Viruses Vs. Bacteria – Debate Rebuttals

ResearchBlogging.org

 

Thomas and I will present our rebuttals below. Feel free to read through them, the original posts which can be found here and here. After taking in both arguments vote for the winner on our first poll. Or just skip to the poll, it’s your vote to cast as you wish 🙂

We tried to limit ourselves to 1000 words each so it didn’t get out of hand, length-wise. Enjoy.

A couple of things first though.

Hits on Thomas’ post (1 week) – 220

Hits on James’ post (1 week) – 165

Comments in favor of Thomas – 3

Comments in favor of James – 8

Number of ‘Editors Selections’ on researchblogging.com – 1 (DAMN YOU THOMAS!!!)

Number of twitter tags generated for this post – 1 (#teambacteria) (SUCK IT THOMAS! WOOOOO!!!)

Now to Thomas for his rebuttal…

So many things wrong with your argument, it’s hard to know where to start. I had 2000 words by the time I realised that it was too long. So here’s the shortened version.

Our best conservative estimate is that 10% of all deaths are directly related to bacterial infections and indirectly.

The vast majority of those 10000000000000000000000000000000 viruses in the oceans feed on bacteria. Where there are bacteria, there are viruses. Viruses kill ungodly numbers of cells daily and are the cause of the most cell death of any known organism. So, the question of who would win in a fight between viruses and bacteria, easily goes to viruses.

But if we want to get to humans, the real threat is sudden changes in death causing collapse in societies and killing even more people. Many of the big emerging diseases you can think of are viruses: bird and swine flu, Ebola, SARS, dengue. Even in the past, large fearsome diseases that swept through communities were virus-caused: The Spanish flu epidemic, killing 3% of the world’s population in 2 years; polio, paralysing entire hospitals of patients; and smallpox, which slaughtered entire tribes of Native Americans. All caused by viruses. We can adapt to the slow burn of death of the bacterial diseases, but the sudden bursts of morbidity and mortality from new diseases disrupt societies and collapse civilisations.

So why viruses rather than bacteria? Many new diseases come from jumping the species gap. Viruses are produced in such large numbers and with so many variants that at least some can infect a new species of host. These new hosts have never seen this virus before so don’t know how to deal with it. More often than not, this causes a great amount of disease as their immune system thrashes about trying to get rid of this new pathogen.

These large numbers and variants (much more than a bacteria) also make it more likely that one of the viruses are resistant to a treatment (say, antivirals) and can spread onto infect others. This is how antiviral resistance occurs and is still a big problem with the small number of virus infections that we do have treatments for.

Thus, viruses are the greater threat to our societies and humankind.

So all eukaryotic cells only exist because of the incorporation of bacteria.

Pfft, try the origin of all known life. With viruses infecting all known cellular lifeforms, viruses were probably present before the evolution of cells. The Virus World theory says that viruses were essential for the evolution of cells as the inventors, vehicles and amplifiers of crucial factors for cellular life (such as nuclei, the enzymes that copy DNA, make RNA and proteins, etc.). Early viruses continually battled it out and reinvented themselves struggling for replicative supremacy; and in their wake, provided fruitful conditions for cellular life to occur. Basically, viruses acted as both ingredients and blenders in the primordial soup, and thus have had a greater contribution to today’s life than bacteria.

The Virus World theory posits that there are 5 main groups of viruses [all of which reproduce in different ways, compared to the one way that bacteria divide (i.e. viruses are more diverse)] that emerged separately at different stages of cellular evolution. This helps explain how viruses infecting completely different hosts (say, bacteria and eukaryotes) can share similar genes, while viruses infecting the same hosts are completely different makeups.

Without bacteria we wouldn’t have eukaryotic cells. […] Way back in the primordial sludge one BACTERIA engulfed another BACTERIA.

Actually prevailing evidence says that an archaeon enveloped a bacterium. The archaea are a domain of organisms that are closer related to humans than any bacteria. Close, James, but it’s a completely different organism. I hold no grudge against the Archaea.

In fact 10% of our genome is incorporated and now defunct retroviruses. For the most part these DNA sequences don’t do anything anymore.

Retroviruses make up more of our genome than our own genes do. While they might not producing virus particles any more, they’re fantastically important to who we are. When the human and mouse genome projects were completed, they saw that 99% of our proteins had a corresponding protein in the mouse. There really isn’t that much to separate us from our cousins. Why are we not mice? Because of regulation: how much of what protein is produced in what tissue at what time. A huge amount of regulation have come from the retroviruses via promoters.

Genes are regulated by molecular switches called “promoters”, DNA sequences that turn on any genes close by. Promoters can be turned on only in certain tissues, some genes need to turn on multiple promoters for them to be expressed, some promoters are only turned on in certain environmental conditions. Promoters add a huge amount of complexity. Viruses carry promoters so that their genes can be activated in a cell. But some retrovirus promoters have been incorporated into our genome and are now used by the cell to alter the expression of our own genes.

About half our genes have retrovirus promoters that contribute to gene expression. 1000 of these use ONLY retrovirus promoters to determine when they are switched on, i.e. if it wasn’t for retroviruses, they wouldn’t be made at all. Many other promoters are in “junk” regions of the genome, i.e. they do not code for proteins. However, these could be regulating expression in other ways, e.g. using siRNAs. All of these examples are proof that retrovirus sequences can not only be active, but are an important part of our identity. Yes, more important that the bacterial contribution.

Viruses cannot move on their own, cannot utilise energy in the environment if they are not parasitising a cell, cannot sense the environment, cannot growth un-assisted, cannot reproduce un-assisted and do not generate metabolic waste.

(Much of this argument was inspired by Prof. Vincent Racaniello’s post at Virology Blog )

OK. Apart from the fact that something is alive doesn’t make it better (see chlamydia/Ferrari comment in my argument post), the line between living and dead isn’t that clear-cut.

  • Rickettsiae, Coxiella and some mycobacteria are bacteria and all need to be inside their host cell to reproduce. Does this make them non-living creatures?

  • Many virus capsids continually change between metastable states (capsid breathing). Capsid breathing is very important for the virus to attach to, enter, and release its genome into a cell using the same capsid proteins. Capsid breathing is powered by ambient heat. Does this count as moving and utilising energy?

  • Once inside the cell, many viruses count on changes in pH to alter their structure and penetrate the cellular wall. Does this count as sensing the environment? When they infect cells, they throw away their spent outer coats. Is this metabolic waste?

MRS GREN is becoming more and more outdated as we find out more about the world.

Some scientists have mentally separated the virion (the freeform that floats around in the environment) from the virus proper (the virion-producing factory that a cell becomes when infected). Virologist J.M. Claverie said comparing the virion to the virus would be like comparing a sperm cell to a human (or a bacterial spore to a living bacterium).

To quote an article entitled “Defining Life: The Virus Viewpoint”:

“… [A]fter destruction or inactivation of the cellular genome, when the viral genome is the only one that is expressed, one can really consider that the infected “cell” is no more a bacterium, but a virus with a cellular appearance. A nice example of this conversion is provided by cyano-bacterioviruses that encode their own photosynthetic proteins to replace the decaying cellular ones in order to get the proper energy required for the production of virions. The former cyanobacterial cell thus becomes a photosynthetic virus.”

The fact that viruses attain this state of living by using such minimalist techniques certainly makes them more elegant than bacteria.

While I’ll concede that bacteria may have a greater impact on the environment, I contend and have shown that viruses are more deadly, more dangerous, more elegant and greater contributors to today’s life and our own identities than bacteria. And I didn’t even invoke Twilight references to do it.

TT

P.S. Also, if it wasn’t for bacteria we could eat raw sausage. (Argument from Erica Southern)

And now my rebuttal…

Oh Thommy Tom Tomo. Your misguided and at times inappropriate and creepy love for viruses or as I like to call them, protein bags, borders on the fanatical. I’m sure if viruses could organise themselves into some sort of tangible entity capable of slapping together a restraining order, you Sir would receive one from them. Having said this, you raise some interesting but inevitably inadequate points that I would like to address.

Unless you wish to pull out now?

No?

Game on then it seems.

Thomas’ opening paragraph suggests that viruses are many things including;

They’re more populous, more deadly, more diverse, more resistant, more elegant, more beautiful and more important than anything bacteria have to offer

My direct response to these are as follows ; true, lies, perhaps, situationaly, lies, subjective and big lie, but I’ll get round to covering these as we move through his elaborated arguments.

First, they’re everywhere.

Oh are they Thomas? Ever looked into a deep sea vent for a virus? You will find bacteria there living in some of the most intense conditions on the planet. What about below the sea ice in Antarctica? Boom! Bacteria there too! 40 miles high in the atmosphere? You got yourself some bacteria!

Everything viruses live in?

Think about all the different types of the organisms you can see (a dog, an ant, a fly, a tree outside, that guy creepily watching you read this article…), then think of the organisms that live off those organisms (mites, bacteria, parasites, fungus…); for every species, there are 10 different viruses that will infect it.

Yep, all of those are harboring commensal bacteria as well. Point nullified.

The only point here that Thomas makes that can’t be directly refuted is the suggestion that viruses outnumber bacteria. At this stage it is expected that there are 10 viruses for each bacteria on this planet. So, okay yes you get that small win but with the number of bacteria on this planet being estimated between 1 × 1030 and 5 × 1030 is it actually relevant? I would say nope.

Hell, there’s even a virus that infects viruses.

I don’t understand why Thomas would bring this up. So what? You have so many viruses that you got some fat ones and some that like to attack other viruses. First you want a big microbe? Check out Thiomargarita namibiensis which measures 0.1-0.3 mm (milimeters for Christ sake!) and has been seen as large as 0.75 mm!

Mamaviruses could be infected by completely different tiny virus, called Sputnik

Are you actually going to bring up inter-species competition? Ummm, bacteria rule competition. We have antibitotics because of this competition. In fact didn’t I just write about the possibility of a newly discovered anti-microbial product being isolated from a bacterial biofilm? Yeah, I totally did.

Some viruses (for example, HIV) insert themselves into your genome

Ha ha ha ha ha ha ha ha ha! Endosymbiotic theory. Win. How many whole viruses is there that remain crucial to cellular function? There are at least two whole ancient bacteria making up every cell in your body. Even though you don’t deserve them Thomas :).

scientists found that only 1.5% of the genome codes for proteins, but 5% of our genome is composed of retrovirus sequences.

I think that I actually covered this quite well in my own argument. If the viruses are defunct then they failed at whatever they were doing. Whereas the endosymbiotic mitochondria and chloroplasts have their own DNA, replicate independent of the host cell and even retain a number of structures like their own membranes which keep them separate in many ways from the cell.

The last argument Thomas uses is one of evolution and adaption.

the 5% difference in the genomic sequence between humans and chimps took 8 million years to develop. To produce the same 5% change, Poliovirus takes 5 days

And while he is spot on that viruses have very high mutation rates what difference does it make? Bacteria have high mutation rates and are, similarly to viruses, evolving around all the weaponry we aimed at them even though bacteria evolve more slowly than viruses do.

Thomas has presented a number of arguments to try and support he unfounded belief that viruses are objectively better than bacteria. After looking at his arguments I would hope you see that his points are in fact blunt, they really lack substance when stacked against bacteria, the most miraculous organisms on this planet.

I wish to make only two more quick points.

First, Thomas, if you don’t make sure I win then I will spike all your experiments with bacteria which I know will ruin your PhD knowing full well that you HepB virus would have no effect on my experiments :).

Finally, Thomas chose the statement that we have argued and in doing so has shot himself in the foot. In order for him to win he must show that viruses are ‘objectively better’ than bacteria. If you finish reading these arguments and walk away liking bacteria better I win, if you walk away liking or hating both equally then I win. So I urge you to think carefully before aligning yourself one way or another as only under the specific case that you believe that viruses are objectively better than bacteria in every way can you vote for Thomas.

Also, I promise to deliver tax cuts while my opponent is a hack. Thank you for your time.

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References

http://www.sdearthtimes.com/et0998/et0998s8.html

http://www.expeditions.udel.edu/extreme08/microbes/virus-myth.php

Conley AB, Piriyapongsa J, Jordan IK. Retroviral promoters in the human genome. Bioinformatics. 2008 Jul 15;24(14):1563-7. Epub 2008 Jun 5. PubMed PMID:  18535086.

Forterre P. Defining life: the virus viewpoint. Orig Life Evol Biosph. 2010 Apr;40(2):151-60. Epub 2010 Mar 3. PubMed PMID: 20198436; PubMed Central PMCID: PMC2837877.

Koonin EV, Senkevich TG, Dolja VV. The ancient Virus World and evolution of cells. Biol Direct. 2006 Sep 19;1:29. PubMed PMID: 16984643; PubMed Central PMCID: PMC1594570

Claverie JM. Viruses take center stage in cellular evolution. Genome Biol. 2006;7(6):110. PubMed PMID: 16787527; PubMed Central PMCID: PMC1779534.

Bennett Hellman, A. (2010). Gut bacteria gene complement dwarfs human genome Nature DOI: 10.1038/news.2010.104

Ricchetti M, Tekaia F, & Dujon B (2004). Continued colonization of the human genome by mitochondrial DNA. PLoS biology, 2 (9) PMID: 15361937

Morris CE, Sands DC, Vinatzer BA, Glaux C, Guilbaud C, Buffière A, Yan S, Dominguez H, & Thompson BM (2008). The life history of the plant pathogen Pseudomonas syringae is linked to the water cycle. The ISME journal, 2 (3), 321-34 PMID: 18185595

Iwase T, Uehara Y, Shinji H, Tajima A, Seo H, Takada K, Agata T, & Mizunoe Y (2010). Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature, 465 (7296), 346-9 PMID: 20485435

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9 Comments

Filed under James' Corner, Thomas' Corner

9 responses to “Viruses Vs. Bacteria – Debate Rebuttals

  1. Meow-Ludo

    I would like to join the debate and argue for fungi. I feel that they unfairly not getting the representain they deserve in this debate!

  2. Pingback: Tweets that mention Viruses Vs. Bacteria – Debate Rebuttals « Disease of the Week! -- Topsy.com

  3. A Surname like Smith (times 100)

    So, it’s a two-party preferred poll? A plague upon both your houses! Even (one member of) the media is commenting on the media’s commentry of the polls:

    http://www.theage.com.au/opinion/politics/uninspired-spruiking-tests-publics-patience-20100806-11oia.html

    But really, James, you know which way I voted. I assume the verbose Thomas has already prepared his concession speech.

    • You voted against us both didn’t you 🙂
      We’ll leave the poll open indefinitely but I know I would concede by Wednesday if I was losing in the poll. HINT HINT.

  4. A Surname like Smith (times 100)

    I wonder about the one vote for an excercise in futility. Personally, I choose bacteria over viruses any day of the week and twice on Sundays.

  5. Uwe

    Just 1 comment I think you need to take back your Spanish flu comment Thomas since recent or not so recent evidence suggest that although many people were infected with the Spanish flu virus most people actually died of bacterial pneumonia (PNAS paper on this). Also have included a web link to make it easy “Bacterial Pneumonia Caused Most Deaths In 1918 Influenza Pandemic” http://www.sciencedaily.com/releases/2008/08/080819160107.htm
    Sorry to rain on this aspect of your debate. Also if your going to go historical I think you cn’t use the Spanish flu and leave out the great plague (or the black death as we bateriaologist like to call it). Thats got to be a scarier than any virus disease name “BLACK DEATH”.
    Cheers

    Uwe

    • I’m trying my hardest to not rebut Thomas’ rebuttal but I’m so glad you are Uwe. There’s so many things I would argue but this has to stop somewhere doesn’t it?

    • I had intended on addressing this point in my original argument, but ran out of space.

      Yes, I am familiar with that paper, Uwe, and am sure it’s correct. But the Spanish flu had to be there for the bacteria to take over. It’s the same thing with HIV. It’s never HIV that kills you, but it increases susceptibility. Anything can come along to finish the job off after that. It just so happens there are bacteria around to do it. In both cases, it’s the virus that signs the death notice by changing the host. Spanish flu is still a point in favour of “Viruses”.

      You could have HIV-AIDS and keep the tuberculosis away by taking antibiotics, but something else is going to get you. And the underlying cause will be HIV.

      TT

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