On the temptations of Christ the Watchtower Society's commentary.

Did Satan physically take Jesus to the temple when tempting him?
Put simply, we cannot be certain whether Jesus actually stood in the temple or he did so only by means of a vision. At times, both possibilities have been presented in our publications.

Consider first what the Bible record says. In his Gospel account of this event, the apostle Matthew was inspired to write: “Then the Devil took him [Jesus] along into the holy city, and he stationed him on the battlement [“parapet; highest point,” ftn.] of the temple.” (Matt. 4:5) Luke’s parallel account puts it this way: “He then led him into Jerusalem and stationed him on the battlement of the temple.”—Luke 4:9.

In the past, our publications have reasoned that this event may not have happened literally. For example, in the issue of March 1, 1961, The Watchtower explained: “It does not seem reasonable to place a literal construction on all that appears in the account of Jesus’ temptation in the wilderness. Certainly there is no mountain from which one could be shown ‘all the kingdoms of the world and their glory.’ So too, we must reasonably conclude that Satan did not literally, bodily, physically, take Jesus ‘along into the holy city’ and station him ‘upon the battlement of the temple.’ Such was not at all necessary for the temptation to have force.” However, in subsequent issues of this journal, we have observed that Christ’s complying with Satan’s request could have resulted in Jesus’ suicide.

Some have stated that, as a non-Levite, Jesus was not authorized to stand on top of the temple sanctuary. So it was assumed that Jesus may have been ‘taken along’ to the temple by means of a vision. That is similar to what happened centuries earlier to the prophet Ezekiel.—Ezek. 8:3, 7-10; 11:1, 24; 37:1, 2.

However, if this temptation occurred only in the form of a vision, the following questions arise:

Was the temptation real or imaginary?
If the other temptations were efforts to lure Jesus into carrying out physical actions such as turning literal stones into bread or performing a real act of worship before Satan, would not this temptation have been similar—requiring Jesus physically to jump from the temple?
On the other hand, if Jesus did stand physically on the battlement of the temple, other questions arise:

Did Jesus violate the Law by standing on top of the sanctuary?
How did Jesus get from the wilderness to Jerusalem?
Further research helps us to see some possibilities that may answer these last two questions.

First, Professor D. A. Carson notes that the Greek word hi·e·ron’, translated “temple” in both accounts, “probably refers to the entire complex, not the sanctuary itself.” So Jesus would not necessarily have had to stand on top of the sanctuary itself. He could have stood, for example, on the southeastern corner of the temple area. From that location, there was a drop of some 450 feet (137 m) to the floor of the Kidron Valley. The southeast structure had a flat roof with a parapet and was the highest in the temple. The ancient historian Josephus stated that if a person stood there and looked down, he “would become dizzy” because of the height. As a non-Levite, Jesus would have been allowed to stand in that location, and his doing so would not have caused any commotion.

But how could Jesus have been taken along to the temple when he was in the wilderness? The basic answer is that we cannot know for certain. The brief description of the temptations does not state how long a period was involved or where Jesus was in the wilderness. We cannot rule out the possibility that Jesus may have walked back to Jerusalem, even though doing so may have taken some time. The account does not specifically say that Jesus remained in the wilderness throughout the time of the temptations. Rather, it merely says that he was taken into Jerusalem.

What, though, of the temptation wherein Jesus was shown “all the kingdoms of the world”? Obviously, he did not literally see all the kingdoms; there is no literal mountain from which all of them can be seen. So Satan may have used some sort of vision to show these to Jesus, similar to the way a projector and a screen can be used to show someone pictures of various places on earth. However, although a vision may have been used, the “act of worship” would have been real, not imaginary. (Matt. 4:8, 9) It could be argued, then, that the temptation to jump off the battlement of the temple involved a real action with real consequences—adding a greater seriousness to this temptation than would be the case were it a mere vision.


The fact is, as stated at the outset, we cannot be dogmatic about this matter. Hence, we cannot rule out the possibility that Jesus actually went to Jerusalem and stood on the battlement of the temple. But one thing we can be sure about is that these temptations were real and that Jesus gave a conclusive answer to the Devil in each case.

Jehovah's Spirit the Watchtower Society's commentary.

What Is the Holy Spirit?

The Bible’s answer
The holy spirit is God’s power in action, his active force. (Micah 3:8; Luke 1:35) God sends out his spirit by projecting his energy to any place to accomplish his will.—Psalm 104:30; 139:7.

In the Bible, the word “spirit” is translated from the Hebrew word ru′ach and the Greek word pneu′ma. Most often, those words refer to God’s active force, or holy spirit. (Genesis 1:2) However, the Bible also uses those words in other senses:

Breath.—Habakkuk 2:19; Revelation 13:15.
Wind.—Genesis 8:1; John 3:8.
The vital, or animating, force in living creatures.—Job 34:14, 15.
A person’s disposition or attitude.—Numbers 14:24.
Spirit persons, including God and the angels.—1 Kings 22:21; John 4:24.
These meanings all share the sense of something invisible to humans that produces visible effects. Similarly, the spirit of God, “like the wind, is invisible, immaterial and powerful.”—An Expository Dictionary of New Testament Words, by W. E. Vine.

The Bible also refers to God’s holy spirit as his “hands” or “fingers.” (Psalm 8:3; 19:1; Luke 11:20; compare Matthew 12:28.) Just as a craftsman uses his hands and fingers to do his work, God has used his spirit to produce such results as the following:

The universe.—Psalm 33:6; Isaiah 66:1, 2.
The Bible.—2 Peter 1:20, 21.
The miracles performed by his ancient servants and their zealous preaching.—Luke 4:18; Acts 1:8; 1 Corinthians 12:4-11.

The fine qualities displayed by people who obey him.—Galatians 5:22, 23.

The holy spirit is not a person

By referring to God’s spirit as his “hands,” “fingers,” or “breath,” the Bible shows that the holy spirit is not a person. (Exodus 15:8, 10) A craftsman’s hands cannot function independent of his mind and body; likewise, God’s holy spirit operates only as he directs it. (Luke 11:13) The Bible also compares God’s spirit to water and associates it with such things as faith and knowledge. These comparisons all point to the impersonal nature of the holy spirit.—Isaiah 44:3; Acts 6:5; 2 Corinthians 6:6.

The Bible gives the names of Jehovah God and of his Son, Jesus Christ; yet, nowhere does it name the holy spirit. (Isaiah 42:8; Luke 1:31) When the Christian martyr Stephen was given a miraculous heavenly vision, he saw only two persons, not three. The Bible says: “He, being full of holy spirit, gazed into heaven and caught sight of God’s glory and of Jesus standing at God’s right hand.” (Acts 7:55) The holy spirit was God’s power in action, enabling Stephen to see the vision.

Misconceptions about the holy spirit

Misconception: The “Holy Ghost,” or holy spirit, is a person and is part of the Trinity, as stated at 1 John 5:7, 8 in the King James version of the Bible.

Fact: The King James version of the Bible includes at 1 John 5:7, 8 the words “in heaven, the Father, the Word, and the Holy Ghost: and these three are one. And there are three that bear witness in earth.” However, researchers have found that those words were not written by the apostle John and so do not belong in the Bible. Professor Bruce M. Metzger wrote: “That these words are spurious and have no right to stand in the New Testament is certain.”—A Textual Commentary on the Greek New Testament.

Misconception: The Bible personifies the holy spirit, and this proves that it is a person.

Fact: The Scriptures do at times personify the holy spirit, but this does not prove that the holy spirit is a person. The Bible also personifies wisdom, death, and sin. (Proverbs 1:20; Romans 5:17, 21) For example, wisdom is said to have “works” and “children,” and sin is depicted as seducing, killing, and working out covetousness.—Matthew 11:19; Luke 7:35; Romans 7:8, 11.

Similarly, when the apostle John quoted Jesus, he personified the holy spirit as a “helper” (paraclete) that would give evidence, guide, speak, hear, declare, glorify, and receive. He used masculine personal pronouns such as “he” or “him” when referring to that “helper.” (John 16:7-15) However, he did so because the Greek word for “helper” (pa·ra′kle·tos) is a masculine noun and requires a masculine pronoun according to the rules of Greek grammar. When John referred to the holy spirit using the neuter noun pneu′ma, he used the genderless pronoun “it.”—John 14:16, 17.

Misconception: Baptism in the name of the holy spirit proves that it is a person.

Fact: The Bible sometimes uses “name” to stand for power or authority. (Deuteronomy 18:5, 19-22; Esther 8:10) This is similar to its use in the English expression “in the name of the law,” which does not mean that the law is a person. A person who is baptized “in the name of ” the holy spirit recognizes the power and role of the holy spirit in accomplishing God’s will.—Matthew 28:19.

Misconception: Jesus’ apostles and other early disciples believed that the holy spirit was a person.

Fact: The Bible does not say that, nor does history. The Encyclopædia Britannica states: “The definition that the Holy Spirit was a distinct divine Person . . . came at the Council of Constantinople in ad 381.” This was over 250 years after the last of the apostles had died.

Waiting for the other shoe to drop?

Homochirality: The Truth Is Out Where?
Evolution News & Views January 31, 2011 7:00 AM

When it comes to origin of life scenarios, the only way to explain the emergence of life from purely naturalistic premises is that life, and all of its necessary components, arose by chance, or by natural laws or by some combination of both.

Whether life arose in a "warm little pond" or in heat vents or in ice crystals, origin of life scenarios must rely only on chance and natural laws (chemical and physical properties) to explain seemingly impossible phenomenon, such as how DNA first arose.

Right-handed amino acids are found in nature, but for whatever reason proteins only employ left-handed amino acids. Laboratory synthesis of amino acids produces a 50/50 mixture, as is expected with chiral molecules, and both are chemically equivalent. Obviously this cannot be attributed to chance any more so than someone flipping a coin 100 times and getting all heads can. So from naturalistic premises, the only way to solve this is to find some reason why the chemistry favored a particular orientation of biomolecules.

One piece of the origin of life puzzle is that biological molecules have a particular chemical orientation. Biological molecules are composed of carbon, and carbon can form four bonds. When there are different things coming off of those four bonds, it makes a difference where those bonds are with respect to each other. For example, when you look at your hands, your thumb could come off of the right side of the hand or the left side of the hand. The orientation of your thumb and fingers relative to each other makes a difference. Your hands are not superimposable (the same); they are mirror images. Carbon bonds have a similar characteristic. When a carbon-containing molecule has a bond structure around a carbon such that if the bonds were arranged differently the molecules would not be superimposible, it is said to be a chiral carbon or a chiral molecule (from the Greek for "hand"). An interesting thing about chirality is that it does not change the chemical nature of the carbon bonds. So if you have a reaction that ends up making a chiral carbon, you will probably get a 50/50 mixture of left- and right-handed molecules.

All of the amino acids, except glycine, have a chiral carbon. Here is the rub: Amino acids that are from naturally occurring proteins are all left-handed.

The two pervading naturalistic theories on this are: 1) Evolution selected left-handed biomolecules or 2) they were formed in outer space. The exact mechanism for these two theories is the fuel for research and publications. Recently, the Astrophysical Journal published a paper that studies ultra-violet circularly polarized light because this is one of the few ways that can produce a particular handedness (e.g. more right-handed molecules than left-handed molecules) in organic molecules (The Astrophysical Journal Letters, 727:L27, February 2011). Since the mirror images of chiral molecules are called enantiomers, a mixture that has more than 50% of one enantiomer over is another is said to have an enantiomeric excess (e.e.).

Some primitive meteorites contain a small enantiomeric excess of certain chiral amino acids, leading many people to believe that perhaps the origin of homochirality is found in outer space. The authors of the Astrophysical Journal paper sought to investigate what kind of cosmic phenomenon would cause this. One possibility is UV-circularly polarized light (UV-CPL) acting on cosmic "ices" or chunks of cold rock that eventually become meteors. "...we tested such a scenario in a laboratory simulation using UV-CPL to drive the photochemistry of cosmic ice analogs under plausible astrophysical conditions and search for the generation of chiral species with significant e.e.'s..."
They decided to compare their experiments to the Murchison Meteorite, which landed in Australia on September 28, 1969 (Garrett & Grisham Biochemistry 2nd Ed, Harcourt, Inc, 1999). This meteorite showed an enantiomeric excess of several amino acids of 2-9%. The authors looked at alanine, which had an enantiomeric excess of 1.2% on the Murchison Meteorite.

For the experiment, the authors selected a particular photon energy that they knew was close to the maximum needed for alpha hydrogenated amino acids, and directed those photons to a synthesized ice mixture that is theoretically similar to cosmic ice mixtures. To simulate interstellar conditions, they used ice mixtures of the composition H2O:CH3OH:NH3 (2:1:1).

This experiment resulted in a 1.34% e.e. of left-handed alanine, close to the 1.2% reported for the Murchison Meteorite. Other amino acids of interest were too dilute to take meaningful measurements. Usually with these syntheses the smallest amino acids are formed in greater amounts. Alanine is the smallest chiral amino acid. The authors' assumptions are first, amino acids formed in outer space under similar conditions to what they have reconstructed in the lab, and secondly, that these molecules were exposed to UV-CPL under the appropriate conditions to cause an enantiomeric excess of left-handed amino acids.

A couple of experimental procedural notes:

First, to get the laboratory experiment to work, the UV-CPL radiation temperature was increased to higher levels than what is thought to be in outer space, but the authors explain that this is still reasonable since the meteor will likely go through various temperatures: "The use of a higher temperature (80 K), rather than observed temperatures for interstellar ices (10-20 K), was decided to enhance diffusivity and recombination of photoproducts within the ices...However, since the complete cycle of inter and circumstellar grain evolution comprises cycles through warmer regions (hot cores) in which grain temperatures rise significantly (200 K), astronomical organic residues should be produced via pathways similar to those in our laboratory simulations." The authors justify this by referencing experimental studies that showed irradiation temperature (10 or 80 K) does not greatly influence product composition.

Second, they chose to irradiate for 10 hr with the molecules at room temperature (this would be about 20 C or 293 K) "to potentially favor enantioselective photoreactions based on a photon-molecule asymmetry transfer..." In other words, they shot photons at the compounds for a particular amount of time at a particular temperature that they knew would favor the reactions they were pursuing. The authors still contend that this remains astrophysically relevant particularly in "hot molecular core environments, where grains are heated and complex gas-phase molecules, thermally desorbed from the ices, are observed..."

While the authors may have a point that there are hot cores in outer space, they are adding an additional factor by assuming that the meteor must apparently pass through a hot core for a period of time and under certain conditions. At this point, there has been quite a bit of experimenter intervention for what they consider a "natural" process.

A 1.34% enantiomeric excess is significant enough to measure, but does this experiment solve the mystery behind homochirality? Let's consider what is most reasonable and probable. Obviously scientists are looking for an explanation for homochirality because the chances of nature accidentally selecting left-handed amino acids in a pool of a 50/50 mix are impossible. So, instead, the possibility presented here supposes that a meteor somehow went through a heat core and was exposed, apparently within the heat core, to UV-CPL with particular helical properties ended up with some amino acids with a slight e.e. on it. It hit the earth, and happened to hit in such a way that the amino acids were not destroyed upon entry, which is possible given the Murchison Meteorite, but then landed in a place conducive for reactions to take place. Furthermore, the authors mention that other amino acids on the Murchison Meteorite show a greater e.e for molecules such as isovalene "that cannot be explained solely by the asymmetric effect of UV-CPL," meaning that the meteor had to have gone through yet another process to produce the enantiomeric excess of other amino acids. Then those reactions apparently beginning with anywhere from 1.2 to 9% e.e. of left-handed amino acids ended up producing 100% e.e. of the chiral amino acids, which is still inexplicable. How is this any more probable than nature just happening to find the one place where a 50/50 racemic mixture was not made and chemistry did not behave as it normally would? 


This paper is interesting because it may account for the 1.2% e.e. of L-alanine in the Murchison Meteorite, although even this is questionable since their procedure does not account for the other amino acids on the meteorite. However, it does not offer much by way of explaining this very difficult origin of life puzzle. The final section of the paper speculates on where UV-CPL sources of the particular helical value necessary for hydrolyzed amino acids might be found. They suggest this type of UV-CPL was "most probably produced by dichroic scattering [ref removed] on aligned grains by a magnetic field in reflection nebulae close to regions containing massive stars." They speculate that this might be similar to where the Sun was formed. By continuing to add specific conditions upon specific conditions, the likelihood that a meteor brought left-handed amino acids to earth which lead to the subsequent beginning of life is quickly diminishing.

Isaiah Ch.3 NASB

1For behold, the Lord GOD of hosts is going to remove from Jerusalem and Judah
            Both supply and support, the whole supply of bread
            And the whole supply of water;
      2The mighty man and the warrior,
            The judge and the prophet,
            The diviner and the elder,      3The captain of fifty and the honorable man,
            The counselor and the expert artisan,
            And the skillful enchanter.      4And I will make mere lads their princes,
            And capricious children will rule over them,      5And the people will be oppressed,
            Each one by another, and each one by his neighbor;
            The youth will storm against the elder
            And the inferior against the honorable.      6When a man lays hold of his brother in his father’s house, saying,
            “You have a cloak, you shall be our ruler,
            And these ruins will be under your charge,”      7He will protest on that day, saying,
            “I will not be your healer,
            For in my house there is neither bread nor cloak;
            You should not appoint me ruler of the people.”      8For Jerusalem has stumbled and Judah has fallen,
            Because their speech and their actions are against the LORD,
            To rebel against His glorious presence.      9The expression of their faces bears witness against them,
            And they display their sin like Sodom;
            They do not even conceal it.
            Woe to them!
            For they have brought evil on themselves.      10Say to the righteous that it will go well with them,
            For they will eat the fruit of their actions.      11Woe to the wicked! It will go badly with him,
            For what he deserves will be done to him.      12O My people! Their oppressors are children,
            And women rule over them.
            O My people! Those who guide you lead you astray
            And confuse the direction of your paths.
God Will Judge
13The LORD arises to contend,
            And stands to judge the people.      14The LORD enters into judgment with the elders and princes of His people,
            “It is you who have devoured the vineyard;
            The plunder of the poor is in your houses.      15“What do you mean by crushing My people
            And grinding the face of the poor?”
            Declares the Lord GOD of hosts.
Judah’s Women Denounced
16Moreover, the LORD said, “Because the daughters of Zion are proud
            And walk with heads held high and seductive eyes,
            And go along with mincing steps
            And tinkle the bangles on their feet,      17Therefore the Lord will afflict the scalp of the daughters of Zion with scabs,
            And the LORD will make their foreheads bare.”18In that day the Lord will take away the beauty of their anklets, headbands, crescent ornaments, 19dangling earrings, bracelets, veils, 20headdresses, ankle chains, sashes, perfume boxes, amulets, 21finger rings, nose rings, 22festal robes, outer tunics, cloaks, money purses, 23hand mirrors, undergarments, turbans and veils.      24Now it will come about that instead of sweet perfume there will be putrefaction;
            Instead of a belt, a rope;
            Instead of well-set hair, a plucked-out scalp;
            Instead of fine clothes, a donning of sackcloth;
            And branding instead of beauty.      25Your men will fall by the sword
            And your mighty ones in battle.      26And her gates will lament and mourn,
            And deserted she will sit on the ground.

universal common ancestry in the hotseat IV

The Naked Ape: An Open Letter to BioLogos on the Genetic Evidence, Cont.
Cornelius Hunter

In a previous article I reviewed BioLogos Fellow Dennis Venema's articles (here and here) which claimed that the genomes of different species are what we would expect if they evolved. For instance, allied species have similar genomes, and genetic features fall into evolution's common descent pattern. I argued that this claim is inaccurate and that the scientific evidence tells a very different message.
In a later article Venema focused his claim on the specific case of human evolution, and the similarity between the human and chimpanzee genomes. As before, Venema finds this genetic evidence to be a compelling confirmation of evolution:

The first line of evidence in favor of humans sharing ancestry with other forms of life is straightforward -- there are other species that have a genome that is nearly identical to our own -- the genomes found in great apes such as chimpanzees, gorillas and orangutans. Compared to our "book," the "books" of these species match at the chapter and paragraph level -- all three species have DNA sequences that have the same genes in the same basic order as we do. There are subtle differences, of course -- blocks of sequence that have been rearranged through breakage and rejoining of chromosomes, as expected -- but the overall pattern is clear.
...
Taken together, what we observe when comparing the overall structure of the human genome to other primates is that (a) our genomes do indeed have the features one would predict them to have if they are copies of a shared ancestral genome, and (b) the differences we do observe are easily accounted for by well-known mechanisms. These observations strongly support the hypothesis that our species arose through an evolutionary process.

It does not seem that the evidence supports evolutionary theory as Venema concludes. In fact, there appear to be several significant problems with this claim, as I will explain.
First, as we saw in my previous article, the genetic data from the different species do not fall into the expected evolutionary pattern. Here Venema focuses on the high genetic similarity between the primates, claiming it confirms evolution. But if this is what is required to confirm evolutionary relationships, then the substantial genetic differences that are so often found between otherwise similar species must falsify evolutionary relationships in those cases.
But evolutionists have never entertained any such doubts. Those evolutionary relationships are intact, according to evolutionists, and this suggests that the high similarity between the primate genomes never was required for evolutionists to believe they evolved from a common ancestor.
So it appears that Venema's claim, that the high genetic similarity between the primates confirms their evolutionary relationship, is more of an "after the fact" claim rather than a confirmation of a genuine evolutionary prediction. In fact, given the substantial morphological differences between humans and the other primates, evolutionists had indeed expected greater genetic differences:

The chimpanzee is our closest living relative. The morphological differences between the two species are so large that there is no problem in distinguishing between them. However, the nucleotide difference between the two species is surprisingly small.

So it does not appear that the high similarity between the chimp and human genomes was predicted by evolution, or is required by evolution. Beyond that, given the high similarity between the chimp and human genomes, there are many inconsistencies with evolution, as we shall see next.
The Gorilla Genome Is Strangely Similar to Both the Chimp and Human Genomes
When the human and chimpanzee genomes were compared a few years ago, the human genes showed some surprising differences in a few places, such as in genes thought to be related to hearing. Evolutionists called it "accelerated" evolution and they said that it was due to the development of human language. However it turns out that the gorilla genome has a similar pattern. And that doesn't make sense since gorillas don't have our advanced verbal skills:

Much of the 15% is in sections of the genome that do not code for proteins. But the researchers also looked at functional gene changes. They found that certain genes -- including some involved in hearing and brain development -- had gone through more rapid changes than expected in both the gorilla and human lineage. Some of these rapid changes are puzzling: the gene LOXHD1 is involved in hearing in humans and was therefore thought to be involved in speech, but the gene shows just as much accelerated evolution in the gorilla. "But we know gorillas don't talk to each other--if they do they're managing to keep it secret," says [lead author] Scally.

So now evolutionists are calling it "parallel accelerated" evolution, because the same accelerated evolution, by random mutation, must have happened independently, in the human and gorilla genomes. But why would the same "accelerated evolution" occur in the gorilla? It wasn't developing human language. Perhaps there is some other reason, but why then wouldn't that "accelerated evolution" occur in the chimpanzee? It doesn't make sense with evolution, for we must say that random mutations just happened to create the same pattern twice.
The gorilla genome also shows similarities to the chimp genome, including duplications that are not present in the other primates. Evolutionists say these various chimp-gorilla similarities were coincidences, occurring repeatedly by chance in the two different species:

We show that both the gorilla and chimpanzee genomes have experienced independent yet convergent patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications, and bursts of retroviral integrations.

These events must have occurred independently and in parallel.
Viruses
Human uniqueness is expansive. Relative brain size, hairless sweaty skin, striding bipedal posture, long-distance running, ability to learn to swim, innate ability to learn languages in childhood, prolonged helplessness of the young, ability to imitate and learn, inter-generational transfer of complex cultures, awareness of self and of the past and future, theory of mind, increased longevity, provisioning by post-menopausal females, difficult childbirth, and cerebral cortical asymmetry are just a few from a long list of features that make humans exceptional.
Another such unique feature is at the genome level: the lack of endemic infectious retroviruses in humans. The problem is that these viruses are present in the other primates, and so according to evolution these viruses must be present in their common ancestor which, again according to evolution, would be an ancestor of humans as well. Therefore this lack of endemic infectious retroviruses in humans is inconsistent with evolution:

Other than the recent introductions of HIV and human T leukaemia virus (HTLV) into humans from other animals, humans seem to be devoid of species-wide endemic infectious retroviruses. By contrast, like most other mammals studied, other hominids and non-human primates (NHPs) do have such viruses. Indeed, given the remarkable corroboration between the phylogenetic trees of primates and their lineage-specific simian foamy viruses (SFVs) our common ancestors with other hominids almost certainly had SFVs. The same is probably true of the lineage-specific simian infectious retroviruses (SIVs) found in most NHPs. Assuming that the common ancestors of hominids carried multiple endemic infectious retroviruses, how did the human lineage eliminate them? Given that humans remain susceptible to re-infection with both SFVs and SIVs from other hominids, this seems unlikely to be explained solely on the basis of more efficient host restriction systems. Rather, there seems to have been an episode in which the ancestral human lineage was somehow 'purged' of these endemic viruses.

In other words, the endemic infectious retroviruses do not align with the expected evolutionary pattern. The human lineage must, somehow, have been purged of these endemic viruses. Perhaps such a purging occurred, and future research may be able to strengthen that hypothesis. But as it stands, this evidence is not consistent with evolution.
Chimp-Human Genome Beneficial Differences Are Few
As noted above, evolutionists were surprised by the high similarity between the chimp and human genomes. With so few differences, how could evolution construct such tremendous differences? But not only is evolution limited to a relatively few genetic modifications to create the human, but according to evolution the majority of even those modifications would likely have had little or no consequence or even would have been slightly harmful. Here is how a 2005 paper on the chimpanzee-human genome comparisons put it:

In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.

The paper is written from an evolutionary perspective, assuming that humans and chimpanzees share a common ancestor. Given that a priori assumption, they were forced to conclude that most of the mutations affecting protein-coding genes led to "neutral and slightly deleterious alleles." So not only are evolution's random mutation resources meager, in terms of both quality and quantity as explained above, but even worse, those mutations mostly led to "neutral and slightly deleterious alleles."
In fact the beneficial mutations in protein-coding genes, which presumably would be important in evolving the human from a small, primitive ape, literally number only in the hundreds. It would be astonishing if the human could be evolved from so few mutations.
Chimp-Human Genome Differences Have Discrepancies
Furthermore, the chimp-human genome differences show some strange patterns, with unexplainable variation towards the ends of most chromosomes, and with the chromosomal banding patterns.
A common response from evolutionists is that these discrepancies are small in magnitude. That is true, they are small in magnitude. But that is not what counts. Molecular spectra that make magnetic resonance imaging (MRI) possible are also small in magnitude. That doesn't mean they don't count. What is important is that the chimp-human genome differences show patterns that evolutionary theory struggles to account for. The evidence is not consistent with the theory, by a wide margin.
The chimp-human genome differences have also been described using sliding 1-Mb windows. Those results also showed nonrandom variations, but later research found that those variations correlate with the observed de novo human mutation rate patterns. The research paper concluded that the variation in chimp-human genome differences "is only partly explained" by the mutation rate patterns. But these results raise the specter that the variations in the chimp-human genome differences seen in 1-Mb windows may be explainable by a known phenomenon.
This suggests the possibility that future research may also explain the variation towards the ends of chromosomes, and with the chromosomal banding patterns. But that was not the claim. Evolutionists such as Venema claim that today's evidences "strongly support the hypothesis that our species arose through an evolutionary process."
Chimp-Human Alternate Splicing Differences
You may have learned in your high school biology class that genes are segments of DNA, but it is a bit more complicated than that. For starters, in the higher species a gene is often not a simple continuous segment of DNA but rather is interrupted several times by intervening segments. So there are the coding segments (called exons for expressed regions) and then there are the intervening segments (called introns for intervening regions).
When a gene is transcribed, the transcript contains both the exons and introns. It is then spliced by a complicated spliceosome machine that removes the introns from the gene copy and glues the exons together.
One of the features of the exon/intron genetic architecture is that it allows for alternative splicing schemes. In fact, incredibly, a given gene can have thousands of different forms depending on how the spliceosome machine edits the gene.
When it was discovered that the human genome contained about twenty five thousand genes it seemed too few. Are not more genes required for a human body? More recently it has been discovered that we make up for that small number of genes with alternative splicing schemes. Most of our genes may undergo such editing, and the result can be a completely different function for the resulting protein.
We have an enormous alternative splicing program in our cells, far more than chimps have. And this is another inconsistency with evolutionary theory.
Given the high similarity between the chimp and human genomes, and the relatively few beneficial mutations in protein-coding genes (discussed above), evolutionists have considered the possibility of evolution by splicing. In other words, our enormous alternative splicing program may have been an important factor in our evolving from a small, primitive ape.
But there are many thousands of these gene-splicing changes that would have to evolve. And unlike bacteria whose populations are large and generation times are short, our gene splicing changes would have to evolve in smaller populations with longer generation times.
It is difficult to see how evolution would have the resources to make this happen. The problem quickly becomes astronomically improbable if groups of genes would need to implement their new splicing logic together. And how could that not be the case?
In fact, even if only the order of implementing splicing for a small number of genes is important, the problem quickly becomes astronomically improbable. And again, how could that not be the case?
But this is only the beginning. In addition to the fact that the evolution of our enormous gene splicing changes is unlikely, it also represents an enormous serendipity problem. We would have to say that random mutations constructed complicated genes, with exons and introns and splicing codes, and the incredible splicing machinery, which, it would just so happen, would luckily be just what was needed to evolve humans.
It is even worse than this when one considers the exons themselves. Those random mutations would have divided the genetic instructions into so many exons, and it just so happened that they would be the right building blocks that, when rearranged, would lead to humans. The serendipity is astronomical here.
Imagine if you were building a tricycle and your friend modified each part you had crafted (not adding anything), and now the parts fit together to construct the space shuttle rocket motor.
The Kangaroo-Human Genomes
In my previous article I explained that, in addition to striking differences in otherwise allied species, striking similarities in otherwise distant species are also inconsistent with evolution. This problem arises also with the human genome. Consider the kangaroo genome, which turned out to be similar to the human genome. As one evolutionist explained:

There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order. Which really surprised us, we thought they'd be completely scrambled, but they're not, there's great chunks of the human genome which is sitting right there in the kangaroo genome.

It was a surprise because under evolution humans and kangaroos must be quite distant relatives. Evolutionists believe a small mouse-like species split into two lineages -- the marsupials and the placentals -- about 150 million years ago. And according to evolutionists that mouse-like species eventually evolved by random mutations into, among other things, a kangaroo in the one lineage and into a human in the other. With that much evolutionary distance the kangaroo and human genomes should have evolved substantial differences.
Conclusion
The genomes of primates do not support evolutionary theory. As we have discussed, there are always speculations for whatever evidence is discovered. Perhaps evolution did this, perhaps it did that. But that does not change the fact that the primate genomes do not "strongly support the hypothesis that our species arose through an evolutionary process," as Venema and fellow evolutionists claim. There are a wide variety of substantial contradictions and problems with this theory.

A clash of Titans XIX

File under "Well said" XXVII

A man should be upright, not be kept upright. 
Marcus Aurelius

Neanderthals continue to prove more human than convenient for Darwinists.

Neanderthals Built Mysterious Stone Circles

Rings of stalagmites found in a cave in France suggest that our ancient relatives were surprisingly skilled builders.

By Nadia Drake

Once illuminated by the flickering fires of prehistoric builders, an array of mysterious stone circles hid in darkness for millennia, tucked into the recesses of a cave in France. Now, these ancient structures are again emerging from the shadows.

The strange rings are crafted from stalagmites and are roughly 176,000 years old, scientists report today in Nature. And if the rings were built by a bipedal species, as archaeologists suspect, then they could only be the work of Neanderthals, ancient human relatives that are proving to be much more “human” than anticipated.

“This discovery provides clear evidence that Neanderthals had fully human capabilities in the planning and the construction of ‘stone’ structures, and that some of them penetrated deep into caves, where artificial lighting would have been essential,” says paleoanthropologist Chris Stringer of the Natural History Museum in London.

However, why Neanderthals ventured deep into the darkness and constructed such elaborate structures is an enigma, at least for now.

Time Capsule

Sealed since the Pleistocene, Bruniquel Cave is located in southwest France, in a region littered with decorated caves and other Paleolithic sites. In 1990, spelunkers excavated its entrance and squeezed through, finding signs of long-vanished cave bears and other extinct megafauna just inside.

But the cave’s real treasure lay in a damp chamber more than 1,000 feet (330 meters) from the entrance. There, several large, layered ring-like structures protruded from the cave floor, the seemingly unmistakable craftwork of builders with a purpose.

“All visitors have noticed the presence of these structures, from the first speleologists,” says Jacques Jaubert of the University of Bordeaux, a coauthor of the study describing the finding.

It would take decades for scientists to begin deciphering the enigmatic circles, an endeavor slowed by restricted access to the cave and the untimely death of the archaeologist who began work on the site in the 1990s.

In 2013, Jaubert and his team were finally able to bring Bruniquel’s secrets into the light.

“The cave was very well preserved, with very few visits, almost none,” he says, noting that the site is on private property and is regulated by the French government. “The structures are spectacular and have virtually no equivalent for that period, and even for more recent periods.”

Stony Mysteries

The mysterious structures are built from nearly 400 stalagmites—the cone-shaped rock formations that rise from cave floors as dripping, mineral-rich water accumulates over time.

Hewn to roughly the same length, some of the stalagmites were crafted into a large circular structure measuring nearly 22 feet (6.7 meters) across. Others were aligned in a smaller semicircle, and the rest were stacked in heaps.

Cracked areas of red and black discoloration indicate that fires had been lit atop the stalagmites, and charred bits of bone, including the burnt bone of a bear or large herbivore, were found near the smaller circle.

Even to a trained eye, the scene looked like it could be the work of early modern humans, who first appeared in Europe about 40,000 years ago. But uranium dating of the stalagmites, as well as dates for a mineral cloak that had grown over them and the bone bits, revealed an age the team didn’t expect.

At around 176,000 years old, the structures vastly predate the arrival of Homo sapiens, not just by a smidge, but by more than 100,000 years.

“These must have been made by early Neanderthals, the only known human inhabitants of Europe at this time.” Stringer says.

Neanderthal Behavior

Neanderthals thrived for 300,000 years, coexisting with and occasionally breeding with modern humans. Like us, they were big-brained and clever, with a mastery of fire. But scientists argue about how similar the two species really were, and debate whether Neanderthals were capable of symbolic thought and ritual behaviors.

Unlike us, Neanderthals didn’t survive, and the reasons why they vanished from the landscape some 30,000 to 40,000 years ago are still a source of contention.

Until now, anthropologists had thought it unlikely that Neanderthals had mastered the art of subterranean living, which is a bit trickier than traipsing around above ground. The Bruniquel cave could prove otherwise.

“The find is solid, and it is an important documentation of the advanced behaviors of the Neanderthals,” says paleoanthropologist Erik Trinkaus of Washington University in St. Louis.

To craft those enormous stone rings, Jaubert and his colleagues argue, the cave’s occupants needed a reliable source of illumination, some kind of social organization, and the ability to conceive of and construct the patterns, which are made from more than two tons of stalagmites.

“This requires the mobilization of people who choose, who lead, who advise, manufacture—and with continuous light,” he says. “All this indicates a structured society.”

Clan or Cave Bears?

That’s one interpretation, but some scientists say it’s too soon to draw these kinds of conclusions about the site. To begin with, it’s not yet clear how widespread such complex behavior may have been among Neanderthals, or if the structures were built by one person or many.

“We don’t know how many people were involved, if the structures were done in one event or during several events, by one person or by several,” says anthropologist Marie Soressi of Leiden University. “I don’t know what to expect, because such a discovery is very unusual.”

Other scientists question the presumed human origin for the structures and instead suggest they could be the work of hibernating cave bears.

“Who in their right minds builds structures 300 meters underground inside of a cave? Seeking refuge in a cave is a way of avoiding having to make an artificial structure,” says paleoanthropologist John Shea of Stony Brook University. “When bears settle in for the winter hibernation, they push all kinds of litter to the side. This looks like a place where cave bears settled in for a nice nap over and over through time.”

But bear dens are generally smaller than the largest ring, Soressi says, and the animals don’t stack stalagmites so much as excavate hollows and brush things aside. Plus, Jaubert notes, “bears do not make fire.”

Subterranean Secrets

If the structures are indeed the work of Neanderthals and not cave bears, their purpose is still a mystery. No one knows what the Neanderthals might have been doing in that cave, or how long they used it. Jaubert and his colleagues refuse to speculate about the structures’ purpose until further work at the site tells more of the story.

In the meantime, it’s hard to resist wondering what our ancient relatives were doing deep inside that cavern, with their fire-lit rings of stone.

“The complex Bruniquel structures are well-dated to within a long cold glacial stage, and at that time the cave might have provided a temporary, more temperate refuge,” Stringer says.

“If there is still-buried debris from occupation, it would help us to determine whether this was a functional refuge or shelter, perhaps roofed using wood and skins, or something which had more symbolic or ritual significance.”

Universal common ancestry in the hotseat III

Toward a Consensus: An Open Letter to BioLogos on the Genetic Evidence
Cornelius Hunter

Dennis Venema, professor of biology at Trinity Western University and Fellow at BioLogos, has written a series of articles that have been noted by evolutionists for their clarity and persuasiveness. So as a collector of evidences and reasons why evolution is a fact, I was interested to see Venema's articles. What does the professor have to say to help confirm what Samuel Wilberforce rhetorically called "a somewhat startling conclusion"?


One of Venema's basic points (see  here and here ) is that the genomes of different species are what we would expect if they evolved. Allied species have similar genomes, and genetic features fall into evolution's common descent pattern:If indeed speciation events produced Species A-D from a common ancestral population, we would expect their genomes to exhibit certain features when compared to each other. First and foremost, their overall genome sequence and structure should be highly similar to each other -- they should be versions of the same book, with chapters and paragraphs of shared text in the same order. Secondly, the differences between them would be expected to fall into a pattern.
Does the evidence confirm these evolutionary expectations? Venema answers with an emphatic yes.

Here Venema is appealing to the empirical evidence. He is comparing the evidence to the theory of evolution, and finding that the evidence confirms evolution's predictions. This means the theory can be empirically evaluated. And if evolution can be genuinely evaluated empirically, then it is, at least theoretically, possible for evolution to fail. If the evidence can confirm evolution, then it also can disconfirm evolution.

This is important because focusing the attention on the evidence means the non-scientific arguments go away and science is allowed to speak. What does it say? Here I will take the opposing view, for it seems that what the science shows is that Venema's claim, that the genetic evidence confirms evolutionary predictions, is inaccurate.

This is not to say that evolutionary explanations cannot be offered. As philosophers well understand, another sub-hypothesis is always possible. Such hypotheses raise more profound questions of parsimony, likelihood, and so forth. But it seems that such philosophical questions ought to be addressed after there is a consensus on what the empirical evidence has to say. The goal here is to move toward that consensus. Venema, and evolutionists in general, make a straightforward claim about the evidence. We ought to be able to dispassionately evaluate that claim.

Of course I realize that reaching consensus is not as simple as reading an article. There will be differing interpretations by fair-minded critics. And the topic of origins is certainly not always dispassionate. If you argue against evolution you will be disparaged. My response to such attacks has and always will be to forgive.

One final preliminary is simply to point out that it is a challenge just to do justice to this story. A thorough treatment could easily require an entire volume. But a few, typical, examples will have to suffice. They can provide readers with an approximate understanding how the evidence bears on Venema's claim.

What Does the Evidence Say?

For starters, phylogenetic incongruence is rampant in evolutionary studies. Genetic sequence data do not fall into the expected evolutionary pattern. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits. This paper reports on incongruent gene trees in bats. That is one example of many.

MicroRNAs are short RNA molecules that regulate gene expression, for example, by binding to messenger RNA molecules which otherwise would code for a protein at a ribosome. Increasingly MicroRNAs are understood to be lineage-specific, appearing in a few species, or even in just a single species, and are nowhere else to be found. In fact one evolutionist, who has studied thousands of microRNA genes, explained that he has not found "a single example that would support the traditional [evolutionary] tree." It is, another evolutionist admitted, "a very serious incongruence."

Trichodesmium or "sea sawdust," a genus of oceanic bacteria described by Captain Cook in the 18th century and so prolific it can be seen from space, has a unique, lineage-specific genome. Less than two-thirds of the genome of this crucial ammonium-producing bacteria codes for proteins. No other such bacteria has such a low value, and conversely such a large percentage of the genome that is non-coding. This lineage-specific genome, as one report explains, "defies common evolutionary dogma."

It is not unusual for similar species to have significant differences in their genome. These results have surprised evolutionists and there does not seem to be any let up as new genomes are deciphered.

The mouse and rat genomes are far more different than expected. Before the rat genome was determined, evolutionists predicted it would be highly similar to the mouse genome. As one paper explained:

Before the launch of the Rat Genome Sequencing Project (RGSP), there was much debate about the overall value of the rat genome sequence and its contribution to the utility of the rat as a model organism. The debate was fuelled by the naive belief that the rat and mouse were so similar morphologically and evolutionarily that the rat sequence would be redundant.
The prediction that the mouse and rat genomes would be highly similar made sense according to evolution. But it was dramatically wrong.

One phylogenetic study attempted to compute the evolutionary tree relating a couple dozen yeast species using 1,070 genes. The tree that uses all 1,070 genes is called the concatenation tree. They then repeated the computation 1,070 times, for each gene taken individually. Not only did none of the 1,070 trees match the concatenation tree, they also failed to show even a single match between themselves. In other words, out of the 1,071 trees, there were zero matches. It was "a bit shocking" for evolutionists, as one explained: "We are trying to figure out the phylogenetic relationships of 1.8 million species and can't even sort out 20 yeast."

What is interesting is how this false prediction was accommodated. The evolutionists tried to fix the problem with all kinds of strategies. They removed parts of genes from the analysis, they removed a few genes that might have been outliers, they removed a few of the yeast species, they restricted the analysis to certain genes that agreed on parts of the evolutionary tree, they restricted the analysis to only those genes thought to be slowly evolving, and they tried restricting the gene comparisons to only certain parts of the gene.

These various strategies each have their own rationale. That rationale may be dubious, but at least there is some underlying reasoning. Yet none of these strategies worked. In fact they sometimes exacerbated the incongruence problem. What the evolutionists finally had to do, simply put, was to select the subset of the genes that gave the right evolutionary answer. They described those genes as having "strong phylogenetic signal."

And how do we know that these genes have strong phylogenetic signal. Because they gave the right answer. This raises the general problem of prefiltering of data. Prefiltering is often thought of merely as cleaning up the data. But prefiltering is more than that, for built-in to the prefiltering steps is the theory of evolution. Prefiltering massages the data to favor the theory. The data are, as philosophers explain, theory-laden.

But even prefiltering cannot always help the theory. For even cleansed data routinely lead to evolutionary trees that are incongruent (the opposite of consilience). As one study explained, the problem is so confusing that results "can lead to high confidence in incorrect hypotheses." As one paper explained, data are routinely filtered in order to satisfy stringent criteria so as to eliminate the possibility of incongruence. And although evolutionists thought that more data would solve their problems, the opposite has occurred. With the ever increasing volumes of data (particularly molecular data), incongruence between trees "has become pervasive."

What is needed now is less data. Specifically, less contradictory data. As one evolutionist explained, "if you take just the strongly supported genes, then you recover the correct tree." And what are "strongly supported" genes? Those would be genes that cooperate with the theory. So now in addition to prefiltering we have postfiltering.

Another issue are the striking similarities in otherwise distant species. This so-called convergence is rampant in biology and it takes on several forms.

Consider a paper from the Royal Society on "The mystery of extreme non-coding conservation" that has been found across many genomes. As the paper explains, there is currently "no known mechanism or function that would account for this level of conservation at the observed evolutionary distances." Here is how the paper summarizes these findings of extreme sequence conservation:

... despite 10 years of research, there has been virtually no progress towards answering the question of the origin of these patterns of extreme conservation. A number of hypotheses have been proposed, but most rely on modes of DNA : protein interactions that have never been observed and seem dubious at best. As a consequence, not only do we still lack a plausible mechanism for the conservation of CNEs -- we lack even plausible speculations.
And these repeated designs, in otherwise different species, are rampant in biology. It is not merely a rare occurrence that perhaps evolution could explain as an outlier. That the species do not fall into an evolutionary tree pattern is well established by science.

Furthermore, these repeated designs do not merely occur twice, in two distant species. They often occur repeatedly in a variety of otherwise distant species. So now the evolutionist must not only believe that there are many of these repeating design events, but that in most cases, they repeat multiple times, in disparate species.

Evolutionists have labeled this evidence as recurrent evolution. As a recent paper  explains:

The recent explosion of genome sequences from all major phylogenetic groups has unveiled an unexpected wealth of cases of recurrent evolution of strikingly similar genomic features in different lineages.
In addition, many instances of a third more puzzling phylogenetic pattern have been observed: traits whose distribution is "scattered" across the evolutionary tree, indicating repeated independent evolution of similar genomic features in different lineages.

Of course these puzzling, striking similarities cannot be explained by common evolutionary history. Instead, they are explained by common evolutionary forces:

As ancestrally shared features are the result of a common evolutionary history, shared features evolved by recurrent evolution are often the result of common evolutionary forces acting on different lineages.
If the pattern fits the evolutionary tree, then it is explained as common evolutionary history. If not, then it is explained as common evolutionary forces.

With all of this contradictory evidence, even evolutionists have realized in recent years that the traditional evolutionary tree model is failing. As one evolutionist  explained, "The tree of life is being politely buried."

There are many more fascinating examples of biological patterns that are not consistent with the expected evolutionary pattern. These are not anomalies or rare exceptions. Here we have focused on the genetic level since that was the theme of Venema's article. It seems that the species and their genomes do not fall into a consistent evolutionary pattern as evolutionists such as Venema claim. This does not mean evolutionists cannot explain any of this. They have a wide spectrum of mechanisms to draw upon, of varying levels of speculation and likelihood. These explanatory mechanisms greatly increase the theory's complexity. They raise questions of realism, and whether the theory is following the data, or the data is following the theory.

But such questions are for another day.

The point here is that evolutionist's claims that the genomic data broadly and consistently fall into the evolutionary pattern and expectations do not seem to reflect the empirical data. This is the first step in moving the discourse forward. We need to reach consensus on what the evidence reveals.

In a subsequent post I will continue with an examination of the next evidences Venema presents.