An important premise in some arguments for God’s existence is that anything that begins to exist has a cause. That is, things that come into being don’t just pop into existence for no reason. There is some cause that explains why that thing started to exist when it did. There is a causal story involving your parents that explains why you exist, for instance, and it would be odd, to say the least, if there weren't. This premise – anything that beings to exist has a cause - seems intuitive, reasonable and attractive to most people. Check out the video below for a neat summary of one argument for God’s existence – the Kalam Cosmological Argument – that features this premise.  

On occasion it would be very convenient if human beings could read minds,
perhaps when interrogating crime suspects or when waiting for the moment to ask a girl out on a date. On balance, however, it's probably a good thing that they can't. Aside from laying bare all our deepest hopes and the ideas we'd never speak aloud, it would completely devastate a good game of chess.  Ah well, such is fantasy. As fantasy, it cannot serve as a neat little answer to a more fundamental question: how do we know things?

Some things, of course, we know because our senses tell us. We feel a switch flick beneath our fingers and see the room be bathed in light. While philosophers argue about the trustworthiness of our senses, broadly speaking we all agree that they're normally reliable.

A few weeks ago I gave a talk at my church on the title 'Has science killed God?'. I am certainly no specialist in this area but hopefully Christians will still find enough in there to help them feel more confident in God and about the nature and role of science. But just so you know, science has not killed God!

Let me know your thoughts and I would be happy to pass on my notes by email if you would like them.

Has Science killed God?

Computers can usually be considered fairly predictable. They work to rule; rules determine how they accept your input and rules determine what they give you back. In fact, you could use the experimental scientific method to find out and document exactly how those rules work. They might say "in response to pressing the 'W' key the car accelerates in a forward direction by 10 miles per hour per second" or "When the car hits a wall head on it comes to a complete stop." The tenth wall will stop you just as effectively as the first. These investigations in cyberspace could be as rigorous as those used to investigate the physical world around us.

Now let us imagine that you're racing around this virtual universe when another car, completely unlike any other, appears from nowhere right in front of you. You see a steep bend coming up and hope to overtake when this mysterious vehicle slows down for it. Instead the other car runs toward, into and straight through the wall! As it happens, one of your opponents is the programmer who designed the game and he is using his knowledge of the inner workings of the game to subvert the basic laws of that in-game universe. The laws you so painstakingly measured aren't wrong, they just can't address the possibility of an external influence like the cheating programmer.

Going back to my undergraduate days, I have long been struck by the engineering elegance and intrinsic beauty of that familiar icon of intelligent design, the bacterial flagellar nano-motor. In tribute to this masterpiece of design, I have just published a detailed (31 pages, inclusive of references) literature review in which I describe the processes underlying its self-assembly and operations.

My essay also attempts to evaluate the plausibility of such a system having evolved by natural selection. Here’s a short excerpt to whet your appetite.

The bacterial flagellum is a reversible, self-assembling, rotary nano-motor associated with the majority of swimming bacteria. There exists a number of different models of this rotary motor (Pallen and Matzke, 2006; Soutourina and Bertin, 2003). Flagella are produced by a very tightly regulated assembly pathway (Chevance and Hughes, 2008; Macnab, 2003; Aldridge and Hughes, 2002), and the archetypical system for understanding flagellar assembly belongs to Salmonella enterica serovar Typhimurium, a rod-shaped gram negative bacterium of the family Enterobacteriaceae.

Flagella receive feedback from the environment by virtue of an elegant signal transduction circuit and can adjust their course in response to external stimuli by a mechanism known as chemotaxis (Baker et al., 2006 Bourret and Stock, 2002; Bren and Eisenbach, 2000). The most extensively studied chemotaxis system belongs to Escherichia coli.

By itself, the rotor is able to turn at a speed between 6,000 and 17,000 rotations per minute (rpm) but normally only achieves a speed of 200 to 1000 rpm when the flagellar filament (that is, the propeller) is attached. Its forward and reverse gears allow the motor to reverse direction within a quarter turn.

The bacterial flagellum, which has been described as a “nanotechnological marvel” (Berg, 2003), has long been championed as an icon of the modern intelligent design movement and the flagship example of “irreducible complexity” (Behe, 1996). But even biologists outside of this community have been struck by the motor’s engineering elegance and intrinsic beauty. As one writer put it, “Since the flagellum is so well designed and beautifully constructed by an ordered assembly pathway, even I, who am not a creationist, get an awe-inspiring feeling from its “divine’ beauty” (Aizawa, 2009).

The mechanistic basis of flagellar assembly is so breathtakingly elegant and mesmerizing that the sheer engineering brilliance of the flagellar motor — and, indeed, the magnitude of the challenge it addresses to Darwinism — cannot be properly appreciated without, at minimum, a cursory knowledge of its underlying operations. The purpose of this essay is to review these intricate processes, and evaluate the plausibility of such a system evolving by natural selection.

Click here to continue reading.

A common objection to the theory of intelligent design is that it makes no testable predictions, and thus there is no basis for calling it science at all. While recognizing that testability may not be a sufficient or necessary resolution of the "Demarcation Problem," my article, which I invite you to download, will consider one prediction made by ID and discuss how this prediction has been confirmed.  

Click here to continue reading>>>

Readers will likely recall the ENCODE project, published in a series of papers in 2007, in which (among other interesting findings) it was discovered that, even though the vast majority of our DNA does not code for proteins, the human genome is nonetheless pervasively transcribed into mRNA. The science media and blogosphere is now abuzz with the latest published research from the ENCODE project, the most recent blow to the “junk DNA” paradigm. Since the majority of the genome being non-functional (as has been claimed by many, including notably Larry Moran, P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and Richard Dawkins) would be surprising given the hypothesis of design, ID proponents have long predicted that function will be identified for much of our DNA that was once considered to be useless. In a spectacular vindication of this hypothesis, six papers have been released in Nature, in addition to a further 24 papers in Genome Research and Genome Biology, plus six review articles in The Journal of Biological Chemistry.

The lead publication of the finding (“An Integrated Encyclopaedia of DNA Elements in the Human Genome“) was released in Nature. The abstract reports,

“The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.” [emphasis added]

They further report that,

“[E]ven using the most conservative estimates, the fraction of bases likely to be involved in direct gene regulation, even though incomplete, is significantly higher than that ascribed to protein- coding exons (1.2%), raising the possibility that more information in the human genome may be important for gene regulation than for biochemical function. Many of the regulatory elements are not constrained across mammalian evolution, which so far has been one of the most reliable indications of an important biochemical event for the organism. Thus, our data provide orthologous indicators for suggesting possible functional elements.”

As this Nature press release states,

“Collectively, the papers describe 1,640 data sets generated across 147 different cell types. Among the many important results there is one that stands out above them all: more than 80% of the human genome’s components have now been assigned at least one biochemical function.” [emphasis added]

The UK Guardian also covered the story, noting that

“For years, the vast stretches of DNA between our 20,000 or so protein-coding genes – more than 98% of the genetic sequence inside each of our cells – was written off as “junk” DNA. Already falling out of favour in recent years, this concept will now, with Encode’s work, be consigned to the history books.” [emphasis added]

This new research places a dagger through the heart of the junk DNA paradigm, and should give adherents to this out-dated assumption yet further cause for caution before they write off DNA, for which function has yet to be identified, as “junk”. Be sure to also check out Casey Luskin’s coverage of the findings at ENV.

Ask a typical geologist, or even a competent GCSE student, how sand forms on the beach and you can expect a step by step procedure as large chunks of rock are split and weathered by the relentless beating of the ocean tides. This is a very slow, perfectly natural process that has been going on for millennia.
Ask how the famous Giant's causeway came about, those striking arrays of hexagonal pillars rising out of the sea on the Irish coast. You'll get a story that starts violently, with a rush of lava at hundreds of degrees, but again is both perfectly natural and unguided.
Ask about any rock form of any size on any continent, and through the gnarled roots of trees, the whipping of the desert winds, the pounding of rivers or the surging of magma from far below us they will provide an explanation, and for the most part those explanations will be perfectly solid.

Now ask instead about David.  The seventeen foot tall marble replica of a man, complete with muscles, bones, joints, and even sideburns, has and can have no unguided natural explanation. The only explanation that explains this phenomenon is the meticulous planning and dexterous hand of the great Renaissance artist and sculptor Michaelangelo. Geologists all agree with the accepted account of the origin of this sculpture, even as they agree on the natural processes that formed the smooth river stones the original David used in his most famous accomplishment.

This article was originally published at Uncommon Descent.

We’ve all heard it before. Time and time again the somewhat tiresome and predictable Darwinian propagandists, in a fit of florid indignation, assert that intelligent design will be the death of science and the dawn of theocracy. The claim that ID is nothing more than warmed-over creationism is one that has been thoroughly addressed by ID proponents, yet, the vacuous claim continues to be thrown around.

Over at Evolution News And Views, John West recently highlighted the upcoming release of Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False (Oxford University Press, 2012), a new book by New York University’s atheist philosopher Thomas Nagel. Those immersed in the debate over ID and Darwinism will be familiar with Nagel’s open scepticism towards neo-Darwinian theory and his sympathetic attitude towards ID theory. Though Nagel does not accept ID, he goes as far as to say that it has much merit and that it is science. Good on him! Nagel’s views on this issue can be found in his 2008, Philosophy & Public Affairs article Public Education and Intelligent Design. It will be good to read more about his views as they are further expressed in his new book Mind and Cosmos. West includes a couple of delicious quotes from chapter 1 of Nagel’s book:

This article was originally published on Evolution News & Views.

A correspondent recently asked me about the evolution of the mammalian middle ear in relation to the fossil record. Based on data gathered from embryology, it is widely thought that the bones of the mammalian middle ear (the region just inside the eardrum) evolved from bones of the reptilian lower jaw joint. Besides the paleontological data, this hypothesis is based on the fact that, in mammals, Meckel's cartilage plays a role in forming the middle ear bones and mandible before subsequently disappearing. In reptiles, it ossifies to become part of the jaw.

Two of the three bones that comprise the mammalian middle ear are located in the lower jaw joint of reptiles. During the transition of mammals to reptiles, therefore, it is supposed that the quadrate and articular (as well as pre-articular) bones became separated from the posterior lower jaw and evolved into the incus and malleus, two of the bones associated with the mammalian ear.

I had the great pleasure yesterday of attending the debate "Does the universe show evidence for a creator?" at Imperial College, London. Arguing in the affirmative was astrophysicist Hugh Ross of Reasons To Believe,  a science-faith think tank from the USA; arguing the negative was Lewis Wolpert, Emeritus Professor of biology and British Humanist.

Before the debate, however, I had the privilege of meeting the participants. Hugh Ross and his wife Kathy were a delight. Kathy remarked that the weather was hotter here than in California! I made sure she appreciated how rare an occurrence this is (have to say, I've been loving it! I can walk down the streets of London in shorts and t-shirt at 9pm)!

Then Lewis Wolpert showed up! A really nice guy! Winsome and congenial. He seemed to get on very well with Hugh and Kathy. I discovered that his son Matthew appears three times a week on the comedy circuit in Leicester Square, so that's an act I definitely need to check out! We also had a great talk about the fascinating complexity of the cell, which Wolpert happily admits is truly mindboggling.

But, onto the debate itself! A good turn-out. The lecture theatre was packed. It was hosted by Imperial College's Christian Union, but a decent number of atheists and sceptics showed up too - which is quite something given that AC Grayling was giving a lecture in the next room (he passed by me earlier as I was editing my latest Dawkins-critical video on my laptop... I don't think he noticed)!

This is where it gets interesting. Hugh Ross went first, and outlined for 20 minutes his Creation Model, arguing that the Bible - and only the Bible - contains consistent, scientifically accurate predictions about the cosmos, the empirical data for which is only being discovered recently in the modern age. His case is essentially that the more we discover about the universe, the more the evidence for design and a transcendent creator piles up and confirms what the Bible has been telling us for the past thousands of years. Of particular note were passages from Jeremiah and Romans, which Hugh claims tell us about the expansion of the universe and the law of entropy. Alongside we have the opening of the Bible, that in the beginning God created the heavens and the Earth - the Big Bang is this beginning. When this was discovered, a great many scientists were reluctant to accept it, fearing that an absolute beginning of space and time gave too much leverage to those who believe in theistic creation.

It was fascinating also to hear Hugh cite an article written by atheist physicists called "Disturbing Implications of the Cosmological Constant". In this article, its atheist authors were forced to concede that this particular cosmological constant left them no choice but to invoke a transcendent causal agent. Their solution? To "do a Daniel Dennett": conclude that this cosmological constant must, therefore, surely be false (!)

Before moving on to Wolpert's response, I cannot help but also comment on the audience. Well, specifically, the students in front of me. They were clearly "sceptics"! Though not just sceptics, rather restless sceptics. The kind I can remember being while I was at university and convinced of my own immortality. There was an evident aggression and desire for peer-approval in the way they increasingly shot each other smirks and disapproving glances as Hugh spoke (one seemed to think it especially important that his lady friend understood unequivocally that this religious nutter wasn't going to sway his opinion one jot)!

It was a touch depressing how superficial some of their reactions were - one questioner claimed to "understand what it's like to be arrogant" before accusing Hugh Ross of being so for claiming that the universe was designed (I don't think that guy actually does understand arrogance). Another student was taking numerous notes while shaking his head. I've no problem with critical note-taking, but I found it curious that one of his bullet-points read "where the f*** did that graph come from". Why the expletive? Where does this extra infusion of hostile energy come from? Why not just write "where did that graph come from"?

Onto Lewis Wolpert's rebuttal. Now, I've seen and heard quite a bit of Wolpert in debates on the existence of God. Indeed, one of my earliest memories of discovering apologetics was watching his 2007 debate against William Lane Craig. His arguments back then were pretty weak, so I wondered what he'd produce this time, five years on...

Exactly the same arguments! Specifically:

1. "Who made God?"

2. "We believe in God because we evolved an over-active sense of cause and effect".

3. "Absence of evidence is evidence of absence"

4. "Why is your religion any better than the thousands of other religions out there"?

I was astonished! Craig had addressed and exposed all these arguments as completely fallacious during their debate in Westminster:

1. Asking "who made God?" has nothing to do with the question of whether the universe shows evidence for a creator (it's a secondary question, and makes the same anti-scientific demand Dawkins does: of "who designed the designer?" leading to the requirement of an infinite regress of explanations in one go, so no explanation could be accepted). This is not to speak of the fact that God is uncaused, which is precisely the position Lewis Wolpert would have to hold about the universe (i.e. his objection is special pleading).

2. The second argument commits the genetic fallacy: of trying to invalidate a view by explaining how someone comes to hold it. Imagine if I walked up to an atheist and said, "you deny God because you have a bad relationship with your father, so you can't stand the idea of a bigger authority figure behind the universe". Even if that were true, would it mean therefore that atheism is false and that God exists?! Clearly not. Why has Wolpert not come to terms with this fallacy, especially given that it has already been pointed out to him?

3. As for evidence of absence, this was something I took upon myself to point out to Lewis during audience Q&A: that it's logically fallacious to rely upon absence of evidence. Having no evidence, say, that there's a person lurking in the corridor outside the lecture theatre, does not mean that we therefore do have evidence there is nobody outside!

4. As for asking "what makes you think your religion is truer than any other"? I can understand this having rhetorical appeal to those who are already sceptical of the idea of God. However, at the end of the day, it's not even an argument. It's a question. And the answer to that question would be... in Hugh's opening speech!

Now, as for those specific arguments Hugh laid out, to show that there is evidence for the Christian God, Wolpert responded:

"There isn't any evidence for God, and you certainly can't get it from physics."

...wasn't that the very title of the debate? About whether or not the physical universe shows evidence for God? So, essentially, Wolpert used up his time recycling fallacious arguments, which had nothing to do with Hugh's presentation, and dismissed the presentation itself in a single sentence consisting of a mere question-begging assertion. In fact, the most telling moment was when he said "I'm not a physicist, I don't understand any of it, but I'm sure that even if I did... it would still not be evidence for God"!

What he did do, which I have to admit was quite a clever tactic, was to divert the audience's attention away from Hugh's astrophysics to biology. Evolution! "Do you think we evolved"? "Did Eve come from Adam's rib"? This manoeuvre set the tone for the lengthy cross-examination and Q&A which was to follow, as Ross's views here certainly aren't in line with the popularly accepted interpretations of evolutionary development (though one cannot be left in any doubt he's comfortable offering evidence for them).

There were no rebuttal rounds after those opening speeches. The rest was cross-examination and audience Q&A, which went on for quite a while and allowed many questions to be raised from the floor. I had to admire Hugh's stamina: he'd only recently come off the plane, must have been jet-lagged, but calmly carried on simply providing answers to the many questions which came his way (and kept doing so for two hours solid after the event had finished). Indeed the questions were very Hugh Ross-heavy. At one point it seemed to be simply a "grill Hugh" session, with Wolpert only becoming involved for the occasional extra point of view. You could almost forget he was there sometimes. He didn't seem to be trying. I wonder if Hugh Ross gave him something new to think about?

Much, much more could be said, but I reckon I can leave it here. Doubtless the recording will be released soon and you can go through it all in greater detail (I'll link it in this post when it's out). Some students appeared unimpressed with Hugh's case, expressing that it was too vague and vulnerable to differing biblical interpretations. Others were coming out with remarks of surprise and interest, admitting they'd not expected to encounter a Christian scientist who was prepared to answer all their questions in such depth. Only time can tell what ripples these events cause.

Speaking of which, you do know how God created different dimensions of time and exists in a time dimension all of his own, don't you? If not, you will soon!

This article was originally published on Evolution News & Views.

I have recently been reading George McGhee's Convergent Evolution: Limited Forms Most Beautiful. McGhee's book is a gripping read, and it favorably cites the work of both Michael Denton and Douglas Axe, ID-friendly scientists well known to readers of ENV. The book documents a multitude of cases of convergent evolution (homoplasy), the phenomenon of repeated evolution. When similarity is thought to have arisen by means of common ancestry, the features in question are said to be "homologous." When similarity is thought to have arisen by means other than common ancestry, the features are said to be "analogous."

Those who subscribe to universal common ancestry interpret biological similarity of sequence, structure and anatomy as resulting from descent with modification from a common ancestral source. ID proponents who question common ancestry typically interpret biological similarity as resulting from a common blueprint. Is there a way to evaluate which of these two competing hypotheses better fits the evidence?

If you take such similarity as pointing to common descent, then you would expect to see it exhibiting a nested hierarchical distribution, the more seamless the better. In other words, the patterns of distribution of this similarity ought to mutually corroborate a single family tree. Sure, there might be occasional deviations from that tree, the results of phenomena such as incomplete lineage sorting. One would not expect to see the pervasive occurrence of a high degree of similarity -- what would normally be regarded as "homology" -- that decidedly cannot be accounted for within the framework of common descent. Yet that is in fact what we do observe.

This article was originally published on Evolution News & Views.
A correspondent recently referred me to an article in the TalkOrigins Archive responding to the argument that "Complex life forms appear suddenly in the Cambrian explosion, with no ancestral fossils." TalkOrigins is a popular online resource that collects attempted answers to some often-heard challenges to Darwinian evolutionary theory. The article offers seven responses to the contention that the Cambrian explosion, which occurred some 530 million years ago, represents a significant difficulty for the neo-Darwinian view on how animal body plans evolved.

Since this subject comes up frequently in the evolution debate, as indeed the seeming dilemma posed by the Cambrian event troubled Darwin himself, I here offer a brief reply to TalkOrigins.