Darwin re-visited

[Biochemist]

Excellent coverage on this from Carl Zimmer over at The Loom: [quote name=

Originally Posted by Zimmer]

Festooning The Tree Of Life | The Loom | Discover Magazine

Bacteria and other single-celled microbes make up much more of life’s genetic diversity, and they were around for three billion years before animals showed up for the party. So much of the history of life may not fit the tree metaphor very well any more. No longer can we assume that the genes in a species all have the same history. Some of them may have leaped from species to species.

Doesn't this directly contradict Moon's assertion that bacteria are quite sophisticated and have evolved as much as humans?

 

Bio

[Biochemist]

And this portion...

Analyzing this tree bush mangrove thicket Gordian knot, Dagan and her colleagues found a fascinating interplay between vertical and lateral gene transfer. If you look at any one of the 181 genomes, 81% on average of its genes experienced lateral gene transfer at some point in its history. So clearly lateral gene transfer is rampant. But once genes made the jump, they tended not to make another one–in fact, Dagan and her colleagues conclude that most became trapped in vertical descent.

is at odds with Moon's assertion that lateral gene transfer somehow resulted in a "merging" of life into a single common tree.

 

Informative post, G, but I don't know what point you were trying to make.

 

Bio

[Biochemist]

Also, I didn't directly link to this in my previous posts, but to anyone who hasn't seen it here is a link to the relevant court rulings on Intelligent Design from Kitzmiller v. Dover Area School District.

Also, recently Ken Miller guest blogged over at The Loom further debunking Intelligent Design. Probably of interest to anyone following this thread:

 

Smoke and Mirrors, Whales and Lampreys: A Guest Post by Ken Miller | The Loom | Discover Magazine

 

Ken Miller’s Guest Post, Part Two | The Loom | Discover Magazine

 

Ken Miller’s Final Guest Post: Looking Forward | The Loom | Discover Magazine

You guys are really fixated. I have said nothing about ID in my discourses. Moon offered Behe's nomenclature of "front loading" in a post a while back, and I used that for his convenience (instead of my "precoding" or "proscribed speciation". You might recall (or maybe not) that my core argument is statistical, in that the probability of an enzyme system of 6 enzymes occurring is still on the order of 1 in 10^1000. Every other enzyme system you add would incrementally increase the number. That is, if a life form needs the Kreb's cycle AND the urea cycle AND beta oxidation, the probabilistic assessment (even with a large number of favorable assumptions) come out to 1 in 10^3000. No one (not ever here) has offered a data-driven counterpoint, other than to say "oh, that old creationist argument".

 

This is NOT a creationist argument. It is a DATA problem!!!!!!

 

I am discussing data, not ideology. This thread's constant reversion to debunking irrelevant straw men is really distracting.

 

Bio

[Moontanman]

Doesn't this directly contradict Moon's assertion that bacteria are quite sophisticated and have evolved as much as humans?

 

Bio

 

No this has nothing to do with complexity, it just shows bacteria operate differently, Again you are making an assumption about sophistication that just simply doesn't hold up.

[Biochemist]

You might recall (or maybe not) that my core argument is statistical, in that the probability of an enzyme system of 6 enzymes occurring is still on the order of 1 in 10^1000. Every other enzyme system you add would incrementally increase the number. That is, if a life form needs the Kreb's cycle AND the urea cycle AND beta oxidation, the probabilistic assessment (even with a large number of favorable assumptions) come out to 1 in 10^3000. No one (not ever here) has offered a data-driven counterpoint, other than to say "oh, that old creationist argument".

But it gets worse. The standard counterpoint by the speciation-by-mutation crowd is that the majority of the steps in the process are not really random.

 

Obviously.

 

But if they are not really random, exactly how non-random are they? If the extant biochemical state (or series of historical states) is such that it can alter the probability of a random event from 1 in 10^3000 down to say 1 in 10^100 or 1 in 10^3 or 1 in 10, where would we bite the bullet and suggest that the probability for a particular outcome was "front loaded"?

[Galapagos]

And this portion... is at odds with Moon's assertion that lateral gene transfer somehow resulted in a "merging" of life into a single common tree.

 

Informative post, G, but I don't know what point you were trying to make.

 

Bio

 

No, not at all.

You could have actually clicked on the articles and read them(there is no way you had enough time given the time elapsed between your responses). Making things up and just asking silly questions is not good science or debate. Would it have hurt you to try google?

 

 

From the wiki page on horizontal gene transfer, a quoted article by biochemist Ford Doolittle, as published in Scientific American:

Horizontal gene transfer - Wikipedia, the free encyclopedia

"If there had never been any lateral gene transfer, all these individual gene trees would have the same topology (the same branching order), and the ancestral genes at the root of each tree would have all been present in the last universal common ancestor, a single ancient cell. But extensive transfer means that neither is the case: gene trees will differ (although many will have regions of similar topology) and there would never have been a single cell that could be called the last universal common ancestor.[22]

 

"As Woese has written, 'the ancestor cannot have been a particular organism, a single organismal lineage. It was communal, a loosely knit, diverse conglomeration of primitive cells that evolved as a unit, and it eventually developed to a stage where it broke into several distinct communities, which in their turn became the three primary lines of descent (bacteria, archaea and eukaryotes)' In other words, early cells, each having relatively few genes, differed in many ways. By swapping genes freely, they shared various of their talents with their contemporaries. Eventually this collection of eclectic and changeable cells coalesced into the three basic domains known today. These domains become recognisable because much (though by no means all) of the gene transfer that occurs these days goes on within domains."[22]

http://shiva.msu.montana.edu/courses/mb437_537_2004_fall/docs/uprooting.pdf

 

 

From the first Zimmer article, may illustrate the point better for you:

Festooning The Tree Of Life | The Loom | Discover Magazine

(read the explanation for the coloring in the article.)

 

 

Informative post, G, but I don't know what point you were trying to make.

 

Bio

Just wanted to further point out that you have no idea what you are talking about :doh:

[Moontanman]

And this portion... is at odds with Moon's assertion that lateral gene transfer somehow resulted in a "merging" of life into a single common tree.

 

Informative post, G, but I don't know what point you were trying to make.

 

Bio

 

No, the lateral transfers i was talking about occurred in the beginning of life when life was simple and differences much less pronounced than today. Once real species came about lateral gene transfers slowed down considerably and it occurs most often between closely related microbes. But as the chart shows they still occur at a rate higher than most people thought. You originally said you thought it was a rare event.

[Galapagos]

You guys are really fixated. I have said nothing about ID in my discourses. Moon offered Behe's nomenclature of "front loading" in a post a while back, and I used that for his convenience (instead of my "precoding" or "proscribed speciation". You might recall (or maybe not) that my core argument is statistical, in that the probability of an enzyme system of 6 enzymes occurring is still on the order of 1 in 10^1000. Every other enzyme system you add would incrementally increase the number. That is, if a life form needs the Kreb's cycle AND the urea cycle AND beta oxidation, the probabilistic assessment (even with a large number of favorable assumptions) come out to 1 in 10^3000. No one (not ever here) has offered a data-driven counterpoint, other than to say "oh, that old creationist argument".

 

This is NOT a creationist argument. It is a DATA problem!!!!!!

 

I am discussing data, not ideology. This thread's constant reversion to debunking irrelevant straw men is really distracting.

 

Bio

 

Nice attempt at a dodge, but you are very obviously religiously motivated. You haven't quoted any scientists or posted any actual science to support your position. All you have is questions. The same as the rest of the ID crowd. Just like you, the Discovery Institute is yet to publish any of the promised supporting data in the past three years since you have been pretending evolution didn't happen on this forum. Got any actual science?

[Moontanman]

You guys are really fixated. I have said nothing about ID in my discourses. Moon offered Behe's nomenclature of "front loading" in a post a while back, and I used that for his convenience (instead of my "precoding" or "proscribed speciation". You might recall (or maybe not) that my core argument is statistical, in that the probability of an enzyme system of 6 enzymes occurring is still on the order of 1 in 10^1000. Every other enzyme system you add would incrementally increase the number. That is, if a life form needs the Kreb's cycle AND the urea cycle AND beta oxidation, the probabilistic assessment (even with a large number of favorable assumptions) come out to 1 in 10^3000. No one (not ever here) has offered a data-driven counterpoint, other than to say "oh, that old creationist argument".

 

This is NOT a creationist argument. It is a DATA problem!!!!!!

 

I am discussing data, not ideology. This thread's constant reversion to debunking irrelevant straw men is really distracting.

 

Bio

 

Your fixation of assuming a preloaded code and then saying no intelligence is required to preload that data is disingenuous and you know it. If it is indeed there then it had to be preloaded by some intelligence. Your idea answers nothing, it just raises more unanswerable questions. Your argument is weak, it has no supporters other than creationists/ID'ers. Not to mention there is absolutely no evidence for it. I for one no longer believe you are serious about any of this after the dishonesty you have shown in other threads.

[Biochemist]

Making things up and just asking silly questions is not good science or debate. Would it have hurt you to try google?

This lack of courtesy is what ruins this site.

 

1) I don't think there is anything silly in my position. I held to pretty much the standard dogma for speciation for most of my career. I changed my mind because of the data.

 

2) the anti-theist bent of this site (and this thread) is remarkably derogatory. It clouds your ability to engage in discussion about relevant data.

 

3) It is true that I don't spend HOURS researching every item in every post. I don't expect posters to read every item in every post of mine either. I don't attack them for missing something.

 

Maybe I will come back in a couple years and try again.

 

Bio

[Biochemist]

Your fixation of assuming a preloaded code and then saying no intelligence is required to preload that data is disingenuous and you know it.

I MOST CERTAINLY DO NOT KNOW IT. WHY CAN'T YOU JUST TAKE THE FACTS AS THEY SIT?????

 

You have the fixation, not me.

[Galapagos]

You guys are really fixated. I have said nothing about ID in my discourses. Moon offered Behe's nomenclature of "front loading" in a post a while back, and I used that for his convenience (instead of my "precoding" or "proscribed speciation". You might recall (or maybe not) that my core argument is statistical, in that the probability of an enzyme system of 6 enzymes occurring is still on the order of 1 in 10^1000. Every other enzyme system you add would incrementally increase the number. That is, if a life form needs the Kreb's cycle AND the urea cycle AND beta oxidation, the probabilistic assessment (even with a large number of favorable assumptions) come out to 1 in 10^3000. No one (not ever here) has offered a data-driven counterpoint, other than to say "oh, that old creationist argument".

 

This is NOT a creationist argument. It is a DATA problem!!!!!!

 

I am discussing data, not ideology. This thread's constant reversion to debunking irrelevant straw men is really distracting.

 

Bio

 

Yes, and this was rejected as the same old silly creationist arguments:

Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations

 

Do you have any credible citations for you claims?

 

 

But it gets worse. The standard counterpoint by the speciation-by-mutation crowd is that the majority of the steps in the process are not really random.

 

Obviously.

 

But if they are not really random, exactly how non-random are they? If the extant biochemical state (or series of historical states) is such that it can alter the probability of a random event from 1 in 10^3000 down to say 1 in 10^100 or 1 in 10^3 or 1 in 10, where would we bite the bullet and suggest that the probability for a particular outcome was "front loaded"?

 

:doh:

 

That whole "speciation-by-mutation crowd" actually publishes papers:

THE EVOLUTION OF F1 POSTZYGOTIC INCOMPATIBILITIES IN BIRDS

Abstract.—We analyzed the rate at which postzygotic incompatibilities accumulate in birds. Our purposes were to assess the role of intrinsic F1 hybrid infertility and inviability in the speciation process, and to compare rates of loss of fertility and viability between the sexes. Among our sample more than half the crosses between species in the same genus produce fertile hybrids. Complete loss of F1 hybrid fertility takes on the order of millions of years. Loss of F1 hybrid viability occurs over longer timescales than fertility: some viable hybrids have been produced between taxa that appear to have been separated for more than 55 my. There is strong support for Haldane's rule, with very few examples where the male has lower fitness than the female. However, in contrast to Drosophila, fertility of the homogametic sex in the F1 appears to be lost before viability of the heterogametic sex in the F1. We conclude that the time span of loss of intrinsic hybrid fertility and viability is often, but not always, longer than the time to speciation. Premating isolation is an important mechanism maintaining reproductive isolation in birds. In addition, other factors causing postzygotic reproductive isolation such as ecological causes of hybrid unfitness, reduced mating success of hybrids, and genetic incompatibilities in the F2s and backcrosses may often be involved in the speciation process.

SEXUAL ISOLATION EVOLVES FASTER THAN HYBRID INVIABILITY IN A DIVERSE AND SEXUALLY DIMORPHIC GENUS OF FISH (PERCIDAE: ETHEOSTOMA)

Abstract.Theory predicts that sexual (or behavioral) isolation will be the first form of reproductive isolation to evolve in lineages characterized by sexual selection. Here I directly compare the rate of evolution of sexual isolation with that of hybrid inviability in a diverse and sexually dimorphic genus of freshwater fish. The magnitude of both sexual isolation and hybrid inviability were quantified for multiple pairs of allopatric species. Rates of evolution were inferred by comparing genetic distances of these species pairs with the magnitude of each form of reproductive isolation: the slope of the regression of genetic distance on the magnitude of reproductive isolation represents the rate of evolution. Of the two forms of isolation, the magnitude of sexual isolation exhibited the steeper slope of regression, indicating that sexual isolation will tend to evolve to completion earlier than hybrid inviability, strictly as a by-product of evolution in geographically isolated populations. Additional evidence from the literature is used to qualitatively compare rates of evolution of sexual isolation with that of other forms of reproductive isolation. Preliminary comparisons support the prediction that sexual isolation will evolve more rapidly than other forms. Because Etheostoma is characterized by striking sexual dimorphism, these results are consistent with the hypothesis that sexual selection for exaggerated mate-recognition characters causes the relatively rapid evolution of sexual isolation.

Correspondence between sexual isolation and allozyme differentiation: a test in the salamander Desmognathus ochrophaeus ? PNAS

Ethological reproductive isolation and genetic divergence across 26 protein loci were measured among populations of the salamander Desmognathus ochrophaeus in the southern Appalachian Mountains. Levels of ethological isolation varied from none to complete and were statistically significant for all but two pairings between populations inhabiting different mountain ranges. When geographic and genetic distances were treated as independent variables in multiple correlation analyses, they accounted for about half the variance in levels of ethological isolation. When genetic distance is held constant, the remaining relationship between ethological isolation and geographic distance is still statistically significant. When geographic distance is held constant, the remaining relationship between genetic distance and levels of ethological isolation is nonsignificant, as is the relationship between geographic distance and genetic distance when ethological isolation is held constant. Ethological isolation and genetic divergence evidently both reflect the gradual divergence of allopatric populations, but genetic distance is a poor predictor of ethological isolation in these salamanders.

 

 

Patterns of Speciation in Drosophila

Speciation in Drosophila: From Phenotypes to Molecules

Study of the genetics of speciation—and especially of the genetics of intrinsic postzygotic isolation—has enjoyed remarkable progress over the last 2 decades. Indeed progress has been so rapid that one might be tempted to ask if the genetics of postzygotic isolation is now wrapped up. Here we argue that the genetics of speciation is far from complete. In particular, we review 2 topics where recent work has revealed major surprises: 1) the role of meiotic drive in hybrid sterility and 2) the role of gene transposition in speciation. These surprises, and others like them, suggest that evolutionary biologists may understand less about the genetic basis of speciation than seemed likely a few years ago.

more:

patterns of postzygotic isolation - Google Search

 

And you ignored this in a previous post, full issue on "Genetics of Speciation" in the journal Heredity:

Heredity-The Genetics of Speciation

 

Care to offer alternative explanations for any of this?

[Biochemist]

Your idea answers nothing

Not true: It addresses the apparent incongruity of the 3 billion years from life to mammal, when the statistical probability is in the range of 1 in 10^3000

, it just raises more unanswerable questions.

Unanswerable? How? They are just different questions. That is how science works.

[Biochemist]

Nice attempt at a dodge, but you are very obviously religiously motivated.

How can something that is factually not true be obvious?

[Moontanman]

Maybe I will come back in a couple years and try again.

 

Bio

 

Go with God Bio, :applause: :doh:

[Galapagos]

How can something that is factually not true be obvious?

 

:doh: I think this post was clear enough the first time:

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:

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:

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

 

 

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:

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?

 

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.

[Galapagos]

2) the anti-theist bent of this site (and this thread) is remarkably derogatory. It clouds your ability to engage in discussion about relevant data.

:doh:

 

Recall this post:

Also, I didn't directly link to this in my previous posts, but to anyone who hasn't seen it here is a link to the relevant court rulings on Intelligent Design from Kitzmiller v. Dover Area School District.

Also, recently Ken Miller guest blogged over at The Loom further debunking Intelligent Design. Probably of interest to anyone following this thread:

 

Smoke and Mirrors, Whales and Lampreys: A Guest Post by Ken Miller | The Loom | Discover Magazine

 

Ken Miller’s Guest Post, Part Two | The Loom | Discover Magazine

 

Ken Miller’s Final Guest Post: Looking Forward | The Loom | Discover Magazine

 

There is nothing "anti-theist" about debunking the junk science of ID:

Kenneth R. Miller - Wikipedia, the free encyclopedia

Kenneth R. Miller (born 1948) is a biology professor at Brown University. Miller, who is Roman Catholic, is particularly known for his opposition to creationism, including the intelligent design movement. He has written two books on the subject. The first, Finding Darwin's God: A Scientist's Search for Common Ground Between God and Evolution, argues that a belief in evolution is compatible with a belief in God. In Only a Theory, his second on the subject, explores ID and the Kitzmiller v. Dover Area School District as well as its implications in science across America.