Darwin re-visited

[Moontanman]

[quote]

Originally Posted by Biochemist

Hang on here. We are (for the sake of discussion) characterizing higher phyla as "more complex". No one is picking on on bacteria. And I am a little surprised to hear you suggest that bacteria are significantly more complex than early life forms, or that they are just as evolved as humans. Isn't that a minority position? Is there evidence of evolutionary history of bacteria?Why?

Bacteria are far more complex than he original life forms on this planet, bacteria, and I use the word loosely since there are vastly different types of bacteria. bacteria are for more complex than they need to be just to survive, bacteria have been taken apart on the gene level to reveal how much of their genome is necessary for them to survive. They are very complex organisms and did not just arise at their current level of complexity out of nothing. No it is not a minority position, modern bacteria are far more complex than the first cells.

If we are just another example of elegant, complex chemistry, why does this matter?

It matters because of how rare complex is, if indeed complex life was common then the deletion of one organism would be sad but not horrendous, but if complex life is indeed extremely rare then becomes all the more valuable, to some people anyway and I am one of them.

[Biochemist]

Originally Posted by Moontanman

It doesn't suggest that to me, to me it only suggests that conditions on the Earth became conductive to complex life after life was well developed. If conditions hadn't settled down to what we see then complex life would not have come about.

Well then, how about a softer position. How about the notion that one tree was favored is"plausible" given the evidence, and is in contrast to your position that multiple serial environments on the planets favored serial life architectures?

Originally Posted by Moon

Transfer of information, gene based or other wise, was how working cells formed, lateral gene transfer was how life adapted to it's envionment, akin to sexual reproduction of complex life forms. Lateral gene transfer goes on today in microbes in rare cases even in complex life forms, virus's help this process.

Are you saying this definitively, or that this is the reigning paradigm?

Originally Posted by Moon

Gene transfer would have not only given those organisms able to transfer genes with each other an advantage it would have pretty much merged all life into an amalgam of traits shared more or less in some degree with all others.

I assume you are aware the gene transfer in bacteria does the opposite. It creates diversity not homogeneity.

Originally Posted by Moon

Even to day lateral gene transfer still occures occasionally between widely disimilar microbes, often it's how resistence to antibiotics is passed from one type of organism to another.

I am pretty familiar with episomal tranfer (I am a Doctor of Pharmacy). This process does distribute some genes across a heterogeneous population, but it certainly does not move the population toward homogeneity. The mechanism you described above where life "merged" does not have a biological example that I know of. Do you?

Originally Posted by Moon

No faith needed, when humans only had their eyes to see we were completely unaware of the rest of the electromagnetic spectrum, once we developed ways to detect other waves then we began to see the wider world. At this time when tests are done to detect DNA in other organisms the test is indeed blind to anything other than specifically what it looks for.

Hebrews 11:1 defines faith as "evidence for things unseen". This seems to be a good fit.

[Biochemist]

[quote=Moontanman;252327]

They are very complex organisms and did not just arise at their current level of complexity out of nothing. No it is not a minority position, modern bacteria are far more complex than the first cells.

So all of the early single cell creatures are extinct, and have been replaced by more complex entities?

Originally Posted by Moon

It matters because of how rare complex is, if indeed complex life was common then the deletion of one organism would be sad but not horrendous, but if complex life is indeed extremely rare then becomes all the more valuable, to some people anyway and I am one of them.

Again, so what? If we are just chemicals, there are lots of other chemicals extant in the universe. And lots of other unique things. Why should we care? And how could any of this have "value"? How could people have "value" for that matter?

[Turtle]

Originally Posted by Biochemist

I lost your point, T. My argument is that you either have to accept that the one tree is significantly more likely than the others, or that there really should be lots of trees. Why is this absurd?

Yeah; sure ya lost me. You can hold all these complex chemical arguments together, but my straightforward point is suddenly too complex. Really?. Really!!?? My point is, all your objections ultimately lie on the reducto ad absurdum and they are all cherry picked to make your god belief a perfect fit once we accept , read, "don't object to", the implied absurd conclusion that life can arise spontaneously, which is to say without your god, or creator, intelligent designer or whatever dress you're hiding it behind today.

[Moontanman]

Originally Posted by Biochemist

I lost your point, T. My argument is that you either have to accept that the one tree is significantly more likely than the others, or that there really should be lots of trees. Why is this absurd?

It's absurd because of the timing, for there to be more than one tree of complex life such life would have had to start at almost precisely the same time and been able to compete exactly the same as the other complex life. I think this is highly unlikely, the first complex life would hog all resources available to complex life and suppress the possible development of any other complex life. On top of that is the fact that complex life didn't just jump up off the ocean floor from some random bacteria. complex life developed from a certain type of microbe called a Eukaryote, if this type of organism had not developed via fusion of two or more other organisms then complex life might still be "front loaded" as you call it and waiting to be down loaded.

[Moontanman]

[quote]

Originally Posted by Biochemist

Well then, how about a softer position. How about the notion that one tree was favored is"plausible" given the evidence, and is in contrast to your position that multiple serial environments on the planets favored serial life architectures?

There is no evidence one tree was favored or even if there was more than one tree. lateral gene transfer in early microbes homogenized life before it speciated into life forms too dissimilar to gene transfer with all other organisms.

Are you saying this definitively, or that this is the reigning paradigm?

Nothing about that far back can be completely definitive but it is a very strong paradigm.

I assume you are aware the gene transfer in bacteria does the opposite. It creates diversity not homogeneity.

Now it does, bacteria have speciated to the extent that lateral gene transfer is no long occurring at the rate that would cause homogeneity.

I am pretty familiar with episomal tranfer (I am a Doctor of Pharmacy). This process does distribute some genes across a heterogeneous population, but it certainly does not move the population toward homogeneity. The mechanism you described above where life "merged" does not have a biological example that I know of. Do you?

Not now because it doesn't happen very often, even less so the less related different species are. At the begining lateral gene transfer was the rule rather than the exception.

Eukaryotes are thought to be the merger of separate organisms, things like mitochondria, chloroplasts, and other cell bits and pieces are thought to be due to the Eukaryotes ability to merge with other cells. Eukaryotes are more complex internally than archia or eubacteria.

Hebrews 11:1 defines faith as "evidence for things unseen". This seems to be a good fit.

No evidence unexplained is evidence of unseen things, faith is just hope with a fancy name.

[Galapagos]

Originally Posted by Biochemist

Thanks for the response, Gala. I will take this one at at time.

1) Thanks for the nomenclature. I will use "front loading" in this post. I did not suggest that "God did it". I suggested that the evidence support that the code is front loaded.

And you also stated that people who think "aliens did it" would like your beliefs:

Originally Posted by Biochemist

My hypothesis puts even more complexity onto the first life form, but it is probably only a several orders of magnitude greater than it was already.

I suspect the folks that are interventionists (i.e. "aliens did it") would like my hypothesis.

Without getting into what the orders of magnitude of complexity you would have to be talking about in order for genetically engineering space-traveling aliens to have existed 3.8 million years ago, the only group I can think of who are crazy enough to believe this would be the adherents of the UFO religion Raelism:

Raëlism - Wikipedia, the free encyclopedia
Raëlians believe that all life on Earth, humans included, was created scientifically by human-like extra terrestrials that are more scientifically advanced than us, called the Elohim, using DNA synthesis and genetic engineering and thus believe in intelligent design. Throughout the ages, Elohim sent different prophets: Moses, Jesus, Buddha, and many others to guide humanity and to prepare us for the future. Largely left to progress on our own, until the time of the Apocalypse/Revelation when Elohim would send their final messenger and reveal the truth for all to know. Raëlians desire to spread that message and work towards building an Embassy where we can officially welcome the Elohim back, and for the first time in human history, actually understand them for who they are, instead of worshiping them as gods as our primitive ancestors did.[5]

You are lying. You are very obviously a proponent of Intelligent Design.
Here is a post by you from March of 2008, for example, both claiming that ID is science(it is not, and the court systems and major scientific organizations regard it as religious pseudoscience/junk science), and discussing the work of Michael Behe:

Originally Posted by Biochemist

Whether or not you weight the credibility of Michael Behe's original arguments as high, medium or low (I would put it at medium), or Dembski's mathematical assessments (I would put these slightly lower), they have credible positions.
[...]
Behe started with simple observational points that some complex structures do not seem to have practical paths for serial mutation to result in a complex endpoint. Credible antagonists have countered that some elements of his complex structures do (in fact) pre-exist in other locales and for other purposes. But the key point is that neither position is proof.
[...]
If we can leave open some of the questions about abiogenesis, we can certainly leave open some of the questions about ID. ID folks are NOT saying "God did it". All they are saying is we cannot assert (based on the fact base) that this was exclusively serial mutation.

That, in my opinion, is science.

Bio

Originally Posted by Biochemist

2) Ken Miller's "refutation" (above) doesn't really refute anything. He posits a problem with "runaway mutations" that would have nothing at all to do with front loading. His refutation is essentially a non-sequitur to my position. Mutations could do whatever they do. They usually result in dysfunctional systems that expire. Let them.
Bio

There is no evidence that the majority of non-coding DNA is functional(from Larry Moran's blog, junk in the human genome):

Sandwalk: Theme: Genomes & Junk DNA
Junk in Your Genome

Transposable Elements: (44% junk)1
DNA transposons: 3%
retrotransposons: 8%
L1 LINES: 16%
other LINES: 4%
SINES: 13%

Pseudogenes (from protein-encoding genes): 1.2% junk

Ribosomal RNA genes: essential 0.05% junk 0.09%

Protein-encoding genes:
transcribed region: essential 1.8% junk (not included above) 7.4%
regulatory sequences: essential 0.6%

Repetitive DNA
α satellite DNA (centromeres)
essential 2.0%
non-essential 1.0%%
telomeres
essential (<1000 kb, insignificant)


Total Essential (so far) 4.5%

Total Junk (so far) 54%

1. A small percentage (<1%) of all transposable elements have acquired a function in the human genome.

The fact that a fugu fish requires a genome only 1/8th our size(with only 1/3 of that 1/8th functional), a species of onion requires five times as much non coding DNA as humans do, and why some species of onion have genomes ten times as large as some others implies much of it is in fact junk(according to the scientists. this is not my opinion as a hypographer).
I quote the Onion Test once more:

Originally Posted by T R Gregory

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

Originally Posted by Biochemist

I appreciate you confirming my main point. In fact, if I were going to preload code for a couple of kingdoms, I would probably explode the initial genome as quickly as possible, then winnow it down as phylogenation occurred. But then, I wasn't there when it happened.

Your picture does a better job of supporting my position that my earlier brief statement.

Bio

So your explanation for the vast variation in genome sizes(and amounts of non-coding DNA) is that if you (an intentional agent) were to Intelligently Design life, you would "front-load"(as suggested by dispenser of religious and confirmed pseudoscience, Michael Behe) , then start "winnowing down" until you reached your goal.


Feel free to address any of the posts by T Ryan Gregory(he says hes welcoming comments, but also notes that most ID people probably aren't interested in any real science) if you still want to carry on with this:
Genomicron: An opportunity for ID to be scientific.
Genomicron: Junk DNA and ID redux.

[Moontanman]

BTW, if you really want to explore the alternate tree thing here are some possibilities.

Nanobe - Wikipedia, the free encyclopedia

Nanobacterium - Wikipedia, the free encyclopedia

Prion - Wikipedia, the free encyclopedia

While these are only indicators of possibilities it is evident that life as we know it might have some competition and how difficult it would be to detect that life.

[Galapagos]

Originally Posted by Biochemist

Your own quote states that these discoveries "dampen the bang" of the explostion. The probabilistic issues with generating a new enzyme system de novo still remain. Gould was still defending PE when he passed away (2006, I believe)

You are both incorrect about genetic probabilities and misconstruing PE. I now quote Niles Eldridge himself, from the peer-reviewed page curated by him on Scholarpedia:

Punctuated equilibria - Scholarpedia
Curator: Dr. Bruce S. Lieberman, Department of Geology and Natural History Museum, University of Kansas, Lawrence, KS
Curator: Dr. Niles Eldredge, The American Museum of Natural History, New York, NY
Punctuated equilibria - Scholarpedia
As is often typical of any new idea, punctuated equilibria sparked considerable discussion and generated significant controversy. One aspect of disagreement was the disconnect between what biologists and paleontologists meant by “rapid change.” To a paleontologist, the 5,000 to 50,000 years typical for a speciation event would seem incredibly rapid, especially due to the limits of resolution in the fossil record and in the face of millions of years of otherwise morphological stability. By contrast, to a biologist, the 5,000 to 50,000 years that Eldredge and Gould consigned to speciation events seemed like a tremendous stretch of time: more than long enough to accommodate “gradual evolutionary divergence.” Because of the disconnect between what “rapid” meant to biologists and paleontologists, some biologists were inclined to view punctuated equilibria as necessitating effectively instantaneous evolutionary change (which was incorrect). Also, and in a related vein, Eldredge and Gould (1972) and Gould and Eldredge (1977) were careful to stipulate that only relatively small morphological differences separated closely related species, and in particular that different species were not separated by unbridgeable evolutionary gaps; however, there was also confusion and controversy on this point as well.

More from Larry Moran:

Originally Posted by Moran

Sandwalk: Macromutations and Punctuated Equilibria

What kind of changes are we talking about here? Very small changes. So small, in fact, that it often takes an expert to recognize them in the fossil record. We're talking about the differences between snails in the same genus, or different species of trilobites, or changes in the surface marking of diatoms. We aren't talking about saltations when we look at punctuated equilibria patterns. People who think that the normal pattern of punctuated equilibria represent big leaps in evolution are confusing two different aspects of evolution.

And T R Gregory:

Genomicron: Punctuated equilibria is not saltationism.
Gould did maintain an interest in macromutations in his discussion of development in the 1970s and 80s, but this was separate from punk eek. Linking them just because the same author discussed them would be like calling natural selection a Lamarckian theory because Darwin considered the inheritance of acquired characteristics in the Origin.

I'm not interested in your personal opinion on the fossil record. Please cite your claims with references to the work of actual scientists.

My comments were on your misconstruing of the Cambrian, yet you responded with more confusion about PE and the work of SJ Gould(you were clearly misrepresenting him).
This is still much more well supported than anything you have posted:

Cambrian explosion - Wikipedia, the free encyclopedia
The fossil record as Darwin knew it seemed to suggest that the major metazoan groups appeared in a few million years of the early to mid-Cambrian, and even in the 1980s this still appeared to be the case.[12][13]

However, evidence of Precambrian metazoa is gradually accumulating. If the Ediacaran Kimberella was a mollusc-like protostome (one of the two main groups of coelomates),[56][17] the protostome and deuterostome lineages must have split significantly before 550 million years ago (deuterostomes are the other main group of coelomates).[74] Even if it is not a protostome, it is widely accepted as a bilaterian.[74][60] Since fossils of rather modern-looking Cnidarians (jellyfish-like organisms) have been found in the Doushantuo lagerstätte, the Cnidarian and bilaterian lineages must have diverged well over 580 million years ago.[74]

Trace fossils[54] and predatory borings in Cloudina shells provide further evidence of Ediacaran animals.[64] Some fossils from the Doushantuo formation have been interpreted as embryos and one (Vernanimalcula) as a bilaterian coelomate, although these interpretations are not universally accepted.[45][46][75] Earlier still, predatory pressure has acted on stromatolites and acritarchs since around 1,250 million years ago.[41]

The presence of Precambrian animals somewhat dampens the "bang" of the explosion: not only was the appearance of animals gradual, but their evolutionary radiation ("diversification") may also not have been as rapid as once thought. Indeed, statistical analysis shows that the Cambrian explosion was no faster than any of the other radiations in animals' history.[4]

There is little doubt that disparity – that is, the range of different organism "designs" or "ways of life" – rose sharply in the early Cambrian.[5] However recent research has overthrown the once-popular idea that disparity was exceptionally high throughout the Cambrian, before subsequently decreasing.[76] In fact, disparity remains relatively low throughout the Cambrian, with modern levels of disparity only attained after the early Ordovician radiation.[5]

The diversity of many Cambrian assemblages is similar to today's.[77][71]

The same goes for your personal version of PE. You are either being purposefully deceptive, or are just simply ignorant and mistaken.

[modest]

Originally Posted by Biochemist

Hebrews 11:1 defines faith as "evidence for things unseen". This seems to be a good fit.

Lethargic Sundays...

I don't suppose you gave half a definition in your quote up there. Maybe the half definition goes well with the half argument and the half "theory" it half supports? Probably so, but I'm sure the point is lost on you, so... I'll be direct...

Faith is the "substance of things hoped for" (Heb. 11.1), and that's the problem BioChem. The only support you have for this preposterous front loading assertion is "hope". You've described an intelligence (like a program) that exists in, apparently, every cell on earth. This program has the ability to create from scratch every species in existence, making it god-like in power and complexity—and yet, nobody has ever found evidence that it exists. No evidence. All you have is a hope that it's there, hope that somebody put it there, and hope that it means what you hope it means.

Yes, I think you could not have picked a better verse to describe what's wrong here. Hope and faith are not evidence, and neither can support a hypothesis.

~modest