Genomics Intelligent Design News Plants

Mistletoe plant has unique genome, lacks common genes

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Mistletoe genome/Jeff Palmer

We are told that the mistletoe species lacks genes found in all other complex organisms.

From ScienceDaily:

A discovery made during an analysis of a species of mistletoe whose apparent ability to survive without key genes involved in energy production could make it one of the most unusual plants on Earth.

“This loss of genes very likely corresponds to the loss of an entire respiratory complex,” said Jeff Palmer, IU Distinguished Professor in the IU Bloomington College of Arts and Sciences’ Department of Biology, who led the study. “This is something that hasn’t been reported before for any multicellular organism.”

The genes that have been lost from V. scurruloideum typically reside in the mitochondrial genomes of plants and animals. Mitochondria play an important role in the overall metabolism of cellular organisms, serving as generators that produce energy to power other functions of the cell through respiration.

Contained within all eukaryotic cells, mitochondria possess their own DNA due to their evolutionary history as an “enslaved” bacterium swallowed up billions of years ago by a primitive eukaryotic organism.

Biologists regard the mitochondrial genomes, or mitogenomes, of flowering plants as “extreme and often perplexing” in their wide range of sizes, structures and mutation rates, Palmer said. But this genetic diversity has never before been shown to include the loss of genes involved in the mitochondria’s primary genetic function of respiration. More.

In short, evolution is a science that can make no predictions as to what to expect.

It is relevant that mistletoe is a semi-parasite, typically on deciduous trees:

“This plant has taken a unique overall tack in evolution, presumably related to its parasitic lifestyle,” said Elizabeth Skippington, a postdoctoral fellow at IU who is first author on the study. “Whether cause or cure, parasitism is most likely at the root of its extremely small mitochondrial genome, which shows clear signs of both rapid and degenerative evolution.”

How do we know that the mistletoe’s development direction is a “unique overall tack” in evolution, as opposed to the first example discovered?

Also, what does “degenerative” mean if the plant has been around successfully for millions of years and not expected to die out naturally soon?

When we use the term “degenerative disease,” we mean a disease a disease that will probably kill or fatally weaken the patient. Maybe “degenerative” is still correct here, but we need to be clear how we are using the term. What if, in its niche, the mistletoe is better off without the extra programming? How is that degeneration?

Despite their familiar role in Christmas traditions, however, Palmer said the broader ecological importance and prevalence of mistletoes across the world is commonly unrecognized.

So it appears to be a niche that works for the mistletoe.

We have only begun to find out enough to have the right questions. Fortunately, with Darwin in charge, we already have all the answers in place to jam the questions into, and hammer them down hard if they don’t fit.

Here’s the abstract:

Despite the enormous diversity among parasitic angiosperms in form and structure, life-history strategies, and plastid genomes, little is known about the diversity of their mitogenomes. We report the sequence of the wonderfully bizarre mitogenome of the hemiparasitic aerial mistletoe Viscum scurruloideum. This genome is only 66 kb in size, making it the smallest known angiosperm mitogenome by a factor of more than three and the smallest land plant mitogenome. Accompanying this size reduction is exceptional reduction of gene content. Much of this reduction arises from the unexpected loss of respiratory complex I (NADH dehydrogenase), universally present in all 300+ other angiosperms examined, where it is encoded by nine mitochondrial and many nuclear nad genes. Loss of complex I in a multicellular organism is unprecedented. We explore the potential relationship between this loss in Viscum and its parasitic lifestyle. Despite its small size, the Viscum mitogenome is unusually rich in recombinationally active repeats, possessing unparalleled levels of predicted sublimons resulting from recombination across short repeats. Many mitochondrial gene products exhibit extraordinary levels of divergence in Viscum, indicative of highly relaxed if not positive selection. In addition, all Viscum mitochondrial protein genes have experienced a dramatic acceleration in synonymous substitution rates, consistent with the hypothesis of genomic streamlining in response to a high mutation rate but completely opposite to the pattern seen for the high-rate but enormous mitogenomes of Silene. In sum, the Viscum mitogenome possesses a unique constellation of extremely unusual features, a subset of which may be related to its parasitic lifestyle. (paywall) – Elizabeth Skippingtona, Todd J. Barkmanb, Danny W. Ricea, and Jeffrey D. Palmera. Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes. PNAS, 2015 DOI: 10.1073/pnas.1504491112

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31 Replies to “Mistletoe plant has unique genome, lacks common genes

  1. 1
    Mapou says:

    Wow. This is guaranteed to wreak havoc on the Darwinist’s sacred nested hierarchy.

    Well, seeing that the exceptions are piling up daily, it must not be so sacred any more. There’s no need to fear, though. We’ve been down this road before. Just add some duct tape and some spit, et voila!

  2. 2
    daveS says:

    Also, what does “degenerative” mean if the plant has been around successfully for millions of years and not expected to die out naturally soon?

    When we use the term “degenerative disease,” we mean a disease a disease that will probably kill or fatally weaken the patient. Maybe “degenerative” is still correct here, but we need to be clear how we are using the term. What if, in its niche, the mistletoe is better off without the extra programming? How is that degeneration?

    It’s just referring to the loss of those genes and corresponding function. From the definition of “degenerate” (as a verb), pertaining to evolution:

    to revert to a simple, less highly organized, or less functionally active type, as a parasitic plant that has lost its taproot or the vestigial wings of a flightless bird.

  3. 3
    Dr JDD says:

    Hmm. In the Christian faith a big curse was placed on the ground and that which grew forth from it. New types of plants appeared which did not exist prior. All fruit previously had been safe to eat (except 1 tree). Mistletoe has poisonous berries.

    For those that claim genetic entropy (Sandford et al) this might be exactly in line with expectations. It surely is with the Christian faith and is no surprise to hear of degenerate evolution or how so many different genetic components of different plants are messed up!

  4. 4
    Mung says:

    Where does this young earth creationist nonsense come from and what does it have to do with intelligent design?

    There’s nothing in the Genesis text to indicate that plants were cursed or that previously edible plants would become poisonous or any other such nonsense.

    http://www.godandscience.org/y.....esis3.html

  5. 5
    Davem says:

    Genesis 3:17
    Cursed is the ground because of you;
    through painful toil you will eat food from it all the days of your life.
    18
    It will produce thorns and thistles for you…”

    Although it doesn’t specifically say that that plants were cursed or that previously edible plants would become poisonous, I wouldn’t say that there is nothing to indicate this.

    Genesis 5:29
    He named him Noah and said, “He will comfort us in the labor and painful toil of our hands caused by the ground the LORD has cursed.”

    This contradicts your link.

  6. 6
    Dr JDD says:

    Mung, study the text of Genesis 2:5 and you can see that other plants came after man – these are different to “day 3” plants.

    Then look at Gen 3 as per davem above. It is very clear that
    a) the ground is “cursed”
    b) man will work hard for his food (implying this was not the case before) – note the same use of “herb of the field” as per 2:5
    c) thorn and thistle appear – strongly implying these were not present prior to sin and the fall

    What is therefore abundantly clear is that the creation pre-fall would have looked, acted, behaved very different to post-fall if you take those events literally. Now applying thar to what we see around us and we see things that look wild, broken, degenerate and imperfect. We also see things that need taming, looking after and work. Not all fruit borne of trees or plants are good for food contrary to what we were told before.

    now the YEC might therefore conclude that there was a dramatic change not only in phenotype but more crucially, the genotype of plant life. Perhaps God could have used rapid evolutionary degeneration to achieve this “curse”. The point – it’s what we see around us today, mistletoe could be one such example.

    It has little to do with ID per se but ID does not have the power to save souls so ID without knowing the D and accepting who they are and your position before them is ultimately quite useless on its own.

  7. 7
    Mung says:

    Dr. JDD, if you study the text of Revelation 19 you might be led to believe that Jesus is actually going to come back to earth riding a literal white horse with his clothing soaked in literal blood and with a literal sword coming out of his mouth.

    And that absurd reading of the text would probably involve less eisegesis than what you’re encouraging people to do with the text of Genesis.

  8. 8
    Mapou says:

    The YEC crowd’s interpretation of Genesis is so far off target, it’s not even in the ballpark of being right. In fact, it’s on a different planet. Planet Wrong.

    The entire story of Adam and Eve, the trees of life and knowledge, the devious talking snake, paradise, garden, etc., is purely metaphorical. The talking snake alone should be a rather easy clue to anybody with two neurons between their ears. A close study of Genesis reveals that it is a collage of several smaller books speaking about different things that were not necessarily related. One thing is certain: the Adam and Eve in the garden are not the same Adam and Eve who had Cain and Abel. The first two are metaphorical.

    Here’s my interpretation. The trees in the garden are symbols of sacred knowledge that Yahweh made available to humanity. The tree of life symbolizes the genome which is organized hierarchically, like a tree. The tree of the knowledge of good and evil is a metaphor for the organization of intelligence and the brain, The brain, too, is hierarchical, like a tree. The secret of the two trees was freely accessible to mankind but Yahweh did not think they were ready for it and forbade them to learn it. When they disobeyed (the women were the first experts on the brain and intelligence), Yahweh kept them from discovering (eating of) the tree of life for fear that they would learn the genetic secret of immortality and live forever. It seems certain that, hundreds of thousands, if not millions of years ago, there was an advanced human civilization on earth. It eventually collapsed and we are the remnants. That’s my current take on it. Take it or leave it.

  9. 9
    Box says:

    Mapou: The secret of the two trees was freely accessible to mankind but Yahweh did not think they were ready for it and forbade them to learn it.

    But then along came Darwin and Yahweh understood that people were finally ready to learn the sacred knowledge about brains and DNA. So he send an angle named Francis Harry Compton Crick.
    It’s all starting to make sense now.

  10. 10
    Mapou says:

    Box,

    Crick is a feeble-minded moron. The real discoverer of DNA is Watson who understood the ubiquitous “twoness” of the natural world. Crick wanted some complicated structure. He ended up collaborating with another mediocre mind called Christof Koch on the neural correlates of consciousness. After many years of research, Koch and Crick eventually concluded that consciousness is an intrinsic property of matter like mass or charge. Even electrons, rocks and thermostats are conscious. It’s amazing the amount of damage a little Darwin can do to someone’s brain.

    Needless to say, Darwin, too, was a mediocre mind. LOL.

  11. 11
    Box says:

    Mapou:

    Crick is a feeble-minded moron. (…) Needless to say, Darwin, too, was a mediocre mind. LOL.

    Compared to who? You?

  12. 12
    Mapou says:

    Box:

    Compared to who? You?

    Not me. I’m a fruitcake and a crackpot, an internet kook. 😀 Compared to real scientific giants like several ancient Greek and Arab thinkers, and others who came much later like Newton, Leibniz, Maxwell, Faraday, Galileo, Marie Curie, Von Neumann and many others.

  13. 13
    Querius says:

    So Mistletoe is apparently “devolving” according to the article. One wonders whether everything else is devolving as well, and how this could be determined.

    Extinction is one measure. The fossil record seems to support this perspective.

    The major mass extinction events of the Phanerozoic include the following (after Lucas, 2005; Raup and Sepkoski, 1982, 1984; Courtillot, 1999):

    450 Myr (Late Ordovician) – estimated 85% of marine species became extinct

    374 Myr (Late Devonian) – estimated 70-80% of marine species became extinct

    251 Myr (end of the Permian) – estimated 90% of all species became extinct, perhaps 99% of all animals — the greatest mass extinction known in Earth history

    200 Myr (end of the Triassic) – most ammonites, half the genera of bivalves, many brachiopods and gastropods, 20% of foraminifera families, 80% of quadrupeds, and all conodonts became extinct

    65 Myr (end of the Cretaceous) – dinosaur extinction, along with ~2/3 of all species and perhaps 80% of all individual organisms

    http://www.baylor.edu/geology/index.php?id=62339

    The degeneration of various genomes (and their interdependent biomes), may have made these organisms less able to adapt.

    -Q

  14. 14
    mike1962 says:

    Mapou: The secret of the two trees was freely accessible to mankind but Yahweh did not think they were ready for it and forbade them to learn it.

    Small correction: In the story, the two are not forbidden to eat from the Tree of Life until after they disobeyed and ate from the Tree of Experiential Knowledge.

    I agree with you about the allegory part. Whatever the writer was trying to convey, it was not about a literal couple. An origins story for the simple, with the real allegorical meaning for the initiates.

    It is interesting how the writer took some of the Sumerian creation tales and reworked the outer story into the allegorical Genesis story. (No, I’m not a follower of Zitchen. I think he’s a hack and a dilettante.) But it is nevertheless interesting (and significant) that the writer of Genesis borrowed heavily from the Sumerian tales and flipped their meaning around to fit the allegory they were “hiding” in plain sight.

    But this is way off topic.

  15. 15
    Mapou says:

    mike1962, thanks for the correction. Maybe it was the other way. Maybe the Genesis account was first and the Sumerians borrowed from it to weave their own mythological creation story. I surmise that, if the book of Genesis was compiled by Moses, it’s a good bet that Moses could have had access to the original texts, having been a high official in the court of his highness the Pharaoh. And being Hebrew, it’s a sure bet that he might have kept historical or genealogical documents related to the history of the Hebrews. After all, we are told that Moses was instructed in all the wisdom of the land of Egypt.

  16. 16
    logically_speaking says:

    Mapou,

    “The entire story of Adam and Eve, the trees of life and knowledge, the devious talking snake, paradise, garden, etc., is purely metaphorical”.

    Except that Genesis repeatedly states that “this is the history of….” so you are wrong.

    “Here’s my interpretation”.

    That’s your problem right there.

  17. 17
    Dr JDD says:

    Revelation is prophetic vision and written as such. Genesis is written as history. Are things still described in ways that might not be literal as if we were there? Sure. But where does the allegory stop and the history start? The flood? Is that allegory? So what about Jesus’ words on the flood? Did he misunderstand who Noah really was?

    And what about the talking donkey? Is that small portion of the old testament allegory but that either side is history? Did God use a donkey to speak? Could the most powerful being created (Satan) who was of the spiritual dimension impersonate or talk trough an animal of sorts that was probably very different to our understanding of what that was today (a serpent )?

    Then let us move on to the real issue at hand. How did Jesus view Scripture? What works did Jesus do to validate his message? Jesus clearly even held that the very tense of a statement in the old testament could be taken literally as speaking of the nature of God. Jesus affirmed Noah, that from the beginning there was male and female. He clearly had a high regard for the Torah and the prophets and the Psalms, and viewed them as inspired.

    Jesus also created. Instantaneous creation. He healed a man with a shrivelled arm. He restored sight to those born blind. Hearing to the deaf. Those who were lame to walk. And most crucially, raised someone who had been dead and decomposing 4 days back to full life. That is instantaneous creation miracles. Note his objectors did not try to say he did not do these works, they just refused to believe his message (that he was God incarnate) even though his extensive miracles should have validated his message.

    So I always ask and wonder – why is the garden of Eden and those details so hard for people to see as real yet as Christians most accept Jesus, limited to human form, performing such creative miracles? And where do we stop with our allegory? Is the resurrection allegory? Did the risen Jesus really walk through walls and ascend into heaven visibly?

    Again, if you apply the rule of “I cannot imagine that happening” (eg Satan possessing a serpent and talking to Adam and Eve through it) then you have far more problems than Gen 1-12 to deal with in the Bible.

  18. 18
    mike1962 says:

    Mapou: Maybe the Genesis account was first and the Sumerians borrowed from it to weave their own mythological creation story.

    Any evidence for that? The philological evidence points the other way. But this probably isn’t the place to discuss such things.

  19. 19
    ppolish says:

    Mike, the Creation predates Moses. It predates the Sumerians too. Nothing wrong with the Sumerians being on the right track.

  20. 20
    Mung says:

    Dr. JDD you are missing the point.

    So there was a talking donkey. From this do you extrapolate to the belief that all animals could talk? No? Why not?

    Why then treat Gen 3:17 differently? Why do people try to read into the text something that is simply not there?

  21. 21
    Mapou says:

    mike1962, nothing is written in stone in this discussion. I’m speculating that Moses, the presumed author of Genesis, was a highly educated and powerful man in the Egyptian kingdom and thus had access to all their records. Ancient Egyptian nobles also had a love of knowledge, libraries and books. One of the worst disasters in history was the burning of the library at Alexandria. So it makes sense to suppose that Moses could have had access to ancient (even in his day) documents/tablets that few others had.

  22. 22
    Mapou says:

    logic:

    Mapou,

    “The entire story of Adam and Eve, the trees of life and knowledge, the devious talking snake, paradise, garden, etc., is purely metaphorical”.

    Except that Genesis repeatedly states that “this is the history of….” so you are wrong.

    “Here’s my interpretation”.

    That’s your problem right there.

    It’s your problem too, apparently.

  23. 23
    Mapou says:

    Mung @20, the difference is that the talking snake is identified in other scriptures as Satan, the ancient serpent, the dragon, the accuser, the Devil, the fallen angel, etc. There is also the fact that the tree of life and the serpent are also used in the book of Revelation, a purely metaphorical book.

    Of course, a bunch of people throughout history have read and continue to read the book of Revelation as if it were literal. I once saw a fundamentalist preacher of hellfire and damnation use Revelation to preach that sinners will burn in hell for eternity. It’s sickening.

  24. 24
    Dr JDD says:

    Eh Mung? I think you are missing the point. I spoke of a talking donkey because you specifically used the example of a talking serpent as a reason to not take the text literally. That says nothing of Gen 3:17.

    The theology that the whole of the land and creation is cursed and subject to sin is a broadly taught principle throughout the bible which is one of several reasons the plain interpretation of Gen 3:17 refers to a curse on the entire ground and the introduction of features as a result of the curse not formerly present.

    It all comes down really to whether you believe the Bible is the inspired Word of God or not. True Christianity swims or sinks on that premise.

  25. 25
    ppolish says:

    Mapou, there were no books when Moses lived. Scrolls and stuff written on stone. And he certainly was not a world traveled highly educated guy.

  26. 26
    logically_speaking says:

    Mapou,

    “It’s your problem too, apparently”.

    Yeah it sure is, I tried translating Genesis myself once from different sources, and gave up as it was just to difficult for me. At the time I dubbed it the Modern Interpretation, so if I was ever asked what version of the Bible I was using, I could say I was using MI version.

    “There is also the fact that the tree of life and the serpent are also used in the book of Revelation, a purely metaphorical book”.

    The book is called REVEAL-ation for a reason, the whole point of the book is to reveal stuff to us so we can finally see the big picture.

  27. 27
    Mapou says:

    Ok. I’m outta here.

  28. 28
    Mung says:

    Mapou, I didn’t say anything about a talking snake.

  29. 29
    Mapou says:

    Mung,

    Sorry.

  30. 30
    Querius says:

    If you’re not already familiar with the Genesis tablet theory, you might want to read this:

    http://www.talkgenesis.org/gen.....h-mystery/

    Basically, PJ Wiseman presented internal evidence that Genesis (until the account of Joseph) was written on clay tablets, very similar in style to those used in ancient Mesopotamia. Using the “Toledoths” within the text along with “catch phrases,” He concluded that there were about a dozen, clearly identified authors of Genesis, and Moses was not one of them. The tablet pattern ends with the start of the story of Joseph, perhaps because in Egypt, they used papyrus rather than clay tablets.

    The evidence is compelling and many scholars have come to accept it as the most likely explanation.

    -Q

  31. 31
    Mapou says:

    Querius @30,

    Thanks for the link.

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