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Let's get another featured article

I know Evolution is already a Featured Article but I think we can do one better and get another evolutionary biology-related article up to Featured Article Status. I have access to all research materials at the University of Maryland (including all notable biological journals), and more importantly, I have the desire to see this through and get it done. I just don't have the subject matter down pat quite yet. I was thinking maybe evolutionary developmental biology. This is still in the planning stages though so I welcome any other suggestions. --Cyde Weys talkcontribs 16:45, 14 December 2005 (UTC)

If you'd like to do that, I propose the natural selection article, which is probably much more trafficked (I'm inventing this usage of the word "trafficked" right now) and has more grist for the mill. Graft 18:04, 14 December 2005 (UTC)

I would like to inquire upon the general consensus as to whether or not the following link, detailing the general increase in elemental composition in the common lineage of species from reacting chemicals (4.6 BYA) to H. sapiens (0.2 MYA), would be appropriate for the evolution article:

[link removed from live page -- still self-promotional spam on the talk page - anyone interested in seeing the site can see the history, otherwise enough people have weighed in against it to show consensus to remove it, so removing here too to avoi free advertising.]DreamGuy 01:39, 15 December 2005 (UTC)

I understand that this article is focused on biological evolution, but in my opinion the random researcher key-word searching for "evolution", we can assume, might be searching for the "big picture" of evolution (4.6 BYA to present), not just biological evolution (1 BYA to present). I already know that user:Vsmith is against this proposal; however, the only contribution Vsmith makes to Wikipedia is to remove peoples' edits, links, and work, etc.; he is more of a de-contributor. Based on his user contributions page, he reverts about 15-20 edits per day; thus I assume he is biased in this direction. Hence, I would greatly appreciate it if evolution-focused Wiki-members could comment on this proposal? Thanks:--Wavesmikey 17:29, 14 December 2005 (UTC)

the "big picture" of evolution (4.6 BYA to present), not just biological evolution (1 BYA to present) What??? Maybe by "biological evolution" you mean "evolution of sexually reproducing species"? Bacteria have been around for most of the age of the Earth. --Rikurzhen 18:09, 14 December 2005 (UTC)

Why should I trust what is on that site? It lists off line references but googling "www.humanthermodynamics.com" shows me its original research MAYBE backed by good references ... but maybe not. Its not sound source and barely relevant. I believe most of it and find the intent of it interesting. It just doesn't belong here. In my opinion. WAS 4.250 20:00, 14 December 2005 (UTC)

The user seems to be interested mainly in adding links to his site, on which he has a book to sell. He placed the link on the evolution page at the top of the list. These clues suggest spamming. Wikipedia is not a collection of everyone's favorite links. His other link addition edits should be scrutinized also. Wiki is not for self-promotion - the object is to write an encyclopedia. Vsmith 21:10, 14 December 2005 (UTC)

Not to speak inappropriately, but let’s just cut through all the baloney. I don’t like Vsmith and I hide nothing. I have written four books and I'm working on a fifth. All of these books are more or less just for fun and have press runs of less than 100 copies (all copies provided free of charge). I also run and organize an information website that neither sells nor advertises nothing. I don't see why I should be penalized for being an author or for having an association to an educational, group-run, website. I do not link to any books nor to anything attempting to promote. If I happen to have a collection of data, such as a list of elemental mass composition data tables, fully-sourced, from various organisms in evolutionary development, then I see no reason not share my information; in the same manner as each of us editors are sharing our intellectual information by editing and adding to articles.
Regarding "why should I trust what is on that site?", my credentials are full-listed on my user page User:Wavesmikey, plus the proposed page contains a link to the about us section, which lists those scientists who have contributed to, support, and or are active memmbers of the site. Furthermore, this link is in full accord with the Wiki link protocol section, which is to refresh everyone is Wikipedia:External links.
I began editing on Wikipedia after I noticed that pages that I was linking words to, from the humanthermodynamics.com website, were of poor quality, and thus reflecting poorly on me. So I began editing. With this said, the proposed attachment is fully-referenced, there is no hidden agenda, there is no advertising, java applets, fees, etc., it is only there for those interested in a molecular perspective of evolution, not just Darwin evolution, or genetic evolution, chemical evolution, etc., but full evolution: 13.7 BYA straight through to the present.
Let me remind us all that wikipedia is a group project. Yet trying to add contributions editing contributions to the actual text of this article seems to be a big ordeal. Unless someone wants to rename this article as Evolution (biological) and start a new article Evolution (general), or have me add content into the article in small amounts, then I don't see how this article fully reflects on all groups interested in evolution from the big bang to the present, which by definition is evolution, in the general sense. If need be, I will be glad to start a new evolution article with a different name, with the help of anyone who wishes to contribute, which fully reflects evolution from 13.7 BYA to the present, which the present article does not.
P.S. the thermodynamics of human life, does not define original research, it is a branch of science over 2,500 years old beginning with the works of Hippocrates, the father of medicine, who theorized that:
“Heat, a quantity which functions to animate, derives from an internal fire located in the left ventricle.”
Lastly, my issue is not with Vsmith (I'm sure we all make both good and bad contributions), I am only asking for people to read the attachment and decide if the "content" is amenable for the evolution article. Thanks again:--Wavesmikey 01:09, 15 December 2005 (UTC)
Let me agree with the other editors above... your link is inappropriate, yopur pushing for it is self-promotional, and your personal attacks on other editors who removed your edits in the past do not help your cause. If anything you've alerted a group of editors to your inappropriate activity and have made more of us likely to revert your edits on sight. DreamGuy 01:31, 15 December 2005 (UTC)
Keep this cruft of my wiki. It's pseudoscience and doesn't belong. Thank you. Your other articles are going to AfD --JPotter 01:43, 15 December 2005 (UTC)

Reverted Wavesmikey's deletion of discussion, it remains as a record of the discussion. Removal was innappropriate. Vsmith 02:29, 15 December 2005 (UTC)

Link is inappropriate, don't include. One puppy's opinion. KillerChihuahua?!? 03:03, 15 December 2005 (UTC)

Sections in limbo

Folks, I must say I think this article is looking much tighter recently. Two sections that seem to be in limbo are "Ancestry of organisms" and "History of life". I'm not sure what the best place for these things is... Graft 20:45, 15 December 2005 (UTC)

Suggestions. We need suggestions. Don't be so shy. WAS 4.250 22:29, 15 December 2005 (UTC)

What about you, eh? I'm not being shy, I honestly don't have any good idea. I think some further reorganization is still in order, specifically moving the "fact vs. theory" discussion earlier, before the "evidence of evolution" bit. That whole latter section might belong in a discussion of the "Fact" of evolution, perhaps broadly under the rubric of "Common descent". So:
  • Fact vs. theory bullshit
  • Common descent
    • Fossil evidence
    • Genetic evidence
    • Morphological evidence
    • History of life (synthesis from the above)
That's my suggestion. Satisfied? Graft 22:53, 15 December 2005 (UTC)

"Matter cannot organize itself"

I'm confused by the significance of the statement in the Misconceptions section, "Matter cannot organize itself." The article should explain 1. what this means. 2. why it would be in conflict with evolution. 3. why it is wrong. 4. why anyone would think it is true (its historical context). Theshibboleth 04:43, 16 December 2005 (UTC)

I got it from a cardinal, and posted in the talk page above, but I'll do a cut and paste for ya:
"Common sense tells us that matter cannot organize itself," he said. "It needs information to do that, and information is a manifestation of intelligence." - Vienna cardinal draws lines in Intelligent Design row
To answer your excellent questions, I assume it speaks to abiogenesis and their skepticism thereof. Historically speaking, not sure if you'd find much, as I had previously outlined (it has been removed by the revision process), this is a neo-creationist position... so my understanding was its a relatively recent assertion. - RoyBoy 800 05:19, 16 December 2005 (UTC)

I think the actual law that is being referred to in this case over this particular "Misconception" is the Law of Entropy, as I understand it not only does it imply that all things lose energy over time but that they also become more chaotic as they do so? Certainly the order exibited in the Earth would therefore interfere with that and imply that it was never less ordered (And thusly started out organized and, logically flowing from that, created) , but I might be wrong on this being the Law of Entropy, at any rate, just some food for thought :/ Homestarmy 02:41, 29 December 2005 (UTC)

Whatever increase in order is produced by biological processes is far offset by the amount of entropy they produce. That's why, for instance, even a minimally active or comatose person needs food and oxygen (converting chemical energy to heat), to maintain the complex structures. Activities like thinking and moving produce even more entropy. Despite the order created by life on earth, far more order has been lost. — Knowledge Seeker দ 03:14, 29 December 2005 (UTC)
  • For what it's worth, if the 2nd Law of Thermodynamics was really as prohibitive as you thought, day-to-day life wouldn't be possible. It is possible, therefore your conception of 2LoT is wrong. Modus tollens, QED. --Cyde Weys votetalk 03:17, 29 December 2005 (UTC)

Knowledge Seeker, I can understand biological processes creating far more energy expenditure than there would be without them, but despite that, wouldn't biological life still count as becoming increasingly more ordered and complex under the theory of evolution? I mean first we had a puddle of goo, then a cell, then bigger clumps of cells, then cells that made themselves into lots and lots of patterns, and then algae and trees and starfish and flowers etc. etc., you see what I mean? Im not saying more energy isn't being lost per se through biological life, but how exactly does evolution embrace the idea that the creation of life has produced less order in living beings as time has moved on? :/ Homestarmy 22:11, 29 December 2005 (UTC)

Because thermodynamics is about energy and heat, not order, it's not an issue. Living (and non-living) things on earth can tie up energy temporarily because we are constantly receiving additional energy from the sun. thx1138 12:40, 4 January 2006 (UTC)

Well I don't mean all thermodynamics, im just talking specifically about the Law of Entropy here, I think that's what the person who brought this topic up at first was trying to discuss, and this specific law does indeed say that all things must tend to proceed to a state of less and less organization :/. Homestarmy 13:58, 5 January 2006 (UTC)

There is no Law of Entropy, its the Second Law of Thermodynamic. And it states that disorder will increase a *closed system*. Earth is not a closed system. Varith 14:40, 5 January 2006 (UTC)
The second law of thermodynamics, in a concise form, states that the total entropy of any thermodynamically isolated system tends to increase over time, approaching a maximum value. Read and enjoy. Since the good cardinal thinks matter cannot organise itself, presumably he thinks that God individually crafts snowflakes, but others think She has better things to do with Her time. ...dave souza 18:20, 5 January 2006 (UTC)
It is a popularized misconception that the second law of thermodynamics has anything to do with order as order is normally thought of. Visualize a universe that consists of nothing but a gallon of steam. As time passes, photons remove the heat and the water molecules form beautiful perfectly symmetrical snowflakes. This transformation from steam to snowflakes and photons represents a loss of useable energy and that is what the second law is refering tp. A human comparing the perfect ice crystal flakes to the unstructured steam would be right in saying the snow flakes possessed more "order". The 2nd law DOES NOT say as time passes there will be more disorder (as the tern is commonly understood) EVEN in a closed system. In arguing about this decades ago with a close friend, I had to explain "The second law is a math equation. ALL transformations of that equation into common English terminology will misrepresent it." WAS 4.250 18:26, 5 January 2006 (UTC)
Says here that "the second law is only a tendency, hence, it is only means that it is highly unlikely that entropy will decrease in a closed system at any given instant." how does entropy decreasing not equate to the creation of order, and if it can't be translated into common English at ALL, how can you say what it isn't if we can't even say what it is? If it can only be used as a mathematical formula, how can anyone actually talk about it and have any chance of representing it properly? and not to nit-pick, but in your example, if there is nothing but a gallon of steam where did the photons come from? Sorry about all these questions it's just im having a hard time understanding this here :/ Homestarmy 16:13, 6 January 2006 (UTC)
The second law is really just related to probabilities. When a physicist says something is "highly unlikely" it means "probably won't happen once in billions of years." There are certainly real life examples of the second law of thermodynamics. Let's pretend that you have a hot tub with an insulated, waterproof sheet splitting it down the middle so that water on one side can't get to water on the other side. Now let's pretend that on one side you have hot water and on the other side you have cold water. Now, if you remove the sheet, the second law says that the hot side should not get hotter, and the cold side should not get colder. Instead, it can at best remain the same, and will most likely begin to even out. Before you remove the sheet, the system is more ordered than when you remove it. The second law is so fundamental and obvious that sometimes people can't even see it. However, (this has been said many many times) it assumes a closed system, which the Earth alone is not. The Sun provides an influx of energy to the Earth that can be used to increase organization. --Ignignot 16:43, 6 January 2006 (UTC)

Ignignot is absolutely correct. If s/he doesn't make sense to you, Homestarmy, let me try to explain it in more detail. The second law of thermodynamics basically states that energy cannot be created without expending energy; therefore over time all energy will be dissipated. Note that even in this formulation the creation of energy is possible. But the 19th century saw a revolution in our understanding of all so-called laws of nature. Perhaps you have heard that in the 17th century some physicists claimed that the universe worked like a clock - that is, a system in which there is a mechanical relation between cause and effect. Some believed that if you knew the position and direction of movement of all the contents of the universe, and the laws that govern the universe, you would know without any doubt what the state of the universe would be at any future point in time. In other words, the laws of nature were thought of as deterministic. The revolution in the 19th century was to replace this deterministic view with a probabalistic view; much of the credit goes to Pierre Simon Laplace, and its foundation is the law of errors. When you roll two dice, you always end up with a combination of two numbers which can be added together to form one number. Some combinations (2 and 3, 3 and 4) lead to different sums; some combinations (2 and 5, 3 and 4) lead to the same sum. We can work out a table of all the possible combination of numbers, and determine that certain sums are more likely than others. You can chart thse sums on a piece of graph-paper and come up with a bell-curve. And then, a person can actually roll two dice over and over again a thousand times, recording what sums actually come up, and the results will more or less conform to that bell-curve. Now, apply this to physics. Say astronomers want to calculate the position of a star. A hundred astronomers make a hundred calculations. Mot of them are actually different (for any number of reasons, there are tiny errors in the observations and calculations). Nevertheless, you can arrange all the calculated positions on a piece of graph paper and — come up with the same kind of bell-curve you get rolling dice. We have a range of contradictory data, but assume that the top of the bell-curve is the "right" answer. Laplace was so important because in his study of "celestial mechanics" (where planets and stars and satellites are located, and how their positions change over time) he openly acknowledged that his analysis was probabalistic. That is, he made a very strong, compelling argument that when studying nature, we can never, never, never ever come up with certainties, only with very high probabilities.

Then, the physicist James Clerk Maxwell applied Laplace's ideas to the study of heat (here is where entropy comes back in). Recall that the "law of entropy" applies to a closed system. Okay, let's say you have a sealed container (thus, a closed system). The temperature within the container is determined by the velocity of the molecules within it (faster molecules collide more often producing more heat). But the fact is, molecules are moving at different velocities. Now, how can one measure the velocity of all these different molecules? The measure of the temperature of the gas within the container is an average. Maxwell claimed that the different velocities of the molecules are distributed just like the different erroneous observations of astronomers, just like the different sums of the roll of the dice, in other words, by that bell curve established by the law of errors (the math is a little more complicated but this is the basic idea).

In other words, the second law of thermodynamics is not deterministic, it is probabalistic. Maxwell then came up with a thought experiment to see what the implications of this would be. First, he supposed that within this closed vessel is a partition, a wall dividing it into two and there is a small hole, and that we can control the opening and closing of the hole so that faster molecules are allowed to pass through from side a to side b, and slower molecules can pass through from side b to side a. Without any work (i.e. without actually changing the velocity of the molecules) we can make side a cooler and side b warmer. This would violate the second law of thermodynamics.

Maxwell's point is not how the second law could be broken. He used this "thought experiment" to reveal a fact about the second law when it is not broken. Let's say that this partition and hole do exist, but we cannot control which molecules can move (this is more like the real world). The temperture of the vessel will appear to remain constant only because the chance of a faster molecule moving from side a to side b is the same as the chance of a faster molecule moving from side b to side a. The chance of a slower molecule moving from side a to side b is the same as the chance of a slower molecule moving from side b to side a. The even distribution of molecules moving at different velocities is a function of the law of errors, of that bell curve.

BUT there is always a chance — however slight (like rolling two dice and getting the sum of "two") — that for a while more faster molecules will enter side a, and more slower molecules will enter side b. IT IS JUST A MATTER OF CHANCE, BUT at tht time, side a will become warmer, and side b will become cooler. This appears to violate the second law of thermodynamics IF you believe that it is a deterministic law. But once you understand that it is a probabalistic law and NOT deterministic, you will understand that within this box the temperature will be uniform most of the time for probabalistic reasons, and for probabalistic reasons sometimes one side will become hotter than the other.

To sum it up, Maxwell wrote "the second law of thermodynamics has th same degree of truth as the stateent tht if you throw a tumblerful of water into the sea, you cannot get the same sumblerful of water out gain." The fact is, you can get the exact same tumblerful of water out again — it is just very very unlikely. Physical laws are about chances, not certainties.

Darwin's theory of evolution through natural selection operates in exactly the same way. Finches reproduce and there is a variation in the size and shape of beaks. Before Darwin naturalists thought tht each species had an ideal form, and that any actual member of the species that varied from the ideal was somehow flawed. But Darwin looked at species not in terms of an ideal, but statisticaly. Once could describe the "average" finch, just as Maxwell measured the average temperature of the molecules in the container. But this is nothing more thn an average. Darwin looked at variations among finches not as examples of imperfections, but as natural variation. The variation could even fall along a bell curve, with the aerge beak at the top of the curve, and the shortest at one end of the curve, and the longest at the other end of the curve.

So there is variation within this population of finches, It is unlikely, but possible, that a few finches of a population of a thousand will have very long beaks (they would be on one of the far sides of the bell curve). The larger the population, the greater the chances. A chance event — let's say, soemthing that separates those finches from the others — will lead to the evolution of a new, long-beaked, species of finch. That is the whole point: random forces can create new orders. It is not likely in a small population and so it hardly ever happens in a small population. It is not likely in a short period of time and so hardly ever happens over a short period of time. But when you have a large population over a long period of time, the chances improve. And new species form.

So far from violating the second law of thermodynamics, Darwin's theory of evolution is entirely consistent with the law.

Does this make sense? Slrubenstein | Talk 17:13, 6 January 2006 (UTC)

Yea, it does, but I think its weird how I could be a product of America's fine education system and never have the second law of thermodyanics explained to me like that :D. But there's still 2 things that gets me, if a "large" population like earth's when it supposedly started evolving beat the odds, why wouldn't a galaxy containing like several million orders more of matter, sunlight energy, and raw materials not of been capable of beating the odds in a similar manner? it seems so unlikely that this all was random rather than created that its sort of ridiculous, you know? and in your thing with the Maxwell idea, isn't that saying that statistically the temperature between 2 areas reaching an equilibrium temperature is the same chance as it is for the temperatures to become even more different on each side?Homestarmy 20:04, 7 January 2006 (UTC)

Alas, I think virtually every scientist in the USA is upset at the poor quality of science education at least at the secondary level. To answer your question about Maxwell, no, the chances are not equal, thy are distributed according to a bell curve. See Normal distribution Gauss–Markov theorem and of course entropy. Also, remember that this beating the odds is not a permanent thing. To return to Maxwell's chamber, all he is saying is that it is possible that over time, at one time or another, one side will become hotter and the other cooler. But over time it will most probably all even out. Now let's look at the real world (the universe): Energy is unevenly distributed throughout the universe, and life has evolved on earth and probably other places. Still, IF the second law of thermodynamics is valid (and remember, scientific laws are not laws because some legislature declares them laws; they are just models based on observation; it is always possible that new observations in the future will require us to revise or reject the second law of thermodynamics. For example, astrophysicists and cosmologists still argue over whether "dark matter" exists and if it does what consequences that has for the universe), entropy will increase over time (but as far as I know there is no reason to think that it will increase at a steady rate). Sooner or later the sun will turn into a red giant or go nova and then exhaust all its energy. Life on earth will all die out within about two billion years.Slrubenstein | Talk 19:53, 7 January 2006 (UTC)

Purifying selection is identical with balancing, not background selection

I have removed the link to purifying selection in front of the background selection line as I believe it to be erroneous. All kinds of selection remove deleterious alleles by definition. Purifying and stabilising selection are the same, as are positive and directional selection. - Samsara 01:13, 17 December 2005 (UTC)

Siller's article

This is a comment directed at user Marcosantezana. It's great to see you doing so much work on this section. After having a look at the revision history, I am wondering, why did you include the Siller article? The article is quite specific in scope, and in my personal view does not work well for general reading. - Samsara 01:13, 17 December 2005 (UTC)

Rooted tree?

As far as I know, it has not been possible to root the tree of life. As such, I would suggest we find a picture without a root indicated, unless anyone can produce a recognised citation to the contrary. - Samsara 01:17, 17 December 2005 (UTC)

I'm not sure I understand. Are you saying that not all known examples of life share a common organism or that we can't identify such an organism? Alienus 01:22, 17 December 2005 (UTC)
We don't know where it sits. We don't know whether the root should be between, say, bacteria and archaea, or archaea and eukaryotes, or even within archaea or any of the other two groups. Unless we obtain a lot more sequence data and as a side-effect, a lot more information about relative rates of evolution, it will not be possible to place the root to this tree. Classical tree-rooting relies on outgroups. This tree has none (unless we find them in outer space somewhere). Also note that even outgroups are chosen either as a best guess, or from rooted trees that rely on other outgroups, so strictly speaking, it is a recursive problem! - Samsara 01:30, 17 December 2005 (UTC)
Ok, that's a reasonable point. I would add that, even if the tree is accurate, it's zoomed out a bit too far to be a good example. Maybe we could substitute something more concrete and well-studied, such as primate evolution. Alienus 01:34, 17 December 2005 (UTC)
I think the tree of life is good to have at the top; I just think it should be unrooted, like this, for example (although it's probably not as visually appealing to the average reader). I'll try and find a better one on PLoS Biology - all of theirs should be suitable for use on wikipedia. Cheers. - Samsara 01:44, 17 December 2005 (UTC)
Most of the trees that I was able to find indicate a root, although sometimes less invasively, as here and here. While the former is somewhat visually appealing, only the latter is known to be available under an open license. The former would need an inquiry. I have contacted the presumed content owner for clarification. I meanwhile, people could comment in case they like the old picture better - I have added a little note in the picture caption about the position of the root being controversial. - Samsara 02:20, 17 December 2005 (UTC)
I've asked the copyright holder of the first link in the above post if we can use it, but she rejected. Since lots of images seem to have been generated from the data it's based on, including the one currently at the top of Evolution, it might not be so bad to make a copy of it? Thoughts? - Samsara 23:37, 20 December 2005 (UTC)
I can easily make a new version of that one... however, I think we should install caveats about the whole thing in the caption, including the notion that the tree of life may not be a "tree" at all. Graft 05:18, 21 December 2005 (UTC)
I've actually made one but was put off submitting it due to the fact that it was very similar to the one published by the Biorealm group. I could submit it for people to make suggestions for obfuscation if necessary.
I've also changed the caption for the tree picture page. Not sure how to change the caption displayed in the article, though. - Samsara 10:34, 21 December 2005 (UTC)
Okay, here we go - comments welcome; colours, positioning, rotation, anything? Easy to change. - Samsara 13:23, 21 December 2005 (UTC)
It ought to be a PNG, not a JPEG... JPEG is terrible for flat-color images like diagrams and charts (gets all splotchy). Also I'd get rid of the big circular bubbles and color the branches instead, possibly making them fatter. Graft 18:29, 21 December 2005 (UTC)

Scaled to size of current front page insert. - Samsara 13:27, 21 December 2005 (UTC)

I suggest replacing the root with a circle that includes a bit of the surrounding three circles and unlabeled, labeled unknown, labeled gene pool, or some such thing. WAS 4.250 17:40, 21 December 2005 (UTC)

Hi WAS 4.250. Thanks for the comment. I'm not quite sure what you mean. Could you explain in more detail? Thanks.
I'm also now thinking it might be an idea to place "bacteria", "eukaryotes" and "archaea" on the branches leading to these groups. However, this would necessitate indicating a sort of confidence interval for the position of the root, as in this version, so that it's clear that they are meant to be monophyletic groups. The big bubbles around the three groups could be misleading in a number of ways. - Samsara 17:08, 22 December 2005 (UTC)

further discussion

  1. The examples given by Samsara all have a "root".
  2. The nature of the "root" is unknown to science.
  3. A tree of life indicating that or else a subset of the tree of life would be more ... evidence based. WAS 4.250 02:59, 17 December 2005 (UTC)
  1. I am aware of this; however, the root could be edited out easily, and is indicated in a more suggestive fashion in the first place.
  2. I'm not sure what you mean. I haven't met anyone recently that's suggested that any of the life forms currently on Earth does not share a common ancestor with any other - there is good evidence from the biochemistry that all life does have a common origin.
  3. Agree. - Samsara 03:40, 17 December 2005 (UTC)
I had this in mind. WAS 4.250 20:07, 17 December 2005 (UTC)
Well, horizontal gene transfer is only possible among organisms that already share basic mechanisms; most importantly, the two organisms would have to have the same mechanism for transfer of genetic material, i.e. DNA, RNA, protein, or some other construct, since extinguished. It is true that networks are now used to represent the relationships within some taxa, although that is simply brushing over the fact that there are underlying trees that now overlap, as each haplotype block is still inherited unidirectionally, from progenitor to offspring. - Samsara 21:19, 17 December 2005 (UTC)
"According to Gogarten, Horizontal Gene Transfer or HGT leads to a radical new organizing principle. Gogarten's and his colleagues work shows that genetic information is not only handed down from ancestor to descendent, but also is exchanged horizontally among and between contemporaries; even among different species and sometimes even between species belonging to different domains. Because evolution was first discovered and studied in animals and plants, the standard belief in biology has been that genes would mainly be transferred vertically, but in the microbial world, this paradigm does not appear to be the best way to explain what occurs. The frequent exchange of genetic information among organisms requires a reassessment of traditional ideas." [1] "While horizontal gene transfer is well-known among bacteria, it is only within the past 10 years that its occurrence has become recognized among higher plants and animals. The scope for horizontal gene transfer is essentially the entire biosphere, with bacteria and viruses serving both as intermediaries for gene trafficking and as reservoirs for gene multiplication and recombination (the process of making new combinations of genetic material)." [2]. WAS 4.250 21:27, 17 December 2005 (UTC)
Well, do note that viruses are usually left off such trees, since they are not usually considered living entities, and because their sequence is not usually sufficiently homologous to other organisms to allow meaningful alignments to be made. In fact, the household genes commonly used in such comparisons, such as genes for ribosomal RNA, are exactly what is missing in most viruses - they often have just an envelope, less than a handful of genes to get them into and out of host cells, and some basic kit to get their RNA or DNA replicated. But with respect to replacing the picture of a rooted tree, I'm not sure what you're suggesting. - Samsara 21:40, 17 December 2005 (UTC)
subset of the tree of life WAS 4.250 23:45, 17 December 2005 (UTC)
continued below at "Tree of life, viruses, continuation of earlier nested thread" WAS 4.250 00:39, 18 December 2005 (UTC)
All of this is not quite accurate. While it's not possible to "root" a tree in a phylogenetically satisfactory sense without an outgroup, that doesn't mean you don't know where the root belongs. As an example, consider human, chimp and baboon. It's evident that human and chimp are sisters and baboon is the outgroup just from sequence, and we need not be that confused by it. However, placing a root along the gorilla branch is very difficult without an outgroup, since it's hard to say how much of the human-chimp vs gorilla divergence is due to gorilla evolution and how much is due to human/chimp evolution. But we should be able to at least decide the correct topology of the tree without an outgroup. And topology is all we're concerned about in this case. Not that deciding the topology is EASY in this particular case (no sir) - we just don't NEED an outgroup. Graft 04:12, 17 December 2005 (UTC)
Graft, you are neglecting the important assumption, implicit in human-chimp-gorilla comparisons, that rates of evolution are the same in gorilla, chimp and human. In many phylogenies, this assumption is flawed, and it's too close to bed-time for me to think about how you actually test for rate equality without confounding the rest of your comparisons, or using the same data twice! - Samsara 04:22, 17 December 2005 (UTC)
You're right, there are of course difficulties with doing reconstructions in this way. But I only mean to say that there are ways to judge tree topology that don't involve outgroups. I think for the tree of life the problem is more that the data is so old and fractured, confused because of horizontal gene transfer, and maybe the truth is that there IS no tree to begin with, there's a ring!
This is obviously still an open question, though, so I don't think we should fret about it too much - just point out that the rooting is in dispute and stick with something reasonably pretty. Graft 07:18, 17 December 2005 (UTC)

FWIW, there's a discussion of the problem of rooted vs. rootless trees in Dawkins's The Ancestor's Tale, near the end. Basically, depending on which information we're comparing we can come up with different roots. And yes, horizontal gene transfer does rather bollix the whole do. --FOo 23:53, 17 December 2005 (UTC)

Continued below at "Tree of life, viruses, continuation of earlier nested thread" WAS 4.250 00:39, 18 December 2005 (UTC)

Pictures in this article: Stephen Jay Gould?

I'd like to question the rationale for including a picture of Stephen Jay Gould. There are theories in evolution that are more accepted than punctuated eqm, and there are minds that are more important and should follow more immediately after Darwin. These are Mendel, Alfred Russell Wallace, T.H. Huxley, Haldane, Wright, Fisher, Dhobzhansky, George Gaylord Simpson, Mayr. - Samsara 04:55, 17 December 2005 (UTC)

I thought it was too close to bedtime... Anyhow, yeah, I'm ok with Gould being replaced by someone whose scientific accomplishments are more significant and relevant. Alienus 05:02, 17 December 2005 (UTC)

I recommend Mayr. --Rikurzhen 06:19, 17 December 2005 (UTC)

If anyone has a picture of him, R.A. Fisher is my favorite. I think I use Fisher's exact test every day. Graft 07:19, 17 December 2005 (UTC)
his picture's a bit grainier. --Rikurzhen 07:52, 17 December 2005 (UTC)

the pic of WD Hamilton is aweful. --Rikurzhen 07:56, 17 December 2005 (UTC)

Image:W D Hamilton.jpg

Shouldn't be a problem finding a better one... there's a website dedicated to him with some nice additional pictures. I also seem to remember that Alan Grafen's Biographical Memoir of Hamilton had a nice pic that we could probably use. - Samsara 13:03, 17 December 2005 (UTC)
Perhaps we could also edit out the orange in this one? Looks a bit glaring... - Samsara 13:04, 17 December 2005 (UTC)

Tree of life, viruses, continuation of earlier nested thread

Sorry for the "horizontal tranfer" so to speak of a deeply nested thread and the end of a subsection to here, but it seemed the thing to do.

On the table are two related issues: choice of the intro image and representation of "tree of life".

Subset(s) of the tree of life might be better or might be a good addition.

An "unrooted" tree of life is closer to the evidence (think communal pool of genes replacing an adam and eve bacteria).

Here is what the tree of life looks like at the twig level.

Life, like a river, is more a process than a thing and some things play a greater part in the process and some things playa lesser part. Viruses play a big part, mutate, evolve, have genes. So they can't survive without other life forms. Same with humans. Only plants are "life" because they can do it without the rest of the ecosystem? I guess plants that need insects to pollinate aren't alive any more than viruses.

Communities of life evolve. The division into parts is sometimes useful and sometimes not. WAS 4.250 00:50, 18 December 2005 (UTC)

Conveniently, wikipedia has a section Life#Defining the concept of life. As for a subtree, I would recommend Drosophila, as it's very well studied and uncontroversial; the latter is probably rare to find. I also like the H5N1 example because it's topical and people won't care too much about the exact structure because it's very transient in any case. If they get it roughly right, it's a success. Maybe I'll have time to hunt a Drosophila example later. - Samsara 01:39, 18 December 2005 (UTC)
I'd recommend the vertebrate phylogeny, actually. It's pretty well-studied and much more familiar than Drosophila. Here[3] is an accurate mammalian tree... it's pretty easy to duplicate this if someone wants to make a better one. Graft 05:26, 18 December 2005 (UTC)
Yes, it would need to be shrunk a bit. The link doesn't work in Firefox 1.0.7 btw, you just get a page telling you off for externally linking to it. - Samsara 11:39, 18 December 2005 (UTC)

Here is the "tree of life" showing the evolution by reassortment of H5N1 that created the Z genotype in 2002 and here is evolution by antigenic drift that created dozens of highly pathogenic varieties of the Z genotype of avian flu virus H5N1, some of which are increasingly adopted to mmammals. Evolution. Right before our eyes. WAS 4.250 23:13, 18 December 2005 (UTC)

Linkage

I put in a discussion of linkage and heterozygosity. It's somewhat ancillary to the subject, although the study of haplotypes and linkage is invaluable to evolutionary biology... I'm sure this is probably not clear to the lay reader and won't ever be. Do people think this discussion is going too far afield? What sort of limits on scope should we have here, to keep ourselves from running loose with the genetics? Graft 06:56, 19 December 2005 (UTC)

Please don't dumb anything down. That said; I don't understand "Deviations from the ideal, random distribution of alleles may appear in the form of decreased heterozygosity - that is, the fraction of the population which has one copy of each allele.". WAS 4.250 07:12, 19 December 2005 (UTC)

Species that reproduce by sex have heterozygosity; they carry a different versions of most genes on each of the two corresponding chromosomes. You are saying something about those versions being the same rather than different. I don't get what you are saying. Ideal? Random? I don't know what those words mean IN THIS CONTEXT. WAS 4.250 07:23, 19 December 2005 (UTC)

In a population where alleles are truly independently assorted, with frequency p and q = 1 - p, the frequency of heterozygotes is 2pq. However, this is not necessarily the same as the ACTUAL frequency of heterozygotes. Graft 07:45, 19 December 2005 (UTC)
Graft, why did you take out the bits about twofold cost of sex? It seems to me if we're discussing sexual recombination at all, that belongs in there. - Samsara 11:17, 19 December 2005 (UTC)
If you meant the parasitism, I thought that was inaccurate... most sexual organisms aren't parthenogenetic, so the female haploid gamete can't really be said to be an independent organism. I chopped that bit about half-the-rate because I meant to put it in somewhere else as "half the effective population size" (once the reader knew what effective population size was), but I forgot. Graft 16:50, 19 December 2005 (UTC)
The parasitism is an analogy that is often used. In fact, there is a species of ant where males and females are effectively different species; the male simply abuses the female for reproduction. Their genomes do no longer mix. I can try and find that reference if required. But essentially, it's just a useful way of thinking about the fact that the male contributes little to reproduction in the vast majority of species - other than perhaps a sexy sons effect, which is somewhat tautological.
The effective population size for any given locus actually decreases dramatically when you lose meiosis-syngamy, as the most selected locus on any given chromosome in the population determines the fate of all other variation on that chromosome! Hence, effective population size is not a particularly useful concept w.r.t. sexual-asexual comparisons, nor does it have any direct connection with the twofold cost! - Samsara 17:09, 19 December 2005 (UTC)
These are two different ideas at play here: one is the benefit of recombination, and the other is the fact that because males can only mate with females (as opposed to truly random mating, e.g. with a fully hermaphroditic population), there is a reduction in effective population size.
As to the ants example, if it's the one I remember, both males and females are fully parthenogenetic in that species, and their offspring are sterile. You're right that there are some examples where males can be seen as parasitic, but that's a small minority of cases, and even there I think the analogy is poor. Graft 17:19, 19 December 2005 (UTC)
Different ant. I'll find the reference when time allows. I think it was a talk at a recent conference I went to, so it may not even be published yet. - Samsara 17:01, 22 December 2005 (UTC)

ANti Anti Proof against evolution

many creationists use this arguments and i´ll tell why they are wrong and work.

  1. Evolution has never been observed.
  2. Evolution violates the 2nd law of thermodynamics.
  3. There are no transitional fossils.
  4. The theory of evolution says that life originated, and evolution proceeds, by random chance.
  5. Evolution is only a theory; it hasn't been proved.


  1. it have been, a fly were onces different races that could mate (still the same species) then 20 years later they couldnt mate, wich means they are different species.
  2. no it doesnt, that law only work on closed system, earth isnt, we get low entropy energy from the sun, and it is by life transformed into high entropy heat. Face it. life increase it aswell. If it decrease the entropy by 20 it increase it aswell with 21.
  3. the chance of all individuals becoming a foosil is so small, like in sweden the chance for one of us become a fossil is very small, its even small that anyone in the world today shall. So its logical that the arts in the middle get jumped, and if the differens is to small they fall in the same species as the one before or after.
  4. it did, if we put a bacteria in a ppol of water, where we have 2 places spitting out different chemicals they will evolve into 2 different specieses that live on each chemical spitter, wich im pretty sure have been shown. we have 2 different specieses from 1.
  5. it have been proved, this is acctualy one of the stupidiest arguments you can come with. A theory can be prown and still be called theory, einsteins theory of general relativity have been so proved as it can and is still called a theory. —The preceding unsigned comment was added by 217.208.244.194 (talk • contribs) 15:33, 19 December 2005 (UTC)

Edited for formatting but not for anything else (including even capitalization). --Cyde Weys talkcontribs 20:39, 20 December 2005 (UTC)

I'd suggest that if you want your anti creationist arguments to be taken seriously that you not use putrid grammar and putrid spelling. --Cronosquall 04:29, 2 January 2006 (UTC)

Ecological niche

Hi RoyBoy, I removed your edit because there is some research indicating that new niches keep becoming available. - Samsara 21:25, 19 December 2005 (UTC)

Stable niches? I'm willing to concede the point and felt it was possible when I wrote it; I'd think that would call for a tweak rather than a removal. I'll follow your lead. - RoyBoy 800 21:34, 19 December 2005 (UTC)
Actually keep in mind the context is about "kinds", not species. - RoyBoy 800 21:35, 19 December 2005 (UTC)
Well, I've thought about that for a few minutes, and I don't see how acknowledging that some ecosystems may be full up (surely not with the current mass extinction?!) makes the point any stronger. In fact, it seems almost contradictory because we can observe allele frequency change even in populations in ancient and pristine ecosystems, whenever the species have sufficient turnover rates for us to have any hope of observing change within a human lifetime.
Hmm... maybe it would fit in some other part of the article... - Samsara 21:56, 19 December 2005 (UTC)
Right. I've put a rudiment of your argument in speciation - please do edit it as you see fit. I think it's a better place, and that page needs some work in any case. See you there? Cheers. - Samsara 22:05, 19 December 2005 (UTC)

There really isn't any such thing as a vacant niche, so to say that "new niches become available" isn't really accurate. A niche is defined by two factors, the plant itself ("fundamental niche") and interactions with other species ("realised niche"). A species can expand its fundamental niche evolutionarily, or it can expand its realised niche either evolutionarily (by gaining some advantage over other species) or through the disappearance of a competitor. However, gaining an advantage over another species is likely to act as a selective pressure on that species (as in the Red Queen hypothesis), which expansion of the fundamental niche may result in disruptive selection (since there is likely to be some cost or trade-off associated with exploiting a new resource). It's worthwhile to note that, for almost all (if nto all) trees in North America for which it has been tested, optimal growth is at the southern end of their range - assuming a Gaussian or peak and tail distribution, optimal growth should be at in the middle of their fundamental niche. So, it would appear that competition keeps trees away from their optimal habitat - the realised niche is skewed far off from the fundamental niche. So the idea of stable niches, empty niches or new niches is an unreasonable simplification, if not flat out inaccuracy. Guettarda 22:25, 19 December 2005 (UTC)

I'm going on gut feeling that if an ecosystem is relatively stable fundamental new types (taxa?) of species (new kinds) would find it difficult, if not fundamentally impossible to evolve. As established "kinds" would simply speciate to fill niches as they come about. I think it important to include this meme here, not on speciation. While my initial edit was misleading and inaccurate I consider the meme important to rewrite and include here. - RoyBoy 800 22:39, 19 December 2005 (UTC)

About "if an ecosystem is relatively stable"; there is no "balance of nature"; nature is in constant flux: both the physical world and the biological world change:day/night. summer/winter, species invation, biological mutation, hurricane, meteor strike, ice age, ... Ecosystems are NEVER stable. Their parts change as fast as they can just to keep up with each other. WAS 4.250 23:51, 19 December 2005 (UTC)

Isn't "parts change as fast as they can just to keep up with each other" a balanced stable (stable does not mean static) ecosystem? And that's the whole point; it takes world changing events (ice age), meteor to make room for new "kinds" to come about. Our ecosystem has been quite stable over humanities time here; I want to clarify that for creationists; and that plays a role in "kinds" not popping up as there is no room (no need) for new kinds if existing kinds can speciate to fill niches. - RoyBoy 800 16:52, 20 December 2005 (UTC)
When population geneticists talk about macroevolution, they usually mean speciation. And speciation is happening all the time in taxa that most of us pay little attention to - fruitflies, nematodes, bacteria, viruses (the last two obviously needing customised definitions of species due to their reproduction working in a different way). Just see the H5N1 example in the tree discussion, above.
Now, it is fair to say that we don't see as much of that in higher animals such as vertebrates, since they have mostly internalised the coevolutionary response - I suspect this will be described somewhat in immunity.
I think I saw an article on niche construction, which is essentially the process by which species are added. Typically, this can be observed in microcosm experiments, where one species uses one substrate for nutrition, and produces a waste product, on which yet another new species can feed, and so on (admittedly not quite ad infinitum in any closed system, but most observations suggest that Earth is far from eqm). - Samsara 17:20, 20 December 2005 (UTC)
With regards to stability and the recent period - we are still very much in transition from the last ice age - for example, more Canadian earthworms are European species - North American species had not yet recolonised large areas post-ice age.
As for the creationist argument about "kinds" - it's just rubbish. The reason you haven't seen new families arising has to do with the rate of evolution. Some families are rooted a million years ago, some ten million years ago - if the split that will lead to a new family happened 1000 years ago, we would probably still see the sister taxa as members of the same genus. Asking why we haven't seen new "kinds" arise is like asking why we haven't seen more ice ages. Guettarda 17:47, 20 December 2005 (UTC)
If you think that's adequately conveyed by the millions of years, that's coo, but I wanted some icing on the cake. Gimme tasty CAKE you guys! - RoyBoy 800 20:25, 20 December 2005 (UTC)

Complete bias towards biology

Evolution is not the sole domain of biology. On the contrary, both Darwin and Wallace were inspired by Malthus (who is not even mentioned on the page). Malthus was thinking of social and economic evolution, not of biology. The reason evolution is so strongly associated with biology is that it can actually be proven there (yes, I know this is disputed), and both Darwin and Wallace understood that perfectly well. But we have evolutionary economics, evolution of languages, evolution of networks, and many other fields of science where systems evolve by quasi-random generation and selection of individuals. Some of them have nothing to do with the genetic mechanism of evolution--string mutation and crossover--yet they are evolutionary systems by all means. Why then are these systems not discussed under evolution? Why is biological evolution not what it should be - an entry called Biological evolution, just as there is an entry Evolutionary economics? (In fact the entry Biological evolution is a redirect to the entry Evolution.)

So, how are we going to introduce such a fundamental change to a featured article that so happens to be the ideological battlefield of this time? My humble suggestion is to first use the entry Theory of Evolution (which also redirects here) to build the entry that should really be called `evolution', and to say so explicitly in the beginning of both entries. Then, if by common consent the new article has reached the maturity it should have to replace such a fundamental article, we could change the redirects. Any ideas? Nannen 19:09, 20 December 2005 (UTC)

Yes. See the evolution (disambiguation) article. The decision was made long ago that this, the biological meaning, is far and above the major meaning of the word "evolution" in modern parlance, and thus the appropriate subject for this article. Graft 19:17, 20 December 2005 (UTC)
This is not true. Just have a look at Merriam-Webster. There, biological evolution is listed as meaning number four, out of a total of six. When people speak of the evolution of a song for example, they do not think of any kind of random cross over between songs, simply because "biological evolution" that is not the major meaning of the word. The modern parlance argument does not hold. Nannen 11:28, 22 December 2005 (UTC)
I agree with the obvious consensus here. M-W doesn't rule. And please don't change other user's words. I replaced the ::Yes indeed. in DS comment below and fixed the indentation. Vsmith 12:25, 22 December 2005 (UTC)
I personally get confused with complex indentations and didn't want to create the impression DS meant my statement and not that of Graft. My apologies to DS. Nannen 13:15, 26 December 2005 (UTC)
Yes indeed. A minor point: I don't think the Reverend Thomas Malthus was thinking about evolution of any kind, and certainly his Whig followers were very much against both evolutionism and the Radicals who were promoting it to undermine aristocratic society. ....dave souza 20:47, 20 December 2005 (UTC)
Yeah, Malthus was not thinking about evolution, not even evolutionary economics. Evolution is not the same thing as the Malthusian problem; it is more of an "answer" to the problem than being the same thing of it. --Fastfission 17:34, 21 December 2005 (UTC)
I have a question and a point. First, did Malthus actually use the word "evolution?" (not rhetorical, I do not know). Second, I believe Darwin avoided the word. The reason he did is of historical interest. The fact rememans that encyclopedias distinguish between words as used colloquially and as terms of art (or as scientific concepts). When people talk about a quantum difference or quantum leap in ordinary conversation, they actually mean close to the opposite of what scientists mean. And dictionaries should acknowledge that. But this is an encyclopedia, not a dictionary. Encycdlopedias are not compendia of words and how all people use them. They are compendia of accumulated knowledge. It's apples and oranges. Today, people use the word "evolution" in many ways, but the most common understanding of evolution is the theory of the evolution of species. I agree that there are other uses of evolution among scientists (e.g. stellar evolution) which is why we have diambiguation pages. Slrubenstein | Talk 14:12, 22 December 2005 (UTC)
The concept of evolution itself also evolved, and Malthus had an early and important part in it. If I remember correctly, the concept of natural selection is strongly associated with his name. Other scientists contributed or refined fundamental evolutionary concepts like trait, inheritance, mutation, fitness, genotype, phenotype and so on. It is a fundamental mistake to attribute the theory of evolution to any one particular scientist or instance in time. This is one of the reasons why I need an entry about evolution in general, to sort these things out. To discuss Malthus in the context of biology is really not serving the topic. Nannen 13:15, 26 December 2005 (UTC)


Maybe I should make the problem more precise: I usually have to do with evolution in two contexts, both of which have little to do with biological evolution: natural languages and economic innovation. Some colleagues of mine are physicists and use evolution in yet another nonbiological way. There is quite a body of theory and thought behind this broader scientific view on evolution where biological evolution would be just another case, but certainly not the dominating one. The annoying thing is that there is no entry where you can formulate this broader view on evolution as both the terms 'evolution' and 'theory of evolution' are taken by 'biological evolution'. Even more annoying, wikipedia suggests that evolution and biological evolution are effectively the same, which is just not true. And it is really not sufficient to discuss evolution as used in the context of languages and economic innovations in their respective entries, as suggested by the use of the disambiguation advocates. Each of these entries, like biological evolution, should not need to discuss the concept of evolution any further than is needed for the field, and then refer to the broad entry. And this broad entry should certainly not define evolution in the narrow biological sense of mutation, random cross over and natural selection, because that is not how languages and economic innovations evolve.
What I request for now is to use the entry Theory of evolution, which unfortunately also redirects to biological evolution, to discuss the broader concept. First, because the redirect is really not justified, and second in order to avoid a ridiculous entry like. Evolution for Non-Biologists. Nannen 13:15, 26 December 2005 (UTC)
Nannen, first of all, I would like to suggest that you properly research such matters as Malthus' role in the history of evolutionary thought before bringing them to the table, at the very least before making the second comment here. Malthus was concerned mostly with population growth, and it is in that context that his name is still used - Malthusian fitness, Malthusian growth curves etc.
Second, calling it biological evolution is not justified exactly because evolution is relevant to psychology and biochemistry, and because essentially the same principles apply in evolutionary programming/genetic algorithms and related biotechnology applications.
To my mind, this article does succeed in discussing the principles of natural selection in broader terms (random variation, at least partly heritable, selection, reconstitution of variation etc. ad infinitum), while also keeping the meaning strict. In all ages, people have tried to link their own research to appealing principles borrowed from related sciences. Hence, too many things nowadays have illegitimately taken on the label "nanotechnology". Well, same with evolution, and I think that Wikipedia is playing a much-needed and exemplary role in preserving the strict meaning of evolution.
You may want to have a look at this. Now, to anticipate any further discussion that may arise from perusing the aforementioned source, we talk about evolution rather than natural selection to acknowledge the occasional role of genetic drift in (trying to avoid the word) heritable change between generations. - Samsara 19:13, 26 December 2005 (UTC)

I created Evolution (term). Maybe it will help with Nannen's concerns. Aplace he can work out an article on the term itself, its useage, the evolution of the use of the term, and so on. As for a "broader theory", well, when ripe, it can be removed from Evolution (term) and given its own article. WAS 4.250 22:54, 26 December 2005 (UTC)

On the subject of "In biology, evolution" vs. "Biological evolution", I favour the former, as it does not constrain evolution to only be valid in biology, but allows that it may have the same meaning in other fields, such as psychology, which would seem to fit with this discussion. - Samsara 10:27, 27 December 2005 (UTC)

To me "biological evolution" refers to the genetic evolution that has been identified as the mechanism for creating new biological species. While, to me, "in biology" refers to what is done in the field of biology which can include the use of computers that run programs that exhibit software evolutionary behavior and come up with theories that exhibit evolutionary development of ideas. WAS 4.250 17:38, 27 December 2005 (UTC)

Should "See also" be comprehensive?

I noticed a good number of links that are missing in the "See also" section and I realized it was because they were already distributed throughout the article in the form of "Main article here". It is my contention that all of the links should be at the bottom of the See also section anyway. It didn't make sense that natural selection wasn't there. I'm just trying to get consensus before I make this change. Thanks for the advice. --Cyde Weys talkcontribs 20:16, 20 December 2005 (UTC)

Is there any way that Template:Main can be rewritten to effect this? - Samsara 20:17, 20 December 2005 (UTC)
  • Huh? I don't see how that's even remotely possible. {{Main}} just creates italicized links to the main article. It doesn't have anything to do with the See also section. Heck, some pages that use {{Main}} don't have See also sections anyways. --Cyde Weys talkcontribs 20:47, 20 December 2005 (UTC)
Well, a new template could definitely be created that achieves this. There are other templates that manage to produce links within articles and in a separate section at the bottom, e.g. Template:Babel - Samsara 16:59, 22 December 2005 (UTC)

I recommend adding useful further reading links to the bottom even if they are also used as inline source in the text. The conversion of inline links to links to sources all listed together at the bottom is a related issue. Using the less ambiguous subsection headers "Sources" and "Further reading" is another related issue. BE BOLD ! cautiously ;) WAS 4.250 23:25, 20 December 2005 (UTC)

Semi-protection

I would rather not have Evolution be semi-protected. Is the vandalism worse than usual? I'm not sure I understand why it was semi-protected, and I definitely do not like that large warning on the article page. — Knowledge Seeker দ 10:58, 22 December 2005 (UTC)

Seems to me like it is. Persistent text removal for the last two days, all from similar IPs. Granted, it could just be a very persistent editor who means well, but there doesn't seem to be any way we can explain how the system works to him/her before he signs up for a username. I've put the semi-protection back on for now, will remove it later today. Cheers. - Samsara 11:51, 25 December 2005 (UTC)
I've removed the semiprotection. It should never have been applied in the first place. Raul654 19:20, 26 December 2005 (UTC)
I have now read the policy, and appreciate that it was wrong to apply it. However, I would also be interested to learn how edit wars in which one editor stands alone against the rest, and is not signed in (thus making it impossible to communicate with said editor) are usually resolved. In this case, the editor repeated his edit (a gramatically unsound deletion of an uncontroversial passage) four times.
Furthermore, as far as I understand, the semi-protection was actually removed by me last night. The edit history seems to indicate this, unless there is something deeper about semi-protection that I do not appreciate, in which case, I would like to know! - Samsara 19:40, 26 December 2005 (UTC)

I see no record of you doing anything to change the protection of this article. From special:log:

  • 19:20, December 26, 2005 Raul654 unprotected Evolution
  • 21:43, December 25, 2005 Voice of All(MTG) protected Evolution (no moves, vandalism [edit=autoconfirmed:move=sysop])
  • 21:43, December 25, 2005 Voice of All(MTG) protected Evolution (activate SemiPro [edit=autoconfirmed:move=autoconfirmed])
  • 12:53, December 22, 2005 Splash unprotected Evolution (no reason given for protection, history now showing heavy vandalism)
  • 10:27, December 22, 2005 Fuzheado protected Evolution (one of the most vandalized pages, testing new page semi-protection [edit=autoconfirmed:move=autoconfirmed]) Raul654 19:48, 26 December 2005 (UTC)
Samsara, it does not appear that you are an administrator, which would mean that you do not have the ability to protect or unprotect pages. — Knowledge Seeker দ 20:04, 26 December 2005 (UTC)
Thanks for that significantly more helpful reply! - Samsara 10:19, 27 December 2005 (UTC)

Quotes

According to the BBC: Colin Norman, news editor of Science, said "[S]cientists tend to take for granted that evolution underpins modern biology [...] Evolution is not just something that scientists study as an esoteric enterprise. It has very important implications for public health and for our understanding of who we are" and Dr. Mike Ritchie, of the school of biology at the University of St Andrews, UK said "The big recent development in evolutionary biology has obviously been the improved resolution in our understanding of genetics. Where people have found a gene they think is involved in speciation, I can now go and look how it has evolved in 12 different species of fly, because we've got the genomes of all these species available on the web." [4] WAS 4.250 04:25, 24 December 2005 (UTC)

Or how about this one: "Nothing in biology makes sense except in the light of evolution." - Theodosius Dobzhansky. - Samsara 08:25, 24 December 2005 (UTC)
We have an article on Nothing in Biology Makes Sense Except in the Light of Evolution already, but let's try to keep clear of witty quotes. You can quote Haldane till the cows come home but it won't improve the article and just attract some quote miners with their own. — Dunc|☺ 11:25, 24 December 2005 (UTC)
I'm not sure that the suggestion was to put them in the article... Not my suggestion, anyway! - Samsara 11:29, 24 December 2005 (UTC)

H5N1 and evolution

"Through a series of evolutionary analyses, the six internal genes of human H5N1 viruses were also found to have diverged generally into two distinguishable evolutionary groups." from Evolutionary characterization of the six internal genes of H5N1 human influenza A virus WAS 4.250 04:58, 27 December 2005 (UTC)

Ape chromosomes and human chromosomes

I know that the human chromosome is a result of the merger of chromosomes 2p and 2q in our simian ancestors, but I was unable to find anything discussing this on Wikipedia. I'm posting this message here first as I want to make sure I'm not duplicating before I create an article on it and because it's related to evolution as it is very compelling evidence of our common descent with the apes. Here's a good article with citations. --Cyde Weys votetalk 15:39, 27 December 2005 (UTC)

The image called "Human Chromosome 2 and its analogs in the apes" in the online article you cite gives new meaning to the phrase "missing link". We literally have a picture of a link in humans that links two seperate chromosomes in the nonhuman apes creating a single chromosome in humans. Furthermore, it is truly THE missing link since it is the ape-human connection that is the big deal in the first place. And while the term originally refered to fosil evidence, this too is a trace from the past corresponding to some living beings that when alive were the physical embodiment of this link. Link found. Case over. WAS 4.250 17:30, 27 December 2005 (UTC)

So I was thinking maybe this bit could be added to Chromosome 2 (human) and then linked to from the "Evidence for Evolution" section on this article. What do you think? --Cyde Weys votetalk 17:53, 27 December 2005 (UTC)

Justbob's addition on Hawthorn flies

Justbob added the following paragraph to the evidence of "macroevolution" section: 

However, one needs to also understand that noone knows for sure if these new hawthorn flies
just appered or maybe they were there all the time and noone ever descovered them untill now
so how would they know if they spontaneously emerged? Also we must take into consdieration
the fact that these flies could have been brought with apple trees. Not only that, but the
other thing we must keep in mind is the fact that adaptations do happen, but it was in there
genes to start with that allows things to Adapt to there surroundings. Also if there is
little evidence of interbreeding then that can not be rulled out as a possabillity.

I reverted his changes because they were poorly written, and frankly, I don't think they deserve to be rewritten in better English as these "objections" read like mindless creationist claptrap. "Ohhh, they didn't evolve, they were always there, we just didn't find them until now!" Yeah, uh-huh. Keep non-scientific nonsense out of the article, please. --Cyde Weys votetalk 18:06, 27 December 2005 (UTC)

Some of his concerns are addressed by Evolvability. - Samsara 18:25, 27 December 2005 (UTC)
A while back I saw two other editors have this interaction: some completely off the wall comment added to an article, then reverted with the comment "Original research is not allowed so please provide a source". It's polite, true, gets the job done, and sometimes they are actually right AND have a source! WAS 4.250 18:30, 27 December 2005 (UTC)
Not quite sure what you're implying here. The hawthorn story holds as originally written in the article. Don't go believing that scientists lack scepticism! It can be shown by DNA studies of the two races that they diverged as recently as the hypothesis of divergence post-apple-introduction requires. The explanation given in the article is the most parsimonious for the data. All further discussion should take good note of Occam's razor. - Samsara 20:46, 27 December 2005 (UTC)
You say "Not quite sure what you're implying here." I am sorry for not being clear. Being terse to the point of cryptic is one of my many uncountable failings. My comment ONLY dealt with what to say in the "edit summary". WAS 4.250 22:51, 27 December 2005 (UTC)

Need some expert opinion

Over at Talk:Charles_Darwin an editor has made some changes to remove all references to evolution as a theory and referring to natural selection a the theory and evolution as a proposition/observation. I reverted once, but I thought I'd solicit some opinions here. --JPotter 01:59, 28 December 2005 (UTC)

  • You're right to make those revisions. It sounds like we have some over-enthusiastic "evolutionist" at work (for lack of a better word). Just point him to Stephen Jay Gould's groundbreaking seminal essay, Evolution as Fact and Theory. --Cyde Weys votetalk 02:02, 28 December 2005 (UTC)
    • The actual changes were exactly in line with Stephen Jay Gould's groundbreaking seminal essay; and well done. But his comments in the talk page misrepresented what he actually did. I retitled the talk subsection involved to better represent his actual very good changes. His changes didn't so much represent evolution as not a theory as much as use language that was more clear about whether the use of the word in each instance in the article was evolution as fact or evolution as theory. As it is both as the essay points out. WAS 4.250 20:57, 28 December 2005 (UTC)
      • I've had fun with the adjectives on that essay. At first I just called it by name. Then I said great. Then I said revolutionary. Then I said seminal. Then I said seminal and groundbreaking. I've referenced the article over ten times now on Wikipedia alone and each time I up the adjectives. What do you think is next? "Stephen Jay Gould's better-than-Christ groundbreaking revolutionary seminal essay, Evolution as fact and theory" ... --Cyde Weys votetalk 03:19, 29 December 2005 (UTC)

Common descent

Actually, common descent from a single progenitor really isn't disputed. First of all, all life is related ... it's not like half of it uses a different system of DNA than the other half. Also, using Occam's Razor, the chance of two abiogenesis events occurring and then both of their life products taking hold is vanishingly slim. But the purpose of my edit was to fix the wording in the article, and by reverting a part of it, you just messed up the wording again. --Cyde Weys votetalk 19:36, 28 December 2005 (UTC)

Perhaps disputed is the wrong word. Claiming a single proginator without sourcing is questionable, as at least some noted evolutionary biologists have stated that like the eye, life in general could have arisen in multiple instances. KillerChihuahua?!? 19:42, 28 December 2005 (UTC)
While it is plausible that life may have evolved multiple times, the similarities between extant life forms at a molecular scale (!) are so compelling to eradicate that possibility. Life in all likelihood has evolved multiple times (in the primordial environment, whatever that may have been), of which only one has survived. The evolution of three domains of life is not currently disputed by any respectable scientist afaik. Please give a source if you think I'm wrong. - Samsara 20:51, 28 December 2005 (UTC)

gene pool" rather than "common proginator

From Common descent "A group of organisms is said to have common descent if they have a common ancestor. In biology, the theory of universal common descent proposes that all organisms on Earth are descended from a common ancestor or ancestral gene pool." and "The earliest life-like forms probably exchanged genetic material laterally in a manner that is analogous to lateral gene transfer amongst bacteria. For this and other reasons, the most recent common ancestor may have been a genetic pool rather than an organism."

From Horizontal gene transfer "Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes." [1] Horizontal gene transfer is called by some "A New Paradigm for Biology " [2] and emphasised by others as an important factor in "The Hidden Hazards of Genetic Engineering". "While horizontal gene transfer is well-known among bacteria, it is only within the past 10 years that its occurrence has become recognized among higher plants and animals. The scope for horizontal gene transfer is essentially the entire biosphere, with bacteria and viruses serving both as intermediaries for gene trafficking and as reservoirs for gene multiplication and recombination (the process of making new combinations of genetic material)." and "Biologist Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research" therefore "biologists [should] use the metaphor of a mosaic to describe the different histories combined in individual genomes and use [the] metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes.". WAS 4.250 20:47, 28 December 2005 (UTC)

(I moved the above two comments from Clyde's talk page) WAS 4.250 21:05, 28 December 2005 (UTC)

You get to the "first organism" by Horizontal gene transfer among entities in the earth's gene pool's almost-organisms: viruses and almost-bacteria and whatnot. You don't get to a "first cell" without millions of similar cells just one molecule different and so on back to the first amino acids randomly sticking together. WAS 4.250 21:05, 28 December 2005 (UTC)

In other words, there is no first cell,just a pool of genes evolving into a variety of life forms. Life is a process, there is no neat dividing line between life and nonlife. WAS 4.250 21:10, 28 December 2005 (UTC)

Alright alright you make good points. The better term is, what, "first gene pool"? --Cyde Weys votetalk 21:20, 28 December 2005 (UTC)

Within biological evolution, so far the consensus is use of the phrase "common descent" and the deatil can go to that article. Within the chemical evolution that preceded biological evolution and continues with it to some degree, I'm not sure it makes any sense to draw up any dividing lines similar to the term "first gene pool". WAS 4.250 22:04, 28 December 2005 (UTC)
What about "common descent from a single gene pool" or "common descent from an the ancestral gene pool"? KillerChihuahua?!? 21:59, 28 December 2005 (UTC)

"common descent from an the ancestral gene pool" is accurate at least. We have no firm evidence on the "single" part. Lots of debate tho. WAS 4.250 22:08, 28 December 2005 (UTC)

You are correct, of course. That is almost identical to my original objection to "single progenitor" - I must be getting tired. KillerChihuahua?!? 22:15, 28 December 2005 (UTC)

No one knows the relative importance of 1 outer space molecules 2 molecules chemiclly evolving in clay and other mostly nonwater places 3. Surfaces between air/water or water/land or 3 free floating in water molecules. WAS 4.250 22:13, 28 December 2005 (UTC)

Hang on guys, we're getting into really muddy waters here. In order for any organisms to be sharing genes, they need the whole basic machinery necessary for doing so, and this will come together in one place in space and time, a single ancestor, from which everybody else gets their "Lego". So no matter how much gene exchange, horizontal or vertical, happens later, somebody comes up with a set of Lego that works. And that's the single common ancestor. This is why everybody has rRNA, tRNA, and mRNA as a minimum; almost the same set of amino acids and hence the same genetic code (there are a few deviations in single codon assignments, but most assignments are common to all life today). Also, by the principles of Coalescence_(genetics), there is bound to be a single common ancestor somewhere way back. I oppose the change. - Samsara 23:36, 28 December 2005 (UTC)

You irreducible complexity belief that "for any organisms to be sharing genes, they need the whole basic machinery" is unjustified. WAS 4.250 23:51, 28 December 2005 (UTC)

You were saying earlier about cryptic comments? - Samsara 00:19, 29 December 2005 (UTC)
I don't know which part is cryptic until you point it out and indicate what you didn't get. WAS 4.250 00:53, 29 December 2005 (UTC)
You are speaking of the genetic "Eve", yes Samsara? That much is accurate... but does that make the current wording inaccurate? KillerChihuahua?!? 23:55, 28 December 2005 (UTC)
there is no genetic eve for all things on Earth that evolve or have evolved. WAS 4.250 00:53, 29 December 2005 (UTC)
Yes, the current wording is less accurate than the previous one which referred only to the concept of common ancestry. I would not call it genetic Eve, as I prefer to avoid religious analogies, but I'll give a quick sketch of coalescence. Basically, with the same random sampling that causes genetic drift, you also get the histories of individual genes merging in the past, because some of the original progenitors eventually leave no more offspring, by chance (this effect is attenuated if you have rapid population growth, but obviously only until (invariably) growth stops). Hence, the most recent common ancestor keeps moving forward as more and more of the anciently diverged lineages go extinct by chance. (Let's avoid discussing the relevance of genetic drift and chance to deterministic vs. probabilistic world views, as it doesn't help the discussion.) - Samsara 00:19, 29 December 2005 (UTC)
Revert if you want. Only refering to common descent is good enough. WAS 4.250 00:53, 29 December 2005 (UTC)
IMHO, reference to a single point in the past should be avoided, regardless of how it is phrased. Reasons per WAS and myself, above, as well as generally lending itself to confusion. KillerChihuahua?!? 00:57, 29 December 2005 (UTC)
I think we should keep asking each other questions rather than making assertions. I'm not sure what it was about my above comments that didn't make sense? Because my feeling was that I'd addressed all points brought in favour of the motion, and made a good argument for keeping the shorter, original version. Comments like "there is no genetic eve for all things" should perhaps be somewhat elaborated, otherwise the rest of us are just left puzzled? Someone once (don't recall if it was this Talk page or some other) referred to avoiding dumbing down as though it was a kind of unwritten rule on wikipedia. So what kind of confusion is produced by referring to a common ancestor? Does addressing this confusion constitute a dumbing down? And more importantly, do these talk pages need the ability to make comments line by line, like is customary style on mailing lists? (Maybe open a new section for this one?
If there's anything cryptic in what I wrote in this message or any previous one, please tell me! - Samsara 17:04, 29 December 2005 (UTC)

The "genetic eve" is a red-herring. I mean, it is an interesting and legitimate isue that chould be discussed on the talk page for Homo sapiens of Human evolution. But the claim that all human beings hve a common ancestor is not the issue here. The issue here is whether all live is descended from a common ancestor. The fact is, this is a fundamental principle of Darwinian theory, and has been accepted by the modern synthesis. This does not mean that it is immune from questioning or revision as our knowledge grows. If there are verifiable scientif cources that today question this claim (e.g. published in peer-reviewed evolutionary biology journals) than we certinly should include it with the appropriate citation. Be that as it may, my understanding is that this is still something virtually all evolutionary theorists and philosophers of science (who address the theory of evolution) agree on. Samsara, as far as I can tell, is not using an intelligent design ("irreducible complexity" argument, as WAS 4.250 suggests, but simply stating a principle set forth by Darwin that evolutionary scientits still consider fundamental. And Samsara was not referring to a "genetic eve as KillerChihuahua states. Even if all living organisms are descended from one ancestor, it is possible (though, according to almost all physical anthropologists) that H. Sapiens evolved independently in different paqrts of the world. That would mean that all H. Sapiens do not share one H. sapien ancestor (of course, they would still share a non H. sapien ancestor). But this issue is a very different kind of debate, with different stakes, requiring different evidence, than Darwin's postulate thall all living organisms have a common ancestor. That's not a "genetic eve." Slrubenstein | Talk 17:20, 29 December 2005 (UTC)

The scientific consensus is "Common descent" which is defined as coming from a common gene pool, not necessarily a single individual. Tracing back Bacteria ancestory is like following a net not a tree (see Horizontal gene transfer). There is not even an agreed upon definition of "life" (see life). Whatever your definition of life, there was a pool of reproducing objects before that (See Bacteria, Virus, Viroid, Prion, Satellite (biology), Autocatalysis.) I get the feeling you guys are thinking humans and horses today and I'm thinking of Bacteria billions of years ago. WAS 4.250 18:40, 29 December 2005 (UTC)
Yes, and I'm about to give up on trying to tell you that if it comes from a single gene pool, by coalescence (genetics), it also comes from a single individual. Please reread my comments above and tell me what is not clear! If you need a reference, please read Hein, Schierup and coauthor, reference found on Jotun Hein. - Samsara 19:25, 29 December 2005 (UTC)
I agree completely we should give up. I would have given up earlier but I didn't want to be rude. WAS 4.250 21:15, 29 December 2005 (UTC)
Couldn't two individual cells have come into being, through the same pathway, but with a differing genome? Coalescence is hardly an idea set in stone. Alternatively, couldn't a pool of self replicating polymers have existed, in a state between life and death, sharing coding and enzymatic properties? I don't understand why it must be true that all life had a single, living progenitor. -- Ec5618 21:23, 29 December 2005 (UTC)
The question is, more or less, whether all DNA sequences had a single point of origin. Even if we believe that there was a pool of pseudo-life, all -extant- creatures must have had their origin in a single organism. Let's say that a hundred progenitor life-forms sprung up, fully formed, with more or less in dependent genomes. What you're saying is that these gave rise to independent lineages, more than one of which survives today. Possible. But extremely unlikely. The characteristics that all life holds in common are NOT those of a primitive progenitor organism - they're of a very sophisticated self-replicating entity. We all employ the same genetic code because we had a common point of origin. That's parsimonious. How could it be otherwise? Graft 21:47, 29 December 2005 (UTC)
Well-written comment there from Graft. I'll also just comment on Ec5618's suggestion that
Coalescence is hardly an idea set in stone.
Coalescence is logically and mathematically inevitable under the assumption of heterogeneity in survival rate - an assumption that anyone who believes that either natural selection or genetic drift play any role in evolution, has already signed his name to, and that, again, is highly parsimonious. - Samsara 22:04, 29 December 2005 (UTC)
I'll concur, well-written comment.
It seems that you assume that lateral transfer didn't occur, at that point, which may be fair, if the organisms were very different, chemically. If lateral transfer could occur however, it's possible two organisms formed interdependently, and survived to share genetic code later on, after which one of the organisms was free to die. Only a single organism would survive, but it would have no single progenitor. So, some sort of 'primeordial pool of pseudolife' may have existed before any 'most recent common ancestor to all life'.
Isn't this argument similar to the argument that proves mitochondrial eve did have parents? All other potential humans were unsuccessful in spawning progeny, but that doesn't mean they didn't exist.
And obviously, the line between life and 'pseudolife' is almost arbitrary.
Finally, since coalescence seems to be the issue of this discussion, I still am not convinced that it must be true. I'll agree that it seems parsimonious, but that alone doesn't merit inclusion into the article as fact.-- Ec5618 22:11, 29 December 2005 (UTC)
For clarification, I'll agree that it is extremely likely that all life on Earth currently has a single progenitor. I may have issue with the idea that all life always had a single progentior, though, for the reasons above. If the issue is 'gene pool' versus 'progenitor', I'd suggest avoiding either, unless we are willing to decicate a line (or more) to an explanation of the difference. -- Ec5618 22:15, 29 December 2005 (UTC)
The point is, Mitochondrial Eve existed. All human mitochondria descended from a single individual, regardless of whether that individual had parents or not. Similarly, saying that there was a LUCA (last universal common ancestor) does NOT mean that the LUCA was the "first organism", or that the LUCA emerged from a single source. But it's undeniable that there WAS such a beast. Thus, common descent. As I said above, this is different from the question of the origin of life, which probably preceded the LUCA by a good long time. Graft 22:19, 29 December 2005 (UTC)
I agree 100% with Graft. WAS 4.250 23:13, 29 December 2005 (UTC)

One last point about coalescence

I just want to clear up one last possible misunderstanding before I let things be on the coalescence issue. I put it here rather than the bottom of the page because I think the portal biology post should garner all the attention by being at the bottom of the page. So here goes...

Coalescence applies whether or not recombination happens, because, although different bits of genome (haplotype blocks) may have different ancestries, all current copies of one particular haplotype block will coalesce to a common ancestor, who may be more or less recent. These ancestors then again coalesce. Hence, everything eventually coalesces! - Samsara 00:49, 30 December 2005 (UTC)

No. Not true. Read the first paragraph of [5]. WAS 4.250 11:45, 30 December 2005 (UTC)

I'll read the whole article and give you a full critique. First paragraphs are not reliable. - Samsara 12:25, 30 December 2005 (UTC)

Here is the last paragraph:

"Using single genes as phylogenetic markers, it is difficult to trace organismal phylogeny in the presence of HGT [horizontal gene transfer]. Combining the simple coalescence model of cladogenesis with rare HGT [horizontal gene transfer] events suggest there was no single last common ancestor that contained all of the genes ancestral to those shared among the three domains of life. Each contemporary molecule has its own history and traces back to an individual molecule cenancestor. However, these molecular ancestors were likely to be present in different organisms at different times." [6] WAS 4.250 13:04, 30 December 2005 (UTC)

I get a feeling that you will still get coalescence if you pick a small enough set of genes, which is tautological if you consider that if you pick derived genes at today's terminal nodes, they will not coalesce in the MRCA because it will not even have a copy of the gene. Unless you consider the "null" (i.e. absent) variant an allele, in which case, everything does converge on an ancestor with no genes at all! ;)

I suppose the conclusion of the trees vs. networks argument also rather depends on whether you want to represent individual species as the consensus sequence for that species, or somehow represent the entire genetic diversity, in which case, you will end up with a network even for haplotypes if you want to keep members of the same species at the same terminal node. It does beg asking how useful a representation that is, however, because it would not be biologically based. - Samsara 11:39, 7 January 2006 (UTC)

Common Descent Revisited

I've been reading this with some interest. And, after timne spent searching in the loft, found the issue of Scientific American that contained the article of interest here. Uprooting the Tree of Life by W. Ford Doolitte (Scientific American, February 2000, pp 72-77) contains a discussion of the Last Universal Common Ancestor, and the problems that arose with respect to that concept when one considers horizontal gene transfer. The article covers a wide area - the endosymbiont hypothesis for eukaryotes, the use of small subunit ribosomal RNA (SSU rRNA) as a measure of evolutionary distances (this was the field Carl Woese worked in when formulating the first modern "tree of life", and his research results with SSU rRNA led him to propose the Archaea as a third domain of life) and other relevant topics. Indeed, it was while examining the new three-domain view of life that horizontal gene transfer arose as a complicating issue: Archaeoglobus fulgidus is cited in the article (p.76) as being an anomaly with respect to a phylogenetic tree based upon the encoding for the enzyme HMGCoA reductase - the organism in question is a definite Archaean, with all the cell lipids and transcription machinery that are expected of an Archaean, but whose HMGCoA genes are actually of bacterial origin.

Again on p.76, the article continues with:

"The weight of evidence still supports the likelihood that mitochondria in eukaryotes derived from alpha-proteobacterial cells and that chloroplasts came from ingested cyanobacteria, but it is no longer safe to assume that those were the only lateral gene transfers that occurred after the first eukaryotes arose. Only in later, multicellular eukaryotes do we know of definite restrictions on horizontal gene exchange, such as the advent of separated (and protected) germ cells."

The article continues with:

"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.
"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 haing 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."

If required, I could, on request, scan the altered 'tree of life' given toward the end of the article for perusal by interested parties (even though it may not be directly useful within the article itself for copyright reasons unless the editors of Scientific American choose to release it thus). Given the above references, however, it should not be hard for other editors of this article to track down the relevant material.

The point I am making here is that the hypothetical 'last common universal ancestor' was not, at the time that article was published, regarded with consensus as being a single species of cell. More correctly, one could not reliably point to a possible single species contender because information about that contender may have been obfuscated by multiple horizontal gene transfers. Admittedly the information I am quoting is six years old, but unless someone has alighted upon a means of resurrecting the LUCA as a single species in that time that I've missed, the above should be noted. Calilasseia 11:07, 10 January 2006 (UTC)

See if you like my recent addition to Horizontal gene transfer (and its talk). WAS 4.250 18:39, 10 January 2006 (UTC)
WAS, thanks for seeking peer review on this. you are definitely living too close to the cutting edge for science on wikipedia. My first disagreement would be that wikipedia should not be stating as fact what is still being debated within the profession. Many people still adhere to the use of trees and the hypothesis of a LUCA.
My second point would be about the appropriateness of quoting large chunks of recent research papers. It would be much better if you could illustrate the same thing in shorter terms and give the reference at the end. - Samsara 18:51, 10 January 2006 (UTC)
And I think you need to explain why HMGCoA is interesting - does it fulfil a very basic biochemical function, i.e. evolved early and been replaced by a diverging copy? - Samsara 18:54, 10 January 2006 (UTC)
HMGCoA reductase is a basic structure synsthesis membrane responsible for building membrane lipids. In humans, the enzyme is part of the pathway involved in cholesterol synthesis, and is important medically. A quick Google search yielded several pages of interest, includng this page on its effects on statin drug efficacy in humans with cholesterol-mediated complications, and this page detailing some of the important reactions that the enzyme takes part in. Furthermore, this page cites that the enzyme is important in germ cell mgration, and that use of inhibitors caused morphological defects in both Drosophila melanogaster and the Zebrafish Danio rerio. Defects in the gene also cause germ cell migration errors. The gene would therefore seem to be of importance throughout a vast array of living organisms, and its presence in living creatures ranging from bacteria to humans suggests that it plays an important role in sustaining life in all of these organisms. That it is found across the domains of life in various incarnations also makes it important as a phylogenetic tracking device in the study of evolution. Calilasseia 23:27, 10 January 2006 (UTC)

Fossils

Just realized the "not enough" fossils issue was removed from the misconceptions section. That is one of the major misconceptions I encounter with creationists (ie: Evolution requires lots of transitional species, that means there should be lots of transitional fossils); and it should be put back in some form. I realize other parts of the article mention fossilization is rare; but I think it could bare repeating as a direct response to this prevalent misconception. - RoyBoy 800 01:40, 29 December 2005 (UTC)

The least we can do is link to the fossil record which elaborates on it; so me do. - RoyBoy 800 01:45, 29 December 2005 (UTC)

Help with Portal Biology

Hey guys, I'm the current maintainer of Portal:Biology and since I figure I "hang" with you guys a lot, you could perhaps help me. Just check out the portal and comment on things you think should be changed (or make the changes yourself). I especially need some more "Did you knows". Also, I'm currently in the process of taking over Portal:Science, so if you want to help me with that too I'd be grateful. Note that I set the current Featured article on the science portal to evolution. Just trying to get some exposure for us! The Science Portal is important because it's linked from the top of the main page. Not a bad spot, eh? --Cyde Weys votetalk 02:57, 29 December 2005 (UTC)

Continued at Portal talk:Biology#Help

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