Pharyngula

Plant and animal development compared

Blogging on Peer-Reviewed Research

Since I wrote about the wacky creationist who couldn’t wrap his mind around the idea that plants and animals are related, and since I generally do a poor job of discussing that important kingdom of the plants (I admit it, I’m a metazoan bigot…but I do try to overcome my biases), I thought I’d briefly mention an older review by Elliot Meyerowitz that compares developmental processes in plants and animals. The main message is that developmental processes, the mechanisms that assemble the multicellular whole, are very different in the two groups and are non-homologous, but don’t get confused: the basic cellular processes are homologous, and there’s no doubt that we are related. The emphasis in this paper, though, is the evidence that plants and animals independently evolved multicellular developmental strategies. There is some convergence, but the tools in the toolbox are different.

First, here is a basic overview of the evolutionary history of these two groups.

i-588e56d8f800081fa600e4f3fa6943bb-plant_evo.jpg

Notice that we’re talking about events in deep time here: we eukaryotes (organisms with a true cell nucleus) evolved as single-celled animals 2.7 billion years ago, and we only know this because we find smears of characteristic hydrocarbons in the rocks of that age. The last common ancestor of plants and animals is estimated from molecular clock data to have lived 1.6 billion years ago — that’s a very long time ago. It’s hard to get the concept of that huge amount of time across to people, but look at the relative amounts of time: complex, multicellular animals evolved a bit more than 0.5 billion years ago, and all of the macroscopically large animal diversity we see now evolved since then; but there’s a period twice as long as that before arthropods and molluscs developed hard shells in which change was percolating in single-celled eukaryotes, laying the foundation for the current differences between orange trees and cats.

But wait…what was the plant-animal common ancestor like? Was it a single-celled organism, or did it have a more complex multicellular organization? Meyerowitz catalogs the different molecular tools that plants and animals use in development, and concludes that development evolved completely independently in the two, with a few hints of some shared elements that tell us a bit about the genetic heritage we have received from that mysterious Proterozoic cell.

Meyerowitz summarizes a few broad categories of similarities and differences in plant and animal development.

  • Pattern formation: Pattern formation is a very wide assortment of developmental processes that define regions of an embryo — the events that put a head on one end and a tail on the other, or a flower above ground and roots below ground, are examples of pattern formation. In animals, the classic example of pattern forming genes are the Hox genes, which establish regional specifications in the early embryo. Plants have similar genes, the MADS box genes, that also set out overlapping regional identities in the growing plant — but MADS boxes and Hox genes are not homologous. Animals have MADS box genes, but don’t use them in pattern formation; plants have Hox genes, but also don’t use them in pattern formation. This suggests that the last common ancestor of plants and animals was single-celled or at best colonial, and lacked any differently developed regions; when regional specialization evolved later in each lineage, different sets of transcription factors were arbitrarily used for the job.

    Another example is dorsoventral specification. We know quite a bit about how that axis is defined in animals, and it’s an elaborate process involving a TGF-α-family protein, an EGF receptor, a receptor tyrosine kinase, a Ras activated cascade, etc. Trust me, it’s detailed, and to developmental biologists with a metazoan bias, like me, the components are all familiar friends. Plants have a similar task, setting up the adaxial-abaxial axis (you’ve certainly noticed that the top and bottom sides of leaves are different), but the molecules involved are completely different, and plants lack homologs of many of them altogether. Instead, plants use REVOLUTA/PHABULOSA/PHAVOLUTA receptors and REV/PHAB/PHAV homeobox proteins, KANADI genes, and the YABBY family of transcription factors. It’s a whole new language as far as I’m concerned, but fascinating — plants use a similar logic to animals, but the pieces are alien to me.

  • Chromatin processes: Another critical step in development is the maintenance of a pattern. After pattern formation initializes the organization, cells in the embryo that descend from an early cell with a particular identity have to maintain that specification; development is a strongly hierarchical process. There are gene products that maintain the pattern of activators and repressors of gene activity and that are inherited by daughter cells in mitosis. In flies, for example, there is a gene called Enhancer of zeste, E(z), that helps lock in expression of some of the Hox genes. Plants have similar genes, and in some cases at least, they’ve been found to be homologous. Arabidopsis has a gene called CURLY LEAF (CLF) that is an E(z) homolog, and there are other chromatin-regulatory proteins that are found in both plants and animals. CLF and E(z) are clearly related genes, and they carry out similar functions in the regulatory logic, but note that while E(z) regulates a Hox gene, CLF regulates a MADS box gene.

  • Cell:cell signaling: During development, cells must communicate with each other, and they do so with molecules, ligands and receptors, that can activate signal transduction cascades inside the cell that lead to changes in metabolic activity or gene regulation. In animals, one common and important family of cell signaling receptors are the receptor tyrosine kinases (RTKs). A kinase is an enzyme that phosphorylates other proteins, attaching a phosphate group to certain amino acids. A tyrosine kinase is one that phosphorylates tyrosines. Plants don’t have any RTKs at all — they are unique to the animal (well, opisthokont) lineage. Plants certainly do have receptor kinases, and carry out cell signaling quite well, but are more likely to use a receptor serine/threonine kinase. Again, we find similar logic carried out by nonhomologous components.

    Another example are the familiar steroid hormones. Both plants and animals use steroid signaling, but animals receive that signal in each cell via members of the nuclear hormone receptor family, while plants use a receptor kinase. Steroid synthesis is common to both lineages, but each has its own way of using it as a signal.

  • Horizontal transfer: Don’t get the impression that animals have all the cool, unique, new stuff, though — that isn’t true. Plants also have their own unique flavors of proteins for which we animals have no homolog. One example are the families of ethylene receptors, a chemical plants use as a signal. These receptors resemble bacterial two-component receptors, and are thought to have aisen by horizontal transfer from cyanobacteria. This transfer event probably occurred after the divergence of plants and animals, so we missed out.

    Another example are the phytochromes, red and far-red light receptors that are similarly related to bacterial two-component receptors. We have nothing similar. What’s particularly interesting about these is that in cyanobacteria, they act as histidine kinases, but in plants, they fit into the more common plant pathways by working as serine/threonine kinases. While horizontal transfer may be a common phenomenon, retention and expansion of such genes shuffled across species also requires some modification to incorporate them into a functional pathway.

The bottom line is that plants and animals clearly arose from a common ancestor, almost certainly single-celled, and that they’ve evolved the processes that allow cells to cooperate and communicate and assemble into complex, elaborate entities with tissues and organs nearly completely independently. We don’t need to go to Mars or Betelgeuse to find aliens, they’re living side-by-side right here on planet Earth. Most importantly, if evo-devo wants to find truly general, universal principles of multicellular development, we can’t get too fixated on gene identities in metazoans (and especially not on the specifics of development in one beastie, Drosophila melanogaster) — we have to throw a wider phyletic net and distill out a bigger picture of the mechanisms involved. The important focus should be on developmental logic, rather than developmental details.


Meyerowitz EM (2002) Plants Compared to Animals: The Broadest Comparative Study of Development. Science 295(5559):1482-1485.

Comments

  1. #1 Holydust
    February 17, 2008

    hoohoo. best way to spend a sunday — biology lesson. :D I’m not being sarcastic. serious. that’s sad, isn’t it? :’D

  2. #2 raatrani
    February 17, 2008

    I agree. The more I learn about the world, and the organisms in it, the greater is my wonder at the very nature of existence. I’m really baffled by the insistence of religious dogma that, as humans, it is somehow beneath our dignity to be related to, and associated with, animals.

  3. #3 tsig
    February 17, 2008

    I could only live up to the dignity of my cat.

  4. #4 danley
    February 17, 2008

    Pomegranates for Christ.

  5. #5 Matt
    February 17, 2008

    Holydust: Ha! I completely agree. When the new addition of “Biology” came out and the 6th edition dropped to less than $20 on amazon, guess who was one of the first to pick it up?

    I’ve got a fort of books on biology and physics right now, keeping out the religious heebie-jeebies.

  6. #6 Blake Stacey
    February 17, 2008

    Fascinating post! I don’t know how a physics geek like me could keep up with biology if it weren’t for Pharyngula and its fellows. It’s unfortunate that these posts seem to attract less discussion than the straight-up creationist bashing — harder for people to think of things to say, I guess, other than “Jebus, 1.6 billion years is a long time!”

    (And Jebus, 1.6 billion years is a long time!)

    If I might continue in the tradition of using and abusing analogies to computers, it sounds like PZ is advocating an approach which looks at developmental rules coded in a high-level language; plants and animals “compile” that code to the “machine language” of particular genes in different ways.

    Well, we know where PZ stands on the usefulness of evo-devo, so I guess we’re just waiting for his statement on multilevel selection — betcha that’ll spark some discussion. . . .

  7. #7 negentropyeater
    February 17, 2008

    “This suggests that the last common ancestor of plants and animals was single-celled or at best colonial, and lacked any differently developed regions; when regional specialization evolved later in each lineage, different sets of transcription factors were arbitrarily used for the job.”

    Something I still don’t understand ; that single celled common ancestor must have had a very short genome. How does one explain that it grew in size, added more base pairs and enabled the evolution of different regional spezializations ?

  8. #8 spurge
    February 17, 2008

    “Something I still don’t understand ; that single celled common ancestor must have had a very short genome.”

    Why must the common ancestor have had a short genome?

    Were they not evolving for a billion years before the split?

  9. #9 Physicalist
    February 17, 2008

    @ #2: Their problem (or part of it) is that they’re so focused on their fairy tales and magic lands that they’re happy to ignore the truly wonderful nature of the actual world. Sad.

    Great post, PZ. Thanks for the learnin’.

  10. #10 Dee
    February 17, 2008

    Nice way to spend a Sunday morning. Brisk walk in the cold sunshine and back to a cool biology lesson. Thanks for these, I really enjoy them. I haven’t had biology since junior high or high school, and yes that means it’s been so long ago that I can’t remember anymore. It’s a lot more interesting than I remember. Keep ‘em coming.

    One question – looking at the chart, does this mean plants have mitchondria as well as chloroplasts?

  11. #11 alias Ernest Major
    February 17, 2008

    Re #6 – the assumption that the common ancestor of plants and animals had a short genome is not obviously true; the size of the genomes of organisms is not well correlated (this is known as the C-value paradox) with complexity (with caveats as to the problems in defining a measure of organismal complexity) – for example certain amoebae are notorious for their large genomes.

    One living single-celled eukaryate (a dinoflagellate) has more cell types than some animals.

    There are processes which increase genome size; polyploidy (which doubles genome size in a short period of time) may be the most important.

  12. #12 windy
    February 17, 2008

    “Two groups”? Fungi don’t get respect…

  13. #13 The Science Pundit
    February 17, 2008

    Great post PZ! It complements the Neil Shubin book I’m reading quite well. Back to Your Inner Fish for me.

  14. #14 Blake Stacey
    February 17, 2008

    Dee:

    One question – looking at the chart, does this mean plants have mitchondria as well as chloroplasts?

    Yep!

  15. #15 Dan
    February 17, 2008

    negentropyeater asks (#6)

    “Something I still don’t understand … How does one explain that [the genome] grew in size, added more base pairs and enabled the evolution of different regional spezializations?”

    Gene duplication

    http://www.sciencemag.org/cgi/content/full/293/5535/1551a

  16. #16 Dee
    February 17, 2008

    Thanks for the link, Blake. I must not have been paying attention that day in class. All these years I thought plants had chloroplasts instead of mitochondria.

    Another chance to display my ignorance (and I hope you don’t mind; I’m supposed to be working and it’s easier to ask than read the book you linked to) – but don’t these two play the same kind of role in the cell? Mitochondria uses oxygen to react with ATP to make chemical energy available to the cell, and chloroplasts use photons to do something similar? Or is the role of mitochondria modified in plants?

    Cool.

  17. #17 andy
    February 17, 2008

    Where do fungi branch off on that diagram, before or after the plant/animal split?

  18. #18 Paul Burnett
    February 17, 2008

    “alias Ernest Major” posted (#10): “There are processes which increase genome size; polyploidy (which doubles genome size in a short period of time) may be the most important.”

    Diploidydoubles genome size” – polyloidy is just “many” – there’s triploidy, tetraploidy, pentaploidy, hexaploidy…

    Yeah, thanks for the lesson, PZ. Question: If the subject predates the split between prokaryotes and eukarotes, is it a biology lesson or a botany lesson?

  19. #19 PZ Myers
    February 17, 2008

    Fungi and animals split later, and animals and choanoflagellates later still. (Be patient, I’m working on another post about these recent papers on the choanoflagellate genome that were recently published — evolution of multicellularity must be my theme this week!)

  20. #20 dzho
    February 17, 2008

    Gawd, I feel so old: Back in the 70s when I studied botany, did anybody know anything? At the library today I’m gonna look for a basic biology textbook. Should be like exploring a whole new world. Thanks, PZ.

  21. #21 Beth B.
    February 17, 2008

    Fascinating post! I hadn’t realized eukaryotic cells are so ancient — that 2.7ish time window around the end of the Archean eon must have been a happening time in earth history. Photosynthesis is thought to have evolved at around the same time or slightly later.

  22. #22 Jim Thomerson
    February 17, 2008

    Does anyone know why flowering plants have double fertilization? Maybe this is one the ID folks could work on.

  23. #23 Chris
    February 17, 2008

    Andy (#16): “Where do fungi branch off on that diagram, before or after the plant/animal split?”

    Fungi branch off after the plant animal split. If fungi were included in the above tree, they would split from the red branch that shows animals as an extant group. The fungi and animals are thus sister groups.

    http://www.tolweb.org/Eukaryotes
    http://www.pnas.org/cgi/reprint/90/24/11558.pdf

  24. #24 Ned in Zurich
    February 17, 2008

    Somehow this reminds me of something I read not too long ago: Two types of bacteria were said to be less closely related to one another than humans are to potatoes. A very striking analogy. Unfortunately I can’t remember what the bacterial strains were.

    Ned

  25. #25 David Marjanovi?, OM
    February 17, 2008

    What happened to the 2.1 Ga old fossils of multicellular red algae? Did they get radically reinterpreted? And aren’t the 2.7 Ga old chemofossils dinosteranes, something that only dinoflagellates produce? (The dinoflagellates are nested deep inside a large tree, so most of eukaryote diversity must have been present when the first dinoflagellates appeared.)

    The horizontal transfer from cyanobacteria — is there any evidence that this didn’t happen at the same time as the origin of chloroplasts?

    Something I still don’t understand ; that single celled common ancestor must have had a very short genome.

    Not at all, why?

    but don’t these two play the same kind of role in the cell? Mitochondria uses oxygen to react with ATP to make chemical energy available to the cell, and chloroplasts use photons to do something similar?

    Yes, but chloroplasts work only when and where the sun shines. The stem and roots (and the epidermis) have no choice but to breathe, and at night the whole plant does so.

    This is the whole point of making sugar in the chloroplasts.

    Where do fungi branch off on that diagram, before or after the plant/animal split?

    Long after. Fungi and animals are very close relatives. (Together they are called Opisthokonta because they — originally — have a single cilium that inserts at the back end of the cell.)

  26. #26 David Marjanovi?, OM
    February 17, 2008

    What happened to the 2.1 Ga old fossils of multicellular red algae? Did they get radically reinterpreted? And aren’t the 2.7 Ga old chemofossils dinosteranes, something that only dinoflagellates produce? (The dinoflagellates are nested deep inside a large tree, so most of eukaryote diversity must have been present when the first dinoflagellates appeared.)

    The horizontal transfer from cyanobacteria — is there any evidence that this didn’t happen at the same time as the origin of chloroplasts?

    Something I still don’t understand ; that single celled common ancestor must have had a very short genome.

    Not at all, why?

    but don’t these two play the same kind of role in the cell? Mitochondria uses oxygen to react with ATP to make chemical energy available to the cell, and chloroplasts use photons to do something similar?

    Yes, but chloroplasts work only when and where the sun shines. The stem and roots (and the epidermis) have no choice but to breathe, and at night the whole plant does so.

    This is the whole point of making sugar in the chloroplasts.

    Where do fungi branch off on that diagram, before or after the plant/animal split?

    Long after. Fungi and animals are very close relatives. (Together they are called Opisthokonta because they — originally — have a single cilium that inserts at the back end of the cell.)

  27. #27 KM
    February 17, 2008

    PZ:

    I always enjoy your posts calling out Creationists but this bit ‘o biology was refreshing. Thanks for a great and fascinating post.

  28. #28 thalarctos
    February 17, 2008

    Most importantly, if evo-devo wants to find truly general, universal principles of multicellular development, we can’t get too fixated on gene identities in metazoans (and especially not on the specifics of development in one beastie, Drosophila melanogaster) — we have to throw a wider phyletic net and distill out a bigger picture of the mechanisms involved. The important focus should be on developmental logic, rather than developmental details.

    This quote would be the icing on the cake for the paper I’m currently revising. Do you mind if I use it, PZ?

  29. #29 thalarctos
    February 17, 2008

    PS, PZ (heh!)–if you want to see a draft before you answer my previous question, that can certainly be arranged.

  30. #30 Bing McGhandi
    February 17, 2008

    I don’t know if anyone else feels the same way, but the simplicity and elegance of evolutionary theory, as well as the complexity it gives rise to, not only satisfies the rational part of my mind, but also tickles my aesthetic sense.

    Because evolution has such inherent aesthetic appeal, I wonder how often artists have been able to make use of it. What occurs to me first is Bruce Sterling’s short story “Swarm,” which you should read. Vonnegut’s Galapagos also comes to mind. In an oblique sort of way, cyberpunk and posthuman fiction deal with the possiblities of human evolution. Any others?

    HJ

  31. #31 Cuttlefish, OM
    February 17, 2008

    I took this post and ran it through
    A New-Age Verbiage Filter–
    Resulting in conclusions which
    Are just a bit off-kilter.

    It seems you’ve given evidence
    For many a woo-woo notion,
    And I predict the following
    Will soon be set in motion:

    If just two billion years ago,
    In some primordial goo,
    We shared a common ancestor
    Then plants have feelings too!

    And surely you have proved beyond
    A shadow of a doubt
    That houseplants are much happier
    When folks don’t scream or shout.

    Indeed, the information that
    This science paper cites
    Becomes a legal argument
    That plants have civil rights!

    The converse, also, must be true
    That deep inside, we’re plants,
    And we can photosynthesize
    In meditative trance!

    If just two billion years ago
    The plants and we were one
    It’s proof that man can live while
    Eating only air and sun.

    Of course, since none of this is true
    No matter our desires–
    The scientists are clearly wrong
    And all a bunch of liars.

    http://digitalcuttlefish.blogspot.com/2008/02/science-through-new-age-filter.html

  32. #32 Sili
    February 17, 2008

    What’s with all this Science?!

    I come here for the snarky relidiot-bashing. Not this hoiti-toiti biology.

    (Sorry – it had to be said.)

  33. #33 Malky
    February 17, 2008

    A good analogy of the difference in time is that 1m seconds is @ 11.6 days but 1bn seconds is @ 31.7 years

  34. #34 HP
    February 17, 2008

    Great post, and it leaves me wanting more.

    I generally do a poor job of discussing that important kingdom of the plants

    So that reminds me: When, oh, when is the ScienceBlogs hive mind going to assimilate a plant biologist?

  35. #35 Ron
    February 17, 2008

    Dee-

    Mitochondria rip carbon skeletons apart and use some of the energy of the bonds to build a hydrogen ion gradient across the inner mitochondrial membrane. That’s right, inner membrane; mitochondria have two membranes! The hydrogen ion gradient is built using an electron transport chain found in the inner membrane. The energy in the hydrogen ion gradient is used to produce ATP. This process requires molecular oxygen to stick the electrons on at the end of the electron transport chain, and results in water being produced.

    Chloroplasts build carbon skeletons up using the carbon in carbon dioxide to generate a three-carbon sugar (which you can stick together to make glucose if you want) using some similar processes. Light energy is “captured” by pigment molecules and the energy is used to build a proton gradient across a membrane using an electron transport chain. In this case, electrons are pulled from water at the start and oxygen is produced as a “waste” product. This all takes place in a membrane (the thylakoid membrane) that is found inside the inner and outer chloroplast membranes. The process does generate ATP, but the ATP is used in the chloroplast to help build the carbon skeletons.

    So the two organelles use some very similar processes to do almost exactly opposite things. :-)

    Jim-

    Why do plants have double fertilization? People are still arguing about why, but the result is the production of a triploid endosperm. In some plants (mainly monocots), the endosperm persists and is used as a nutrient source for the germinating seedling. In other plants (mainly dicots), the endosperm is transient, and the reserves are moved to the cotyledons. We, of course, take advantage of this storage process to feed ourselves and our animals. A good example of endosperm that most of us have seen is the big fluffy part of popcorn.

  36. #36 Dee
    February 17, 2008

    re #34
    Taking a short break from a paper I don’t really want to write, and I find #34. It’s a pleasure to read your response, Jim, thanks for the time.

    So does the mitchondiral double membrane(sounds like chloroplasts have them too, and for the same reason?) have any thing to do with the fact that they used to be free bacteria?

    This thread isn’t making it any easier for me to get my damn work done, you know.

  37. #37 Sam
    February 17, 2008

    Thanks for the fascinating post PZ! I never thought I’d be reading about pattern formation, chromatin processes, cell:cell signaling and horizontal transfer today! I always learn something new at this blog which keeps me coming back.

  38. #38 truth machine
    February 17, 2008

    @Cuttlefish

    Fucking genius. I hate you for making me feel puny.

  39. #39 harley gee
    February 17, 2008

    Nobody covers this area as well as Dawkins does with ‘Ancestors Tale’. It is elegant and it is authoritative and it is one of the best books I have ever read.

  40. #40 Nick Kanellos
    February 17, 2008

    Thanks PZ.

    Did you say you’d be blogging on the evolution of multi-celled organisms. I’d love a post on the transition from single celled organisms to multi-celled ones. Just hypothesizing here, not being a biologist, but could it be that colonies of single celled organisms developed sub-colonies with their own areas of specialization? What would have been the mechanisms of differenation back then?

    Very interesting stuff. Thanks again. I love these Sciencey posts (but the snarky creationist-bashing ones are great too!!!)

  41. #41 Ron
    February 17, 2008

    Dee-

    It’s Ron, actually, but that’s okay. From what I remember, the outer membrane of mitochondria is thought to have been derived from the membrane surrounding the critter as it was endocytosed (so from the “host” organism) and the inner membrane is the critter’s membrane. It’s been a long time since I read the literature on this so the viewpoint may have changed. I don’t have a clear recollection of how the three membranes of plastids got there, and I can’t remember if some photosynthetic bacteria have elaborations of their plasma membrane. Time to go back and do some reading.

  42. #42 kc
    February 17, 2008

    Paul (#18)

    Well, diploidy isn’t quite just the lowest level of polyploidy, because the “diploid” number of chromosomes is that which gets divided at meiosis in a eukaryote into “haploid” gametes/spores, etc. You can have a (allo)tetraploid with a diploid number of, say, 24 chromosomes, which come from two parental lines (say 11+13). It’s still a polyploid (tetraploid), but also a functioning (meiotically) diploid at the same time. It can get real messy with various types of polyploids, aneuploids, etc., but it’s really a fascinating area (especially in plants!)

  43. #43 Dee
    February 17, 2008

    Oops, sorry Ron. I know I’m bad with names, but that’s really bad. I’ve been staring at a computer screen all day, so my eyes are pretty crossed. But thanks!

  44. #44 negentropyeater
    February 17, 2008

    DELIRIUM ON

    < Ah these evil scientists who need billions of years to explain how everything was made, when it took God only seven days. They want to make us believe that if you left a bucket of dirt outside in your backyard, after some billions of years, it 'd transform itself, without any miracle, into cabbages, ceiling wax and kings. Do they think we're stupid or what ? No wonder with this kind of beliefs, we're all gonna become communist embryo eating homosexuals ! >

    DELIRIUM OFF

    (sorry for the very sudden attack)

  45. #45 negentropyeater
    February 17, 2008

    DELIRIUM ON

    - Ah these evil scientists who need billions of years to explain how everything was made, when it took God only seven days. They want to make us believe that if you left a bucket of dirt outside in your backyard, after some billions of years, it ‘d transform itself, without any miracle, into cabbages, ceiling wax and kings. Do they think we’re stupid or what ? No wonder with this kind of beliefs, we’re all gonna become communist embryo eating homosexuals !

    DELIRIUM OFF

    (sorry for the very sudden attack)

  46. #46 David Marjanovi?, OM
    February 17, 2008

    The thylakoids are simply budded-off infoldings of the inner membrane. The inner membrane, like that of mitochondria (which also has lots of infoldings), is the chloroplast’s own membrane, and the outer one ultimately results from the endocytosis event that led to the origin of chloroplasts.

    The chloroplasts of the glaucophytes, called cyanelles, have a bacterial cell wall in the expected place: between the two membranes.

  47. #47 David Marjanovi?, OM
    February 17, 2008

    The thylakoids are simply budded-off infoldings of the inner membrane. The inner membrane, like that of mitochondria (which also has lots of infoldings), is the chloroplast’s own membrane, and the outer one ultimately results from the endocytosis event that led to the origin of chloroplasts.

    The chloroplasts of the glaucophytes, called cyanelles, have a bacterial cell wall in the expected place: between the two membranes.

  48. #48 Nomen Nescio
    February 17, 2008

    re. #11:

    One living single-celled eukaryate (a dinoflagellate) has more cell types than some animals.

    er, how’s a single-celled organism have more than one cell type? i don’t get it.

  49. #49 windy
    February 17, 2008

    “how’s a single-celled organism have more than one cell type?”

    How could Liz Taylor have seven husbands? :)

  50. #50 JohnnieCanuck, FCD
    February 17, 2008

    I think he may have phrased it like that on purpose, Nomen.

    Sort of an answer begging for your question.

  51. #51 foxfire
    February 17, 2008

    PZ, thank you so much for this article – and thanks to the folks posting comments too. The links, additional information, thoughts and comments are wonderful.

    To Holydust @ #1: Today is my 57th birthday and I feel the same (except did go to a dynamite brunch and Sagan’s Cosmos is now mine, plus some really awesome fish-art!)

    To Matt @ #5: Oh wow! You too? Cool! Unfortunately, age takes its toll and it’s annoying that learning takes longer nowdays.

    To Ron @ #34: Thank you for yet another perspective of what I’m learning – that is a really cool and thanks to Dee for asking.

    And then there is Cuttlefish:

    Delightful rhymer,
    science love showing,
    faces ID whiner
    by poem-ing with knowing.

    Be it YEC* or ID
    they can have no hopes,
    as science and C-Fish
    reveal they are dopes

    Delightful writer,
    clever and true;
    making threads brighter,
    we really like you!

    * YEC – pronounced like Heck, but with Y instead of a H.

  52. #52 Monado, FCD
    February 17, 2008

    If you want a good basic biology book online, here’s Miller and Levine’s Biology, also called “the Dragonfly book” (the one recommended for teachng actual science in Dover, Pennsylvania).

    Evolutionary theory has advanced so much since I took Bio. in university that I think I’d start there.

  53. #53 ColinB
    February 17, 2008

    Ok, so finding my biological knowledge a bit stretched, I had to look up the word – opisthokont. My google search took me to wikipedia (http://en.wikipedia.org/wiki/Opisthokont) where to my surprise the topic was labelled “controversial”?

    What gives – is there a serious scientific controversy or has some fundy simply complained about grouping animals with fungi?

  54. #54 Alan Kellogg
    February 18, 2008

    From what I’ve seen it would appear that a that a plant/animal split is an oversimplification. The actual sequence was probably more like…

    Algae arise from protists incorporating cyano bacteria. Plants will later evolve from algae in the transition to the land.

    Slime molds arise from a different protist group. This event will occur twice more. Of these three groups one might be the ancestor of fungi and animals, or those two might have arisen from different slime mold kingdoms.

    Then you get into phyta and phyla, which gets complicated. Then add in red plants, which are descended from red algae and so form a phytic kingdom all their own. Making matters even murkier you have viral lateral transference, bacterial lateral transference, and even (maybe) eurkaryotic lateral transference of DNA. We may have gotten the gene for creativity from an African shrub who used it to regulate cell communication.

    Think of biology as a soap opera murder mystery with 50 years of backstory, missing film and video, and no organization to the records other than what one can devise for one’s self.

  55. #55 DrFrank
    February 18, 2008

    Great post, PZ – it’s corrected a couple of misconceptions I had about plant/animal relatedness, which isn’t something I’d really read about :)

  56. #56 zer0
    February 18, 2008

    I thoroughly enjoyed the post PZ and hope you find the time to do posts like these more often. You explain things very well, it’s almost as if you know this stuff ;)

    Cuttlefish, great poem. Always a pleasure.

  57. #57 DrA
    February 18, 2008

    RE: Jim Tomerson’s question “Does anyone know why flowering plants have double fertilization? Maybe this is one the ID folks could work on. ”

    As mentioned above, the 2nd fertilization makes endosperm, both diploid (in basal lineages of flowering plants) and triploid (2n) in the rest. It functions in nutrition of the embryo, and when the embryo is large (one strategy, and not all dicots do this, and dicots aren’t a group anymore anyways) the endosperm is totally absorbed. But that doesn’t answer why make endosperm?

    In all other land plants, including the other seed plants, the embryo (diploid organism) grows within and receives nutrition from the maternal parent (a haploid organism), so it has been proposed that there is an genetic compatibility advantage to endosperm which is a genetic twin to the embryo. Great idea, but no real proof.

    However the production of endosperm has one fairly clear reproductuve advantage. Flowering plants do not start packing food reserves into a seed until after a successful fertilization produces an embryo, whereas in other seed plants, the gymnosperms, a fairly large female gametophyte with food reserves had to reach maturity before fertilization could take place. The female gametophyte in flowering plants is greatly reduced, minimally consisting of just 4 cells, although usually illustrated as 8 nuclei in 7 cells where the 2 nuclei together fuse with a sperm to make 3n endosperm.

    RE: “So that reminds me: When, oh, when is the ScienceBlogs hive mind going to assimilate a plant biologist?”

    Good question. A few of us are out there, and we resist assimilation. Oh, that’s the Borg not the Blog. Sorry.

  58. #58 John Scanlon, FCD
    February 18, 2008

    ColinB #51, maybe it’s the term itself that’s seen as a little risqué. My Greek’s just a little rusty, but it reads to me as ‘rear-konts‘ or ‘having a kont at the back end’. Many of those little words in English go all the way back to Proto-Indo-European and have cognates in other IE languages…

  59. #59 Abhishek
    February 20, 2008

    Just in case you take questions after class – what exactly is ‘developmental logic’? I read Endless forms most beautiful and it talks about the ‘combinatory logic’ of gene regulation (I assume this has nothing to do with that term as used in comp sci) with a few diagrams that resemble flowcharts, but no more details.

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