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Can an organism exist as a single cell but come together as multi-cellular during certain times?

Can an organism exist as a single cell but come together as multi-cellular during certain times?


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I am trying to remember a particular segment from a BBC special, about a single celled species. However, at certain times all the individual cells came together to form a structure, not unlike a mushroom, to scatter something like spores into the wind. Afterward, the individual cells separated and continued on as individuals.

Am I remembering this incorrectly? Is this even possible?


Welcome to Biology StackExchange.

Am I remembering this incorrectly?

No, you're remembering it correctly.

I think you're talking about slime molds. You'll find more information on the wiki page

Is this the video you saw? These images are pretty cool.

Is this even possible?

Yes (given that it exists). There is no way to correctly answer this question as it really is an open-ended question. But here are a few words that may push you writing further posts.

Just a few words on the evolution of altruism

The main interest behind this life-cycle is that not all individuals reproduce. Some individuals form the stalk while others go through meiosis (see below on the life-cycle).

How unfair does it seem to those who form the stalk! Why would those individuals forming the stalk spend energy to help other individuals to reproduce?

Kin selection

Let's think about us, vertebrates, "real multicellular" organisms. The cell that is in your eye is never going to reproduce. Although it is spending all its energy into helping your ovules/spermatozoids to fuse. Why would this cell in the eye make such an effort? The genes in the spermatozoids/ovules are essentially the same as those in the "eye cell". Therefore, by helping your spermatozoids/ovules the eye cell is actually contributing to spreading copies of the genes that it is carrying. This is referred to as kin selection.

Slime molds and altruism

Now, the story is not exactly the same for the slime molds. The cells in the stalk can be quite different from those that are undergoing meiosis. Altruism can exist in a variety of different mechanisms and it would take several books to go over the literature about the evolution of altruism. Without knowing the literature specific to the slime molds reproduction, I just want to notice that the cell in the stalk will die anyway, whether or not it spend energy helping other cells reproducing. There is, therefore, no fitness cost into construction a stalk. Little population structure (causing higher relatedness within deme than among demes) could be enough to allow this behaviour to evolve.

Just a paper (that I haven't read) on the subject

Hudson et al. 2002

Genetics of the fruiting body

Interestingly, similar genes are being used in Dictyostelium discoideum (slime mold) to create this fruiting body than what is used in multicellular eukaryotes (ref.). Thanks to @Tim Cutts for this info.


Eukaryotic Cell Study Guide (PART 1)

* If a single cell is living on its own, it is called a unicellular organism.

* Heredity material: All cells have DNA it controls all the activities of a cell and contains the information needed for a cell to make new cells.

* Cytoplasm and organelles: All cells have chemicals and structures that enable the cell to live, grow, and reproduce.The structures are called organelles. Organelles are organs inside your cells. The chemicals and structures of a cell are surrounded by a fluid. This fluid and almost everything in it are collectively called cytoplasm.

* 10 times larger than prokaryotic cells.

* Plants, Fungi, Animals,and protists are eukaryotes.

* Have many membrane covered organelles.

* Its stores DNA that has information on how to make all of the cells proteins.

* The dark spot inside the nucleus is called a nucleolus.

* The nucleolus stores the materials that will be used later to make the ribosomes in the cytoplasm.

* The cytoplasm is the gooey liquid in the cell.

* Amino acids are hooked together to make proteins at very small organelles called ribosomes.

* Inside all cells, food molecules are broken down to release energy. The energy is then transferred to a special molecule that the cell uses to get work done.

* These organelles are surrounded by two membranes. The inner membrane, which has many fields in it, is where most of the ATP is made.

* Mitochondria needs oxygen in order to make ATP. Animals and humans get that oxygen by breathing in oxygen.

* Some organs such as the heart or brain may have thousands of mitochondria, while other cells such as skin cells may have only a few.

* Vacuoles store water and other liquids.

* They are full of water to help support the cell.

* Most plant cells have a very large membrane covered chamber called a vacuole.

* Some unicellular organisms that live in a freshwater environments have a problem with too much water entering the cell.

* They have a special structure called a contractile vacuole that can squeeze excess water out of the cell.

* Lysosomes are special vessels in animal cells that contain enzymes.

* When a cell engulfs a particle and encloses it in a vessel, lysosomes bump into these vessels and pour enzymes into them. The particles in the vessels are digested by the enzymes.

* Sometimes, lysosome membranes break, and the enzymes spill into the cytoplasm, killing the cell. This is what must happen for a tadpole to become a frog.

* Before you were born, Lysosomes also caused the destruction of cells that formed the webbing between your fingers.

* Lysosomes destruction of cells may also be one of the factors that contribute to the aging process in humans.

* Lipids and proteins from the ER are delivered to the Golgi complex where they are modified for different functions.

* The final products are enclosed in a piece of the Golgi complex's membrane that pinches off to form a small compartment.

* Small compartment's transport its contents to other parts of the cell or outside of the cell.

* When proteins and other materials need to be processed and shipped out of a eukaryotic cell, the job goes to an organelle called the Golgi complex.

* The endoplasmic reticulum (ER), is a membrane covered compartment that makes lipids and other materials for use, inside and outside the cell.

* It is also the organelle that break down drugs and certain chemicals that could damage the cell.

* Substances in the ER can move from one place to another through its many tubular connections.

* Some ER may be covered with ribosomes that makes its surface look rough, also known as rough ER.


In one of nature's innovations, a single cell smashes and rebuilds its own genome

A study led by Princeton University researchers found that the pond-dwelling, single-celled organism Oxytricha trifallax (above) has the remarkable ability to break its own DNA into nearly a quarter-million pieces and rapidly reassemble those pieces when it's time to mate. This elaborate process could provide a template for understanding how chromosomes in more complex animals such as humans break apart and reassemble, as can happen during the onset of cancer. Credit: John Bracht, American University and Robert Hammersmith, Ball State University.

Life can be so intricate and novel that even a single cell can pack a few surprises, according to a study led by Princeton University researchers.

The pond-dwelling, single-celled organism Oxytricha trifallax has the remarkable ability to break its own DNA into nearly a quarter-million pieces and rapidly reassemble those pieces when it's time to mate, the researchers report in the journal Cell. The organism internally stores its genome as thousands of scrambled, encrypted gene pieces. Upon mating with another of its kind, the organism rummages through these jumbled genes and DNA segments to piece together more than 225,000 tiny strands of DNA. This all happens in about 60 hours.

The organism's ability to take apart and quickly reassemble its own genes is unusually elaborate for any form of life, explained senior author Laura Landweber, a Princeton professor of ecology and evolutionary biology. That such intricacy exists in a seemingly simple organism accentuates the "true diversity of life on our planet," she said.

"It's one of nature's early attempts to become more complex despite staying small in the sense of being unicellular," Landweber said. "There are other examples of genomic jigsaw puzzles, but this one is a leader in terms of complexity. People might think that pond-dwelling organisms would be simple, but this shows how complex life can be, that it can reassemble all the building blocks of chromosomes."

From a practical standpoint, Oxytricha is a model organism that could provide a template for understanding how chromosomes in more complex animals such as humans break apart and reassemble, as can happen during the onset of cancer, Landweber said. While chromosome dynamics in cancer cells can be unpredictable and chaotic, Oxytricha presents an orderly step-by-step model of chromosome reconstruction, she said.

"It's basically bad when human chromosomes break apart and reassemble in a different order," Landweber said. "The process in Oxytricha recruits some of the same biological mechanisms that normally protect chromosomes from falling apart and uses them to do something creative and constructive instead."

Gertraud Burger, a professor of biochemistry at the University of Montreal, said that the "rampant and diligently orchestrated genome rearrangements that take place in this organism" demonstrate a unique layer of complexity for scientists to consider when it comes to studying an organism's genetics.

"This work illustrates in an impressive way that the genetic information of an organism can undergo substantial change before it is actually used for building the components of a living cell," said Burger, who is familiar with the work but had no role in it.

"Therefore, inferring an organism's make-up from the genome sequence alone can be a daunting task and maybe even impossible in certain instances," Burger said. "A few cases of minor rearrangements have been described in earlier work, but these are dilettantes compared to [this] system."

Burger added that the work is "extremely comprehensive as to the experimental techniques employed and analyses performed." The project is one of the first complex genomes to be sequenced using Pacific Biosciences (PacBio) technology that reads long, single molecules.

Oxytricha already stands apart from other microorganisms, Landweber said. It is a large cell, about 10 times the size of a typical human cell. The organism also contains two nuclei whereas most single-celled organisms contain just one. A cell's nucleus regulates internal activity and, typically, contains the cell's DNA as well as the genes that are passed along during reproduction.

An individual Oxytricha cell, however, keeps its active DNA in one working nucleus and uses the second to store an archive of the genetic material it will pass along to the next generation, Landweber said. The genome of this second nucleus—known as the germ-line nucleus—undergoes the dismantling and reconstruction to produce a new working nucleus in the offspring.

Oxytricha uses sex solely to exchange DNA rather than to reproduce, Landweber said—like plant cuttings, new Oxytricha populations spawn from a single organism. During sex, two organisms fuse together to share half of their genetic information. The object is for each cell to replace aging genes with new genes and DNA parts from its partner. Together, both cells construct new working nuclei with a fresh set of chromosomes. This rejuvenates them and diversifies their genetic material, which is good for the organism, Landweber said.

"It's kind of like science fiction—they stop aging by trading in their old parts," she said.

It's during this process that the scrambled genes in the germ-line nucleus are sorted through to locate the roughly 225,000 small DNA segments that each mate uses to reconstruct its rejuvenated chromosomes, the researchers found. Previous work in Landweber's lab—a 2012 publication in Cell and a 2008 paper in the journal Nature—showed that millions of noncoding RNA molecules from the previous generation direct this undertaking by marking and sorting the DNA pieces in the correct order.

Also impressive is the massive scale of Oxytricha's genome, Landweber said. A 2013 paper from her lab in PLoS Biology reported that the organism contains approximately 16,000 chromosomes in the active nucleus humans have only 46. Most of Oxytricha's chromosomes contain just a single gene, but even those genes can get hefty. A single Oxytricha gene can be built up from anywhere between one to 245 separate pieces of DNA, Landweber said.

The exceptional genetics of Oxytricha protect its DNA, so that mainly healthy material is passed along during reproduction, Landweber said. It's no wonder then that the organism can be found worldwide munching on algae.

"Their successful distribution across the globe has something to do with their ability to protect their DNA through a novel method of encryption, then rapidly reassemble and transmit robust genes across generations," Landweber said.


Cell Biology Blog

4 What is significant about the concept that all living creatures are multicellular?

38 comments:

Okay. I still have not found an answer to the first and third questions but I have started to grasp the second and the fourth question and will attempt to answer them.

It seems that because of their extremely small size, bacteria and viruses are quite difficult, if not impossible, to isolate. This rules out the traditional micromanipulator and microinjector method. It seems that there is a new method of isolating these small organisms by using a non destructive laser beam to set up an "optical trap." How this method works, I have yet to find out.
http://resources.metapress.com/pdf-preview.axd?code=p213088016118501&size=largest

About the fourth question, it seems to me that because all creatures are multicellular in the fact that even the single celled organisms are found in a community of other single cells, this only proves the point that macroevolution could not be possible. Just as us humans need plants and animals to survive here on earth, there is a community, an essential co-existence of all organisms, even to the microscopic group of cells, in order to continue to survive.

1.Now this is the definition of what I got for the first question from Answers.com:
"The larger of two nuclei present in ciliate protozoans, which controls nonreproductive functions of the cell, such as metabolism."
Then I had to look up what a ciliate protozoan (because I'm imperfect, and I can't remember everything I learn) and SO this is what I got:"ciliates, A group of single celled eukaryotic organisms characterized by the presence of hair-like organelles called cilia, which are identical in structure to flagella but typically shorter and present in much larger numbers with a different undulating pattern than flagella."
Controls metabolism. in a single celled organism? That's crazy! I don't think it would be a cozy home Dr. Francis. It may not have reproductive functions, but it still has work to do!
3. Now, how it doesn't digest some of the algae is something I don't completely understand..but I know that God doesn't always want us to understand all things. It gives us all the more reason to praise Him for His mighty works! From what I understand though. is that it has something that humans don't have (although it reminds me of how humans store fat and how some is used..). is it true that they have some food vacuole that stores the algae after the stomach fills up? That's just what I got from a website, but I wasn't sure..
2. Now this question just made me think about how most people isolate things..we use ordinary items such as petri dishes, certain scientific tools, etc. Personally, I don't think it would be possible for me to isolate something so small. I know with God all things are possible, but to do it in an ordinary laboratory, I would definitely seek you Dr. Francis for help, because I have no clue!
4. What is significant about about the concept that all living things are multicellular? Well, this would make me ponder upon what Sean said..if single celled organisms are found in communities of other single celled organisms, then technically they are never alone, (unless of course, a human were to isolate it). But once isolated, is it living? I just don't know. Thanks for the blog Dr. Francis! It makes me all the more grateful that God is in control of all things and brings life to things, that even I don't understand. :)

1) So since Beth got her answer from Answers.com, I'll go the less credible way (Wikipedia). Wikipedia also says that the macronucleus is the larger type of nucleus in Ciliates. Wikipedia also said that the macronuclei are polyploid (they have more than one pair of chromosomes) and does not divide through mitosis but through direct division. Also macronuclei are involved every day tasks and functions of the cell such as metabolism, but they are not involved in reproduction. So in the end, I would not want to be a tiny bacteria living in a macronucleus! The poor bacteria are happily swimming along when they are engulfed by a unicellular (or is it?) organism and enslaved to do its bidding or worse, digested!

3)I found a website that talks about how some plants and bacterial cells that produce chemicals that warn others not to eat it. It then talks about how some paramecium form symbiosis relationships with algae. So the question is: do some algae emit chemicals that allow the paramecium to see they shouldn't be digested, but they are allowed to engulf them? This is crazy seeing that these tiny creatures have no brains to think this through!
http://www.morning-earth.org/graphic-e/biosphere/Bios-C-ProtistsProtozoa.htm

4) Well if all creatures are multi cellular then it shows that all of creation is dependent on something. Even these seemingly "unicellular" creatures rely on bacteria or other things in order to survive and maintain homeostasis. Nothing is truly independent. This is a great concept to think about, especially for Christians, we are truly dependent on God and we cannot hope to see eternal life with HIm without relying on Him.

Thanks Dr. Francis for these thought provoking questions. See you soon!

2.)Stop a culture of cells from reproducing maybe using hormones that stall the process and then patiently wait until they all die until there are only a few left. Then kill the few that are left. I wouldn't know how to do that. Then I would take the last infertile cell stain it and put it on a slide.

3.) Same reason we can't digest certain foods

4.)If we look at larger organism in nature such as the African Savanna we see that all of them are interlinked but that doesn't mean we can isolate a single species and keep it alive by providing food for it the only thing is that a single cell can reproduce all by it's self so its hard to isolate a single one unlike oh say zebras.

1) According to britannica.com, a macronucleus is a "relatively large nucleus believed to influence many cell activities. It occurs in suctorian and ciliate protozoans (e.g., Paramecium). The macronucleus is associated with one or more smaller micronuclei, which are necessary for conjugation and autogamy (reproduction by exchange between the nuclei of different individuals and of the same individuals, respectively). When these reproductive processes occur, the macronucleus degenerates. It is re-formed from nuclear material in the zygote."

As to why a "pond critter" would host a bacterium in its macronucleus, I do not know. It seems detrimental to have a foreign entity living in one's "brain," if you will. A guess would be that perhaps there is a parasitic relationship occurring.

2) Honestly, I don't know, and I won't pretend to. All I do know is that I researched the topic a little bit online and found that cells can be isolated using a very complicated microfluidic device. However, any such device is not in the tool bag of us students, and may not even allow for the placing of a single cell on a basic microscope slide.

3) There must be a complex chemical reason why the lysosomes of a Paramecium do not digest consumed algae. In awfully basic enzyme terms, the "key" must not fit the "lock."

4) If it were proven that all living creatures are multicellular, then the reasons for unhealthy ecosystems could become more clear this would be so because previously the weakness in an ecosystem may not have been associated with the loss or gain of seemingly independent life forms.

Sean, I am not sure that the existence of community is a closed and shut case against evolution. However, there seems to be a massive community of microbes on earth which support life. Could they exist on their own without other creatures perhaps. However, it does not appear that macro-organisms can exist without this biomatrix. In addition, there is interdependency within this biomatrix. So it is difficult to conceive of life starting on earth with abiotic factors only.

Sarah and David, good thoughts on the isolation of bacteria. Sean is on to something I think with his idea of optical trapping.

Gage. Great thoughts about interdepency. Creation appears to exude this idea at every level.
Great work everyone

I would still like to know what a bacterium does in a macronucleus. Seems like a scary place to keep your symbionts.

okay so question 1: a macronucleus as defined by biology-online.org describes it as a larger nucleus nucleus in ciliates. I remember from org bio that ciliates are super tiny organisms that have hair-like structures all around them. part of this nuclei in the ciliate protozoans later go through cell division. So why would they want to live there? Well, from everything that I DONT know yet, all I can say is that a macronucleus' job is to transcribe DNA, that's it, then it divides and transcribes more DNA. It starts off as one, and then is divided into many other cells. Who doesn't want to be in more than one place at once?
2: Okay so at first I didn't think this was possible but after thinking about and reading over your post again. I started thinking- you say that with bacterial cells they start growing and reproducing and you can't stop them fast enough to isolate one cell. Well what if you went backwards? What if you took a group of cells and took away the things that make them multiply. Factors would be it's nutrients and good conditions like light, oxygen, water, temperature, etc. Maybe if you slowly took those things away, it would start dying off. Not all at once though. (hopefully) You can keep removing the dead bacterial cells and then you could eventually be left with one. Just maybe.
3: are eating and digesting different from each other? my guess is that eating means that the organism takes the nutrients from whatever it's eating. digesting then must mean that it just swallows is but doesn't actually take nutrients from it. basically just meaningless space within itself. I don't know how the paramecium could not 'eat' the algae unless it would be harmful to the paramecium.. but then that raises the question if it was harmless, why would it be eating something that could have catastrophic consequences. and now Im back to I don't know.
4. why are all living creatures multicellular? well I can't help but think are they? Have we as human beings discovered ALL living organisms? no. but I understand what you're asking. I don't know. maybe it's like Gage said and that it shows that all creation is dependent on something. It could be, and I think probably because everything leads back to God. He is very purposeful in His creation.
thanks for the post Dr. Francis. Definitely has my brain turning.

Concerning the second question again, it seems that there is a method called "laser tweezers" or "optical trap," in which a high powered laser that is focused into a cone is able to lay hold of a small particle at its focal point because it can effect a small force on that particle.
http://www.youtube.com/watch?v=IiIRPk81bpk

This method has been used to move cell organelles and to manipulate microscopic particles and organelles. The only problem would be to only isolate one bacterial cell as they are very small.
http://www.youtube.com/watch?v=KC4rHjxWCDg

And about the first question, I cannot find any reasons why the virus resides in the macronucleus. Maybe it is just because the macronucleus is bigger than the micronucleus and thus contains more strains of DNA and also more space to reside in?

1. macronucleus: The larger the two nuclei present in ciliate protozoans it controls the nonreproductive functions of the cell.
I looked up why a bacteria would want to live in the macronucleus of a paramecium and found this example. "Paramecium caudatum hosts Holospora obtusa in its macronucleus. This bacteria is specific to the macronucleus of Paramecium caudatum they cannot grow outside of this organism. This species acquires heat-shock resistance when infected with Holospora obtusa, which contributes to ciliary motion (http://microbewiki.kenyon.edu/index.php/Paramecium). So this implies that it would be a mutualistic relationship. It just shows how complex God created even these single-celled organisms. So this bacteria wants to live in the paramecium because it cannot grow outside of the organism and the paramecium want him there because of the heat-shock resistance from the bacteria that helps in its ciliary motion.
2. No idea on this. I know we could not just isolate a single bacterial cell in our lab without any technology other than a microscope, but I don't know the method by which we could isolate one.
3. I was thinking that maybe God gave them a certain mechanism so that they can know which algae they should digest and which to keep as energy harvesting slaves. Or maybe He just made it so that it is natural within them and they do not even have to do any delineating and whichever ones will be helpful are just naturally not digested.
And to try to answer the question perhaps the mechanism goes off and there is some way that the organism knows not to digest the organism and releases it into the cytoplasm or wherever it would decide to keep this algae. But I honestly don't know.
4. The concept that all living creatures are multicellular in that you cannot naturally isolate a unicellular organism without going through some crazy process is quite significant. It shows God's design in that we were all created to live together in a truly complex and amazing way and life is not really meant to exist on its own. Things build on each other in God's creation and there is complexity on every level. Even these unicellular organisms were made so that they do not have life on their own and truly do not live completely independent lives. It's fascinating to look into the complexity of life.
Thanks for making us think :)

1 What is a macronucleus and why would you want to live there? cheap rent? cozy? macronucleus, relatively large nucleus believed to influence many cell activities. Also thought to have something to do with further cell division, so maybe the virus resides in macronucleus is that when further cell division takes place then the virus spreads further. Just a thought not sure:)
2 How would you isolate a single bacterial cell on a microscope slide? This would be rather difficult since many microorganisms are unicellular (single-celled), but this is not universal, since some multicellular organisms are microscopic.

1. It looks like the definition of macronucleus has been mentioned several times, but here is a definition that I found from the free dictionary online "The larger of two nuclei present in ciliate protozoans, which controls nonreproductive functions of the cell, such as metabolism". I don't ever remember learning about macronucleus' before, so this is interesting to me! There are 2 nucleui in cells? Wow! God is creative! Bacteria must want to live there because they get something out of the deal, like a symbiotic relationship. I imagine it could be cozy and warm, but at this point, I don't know enough to say that is true.

2. I don't know exactly how to do this, but it would be interesting to see it done! I think that to isolate a bacteria, you must be able to make it stop reproducing. You also might need to sterilize a petree dish so there is no food for the bacteria, but you can't kill it, either.

3. I think this might be some kind of symbiotic relationship as well. I wonder if the algae has some sort of shell that is resistant to the paramecium's digestion. God can do anything!

4. This is a very interesting thought. I think that God might be using this as an example to say that all living forms cannot live by themselves, independent from God and other species. In our Christian walk, we grow best while walking alongside each other to encourage and exhort. This is also why God created Eve to be a helpmate for Adam in the garden, even while everything was perfect!

"A macronucleus (formerly also meganucleus) is the larger type of nucleus in ciliates. Macronuclei are polyploid and undergo direct division without mitosis. It controls the non-reproductive cell functions, the everyday tasks, such as metabolism. During conjugation, the macronucleus disintegrates, and a new macronucleus is formed by karyogamy of the micronuclei. The macronucleus contains hundreds of chromosomes, each present in

50 copies. The macronucleus lacks a mechanism to precisely partition this complex genome equally during nuclear division thus how the cell manages to maintain a balanced genome after generations of divisions is a mystery."

Perhaps the reason why the macronucleus would be benefited by having a bacterium live inside of it is that the bacterium somehow plays a role in partitioning the complex genome and helping to maintain a balanced genome. The next question would be, what benefit does the bacterium get by living in a macronucleus. I was not able to find any more details about what else a macronucleus contains. Maybe there is something produced in the macronucleus that the bacterium uses.

3. When a Paramecium eats algae, the algae go into the cytoplasm through the gullet. At this point, the Paramecium may or may not release proteins to digest the algae. If the proteins are not released, either the Paramecium does not have necessary proteins to digest that particular algae, or the appropriate proteins are somehow prevented from being released. The Paramecium does not choose to digest one kind of algae and then only ingest another kind of algae. Rather, the Paramecium is able to digest one kind of algae and unable to digest other kinds.

I appreciate everyone's input here. Elizabeth has perhaps one of the more interesting and creative ideas about the bacterium that it is involved in partioning the DNA. fascinating.
Dr Francis


Domains and Kingdoms of Life

For each question, choose the best answer. The answer key is below.

  1. The Three Domains of Life are:
    • Bacteria Domain, Eukarya Domain, Iglobin Domain
    • Bacteria Domain, Archaea Domain, Eukarya Domain
    • Protista Domain, Animalia Domain, Fungi Domain
    • Eating, Sleeping, Playing
  2. The 6 Kingdoms of Life are:
    • Eubacteria, Archaebacteria, Protista, Fungi, Plantae, and Animalia
    • Eubacteria, Archaebacteria, Protista, Fungi, Plantae, and Humans
    • Eubacteria, Antibacteria, Protista, Fungi, Plantae, and Animalia
    • Plants, Bacteria, Mushrooms, Birds, Humans, Mammals
  3. Mushrooms are in the
    • Protista Kingdom
    • Plantae Kingdom
    • Fungi Kingdom
    • Eubacteria Kingdom
  4. Humans are in the:
    • Protista Kingdom
    • Plantae Kingdom
    • Animalia Kingdom
    • Nonextreme Archabacteria
  5. Birds are in the:
    • Reptile Kingdom
    • Bird Kingdom
    • Animalia Kingdom
    • Flying Kingdom
  6. Inchworms are in the:
    • Insect Kingdom
    • Animalia Kingdom
    • Archaebacteria Kingdom
  7. Whales are in the:
    • Animalia Kingdom
    • Ocean Life Kingdom
    • Fungi Kingdom
    • Protista Kingdom
  8. Euglena are in the:
    • Fungi Kingdom
    • Plantae Kingdom
    • Animalia Kingdom
    • Protista Kingdom
  9. Extremophiles are in the:
    • Methanogens Kingdom
    • Archaebacteria Kingdom
    • Euglena Kingdom
    • Animalia Kingdom
  10. Last question! Bacteria (cell walls that contain peptidoglycan) are in the:
    • Eubacteria kingdom
    • Archaebacteria kingdom
    • Protista Kingdom
    • Animalia Kingdom

Answer Key

  1. Bacteria Domain, Archaea Domain, Eukarya Domain
  2. Eubacteria, Archaebacteria, Protista, Fungi, Plantae, and Animalia
  3. Fungi Kingdom
  4. Animalia Kingdom
  5. Animalia Kingdom
  6. Animalia Kingdom
  7. Animalia Kingdom
  8. Fungi Kingdom
  9. Archaebacteria Kingdom
  10. Eubacteria kingdom

Reference Articles

6:1 Supposed eukaryote evolution pushed back one billion years, Oard, www.answersingenesis.org/tj/v15/i1/eukaryote.asp

Traces of compounds (hydrocarbons called “steranes”) produced by eukaryotes (single-celled organisms with membrane-bound organelles) found in 1999 pushed back the arrival of eukaryotes from 1.2 to 2.7 billion years ago. The evolutionary story that had supposed it was difficult for eukaryotes to evolve had to be dramatically reworked. This also presents a challenge to thinking about the early atmosphere because oxygen would have needed to be present to produce the compounds found. This is just another example of the history of life being dramatically changed based on new fossil evidence found and interpreted in the evolutionary framework. Of course, there is no need to change the creation model in light of this evidence. The organisms were all created at the same time and are expected to occur in the oldest sedimentary rocks correlating to the Flood.

6:2 Ancient organisms stay the same, Creation , June 1999, pp. 7–9.

A while ago, evolutionists would not have expected to find any fossils in rocks that they thought were, say, three billion years old—life supposedly hadn’t evolved yet. However, fossils of bacteria kept turning up in progressively older rocks (no surprise to creationists), which allowed less and less time for the first life to evolve in the hypothetical, oxygen-free early atmosphere. Now an Austrian/Swiss team of scientists has looked at rock from Western Australia’s Pilbara region, supposedly around 3.5 billion years old, and found fossilized cyanobacteria. These appear to be indistinguishable from the same (oxygen-producing) creatures making the mat structures called stromatolites in the shallows of Shark Bay, some 500 kilometers away on the coast.

6:3 “Snowball Earth”—a problem for the supposed origin of multicellular animals, Oard, www.answersingenesis.org/tj/v16/i1/snowball.asp

Evolutionary scientists suggest that several ice ages that occurred hundreds of millions to billions of years ago actually extended to the equator—the “snowball earth” hypothesis. A major problem is that the snowball condition would be permanent unless there was some catastrophic event to reverse it. Evolutionists face a major problem. Life was supposed to be evolving into multicellular forms at this time— a difficult task in light of a global ice age. Rock formations also suggest a very hot period immediately after, and sometimes during, these ice ages.

To accommodate this, a freeze-fry model was created that allowed the rapid diversification of multicellular life. Volcanoes penetrated the ice and spewed carbon dioxide into the atmosphere, increasing temperatures through the greenhouse effect. A rapid reversal of temperature provided an opportunity for organisms to diversify. Not only did this happen once but five times in the evolutionary model. These cycles limit the likelihood of evolution occurring even further. There are many other significant problems with the model, and computer simulations have failed to show its viability. Trying to explain the explosion of life at the beginning of the Cambrian Period while accommodating climate extremes has proven an impossible puzzle for evolutionists to solve. Creationists can explain the rock evidence in terms of underwater landslides and rock formation during the hot-ocean phase of the Genesis Flood. The abrupt appearance of multicellular organisms is also easily accounted for in the account of creation .

6:4 Round and round we go—proposed evolutionary relationships among archaea, eubacteria, and eukarya, Purdom, http://www.answersingenesis.org/articles/2006/10/04/evolutionary-relationships

In 1977 Carl Woese first identified what he called a third domain of life, named archaea, based on ribosomal RNA (rRNA) sequence comparisons. The other two domains of life are eubacteria (true bacteria, prokaryotes) and eukarya (protists, fungi, plants, animals, and humans). Archaea share some physical characteristics with eubacteria but tend to live in more extreme environments, such as hot springs and high-salt environments. These extreme environments were believed to be present on early earth hence archaea were thought to be the ancestor to both eubacteria and eukarya. However, further analyses of archaea showed them to be genetically and biochemically quite different from eubacteria, and they are no longer believed to be ancestral to eubacteria.

Archaea are actually more genetically similar to eukaryotes than eubacteria and are often represented as a “sister” to eukarya on evolutionary trees of life. Eukarya have genes that appear to have come from both archaea and eubacteria, and so a genome fusion has been proposed. Archaea have given eukarya their informational genes (genes for transcription, translation, etc.), and eubacteria have given eukarya their operational genes (genes for amino acid biosynthesis, fat biosynthesis, etc.). Rather than an evolutionary “tree” of life, a “ring” of life has been suggested. The archaea and eubacteria (possibly multiple ones) fused using the processes of endosymbiosis and lateral gene transfer to give rise to eukarya.

A subheading in a recent article discussing the challenges of determining evolutionary relationships among these three groups says it well: “More good theories for eukaryotic origins than good data.” The scientists are so locked into their evolutionary assumptions that they must keep reinterpreting the data to fit their theories. If they would interpret their data in light of the truth found in the Bible , they would find that the data fits the creation model much better.

God created many individual kinds of archaea, eubacteria, and eukarya. Through the processes of natural selection and speciation, the many different bacterial, plant, and animal species we have today have developed. The common traits seen among these living organisms point to a common designer not a common ancestor.

6:5 Shining light on the evolution of photosynthesis, Swindell, www.answersingenesis.org/tj/v17/i3/photosynthesis.asp

The evolution of photosynthesis appears to be an impossible process as the intermediate products are toxic to the cell. In the absence of all of the enzymes being present at once, the process would kill the cells it was happening in. The probability of all of the enzymes evolving simultaneously makes it virtually impossible that photosynthesis occurred by chance in “primitive” bacteria. This article describes the process of photosynthesis to expose the evolutionary hurdles that would need to be overcome. The challenges to the evolution of photosynthesis include the presence of 17 enzymes required to assemble chlorophyll and the toxicity of intermediate molecules required to chemically synthesize the enzymes. Natural selection cannot explain the presence of useless enzymes waiting for a functional product, or the presence of other irreducibly complex components.

It defies common sense to imagine that the irreducible complexity of photosynthetic systems would have formed according to evolutionary theory. Rather, the incredible organization and intricacy evident in photosynthesis—a process man has yet to fully understand, let alone copy— screams for a designer. If photosynthesis was present from the beginning, the “oxygen revolution” was never a condition that evolving life had to deal with. Having been created by God , life on earth was already equipped to deal with such issues.

6:6 “Nonevolution” of the appearance of mitochondria and plastids in eukaryotes—challenges to endosymbiotic theory, Purdom, http://www.answersingenesis.org/articles/2006/10/11/endosymbiotic-theory

Endosymbiont theory was first developed and popularized by Lynn Margulis in the early 1980s. The idea proposes that mitochondria were originally protobacteria that were engulfed by an ancestral cell but not digested. As a result, this ancestral cell became heterotrophic (i.e., human and animal cells). Plastids (i.e., chloroplasts) were originally cyanobacteria that were engulfed by an ancestral cell but not digested. This ancestral cell became autotrophic (i.e., plants). These organelles share some characteristics with bacteria including circular DNA, division by binary fission, and membrane and ribosome similarities.

On the surface this process seems simple, but these organelles and their relationship to the cell are extremely complex. For example, not all the proteins necessary for the functioning of the organelles are found in their own genomes. Instead, some of the protein codes are found in the nucleus of the cell. Organelle proteins not made in the organelle must be transferred into the organelle. This involves complex protein transfer machinery comprised of multiple pathways, each involving numerous proteins for the transport of proteins into mitochondria and plastids. How does a transport pathway made of multiple parts, all necessary for the proper functioning of that pathway, evolve in slow incremental steps? It can’t because of evolution ’s “use it or lose it” mechanism so it must have been designed by a Creator God all at once and fully functional.

6:7 Evolutionary theories on gender and sexual reproduction, Harrub and Thomson, www.trueorigin.org/sex01.asp

One concept that is rarely mentioned in the evolutionary storytelling is the origin of sexual reproduction (sex). The idea of survival of the fittest seems to fail to explain the origin of sex, even if it may be able to explain why it would be maintained once it had developed. Asexual reproduction is a very effective method of reproduction compared to sex. Several hypotheses have been proposed to explain the origin of sex.

The Lottery Principle suggests that asexual reproduction is like buying many lottery tickets with the same number. Sex allows a mixing of genes so it is like buying many tickets with many different number combinations.

The Tangled Bank Hypothesis suggests that sex originated to simply prepare the offspring for the variety of challenges they would face in the environment. The intense competition makes sex an advantage.

The Red Queen Hypothesis suggests that sex gives the offspring an advantage in the constant competition to simply maintain its position in the “genetic arms race.” Organisms must be constantly undergoing genetic changes just to be able to continue to survive in their environment— they must constantly run just to stay in place. Sex would certainly be an advantage in such a scenario.

The DNA Repair Hypothesis suggests that an advantage is obtained if an organism has two copies of any given gene. The bad copy is less likely to cause problems if there is a chance that the other copy is good. The more genes you have, the less likely you are to suffer from genetic diseases. This would prevent bad genes from affecting a population rapidly and provide a mechanism for the preservation of favorable traits.

Each of these hypotheses, or some combination of them, provides a reasonable explanation for the benefit of sex once it is present, but none address its actual origin. Just because something has a benefit does not mean that it must happen. Neither do these hypotheses address the physical development of male and female sex organs and behaviors. The language used by evolutionists when discussing the particulars of the origin of sex is riddled with phrases like “perhaps some could,” “may have been,” “by chance,” and “over time.” All of these are devoid of any evidence. The highly complex nature of sexual reproduction and life on earth clearly points to God as the Intelligent Creator.


Learning from Earth's Smallest Ecosystems (Kavli Hangout)

Alan Brown, writer and blogger for the Kavli Foundation, contributed this article to Live Science's Expert Voices: Op-Ed & Insights.

From inside our bodies to under the ocean floor, microbiomes — communities of bacteria and other one-celled organisms — thrive everywhere in nature. Emerging at least 3.8 billion years ago, they molded our planet and created its oxygen-rich atmosphere. Without them, life on Earth could not exist.

Yet we know surprisingly little about the inner workings of nature's smallest and most complex ecosystems.

Microbiomes have a great deal to teach us. By learning how members of microbiomes interact with one another, scientists might discover innovative green chemistry and life-saving pharmaceuticals, or learn how to reduce hospital infections, fight autoimmune diseases, and grow crops without fertilizers or pesticides.

The sheer complexity of microbiomes makes them difficult to study by conventional biochemical means. Nanoscience provides a different and complementary set of tools that promises to open a window into this hidden world. [The Nanotech View of the Microbiome]

Earlier this month, The Kavli Foundation hosted a Google Hangout with two leaders in the emerging applications of nanoscience for studying microbiomes. They discussed the potential of natural biomes, why they are so difficult to understand, and how nanoscience may help us unlock microbiome secrets.

Joining the conversation were:

Eoin Brodie, a staff scientist in the Ecology Department at Lawrence Berkeley National Laboratory. He was part of the team that pioneered a device capable of identifying thousands of the bacterial species found in microbiomes, and is currently developing ways to combine data from many different types of measurement tools into a more coherent picture of those ecosystems.

Jack Gilbert is a principal investigator in the Biosciences Division of Argonne National Laboratory and an associate professor of ecology and evolution at the University of Chicago. He has studied the microbiomes of hospitals and is working on ways to use nanostructures containing bacteria to help infants fight immune diseases.

Below is a modified transcript of their discussion. Edits and changes have been made by the participants to clarify spoken comments recorded during the live webcast. To view and listen to the discussion with unmodified remarks, you can watch the original video.

The Kavli Foundation: So let's start with an obvious question, what exactly is a microbiome?

Eoin Brodie: A microbiome is a connection of organisms within an ecosystem. You can think of the ecosystem of microbes in the same way you think of a terrestrial ecosystem, like a tropical forest, a grassland, or something like that. It is a connection of organisms working together to maintain the function of a system.

Jack Gilbert: Yes. In a microbiome, the bacteria, the archaea (one-celled organisms similar to bacteria), the viruses, the fungi, and other single-celled organisms come together as a community, just like a population of humans in a city. These different organisms and species all play different roles. Together, they create an emergent property, something that the whole community does together to facilitate a reaction or a response in an environment.

TKF: How complex can these microbiomes? Are they like tropical forests? Are they more complex, less complex?

J.G.: The diversity of eukaryotic life — all the living animals and plants that you can see — pales into insignificance beside the diversity of microbial life. These bacteria, these archaea, these viruses — they've been on the earth for 3.8 billion years. They are so pervasive, they have colonized every single niche on the planet.

They shaped this planet. The reason we have oxygen in the atmosphere is because of microbes. Before they started photosynthesizing light into biomass, the atmosphere was mostly carbon dioxide. The reason the plants and animals exist on Earth is because of bacteria. The diversity of all the plants and animals — everything that's alive today that you can see with your eyes — that's a drop in the proverbial ocean of diversity contained in the bacterial and microbial world. [Can Microbes in the Gut Influence the Brain?]

E.B.: We tend to think of the earth as being a human planet and that we're the primary organism, or the alpha species. But we're really passengers, we're just blow-in's on a microbial planet. We're recent, recent additions.

TKF: You both wax so poetic about it. Yet we know so little about microbiomes. Why is it so hard to understand what goes on in these ecosystems?

E.B.: Jack eluded to it. The first problem is that microbiomes are very small. We can't see them, and it's very difficult to understand how things work when you can't see them. So tools are needed to be able to see these organisms.

We also can't grow them. It's very hard to bring them from the natural ecosystem into the lab for study. Probably less than one percent, depending on the ecosystem, can actually be cultivated on growth media in the lab so that we can do experiments and understand what functions they carry out. That leaves 99 percent — the vast majority of the microbes on Earth and most of their ecosystems — unknown to us, apart from their DNA signatures and things like that.

Now, Jack has pioneered DNA analyses. When you look at the DNA signatures from these environments, there are all these new organisms, new proteins, and new functions that we have never really seen before. This has been called earth's microbial dark matter. Just like dark matter and energy in the universe, this has been unknown to us, but it is extremely important if the planet — and humans — are to continue to function.

TKF: So, what makes it so hard to grow these microbes in a Petri dish?

E.B.: They're very fussy. You can think of it that way. They don't like to eat the food that we give them, in many cases. They eat things that we don't know they can eat. They breathe things that we don't know that they can breathe.

We breathe oxygen, they breathe oxygen, but they also breathe nitrates, iron, sulfur, even carbon dioxide. Getting the right concentrations and combinations of what they eat and breathe is very difficult.

In some cases, even if you can work that out, there may be something that they need to get from another member of the ecosystem. That member may supply an essential nutrient or a cofactor for them to grow.

So getting all of those possible permutations and combinations right is extremely challenging. A lot of people are working on it, and there's a lot of expertise being put into this, but it's extremely difficult and complicated.

J.G.:& That's an interesting point. I liken it to having a baker. You know, if you have a baker in a human community, the baker needs somebody who can make the flour, somebody who can provide a bit of yeast, and someone who will buy the bread. They exist as a network of individuals living in a community.

If you take the baker out of the community, he or she cannot make the bread and so they are no longer a baker. Removing a microbe from its community reduces the likelihood that it will be able to perform the roles and tasks that it does in that environment.

So it's almost like you don't want to try and grow these things in isolation. Because, while isolating them makes our job as a microbiologist easier, it's also much more difficult to understand what they actually do in the environments in which they live. We can't figure that out in isolation because they are community players.

TKF: What are some of the tools that we can use today to look at microbiomes? Is there a state of the art?

J.G.: So I'll take on that. I mean this is a very dynamic evolving field. It is not a field where everyone seems to rest on their laurels.

To understand microbes, we have a couple of tools that are available to us. One of those tools is genomics, so we can sequence the genome of bacteria, archaea, viruses and fungi, just as we've done for the human genome.

The second one is the transcriptome, which looks at RNA, a transient molecule that creates the cell by translating what's in the genome into proteins. That's useful, because it tells us which genes are being turned on and off when we put those microbes under different conditions.

Then we have the proteome, the proteins that actually make up the cell. They are the enzymes that enable the organism to interact with its environment, to consume its food, to respire carbon dioxide, oxygen or iron, and so on.

Then you have the metabolome, the metabolic molecules living organisms consume as food and produce as waste products.

The genome, transcriptome, proteome, and metabolome are four of the tools in our toolbox that we can actually use to examine the microbial world. But they are by no means the limit of our tools or our goals. We have ambitions far beyond just examining those components. Eoin is developing some of these, and maybe Eoin, you want to jump in now?

E.B.: Yes, I'd add to that. The challenge of understanding the microbiome, and even individual microbes, is that they're just so small. They're complicated and small, so understanding their activity — their transcriptomes or proteins or metabolites — at the scale at which they exist, is extremely challenging.

All the technologies that Jack mentioned are being developed with larger organisms in mind. Scaling them down to deal with the size of microbes, but then increasing their throughput to deal with the complexity of microbes, is a huge, huge challenge.

I'll give you an example. When you look at the activity of an ecosystem, say a tropical forest, you look at the distribution of trees and animals, and look for the association between the vegetation and animals.

So if you want to understand insects, you have a space in mind. You think, "This lives near this. It interacts in this area." So there's an interaction, a fundamental association between those members of the ecosystem.

The way we typically looked at microbiomes — though this is changing now — was to mash up the entire forest in a blender. Then we would sequence all of the DNA, and look at the RNA and proteins, and the metabolites.

Then we try to go back and say, "This tree is interacting with this insect." Whereas, in reality, that tree is hundreds or thousands of kilometers away from that insect, and they never see each other.

That's the problem we have in the microbiome. When we mash up those organisms to look at their DNA, RNA, proteins and metabolites, we get rid of that spatial structure and its associations. And we lose the importance of space in terms of facilitating interactions. [The Nanotech View of the Microbiome (Kavli Roundtable)]

So, really, I think the next wave in microbiome research has to target this microbial activity and interactions at the scale of the microbe. Do they see each other? Do they interact, and how do they interact? What chemicals do they exchange, and under what conditions? I think that's the real challenge. That's why we're talking to the Kavli Foundation, because that's where nanoscience comes in.

TKF: This is an excellent transition to my next question: How do we use nanoscience to learn about microbiomes? For example, could we use some of the same nanoscale probes we are developing to study the brain to, say, investigate microbiomes in the ocean or soil?

E.B.: I think there are some interesting parallels. I mean, you can think of the brain as this extremely complicated network of neurons. The BRAIN Initiative is attempting to map those neurons and to follow their activity.

Similarly, the microbiome is a network of interacting organisms that turn on and turn off. The connections and the structure of that network are extremely important to the functioning of the system, just as it is for the functioning of the brain.

For the BRAIN Initiative, people got together and said, "Well what do we need to do to look at electrical charge and electrical flow through neurons, noninvasively, and in real time?" And they came up with some technologies, that can potentially, do remote sensing on a very small scale, and watch how the system changes noninvasively.

So, one approach to understanding the brain is to use external imaging, and another approach is to embed sensors.

In the BRAIN Initiative some sensors are being developed here at Berkeley lab and elsewhere that use RFID — radio frequency identity — technology. They are similar to tags used to track shipping containers, goods in department stores, and things like that. They both transmit information and harvest energy from radio frequencies, so they're autonomous devices. I think that the challenge now is coupling that technology to sensors that can monitor something in the environment and send that information autonomously — no batteries required — to receivers. Then, if these sensors are distributed in an intelligent way, just like with GPS, you can triangulate where that information is coming from.

How could you use this to understand a microbiome? Well, the sensors that are being developed are still relatively large scale, about one square millimeter in size. That's pretty small for us, but very large for a microbe.

So you can think about this in soil. Let's say we want to understand what happens when a root grows through soil. The root stimulates microbes, and there are ten times more microbes near the root than there are away from the root in soil. They all have different chemistries and different functions that are very important for the nutrition and health of the plant.

If you could distribute very small sensors in the soil and have them sense things like carbon from roots or oxygen consumed by microbes, then you can build a three dimensional picture of how the soil microbiome is changed and altered as a root moves through the soil. That's one example of how advances in other fields, driven by nanotechnology, could be applied to microbiome.

TKF: These RFID sensors would be based on semiconductor chips, right? So you could take a wafer, make a lot of them cheaply, distribute them in the soil, and get a picture you couldn't get any other way?

E.B.: Yes. There's an emerging field called predictive agriculture. It's like personalized agriculture, where fertilizer addition, for example, in a field would not be uniform. Instead, you would deliver the fertilizer where it's needed. You would irrigate the field exactly where it's needed. So you have this massive network of distributed autonomous sensors, and that would allow us to more efficiently use fertilizer. Then it wouldn't be leached or lost from the system, and cause water pollution and things like that. These examples are not on a microbial scale, but microbial processes control the availability and uptake of these fertilizers.

TKF: Thank you. Hold that thought and we'll come back to it in a few moments. In the meantime, Jack has been studying microbiomes in a new hospital to see how they evolve and affect the spread of disease. Could you tell us what you are doing, and how nanotechnology might help?

J.G.: Yes. The microbes that exist in a hospital have been a focus of clinicians and medical researchers for a couple of hundred years. Ever since we uncovered that bacteria might actually be causing disease, we've been trying to eradicate as much microbial life as possible.

That paradigm is shifting to one where we're more interested in trying to understand how bacterial communities in a hospital may facilitate the spread of disease and antibiotic resistance, and maybe promote health as well.

We've been going into hospitals and, with a very, very high temporal resolution, exploring how their bacterial communities change over time. So, looking at a scale of hours to days, we're trying to understand how — when a patient moves into a new room to have an operation or to undergo a procedure — the microbes that are already in that room affect the outcome of the patient's stay in the hospital. We want to know if it makes them either healthier or sicker.

So, we've been cataloging the microbes at these very fine scales. And what we see is an exchange between the bacteria in the room and inside the patient's body.

But we've also discovered that the vast majority of bacteria that we would normally associate with so-called healthcare-associated infections — pathogens that we thought people acquire during hospital stays — appear to be bacteria that patients brought into the hospital themselves. They're bacteria that we have inside us.

Remember, we have one hundred trillion bacteria living inside us. They weigh about two pounds, about the same as the brain. So if you think that the BRAIN Initiative is important, well maybe a microbiome initiative would also be important, because it weighs about the same as the brain.

The human microbiome has a lot of players. Most of them are friendly to us, but they can turn on us too. I liken this to a riot spreading in the city. You know, if you take things away from people, they will generally rise up and try to overthrow the very thing which was supporting them in the first place.

Microbes are the same way. We give a hospital patient antibiotics and radiation therapy to kill bacteria. Then we cut open his or her intestine and expose the bacteria to oxygen, which they don't like, and stitch the gut back up. When we look at the bacteria, we see that previously friendly bacteria have started to riot. They've been insulted so many times by the patient's treatment that they've decided that they've had enough. Then they go and attack the host to regain the resources which are being taken away from them.

This is very important. Understanding a patient's hospital stay from the microbes' perspective is helping us to design better ways to treat patients and reduce the likelihood that those microbes inside us will rebel, attack us, and make us sick.

Nanotechnology is helping us to achieve a finer scale of visual resolution, so we can see exactly when, during a surgical procedure, bacteria go rogue and start to attack the host, and the molecular mechanisms that underpin that behavior.

We have a great example that we found by placing nanoscale molecular biosensors in the gut. It measures phosphate levels. Phosphate is a very important molecule that is used to create the DNA and proteins in our body, and in the cells of those bacteria.

When the phosphate level drops below a certain threshold, the microbes turn on a mechanism to acquire phosphate from their environment. And where's the best source of phosphate? It's in the gut lining of their host. So they migrate to the gut and start to break down the human cells. We experience that as a several pathogenic infection, which often kills us.

Because we understand that process, we are developing mechanisms to release phosphate at exactly the right time during surgery to prevent those bacteria from ever experiencing that phosphate reduction. To do those micro phosphate releases, we're developing nanotech scaffolds to hold phosphate, and placing them into the gut during surgery. This will reduce the likelihood that microbes will become pathogenic.

TKF: Not only is that interesting, but it leads one of our viewers to ask whether we can adjust microbiomes so that they can target diseases and other human conditions. Can they go beyond just adjusting acidity or phosphate levels and do something more aggressive?

J.G.: Yes. The case where we've had the best success is in treating chronic infections caused by Clostridium difficile bacteria. C. diff infections are chronic gastrointestinal infections. Our treatments use a shotgun approach. We take the bacteria from a healthy person and transplant them into somebody with a chronic C. diff infection. That's overridden the C. diff infection, and established a healthy microbiome in the patient's gut so that he or she is no longer sick.

The Chinese did this about 2,000 to 3,000 years ago. They called it yellow soup, and they fed the stool from a healthy person to a sick person, and that made the sick person healthy. We just rediscovered this process, and we are now applying it in a more clinical setting.

So far, it's a very untargeted approach. What we're trying to do with our research arm, American Guts, and programs associated with autism, Alzheimer's, and Parkinson's, is to identify specific bacterial community members that are either absent or overgrown in those patients. Then we want to explore how to adjust them — maybe we implant one that is missing or knock one back that is over-grown, to make that person healthier.

E.B.: I'd like to add something to that. There's an interesting analogy, I think, in what we're doing for C. diff — fecal transplants — and restoration ecology. That's where you weed out an invasive plant species and plant another species to out-compete that invasive plant species. It's the exact same process, so the same ecological principles and ecological theory that's used in restoration ecology can be used in medicine. In some cases, it may not be as simple as removing one organism or adding one or two other organisms. It might be a community function, where we may actually need that complexity to be able to out-compete the organism that's causing the disease.

J.G.: That's a really interesting point. Both Eoin and I are microbial ecologist at our core. I started out in marine microbial ecology, and now I work in soils, plants, humans, and disease. Eoin does the same. And both of us can apply the ecological principles of microbes to any environment because microbes are everywhere.

TKF: Good. So, Eoin, we have two questions for you from our audience. The first involves agriculture. A viewer want to know whether nanoscience help us alter microbiomes in ways that change how we grow, fertilize, and protect plants from pests?

E.B.: That's a great question, and I think a really timely one as well. The world population is seven billion, heading to nine, and then 11 billion. We're going to run out of fertilizer, we're going to run out of space to grow food, and we're running out of water — we're in a severe drought in California. These are our challenges, feeding a global population and providing fuel for a global population.

The things microbes and nanotechnology can do mainly revolve around improving the resistance of plants to stresses, such as drought. Microbes can help plants acquire water. For example, mycorrhiza fungi can increase the root system, improve its drought tolerance, and improve nutrition.

We can also identify bacteria that can produce fertilizer in or near the plant. So bacteria that can take nitrogen from the atmosphere and fix nitrogen can potentially offset the use of nitrogen fertilizer, which takes a lot of energy and causes a lot of pollution to manufacture.

Bacteria can also mine critical minerals from the soil. We can have bacteria growing with the plants that acquire phosphorous, like Jack was saying. We can choose bacteria so that they mine more phosphorous than they need and supply that to the plant.

All of these things would reduce our reliance on mining phosphorous from strip mines or using five percent of our world's energy to product nitrogen fertilizer. I think it's a big, big challenge.

Nanotechnology, as I mentioned earlier, can be used to characterize these organisms and understand how they work. We can also build sensor systems to identify when nutrients are limiting growth. So instead of spreading nutrients and fertilizer in a very inefficient way, we can use it in a very targeted, specific, and much more sustainable way.

TKF: Can we take a step beyond that, and perhaps use microbiomes to control pests?

E.B.: Actually, that's been done for a long time. As you know, there are GMO crops out there that have taken genes from microbes that are used to kill insects. This could be carried out in a more natural way, as well, for example, by growing these bacteria with the plants and potentially inhibiting insects from grazing and feeding on the plants. We can learn a lot from nature. Nature has already developed these strategies for pest control, and we can learn from that to design our protections in a more, controllable and intelligent way.

TKF: Another question from a viewer: Is it possible to make an artificial microbiome community do a particular task?

J.G.: Yes. We've actually been working in that area, trying to create what we call a simple minimal community. This is a community of organisms that performs a task, such as creating acetate or generating hydrogen or butanol as potential biofuel source. So we're looking at microbes that grow on the surface of cathodes, and take raw electrons from those cathodes and integrate them with a carbon dioxide source, such as blue gas from a factory. We want to create a community that drives it's metabolism towards a set goal.

That will take a mathematical modeling approach. So metabolic modeling, trying to synthesize in a computer how these microbes interact to release a certain product. So, in that sense, you need nanotechnology to sense the metabolic relationships that exist between those organisms, so that you can engineer that community towards producing a particular product. That's going to be very important to achieve biotechnology results.

E.B.: Actually, I've got to turn that question on its head. I would like to take a natural microbial community and stop it doing something, in certain cases.

Let's say, for example, you've got cattle livestock. They are a significant source of global methane that contributes to global warming. Part of that is because of their diets, which provide an excess energy. That results in increased hydrogen, which results in a lot of methane, and cows release a lot of methane.

So, could we go in and use targeted synthetic biology or chemical interference approaches to stop the production of methane? To alter the balance of the cow's rumen, the cow's gut microbial ecosystem? We could not only inhibit methane production, but improve nutrition to the animal, because it's microbes that control the flow of energy to the animal from the food that it eats.

It's a complicated ecosystem, but specifically tweaking it for the benefit of the animal and the benefit of the planet, is an interesting challenge and there are people working on that.

J.G.: I'd like to take that exact system and apply it to coal, in order to make more methane that we can then capture and pump into people's homes as biofuel.

TKF: Interesting thought. I have another question from a viewer, and Jack, I think you are the one to answer this. She has of experimental treatments that involve implanting health gut bacteria into people with autism. Why might this work? And will this be something that we see soon?

J.G.: The bacteria in our gut have an impact upon neurological behavior — the way we behave — through our immune system. They elicit a certain immune response in our gut, which feeds back on our nervous system to create a certain characteristic behavior in our brain.

We've known this in animal models for a number of years now. We're just starting to understand the extent to which neurological diseases, such as autism, Parkinson's, and conditions such as Alzheimer's, are attributable to a disruption in the bacterial community in somebody's intestine.

There have been several experiments with very low numbers of children. In several cases in South America and a number in Australia, the children have had a fecal microbiome transplant, a healthy microbial community implanted into their own gut.

The results are variable, and not exactly something that you would want to try at home. But they do hint, in some instances, of a favorable outcome where the child's neurological disorder is lessened, or significantly reduced.

There are groups at Cal Tech are generating probiotics, particular bacteria species, that they hope to add to a child's diet or put into a capsule that can be swallowed. They seem to have a benefit in reducing the neurological abnormalities associated with autism, though they are still in their early days.

TKF: That leads to another question I wanted to ask you. Jack, you're also working on encapsulating microbiomes in some sort of nanostructure and applying them to homes or offices. Your hope is that these biomes will expose people to microbiomes that will help their immune system develop resistance to these neurological problems. Could you tell us about that?

J.G.: Yes, we're working on animal models at the moment. Imagine recreating structures that these animals can interact with. Imagine I build you a building that was biologically alive, where the walls were deliberately teeming with a healthy microbial community.

Now, we have only a very limited idea what healthy means, but essentially what we're doing is creating structures, 3D printable structures, impregnated with certain nutrients. We're working with Ramille Shah at Northwestern University to create a 3D structure which allows that bacterial community to thrive.

We can then introduce these structures into a mouse's cage. The bacteria associated with the 3D surface will colonize that mouse, and reduce certain abnormalities that we see in that mouse, such as an allergy response. So we've been growing bacteria which can produce a chemical that, once released into the gut of the mouse, will form a colony and reduce the likelihood of that mouse having a food allergy.

I'm also working with Cathy Nagler at the University of Chicago. We're hoping to prove that we don't have to pump kids full of probiotics. Instead, we can just redesign homes, schools, and maybe daycare centers, so that children will get an appropriate microbial exposure that would mirror how they would have grown up if they were in a natural ecosystem. Hopefully, that will be the future of architecture.

E.B.: And, you know, as a possible alternative, we can send our kids outside to play more.

J.G.: You got it.

E.B.: Not bad.

Follow all of the Expert Voices issues and debates — and become part of the discussion — on Facebook, Twitter and Google+. The views expressed are those of the author and do not necessarily reflect the views of the publisher. This version of the article was originally published on Live Science.


Lecture 1: Introduction

Download the video from iTunes U or the Internet Archive.

Topics covered: Introduction

Instructors: Prof. Robert A. Weinberg

Lecture 10: Molecular Biolo.

Lecture 11: Molecular Biolo.

Lecture 12: Molecular Biolo.

Lecture 13: Gene Regulation

Lecture 14: Protein Localiz.

Lecture 15: Recombinant DNA 1

Lecture 16: Recombinant DNA 2

Lecture 17: Recombinant DNA 3

Lecture 18: Recombinant DNA 4

Lecture 19: Cell Cycle/Sign.

Lecture 26: Nervous System 1

Lecture 27: Nervous System 2

Lecture 28: Nervous System 3

Lecture 29: Stem Cells/Clon.

Lecture 30: Stem Cells/Clon.

Lecture 31: Molecular Medic.

Lecture 32: Molecular Evolu.

Lecture 33: Molecular Medic.

Lecture 34: Human Polymorph.

Lecture 35: Human Polymorph.

As I'm going to argue repeatedly today, biology has become a science over the last 50 years. And, as a consequence, we can talk about some basic principles. We can talk about some laws and then begin to apply them to very interesting biological problems.

And so our general strategy this semester, as it has been in the past, is to spend roughly the first half of the semester talking about the basic laws and rules that govern all forms of biological life on this planet. And you can see some of the specific kinds of problems, including the problem of cancer, how cancer cells begin to grow abnormally, how viruses proliferate, how the immune system functions, how the nervous system functions, stem cells and how they work and their impact on modern biology, molecular medicine, and finally perhaps the future of biology and even certain aspects of evolution. The fact of the matter is that we now understand lots of these things in ways that were inconceivable 50 years ago. And now we could begin to talk about things that 50 years ago people could not have dreamt of. When I took this course, and I did take it in 1961, we didn't know about 80% of what we now know. You cannot say that about mechanics in physics, you cannot say that about circuit theory in electronics, and you cannot say that, obviously, about chemistry.

And I'm mentioning that to you simply because this field has changed enormously over the ensuing four decades. I won't tell you what grade I got in 7. 1 because if I would, and you might pry it out of me later in the semester, you probably would never show up again in lecture.

But in any case, please know that this has been an area of enormous ferment. And the reason it's been in such enormous ferment is of the discovery in 1953 by Watson and Crick of the structure of the DNA double helix. Last year I said that we were so close to this discovery that both Watson and Crick are alive and with us and metabolically active, and more than 50 years, well, exactly 50 years after the discovery. Sadly, several months ago one of the two characters, Francis Crick died well into his eighties, and so he is no longer with us. But I want to impress on you the notion that 200 years from now, we will talk about Watson and Crick the same way that people talk about Isaac Newton in terms of physics. And that will be so because we are only beginning to perceive the ramifications of this enormous revolution that was triggered by their discovery. That is the field of molecular biology and genetics and biochemistry which has totally changed our perceptions of how life on Earth is actually organized.

Much of the biology to which you may have been exposed until now has been a highly descriptive science. That is you may have had courses in high school where you had to memorize the names of different organisms, where you had to understand how evolutionary phylogenies were organized, where you had to learn the names of different organelles, and that biology was, for you, a field of memorization. And one point we would like, hopefully successfully, to drive home this semester is the notion that biology has now achieved a logical and rational coherence that allows us to articulate a whole set of rules that explain how all life forms on this planet are organized. It's no longer just a collection of jumbled facts. Indeed, if one masters these molecular and genetic principles, one can understand in principle a large number of processes that exist in the biosphere and begin to apply one's molecular biology to solving new problems in this arena.

One of the important ideas that we'll refer to repeatedly this semester is the fact that many of the biological attributes that we posses now were already developed a very long time ago early in the inception of life on this planet. So if we look at the history of Earth, here the history of Earth is given as 5 billion years, this is in thousands obviously. The Earth is probably not that old.

It's probably 4.5 or 4 or 3 billion years but, anyhow, that's when the planet first aggregated, as far as we know.

One believes that no life existed for perhaps the first half billion years, but after half a billion years, which is a lot of time to be sure, there already begins to be traces of life forms on the surface of this planet. And that, itself, is an extraordinary testimonial, a testimonial to how evolutionary processes occur. We don't know how many planets there are in the universe where similar things happened.

And we don't know whether the solution that were arrived at by other life systems in other places in the universe, which we may or may not ever discover, were the similar solutions to the ones that have been arrived at here.

It's clear, for example, that to the extent that Darwinian Evolution governs the development of life forms on this planet that is not an artifact of the Earth. Darwinian Evolution is a logic which is applicable to all life forms and all biosystems that may exist in the universe, even the ones we have not discovered.

However, there are specific solutions that were arrived at during the development of life on Earth which may be peculiar to Earth.

The structure of the DNA double helix.

The use of ribose in deoxyribose. The choice of amino acids to make proteins. And those specific solutions may not be universal.

Whether they're universal in the sense of existing in all life forms across the planet, the fact is that many of the biochemical and molecular solutions that are represented in our own cells today, these solutions, these problems were solved already 2 and 3 billion years ago. And once they were solved they were kept and conserved almost unchanged for the intervening 2 or 3 billion years. And that strong degree of conservation means that we can begin to figure out what these principles were early on in evolution of life on this planet and begin to apply them to all modern life forms.

From the point of view of evolution, almost all animals are identical in terms of their biochemistry and in terms of their physiology.

The molecular biology of all eukaryotic cells, that is all cells that have nuclei in them, is almost the same.

And, therefore, we're not going to focus much in this course this semester on specific species but rather focus on general principles that would allow us to understand the cells and the tissues and the physiological processes that are applicable to all species on the surface of the planet. Let's just look here and get us some perspective on this because, the fact of the matter is, is that multicellular life forms, like ourselves, we have, the average human being has roughly three or four or five times ten to the thirteenth cells in the body. That's an interesting figure.

The average human being goes through roughly ten to the sixteenth cell divisions in a lifetime, i.e. ten to the sixteenth times in your body there will be cells that divide, grow and divide.

Every day in your body there are roughly ten to the eleventh cells that grow and divide. Think of that, ten to the eleventh.

And you can divide that by the number of minutes in a day and come up with an astounding degree of cellular replication going on.

All of these processes can be traceable back to solutions that were arrived at very early in the evolution of life on this planet, perhaps 550, 600 million years ago when the first multicellular life forms began to evolve. Before that time, that is to say before 500 to 600 million years ago, there were single-cell organisms.

For example, many of them survive to this day. There were yeast-like organisms. And there were bacteria. And we make one large and major distinction between the two major life forms on the planet in terms of cells. One are the prokaryotic cells. And these are the cells of bacteria, I'll show you an image of them shortly, which lack nuclei.

And the eukaryotic cells which poses nuclei and indeed have a highly complex cytoplasm and overall cellular architecture.

We think that the prokaryotic life forms on this planet evolved first probably on the order of 3 billion years ago, maybe 3.

billion years ago, and that about 1. billion years ago cells evolved that contained nuclei. Again, I'll show them to you shortly. And these nucleated cells, the eukaryotes then existed in single-cell form for perhaps the next 700 or 800 million years until multi-cellular aggregates of eukaryotic cells first assembled to become the ancestors of the multi-cellular plants and the multi-cellular animals that exist on the surface of the Earth today. To put that in perspective, our species has only been on the planet for about 150, 00 years. So we've all been here for that period of time.

And a 150,000 sounds like a long time, in one sense, but it's just “a blink in the eye of the Lord” as one says in terms of the history of life on this planet, and obviously the history of the universe which is somewhere between 13 and 15 billion years old.

You can begin to see that the appearance of humans represents a very small segment of the entire history of life on this planet.

And here you can roughly see the way that life has developed during this period of time from the fossil record. You see that many plants actually go back a reasonable length of time, but not more than maybe 300 or 400 million years. Here are the Metazoa.

And this represents -- Well, can you hear me? Wow, 614 came in handy.

OK. So if we talk about another major division, we talk about protozoa and metazoa. The suffix zoa refers to animals, as in a zoo. And the protozoa represents single-cell organisms.

The metazoa represent multi-cellular organisms. And we're going to be focusing largely on the biology of metazoan cells this semester, and we're going to be spending almost no time on plants.

It's not that plants aren't important. It's just that we don't have time to cover everything. And, indeed, the molecular biology that you learn this semester will ultimately enable you to understand much about the physiology of multi-cellular plants which happen to be called metaphyta, a term you may never hear again in your entire life after today. That reminds me, by the way, that both Dr. Lander and I sometimes use big words.

And people come up to me afterwards each semester each year and say Professor Weinberg, why don't you talk simple, why don't you talk the way we heard things in high school?

And please understand that if I use big words sometimes it's to broaden your vocabulary so you can learn big words.

One of the things you should be able, one of the big take-home lessons of this course should be that your vocabulary is expanded.

Not just your scientific vocabulary but your general working English vocabulary. Perhaps the biggest goal of this course, by the way, is not that you learn the names of all the organelles and cells but that you learn how to think in a scientific and rational way. Not just because of this course but that this course helps you to do so. And as such, we don't place that much emphasis on memorization but to be able to think logically about scientific problems. Here we can begin to see the different kinds of metazoa, the animals. Here are the metaphyta and here are the protozoa, different words for all of these.

And here we see our own phylum, the chordates. And, again, keep in mind that this line right down here is about 550 to 600 million years ago, just to give you a time scale for what's been going on, on this planet.

One point we'll return to repeatedly throughout the semester is that all life forms on this planet are related to one another.

It's not as if life was invented multiple times on this planet and that there are multiple independent inventions to the extent that life arose more than once on this planet, and it may have. The other alternative or competing life forms were soon wiped out by our ancestors, our single-cellular ancestors 3 billion years ago.

And, therefore, everything that exists today on this planet represents the descendents of that successful group of cells that existed a very long time ago. Here we have all this family tree of the different metazoan forms that have been created by the florid hand of evolution. And we're not going to study those phylogenies simply because we want to understand principles that explain all of them.

Not just how this or that particular organism is able to digest its food or is able to reproduce. Here's another thing we're not going to talk about. We're not going to talk about complicated life forms. We're not going to talk very much, in fact hardly at all, about ecology. This is just one such thing, the way that a parasite is able to, a tapeworm is able to infect people.

This is, again, I'm showing you this not to say this is what we're going to talk about, we're not going to talk about that.

We're not going to talk about that. There's a wealth of detail that's known about the way life exists in the biosphere that we're simply going to turn our backs on by focusing on some basic principles.

We're also not going to talk about anatomy. Here in quick order are some of the anatomies you may have learned about in high school, and I'm giving them to you each with a three-second minute, a three-second showing to say we're not going to do all this.

And rather just to reinforce our focus, we're going to limit ourselves to a very finite part of the biosphere.

And here is one way of depicting the biosphere. It's obviously an arbitrary way of doing so but it's quite illustrative.

Here we start from molecules. And, in fact, we will occasionally go down to submolecular atoms. And here's the next dimension of complexity, organelles. That is these specialized little organs within cells. We're going to focus on them as well. We're going to focus on cells. And when we start getting to tissues, we're going to start not talking so much about them.

And we're not going to talk about organisms and organs or entire organisms or higher complex ecological communities.

And the reason we're doing that is that for 40 years in this department, and increasingly in the rest of the world there is the acceptance of the notion that if we understand what goes on down here in these first three steps, we can understand almost everything else in principle.

Of course, in practice we may not be able to apply those principles to how an organism works or to how the human brain works yet.

Maybe we never will. But, in general, if one begins to understand these principles down here, one can understand much about how organismic embryologic develop occurs, one can understand a lot about a whole variety of disease processes, one can understand how one inherits disease susceptibilities, and one can understand why many organisms look the way they do, i.e. the process of developmental biology.

And so, keep in mind that if you came to hear about all of these things, we're going to let you down. That's not what this is going to be about. This also dictates the dimensions of the universe that we're going to talk about because we're going to limit ourselves to the very, very small and not to the microscopic. On some occasions we'll limit ourselves to items that are so small you cannot see them in the light microscope. On other occasions we may widen our gaze to look at things that are as large as a millimeter, but basically we're staying very, very small. Again, because we view, correctly or not, the fact that the big processes can be understood by delving into the molecular details of what happens invisibly and cannot be seen by most ways of visualizing things, including the light and often even the electron microscope. Keep in mind that 50 years ago we didn't know any of this, for all practical purposes, or very little of this. And keep in mind that we're so close to this revolution that we don't really understand its ramifications.

I imagine it will be another 50 years before we really begin to appreciate the fallout, the long-term consequences of this revolution in biology which began 51 years ago. And so you're part of that and you're going to experience it much more than my generation did.

And indeed one of the reasons why MIT decided about 10 or 12 years ago that every MIT undergraduate needed to have at least one semester of biology is that biology, in the same way as physics and chemistry and math, has become an integral part of every educated person's knowledge-base in terms of their ability to deal with the world in a rational way. In terms of public policy, in terms of all kinds of ethical issues, they need to understand what's really going on. Many of the issues that one talks about today about bioethics are articulated by people who haven't the vaguest idea about what we're talking about this semester.

You will know much more than they will, and hopefully some time down the road, when you become more and more influential voices in society, you'll be able to contribute what you understood here, what you learned here to that discussion.

Right now much of bioethical discussion is fueled by people who haven't the vaguest idea what a ribosome or mitochondrion or even a gene is, and therefore is often a discussion of mutually shared ignorance which you can diffuse by learning some basics, by learning some of the essentials. Here is the complexity of the cell we're going to focus on largely this semester, which is to say the eukaryotic rather than the prokaryotic cell.

And this is just to give you a feeling for the overall dimensions of the cell and refer to many of the landmarks that will repeatedly be brought up during the course of this semester.

Here is the nucleus. The term karion comes from the Greek meaning a seed or a kernel. And the nucleus is what gives the eukaryotic cell its name. Within the nucleus, although not shown here, are the chromosomes which carry DNA.

You may have learned that a long time ago. Outside of the nucleus is this entire vast array of organelles that goes from the nuclear membrane, and I'm point to it right here, all the way out to the outside of the cell. The outside limiting membrane, the outer membrane of the cell is called the plasma membrane.

And between the nucleus and the plasma membrane there is an enormous amount of biological and biochemical activity taking place.

Here are, for example, the mitochondria. And the mitochondria, as one has learned, are the sources of energy production in the cell. And, therefore, we'll touch on them very briefly. This is an artist's conception of what a mitochondrion looks like. Almost always artists' conceptions of these things have only vague resemblance to the reality.

But, in any case, you can begin to get a feeling for what one thinks about their appearance. Here are mitochondria sliced open by the hand of the artist. And, interestingly, mitochondria have their own DNA in them. One now accepts the fact that mitochondria are the descendents of bacteria which insinuated themselves into the cytoplasms of larger cells, roughly 1.5 billion years ago, and began to do a specialized job which increasingly became the job of energy production within cells. To this day, mitochondria retain some vestigial attributes of the bacterial ancestors which initially colonized or parasitized the cytoplasm of the cell.

When I say parasitized, you might imagine that the mitochondria are taking advantage of the cell.

But, in fact, the mitochondria represent the essential sources of energy production in the cell. Without our mitochondria, as you might learn by taking cyanide, for example, you don't live for very many minutes. And the vestiges of bacterial origins of mitochondria are still apparent in the fact that mitochondria still have their own DNA molecule, their own chromosome. They still have their own ribosomes and protein synthetic apparatus, even though the vast majority of the proteins inside mitochondria are imported from the cytoplasm, i.e., these vestigial bacteria now rely on proteins made by the cell at large that are imported into the mitochondrion to supplement the small number of vestigial bacterial proteins which are still made here inside the mitochondrion and used for essential function in energy production. Here is the Golgi apparatus.

And the Golgi apparatus up here is used for the production of membranes.

As one will learn throughout the semester, the membranes of a cell are in constant flux and are being pulled in and remodeled and regenerated. The Golgi apparatus is very important for that.

Here's the rough endoplasmic reticulum. That's important for the synthesis of proteins which are going to be displayed on the surface of cells, you don't see them depicted here, or are going to be secreted into the extracellular space.

Here are the ribosomes, which I might have mentioned briefly before. And these ribosomes are the factories where proteins are made.

Again, we're going to talk a lot about them. And, finally, several other aspects, the cytoskeleton. The physical integrity, the architecture of the cell is maintained by a complex network of proteins which together are considered to be the cytoskeleton. And they enable the cell to have some rigidity, to resist tensile forces, and actually to move.

Cells can actually move from one place to the other.

They have motile properties. They're able to move from one location to another. The process of cell motility, if that's a word you'd like to learn.

Here is what a prokaryotic cell looks like by contrast.

And I just want to give you a feeling. First of all, it looks roughly like a mitochondrion that I discussed before. But you see that there is the absence of a nuclear membrane. There's the absence of the highly complex cytoarchitecture. Cyto always refers to cells.

There's the absence of the complex cytoarchitecture that one associates with eukaryotic cells. In fact, all that a bacterium has is this area in the middle. It's called the nucleoid, a term which you also will probably never hear in your lifetime.

And it represents simply an aggregate of the DNA of the chromosomes of the bacterium. And, in most bacteria, the DNA consists of only a single molecule of DNA which is responsible for carrying the genetic information of the bacteria. There's no membrane around this nucleoid. And outside of this area where the DNA is kept are largely ribosomes which are important for protein synthesis. There's a membrane on the outside of this called the plasma membrane, very similar to the plasma membrane of eukaryotic cells. And outside of that is a meshwork that's called the outer membrane, it's sometimes called the cell wall of the bacterium, which is simply there to impart structural rigidity to the bacterium making sure that it doesn't explode and holding it together. And then there are other versions of eukaryotic cells. Here's what a plant cell looks like.

And it's almost identical to the cells in our body, except for two major features. For one thing, it has chloroplasts in it which are also, one believes now, the vestiges of parasitic bacteria that invade into the cytoplasm of eukaryotic cells. So, in addition to mitochondria which are responsible for energy production in all eukaryotic cells, we have here the chloroplasts which are responsible for harvesting light and converting it into energy in plant cells. The rest of the cytoplasm of a plant cell looks pretty much the same.

One feature that I didn't really mention when I talked about an animal cell is in the middle of the nucleus, here you can see, is a structure called a nucleolus. And a nucleolus, or the nucleolus in the eukaryotic cell is responsible for making the large number of ribosomes which are exported from the nucleus into the cytoplasm. And, as I mentioned just before, the ribosomes are responsible for protein synthesis.

It turns out this is a major synthetic effort on the part of most cells. Cells, like our own, have between 5 and 10 million ribosomes in the cytoplasm. So it's an enormous amount of biomass in the cytoplasm whose sole function is to synthesize proteins.

As we will learn also, proteins that are synthesized by the ribosomes don't sit around forever. Some proteins have long lives.

Some proteins have lifetimes of 15 minutes before they're degraded, before they're turned over. One other distinction between our cells, that is the cells of metazoa and metaphyta, are the cell walls, analogous to the cell walls of bacteria, this green thing on the outside. As I said before, we do not have cell walls around our cells. And we will, as the semester goes on, go into more and more details about different aspects of this cytoarchitecture during the first half of the semester. Here, for example, is an artist's depiction of the endoplasmic reticulum.

Why it has such a complex name, I cannot tell you, but it does.

It's called the ER in the patois of the street. The ER.

And the endoplasmic reticulum is a series of membranes.

Keep in mind, not the only membrane in the cell is the plasma membrane.

Within the cytoplasm there are literally hundreds of membranes which are folded up in different ways.

Here you see them depicted. And one set of these membranes, often they're organized much like tubes, represents the membranes of the endoplasmic reticulum which either lacks ribosomes attached to it or has these ribosomes attached to it which cause this to be called the rough endoplasmic reticulum to refer to its rough structure which is created by the studding of ribosomes on the surface.

As we will learn, just trying to give you a feeling for the geography of what we're going to talk about this semester, these ribosomes on the surface of the endoplasmic reticulum are dedicated to the task of making highly specialized proteins which are either going to be dispatched to the surface of the cell where they will be displayed on the cell's surface or actually secreted into the extracellular space. Many of the proteins that are destined for our body are not kept within cells but are released into the extracellular space where they serve important functions, and so we're going to focus very much on them.

Here's actually what some of these things look like in the electron microscope to see whether we can either believe or fully discredit the imaginations of the artists. Here's the rough endoplasmic reticulum I showed you in schematic form before. And you can see why it's called rough. All these black dots are ribosomes attached on the outside. Here's the Golgi apparatus.

You see these vesicles indicated here. And a vesicle, just to use a new word, is simply a membranous bag.

And keep in mind, by the way, that we're not going to spend the semester with these highly descriptive discussions.

Our intent today is to get a lot of these descriptive discussions out of the way so that we can begin to talk in a common parlance about many of the parts, the molecular parts of cells and organisms.

Here is the mitochondrion which we saw depicted before.

It looks similar to, but not identical to the artist's description of that. And keep in mind that the mitochondrion in our cells, as I said before, are the descendents of parasitic bacteria. Here's the endoplasmic reticulum, and the way it would look, as it does in certain parts of the cell when it doesn't have all of these ribosomes studded on the surface. The endoplasmic reticulum here is involved in making membranes.

The endoplasmic reticulum here is involved in the synthesis and export of proteins to the cell's surface and for secretion, as I mentioned before. Much of what we're going to talk about over the next days is going to be focused on the nucleus of the cell, that is on the chromosomes on the cell and on the material which is called chromatin which carries the genetic material.

So the term chromatin is used in biology to refer simply to the mixture of DNA and proteins, which together constitutes the chromosomes. So chromatin has within it DNA, it has protein, and it has a little bit of RNA in it.

And we're going to focus mostly on the DNA in the chromatin, because if we can begin to understand the way the DNA works and functions many other aspects will flow from that.

I mentioned the cell's surface, and I just want to impress on you the fact that the plasma membrane of a cell is much more complicated than was depicted in these drawings that I showed you just before.

If we had a way of visualizing the plasma membrane of a cell, we would discover that it's formed from lipids. We see such lipids there, phospholipids, many of them. We'll talk about them shortly. That the outside of the cell, there are many proteins, you see them here, which thread their way through the plasma membrane, have an extracellular and intracellular part.

And these transmembrane proteins, which reach from outside to inside, represent a very important way by which the cell senses its environment. This plasma membrane, as we'll return to, represents a very effective barrier to segregate what's inside the cell from what's outside of the cell to increase concentrations of certain biochemical entities.

But at the same time it creates a barrier to communication.

And one of the things that cells have had to solve over the last 700 to 800 million years is ways by which the exterior of the cell is able to send certain signals and transmit that information to the interior of the cell. At the same time, cells have had to use a number of different, invent a number of different proteins, some of them indicated here, which are able to transport materials from the outside of the cell into the cell, or visa versa. So the existence of the plasma membrane represents a boon to the cell in the sense that it's able to segregate what's on the inside from what's on the outside.

But it represents an impediment to communication which had to be solved, as well as an impediment to transport. And many of these transmembrane proteins are dedicated to solving those particular problems.

Here you see, once again an artist's depiction form, aspects of the cytoskeleton of the cell. And when we talk about the cytoskeleton we talk about this network of proteins which, as I said before, gives the cell rigidity.

Keep in mind that the prefix cyto or the suffix cyt refers always to cells. Allows the cell to have shape. And here you can see this network as depicted in one way, but here it's depicted actually much more dramatically. And here you begin to see the complexity of what exists inside the cell. Here are these proteins.

These are polymers of proteins called vimentin which are present in very many mesenchymal cells. Here are microtubules made from another kind of protein. Here are microfilaments, in this case made of the molecule actin. And if we looked at individual molecules of actin they would be invisible.

This is end-to-end polymerization of many actin molecules.

And we're looking here under the microscope from one end of the cell to the other end of the cell. And you can see how these molecules, they create stiffness, and they also enable the cell to contract and to move. Some people might think that the interior of the cell is just water with some molecules floating around them. But if you actually look at what's present in the cell, more than 50% of the volume is taken up by proteins.

It's not simply an aqueous solvent where everything moves around freely.

It's a very viscous slush, a mush. And it's quite difficult there for many cells to move around from one part of the cell to the other. Here you begin to get a feeling now for how the connection, which we'll reinforce shortly in great detail, between individual molecules and the cytoskeleton.

And here you see these actin fibers. I showed them to you just moments ago stretching from one end of the cell to the other.

And each of these little globules is a single actin monomer which polymerize end-to-end and then form multi-strand aggregates to create the actin cytoskeleton. Here's an intermediate filament and here's the microtubules that are formed, once again giving us this impression that the cell is actually highly organized and that that high degree of organization is able to give it some physical structure and shape and form. I think we're going to end today two minutes early. You probably won't object.


Structure

All organisms consist of monomeric units called cells some contain a single cell (unicellular), others contain many (multicellular). Multicellular organisms are able to specialise cells to perform specific functions, a group of such cells is tissue the four basic types of which are epithelium, nervous tissue, muscle tissue and connective tissue. Several types of tissue work together in the form of an organ to produce a particular function (such as the pumping of the blood by the heart. This pattern continues to a higher level with several organs functioning as an organ system to allow for reproduction, digestion etc. Many multicelled organisms comprise of several organ systems which coordinate to allow for life.

The cell

The cell theory, developed in 1839 by Schleiden and Schwann, states that all organisms are composed of one or more cells all cells come from preexisting cells all vital functions of an organism occur within cells, and cells contain the hereditary information necessary for cell functions and for transmitting information to the next generation of cells. There are two types of cells, eukaryotic and prokaryotic. Prokaryotic cells are usually singletons, while eukaryotic cells are usually found in multi-cellular organisms. Prokaryotic cells lack a nuclear membrane so DNA is unbound within the cell, eukaryotic cells have nuclear membranes. All cells have a membrane, which envelopes the cell, separates its interior from its environment, regulates what moves in and out, and maintains the electric potential of the cell. Inside the membrane, a salty cytoplasm takes up most of the cell volume. All cells possess DNA, the hereditary material of genes, and RNA, containing the information necessary to build various proteins such as enzymes, the cell's primary machinery. There are also other kinds of biomolecules in cells.

All cells share several abilities [5] :

  • Reproduction by cell division (binary fission, mitosis or meiosis).
  • Use of enzymes and other proteinscoded for by DNAgenes and made via messenger RNA intermediates and ribosomes. , including taking in raw materials, building cell components, converting energy, assembling molecules and releasing by-products. The functioning of a cell depends upon its ability to extract and use chemical energy stored in organic molecules. This energy is derived from metabolic pathways.
  • Response to external and internal stimuli such as changes in temperature, pH or nutrient levels.
  • Cell contents are contained within a cell surface membrane that contains proteins and a lipid bilayer.

Earth was a frozen Snowball when animals first evolved

The ice brought Earth to a standstill. Where there were once waves lapping onto a tropical shore and warm waters teeming with life, there was just the whistling of the wind and a cold barren landscape, covered in ice as far as the eye could see. Even at the equator &ndash the warmest place on Earth &ndash the average temperature was a frigid -20°C, equivalent to modern-day Antarctica. Most life was wiped out, and the creatures that did survive huddled in small pockets of open water, where hot springs continued to bubble up.

This was "Snowball Earth" &ndash a deep freeze that began around 715 million years ago and held Earth in its icy grip for a good 120 million years. "There are no other comparable glacial periods on Earth. This one was really quite catastrophic," says Graham Shields of University College London in the UK.

However, some scientists now believe that this crushing catastrophe drove one of the most incredible steps in evolution: the development of the first animals, and a dramatic flourishing of life known as the Cambrian explosion.

Around 540 million years ago, a host of exotic creatures suddenly appeared. They included giant woodlouse-like creatures known as trilobites, the five-eyed Opabinia, and the spiny slug-like Wiwaxia. Suddenly, Earth leapt from being dominated by single-celled bacteria to a world teeming with exotic multicellular creatures, all in a geological blink of an eye.

The Cambrian explosion remains a puzzle

For Charles Darwin, trying to demonstrate his theory of natural selection, this sudden burst of evolution was a major problem. "The case must at present remain inexplicable and may be truly urged as a valid argument against the views here entertained," he wrote in On the Origin of Species in 1859.

To this day the Cambrian explosion remains a puzzle. But maybe a planet-encasing icy catastrophe could help explain it.

The evidence for a Snowball Earth first emerged in the early 1990s. Unexpectedly, geologists discovered evidence of glaciers &ndash such as stones that had clearly been carried on ice rafts and then dropped - in the tropics. Since then, a growing body of evidence has shown that the global deep freeze began around 715 million years ago, and lasted nearly 120 million years.

Most scientists agree that the Snowball formed suddenly

Exactly how far the ice extended is still debated. Some argue that the entire Earth was encased in ice, with just a few small pockets of open water where hot springs bubbled up. Others believe that a belt of open water remained around Earth's equator.

Regardless of how far the ice stretched, most scientists agree that the Snowball formed suddenly. It was probably caused by rapid weathering of Earth's continents, which sucked carbon dioxide &ndash a planet-warming greenhouse gas &ndash out of the atmosphere and caused temperatures to plummet. There were two distinct pulses of extreme glaciation, interspersed with a 20-million-year warm period. Finally, around 660 million years ago, Earth's volcanoes topped up the atmospheric carbon dioxide enough to haul the climate out of its frozen state.

So why on Earth would this period of extreme cold cause life to switch gear so rapidly? Maybe, say many geologists, because it pumped lots of life-giving oxygen into the air.

The idea is that the ice gave a boost to microscopic plants, which released oxygen as a waste product. During the Snowball, the glaciers would have worn huge amounts of phosphorus-rich dust away from the underlying rocks. Then, when the ice retreated at the end of the Snowball, rivers washed this dust into the oceans, where it fed the microbes.

"High phosphorus levels would have increased biological productivity and organic carbon burial in the ocean, leading to a build-up of atmospheric oxygen," says Noah Planavsky of Yale University in New Haven, Connecticut. In 2010 he identified a massive spike in phosphorus levels in sediments from around the world, just as Snowball Earth was ending.

Some animals can survive with much less oxygen than previously thought

That was suggestive, but in 2014 Planavsky found more direct evidence. His team estimated oxygen levels prior to Snowball Earth, by studying chromium &ndash which exists in different states depending on the amount of oxygen in the air &ndash in ancient rocks. Until 800 million years ago, atmospheric oxygen levels were just one-hundredth of today's levels.

Planavsky thinks that is far too low to support complex animal life. "In modern low-oxygen environments there is less ecosystem complexity and a more limited range of animal behaviours," says Planavsky. "So it is reasonable to expect that an oxygen rise would pave the way for animal and ecosystem diversification."

But there's a problem with that idea. Experiments published in 2014 showed that some animals can survive with much less oxygen than previously thought. Sponges, one of the oldest kinds of animal, need just 0.5% of modern oxygen levels. That suggests oxygen wasn't enough of a trigger.

In recent years another idea has come to prominence. Maybe it was the ice itself that drove the evolutionary leap, says Richard Boyle of the University of Southern Denmark in Odense. "There are no animals more complex than a sponge prior to the last of the Snowball glaciation events, and in my opinion this is not coincidence," says Boyle.

Snowball Earth may have pushed animal cells to specialise

For Boyle the real puzzle isn't the appearance of multicellular animals. Instead, it's the rise of cellular differentiation &ndash cells with specific roles like liver, muscle and blood. These specialised cells allowed animals to become much more intricate. "What sets animals apart from plants and fungi is this irreversible cellular differentiation, which, for instance, is what allows animals to have more cell types," says Boyle.

It's hard to see how this could have evolved, because specialised cells lose the ability to reproduce on their own. Instead they have to be distinctly self-sacrificing, cooperating with other cells in the body for the greater good of the animal. Only the specialised reproductive cells, the sperm and eggs, get to create a new generation.

By contrast, plants don't just rely on specialist sex cells to reproduce. They can also reproduce themselves from cuttings taken from their stems or roots. "You can't take a cutting from an animal," says Boyle. He thinks the severity of Snowball Earth may have pushed animal cells to abandon this flexibility, and specialise.

"During the Snowball period, life will have been confined to small geothermally heated areas, and will have experienced frequent extinctions and population crashes," says Boyle. The populations that did survive were often reduced to just a handful of organisms. Boyle suggests that these little groups of survivors were often closely related, encouraging them to cooperate more than usual.

Most geologists don't buy the idea of a hard Snowball Earth anymore

Biologists have long known that animals are more likely to help close relatives, because by doing so they can benefit their own genes, which the relative will also carry. For example, wild animals are likely to adopt orphans that are related to them, but not orphans that are unrelated. Boyle thinks that Snowball Earth may have forced cells to behave altruistically. "Until that point, the cost of being an animal cell had been too high," he says.

Boyle's notion is controversial and other scientists are sceptical. "Boyle's melt-hole idea for the origin of animals is fun," says palaeontologist Nick Butterfield of the University of Cambridge, UK. "But most geologists don't buy the idea of a hard Snowball Earth anymore, so the isolated hot-spring refugia ponds wouldn't have actually existed."

Butterfield argues that life probably retreated to the open waters of the tropics during Snowball times, but otherwise carried on as normal.

It would really help to find some definitive fossils to resolve this. Unfortunately, the fossil record is very patchy in such ancient rocks. So far, the oldest definitive fossils of complex animals date to around 560 million years ago. That could fit with either hypothesis.

Genetics doesn't help much either. By working backwards through the animal family tree and estimating rates of genetic change, scientists have estimated that the first animals are likely to have emerged around 750 million years ago. But these "molecular clock" estimates are notoriously unreliable.

It is no coincidence that these animal precursors appear right after the Snowball

Nonetheless, recent discoveries hint that animal life may have started to gain a foothold during Snowball Earth. In 2014, Malcolm Wallace of the University of Melbourne in Australia discovered strange clumps of fossils in remote regions of Australia and Namibia. In the remains of ancient reefs, Wallace found bubble-shaped fossils up to 3cm across. Many of the bubbles appeared to interconnect into a network of finger-like strands.

"These fossils are big and complex, but they don't really fit exactly into any of the animal phyla," says Wallace. They date from around 700 million years ago, soon after Earth first became a Snowball.

So Wallace and his colleagues think they may have found the precursors to animals &ndash very early sponge-like creatures, which lived in low-oxygen waters and represented a halfway stage between single-celled microbes and multicellular animals. And they think it is no coincidence that these animal precursors appear right after the first major Snowball glaciation.

"Intuitively, you might think that Snowball Earth would hinder evolution, and yet animals appear soon after the big glaciations," says Wallace. "It seems clear that these big glaciations have disrupted the Earth's ocean-atmosphere system in some way that was favourable for complex life to develop."

Boyle agrees that this kind of primitive animal life may have evolved before the end of Snowball Earth, but he argues that this wasn't the crucial step. Instead, the key threshold is when individual cells forgo their ability to reproduce, and instead take on specific roles within an animal.

Butterfield suspects we have got the whole story backwards

So far, animals more complex than sponges, with specialised organs that do different jobs, have only been found in rocks laid down after the Snowball. Boyle predicts that they will never be found in older rocks, certainly not in rocks laid down before the Snowball. "If such fossils are found then my hypothesis will be proven incorrect," he says.

Butterfield agrees that such ancient animal fossils may never turn up, but that could simply be because they haven't been preserved. He now suspects that Boyle, Planavsky and Wallace have got the whole story backwards. Instead of the ice creating complex animals, he suggests that the first animals appeared 750 million years ago and transformed the planet, cooling the climate. "I think there is a good case to be made for the evolution of animals actually triggering the glaciations," says Butterfield.

"Animals have an enormous capacity to modify physical environments," says Butterfield. So he thinks the first animals upset the delicate balance of ocean chemistry, with knock-on effects for the rest of the planet.

The first animals could have thrown Earth into a deep freeze

Animals can certainly have big effects on the planet. For instance, burrowing animals like worms can break up rocks faster. The resulting rock dust reacts with carbon dioxide in the air, and the minerals produced get washed into the oceans &ndash removing the carbon dioxide from the air. Meanwhile, marine animals boost oxygen levels by eating the remains of dead organisms, which would otherwise consume oxygen. Butterfield also thinks animals may have driven the evolution of new microscopic plants that sank faster, taking carbon dioxide with them.

There is some evidence that the first animals could have thrown Earth into a deep freeze. In 2011, Eli Tziperman of Harvard University in Cambridge, Massachusetts and his colleagues modelled the chemical cycles in the ocean. They found that the evolution of new marine organisms could have helped transport more carbon to the ocean floor and forced a major change in climate. "It's certainly not unreasonable to suggest that the evolution of animals initiated glaciation," says Butterfield.

Right now there's not enough information to decide whether animals created Snowball Earth, or Snowball Earth triggered animal evolution. But either way, the two events are linked.

Whether our planet goes hot or cold, it will be a seriously bumpy ride

They are also a sobering reminder of how quickly conditions on Earth can change. Our planet has been just right for us for thousands of years, but there is no reason to believe it will stay that way.

Right now our appetite for fossil fuels is hotting things up dangerously fast. But a large asteroid impact, like the one that did for the dinosaurs, would throw up enough dust to block sunlight and cause a dangerous chill. And because today's oceans are cooler than they were in the dinosaurs' time it's conceivable that the oceans would freeze and Earth would revert to a Snowball state.

Whether our planet goes hot or cold, it will be a seriously bumpy ride. Maybe we should learn from those early animal cells, and learn to work together.



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