Darwin re-visited

Biochemist · January 15, 2009

Clearly someone is confused.

Mod- I am not sure why you are not getting this. I must be a poor writer.

We use the word "gene" to describe protein-encoding DNA. In eukaryotes, most DNA is not protein encoding. Further, we know of multiple processes (e.g., transposons) where DNA modifies DNA without the use of a protein as an intermediate. Most folks regard transposon activity as quasi-random or accidental.

I suggest that is conjecture.

I an also suggesting that transposons (or any other chromosome alteration service) could be coded in the DNA just like protein replication is. Ergo, daughter species would have genes that were not in the parent species, because DNA encoding in the non-protein-transcribing zones created new genes. The daughter genes were still specified in the code, but they were not copied from pre-existing parent genes. They were created de novo by the DNA to DNA encoding

Bio

modest · January 15, 2009

I an also suggesting that transposons (or any other chromosome alteration service) could be coded in the DNA just like protein replication is

Yes, in other words, you think eukaryotes some one and a half or two billion years ago had (in its DNA) the coding to make the modern plant and animal phyla.

If that were the case then that DNA should still be around. If you looked at the DNA of algae or any protozoan life today you would find the coding to make a mammalian placenta or a reptilian eye.

It's not there.

~modest

Biochemist · January 15, 2009

Yes, in other words, you think eukaryotes some one and a half or two billion years ago had (in its DNA) the coding to make the modern plant and animal phyla.

If that were the case then that DNA should still be around. If you looked at the DNA of algae or any protozoan life today you would find the coding to make a mammalian placenta or a reptilian eye.

It's not there.

It could be. We could not (yet) tell if it is. We would have to know how DNA "codes" for DNA changes. We only know an infinitessimal fraction of this now.

Do recall that the existing standard biochem dogma assumes that DNA builds mRNA, rRNA and tRNA which work together to build proteins which in turn build other structure or manage other processes. DNA also replicates DNA. This means that we assume that little machines (DNA) build little machines (replicated DNA) which build more little machines (the three kinds of RNA) which build yet more machines (proteins) which construct the cell (the last machine- unless you consider the end multicellular organism another "construction" generation).

Summarizing: Machine 1 replicates machine 1 (i.e. becomes machine 2), build machines 3,4,and 5, which build machines 6 and possibly 7.

Is it really a great stretch to suggest that DNA could code to modify DNA? This would occur before machine 1 above. If this happens, the historical DNA could be right there in front of us, and we could not read it.

It would be easier to use weather data to predict weather.

Galapagos · January 17, 2009

That would be an abiogenesis discussion. Should be the topic for another thread. Yes, I am dodging the topic. All views of abiogenesis are so poorly supported (in my view) that they are all equally weak.Sort of. The current view of natural selection is that rare variants in the population are advantaged in particular niches, hence those variants are favored. Natural selection per se really only applies after the point where a genomic changed can express itself in the population (and hence have the potential for selection). What we are discussing how the genomic change got into the population.

What you are explaining is known as "front-loading", where the genetic information is placed in the DNA in advance by God.

It was put forth in ID biochemist and fellow of the Discovery Institute Michael Behe in his book "Darwin's Black Box", and was subsequently shot down by biologist Ken Miller:

Dispatches from the Culture Wars: Exaptation vs Front Loading: Why Evolution Wins
Front loading is the idea that God (no, I'm not going to engage in the ridiculous fiction that the generic designer they posit is anything other than God) programmed in all of the genetic information necessary for later developments in to the first cell. Michael Behe famously proposed this in Darwin's Black Box:
Suppose that nearly four billion years ago
the designer
made the first cell, already containing all of the irreducibly complex biochemical systems discussed here and many others. (One can postulate that the designs for systems that were to be used later, such as blood clotting, were present but not "turned on." In present-day organisms plenty of genes are turned off for a while, sometimes for generations, to be turned on at a later time.)

Back when Behe proposed this idea, Ken Miller pointed out the most obvious problem with it: runaway mutations. Natural selection can only work on genes that are expressed. If a gene is "turned off" then it is subject to runaway mutations that will render if useless in short order. Miller wrote:

This means that billions of years ago a humble prokaryote was packed with genes that would be turned off for hundreds of millions of years before they produced the eukaryotic cilium, and genes for blood clotting proteins that would pass more than a billion inactive years in genetic "cold storage." And what happens during those billions of years? As any student of genetics will tell you, because those genes are not expressed, natural selection cannot weed out genetic mistakes. This means that mutations will accumulate in these genes at breathtaking rates, rendering then hopelessly changed and inoperative hundreds of millions of years before Behe says that they will be needed.

Not only is the idea not scientifically sound(the problem of runaway mutations, as mentioned above), it is also a religious idea.

Let me give it a shot, one-by-one:
The fossil record still reflects the uneven rate of development of phyla as first described by Gould and Eldredge in 1972.... This rapid acceleration in genesis of phyla, followed by cessation of new phyla creation is grossly at odds with a serial mutation mechanism.

The section on wiki(which is supported by citations from major peer reviewed journals) paints a very different picture than your description above:

How real was the explosion?

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]

Current evolutionary theory offers much better explanations for the Cambrian biota than anything you have posted in this thread. We can discuss the validity of scientific literature(with citation), but I am not interested in your own personal narrative about fossil strata or the evolution of genomes.

I think I discussed this above.This is a particularly odd one, and rarely discussed, since it is really more related to abiogenesis than speciation, but it relates to our current discussion. All life forms use exactly the same life architecture (DNA, RNA, and 20 amino acids). Why is there no other life architecture? Why are there no DNA variations? ...

Questions of this nature are considered in detail with reference to published research in "The Major Transitions in Evolution" by Smith and Szathmary, which I mentioned back in this post. See specifically, section 5.5 "What Determines the Size of the Genetic Alphabet" and section 6.3 "The Origin of the Code II: The bottom up approach"(the section "Why are there 20 amino acids?"), although those interested would do well to read chapters 4, 5, and 6, or perhaps the whole thing.

See also section on "Junk DNA" here:

The best of Genomicron.

http://genomicron.blogspot.com/2008/01/junk-dna-and-id-redux.html

As I mentioned above PE better supports my position than speciation-by-mutation....

Disagree, the current evolutionary theory is much more well supported. It might help if you start supporting your stories about the history of life or biology with objective citation.

In the mean time, if you would like to discuss any of the science on speciation and genetics: available for free in the January 1, 2009 issue of the journal Heredity:

Heredity - Special Issue on Genetics of Speciation

Galapagos · January 17, 2009

Two more items I would like to post because I believe they shed light on where the disagreement in this thread is coming from:

Wedge strategy - Wikipedia, the free encyclopedia
The Wedge strategy is a political and social action plan authored by the Discovery Institute, the hub of the intelligent design movement. The strategy was put forth in a Discovery Institute manifesto known as the Wedge Document,[1] which describes a broad social, political, and academic agenda whose ultimate goal is to "defeat [scientific] materialism" represented by evolution, "reverse the stifling materialist world view and replace it with a science consonant with Christian and theistic convictions"[2] and to "affirm the reality of God."[3] Its goal is to "renew" American culture by shaping public policy to reflect conservative Christian, namely evangelical Protestant, values.[4]

The wedge metaphor, attributed to Phillip E. Johnson, is that of a metal wedge splitting a log and represents using an aggressive public relations program to create an opening for the supernatural in the public’s understanding of science.[5]

Intelligent design is the religious[6] belief that certain features of the universe and of living things are best explained by an intelligent cause, not a naturalistic process such as natural selection. Implicit in the intelligent design doctrine is a redefining of science and how it is conducted. Wedge strategy proponents are opposed to materialism,[7][8][9] naturalism,[8][10] and evolution,[11][12][13][14] and have made the removal of each from how science is conducted and taught an explicit goal.[15][16]

The strategy was originally brought to the public's attention when the Wedge Document was leaked on the Web. The Wedge strategy forms the governing basis of a wide range of Discovery Institute intelligent design campaigns.

And this article from Dan Dennett belongs in any thread about evolution/creationism:

Edge: SHOW ME THE SCIENCE by Daniel C. Dennett
[...] the proponents of intelligent design use a ploy that works something like this. First you misuse or misdescribe some scientist's work. Then you get an angry rebuttal. Then, instead of dealing forthrightly with the charges leveled, you cite the rebuttal as evidence that there is a "controversy" to teach.

Note that the trick is content-free. You can use it on any topic. "Smith's work in geology supports my argument that the earth is flat," you say, misrepresenting Smith's work. When Smith responds with a denunciation of your misuse of her work, you respond, saying something like: "See what a controversy we have here? Professor Smith and I are locked in a titanic scientific debate. We should teach the controversy in the classrooms." And here is the delicious part: you can often exploit the very technicality of the issues to your own advantage, counting on most of us to miss the point in all the difficult details.

...

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.

;)

HydrogenBond · January 17, 2009

The Cell's Energy Balance

I have been trying to discuss the middle zone of evolution, between the alpha of a genetic change and the omega of a selective advantage. This middle area turns genetic potential into the practical reality of selective advantage.

One way to begin addressing this middle area is by using a simple energy balance. If you look at a cell, it is highly efficient, which means it tries to use the least amount of energy to accomplish its tasks. Enzymes are catalysts that lower the energy requirement to perform any task. Regardless of how these evolve, selective advantage implies efficiency which also implies minimizing the energy requirement for any and all the tasks. That is the goal in the middle.

If we do an energy balance around the cell cycle, the cell cycle begins when the cell has the most potential energy as stored food. The cell is an maximum energy potential. The cell cycle is energy intensive. By the time the cell divides into daughter cells, this potential energy storage is at its lowest since so much energy was needed for all the steps.

In terms of an energy curve, we start at a maximum. This maximum decays and reaches a minimum when daughter cells form. After that there is another climb up the energy hill. When it reaches the top the cycle can begin again. Early cells where only riding the energy curve. Efficiency was always the implied future goal since selective advantage implies efficiency.

If you look at any chemical reaction, the energy curve looks the same. It has to climb an energy hill called the activation energy. Once it reaches the top it can slide down to lower energy. The duplication of a cell is just another complex integrated bunch of chemical reactions following this precedent common to all chemistry.

If we look at the DNA, if we made a perfect duplication, all the hydrogen bonding is perfect and therefore the double helixes are at minimum energy. If add any defects we add imperfect hydrogen bonding. Any defect means the DNA has increased its potential energy. This is part of the activation energy for change leading to the efficiency implicit of selective advantage. A genetic change is implicit of the beginning of an ascent up an activation energy hill, but it is not enough to put it over the hump.

The next step is we need to make and add the protein that results from a genetic change into a cell. We are initially adding inefficiency since the cell may not be initially equipped to deal with this. This adds more potential energy to push the process further up the activation energy hill.

Say the cell body has increased potential energy due to the new inefficiency. This means the potential energy of the DNA will increase even further since the DNA is part of the cell. There are many ways to increase the energy potential of the DNA. One way is to separate the double helix in as many places as needed to form an equilibrium, since this will break a bunch of hydrogen bonds and increase the potential of the DNA, etc. Say this allows us to make another protein. This may help or make things worse. Either way, the cell needs to climb the activation energy hill with the hope of reaching the top, before both can slide down the energy hill into selective advantage.

Another way is to reverse some of the packing, since packing proteins help to lower the energy of the DNA. This makes more DNA available. Maybe the needed gene is tucked away, which will allow the slide down into selective advantage or the bottom of the energy curve.

This analysis is only an energy balance and does not attempt to address the biochemical details. But the details need to add up to the energy balance.

modest · January 17, 2009

What you are explaining is known as "front-loading", where the genetic information is placed in the DNA in advance by God.
It was put forth in ID biochemist and fellow of the Discovery Institute Michael Behe in his book "Darwin's Black Box", and was subsequently shot down by biologist Ken Miller:
Dispatches from the Culture Wars: Exaptation vs Front Loading: Why Evolution Wins
Front loading is the idea that God (no, I'm not going to engage in the ridiculous fiction that the generic designer they posit is anything other than God) programmed in all of the genetic information necessary for later developments in to the first cell. Michael Behe famously proposed this in Darwin's Black Box:
Suppose that nearly four billion years ago
the designer
made the first cell, already containing all of the irreducibly complex biochemical systems discussed here and many others. (One can postulate that the designs for systems that were to be used later, such as blood clotting, were present but not "turned on." In present-day organisms plenty of genes are turned off for a while, sometimes for generations, to be turned on at a later time.)

Back when Behe proposed this idea, Ken Miller pointed out the most obvious problem with it: runaway mutations. Natural selection can only work on genes that are expressed. If a gene is "turned off" then it is subject to runaway mutations that will render if useless in short order. Miller wrote:

This means that billions of years ago a humble prokaryote was packed with genes that would be turned off for hundreds of millions of years before they produced the eukaryotic cilium, and genes for blood clotting proteins that would pass more than a billion inactive years in genetic "cold storage." And what happens during those billions of years? As any student of genetics will tell you, because those genes are not expressed, natural selection cannot weed out genetic mistakes. This means that mutations will accumulate in these genes at breathtaking rates, rendering then hopelessly changed and inoperative hundreds of millions of years before Behe says that they will be needed.

Not only is the idea not scientifically sound(the problem of runaway mutations, as mentioned above), it is also a religious idea.

Thank you Galapagos. This is very good information :hyper:

~modest

Biochemist · January 18, 2009

What you are explaining is known as "front-loading", where the genetic information is placed in the DNA in advance by God.
It was put forth in ID biochemist and fellow of the Discovery Institute Michael Behe in his book "Darwin's Black Box", and was subsequently shot down by biologist Ken Miller:

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.

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

Biochemist · January 18, 2009

The section on wiki(which is supported by citations from major peer reviewed journals) paints a very different picture than your description above...Current evolutionary theory offers much better explanations for the Cambrian biota than anything you have posted in this thread. We can discuss the validity of scientific literature(with citation), but I am not interested in your own personal narrative about fossil strata or the evolution of genomes.

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)

Moontanman · January 18, 2009

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.

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

It might be ok for some to just say it was front loading and let it drop but since it obviously wasn't abiogenesis where did the original loaded genes come from? Don't avoid the $64,000,000 question, if you truly believe the genes were front loaded then where did they come from?

Biochemist · January 18, 2009

With respect to the restricted genetic alphabet:

Questions of this nature are considered in detail with reference to published research in "The Major Transitions in Evolution" by Smith and Szathmary, which I mentioned back in this post. See specifically, section 5.5 "What Determines the Size of the Genetic Alphabet" and section 6.3 "The Origin of the Code II: The bottom up approach"(the section "Why are there 20 amino acids?"), although those interested would do well to read chapters 4, 5, and 6, or perhaps the whole thing.

This is a perfectly reasonable counter hypothesis. It is just entirely hypothetical and not particularly well supported. The "complex RNA" environment precursor environment has to have essentially disappeared. It would have been more reasonable for two separate life pools to have emerged from this biogenesis model. But this is still a reasonable hypothesis. It certainly does not refute my position. It is just (probably) the best counterposition.

Biochemist · January 18, 2009

Genome sizes vary in ways that are not yet fully understood.

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

Biochemist · January 18, 2009

Two more items I would like to post because I believe they shed light on where the disagreement in this thread is coming from...And this article from Dan Dennett belongs in any thread about evolution/creationism:

Gala- You seem a little hung up on creationism. I am not making any references to divine intervention at all. I am offering a data-driven argument. I don't really care if someone else sees this as theistic. Have at it.

Biochemist · January 18, 2009

Don't avoid the $64,000,000 question, if you truly believe the genes were front loaded then where did they come from?

How about: I don't know? I recognize that this is a little disturbing, but so is the big bang (What happenned before? Why did it start here?). Or the incongruities of particle physics (light is both a particle and a wave, depending what you measure?).

I truly thought abiogenesis was infeasible even when I still thought speciation-by-mutation was reasonable. That fact that my view on speciation makes abiogenesis even more problematic is pretty consistent with nearly every discovery in basic science: The more we know, the more complex the model gets.

I just don't have an answer, and it is very difficult to model abiogenesis. But I really don't expect to find out that there was a "poof" and God stuck the first totipotential cell here. It will have arisen from someplace.

Moontanman · January 18, 2009

Gala- You seem a little hung up on creationism. I am not making any references to divine intervention at all. I am offering a data-driven argument. I don't really care if someone else sees this as theistic. Have at it.

If what you say is true then answer my question, who or what preloaded the genome? Your conjecture doesn't answer anything it just asks the question of who preloaded the genome.

Moontanman · January 18, 2009

How about: I don't know? I recognize that this is a little disturbing, but so is the big bang (What happenned before? Why did it start here?). Or the incongruities of particle physics (light is both a particle and a wave, depending what you measure?).

All you are doing is obfustacating the issue your premise only asks more questions than it answers.

I truly thought abiogenesis was infeasible even when I still thought speciation-by-mutation was reasonable. That fact that my view on speciation makes abiogenesis even more problematic is pretty consistent with nearly every discovery in basic science: The more we know, the more complex the model gets.

Current Abiogenic theory is completely plausible, far more plausible than front loaded gens. Your idea of pools of water is so far from current theory it's not even in the same universe. You are going on out dated material and using that material as defense of your stand.

I just don't have an answer, and it is very difficult to model abiogenesis. But I really don't expect to find out that there was a "poof" and God stuck the first totipotential cell here. It will have arisen from someplace.

No abiogenesis is not hard to model, do some research somewhere other than creationist web sites and you'll see this. No "Pool" no need for god or preloaded genes. I am very disappointed bio, I thought you were up front but you are just another disingenuous creationist trying to get your ideas inserted into the main stream by obfuscation.

Biochemist · January 18, 2009

All you are doing is obfustacating the issue your premise only asks more questions than it answers.

If only I knew everything.

Current Abiogenic theory is completely plausible, far more plausible than front loaded gens.

I think I agree with the second part of your point, but not the first. You are going to honestly say that we got the first self replicating life form with our four nucleic acids and 20 amino acids in the roughly 500 million years between when the earth cooled and 3.5 billion year ago????? Completely randomly???? Did it happen seven more times (in nearly exactly the same way) since???? Heck, we have had time and the environment is a lot less hostile now. Why aren't there a half dozen common descent trees? Get real. This is a perfectly reasonable position as a hypothesis, but it is not high on the plausibility scale.

No abiogenesis is not hard to model, do some research somewhere other than creationist web sites and you'll see this.

I don't look at creationist web sites. I leave that to you unbiased scientists.

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