Primate phylogeneticists out of their tree?

Primate Phylogenetics Researchers Swinging from Tree to Tree
Casey Luskin

A recent article on ScienceDaily, titled "A New Evolutionary History of Primates," claims that by combining genetic data from 54 genes (totalling 34,927 base pairs) from a variety of primates, researchers have created "[a] robust new phylogenetic tree" which "resolves many long-standing issues in primate taxonomy." That sounds great--until you read the fine print. The paper used dozens of genes or "large-scale sequencing" to create the phylogeny--a method which is designed to smooth over conflicts between trees based upon individual genes. This method fails to test whether individual genes paint a consistent picture of common descent. Moreover, even after using this method, not everything about the tree is neat and tidy. Even when using many genes to construct the tree, the paper reports there were a variety of potential sub-trees which conflicted with one another:

However, greater frequency of phylogenetic inconsistencies or unresolved nodes occur in these subset trees, compared with the entire concatenated data set.

(Perelman et al., "A Molecular Phylogeny of Living Primates," PLoS Genetics, Vol. 7(3):e1001342 (March, 2011) (internal figure citations removed).)

Indeed, such phylogenetic inconsistencies between different phylogenetic trees are not uncommon at all, particularly in important parts of the purported primate tree. While this paper used methods that smoothed over conflicts between trees, another recent paper found primate phylogenetic data that pointed in opposite directions. A recent article on ScienceDaily, titled "Genetic Archaeology Finds Parts of Human Genome More Closely Related to Orangutans Than Chimps," stated:

In a study published online in Genome Research, in coordination with the publication of the orangutan genome sequence, scientists have presented the surprising finding that although orangutans and humans are more distantly related, some regions of our genomes are more alike than those of our closest living relative, the chimpanzee.
Of course this finding is "surprising" because it contradicts the phylogeny preferred by most evolutionists. The ScienceDaily article noted: "[I]n about 0.5% of our genome, we are closer related to orangutans than we are to chimpanzees ... and in about 0.5%, chimpanzees are closer related to orangutans than us," and the paper cited concluded:

Our analyses find that for ~0.8% of our genome, humans are more closely related to orangutans than to chimpanzees.

(Asger Hobolth et al., "Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection," Genome Research, Vol. 21:349-356 (2011).)

Since humans are typically said to be most closely related to chimps, this data conflicts with the standard supposed tree. As discussed here, the basic problem is that one gene (or portion of the genome) gives you one version of the tree, while another gene (or portion of the genome) gives you a very different version of the tree. This leads to discrepancies between molecule-based trees, wherein DNA data fails to provide a consistent picture of common ancestry. (We've discussed a number of such examples lately, such as here, here, and here. Jonathan M. also cites some discordant data pertaining to human/chimp phylogenetics here.)

0.8% of our genome might not sound like a lot, but that equates to over 20 million base pairs. That's means that over 500 times more raw genetic information than was used in the PLoS Genetics paper (to purportedly create a "robust new phylogenetic tree") is supposedly pointing in the wrong phylogenetic direction. Perelman et al.'s paper in PLoS Genetics could only find a "robust new phylogenetic tree" after using methods that are designed to avoid this problem and ignore conflicts between trees. That might sound good, but their methods are wholly assuming, rather than testing, common descent.

That brings us to the final point of this discussion. In the end, molecular trees are based upon the sheer assumption that the degree of genetic similarity reflects the degree of evolutionary relatedness. One paper makes this assumption explicit:

molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the 'molecular assumption.' ... For historians and philosophers of science the questions that arise are how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central ...

(Jeffrey H. Schwartz, Bruno Maresca, "Do Molecular Clocks Run at All? A Critique of Molecular Systematics," Biological Theory, Vol. 1(4):357-371, (2006).)

Clearly this assumption fails when different genes paint contradictory pictures of evolutionary relationships. But are there other mechanisms that can explain DNA similarities besides inheritance from a common ancestor? As explained here, one equally good explanation for the reason that genetic similarity is continuously being found in places both predicted, and unpredicted, by common descent, could be common design.

The Watchtower Society's commentary on the coming day of Jehovah.

The Day of Jehovah—A Vital Theme:
“THE great day of Jehovah is near. It is near, and there is a hurrying of it very much.” (Zephaniah 1:14) God’s prophets time and again warned of the approaching day of Jehovah. Usually, they pointed out how its coming should affect people’s daily life, their morals, and their conduct. Urgency was always attached to their proclamations. If you had heard these messages with your own ears, how would you have reacted?

2 In reading the 12 prophets, you will find that they all, directly or indirectly, spoke of the day of Jehovah.* Thus, before considering in the following chapters the valuable information that these prophets delivered, think of the recurring theme: the day of Jehovah. Six of the prophets directly used that expression or similar terms. Joel graphically described “the great and fear-inspiring day of Jehovah.” (Joel 1:15; 2:1, 2, 30-32) Amos told the Israelites to get ready to meet their God, for the day of Jehovah would be one of darkness. (Amos 4:12; 5:18) Later, Zephaniah spoke the words quoted in paragraph 1. And near the time of the destruction of Jerusalem, Obadiah warned: “The day of Jehovah against all the nations is near.”—Obadiah 15.3 You will also see that two prophets who were sent to the Jews after their return from exile used similar expressions. Zechariah told of the day when all nations coming against Jerusalem would be annihilated. He described vividly what would take place on “one day that is known as belonging to Jehovah.” (Zechariah 12:9; 14:7, 12-15) And Malachi alerted God’s people to the coming of “the great and fear-inspiring day of Jehovah.”—Malachi 4:1-5.4 Though not using the expression “the day of Jehovah,” the others of the 12 alluded to that day. Hosea talked of Jehovah’s settling accounts with Israel and later with Judah. (Hosea 8:13, 14; 9:9; 12:2) These messages often related to what Jehovah did back in those days. For example, Jonah proclaimed God’s judgment on Nineveh, and Micah described what would happen when God acted against rebellious peoples. (Jonah 3:4; Micah 1:2-5) Nahum promised that Jehovah would take vengeance on His adversaries. (Nahum 1:2, 3) Habakkuk cried out for justice and described “the day of distress.” (Habakkuk 1:1-4, 7; 3:16) Some messages in these books definitely pointed to developments that would involve true Christians. For instance, Haggai, one of the postexilic prophets, foretold the rocking of the nations. (Haggai 2:6, 7) The apostle Paul quoted from the words of Haggai 2:6 to urge Christians to be in a fit condition when God removes the symbolic wicked heaven.—Hebrews 12:25-29; Revelation 21:1.
THE DAY OF JEHOVAH—WHAT IS IT?
5 You have good reason to wonder what the day of Jehovah will be like. You may ask, ‘Does the day of Jehovah have any bearing on how I live now and on my future?’ As the prophets indicated, the day of Jehovah is a period when Jehovah acts against his enemies to execute judgment, a day of battle. That fear-inspiring day will likely be a day of celestial phenomena. “Sun and moon themselves will certainly become dark, and the very stars will actually withdraw their brightness.” (Joel 2:2, 11, 30, 31; 3:15; Amos 5:18; 8:9) What will happen on the earth, where we live? Micah stated: “The mountains must melt under [Jehovah], and the low plains themselves will split apart, like wax because of the fire, like waters being poured down a steep place.” (Micah 1:4) This description may be figurative, but we can conclude from it that God’s acts will bring disastrous effects on the earth and its inhabitants. Not on all humans, though. The same prophets pointed to abundant blessings for those who “search for what is good” and thus keep living.—Amos 5:14; Joel 3:17, 18; Micah 4:3, 4.

6 Others of the 12 prophets painted more graphic pictures of the day of Jehovah. Habakkuk vividly portrayed how Jehovah will smash “the eternal mountains” and bring low “the indefinitely lasting hills,” fitting representations of human organizations, which might seem enduring. (Habakkuk 3:6-12) Yes, the day of Jehovah “is a day of fury, a day of distress and of anguish, a day of storm and of desolation, a day of darkness and of gloominess, a day of clouds and of thick gloom.”—Zephaniah 1:14-17.
7 Imagine what a scourge will come upon those fighting against God! “There will be a rotting away of one’s flesh, while one is standing upon one’s feet; and one’s very eyes will rot away in their sockets, and one’s very tongue will rot away in one’s mouth.” (Zechariah 14:12) Whether this vision will be fulfilled literally or not, you can tell that it portends tragedy for many. At the very least, the tongues of God’s enemies will rot in the sense that their defiant speech will be silenced. And any vision of taking unified action against God’s people will be blurred.
WHY A GOD OF LOVE ACTS
8 You may have heard people ask: ‘How can a loving God bring such a disaster upon his enemies? Does God have to wreak havoc on the earth? Did not Jesus urge continuing to love even enemies and thus proving to be sons of the Father in the heavens?’ (Matthew 5:44, 45) In response, you might direct attention to the very beginning of mankind’s troubles. God created the first human couple in his image and likeness—they were perfect. Yet, they introduced sin and death into the human family and thus into our life. They took sides with Satan the Devil on the issue of who has the supreme right to rule mankind. (Genesis 1:26; 3:1-19) Over the centuries, Satan has tried to prove that if humans are given an incentive to do otherwise, they will not serve Jehovah. You know that Satan has failed. Jesus Christ and many other servants of Jehovah have kept integrity to God and have shown that they serve him out of love. (Hebrews 12:1-3) Can you not think of many by name who are thus serving God loyally?

9 Moreover, you are involved in this issue that will end in Jehovah’s eliminating wickedness. For example, as you read these 12 books, you will note that some of the prophets drew attention to the luxurious lifestyle of people who were neglecting the worship of Jehovah. The prophets admonished God’s people to ‘set their heart upon their ways’ and to transform their lives. (Haggai 1:2-5; 2:15, 18; Amos 3:14, 15; 5:4-6) Yes, the prophets were showing the people how to live. Those who accepted that exhortation showed that Jehovah is their Sovereign, thereby proving Satan a liar. Jehovah will prove loyal to such ones when he annihilates his enemies.—2 Samuel 22:26.10 There is another reason for God to act. Turn your attention back to the eighth century B.C.E. when Micah prophesied in Judah. Speaking as if he were the nation, he likens the situation to a vineyard or an orchard after the harvest, with no leftover grapes or figs. That was how it was in Judaean society, where upright ones could hardly be found. Israelites were hunting their fellow citizens, lying in wait to shed blood. Their leaders and judges were out for selfish gain. (Micah 7:1-4) If you lived in that kind of situation, how would you feel? Likely, you would feel compassion for the innocent victims. Thus, how much more Jehovah feels for the oppressed! Today Jehovah scrutinizes mankind. What do you think he finds? Oppressors are viciously taking advantage of others and violently attacking their neighbors. As for loyal ones, they are relatively few compared with the world population. But we need not despair. Out of love for the victims, Jehovah will render justice.—Ezekiel 9:4-7.
  11 Clearly, Jehovah’s day means destruction for his enemies and deliverance for those who fear and serve him.* Micah foretold that nations would stream to the mountain of Jehovah’s house, resulting in worldwide peace and unity. (Micah 4:1-4) Back in that time, did the fact that the prophets were proclaiming the day of Jehovah make any difference in people’s lives? For some, it did. Recall that when Jonah proclaimed a judgment against Nineveh, the violent, wicked inhabitants of that city “began to put faith in God” and “turned back from their bad way.” As a result, Jehovah refrained from causing calamity then. (Jonah 3:5, 10) The message about the impending day of Jehovah’s judgment did affect the lives of the Ninevites!
 HOW DOES THAT DAY AFFECT YOU?
12 ‘But those prophets lived centuries ago,’ someone might object. ‘What do their messages about Jehovah’s day have to do with me?’ Granted, those prophets lived many years even before Jesus’ birth, yet we should consider how their words about Jehovah’s day are relevant in the 21st century. What practical benefits can we derive from what they said about Jehovah’s great day? There is a key to seeing the relevance and benefiting from their message. It is our recognizing that the prophets warned of Jehovah’s day against Israel, Judah, surrounding nations, and certain world powers of the day.* The point is that such prophecies were fulfilled! The Assyrians did invade Samaria, Judah was desolated in 607 B.C.E., and the surrounding hostile nations were soon devastated. Eventually, the Assyrian and Babylonian world powers fell, all in fulfillment of specific prophecies.
13 Now turn your thoughts to the day of Pentecost 33 C.E., long after many of those prophecies saw their first fulfillments. On that day, the apostle Peter applied Joel’s prophecy to the pouring out of God’s holy spirit. Then Peter quoted from the book of Joel: “The sun will be turned into darkness and the moon into blood before the great and illustrious day of Jehovah arrives.” (Acts 2:20) This shows that there would be still further fulfillments of the prophecies about the day of Jehovah. As for Joel’s prophecy, it had a second fulfillment in 70 C.E. when the Roman army destroyed Jerusalem, certainly a time of darkness and blood.
  14 However, Joel’s prophecy and other prophecies about the day of Jehovah are yet to have a final fulfillment, which applies to us living in the 21st century. How so? Peter admonished Christians to keep “close in mind the presence of the day of Jehovah.” The apostle went on to say: “There are new heavens and a new earth that we are awaiting according to his promise, and in these righteousness is to dwell.” (2 Peter 3:12, 13) No new heavens (a new theocratic government) with a new earth (a society of righteous people under that government) was established right after the destruction of Jerusalem in 70 C.E. So the prophetic words about the day of Jehovah must have another fulfillment. Yes, these prophecies concern us today, who are living in “critical times”!—2 Timothy 3:1.

15 The combined description of Jehovah’s day as presented in these 12 Bible books makes us think of Jesus Christ’s words: “There will be great tribulation such as has not occurred since the world’s beginning until now, no, nor will occur again.” He said that “immediately after” the beginning of that great tribulation, “the sun will be darkened, and the moon will not give its light, and the stars will fall from heaven, and the powers of the heavens will be shaken.” (Matthew 24:21, 29) This helps us to pinpoint the timing of the day of Jehovah. It is just ahead. The Scriptures indicate that the great tribulation will destroy “Babylon the Great,” the world empire of false religion. Then, as the climax of the great tribulation, Jehovah’s day will wipe God’s enemies off the face of the earth.—Revelation 17:5, 12-18; 19:11-21.16 Jehovah’s Witnesses have discerned the nature of fulfillments of prophecies about Jehovah’s day. Often and in various ways, apostate Jerusalem, renegade Samaria, the hostile Edomites, the violent Assyrians, and the Babylonians prefigured aspects of false religion. All such religion will be destroyed in the initial phase of the great tribulation. In the following “great and fear-inspiring day of Jehovah,” her political and commercial lovers will meet their end.—Joel 2:31.
 17 Because the judgment messages apply mainly to false religion, some Christians might feel that they will not be affected by the fulfillment of these prophecies. However, what Amos told the Israelites has practical value to all: “Woe to those who are craving the day of Jehovah!” Some Israelites in Amos’ day thought that Jehovah’s day would mean only blessings for them, believing that it would be the day when God acts for his people. They even craved that day! To self-conceited ones, though, the day of Jehovah would “be darkness, and no light,” Amos continued. Yes, those Israelites were on the receiving end of Jehovah’s wrath!—Amos 5:18.

18 Amos then described what would happen to those who were craving the day of Jehovah. Think of a man who flees from a lion and ends up meeting a bear. Running away from the bear, he takes refuge in a house. Panting for breath, he closes the door behind him and leans on the wall, only to be bitten by a snake. In a way, that is the destiny of the ones who are not really ready for the day of Jehovah.—Amos 5:19.
19 Do you see the practical value this account might have for you? Recall that Amos was directing his words to people who were in a dedicated relationship with God. Still, there were things about their actions and attitudes that needed adjustment. Is it not worthwhile to examine your life to see whether you are proving yourself ready for that vital day or whether some adjustments are in order? How can you prove that you really are ready? Obviously, it is not by building a shelter, storing basic food items, learning how to purify water, or stockpiling gold coins, as some survivalists have done. “Neither their silver nor their gold will be able to deliver them in the day of Jehovah’s fury,” says Zephaniah. So being ready would not depend on the storing up of material items. (Zephaniah 1:18; Proverbs 11:4; Ezekiel 7:19) Rather, we have to be alert spiritually and live day by day as ones who are ready. We need the right attitude—and actions to match. Micah said: “As for me, it is for Jehovah that I shall keep on the lookout. I will show a waiting attitude for the God of my salvation.”—Micah 7:7.
  20 If you have this waiting attitude, you will give evidence that you are ready, on the lookout for the day of Jehovah. You will not be concerned about the date on which that day may come or how long you have waited for it. All the prophecies regarding that day will be fulfilled in Jehovah’s due time and will not be delayed. Jehovah told Habakkuk: “The vision is yet for the appointed time, and it keeps panting on to the end, and it will not tell a lie. Even if it should delay [from a human standpoint], keep in expectation of it; for it will without fail come true. It will not be late [from Jehovah’s viewpoint].”—Habakkuk 2:3.
 21 In this book, you will learn how you can show a waiting attitude for the God of salvation. What benefits can you expect? Well, the focus will be on a part of the Bible that may be somewhat unfamiliar to you—the 12 so-called Minor Prophets. Hence, there will be stimulating insights. For example, in Section 2, you will consider how to “search for Jehovah” and keep living. (Amos 5:4, 6) Based on these 12 books, you might discern how to get to know Jehovah better and sharpen your view of serving him, even in expanded ways. With help from these prophets, you will doubtless deepen your understanding of his personality. In Section 3, you will see more clearly what Jehovah expects of you in your dealings with your family members and others. That can help you to be ready for his great day. Finally, in Section 4, you will look into the prophets’ advice on what your attitude should be as Jehovah’s day draws nearer, learning, too, how your Christian ministry may be impacted. No doubt, you will be thrilled as you consider the prophets’ message about what your future can be like.
22 Do you recall the urgent words of Zephaniah quoted at the outset of this chapter? (Zephaniah 1:14) His message affected the life of young King Josiah. When he was but 16 years of age, Josiah started to seek Jehovah. When he turned 20, he set out on a campaign against idol worship, in line with Zephaniah’s encouragement to the people of Judah and Jerusalem. (2 Chronicles 34:1-8; Zephaniah 1:3-6) Has the warning about the day of Jehovah touched your daily life as much as it did Josiah’s?

On the periodic table's case for design.

Rare Earth Elements and Intelligent Design
Evolution News | @DiscoveryCSC

Can we explain human technology merely by supernova explosions and blind chance? Some do. But in rare earth elements, we find hints of a better explanation.  Science Magazine posted a look at the so-called “rare earth elements” of the periodic table. Consider some design implications of these elements. Introducing the rare earth elements (REEs), Thibault Cheisson and Eric J. Schelter call them “Mendeleev’s bane, modern marvels.”

The archaeological three-age system (Stone, Bronze, and Iron) organizes the history of humankind according to the central role of metals in technological evolution. From antiquity to the modern day, the exploitation of metals has required technologies for their mass extraction and purification, creating strategic importance for mineral deposits and metallurgical knowledge. Unlike other resources, metals are relatively amenable to recycling and to the creation of circular supply chains. This scenario is evident in historical developments for Fe, Cu, Al, Ti, Zn, Ni, and Sn with recycling rates representing between 15 and 70% of the current usage for those metals in the United States and the European Union. However, in recent decades, new technologies have emerged that rely on metals of previously limited use: lithium, cobalt, and the rare earth (RE) elements, among others. Rare earths are finding increasing use in communications — and display devices, renewable energy, medicine, and other practical applications that affect daily life. In this Review, we examine the past and present separation methods that have developed REs into an industrial sector, with a focus on recent advances.

Rare Earths and Chemistry

As Evolution News touched on in January, Dmitri Mendeleev was the key player in describing a natural pattern among the elements that led to the modern periodic table. In his day, only six of the rare earth elements were known. His belief in an orderly universe led him to predict in 1869 that elements in the gaps would be found — as indeed they were  — where he only had question marks. Cheisson and Schelter call these REEs “Mendeleev’s bane” because they frustrated his scheme.

  To accommodate some of these troublesome elements, Mendeleev himself examined and confirmed their trivalent natures in oxides (RE2O3), materials that were initially assumed to be divalent. In the latter iteration of his Natural System of the Elements, Mendeleev tried to accommodate the known REs in analogy to the d-block metals, but this placement led to inconsistencies. Ultimately, Mendeleev never successfully set the REs in his periodic system, a frustration that may have contributed to his shift in research interest away from the periodic table after 1871. Without easily discernable periodic trends, and owing to the limited characterization techniques of the time, close to 100 erroneous new RE claims were made during the last part of the 19th century. By 1907, all REs had finally been isolated….

   In spite of these challenges, Mendeleev stuck to his conviction that order would persist. 1907 was the year of Mendeleev’s death, so he had been partly vindicated by the time the REEs were found. Some of the REEs were fit into an “f-block” in the periodic table, consisting of two expanded rows called the lanthanide series (elements 58 to 71) and the actinide series (elements 90 to 103). This maintained the periodicity of the bottom two rows of the table by adding 14 elements between lanthanum-57 and hafnium-72, and 14 elements between actinium-89 and rutherfordium-104 (elements above 94 being artificially created in the atomic age). Specifically, “The REs are a family of 17 metallic elements formed by the group III (Sc, Y) and the lanthanide series (La–Lu).”

Considered to be metallic, they are called “rare earths” not because they are all geologically scarce, but because they are hard to isolate. “Chemically, REs demonstrate very similar properties with the prevalence of the +3 oxidation state under ambient conditions, a large electropositivity, and kinetic lability,” the article explains. These factors made them a bane to poor Mendeleev in the 19th century, but we know much more about them now, after years of perfecting techniques to isolate them. Their difficult identification provides a first take-home on rare earths: they were predicted, and eventually discovered, because of a man who believed in an orderly system of chemistry.

Rare Earths and Biology

Life uses comparatively few of the 103 natural elements. Most of them are abundant on the earth. The big four are carbon, hydrogen, oxygen, nitrogen. Next in line, according to David Nguyen at Sciencing, are seven other major elements, phosphorus, sulfur, sodium, chlorine, potassium, calcium, and magnesium, making up about 3.5 percent of our bodies. The last 0.5 percent consists of the 13 trace elements, iron, iodine, manganese, molybdenum, selenium, silicon, tin, vanadium, boron, chromium, cobalt, copper, and fluorine. Despite their minor appearance by volume, “living things would not be able to survive without trace elements,” Nguyen says. So far, that’s 24 of the 94 naturally occurring chemical elements to be essential for the human body.

Tin, by the way? Really? It is found in our tissues, but there is no evidence it has any essential biological function at this time, says the Agency for Toxic Substances and Disease Registry. Search the Internet for Search the Internet for the body’s need for trace amounts of cobalt, chromium, silicon, and vanadium. It’s quite fascinating. Silicon, for instance, is used in our balance organs, and cobalt is used to absorb and process vitamin B12 and repair myelin around nerve cells.

In any event, one cannot always discount an element’s importance by its absence in the body. Not that long ago, scientists identified bromine as a vital element. It doesn’t abide in the body, but takes part in essential processes during the construction of collagen. “Without bromine, there are no animals,” concluded scientists at Vanderbilt University in 2014. They call it the 28th essential element.

Do We Need Them?

his brings us to REEs and biology. Do we need them? Do we rely on them? Cheisson and Schelter spend most of their article discussing the historical progress of isolating REEs. But then, they describe a new, young field of research looking into this question:

      Rare earths are used extensively in medicine, especially as imaging agents. But until recently, they were believed to have no natural, biological importance. Surprisingly, Jetten, Op den Camp, Pol, and co-workers reported in 2014 an essential dependence of methanotrophic bacterium on LREs [“light” rare earths, belonging to the Cerium group]. They rationalized this requirement by the replacement of the generally encountered Ca2+ cation by a LRE3+ cation in the active site of the methanol dehydrogenase (MDH) enzyme (61, 62) (Fig. 3A). Following that discovery, RE-dependent bacteria have been found in many environments and have initiated a new field of research.

      t’s too early to say if humans need rare earths, but now that bacteria — the supposedly most primitive life forms on earth — depend on some of them, the possibility exists that REEs will prove to be vital to all life on earth, perhaps in indirect ways. “Without doubt, these confounding elements will continue to provide surprises and opportunities for the progress of humankind,” the authors say.

Rare Earths and Applied Science

It’s only recently that rare earths have become vital to modern engineering. Now, they are eagerly sought elements for computers, cell phones, “communications — and display devices, renewable energy, medicine, and other practical applications that affect daily life.” Ions of yttrium and lutetium, for instance, have become useful for identifying and treating cancer. We rely on REEs when we use cell phones and computers and TV sets. While it is true that humans got along fine without REEs during the Stone Age, Bronze Age, and Iron Age, how much richer our lives have become recently because of the availability of these elements.

Rare Earths and Geology

Essential elements cannot just be part of a planet’s makeup. They have to be accessible at the surface. Astronomers say that all the elements heavier than iron-26 had to come from supernovae. What are the chances that sufficient quantities of heavier elements, including the cobalt, copper, zinc, bromine, and molybdenum in our bodies, and potentially the REEs that give humans technological opportunities, would have arrived at the sun or earth from a nearby supernova? What are the chances that they would percolate up to the crust from a molten planet during its formation? These sound look good questions for design scientists.

Rare Earths and Cosmology

The same questions apply to other stars and planets. Astrobiology is big these days: NASA tries to look for life beyond the earth. They look for habitable zones around other stars, and get excited when earth-size planets appear to orbit a star at a radius that allows the existence of liquid water. They try to identify biomarkers such as methane or oxygen in an exoplanet’s atmosphere. Many astrobiologists feel it is sufficient to “follow the water,” even speculating that life might exist in subsurface oceans of moons in the outer solar system, like Europa at Jupiter and Enceladus at Saturn. Water is remarkably well-suited for life, as Michael Denton has written in his book, The Wonder of Water.We know, however, that earth life needs far more than H and O. What about the other 26 essential elements? And what about those rare earths? Even though they are apparently not essential for life, did an intelligent creator supply those on the surface of our planet with the foreknowledge that designed beings would someday make good use of them?

Rare Earths and Rare Earth

In 2000, Ward and Brownlee published a controversial book, Rare Earth: Why Complex Life Is Uncommon in the Universe. At a time when most scientists assumed there must be millions of complex civilizations in the Milky Way alone, the authors rained on their parade, arguing that the requirements for complex life are so stringent, living worlds like ours could be rare exceptions — perhaps unique. 

This brief look into rare earth elements may provide additional support for their rare earth hypothesis. The more stringent the requirements, the better the evidence for design. REEs offer a new generation of chemists, biologists, geologists, physicists, engineers, astronomers, cosmologists, and philosophers opportunities to investigate profound questions about these elements. Why are they here? Where did they come from? Is the naturalistic answer plausible? Do they serve a purpose? The answers could inspire additional chapters to The Privileged Planet.

In the beginning...

Confirming the Big Bang: The Early Decades
Guillermo Gonzalez

Cosmologists have come a long way since Edwin Hubble published that ratty looking plot of galaxy recession velocities versus distance. Hubble wasn’t the first to discover what we now call Hubble’s law, but the name stuck. Extragalactic distance measurements have improved greatly since then. Cosmologists have measured more galaxies, at much greater distances and with greater accuracy and precision. 

  Of the four forces, only the gravitational force is important for determining motions of matter at large scales. By the 1920s Einstein’s general theory of relativity (GR) had displaced Newton’s theory of gravity. Any theory attempting to describe the dynamics and history of the universe must ultimately depend on GR.

    

Alternative Proposals

To be sure, there were and continue to be alternative proposals to explain the observations. One early theory was called“tired light.”  It was first proposed by Fritz Zwicky in 1929. In this theory, light becomes more redshifted the farther it travels through the intergalactic medium. More on this proposal below.

The Big Bang theory developed from Georges Lemaître’s earlier “primeval atom” or “Cosmic Egg” hypothesis. The Big Bang theory simply says the universe was much smaller, denser, and hotter compared to the present. It has expanded over its history, causing matter on large scales to spread out. On small scales, gravity caused matter to clump together.

Originally, the Big Bang theory was built on the theoretical foundation of GR and the empirical foundation of Hubble’s law. GR has faired extremely well over the past century. It has passed many stringent observational and experimental tests, including, in 2015, the first direct detection of gravitational waves.

  Alexander Friedmann, and later independently Georges Lemaître, Howard Robertson, and Arthur Walker, derived the cosmological solution to the GR field equations describing an isotropic and homogeneous dynamic universe. Not only did these equations form the foundation of the Big Bang theory, they also equally supported its main competitor, Steady State. The Steady State theory was proposed by Fred Hoyle, Thomas Gold, and Hermann Bondi in 1948 to do away with the need for a beginning, which the Big Bang theory implied.

Predictions and “Postdictions”

Each cosmological theory makes different predictions, but they “postdict” already available data. Prior to the 1960s, the Big Bang and Steady State models explained the Hubble law within their respective frameworks, and they were both consistent with everything else we could observe in the universe. Continued advancements in observational cosmology, however, soon provided ways of testing them. The first important test came in 1964 with the discovery of the cosmic microwave background (CMB) radiation. Arno Penzias and Robert Wilson of Bell Labs measured the temperature associated with the radiation to be 3.5 +/- 1 degrees K. For an interesting historical overview of the early “near misses” of the discovery of the CMB radiation, see here. The modern value is 2.7 degrees K.

Caught with Its Pants Down

This was an important discovery for several reasons. First, the Big Bang theory required the CMB radiation, while Steady State was silent about it. Steady State was caught with its pants down; its proponents tried to explain the CMB radiation after the fact. 

Second, in 1948 Ralph Alpher and Robert Herman actually predicted the temperature associated with the CMB to be 5 degrees K (see here for a detailed history of predictions of the CMB radiation temperature written by Alpher’s son). George Gamow predicted a value of 7 degrees K in 1953 and 50 degrees K in 1961. It is important to note that the predicted values of the CMB radiation temperature depend on knowing such quantities as the value of the Hubble constant and the age of the universe. Neither of these was known very accurately at the time. For example, correcting Gamow’s 1961 temperature estimate for his too-small value for the age of the universe reduces it by a factor of two (see here). Third, the CMB radiation was measured to be uniform in all directions, or isotropic, which also confirms its cosmic status. 

The Temperature of Space

However, prior to 1964, Big Bang proponents were not the only ones talking about the “temperature of space.” For example, in 1926 Arthur Eddington calculated a temperature of space due to the energy density of the radiation from stars around the Sun to be about 3.2 degrees K. As  explained here, this is just the local radiation field and not the CMB radiation that fills all of space. In addition, this radiation is most intense in the visible region of the spectrum and is far weaker in the radio, where the expected CMB radiation peaks. Eddington never gave his estimate any cosmological significance. The close agreement with the CMB radiation temperature is a coincidence due to our particular location in the Milky Way galaxy.

Others did make explicit predictions of the CMB temperature within the context of a nonexpanding universe. They included a who’s who of scientists: Walther Nernst, Louis de Broglie, and Max Born. They worked within the framework of various tired light models. Unlike the Big Bang and Steady State theories, tired light models were proposed as alternatives to GR to explain the redshifts. Although the “space temperatures” calculated for these models are close to the measured value of the CMB temperature (see here) they never gained much following because they failed to provide a plausible physical mechanism for the light to become tired (see here and here). What’s more, the success of GR over the course of the 20th century chipped away at theories based on alternatives.

Was this the only Big Bang prediction? Not by a long shot! In another post I will discuss the many additional observational tests of the Big Bang theory in the years following Penzias and Wilson’s important discovery.

The design debate devolves?

Listen: Behe, McDiarmid Continue a Discussion of the Lents Review
David Klinghoffer | @d_klinghoffer

On a new episode of ID the Future, host Andrew McDiarmid continues his conversation with biochemist Michael Behe about the response to Behe’s just released book, Darwin Devolves. Their focus is the review in Science by lead author Nathan Lents, with Joshua Swamidass and Richard Lenski.

Mike and Andrew have a good time considering the range of ways in which the preemptive, prepublication review fell short. Download the podcast or listen to it here.As I’ve noted, the extensive discussion of the review, by Behe himself and others at Evolution News, is simply due to the fact that Science is such a major and respected venue. It is the New York Times of the science community here in the United States. On ID the Future, Behe has some further, sharp words for the Lents document. I will add that after Professor Lents lashed out rather wildly this week, writing at the website Peaceful Science, I agreed with Joshua Swamidass, who administers the site, that it was time to cool things off a bit.

In that spirit, I offer no commentary other than to say, it’s very much worth your time to listen to this podcast, the second in a series. (See  here  for the first part.) Behe summarizes well where the review goes wrong, and what that indicates about the future of the evolution debate.

Some newborns are less equal than others?

Darkness Rising: As It Turns Out, Not All Newborns Have a Right to Life
Michael Egnor

If you had any doubt that darkness is overtaking our culture, this should remove it. Last week Nebraska Senator Ben Sasse introduced the Born-Alive Abortion Survivors Protection Act, intended to protect babies who are born during the process of abortion. The bill required physicians to provide babies who survive abortion with the same medical care that would be provided to any newborn. Forty-four senators voted against the bill, which precluded it from being considered for legislation because 60 votes were needed to override the anticipated filibuster. 

An Anti-Infanticide Bill

Sasse’s bill was essentially an anti-infanticide bill. The 44 senators who voted to oppose the bill voted to deny life to children who are born despite the fact that their mothers don’t want them. “You paid for a dead baby, you deserve a dead baby” is the most succinct justification for their opposition to the bill. 

Opponents of the bill argued that it amounts to interference in the medical relationship between a woman and her doctor. Nonsense. Once the baby is alive outside the womb — whether by ordinary childbirth or by a botched abortion — he or she is a newborn, not a “product of conception.” Sasse’s bill merely requires that all newborns — all live babies — receive competent medical care, regardless of the circumstances immediately preceding their birth. 

Two Classes of Newborns

Opponents argue — implicitly, though of course not explicitly — that there are two different classes of newborns: the wanted and the unwanted. They argue that only the wanted deserve medical care. The unwanted have no right to life. 

Opposition to this bill by even one senator would be a sign of moral rot; in a healthy culture, no legislator would dare endorse infanticide. Endorsement of infanticide by nearly half of the Senate is astonishing. 

The culture of death — the dehumanization of the vulnerable and the unwanted — is fast upon us. The rapidity of its advance is hard to believe, even for a cynic like me. If the widespread opposition to Senator Sasse’s simple bill that protects all newborns — wanted and unwanted — doesn’t horrify you, you’re not paying attention. 

Toward a theory devolution? IV

Listen: Behe, McDiarmid Continue a Discussion of the Lents Review
David Klinghoffer | @d_klinghoffer

On a new episode of ID the Future, host Andrew McDiarmid continues his conversation with biochemist Michael Behe about the response to Behe’s just released book, Darwin Devolves. Their focus is the review in Science by lead author Nathan Lents, with Joshua Swamidass and Richard Lenski.

Mike and Andrew have a good time considering the range of ways in which the preemptive, prepublication review fell short. Download the podcast or listen to it here.

As I’ve noted, the  extensive discussion of the review, by Behe himself and others at Evolution News, is simply due to the fact that Science is such a major and respected venue. It is the New York Times of the science community here in the United States. On ID the Future, Behe has some further, sharp words for the Lents document. I will add that after Professor Lents lashed out rather wildly this week, writing at the website Peaceful Science, I agreed with Joshua Swamidass, who administers the site, that it was time to cool things off a bit.

In that spirit, I offer no commentary other than to say, it’s very much worth your time to listen to this podcast, the second in a series. (See here for the first part.) Behe summarizes well where the review goes wrong, and what that indicates about the future of the evolution debate.

Long dead,human exceptionalism is gradually being buried unlamented.

Peter Singer Thinks Intellectually Disabled Less Valuable than Pigs

Wesley J. Smith

In his apologetics for infanticide, Princeton bioethicist Peter Singer has used a baby with Down syndrome as an example of a killable infant based on utilitarian measurements. (He actually supports infanticide because babies -- whether disabled or not -- are, in his view, not "persons.")

To Singer, moral value primarily comes from intellectual capacities, and that means developmentally and cognitively disabled human beings (also, the unborn and infants) have less value than other human beings, and indeed, a lower worth than some animals.

Were society ever to adopt Singer's bigoted anti-human exceptionalism views, it would mark the end of universal human rights, opening the door to tyrannical campaigns against the most weak and vulnerable -- you know, the kind of people that the Singers of the world deem resource wasters.

It would also break the spine of unconditional love, as our children would have to earn their place by possessing requisite capacities.

Consider the recent statements by Singer, published in the Journal of Practical Ethics, in which he explains why he would adopt out a child with Down syndrome. He then expresses a profound bigotry against people with cognitive and developmental disabilities (emphasis added):

For me, the knowledge that my [hypothetical Down] child would not be likely to develop into a person whom I could treat as an equal, in every sense of the word, who would never be able to have children of his or her own, who I could not expect to grow up to be a fully independent adult, and with whom I could expect to have conversations about only a limited range of topics would greatly reduce my joy in raising my child and watching him or her develop.

"Disability" is a very broad term, and I would not say that, in general, "a life with disability" is of less value than one without disability. Much will depend on the nature of the disability.

But let's turn the question around, and ask why someone would deny that the life of a profoundly intellectually disabled human being is of less value than the life of a normal human being. Most people think that the life of a dog or a pig is of less value than the life of a normal human being.

On what basis, then, could they hold that the life of a profoundly intellectually disabled human being with intellectual capacities inferior to those of a dog or a pig is of equal value to the life of a normal human being? This sounds like speciesism to me, and as I said earlier, I have yet to see a plausible defence of speciesism. After looking for more than forty years, I doubt that there is one.

Invidious discrimination exists when equals -- e.g., all human beings -- are denigrated as unequal based on some category that the bigot believes reduces the status of the discriminated against human, e.g., racism, sexism, and Singer-style discrimination against people with cognitive or developmental disabilities.

But human beings and animals do not inhabit the same moral realm. It is not wrong or discrimination to view and treat us differently than we do them.

Moreover, the very concept of "speciesism" -- used liberally in animal rights activism and bioethics -- is inherently and invidiously anti-human because it reduces us to so many carbon molecules with no inherent value beyond our cognitive capabilities at the moment of measurement. To repeat myself, the idea of speciesism, like utilitarianism, makes universal human rights impossible to sustain intellectually.

Assuming such utilitarian values would destroy the principles of Western civilization. And never mind the real capacities of many people with Down, whom Singer mischaracterizes, or their extraordinary loving natures -- which I have yet to see Singer opine much about. To Singer, intellect trumps all.

That's bigotry any way you look at it, no different from racism, except that his victims are less able to defend themselves.

I have always found it odd that Singer faces little of the opprobrium society metes out to other bigots. Indeed, he was brought to Princeton from Australia and given one of the world's most prestigious chairs in bioethics precisely because of these attitudes.

Despite supporting the propriety of killing babies, I have no doubt that Singer will continue to be the New York Times' favorite philosopher.

Yet more parody defying absurdity From OOL science.

Here We Go Again: For Complex Life, Just Add Fertilizer
Evolution News & Views

It's such an easy point. A child can grasp it. You may have all the ingredients you want, in the right quantities, but without a builder, nothing functionally complex will emerge. Here, we'll bring you tons of lumber, nails, and pipe. Need wire? Have all you want. Anything else? Just ask, and we'll throw it in at no extra charge: screws, paint, glass. Why, we will even lay a bunch of tools on the ground beside the pile.

Now, let it sit there, exposed to the sun and rain for as long as you like. Billions of years even. How many expect a house or a skyscraper to emerge by natural causes alone?

Evolutionists seem strangely immune to the obviousness of the logic here. They want to explain life's origin and complexity by reference to the availability of building blocks alone. Remember those who tried to account for the  Cambrian explosion by the rise of oxygen? And  origin of life by "a pinch of thickener" in a jumble of common molecules? Look, we can make it much, much easier for evolution. We will even arrange all the atoms into amino acids, sugars, fats and complex organic compounds and dump them into the oceans. Have some polycyclic aromatic hydrocarbons, citric acid, purines and pyrimidines, all brought special delivery by comets and asteroids. Plop! Into the primordial soup they go. Here, have some energy! Have all the UV light, lightning, and volcanoes you want.

The only rule is: no chemists, no mind, and no intelligence.

In  Illustra's film Origin, Discovery Institute biologist Ann Gauger has a pithy way of explaining the hopelessness of natural processes acting on building blocks. "If I put amino acids in a test tube in my lab, even if I added heat and shook it up real well, and kept doing that for a hundred years, or a thousand years, or ten thousand years, or a million years, nothing would happen."

Evolutionists must play by the rules they agreed to. Discovery Institute's Paul Nelson explains the rules in the film:

When you come to the origin of life, the rules -- and this isn't the science itself, this is the underlying philosophy -- the rules say, to solve the problem, you can use matter and energy, and natural law, natural regularities and chance processes, but that exhausts your toolkit. What you're not allowed to use, fundamentally by the rules, so-called rules of science, is mind or intelligence. If you had to attach a name to this position, you can't do better than scientific materialism: a philosophy that tells you "the only acceptable explanation has to be rendered in terms of matter and energy." And if you can't solve the problem using those tools, you're not allowed to change the rules. So from that perspective, how did life come to be via matter and energy alone? Now: try to solve the problem. [Emphasis added.]
To go from microbes to animals presents the same problem, because the same rules apply. Put building blocks into the hand of natural selection, add energy, and once again, nothing will happen. Natural selection is natural, not intelligent. It is matter and energy in motion. It has no foresight. It has no direction. It has no goal. Mindless entities do not compete. They do not try to outdo each other in the struggle for life. Without a mind or plan, natural selection cannot select. In a real sense, natural selection is a restatement of, "Whatever will be, will be." If everything goes extinct in the next meteor strike, so be it. Nobody cares in Darwin's world.

Yet paper after paper appears that fudges on the established rules. A recent example is found in Nature, where Reinhard et al. try to account for the rise of complex life by linking it to the rise of available phosphorus after billions of years. The news from Georgia Tech reads like a myth:

For three billion years or more, the evolution of the first animal life on Earth was ready to happen, practically waiting in the wings. But the breathable oxygen it likely required wasn't there, and a lack of simple nutrients may have been to blame.
Then came a fierce planetary metamorphosis. Roughly 800 million years ago, in the late Proterozoic Eon, phosphorus, a chemical element essential to all life, began to accumulate in shallow ocean zones near coastlines widely considered to be the birthplace of animals and other complex organisms, according to a new study by geoscientists from the Georgia Institute of Technology and Yale University.

Here we go again. Poor animals; they were trying to evolve, but they couldn't breathe. They needed fertilizer.

Picture again our lumber pile, now with bags of fertilizer next to everything. Picture Ann Gauger's test tube. Add some phosphorus. Bubble in some oxygen. Any help? How will simply adding more building blocks build a building?

But, the scientists object, we're talking about living cells before the first animals. Right. Saturate the oceans with bacteria, toss in the phosphorus, and watch the oxygen levels rise. Do they really expect trilobites, worms, and crustaceans to appear?

We place our phosphorus record in a quantitative biogeochemical model framework and find that a combination of enhanced phosphorus scavenging in anoxic, iron-rich oceans and a nutrient-based bistability in atmospheric oxygen levels could have resulted in a stable low-oxygen world. The combination of these factors may explain the protracted oxygenation of Earth's surface over the last 3.5 billion years of Earth history. However, our analysis also suggests that a fundamental shift in the phosphorus cycle may have occurred during the late Proterozoic eon (between 800 and 635 million years ago), coincident with a previously inferred shift in marine redox states, severe perturbations to Earth's climate system, and the emergence of animals.
The "emergence of animals." Evidently, those animals were waiting for their phosphorus order to arrive.

Let's review what's required for animal body plans that appeared abruptly at the Cambrian explosion: (1) new cell types, (2) new tissues, (3) new organs, (4) new genes, (5) new gene regulatory networks (GRNs), (6) new systems (digestive, muscular, skeletal, reproductive, central nervous systems, brains, etc.), (7) new levels of hierarchical integration of these systems, (8) new behaviors, (9) new defenses, (10) the ability to grow all these things from a single zygote.

The authors of the paper collected thousands of samples of shallow ocean sediment deposits, and carefully measured their phosphorus levels.

Theoretical predictions and observations from the geochemical record provide strong evidence that the first 80%-90% of Earth's 4.5-billion-year history was characterized by limited P burial in near-shore sediments, a pattern that we link to high C/P ratios in primary producers resulting from an Fe-based nutrient P trap. The shale record we present here, when coupled with our ocean-sediment biogeochemical model, illuminates an Earth system state in which dynamically coupled P- and N-limitation stabilized surface oxygen levels on billion-year timescales. However, there is evidence for at least periodic shifts away from pervasive Fe-rich waters in the late Tonian, or Ediacaran periods, coincident with our observed increase in sedimentary P enrichments. We propose that models seeking to explain the transition to an oxygen-rich ocean-atmosphere system in which early animals thrived and complex ecosystems developed should focus on mechanisms for overcoming enhanced P scavenging and transiting the N-fixation barrier that would act to prevent P-driven increases in ocean-atmosphere O2 levels during nascent global oxygenation events.
Minus the jargon:

The elevated availability of nutrients and bolstered oxygen also likely fueled evolution's greatest lunge forward.
They backpedal a little, saying, "The researchers are careful not to imply that phosphorous necessarily caused the chain reaction, but in sedimentary rock taken from coastal areas, the nutrient has marked the spot where that burst of life and climate change took off." So instead, they explain, "That first signal of phosphorus in Earth's coast shallows pops up in the shale record like a shot from a starting pistol in the race for abundant life."

Ah, now it all makes sense. Someone go over to our pile of lumber and fire a pistol.

The daily mail is Britain's blight?:Pros and cons.