proposal?

Quadrune BrainQuadrune Brain
[Drawing by Nancy Margulies, reproduced with permission]

Remember that the "Lizard Legacy" represents the R-Complex, the "Lil’ Furry Mammal" is the lymbic system, the "Monkey Mind" is the Neocortex, and the "Higher Porpoise" is the Executive part of our brain.

The R-Complex, which is precisely the brain stem, is the one which causes hiccups when the nerves which control the diaphragm are affected in some way. Reptiles evolved from amphibians and still preserved the brain stem. The R-Complex, as it happens with fish and amphibians, also controls in great measure our heart beating, breathing, digestive system, sexual drive, and everything else involuntary but which keeps us alive.

However, the R-Complex is also the seat of other things. In humans, it also assumes other functions such as hierarchical thinking derived from the instinct of territoriality. There is a sense that a certain piece of land or place "belongs to us". Let’s not misrepresent this as a justification for capitalism’s ideal of private property. It is not about exploiting "what you buy or sell". What matters for the reptile is survival, and the place where it lives is essentially a scarce resource.

Not everything on Earth holds the same quality of life for a reptile. It is not the same to live near water, or to live in a forest, than to live in a desert or dry land. It is this reptilian instinct of territoriality which lets it defend its territory where it can prosper, nourish itself and reproduce. It is not a big surprise, then, that the reptilian part of our mind is the source of our inherent aggressive behavior. In the animal world, if you are not aggressive, you cannot defend "your territory", you cannot reproduce, hence your species will not survive. Aggressive behavior exists because of natural selection.

Of course, this insight made by Paul MacLean when he proposed the triune-brain theory (today the quadrune brain-theory) could be used by Social Darwinists to state that forms of violence in order to preserve a group, or race, or oppressive economic systems, are morally justified. The problem is that this perspective actually ignores other parts of the brain that evolved ,precisely because they also helped us survive and make better decisions than the R-Complex alone would ever do.

The Moral Importance of the Limbic System

She was all smiles, lovely as ever! Beautiful, slender, gorgeous, attractive. She was there to visit António Damásio, one of the most renowned neurobiolotists in the field.

António Damásio

She has had some seizures, which was the reason why she wanted Damásio to check her brain out. And she had something that we, a prima facie would regard as something charming about her: she had a very positive view of life. Yet, the problem was that she was too positive about life’s outcomes.

She was always cheerful, she could be very friendly, formed romantic relationships easily, and so on. But she had attitudes of positive thought that were inappropriate for any regular person to have under certain circumstances. In fact, she had no fear, nor anger in any way. She happened to be a great artist, dedicated to drawing. She could draw practically facial expressions which communicated all sorts of emotions … except fear.

So, Damásio carried out an experiment. He would show one hundred human faces so she would judge them: are they "trustworthy" or "approachable" people? If you showed them to any normal person, usually they all agree which faces seem as trustworthy and which are not. But the woman of our story was not able to do that. For her, all faces were "trustworthy".

The problem with not having particular negative emotions such as anger or fear is that you cannot make certain judgments according to states of emotions in other people, therefore making it impossible to know which situations could be risky, or call for caution, or even to be avoided altogether.

This woman had seizures, and at the same time was fearless because one of the amygdalae of her brain was almost completely calcified. The amygdala is a very important part of the limbic system, which regulates our emotions. As we have said in Part V, the limbic system is a legacy from our ancestors, the first primordial mammals, which developed through natural selection and genetic mutation a way to feel empathy towards their offspring, or towards other members of their group or species. It also helps drive our emotions towards feeding and reproducing. It is said that the limbic system mediates and regulates some aspects of our behavior which can be summed up with the four F’s: feeding, fighting, fleeing, and f … sexual behavior. 😛

As we can see, emotions play a vital role in making moral decisions, since they enable us to have empathy towards another, or to avoid circumstances, or to recognize a state of emotion in other people that will let us deal with them better under certain circumstances. Also, with the limbic system we find the residence of care and bonding. Many people who have an affected limbic system are unable to bond, love, or care appropriately, sometimes to the point of completely nullifying moral behavior. For instance, much of the most horrid serial killers have their amygdalae and/or the temporal lobe affected in some way (see more factual research here).

Also another point I want to bring, a little criticism to post-feminism. Post-feminism thrives in the idea that much of our stereotypes regarding women are of cultural origin and they need to be deconstructed. However, Steven Pinker, John Eccles and many cognitive scientists and neurobiologists have shown that usually most stereotypes people have are based on actual experience, it is not something instilled by culture in order to oppress the "other". For example, post-feminists criticize that most of society holds that females are generally more emotional than males, and that this is a male construct in a male-dominated society to place women as inferior. Quite the contrary, females in general are more emotional in many aspects than males, especially when it comes to bonding and empathy, and this in no way makes them inferior or completely irrational, or that males lack emotions or should not use emotions. The reason why they are emotional is that the connection among amygdalae in both hemispheres of the brain is usually larger than males. For this, and many other reasons, women are usually far better than males in detecting another person’s state of emotions.

This fact does not make females inferior or more irrational, especially when making moral and ethical judgments. One day a dear friend of mine, whom I hold as a model of kindness, humanity and spirituality, wrote me some months ago feeling somewhat frustrated, because most people didn’t feel as outraged as she was when she saw some injustice in the world, or when she saw hate-speech online, or when she saw some excesses by government or corporations. She felt naïve for having these feelings, because no one else seemed to care. I told her that if everyone had her sense of outrage, the world would be a much better place.

Anosognosia and the Neocortex

Of all mental illnesses, one of the most curious is anosognosia. Vilayanur Ramachandran had a very interesting patient. Mrs. Dodds had a physical problem, her left arm was paralyzed as a result of a stroke in the right hemisphere of the brain, but what was more amazing about her is that she denied that it was paralyzed. When Ramachandran asked her if she could move her arm, she did not do so, but she claimed that it was perfectly fine. When he asked her to touch his nose with her left hand, she claimed she was doing it despite the fact that it was "too obvious" that she was not doing it. She would also claim that she could clap, and if he asked her to do so, her paralyzed arm would remain unmoved, but claim she was clapping.

António Damásio had his share of patients like this:

My patient DJ had a complete left-side paralysis, but when I would ask her about her left arm, she would begin by saying that it was fine, that once, perhaps, it had been impaired but not any longer. When I would ask her to move her left arm, she would search around for it and, upon confronting the inert limb, she would ask whether I "really" wanted "it" to move. It was only then, as the result of my insistence, that she would acknowledge that "it doesn’t seem to do much by itself." Invariably, she would then have the good hand move the bad arm and state the obvious: "I can move it with my right hand." (Damásio, 1999, p. 211).

Sometimes, patients, after being told that they have something wrong, forget about such statement minutes later.

Why are there patients who behave this way? Most people in psychology have always tried to explain it a la Freud. The Freudian proposal is that the patient simply will not recognize something as unpleasant as his or her problem. It is simply a gross form of denial (understood as Freudian denial). The problem with this view is that even the patient is surprised that it is so amazingly evident to everyone else what he or she is denying is happening. This cannot be explained simply by a psychological defense mechanism.

A better explanation might be neurological. These are patients with a systematic damage of certain areas of the right hemisphere of the brain as the result of a stroke or an accident. This is due in part because the brain’s right hemisphere also deals with emotions in some way in a higher level. When it is affected, the patient doesn’t seem to respond emotionally well about it, and doesn’t seem to understand the magnitude of what is happening to him or her. Ramachandran theorizes that the story would be incomplete without the intervention of the left hemisphere, which is the part of the brain that "rationalizes" and "calculates" out of experience. When the brain is affected in the right hemisphere in such a way that belief systems mostly elaborated in the right side of the brain conflict with experience, the left side of the brain tries to deny the experience to keep the status quo so-to-speak.

Damásio’s perspective, different from Ramachandran’s in some aspects (though not mutually exclusive), proposes that these affected parts of the brain are essential for the development of the autobiographical self and the extended consciousness, and when they are damaged they affect these levels of our mental activity. As a result, they affect consciousness to a certain degree.

Of course, the right and left hemispheres exist only in one place, the Neocortex. As we discussed in Part V, it is the part of the brain that was developed by some of our ancestors, namely earlier forms of primates. This is where all the processes of emotion, recognition of faces, basic instincts, etc. are processed by the brain to a higher level. It is also the place where most of our rationalization and calculation takes place. In the case of humans, the Neocortex has grown so much that it constitutes 90% of our brain mass. It has developed so much, that it actually enhances our cognitive abilities such as language and working memory (the understanding and reasoning of certain complex tasks). No other primate has the brain development that we do. As patients of anosognosia can show very clearly, we can rationalize well our situation, even to the point of self-deception. On the other hand, having developed such higher level emotions and calculations has given us a very clear advantage over other animals.

As you might imagine, the Neocortex is also important to make moral decisions, because it helps us consider courses of action regarding difficult ethical circumstances and prioritize our values so we can carry out whatever it is that we should do.

However, a big Neocortex is not the only part of our brain that makes us uniquely human.

Our Executive Brain, or Why Phineas Gage Lost his Sanity

If there is a part of the brain that makes us uniquely human, that would be our frontal lobes, where the highest concentration of nerve-cells and nervous activity takes place in the brain. Paul MacLean’s original model conceived this area as part of the Neocortex, but the more recent model of the quadrune brain considers it a different area, because they have very unique properties that are not shared by the rest of the Neocortex. The frontal lobes of our brain are called the Executive Area, or the Executive Brain.

In Phineas Gage’s case, this part of the brain was suddenly missing.

Gage had an accident that would change the rest of his life. In 1848, while blowing up some rocks in order to place railroad tracks, one bar flew at him and literally went through his skull, more or less this way:

Phineas Gage

The fascinating thing about this incident is that he survived. When he recovered, he could speak, reason, recall his past, no paralyzed limbs, no blindness, and so on. Later, his wife, colleagues and friends claimed: "Gage is no longer Gage". There was a significant change in his character. He practically became profane, most irreverent, and disrespectful towards his family and friends. But there was more than that. Phineas Gage was described by his boss as been one of the most efficient men he had ever seen …. before the accident. What about after the accident? Gage would try engaging in projects which were proposed, but then abandoned instantly. Nothing ever suited him to do absolutely anything. He became so inefficient in trying to plan ahead or make decisions about those plans, that his boss had to fire him. As a result, he ended up as a "circus freak show" to be able to earn a bit of money.

Phineas Gage

He worked for a theatrical group for a while, with which he left for South America. By 1859, his health deteriorated, and after returning to the United States, he died in 1860. Apparently, such an accident made Gage an amoral animal, it made him lose his moral sense.

The reason why Gage changed drastically may have to do with the fact that the bar that went through his skull literally destroyed some part of his limbic system (explaining his profanity and attitude), but also the frontal lobes of the brain. We know that this may be true for the simple reasons that people today have endured some loss of that frontal part of the brain, and had similar problems.

For instance, Damásio does tell the story of how he met one man who lost part of the frontal lobe of his brain due to surgery to extirpate a brain tumor, he called him Elliot. Damásio was extremely surprised at the fact that, as Elliot was telling his story, he never showed any sort of emotion whatsoever, not a feeling of sadness, not joy, not happiness, not anger, not anything! Unlike Gage, he remained always respectful, but he was totally emotionless. However, like Gage, he had a problem: he could not be satisfied with a planned project. As a matter of fact, he found it difficult to plan a project in the first-place. He could not make any decisions about anything anymore, nor learn from his mistakes. Gage and Elliot lost all free will. This video shows another example:

Yes, it seems that the frontal lobes of the brain, the Executive Area, is the one part of the brain that lets us make a plan, foresee consequences, and make decisions. We could even say that this is the teleological part of our brain: it seeks a purpose and an end. Notice that in both Gage’s and Elliot’s cases, emotions seem to play a role. It is as if without emotions they were unable to make any decisions. This is not surprising given the fact that for our brain to function socially, it needs to use a means to an end, and that this end must be desired in some way, there must be an emotion that pushes us (so to speak) towards it. No emotions, no purpose, no decision-making. The Executive Area of the brain is that part of the brain that coordinates feelings and rational calculation.

This practically destroys one of the greatest myths that have been supported by philosophy and religious thinking for millenia: the opposition between reason and emotion. I call it the "Star Trek view". There is Dr. McCoy, who is all emotion, little reason; then there is Mr. Spock, who is a Vulcan, all reason and no emotion; and then there is James T. Kirk, who is sort of "in between". He listens to reason (Spock), and emotion (McCoy), and makes a decision. This is a false dichotomy. You cannot make any rational decisions without emotions. The false dichotomy arises from the fact that if we are too emotional, then we are not able to think straight. We agree. However, that does not mean that emotion does not play a role in our rational decisions. Having no faculty for empathy (as determined by the limbic system) would not enable us to ethically and rationally reflect on the pleasures and the pain of another person. To have no faculty of anger, we would not be able to be outraged against certain situations of human relations that call for it. As with everything, if you keep yourself emotionally balanced, you can make rational decisions.

As we have seen in this exposition all of the components of our brain are necessary to make moral and ethical decisions. This is the evolutionary recipe to forge a human brain, to make humans moral beings.

Evolutionary Explanation for Humanity Being Moral

Jorge José Ferrer, a Puerto Rican Jesuit priest and renowned bioethicist, gives us the most plausible explanation, from an evolutionary standpoint, for how we came to be moral beings.

  1. Instinct is not enough for humans: An instinct is a set of natural inclinations and impulses which drive any animal to act a certain way. Our R-Complex is the most instinctive of all of the parts of our brain, and enables us to adapt to an environment. Humans have some instincts: when we stumble, immediately our instinct is to move our body a certain way to be in equilibrium again. We could include here the instincts that drive us to feed, to sexual acts, and so on. Unlike other animals, though, instincts in humans are not as developed. For this reason, says Ferrer, we need longer care than other animals and we depend greatly on the protection of other humans. Humans also require a long process of learning, socialization and adaptation (Ferrer, 2007, pp. 31-32).
  2. Human intelligence: We have the most developed intelligence in the animal kingdom, which is the part that compensates our lack of instincts. As we have seen, our Neocortex is 90% of our brain, and our Executive Area is so well developed that it lets us make rational and moral decisions. Through intelligence, humans are able to understand reality, make plans for the future, and even modify the world according to our needs. It is for this reason that all humans have true moral and social duties. Due to intelligence, humans are the only ones who can foresee the long-term consequences of their actions (Ferrer, 2007, pp. 32-33).
  3. Autonomy: Also, because of intelligence, human beings in general have free will. A human being is not independent of his or her environment, but given certain circumstances, he or she can make a choice. Autonomy is defined by Ferrer as the capacity that people have to self-determine in order to achieve self-realization, choosing among many good means and ends they have before them (Ferrer, 2007, p. 34).
  4. Responsibility: Due to the fact that we are autonomous, we have responsibility, we are accountable for our actions. This arises from our sense of duty towards our conscience, towards society, and (if you are a religious person) towards God, Goddess, or Supreme Being, or Wholeness of the Universe, and so on (Ferrer, 2007, pp. 35-36).
  5. Sociality of humanity: Aristotle said "man is a political animal", i.e. animal of the polis, the community. Our best evolving mechanism is the fact that we live in communities, and we can only grow and develop individually when we are in a community. This is part of the reason why we developed a sense of duty and responsibility towards the community (Ferrer, 2007, pp. 36-37).
  6. Human vulnerability: Every living being is vulnerable: its life can come to a sudden end. However, unlike much of the animal kingdom, humans are highly vulnerable, and capable of being easily hurt or killed. We need to develop protection. This is part of the reasons we are able to recognize, from an evolutionary standpoint, the most basic moral norms of the community: no assassinating, no lying, no stealing, etc. This could be the evolutionary beginning of the development of an idea of morals as a whole, and the morals of virtues, which promote moral excellence (Ferrer, 2007, p. 37).

These are the six basic traits that constitute humanity as moral beings, and why we construct moral norms.


Begley, S. (2007, April 9). In our messy, reptilian brains. MSNBC. Available online:

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Damasio, A. (1999). The feeling of what happens: body and emotion in the making of consciousness. San Diego, US: Hancourt.

Dowd, M. (2007). Thank God for evolution: how the marriage of science and religion will transform your lie and our world. US: Plume.

Ferrer, J. J. (2007). Deber y deliberación: una invitación a la bioética. PR: Centro de Publicaciones Académicas, UPR-RUM.

Gazzaniga, M. S. (2006). The ethical brain: the science of our moral dilemmas. US: Harper Perennial.

MacLean, P. D. (1990). The triune brain in evolution: role in paleocerebral functions. Springer.

Ramachandran, V. S. (2004). A brief tour of human consciousness. NY: Pi Press.

Ramachandran, V. S. & Blakeslee, S. (1998). Phantoms in the brain: probing the mysteries of the human mind. NY: Harper Perennial.

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Humans’ Complicated Way of Seeing and Thinking

(c) 2010 Pedro M. Rosario Barbosa

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A Preacher on the Road …

Last year, I found the most amazing book called Thank God for Evolution. It stressed the importance on "marrying" science and religion in order to transform our lives, and the world. Bold claims! Here is the author: Michael Dowd.

Michael Dowd

If he looks like a preacher, that’s because he is. He is an ordained minister who preaches wherever he is invited in the United States. He used to be a young-earth Creationist, today he is a renowned preacher for evolution, not only of living things, but of evolution of the universe as a whole. He married an atheist called Connie Barlow, who is a biologist who is today struggling for the environment. One day, he told her that he wished to live on the road in order to preach a new perspective on God and creation, one meta-religious view which integrates evolution. He was surprised when she agreed. So, an act that almost makes us remember Christ’s call to "leave everything and follow Him", both of them left everything and dedicated to preach this new view of God. Today Dowd considers himself a crea-theist, while Barlow considers herself a cre-atheist. They preach the Gospel according to St. Charles … Darwin, of course.

They have a van, which they use to travel everywhere in the United States. On the side of it you’ll find the following image:


Dowd says that this image alone is enough to make people wonder. Of course, when he drives in the south of the United States, some people are not amused by it. According to him, he even gets some "interesting" gestures from people. When he pulled over to park his van in Lawrence, Kansas, a biology professor said: "Oh great! Now you piss everybody off!"

I have to confess that I was skeptical about his book when I picked it up. I was already acquainted with several efforts by some "spriritual" people to mix science with spiritual beliefs. I’m not fond of Deepak Chopra’s use of quantum physics, which tends to confuse rather than clarify. I’m not particularly crazy about What the [Bleep] do We Know? (much less about Down the Rabbit Hole), which is filled with misinformation and pseudoscience, and I most certainly despise The Secret, which is a scam in my opinion.

But here comes the interesting part: with the exception of academic books, I usually ignore book recommendations on the book, be it by The New York Times, or The Boston Globe, or, etc. Usually, they never help me distinguish between a good book or a bad one. recommended the Da Vinci Code only to write nasty articles about it afterwards.

Dowd’s book is the exception to the rule. Who endorses the book? Eugenie Scott (the director of the National Center for Science Education [!]), Michael Shermer (publisher of Skeptic magazine [!!]), Francisco Ayala (renowned scientist [geez whiz!]), John Haught (renowned Catholic theologian), five Nobel Prize winners (Craig Mello, John Mather, Thomas Schelling, Frank Wilczek, and Lee Hartwell), among many other credible people. So, I thought that the book may be worthy of being read.

When I opened it and gazed at it, the following two illustrations surprised me:

Quadrune Brain IQuadrune Brain II
[Drawing by Nancy Margulies, reproduced with permission]

It is interesting that this illustration appears in the chapter on original sin. Dowd claims in this chapter you cannot realize grace or sin if you don’t pay attention to your brain. According to him, the brain contains the "Great Story" of evolution. In order to "realize" original sin (this is, understand original sin in a way that is universally valid), we have to understand the Lizard, the Furry Li’l Mammal, the Monkey Mind, and the Higher Porpoise. As I kept reading it, I started smiling at the explanation he gave in the book regarding our brain.

Ah! And I bought the book …

Some People are Blind, and Yet, They can See!

Neuroscientists carry out all sorts of weird experiments every day. For instance, they carry out experiments on whether a blind man can see motion. This is not something that they come up because they have nothing to do. On the contrary, they are studying a well-documented phenomenon called "blind-sight". This phenomenon is due to the way the brain is "wired up". To help you with the explanation, I give you the following illustration.

Human Brain

Now, here is an illustration of how our eyes are connected to our brain:

[Modified version of an illustration of the brain by Patrick J. Lynch.
It includes illustration of the eye by
Joël Gubler and Jakov.
This illustration can be reproduced under the terms of
CC-BY-SA 3.0.]

From the eyeballs there are two separate pathways to the brain, one which goes to the thalamus, and then ends in the occipital lobe of the brain (black), while another one goes to the brain stem, and from it goes to the parietal lobe (green). The former is where the visual cortex of the brain can be found, the area used for conscious sight. This is the area that lets us see the objects around us. It is very important to point out that the other pathway goes to the brain stem, and from it there is a path to the higher centers of the brain.

The fascinating thing about the higher centers of the brain is that they are concerned with reaction to stimulus from a visual field, it directs your attention to something significant. People with blind-sight have the problem that one of the pathways (represented by black in the illustration) is non-functional, either because of an accident or a stroke, but they have the other pathway intact. As a result, they can "see" motion and react to it, but they cannot consciously see.

The funny thing is that many reptiles today cannot see the way we humans see. You may ask why do they have eyes in the first place? The answer is that reptiles can see motion, direction, and orientation of the eyes towards something significant. Even the novel and movie Jurassic Park exploited this trait for Tyrannosaurus rex. The reason why lizards can be so accurate in capturing flies with their tongue is not because they see them "just" as we do, but because they see motion and they react.

This reptilian quality that our brain carries out a subconscious or unconscious mental activity. Imagine that you are driving. You may be consciously focused ahead of you, or on the music that you are listening to, or in a conversation you are carrying out in the car, and so on. Your mind is focused on those activities, yet you keep driving perfectly well without problems, being aware that some stuff is happening in the periphery. Why is that? This is due in part to that "reptilian" trait, of being able to react if something unexpected happens in the street in the periphery of our attention. This unconscious activity of the brain will let us have a minimum attention on the street at a subconscious level, while we are consciously focusing on other things. It seems to be a survival mechanism. It not only lets us drive, but also let us walk. Thanks to it, we do not stumble with everything we find (unless our thoughts are too lost in space).

The Complexity of the Eye and the Brain

One of the arguments presented by Creationists or Intelligent Design (ID) proponents is that evolution itself cannot account for the complexity of the most complex organ that we have, which is the brain. I don’t blame them for thinking this. V. S. Ramachandran describes our brain this way:

… it has been calculated that the number of possible permutations and combinations of brain activity, in other words the numbers of brain states, exceeds the number of elementary particles in the known universe (Ramachandran, 2004, p. 3).

Even it has been argued that evolution cannot account for the complexity of something as perfect as the human eye. This is not surprising either, since vision is the sense that we all preer most. Aristotle in the Metaphysics begins by talking about human’s thirst for knowledge, and that evidence of this is the importance we give to our senses, especially the sense of sight. It is said that only an "intelligent designer" can account for a complexity that lets us function so well. I want to argue the opposite: the degree of complexity of the eye and the brain are exactly the sign that they were not intelligently designed, but forged by continuous mutation and adaptation.

Most of us marvel at our eyes, but not everyone is impressed. Hermann von Helmholtz, a physicist, took a look at the way the eye is arranged, and he was dismayed. His thought was that humans are able to build today better lens and cameras which do a much better job than the human eye! Helmholtz stated the following about the human eye:

If an optician wanted to sell me an instrument which had all these defects, I should think myself quite justified in blaming his carelessnesss in the strongest terms, and giving him back his instrument (quoted in Dawkins, 2009, p. 353).

Let’s look at the human eye.

Human Eye

[Illustration of the eye by Joël Gubler and Jakov.]

In the case of the eye we can look that the light enters through the pupils (on the left of the illustration) through the pupils so that it can be perceived by the retina (the fine dark-green line at the right). Immediately we notice that something is wrong with the architecture. For instance, the retina seems to be attached to another layer (represented in red) at the back of the eye. In reality, these two are not attached to each other. In some cases, as we age, the jelly inside the eye liquifies, and it can cause the retina to tear. This liquid then fills the in between layers, so that it creates a retinal detachment.

In the retina itself we can find other significant problems. For instance, there is a little dip which is our "blind spot". This is created by a set of nerve endings which curl up right behind that spot and create a pathway to the brain. But it gets weirder than this because the image perceived by the eye is inverted. Most of us notice this when we took anatomy and biology class in middle school or high school, but we never reflect on this as an imperfection in the eye.

Think about that. There is a blind spot in our eyes, yet, we have no "blind spot" in our vision. We can see everything "just fine"! This happens because our brain "fills" the gap in our vision. Let’s do the following experiment. When looking at the following image, cover your left eye, fix your right eye at the star and slowly move towards the screen. At some point you will notice the spot on the right disappear.

Blind Spot

Why does this happen? In order to compensate the loss of vision due to the blind spot, our brain fills whatever it cannot see due to the blind spot. That means that to compensate for the blind spot, the brain has to develop structures and signals. The blind spot, which is an imperfection of the eye, complicates the brain. If there were no blind spot, there would be no need for these brain sturctures.

The same thing happens with the "inverted" image that stimulates our retina. There should be brain structures to "invert" the image "inversion" by the eye. Once again this particular imperfection of the eye complicates the brain.

Another imperfection of the eye is its inability to perceive the vast majority off the radiation spectrum. We can only see a very small part of the radiation spectrum. And it assigns colors to different frequencies our eyes perceives. This further complicates the brain. Many people think that objects "have color". In reality, objects have no color themselves, they emanate light frequencies that reach our eyes, and our brain interpret these frequencies as colors.

Last, but not least, there is one major imperfection of the human eye. If you look at the way our retina is internally structured, you notice something very peculiar. If you design a camera to perceive everything very well, you try the best for the photosensible part of the camera to be exposed to the light. This is not the case with our retina. There are photocells (cells responsive to light) in the retina, but ironically they are away from the light. There are cells with several nerve endings in the side of the retina that receives the light, and these nerve endings deliver the information of the light to photocells inside the retina. Then this signal from the photocells goes to the nerves at the blind spot, to then send the signal to the brain. So, the brain not only has to compensate for the blind spot, but it also needs to compensate for the imperfection of having the photocells in the wrong place in the retina. Needless to say that the ill-designed retina complicates the brain further.

It is not a surprise that if you take into account all the regions of our brain dedicated to vision (thirty regions), they are a bit more than 1/3 of our brain.

Why in heaven’s name are our eyes so ill-made? Unfortunately neither Creationism nor ID can solve this problem. In the case of ID they would have to suppose that the designer must be REALLY stupid, a position not acceptable by Creationists in any way. Now, if we look at the evolution of the eyes, we can understand perfectly why the eye is the way it is.

See … nature is a "blind watchmaker", it is not "trying" to create an eye. It is not "trying" to create an ear, or teeth, or limbs. Evolution is a long process of gene mutation and natural selection. Metaphorically speaking, what nature does is not create an organ out of the blue, but slowly "use" mutation of the genetic code that is already there, and evolution "builds" from that genetic material that makes the phenotypical traits change enough so that through exaptation it creates a new organ.

Even if we were lacking fossils, we can look at different sorts of organisms alive today and present a theoretical model on how the human eye evolved. Why can we do it? Because many of the organisms alive today did not need to develop eyes the way we have in order to survive, they developed other means of survival that did not require a completely evolved human eye. We could ask: "if nature designs every species to survive, then why those organisms that don’t have eyes did not evolve eyes? Besides, it would have more survival value." Remember that since nature is not a conscious designer, it does not seek to "maximize" survival of each organism. Natural selection just lets be the mutations that are adequate (not perfect) for survival.

We can pick several organisms that could represent different stages of the evolution of the human eye. Here is the model itself:

Evolution of the Human Eye
[Illustration created by Matticus78]

Dan Eric Nilsson was the person who proposed this model. We can find many organisms in nature which represent these different stages of the evolution of the human eye. (a) From a set of photocells in an organism, nature would favor any tendency for those photocells to form a sort of cup that would give the organism more visual information on the surroundings. (b) The cup-structure would help shade the photocells from aspects of the environment. This "eye" can do little more than detect movement, such as in the case of flatworms. (c) That cup-structure made possible an additional measure for creating a "pinhole" that would control the amount of light it received by the "photocells", just as we see in the chambered nautilus. Essentially it helps focus light up to a point. (d) This made possible the development of an enclonsed chamber, (e) and later some lens filled with liquid jelly, which helped eyes to focus light more sharply on the photocells, we can find this in many animals such as birds and mammals. (f) As the eye kept filling with jelly and water, the images grew sharper, and sharper, until we (and many mammals) have the eye that we have today.

But What about the Brain?

A Messy Way Through our Mental Operations

Contrary to what many people think, the brain is not a simple organ. Quite the contrary. Some neurologists think the brain as a composite organ, while others think of it in terms of a system of organs. These organs of the brain are not very well organized either. If you didn’t know better about the relation between vision and the brain, you would swear that the logical place for vision is just at the frontal lobes of the brain. In fact they are all the way back.

Those parts of the brain that deal with motor skills and sensory areas are not well organized either. How are these sensory and motor organs spread in these areas of the brain? Let’s look at the Homunculi drawn by the famous neurologist Wilder Penfield:

PreCentral GyrusPostCentral Gyrus
[Illustrations of the Primary Somatosensory Cortex (left) and the Primary Motor Cortex (right)
Life Science Database Archives in Japan and available under a CC-BY-SA 2.1 JA]

Sensory and Motor Homunculi
[Illustration in Penfield & Rasmussen (1950): click to enlarge]

It should be noted that, after a thorough study of the brain, it has been found that the faces in these homunculi are actually inverted: the jaw and mouth are closer to the fingers, and the eyes are away from them.

We could ask, why is this so important? These illustrations help us realize something very important: brain development does not follow the reasoning of an intelligent designer. And these illustrations in turn help us explain why did we evolve certain behaviors, some of which we are not even aware of. For instance, Charles Darwin noticed that when some people are cutting with scissors, they clench and unclench their jaw mimicking the motion of the hand. Why is that? Again loot at the homunculus of the primary motor complex, noting that the face is actually inverted, the fingers (particularly the thumb and the index) are right next to the mouth and the jaw. The neural proximity of these areas can explain that kind of behavior (Ramachandran, 2004, p. 79).

Not only that, but it can also explain the phenomenon called "phantom limbs" so to speak. What is a phantom limb? Many people who have had accidents, or have been subject to surgeries, have lost an arm, or a leg. After it happens, they report that they still feel the arm or hand: they feel that they are waving goodbye, or petting their cat, or grabbing objects. What is interesting about this phenomenon is that when they are touched in some areas of the face, or even in a part of the arm that is not off the body, they can actually feel the same sensation in their phantom limb (especially phantom fingers and phantom hand). The reason is that both the part of the somatosensory cortex that controls the sensations of the hands are just next to the arm and to the face (again, remember that the face of the homunculus is inverted). So, when a person loses an arm the part of the somatosensory cortex of the arm and the hands are "hungry" for sensations. So, they literally invade the part of the cortex of the face and the jaw. So, when you are touched on the face or the jaw, you will feel the same sensation in the phantom hand or arm.

"The Great Story" in Our Heads

Now, according to Michael Dowd and his wife Connie Barlow, our brain tells us the Great Story: the story of the whole of reality, that reality called God. This story includes our evolution as a species. As I said before, they illustrate it like this.

Quadrune Brain

Now, why in the heavens would I buy a book that would represent the brain in an apparently weird, even childish manner? The answer is: it accurately represents how our brain evolved! It is actually based on a refinement of a model of the brain called the "Triune Brain" as it has been developed by the neurologist Paul D. MacLean. His proposal of the Triune Brain has been modified slightly due to the importance of the frontal lobes of the brain, as we shall see later, turning it into the Quadrune Brain proposal. Let’s begin with the exposition, shall we?

The Lizard Legacy

Lizard Legacy

The first significant evolutionary stage when our ancestors evolved from amphibians to reptiles is what Dowd calls "The Lizard Legacy", or as McLean called it: the R-Complex ("R" for "reptilian"). This complex consists in the brain stem and the cerebellum. Remember the phenomenon of "blind-sight"? Why do we have a reptilian quality of reacting and directing our eyes at something that seems important? The part of the brain that deals with that subconscious process is connected to the brain stem … precisely part of our R-Complex.

According to McLean, the R-Complex has to do with the most basic sexual instincts, impulse to search for food, and territoriality. Also, it reacts towards whatever is interpreted as a threat either to it or its territory. Hence, one of the most basic traits of the R-Complex is that in it resides the ability we have to aggressive behavior when we think we are threatened in some way, or if we are going to attack. Finally, because it is concerned with territorial protection, its conception of nature is hierarchical, there is a tendency to dominate others in order to protect itself or its territory. Also it deals with our ability to involuntarily breathe, respond to stimuli, and even "acquired muscle memory" (so to speak).

Furry Li’l Mammal

Furry Li'l Mammal

Dowd calls the next stage of our brain development as "Furry Li’l Mammal", also called the "paleomammalian complex", or as MacLean and neurobiologists call it: the Limbic System. It is a complex made up of the hippocampus, septum, thalamus, hypothalamus, insula, cingulate cortex, and amygdala.

This is the emotional region of the brain. This limbic system is shared by all mammals alike. Why is being a mammal linked to emotional states? There is a difference between mammals and reptiles: mammals in general care for their offspring, reptiles usually don’t. Emotional states can help bond parents (especially mothers) and offsprings. Love, in the emotional sense of the word, originates in the Limbic System. It also provides the biological basis for emotional responses to certain sense-stimuli, especially taste and smell. There is also a part of the limbic system dedicated to emotional responses to sexual stimuli.

The Monkey Mind

Monkey Mind

For Dowd there is also what he calls "The Monkey Mind", but called by neurobiologists "Neocortex". Dowd borrows the term "Monkey Mind" from Buddhism to somehow describe what the Neocortex does: calculation (e.g. it calculates risk or safety). However, this term is somehow imperfect, because in Buddhism’s case, they see the Monkey Mind as describing often capricious, uncontrollable, or confused behavior. On the other hand, our Neocortex lets us have an organized way to view the world, since it has spatial and mathematical reasoning, it makes language possible, it contains the higher functions that deal with what we perceive and our motor commands (as we saw in the case of the primary motor cotex). Conscious thinking and experience seems to take place in the Neocortex, as well as our ability to abstract from experience and forge abstract notions and concepts.

However, the term "Monkey Mind" may describe accurately how our brain evolved, since the development of the Neocortex came to be as our mammal ancestors evolved into primates. Humans have the most developed Neocortex in the animal kingdom.

Our Neocortex has been adapted to evolving two hemispheres. The left hemisphere controls operations of the right side of our body, and also engages in analytic and rational thinkin. The right hemisphere controls the left side of our body, and also engages in intuition and creativity.

Higher Porpoise

Higher Porpoise

Finally, Dowd calls the most developed part of the human brain (where our nerve cells concentrate the most) the "Higher Porpoise". MacLean assumed that the frontal lobes were part of the Neocortex, as indeed it is. However, careful studies have led some neurobiologists to make an essential distinction between the frontal lobes of the brain and the rest of the Neocortex. Some o them call "Executive Brain" to the frontal lobes of the brain. When this part of the human brain is recognized, MacLean’s proposal of the Triune Brain becomes the Quadrune Brain Model.

This is the part of the brain that carries out what Elkhonon Goldberg calls "executive functions", the most complex operations of the brain. According to Goldberg we can find in it four very important operations of the human brain: intentionality, purposefulness, self-awareness, and complex decision making. This has been developed only in humans, and, according to Goldberg, it is what makes us human. This is the part of the brain that can actually drive us into action, make moral commitments, make moral decisions, and even refrain us from expressing all of the impulses from other areas of the brain, especially the Limbic System and the R-Complex. It is also the part of the brain that lets us build a plan we are going to carry out in the future.

Our Evolved Brain

Just as we can correlate many stages of the evolution of the human eye with many organisms around the world, it is this methodology that lets us identify different evolutionary stages of the human brain. And we also find that each one of these stages has a very significant component of human behavior, especially regarding survival. We cannot regard all of these regions of the brain or all these stages of evolution as just "separate" operations. Each one of these regions and stages of the brain has an organic relationship with the rest of it. This organic interaction of the organs of the brain that makes it a system is what is the origin of human nature.

Without evolution, there is no human nature. The brain is very important evidence for exaptation, since much of the organs (or parts) of the brain once developed make the whole system have a new function, a new behavior. It shows evidence that it was not intelligently designed, but it is an important evidence that it has been designed by evolution. Everything in our brain has evolved according to natural selection, giving us an enormous advantage over many other organisms. Indeed, human intelligence and mental states have made us one of the most successful organisms on the face of this planet. So successful, in fact, that we represent a very real threat to the existence of other organisms everywhere in the world. This is an issue we will talk about in a future article.


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Darwin, C. (2008a). On the origin of species by means of natural selection of the preservation of favoured races in the struggle for life. NY: Bantam. (Originally published in 1859).

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Forget About Monkeys! We Came from Fish

(c) 2010 Pedro M. Rosario Barbosa

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This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.

Missing Link? What do you Mean “Missing”?
-Richard Dawkins

The Missing Link Regarding On Pandas and People: “Cdesign Proponentsists”

Remember we talked about the ID book On Pandas and People? During the Dover case, philosopher Barbara Forrest was scheduled to appear on trial regarding the background on that textbook. Many critics of ID thought that in essence ID was Creationism repackaged. There is a difference between both views. Creationism is the doctrine that creation happened the way the Bible says it happened. ID on the other hand can admit the existence of a very old Earth, but due to the high improbability of life happening, some intelligent agent (be it God, gods, extraterrestrials, and so on) intervened for life to be possible. ID, in this sense, sounds far more scientific than Creationism. Michael Behe, for instance, adopts this view in science. Since he produced the “irreducible complexity” principle, and neither ID proponents admit the concept exaptation, necessarily it requires that every new organism be created whole. Yet, critics did not believe that there was no relationship between both views. On Pandas, they found the “missing link” between those two different ways of looking at creation.

During the Dover trial, the plaintiff wanted to show that Pandas was essentially religion disguised as science. Pandas‘ publisher was subpoenaed and was asked for any drafts connected to the textbook. In a few months, the plantiff’s lawyers received two boxes full of papers and drafts related to Pandas’ publication. Forrest dug into all of the almost seven thousand pages they received. Beneath them all, there were two drafts of Pandas that were quite significant. She was very surprised and was amused when she read them. She called Kenneth Miller and said: “Ken, you are not going to believe what I’ve found in these drafts!” She told him about their content, and Miller was asking himself: “Haven’t these people learned anything from the Nixon administration. Burn this stuff!”

What did Forrest find? Well, as it turns out the two drafts in question were written at different times. One of them was written before 1987, the other was written after it. Why is 1987 relevant? Because that is the year the Supreme Court decided that teaching Creationism was essentially teaching religion, and that teaching it in public schools was a violation of the separation of Church and State, hence unconstitutional (Edwards v Aguillard, 482 US 570 (1987)). The first draft, which was written in 1987 before the Supreme Court decision, defined Creationism this way:

Creation means that various forms of life began abruptly through the agency of an intelligent Creator with their distinctive features already intact — fish with fins and scales, birds with feathers, beaks, and wings, etc.

But the draft written just after the decision defines ID this way:

Intelligent design means that various forms of life began abruptly through an intelligent agency, with their distinctive features already intact — fish with fins and scales, birds with feathers, beaks, and wings, etc.

So, for all purposes, it is almost exactly the same definition. One is worded in terms of Creationism, and the other is worded in ID language. But this is not the funny part.

Apparently what ID proponents did was to use their word processor and carry out an extensive “search and replace” operation throughout the text, substituting the word “creation” and similar terms with “intelligent design”. In doing so, apparently they did so in such a hurry, that they left a mistake. In one of the cases, they tried substituting “creationists” with “design proponents”. The result was the “missing link” between creationism and ID in Pandas: “cdesign proponentsists”. In the Kitzmiller v. Dover case, the draft showed Judge John Jones III that there was a “transitional form” between a creationist textbook and an ID textbook.

What did Darwin Mean by “Missing Link”?

Besides The Origin of Species, Darwin wrote another very important work called The Descent of Man, Selection in Relation to Sex, where he formulates hiw own views regarding the origin of humankind. He stated there that possibly primates, including us, originated from Africa. And also he hypothesized that humans and the rest of the primates share a common ancestor which is now extinct. He talked about the “missing link” between earlier forms of primates and humans.

The term “missing link” has been abused by both, those favoring Creationism and those favoring evolution. Sometimes it assumes that every single newly discovered form of life has to have a transitional form (a missing link). Richard Dawkins complains about this stating that in many cases evolutionists have met the goal of showing a transition form between one earlier life form and a later life form, but Creationists and ID proponents are unsatisfied. Why? Because both of these groups have a logical-strategic means to avoid recognizing these transition forms as transition forms.

Notice that in none of my earlier articles about evolution we talked about fossils. Dawkins and many others have pointed out that we know evolution to be what most probably occurred even if we had no fossils. They would hold fossils as a nice bonus. The evidence for evolution is overwhelming. It is based on the morphology of bones, fetal development, genetic material, neurology, structure of the organs, studies on speciation on monocellular organisms and some multi-cellular organisms, and so on. Several observations on the bacterial flagellum, comparative works on the factors involved in blood clotting among animals, on the eyes-structure, on customs adopted by organisms, lead with almost absolute certainty that evolution through natural selection is the strongest theory. For this reason, Dawkins compares the labor of scientists and a biologists as one of the detective arriving to the scene of a crime, and the way the evidence appears before us leads us to different theories of what happened. After long guesswork by proposing by conjecturing and refuting, we are led to who was probably the perpetrator of the crime.

The Problem of Transitional Forms

But then, there are fossils. And ironically Creationists and ID proponents love fossils. One might wonder why. Dawkins compares these groups to a defense attourney. Using the analogy of the evidence gathered at the scene of a crime, he tells us a short story:

Creationists are deeply enamoured of the fossil record, because they have been taught (by each other) to repeat, over and over, the mantra that it is full of ‘gaps’: ‘Show me your “intermediates”!’ . . . Let’s again make use of the analogy of the detective coming to the scene of a crime to which there were no eye witnesses. The baronet has been shot. Fingerprints, footprints, DNA from a sweat stain on a pistol, and a strong motive all point towards the butler. It’s pretty much an open and shut case, and the jury and everybody in the court is convinced that the butler did it. But a last-minute piece of evidence is discovered, in the nick of time before the jury retires to consider what had seemed to be their inevitable verdict of guilty: somebody remembers that the baronet had installed spy cameras against burglars. With bated breath, the court watches the films. One of them shows the butler in the act of opening the drawer in his pantry, taking out a pistol, loading it, and creeping stealthily out of the room with a malevolent gleam in his eye. You might think that this solidifies the case against the lawyer astutely points out that there was no spy camera in the library where the murder took place, and no spy camera in the corridor leading from the butler’s pantry. He wags his finger, in that compelling way that lawyers have made their own. ‘There’s a gap in the video record! We don’t know what happened after the butler left the pantry. There is clearly insufficient evidence to convict my client.’

In vain the prosecution lawyer points out that there was a second camera in the billiard room, and this shows, through the open door, the butler, gun at the ready, creeping on tiptoe along the passage towards the library. Surely this plugs the gap in the video record? Surely the case against the butler is now unassailable? But no. Triumphantly the defence lawyer plays his ace. ‘We don’t know what happened before or after the butler passed the open door of the billiard room. There are now two gaps in the video record. Ladies and gentlemen of the jury, my case rests. There is now even less evidence against my client than there was before’ (Dawkins, 2009, pp. 145-146).

This amusing analogy shows exactly what is wrong with Creationists and ID proponents. Sometimes, evolutionists fall into what I call “the inductive trap”, that is, that you arrive at a theory via “data accumulation”. Anti-Darwinians simply thrive on it, as we have just seen. As I have said before (Part II), theory always comes first and will tell the scientist which data are pertinent, which aren’t. The second problem is that you can have all the “pertinent” data that confirms your theory, but the theory itself might still be wrong. Aristotle’s theory of gravity was overwhelmingly confirmed by evidence: solid objects have the tendency to move to its natural state. Yet, it was wrong. Even Newton’s theory was itself was wrong, as Einstein showed.

Evolution through natural selection has a special status regarding this issue. As we keep digging for fossils, we keep finding intermediate forms. In fact, there are so many fossils of intermediate forms that they create heated debates among paleontologists (e.g. “Is this the fossil of a mammal-like reptile or a reptile-like mammal?!”) But there is a very important trait of evolutionary theory: between two life forms there could be an intermediate form. Unfortunately this leads the opponents of evolution to say: between two different life forms there must be an intermediate form. So, let us say that we have two different life forms in two stages in prehistory. If a intermediate form is found, then we have three life forms, and it would require two new intermediate forms. If a paleontologist finds them, then it would require four intermediate forms, and so on. So, every time a paleontologist finds a transitional form, in a an anti-evolutionist mind, it will mean that there is less evidence for evolution.

Solving the Induction Trap

This is due to the induction trap: from a frequentialist point of view of probabilities, each instance cannot verify by itself a theory. Karl Popper made this criticism in Conjectures and Refutations and has received very little attention in the scientific community. For Popper, induction is never the way to go in scientific practice. An accumulation of data never says anything about the forces behind anything. First you must posit a theory or a theoretical body to then try to test it experimentally and try to refute it.

But he also discovered something very important, if we focus on the content of theories, we cannot fall into what I call the “induction trap”. When we talk about the “content” of a theory we are talking about the amount of state-of-affairs (facts) that the theories themselves are accounting for. For Karl Popper, from the point of view of the logical content of theories (he called it “logic of probabilities”) we should formulate theories that are less probable. What does Popper mean by that?

Let us suppose that we have three hypotheses:

  • hypothesis (a) = “today rains”
  • hypothesis (b) = “tomorrow will be sunny”
  • hypothesis (ab) = “today rains and tomorrow will be sunny”

The letter p will represent “probability”, and Ct will represent “content”. We can represent the relationship among these hypotheses the following way:

If Ct(a) ? Ct(ab) ? Ct(b), then p(a) ? p(ab) ? p(b)

In laymen terms, what does this mean? Let’s say that the probability of a happening is 50%, and the probability of b is 50%. So, far so good. Now, what is the probability for both a and b to actually happen? Actually much less. So, the more content a theory has, the less probability for it to happen.

Still, why should we prefer a theory that is less probable? Here is the kicker: If we start from a frequentialist view of probability, sometimes there is no way to decide which theory is better: the Aristotelian, or the Newtonian, or the Einsteinien theories of gravity. We could observe solid objects fall 100% of the time, with perfect confirmation for all of these theories. But what makes the Newtonian theory better than the Aristotelian theory? The content of Newtonian theory, the amount of phenomena the theory is supposed to account for, is greater! Aristotle can only explain one phenomenon, the gravitation of solid objects and their tendency to go down. On the other hand, Newtonian theory can explain that and it can explain the tides, planets’ orbits, the next arrival of Halley’s comet, and so on. Einstein’s theory, though, was better! It could account for all of what Newtonian theory accounted for, solved Mercury’s orbit, and explained why light bends close to massive objects, the Doppler effect, the second twin paradox … you name it!

So, the frequentialist point of view of scientific theories (looking how many times a theory is confirmed) is useless to decide which scientific theory is the best. The most successful scientific theories must require:

  1. That they be the simplest possible, and at the same time have greater explanatory power, i.e. their content should be as great as possible.
  2. Although we don’t start from a frequentialist point of view, these theories must have a high degree of corroboration. This means that these scientific theories should be heavily tested, and if they survive any attempt at refutation, then they should be adopted.

How does this solve the inductive trap that Neo-Darwinists and their opponents fall into? Neo-Darwinism should focus on the theory itself and all it accounts for: fossils, the way genetic code is structured, the way our bodies are structured, the way embryos grow and develop, behavioral patterns, and so on. Our focus is not on how many intermediates paleontologists find. Our focus should be on what Neo-Darwinism accounts for. What is one of the advantages ofNeo-Darwinism over ID or Creationism? In that the former accounts for more natural phenomena, including transitional forms. ID and Creationism are not able to account for the appearance of transitional forms. Too bad, so sad!

“Missing Links” between Ancient Primates and Humans?

Give me a nickle for every person who has been taught to believe that Darwin said that humans come from monkeys, chimpanzees or gorillas. Darwin never said so, and no evolutionist claims it. For some reason, when I invite much of these people to read Darwin’s The Descent of Man, they never do so on the basis that too much time has passed, and that the book is obsolete by now. When I ask them to read lots of works on the primates which were our ancestors, then they say that it is “full of frauds” because of the Piltdown Man (a fraud), which for many years was presented in the press as “the missing link” between ancient primates and humans. They also cite the Nebraska man, the Rhodesian man, among some others. But Creationists miss the point about science: it is a self-correcting field. In Part II we discussed scientific theories that can serve as a jigzaw puzzle to understand given phenomena. This is true of Neo-Darwinism. Evolutionists themselves were the ones who discovered that the Piltdown Man was a hoax.

On the other hand, people who favor Creationism or ID have not been able to show that much of the fossils available world-wide of our ancestors are indeed frauds. Such fossils include: Australopithecus afarensis, Homo habilis, Homo ergaster, Homo rhodesiensis. There are other fossils of primates which could be candidates for our ancestry, but we don’t know for sure: Homo rudolfensis, Homo georgicus, Homo erectus, Homo antecessor, Homo cepranensis, among others. Thanks to genetics, sometimes, those we thought were our ancestors are no longer considered such by paleontologists. This is the case of Homo neanderthalensis. Nenanderthals coexisted with ancient humans (sometimes called “cro-magnon”), but seem to never interbreed with them, which indicates that both were separate species. Some scientists theorize that humans drove Neanderthals to extinction, but we do not know for sure. The research and puzzle-solving goes on, and on.

At this level of research, though, many paleontologists agree that there are no “missing links” between ancient primates (such as Australopithecus afarensis) and Homo sapiens. What we need to solve is how we organize these fossils in a manner that is consistent with all the other evidence available.

By the way, paleontology has confirmed that we don’t come from monkeys, gorillas or any other primate alive today. Capiche?!

Why are You the Way you Are? You Came from Fish!

During the Dover trial, there was a great discovery of a very beautiful intermediate. This intermediate showed that we didn’t come from monkeys, but that we certainly came from fish! This explains why our bodies were built the way they were built. You may think that your body is too complicated to have evolved. Maybe, maybe it is not too complicated.

Of course, the way I was taught biology, it seems that fish had fins, and then they evolved limbs after they climbed out of the water. However, if you think about it, it does not make any sense. Do you see your goldfish using fins to climb out of the water to land? Have you seen salmon or tuna doing that? Fins are not enough to get a fish out of the water, it is not developed for that. It sucks for walking, but it works well for swimming.

The answer to this riddle would be found in 2004, when a transitional fossil was discovered. Here it is!!!

Neil Shubin and the Tiktaalik

No. It’s not the guy in the left. He is Neil Shubin, the paleontologist who discovered the fossil, the one in the right (which seems to be smiling too).

The fossil he is holding is called Tiktaalik roseae, which was discovered in 2004, in Ellesmere Island, close to Greenland, just when the resources Shubin had available were about to run out. He is a paleontologist deeply interested in how organisms developed limbs during the course of evolution. Here are artistic representations of Tiktaalik.



As you can see, this is a perfect transition fossil between fish and amphibians. You cannot even ask a better one if you want to. Amphibians in the late Davorian Age have flat heads, with eyes in the top, with necks, which separate the shoulders from the head, and limbs with elbows and hands. Tiktaalik has a flat head with eyes on the top, with shoulder bones slightly separated from the head, but its head has limited mobility. But the interesting thing I wish you to notice are its fins. Let us look at its bones.

Tiktaalik's Fins

This looks like a mess of bones, even though when it shows an organization. There is a big question regarding how Tiktaalik got this new fin from earlier fin structures. Look at the following image:

Evolution from Fins to Limbs

(From Boisvert, et al., 2008
a. Euthenopteron, b. Panderichthys, c. Tiktaalik, d. Acanthostega)

This picture shows a transition from fins to a hand in the fossil record. As you can see, the bones of Tiktaalik’s fins correspond to the fins of the Euthenopteron, but also of the Acanthostega. If you look at Acathostega’s limb you’ll notice that it is already an arm that serves to walk around. Tiktaalik’s fins, though, didn’t serve to walk. Most of what Tiktaalik can do is push up.

Although not evident in these images, if you look at the fins of the Euthenopteron or any fish, you’ll notice that there are long webs coming out of the bones and make up most of the fins. But if you look at Tiktaalik (again, not evident in this image), you’ll see very short webs coming from the bones. So that means that Tiktaalik’s fins were not made to swim the same way that a fish does, but at the same time it is not developed enough to make it walk or crawl. What does this mean regarding our knowledge of how a limb evolved from a fin?

The key lies in genes themselves. Remember, natural selection does not select anything phenotypical. What is selected is a particular genetic arrangement. So, whatever made fins change into hands is of genetic in origin.

There is this specific gene called Sonic hedgehog that directly deals with fins in some animals (fish) or limbs on other animals (reptiles, mammals, etc.). Experiments using the same gene from mice on sharks have spectacular results of giving shark fins a bone structure similar to that of Tiktaalik. As Neil Shubin would say, you can give a shark a hand, very literally.


Furthermore, when you look Acanthostega, you see a transition from Tiktaalik to amphibians. Acanthostega is mostly amphibians, but it still has gills, which means it can breathe underwater, something that amphibians cannot do. The legs that Acathonstega has were the ones that made amphibians get out of the water and walk on land. And from those limbs, human limbs evolved.

What does this all mean? Our limbs are nothing more than evolved fins. That essentially we are evolved fish out of water. More importantly, from such fish, amphibians evolved, which would lead to reptiles. As I will show in my next article, we would not make rational decisions without the reptilian part of our mind.


Ayala, F. J. (2007). Darwin’s gift to science and religion. Washington, D.C.: Joseph Henry Press.

Boisvet, C. A., Mark-Kurik, E., & Ahlbert, P. E. (2008, December). The pectoral fin of Panderichthys and the origin of digits. Nature. 406, 636-648. doi: 10.1038/nature07339.

Darwin, C. (2004). The descent of man, and selection in relation to sex. US: Penguin. (Originally published in 1879).

Darwin, C. (2008a). On the origin of species by means of natural selection of the preservation of favoured races in the struggle for life. NY: Bantam. (Originally published in 1859).

Darwin, C. (2008b). On the origin of species: the illustrated edition. D. Quammen (Ed.) NY & London: Sterling.

Dawkins, R. (2009). The greatest show on Earth: the evidence for evolution. NY: Free Press.

Futuyma, D. J. (2009). Evolution. US: Sinauer Associates.

Miller, K. (2008). Only a theory: evolution and the battle for America’s soul. U.S.: Viking.

NOVA. (2007). Judgment day: intelligent design on trial. [DVD]. Video can be watched online in:

Popper, K. (1979). Objective knowledge: an evolutionary approach. Oxford: Clarendon Press. (Originally published in 1972).

Popper, K. (1999). The logic of scientific discovery. London & NY: Routledge. (Originally published in 1959).

Popper, K. (2000). Realism and the aim of science. London & NY: Routledge. (Originally published in 1983).

Popper, K. (2002). Conjectures and refutations. London & NY: Routledge & Kegan. (Originally published in 1963).

Rebato, E., Susanne, C., & Chiarelli, B. (Eds.). (2005). Para comprender la antropología biológica: evolución y biología humana. España: Editorial Verbo Divino.

Shubin, N. (2009). Your inner fish: a journey into 3.5-billion year history of the human body. NY: Vintage Books.

Exaptations and the Dover Case

(c) 2010 Pedro M. Rosario Barbosa

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This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License.

Maybe Darwinism is the most prevalent theory
out there today, but it is a theory. It isn’t a law
of science, it isn’t a fact. It is just a theory.

-Alan Bonsell
Ex-Member of the Dover School Board

Intelligent Design is a science stopper.

-Kenneth Miller
Co-author of Biology, published by Prentice Hall

A Decisive Moment in the Case

The Dover Area School District and the school board of the Dover High School, in the small community of Dover, Pennsylvania, were sued by Tammy Kitzmiller and other parents who thought their constitutional rights were being violated. The school board of the Dover High School was pretty angry over a text book used by the science teachers. Written by two authors, Kenneth Miller and Joseph Levine, the book Biology, published by Prentice Hall, was regarded as annoying, insulting and dangerous.

Biology - by Kenneth Miller and Joseph Levine

According to some of the now ex-members of the board, the reason why they hated this text is because Darwin and evolution were discussed throughout the book without considering other competing “scientific” theories. One of the things they did was to place a disclaimer on it that said the following:

This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully and critically considered.”

Much later, other textbooks appeared out of nowhere. An unknown person sent a box full of textbooks called On Pandas and People, which presented an alternative point of view: something called “Intelligent Design”.

Of Pandas and People

Intelligent Design (ID) is not traditional Creationism (the doctrine that God created the world in six days about 6,000 years ago). ID basically states that organisms appeared on Earth fully formed by an “intelligent designer” (God, gods, extraterrestrials, and so on). Some of the parents of the Dover High School students felt their first amendment constitutional rights were being violated, they were trying to teach religion in a public school instead of science.

The trial was presided by Judge John Jones III. Now, let me give you a background on this guy. First, he looks like this:

Judge John E. Jones III

This is a judge with a very conservative record: very devout traditional Lutheran, was chairman of the Liquor Control Board form 1995 to 2002, tried to privatize state stores, banned the Bad Frog Beer because of an interesting gesture it made (the finger!), and was appointed by Pres. George W. Bush recommended by none other than Rick Santorum. Let us remember that Santorum declared himself in favor of ID, and President Bush said that “the jury is still out on evolution”. Certainly if anyone would rule in favor of ID and the school board of Dover High School would be Judge Jones!

It is time for closing arguments. After an intense trial, and the testimony of scientists, philosophers, parents, teachers, and members of the school board, there was nothing left but to close.

One of the defense attourneys of the school board stated during his closing argument: “Your honor. I don’t know if you have noticed that this trial lasted forty days and forty nights.”

And the judge interrupted, gave him a smile and a wink, and said: “But it wasn’t by design.” This was a clue of what was going to be ruled in the end. You may read the full text of his ruling, it is an amazing document! A masterpiece! Click here to download it.

Why in the heavens would a hardcore conservative, religious judge rule the way he did?

God vs. Science? Conservatives vs. Liberals?

One of the big problems the judge found so unacceptable regarding ID, is that usually the people who propose it establish a false dichotomy between the belief in God and science, specifically the theory of evolution through natural selection. The judge found this unacceptable. If anyone has any questions about the religious background (or lack of it), it should be noted that most of the parents who sued the school board and all of the science teachers who refused to teach ID are Christians, some of them very active in the Church, and even running Bible school programs. One of the scientists who argued in favor of evolution in the Dover case is a traditional Roman Catholic, Dr. Kenneth Miller, and another person who assisted these parents in the case was John Haught, a well known theologian.

It would also be wrong to say that this is a conservative vs. liberal issue. Most of those who sued the school board are also hard core conservatives. In fact, some other communities have had the experience that conservatives were more fervent defenders of evolution than liberals, when Democratic support was sorely lacking. Why would conservatives favor evolution instead of ID? The reasons explained by the judge were those of a true conservative:

In an era when we are trying to cure cancer, when we are trying to prevent pandemics, when we are trying to keep science, math, and education on the cutting edge in the United States, to introduce and teach bad science to ninth grade students makes makes little sense to me. You know, garbage in, garbage out. It doesn’t benefit any of us, who benefit daily from scientific discoveries. (NOVA, “Judgment Day”)

The theory of evolution is a scientific theory that has been tested rigurously for many years now, and in itself makes no claims about God or political ideals of any kind. Of course, the theory of evolution is not consistent with the literalist view of the Bible, but it can be fully compatible with other religious views about God. We will discuss this in a future part of these series on evolution, ethics and spirituality.

Testimony of Dr. Kenneth Miller

There were two scientists who testified at the Dover trial, but for the purpose of our discussion I wish to talk about Dr. Miller’s own contribution to the case.

As we have said before, Dr. Miller was co-author of the biology textbook in case. He tells the story of how, in his small community, he was the commissioner of the girl softball program. One day, the highschool adopted the Biology textbook, and teachers and parents saw his name on the cover and his picture was inside the book. One of the other coaches in the softball program was all emotional and said: “Ken! Ken! You wrote the book that we are using in the high school!” Miller smiled, with much pride and said: “Yes, Bonnie. I did!”. Then she told him: “Funny thing is you don’t seem that smart.” Miller last comment when he tells the story is: “You may make of that as you will.”

Miller used to be a Goldwater Republican, is a traditional Roman Catholic, renowned cell biologist, and one of the most ardent defenders of evolution. As an ex-Republican he was interested in the 2008 Republican debates for the primaries to elect their candidate for President of the United States. During one televised debate, the host asked all of the Republican pre-candidates if any of them did not believe that evolution was true. Three of the pre-candidates raised their hands: Tom Tancredo, Sam Brownback and Mike Huckabee. Later, Ron Paul said that if he had heard the question correctly, he would have raised his hand as well.

Miller felt disappointed at Huckabee, because he was his favorite pre-candidate. He looked at why Huckabee did not think evolution was true:

In the beginning, God created the Heavens and the Earth. A person either believes that God created the process or believes it was an accident and that it just happened all on its own … If anybody wants to believe that they are the descendants of a primate, they are certainly welcome to do it.

Miller thought long and hard about that last sentence, and he sincerely wanted to see Governor Huckabee during the primaries campaign and say:

“You know, Governor, you are a great candidate, I love your candor, and your sense of humor … But Governor, between you and me, I have to tell you sir … you are a primate. And so are your mom and dad. Therefore, you did descend from primates.”

Humans are indeed primates, says Miller, and this is not Darwin’s fault. It was a classification made by Carl von Linné (or, as he called himself, Linnaeus Carolus). Linné was a creationist, and he made it very clear in a very modest claim: “Deus creavit; Linnaeus disposuit” (God creates; Linnaeus arranges). He lived before Darwin, but he was the father of the classification of living beings. He was the one who classified humans are being primates.

The Whole Case for ID: Irreducible Complexity

Of course, Huckabee belonged to a group of people within the Republican Party who embraced a form of ID. The Dover case was indeed about evolution against ID. The scientist whom the plaintiff relied on most was Michael Behe. Behe in his book, Darwin’s Black Box, formulated a principle which is regarded today as the cornerstone of the whole ID movement: the principle of irreducible complexity. For Behe, we see purposeful design in nature, a design directed to assume a function that serves that organism to survive. If we look at the intrinsic mechanisms of an organism, we find that if one part of the system is missing, then the system itself would cease to function. When this happens, it is said that the system itself is “irreducibly complex”. This necessarily means that all parts must be there simultaneously for it to work properly. Since evolution through random mutations and events cannot make such a “perfect” system for that particular purpose, the choice left is to suppose an intelligent designer. This designer can be God, or spirits, or fairies, or extraterrestrials, but they cannot be made by unintelligent evolution.

Examples of this? Behe, being a biochemist, was amazed at the structure and performance of the flagellar bacterial motor. Those bacteria with a flagellum are propelled by a very sophisticated motor that rotates the flagellum making the bacteria displace itself. Look at it and be amazed:


Bacterial Flagellar Motor

As you can see, these structures are very well built! At the bottom we see the image of the flagellar motor as reconstructed visually by NOVA, for the Episode “Judgment Day”. The bacterial base is one very sophisticated motor, one that existed before men inveted motors. Let us see this motor closely:

Flagellum Base Diagram

Now, I don’t care whether you believe in ID or evolution, you have to simply MARVEL at this. No wonder this served for a long time as the poster child for ID, especially as a case of irreducible complexity. And Behe is right, if you take one of these pieces away, the flagellar motor would cease to function as propellar. The flagellar base is made up of 50 different proteins, all very well “arranged” to function as they do. Point made: it is simply almost impossible that pure random of combinations of proteins would form a very sophisticated bacterial motor. A bacterial motor is not evolvable.

This is a tough case for evolutionists to account for … or is it?

Not All Motors Are Created Equal: Some are Built from Earlier Stuff

Of course, a prima facie it would seem that the bacterial motor is irreducibly complex. However, Ken Miller replied to Behe’s argument for irreducibly complexity by stating that … well … the bacterial motor, as impressive as it may be, is not irreducibly complex. How did he show it? By looking at the evidence already gathered by many other scientists over the years, whose work were conveniently ignored by Behe during his testimony.

Miller showed on trial, based on well documented scientific findings, that you can take away parts, and it would still be functional. But let us be more specific about this claim. Again, the flagellar motor is formed by fifty different proteins. Miller argued: “let’s take some parts away … ummm… maybe ten … Nah! .. Maybe twenty … Nope! … Maybe thirty … Not enough! Maybe forty parts! Yes! Let’s take forty of those fifty proteins, and see what happens!” And all you have left with is this (another NOVA visual recreation):

Bacterial Type-III Secretory System

If this illustration looks a lot like the illustration of the flagellar bacterial motor, it is not a coincidence. This thing is an exact subset of the flagellar motor. Let us have a second look at both structures (NOVA visual recreation):

Bacterial Flagellum and the Type-III Secretory System

Now, what is this new thing at the right of the illustration? It is called the Type-III Secretory System. Is it functional? Yes, it is! But let us be honest. Does it rotate? Does it propel? No. What it does, though, is to secrete into a cell a poisonous substance. The bacteria of the bubonic plague is one example of this, it can be pretty nasty.

Despite this, much later, long after the trial ended, William Dembski, another major figure in the ID movement, protested Miller’s observation on irreducible complexity saying essentially that Miller missed the point. Why? Because despite the fact that the Type-III Secretory System is a subset of the flagellar motor, and that it is functional, it does not carry out the original function of propelling the bacteria. THAT is what Behe meant in the first place.

But in this issue, Dembski is the one missing the point!

Evolution 101 — New Term to Learn: “Exaptation”

If you are going to refute Darwin, it is necessary to know Darwin’s actual theory of evolution before make believe you are refuting him. Proponents of ID absolutely love the following passage in Darwin’s The Origin of Species:

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down (Darwin, 1859/2008, p. 189).

Yet, for some reason, they forget to quote the next sentence: “But I can find out no such case” (Darwin, 1859/2008, p. 189). He then proceeds to state a series of ways these “highly improbable” complex organs evolved. He noticed that in many species, the same organs can assume different functions in different species that are respectively advantageous for them. Sometimes the same organ can carry out two functions at once. Sometimes two different organs assume the same function, and so on. He gives several examples of this, which I will not discuss here, but invite you to read The Origins of the Species. How ever vaguely, Darwin was proposing in that specific section the idea of what is now called exaptation (previously called “pre-adaptation”).

What is an exaptation? It means that the way complex organs evolve is that from simpler organs that carry out different disparate functions, because certain random mutations and changes in the environment, they combine to form another organ or system that assumes a new function. Do you want an example? The bacterial flagellum!

It may well be that both the base of the bacterial flagellum and the Type-III Secretory System share a common ancestor. But, it may also suggest, due to the degree of complexity among both, that the Type-III Secretory System may be the base flagellum’s ancestor itself, since it has all the proteins that conceivably through mutation and combining itself with other proteins, could make the flagellum come to be.

To make matters worse (for ID that is), the rest of the 40 proteins that would transform a Type-III Secretory System into a bacterial motor exist in other parts of the bacterial cell as simpler structures assuming other functions (just as Darwin described in general): type-II secretory system, axial proteins, ion transport, and signal transduction.

So again, the notion of irreducible complexity breaks apart in light of the evidence: the idea that the components of a flagellum cannot be functional until they are assembled into a flagellum is simply wrong.

Another example we can see of exaptation (and refutation of irreducible complexity) stems from blood clotting. According to Michael Behe, if you look at the blood clotting cascade, we can see design. Remove one of the components of the cascade, and you realize that blood can no longer clot. Therefore, it is another example of irreducible complexity.

Blood Clotting Cascade

(Illustration by Jay D.)

I won’t go into the details of this diagram, suffice to say that each component that you see here in Roman numbers are proteins necessary for blood to coagulate. Behe says that they must be there for the whole thing to work. Evolution could not have produced the system, because all of the factors must be there at the same time for it to work. Of Pandas and People gives this specific example as evidence of ID.

However, Miller could show in the trial that this is not an example of irreducible complexity. It is true that in the case of humans, if any of the components are missing, the blood will not clot. Is it true of other animals? Miller showed what would happen if we eliminate factor XII. This factor XII is very important for humans, because that is the one protein that starts the cascade. Does any other organism lack factor XII and still have a functional clotting system of proteins? Yes! As it happens, whales lack factor XII, because they are not needed for animals that live in the ocean. Now, let us eliminate factors XII and XI, what happens? The puffer fish lacks these factors, and yet, they have a perfect clotting system.

From an evolutionary standpoint, what do scientists theorize happened? Our ancestors came from the ocean. As they adapted to the air and being on land, they developed through natural selection a more complex clotting system, the one we humans have today. Exaptation is considered here, because, from comparative genetic analysis, we know today where did these factors come from. Again, they were proteins that assumed a role in our ancestor’s organisms, and which, through exaptations, combining itself with other proteins already formed in the clotting system, assumed a new function.

The same can be argued of another example, the immune system, eyes, arms, teeth, bones, and so on. It doesn’t matter.

Everything in humans is the result of this long evolutionary process. As we shall see, exaptation is precisely the evolutionary mechanism that forged what we consider today to be “human nature”, even its capacity to make moral decisions.


Ayala, F. J. (2007). Darwin’s gift to science and religion. Washington, D.C.: Joseph Henry Press.

Darwin, C. (2008). The origin of species by means of natural selection of the preservation of favoured races in the struggle for life. NY: Bantam. (Originally published in 1859).

Futuyma, D. J. (2009). Evolution. US: Sinauer Associates.

Hess, P. M. J., & Allen, P. L. (2008). Catholicism and science. Westport: Greenwood Press.

Miller, K. (1999). Finding Darwin’s God: a scientist’s search for common ground between God and evolution. NY: Harper Perennial.

Miller, K. (2008a). Kenneth Miller on Evolution and Intelligent Design. Online video:

Miller, K. (2008b). Only a theory: evolution and the battle for America’s soul. US: Viking.

Musgrave, I. (2004). Evolution of the bacterial flagellum. Why intelligent design fails: a scientific critique of the new creationism. New Brunswick: Rutgers University Press.

NOVA. (2007). Judgment day: intelligent design on trial. [DVD]. Video can be watched online in:


(c) 2010 Pedro M. Rosario Barbosa
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The Old Ways of Explaining Nature: Religion, Philosophy, and Science

The path to discover human nature is not easy. The first questions were asked in the realm of religion as well as the origins of the cosmos. Then another different field, philosophy started to question religious beliefs, and called for a secular approach to the universe. With philosophy, natural science began. Thales of Mileto did provide the first secular theory on the world, even though much of the ideas in it came from different parts of the Mediterranean Sea. He looked at many of the religious traditions and saw something in common: that the Earth was essentially land floating on water, or spread on the water. Before that, science was intrinsicably mixed with religion. Today we tend to laugh at ancient religious ideas of the past, practically arguing that they were non-sense and essentially irrational. We read Genesis, and mock the two very different incompatible stories of creation (Gen. 1-2:4a; 2:4bff.), regard at the story of Adam and Eve as amusing, and so on. In reality the first version of creation is a proto-theory of how the universe came to be, the second story of creation has a more existential aspect to it: not only did God create everything, but also it tries to explain where does evil in the world come from.

It is not correct to say that these are just pure irrational fantasies of religious people whose thoughts were superstitious. Of course, there are political, sociological and conceptual aspects to both stories of creation that deserve to be studied in context. For any such analysis, I highly recommend Richard Elliot Friedman’s Who Wrote the Bible? But right now I’m not going to dwell on the sociological backgrounds of both of these stories. The idea that God or gods created the universe is not crazy. It is perfectly reasonable. Just go out and look at nature itself, with all its order, beauty, natural laws, and complexities that operate in an organized manner to make life possible. The God hypothesis, in lack of any other reasonable hypothesis at the time, was valid.

As a matter of fact, a lot of ideas developed by religion were perfectly rational. Most people consider the Middle Ages to be the "dark ages". When we say "Medieval", we mean almost living in a period of pure ignorance. However, science did thrive during the so-called "dark ages". On the second half of the Middle Ages, universities were established all over the Italian Peninsula, clergymen and monks carried out experiments and discoveries, architecture evolved (think of the Gothic cathedrals), there were advances in medicine, chemistry, optics, geography, mechanics, reconceptuation of physics and biology, even theory of flight (Jones & Ereira, 2007, pp. 115-138). The basis for future philosophy of science and the much of the principles of knowledge we still discuss today were also established during the Middle Ages. Think of Robert Grosseteste, Roger Bacon, Duns Scotus, William of Occam, Nocholas of Autrecourt, among many others (Losee, 2001, pp. 26-45; see Grendler (2004)). Roger Bacon, a monk himself, discovered that white light contained the colors of the rainbow, long before Newton. The Galilean, Keplerian and Newtonian scientific theories would never have come to be without these important contributions. Many people even insist on clinging to total falsehoods to hold that the Middle Ages was decadent. The famous dispute that, according to popular culture, between Columbus and the theologians in Salamanca were a complete fabrication by Washington Irving. In reality, everyone knew at the time that the Earth was a sphere, and not flat. This was known since Ancient times, even Erastothenes was pretty close to the Earth’s actual size! Hey, even the Bible says that the Earth is a sphere! Haven’t you noticed? (Prov. 8: 31) St. Thomas Aquinas and Roger Bacon made very clear reference to this fact. Why in heavens would religious people in the Middle Ages be so interested in science? Answer: they were trying to understand God by studying His creation, the better we understand how the universe works, the more we understand God Himself. In fact, technological innovation on the basis of science would help us be His co-creators along the process.

The Renaissance, though, regarded today as a period of recovering the "light of knowledge" was a period of decadence in many ways. For instance, the Renaissance comes to be at the end of the bubonic plague that swept Europe. Contrary to what people think, there were no witch hunts during the Middle Ages, they happened during the Renaissance. The infamous Malleus Maleficarum was written during this period (1487). If you are woman, you would prefer to live in the late Middle Ages than during the Renaissance, when women in general were very much repressed. Europe was in religious, political and social decadence. The "Galileo Affair" took place during this period. Most people who haven’t read at all about the subject, take it to be a science vs. religion affair, showing that religion is in a constant battle with science. Although religious elements were involved in the affair (e.g. Joshua commanding the sun to stop), but in reality what the depth of the discussion had to do with the Aristotelian-Ptolemaic scientific view of the world. I recommend the works of Maurice Finocchiaro and Ernan McMullin about this important subject (see the Reference section below).

Two Doors to Understand Human Nature

However, it was not even until recently, the second half of the nineteenth century, that two doors were open to understand human nature. They were opened by three eminent figures: Alfred Russel Wallace (1823-1913), Charles Darwin (1809-1882), and Georg Mendel (1822-1884). The first two elaborated separately a theory of evolution through natural selection. At that time, many scientists and learned people, including some people in the clergy, knew that the Earth was far older than six thousand years, and even that everything pointed out to the Earth as being beyond a million years old. Everyone knew that animals evolved, and that there were animal species that became extinct while other species came into being. Wallace and Darwin said that gradual mutation and natural selection were both keys to understand how species came to be. It was first known by Wallace in an article titled "On the Law which has Regulated the Introduction of Species", published in the Annals and Magazine of Natural History (1855). However, we know more about this theory because of Darwin’s later publication The Origin of Species (1859). Even when it was published after Wallace’s article, the latter did recognize that Darwin did not plagiarize him. Much later, due to the elegant way that Darwin explained their theory of evolution, Wallace created the term "Darwinian" to describe it.

If we look at the theory of evolution proposed by Wallace and Darwin, we discover that the theory is a set of five different theories (Futuyma, 2009, pp. 8-9):

  1. Evolution occurs because of changes in organisms’ traits over time.
  2. Every single organism that exists on this Earth has common ancestors with other organisms. All living beings share a common ancestor. This essentially means that we cannot conceive evolution as being a "linear" process, but more like a tree or a bush, where branches of species come from other branches.
  3. New species and subspecies of organisms come to be in a gradual manner, i.e. given enough time. Speciation can happen in hundreds, thousands or millions of years.
  4. Changes among species often happen because of isolation of populations due to external factors or due to different phenotypical traits that let some survive in one environment while others are best suited for another.
  5. Finally, there is natural selection, that is, an organism has the specific traits that are necessary to survive a certain environment in nature, those organisms lacking it will not. Only those adapted to a certain environment will eventually survive in it.

The second door was opened by Georg Mendel and his pioneering work on genetics. He did notice that there were natural laws ruling the way organisms inherit their traits. In 1909, this new field of genetics elaborated the notion of "gene", which was defined back then as a single unit that is inherited from an ancestor or ancestors. Today we know that genes are associated with a molecule called Desoxyrribonucleic Acid (DNA), our own genetic code. DNA is a very long molecule with a sequence of units called nucleotides, molecules which determine the way an organism will develop. A specific sequence of nucleotides that produce a particular protein constitutes a gene. Depending on the location of the gene within the genetic code, and whether it is turned "on" or "off", a phenotypical trait will be present or not in a living being.

Richard Dawkins has pointed out that it would be wrong to describe DNA as a blueprint or set of instructions. The reason is that it gives the false impression that "someone" wrote the instructions down, or that "someone" made a blueprint. Logically, whoever makes a blueprint has a "plan" to make a building in such and such a way. When you look at the DNA, the least you see is a "set of instructions" or a blueprint. It gives no sign of being "designed" by anyone. Dawkins explains why thinking of the DNA as a blueprint is a fallacy at best:

A true blueprint of, say, a car or a house embodies a one-to-one mapping from paper to finished product. It follows from this that a blueprint is reversible. It is as easy to go from house to blueprint as the other way around, precisely because it is a one-to-one mapping. Actually, it’s easier, because you have to build the house, but you only have to take some measurements and then draw the blueprint. If you take an animal’s body, no matter how many detailed measurements you take, you can’t reconstruct its DNA. That’s what makes it false to say that DNA is a blueprint.

It is theoretically possible to imagine — maybe that’s the way things work on some alien planet — that DNA might have been a code description of a body; a kind of three-dimensional map rendered into the linear code of DNA ‘letters’. That really would be reversible. Scanning the body to make a genetic blueprint is not a totally ridiculous idea. If that is how DNA worked, we could represent it as a kind of neo-preformationism. It wouldn’t raise the spectre of the Russian dolls. It isn’t clear to me whether it would raise the spectre of inheritance from only one parent. DNA has breathtakingly precise way of intersplicing half the paternal information with exactly half the maternal information, but how would it go about intersplicing half a scan of the mother’s body with half a scan of the father’s body? Let it pass; this is all so far from reality (Dawkins, 2009a, pp. 214-215).

Genetics was later integrated to the Wallace-Darwin theory of evolution to constitute what is now known as Neo-Darwinism, or the Neo-Darwinian theory of evolution. What is the difference between Darwinism and Neo-Darwinism? The difference is not much in terms of what we have described above, except for one fact. Darwin nor Wallace paid much attention to Mendel’s work, and had absolutely no idea what DNA was, not even what a "gene" was. We now do! Neo-Darwinism states that what is being selected by natural selection is not a set of phenotypes, but the genes that make those phenotypes possible. It also states that the reason why organisms change is because of accumulation of genetic "errors" over time, making a set of organisms to mutate. Today geneticists know that genetic errors happen every now and then, and that generally these changes are harmful to organisms. However, from time to time, there is this significant genetic change that will be beneficial to an organism. Because that particular genetic change lets an organism survive an environment, then THAT genetic "error" is selected because it is the one that keeps replicating through an organism’s reproduction.

Richard Dawkins invites us to use a metaphor in order to think on how evolution works: the selfish gene! (Dawkins 1976/2009b). Let’s imagine that genes replicate so that they will keep existing, and they are competing against other organisms which carry rival genes. Thought of this way, a gene "uses" the organism (so-to-speak) as a mechanism to guarantee its survival and continue replicating. Get it?! It is not about us … we are just here for the ride! In reality, genes drive us to survive. For purely selfish reasons, genes enable us to have all kinds of behavior to guarantee its existence, including, being altruistic, or being able to create solidarities and systems so that it survives! Now, let’s remember, this is all a metaphor. Obviously genes cannot be selfish, but if we are careful and keep away on several misunderstandings and shortcomings regarding the metaphor, it can be pretty useful. In fact, it can also open the door to understand what human nature is, our own unique characteristics as a species, why we have been so successful surviving, why are we selfish or why we cooperate, why are our instincts there, what is behind our intelligence, and whether we can rebel against our "selfish" genes. It might even go as far as to tell us why there is religion, why are there nations, why certain economic and political systems work and why others simply won’t.

All of these questions pertain directly to three subjects: human nature, ethics and spirituality.

Evolution, Religion, and Spirituality

Without a doubt science has always been a challenge to many religions around the world. I’m not saying that science and religion are in mortal combat. As we have seen, this has been rarely the case, most of the challenges by religion towards science are due to sociological reasons, and some few times have to do with religious beliefs themselves. However, when religious beliefs themselves become a sociological problem for the advance of science, we should seriously question religious beliefs if the grounds for opposing a scientific theory or scientific practice are not ethical, and if the grounds are ethical we should question them.

Richard Dawkins’ The God Delusion or The Root of All Evil?, or Daniel Dennett’s Breaking the Spell are a disgrace in this area, not only because they show huge ignorance on religion, theology, and even the most basic sociological aspects of religion, but also because it does not help in this dialogue between the best theologians religions have to offer and scientists. Ironically, books like Dawkins’ or Dennett’s, which pretend to make a scientific approach to religion to say it is all a delusion, suppose the existence of metaphysical and untestable entities (such as memes), only look at those scientific data that favor their views (which they accuse religious people of doing), and use a lot of clichés and stereotypes without looking futher into the many sociological aspects of religious movements. They even agree a hundred percent with the most fundamentalist sectors of certain religions when they say that there is inconsistency between God and evolution. There have been extensive works by serious theologians and philosophers which respond to their statements (see below: Haught (2008), McGrath (2007), McGrath & McGrath (2007), Miller (1999), Mooney & Kirshenbaum (2009), Ruse (2000), Ruse (2010), and Wade (2009)), so I won’t elaborate on Dawkins or Dennett here. I only wish to point out that such positions on the side of science are really counterproductive to science. Contrary to what Sam Harris (2004, p. 15) believes, it is they (the radical atheists), not us the religious moderates or the atheist moderates, who engage radicalism in religion, because in the eyes of fundamentalists they prove exactly their own point of view: evolution and God are mutually exclusive, and that holding evolution as true means that ethical norms are illusory and inexistent (a belief that Dawkins and Dennett seriously hold).

On the other hand, it would be incredibly naïve if we suppose that there is no unease between science and religion. Some like Francisco Ayala, Kenneth Miller, John Haught, Denis Edwards, Karl Giberson, Alister McGrath, Darrel Falk, Francis Collins, and others have been working on a new understanding of God in light of the discoveries of science, trying to "bridge the gap" between science and faith. There are even those like Michael Dowd who brilliantly integrate evolution, neuroscience, physics, hermeneutics and spiral dynamics into a metareligious theology which can enrich many religions, spiritual paths, and even sketpticism and atheism.

These articles are the result of certain reflections I’ve carried out regarding evolution, ethics and spirituality. My view is that of a Catholic, although people of other denominations and religions can be able to appreciate the very important implications of human nature towards ethics, religion and spirituality. I hope you will join me in this exciting trabel I’m going to embark.


Ayala, F. (2007). Darwin’s gift to science and religion. Washington, D.C.: Joseph Henry Press.

Darwin, C. (2008). The origin of species by means of natural selection or the preservation of favoured races in the struggle for life. US: Bantam Classic. (Originally published in 1859).

Dawkins, R. (2009a). The greatest show on earth: the evidence for evolution. NY: Free Press.

Dawkins, R. (2009b). The selfish gene. US: Oxford University Press. (Originally published in 1976).

Dowd, M. (2009). Thank God for evolution: how the marriage of science and religion will transform your life and our world. US: Penguin Group.

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