Calculating the odds of life

[Ulven]

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.

Really? You're telling me that a quarter of all the atoms in the universe can be found as oxygen in a drop of water? Really?

Listen, Spinoza, you are obviously no mathematician. Your probabilistic calculations are totally meaningless in a discussion on the odds of life. The only true statement in your opening post was that the probability of life is difficult to calculate. I can't understand whatever gave you the idea that you would be the one to solve this problem.

[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...

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.

The sequence precision assertion is nonsense, the alignment I carried out and have posted before demonstrates that clearly. Drop this nonsense, the fact that there are transposons and chromosomal rearrangements that can still have no major effect shoots down this assertion, the precise sequencing is not necessary, and sequences from organisms ARE NOT precisely sequenced, and I will continue to point this out until you cite something in opposition from the apposite peer reviewed literature (unlikely) or retract this canard and alter your calculations such that this faulty premise is removed.

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?

I do not "believe" anything, the empirically valid answer, aka the objectively real answer, will come up when the answer is found empirically. I will deal with a relevant paper in the next paragraph.

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 article is plain wrong, Chlamydomonas reinhardtii, which has NO pax6 , has an eyespot which can regulate movement towards light in the absence of a nervous system, requiring the involvement of just 202 genes.

Flagellate green algae have developed a visual system, the eyespot apparatus, which allows the cell to phototax. To further understand the molecular organization of the eyespot apparatus and the phototactic movement that is controlled by light and the circadian clock, a detailed understanding of all components of the eyespot apparatus is needed. We developed a procedure to purify the eyespot apparatus from the green model alga Chlamydomonas reinhardtii. Its proteomic analysis resulted in the identification of 202 different proteins with at least two different peptides (984 in total). These data provide new insights into structural components of the eyespot apparatus, photoreceptors, retina(l)-related proteins, members of putative signaling pathways for phototaxis and chemotaxis, and metabolic pathways within an algal visual system. In addition, we have performed a functional analysis of one of the identified putative components of the phototactic signaling pathway, casein kinase 1 (CK1). CK1 is also present in the flagella and thus is a promising candidate for controlling behavioral responses to light. We demonstrate that silencing CK1 by RNA interference reduces its level in both flagella and eyespot. In addition, we show that silencing of CK1 results in severe disturbances in hatching, flagellum formation, and circadian control of phototaxis.

http://www.plantcell.org/cgi/content/abstract/18/8/1908

The precise sequence assertion is nonsense

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

<facepalm>

There can be a variety of functional sequences without sequences having to be precise =/= moving DNA around has no effects, how stupid is that equivocation? (The alignments are there and I have shown this to be nonsense, so I suggest you drop it immediately)

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?

Organisms share genes =/= organs share genes , an example I already posted was about Pax6 being absent and Chlamydomonas reinhardtii, Warnowiids (a class of dinoflagellates, also with Ocelloids or eye-organelles that are pretty complex) also have this organ(elle) since it is unicellular developing in the absence of pax6, a master regulator of eye development. In other words, there is more than one way an organ can be formed, including the recruitment and usage of different genes , organisms that diverged from a common ancestor will share genes, but the dynamics of development and co-optation and expression means that this will not mean that organogenesis and organs are similar,too.

Basically, the mechanisms of development and the fuzzy nature of gene interactions (given that small changes can introduce massive variables into the system) don't imply that similar genes must produce similar organs, or conversely, that similar organs must be produced by similar genes.

The "common genes" argument is a canard because of the nature of development.

* Time to reiterate again, given that you've been missing this point, "common genes" is a misnomer, homologous genes is the correct term, and homologous genes do not make for homologous development as a general rule at all, which is where your naivete shows, this also explains why random mutations can generate such a wide range of morphological diversity. If you were going to accuse me of "hating" a proper appreciation or understanding of the processes involved, something you showed improper understanding of, I'm having a larf again.

[GenesForLife]

Just found another relevant paper, where two organisms share homologous genes, but produce a morphological characteristic , or "organ" if you will, by different mechanisms even if they have the same genes.

BACKGROUND: Butterfly and moth eyespots can share a similar appearance, involving multiple concentric rings of colored scales, but usually occurring in non-homologous positions on the wing. Within the butterflies, on the other hand, spots that share the same homologous position may not share the concentric ring structure; and, in butterfly species that have eyespots with concentric rings, ectopic eyespots with a similar ring structure can be induced by means of a simple epidermal wound. The extent to which all these eyespots, natural or induced, share similar genes and developmental mechanisms is investigated here by means of protein in-situ localizations in selected butterfly and moth species. In addition to looking at some of the transcription factors previously identified as being involved in eyespot formation, we also tested the involvement of candidate genes from the Wingless and TGF-beta signaling pathways as putative morphogens for eyespot development. RESULTS: Saturniid moth and nymphalid butterfly eyespots with concentric rings of color express at least two transcription factors, Distal-less and Engrailed, in the center of the future pattern. Nymphalid eyespots centers also express the ligand Wingless and an activated signal transducer, a phosphorylated Smad protein, but neither these proteins nor the previous two proteins are found in pierid spot centers, which consist of a single patch of color. Both butterfly wing patterns, however, express a third transcription factor, Spalt, a portion of whose expression domain maps to the black scales on the adult wing. Wounding a nymphalid wing, on the other hand, leads to upregulation of Distal-less, engrailed and spalt in subsets of cells around the wounding site, mimicking concentric eyespot development. CONCLUSION: Wingless and TGF-beta ligands are both candidate morphogens involved in nymphalid butterfly eyespot formation. These eyespots, as well as saturniid moth eyespots with concentric circles, share two genes that are associated with the differentiation of the signaling cells in nymphalid eyespots. This commonality suggests that they may be produced via the same developmental mechanism despite their non-homologous location. By contrast, pierid butterfly spots of a single color share some of the same genes but appear to be produced by a different mechanism. Eyespots with concentric rings may have co-opted a wound healing genetic network during their evolution.

http://www.ncbi.nlm.nih.gov/pmc/article ... ool=pubmed
1.See , similar organs =/= similar genes, nor does similar genes =/= same organs.
2. Notice the italicized spot, different locations still led to the formation of similar morphological features using the same genes, shaking up the DNA in terms of genomic location had no effect on the phenotype.

[GenesForLife]

Spinoza99, if you really want to read "The Regulatory Genome", one of the basic starting points in understanding the nature of development and the role of evolution in development I am making an offer, I will upload a copy of the book so that you can download it.

[ScholasticSpastic]

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.

Really? You're telling me that a quarter of all the atoms in the universe can be found as oxygen in a drop of water? Really?

Listen, Spinoza, you are obviously no mathematician. Your probabilistic calculations are totally meaningless in a discussion on the odds of life. The only true statement in your opening post was that the probability of life is difficult to calculate. I can't understand whatever gave you the idea that you would be the one to solve this problem.

I didn't spot this. Also, it's wrong in other terms. The total number of oxygen atoms in 18 mL of pure water at 20 degrees C is only 6.022*1023, after all (one mole of molecules, one oxygen in each, molecular weights, density of water), so nothing in this drop of water claim is true. Nothing at all.

[GenesForLife]

More dodgy premises, quelle surprise!

Listen Spinoza, there are plenty of peer-reviewed journals, write your calculations down, send it to them, and come back when you have the results.