The Word Became Flesh
1 In the beginning was the Word, and the Word was with God, AND THE WORD WAS GOD. 2 He was in the beginning with God. 3 All things were made through him, and without him was not anything made that was made. 4 In him was life, and the life was the light of men.5 the light shines in the darkness, and the darkness has not overcome it.
6 There was a man sent from God, whose name was John. 7 He came as a witness, to bear witness about the light, that all might believe through him. 8 He was not the light, but came to bear witness about the light.
9 The true light, which gives light to everyone, was coming into the world. 10 He was in the world, and the world was made through him, yet the world did not know him. 11 He came to his own, and his own people did not receive him. 12 But to all who did receive him, who believed in his name, he gave the right to become children of God, 13 who were born, not of blood or of the will neither of the flesh nor of the will of man, but of God.
14 And the Word became flesh and dwelt among us, and we have seen his glory, glory as of the only Son from the Father, full of grace and truth. 15 (John bore witness about him, and cried out, “This was he of whom I said, ‘He who comes after me ranks before me, because he was before Me.’”) 16 For from his fullness we have all received, grace upon grace. 17 For the law was given through Moses; grace and truth came through Jesus Christ. 18 No one has ever seen God; the only God, who is at the Father’s side, he has made him known.
The Creation of the World
1 In the beginning, God (JESUS) created the heavens and the earth. 2 The earth was without form and void, and darkness was over the face of the deep. And the Spirit of God was hovering over the face of the waters.
3 And God said, “Let there be light,” and there was light. 4 And God saw that the light was good. And God separated the light from the darkness. 5 God called the light Day, and the darkness he called Night. And there was evening and there was morning, the first day.
6 And God said, “Let there be an expanse in the midst of the waters, and let it separate the waters from the waters.” 7 And God made the expanse and separated the waters that were under the expanse from the waters that were above the expanse. And it was so. 8 And God called the expanse Heaven. And there was evening and there was morning, the second day.
9 And God said, “Let the waters under the heavens be gathered together into one place, and let the dry land appear.” And it was so.10 God called the dry land Earth, and the waters that were gathered together he called Seas. And God saw that it was good.
11 And God said, “Let the earth sprout vegetation, plants yielding seed, and fruit trees bearing fruit in which is their seed, each according to its kind, on the earth.” And it was so. 12 The earth brought forth vegetation, plants yielding seed according to their own kinds, and trees bearing fruit in which is their seed, each according to its kind. And God saw that it was good. 13 And there was evening and there was morning, the third day.
14 And God said, “Let there be lights in the expanse of the heavens to separate the day from the night. And let them be for signs and for seasons, and for days and years, 15 and let them be lights in the expanse of the heavens to give light upon the earth.” And it was so.16 And God made the two great lights—the greater light to rule the day and the lesser light to rule the night—and the stars. 17 And God set them in the expanse of the heavens to give light on the earth, 18 to rule over the day and over the night, and to separate the light from the darkness. And God saw that it was good. 19 And there was evening and there was morning, the fourth day.
20 And God said, “Let the waters swarm with swarms of living creatures, and let birds fly above the earth across the expanse of the heavens.” 21 So God created the great sea creatures and every living creature that moves, with which the waters swarm, according to their kinds, and every winged bird according to its kind. And God saw that it was good. 22 And God blessed them, saying, “Be fruitful and multiply and fill the waters in the seas, and let birds multiply on the earth.”23 And there was evening and there was morning, the fifth day.
24 And God said, “Let the earth bring forth living creatures according to their kinds—livestock and creeping things and beasts of the earth according to their kinds.” And it was so. 25 And God made the beasts of the earth according to their kinds and the livestock according to their kinds, and everything that creeps on the ground according to its kind. And God saw that it was good.
26 Then God said, “Let us make man in our image, after our likeness. And let them have dominion over the fish of the sea and over the birds of the heavens and over the livestock and over all the earth and over every creeping thing that creeps on the earth.”
27 So God created man in his own image, in the image of God he created him; and female he created them.
28 And God blessed them. And God said to them, “Be fruitful and multiply and fill the earth and subdue it, and have dominion over the fish of the sea and over the birds of the heavens and over every living thing that moves on the earth.” 29 And God said, “Behold, I have given you every plant yielding seed that is on the face of all the earth, and every tree with seed in its fruit. You shall have them for food. 30 And to every beast of the earth and to every bird of the heavens and to everything that creeps on the earth, everything that has the breath of life, I have given every green plant for food.” And it was so. 31 And God saw everything that he had made, and behold, it was very good. And there was evening and there was morning, the sixth day. Incidentally, the above order of scripture is how one should read the Bible.
And now Scientists offer a new rendition of “The Tree of Life”
Scientists who wanted to add new species to this tree of life have faced a daunting challenge: They do not know how to grow the vast majority of single-celled organisms in their laboratories.
A number of researchers have developed a way to get around that. They simply pull pieces of DNA out of the environment and piece them together.
In recent years, Jillian F. Banfield of the University of California, Berkeley and her colleagues have been gathering DNA from many environments, like California meadows and deep sea vents. They have been assembling the genomes of hundreds of new microbial species.
The scientists were so busy reconstructing the new genomes that they did not know how these species might fit on the tree of life. “We never really put the whole thing together,” Dr. Banfield said.
Recently, Dr. Banfield and her colleagues decided it was time to redraw the tree.
They selected more than 3,000 species to study, bringing together a representative sample of life’s diversity. “We wanted to be as comprehensive as possible,” said Laura A. Hug, an author of the new study and a biologist at the University of Waterloo in Canada.
The researchers studied DNA from 2,072 known species, along with the DNA from 1,011 species newly discovered by Dr. Banfield and her colleagues.
The scientists needed a supercomputer to evaluate a vast number of possible trees. Eventually, they found one best supported by the evidence.
It’s a humbling thing to behold. All the eukaryotes, from humans to flowers to amoebae, fit on a slender twig. The new study supported previous findings that eukaryotes and archaea are closely related. But overshadowing those lineages is a sprawling menagerie of bacteria.
Remarkably, the scientists didn’t have to go to extreme places to find many of their new lineages. “Meadow soil is one of the most microbially complex environments on the planet,” Dr. Hug said.
Another new feature of the tree is a single, large branch that splits off near the base. The bacteria in this group tend to be small in size and have a simple metabolism.
Dr. Banfield speculated that they got their start as simple life-forms in the first chapters in the history of life. They have stuck with that winning formula ever since.
“This is maybe an early evolving group,” Dr. Banfield said. “Their advantage is just being around for a really long time.”
Brian P. Hedlund, a microbiologist at the University of Nevada, Las Vegas who was not involved in the new study, said that one of the most striking results of the study was that the tree of life was dominated by species that scientists have never been able to see or grow in their labs. “Most of life is hiding under our noses,” he said.
Patrick Forterre, an evolutionary biologist at the Pasteur Institute in France, agreed that bacteria probably make up much of life’s diversity. But he had concerns about how Dr. Banfield and her colleague built their tree. He argued that genomes assembled from DNA fragments could actually be chimeras, made up of genes from different species. “It’s a real problem,” he said.
Dr. Banfield predicted that the bacterial branches of the tree of life may not change much in years to come. “We’re starting to see the same things over and over again,” she said.
Instead, Dr. Banfield said she expected new branches to be discovered for eukaryotes, especially for tiny species such as microscopic fungi. “That’s where I think the next big advance might be found,” Dr. Banfield said.
Dr. Hug disagreed that scientists were done with bacteria. “I’m less convinced we’re hitting a plateau,” she said. “There are a lot of environments still to survey.”
The new tree of life that researchers published on Monday shows that much of Earth’s biodiversity is bacteria, top half of which includes “candidate phyla radiation” that are still waiting to be discovered. Humans are in the bottom branch of eukaryotes. Credit Jill Banfield/UC Berkeley, Laura Hug/University of Waterloo