nodalpoint.org - Evolution - Comments

writing style

chris — Fri, 23 Dec 2005 13:25:37 -0500

I'm a big fan of these sorts of articles. The best writing usually tells a story: a continuous narrative for some reason resonates deeply with the human mind and allows us to absorb information and place things into perspective. It's an old trick, going back to the legends and parables of the ancient worlds of Gilgamesh and Homer.

One of the things we often miss when reading/writing a scientific paper is this narrative: the introduction should at least set the scene, but in truth so many scientists are so poor at writing that their papers become garbled and abstruse, even for other experts in their field.

Maybe we should all try to tell stories in our next papers?

More avian flu resources, and a note on the Connotea resources

Declan Butler — Sat, 05 Nov 2005 05:12:05 -0500

Hi, I'm the keeper of the avian flu firehose on Connotea -- its meant to be used via its RSS feed as a sort of daily newswire. At Nature we also have an updated focus section on avian flu. I've also made some rough Google Earth maps of avian flu outbreaks, that will be refined when I get a moment.

Declan

Quite

chris — Wed, 26 Oct 2005 04:47:32 -0400

The logistics angle may be the defining criterion for pandemic threat status. That we are more prepared now than in 1918 is a disingenuous point to make - there is a much greater population to contend with, travel (and hence geographical spread) is much faster, and our medical facilities - where they exist - are probably under more strain than a century ago.

We didn't stop AIDS, and we didn't stop Ebola (it wiped itself out). Granted, we didn't know how to cure those diseases. But we do know a lot about TB, and we don't seem able to stop a resurgence of resistant strains - everyone just seems to be praying very hard it doesn't escalate. And that's a bug, not a virus, which would normally make it easier to treat...

It seems to non-specialist me that the one thing that is really keeping a serious wave of infection at bay is the relatively low frequency of transmission from animal to human host, and the even lower ability of the virus to spread between humans. But how long will that last? Any virologists care to comment?

NCBI Influenza Virus Resource

Tobi — Tue, 25 Oct 2005 16:31:55 -0400

Maybe also interesting in this context: A database of all influenza sequences in Genbank is provided by the NCBI.

links on Connotea

alf — Tue, 25 Oct 2005 15:10:34 -0400

I found Nature journalist Declan Butler's 'AvianFlu'-tagged links on Connotea to be a useful resource too, though it's quite a firehose of information.

Have seen an interesting

Stewb — Mon, 24 Oct 2005 06:50:59 -0400

Have seen an interesting post on Instapundit blogged a few times... "is avian flu being overhyped?". It's a letter from a doctor at the University of Chicago saying that we're much better prepared to deal with a flu pandemic than we were in 1918, so no worries.

Though I agree with what he writes, I couldn't help thinking: sure, with the help of modern medicine we shouldn't have that much to fear, but isn't any possible avian flu pandemic a logistical nightmare rather than a medical one? We know how to treat it, will know how to vaccinate people against it in fairly short order and so on but that's no good if you don't have enough hospital beds / respirators / vaccines to go round.

I would point out that evolut

chris — Wed, 29 Jun 2005 21:12:16 -0400

I would point out that evolution is NOT a smooth motion from less to more 'evolved'. Put crudely, it states that stuff happens over (geological) time, (largely) in response to external factors. Although it's tempting to assume that things get better/more complex/more refined over time, this is not necessarily true. Things change: attributing subjective values like "good" or "better" is a (natural) human fallacy, as is assuming that evolution has stopped. It's still going, and will continue for the forseeable (geological) future.

So the fact is that you can't cause something to devolve. Evolution isn't a linear process. Here's a hand-wavy thought experiment (bear with me here, and assume we could actually do all this).

Let's assume that an external factor F causes selection for a particular trait in an organism. If you then applied the opposite of F, you probably wouldn't reverse the trait (ie cause what I assume you mean by devolution); instead, you'd modify it in some unpredictable way.

One of the paradoxical things about evolutionary theory is the concept of contingent history: once something has happened, you can point out its causes; but you would not have been able to predict that outcome before it happened, because (i) it is impossible to know what the acting causes are or how they change over time, and (ii) even if you did, the element of chance (which after all helps generate diversity) means you couldn't predict the outcome.

more thanks!

Will Von Wizzlepig — Mon, 02 May 2005 15:06:21 -0400

Wow, awesome. Thank you. I will look into that.

I see now that the experiment had different intentions. Craig Venter's work seems more like what I am looking to find out about. Can we show that a certain creature can be caused to devolve? Can we show the theory of evolution in real time?

With the 'alive' issue I am on the same page with you- I'm here for several reasons- It's interesting, I want to know, but moreover, I want to be able to show people what I have found and make it meaningful, and I am not one to leave out footnotes and endnotes and call it a success- if I have to include 'alive' in the debate because some contend its application, I will lose some of my audience- mostly, those who are eager to throw it out to begin with.

Thanks again.

-WVW

Complexity

chris — Fri, 29 Apr 2005 21:49:49 -0400

I think you've got the experiment the wrong way round. Although Speigelman started with a virus, the point was to try and reverse-engineer abiogenesis - the process where (relatively) simple chemical entities eventually come together to form a replicator, such as an RNA strand. Eigen then attacked the problem directly, simulating a 'primordial soup' environment complete with bolts of lightning to set things going [a model now widely questioned, I believe - Neil?].

The overall aim was to see if you could go from 'stuff' to 'stuff that copies itself' - abiogenesis. The simplest self-replicating entities we know of today - viruses, prions, other bits and pieces - are many times more complex than these (largely hypothetical) progenitors. Truly 'living' things, such as bacteria, are in turn orders of magnitude more complex than even pretty sophisticated viruses with protein coats. So the experiment to generate a bacterium from 'stuff' is probably flawed, because that's probably not how it happened.

What people are trying to do is to see what the simplest possible bacterium is - Craig Venter has been trying for years to induce one of the smallest ones, a Mycobacterium, to shed as much of its DNA as possible. The overall aim is to see how simple a cell (which most reasonable people would agree is alive) can be. Although it's a very artificial setup, it would be interesting to see the results.

I'll save up the rant about the human tendency to divide everything into two neat categories (alive/non-alive) for another time :-)

me again

Will Von Wizzlepig — Fri, 29 Apr 2005 17:13:44 -0400

Thanks again for the help, but now I have another question and I did not find the answer in the archives.

Spiegelman's experiment shows that a virus can be goaded into devolving to nearly useless form (from 4500 nucleotides to 220.)

It seems a given that the 'aliveness' of viruses is questionable.

Can't a similar experiment from be performed using some other microscopic entity which is actually considered 'alive'? Has it been tried? If not, what prevents it?

Thanks again,

WVW

Thanks!

Will Von Wizzlepig — Fri, 29 Apr 2005 12:06:48 -0400

I will check it out, now that I know what to look for it should be easy. Thanks a lot!

-WVW

try talk.origins

Neil — Fri, 29 Apr 2005 00:56:00 -0400

All your evolutionary questions are answered at the Talk.Origins archive. I believe the experiment that you refer to is "Spiegelman's monster" and involved viruses; try those search terms at the Talk.origins search page or on Google.