Research Blogging Rage and ERV live

More puppeh pix pl0x. :p

My definition of "alive", which is a work in progress, is that anything that is both a) a product of natural selection, b) contains genetic information that is inherited from its ancestors, and c) is not dead, is alive. Or something like that. The trick is to capture those things that we intuitively think of as alive. I think that the main thing that our intuition is picking up on is self interest and intent. I don't mean these in a cognitive sense. "Self interest" comes from natural selection (that is why AIs won't automatically have self interest just because they are self-aware). So a virus (or dandylion or lion) has "goals" which are achieved (or attempted) and these goals, and the actions which tend to realize them, are a result of natural selection. That is, all living products of natural selection have adaptations and these adaptations have functions and sere the 'interests' of the living entity. The genetic bit (part b) is included in order to exclude things like beaver dams which are products of natural selection (a la the Extended Phenotype) but are obviously not alive. I have tried not to say anything about reproduction because some things will never reproduce but are obviously alive (e.g. a neutered dog). The last bit (part c) is apparently something that I have not worked out yet.

Interestingly, this means that my definition of alive includes the erythrocytes of reptiles (including birds) but not mammals (since mammal erythrocytes are anucleate and therefore don't carry genetic information)

Another interesting consequence is that things that are designed are not alive. If the YECs are correct then we none of us are living.

Anyway, this is one of these things that makes sense until I try to explain it.

I can't access the paper so I'm not sure what the objections to viruses as living things are but a few that I have heard elsewhere are problematic. One is that they have no metabolism. Tardigrades are also metabolically inert when they encysted. Lots of other things too (resting spores of bacteria for example). I have also heard objections based on the fact that viruses can't reproduce except inside a host. Of course this applies to all parasites so it seems to be a non-starter.

In fairness, I'm pretty sure a pit bull would savage a manuscript if you gave it one to play with. I mean, look what that guy's doing to the shoe.

I don't really get the virus thing. If they can make more of themselves, and evolve over time, what else would you call them? Undead? I'll have to read the paper carefully tomorrow.

I'm looking forward to these videos!

Don't forget to take Arnie with you to the church.

If they can make more of themselves, and evolve over time, what else would you call them?

That's part of the rub. Technically, they don't make more of themselves. They hijack another organism and use their machinery to make more of them.

So, as MattK said ... it depends on how you define "alive". Some days, my definition doesn't include viruses either.

Good luck!

Viruses contrive to reproduce without even having the innards to do so. How elegant is that?

I think we should add viroids as examples of chemical evolution almost-life... the great Missing Link between organic chemicals and viruses.

Technically, they don't make more of themselves. They hijack another organism and use their machinery to make more of them.

*shrug* So do cuckoos, and plants which need animals to pollinate them, and those weird parthenogenetic species which need sperm from related species' males to activate their eggs. Heck, no heterotroph can complete its life cycle without "borrowing" vital molecules from other organisms.

I mean, sure, viruses have managed to outsource more of life's necessary chores than any other organism, but to my mind, that just makes them incredibly successful in the parasite business.

On viruses: It seems to this layman that the prejudice against the virus as a living thing comes mainly from one fact:

People just don't like parasites.

A virus is a parasite upon eukaryotes (cellular life) and cannot live its full life cycle without such eukaryotes.

But is a flea not a living creature? Even though it depends completely upon its host?

The virus, though generally simpler than the eukaryote, seems in its present form to be unlikely to have been the first life. It either evolved from the eukaryote, or (more likely, I'd guess) from a common, cell-less ancestral replicating chemical (itself already a distant descendant of the Last Universal Ancestor) losing its independence in the process. The rise of the eukaryote must have reduced the chemical soup in the early environment, causing its membrane-less cousins to adapt for parasitism or die.

I suspect that some of these pre-cellular lifeforms evolved cell membranes and became eukaryotes, while the ancestors of the viruses evolved to exploit the eukaryotes as rich concentrations of amino acids. The virus didn't need an independent ability to reproduce, and so lost it. After all, it has the eukaryote to supply all it needed for food and a nursery for its young.

Those who would deny the stately virus its rightful place in the country club of life have to come up with quite arbitrary membership restrictions.

Actually, eukaryote is a specific group of cellular life. Viruses infect prokaryotes (bacteria and archaea) as well as eukaryotes.

Still, terminology aside, that is a popular theory, that viruses are descended from free-living creatures. Many also say that they're polyphyletic.

I myself don't know enough to have an informed opinion.

Do not go on the web tubes when you are preparing for a talk.

Srsly.

Your stress level will temporarily go down as you troll about. But later if you haven't prepared for typical snags - e.g., laptop crashes (PowerPoint on thumb drive as backup), need to get on the 'nets last minute for something (bring your own LAN cable)-- you will pay a price.

I hope your are not reading this because you're in the pre-talk groove.

Don't prions make more of themselves? And they have heritable sequences of amino acids rather than nucleotides but the two systems are complementary. Are prions alive?

PS - YAY Tom Coburn!

Paper Hand wrote: "Actually, eukaryote is a specific group of cellular life. Viruses infect prokaryotes (bacteria and archaea) as well as eukaryotes."

Thank you for the correction. I'm always glad to learn. (At least I began by warning that I'm a layman.)

Abby: As I see it, there are two questions with respect to the second citation, and they may deserve different responses.

Q1: Are viruses 'alive' or 'not-alive'?

All sorts of answers are possible here. Generally speaking, it is not necessary to answer this question in order to study viruses or to use viruses as part of the molecular biology tool kit. In addition, we should keep in mind that even in cases where some sort of answer might seem useful, it might ultimately not be all that meaningful. It might be more helpful in such cases to think merely in terms of replicators with varying levels of complexity, rather than a strict dichotomy between the living and the dead.

Q2: Are viruses ancient lineages from the very roots of the 'tree of life', or are they more recent additions to the network?

I find this question more interesting, and probably more important in answering questions of function, precisely because we can pretty much uncouple it from the vagaries that plague question 1!

Are the videos going to be linked here? I'd really like to see the YEC vid.

Jon-- Yup!

A friend just sent me the 'promo' the local pastor ran in the newspaper.

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If youâve been a faithful reader of the âLetters to the Editorâ over the past couple of months then youâve certainly read the lively interaction Iâve had with Matt Hardison over the Creation/âEvolution issue.

We last talked about setting up an open debate and weâve been working behind the scenes to make this debate a reality.

It should be lots of fun and very educational.

Hereâs the info on the debate: the topic will be âDoes Molecular Genetics Support Human Evolution?â Each side will have 20 minutes to present their case followed by a 10-minute rebuttal from each followed by a time of question and answer from the audience.

Weâll be looking at empirical evidence which will support the scientific position of each side.

This is going to be science put to the test to see if the evolutionary theory has a solid foundation or are the creationist on a more solid footing?

Matt has asked Abbie Smith to present the evolutionary view point.

I have corresponded with Abbie and see seems like a very intelligent person. Ms. Smith is a research scientist at the O.U. Health Science Center with her research focusing on AIDS. It is my understanding that Ms. Smith has participated in a couple of other debates and has done a masterful job of laying out her position. I have asked Dr. Charles Jackson to present the creationist point of view. Dr. Jackson is the scientist for the Creation Truth Foundation. He too has been in several debates and carries a strong reputation in his debate skills.

The debate will be held on Thursday evening, March 26 at 7 p.m.

It will be hosted by Christâs Church of Yukon, 620 W. Vandament.

Everyone in the community is invited to come and be a part of this debate.

I especially want to encourage our parents to come and bring your older children as in school they only receive one side of this information.

If you are a Christian parent trying to raise your children with a Biblical World View then you must realize that the school system is not your friend in the area of science as they only teach evolution and will not even open the door to the possibility that science stands behind a creator.

I asked the school if they would be a neutral site and host this debate but they refused citing the separation of church and state.

I personally thought we were talking about science not religion.

I would like to personally invite every science teacher in the Yukon school district to come and sit in on this debate and be ready to ask your questions when the opportunity arises.

You might be surprised at the truth of science, for there is another side even though the school system (not just Yukon) worships at the altar of evolution and turns a blind eye to that which they do not want to address.

Saying that probably doesnât sit very well with some folks, so come and prove me wrong.

But if there is scientific proof behind creationists view point, then letâs make some educational changes.

I know that is a big challenge but I believe weâve been taken for a ride down a dead end street for way too long.

Come join us at the debate on Thursday, March 26.

I promise you that it will be very interesting to say the least.

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I love this announcement.

1) This pastor did not use the bio I sent him. I told him I am a student, currently researching the evolution of HIV-1 to design vaccines. He carefully left out the fact Im a student, but added that Ive been in lots of debates. Ive never debated a Creationist. I guess you could kinda consider my Horowitz show on Infidel Guy a 'debate', but it was more like a conversation with a nutbar. *shrug*

2) Im not presenting any 'science to be put to the test'. Im presenting really old information that is probably new to the audience in an elementary, easily accessible format. For example, one of my images is a connect-the-dots Easter bunny. Easter. Bunny.

3) Im so happy the pastor invited children! I didnt know this event was going to be catered!!

Looks like a hostile environment. Good luck!

Also, 20 bucks says that someone asks the "why are there still monkeys?" question at the debate.

Weâll be looking at empirical evidence which will support the scientific position of each side.

Seriously, how is Jackson going to present any evidence without making it up? Perhaps he'll try to veer completely off topic to a debate on the existence of God? This will be interesting. More power to you, you have more patience than I do!

I think I found this Jackson guy's site

http://www.pointsoforigins.com/

Seems like the garden variety creotard...

aaand here's a post from the site:

Chromosome Proof we're Monkeys?
12/28/2006

A tough evo-proof is, only chimps and humans have the same parts of certain chromosomes, flipped 'round backwards (called inversions). Evo's say this comes from back when we were in the same gene pool. Now we know more of this story. The 9/22/06 issue of Science reports fruitfly inversions are "in some individuals and not in others ... follow a pattern ... in response to climate." When global warming started, some northern flies went ahead and inverted the same genes their tropical cousins had. (Science News, 12/2/06, p363)
Hey, if all it takes is being in the same climate, to get the same inversions ... and people and chimps (whose genes are alot the same anyway) came from the same climate off the Ark ... then it would make perfect sense that when genes were flippin' ... we'd both flip ... the same ways! Then millennia later ... evo's end up saying it means -- you're a monkey !
Keep thinking.

Dr J

IT WAS TEH ARK! LOL!

Abbie wrote: Im so happy the pastor invited children! I didnt know this event was going to be catered!!

I hope you invited a few friends too. Take Arnie with you so you can show the kids that Pit Bulls are pretty cool critters.

In the event no kids are there and a lot of bubbas are, you would be well armed.

Just being paranoid.

I'll give you twenty bucks if wear your lab coat and eye protection, proceed to pour chemicals into a top hat, produce a rubber fetus and throw it at your opponent shouting, "TAHHHH DAHHHHHH!".

"If you are a Christian parent trying to raise your children with a Biblical World View...."

Neato. "Sorry kids, no Legos for you. Every thing since 65 A.D. is uvvvv the Debbbil !!"

Maybe you should eat the babies. A life without Nerf products is not worth living.

P.S. It's spring and we are all watching Black Cat Bob's galleries for new bugs. Have you guys seen his work?
http://www.blk-cat-mtn-trilobites.com/

Remarks like this always make me roll my eyes:

worships at the altar of evolution

Sounds like a fun debate (or not), and I work on the west side of OKC. I'll try to be there, and I promise to try to ask a semi-decent question, but it probably won't mention monkeys.

worships at the altar of evolution = spank me with a novelty rubber coelacanth and call me Monsignor.

Speaking of slap fights I read the summation of the 10 reasons blah blah at http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/

Isn't this just the bag-o-genes versus reductive evolution pissing match that Marseilles has been having with Paris for the last five years over the mimivirus?

Has anybody had time to duplicate/review David Moreira et al.'s data since last years wave of articles about mimivirus?

I can't wait! And, I think my brother and I should have some marginally good questions for the creo. Maybe Silly Sally Kern and her husband will make an appearance! One can only hope.

Hey, what does that debate topic even mean? âDoes Molecular Genetics Support Human Evolution?â What's human evolution? The evolution of modern humans from ape-like ancestors? Or of modern humans into something else? Is human evolution being thought of as separate to the rest of life?

And how does Molecular Genetics support it? Does it mean its evidence? Or does it mean that it enables it?

To my mind, that question is full of unspoken assumptions that could get very murky very quickly.

When reading Dawkins' The Ancestors Tale I was looking forward to the gripping climax and seeing how viruses fit in. I felt a bit let down.

PS - Right now I'm listening to Check It Out by Handsome Boy Modeling School.
Check It Out, y'all!

The pastor is inflating your credentials for some reason.

Whoever mentioned "evo-proof" above seems to have missed the point that our chromosome 2 is a chimp's chromosome 15 & 16, fused, or some such. That's not an inversion that shows up in some individuals and not others. And conflates apes with monkeys. That's like... like.... referring to sparrows as ostriches?

How did it go???

Abbie,

where's the video,I need a laugh !