Oldest vertebrate fossil found in Australia, scientists say

Of course, it might be noted that my statement that deer cannot pass on traits to their ancestors is -- well, it's not wrong, anyway. I meant descendants, of course.

ican, if you refuse to read the texts such as Behe, you will miss much of the basic knowledge from which your argument could appreciate vastly.
Your comment that exteinctions cause immediate reductions in species IS correct , where you depart from data , is that there is no evidence that there is a march toward more complex brains(whatever the hell that supposed to mean). In the Paeocene through the Miocene were a vast number of mega fauna who were far less niche specialized in their food habits (and inferred TACTICS) than were specific dinosaurs.The really smart dinosaurs like the earlier Allosaurs or therapsids, were evolving in specialized niche areas that later became separate continental masses. Mammals, when dinosaurs were no longer around, evolved at least seven different orders in different proto continents. Luck of the climatic draw yielded larger furrier body masses able to witstand cold by a smaller mass volume, or in warmer land masses, the trend toward tactics and opportunistic feeding was a mere modification of the red queen. All the faster and sabre toothed individuals evolved within a limited proto geographic zone and no data has supported that , except for man, that a "big b rain" was even needed to survive. So the Universal rule you claim is not borne out by evidence , which, if you would take time to learn rather than constantly repeating your own version of reality, youd argue this from a greater base of knowledge. Now you are doggedly asserting that such knowledge is irrelevant. Id hate to have you design a bridge without a secure basis in civil structural.

The entire point youve made has, in my estimation, been adequately refuted and shown where you need to dress up your windows.
Your comment that evolution only prunes the bush is one of complete ignorance of cladistics and paleogeography. Yet you continue this effort with absolutely no grounding. Once or twice, ok. But youve not discovered anything new in your readings. You said you read Goulds "STructure..." then, I submit, youve missed the whole point .

Gentlemen, I dont think there is any cross communication possible herein. I either think ican is just having a personal joke at our expense or , his self proclaimed reverence for knowledge only goes as far as his prejudices.

Sorry to be so blunt but the thought just occured when I reread some of your posts and discovered you are merely restating positions in slightly different means. To that Im gonna say "ASKED AND ANSWERED"... move on to something substantive.

rosborne --

Yep, endosymbiosis is a very cool thought. I've only briefly looked at the link and don't have much time to do so, so I don't know how far it goes into this -- but one of the principal pieces of evidence for this is the dual membrane on mitochondria and on plastids -- as though they were floating around in the cell as vesicles that never got everted! (Unless Campbell's textbook is wrong; I've certainly hear a mycologist go on about it.)

I'd also tend to question the classification of plants and animals as the two major kingdoms of life, but that's just quibbling...



I took this statement by ican to mean that reduction happened within species during mass extinctions, not as a statement of the impact on overall biodiversity. I realize now I probably misread it.



Ah, well, it's caused my young, mushy brain to revisit some things.

me too dog, but apparently not our dabtaing friend. "Consistency is often not to be rewarded by conferring credibility"

Im applying a forensic approach now, Never ask a question whose answer you dont want to hear.

Science doesnt work like that, the arguments being pursued in the name of advancing knowledge, never start with a predetermined position and then discount everything that doesnt match your hypothesis. This is a bit disengenuous.

Anyway, Im tiring of the 'dueling quotes " method wherein , If I , or you say something, we get an incomplete sound byte which incorrectly argues itself as evidence

Yes, but they sure do cause a reduction in total species however relatively short lived.



Perhaps this will merely reveal my engineer's bias regarding cause and effect, but here goes anyway.

Natural selection (NS) is characterized, in everything I have thus far read, as the equivalent of a mindless, random killer of species or major percentages of members of species. This occurs as a consequence of NS mindlessly creating conditions within which certain species cannot survive. The only thing truly natural about mindless NS are the environmental changes it mindlessly creates. Being mindless, NS cannot contemplate improvements and attempt to influence outcomes accordingly.

So, by analogy, NS mindlessly prunes the alleged mindless bush. It is the alleged mindless bush that somehow causes itself to attempt to regenerate under the new conditions the life it heretofore possessed. Generally, however, it succeeds in not so much regeneration of what was but in generation of new life. I have hypothesized that the bush does this with a little help from 2ndI.

.
I think calling NS a pressure initial or otherwise is mere metaphor. There is no pressure for change; there is only variable opportunity for change. The change is strictly caused by the actual propensity of life itself to allegedly mindlessly seek survival. In other words, NS doesn't create, it destroys.

To attribute to NS the attribute to create is no less repugnant to me than the idea that militant jihadists by virtue of their killing create opportunity for new forms of life to be bred. Yes, kill some life and other life will benefit. But the acts of benefiting are not caused by the killers but the propensity of the surviving life itself to endure.



In that regard then, there appears to be developing a 3rdI, mindful humans, which up to recent times had given little thought to these unintended consequences, but created conditions that nontheless fostered these consequences. But it's the deer genomes that did the "real work".

2ndI can be nothing more than life's mindless compulsion to, through mindless trial and error, seek ways to maximize its existence, and out of its successes to mindlessly emphasize future trials that are consistent with the experience of that which has and has not worked.

Wait a minute While this may apear mindless to our bone-headed brains, it may not be mindless to procreating genomes. Hmmmm



(my emphasis added.)

A purposeless efficient exploitation of available resources? I've got to think more about this.

For now, just for grins, I hypothesize 2ndI to be that quality found within all life that exhibits purposefulness. Can a bunch of protein molecules not encased in a brain have purpose? Why not?

Oh, for God's sake -- you're allowed to use free-and-lose interpretations of language and I am to be held to the strictest standards? Nothing I've postited to you is in the least wy objectionable. "Pressure" simply means that certain changes are prohibited, just as a boulder on Route 1 at Devil's Slide means that you can't take the highway. It doesn't tell you what highway you can take, it simply blocks one. If you don't understand the simple concept of a diversifying pressure (and, again, "pressure" doesn't signify intent in evolution any more than it does in a garden hose), you haven't grasped one of the most basic precepts of the model of natural selection. Have you ever read a basic biology text, or did you just jump to the ones, like Gould's, that presuppose a degree of familiarity of basic concepts before expanding on them? Surely you wouldn't gather much from reading Hawking without knowing a bit of physics first. I'm a little surprised -- OK, not surprised, but irritated -- that you feel you can challenge one of the most widely studied scientific models around (and the proof of how closely it is scrutinized is in how many studies are published every day that corroborate or modify some small part of the model) when you display such an inadequate knowledge of the basic subject matter.

I mentioned the Campbell text earlier. It's a pretty good one, very approachable, excellent diagrams (again, though, don't put too much stock in their life histories of fungi), and earlier editions can be got pretty cheap. Again, cheers. Have fun arguing for the sake of arguing.

You lost me with that comment. I inferred from what you previously wrote that Behe's stuff was no longer accepted by the scientific community. Of course my reason for avoiding him was what I infered from you was his prior commitment to devine intervention as the cause of evolution.



Irrelevant to my hypothesis, YES. Irrelevant to determining the nature of 2ndI, NO. Irrelevant in general, NO. We are not designing a bridge or a computer system here. I, at least, am trying to make sense out of what often appear to me to be conflicting and sometimes absurd claims.

Please provide me your recommended reading list. I am confident it will help me.



GRRRRR
I did not write that evolution only prunes the bush. I did not mean that evolution only prunes the bush. I wrote and mean that Natural Selection only prunes the bush.



No, I never wrote that I read Gould's "Structure ... " I did quote from that part I have thus far read. I'm still reading and studying it and trying to get past the man's seeming propensity to dress up questionable ideas with a plethora of erudition serving perhaps to impress his colleagues, but certainly NOT serving to impress me. I keep trying because for reasons unknown to me, "I think that with all that .... in there, there's got to be a pony in there someplace".



Well, ok, it's time for me to be blunt too.

One principal you, farmerman, continually appear to misunderstand and improperly practice is that knowing the history of a series of events is NOT equivalent to knowing the causes of those events. The determination of cause requires an accurate knowledge of history (like you apparently have) but that knowledge by and of itself is insufficient -- dare I say, inadequate.

Another principal about which you demonstrate significant ignorance is the principal that argment should be directed to the arguments offered by their arguer and not to their arguer himself. Everytime you flip into your criticism of me whom you don't know (which you do with childishly increasing frequency), I infer you are either criticising yourself whom you do know, or are so terribly frustrated about what you are discovering you do not know that you want to blame the messenger.

Ok, so blame the messenger, if it makes you feel any better. But self-rectification has a more lasting satisfying result.

Ican, if you have not already read it, get yourself a copy of "What Evolution Is", by Ernst Mayr., Basic Books, 2001. Almost every issue you have raise is addressed in that book. It is also simple, straight forward, and provide with much of the basic back ground (other than genetics which is a specialized field) on evolution that patiodog recommended. For genetics I would recommend "Evolutionary Analysis" by Freeman and Herron, Prentice Hall, 2001. It is an introductory text.

Thank you very much. First, I'll try to order both through Amazon Books. Thanks again.

You've misunderstood this example. You stated that natural selection cannot create branches. I have provided an example of case where that is not true -- one gene pool got split into two, and there is a selective pressure against the two merging back into one. This is neither good or bad: it just is. The two populations have clearly adapted to different terrains, and are/were on there way to speciation because natural selection acted against homegenization of their collective gene pool. The reason I mention the human factor is because this is the only reason we've noticed this: human interference has allowed us to see what happens when individuals from these two species mate. This is actually a case of one form of natural selection -- predation -- potentially causing speciation (through increased genetic hetergogeneity) while another -- environmental shift, caused by humans in this instance -- potentially increasing genetic homogeneity. It's actually a very good model for thinking about homogeneity.

And as for positing humans as 3rdI -- why do you feel the need to separate humans from the natural world? Competition and symbiosis between species is one of the driving factors behind macroevolution; why should our actions require a new category?

Truer words have never been spoken. There is a limited amount of energy available on the planet. Those species that make better use of it are going to be more competitive than those who don't.

It does bring up an interesting point regarding complexity and intelligence, though. One of the most complex and highly conserved biological products around is the pyruvate dehydrogenase complex. It has three different enzymatic subunits, is regulated in at least three different ways (probably more, but studies are still progressing; the first low-resolution crystallographic images were published fairly recently; the damn thing is so big that you can look at it -- a protein, for the love of God -- with an electron microscope). It requires five different coenzymes to function, and, in addition to its high degree of organization, appears to form highly organized supramolecular complexes that effectively catalyze reactions in two dimensions rather than three. And where is this thing? In the mitochondrion, that simple, ancient endosymbiont that was phagocytized by an old eukaryote -- probably my great-great-grandpappy. Nothing to do with intelligence, except that our big brains and their need for a very closely controlled thermal and chemical environent demand a lot of energy. Just a bit of trivia for you.

no ican, I can go back to sections of your posta and show where you either purposefully contradict yourself or have apoor memory.
As for knowing the history is not knowing the cause, this has been your everlasting mantra , and up, is with which, it shall not be put. Maybe I cannot understand the cause, but by NOT knowing as you so proudly admit, you arent even able to pose intelligent questions. Thats a silly point youve been stuck with, why not lose it.

Im not really angry at you,Im more angry at me for thinking that, with your additional reading since last year, your misunderstandings would be on a higher plane of understanding, they are, alas, not. Consequently, Ive been quoting things that were in some of those works and I think they went right over your head. I didnt catch that until your "pruning the bush" statement, ahhh well,

Dog argues a point for sympatry, an idea that Mayr had renounced as not consistent withnatural selection. He has since , in the 1990s, changed his mind based upon data and field evidence. His newest points are within the very Mayr book Acquiunk has mentioned. The combination of gene drift (not the statistical autocorrelation aspect but the place motion of the great variability in a genome or a single gene sequence) and nat selection is now espoused by Mayr as the most important initiator in macroevolution.This is quite common, in that for speciation and higher taxa, animals need not be isolated for selection to be the only causation.Sympatry often occurs as the great variability and genetic diversity allows animals who dwell together to exploit totally different niches so as not to overstress a resource that is the limiting resource.( some owls fly in the day, There are rats that are evolving dentition toward an omnivorous diet, etc etc)


The only reason you should read Behe is to see your very


own argument told in a very ordered fashion. Of course Behe isnt doing a running gun battle. His argument has been pretty much taken apart but so has Cuviers, Lamark, Werner, Buffon, Jameson and others , We do, however read them to gain a sense of history of how even the thought of evolution and an old earth "evolved"


patiodog, what does the pyruvate d .c look like in the diffraction patterns? Is it distinguishable from others. Im familiar with Margulis genome capture theories but she was always taking of eukaryote to eukaryotic cell. You seem to indicate that the capture was between a euk and a pro.? Is that right?
See that could speed up genome capture a huuuge amnt. Ill bet Lynn Margulis gets some kind of medal for her work. Shes always sort of been considered a crackpot, but her chemistry seemed sound to me (although Biomole' reactions are not my forte)


Heres some more lit ican.
PAul Ehrlich and C Wills-The Children of Prometheus
Knoll AH-eArly animal evolution:views from comparitive biology and geology SCIENCE 1999 (cant remember the issue
Ive got it as a PDF

Averof M. 1995. HOx genes and the diversification of body plans. NATURE
376,p420

This has been demonstrated exhaustively with microorganisms in vitro, hasn't it?



Haven't seen the diffraction -- it was today's biochem lecture, thought I'd throw it out there to help cement it in my own brain. We just looked at the TEM and plowed on into the Krebs cycle.

I've always heard the capture was most likely of a prokaryote. The mitochondria and plastid chromosomes are circular (a la bacteria), aren't they? I could be misremembering. My biochem. prof has said the origin was what I'd always thought it was -- prokaryote -- but folks don't always agree or even speak rightly on their feet. Gotta go to ecology. Cheers.

well, if thats the case (mitochondrils from a pro to a euk) weve nocked off a couple bazillion years in systematics


microrogas and saympatry, yes, I believe e coli and e (stratumname here) were sequenced as such

They don't require a new category. For now, I wanted to avoid analyzing influences caused by intelligent things, so I thought I could achieve that by putting all intelligent influences in a 3rd category.

CAUSE AND EFFECT

A population of a single species of animal is transferred from its home environment into two different environments: Environment H and Environment T. The anmals are lined up and a coin is flipped for each animal to decide whether it shall be transferred into H or T. After many generations have elapsed, significant physical difference are perceived to exist between the two populations.

What do you think caused these differences to evolve?

Did the coin do it?
Did the coin tosser do it?
Did the transferor do it?
Did the respective environments do it?
Did the chance editing of procreating genes do it?
Did natural selection acting within each environment do it?
Did 2ndI do it?
Did something else do it?

Did none of the above do it?
Did all of the above do it?

I don't believe you!

Lecture cancelled. Would have left hours ago if I'd known that was coming. Now gotta wait for my bus...



Thinking about it again, I think you're right about the membranes. I'd confused the nuclear envelope -- which has two layers -- with the plastids et al, which have three. If bacterial this could have been because they were engulfed twice, or they could have been gram-negative, which have two membranes and minimal whatchamacallit -- the membrane glycoprotein that's peculiar to prokaryotes.


ican --
Genetic drift did it. But the question is -- what causes populations to become separated and drift apart? Could be continental drift, could be a fire that wipes out a swath of forest (so that whatever lives in the leaf litter on one side of the burn is now separated from its conspecifics on the other side of the burn), it could be a road. If something presents either/both populations from exchanging genetic material, they can speciate.

Doesn't have to be a physical separation, either. Competition can drive some individuals subject to intraspecific competition to seek out* other resources and establish a new niche.

*Again, I'm just describing possible behaviors; I'm not suggesting that anything tries to adapt any more than Norwegians centuries ago tried to retain lactase throughout their life so that they could subsist on a diet extremely high in animal milk.

I don't understand the point of this little exercise at all...
How does flipping a coin and having an animal choose where it will go relate to anything in the natural world? What's the analogy you are trying to present?

Heres a short article on the need for further sequencing to draw the conclusions tha ican wants . The difference is that the molecular evolution researchers dont make wags about their work, and ,as you can see, its expensiveHow many genomes are enough?
The more, the merrier, researchers declare. Is the sky the limit? | By Tabitha M Powledge

How many sequenced genomes are enough? The minimum number for comparative genomics, researchers say, depends on what you want to learn. The optimum number is a still a mystery.

For identifying cis-regulatory regions such as enhancers and promoters, the genomes of three species that are roughly equidistant evolutionarily is the bare minimum, and more is better, according to Lincoln Stein. Stein, who is at Cold Spring Harbor Laboratory, is first author of a paper on the Caenorhabditis briggsae genome in the first issue of PLoS Biology, an open-access online journal published by the Public Library of Science. He pointed out that having the genomes of at least three species permits distinguishing between the signal?-bases conserved because they actually do something?-and noise?-bases conserved simply because they haven't mutated yet. "As you add more species to the alignment, the signal remains the same while the noise decreases because there are fewer and fewer bases that are the same because of an accident of history," he told The Scientist.

For finding conserved sequences in mammals, with their more complicated genomes and long stretches of repetitive DNA, some half-dozen species might be enough, said Eric Green, scientific director at the National Human Genome Research Institute (NHGRI). His estimate comes from his lab's unpublished work and from a paper in the August 14 Nature comparing a single large genomic region in 13 vertebrate species.

"By the time you get to about five or six mammals, you start to plateau in the detection of these highly conserved sequences," Green said. "But," he cautioned, "we don't know if we've found everything we need to find, and we don't know if our algorithms are properly developed to find everything we're trying to find. It just means that with our algorithms, you plateau. In the absence of knowing what it is that you're really trying to find, it's hard to assess the methods and the datasets that you're using to find it."

Studies of evolutionary change require another comparative approach. Caenorhabditis elegans and C. briggsae differ in their ability to respond to RNAi, Stein pointed out. Did C. elegans acquire the ability or did C. briggsae lose it? To determine the direction of change, worm researchers need the genome of a third, somewhat distant species. If it has the elegans form of the hypothetical systemic RNAi gene, then the common ancestor of C. elegans and C. briggsae probably possessed that form, and it was lost in the C. briggsae lineage, Stein noted. If the third species has the briggsae form, then elegans probably learned a new trick in the hundred million years or so that separates them.

That's why the C. briggsae paper urges sequencing of Caenorhabditis remanei, a genome project that NHGRI has already accorded moderate priority. John Spieth, of the Genome Sequencing Center at Washington University School of Medicine in St. Louis, who is first author of the remanei "white paper" (proposal), says he and his coauthors are thinking about rewriting the paper in an attempt to persuade NHGRI to bump remanei up to high priority. That strategy has already worked for partisans of the rhesus macaque, which made the A list at the second attempt.

The C. briggsae paper also suggests sequencing the more distant nematodes Caenorhabditis japonica, Caenorhabditis drosophila, or Brugia malayi. A B. malayi project is underway at The Institute for Genomic Research, said Avril Coghlan, a comparative genomicist at the Smurfit Institute of Trinity College Dublin. "It will be possible to compare B. malayi to C. elegans and C. briggsae across their entire genomes. This three-genome data set will be a treasure trove to nematode geneticists and molecular evolutionists."

Will three genomes really be enough for evolution studies? "If you're trying to understand details about genome evolution, there's probably never enough genomes. Every genome you get more data from, you're getting insight about the evolution of that genome relative to all other genomes," Green said. Green has put his resources where his mouth is. The Nature paper presented comparisons of a single swath of DNA from a mere 13 far-flung vertebrates. But his lab is beavering away on more than 30?-a list that does not yet include beavers, although there is a hedgehog, along with marsupials, bats, and several primates.

"I'd say we're just scraping the surface right now," noted Hugh Robertson, who studies the evolution of insect transposons at the University of Illinois at Urbana-Champaign. He forecasts eventual genome projects on several insect orders, including beetles, moths, and bugs (Hemiptera). To say nothing of fruit flies: Drosophila simulans and Drosophila yakuba have already been added to NHGRI's high-priority roster, and a white paper in preparation urges an additional eight Drosophila species. "The bacterial people are already way ahead of this. They're doing tons of comparative genomics," Robertson points out. "Look at what the yeast people learned when they sequenced five yeast species closely related to Saccharomyces cerevisiae. And that was a relatively cheap project."

The main barrier to the immediate sequencing of many more genomes remains cost. "The reason there is so much discussion about which vertebrates to sequence is simply because it still costs between $50 million and $100 million to sequence a vertebrate genome, and that's real money," Green pointed out. "There's no question that if the cost of a sequence were ten or a hundred times cheaper, we wouldn't be worried about whether we were going to sequence three mammals, or six, or ten. We would just sequence a lot of them."

Even at present prices, sequencing is a bargain, Robertson argued. "When you think about it relative to the enormous amount of resources that NIH puts into grants to characterize individual genes of different species, sometimes it just seems ludicrous not to be sequencing their genomes." Sequencing an insect genome, he declared, would cost no more than a few National Institutes of Health (NIH) grants.

Sequencing costs have dropped several orders of magnitude, from $10 per finished base in 1990 to today's cost, which Green estimates at about 5 or 6 cents per base for finished sequence and about 2 to 4 cents for draft sequence. For some comparisons, draft sequence is adequate. Last spring NHGRI projected future cost at about a cent per finished base by 2005.

Although the plummeting price of sequencing is welcome, it is due to incremental improvements on the basic technology. "What we're all praying for is one of those great breakthroughs?-a new technology that will allow us to read single-molecule sequences, or whatever the trick is going to be that will give us several orders of magnitude increase in speed and reduced cost," Robertson said. Teams of competitive technology developers around the world are racing toward that goal, cheered on by a lot of casual prophecy about the $1000 genome.

Nor is cost the only challenge. "The really big questions about genome dynamics, selection, adaptation, and gene networks await better theory, methods, and clever hypothesis testing," said Cristian I. Castillo-Davis, who studies regulatory sequence evolution at Harvard University. "Currently, the field is very thin on biological analysis and very heavy on technology and the reporting of numbers for numbers' sake." Castillo-Davis' solution? "We are in great need of biologists who can develop novel analytical tools and theory to make biological sense of comparative genomic data."

But the infrastructural problems of comparative genomics tend to fade in the dazzle of its prospects. With the data that will flood public databases in the next few years, Coghlan expects researchers to take on questions such as: How does regulatory DNA evolve? How is chromosome and protein evolution related to population size and structure? How do differences in meiosis and recombination in different species, such as those with holocentric chromosomes versus those with a true centromere, affect the structure of chromosomes and proteins?

"Research communities are realizing that they're going to wither if they don't have a genome project," Robertson said. "I suppose we're not going to sequence every genome on the planet, and that's certainly true if technology stays the way it is. But if technology changes as radically as some people think it will, then yes, why not sequence most of the species on earth?"
Links for this article
C. Holding, "Caenorhabditis comparative genomics," The Scientist, November 17, 2003.
http://www.biomedcentral.com/news/20031117/04/

Cold Spring Harbor Laboratory
http://www.cshl.org/

L.D. Stein et al., "The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics," PLoS Biology, October 2003.
http://biology.plosjournals.org/

National Human Genome Research Institute (NHGRI)
http://www.genome.gov/

J.W. Thomas et al., "Comparative analyses of multi-species sequences from targeted genomic regions," Nature, 424:788-793, August 14, 2003.
[PubMed Abstract]

NHGRI Genome Sequencing Proposals, Status of Organisms in the Prioritization Process for Genome Sequencing and their 'White Paper' Proposals
http://genome.gov/page.cfm?pageID=10002154

Genome Sequencing Center, Washington University School of Medicine in St. Louis
http://genome.wustl.edu/

T.M. Powledge, "Macaque advocates seek higher status," The Scientist, September 16, 2002.
http://www.biomedcentral.com/news/20020916/04/

The Institute for Genomic Research
http://www.tigr.org/

Smurfit Institute, Trinity College Dublin
http://www.tcd.ie/Genetics/


M. Kellis et al., "Sequencing and comparison of yeast species to identify genes and regulatory elements," Nature, 423:241-254, May 15, 2003.
[PubMed Abstract]

L. Pray, "A cheap personal genome?" The Scientist, October 4, 2002.
http://www.biomedcentral.com/news/20021004/04/

In this exercise, the animal does not flip the coin; something else flips the coin.

In this exercise, the animal does not choose where it will go; something else chooses where the animal will go.

It has been alleged that natural selection is the cause of procreating genomes NOT surviving.

It has been alleged that chance is the cause of the edits of procreating genomes. In particular, it is alleged that these edits of procreating genomes are the cause of genetic-drift.

Regardless, what do you think caused the physical differences to evolve?