Calculating the odds of life

[GenesForLife]

In what logically consistent universe is the statement "6 million base pairs in the exact same order to the genomic extent" equal to saying "one can expect something to happen by shuffling DNA anyway" ? Another case of lying, keep it coming.

Ok, let me ask you directly to state some hard numbers:

1) do you agree that all mutlicelled organisms go back to one root, if not state exactly how many roots do you think there possibly are

The evidence points towards all multicellular organisms sharing a common ancestor. Then again you cannot use this as a starting point for your calculations, reason being that multicellularity has been observed forming in vitro, quoting the relevant abstract, we have this...


Phagotrophy by a flagellate selects for colonial prey: A possible origin of multicellularity

MARTIN E. Boraas, DIANNE B. Seale and JOSEPH E. Boxhorn

Predation was a powerful selective force promoting increased morphological complexity in a unicellular prey held in constant environmental conditions. The green alga, Chlorella vulgaris, is a well-studied eukaryote, which has retained its normal unicellular form in cultures in our laboratories for thousands of generations. For the experiments reported here, steady-state unicellular C. vulgaris continuous cultures were inoculated with the predator Ochromonas vallescia, a phagotrophic flagellated protist (‘flagellate’). Within less than 100 generations of the prey, a multicellular Chlorella growth form became dominant in the culture (subsequently repeated in other cultures). The prey Chlorella first formed globose clusters of tens to hundreds of cells. After about 10–20 generations in the presence of the phagotroph, eight-celled colonies predominated. These colonies retained the eight-celled form indefinitely in continuous culture and when plated onto agar. These self-replicating, stable colonies were virtually immune to predation by the flagellate, but small enough that each Chlorella cell was exposed directly to the nutrient medium.

They started with a unicellular pure culture and reported a mutant variety that was multicellular, it is immediately apparent that the evolution of multicellularity from unicellular forms can happen, and in extremely short periods of time, which means, we now go back to unicellular organisms, and going back further, to the initial replicator, which may need as less as the 50 + something base pairs reported in one of the papers I already posted.

Once we have a replicator, any length of sequence can be built up in various copies of said replicator given the time, with an event being gene duplication at the most basic level and whole genome duplication (where whole genomic content doubles) at a given time, there are no barriers to the formation of any minimal genome complement necessitated for by muticellular organisms.

2) what is the minimum amount of DNA needed for a mutli-celled creature in your opinion

I have no opinion on this, except that we need genomic sequences from all kinds of multicellular organisms (our collection of sequenced genomes is quite small) to arrive at a tentative value of that, but this does not matter or may not prove useful at all in light of the answer to the first question and in light of the nature of evolution.

To put it extremely simply, while extant forms may require minimal genomic complements, this doesn't hold true for ancestral organisms to the point of the replicator, and because of the way evolution can co-opt previously unnecessary genes as part of newer pathways and phenotypes while rendering them integral in the process, something that contributes to the illusion of irreducible complexity.

[GenesForLife]

The link to the abstract on the Boraas paper I posted is http://www.springerlink.com/content/q239365007h43465/

He apparently also recorded such a mutational transition driven by predation as the selective pressure and reported his findings in the paper to which a citation follows, which I may try to procure from elsewhere and post it because it is not available online now.

Boraas, M. E. 1983. Predator induced evolution in chemostat culture. EOS. Transactions of the American Geophysical Union. 64:1102

[spinoza99]

The evidence points towards all multicellular organisms sharing a common ancestor. Then again you cannot use this as a starting point for your calculations, reason being that multicellularity has been observed forming in vitro, quoting the relevant abstract, we have this...


Phagotrophy by a flagellate selects for colonial prey: A possible origin of multicellularity

MARTIN E. Boraas, DIANNE B. Seale and JOSEPH E. Boxhorn

Predation was a powerful selective force promoting increased morphological complexity in a unicellular prey held in constant environmental conditions. The green alga, Chlorella vulgaris, is a well-studied eukaryote, which has retained its normal unicellular form in cultures in our laboratories for thousands of generations. For the experiments reported here, steady-state unicellular C. vulgaris continuous cultures were inoculated with the predator Ochromonas vallescia, a phagotrophic flagellated protist (‘flagellate’). Within less than 100 generations of the prey, a multicellular Chlorella growth form became dominant in the culture (subsequently repeated in other cultures). The prey Chlorella first formed globose clusters of tens to hundreds of cells. After about 10–20 generations in the presence of the phagotroph, eight-celled colonies predominated. These colonies retained the eight-celled form indefinitely in continuous culture and when plated onto agar. These self-replicating, stable colonies were virtually immune to predation by the flagellate, but small enough that each Chlorella cell was exposed directly to the nutrient medium.

as far as I can tell the article offers a theory for how multicellular organisms arose from one cell, not that multi-celled organisms go back to thousands of roots. The point I'm trying to make is that in order to get mult-cellular organism DNA has to be arranged in a precise order.

I need you to tell many how ancestors you think there are for complex life.


Now, here is evidence that all eyes share a common root. You can't just shuffle DNA any way you want and get an eye. It has to be precisely sequenced. Do you believe that there are several ways that the eye arose and if so how many? Do you believe you can form an eye with less than 5000 genes? If so how many?

Name any organ, name any organism-- chances are the genes that put it together are strikingly similar.

Though eyeless may set eye formation in motion, events of staggering complexity follow. Maybe 5,000 genes act together to build up an eye, and researchers are only beginning to figure out which these are, and how and when they do what they do.

But it takes far more than one or two genes to assemble an eye. Whole hordes of them lend a hand in getting the furrow moving and in nudging cell eight into being--in helping create all the other frills and furbelows that go into making a fully functional eye.

In the textbooks--including my own--you’ll read that a prototype eye arose independently some 40 times, says Gehring. Many a detailed study of eyes went into that conclusion, yet what it means precisely has never been clear. Did different eyes evolve completely independently, each time? After all, the light-sensing pigment rhodopsin is basically the same in all animals--it’s not very likely that it evolved 40 times. Thus, many people suspect that somewhere in our deep past there was a rudimentary eye that great-great-grandfathered all the different kinds of eyes we see today.

What’s more, in people and mice at least, the gene’s role seems awfully close to its role in flies. There’s a genetic condition in humans called aniridia, in which the retina, iris, lens, and cornea are flawed. The imperfections stem from damage to the human counterpart to eyeless. Deleting one copy of the eyeless counterpart in mice--a gene called pax-6-- causes similar problems; deleting both copies leads to mice with no eyes, no nose, and an incomplete nervous system. Gehring even did an experiment in which he inserted the mouse pax-6 gene into a fly and turned it on inappropriately. Eyes--fly eyes--formed all over. In both vertebrates and invertebrates, the genes really do seem to work the same way.

And yet now we see that some part of the developmental process is homologous, because it’s done with the same gene. That points to a common, ancestral eye. It might not have been much of an eye--perhaps just a sheet of light-sensing cells, the kind that exist in primitive creatures like flatworms. And lots and lots of independent evolution happened later. But there’s no reason to talk anymore about eyes evolving dozens of times from scratch.

http://discovermagazine.com/1996/jul/se ... aflysey816

[GenesForLife]

Also check out myxomycetes, which are unicellular organisms which can come together to form functionally multicellular units, there isn't really much of a barrier that would prevent transitions from unicellularity to multicellularity (the fact that we've seen this happen and have documentation pooh poohs all over that assertion)

[PsychoSerenity]

[spinoza99]

Also check out myxomycetes, which are unicellular organisms which can come together to form functionally multicellular units, there isn't really much of a barrier that would prevent transitions from unicellularity to multicellularity (the fact that we've seen this happen and have documentation pooh poohs all over that assertion)

So answer the question, how many roots do you think multi-celled organisms have?

Also, answer the question about eyes sharing a common ancestor, do you believe this is true?

[Thinking Aloud]

ANSWER THE QUESTION, DAMMIT!!!

[Coito ergo sum]

I think it's pretty clear that the odds of life forming on a given world are pretty small. But, if we live in on an average planet in an average solar system - there could be about ( 32 to the power of 10) squared planets in the known universe - that's about 1,024 to the power of 21 planets. Right? Something around there?

What are the odds that spinoza99 is talking about? Maybe we're the only planet with life on it, and the odds are 1 in 1,024 to the power of 21. Pretty long odds, but we have the dice rolls....

[GenesForLife]

The evidence points towards all multicellular organisms sharing a common ancestor. Then again you cannot use this as a starting point for your calculations, reason being that multicellularity has been observed forming in vitro, quoting the relevant abstract, we have this...


Phagotrophy by a flagellate selects for colonial prey: A possible origin of multicellularity

MARTIN E. Boraas, DIANNE B. Seale and JOSEPH E. Boxhorn

Predation was a powerful selective force promoting increased morphological complexity in a unicellular prey held in constant environmental conditions. The green alga, Chlorella vulgaris, is a well-studied eukaryote, which has retained its normal unicellular form in cultures in our laboratories for thousands of generations. For the experiments reported here, steady-state unicellular C. vulgaris continuous cultures were inoculated with the predator Ochromonas vallescia, a phagotrophic flagellated protist (‘flagellate’). Within less than 100 generations of the prey, a multicellular Chlorella growth form became dominant in the culture (subsequently repeated in other cultures). The prey Chlorella first formed globose clusters of tens to hundreds of cells. After about 10–20 generations in the presence of the phagotroph, eight-celled colonies predominated. These colonies retained the eight-celled form indefinitely in continuous culture and when plated onto agar. These self-replicating, stable colonies were virtually immune to predation by the flagellate, but small enough that each Chlorella cell was exposed directly to the nutrient medium.

as far as I can tell the article offers a theory for how multicellular organisms arose from one cell, not that multi-celled organisms go back to thousands of roots. The point I'm trying to make is that in order to get mult-cellular organism DNA has to be arranged in a precise order.

I've already showed that there is no precision required even in genes that do the same function, missed the alignment , did you? Or are you too unacquainted with sequence alignments?

This article has DEMONSTRATED that multicellular organisms can form from unicellular ones, I half expected obfuscation and the execution of specious apologetics with respect to that, an actual experiment was conducted.

I need you to tell many how ancestors you think there are for complex life.

How did you contrive to miss the very first line of my post?

Now, here is evidence that all eyes share a common root. You can't just shuffle DNA any way you want and get an eye. It has to be precisely sequenced. Do you believe that there are several ways that the eye arose and if so how many? Do you believe you can form an eye with less than 5000 genes? If so how many?

No one is asserting that the first complex organisms evolved with eyes intact, and if you assert eye development is the result of a single gene I'm going to laugh at you. Complex organisms can have their genomes formed from pre-existing simpler genomes in simpler organisms going back to a replicator by basic chemistry. The precise sequence assertion is nonsense and it is fuckwittery to persist with it after being shown that this is indeed the case.

Name any organ, name any organism-- chances are the genes that put it together are strikingly similar.

That is not how organogenesis and tissue development works, go read Davidson's "The Regulatory Genome" for a basic grounding and come back when you are actually capable of speaking coherently about the nature of development, your representation of development is extremely naive.

Though eyeless may set eye formation in motion, events of staggering complexity follow. Maybe 5,000 genes act together to build up an eye, and researchers are only beginning to figure out which these are, and how and when they do what they do.

obfuscatory nonsense, this is relevant to the origin of life how exactly? you aren't suggesting the first complex organism had an eye are you? In which case it would be another blatant lie.

But it takes far more than one or two genes to assemble an eye. Whole hordes of them lend a hand in getting the furrow moving and in nudging cell eight into being--in helping create all the other frills and furbelows that go into making a fully functional eye.

A modern eye =/= the multicellular concenstor or the initial concestor, stop your fallacious equivocation.

In the textbooks--including my own--you’ll read that a prototype eye arose independently some 40 times, says Gehring. Many a detailed study of eyes went into that conclusion, yet what it means precisely has never been clear. Did different eyes evolve completely independently, each time? After all, the light-sensing pigment rhodopsin is basically the same in all animals--it’s not very likely that it evolved 40 times. Thus, many people suspect that somewhere in our deep past there was a rudimentary eye that great-great-grandfathered all the different kinds of eyes we see today.

Yup, deep deep past =/= first multicellular organism/first organism, which is what we are talking about here, get that elementary point?

What’s more, in people and mice at least, the gene’s role seems awfully close to its role in flies. There’s a genetic condition in humans called aniridia, in which the retina, iris, lens, and cornea are flawed. The imperfections stem from damage to the human counterpart to eyeless. Deleting one copy of the eyeless counterpart in mice--a gene called pax-6-- causes similar problems; deleting both copies leads to mice with no eyes, no nose, and an incomplete nervous system. Gehring even did an experiment in which he inserted the mouse pax-6 gene into a fly and turned it on inappropriately. Eyes--fly eyes--formed all over. In both vertebrates and invertebrates, the genes really do seem to work the same way.

Similar genes can do similar functions, where did I deny that? the fact that similar genes can do similar functions does not mean different genes cannot do similar functions either, different being sequentially different, as my alignments already demonstrated, yet you persist more obfuscatory sleight of hand, how totally disingenious.

And yet now we see that some part of the developmental process is homologous, because it’s done with the same gene. That points to a common, ancestral eye. It might not have been much of an eye--perhaps just a sheet of light-sensing cells, the kind that exist in primitive creatures like flatworms. And lots and lots of independent evolution happened later. But there’s no reason to talk anymore about eyes evolving dozens of times from scratch.

How does this detour have anything to do with your argument about the initial species, followed by your goalpost shift to the concestor of multicellular organisms or

http://discovermagazine.com/1996/jul/se ... aflysey816

[/quote][/quote]

I already showed you why your gene conservation canard is a canard, if you continue to pretend that that refutation does not exist you it will be intellectually dishonest (as is most of your tripe on this thread) and I will have to start pointing it out until you clean your act up.

And oh, care to post links to proper peer reviewed literature and not diluted gnat's piss that popular science articles are?

[spinoza99]

I think it's pretty clear that the odds of life forming on a given world are pretty small. But, if we live in on an average planet in an average solar system - there could be about ( 32 to the power of 10) squared planets in the known universe - that's about 1,024 to the power of 21 planets. Right? Something around there?

What are the odds that spinoza99 is talking about? Maybe we're the only planet with life on it, and the odds are 1 in 1,024 to the power of 21. Pretty long odds, but we have the dice rolls....

As I stated in my initial post, I believe the odds of life forming are at a minimum of one in 300 googols (though it is certainly higher), the number of events at our disposal is about .8 googols. To give you an idea of how much that is, there are about .2 googol oxygen atoms in a drop of water, but .8 googols of atoms in the entire universe.

[GenesForLife]

Re: the eye does seem to have a common ancestor in terms of the organ...this again doesn't mean that the common ancestor of the eye was again the common ancestor of all complex organisms (time to take note, there are plenty of complex organisms without eyes which would indicate that they diverged from the lineage that did give rise to all eyed organisms before.)

pax6 too is not eye specific and is recruited for cell differentiation leading to organogenesis of many other organs, by the way, which is a reminder of the process of co-optation , that genes previously used for different purposes,due tomutation if they interact with other genes (example - a transcription factor can bind differentially to different promoter sequences and thus affect quantity of gene expression (which in terms of Hox products and gradients can have varying effects, for instance)) should result in a useful product, they will be selected for, in other words, the emergence of complex features from interactions of genes does not require a complex origin of all the components involved in the pathway simultaneously OR a complex common ancestor with all the required genes put in place, reason being divergence can allow the spreading of a trait along lineages as and when a beneficial phenotype manifests.

PS - what you believe is irrelevant, and doesn't stand up to scrutiny , regardless of how much you obfuscate, if you are conviced it does, get it published in a peer-reviewed journal like Science or Nature, or even PNAS or PLoS or anything with a high impact factor, and then I may give it due consideration, but until your argument is validated I will oppose any attempts to pass your asinine argument for fact.

[GenesForLife]

I wonder if Cali has some time to spare

[spinoza99]

The evidence points towards all multicellular organisms sharing a common ancestor. Then again you cannot use this as a starting point for your calculations
reason being that multicellularity has been observed forming in vitro, quoting the relevant abstract, we have this...

This article has DEMONSTRATED that multicellular organisms can form from unicellular ones, I half expected obfuscation and the execution of specious apologetics with respect to that, an actual experiment was conducted.

I'm not saying that multi-cellular organisms do not come from single-celled organisms I'm saying that in order to get multi-celled organisms you need to sequence the DNA precisely. The only thing you have proved about multi-cellular life is that it comes from single-celled life. I already believe that. What we're arguing over is, does the DNA need to be sequenced in a precise way? Since no other complex life comes from a different root, we have no reason to believe that there are numerous ways of sequencing DNA such that complex life can arise.

Now, here is evidence that all eyes share a common root. You can't just shuffle DNA any way you want and get an eye. It has to be precisely sequenced. Do you believe that there are several ways that the eye arose and if so how many? Do you believe you can form an eye with less than 5000 genes? If so how many?

No one is asserting that the first complex organisms evolved with eyes intact, and if you assert eye development is the result of a single gene I'm going to laugh at you. Complex organisms can have their genomes formed from pre-existing simpler genomes in simpler organisms going back to a replicator by basic chemistry.

I'm not asserting that bang eyes appeared out of nowhere and I'm also not asserting that complex organisms can not have their genomes formed from pre-existing simpler genomes in simpler organisms going back to a replicator by basic chemistry. What I'm asserting is that you need to sequence DNA in a precise way to get eyes and the sequence is extremely complicated.

Let me ask you this. The above article quote the number of 5000 genes which is quite a lot of base DNA pairs. What do you think is the minimum number of base dna pairs it takes before an eye carries a minimal survival advantage?

The precise sequence assertion is nonsense

Ok, go ahead and move the dna of fly around and tell me if there are no effects.

Name any organ, name any organism-- chances are the genes that put it together are strikingly similar.

That is not how organogenesis and tissue development works, go read Davidson's "The Regulatory Genome" for a basic grounding and come back when you are actually capable of speaking coherently about the nature of development, your representation of development is extremely naive.

Ok, good, I just want you to admit the fact that you hate the idea that all organs share common genes. If the scientific community reaches a strong consensus that all organs share common genes will you change your mind?

[spinoza99]

the eye does seem to have a common ancestor in terms of the organ...this again doesn't mean that the common ancestor of the eye was again the common ancestor of all complex organisms

You've already admitted the all complex life points to a common ancestor. The only thing were debating is the implications of that fact. You cannot just shuffle dna any way you like and expect a unicelled creature to turn in a multi-celled creature. Do you believe that just any dna sequence can transform a uni-celled creature into a multi-celled? Answer the question, I'm still waiting for you to answer that.

PS - what you believe is irrelevant, and doesn't stand up to scrutiny , regardless of how much you obfuscate, if you are conviced it does, get it published in a peer-reviewed journal like Science or Nature, or even PNAS or PLoS or anything with a high impact factor, and then I may give it due consideration, but until your argument is validated I will oppose any attempts to pass your asinine argument for fact.

I accept almost all of the ideas of the scientific mainstream with the exception of natural selection which is not a scientific theory.

[mistermack]

Spinoza, your whole argument is the pathetic god-of-the-gaps argument.
You're trying to contrive a gap, ie, a missing part of the process from naturally occurring chemicals leading to life as we know it.
A GAP DOES NOT EQUAL A GOD !!.
If you want to convince the world that there's a god, do the honest thing, and find some evidence FOR a god. Not evidence for a GAP!!.

It's such a stupid argument, the god of the gaps, because history shows that as we go on, more and more gaps are being filled. It's sad and pathetic to exploit a gap left in our knowledge, mess it up with dubious maths, and claim that that means there is a god. It's only a matter of time before that gap is filled, and the sad people will be onto something else.

So here's a challenge. Try and prove there is a GOD, not a GAP!!
.