The Edge of Evolution - Michael Behe

Where can we draw the line between the capabilities of random chance and the evidence of intentional and intelligent design? In other words, how far up the complexity scale can random chance really travel and how far down the complexity scale is there evidence of design? Where can we draw the line?

This is the question that Michael Behe both asks and answers in this new and compelling book. Like many in the Intelligent Design movement, he discards the notion that evolution and Darwinism are synonymous and instead examines three smaller concepts, random mutation, natural selection, and common descent, on their own individual merits. The novelty about his approach to the subject is his clarity in explanation and his astronomical empirical data sample upon which he bases his conclusions. His case is overwhelming.

More specifically, he uses the genetic data available on malaria, HIV, and E. coli (as well as the human genetic response to these micro-organisms) over roughly the past fifty years as his data sample. For malaria alone this is a sample size of approximately one hundred billion billion organisms. How much has random mutation accomplished in one hundred billion billion chances? Not much. Nothing new, nothing constructive, no new cellular machinery, no new genes or genetic material, nothing but a few “broken” genes which both damage the malarial organism and yet also make it immune or resistant to the drugs we use to kill it.

So does Darwinism work? Yes. Darwinism is the perfect explanation for the resistance that malaria gained against chloroquine (and other drugs). A random mutation provided resistance to the drug, therefore this new genetic trait caused the mutant parasite to out-compete its rivals and this mutation became a widespread trait in the population. Random mutation, natural selection, common descent all work. The question, however, is not whether Darwinism works. The question is how much random mutation can realistically accomplish. The answer, to repeat myself, is “not much”. So while random mutation (and hence Darwinism when paired with natural selection and common descent), can accomplish some relatively modest changes given a large enough population size, it is severely limited.

For reasons that I will defer to Behe to explain, random mutation can only realistically accomplish a maximum of two simultaneous and specific protein-protein interactions (that is among existing proteins), or single-point mutations. This is exactly what happened in malaria out of one hundred billion billion chances. (The details are important here and I am leaving out a lot, but I can’t give all that to you in this space. Read the book). To recap, if we draw our line where Behe does at the two-binding-sites rule, we are left with the following realization: random mutation could not have accomplished any significant evolution. Not only is this true for single-celled organisms which reproduce quite rapidly, but imagine the problem for higher animals: one hundred billion billion is more mammals than have ever existed and yet the differences between them are much much greater than two protein binding sites. Random mutation can simply not account for such changes. Especially not when you consider that those changes would involve the creation of entirely new and complex genetic material.

Here, then, is the “edge of evolution”. Random mutation can statistically generate small changes given a large enough population but if fails to create anything greater than a two-binding-site difference (see the book for an explanation). Therefore, Darwinism is a good explanation for certain biological phenomena such as antibiotic resistance in micro-organisms and certain genetic diseases like “sickle-cell”. In all of these cases, the operative change is small and although beneficial in an immediate and desperate sense actually decreases the function of the organism in question. The trait is only selected because it provides resistance to a disease or drug. Anything beyond this should be properly understood as the product of intelligent design.

Keep in mind, again, that I have left out a large amount of information in my explanations. My summaries are rough at best.

Goings On

So I still haven't posted anything with much content in it. Shame on me.

Samuel, my son, was born February 13th and my time has revolved around him since.

I do still manage to get a little done, however. I became a sustaining member of the Creation Research Society to receive their quarterly journal: Creation Science Research Quarterly. This also gave me access to their archive of past journals which I've been delighted to peruse. Some of the articles are fantastic. I was especially impressed by an article regarding the encephalization quotients of primates and how, when correcting for body posture and degree of bipedality, extinct primates such as Australopithecus and others do not indicate an increase in brain size other than in a proper ratio to their body mass.

I am reading a book called The Law, Darwinism, and Public Education which Michell had from one of her courses at Baylor. It is a fascinating book and an enlightening glimpse into the current legal arguments surrounding Intelligent Design. I also picked up The God Delusion by Dawkins (I happened across it as one of my new books to process at work) to finally get a taste of today's most outspoken atheist/darwinist.

Anyhow, hopefully I'll manage to post something of value again eventually.

Still here

Since my last post, I've read Darwinism: A Theory in Crisis by Michael Denton, Shattering the Myths of Darwinism by Richard Milton, and I'm currently reading an anti-creationist book called Bones, Rocks, and Stars by Chris Turney.

I haven't posted here because of a million small reasons; basically I've just been busy and distracted. I'll try to get reviews of the above mentioned books up before too long and then I'll try to keep the momentum going. There are always plenty of things to read and talk about!

Tornado in a Junkyard: The Relentless Myth of Darwinism

Author: James Perloff

This book was not quite what I expected, especially for the first ten chapters. Perloff is more of a journalist or a reporter than anything else so instead of gathering evidence and presenting it himself he relies almost entirely on a collection of quotes, many of them lengthy, to state the evidence for him. This isn't always a bad thing, but I think it makes his text somewhat disjointed. In addition, his first ten chapters are mostly his treatment of evolutionary theory as a whole and why, according to the numerous quotes he has collected, it is invalid. Since he treats the theory as a whole and relies almost exclusively on various quotations to combat it, the reader only really learns that the field has a high degree of disagreement within it, not so much that any certain idea has been proven false. Up to this point, I found the book disappointing.

Things changed with chapter eleven. At this point he treats the big bang, radiometric dating, and the age of the earth. Although he still relies largely on quotes, his evidence is more positive than before. Chapter 15 is where things really got interesting. It is here that he changes modes from scientific quotes to an examination of some fascinating historical evidence. Now, instead of discussing natural selection or genetic mutation, where a journalist is somewhat out of place, he investigates history, where a journalist can truly shine.

He begins with the historical accounts, from a multitude of cultures covering every inhabited continent, of the great flood. While the accounts certainly differ, there are striking similarities and common facts that they share. Some of the Chinese versions are stunningly close to the Biblical account, so much so that the name of Noah is Nuah and the details of the flood (the wickedness of the earth, God's punishment, a great boat with the "seeds of life" with eight people on board, even a rainbow as God's sign of a promise afterward) are beyond coincidence. But even if the accounts were all completely different except for the detail that a massive flood once covered the entire earth, it challenges credibility to label the accounts as simple mythological coincidences. There is a reason why the story of the flood is universal: it really happened.

For that matter, why is modern science so adamant in denying the flood? What do they gain from this assertion and on what evidence do they base their conclusion? It becomes rather silly when you think of it this way. What is the problem with acknowleding an event that cultures from every inhabited continent remember? Other than the fear that it would lend to faith in sacred texts like the Bible, why challenge such an account of history? In fact, Perloff points out that some scientists simultaneously theorize that Mars (a planet without a definitive water mass) once had a global flood while completely denying that Earth (a planet covered in ice, water, and water vapor) could ever have possibly had one! Their denial is clearly ideological.

Perloff also covers some positive evidence for a catastrophic world-wide flood and then moves on to dinosaurs; or perhaps I should say dragons. I had known that a large number of cultures have dragon legends, but I wasn't quite aware of how matter-of-fact many of the dragon accounts were or how truly universal the stories are. It seems that even more cultures remember dragons than remember the flood. Not only that, but their description of the dragons, in many cases, is so similar to our modern reconstructions of some dinosaurs that it becomes clear that these people once saw and lived alongside these creatures. Add to this the evidence from cave paintings, burial stones, and other ancient depictions all clearly of dinosaurs and you have a phenomenal amount of evidence that man and dinosaurs very obviously coexisted for a great length of time.

But what really caught my attention was how recent some of these accounts were! Some very serious and careful descriptions of "dragons" are as modern as 1793 (Scotland), 1856 (Britain), and 1890 (America - Arizona). I was shocked at these accounts and am convinced that they are more likely legitimate than hoaxes. They are well worth a read and I may post them here after this review. There are also numerous reports from ancient historians on dragons, many of them not as fanciful as legend has it. This was by far my favorite chapter in the book.

It seems that, for whatever reason, the flying dragons (what we call pterosaurs or pterodactyls) survived the longest in history. This is probably why the famous dragon accounts are all of flying monsters. The Americas have a fantastic and terrifying legend of a flying monster called the Piasa that constantly attacked humans and animals. It is of flying monsters that all of the recent accounts I previously listed describe. It seems reasonable that flying creatures could survive longer than the larger land lizards. But even the larger land creatures have accounts from the 15th century in Ireland and even Marco Polo's travels (in which he calls them lindworms), among others. Much like the flood, it becomes clear that denial of these accounts is ideological; science is so deathly afraid that any evidence might encourage creationism that they betray their own objectivity.

Perloff ends his book with a thorough description of the actual Scopes trial versus the popularized play and hollywood accounts of the event; and then he wraps up the work with a chapter on God and how to become a Christian. I enjoyed this book from about the middle on and I especially enjoyed the dragon and flood discussions. This book is clearly a young earth creationist work (one of the very few, contrary to popular belief).

I would recommend this book, with the caveat that the first 10 chapters aren't so hot compared to many of the other books available.

Darwin's Black Box: The Biochemical Challenge to Evolution

Author: Michael J. Behe, Professor of Biological Sciences - Lehigh University

This book is amazing. It easily ranks along with Uncommon Dissent and Darwin on Trial to make the top three books I've read so far. In fact, I might put it in the top two.

Behe's book is straightforward and profound; he presents five very specific examples of biochemical irreducible complexity within cellular structures and concludes that Darwinian gradualism is incapable of creating such structures.

Those five structures/systems are:

1.) Cilia/Flagella

2.) Blood Clotting

3.) Delivery of molecules from one cell compartment to another, particularly to lysosomes

4.) Immune Systems, particularly the work of antibodies

5.) The creation of nucleotides, particularly the form of adenine known as AMP

The first four are irreducibly complex, the fifth is not necessarily so but the statistics of its gradual evolution are beyond reasonable measure and the process involves unreasonable assumptions.

You'll have to read the book to see the processes involved in these examples and to see why they are irreducibly complex. Behe's conclusions are very clear and he explains his evidence and reasoning thoroughly. He also takes much effort to explain what irreducible complexity is and what it is not.

With these examples, it becomes abundantly clear that Darwinian gradualism can not account for the evolution of cells, prokaryotes or eukaryotes. There has to be another explanation and the evidence all points toward design of some kind. The designer can remain anonymous; design can be inferred without knowing the identity of who or what did the designing.

As if this wasn't enough, Behe goes on to give a thorough account of Intelligent Design theory in greater detail. This book almost becomes an introductory text into ID as a whole.

The meat of Behe's argument goes like this: Now that science has looked inside the cell in detail and seen all the minute machinery that makes it up, this is now the level on which life must be explained. It does not do to explain the progression of structures on the level of gross anatomy, like a progression of eyes or limbs, these explanations mean nothing unless they include biochemical explanations and examples of how such strutures actually evolved. Saying that one form of eye evolved into another would be like saying that one form of computer evolved into another. It is an argument of irrelevance unless you can explain how the processor, RAM, video card, sound card, network card, power supply, case, motherboard, lights, etc... all evolved together. Such an account must involve specifics! Just saying that the pieces evolved by some fantastical story without any specific and thorough steps of exact change with exact selective pressures, exact reasons for increased fitness, etc... is worthless.

With that established, Behe gives four specific examples of systems that are irreducibly complex. He then goes to show that no explanations have been given for these or any other biochemical strutures in evolutionist literature. There are a few "just so" stories but a complete lack of specific evolutionary steps and examples. Darwinism can not explain these things, but it must if it is a valid theory of life's origin and diversity.

Behe's challenge has been met only with ad hominem attacks (big surprise) and distortions of his original arguments. He includes an afterword in this edition that explains the response his book has generated and his response to that response. It is a simple scenario; biochemistry has raised the bar of life's explanation and Darwinism can not foot the bill. There is strong and specific evidence for design in nature and Darwinists are completely unable to refute it.

After reading this book, the reader will understand Intelligent Design quite well. Not only that, but the reader will be surprised to see that Darwinists have not, and can not, explain away the evidence that ID presents. It is a shame that the arguments of this book are suppressed and waved over by the scientific community. It's about time that science pursued facts without being chained to a presumptive framework that rules certain things, like ID, out of court without evidence or explanation.

Darwin on Trial

Author: Phillip E. Johnson, Professor of Law - University of California at Berkeley

In this amazing book of only around 200 pages, Johnson succeeds in fairly evaluating the evidence that Darwinists use to support their theory of evolution. I think he has legitimately analyzed the data at hand absent metaphysical assumptions or biases. This makes this work similar to that of Wells in one respect, but very different in terms of content, purpose, and style.

Johnson is a professor of law and naturally views this topic from a legal standpoint as well as from the standpoint of argument style. He has very little to say about "creation-science" or "fundamentalism" since they have nothing at all to do with his topic at hand. He is concerned, rather, with considering whether or not valid and convincing evidence for Darwinist evolution exists when taken out of a naturalistic presumptive framework or metaphysical model. After he has examined the evidence and taken the reader through these steps, he confidently concludes that the evidence at hand does not support the theory that life on earth is the product of purely naturalistic forces acting through natural selection and random mutation. In fact, such evidence is not only rare but nonexistent.

He is well aware that organisms change within population groups to very limited degrees. Bacteria populations can change to resist antibiotics; insect populations change to resist insecticide; and, yes, finches' beaks within a population can change sizes from small to large and back again due to environmental pressures. Johnson is even convinced that the peppered moth example of natural selection is valid which Wells competently defeats in Icons of Evolution. None of this supports anything more than what I just typed. Those small changes occur, but the jump from this data to the assumption that such changes account for the existence of bacteria, insects, and finches in the first place is not empirical but rather the consequence of a certain philosophical presupposition.

While Johnson and Wells both examine Darwinist evidence and the metaphysical assumptions behind that evidence, Wells does more of the former while Johnson does more of the latter. The difference between Wells and Johnson is that Wells took ten specific icons of evolution, examined and debunked them, and lamented the modern state of scientific affairs; Johnson examines more general categories of Darwinist evidence, though he does take time to illustrate their lack of empirical justification, and focuses more intently on the arguments employed in the process.

This book is phenomenal and monumental. Johnson begins by categorically surveying the evidence: the legal setting, natural selection, mutations, the fossil record, evolutionary "fact" vs. "theory", the vertebrate sequence, molecular evodence, and prebiological evolution. Johnson has the genius ability to point out serious problems in reason and argument that may be hard to recognize for the layman. He also has a thorough knowledge of these topics, no doubt through extensive research.

After this he has concluded that Darwinism lacks the evidence it claims to have. He then discusses that given the rules of science that they employ, the lack of evidence is not a problem for them; their theory is metaphysical and doesn't even require empirical data. He then discusses the Darwinist cultural monopoly in regard to religion and education and concludes his book with a chapter titled "Science and Pseudoscience" where he makes the distinction between science (falsifiable) and pseudoscience (not falsifiable).

I was intriguied by his references to Popper and Kuhn in relation to the discussion of scientific paradigms and falsifiable theories. In order for a theory to truly validate itself it must make a risky claim or prediction and then discover that the prediction or claim was specifically true or false. There need to be specific and clear criteria for both the vindication and falsification of the theory in question. Darwinism, as it stands, is not falsifiable since it makes no risky predictions and absorbs everything it comes across as more "evidence" for itself. It therefore explains everything which by consequence explains nothing. Instead of using the theory to predict certain things (data), it merely gathers data and explains it in terms of the theory. This is completely backwards.

As for the scientific paradigms, Johnson mentions Kuhn's theory that science (and really humankind in general) takes on a certain paradigm which it uses to create questions and the rules on how to answer them. Conflicting data is explained away but rarely considered threatening to the paradigm since the paradigm is essentially a worldview through which science views everything. Kuhn postulates that science goes through paradigm shifts from time to time. I think his observation is quite accurate and, more significantly, important for our society to recognize. Our assumptions, metaphysical or otherwise, need to be acknowledged candidly and openly.

This book is amazing. If I hadn't already read Uncommon Dissent I would declare this the best anti-Darwinist book that I have ever read. It certainly lives on the same level as Uncommon Dissent but is different and unique in its own right. Every American student should read this book; it is that profound and important.

Icons of Evolution: Science of Myth?

Author: Jonathan Wells, Senior Fellow at Discovery Institute's Center for the Renewal of Science and Culture

I have to admit that my expectations for this book were a bit low, but I was pleasantly surprised in spite of this and was happy to be wrong in my assumptions. The book is topically arranged around ten "Icons of Evolution", the often repeated and publicly famous "evidences" for Darwinism. Wells points out that, in various degrees of severity, these icons all misrepresent the actual evidence. Each topic has its own chapter and contains more than enough research to completely debunk Darwinian orthodoxy.

One icon (the Miller-Urey experiment) gives the false impression that scientists have demonstrated an important first step in the origin of life. One (the four-winged fruit fly) is portrayed as though it were raw material for evolution, but it is actually a hopeless cripple - an evolutionary dead end. Three icons (vertebrate limbs, Archaeopteryx, and Darwin's finches) show actual evidence but are typically used to conceal fundamental problems in interpretation. Three (the tree of life, fossil horses, and human origins) are incarnations of concepts masquerading as neutral descriptions of nature. And two icons (Haeckel's embryos, and peppered moths on tree trunks) are fakes...

This is not science. This is not truth-seeking. This is dogmatism, and it should not be allowed to dominate scientific research and teaching. Instead of using the icons of evolution to indoctrinate students in Darwinian theory, we should be using them to teach students how theories can be corrected in light of the evidence. Instead of teaching science at its worst, we should be teaching science at its best.

And science at its best pursues the truth. Dobzhansky was dead wrong, and so are those who continue to chant his anti-scientific mantra ["nothing in biology makes sense except in the light of evolution"]. To a true scientist, nothing in biology makes sense except in the light of evidence.

Since this book covers so many different topics, it can only briefly introduce them. Each topic could easily warrant its own book of thorough treatment. This gives Icons of Evolution a wonderful assortment of information at the cost of more detailed study. Wells makes up for this, however, through skillful summary. He artfully reduces mass research into carefully chosen and pertinent statements on each subject.

Wells also has a thorough grasp of the metaphysical assertions and assumptions that accompany these various icons of evolution. In most chapters, he precisely juxtaposes the available evidence against statements by leading biologists and examines the philosophical conclusions that they make. The reader is treated to abundant non-sequiturs and mental gymnastics as evidence is twisted beyond recognition by various outspoken Darwinists.

Perhaps the most unique contribution of Wells's book is his examination of current biology textbook material. In each of his sections he compares the available evidence with the current information printed in biology textbooks. In each case, the reader shudders at the rampant dishonesty and, in some cases, intentional deception that these books inflict upon American education. This is one of the more disturbing aspects of Wells's research. The presence of dishonesty is bad enough, but the amount Wells uncovers, bold and flagrantly displayed in publication after publication funded largely by public money, is enough to evoke genuine outrage. At the end of the book Wells includes an audit of some popular textbooks and grades them on their presentation of the various "icons". The results are dismal.

After reading this book, the evidence Darwinists use to promote their worldview seems much less intimidating. In fact, it seems sad and twisted and the reader is left with feelings of anger at the outright lies promoted in public education and feelings of despair at the state of American science. Why can't biology be honest with the more noble sciences like physics and chemistry? Why do biologists cheat and lie and why do we have to put up with it?

This critique of the most famous and propogandized evidences for Darwinism is an item that every educator should be required to read. Nowhere does Wells base any arguments on religion, faith, the Bible, God, or anything of the sort. He keeps to the evidence, quite unlike the Darwinists he discusses, and amply disarms these iconographic pillars of evolution. Is evolution true or false? Wells doesn't seem to care; but he certainly doesn't want lies and deception infiltrating our schools and society and he therefore rightly throws these "icons" in the garbage where they belong. The problem, as he points out, is that these icons are the evidence for evolution. Why should we believe a theory based on misinformation?

Transitional Fossils

Something David Berlinski said got me thinking:

"I am happy to salute Archaeopteryx, recognizing the little monster as half-bird and half-reptile"

Now, Berlinski isn't a creationist but he does have a problem with Darwinist evolution. His comment, however, struck me in an interesting way. Why do creationists fret over the supposed "transitional" fossils? What is there really to worry about? So what if a creature is half-bird and half-reptile, that doesn't mean it evolved from either or into either. It just means it's half-bird and half-reptile. Peculiar, sure; proof of evolution, hardly.

The simple facts of reality are on our side. The past is inscrutable. Even if there was a perfect procession of fossils (which there absolutely isn't); even if we could create life from non-life in the lab by purely random processes (which we absolutely can not); even if we could observe macroevolution from one creature into another (which we absolutely have and will not) what would it prove? Nothing! It would only open up the possibility that such things might or can happen, not that they did in fact occur in the past. None of this can be proven empirically. Thus should cause science to step back and stop making dogmatic statements about such uncertain ground. Science is a fine thing as long as it keeps itself in check by its own standards of empirical observation and it remains purely objective and impartial. The past is not an object that can be reliably studied through these methods. It is therefore not the proper domain for scientific study, especially not dogmatic scientific conclusions.

Thought Police (aka "scientists")

"Science", if you can refer to such a broad concept as a single entity, has become an ideological bulwark. The establishment today has so long ago lost its roots that it has become what it once fought against: dogmatic metaphysical indoctrination.

Science, as a term, is simply the quest for knowledge and understanding. Technically, it isn't even the study of "truth"; rather it merely collects and arranges data. It is supposed to be very much like a trial judge: an impartial force with no investment in or desire for a certain conclusion. Just as a trial judge is not supposed to care which side wins or loses, science is not supposed to care what conclusions the data supports. In the words of Carl Sagan:

"The suppression of uncomfortable ideas may be common in religion or in politics, but it is not the path to knowledge, and there's no place for it in the endeavor of science."

Why, then, do we find ourselves in a very different situation? "Science", the establishment, has made it clear that any conclusions supporting creationism, christianity, teology, and many other concepts are not allowed. Wait a minute. That is not an impartial force with no investment in or desire for a certain conclusion. Therefore, I must conclude that these are not the words of science but rather the words of a dogmatic metaphysical system of thought. If the data at hand somehow did indicate that creationism was the best explanation for biological life, why is that not allowed? Where is the quest for knowledge if certain conclusions are ruled out a priori? The discrepancy is so blatant that I just summed it up in a single paragraph. What happened to science?

What if the data at hand indicated that humans have souls, that God does exist, that miracles have occurred, and that this world and universe were intelligently designed? Why should science care? It isn't supposed to prejudge. It doesn't work to simply say that science is the study of only physical things becuase that automatically assumes that nonphysical things can neither be studied nor can be the conclusion from physical study. Where is there evidence for such a conclusion? Science isn't supposed to care.

Take this quote from David Berlinski (not a creationist, by the way) in response to one of his critics:

"Paul R. Gross is anxious lest in criticizing Darwinian theory I give comfort to creationists. It is a common concern among biologists, but one, I must confess, to which I am indifferent. I do not believe biologists should be in the business of protecting the rest of us from intellectual danger."

How poignant a statement! When did science become our thought police? Why should science care what we believe or what we doubt?

It can only be concluded that the behavior of "science", the establishment, indicates an overarching worldview that they seek to enforce. Otherwise they honestly shouldn't care what the data indicates. I say this is a serious problem and gross waste of our society's time and money. Why does science care what we believe? That isn't its business.

Why should "science", the establishment, care if a certain school board wants to teach Intelligent Design? [Adam was waiting for my statement on this]. It isn't science's domain to tell us what to believe, only to present us with its findings. Why does science care if the data can be interpreted to support teleology? It isn't supposed to care if it really is impartialy seeking the truth, no matter what that truth might be. In fact, from this school board reaction, I can tell that science didn't even do its homework (not that it should have been involved in the first place). Even reading a single book on Intelligent Design shows that it strongly supports evolution. In fact, Intelligent Design theorists are primarily staunch evolutionists but not Darwinists; they see design and teleology as inherent properties of the natural world. Again, why should science care?

It really is time to grow up. I don't need thought police, do you?

Mind and Matter, Soul and Substance

After reading Uncommon Dissent for the second time and reviewing each article, I have this topic on my mind. I suppose my inquiry was particularly inspired by Christopher Michael Langan's essay, though I've wondered about this for some time now.

Without getting overly abstract, let me introduce this issue. As Langan points out, there has to exist some medium wherein causes are linked to their effects. Take a bat intersecting with a ball, for example. The bat swings with a certain degree of force and, upon hitting the ball, transfers a degree of that force. We can describe this medium in terms of physical forces: mass, matter, velocity, momentum, etc...

Causality can also exist in more than one plane of reality, however. An example of this is the intersection of mind and matter. How exactly does a mind intersect with a body? I'm not talking about a brain, I'm talking about the nonphysical consciousness that we call "mind". A person can decide to drive to work with their mind and somehow this is causally transferred into the brain which guides their body to complete the task. Mind connects with matter in this way, somehow.

An even better example is the intersection of soul (if you consider that separate from the mind) and matter. How does a soul, what makes a person who he or she is, reside within a body and mind? How does it causally interact with the body and mind?

These are all interesting questions, but I don't intend to answer them here. I'm not concerned with exactly how mind, soul, and body are causally connected as long as it can be acknowledged that mind and soul are nonphysical and yet they causually interact with the physical body somehow.

Along these lines, it seems only natural that when the mind or soul interacts with the body there is a physical manifestation of that causal relationship. In other words, emotions (which can take place within the mind and soul) are still physically manifested in the brain and body. Emotions exist, therefore, in both planes of reality. Not only this, but if these things are true the physical manifestations of the said reactions are the result of the relationship.

This boils down to my point: physical properties are not indicative of a lack of the nonphysical. Just because we have found that seratonin is involved in emotions does not mean that emotions are a purely physical quality. There is no evidence whatsoever to conclude that the discovery of a physical quality, such as seratonin levels, is necessarily a cause; it could just as easily be an effect.

Applying this over all of science, we see examples all around us of people finding new physical manifestations of things once thought nonphysical. This is espeically true in psychology and biology today, but was also true in other disciplines in the past. Meteorology, for example, took "God" out of lightning and thunder. It did this not because of evidence against God, but becuase a physical nature was discovered in weather events.

It strikes me as odd that people think a physical event must therefore lack a nonphysical cause; especially since we observe it constantly between our minds and bodies. How presumptuous of us to eliminate the cause by explaining the effect. This is one of science's favorite tricks and it is step-by-step eliminating every bit of nonphysical reality from our culture. Evidence for this? None, of course; only the charging assumption that nonphysical events are simply not yet "explained".