Darwin re-visited

[Galapagos]

Originally Posted by Biochemist

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.

Excellent coverage on this from Carl Zimmer over at The Loom:

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.

So how should we picture the history of life then? The newest assault on this tough question just came out in the Proceedings of the National Academies of Sciences. Tal Dagan, a biologist at the University of Dusseldorf, and her colleagues have festooned the tree of life with lateral gene transfer. They analyzed 539,723 genes from the completely sequenced genomes of 181 species of microbes. To begin making their new picture of evoluiton, they drew a tree showing how those 181 species are related. They used a gene that doesn’t seem to have been traded around much, and which therefore reflects the common descent of the microbes.
[...]
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.

This new picture is a far cry from Darwin’s sketch, and thank goodness for that. A science that doesn’t move forward for 150 years isn’t much of a science at all. But we may need some new metaphors to help us catch up with it.

Click to view excellent images from the study in the above post.

The image in this post is more interesting(imo) as it contains a bit more content:

Originally Posted by Zimmer

Tangling the Tree | The Loom | Discover Magazine

This picture is a splendid representation of this debate. Scientists at the European Bioinformatics Institute created it by comparing 184 microbes. The scientists first identified genes that the microbes all inherited from a common ancestor that they then passed down in conventional parent-to-offspring fashion. By comparing their different sequences, the scientists were able to draw a conventional tree of the sort Darwin had in mind. Next, they scanned the genomes of these microbes for jumping genes. They drew the jumpers as vines from one branch to the next. They then produced this three-dimensional picture.

As you can see, the branches rise from a common ancestor, but they are enmeshed in vines. What’s particularly fascinating about it is the way in which the vines connect the branches. It is not a random mesh. Instead, a few species are like hubs, with spokes radiating out to the other species. This is the same pattern that turns up in many networks in life, from the genes that interact in a cell to the nodes of the Internet. These hubs can bring a vast number of nodes into close contact. It’s why you can play Six Degrees of Kevin Bacon. In the microbial world, this network allows genes to move quickly through the tree of life, whether those genes provide resistance to antibiotics or allow microbes to cope with some other change in the environment. The Kevin Bacons of the microbial world, at least in the current study, seem to be species that live in habitats where they may come in intimate contact with other species, such as in plant roots. They then act as gene banks from which other species can make withdrawals.

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

[Moontanman]

Great post dude, way to cut to the chase, I'd rep you if I could.

[HydrogenBond]

I keep coming back to an energy balance because it defines what is possible and/or what is most likely. For example, making the first proteins is postulated using clays. The clay lowers the activation energy hill, so the reactions can move forward. Without the clays, the activation energy hill is much higher, even though both mechanisms end at the same final state in terms of a protein energy hill.

Even replicators can only move forward if there is sufficient energy to climb an energy hill. This can occur either with an external energy source or a catalytic mechanism that lowers the height of the activation energy hill. This sets a constraint of what is possible and/or what would need to happen.

If we compare a perfect genetic base pair, to one with a defect due to improper base pairing, the final states exist at two different energy levels, with the defect existing at slightly higher energy. It has potential energy. Genetic defects begin with potential energy. The goal then becomes how to lower this. The result should be predictable since only certain paths reach the bottom of the energy hill. There are also others paths, that lower the potential but these end up with extra potential. It is possible all will occur, but the data we collect millions of years later reflect movement to the bottom of the energy hill.
An example is exploding a mixture of H2 and O2, there may be a bunch of random radicals during the explosion, but lowest energy is defined as H2O. That is the goal of all the random diversity.

[Biochemist]

Originally Posted by Turtle

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.

I don't think I cherry picked anything. I took the same complete data set you are using, and viewed it differently.

Again, I do not attempt to support a divine-intervention model. I just allow for it. Nothing I asserted above required divine intervention.

And I NEVER asserted that life could arise spontaneously. I said I did not know how it happened.

[Biochemist]

Originally Posted by Galapagos

Excellent coverage on this from Carl Zimmer over at The Loom:

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...

Originally Posted by Galapagos

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]

Originally Posted by Galapagos

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]

Originally Posted by Biochemist

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]

Originally Posted by 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]

Originally Posted by Biochemist

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.

Originally Posted by Biochemist

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.../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.)

Originally Posted by Biochemist

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