Another Swipe at “Established Science”

December 26, 2016

One theme of Genesis and Genes is that the public should beware of claims of established science. This means that certain issues are no longer open to discussion, because the evidence is supposedly so solid as to warrant no more doubt. Critics of established science are deemed quacks, obscurantists, anti-science or worse, regardless of how cogent and evidence-based is their criticism.

Claims that certain positions constitute established science are not new. Let me provide one example from astronomy.

For several decades in the late nineteenth and early twentieth centuries, a debate raged among astronomers about whether or not the Milky Way was the sum total of the material universe. Many astronomers believed that there were no stars beyond our galaxy. The galaxy made up everything, and beyond it lay empty space. Others believed that there were other galaxies beyond our own, known at the time as island universes. [Kant and Laplace are credited with developing this view]. The disagreement culminated in the “Great Debate”, a 1920 confrontation between Harlow Shapley and Heber Curtis, in which this issue was discussed.

The pivot around which the debate revolved was the existence of faint, fuzzy patches of light known as nebulae. Were they galaxies that existed very far away from the Milky Way, or were they clouds of gas that existed within (or on the outskirts of) our galaxy? In 1890, Agnes Clerke (1842-1907), an English astronomer and science writer, summed up the prevailing belief about the existence of other galaxies in System of the Stars:

The question of whether the nebulae are external galaxies hardly any longer needs discussion. It has been answered by the progress of discovery. No competent thinker, with the whole of the available evidence before him, can now, it is safe to say, maintain any single nebula to be a star system of co-ordinate rank with the Milky Way. A practical certainty has been attained that the entire contents, stellar and nebular, of the sphere belong to one mighty aggregation…[1]

So you see, it’s settled. There are no galaxies beyond the Milky Way. There is no need for further discussion. If you are a competent thinker, there is nothing more to say (and, of course, if you express doubt, you must be an incompetent thinker).

Needless to say, this established science view turned out to be incorrect. As astronomy progressed it became evident that numerous galaxies exist beside our own. Today, it is believed that there may be 200 billion galaxies in the observable universe.


The Big Bang Theory is a paradigmatic example of established science. Practically everyone knows that the universe began some 13.8 billion years ago in a humongous expansion of spacetime (the less informed imagine something very fiery, like the Mother of All Bombs). There is certainly evidence for this view, but there are problems too (which is the case for all scientific theories). Perhaps the chief difficulty with [the Standard Model of] the Big Bang is the horizon problem.

Here is the bare bones on the horizon problem. If we look in one direction into space to a distance of, say, 10 billion light years, and then look in the opposite direction, again to a distance of 10 billion light years, we would be looking at two regions of space that are 20 billion light years from each other. Since the universe is believed to be only about 13.8 billion years old, no light (or anything else) from one of these regions could have “communicated” with the other region. There would not have been any opportunity for these two regions of space to have physical contact which could have led to temperature differences between these regions, for example,  being averaged out. And yet, we find that the entire observable universe is astonishingly similar in its physical properties in all directions (it is isotropic).

Two possible solutions to this conundrum have been proposed. The first is inflationary cosmology, which solves the horizon problem at the expense of gigantic problems of its own. Basically, accepting inflation to solve the horizon problem is like treating an itchy nose by cutting it off: the itch is cured, but the cure comes at a steep price. Problems with the inflationary model have been noted by top-notch scientists like Roger Penrose and Paul Steinhardt.

The second solution has been proposed independently by several teams. One team is led by Professor João Magueijo, whom I briefly introduced in Genesis and Genes:

Magueijo received his doctorate at Cambridge, and was awarded the research fellowship previously held by the physics Nobelists Paul Dirac and Abdus Salam. He has been a faculty member at Princeton and Cambridge, and is currently a professor at Imperial College London. Magueijo is famous in physics circles for his work on VSL cosmology. The acronym stands for Varying Speed of Light. Undertaken in 1998 together with Andreas Albrecht, VSL proposes that the speed of light was much higher in the early universe – some 60 orders of magnitude faster than its present value. The work is an alternative to inflationary cosmology. Magueijo describes his work in his 2003 book, Faster than the Speed of Light.[2]

If Magueijo and others are right, the horizon problem is solved at the expense of a key aspect of contemporary physics: the immutability of the speed of light.

Recently, Sputnik News provided an update about Magueijo’s research.[3] He and his colleagues are collecting evidence to bolster their claim. If they are right, one of the cornerstones of modern physics – that the speed of light is constant in a vacuum – will come crashing down.

Of course, that’s a big if. But my point is relevant regardless. I wrote this in Genesis and Genes:

In contemporary science, the dominant theory often doesn’t dominate – it monopolizes. This means that the public – and scientists – are often not even aware that there are competing theories.

My (educated) guess is that everyone reading this post has heard of the Big Bang Theory. Far fewer people – those more informed than the average member of the public – have heard of inflationary cosmology. And perhaps one person in a million has heard of VSL, the alternative to inflation that posits a varying value for the speed of light. But VSL is there, a real and legitimate research program.

This state of affairs, in which the dominant theory monopolises the news, distorts the public’s ability to assess the claims made by scientists. An illusion is created whereby the dominant theory is perceived by the public as the only theory. The consequence is that it becomes politically and socially difficult to criticise this entrenched position.

In Genesis and Genes, I went on to describe another incidence of established science, this time in the context of evolutionary biology:

[Beginning of Quote]

Here is another example of the monopoly phenomenon that is directly relevant to the primary focus of this book. This is the evolution of dinosaurs to birds. This hypothesis is a staple of museum displays, documentaries, biology textbooks and encyclopaedia entries. The standard teaching is that birds evolved from maniraptoran theropod dinosaurs. This, too, is portrayed as something that we know. As is the case with Black Death, even well-informed members of the public have virtually no chance of discovering that there are many competent scientists – committed to the Darwinian worldview, so that they cannot stand accused of religious bias – who strongly disagree with the mainstream view for straightforward technical reasons. Here is one example. Larry Martin is a paleo-ornithologist and the curator for vertebrate palaeontology at the University of Kansas Natural History Museum. He is one of the world’s foremost experts on birds of the Mesozoic era. In an article which appeared in the now-defunct periodical The Sciences (March/April 1998), Martin wrote:

I began to grow disenchanted with the bird-dinosaur link when I compared the eighty-five or so anatomical features seriously proposed as being shared by birds and dinosaurs. To my shock, virtually none of the comparisons held up. For example, the characteristic upward-projecting bone on the inner ankle in dinosaurs lies on the outer ankle in birds. In some cases I even discovered that the supposedly shared features occurred on entirely different bones. That is a bit like saying that you and I are related because my nose resembles your big toe.

The simplest argument against the dominant hypothesis is that the fossil record is incompatible with the dino-to-bird scenario. As Professor John A. Ruben of Oregon State University points out, “For one thing, birds are found earlier in the fossil record than the dinosaurs they are supposed to have descended from. That’s a pretty serious problem, and there are other inconsistencies with the bird-from-dinosaur theories.”[4] What are some of these other inconsistencies? Flying is an extremely energy-intensive activity. When they fly, birds need to produce energy at a furious rate. This means that they need to process oxygen very efficiently. Birds, which are, of course, warm-blooded, need about twenty times more oxygen than cold-blooded reptiles. They have a unique lung structure that allows for a high rate of gas exchange which makes flying possible.

Now, it’s been known for decades that the thigh bone (femur) in birds is largely fixed and makes birds into “knee runners”, unlike virtually all other land animals. In 2009, however, the discovery was made by Oregon State University researchers that it is this fixed position of bird bones and musculature that keeps their air-sac lung from collapsing when the bird inhales. Their unusual thigh complex is what helps support the lung and prevent its collapse. “This is fundamental to bird physiology,” says Devon Quick, an OSU zoologist. “It’s really strange that no one realized this before. The position of the thigh bone and muscles in birds is critical to their lung function, which in turn is what gives them enough lung capacity for flight.” Why is this discovery so pertinent to the issue of evolution? The OSU scientists said that every other animal that has ever walked on land has a moveable thigh bone that is involved in their motion – including humans, elephants, dogs, lizards and – in the ancient past – dinosaurs. The implication, the researchers say, is that birds almost certainly did not descend from dinosaurs. Professor Ruben of OSU continues, “But one of the primary reasons many scientists kept pointing to birds as having descended from dinosaurs was similarities in their lungs.” His conclusion: “However, theropod dinosaurs had a moving femur and therefore could not have had a lung that worked like that in birds. Their abdominal air sac, if they had one, would have collapsed.”

Researchers committed to the dino-to-bird hypothesis typically brush aside this criticism. The main reason for this is, of course, their commitment to the evolutionary story. The Science Daily report from which these quotations are taken continues: “The conclusions [of the Oregon State University researchers] add to other… evidence that may finally force many palaeontologists to reconsider their long-held belief that modern birds are the direct descendants of ancient, meat-eating dinosaurs…” Professor Ruben adds, “But old theories die hard, especially when it comes to some of the most distinctive and romanticized animal species in world history.” He continues, “Frankly, there’s a lot of museum politics involved in this, a lot of careers committed to a particular point of view even if new scientific evidence raises questions.” In some museum displays, he says, the birds-descended-from-dinosaurs evolutionary theory has been portrayed as a largely accepted fact, with an asterisk pointing out in small type that some scientists disagree. [Frankly, I have yet to see such an asterisk. The dino-to-bird model is always presented as established fact; something we know.]

 [End of quote]

Informed consumers of science are aware that the history of science is replete with issues that were once settled, until they were upset by new evidence. The consensus position is not always correct. Especially when it comes to fundamental and controversial issues like the origin of the universe and of life, one should harbour some scepticism even when the majority of scientists proclaim that there is nothing left to say.

[1] Edward Harrison, Darkness at Night, Harvard University Press, 1987, page 114.

[2] Magueijo is also the host of the Science Channel series, Joao Magueijo’s Big Bang, which premiered on May 13, 2008.


[4] Discovery Raises New Doubts About Dinosaur-bird Links, ScienceDaily (June 9, 2009).

Dark Matter – An Update

October 9, 2016

In Genesis and Genes, I devoted some space to the notion of Dark Matter. I recently read an article in Nature about developments in this area, and I’d like to update my readers about this fascinating subject.

What follows is an excerpt from Genesis and Genes (for the purpose of this post, I have omitted the endnotes that appear in the book). I will then comment on the article in Nature.


Nobody – including astronomers and cosmologists – knows what the universe is made of. Visible matter – the kind of stuff that people and planets are made of – is outweighed by a factor of 6 or 7 by invisible, cold dark matter. To put it another way, something like 95% of the universe is made up of stuff we can’t detect, except that it seems to exert a gravitational pull. Here is how one distinguished astronomer and author, James Kaler, puts it:

Our Galaxy, its stars revolving around the center under the influence of their combined gravity, is spinning too fast for what we see. Galaxies in clusters orbit around the clusters’ centers under the influence of their mutual gravities, but again, they move faster than expected. There must be something out there with enough of a gravitational hold to do the job, to speed things up, but it is completely unseen. Dark matter… We have no idea what constitutes it. Rather, there are many ideas, but none that can be proven.

A popular history of astronomy weighs in with this:

Over 90 per cent of our Universe is invisible – filled with particles of mysterious dark matter. And astronomers have no idea what it is. Theoretical physicists working on the kinds of particles produced in the Big Bang say that dark matter cannot be anything ordinary – it has to be something very exotic.

I don’t wish to labour the point, but I must. The public is subjected to absolute statements about our knowledge of the universe and its history so frequently that the average person is simply inured to the fact that there remain basic questions about our cosmic abode. To wit, we do not know what it is made of. Consider this. The most ambitious project in astronomy in the early 21st century is the SKA, or Square Kilometre Array, a network of radio telescopes that is gargantuan in every respect: complexity, size and cost. An article in TIME magazine about the instrument begins by asking the project manager what it is that astronomers wish to discover with this machine:

For someone whose job title could read Man Most Likely to Blow Your Mind, Bernie Fanaroff looks pretty conventional… Consider the fact, says Fanaroff, that we have no idea what 96% of the universe is made of. Cosmologists have known for some time that only 4% of the universe is stuff like dust, gas and basic elements. Dark matter, says Fanaroff, accounts for 23% to 30%; dark energy makes up the rest. (Dark, Fanaroff explains, is the scientific term for “nobody knows what it is.”)

That’s not an exaggeration – nobody knows anything significant about what makes up 96% of the universe. And this is acknowledged even by those who pretend to be able to answer ultimate questions in naturalistic terms. Lawrence Krauss is a world-famous physicist and an ardent atheist. His latest book, A Universe from Nothing: Why There Is Something Rather than Nothing (Free Press, 2012) was reviewed in the January 2012 issue of Nature, the world’s most respected science journal. Nature appointed Caleb Scharf, an astrobiologist at Columbia University, to aggrandise Krauss’s ideas about the universe popping out of absolutely nothing, but even he could not hide the gigantic lacuna in Krauss’s thesis:

He notes that a number of vital empirical discoveries are, ominously, missing from our cosmic model. Dark matter is one. Despite decades of astrophysical evidence for its presence, and plausible options for its origins, physicists still cannot say much about it. We don’t know what this major mass component of the Universe is, which is a bit of a predicament. We even have difficulty accounting for every speck of normal matter in our local Universe.

It is crucial to appreciate that dark matter is not something that was initially discovered in a laboratory, and whose existence was then used to explain some phenomenon. It is also not an entity whose existence was implied by some cosmological theory, and then applied to the problem of energetic stars. Dark matter is entirely hypothetical. Its existence was postulated to explain how the stars in spiral galaxies can orbit at such breakneck speeds without being flung off into the void. In other words, when astronomers tallied up all the mass in the universe, they came face to face with a phenomenon which they could not explain using known physical laws: those laws would indicate that stars in spiral galaxies should indeed be flying off in all directions. Since they aren’t, there must be something out there to prevent them from doing so. What that something is remains anybody’s guess, as Professor Kaler pointed out above. Many astronomers believe that there is matter out there; matter which for whatever reason, we cannot see. This is why they refer to this hypothetical entity as dark matter. They appear to have considerable fun in speculating on the nature of this hypothetical matter: is it made up of MACHOs (Massive Compact Halo Objects)? Or is it WIMPs (Weakly Interacting Massive Particles)?

But since the whole exercise is built on speculation as to what could possibly be acting as a brake on those wayward stars, other scientists do not believe that dark matter even exists. And there is nothing to contradict their view. All you have to do is propose a plausible mechanism to restrain energetic stars from flying off into the cosmic sunset. [END OF QUOTATION FROM GENESIS AND GENES.]


A recent article in Nature, written by Jeff Hecht and cleverly entitled Dark Matter: What’s the Matter? provides a welcome update in this regard.[1] Hecht begins by introducing the subject:

Most of the Universe is missing. The motion of the stars and galaxies allows astronomers to weigh it, and when they do, they see a major discrepancy in cosmological accounting. For every gram of ordinary matter that emits and absorbs light, the Universe contains around five grams of matter that responds to gravity, but is invisible to light. Physicists call this stuff dark matter, and as the search to identify it is now in its fourth decade, things are starting to get a little desperate.

A little later, Hecht discusses a new attempt to crack the problem, one that has both supporters and detractors within the scientific community. Hecht is not optimistic about the latest approach:

It looks unlikely that primordial black holes are the mysterious dark matter. And as time passes without a confirmed detection, even the most heavily backed theories are beginning to look less likely. A series of experiments have systematically searched for, and failed to find, the theoretical candidates for dark matter — one by one, the possibilities are being reduced. A raft of experiments designed to finally detect, or refute, the remaining candidates are now underway, each with vastly different approaches to the problem. As more options are crossed off the list, physicists may have to explore new ideas and reconsider alternative theories… — or accept that nature may have hidden dark matter just out of our reach.

When Genesis and Genes was written, MACHOS – massive Compact Halo Objects – were still considered candidates for Dark Matter. No longer:

Decades of research have narrowed down the possibilities. Early favourites included not only black holes, but also other massive compact halo objects (MACHOs) made of ordinary matter. A series of studies, however, gradually ruled out most of the possibilities… But in the view of theoretical physicist John Ellis of King’s College London, “MACHOs are dead.”

The other candidate for Dark Matter I mentioned in Genesis and Genes was WIMPS – Weakly Interacting Massive Particles. WIMPS still hold some promise for resolving the Dark Matter conundrum:

Although MACHOs have fallen by the wayside, another candidate has hung around. A decade ago, physicists were largely convinced that dark matter was made up of weakly interacting massive particles (WIMPs)…

WIMPs remain the leading candidate for dark matter. “Supersymmetry is beautiful mathematically,” says physicist Oliver Buchmueller of Imperial College London. “With just one weakly interacting particle, we can explain all the dark matter we see in the Universe.” Indeed, so well does the lightest of these hypothetical particles fit the bill for dark matter that it has been called “the WIMP miracle”, says physicist Leslie Rosenberg of the University of Washington in Seattle.

But only in theory:

But supersymmetrical particles have proved maddeningly elusive. Physicists at CERN, Europe’s particle-physics laboratory, are searching for WIMPs with the Large Hadron Collider (LHC) by smashing protons or atomic nuclei together to recreate the conditions of the early Universe… The longer the puzzle goes unsolved, the more twitchy the scientific community will become. “People are a little nervous,” says Rosenberg.

Hecht goes on to discuss the difficult – and rather exotic – ways in which scientists use particle colliders to try to detect recalcitrant particles:

Researchers won’t see dark matter directly. Instead, they look for signs that energy and momentum in collisions have gone missing when they should have been conserved. Ellis compares searching for evidence of dark matter to watching billiard balls roll away after the cue ball hits them on the break shot. If the balls on one side of the group were invisible, and only the balls rolling away on the opposite side could be seen, the path and nature of the unseen balls can still be deduced, he says. Physicists are using the paths of the particles they can see to identify the paths of the dark matter that they can’t.

So far, nothing has come up.

Dark Matter is a fascinating scientific problem. For informed consumers of science, a number of issues are important in this context:

  1. We don’t know what 95% of the universe is made of! That’s astonishing. Members of the public should be aware that when peremptory remarks about the universe are made by scientists, or in magazine articles, or in documentaries, they hide enormous assumptions about how much we really know. As I explain in Genesis and Genes, Dark Matter (and Dark Energy) may one day turn out to be made of exotic particles; then again, it is quite possible that the scientific picture of our universe is seriously wrong, a possibility freely acknowledged by astronomers such as James Kaler and physicists like Mordechai Milgrom. Don’t be duped by those who insist that matter and energy form the fundamental substrate of our universe. This view originates in an ideology – scientism – and not in evidence from Nature itself. The only reasonable response to knowing how little we know about the universe is humility.

2. It is worth bearing in mind the similar situation that pertained in biology before the Junk DNA paradigm collapsed (see my previous post, Francis Collins Does Teshuva). In that context, many biologists dismissed about 95% of the human genome as junk, because they did not know what it did. This turned out to be a spectacular failure, delaying by several decades the onset of the age of epigenetics. In my view, physicists and astronomers are generally more open to the possibility of paradigm shifts than are biologists. They are also more likely to admit, in public, that major lacuna remain in our knowledge of the physical world.

 3. All the methods that have been devised to detect Dark Matter rely on complicated statistical analyses to infer particles of Dark Matter. This is not a simple matter of observation, and lends itself to different interpretations. Here, too, the history of science would indicate that healthy scepticism be maintained when certain results are proclaimed.



Retrieved 7th October 2016.

Francis Collins does Teshuva

July 26, 2016

In Genesis and Genes, I mentioned Francis Collins a few times. Recently, important remarks of his have come to light, which I’d like to discuss. Below, I quote the relevant section from Genesis and Genes and then discuss Collins’ statement. In this section of Genesis and Genes, I conduct a conversation with Jonathan, a fictitious character who embodies many individuals with whom I have spoken and corresponded over the past few years. For the purpose of this post, I have omitted the endnotes that appear in the book.


YB: Because he [Francis Collins] has written on the subject of junk DNA.

Jonathan: Junk DNA? I thought the T-shirt said, I know I’m important because God don’t make no junk.

YB: Good point, but not a sentiment shared by evolutionary biologists.

Jonathan: So what is junk DNA?

YB: Here’s the basic story. In the 1970s geneticists discovered that only a tiny percentage of our DNA codes for proteins.

Jonathan: What does “code for proteins” mean?

YB: It means “contains the instructions for manufacturing proteins.” Some DNA contains the encoded information necessary to make the crucial workhorses of the cell – proteins. But most DNA does not have that function.

Jonathan: OK. So what’s the story?

YB: The term junk DNA appears to have been coined by the biologist Susumu Ohno of the City of Hope National Medical Center in Los Angeles. In 1972, he published an article wondering why there is “so much ‘junk DNA’ in our genome.” In 1980, two papers appeared back-to-back in the journal Nature. Both argued that much genetic material has no function, and the second article explicitly argued that much DNA in higher organisms is little better than junk. Two biologists wrote to Nature to express disagreement. Thomas Cavalier-Smith considered it “premature” to dismiss non-protein-coding DNA as junk, and Gabriel Dover wrote that “we should not abandon all hope of arriving at an understanding of the manner in which some [DNA] sequences might affect the biology of organisms in completely novel and somewhat unconventional ways.” But the majority of biologists accepted the notion of junk DNA. The suggestion was that most of our DNA is functionless junk that accumulated in our cells as a by-product of merciless evolutionary processes. This became the dominant view among biologists, and the term junk DNA pervaded the literature – both professional and popular. But that view has turned out to be spectacularly wrong. Since 1990 – and especially after completion of the Human Genome Project in 2003 – many hundreds of articles have appeared in the scientific literature documenting the various functions of non-coding DNA, and more are being published almost every week. Far from consisting mainly of junk, our genome is increasingly revealing itself to be a multidimensional, integrated system in which “junk” DNA performs a wide variety of functions.

Jonathan: Sounds familiar by now.

YB: Yes. We’ve seen how, so often, the glow of evolutionary dawn doesn’t last until noon.

Jonathan: How was junk DNA used to argue for evolution?

YB: Initially, the functions of these stretches of DNA were not understood. It seemed as if they did nothing. So many biologists said that junk DNA just accumulates in the genome like, well, like junk in a junkyard. In retrospect, it’s rather like cavemen coming upon an IPod and declaring that it’s only moderately useful for throwing at peaches high up in the trees.

Jonathan: Can you give me an example of a typical statement along these lines?

YB: I could give dozens of examples. Here is one, from the evolution-populariser Richard Dawkins. It’s a paragraph from an article he wrote in the journal The Skeptic in 1998:

Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn’t even need scare quotes) get on with their business in a different part of the same genome. And there’s lots more DNA that doesn’t even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, “tandem repeats”, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.

Dawkins, like numerous evolution junkies, believes that there is no explanation for this apparently-superfluous material in our genomes, other than the admission that they are the residue of an evolutionary process:

Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.

In one of his most recent books (published in 2009), The Greatest Show on Earth, Dawkins observed that “the greater part… of the genome might as well not be there, for all the difference it makes,” and that this fact is “useful for… embarrassing creationists.” Similarly, in Why Evolution Is True (also published in 2009), Jerry Coyne of the University of Chicago states that it is a “prediction” of neo-Darwinian theory that we will find the genome littered with useless “vestigial genes”. This sort of claim permeated the literature for decades.

Jonathan: But why is it relevant to Collins?

YB: Because atheists like Dawkins and Coyne were not the only people to make the point. Believers like Collins also used the junk DNA argument to argue for evolution.

Jonathan: Really?

YB: Yes. Collins has written a number of best-selling books promoting theistic evolution. In 2006, he published The Language of God. He wrote that

Mammalian genomes are littered with such AREs [ancient repetitive elements] with roughly 45 percent of the human genome made up of such genetic flotsam and jetsam.

Notice that Collins makes a spectacular claim. He says that almost half of the human genome is flotsam and jetsam. And this convinced Collins of the reality of evolution, because he, like Dawkins, could not fathom why God would insert so much of this useless material into the human genome:

Unless one is willing to take the position that God has placed these decapitated AREs in these precise positions to confuse and mislead us, the conclusion of a common ancestor for humans and mice is virtually inescapable.


Jonathan: It seems like a decent argument.

YB: It’s a terrible argument, for a number of reasons, but I’ll focus only on one.

Jonathan: What’s that?

YB: Things changed. We know now that many features of the human genome that were thought to be junk in fact have important functions. It’s fascinating to track how, over the years, the terminology changed.

Jonathan: What do you mean?

YB: In older publications, it was always junk DNA, or, as Collins puts it, flotsam and jetsam, or some other pejorative sobriquet.  As perceptions changed and biologists realised that they might ultimately be humiliated when junk DNA was discovered to be anything but, they changed tack. If you track the evolution of the terminology – excuse the pun – you will see how the prevalence of junk DNA diminishes in favour of non-coding DNA. This is in recognition of the fact that these regions of DNA, even though they do not code for proteins, nevertheless have other, very important, functions.

Jonathan: Has Collins seen the light?

YB: Yes and no.

Jonathan: What do you mean?

YB: Well, Collins published another book, The Language of Life, in 2010, in which he takes a far more cautious stance vis-á-vis DNA. Gone are the strident declarations about how junk DNA constitutes incontrovertible proof of universal common descent.

Jonathan: What does he say?

YB: Read for yourself:

The discoveries of the past decade, little known to most of the public, have completely overturned much of what used to be taught in high school biology. If you thought the DNA molecule comprised thousands of genes but far more “junk DNA”, think again. [Emphasis added].

Jonathan: Mm…

YB: Mm indeed. Furthermore, Collins now has the chutzpah to scold others who dismissively refer to long stretches of non-coding DNA as gene deserts:

It appears there are also long “spacer” segments of DNA that lie between genes and that don’t code for protein. In some instances, these regions extend across hundreds of thousands or even millions of base pairs, in which case they are referred to rather dismissively as “gene deserts.” These regions are not just filler, however. They contain many of the signals that are needed to instruct a nearby gene about whether it should be on or off at a given developmental time in a given tissue. Furthermore, we are learning that there may be thousands of genes hanging out in these so-called deserts that don’t code for protein at all. They are copied into RNA, but those RNA molecules are never translated – instead, they serve some other important functions.

Other than die-hard materialists such as Richard Dawkins, plenty of scientists are coming to see that the junk DNA paradigm must be ditched. For example, Richard Sternberg and James Shapiro, both of whom are prominent biologists, write that one day, we will think of what used to be called junk DNA as a critical component of truly expert cellular control regimes. In the end, it is clear that Collins’ 2010 book is a significant retreat on the claim that junk DNA dominates our genome. He explicitly admits that non-coding DNA has other functions:

It turns out that only about 1.5 percent of the human genome is involved in coding for protein. But that doesn’t mean the rest is “junk DNA.” A number of exciting new discoveries about the human genome should remind us not to become complacent in our understanding of this marvellous instruction book. For instance, it has recently become clear that there is a whole family of RNA molecules that do not code for protein. These so-called non-coding RNAs are capable of carrying out a host of important functions, including modifying the efficiency by which other RNAs are translated. In addition, our understanding of how genes are regulated is undergoing dramatic revision, as the signals embedded in the DNA molecule and the proteins that bind to them are rapidly being elucidated. The complexity of this network of regulatory information is truly mind-blowing, and has given rise to a whole new branch of biomedical research, sometimes referred to as “systems biology.” [Emphasis added].


Jonathan: But still, doesn’t Collins deserve credit for absorbing the new evidence and adjusting his view accordingly?

YB: He deserves very little credit. First of all, in his later book, The Language of Life, he doesn’t tell his readers about what he wrote just four years earlier, in The Language of God. They would have no inkling that the solemn words of rebuke for those who speak of “gene deserts” were written by someone who himself completely botched the junk DNA argument. Secondly, he goes on to argue for universal common descent on the basis of – wait for it – junk DNA.

Jonathan: No!

YB: Yes. His latest book is The Language of Science and Faith, co-written with Karl Giberson and published in 2011. Collins and Giberson look at the vitamin C GULO “pseudogene” found in humans and other primates (as well as some non-primate species), and they contend that it is “not remotely plausible” that “God inserted a piece of broken DNA into our genomes.” They conclude that this “has established conclusively that the data fits a model of evolution from a common ancestor”. So even though Collins himself was forced to retreat from his early tirades about junk DNA by the accumulating evidence that that genetic material actually performs highly-sophisticated tasks that were earlier missed by biologists, he continues to belt out the broken record message of “broken DNA”. This is bound to rebound on Collins. There is a cascade of research these days that’s uncovering more and more crucial functions for genetic material previously dismissed as “junk”. Collins is painting himself into a corner by citing one example – what he considers to be a broken gene – even though his view from just a few years back (that about half the human genome is junk DNA) has proved to be spectacularly wrong.

Jonathan: Can you give me an example of research that is finding surprising functions for non-coding DNA?

YB: Sure. We won’t go into the technicalities, but here is the synopsis of a recent research article from the journal RNA. This is a run-of-the-mill scientific journal whose editors, contributors and readers overwhelmingly subscribe to the evolutionary scenario:

Pseudogenes have long been labeled as “junk” DNA, failed copies of genes that arise during the evolution of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins. Far from being silent relics, many pseudogenes are transcribed into RNA, some exhibiting a tissue-specific pattern of activation… In another remarkable discovery, it has been shown that pseudogenes are capable of regulating tumor suppressors and oncogenes… The finding that pseudogenes are often deregulated during cancer progression warrants further investigation into the true extent of pseudogene function. In this review, we describe the ways in which pseudogenes exert their effect on coding genes and explore the role of pseudogenes in the increasingly complex web of noncoding RNA that contributes to normal cellular regulation.


Jonathan: This is really shocking! If so many functions have been discovered for sections of the genome that were previously not understood, how can anyone continue to argue for universal common descent on the basis of non-coding DNA?!

YB: I agree. When you, as a non-scientist, are trying to form an opinion about evolution, don’t be intimidated by the fact that opinions are expressed by acknowledged experts in their fields. As we have seen in this book, the logic presented is often shoddy and the integrity questionable. [END of QUOTATION]

Now, however, comes news of Collins conceding defeat on this front. Here is what Marvin Olasky writes []:

July 11 is the 10th anniversary of the publication of theistic evolutionist Francis Collins’ The Language of God, which became a New York Times bestseller largely because of Collins’ reputation as director of the National Human Genome Research Institute. That book, in turn, helped Collins gain new fans and a nomination from Barack Obama to head the National Institutes of Health.

Confirmed by the Senate, Collins has been in that position ever since, and I’m glad he’s there. But his book, and a talk about it I heard Collins give in New York, also displayed what Collins now admits was arrogance. Collins claimed on page 136 that huge chunks of our genome are “littered” with ancient repetitive elements (AREs), so that “roughly 45 percent of the human genome [is] made up of such genetic flotsam and jetsam.” In his talk he claimed the existence of “junk DNA” was proof that man and mice had a common ancestor, because God would not have created man with useless genes.

Last year, though, speaking at the J.P. Morgan Healthcare Conference in San Francisco, Collins threw in the towel: “In terms of junk DNA, we don’t use that term anymore because I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome, as if we knew enough to say it wasn’t functional. … Most of the genome that we used to think was there for spacer turns out to be doing stuff.” [END of QUOTATION].

There are a number of lessons to be drawn from this:

  1. Collins deserves at least some credit for conceding defeat and, more importantly, for ascribing his past mistakes to “hubris”. I pointed out again and again in Genesis and Genes that science is done by people. Laymen often stand in awe of scientists, imagining them to be super-heroes who are totally objective, operating without any conditioning, biases or worldviews. The reality is, alas, completely different. Scientists are ordinary individuals (albeit often highly-intelligent and possessing an aptitude for mathematics) who receive no training other than in their narrow, technical fields. The vast majority of scientists have never taken a course in the psychology of research. They know as little as the man in the street does about the history and philosophy of science, and are therefore often pathetically unaware of their own weaknesses as individuals and of historical failures in their respective fields. The admission by Collins that he has retracted from his previous position, and that he was blinded by hubris, is as refreshing as it is rare. One can hardly imagine someone like, say, Richard Dawkins making the same admission.

  1. SCIENCE CAN BE WRONG. It is astonishing how difficult it is to get ordinary members of the public to appreciate this elementary fact of the history of science. Don’t confuse Nature with Science. Nature is what it is, and Science is the attempt by humans to understand Nature. Like all human endeavours, Science is fallible.

  1. Decades of fruitful research were lost because students were taught the dogma of junk DNA and thus discouraged from investigating the properties and functions of these sections of the genome.

  1. Don’t be fooled by peremptory pronouncements. Over the past half-century, scientists insisted that we know that most of the human genome is junk. It is common in these situations for dissenters to be ridiculed and frozen out of research grants. Especially when it comes to fields that have bearing on profound philosophical questions, one should treat absolute statements by scientists with a sack of salt. There is much more that we don’t know about nature than we do

Poor Review

April 17, 2015

The latest issue of Dialogue Magazine contains an essay I submitted, entitled Poor Review. It is reproduced below.

Your life depends on the Krebs cycle.

Even if you haven’t heard of it, your body is powered by the string of chemical reactions named after a German Jewish scientist who was forced to flee his homeland in 1933. In 1953, Hans Krebs was awarded the Nobel Prize in medicine/physiology for his seminal discovery of the eponymous cycle. But there’s a twist to this happy story. In June 1937, when Krebs submitted his crucial paper to Nature, it was returned to him. The paper was eventually published in the obscure journal Enzymologia.

Copernicus’s heliocentric cosmology, Galileo’s mechanics, Newton’s gravity and equations of motion – these ideas never appeared in journal articles. They appeared in books that were reviewed, if at all, by associates of the author. The peer-review process as we know it was instituted after the Second World War, largely due to the huge growth of the scientific enterprise and the enormous pressure on academics to publish ever more papers.

When it comes to peer review of scientific papers, the general public entertains unrealistic, highly-idealized visions of a process by which scientific research is assessed. In theory, peer review is supposed to act as a filter, weeding out the crackpots; in practice, it often turns out to be a way to enforce orthodoxy.

Since the 1950s, peer-review has worked as follows: a scientist wishing to publish a paper in a journal submits a copy of the paper to the editor of a journal. The editor forwards the paper to several academics whom he considers to be experts on the matter, asking whether the paper is worthy of publication. These experts – who usually remain anonymous – submit comments about the paper that constitute the “peer review”. The referees judge the content of the paper on criteria such as the validity of the claims made in the paper, the originality of the work, and whether the work, even if correct and original, is important enough to be worthy of publication. Often, the journal editor will require the author to amend his paper in accordance with the recommendations of the referees.

Prior to the War, university professors were mainly teachers, carrying a teaching load of five or six courses per semester (a typical course load nowadays is one or two courses). Professors with this onerous teaching burden were not expected to write papers. The famous philosopher of science, Sir Karl Popper, wrote in his autobiography that the dean of the New Zealand university where Popper taught during World War II said that he regarded Popper’s production of articles and books a theft of time from the university.

But at some point, universities came to realize that their prestige – and with it the grants they received from governments and corporations – depended more so on the scholarly reputation of their professors than on their teaching skills. And this reputation could only be enhanced through publications. Teaching loads were reduced to allow professors more time for research and the production of papers; salaries began to depend on one’s publication record. Before the War, salaries of professors of the same rank (associate professor, assistant professor, adjunct professor, full professor etc.) were the same (except for an age differential, which reflected experience). Nowadays, salaries of professors in the same department of the same age and rank can differ by more than a factor of two, based on their publication output.

One consequence of all this is that the production of papers has increased by a factor of more than one thousand over the past fifty years. The price that has been paid for this literary fecundity is a precipitous decline in quality. Before the War, when there was no financial incentive to publish papers, scientists wrote them as a labor of love. These days, papers are written mostly to further one’s career. One thus finds that nowadays, most papers are never cited by anyone except their author(s).[1]

Philip Anderson, who won a Nobel Prize for physics, writes that:

“in the early part of the postwar period [a scientist’s] career was science-driven, motivated mostly by absorption with the great enterprise of discovery, and by genuine curiosity as to how nature operates. By the last decade of the century far too many, especially of the young people, were seeing science as a competitive interpersonal game, in which the winner was not the one who was objectively right as [to] the nature of scientific reality, but the one who was successful at getting grants, publishing in Physical Review Letters, and being noticed in the news pages of Nature, Science, or Physics Today… [A] general deterioration in quality, which came primarily from excessive specialization and careerist sociology, meant quite literally that more was worse.”[2]

More is worse. As Nature puts it, “With more than a million papers per year and rising, nobody has time to read every paper in any but the narrowest fields, so some selection is essential. Authors naturally want visibility for their own work, but time spent reading their papers will be time taken away from reading someone else’s.”[3] The number of physicists has increased by a factor of one thousand since the year 1900. Back then, ten percent of all physicists in the world had either won a Nobel Prize or had been nominated for it. Things are much the same in chemistry. The American Chemical Society made a list of the most significant advances in chemistry over the last 100 years. There has been no change in the rate at which breakthroughs in chemistry have been made in spite of the thousand-fold increase in the number of chemists. In the 1960s, United States citizens were awarded about 50 000 patents in chemistry-related areas per year. By the 1980s, the number had dropped to 40 000. But the number of papers has exploded. One result of this publish-or-perish mentality is that groundbreaking papers are often rejected because they are submitted to referees who are incapable or unwilling to recognise novel ideas. Consider these examples:

1. Rosalyn Yalow won the Nobel Prize in Physiology or Medicine in 1977. She describes how her Nobel-winning paper was received: “In 1955 we submitted the paper to Science… the paper was held there for eight months before it was reviewed. It was finally rejected. We submitted it to the Journal of Clinical Investigations, which also rejected it.”[4]

  1. Günter Blobel also won a Nobel Prize in Physiology or Medicine, in 1999. In a news conference given just after he was awarded the prize, Blobel said that the main problem one encounters in one’s research is “when your grants and papers are rejected because some stupid reviewer rejected them for dogmatic adherence to old ideas.” According to the New York Times, these comments “drew thunderous applause from the hundreds of sympathetic colleagues and younger scientists in the auditorium.”[5]
  1. Mitchell J. Feigenbaum thus described the reception that his revolutionary papers on chaos theory received: “Both papers were rejected, the first after a half-year delay. By then, in 1977, over a thousand copies of the first preprint had been shipped. This has been my full experience. Papers on established subjects are immediately accepted. Every novel paper of mine, without exception, has been rejected by the refereeing process. The reader can easily gather that I regard this entire process as a false guardian and wastefully dishonest.”[6]
  1. Theodore Maiman invented the laser, an achievement whose importance is not doubted by anyone. The leading American physics journal, Physical Review Letters, rejected Maiman’s paper on constructing a laser.[7]
  1. John Bardeen, the only person to have ever won two Nobel Prizes in physics, had difficulty publishing a theory in low-temperature solid-state physics that went against the paradigm.[8]
  1. Stephen Hawking needs no introduction. According to his first wife Jane, when Hawking submitted to Nature what is generally regarded as his most important paper on black hole evaporation, the paper was initially rejected.[9] The physicist Frank J. Tipler writes that “I have heard from colleagues who must remain nameless that when Hawking submitted to Physical Review what I personally regard as his most important paper, his paper showing that a most fundamental law of physics called ‘unitarity’ would be violated in black hole evaporation, it, too, was initially rejected.”
  1. Conventional wisdom in contemporary geophysics holds that the Hawaiian Islands were formed sequentially as the Pacific Plate moved over a hot spot deep inside the Earth. This idea was first developed in a paper by the Princeton geophysicist Tuzo Wilson. Wilson writes: “I… sent [my paper] to the Journal of Geophysical Research. They turned it down… They said my paper had no mathematics in it, no new data, and that it didn’t agree with the current views. Therefore, it must be no good. Apparently, whether one gets turned down or not depends largely on the reviewer. The editors, too, if they don’t see it your way, or if they think it’s something unusual, may turn it down. Well, this annoyed me…”[10]

In a paper playfully entitled Not in our Nature but nonetheless published in Nature, Juan Miguel Campanario gives many examples of papers, now considered classics, which were rejected by the world’s most prestigious science journal. Here are two examples:

  1. In 1981, Nature rejected a paper by the British biochemist Robert H. Michell on signalling reaction by hormones. This paper has since been cited more than 1800 times.
  1. A paper by Michael J. Berridge, rejected in 1983 by Nature, ranks at 275 in a list of the most-cited papers of all times, having been cited more than 1900 times.[11]

In 2006, Nature published an essay by Charles G. Jennings, a former editor with the Nature journals and former executive director of the Harvard Stem Cell Institute. As an editor, Jennings was intimately familiar with the peer-review system, and knows full well how badly misunderstood this process is by the public. He writes:

“Whether there is any such thing as a paper so bad that it cannot be published in any peer reviewed journal is debatable. Nevertheless, scientists understand that peer review per se provides only a minimal assurance of quality, and that the public conception of peer review as a stamp of authentication is far from the truth.”

Jennings writes that “many papers are never cited (and one suspects seldom read)”. These papers are written, to a large extent, because “To succeed in science, one must climb this pyramid [of journals]: in academia at least, publication in the more prestigious journals is the key to professional advancement.”[12] Advancement, in this context, is measured by career rewards such as recruitment and promotion, grant funding, invitations to speak at conferences, establishment of collaborations and media coverage.

In September 2001, Science reported on a conference on peer review. The article states that traditionally, peer review was considered the “least bad way” to weed out weak manuscripts or research proposals and improve promising ones. But

“that common wisdom was questioned last weekend at a meeting attended by hundreds of editors of medical journals and academics. In a meta-analysis that surprised many – and that some doubt -researchers found little evidence that peer review actually improves the quality of research papers.”

The article continued

“Mention ‘peer review’ and almost every scientist will regale you with stories about referees submitting nasty comments, sitting on a manuscript forever, or rejecting a paper only to repeat the study and steal the glory.”[13]

Sydney Brenner received a Nobel Prize in Physiology or Medicine in 2002, and is revered for his contributions to molecular biology. He was interviewed in February 2014, and the title of the interview is itself illuminating: How Academia and Publishing are Destroying Scientific Innovation.[14] Brenner is fiercely critical of peer review:

“But I don’t believe in peer review because I think it’s very distorted… I think peer review is hindering science. In fact, I think it has become a completely corrupt system. It’s corrupt in many ways, in that scientists and academics have handed over to the editors of these journals the ability to make judgment on science and scientists… Now I mean, people are trying to do something, but I think it’s not publish or perish, it’s publish in the okay places [or perish]. And this has assembled a most ridiculous group of people… I campaigned against this [culture] because I think it is not only bad, it’s corrupt. In other words it puts the judgment in the hands of people who really have no reason to exercise judgment at all. And that’s all been done in the aid of commerce, because they are now giant organisations making money out of it. “

The 2013 Nobel Prize-winning biologist Randy Schekman recently announced that he will no longer submit papers to ‘luxury’ science journals because they corrupt the publication process. Writing in The Guardian, he titled his piece How Journals like Nature, Cell and Science are Damaging Science.[15]


The very existence of a blog called Retraction Watch is telling.[16] The site tracks retractions “as a window into the scientific process.” Typical entries, of which there are hundreds, read “Another Nature stem cell paper is retracted”[17] or “University of Texas Southwestern cancer research group notches ninth retraction.”[18] The blog’s editor, medical doctor turned journalist Ivan Oransky, explains that “A retraction means there is something deeply wrong” with a given academic paper. “About two thirds of the time, that’s actually something that’s considered misconduct – the official federal definition of which is falsification, fabrication, or plagiarism.”[19]

But Retraction Watch’s latest scoop made the regular entries pale into insignificance. In July of this year it reported on the busting of a “peer review and citation ring”, causing SAGE Publishing, a major publisher of scientific journals, to retract sixty (!) papers from its Journal of Vibration and Control.[20] Among the scandal’s victims was Taiwan’s education minister, who resigned “to uphold his own reputation and avoid unnecessary disturbance of the work of the education ministry, after the incident ignited a wave of public criticism.”[21] This is what Slate wrote about the debacle:

It may not be entirely fair to liken a “peer review and citation ring” to the academic version of an extortion ring, but there’s certainly fraud involved in both. Retraction Watch, a blog dedicated to chronicling which academic papers have been withdrawn, is reporting that SAGE Publishing, a group that puts out numerous peer-reviewed journals, is retracting 60 papers from its Journal of Vibration and Control after an internal investigation uncovered extensive evidence of severe peer-review fraud.

Apparently researcher Peter Chen, formerly of National Pingtung University of Education in Taiwan, made multiple submission and reviewer accounts – possibly along with other researchers at his institution or elsewhere – so that he could influence the peer review system. When Chen or someone else from the ring submitted a paper, the group could manipulate who reviewed the research, and on at least one occasion Chen served as his own reviewer.[22]

The Washington Post [23] and The Guardian [24] carried similar stories.


Why does all of this matter?

First, the narrow point. In Big Science, certain topics – like, say, the weaknesses of evolutionary biology, are well nigh verboten. I hope that by now, the following point is obvious: The claim that scientists critical of evolutionary biology who are not published in Nature, Science et al cannot be accomplished scientists (why, otherwise, haven’t they published there?) is hollow. These journals will not publish material which undermines the cherished paradigm. Contrary to popular misconceptions, Big Science is not open, objective, and tolerant. Even those scientists whose research is done within the paradigm – including virtually all those named above – often find the system to be rigid and even hostile towards those who are truly innovative.

But there’s a broader point to be made as well. I have written and lectured on the interface of Judaism and science for many years. I mostly deal with issues of ultimate origins – of the universe and humanity. These are controversial and fascinating issues, and should be explored dispassionately and in detail. Probably the biggest obstacle I face in trying to convey Judaism’s views on these matters is the public’s distorted view of what scientists are like and what scientific work consists of. Among the general public, there is a pervasive view of scientists as paragons of morality and objectivity. It’s as if the mere fact that one has an aptitude for mathematics or wears a lab coat somehow bestows immunity from human vices.

In Genesis and Genes, I wrote:[25]

The physicist Sir John Polkinghorne is a prominent writer about the intersection of science and theology. In Science and Theology he coins a marvellous phrase:[26]

Scientists do not look at the world with a blank gaze; they view it from a chosen perspective and bring principles of interpretation and prior expectations… to bear upon what they observe. Scientists wear (theoretical) “spectacles behind the eyes”.

Theoretical spectacles behind the eyes. Why does Polkinghorne need to tell his readers that scientists view the world not with a blank gaze, but from a chosen perspective and with prior expectations? Isn’t that only human? The answer:[27]

“Many people have in their minds a picture of how science proceeds which is altogether too simple. This misleading caricature portrays scientific discovery as resulting from the confrontation of clear and inescapable theoretical predictions by the results of unambiguous and decisive experiments… In actual fact… the reality is more complex and more interesting than that.”

The caricature of scientists as supermen is pervasive. The layman is so removed from the experience of actual research that he harbors an image of this profession that is massively distorted. We picture the scientist as popping into existence in the laboratory, like the Greek goddess Athena popping out of Zeus’ head, without any experiences, prejudices, views and background that could impinge on her interpretations and expectations. But scientists are human beings, subject to all the weaknesses, foibles and failings of other human beings.[28]

When I wrote these words in Genesis and Genes, I was focusing on the conditioning to which all scientists are subject and which deeply influences their research. This essay, with its exploration of the mechanics of a crucial component of the scientific edifice – the institution of peer review – is intended as a cautionary note to those who do not understand that scientists are indeed subject to all the weaknesses, foibles and failings of other human beings. They are subject to many forces which influence their research agendas, assumptions and conclusions.

The general public, blissfully shielded from the sludge-like reality of science publishing, takes peer-review to be flawless. Non-experts often mistakenly believe that individual scientists who serve as editors or referees on papers are always open-minded and completely objective in reviewing papers. Peer-review is seen as a gold-standard which guarantees the legitimacy of a paper. Indeed, this mirage is promoted by science propagandists like Jerry Coyne, an evolutionary biologist at the University of Chicago, who wrote in 2005 that “The gold standard for modern scientific achievement is the publication of new results in a peer-reviewed scientific journal.”[29] But the examples in this essay are more than sufficient to demonstrate that the peer-review system is deeply compromised. It is an efficient way of strangling new ideas, rather than a vehicle for promoting truly novel ideas. The peer-review system often stifles true innovation, allowing the reigning paradigm to squash all competition unfairly.

Stephen Jay Gould, one of the most prominent evolutionary biologists of the late 20th Century, sought to dispel the myths promoted by the likes of Coyne when he observed that “[t]he stereotype of a fully rational and objective ‘scientific method,’ with individual scientists as logical (and interchangeable) robots, is self-serving mythology.”[30] The mathematician John Lennox echoed these sentiments, writing that “… the Enlightenment ideal of the coolly rational scientific observer, completely independent, free of all preconceived theories, prior philosophical, ethical and religious commitments, doing investigations and coming to dispassionate, unbiased conclusions that constitute absolute truth, is nowadays regarded by serious philosophers of science (and, indeed, most scientists) as a simplistic myth.”[31] Lawrence K. Altman made a similar point in an article in the New York Times:

“Many nonscientists perceive reviewers to be impartial. But the reviewers, called independent experts, in fact are often competitors of the authors of the papers they scrutinize, raising potential conflicts of interest.”[32]

Professional jealousy is not the only vice involved. Dr. Altman explains that good old-fashioned greed is also a factor. Journals have huge economic interests in preserving the current flawed system, and research scientists play along because peer-reviewed papers are necessary for them to maintain their positions:

The public and many scientists tend to overlook the journals’ economic benefits that stem from linking their embargo policies to peer review. Some journals are owned by private for-profit companies, while others are owned by professional societies that rely on income from the journals. The costs of running journals are low because authors and reviewers are generally not paid.

A few journals that not long ago measured profits in the tens of thousands of dollars a year now make millions, according to at least three editors who agreed to discuss finances only if granted anonymity, because they were not authorized to speak about finances.[33]


What’s the solution? Many scientists believe that the system is broken beyond repair. But others, who certainly recognise the ills that plague the peer-review process, believe it’s salvageable. Experiments are being conducted to improve – or sidestep – the current system. For example, some journals no longer grant referees the protection of anonymity. Instead, reviewers are identified and their critiques of papers are made available to the author of the paper being reviewed. The author is then able to defend his paper. This may ameliorate the problem of reviewers who hamper the publication of a paper for less than noble reasons (such as professional jealousy). Another possible solution, already being tried, is the creation of websites that will publish any research paper, whether it is deemed “acceptable” by the establishment or not, as long as it is submitted by credentialed scientists. But this debate, I think, misses the point.

The point is that scientists are human beings. They are fallible; they suffer from professional jealousy, prejudice, greed and every other human failing, to the precise extent that other human beings suffer from these moral maladies. There is nothing in the typical scientist’s training that makes him less vulnerable to subjectivity and prejudice than any other person.

Nothing fundamental is going to change until the science establishment realises that facility with partial differential equations or the ability to fiddle with the knobs and switches of an electron microscope are not guarantors of ratiocination. Character training is just as important. Until the “self-serving mythology” of a scientific method that is impervious to human frailty and is thus rational and objective is recognised as such by scientists and the wider public, and until such time as scientific training incorporates elements of self-analysis and character improvement, one can expect that peer-review, as well as all other elements of modern science, will fall far short of the ideal.


[1] See the essay by the physicist Frank J. Tipler entitled Refereed Journals: do they insure quality or enforce orthodoxy? The essay appeared in Uncommon Dissent: Intellectuals who find Darwinism Unconvincing, William A. Dembski (editor), ISI Books, 2004. Several of the quotations in this article come from this essay.

[2] Philip Anderson, in Brown, Pais and Pippard, editors, Twentieth Century Physics, American Institute of Physics Press, 1995,page 2029.


Retrieved 1st June 2014.

[4] Walter Shropshire Jr., editor, The Joys of Research, Smithsonian Institution Press, 1981, page 109.

[5] New York Times, 12th October 1999, page A29.

[6] Mitchell J. Feigenbaum, in Brown, Pais and Pippard, editors, Twentieth Century Physics, American Institute of Physics Press, 1995, page 1850.

[7] Ibid. page 1426.

[8] Lillian Hoddeson, True Genius: The Life and Science of John Bardeen, Joseph Henry Press, 2002, page 300.

[9] Jane Hawking, Music to Move the Stars: A Life with Stephen Hawking, Trans-Atlantic Publications, 1999, page 239.

[10] Walter Shropshire Jr., editor, The Joys of Research, Smithsonian Institution Press, 1981, page 130.

[11] Campanario, J.M. 1993, Not in our Nature, Nature 361:488.


Retrieved 1st June 2014.

[13] Science 21 September 2001: Vol.293 no. 5538 pp. 2187-2188:


Retrieved 27th May 2014.


Retrieved 27th May 2014.


Retrieved 31st July 2014.


Retrieved 4th August 2014.


Retrieved 4th August 2014.


Retrieved 6th August 2014.


Retrieved 4th August 2014.


Retrieved 4th August 2014.


Retrieved 30 July 2014.


Retrieved 30 July 2014.


Retrieved 30 July 2014.

 [25] Yoram Bogacz, Genesis and Genes, Feldheim, 2013, pages 10-11.

[26] Science and Theology, John Polkinghorne, Fortress Press, 1998, page 10.

[27] Ibid. page 9.

[28] Dr. Niles Eldredge, a distinguished paleontologist at the American Museum of Natural History in New York, put it this way, “Many scientists really do seem to believe that they have a special access to the truth. They call press conferences to trumpet new discoveries… and they expect to be believed – by their peers, and especially by the public at large. Throwing down scientific thunderbolts from Olympian heights, scientists come across as authoritarian truth givers, whose word must be taken unquestioned.” Speaking as a highly accomplished scientist himself, he unceremoniously shatters this misleading façade: “That all the evidence shows the behavior of scientists to be no different from the ways in which other people behave is somehow overlooked in all this.” See this article Retrieved 14th June 2011.


Retrieved 5th August 2014.

 [30] See Stephen Jay Gould, “In the Mind of the Beholder,” Natural History, Vol. 103 (2):15 (1994). I came across this comment in the following article by Casey Luskin:

Retrieved 4th August 2014.

 See also

Retrieved 4th August 2014.

[31] God’s Undertaker: Has Science Buried God? John C. Lennox, Lion, 2009, page 33.


Retrieved 4th August 2014.

[33] Ibid.

Review of Awesome Creation

July 30, 2014

The Cosmos is all that is, or was, or ever will be. Thus spake the late astronomer and author Carl Sagan, expressing his belief that reality consists of nothing but matter and energy. Sagan’s atheist slogan may have been borrowed from the ancient Greek philosopher Heraclitus (circa 500 BCE): “This cosmos, the same for all, was neither made by God nor man, but was, is, and always will be.” Heraclitus was conveying a notion that held sway for millennia and was endorsed by modern science until very recently – that the universe has always existed. He is quoted in Awesome Creation, a Study of the First Three Verses of the Torah, by Rabbi Yosef Bitton (Gefen Publishing House, 2013).

Rabbi Bitton eloquently presents the Jewish response to claims of the universe’s eternity: Bereshis bara! The universe was created by God out of nothing; it has not always existed. And Big Bang cosmology, now accepted by the overwhelming majority of the scientific community, involves a rather reluctant acknowledgement by many scientists that a cherished philosophical notion had to be forsaken.

In recent decades, a veritable cottage industry has arisen within the Torah community, with authors claiming to harmonise the respective viewpoints of the Torah and Science on the question of ultimate origins (of the universe and humanity). These authors make it their business – a lucrative business at that! – to pander to readers whose point of departure is, “How do you reconcile Judaism and Science?” without realising that they are not asking a question but rather expressing a prejudice. It never occurs to them to ask, “Are Judaism and Science necessarily reconcilable?” Having decided at the outset that the two viewpoints must always coincide, these authors proceed to make sure – if necessary by torturing classical sources until they confess – that Torah sources submit to political correctness.

Awesome Creation, for the most part, avoids this pitfall. It does an excellent job of elucidating the key terms in the first three verses of the Torah. What does tohu really mean? And bohu? How about raqia’? Does darkness mean the mere absence of light or is it a tangible entity? Rabbi Bitton analyses these words on the Torah’s own terms, using the Hebrew text, Chazal and classical authorities. And in pursuing the legitimate meanings of obscure terms, the author is sufficiently confident to criticise well-known writers – Rabbi Aryeh Kaplan, for example – for mistranslating certain phrases. Mostly, the author succeeds in sticking to his objective that “Science is used in this work only to the extent it contributes to the understanding of the Biblical text, which is the main goal of this book.”

But not always. Rabbi Bitton, too, sometimes succumbs to the urge to show that, as he puts it, the “Biblical Creation story… is completely compatible with science’s modern discoveries.” Nu nu… At any rate, writing that Ramban anticipated a post-Newtonian conception of physics or that Rambam identified primeval darkness as… [an] invisible form of energy was unnecessary. Overall, however, Rabbi Bitton’s scholarship is dispassionate and focused.

Awesome Creation makes the occasional innocent mistake. The famous astrophysicist Arthur Eddington was not an uncompromising atheist (he was a committed Quaker, and, because of his pacifism, faced imprisonment in 1918, when he was 35 years old and still subject to conscription in WWI) and citizens of the “eternal and stationary universe of Aristotle” did not ponder elliptical orbits (nobody did that until Kepler). But I quibble. On scientific matters, Awesome Creation is almost always accurate and informative.

One of the novel features of Awesome Creation is its willingness to cite lesser-known sources (a point the author acknowledges in a recent interview (see This is innocuous and even illuminating, except for the odd occasion when this practice goes overboard. Do we really need Jorge Luis Borges to tell us that Nature and the Bible are two books written by the same Author? Galileo said so 400 years ago (and Rabbi S.R. Hirsch used the same idea in his 18th Letter). But again, this is nitpicking. Mostly, Awesome Creation sticks to standard sources. And even when novel rabbinic sources are cited, they are not there to convince the reader that radical and fringe views are legitimate Torah viewpoints, because in hashkafa anything goes. [See, however, note 4 on page 63].

Awesome Creation is stimulating, original and accessible and I warmly recommend it to anyone who is interested in the Torah’s account of Creation.

Article on on Free Will

June 23, 2014

My article on Darwinism, Morality and Free Choice is now (Monday, 23rd June 2014) posted on the Aish HaTorah website,

This is the URL:


Article on Aish.Com

May 25, 2014

My article on the wider significance of brain scans is now (Sunday, 25th May 2014) posted on the Aish HaTorah website,

This is the URL:


Vestigial Organs

December 1, 2013


An abridged version of my article on vestigial organs appeared in the Chanukah issue (number 29) of Kolmus, a supplement to Mishpacha Magazine. Below is the full article, with notes.


A newspaper here in Johannesburg recently published an article on the alleged imperfections of the human body. The author of the article would not have had to search far to find material for her article. The Internet buzzes with sites that carry lists of God’s Great Mistakes[1], and Discover Magazine delights in articles that disparage miscellaneous parts of the human body.[2]

 The article is downright silly at times. In describing the human ear, it points out that its exquisite sensitivity is a liability because a sudden explosion could destroy the tiny crystalline rods in the ear whose function is to amplify the vibrations impinging on the eardrum. What next – proof that the human skeleton is shoddily constructed because of its inability to remain intact following a plunge from the tenth storey?[3] But the ear – amazing as it truly is – is not my subject.[4] In this essay, we will focus on the mascot of the vestigial organ movement, the human appendix, with which the article begins:

The human body is a wonder of nature: our brains react faster than a computer, our hearts beat without the need for rest. But it’s not perfect. The appendix, for instance, seems to have no real function yet can be the cause of appendicitis and, if left untreated, life-threatening peritonitis (inflammation of the abdominal lining) – so it could be simpler to get rid of it.

 Seems to have no real function, huh? In order to make that statement, one must be sure that the appendix really does not have a function, and making a negative argument like that is often dodgy.[5] In 1981, the Canadian biologist Steven Scadding argued that although he had no objection to Darwinism, “vestigial organs provide no evidence for evolutionary theory.” The primary reason is that “it is difficult, if not impossible, to unambiguously identify organs totally lacking in function.” Scadding cited the human appendix as an organ previously thought to be vestigial but now known to have a function.[6] What function does it have?

In October 1999, a Scientific American reader submitted the following question to the Ask the Experts column: “What is the function of the human appendix? Did it once have a purpose that has since been lost?”[7] The journal appointed Loren G. Martin, professor of physiology at Oklahoma State University, to answer the query. Professor Martin began by pointing out the contribution made by the appendix before a human being is even born:

For years, the appendix was credited with very little physiological function. We now know, however, that the appendix serves an important role in the fetus and in young adults. Endocrine cells appear in the appendix of the human fetus at around the 11th week of development. These endocrine cells of the fetal appendix have been shown to produce various… compounds that assist with various biological control (homeostatic) mechanisms. There had been little prior evidence of this or any other role of the appendix in animal research, because the appendix does not exist in domestic mammals.[8]

 Professor Martin then notes that in adulthood, the appendix continues to be an important player:

Among adult humans, the appendix is now thought to be involved primarily in immune functions. Lymphoid tissue begins to accumulate in the appendix shortly after birth and reaches a peak between the second and third decades of life… During the early years of development, however, the appendix has been shown to function as a lymphoid organ, assisting with the maturation of B lymphocytes (one variety of white blood cell) and in the production of the class of antibodies known as immunoglobulin A (IgA) antibodies. Researchers have also shown that the appendix is involved in the production of molecules that help to direct the movement of lymphocytes to various other locations in the body.[9]

 Professor Martin also notes that “the appendix probably helps to suppress potentially destructive humoral (blood- and lymph-borne) antibody responses while promoting local immunity… This local immune system plays a vital role in the physiological immune response and in the control of food, drug, microbial or viral antigens.”

 Finally, Professor Martin validates the adage that if something ain’t broken, you shouldn’t try to fix it:

In the past, the appendix was often routinely removed and discarded during other abdominal surgeries to prevent any possibility of a later attack of appendicitis; the appendix is now spared in case it is needed later for reconstructive surgery if the urinary bladder is removed. In such surgery, a section of the intestine is formed into a replacement bladder, and the appendix is used to re-create a ‘sphincter muscle’ so that the patient remains continent (able to retain urine). In addition, the appendix has been successfully fashioned into a makeshift replacement for a diseased ureter, allowing urine to flow from the kidneys to the bladder. As a result, the appendix, once regarded as a nonfunctional tissue, is now regarded as an important ‘back-up’ that can be used in a variety of reconstructive surgical techniques. It is no longer routinely removed and discarded if it is healthy.[10]

So we know that the appendix very definitely does have function. Enter William Parker.[11] Parker is a professor of surgery at Duke University School of Medicine who was sceptical of claims that the appendix is vestigial. His hypothesis was that it serves as a nature reserve of sorts for beneficial bacteria in our guts. When struck by severe gut infections such as cholera – an all-too-common scourge in human history – the beneficial bacteria in our guts are depleted. The appendix serves as a sanctuary for beneficial bacteria, which can ride out a bout of diarrhoea that completely evacuates the intestines, and emerge afterwards to repopulate the gut.[12]

In October 2007, Science Daily reported on this research.[13] “While there is no smoking gun, the abundance of circumstantial evidence makes a strong case for the role of the appendix as a place where the good bacteria can live safe and undisturbed until they are needed,” said Parker, who conducted the analysis in collaboration with R. Randal Bollinger, Duke professor emeritus in general surgery.

 The gut is populated with different microbes – and there are more of them than there are human cells in a typical human body – that help the digestive system break down the food we eat. In return, the gut provides nourishment and safety to the bacteria. Parker believes that the immune system cells found in the appendix are there to protect, rather than harm, the good bacteria.

Science Daily reported that for the previous ten years, Parker had been studying the interplay of these bacteria in the bowels, and in the process had documented the existence in the bowel of what is known as a biofilm. This thin and delicate layer is an amalgamation of microbes, mucous and immune system molecules living together atop the lining of the intestines. “Our studies have indicated that the immune system protects and nourishes the colonies of microbes living in the biofilm,” Parker explained. “By protecting these good microbes, the harmful microbes have no place to locate. We have also shown that biofilms are most pronounced in the appendix and their prevalence decreases moving away from it.”

“Diseases causing severe diarrhea are endemic in countries without modern health and sanitation practices, which often results in the entire contents of the bowels, including the biofilms, being flushed from the body,” Parker said. He added that the appendix’s location and position – the appendix is a dead-end sac that hangs between the small and large intestines – is such that it is expected to be relatively difficult for anything to enter it as the contents of the bowels are emptied.

“Once the bowel contents have left the body, the good bacteria hidden away in the appendix can emerge and repopulate the lining of the intestine before more harmful bacteria can take up residence,” Parker continued. “In industrialized societies with modern medical care and sanitation practices, the maintenance of a reserve of beneficial bacteria may not be necessary. This is consistent with the observation that removing the appendix in modern societies has no discernible negative effects.”[14]

Parker’s idea implies that individuals with their appendix should be more likely to recover from severe gut infections than individuals without an appendix. His hypothesis was tested a few years after he floated it. In its December 2011 issue, the journal Clinical Gastroenterology and Hepatology published a study entitled “The Appendix May Protect Against Clostridium difficile Recurrence”.[15]

Ideally, in order to test Parker’s idea, scientists would compare the fates of individuals who suffer gut infections and have an appendix to those of individuals who suffer the same gut infections and do not have an appendix. But such a study would be easiest in developing countries where cholera and similar diseases are prevalent, and those same regions are the ones where medical records (of appendectomies, for example) tend to be least detailed.

James Grendell, chief of the division of Gastroenterology, Hepatology and Nutrition at Winthrop University Hospital in New York, solved the problem, together with his colleagues. They studied a pathogen called Clostridium difficile. Thisdeadly organism is often encountered in hospitals, particularly when patients must be treated by prolonged courses of antibiotics. It does not appear to compete well with the native biota of patients’ guts, but when the native biota is depleted (as is the case after several courses of antibiotics) Clostridium difficile can grow quickly and take over. It is most dangerous when, after treatment, it recurs, which is to say when the native fauna of the gut and immune system cannot, together, prevent it from reinvading. If Parker was right, individuals without an appendix should be more likely to have a recurrence of Clostridium difficile than those individuals with an appendix.

The researchers were able to find 254 patients at the hospital who met the requirements of their study: there was evidence of their having been infected by Clostridium difficile, and the presence or absence of an appendix was known or discernible. The rest was easy. They compared whether individuals without their appendix were at a higher risk of recurrence from Clostridium difficile. The results were dramatic. Individuals without an appendix were four times more likely to have a recurrence of Clostridium difficile, exactly as Parker’s hypothesis predicted. Recurrence in individuals with their appendix intact occurred in 11% of cases. Recurrence in individuals without their appendix occurred in 48% of cases.

The results do not unequivocally prove Parker’s thesis, but they do provide further strong circumstantial evidence for the hypothesis that the human appendix plays an important role in human health. 


So, through ingenious science, a number of important functions have been found for the appendix, and human knowledge has advanced. Still, if that’s all there was to it, the topic would remain esoteric, limited to specialists in academic medicine. But that’s not all there is to it.

The uselessness of the appendix is a long-standing urban legend, going back at least as far as Charles Darwin. Darwin argued in The Origin of Species that the widespread occurrence of vestigial organs – organs that may have once had a function but are now useless, mere vestiges of the past – is evidence against Creation. “On the view of each organism with all its separate parts having been specially created, how utterly inexplicable is it that organs bearing the plain stamp of inutility… should so frequently occur.” But such organs, he argued, are not only explained by his theory, but would even have been predicted by it: “On the view of descent with modification, we may conclude that the existence of organs in a rudimentary, imperfect, and useless condition, or quite aborted, far from presenting a strange difficulty, as they assuredly do on the old doctrine of creation, might even have been anticipated in accordance with the views here explained.”[16]

This argument was then bequeathed to subsequent generations of biologists. It was endorsed as recently as 2001 by Ernst Mayr, one of the leading biologists of the twentieth century: “Every shift into a new adaptive zone leaves a residue of no longer needed morphological features that then become an impediment. One only needs to think of the many weaknesses in humans that are remnants of our quadrupedal and more vegetarian past, for instance… the caecal appendix.”[17]

When making his overall argument, Darwin used some examples of apparently vestigial organs which, I think, are uncontroversial. Some cave-dwelling fish are completely blind, although they possess eyes; others have no eyes at all. The species Astyanax mexicanus is born with eyes, but, as it matures, skin grows over the eyes and they degenerate completely – there is no need for sight in the dark world of a troglodyte. The eyes of blind cavefish are vestigial, and this appears to have happened through disuse. Darwin wrote that “It appears probable that disuse has been the main agent in rendering organs rudimentary. It would at first lead by slow steps to the more and more complete reduction of a part, until at last it became rudimentary, as in the case of the eyes of animals inhabiting dark caverns…”[18]

But as evidence for biological evolution, sightless cave-dwelling fish are weak. Firstly, as everyone who has built towers with blocks in the company of a two-year-old knows, there is a big difference between constructing and demolishing. A toddler is quite capable of bashing down impressive edifices, but cannot pile more than two or three blocks on one another. The fact that disuse can lead to the atrophying of an organ is by no means indicative of a purposeless, natural process being capable of constructing an organ where none previously existed. Whatever process leads to the loss of an organ’s abilities must be demonstrated to be capable of creative activity, if vestigial organs are to serve as evidence for biological evolution. As the biologist Lynn Margulis put it, “Natural selection eliminates and maybe maintains, but it doesn’t create.”[19]

Secondly, in the case of eyes, there is no doubt as to their function – to provide sight – which is superfluous in pitch-black caves. Even if cave-dwelling fish had perfectly-functioning eyes, they would still be useless, because there is no light in the caves these fish inhabit. It is therefore reasonable to posit that the eyes of blind cavefish functioned in the distant past, but atrophied over time due to lack of use. But when it comes to other apparently-vestigial organs, whose function in the distant past we do not know with certainty, the conclusion does not inexorably follow that they are really vestigial.

The parathyroid gland is a good example of this last point. It was discovered in humans in 1880. All through the early twentieth century biologists surmised that these glands were among the many useless parts they believed existed in the human body. Not anymore. The parathyroid is now known to regulate calcium-phosphorous metabolism,[20] and also plays a role in magnesium metabolism by increasing its excretion.[21] [A similar narrative is associated with tonsils: the removal of tonsils may lead to a higher incidence of throat cancer, but for decades doctors never suspected that this “useless” tissue might actually have a use that escaped their detection.[22]] In the decades when it was claimed that the parathyroid glands are vestigial, the argument rested on ignorance. Not only did nobody know what the parathyroid does now, nobody knew what the parathyroid was ever supposed to have done. To have claimed that these glands are vestigial was to argue from ignorance. We now know better.

Back to the appendix. In The Descent of Man, Darwin cited the human appendix as an example of a vestigial organ.[23] As we saw earlier, Darwin was wrong. In his time, immunology and endocrinology can barely have been said to exist. How wise was it, in retrospect, to label the appendix vestigial? And if we now confront an organ that appears to have no function, how wise is it to label it vestigial? And once we agree that labelling organs as vestigial is premature unless we know with certainty what their function was in the distant past, what happens to these organs’ role as evidence for biological evolution?

A final point. Not only does the appendix not provide evidence for biological evolution, it in fact constitutes a difficulty for the evolutionary paradigm. The appendix is found in both marsupial creatures, like the wombat, and in placental mammals, such as rats, lemmings and humans. But since, according to evolutionary theory, the last putative common ancestor of marsupials and placental mammals did not possess an appendix, evolutionists are forced to believe that the same organ evolved twice, independently.[24] Needless to say, this is fantastically improbable.[25]

Darwin of the Gaps

One of the curious twists in the story we have followed is the role reversal. In the past, proponents of scientism often threw the God of the Gaps argument in the face of believers. The argument is supposed to work like this. Believers, wallowing in ignorance, would explain sundry aspects of nature with a shrug and “God did it” or “That’s how God wanted it to be”. But as science progressed, and one dark corner after another was illuminated by the light of reason and empirical evidence, the believers had to retreat. The gaps in our understanding of the natural universe shrank, leaving less and less for God to accomplish.

The God of the Gaps argument was always silly, but in the case of vestigial organs the shoe – of a decidedly uncomfortable fit – is on the other foot. Biologists made the claim about various organs that they must be the product of evolution. But this argument depended on the claim that these organs had no function and thus had to be vestiges of a more-useful past. But as human knowledge expands, we find that structures that were previously assumed to be without function in fact have important function. With each of these steps, evolutionary biologists have had to retreat.


 And what about the Jewish angle? Well, the Talmud teaches that everything that God created has a purpose.[26] And Maharal (ca. 1520-1609), one of the greatest Jewish philosophers of the past half-millennium, wrote that even if we do not understand every feature of the human body, yet we are quite certain that nothing in it is superfluous.[27] Are those viewpoints compatible with the notion that our bodies are littered with useless vestiges of the past? I am not sure that these statements are sufficient to preclude the conclusion that wisdom teeth, for example, are vestiges of a past in which our diet was substantially different to what it is nowadays. But I do know this. The left atrial appendage is a small muscular ‘pouch’ in the heart. Dr. Amanda Varnava, a cardiologist quoted in the newspaper article I cited at the beginning of this essay, says that “It is completely redundant – it has no functional role.” It would be prudent to reserve judgment.[28]

[1] See

Retrieved 8th April 2013.

[2] See

Retrieved 8th April 2013.

[3] The Star, Wednesday, 20th March 2013, page 36, The Bits of Your Body that Nature Got Wrong, by Lucy Elkins:

The human body is a wonder of nature: our brains react faster than a computer, our hearts beat without the need for rest. But it’s not perfect. The appendix, for instance, seems to have no real function yet can be the cause of appendicitis and, if left untreated, life-threatening peritonitis (inflammation of the abdominal lining) – so it could be simpler to get rid of it.

EARS… Once the ear drum has collected the noise vibrations, they are passed into the inner ear. Here, the noise vibrations are picked up by tiny crystalline rods that look like hairs. “These are very fine and help make our hearing especially sensitive by adding volume and clarity,” [ENT specialist Tony Wright] adds. But this sensitivity also means the rods are prone to damage. “Something like an explosion can destroy them instantly – and persistent loud noise of 85 decibels or more (such as in a noisy factory or a disco) can damage them over years. The problem is that we can’t regenerate them.”

The article can be read online:

Retrieved 17th June 2013.

[4] To read about some of the latest research regarding the astonishing abilities of the human ear, see

Retrieved 14th June 2013.

[5] מסכת מנחות דף קג עמוד ב במשנה: אין לא ראינו ראיה.

[6] Steven R. Scadding, “Do ‘vestigial organs’ provide evidence for evolution?” Evolutionary Theory 5 (1981): 173-176. See this article by Dr. Jonathan Wells:

Retrieved 14th June 2013.

[7] See

Retrieved 10th April 2013.

[8] A report on LiveScience dated 29th May 2006 states:

The appendix is a slimy, dead-end sac that hangs between the small and large intestines.  It’s about a half inch in diameter and three inches long.  As quickly as 11 weeks after conception, the appendix starts making endocrine cells for the developing fetus.  Endocrine cells secrete useful chemicals, such as hormones, and the appendix endocrine cells secrete amines and peptide hormones that help with biological checks and balances as the fetus grows.


Retrieved 14th April 2013.

[9] The same LiveScience report also makes the following point:

After birth, the appendix mainly helps the body stave off disease by serving as a lymphoid organ.  Lymphoid organs, with their lymphoid tissue, make white blood cells and antibodies.

The appendix, by virtue of its lymphoid tissue, is part of a complicated chain that makes B lymphocytes (one variety of white blood cell) and a class of antibodies known as immunoglobulin A antibodies.  The appendix also produces certain chemicals that help direct the white blood cells to the parts of the body where they are needed the most. 

[10] There is a sinister side to this surgical versatility. In 2001, rumours were circulating in Greek hospitals that surgery residents, eager to rack up scalpel time, were falsely diagnosing hapless Albanian immigrants with appendicitis. At the University of Ioannina medical school’s teaching hospital, a newly minted doctor named Athina Tatsioni was discussing the rumours with colleagues when a professor who had overheard asked her if she’d like to try to prove whether they were true – he seemed to be almost daring her. She accepted the challenge and, with the professor’s help, eventually produced a formal study showing that, for whatever reason, the appendices removed from patients with Albanian names in six Greek hospitals were more than three times as likely to be perfectly healthy as those removed from patients with Greek names. “It was hard to find a journal willing to publish it, but we did,” recalls Tatsioni. “I also discovered that I really liked research.” See

Retrieved 6th May 2013.

[11] My account of Dr. Parker’s work is based on an article on the website of Scientific American. It can be read here:

Retrieved 9th April 2013.

[12] See Randal Bollinger R, Barbas AS, Bush EL, Lin SS, Parker W. Biofilms in the large bowel suggest an apparent function of the human vermiform appendix. Journal of Theoretical Biology, 2007 Dec 21; 249(4):826-31.

[13] See

Retrieved 14th June 2013.

[14] About one person in twenty has the appendix removed.

[15] See the abstract here:

Retrieved 9th April 2013.

[16] Darwin, The Origin of Species, Chapters XIV (p. 402) and XV (p. 420). Available online at

Retrieved 14th June 2013.

[17] Ernst Mayr, What Evolution Is, Basic Books, page 143.

[18] Charles Darwin, Origin of Species (1859), sixth edition, page 401. See

Retrieved 8th April 2013.

“By the time that an animal had reached, after numberless generations, the deepest recesses, disuse will on this view have more or less perfectly obliterated its eyes, and natural selection will often have affected other changes, such as an increase in the length of antennae or palpi, as a compensation for blindness.” Charles Darwin, Origin of Species (1859), sixth edition, page 111. See

Retrieved 14th June 2013.

[19] See

Retrieved 14th June 2013.

[20] See

Retrieved 11th April 2013.

[21] parathyroid gland. (2009). Encyclopædia Britannica. Encyclopædia Britannica 2009 Ultimate Reference Suite.  Chicago: Encyclopædia Britannica.

[22] “Tonsillectomies have been linked to dozens of medical complications and conditions, ranging from polio to weight gain. A typical example is a study published in 2011 in the European Heart Journal. The study “found a higher risk of AMI [acute myocardial infarction] related to surgical removal of the tonsils and appendix before age 20. These results are consistent with the hypothesis that subtle alterations in immune function following these operations may alter the subsequent cardiovascular risk…” The Black Swan, Nassim Nicholas Taleb, Penguin Books, 2010, page 55.


Retrieved 14th June 2013.

See this article for a general overview:

[23] Darwin, Charles. The Descent of Man, First Edition (London: John Murray, 1871), Chapter I (page 27). Available at

With respect to the alimentary canal I have met with an account of only a single rudiment, namely the vermiform appendage of the caecum. The caecum is a branch or diverticulum of the intestine… It appears as if, in consequence of changed diet or habits, the caecum had become much shortened in various animals, the vermiform appendage being left as a rudiment of the shortened part… Not only is it useless, but it is sometimes the cause of death… this is due to small hard bodies, such as seeds, entering the passage and causing inflammation.

[24] This process is called convergent evolution.


[26] מסכת שבת דף עז עמוד ב: אמר רב יהודה אמר רב כל מה שברא הקב”ה בעולמו לא ברא דבר אחד לבטלה.

[27] מהר”ל תפארת ישראל פרק ח: וכבר אמרנו שאף אם אין ידוע לנו טעם וסבה של כל דבר ודבר שנמצא באדם למה הוא כך, מכל מקום ידוע לנו שאין דבר אחד לבטלה…

[28] A paper published in November 1999 in the journal Heart states that:

The physiological properties and anatomical relations of the LAA [left atrial appendage] render it ideally suited to function as a decompression chamber during left ventricular systole and during other periods when left atrial pressure is high. These properties include the position of the LAA high in the body of the left atrium; the increased distensibility of the LAA compared with the left atrium proper; the high concentration of atrial natriuretic factor (ANF) granules contained within the LAA; and the neuronal configuration of the LAA… Obliteration or amputation of the LAA may help to reduce the risk of thromboembolism, but this may result in undesirable physiological sequelae such as reduced atrial compliance and a reduced capacity for ANF secretion in response to pressure and volume overload. See

Retrieved 13th May 2013.

Origin of Life and Philosophical Outlook

June 28, 2013

In Signature in the Cell, Dr. Stephen Meyer presented a comprehensive and accessible history of research into the origin of life. In this post, we take a bird’s eye view of research into this area over the past three-quarters of a century. We shall also digress in order to get a snapshot of how ideological commitments shape the views of many scientists.


Let’s begin with Dr. Ernst Chain. Chain won a Nobel Prize for his contribution to the development of penicillin. I mentioned him in Genesis and Genes, in the context of the discussion about whether evolutionary theory is relevant to nuts-and-bolts research in biology. I cited an article by Philip Skell (1918-2010), who was a distinguished professor of chemistry and a member of the National Academy of Sciences in the USA and a prominent Darwin sceptic. In a 2009 article in entitled The Dangers of Overselling Evolution, he made the point that evolutionary theory makes no contribution to actual research:

In 1942, Nobel Laureate Ernst Chain wrote that his discovery of penicillin (with Howard Florey and Alexander Fleming) and the development of bacterial resistance to that antibiotic owed nothing to Darwin’s and Alfred Russel Wallace’s evolutionary theories.[1]

Chain understood the immensity of the task of trying to explain life in naturalistic terms. In The Life of Ernst Chain: Penicillin and Beyond, we read that:

I have said for years that speculations about the origin of life lead to no useful purpose as even the simplest living system is far too complex to be understood in terms of the extremely primitive chemistry scientists have used in their attempts to explain the unexplainable that happened billions of years ago.[2]

In August 1954, Dr. George Wald, another Nobel Laureate, wrote in Scientific American:

There are only two possibilities as to how life arose. One is spontaneous generation arising to evolution; the other is a supernatural creative act of God. There is no third possibility… a supernatural creative act of God. I will not accept that philosophically because I do not want to believe in God, therefore I choose to believe that which I know is scientifically impossible; spontaneous generation arising to Evolution.

 This statement may seem astonishingly frank to many members of the public. Informed consumers of science, in contrast, are aware that much of the debate around the origin of life and biological evolution has precious little to do with drawing inevitable conclusions from straightforward evidence. It is far more about worldviews and ideologies, and only extremely naive observers assume that this does not apply to scientists who participate in the debate. Wald makes it perfectly clear that his direction was dictated by his philosophical leanings, and that is true of many scientists and Western intellectuals. Consider the views of Thomas Nagel. Nagel is a courageous thinker whose latest book, Mind and Cosmos, is a fierce demolition of Darwinian evolution.[3] But Nagel will only go so far. In The Last Word, which appeared in 1997, he offered a candid account of his philosophical inclinations:

I am talking about something much deeper—namely, the fear of religion itself. I speak from experience, being strongly subject to this fear myself: I want atheism to be true and am made uneasy by the fact that some of the most intelligent and well-informed people I know are religious believers… It isn’t just that I don’t believe in God and, naturally, hope that I’m right in my belief. It’s that I hope there is no God! I don’t want there to be a God; I don’t want the universe to be like that.[4]

 The fact that faith – the faith of many scientists in the ability of unguided matter and energy to create life – drives much of the discussion about evolution, was underscored by Dr. Gerald Kerkut, Professor  Emeritus of Neuroscience at the University of Southampton, who wrote in 1960 that: 

The first assumption was that non-living things gave rise to living material. This is still just an assumption… There is, however, little evidence in favor of abiogenesis and as yet we have no indication that it can be performed… it is therefore a matter of faith on the part of the biologist that abiogenesis did occur and he can choose whatever method… happens to suit him personally; the evidence for what did happen is not available.

 Harold Urey won a Nobel Prize for chemistry, but is probably more famous for participating, with his graduate student Stanley Miller, in what became known as the Miller-Urey experiment. Writing in The Christian Science Monitor on 4th January 1962, Urey wrote: 

All of us who study the origin of life find that the more we look into it, the more we feel it is too complex to have evolved anywhere. We all believe as an article of faith that life evolved from dead matter on this planet. It is just that its complexity is so great, it is hard for us to imagine that it did.

 Hubert Yockey, the renowned information theorist, wrote in the Journal of Theoretical Biology in 1977 that:

One must conclude that… a scenario describing the genesis of life on earth by chance and natural causes which can be accepted on the basis of fact and not faith has not yet been written.

Richard Dickerson, a molecular biologist at UCLA, wrote in 1978 in Scientific American that: 

The evolution of the genetic machinery is the step for which there are no laboratory models; hence one can speculate endlessly, unfettered by inconvenient facts. The complex genetic apparatus in present-day organisms is so universal that one has few clues as to what the apparatus may have looked like in its most primitive form.[5]

 Francis Crick needs no introduction. In Life Itself, published in 1981, he wrote that: 

Every time I write a paper on the origin of life, I determine I will never write another one, because there is too much speculation running after too few facts.

 Crick’s conclusion is that:

The origin of life seems almost to be a miracle, so many are the conditions which would have had to have been satisfied to get it going.[6]

 Prominent origin-of-life researcher Leslie Orgel wrote in New Scientist in 1982 that:

Prebiotic soup is easy to obtain. We must next explain how a prebiotic soup of organic molecules, including amino acids and the organic constituents of nucleotides evolved into a self-replicating organism. While some suggestive evidence has been obtained, I must admit that attempts to reconstruct the evolutionary process are extremely tentative.[7]

 The views of Nobel Prize winner Fred Hoyle are particularly interesting. He struggled with the conflict between his ardent atheism and his knowledge of the excruciating difficulty of positing a naturalistic start to life. Writing in 1984, Hoyle stated that: 

From my earliest training as a scientist I was very strongly brain-washed to believe that science cannot be consistent with any kind of deliberate creation. That notion has had to be very painfully shed. I am quite uncomfortable in the situation, the state of mind I now find myself in. But there is no logical way out of it; it is just not possible that life could have originated from a chemical accident.[8]

 The writer Andrew Scott hit the nail on the head when he wrote, in 1986, that most scientists’ adherence to naturalistic accounts of the origin of life owed little to the evidence and much to ideological commitments:

But what if the vast majority of scientists all have faith in the one unverified idea? The modern ‘standard’ scientific version of the origin of life on earth is one such idea, and we would be wise to check its real merit with great care. Has the cold blade of reason been applied with sufficient vigor in this case? Most scientists want to believe that life could have emerged spontaneously from the primeval waters, because it would confirm their belief in the explicability of Nature – the belief that all could be explained in terms of particles and energy and forces if only we had the time and the necessary intellect.[9]

 This conclusion is mirrored in the words of Paul Davies, a theoretical physicist and authority on origin-of-life studies. Writing in 2002, Davies affirms that it is scientists’ adherence to methodological naturalism that drives their agenda and conclusions:

First, I should like to say that the scientific attempt to explain the origin of life proceeds from the assumption that whatever it was that happened was a natural process: no miracles, no supernatural intervention. It was by ordinary atoms doing extraordinary things that life was brought into existence. Scientists have to start with that assumption.[10]

 In 1988, Klaus Dose, another prominent origin-of-life theorist, summed up the situation nicely when he wrote that: 

More than 30 years of experimentation on the origin of life in the fields of chemical and molecular evolution have led to a better perception of the immensity of the problem of the origin of life on Earth rather than to its solution. At present all discussions on principal theories and experiments in the field either end in stalemate or in a confession of ignorance.[11]

 Carl Woese was a pioneer in taxonomy, and one of the major figures in 20th century microbiology. His view of the origin of life: 

In one sense the origin of life remains what it was in the time of Darwin – one of the great unsolved riddles of science. Yet we have made progress…many of the early naïve assumptions have fallen or have fallen aside…while we do not have a solution, we now have an inkling of the magnitude of the problem.[12]

 Paul Davies, too, writes that no substantive progress has been made in this area since Darwin’s time. In a recent short paper suggesting that life be viewed as a software package, Davies writes:

Darwin pointedly left out an account of how life first emerged, “One might as well speculate about the origin of matter,” he quipped. A century and a half later, scientists still remain largely in the dark about life’s origins. It would not be an exaggeration to say that the origin of life is one of the greatest unanswered questions in science.[13]

 Readers of Genesis and Genes will recall Richard Lewontin’s admission that his mathematical models of evolutionary mechanisms are a sham – they do not correspond to reality. The biologist Lynn Margulis reminisced:

Population geneticist Richard Lewontin gave a talk here at UMass [University of Massachusetts] Amherst about six years ago, and he mathematized all of it – changes in the population, random mutation, sexual selection, cost and benefit. At the end of his talk he said, “You know, we’ve tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I’ve told you about.” This just appalled me. So I said, “Richard Lewontin, you are a great lecturer to have the courage to say it’s gotten you nowhere. But then why do you continue to do this work?” And he looked around and said, “It’s the only thing I know how to do, and if I don’t do it I won’t get grant money.” So he’s an honest man, and that’s an honest answer.

 Lewontin, who is one of the most prominent geneticists in the world and a protégé of one of the founders of neo-Darwinism, Theodosius Dobzhansky, was equally forthright about the role that faith plays in moulding scientists’ approach to important issues. In his review of a book by Carl Sagan, Lewontin wrote in 1997 that:

We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.[14]

 Stuart Kauffman of the Santa Fe Institute is one of the world’s leading origin-of-life researchers and a leading expert on self-organisational systems. He writes:

Anyone who tells you that he or she knows how life started on the earth some 3.45 billion years ago is a fool or a knave. Nobody knows.[15]

 In Genesis and Genes, I also quoted the biochemist Franklin Harold. In his book The Way of the Cell, Harold frankly acknowledged that “We must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.”[16] Regarding the origin of life, Harold writes that:

It would be agreeable to conclude this book with a cheery fanfare about science closing in, slowly but surely, on the ultimate mystery; but the time for rosy rhetoric is not yet at hand. The origin of life appears to me as incomprehensible as ever, a matter for wonder but not for explication.[17]

 Massimo Pigliucci was formerly a professor of evolutionary biology and philosophy at the State University of New York at Stony Brook, and holds doctorates in genetics, botany, and the philosophy of science. He is currently the chairman of the department of philosophy at City University of New York. He is a prominent international proponent of evolution and the author of several books. Writing in 2003, Pigliucci writes that “[I]t has to be true that we really don’t have a clue how life originated on Earth by natural means.”[18]

In 2007, we find science writer Gregg Easterbrook writing in Wired: “What creates life out of the inanimate compounds that make up living things? No one knows. How were the first organisms assembled? Nature hasn’t given us the slightest hint. If anything, the mystery has deepened over time.”[19]

 Also in 2007, Harvard chemist George M. Whitesides, in accepting the highest award of the American Chemical Society, wrote: “The Origin of Life. This problem is one of the big ones in science. It begins to place life, and us, in the universe. Most chemists believe, as do I, that life emerged spontaneously from mixtures of molecules in the prebiotic Earth. How? I have no idea… On the basis of all the chemistry that I know, it seems to me astonishingly improbable.”[20] 

As recently as 2011, Scientific American acknowledged that origin-of-life research has gotten nowhere in the last century. In an article by John Horgan, we read that:

Dennis Overbye just wrote a status report for the New York Times on research into life’s origin, based on a conference on the topic at Arizona State University. Geologists, chemists, astronomers, and biologists are as stumped as ever by the riddle of life.[21]

 Also writing in 2011, Dr. Eugene Koonin provided a neat summary of the utter failure of this endeavour: 

The origin of life is one of the hardest problems in all of science… Origin of Life research has evolved into a lively, interdisciplinary field, but other scientists often view it with skepticism and even derision. This attitude is understandable and, in a sense, perhaps justified, given the “dirty” rarely mentioned secret: Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the ultimate goal, the origin of life field is a failure – we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth. Certainly, this is due not to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the origin of life… these make the final outcome seem almost like a miracle.[22]


The area of origin-of-life research is fascinating not only for its own sake, but also in the way that it exposes what many uninformed members of the public take for granted, namely, that scientists are driven by data, and data alone. I elaborated on this misconception in Genesis and Genes, demonstrating that the commitment of many scientists to methodological naturalism is a far more important factor than the scientific evidence in reaching conclusions about life on Earth.


 See Also:

The post Certitude and Bluff:


Some of the quotations in this post come from an article by Rabbi Moshe Averick, published in The Algemeiner. The article can be read here:

Retrieved 26th June 2013.

[1] The article can be read here:

Retrieved 2nd November 2010.

[2] R.W. Clark, Weidenfeld and Nicolson, London (1985), page 148.

[3] To read more about Nagel and his latest book, see these reviews:

[4] See

Retrieved 27th June 2013.

[5] Richard E. Dickerson, “Chemical Evolution and the Origin of Life”, Scientific American, Vol. 239, No. 3, September 1978, page77.

[6] Life Itself, New York, Simon and Schuster, 1981, page 88.

[7] Leslie E. Orgel, “Darwinism at the very beginning of life”, New Scientist, Vol. 94, 15 April 1982, page 150.

[8] Fred Hoyle, Evolution from Space, New York, Simon and Shuster, 1984, page 53.

[9] Andrew Scott, “The Creation of Life: Past, Future, Alien”, Basil Blackwell, 1986, page 111.

[10] Paul Davies, “In Search of Eden, Conversations with Paul Davies and Phillip Adams”.

[11] Klaus Dose, “The Origin of Life: More Questions Than Answers”, Interdisciplinary Science Reviews, Vol. 13, No. 4, 1988, page 348.

[12] Carl Woese, Gunter Wachtershauser, “Origin of Life” in Paleobiology: A Synthesis, Briggs and Crowther – Editors (Oxford: Blackwell Scientific Publications, 1989.

[13] See:

Retrieved 27th June 2013.

[14] “Billions and Billions of Demons”, Richard Lewontin, 9th January 1997, New York Times Book Review.

[15] At Home in the Universe, London, Viking, 1995, page 31.

[16] Franklin Harold, The Way of the Cell: Molecules, Organisms and the Order of Life, Oxford University Press, 2001, page 205.

[17] Ibid. page 251.

[18] Massimo Pigliucci, “Where Do We Come From? A Humbling Look at the Biology of Life’s Origin,” in Darwin, Design and Public Education, eds. John Angus Campbell and Stephen C. Meyer (East Lansing, MI: Michigan State University Press, 2003), page 196.

[19] Gregg Easterbrook, “Where did life come from?” Wired, page 108, February, 2007.

[20] George M. Whitesides, “Revolutions in Chemistry: Priestly Medalist George M. Whitesides’ address”, Chemical and Engineering News, 85 (March 26, 2007): p. 12-17. See

Retrieved 22nd April 2012.

[21] John Horgan, Scientific American, 28th February 2011.

[22] Eugene Koonin, The Logic of Chance: The Nature and origin of Biological Evolution (Upper Saddle River, NJ, FT Press, 2011, page 391.

Genesis and Genes on Television

June 15, 2013

A local television station, SABC 2, recently featured Genesis and Genes. The segment, which is about 7-minutes long, is now available on YouTube. Here is the link: