Category: Biology

Carroll on the Philosophy of Nature

William Carroll writes at Public Discourse (“The Limits of Life: -1359712483qyBBiology and the Philosophy of Nature“):

‘For some time, astrobiologists have been studying what are called extremophiles, organisms that live in extreme conditions. Do we get closer to understanding the origin of life the more we advance in our knowledge of life at its frontiers?

It is precisely such a question that is properly in the domain of the philosophy of nature. It would be of considerable benefit for biologists and other natural scientists to become acquainted with the insights this discipline offers. The philosophy of nature is a more general science of nature than any of the diverse empirical sciences. It depends upon the various natural sciences to understand nature, but the philosophy of nature concerns topics that are not specific to any one of the sciences, but common to them all: the nature of change and time, how physical entities are unities (as distinct from mere heaps of elements), and what the differences are between the living and the non-living.’

Read here.

Reconsidering the “Great Oxidation Event”

Earth’s early atmosphere containedEarth with auroras (NASA) very little oxygen. The rise of photosynthetic organisms, which produce oxygen as a byproduct, led to increasing levels of oxygen in the atmosphere, and later the appearance of nonphotosynthetic organisms (like us) which used oxygen as an ingredient in energy-prducing cellular respiration.

A new study suggest that the oxidation of the Earth’s atomsphere was a longer and more variable process than previously thought:

‘The evidence for the Great Oxidation Event has mainly come from the sudden disappearance in the record of a particular chemical signature of volcanic sulfur that signals the removal of a major oxygen ‘sink’, and the permanent accumulation of oxygen in the atmosphere.

But, in a new review of the latest scientific literature, Lyons and colleagues argue that relying on this record alone has been misleading.

“A big message of this paper is that the Great Oxidation Event is really a very protracted and dynamic transition rather than a single step,” says Lyon. “We suggest it shouldn’t be called an event at all.”

Lyons and colleagues argue photosynthesis probably started earlier around 3 billion years ago but the oxygen it produced was largely removed from the atmosphere by tectonic processes that led to emission of reducing sulfur, hydrogen and methane gases.

Such processes led to a much more complicated rise and fall of oxygen levels over Earth’s history than previously thought, says Lyons.

“There’s a dance between production and consumption of oxygen with huge implications for life on Earth.”

“The oxygen curve was not just low, intermediate and high, which is what has been in everyone’s mind forever.”‘

Read here (ABC Science).


Image: NASA

Lewis, MacDonald, Krauthammer & the Soul

You’ve probably come across this quote before:

You don’t have a soul. You are a soul. You have a body.

I am glad to discover that the source of this quote is not, as is commonly claimed, C. S. Lewis, but rather his literary hero, George MacDonald. I am glad to know that Lewis would not make such a mistake, but surprised that MacDonald would. This post at First Things has more. In response to the reduction of materialism, and given the unconscious, dominant Cartesianism of our society, the quote strikes many Christian ears as right and as a fitting statement of the Christian position, over against materialism. In fact, though, the quote is wrong, and does not accurately convey the classical Christian teaching. A more accurate statement would be: You do not have a soul or have a body, you are a soul and a body. A soul is, by definition, the form of the body. You cannot have one without the other. To separate them is incoherent.

To the materialist claim that the soul is some sort of ghostly woo, unsupported by any empirical evidence, then, the proper response is: the evidence is right before your eyes. The evidence for the soul is just as present as the evidence for the body, which no one denies. The argument that the soul exists is not an argument that there is something over and above the body, or some ethereal thing in addition to the body, for which evidence must be produced. The evidence for the existence of the soul arises from rightly considering the evidence of the body.


Which leads us to our second point, also discussed further in a post atKrauthammer_Final2 First Things. As a Christmas gift, I received a copy of Charles Krauthammer’s recent book of collected columns, Things That Matter, and though I do not agree with all he writes, he is a superb columnist with a great talent for addressing topics thoughtfully and distilling his thoughts concisely with great clarity and force. Nevertheless, in his essay on stem cells contained in that book, he makes a fundamental mistake right out of the gate, declaring that the question of the personhood of the unborn child, or what he calls “ensoulment”, is a “metaphysical” question, a “question of faith”, and such questions are beyond secular consensus. He repeats these claims in a recent National Review column that is discussed at the First Things link.

There are two problems with this. The first is this: it is impossible to stake a neutral claim on this question; or, at least, the supposedly “neutral” postion in this case clearly favors one judgment over the other. We simply cannot avoid taking some metaphysical position on this question. If we say that since we are not sure whether the unborn is a person, we will not restrict the taking of the unborn’s life, we simply to choose to treat it as if it is not a person. It is not a neutral position; it is, practically, a metaphysical decision against personhood.

But the error in fact lies deeper than this. Dr. Krauthammer’s concerns about “ensoulment” are irrelevant. Let us set aside all theological concerns; let us simply stick to the biology. To identify a human being we need do no more than identify a living human body, and the unborn child is just a living human body. On this question it is the Catholic pro-life position that is one of hard-nosed materialism. The soul is the form of the body; find the living body, there is the soul. Reason needs no more than this. It is the other side, with its hand-wringing over defining the beginning of some vague notion of ghost-in-the-machine “personhood”, that invokes the mystical, unscientific woo.


Some follow-up on Stephen Hawking’s black hole comments: New Scientist presents a basic overview of the questions involved; and, from what I can tell, this view seems to be the most sensible.


christ-in-the-garden-of-gethsemane-1584Suppose you asked, about a mass shooting, “How could this happen?” In response, someone offers you a straightforward, scientific, factual forensic report on the various angles and types of weapons used. Although it does, strictly speaking, answer your question, it isn’t quite the answer you were looking for. Philosophy and theology offer answers to the problem of evil, but as skeptics like to note, they’re never quite satisfactory. That is, while they do offer logical and reasonable answers, they don’t really get to the point. Evil and suffering is not a logic problem. Though a logical answer is necessary and a helpful part of understanding the problem, just as a physical answer is a part of understanding something like a mass shooting, it doesn’t get to the heart of the matter. But the heart of the matter is not a question of science, or logic, or reason. Thus I recommend this excellent essay from Martin Cothran, “How Literature Solves the Problem of Evil”:

The problem of evil is, to steal a phrase from The Hobbit, a “riddle in the dark.” And philosophers do not do well in the dark. They fly by day. When darkness comes, pure intelligence is of little avail. Darkness requires wisdom, and wisdom is of the poets. I don’t think Hegel meant it this way, but it is perhaps why the Owl of Minerva, the symbol of wisdom, flies only at dusk.

When people look for a solution to the problem of evil in its rational or logical form, they are looking for a resolution to a technical problem. But this question—the rational question of evil—is not the real problem of evil. At least it is not the question with which people who experience suffering actually struggle. In fact, the vast majority of those who actually struggle with evil couldn’t even tell you what the logical question was. And even if they were aware of the problem—and even if they knew the answer to it—they would not be satisfied.

How would the answer to a logical question assuage their grief? Their grief is not a logical problem. The logical dilemma of evil would not be satisfying to anyone but a logician—and it would only satisfy him as a logician; it would not satisfy him as a human being.

Read here.


And finally, China’s rover trip to the Moon is proving to be short-lived, as Yutu seems to have suffered from a failure that looks increasingly fatal.


Images: Washington Post; Paolo Veronsese, “Christ in the Garden of Gethsamane”, 1584.

Time & Space


SN 2014J in colour (University College London)

Twelve million years ago, a star in the galaxy we call M82 exploded. Since M82 lies 12 million light years away, the light from that explosion just reached Earth last week, being first noticed on January 21st. You may be able to see this supernova for yourself. M82 sits high in the northern sky above the Big Dipper. As of yesterday, Sky & Telescope reports the supernova’s magnitude at 10.6, within the range of backyard telescopes. The explosion was spotted serendipitously on January 21st by a group of undergraduate students and their teacher during a brief workshop at University College London.

One of the aspects that I find most interesting about this process is the extreme juxtaposition of scales of time and space. As noted, the galaxy M82 sits 12 million light years away; therefore, the light from the supernova explosion has taken 12 million years to reach us. Yet compare these huge numbers with the supernova itself: the explosion itself lasted only a matter of seconds. A Type Ia supernova, like this one, occurs when a compact white dwarf star pulls matter (via gravity) off of a much larger companion star. Eventually, enough mass accumulates on the white dwarf so as to suddenly initiate fusion, explosively releasing tremendous amounts of energy. The explosion itself lasts for a minute or so, and the brightly glowing aftermath itself persists for weeks (which at least gives us plenty of time here to catch it). Yet this brief event sheds light and energy out into space that can overpower the luminosity of an entire galaxy and can be seen in skies of a planet—our planet—millions of light years distant and millions of years in the future.


I have not yet read it, but David Bentley Hart’s new book The Experience of God sounds promising. William Carroll reviews it at Public Discourse, and Edward Feser reacts to Jerry Coyne’s comments on it here. Hart writes:

“Any argument for or against the reality of God not so understood—any debate over an intelligent designer, or a supreme being within time and space who merely supervises history and legislates morals, or a demiurge whose operations could possibly be rivals of the physical causes describable by scientific cosmology—may prove a diverting amble along certain byways of seventeenth-century deism or eighteenth-century “natural history,” but it most definitely has nothing to do with the God worshiped in the great theistic religions or described in their philosophical traditions, or reasoned toward by their deepest logical reflections upon the contingency of the world.”

And Carroll adds:

“Hart offers mostly dialectical arguments to show the incoherence of the positions he rejects. We recognize the radical contingency of the world we experience, a recognition that is not the result of a demonstrative argument but a kind of intellectual intuition based on the immediacy of our experience. This insight into the ‘absolute contingency’ of the world eludes those who embrace a materialistic metaphysics. It is also the basis for a reflection that leads to God as the absolutely necessary being.”


In honor of St. Thomas Aquinas’ recent feast day, we have this—over at BioLogos, Fr. Austriaco argues that evolution is a fitting means of creation:

“I propose that it was fitting for God to have created via evolution rather than via special creation because in doing so, he was able to give his creation – the material universe and the individual creatures within it – a share in his causality to create. In this way, he more fully communicates his perfection to his creation, thus, more clearly manifesting his glory. As St. Thomas points out: ‘If God governed alone, things would be deprived of the perfection of causality. Wherefore all that is effected by many would not be accomplished by one.’ (Summa theologiae, I.103.6)”


Stephen Hawking announces that he suspects that black holes aren’t quite what he thought they were. To wit: he thinks that the event horizon has been mischaracterized. Classically, the event horizon marks the point of no return: the line at which the black hole’s gravity becomes inescapable. Once it is crossed, there’s no way out again. Interestingly, though, in the classical view, an astronaut crossing the event horizon wouldn’t notice anything different at first. He’d just ride along across it along with everything else traveling with him. More recent quantum mechanics–based analyses, however, have suggested that the event horizon is marked by a “firewall” of astoundingly high energy created by quantum behavior at the black hole’s boundary. But Hawking now says that the whole idea of the horizon needs to be evaluated. Other physicists remain skeptical.


And, finally, Pope Francis encourages Notre Dame to resist attempts to undermine the university’s commitment to Catholic moral practice.

Image: University College London

Meleagris gallopavo

Wild turkey (R. Burton/USFWS)

Meleagris gallopavo (Wild turkey)

(R. Burton/USFWS)

Alas, Poor Ming!

Ming (Bangor University)

We hardly knew ye.

ScienceNordic reports:

In autumn 2006 a team of researchers went on an expedition to Iceland, where they discovered something that made the headlines across the world. The discovery even made it into the Guinness Book of World Records.

One of the Arctica islandica bivalve molluscs, also known as ocean quahogs, that the researchers picked up from the Icelandic seabed turned out to be around 405 years old, and thus the world’s oldest animal.

However, after taking a closer look at the old mollusc using more refined methods, the researchers found that the animal is actually 100 years older than they thought. The new estimate says that the mollusc is actually 507 years old.


The mollusc’s 507-year-long life came to an abrupt end in 2006 when the British researchers – unaware of the animal’s impressive age – opened up its shell to put it under scientific scrutiny.

Read here.


Image: Bangor University

Life Began in Clay?

Creation of Adam, Sistine Chapel (Michelangelo)

It does have a certain Biblical ring to it.

A new study from Cornell shows that complex molecules that could potentially aid in the rise of cells can be built from reactions embedded deep in clay:

“We propose that in early geological history clay hydrogel provided a confinement function for biomolecules and biochemical reactions,” said Dan Luo, professor of biological and environmental engineering and a member of the Kavli Institute at Cornell for Nanoscale Science.

In simulated ancient seawater, clay forms a hydrogel — a mass of microscopic spaces capable of soaking up liquids like a sponge. Over billions of years, chemicals confined in those spaces could have carried out the complex reactions that formed proteins, DNA and eventually all the machinery that makes a living cell work. Clay hydrogels could have confined and protected those chemical processes until the membrane that surrounds living cells developed.

Read here from Science Daily.

The trouble is that reports like this are becoming all too common. I don’t think a week goes by that there’s not a new report of interesting compounds arising in the deep sea, in hydrothermal vents, in ice, on volcanoes, under lightning strikes, in tidal pools, on comets, on Mars…

But if ostensibly life-giving compounds can spring up practically anywhere, that leaves us precisely nowhere on the question of where it actually did so.

The Mysterious Human Body: Unknown Ligament Discovered

It has been the subject of intense study since time immemorial,Greek sculpture and is known quite intimately by each of us, and yet the human body is still a mystery in its details. In this day and age, new discoveries about the human body are usually made at the microscopic or the physiological scale, but here’s a genuine new discovery in gross anatomy: a whole new ligament in the human knee that had previously gone unnoticed. Ligaments are bands of fibrous tissue that “tie” bones to other bones. The newly discovered anterolateral ligament was found by Belgian surgeons looking for clues as to why some patients still have particular trouble after ACL repair surgeries—and they started with speculation from 1879 about a yet-unknown ligament.

Read here from KU Leuven.

The discovery is reported in the Journal of Anatomy: Claes, S., Vereecke, E., Maes, M., Victor, J., Verdonk, P. and Bellemans, J. (2013), Anatomy of the anterolateral ligament of the knee. Journal of Anatomy, 223: 321–328. doi: 10.1111/joa.12087

Extranuclear Genes Have Disproportionate Effects

One of the changes that was happening in biology at the time this blog was started was the realization that the importance of the gene had been somewhat overemphasized in the previous decades; in addition to learning more and more about the genome, biologists have also been learning more and more about how the gene needs to be understood in a wider organismal context, and life can’t be simply reduced to the expression of genes.

Here’s a new story from UC Davis that illustrates how extranuclear genes, that is, the DNA found in the cell’s organelles (such as mitochondria), have a disproportionate effect on the cell’s activities relative to their small number.

“The influence of genes outside the nucleus was known to an earlier generation of field ecologists and crop breeders, said Dan Kliebenstein, professor in the UC Davis Department of Plant Sciences and Genome Center and senior author on the paper published Oct. 8 in the online journal eLife. This is the first time that the effect has been quantified with a genomic approach, he said.

Bindu Joseph, a postdoctoral researcher in Kliebenstein’s lab, and Kliebenstein studied how variation in 25,000 nuclear genes and 200 organellar genes affected the levels of thousands of individual chemicals, or metabolites, in leaf tissue from 316 individual Arabidopsis plants.

They found that 80 percent of the metabolites measured were directly affected by variation in the organellar genes — about the same proportion that were affected by variation among the much larger number of nuclear genes. There were also indirect effects, where organellar genes regulated the activity of nuclear genes that in turn affected metabolism.”

Since these genes aren’t transmitted in the ordinary Mendelian fashion through the nucleus, I find it interesting to ask what role these extranuclear genes and their patterns of descent may play in evolutionary processes.

On the other hand, knowledge of these genes also plays a role in current attempts to “treat” mitochondrial genetic diseases through IVF; I say “treat” because, rather than treating a developed individual who already has the disease, the technique actually involves creating embryos from the start without the disease-carrying genes, by replacing the mother’s mitochondria with mitochondria from a third individual, hence the “three-parent” embryos that have been in the news lately. Rebecca Taylor writes more about these techniques here.

Robots in Disguise: First Known Gear Found in Nature

Popular Mechanics reports:Issus. Credit: Malcolm Burrows

” In 2 milliseconds it has bulleted skyward, accelerating at nearly 400 g’s—a rate more than 20 times what a human body can withstand. At top speed the jumper breaks 8 mph—quite a feat considering its body is less than one-tenth of an inch long.

This miniature marvel is an adolescent issus, a kind of planthopper insect and one of the fastest accelerators in the animal kingdom. As a duo of researchers in the U.K. report today in the journal Science, the issus also the first living creature ever discovered to sport a functioning gear. ‘Jumping is one of the most rapid and powerful things an animal can do,’ says Malcolm Burrows, a zoologist at the University of Cambridge and the lead author of the paper, ‘and that leads to all sorts of crazy specializations.’”

The strikingly mechanical nature of the adapatation has found its way into the design debate. I leave this, for the moment, for the reader to ruminate for himself.