Water is becoming the new oil.

THE WORLD WILL SOON BE AT WAR OVER WATER
BY JAMES FERGUSSON 

The world is at war over water. Goldman Sachs describes it as “the petroleum of the next century”. Disputes over water tend to start small and local – for instance, with the sort of protests that drought-stricken São Paolo has experienced this year. But minor civil unrest can quickly mushroom, as the bonds of civilisation snap.It is often forgotten that the revolution against Syrian president Bashar al-Assad began this way, when youths of the southern Syrian town of Daraa, angry at the local governor’s corrupt allocation of scarce reservoir water, were caught spraying anti-establishment graffiti. Their arrest and torture was the final straw for the tribes from which the youths came. It was a very similar story in Yemen, whose revolution began in 2011 in Taiz, the most water-stressed city in that country.When we think of Syria now, we cannot see far past the threat posed by Islamists. But Isis, in the end, is a symptom of social malfunction. If order is to be restored, we might do better to start focusing instead on the causes. Then we could perhaps look harder for “soft power” solutions – the restoration of governance and basic services, such as electricity and water supply – rather than for hard power ones, such as missiles and bombs.
1. THE MESOPOTAMIAN WAR As Islamic State’s leaders work to carve out their glorious new state, they have comprehended that political power in Mesopotamia has always rested on the ability to supply its citizens with water. The prosperity of ancient Nimrud, the 7th-century BC ruins that Isis recently bulldozed because they were “unIslamic”, was founded on its irrigation dam across the Tigris. The Sumerian city-state of Ur – the first city, founded in 3800BC – was abandoned by 500BC following a protracted drought and the siltation of the Euphrates.Isis is headquartered at Raqqah, a mere 40km down the Euphrates from the largest reservoir in Syria, Lake Assad. Raqqah’s economy has long depended on the cultivation of cotton irrigated by the reservoir, which was formed by the Russian-assisted construction of the Tabqa dam in 1973, and designed to irrigate some 2,500 square miles of farmland.Last August, Isis fought fiercely for control of the largest dam in Iraq, across the Tigris at Mosul. Its fighters also took over two other dams across the Euphrates, one at Fallujah, the other at Haditha. In all cases, it took American air strikes to drive them off, and the high value the terrorist group places on Mesopotamia’s dams suggests that further offensives against such targets are likely.Even if Isis leaders in Raqqah succeed in holding one of these key pieces of hydro-infrastructure, however, they do not control the headwaters of either the Tigris or the Euphrates, which rise in Turkey. It is the Turks, who have squabbled for 40 years with their downstream neighbours over use of the rivers, who therefore hold the keys to the long-term future of Isis – and the Islamists know it.

2. TURKEY V ISIS Last summer, Isis accused the Turkish government in Ankara, headed by Recep Tayyip Erdogan, of deliberately holding back the Euphrates through a series of dams on its territory, lowering water levels in Lake Assad by a record six metres. Isis was apoplectic.“I pray to God that the apostate [Turkish] government reconsiders its decisions,” a spokesman Abu Mosa reportedly said, “because if they do not reconsider it now, we will reconsider it for them by liberating Istanbul.”Turkey’s dams have given Ankara a vital hold over Isis’s leaders, who, for the present, twitch like puppets on a string. Ankara, it should be said, may not have been wholly responsible for the shrinking of Lake Assad. Local farmers, emboldened by the collapse of governance in Syria, were reported last year to have siphoned off vast amounts of water to irrigate their own cotton plantations. Nature played a role too; there was less than half as much rainfall in the Turkish highlands in the wet season of 2014 as in the previous year.Nevertheless, Turkey’s stranglehold over its downstream neighbours is real – and it is set to tighten further in 2015, with the completion of the controversial Ilisu hydro-dam on the Tigris, which will create a 10 billion cubic metre reservoir just 30 miles north of the Syrian border. The dam is the latest of 22 envisioned under the Southeastern Anatolia Project (or GAP, to use its Turkish acronym), a vast regional development plan that was originally mooted by Kemal Ataturk in the 1930s.The father of modern Turkey could not have foreseen how completely his country’s “blue gold” would one day replace oil as the region’s most important resource. Iraq’s oil industry requires 1.8 billion cubic metres of water a year in order to function at all. Ankara has adopted a canny and forward foreign policy for years now, extending its influence everywhere from Somalia to Afghanistan. What is happening in Anatolia now suggests that “neo-Ottomanism” is not just political posturing: it really is the future for this part of the Middle East.Hydrologists in Sweden recently suggested that by 2040, the volume of water being extracted from the mighty Tigris and Euphrates – rivers that once delineated and sustained the cradle of civilisation – could be so great that they no longer reach the sea.Once the GAP is completed, about half of the water these rivers now carry may never leave Turkey at all. The prediction bodes very ill for the visionaries of Islamic State. Whatever else they may achieve, it is no 1,000-year Reich that they are building in Syria or Iraq.

3. THE YANGTZE PROBLEM There are dozens of potential dam-related flashpoints around the world. The Permanent Court of Arbitration in The Hague, which handles international water disputes, says 263 river basins are contested globally. There are already more than 40,000 large dams around the world. These icons of post-war Western development irrigate millions of square miles of farmland and produce a fifth of the world’s electricity through hydropower.An area the size of California – 0.3% of the world’s total land mass – has been lost to artificial reservoirs since the golden age of dam-building began in the 1950s. The number of major schemes tailed off in the 1990s, as environmental concerns grew and the economic efficiency of the largest projects was called into question. But booming demand has since dramatically revived the industry. New mega-dams are now among the largest and most expensive engineering projects on the planet.The costliest so far is China’s South-to-North Water Diversion Project, a scheme to divert the waters of the River Yangtze via dams, tunnels and three vast canals to the arid north of the country. The project is still only half finished, yet by last year had swallowed more than $79bn (€73bn). Hundreds of thousands of villagers have been forced from their homes by the project. The scheme’s long-term effect on the environment and economy of the south remains uncertain.Far to the south, meanwhile, on the River Mekong, Laos is copying China by building two major dams that could devastate not just the local economies but the lives of its downstream neighbours, Cambodia and Vietnam. The diet of some 50 million people is based on fish caught in the Mekong, which is already the most dammed river in the world.Then there is the Rogun hydro-dam on the Amu Darya in Tajikistan which, when completed, could be 355 metres high: the tallest dam in the world. The possible effect on the Amu Darya worries downstream Uzbekistan, which has responded with sanctions and travel restrictions on the Tajiks.
4. THE CONGO AND THE NILE The most productive hydro-power dam, the Grand Inga, has recently been proposed for the River Congo, 225km south-west of Kinshasa. With a projected price tag of £80bn (€74bn), developers claim it will “light up Africa”. Critics say that the electricity generated will mostly be transmitted to distant cities, and that the continent’s poorest will see little benefit. The cost overruns in this notoriously corrupt part of the world could also end up making the South-to-North China project look cheap.This month, Egypt and Ethiopia signed a treaty over the latter’s half-built Grand Renaissance dam on the Blue Nile, which will be the largest hydro-scheme in Africa when it comes on stream in 2017. Downstream Egypt, whose development has depended on the Nile since ancient times, originally objected so strongly that in June 2013 a meeting of the cabinet of the then president, Mohammad Morsi, was caught on live television discussing ways of destroying the dam, including via covert support for anti-government rebels. Sanity seems now to have prevailed.5. AFGHANISTAN DRIES UP Nato’s recently concluded engagement in southern Afghanistan is not normally cast as a water conflict, although that is largely what it was. Helmand, the most hotly-disputed province, was once one of Afghanistan’s breadbaskets thanks to the Helmand Valley Authority, an irrigation scheme set up in the 1950s by American engineers.But mismanagement of the scheme’s 300 miles of canals, coupled with a period of protracted drought, meant that the area of irrigated land halved between 1979 and 2002. Local tribes, spurred on by the vast profits to be made from the cultivation of poppies, fought over what remained, with the Taliban exploiting the conflict.One of the centrepieces of the HVA was the Kajaki hydro-dam, completed in 1953 by the same US firm that built the Hoover Dam on the River Colorado. The Americans returned in 2001, this time in order to bomb it.Policy changed again in 2006, however, when Nato realised how important the dam was to regional stability. In 2008, in what proved to be the largest set-piece Nato operation of the entire Afghan war, some 5,000 Nato troops fought for six days to deliver by road a new 200-ton turbine to the plant. Seven years on, the turbine, scandalously, has still not been assembled.6. INDIA V PAKISTAN The territorial dispute between India and Pakistan over Kashmir – both the highest and longest-running in the world – is largely about control of the headwaters of the River Indus, on which Pakistan’s agricultural economy downstream has become ever more dependent.There are 200 million people in Pakistan: double the number 30 years ago. Yet Dutch scientists think shrinking glaciers caused by climate change could reduce the Indus by 8% by 2050.India, which has built or proposed some 45 hydro-schemes on the Indus’s upper reaches, insists that flow will never be affected. But Pakistan is as paranoid about India as Isis is about Turkey, with a long track-record of blaming India for social ills at home.The rhetoric of extremists is already hot. Hafiz Saeed, a militant linked to the Mumbai hotel atrocity of 2008, has spoken in the past of India’s “water terrorism”, and campaigned under slogans like “Water flows, or blood”. Could diminishing water supply push these nuclear-armed neighbours towards a new war?

7. ISRAEL V PALESTINE Finally, there is Israel and Palestine, arguably the grand-daddy of all water conflicts. Israel, a state founded on Ben-Gurion’s dream of “making the desert bloom”, diverted the River Jordan half a century ago, east and southwards towards the Negev desert, via a canal called the National Water Carrier.The Dead Sea has lost a third of its surface area as a direct consequence, and the River Jordan of biblical antiquity has become a muddy trickle in a ditch. The reason Israel still occupies the Golan Heights, captured from Syria in the Six-Day War of 1967, is because that is where the Jordan rises.All this has come at the expense of the Palestinians, who accuse Israel of manipulating water supply to suppress them. Some 85% of all the water in the West Bank goes to Israel, according to some estimates. The Palestinian Water Authority says that Israelis consume seven times more water, per capita, than Palestinians: a spur, if ever there was one, for a resumption of the Intifada.Elsewhere in the world, even the hottest conflicts over water supply have been resolved through negotiation. But with the recent re-election of Benjamin Netanyahu, who campaigned on the outright rejection of a two-state solution to the region’s troubles, the prospect of a fairer water-sharing arrangement for Palestine look more remote than ever. 

A simple lifeform?

High Tech, Low Life -- The Amazing Flagellum
David Klinghoffer







As Stephen Meyer puts it in a brief video, the bacterial flagellar motor that Michael Behe spotlighted in  Darwin's Black Box is a marvel of nanotechnology. Yet this miniature motor is found in some of life's humblest organism. Moving up the scale to more complex forms, obviously the wonder increases.

On the other hand, as microbiologist Scott Minnich points out here, the flagellum is so effective at doing its job that if human swimmers could move that fast, we'd be setting some crazy new Olympic records -- 20 body lengths per second, which is to say, on our scale, some 120 feet per second. That's fast.

Dr. Minnich mentions two top Olympic swimmers, Mark Spitz and Michael Phelps. Interestingly, someone  did the math  on Phelps and computed that he swims about 1 body length per second, compared to a gold fish that swims at 4.5 body lengths per second.

So the flagellum is way out of ahead of the fastest human swimmers, and well ahead of a goldfish. It's not the speed alone that's impressive, however, but the incredible micro scale. [Update: Thanks to thoughtful reader Per for a correction here regarding sailfish.]

As we point out in the new hour-long documentary Revolutionary: Revolutionary: Michael Behe and the Mystery of Molecular Machines, the flagellum is just one known molecular machine whose irreducible complexity defies Darwinian explanations but fits well with the hypothesis of intelligent design. Get your copy of Revolutionary now on DVD or Blu-ray!

On origins and the design debate.

Pre darwinian design v. materialistic OOL.

In BIO-Complexity, Meyer and Nelson Debunk DRT
Ann Gauger 

Origin-of-life research has a big problem, and the DRT model purports to solve part of it. In a peer-reviewed paper published this week in BIO-Complexity,  Stephen C. Meyer and Paul Nelson take on DRT. What is DRT, exactly, you ask? Some background will help in explaining.

While DNA carries information necessary to build cells, it performs no chemistry and builds no cellular structures by itself. Rather, the information in DNA must be translated into proteins, which then can carry out the various chemical and structural functions of life. But there is no direct way to convert a given DNA sequence into a protein sequence -- no direct chemical association between DNA nucleotides and amino acids. Some sort of decoding mechanism is needed to translate the information encoded in DNA into protein.

That decoding mechanism involves a whole host of enzymes, RNAs and regulatory molecules, all functioning as an elegant, efficient, accurate and complicated system for copying and translating the information in DNA into a usable form. (For a comprehensive and engaging description of how information is processed in the cell, and how the details of this process have been discovered, see Stephen C. Meyer's  Signature in the Cell.)

The problem is, this decoding system is self-referential and causally circular. Explaining its origin becomes a chicken and egg problem. As it stands now, you need the machinery that translates DNA into protein in order to make the very same machinery that translates DNA into protein. This should give us pause, because causal circularity cannot be explained in purely naturalistic terms. In order to avoid this trap, neo-Darwinian evolution would require the prior existence of another way to specify and carry out protein-like functions in a heritable fashion, but apart from the usual machinery -- DNA, RNA and protein, all three working together.

So when it was discovered that some RNAs could carry out (very limited!) chemical reactions, scientists seeking a purely materialistic explanation for life's origin were thrilled. Perhaps here was the solution to the conundrum. Perhaps RNAs could be both catalysts and heritable information carriers. Perhaps the first living world was RNA-based.

Fast forward to now. Researchers continue to try to design RNAs that can copy themselves, and try to expand the range of chemistries they can carry out. The RNA world, if it ever existed, though, would be a very impoverished place, based on what human designers have been able to produce so far. And the problem of how an RNA world could become a DNA/RNA/protein world would still remain.

Enter the  Direct RNA Templating (DRT) model of Michael Yarus et al. His hypothesis was originally based on the discovery that the activity of one RNA catalyst could be blocked by the presence of the amino acid arginine. From this result Yarus hypothesized that perhaps other RNAs would show an affinity for particular amino acids. In a series of papers he and his coworkers identified other such RNAs. Then, based on statistical analysis,  they argued that these RNAs contained a higher than expected frequency of triplets corresponding to the particular codons or anticodons now used in the modern genetic code to specify the particular amino acid they bound.

But is their analysis correct? Meyer and Nelson carefully examine the claims of Yarus et al. and find them wanting. Inadequate null hypotheses, arbitrary selection of data for analysis, and unrealistic assumptions about prebiotic chemistry are just a few of the problems. Rather than go through their arguments here, I encourage you to read their paper yourself.

Why does it matter? Critics of intelligent design have advanced the DRT model as the answer to the sequencing problem -- how genetic information in RNA (in the hypothetical RNA world) eventually could have been translated into more stable and versatile proteins. Based on the analysis in this paper, however, the sequencing problem has not been solved, even partially. There is no natural affinity between RNAs, amino acids, and codes. And the origin of life remains inexplicable in materialistic terms.

On decanonising scientism.

Lessons from the Wansink Science Scandal

Sarah Chaffee

What pedagogical methods best prepare students to engage with science? Quality science education, especially regarding evolutionary theory, is inquiry-based, not dogmatic. 

Over at the Washington Post, Alan Levinovitz, associate professor of religious studies at James Madison University,  wrote an article reflecting on the recent Brian Wansink science scandal. He comes to the conclusion that science education often errs by omitting instruction about critical thinking. 

Who is Brian Wansink? From the Associated Press:

A prominent Cornell University food researcher resigned after an investigation found he committed academic misconduct, including misreporting data, the school announced Thursday.

Brian Wansink has been removed from all teaching and research positions and will retire at the end of the school year next June, Cornell said in a statement.

Wansink had previously helped update the U.S. dietary guidelines and is known for his research on consumer behavior, which has been widely cited including in articles by The Associated Press.

Cornell says Wansink’s academic misconduct also included “problematic statistical techniques, failure to properly document and preserve research results, and inappropriate authorship.”

Thursday’s announcement comes a day after six more of Wansink’s papers were retracted. The most recent retractions included a 2005 paper that said people eat more when served in large bowls and a 2013 article that said grocery shoppers buy food with more calories when they’re hungry.

Levinovitz describes Wansink’s fall as “painful to watch.” He had written on the professor’s studies in the past, but notes that he no longer trusts any of Wansink’s research: 

Most important, I no longer trust myself. I take pride in being a steely-eyed skeptic, wary of too-good-to-be truths. Yet my critical apparatus was hijacked by Wansink’s apparent altruism and his alignment with my own beliefs about the power of branding…

The State of Science

What does the Wansink ordeal reveal about the state of science? 

“In theory, the scientific method is objective. But in reality, science is produced, interpreted and reported by humans — humans who are fallible, biased and self-interested,” Levinovitz states. 

In the wake of the Wansink scandal, there have been renewed calls for reforming the methods and culture of scientific inquiry: open data to allow for outside verification of results, pretrial registration so researchers can’t sift through results to come up with post hoc conclusions. The intense pressure of academia’s “publish or perish” mantra is no longer seen as an engine of discovery, but rather a possible enemy of honest inquiry.

I agree. Science ought to be subject to more scrutiny. I would also add that biases in science lead to some evidence — such as evidence contrary to evolutionary theory — being excluded from mainstream publications.

“A Big Book of Important Truths”

Professor Levinovitz also wants to reform science education. “When I was a child, scientific knowledge was presented to me as though it came from a big book of Important Truths,” he notes. An approach like that does not prepare citizens to critically evaluate research like Wansink’s. 

“Reforms to the culture of science need to be accompanied by reforms in science education,” says Levinovitz. 

Textbooks should include case studies of how industry funding can skew results. The standard suite of experiments should include at least a few meant to illustrate confirmation bias. Statistical tricks such as post hoc generation of conclusions from a large data set are not difficult to understand, and they should be laid out clearly as cautionary tales.

It is important not only for critical inquiry to be used in evolutionary biology, but also for students to learn about Darwin’s theory and the modern evolutionary synthesis by practicing what it means to weigh the evidence objectively.  Our Science Education Policy calls for teaching the scientific strengths and weaknesses of evolution, noting: “[E]volution should be taught as a scientific theory that is open to critical scrutiny, not as a sacred dogma that can’t be questioned.” Why? Good science avoids dogmatism. 

Beyond Science

This is also worth pointing out: Levinovitz at the end of his article finds himself looking beyond science to the realm of ethics. “STEM education needs to emphasize moral virtues for what they really are: key features of the scientific method,” he writes. 

Wow. 

He concludes this way: 

[R]eflecting on Wansink’s fall, we should remember that what we want to believe — what’s easiest to believe — isn’t necessarily true. Insisting on believing it anyway? That’s the opposite of good science, and good scientists and science educators should lead the fight against it.

Well said. it would be interesting to know whether Professor Levinovitz sees the importance of extending this philosophy to the study of evolution.

On Darwinism's 'simple beginning' problem.

Never mind what your eyes tell you:

New York Times: "We are Sarcopterygian Fish," If You Ignore Contrary Data

Casey Luskin 

Given its prior history of pushing Tiktaalik  as an icon of evolution (now thoroughly toppled), the New York Times has an obvious fascination with the idea that tetrapods (four-limbed vertebrates like frogs, birds, cows, and humans) evolved from fish. Now the Times Science section is at it again with an article titled "Fish's DNA May Explain How Fins Turned to Feet"

The article highlights a recent paper in Nature, reporting on the sequencing of the genome of the coelacanth, a famous fish often called a "living fossil" which is descended from the line of fish that supposedly evolved into tetrapods. Reporter Nicholas Wades writes that "the coelacanth is more closely related to people than to other fish," and he quotes Axel Meyer, an evolutionary biologist who co-authored the study of the coelocanth genome, who says: "Evolutionarily speaking, we are sarcopterygian fish." Sarcopterygians include the lungfish, coelacanth, and "evolutionarily speaking," tetrapods like you and me.

Is Meyer right? According to the NYT, there are two main pieces of relevant evidence. First, the coelocanth has "one gene that is related to those that, in animal species, build the placenta," and "[t]his gene could have been developed by land animals into a way of constructing the placenta."

The real story isn't quite that interesting. According to the Nature paper, a particular region of DNA associated with a Hox gene cluster in the coelocanth genome showed sequence homology with a stretch of Hox gene-related DNA in tetrapods. Hox genes are known to be widely conserved among vertebrates, so the fact that homology was found between Hox-gene-associated DNA across these organisms isn't very surprising. The authors aren't sure exactly what this particular segment of DNA does, though it's probably a promoter region. In mice the corresponding homologous region is associated with Hox genes that are important for forming the placenta. Ergo, we've solved the mystery of how the placenta evolved. Right?

Not really. Again, all that was found was a little homologous promoter region in Hox-gene related DNA in these two types of organisms. Given that we don't even understand exactly what these genes do or how they work, obviously the study offered no discussion of what mutations might have provided an evolutionary advantage. No evolutionary pathway was proposed, or even discussed. So there's not much meat to this story, other than a nice little region of homology between two shared, functional pieces of Hox-gene-related DNA. But of course, such shared functional DNA could be the result of common design and need not indicate common descent or Darwinian evolution.

The NY Times goes on, offering the second piece of evidence: "Another helpful preadaptation is a snippet of DNA that enhances the activity of the genes that drive the formation of limbs in the embryo." When they inserted this enhancer into mice, according to Neil Shubin, "It lit up right away and made an almost normal limb."

What's that he said? "Preadaptation"? Darwinian evolution isn't supposed to have any goals, so whenever I see that term I get suspicious that there's something non-Darwinian going on. So long as we're discussing the coelacanth's supposed "preadaptation" for life on the land, consider what vertebrate paleontologist Barbara Stahl wrote about coelacanth anatomy:

[T]he modern coelocanth shows no evidence of having ... internal organs preadapted for use in a terrestrial environment. The outpocketing of the gut that serves as a lung in land animals is present but vestigial in Latimeria. The vein that drains its wall returns blood not to the left side of the heart as it does in all tetrapods but to the sinos venosus at the back of the heart as it does directly or indirectly in all osteicthyans except lungfishes. The heart is characteristically fish-like in showing no sign of division into left and right sides, and the gut, with its spiral-valved intestine, is of a type common to all fishes except the most advanced ray-fins.

At one time, paleontologists thought that coelocanths, like air-breathing tetrapods, had nasal passages that opened into the mouth cavity, but dissection of Latimeria disroved that idea. Despite their fleshy fins, the coelocanths were no nearer the ancestral stock of land vertebrates than the dipnoans, fishes in which internal nares, or choanae, were also shown to be nonexistent.

(Barbara J. Stahl, Vertebrate History: Problems in Evolution, p. 146 (Dover Publications, 1985).)

The coelocanth's anatomy doesn't make a very compelling case for "preadaptation" for land-based life, but the NY Times story about genetic "preadaptation" isn't very compelling either. Here's what they really found.

An enhancer is a short stretch of DNA that helps to enhance transcription of a gene by serving as an attachment point for proteins that are involved in recruiting RNA polymerase II, and various transcription factors necessary to transcribe the gene into RNA. The study found that an enhancer for a Hox gene involved in fin-development in coelocanths has sequence homology with an enhancer associated with a Hox gene involved in limb-development in mice. When the investigators inserted the coelocanth enhancer into the mouse, the mouse apparently grew what Neil Shubin called an "almost normal limb."

Actually, the technical paper didn't report the growth of any limbs -- whether "almost normal" or totally normal -- but rather only a "limb bud." But that's just a detail -- because even if a limb had grown, this wouldn't mean much for Darwinian evolution.

Again, it's well known that Hox genes are conserved throughout most vertebrates, including fish (like the coelacanth) and tetrapods (like mice). In this case, the genetically homologous enhancer in the two organisms seems to have had a similar, homologous function as well: in coelacanth it enhanced a Hox gene for building fins, and in mice it enhanced a Hox gene for building limbs. This similarity of function and genetic role makes it unsurprising that that these enhancers had a similar DNA sequence. The similarity of function, genetic role, and DNA sequence is thus interesting, but it's not overly surprising to find that it sort of worked when inserted in a mouse.

But what's evolution got to do with any of this? The experiment worked because of functional and genetic similarities between the coelacanth enchancer and the mouse enchancer. Once again, such similarities of sequence and function could be explained by common design and don't necessarily tell us much about common descent.

Inconvenient Immunoglobulin Data

So what are we to make of the NY Times's statement that "the coelacanth is more closely related to people than to other fish" or that "we are sarcopterygian fish"? Well, the article didn't mention one important piece of evidence from the coelocanth genome that contradicts those claims.

According to the  study in Nature, "The fish [coelocanth] is the first vertebrate found to lack genes for immunoglobulin-M [IgM], an almost universal immune-system protein." That's a bit weird, but it gets much weirder. According to the technical paper:

IgM genes cannot be found in coelacanth, despite an exhaustive search of the coelacanth sequence data, and even though all other major components of the immune system are present. Instead, we found two IgW genes; immunoglobulin genes that are found only in lungfish and cartilaginous fish and are believed to have originated in the ancestor of jawed vertebrates but subsequently lost in teleosts and tetrapods.

(Amemiya et al., "The African coelacanth genome provides insights into tetrapod evolution," Nature, Vol. 496:311-316 (April 18, 2013) (internal citations omitted).)

This means that if we were to construct a phylogenetic tree of vertebrates based upon the IgW gene, we would get a bizarre tree that dramatically conflicts with the standard vertebrate tree. To understand why, let's first look at the standard vertebrate phylogeny, shown in the Nature paper:

Figure A: Reprinted from Figure 1, Amemiya et al., "The African coelacanth genome provides insights into tetrapod evolution," Nature, Vol. 496:311-316 (April 18, 2013). Image used under a Creative Commons license, Attribution-Noncommercial 2.5. Usage not intended to imply endorsement by the authors/creators of the image.

This standard phylogeny could be simplified to look something like this:

Figure B: A simplified version of the standard vertebrate phylogeny.

But according to the IgW data, very roughly speaking, the vertebrate phylogeny should look something like this:



Figure C: A very rough sketch of what the vertebrate phylogeny might look like based upon the IgW gene.

Compare Figures B and C. Do you see the difference? In the standard phylogeny (Figure B), tetrapods (like you and me) are much more closely related to the coelocanth or lungfish than we are to ray-finned fish (like the goldfish). But in an IgW-based tree (Figure C), tetrapods should be much more closely related to goldfish than to the coelocanth or the lungfish. That's startling and unexpected -- if you're a proponent of common descent.

How does the Nature paper explain this phylogenetically incongruent data? In the passage I cited above, their explanation is that "immunoglobulin genes that are found only in lungfish and cartilaginous fish and are believed to have originated in the ancestor of jawed vertebrates but subsequently lost in teleosts and tetrapods."

Of course this requires some extremely unparsimonious and unlikely events. Since IgW is found in vertebrates as diverse as lungfish and cartilaginous fish (e.g., sharks), a Darwinian evolutionary view would infer that the gene for IgW was present in the ancestor of all jawed vertebrates. If so, then IgW must have stuck around in vertebrates long enough to end up in the sarcopterygian line. But somehow evolutionary theory must explain why tetrapods and all teleosts lack this gene.

Perhaps the loss of IgW in tetrapods isn't very hard to explain -- maybe IgW was lost in the early stages of the line that branched off other sarcopterygians and led to tetrapods.

But with teleosts, this story is much harder to believe. According to the standard evolutionary account, this ancient group of vertebrates diverged and began to diversify before the sarcopterygians (lungfish, coelocanths, and ultimately tetrapods) branched off. Since lungfish and coelocanths have IgW, somehow IgW was lost in all known teleosts, independently, and after the line that led to sarcopterygians branched off, so that today all teleosts lack this gene.

This highly unparsimonous evolutionary story is the only way (and the way the Nature paper chooses) to explain why teleosts and tetrapods lack IgW, but lungfish and coelacanths don't. A more straightforward and plausible account of vertebrate relationships would suggest a phylogeny (Figure C) that's quite incompatible with the standard vertebrate phylogeny.

No wonder the New York Times decided not to mention this inconvenient data point that has emerged from the coeolocanth genome: it suggests the coelacanth is NOT "more closely related to people than to other fish," and that "we are" -- yes, big surprise -- NOT "sarcopterygian fish."

One Darwinian gatekeeper's journey to the 'dark side'

irreducibly complex and undeniably designed.

To Make a Baby Requires Intelligent Design
Geoffrey Simmons

Like a well-written, trillion-page novel, every micro-step, every macro-step, every twist and turn of our development follows a master plan. Any deviation, at least early on, from the blueprint would be like building a skyscraper and leaving out important parts of a first floor. Trillions of coordinated actions are linked together in time and space to create a human being. Quadrillions of very specific chemical reactions happen in sequence and/or in tandem.

Everything is perfectly timed. Virtually nothing is left to chance. Intelligent design requires intelligent planning.

From a Single Cell

The single cell (a zygote), formed by the union of the egg and sperm, becomes a 15 trillion-cell individual in a matter of nine months with amazing precision and speed. That includes over tens of thousands divisions per second with a greater than 99.99 percent rate of accuracy. By the 16th day the heart starts beating. By 30 days, the embryo will have grown to 10,000 times the size of the fertilized egg. At seven weeks the unborn child is an inch long and has developed all organs (e.g., liver, sex organs, spleen, intestine). At eight weeks, fingerprints and toe-prints can be found and the brain and spinal cord are clearly present. At a specific time, 250,000 neurons (nerve cells) migrate (climb, crawl, swim, slide, squeeze by) every minute to designated places with distinct purpose(s) within the brain. Compared to their size, the distances traveled by some can be compared to humans walking many miles. Noted the 15 trillion will become 75 trillion by adulthood.

At twelve weeks vocal cords show up, but because the lung are still filled with amniotic fluid and not air, a voice and breathing are absent. At four months ultrasound can show the baby sucking its thumbs and playing with its umbilical cord. Between 18 and 20 weeks the senses for pain are mature, virtually the same as they will be at birth. Studies show babies withdrawing their feet in response to irritating stimuli.

A few premature babies at around 23-24 weeks can survive in a neonatal intensive care unit. At 24 weeks, ultrasound can show the baby smiling. At twenty-eight weeks, a baby will track a moving light, such as a flashlight, held against the mom’s belly. Somewhere in this period, the baby learns to recognize her mother’s voice.

Time to Greet the World

When the baby decides it’s time to greet the world, she sends millions of messenger chemicals to the mother’s brain saying, “I’m ready. How about hitting the START button?” Mom’s brain then floods the womb with a different set of chemical messages telling all cells there to start the warm-up process. That mostly means contractions. There’s a shifting and aiming of the baby’s head downward and the placenta is notified to start loosening its grip. Of note, by this time, the uterus is 5 times its usual size, has a capacity of 500 times normal, and weighs in at 15 times heavier. It will return to normal size within a week, but it takes another month or so for complete healing.

The start-up contractions are called false or Braxton Hicks contractions; about this time a small amount of amniotic fluid leaks occurs (“my water broke”). The first contractions are variable in timing and usually mild, but that soon changes to closer timing and increasing intensity (pain). Pressure also comes from the sides of the uterus to line up the baby. An extremely thinned uterus does the pushing.

The baby has to exit to the outside world through the cervix which normally looks a little like a soft, pink bottle cap with a tiny hole in the middle (where the Pap test is done). This opening will slowly dilate to ten centimeters (4.5 inches) before the baby can begin its outward journey.  As it moves, its head fits inside (“engages”) the canal, facing sideways. Sideways is critical. The passageway through the bony pelvis is not wide enough to accommodate our large head (and large brain). FYI: The great apes don’t have this problem. Despite their size, their brains are considerably smaller.

No Room for Experimenting

Four percent of the time, the baby presents feet first or breech. The reason for this is unknown.

The instant the baby passes out of the womb, chemical messages tell the baby’s brain to start the lungs breathing.  There’s no obvious ON switch, START button  or pull cord, but some critical mechanism(s) has to exist. Perhaps, it’s temperature change, air pressure change, and/or the hint of oxygen tickling the baby’s nose. We don’t know, but this messaging is obviously critical. A swat on the butt is more for the movies. If breathing starts too soon, the baby dies of asphyxiation; if too late, the baby incurs brain damage or dies of hypoxia (low oxygen). The decision to start breathing happens in a matter of seconds. It has to be exactly timed. Childbirth has always been this way.

There’s no room here for nature to have experimented.

On occasion, an unborn child will linger part way through the birth canal for hours, even days, especially with the mom’s first pregnancy, yet the baby remains quite stable, without a need to breathe.

By Survival of the Fittest?

At the time of birth, the newborn’s blood, which had been circumventing the lungs for nine months (there was no reason to breathe), must immediately go through lungs to absorb oxygen. There’s a very interesting trick (or change) that happens promptly after birth. A valve-like artery (ductus arteriosus) that was used to bypass the previously dormant lungs (since oxygen came from the mom via the placenta) closes off while the arteries to the lungs become functional.  The lungs’ tissues are ready to roll. The timing has to be exact. The rare baby who survives the non-complete closure of the ductus will need urgent surgery to close off this artery.

The birth of a baby could not have come about by survival of fittest, which is to say, by nature’s experimentation or trial and error. Mutation would have made things more dangerous. Intelligent planning is seen throughout.

Yet more on the Darwinism of the gaps fallacy.

Denis Lamoureux on the God-of-the-Gaps Fallacy
Brian Miller

I previously pointed out the dangers of Denis Lamoureux’s proposed synthesis between Darwinian evolution and religious belief. Today, I will correct his error that arguments for design in life fall into what is referred to as the God-of-the-gaps fallacy. The basic claim is that people of faith, particularly Christians, have often argued that some phenomenon which was not currently understood in nature (e.g., the complex motion of the planets) could only be explained by God’s direct intervention. They were in effect inserting God into the gaps of the current scientific understanding. However, future discoveries eventually demonstrated how natural processes explained the phenomenon, thus obviating the need for God. Therefore, scientists should not make the same mistake today by arguing that many features of life appear designed. For, in the future evolutionary explanations will inevitably explain what was once attributed to a designer. 

This argument appears compelling at first, but it actually demonstrates a misunderstanding of trends in scientific discovery over the past several decades. 

The God-of-the-gaps fallacy has only applied to natural processes related to common matter and energy. It has never applied to life. Living systems and their components represent arrangements of molecules that cannot be comprehended primarily in terms of their physical and chemical properties any more than the arrangement of parts in a car can be understood in terms of the material properties of metal, rubber, and glass. Instead, they can only be fully understood in relation to the purposeful functions they were designed to perform. As a consequence, attempts to explain the origin and development of life purely in terms of natural processes have constantly fallen into the materialism-of-the-gaps fallacy — evolutionary and other materialist narratives that seem plausible at first consistently topple as science advances.  

Origin of Life

The trend is perhaps most pronounced in origin of life research. Advances in organic synthetic chemistry have increasingly demonstrated the implausibility of any undirected process on the early earth producing life’s complex building blocks. And, nearly every step in the development of the first cell appears increasingly intractable as the underlying physics and chemistry are better understood. For instance, the forming of a functional cell membrane had long been assumed to be one of the easiest steps, but it now represents yet another insurmountable hurdle. At an even more foundational level, the thermodynamic challenges have grown increasingly problematic with advances in our understanding of non-equilibrium systems. The obstacles now appear so severe that arguing for a purely materialist account for life’s origin represents a modern day version of the quest for a perpetual motion machine

Evolutionary Narratives

Similarly, attempts to envision evolutionary narratives for the appearance of complex adaptations consistently collapse with advances in our understanding of the underlying biology. For instance, biologists once claimed that they had constructed for the evolution of the vertebrate eye a “detailed step-by-step” description. However, each stage in this cartoonish story proved increasingly implausible with new discoveries in the developmental biology of eye formation. For instance, the undirected origin of the lens requires a series of initial mutations to allocate undifferentiated tissue in front of the photoreceptors. This tissue must have then accumulated more mutations to eventually evolve into a fully functional lens. However, the tissue’s first appearance would have severely degraded the animal’s vision, so the  early mutations would have been strongly selected against and quickly removed from the population. 

In addition, the lens would not have become even marginally functional until a complex network of developmental genes emerged to complete its formation. Such a feat would have required hundreds of coordinated mutations, not to mention numerous changes beyond the developmental network, yet the allowable time would have been sufficient for only two or three,even if negative selection were ignored. Therefore, accumulating even a tiny fraction of the needed changes in a feasible timeframe would have been next to impossible. Other evolutionary scenarios for major transformations also fail upon similar analyses. Those which seem plausible only do so because the underlying biology is not well understood, or simply ignored, and rigorous mathematical calculations of required time scales have been avoided.  

Fossil Record

Evolutionary theory has also faced increasing challenges from the fossil record. Even if one assumed that common ancestry were true, the timescale allowed by the record for the appearance of new complex innovations has typically decreased to within geological instances. In addition, once a species appears, it remains essentially the same throughout its tenure on earth. This pattern is most clearly seen where the fossil record is most complete. Copious documentation of these trends was collected by Walter ReMine in his book The Biotic Message. One particularly illustrative example is from Derek Ager’s The Nature of the Stratigraphical Record (Ager, pp. 16-17, as cited in ReMine, p. 314):  

Peregrinella … is one of the most distinctive brachiopods in the whole record and it has internal structures which make it clear that none of the abundant brachiopods in the strata above or below could possibly be classified as even distant relations. …. In other words, we have fossils that just suddenly appear around the world at one moment in geological history and ‘whence, and whither flown again, who knows’? … the Mesozoic brachiopods are now very thoroughly documented in every stage and the relations of these large and distinctive forms can hardly have been missed.

The most dramatic conflict between evolutionary theory and reality is the sudden appearance of new animal phyla in the Cambrian explosion. The only cogent attempt to explain this event was presented by paleontologist Charles Marshall and his colleagues. They recognized that the transformation of body plans required the rewiring of the genetic networks which controlled the animals’ embryological development. They also understood that such changes were impossible in modern organisms. In response to these facts, they proposed that animals ancestral to each phyla had genetic networks of a completely different nature from today in that they were far more malleable. As a result, animals could transform dramatically though alterations in these networks without harm. After sudden changes occurred in each branch of the tree, the genetic networks in every phylum uniformly transformed into the unchangeable forms we see today. 

The charm of this model is that it is almost completely untestable since it revolves around groups of organisms which left no trace in the fossil record. It also has to make several rather dubious ad hoc conjectures which could never be verified. However, it does rely on one key assumption which can be studied. Namely, the model presupposes that the development of a new phylum of animal does not require large numbers of new genes, and that that claim has been disproven. Consequently, the fact that enormous amounts of information appeared suddenly in the origin of most animal phylapoints clearly to intelligent design since its production is only possible through a mind. 

Most design critics ignore the data mentioned above and instead attempt to defend evolutionary theory by using groups of organisms where the evidence is considerably less complete and atypical (e.g., whale series). In these cases, the gaps in evolutionists’ knowledge provide room for their imaginations to project their assumptions unto the data. Namely, they infer that groups of species/genera are connected through the gradual branching of an evolutionary tree. The challenge is that the presumed tree has no basis in reality. Even common icons such as the whale series do not represent clear ancestor-descendant relationships, but each “transitional link” is simply assumed to reside on a branch of a hypothetical tree near other links on neighboring branches. The animals are believed to be closely related due to similarities in their traits. The problem is that mounting evidence has demonstrated that similarities of every type between different groups of organisms are not reliable indicators of common ancestry. For, the similarities do not imply a consistent evolutionary tree engineer or computer programmer implementing common design modules to meet similar goals. 

Imperfection-of-the-Gaps Fallacy

Another error perpetrated by many evolutionists comes when they encounter some feature of life where the design logic is not immediately obvious. They often claim that such features represent examples of poor design which no competent engineer would have created. Such claims have constantly fallen into the imperfection-of-the-gaps fallacy. The perception of poor design simply reflected a lack in understanding of the underlying biology or ignorance of engineering principles. As biologists or engineers more carefully studied the features, they consistently came to recognize that they represented exceptional design.For instance, biologists in the 19th century identified dozens of what were then believed to be useless organs in the human body. Nearly all have since been shown to be fully functional. Recent examples include the appendix, tonsils, and the tail bone (coccyx). Other refuted examples of poor design include many examples of junk DNA, the backwards wiring of the vertebrate eye, the laryngeal nerve, the panda’s thumb, and pelvic bones in whales. Some examples of currently suboptimal design might exist due to their having degraded over time from deleterious mutations, but such examples no more refute the argument for design in life than rust on a car argues for it being the product of a tornado moving through a junk yard. In reality, the more biology and engineering advance, the more the evidence for design in life increases.     

False Understanding of Nature

Denis Lamoureux’s invoking the god-of-the-gaps argument reflects a false understanding of nature. He conceives of the universe as a well-designed clock that should not need continuous rewinding. A more accurate metaphor is that the universe is like a musical instrument that was designed to interact with its designer. Specifically, our universe was wonderfully engineered to sustain life, but it was also designed to later manifest infusions of information in the origin of the first cell and in the later appearance of complex innovations. This choice for the structure of the cosmos has one particularly important advantage. If the universe were designed to generate and radically transform life, the information required for the first cell and later innovations would have needed to have been built into the laws of physics. The laws would have then been so complicated and intractable that the development of science would have been impossible. 

Lamoureux laments that people of faith would desire to construct sophisticated arguments from science to demonstrate the existence of God. In one sense he has a point. The evidence from life for an intelligent cause is so clear that anyone should recognize it with little effort. Unfortunately, typical science education often conditions the mind to suppress that reality. Attempting to see design then becomes like an art patron who lost nearly all of his or her vision attempting to appreciate an impressionist painting from a distance. The rigorous design arguments function analogously to high-powered glasses that help restore normal vision. Naturally, people who have completely lost their sight or the desire to see altogether will not appreciate such assistance. However, they should not attempt to rob others of the opportunity