PDA

View Full Version : Taxonomy, Aliens, and Artificial Life.



Spherical
2006-Jan-09, 09:00 PM
http://www.spaceflightnow.com/news/n0511/24life/

So what do we do now that we are the Creator?

SolusLupus
2006-Jan-09, 09:41 PM
http://www.spaceflightnow.com/news/n0511/24life/

So what do we do now that we are the Creator?

We party.

Enzp
2006-Jan-10, 04:11 AM
We provide it with inconsisent messages and an implausible mythology and wait to see if it turns out like we did.

SolusLupus
2006-Jan-10, 04:13 AM
We provide it with inconsisent messages and an implausible mythology and wait to see if it turns out like we did.

Okay. A) I find this statement incredibly hilarious.

B) I still think it's crossing the line. Lots of people might get offended.

Huevos Grandes
2006-Jan-10, 08:56 AM
B) I still think it's crossing the line. Lots of people might get offended.

I agree. But with the rules being enforced in an inconsistent manner, who knows how long such a statement may be allowed to exist.

This article is junk, IMO. I'm positive that Peter Ward wants to re-christan the taxonomical tree, the "Wardian Taxonomical Tree". The (non)inclusion of viruses is a problem, yes, but hardly merits its own kingdom, or whatever he chooses to call it.

Exotic alien amino acids- what might those be ? If acids beyond the 20 "native" ones were feasible anywhere (including Earth), then we'd be aware of it in some lifeform by now. Even so, the two decades of manufacturing life in labs that Ward refers to will bear out this fallacy. And the mere mention of silicon-based life makes the entire article laughable. Just as a biochemist why carbon = good, silicon = bad, for a lesson in molecular bonding properties.

Yes, when the aliens drop in for tea several Tuesdays from now, then we can look to re-evaluate the classification tables. Guessing the unknown just complicates biologists' work needlessly.

Halcyon Dayz
2006-Jan-12, 05:12 AM
Artificial life and alien life are not part of our tree of life.
They form their own, independent trees.

SolusLupus
2006-Jan-12, 03:36 PM
Even if we could make an animal that thinks, act, and is just like another animal of it's type, and even breed with that animal? Not saying that we have, but I think it depends on how you define the "tree of life"

Halcyon Dayz
2006-Jan-12, 03:49 PM
Even if we could make an animal that thinks, act, and is just like another animal of it's type, and even breed with that animal? Not saying that we have, but I think it depends on how you define the "tree of life"
Wouldn't that be a high-tech clone, rather than an bio-artifact?

SolusLupus
2006-Jan-12, 03:52 PM
Wouldn't that be a high-tech clone, rather than an bio-artifact?

Is it? If we made it ourselves, and designed it to have a personality we chose, and didn't use the genetic imprint of an exact copy, then how is it a clone?

eburacum45
2006-Jan-12, 05:30 PM
Artificial life might be developed fairly sson, and it might start off by being simpler than any life we find in nature today. There seems to be quite a lot of redundant DNA in the genome of most creatures alive today (although this might be just material we haven't found the reason for yet).

If we can make simplified versions of a microbe's DNA for instance, and the result is viable, the resulting creature would be an entirely new creature.
In OA we call such entirely new creatures 'Neogens'; I don't know if there is any earlier instance of this usage.

Eventually the majority of lifeforms in a civilised galaxy might be neogenic.

Halcyon Dayz
2006-Jan-12, 05:48 PM
Even if we could make an animal that thinks, act, and is just
like another animal of it's type, and even breed with that animal? Not saying
that we have, but I think it depends on how you define the "tree of life".

If we made it ourselves, and designed it to have a personality
we chose, and didn't use the genetic imprint of an exact copy,
then how is it a clone?
I misread your first post.
You could have Frankensteinian spliced gene species.
But a completely new species, with for instance a computer-generated
genetic code, would not be related to any other animal, and therefore
would IMO not belong to the kingdom of animals, but to a completely
new kingdom. I suppose biologists would then have to come up with
some sort of genetic measurement to establish relationships, rather
then rely on decent.
Alien life and technological "life" would not fit in the tree at all.

eburacum45
2006-Jan-12, 05:48 PM
As far as xenobiology is concerned, I think Huevos Grandes might be wrong; on our world twenty amino acids are coded for in DNA; but more that a hundred different amino acids have been discovered, some only in meteorites (carbonaceous chondrites), and apparently there might be billions of possible examples.

On our world the evolution of RNA and DNA replication obviously caused the selection of lifeforms containing these twenty acids.

But before self-replication emerged, life-like organic processes must have existed for an unknown time; we might find worlds where self-replication through DNA never evolves, and on those worlds the many other possible amino acids might be found. It may even be the case that other forms of self replication might emerge, not using RNA/DNA at all;

such life, if possible, could potentially utilise many amino acids not used on Earth.
I don't think that anything we know currently can rule this possibility out, but by all means prove me wrong.

Huevos Grandes
2006-Jan-13, 03:51 AM
As far as xenobiology is concerned, I think Huevos Grandes might be wrong; on our world twenty amino acids are coded for in DNA; but more that a hundred different amino acids have been discovered, some only in meteorites (carbonaceous chondrites), and apparently there might be billions of possible examples.
I don't need "Xenobiology" to be correct, in this instance; regular biology will suffice. You fall into the same trap as the author, making mysterious this prospect that other-worldly amino acids can form new and exciting lifeforms. This is bunk- most complex lifeforms on Earth do not build 20 amino acids (this is one of the reasons I eat food).

In reality, it is not only amino, but imine acids that go into creating proteins, and nature favors simplicity. Other amino acids do go into forming protein secondary and tertiary structures, but are irrelevant, because even minute differences in the 'R' chain into something that won't form bonds to create secondary- and tertiary structures (e.g. a synthetase enzyme with 38 acids "folded", bonded acids will not work properly if say- one of the glutamic acids has a oxygen atom or two replaced by a copper). Other amino acids are possible, sure- but not necessarily ones that work. Amino acids are the basic building blocks because they are basic- not some randomized "Earth" chance.


On our world the evolution of RNA and DNA replication obviously caused the selection of lifeforms containing these twenty acids.
Obviously not. I would ask for your explanation for this, using basic biochemistry, referring to my analysis above.


But before self-replication emerged, life-like organic processes must have existed for an unknown time; we might find worlds where self-replication through DNA never evolves, and on those worlds the many other possible amino acids might be found. It may even be the case that other forms of self replication might emerge, not using RNA/DNA at all;

such life, if possible, could potentially utilise many amino acids not used on Earth.
Again- chemistry doesn't restrict itself to borders in this manner. The same elements that make aspartic acid and amino acid X possible on Ceti Alpha 5 (Khaaaaaaan!), for example, are available on Earth. And while I am unable to disprove your assertion, I will say that complex life can only form where DNA/RNA (other some other stable information-carrying molecule) self-replicates. Before enclosed membranes, organelles, and concentrated agglomerations of nutrients could be counted upon by the DNA/RNA, floating freely in the "soup" of Precambrian life, replication happened by chance. Mutation was abundant, and almost invariably caused problems, rather than improvement.


I don't think that anything we know currently can rule this possibility out, but by all means prove me wrong.
You can make "new" amino acids at home. Your own body is creating them all the time. They simply just don't tend to make working proteins, are are thus destroyed. Ask a biochemist sometime how many potential R-chains a protein can have.

eburacum45
2006-Jan-13, 02:18 PM
most complex lifeforms on Earth do not build 20 amino acids (this is one of the reasons I eat food).
Absolutely; humans are heterotrophic and need to eat protein to survive.

I was refering to the biology of Earth as a whole, which is remarkably consistent in it's amino acid make-up; but it may well have evolved from a small number of instances of abiogenesis- possibly just one.

You are no doubt more familiar with the twenty amino acids coded for in DNA/RNA than I am, but here they are anyway;
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html

My suggestion is that other possible associations of more exotic acids don't get a chance because these twenty and their derivatives out-compete them; and they can do this because of their association with DNA/RNA.


And while I am unable to disprove your assertion, I will say that complex life can only form where DNA/RNA (other some other stable information-carrying molecule) self-replicates.
Do you think it possible then that other stable information-carrying molecules might exist? Any suggestions? If such molecules do exist they might not code for a biology using all the same amino acids as our own.

Or, alternatively, other information carrying molecules might code for a biology remarkably similar to our own. It is certainly possible that the association of proteins and amino acids that we have on Earth is the simplest and most optimised for survival;
but we have only a sample of one to go on.
If all life on Earth descends from a very small initial sample, then the common features might be a result of that limited ancestry rather than a universal rule.

Huevos Grandes
2006-Jan-13, 03:50 PM
My suggestion is that other possible associations of more exotic acids don't get a chance because these twenty and their derivatives out-compete them; and they can do this because of their association with DNA/RNA.

Do you think it possible then that other stable information-carrying molecules might exist? Any suggestions? If such molecules do exist they might not code for a biology using all the same amino acids as our own.

My apologies- I didn't realize you were tying your speculation to DNA/RNA being the dominant genetic information carrier. I became confused when you started invoking that exotic amino acids had been "discovered" in meteorites.

Yes, there could well be another information carrier besides a single or double- stranded DNA/RNA. But interaction with amino acids to make proteins has about zero to do with the genetic information containted in a cell. Sure, even in archaebacteria, there is replicase and other enzymes that work directly with the genome, but the vast number of proteins are synthesized in the cytoplasm, with little help from the "phonebook" DNA genome, besides a mRNA crib note.

It is the proteins that are seen to do, and make structures- it is their interactions that could build a better enzyme, or potentially lyse the cell. For a time, before Watson & Crick, some biologists believed that proteins were the cellular structures that carried the genetic code, simply because of how detailed they could be, and how chains could interact and "fold" within themselves.


Or, alternatively, other information carrying molecules might code for a biology remarkably similar to our own. It is certainly possible that the association of proteins and amino acids that we have on Earth is the simplest and most optimised for survival;
but we have only a sample of one to go on.
If all life on Earth descends from a very small initial sample, then the common features might be a result of that limited ancestry rather than a universal rule.
Nature does favor simplicity- I would think certainly with a couple billion years under its belt, life on Earth would've had a chance to consume a 21st amino acid and incorporate it into a protein. But that amino acid chain was too complex, and interfered with the other amines, which are really very simple molecules. I don't deny that Earth life descends from a small sample- mitochondria and mitochondrial respiration essentially prove this. But in the end, I imagine the same 20 simple amino acids will be utilised on other worlds almost exclusively, and I'll bet you all of my Enron shares that this experimentation yields extremely few, if any, working proteins with a "bizarre" amine contained therein.

SolusLupus
2006-Jan-13, 03:54 PM
So.. there's no chance of other amino acids existing "out there" that can't be found "here"?

Huevos Grandes
2006-Jan-13, 04:39 PM
So.. there's no chance of other amino acids existing "out there" that can't be found "here"?

How about "negligible chance" ? The article talks about manufacturing life here on Earth, inferring use of other amino acids in a lab. But a lab isn't, and hasn't been necessary to "create" an amino acid thus far. If it's SOOOO exotic as to have to come from a deep, dark, mysterious comet/meteorite/etc., then odds are it's too complex to involve regular inclusion into a meaningful protein.

BioSci
2006-Jan-13, 08:10 PM
But in the end, I imagine the same 20 simple amino acids will be utilised on other worlds almost exclusively, and I'll bet you all of my Enron shares that this experimentation yields extremely few, if any, working proteins with a "bizarre" amine contained therein.

I think that the current best model for selection of amino acids is that the list of ~20 amino acids normally found in proteins on earth is a combination of chemical acitvity and random selection of possible amino acids that could be used. To make a typical functional protein, one needs to use a selection of amino acids with general and specific characteristics - general characteristics to include: acidic, basic, hydrophobic, & sulfur reactive groups. Specific attributes include the exact number of carbons in chain & placement of the active group. Extensive experimental evidence shows that most of the amino acids of a protein sequence can be easily changed to an alternate amino acid without large changes in protein structure or function especially if the exchange maintains the same general characteristic (acidic, basic, etc.). Specifc "active sites" or "conserved regions" of specific proteins may have much tighter restrictions on amino acid substitutions based on chemical reactivity and precise localization of chemical groups.

Considerable research has been conducted on incorporation of novel, "unnatural" amino acids into proteins. These novel amino acids include ones with novel elements (iodine, selenium) and reaction groups (photoreactive, fluorescent). The proteins work fine.

I think that the current model for how we ended up with our current list of 20 amino acids includes the concept that the exact chemical structure of our amino acids is essentially a random selection from the 100's of possible amino acids. As long as life has a selection of acidic, basic, hyrophobic, etc. amino acids to build from, the number and potential activity of resulting proteins is essentially unlimited.

This means that if life were to develop proteins from amino acids in a similar fashion elsewhere - the actual amino acids used would be highly, highly unlikely to match our same 20 amino acids. If Allien life made proteins out of amino acids, they would certainly be a different mix of amino acids.

Similar arguments can also be made for DNA/RNA nucleotides. The AGTC of our DNA are not uniquely capable of their function - other nucleotides and related chemical structures are equally possible and suggests that Allien life would be likely to discover/invent an alternative molecule for encoding genetic information

For some research papers on this active area of work one can search PubMed for nonnatural amino acids & genetic code.

SolusLupus
2006-Jan-13, 08:17 PM
How about "negligible chance" ? The article talks about manufacturing life here on Earth, inferring use of other amino acids in a lab. But a lab isn't, and hasn't been necessary to "create" an amino acid thus far. If it's SOOOO exotic as to have to come from a deep, dark, mysterious comet/meteorite/etc., then odds are it's too complex to involve regular inclusion into a meaningful protein.

Well, for use on this earth, yeah, I agree. Good point.