World's Smallest Genome

Foolish EVILutionist. This proves creationism. Since there is no organism with 183 genes, it is a clearly unbridgeable gap that you cannot fill.

Pretty cool, I've seen transcripts that are longer than that. Take Ebf1, whose unspliced transcript clocks in at just under 390 kb.

Entertainingly, the largest (known) virus has 900 genes and 800 kb of DNA:
http://www.newscientist.com/article.ns?id=dn3559

"Variation within the kind", I expect.

After I read this paper I made a bet with a friend whether it would be idthefuture or uncommondescent who will be the first to claim that this proves abiogenesis must involve 180 genes forming simeltaneously from random nucleotides and is therefore too improbable.

At the moment, the researchers are not sure how C. ruddii copes,...

After I read this paper I made a bet with a friend whether it would be idthefuture or uncommondescent who will be the first to claim that this proves abiogenesis must involve 180 genes forming simeltaneously from random nucleotides and is therefore too improbable.

So it's not capable of feeding/reproducing itself?

How small can a genome get and still run a living organism? Researchers now say that a symbiotic bacterium called Carsonella ruddii, which lives off sap-feeding insects, has taken the record for smallest genome with just 159,662 'letters' (or base pairs) of DNA and 182 protein-coding genes.

So how many of the 159,662 bp are "junk"?

Andersson says that C. ruddii might be analogues of mitochondria, caught in the process of changing from separate but dependent organisms into structures that will be engulfed and incorporated into the host cells.

Ok, just for kicks, what are the average number of base pairs in mitochondria that have been sampled so far?

So it's not capable of feeding/reproducing itself?

I guess I was trying to emphasize "feeding/reproducing itself".

It will indeed be interesting to see if it either has co-opted some of the structural proteins produced by the host, or if it actually has somehow transfered portions of its DNA to the host.

really neat.

would love to see a follwup on this in a year or so.

After I read this paper I made a bet with a friend whether it would be idthefuture or uncommondescent who will be the first to claim that this proves abiogenesis must involve 180 genes forming simeltaneously from random nucleotides and is therefore too improbable.

You see, we're all just cursed, deteriorating specimens descended from "front-loaded", "heterozygous" perfection.

Just to be pedantic for the fun of it, how can we be sure this is in fact the world's smallest genome, and not just the smallest identified to date? I personally would be astounded if this were the smallest that will ever be found, much less the smallest there really IS, much less the smallest possible.

smallest possible... for what?

That is, 3 Billion base pairs for the human haploid genome.

Just to be pedantic for the fun of it, how can we be sure this is in fact the world's smallest genome, and not just the smallest identified to date?

— Flint

I wonder, in trying to figure out a minimum number of genes that could work, is it possible to separate genes needed just for eating and growing, from those needed for dealing with enemies and/or competitors? Presumably a species on very early Earth might have only the inanimate environment to deal with, and if it was in a sheltered location, that might not have been a big problem at the time.

Henry

Ohhh, look at the pretty parasite!

Darn creos! Before I got interested in their special brand of pseudoscience, unfortunately I seldom visited biological sites. I used to think parasites were yuckky - now I find them clever little beasts. I blame Dumbsky for my newfound appreciation of all of evolution.

"the idea that the minimally survivable cell must be such and so big is dubious"

Agreed. Algorithmic information theory, the science that Dumbsky perverts so, seems to tell us that simplicity is in general illdefined. AFAIK there is no general method to construct or test for the simplest construction to perform a specific function. Each suspected case of simplest construction must be compared broadely, probably without finding any method for guarantee.

I don't know if that follow over to performing several functions. But if we look at a cell as something that performs a finite number of tasks at any time, it looks like a similar difficulty.

Perhaps specific constraints, say of preexisting cellular machinery, helps to narrow such a search. But as I understand it that is probably not the original solution.

On other threads I have been emphasizing the need for logical argument that the man in the street feels comfortable about, based on fact.

As someone who concentrated in his own feeble way on Geology, I invite you to outline in a rigorous manner the likely history of this beasty. When might it have first appeared? How did it at first survive? Have we a cohesion with the history of other, similar forms?

Is it a bacteria - which I assume has DNA - or a virus - without DNA? Or is it a sort of half-and-half? How would the complexity of this organism compare with the very simple organisms knocking about and perhaps helping precipitate iron etc. in early Pre-Cambrian waters?

If Anton shows up, I looked at his reference on the so-called evolutionary improvement of human genetics, and as far as I can see they were simply documenting the usual and expected selective breeding which happens to all species all the time and which keeps them from sudden extinction. I will ask him and anyone else who wishes to comment, is there any observable evidence that higher life-forms are gaining new and improved information in their genetic makeup, this new information being of a category that is demonstrably turning them into a new species? And, is the genetic information carried by higher life-forms being rendered less concise through genetic damage, and is this degeneration being passed on and not eliminated, or have I been hearing things?
But is the story for beasties such as the one mentioned on this thread the reverse - i.e., are some micro-organisms improving their genetic prowess in a robust way?

We can talk genomes and that technical side all we wish. It's mostly lost on the public. It needs to be straightforward. The man in the street knows that if he sees six words strung together in an intelligent sentence, someone wrote it. Evolutionists talk this complex language, but as soon as they get in an argument with a creationist, the creationist asks how six words in a sentence need a creator but six to the power of something "words" in an organism's genes don't need a creator. I suggest you re-vamp the approach here. Re-vamp it so you are not saying there is no creator, rather, you are aknowledging that possibility but you are phrasing the science so that the deeper questions aren't implicit in the science. (That's what I am attempting at my site.)

PBH:
You should not try to make yourself out to be discussing evolution in any sensible manner, nor attempting to "phrasing the science". You fail miserably, for example here when you show you can't read a simple text.

Try again to find the words "bacterium" and "DNA" above, that may answer your question about the nature of the beast.

Regards your discussion about accumulating genetic damage, it seems to me from an admittedly cursory reading that you both acknowledge that it is observed to not show up in humans (or perhaps you still hold out the hope that it takes an indefinite time) and try to make it inevitable without any observational support for the latter. It is fun to watch you juggle your cognitive dissonance!

PBH:
"or a virus - without DNA"

Forgot this misconception of yours. (Understandably - you have so many.:-) See http://en.wikipedia.org/wiki/Virus for DNA/RNA classifications. Viruses may have both double and
single stranded DNA (as for RNA).

Steve Reuland wrote: In my opinion, I think we'll get to a point where the difference between cell and non-cell becomes ever fuzzier, just as the difference between virus and selfish molecule isn't so clear-cut either.

correction:
fit in?

is there any observable evidence that higher life-forms are gaining new and improved information in their genetic makeup, this new information being of a category that is demonstrably turning them into a new species?

And, is the genetic information carried by higher life-forms being rendered less concise through genetic damage, and is this degeneration being passed on and not eliminated, or have I been hearing things?

This is encouraging news for synthetic biologists who are hoping to make designer bacteria from scratch...

Is this where prions, and the confusion about they-are/they-are-not subject to selection, fit it?

i dont understand how creationists think that endosymbiosis is a problem for evolution .....organisms can get anything from a few base pairs to complete genes to an entire genome from another organism .....they still have to show that hypothetical (and probably imaginary)creationist "barrier between organisms"

secondary endosymbiosis in an organism called "hatena" IIRC, has observed btw....Science had a very short review article on it a few months ago

and about that bacterium we are getting closer to abiogenesis being much more than merely plausible....cool

and about that bacterium we are getting closer to abiogenesis being much more than merely plausible....cool

jeffw --- Yes, but the smallest self-reproducing Turing machine...

jeffw --- Yes, but the smallest self-reproducing Turing machine...

self-reproducing Turing machine...

Is it a bacteria - which I assume has DNA - or a virus - without DNA? Or is it a sort of half-and-half?

— Philip Bruce Heywood

If Anton shows up, I looked at his reference on the so-called evolutionary improvement of human genetics, and as far as I can see they were simply documenting the usual and expected selective breeding which happens to all species all the time and which keeps them from sudden extinction.

I will ask him and anyone else who wishes to comment, is there any observable evidence that higher life-forms are gaining new and improved information in their genetic makeup,

this new information being of a category that is demonstrably turning them into a new species?

And, is the genetic information carried by higher life-forms being rendered less concise through genetic damage, and is this degeneration being passed on and not eliminated, or have I been hearing things?

Well how'd you be, I must have skipped the first main paragraph of the post. This is definitely a bacterium, then, and not a virus? If some virus's have DNA, what is lacking that stops them reproducing independent of a host? Actually I have a suspicion they are going to find simpler bacteria-type organisms even than this one, and although their fossil remains may never be found, they had representitives on Earth way back before everything else. That, of course, doesn't answer my question of when this microbe made its debut, and whether it could ever have existed without a host. Or are microbes actually modifying in such a dramatic way that they are observed to change from non-parasitic to parasitic? Advanced parasitic forms (such as mistletoe) aren't observed to do this, I feel sure, but in the microscopic world, dynamic darwinian style change is a feature? Don't get too excited, Anton; that last question is based on my reading of the Bible: but you have tickled the curiosity re biology.

I don't know whether adults consuming dairy foods - ice creams excepted - was ever not a feature of HOMO SAPIENS. Likewise malaria. Depends on one's view as to how HOMO SAPIENS got here, I suppose. If you check Richard Owen's prognostications, he seemed to have the impression that the whole fossil record was evidence of an unrolling or evolution pre-programmed for future events. And if you look at all the animals and plants that appeared just before Man - excluding such nasties as virus's, bad microbes, snakes, etc., some of which may have appeared AFTER Man! - it's quite difficult to argue that he wasn't correct.

New species imply new information, new programming, new autoimmune responses, new sex cells ..... . That's what we aren't observing, in the higher forms. I do recognize the points you make, and I say, don't abandon any of it, but follow the opening paths of technologic advance.

You know I did geology. Here's a problem neither I nor any of the lecturers could overcome. You know that individuals of any living group sooner or later desperately seek the company of the same or at best a similar species. You know, Love will scale the highest mountain, ford the deepest stream, cross the widest desert .... blah blah blah. There's a biologic truth there. Ask anyone who herds or handles animals. You also know that some pollens and fungi are believed to travel the world in air currents, whilst fish and plankton can do the same in other currents. If indeed speciation depends SOLELY on a) Isolation, followed by b) Divergence, and this isolation must be maintained at all costs against all comers for a long time whilst the divergence occurs - remember the love crossing the highest mountain, etc.? - repeated major world changes bordering on world disasters are called for about every other dozen million years. In the case of the abovementioned plankton, pollen, fish, birds ... there is no known world catastrophe that could cause the prolonged isolation. Even with land animals, things like continental breakup, repeated mega desertification/icification, and mountain construction/removal, would have had to have been frenetic. The evidence just isn't there. Something else had to be involved. What do you think?

what is lacking that stops them reproducing independent of a host?

If some virus's have DNA, what is lacking that stops them reproducing independent of a host?

— Philip Bruce Heywood

Or are microbes actually modifying in such a dramatic way that they are observed to change from non-parasitic to parasitic? Advanced parasitic forms (such as mistletoe) aren't observed to do this, I feel sure, but in the microscopic world, dynamic darwinian style change is a feature?

I don't know whether adults consuming dairy foods - ice creams excepted - was ever not a feature of HOMO SAPIENS. Likewise malaria. Depends on one's view as to how HOMO SAPIENS got here, I suppose.

If you check Richard Owen's prognostications, he seemed to have the impression that the whole fossil record was evidence of an unrolling or evolution pre-programmed for future events. And if you look at all the animals and plants that appeared just before Man - excluding such nasties as virus's, bad microbes, snakes, etc., some of which may have appeared AFTER Man! - it's quite difficult to argue that he wasn't correct.

New species imply new information, new programming, new autoimmune responses, new sex cells ......

If indeed speciation depends SOLELY on a) Isolation, followed by b) Divergence, and this isolation must be maintained at all costs against all comers for a long time whilst the divergence occurs

a better question is, why aren't Heywood's posts automatically being dumped to the wall at this point?

a guess would be that the contributors don't tend to follow other threads (than their own) on PT any more.

besides, what's wrong with continually pointing out Heywood's blatant ignorance wrt the topics he comments on so profusely?

it passes the time.

I suppose many publications such as T/O attract the odd fanatic- come totalitarian, but I recognize the dedication of most of its Operators to democracy and free speech. Almost all developments have been vehemently opposed by a minority, if not a majority, somewhere, sometime. That is written into the history of human technologic advance.
Sometimes, one wonders whether if Darwin himself were to be resurrected and was to contribute, there wouldn't be calls to silence him! Comfort zones are dangerous things to invade.

Everything Anton said is relevant but the day is fast approaching - yea, is arriving - when all the external factors (such as isolation) and all the intriguing observations (such as hybridization) are going to be tied to real microbiological events & processes that gave real, measurable changes in the hidden paraphenalia of the species. I think there are plenty of scientists about who will be able to get out of their comfort zones and handle it. Things like isolation, time, and the pressure of environmental change are not mechanisms - merely factors. The mechanism = the chemical reaction(s) that revolutionize the relevant molecular structures. The triggers of those chemical reactions are gradually beginning to hove into view. That is where empirical science begins to take over. The individual chemical steps necessary to speciation will be deduced. Whatever you do, don't be like the mathematics expert who was holding successful lectures debunking the idea of Man achieving escape velocity, the SAME YEAR that SPUTNIK went up! Ah, we love Science.

If indeed speciation depends SOLELY on a) Isolation, followed by b) Divergence, and this isolation must be maintained at all costs against all comers for a long time whilst the divergence occurs

There's also the idea that once populations become separated long enough, they may still be reproductively compatible, but any interbreeding produces less fit offspring, thus reinforcing the separation (I forget the name of that concept).

— jeffw

Dudes, why on earth are you bothering with a blithering idiot like Heywood?

— 'Rev Dr' Lenny Flank

There's also the idea that once populations become separated long enough, they may still be reproductively compatible, but any interbreeding produces less fit offspring, thus reinforcing the separation (I forget the name of that concept). After that happens, geography is not important. Well, at least not for speciation.

GuyeFaux --- See Jim Thatcher's thesis on the subject. Also Alvyn Ray Smith and his advisor, M. A. Arbib.

The first paper that I know of on the subject of self-reproducing Turing machines is one of J. von Neumann's.

Dr. Lenny spoke thusly: Dudes, why on earth are you bothering with a blithering idiot like Heywood? Stop offering your intestines to the tapeworm.

Everything Anton said is relevant but the day is fast approaching - yea, is arriving ...

get down off your soapbox, tub-thumper.

that you're completely clueless is a matter of obvious record.

get over it already.

"Why would any plant or animal want to reproduce more of its kind since this would only make more mouths to feed and decrease the chances of survival?"

Let's assume for the sake of argument that this critter can't feed/reproduce itself outside of its symbiotic relationship. Does this affect the minimality of the genome?

GuyeFaux --- See Jim Thatcher's thesis on the subject. Also Alvyn Ray Smith and his advisor, M. A. Arbib. The first paper that I know of on the subject of self-reproducing Turing machines is one of J. von Neumann's.

"No such thing possible, I'm afraid: infinate tapes and all that."

Why is that an obstruction? Reallife turing implementations have finite memory, or stacks (minsky machines).

It should be more natural to make an analogy from turing complete languages (ie all practical languages) or formalisations (lambda calculus et cetera). One can write interpretators in other languages, ie turing implementations self-reproduce.

"As far as I can tell the Von Neumann (my hero) paper deals with self-reproducing automata, not self-reproducing TMs."

Selfreproducing turing machines are famously called universal constructors, or von Neumann machines/probes. Originally proposal were cellular automata, but even incredible simple cellular automata like Conway's Game of Life are turing complete. "It is possible to arrange the automaton so that the gliders interact to perform computations, and after much effort it has been shown that the Game of Life can emulate a universal Turing machine." ( http://en.wikipedia.org/wiki/Cellular_automata )

"Whatever you do, don't be like the mathematics expert who was holding successful lectures debunking the idea of Man achieving escape velocity, the SAME YEAR that SPUTNIK went up!"

I don't know why mathematicians argued technological restrictions, but OTOH sputnik didn't prove achievement of escape velocity either. Luna-1 did 1959, more than a year later. ( http://en.wikipedia.org/wiki/Luna_1 )

BTW, do you understand the difference between orbit and escape?

"The only geographical isolation is the location of their food preferences: fish (Strait of Georgia/ Juan de Fuca) vs. mammals (northern Vancouver Island) vs. (speculated) elasmobranchii (west coast VI)."

Here in Sweden there is a suspected speciation reported to be in progress, where a large lake have a fish population with some groups choosing to hide among coastal dense vegetation against a successful predator and some others remaining freeswimming. IIRC differentiated reproductive sites have resulted in markedly different body plans (short and stocky vs long and lean).

"No such thing possible, I'm afraid: infinate tapes and all that."

Why is that an obstruction? Reallife turing implementations have finite memory, or stacks (minsky machines).

It should be more natural to make an analogy from turing complete languages (ie all practical languages) or formalisations (lambda calculus et cetera). One can write interpretators in other languages, ie turing implementations self-reproduce.

"As far as I can tell the Von Neumann (my hero) paper deals with self-reproducing automata, not self-reproducing TMs."

Selfreproducing turing machines are famously called universal constructors, or von Neumann machines/probes. Originally proposal were cellular automata, but even incredible simple cellular automata like Conway's Game of Life are turing complete. "It is possible to arrange the automaton so that the gliders interact to perform computations, and after much effort it has been shown that the Game of Life can emulate a universal Turing machine." ( http://en.wikipedia.org/wiki/Cellular_automata )

"Whatever you do, don't be like the mathematics expert who was holding successful lectures debunking the idea of Man achieving escape velocity, the SAME YEAR that SPUTNIK went up!"

I don't know why mathematicians argued technological restrictions, but OTOH sputnik didn't prove achievement of escape velocity either. Luna-1 did 1959, more than a year later. ( http://en.wikipedia.org/wiki/Luna_1 )

BTW, do you understand the difference between orbit and escape?

"The only geographical isolation is the location of their food preferences: fish (Strait of Georgia/ Juan de Fuca) vs. mammals (northern Vancouver Island) vs. (speculated) elasmobranchii (west coast VI)."

In Sweden there is a suspected speciation reported to be in progress, where a large lake have a fish population with some groups choosing to hide among coastal dense vegetation against a successful predator and some others remaining freeswimming. IIRC differentiated reproductive sites have resulted in markedly different body plans (short and stocky vs long and lean).

Sorry about the double posting, I receieved an error message that was unclear. (Too many postings, try later. Which I did :-(

Ah, Torbjorn: from jotuns to g_nomes, all in the span of a month!

To quote the Beach Boys, you sure get around.

If the Game of Life is a universal Turing machine emulation, then from Alvy Ray Smith's thesis, it is self-replicating, or equivalently, self-describing.

There are even simpler cellular automata which are self-replicating. Universality is sufficient, but not necessary.

Such studies as these ought to be suggestive regarding the minimal biochemistry required for self-replication, but so far, at least, not suggestive enough...

It's so quiet now on the creationist/ID front. Have even the rank-and-file given up completely on arguing that there's actual scientific evidence for their claims?

It'll be at least ten years, maybe twenty, before anyone takes anti-evolutioners seriously again. In the meantime, we all might as well go into brumation.

— 'Rev Dr' Lenny Flank

Rev:
That seems backwards. If creationists stop imposing religion and politics on science, there will be no specific need to discuss religion on a pro-science site.

If so, you might start thinking about your new title...

Heh! I had formed the hypothesis that when thread ends disappeared, there was a data base problem. Now I understand what removed to the Bathroom Wall means.

Please disregard my last comment, the comment that precipitated it disappeared.

Re "Now I understand what removed to the Bathroom Wall means."

Yeah, it means something got flushed. ;)