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Sunday, 2 October 2016

The Watchtower Society's commentary on Isaiah's prophecy Chapter.4 Vol.1

 Chapter Four
Jehovah’s House Lifted Up
THEY shall beat their swords into ploughshares. And their spears into pruning hooks: nation shall not lift up sword against nation. Neither shall they learn war any more.” These words are inscribed on a wall at the United Nations plaza in New York City. For decades the source of that quotation was not identified. Since the aim of the UN is to work toward global peace, it was easy to conclude that the quote originated with the founders of the UN, in 1945.
2 In 1975, however, the name Isaiah was chiseled into the wall below the quotation. It was then evident that the words were not of modern origin. They were, in fact, recorded as a prophecy over 2,700 years ago in what is now the 2nd chapter of the book of Isaiah. For millenniums lovers of peace have pondered over how and when the things Isaiah foretold would occur. There is no longer any need to wonder. Today we see before us the remarkable fulfilment of this ancient prophecy.
3 Who are the nations that beat their swords into ploughshares? Surely, they are not the modern-day political nations and governments. Until now these nations have developed swords, or weapons, both to wage war and to preserve “peace” through strength. If anything, the tendency has always been for nations to beat their ploughshares into swords! Isaiah’s prophecy finds fulfilment in representatives from all nations, people who worship Jehovah, “the God of peace.”—Philippians 4:9.
The Nations That Stream to Pure Worship
4 Isaiah chapter 2 begins with these words: “The thing that Isaiah the son of Amoz visioned concerning Judah and Jerusalem: And it must occur in the final part of the days that the mountain of the house of Jehovah will become firmly established above the top of the mountains, and it will certainly be lifted up above the hills; and to it all the nations must stream.”—Isaiah 2:1, 2.
5 Notice that what Isaiah foretells is not mere speculation. Isaiah is directed to record events that “must occur”—without fail. Whatever Jehovah purposes has “certain success.” (Isaiah 55:11) Evidently to give emphasis to the reliability of his promise, God inspired the prophet Micah, a contemporary of Isaiah, to record in his book the same prophecy that is set out at Isaiah 2:2-4.—Micah 4:1-3.
6 When is Isaiah’s prophecy to be fulfilled? “In the final part of the days.” The NewInternational Version reads: “In the last days.” The Christian Greek Scriptures foretold features that would identify this period. Included among them are wars, earthquakes, pestilences, food shortages, and “critical times hard to deal with.”* (2 Timothy 3:1-5; Luke 21:10, 11) The fulfilment of such prophecies gives abundant evidence that we are living “in the final part of the days,” the last days of this present world system. Logically, then, we would expect to see fulfilled in our time the things that Isaiah foretold.
A Mountain in Which to Worship
7 In a few words, Isaiah paints a vivid prophetic picture. We see a lofty mountain, crowned by a glorious house, the temple of Jehovah. This mountain towers above surrounding mountains and hills. Yet, it is not foreboding or intimidating; it is appealing. Peoples of all nations yearn to ascend to the mountain of the house of Jehovah; theystream to it. This is easy to visualise, but what does it mean?
8 In Isaiah’s day hills and mountains are often associated with worship. For example, they serve as sites for idolatrous worship and for sanctuaries of false gods. (Deuteronomy 12:2; Jeremiah 3:6) However, the house, or temple, of Jehovah adorns the summit of Mount Moriah in Jerusalem. Faithful Israelites journey to Jerusalem three times a year and ascend Mount Moriah to worship the true God. (Deuteronomy 16:16) So the streaming of the nations to “the mountain of the house of Jehovah” pictures the gathering of many peoples to true worship.
9 Today, of course, God’s people do not gather at a literal mountain with a temple of stone. Jehovah’s temple in Jerusalem was destroyed by Roman armies in 70 C.E. Besides, the apostle Paul made it clear that the temple in Jerusalem and the tabernacle that preceded it were pictorial. They represented a greater, spiritual reality, “the true tent, which Jehovah put up, and not man.” (Hebrews 8:2) That spiritual tent is the arrangement for approaching Jehovah in worship based on the ransom sacrifice of Jesus Christ. (Hebrews 9:2-10, 23) In harmony with this, “the mountain of the house of Jehovah” mentioned at Isaiah 2:2 represents the exalted pure worship of Jehovah in our time. Those embracing pure worship do not gather at any geographic location; they gather in unity of worship.
The Elevating of Pure Worship
10 The prophet says that “the mountain of the house of Jehovah,” or pure worship, would become “firmly established above the top of the mountains” and be “lifted up above the hills.” Long before Isaiah’s time, King David brought the ark of the covenant up to Mount Zion in Jerusalem, which was located 2,500 feet [760 m] above sea level. There the ark rested until it was transferred to the completed temple on Mount Moriah. (2 Samuel 5:7; 6:14-19; 2 Chronicles 3:1; 5:1-10) Thus, by Isaiah’s day the sacred ark had already been physically elevated and placed in the temple, in a position higher than the many surrounding hills used for false worship.
11 Of course, in a spiritual sense, Jehovah’s worship has always been superior to the religious practises of those who serve false gods. During our day, however, Jehovah has exalted his worship heaven high, above all forms of unclean worship, yes, far above all “the hills” and “the top of the mountains.” How so? Largely through the gathering together of those who want to worship him “with spirit and truth.”—John 4:23.
12 Christ Jesus referred to “a conclusion of a system of things” as a time of harvest when the angels would gather in “the sons of the kingdom”—those with the hope of ruling with Jesus in heavenly glory. (Matthew 13:36-43) Since 1919, Jehovah has empowered “the remaining ones” of these sons to share with the angels in the harvest work. (Revelation 12:17) Thus, to start with, “the sons of the kingdom,” Jesus’ anointed brothers, are the ones gathered. Then they share in a further gathering work.
13 During this time of harvest, Jehovah has progressively helped the anointed remnant to understand and apply his Word, the Bible. This too has contributed to the elevating of pure worship. Though ‘darkness itself covers the earth, and thick gloom the national groups,’ the anointed are “shining as illuminators” among humankind, having been cleansed and refined by Jehovah. (Isaiah 60:2; Philippians 2:15) “Filled with the accurate knowledge of his will in all wisdom and spiritual comprehension,” these spirit-anointed ones “shine as brightly as the sun in the kingdom of their Father.”—Colossians 1:9; Matthew 13:43.
14 Moreover, others have streamed to “the mountain of the house of Jehovah.” Called by Jesus his “other sheep,” these have the hope of living forever on a paradise earth. (John 10:16; Revelation 21:3, 4) Starting in the 1930’s, they appeared by the thousands, then by the hundreds of thousands, and now by the millions! In a vision given to the apostle John, they are described as “a great crowd, which no man was able to number, out of all nations and tribes and peoples and tongues.”—Revelation 7:9.
15 The prophet Haggai foretold the appearance of this great crowd. He wrote: “This is what Jehovah of armies has said, ‘Yet once—it is a little while—and I am rocking the heavens and the earth and the sea and the dry ground. And I will rock all the nations, and the desirable things of all the nations [those who join anointed Christians in pure worship] must come in; and I will fill this house with glory,’ Jehovah of armies has said.” (Haggai 2:6, 7) The existence of this still-growing “great crowd” and their anointed companions elevates, yes glorifies, pure worship in Jehovah’s house. Never before have so many been recorded as united in the worship of the true God, and this brings glory to Jehovah and his enthroned King, Jesus Christ. King Solomon wrote: “In the multitude of people there is an adornment of a king.”—Proverbs 14:28.
Worship Exalted in the Lives of People
16 Jehovah deserves all credit for the elevating of pure worship in our time. Still, those who approach him are privileged to share in this work. Just as it requires effort to climb a mountain, so, too, it requires effort to learn of and live according to God’s righteous standards. Like Christians in the first century, God’s servants today have left behind life-styles and practises that are not compatible with true worship. Fornicators, idolaters, adulterers, thieves, greedy persons, drunkards, and others have changed their ways and been “washed clean” in God’s sight.—1 Corinthians 6:9-11.
17 Typical is the experience of one young woman who wrote: “I once was lost with no hope. I lived a life of immorality and drunkenness. I had sexual diseases. I also sold drugs and just didn’t care about anything.” After studying the Bible, she made major changes in order to conform to God’s standards. Now she says: “I enjoy peace of mind, self-respect, a hope for the future, a real family and, best of all, a relationship with our Father, Jehovah.”
18 Even after coming to an approved standing before Jehovah, all must continue to elevate pure worship by giving it a place of prominence in their lives. Thousands of years ago, through Isaiah, Jehovah expressed his confidence that there would be multitudes today eager to make his worship the most important thing in their lives. Are you among them?
A People Taught Jehovah’s Way
19 Isaiah tells us more about those who embrace pure worship today. He says: “Manypeoples will certainly go and say: ‘Come, you people, and let us go up to themountain of Jehovah, to the house of the God of Jacob; and he will instruct usabout his ways, and we will walk in his paths.’ For out of Zion law will go forth, andthe word of Jehovah out of Jerusalem.”—Isaiah 2:3.
20 Jehovah does not let his people wander about like lost sheep. Through the Bible and Bible-based publications, he imparts to them his “law” and his “word” so that they learn his ways. This knowledge equips them to “walk in his paths.” Out of hearts filled with appreciation and in harmony with divine direction, they speak to one another about the ways of Jehovah. They gather together at large conventions and in smaller groups—at Kingdom Halls and in private homes—so as to listen to and learn the ways of God. (Deuteronomy 31:12, 13) Thus they imitate the pattern of the early Christians, who met together to encourage and incite one another to abound in “love and fine works.”—Hebrews 10:24, 25.
21 They invite others to “go up” to the exalted worship of Jehovah God. How well this harmonises with the command Jesus gave to his disciples just before his ascension to heaven! He told them: “Go therefore and make disciples of people of all the nations, baptising them in the name of the Father and of the Son and of the holy spirit, teaching them to observe all the things I have commanded you.” (Matthew 28:19, 20) With divine backing, Jehovah’s Witnesses obediently go throughout the earth, teaching and making disciples, baptising them.
Swords Into Ploughshares
22 Now we come to the next verse, part of which is inscribed on the wall at the UN plaza. Isaiah writes: “He will certainly render judgement among the nations and set matters straight respecting many peoples. And they will have to beat their swords into ploughshares and their spears into pruning shears. Nation will not lift up swordagainst nation, neither will they learn war anymore.”—Isaiah 2:4.
23 To achieve this would be no small accomplishment. Federico Mayor, director-general of the United Nations Educational, Scientific, and Cultural Organisation, once said: “All the obscenities of war, brought home to us nowadays by audio-visual equipment, do not seem able to halt the advance of the huge war machine set up and maintained over many centuries. Present generations have the almost impossible, Biblical task of ‘beating their swords into ploughshares’ and making the transition from an instinct for war—developed since time immemorial—to a feeling for peace. To achieve this would be the best and most noble act that the ‘global village’ could accomplish, and the best legacy to our descendants.”
24 The nations as a whole will never achieve this lofty goal. It is simply beyond their reach. Isaiah’s words are fulfilled by individuals from many nations, who are united in pure worship. Jehovah has “set matters straight” among them. He has taught his people to live at peace with one another. Truly, in a divided and strife-ridden world, they have figuratively beaten their “swords into ploughshares and their spears into pruning shears.” How?
25 For one thing, they do not take sides in the wars of the nations. Shortly before Jesus’ death, armed men came to arrest him. When Peter lashed out with a sword to defend his Master, Jesus said to him: “Return your sword to its place, for all those who take the sword will perish by the sword.” (Matthew 26:52) Since then, Jesus’ footstep followers have beaten their swords into ploughshares and have refrained from taking up weapons to kill their fellow man and from supporting war efforts in other ways. They “pursue peace with all people.”—Hebrews 12:14.
Pursuing the Ways of Peace
26 The peace of God’s people goes far beyond a refusal to engage in warfare. Though they are found in more than 230 lands and represent countless languages and cultures, they enjoy peace with one another. In them is found a modern fulfilment of the words of Jesus, who said to his disciples in the first century: “By this all will know that you are my disciples, if you have love among yourselves.” (John 13:35) Christians today are “peacemakers.” (Matthew 5:9, footnote) They “seek peace and pursue it.” (1 Peter 3:11) Sustaining them is Jehovah, “the God who gives peace.”—Romans 15:33.
27 There are dramatic examples of those who have learnt  to be peacemakers. A young man writes of his early life: “Hard experience taught me how to defend myself. It made me tough and angry about life. I would always end up in fights. Each day, I would fight a different kid in the neighbourhood, sometimes with fists, sometimes with rocks or bottles. I grew up being very violent.” Eventually, however, he responded to the invitation to go to “the mountain of the house of Jehovah.” He learnt  God’s ways and became a peaceable servant of God.
28 Most of Jehovah’s servants do not come from such a violent background. Still, even in relatively small things—acts of kindness, forgiveness, and empathy—they strive to promote peace with others. Although imperfect, they endeavour to apply the Bible’s counsel to “continue putting up with one another and forgiving one another freely if anyone has a cause for complaint against another.”—Colossians 3:13.
A Future of Peace
29 Jehovah has done a marvellous thing in this “the final part of the days.” He has gathered from all nations people who want to serve him. He has taught them to walk in his ways, ways of peace. These are the ones who will survive the coming “great tribulation” and pass into a peaceful new world in which war will be abolished forever.—Revelation 7:14.
30 Swords—weaponry—will be no more. The psalmist wrote of that time: “Come, you people, behold the activities of Jehovah, how he has set astonishing events on the earth. He is making wars to cease to the extremity of the earth. The bow he breaks apart and does cut the spear in pieces; the waggons he burns in the fire.” (Psalm 46:8, 9) In view of such a prospect, Isaiah’s following exhortation is as appropriate today as it was when he wrote it: “O men of the house of Jacob, come and let us walk in the light ofJehovah.” (Isaiah 2:5) Yes, let Jehovah’s light illuminate our path now, and we will walk in his way for all eternity.—Micah 4:5.

A non-theist engages in some hard-talk re:the prevailing evolutionary synthesis.






Just enough religion to make us hate.

The end of Christianity in the Middle East could mean the demise of Arab secularism

In a Middle East rebuilt on intolerant ideologies, there is likely to be little place for beleaguered minorities


The past decade has been catastrophic for the Arab world'sbeleaguered 12 million strong Christian minority. In Egypt revolution and counter-revolution have been accompanied by a series of anti-Copt riots, killings and church burnings. In Gaza and the West Bank Palestinian Christians are emigrating en masse as they find themselves uncomfortably caught between Netanyahu's pro-settler government and their increasingly radicalised Sunni neighbours.
In Syria most of the violence is along the Sunni-Alawite fault line, but stories of rape and murder directed at the Christian minority, who used to make up around 10% of the population, have emerged. Many have already fled to camps in Lebanon, Turkey or Jordan; the ancient Armenian community of Aleppo is reported to be moving en masse to Yerevan.
The worst affected areas of Syria are of course those controlled by Isis. Last weekend it issued a decree offering the dwindling Christian population of eastern Syria and northern Iraq a choice: convert to Islam or pay a special religious levy – the jizya. If they did not comply, "there is nothing to give them but the sword". The passing of the deadline led to possibly the largest exodus of Middle Eastern Christians since theArmenian massacres during the first world war, with the entire Christian community of Mosul heading off towards Kirkuk and the relative religious tolerance of the Kurdish zone.
Even before this latest exodus, at least two-thirds of Iraqi Christians had fled since the fall of Saddam. Christians were concentrated in Mosul, Basra and, especially, Baghdad – which before the US invasion had the largest Christian population in the Middle East. Although Iraq's 750,000 Christians made up only 7% of the pre-war population, they were a prosperous minority under the Ba'athists, as symbolised by the high profile of Tariq Aziz, Saddam's foreign minister, who used to disarm visiting foreign dignitaries by breaking into Onward, Christian Soldiers in Aramaic, the language of Jesus.
According to tradition it was St Thomas and his cousin Addai who brought Christianity to Iraq in the first century. At the Council of Nicea, where the Christian creed was thrashed out in AD325, there were more bishops from Mesopotamia than western Europe. The region became a refuge for those persecuted by the Orthodox Byzantines, such as theMandeans – the last Gnostics, who follow what they believe to be the teachings of John the Baptist. Then there was the Church of the East, which brought the philosophy of Aristotle and Plato, as well as Greek science and medicine, to the Islamic world – and hence, via Cordoba, to the new universities of medieval Europe.
Now almost everywhere Arab Christians are leaving. In the past decade maybe a quarter have made new lives in Europe, Australia and America. According to Professor Kamal Salibi, they are simply exhausted: "There is a feeling of fin de race among Christians all over the Middle East. Now they just want to go somewhere else, make some money and relax. Each time a Christian goes, no other Christian comes to fill his place and that is a very bad thing for the Arab world. It is Christian Arabs who keep the Arab world 'Arab' rather than 'Muslim'."
Certainly since the 19th century Christian Arabs have played a vital role in defining a secular Arab cultural identity. It is no coincidence that most of the founders of secular Arab nationalism were men like Michel Aflaq – the Greek Orthodox Christian from Damascus who, with other Syrian students freshly returned from the Sorbonne, founded the Ba'ath party in the 1940s – or Faris al-Khoury, Syria's only Christian prime minister. Then there were intellectuals like the Palestinian George Antonius, who in 1938 wrote in The Arab Awakening of the crucial role Christians played in reviving Arab literature and the arts after their long slumber under Ottoman rule.
If the Islamic state proclaimed by Isis turns into a permanent, Christian-free zone, it could signal the demise not just of an important part of the Arab Christian realm but also of the secular Arab nationalism Christians helped create. The 20th century after 1918, which saw the creation of the different Arab national states, may well prove to be a blip in Middle Eastern history, as the old primary identifiers of Arab identity, religion and qabila – tribe – resurface.
It is as if, after a century of flirting with imported ideas of the secular nation state, the region is reverting to the Ottoman Millet system (from the Arabic millah, literally "nation"), which represented a view of the world that made religion the ultimate marker of identity, and classified Ottoman subjects by their various sectarian religious "nations".
Despite sizeable Christian populations holding on in Lebanon, Jordan and Egypt, there is likely to be little place for Christian Arabs in a Middle East rebuilt on intolerant ideologies like those of Isis. Their future is more likely to resemble that of the most influential Christian Arab intellectual of our day, Edward Said. Born in Jerusalem at the height of Arab nationalism in 1935, Said died far from the turmoil of the Middle East in New York in 2003. His last collection of essays was appropriately entitledReflections On Exile.
• The headline of this article was amended on 24 July 2014.

Yet more on the tree of life

Do All Life Forms Fall into a Nested Hierarchy?

 

 

Casey Luskin June 11, 2015 4:57 AM |


A biology graduate student and alumnus of our Summer Seminar on Intelligent Design recently contacted me to ask where ID comes down on common descent. I explained to him that in the ID camp, some folks accept common descent while others are skeptical. ID proponents can respectfully disagree on that question (and others too), while agreeing on the powerful evidence for design in nature. But my correspondent asked about an argument in favor of common ancestry he had heard that basically went like this:
All life forms fall within a nested hierarchy. Of the hundreds of thousands of specimens that have been tested, every single one falls within a nested hierarchy, or their evolutionary phylogenetic tree is still unknown and not sequenced yet.
This claim (which he wasn't making, by the way) is far from true. We constantly find organisms that don't fit neatly into a phylogenetic tree. Or, what happens is evolutionary biologists attempt to force-fit organisms into the tree only by invoking processes like convergent evolution and loss of traits. In other words, evolutionary biologists are forced to propose that an organism's traits did not arise through common ancestry, because common ancestry fails to explain the data. Does this mean that evolutionary biologists reject common ancestry when they find data that doesn't fit a tree? No, because they assume common ancestry; they aren't interested in testing it. So when they find data that doesn't fit a tree, they just find ways to force-fit the data into the tree. Here's what's going on:
The first and primary assumption of all evolutionary phylogenetic classification methodologies is that common ancestry is true. This assumption nearly always goes unquestioned, even when the data doesn't support it. As Elliott Sober and Michael Steele explain, "It is a central tenet of modern evolutionary theory that all living things now on earth trace back to a single common ancestor," and "This proposition is central because it is presupposed so widely in evolutionary research." They acknowledge that cladistics assumes that a tree exists, and common ancestry is correct:
Whether one uses cladistic parsimony, distance measures, or maximum likelihood methods, the typical question is which tree is the best one, not whether there is a tree in the first place. (Elliott Sober and Michael Steele, "Testing the Hypothesis of Common Ancestry," Journal of Theoretical Biology 218 (2002): 395-408 (emphasis added).)
Likewise, the assumption is made explicit, and primary, in the UC Berkeley Museum of Paleontology's introductory page on cladistics:
What assumptions do cladists make? There are three basic assumptions in cladistics:
1.Any group of organisms are related by descent from a common ancestor.
One textbook cited by Stephen Meyer in Darwin's Doubt concurs about this assumption:
The key assumption made when constructing a phylogenetic tree from a set of sequences is that they are all derived from a single ancestral sequence, i.e., they are homologous. (Marketa Zvelebil and Jeremy O. Baum, Understanding Bioinformatics (New York: Garland Science, 2008), p. 239.)
Together, these authorities make a crucial point: cladistics and other phylogenetics methods do not demonstrate common ancestry; they assume it. In other words, these methods don't test whether all organisms fit into a nested hierarchy (i.e., phylogenetic tree). Rather, evolutionary systematics assumes that common ancestry is true and therefore all organisms belong within a nested hierarchy, and then it uses methods to force-fit any organism into the tree, even if that organisms has traits that don't fit neatly within the tree. Thus, Michael Syvanen -- a rare evolutionary biologist who is open to the possibility that universal common ancestry is false -- laments the pro-tree biases of treebuilding algorithms:
Because tree analysis tools are used so widely, they tend to introduce a bias into the interpretation of results. Hence, one needs to be continually reminded that submitting multiple sequences (DNA, protein, or other character states) to phylogenetic analysis produces trees because that is the nature of the algorithms used. (Michael Syvanen, "Evolutionary Implications of Horizontal Gene Transfer," Annual Review of Genetics, 46:339-356 (2012) (emphases added).)
Common ancestry, therefore, is a starting assumption about the data -- not a conclusion from it. Another key lesson is this: just because you see evolutionary biologists creating an impressive-looking phylogenetic tree doesn't mean that all of the organisms or their traits shown within that tree fit neatly into a nested hierarchy (i.e., a tree structure). One could cite many examples of organisms that don't fit cleanly into a tree. Here are a few:Sahelanthropus tchadensis is widely touted as a human ancestor that lived about 6-7 million years ago, sometime very soon after the supposed split between the human line and the chimp line. But it's rarely mentioned that this specimen doesn't fit into the standard hominin tree at all. Why? Because it has a flat face, a humanlike quality, which shouldn't exist that far back:
If we accept these as sufficient evidence to classify S. tchadensis as a hominid at the base, or stem, of the modern human clade, then it plays havoc with the tidy model of human origins. Quite simply, a hominid of this age should only just be beginning to show signs of being a hominid. It certainly should not have the face of a hominid less than one-third of its geological age. Also, if it is accepted as a stem hominid, under the tidy model the principle of parsimony dictates that all creatures with more primitive faces (and that is a very long list) would, perforce, have to be excluded from the ancestry of modern humans." (Bernard Wood, "Hominid revelations from Chad," Nature, 418 (July 11, 2002):133-35.)
Because of this, some are skeptical that S. tchadensis belongs on the human line. If that's the case then its flat face represents convergent evolution. And if it is on the human line, then you are forced to propose that later species on the human line lost this trait. Either way, S. tchadensis creates major problems for a nice, neat, nested hierarchy of hominins that is consistent with the chronology of the fossil record. Much further back, there are organisms like Diania, thought to be an early arthropod ancestor from the Cambrian period, but which actually cause huge problems for the arthropod tree:
[W]e should caution that dinocaridids, Diania and other potential stem-arthropods typically express mosaics of arthropod-like characters, which makes resolving a single, simple tree of arthropod origins problematic. Indeed, the position recovered here for Diania between Radiodonta and the ostensibly similar-looking Schinderhannes is surprising. DianiaSchinderhannes and the remaining Arthropoda all share the putative apomorphy of jointed trunk appendages, and yet the trunk limbs of Diania resemble the frontal appendages of Anomalocaris and other radiodontans, which themselves lack trunk limbs entirely. If this is a secondary reduction in fossils like Anomalocaris, then Diania may in fact occupy a more basal position with respect to Radiodonta, Schinderhannes and Arthropoda; a scenario that would be more consistent with their fairly simple body morphology. (Liu et al., "An armoured Cambrian lobopodian from China with arthropod-like appendages," Nature, 470 (February 24, 2011): 526-530 (internal citations omitted).)
The reason the authors talk about "mosaics of arthropod-like characters" is that these organisms don't fit into an orderly, sequential, hierarchical, treelike pattern as predicted by common descent. They present a mishmash of traits, not distributed in a treelike pattern that shows some sequential, hierarchy ordering arthropod traits. This is a famous problem in arthropod evolution, rightly described as a mess. As one paper observes: "Arthropod phylogeny is sometimes presented as an almost hopeless puzzle wherein all possible competing hypotheses have support." That's the opposite of a nested hierarchy.  Nor is it just within the Cambrian phyla that we find such an array of phylogenetic misfits. Among the animal phyla more generally, we see traits that make it difficult to create a treelike representation of relationships.
The argument cited by the grad student noted that one reason an organism's classification isn't understood is that "their evolutionary phylogenetic tree is still unknown and not sequenced yet." That's a bit of a rudimentary argument, but it probably means that until we sequence an organism's genome, we don't know where it belongs in the tree of life. But sometimes after we sequence an organism's genome we find that its place in the tree of life is even less clear than it was before.
This is exactly what happened after the comb jelly genome was sequenced. As I wrote last year, comb jellies (phylum ctenophora) have muscles and complex nervous systems, but molecular studies suggest they branch off very close to the base of the animal tree. However, sponges -- which branch off later according to molecular data -- lack such structures. This means that either complex muscle and nervous cells were lost in sponges (even though these are complex, useful traits you'd probably want to keep around) or muscles and brains evolved convergently in later animals. Either way, you're left with a situation where comb jellies don't fit neatly into the animal tree. They show a mosaic of traits that shouldn't be the case under common descent.
Here's one more classic example from the animal phyla: symmetry. Animals can be divided up in many different ways. Some display bilateral symmetry, basically meaning they have a right half and a left half. Such "bilaterian" phyla include vertebrates, arthropods, and mollusks. Others have radial symmetry, where their symmetry is distributed in an essentially circular fashion around a central axis. Phyla with radial symmetry include cnidarians (e.g., jellyfish), ctenophores (comb jellies), and echinoderms (e.g., star fish and sea urchins).
From an evolutionary perspective, you might expect an animal tree to divide up neatly according to whether organisms display bilateral or radial symmetry. Not so. Echinoderms are placed much closer to vertebrates than they are to cnidarians and other phyla with radial symmetry. In fact, in another weird twist, vertebrates (with bilateral symmetry) are thought to be much closer to echinoderms (with radial symmetry) than they are to other bilaterian phyla like the arthropods, mollusks, or annelids. This grouping is made on the basis of early developmental processes. Echinoderms and vertebrates are both deuterostomes, meaning that early in development the first opening in the blastopore becomes the anus rather than the mouth. The upshot is this: animal symmetry is not distributed in a treelike pattern.
Yes, a critic might object that larval stages of echinoderms can have bilateral symmetry. But exactly the same can be said of some cnidarians, which are very far from echinoderms in the animal tree -- showing, again, that symmetry is not distributed in a treelike pattern.
In any case, an evolutionary biologist could decide to group phyla according to early developmental processes, or according to symmetry, and that's fine. If you weight one trait heavily, you'll get one tree. But switch that weight to another trait and you'll get another, conflicting tree. Either way, when you use one character set to create your tree, then the other character set is no longer distributed in a treelike fashion, and vice versa. That's a major problem.
Another good example of an organism whose genome posed problems for phylogenetic classification after it was sequenced is birds. As we reported last December, the sequencing of various bird genomes led to the unexpected conclusion that many types of birds that were previously thought to be closely related -- water birds, birds of prey, and songbirds -- evolved their groups' defining traits convergently. As Nature put it, "the tree of life for birds has been redrawn" by this study. The problem was, once genomic data was sequenced and understood, many basic habits and lifestyles of birds no longer fit into a nested hierarchy.
Again, there are innumerable examples of organismal traits that don't fit into a treelike pattern. But here are two more that came out recently. 
In April, Science Daily reported a study that looked at how different marine organisms swim ("Convergent evolution: Diverse sea creatures evolved to reach same swimming solution"). The scientists found that organisms as diverse as cuttlefish (a mollusk), the black ghost knifefish (a vertebrate), and the Persian carpet flatworm (phylum platyhelminthes) all use the same method of swimming:

The ability to move one's body rapidly through water is a key to existence for many species on this blue planet of ours. The Persian carpet flatworm, the cuttlefish and the black ghost knifefish look nothing like each other -- their last common ancestor lived 550 million years ago, before the Cambrian period -- but a new study uses a combination of computer simulations, a robotic fish and video footage of real fish to show that all three aquatic creatures have evolved to swim with elongated fins using the same mechanical motion that optimizes their speed, helping to ensure their survival.These three animals are part of a very diverse group of aquatic animals -- both vertebrate and invertebrate -- that independently arrived at the same solution of how to use their fins to maximize speed. And, remarkably, this so-called "convergent" evolution happened at least eight times across three different phyla, or animal groups, supporting the belief that necessity played a larger role than chance in developing this trait.
Now they are welcome to invoke convergent evolution if they like, but it's striking how each of these widely diverse organisms has a very similar mode of swimming, where the length of one undulation of the animal's fins divided by the average amplitude of the corresponding sideways movement gives you a ratio of about 20. You can see how distantly related (according to the usual evolutionary paradigm) these similar-swimming organisms are by looking at a tree diagram from the original paperAlso in April there were striking reports of a new vegetarian theropod dinosaur that had traits that made it very difficult to classify within the standard dinosaur tree:
Although closely related to the notorious carnivore Tyrannosaurus rex, a new lineage of dinosaur discovered in Chile is proving to be an evolutionary jigsaw puzzle, as it preferred to graze upon plants. Chilesaurus boasted a proportionally small skull, hands with two fingers like Tyrannosaurus rex and feet more akin to primitive long-neck dinosaurs.
Theropods, of course, include the meat eaters Velociraptor and T. rex, yet this species was a vegetarian. It thus poses a severe puzzle for evolutionary classification, as an article in The Guardian acknowledged:
Fossil hunters in Chile have unearthed the remains of a bizarre Jurassic dinosaur that combined a curious mixture of features from different prehistoric animals. The evolutionary muddle of a beast grew to the size of a small horse and was the most abundant animal to be found 145 million years ago, in what is now the Aysén region of Patagonia.

The discovery ranks as one of the most remarkable dinosaur finds of the past 20 years, and promises to cause plenty of headaches for paleontologists hoping to place the animal in the dinosaur family tree.

"I don't know how the evolution of dinosaurs produced this kind of animal, what kind of ecological pressures must have been at work," said Fernando Novas at the Bernardino Rivadavia Natural Sciences Museum in Buenos Aires.
The technical paper in Nature puts it this way:
For a basal tetanuran, Chilesaurus possesses a number of surprisingly plesiomorphic traits on the hindlimbs, especially in the ankle and foot, which resemble basal sauropodomorphs. These features are here considered as secondary reversals that might be related to a less-cursorial mode of locomotion. Furthermore, derived features of the dentary and teeth shared by Chilesaurus, sauropodomorphs and therizinosaurs are interpreted as homoplasies related to herbivorous habits. ... Chilesaurus represents an extreme case of mosaic evolution among dinosaurs, owing to the presence of dental, cranial and postcranial features that are homoplastic with multiple disparate groups. Using quantitative morphospace analysis, we explored morphospace occupation of different skeletal regions in Chilesaurus with respect to a variety of avian and non-avian theropods. This shows that Chilesaurus has a ceratosaur-like axial skeleton, a 'basal tetanuran' forelimb and scapular girdle, a coelurosaur-like pelvis, and a tetanuran-like hindlimb. General ankle and foot construction does not group with any theropod clade, probably as a result of the characters shared by Chilesaurus, sauropodomorphs and herrerasaurids.
Science Daily explained in less technical terms why this species, with its set of traits resembling many different types of dinosaurs, is difficult to classify:
Other features present in very different groups of dinosaurs Chilesaurus adopted were robust forelimbs similar to Jurassic theropods such as Allosaurus, although its hands were provided with two blunt fingers, unlike the sharp claws of fellow theropod Velociraptor. Chilesaurus' pelvic girdle resembles that of the ornithischian dinosaurs, whereas it is actually classified in the other basic dinosaur division -- Saurischia. The different parts of the body of Chilesaurus were adapted to a particular diet and way of life, which was similar to other groups of dinosaurs. As a result of these similar habits, different regions of the body of Chilesaurus evolved resembling those present in other, unrelated groups of dinosaurs, which is a phenomenon called evolutionary convergence.
Chilesaurus represents one of the most extreme cases of mosaic convergent evolution recorded in the history of life. For example, the teeth of Chilesaurus are very similar to those of primitive long-neck dinosaurs because they were selected over millions of years as a result of a similar diet between these two lineages of dinosaurs.
Martín Ezcurra, Researcher, School of Geography, Earth and Environmental Sciences, University of Birmingham said: 'Chilesaurus can be considered a 'platypus' dinosaur because different parts of its body resemble those of other dinosaur groups due to mosaic convergent evolution. In this process, a region or regions of an organism resemble others of unrelated species because of a similar mode of life and evolutionary pressures. Chilesaurus provides a good example of how evolution works in deep time and it is one of the most interesting cases of convergent evolution documented in the history of life.
What we see here is a dino that doesn't fit with the dino tree not just because it's a herbivorous theropod, but also because different parts of its body appear similar to different types of dinosaurs. Through convergent evolution and loss of traits, you can always find a way accommodate such quirky data. However the bottom line is that organisms like these are the opposite of finding "All life forms fall within nested hierarchy." We explain further in our curriculum Discovering Intelligent Design:
You may recall the "main assumption," mentioned at the beginning of the chapter, that Darwinian evolutionists use when constructing trees: similarity implies inheritance from a common ancestor. But what about situations where that assumption is clearly untrue -- i.e., when two organisms share a trait that their supposed common ancestor could not have possessed? A striking example is the [skull] similarity between marsupial and placental "saber-toothed cats," which are classified as very different types of mammals due to their two distinctly different ways of bearing young.
According to current evolutionary theory, the common ancestor of these two cats was a small rodent-like mammal with a very different body plan. Thus, their highly similar skull structures had to develop independently and could not have been inherited from a common ancestor.
Common descent does not explain these similarities. Evolutionists try  to explain this evidence by claiming these distinctly different cats evolved the same traits independently through convergent evolution.
Does this sort of data absolutely refute universal common descent? Taken on a case-by-case basis, no of course not, and we're not claiming it does. What it shows, collectively, is that the evolutionary case is a lot weaker than is routinely claimed. We commonly -- if not constantly -- find organisms whose traits don't fit into a hierarchical tree.DID-FB-5.jpg
I like how we conclude on this topic in Discovering Intelligent Design:
Perhaps the main assumption of phylogenetic trees should be rewritten as: "similarity implies inheritance from a common ancestor, except when it does not." Rather than being a helpful solution for neo-Darwinists, convergent evolution undermines the reasoning used to construct phylogenetic trees.
In fact, maintaining that "All life forms fall within a nested hierarchy" requires you to ignore huge amounts of data. ID proponents who doubt common descent have, I would say, ample reason for doing so.

 

On reasons to doubt the trinity

On reasons to doubt the trinity II