One more time:artificial selection =natural selection.

How the 2018 Nobel Laureates in Chemistry Harnessed Intelligent Design

Matti Leisola

I am an enzyme bioengineer, so I greeted with enthusiasm Wednesday’s announcement, noted here already by Doug Axe,that part of the 2018 Nobel Prize in Chemistry went to a fellow enzyme bioengineer. She is Frances H. Arnold,a professor of chemical engineering at Caltech. 

Her accomplishments in the field are impressive, as is the work of her co-winners, whose work also involves bioengineering. The three are indeed deserving recipients. 

There is one point of confusion in descriptions of this year’s prize winners. It’s the talk of “directed evolution.” The Nobel Prize organization itself has encouraged such talk. The official announcement is titled “They harnessed the power of evolution.” It continues:

The 2018 Nobel Laureates in Chemistry have taken control of evolution and used it for purposes that bring the greatest benefit to humankind. Enzymes produced through directed evolution are used to manufacture everything from biofuels to pharmaceuticals.

The New York Times goes on in the same vein:

At first, Dr. Arnold attempted “rational design,” employing logic and knowledge of how proteins function to try to build new enzymes — proteins that act as catalysts for chemical reactions. But enzymes are large, complicated molecules — some consisting of thousands of amino acids — and it is hard to figure out how a shift in one twist of the molecule affects how it works.

In desperation, she said, she turned to evolution.

“I copied nature’s inventions, this wonderful process of evolution, to breed molecules like you breed cats and dogs,” she said.

For this “directed evolution” research, she inserted the gene that produced the enzyme she wanted to study into fast-reproducing bacteria. With mutations of the gene, she could then examine how well variations of the enzyme worked. She chose the one that worked best and repeated the process — just like evolution chooses the survival of the fittest over succeeding generations.

Conflating Artificial and Natural Selection 

What’s the problem? First there’s the conflation of artificial and natural selection. More fundamentally, the term “directed evolution” is a contradictio in adjecto, in the same way the term “wooden iron” is. It obscures the reality that the new enzymes were engineered via intelligent design. We’re called bioengineers for a reason, after all.

The role of the term “directed evolution” is contrasted with “rational design.” This second phrase is also a contradictio in adjecto. The placing of the adjective “rational” in front of “design” implies that design can be wholly non-rational, wholly separate from the work of creative intelligence, of mind. But that is contradictory to all generally accepted definitions of design.

The following excerpt from my essay in the recent anthology Theistic Evolution: A Scientific, Philosophical, and Theological Critique describes the random and designed aspects of the so-called “directed evolution” approach to bioengineering:

Enzymes are widely used for many different applications: in washing powders, food manufacturing, textile industry, animal feed, and chemical production etc. Unfortunately natural enzymes are not always suitable for industrial conditions where high temperatures, extremes of pH and variety of other chemicals interfere with enzymatic reactions. Using the tools of genetic engineering it is possible to modify existing enzymes with various methods. One approach is to randomly mutate the gene coding for a given enzyme. The process is called directed evolution (which is an oxymoron since it connects two opposing terms together). One then seeks to find better functioning mutants among the variants so created. Some amazing results have been achieved with this technique1:

Enzyme activity has been improved.

Thermal and pH stability has increased.

Specificity has changed.

Side activities have improved.

Stability against solvents and oxidants has improved.

In spite of these achievements, the technique has its limitations:

There must be a mutational pathway to the new structure.

One must be able to create a large enough mutant library in order to find the rare positive mutants.

One must have a rapid screening method to detect the rare positive mutants.

Hallmarks of Intelligent Design

In his book The Edge of Evolution biochemist Michael Behe draws upon research on E. coli, malaria, and HIV mutations. From this he calculates the upper limit for a random mutational process in nature at two to three simultaneous mutations in one protein. This is in harmony with Barry Hall’s results with lactase mutations.2 

Bioengineers, including the 2018 Nobel laureates in Chemistry, are demonstrating a way beyond this limit — intelligent design. These brilliantly designed experiments involve mutation rates artificially engineered to occur at 10,000 to a million times the rate typical in nature, carefully selected reaction conditions, the intelligently selected use of genetic engineering tools (tools that are themselves intelligently designed), and the mindful selection of variants towards a desired goal. 

All of these are hallmarks of intelligent design.

For more on the promising field of enzyme engineering, how it demonstrates the limits of natural evolutionary processes and the reach of intelligent design, see Chapter 10 of my recently co-authored book  Heretic: One Scientist’s Journey from Darwin to Design.

Matti Leisola, DSc, is a bioengineer and former dean of Chemistry and Material Sciences at Helsinki University of Technology. An expert in enzymes and rare sugars, he has published 140 peer-reviewed articles and won the Latsis Prize-ETH Zürich. He also served as biotech research director for Cultor, an international biotech company, co-founded the International Society of Rare Sugars, and was the founding editor of BIO-Complexity.

Notes:

Matti Leisola, and Ossi Turunen, “Protein Engineering: Opportunities and Challenges,” Applied Microbiology and Biotechnology 75 (2007): 1225-1232, doi:10.1007/s00253-007-0964-2.

Barry Hall, “The EBG System of E. coli: Origin and Evolution of a Novel Beta-Galactosidase for the Metabolism of Lactose,” Genetica 118 (2003): 143-156.

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.