Front loading passes peer review in Cell Cycle

_{September 9, 2007

Intelligent Design}

Share: Facebook; Twitter; LinkedIn; Flipboard; Print; Email

1: Cell Cycle. 2007 Jun;6(15):1873-7. Epub 2007 Jun 6. Links

Universal genome in the origin of metazoa: thoughts about evolution.

Sherman M.

Department of Biochemistry; Boston University Medical School, 715 Albany St., Boston, Massachusetts 02118, USA.

sherma1@bu.edu

Recent advances in paleontology, genome analysis, genetics and embryology raise a number of questions about the origin of Animal Kingdom. These questions include:(1) seemingly simultaneous appearance of diverse Metazoan phyla in Cambrian period, (2) similarities of genomes among Metazoan phyla of diverse complexity, (3) seemingly excessive complexity of genomes of lower taxons and (4) similar genetic switches of functionally similar but non-homologous developmental programs. Here I propose an experimentally testable hypothesis of Universal Genome that addresses these questions. According to this model, (a) the Universal Genome that encodes all major developmental programs essential for various phyla of Metazoa emerged in a unicellular or a primitive multicellular organism shortly before the Cambrian period; (b) The Metazoan phyla, all having similar genomes, are nonetheless so distinct because they utilize specific combinations of developmental programs. This model has two major predictions, first that a significant fraction of genetic information in lower taxons must be functionally useless but becomes useful in higher taxons, and second that one should be able to turn on in lower taxons some of the complex latent developmental programs, e.g., a program of eye development or antibody synthesis in sea urchin. An example of natural turning on of a complex latent program in a lower taxon is discussed.

PMID: 17660714 [PubMed – in process]

HT to Gilbert T. for alerting me to this paper.

Comments

Thanks Bob, for the insight on tracking down Genetic Entropy in humans using genetic data: Thus as a result of your insight, this following quote garnered from the ID antagonists, no less, over at Wikipedia; Existing data on human genetic variation support and extend conclusions based on the fossil evidence. African populations exhibit greater genetic diversity than do populations in the rest of the world, implying that humans appeared first in Africa and later colonized Eurasia and the Americas (Tishkoff and Williams 2002; Yu et al. 2002; Tishkoff and Verrelli 2003). Thus Genetic entropy is readily admitted in the article. They are in effect saying that more information exists in the African population than is younger populations! full article is here: http://en.wikipedia.org/wiki/Human_genetic_variationbornagain77_{September 11, 2007
September
09
Sep
11
11
2007
07:54 AM
7
07
54
AM
PDT}

Bob O'H you stated: The bottleneck wasnÃ¢â‚¬â„¢t a result of natural (or artificial) selection. It was a result of domestication starting from a small base population - the plants that happened to be in the right place at the right time (the story is clearer with bread wheat, which is a hybrid, so the parents in the hybridization form a small base). Are you saying this following statement is false? Ã¢â‚¬Å“Whatever we may try to do within a given species, we soon reach limits which we cannot break through. A wall exists on every side of each species. That wall is the DNA coding, which permits wide variety within it (within the gene pool, or the genotype of a species)Ã¢â‚¬â€but no exit through that wall. Darwin's gradualism is bounded by internal constraints, beyond which selection is useless." R. Milner, Encyclopedia of Evolution (1990) Are you saying that we would get different results from wheat plants in the wild? Are you saying this lack of variation found in sub-species will not consistently occur when pressure of selection is put on a parent species no matter if in the wild are if "artificially selected for by man?? If so why should I think that the chances for CSI generating in the wild for a larger population in the wild are vastly greater than a sample population of same? What are you really trying to say? Is a larger population going to solve your problem of generating CSI? Behe has demonstrated that malaria and HIV, though having a vastly larger population than your wheat will never generate CSI. I think you are barking up the wrong tree Bob!! You are trying to put the problem out of reach with an allusion to a larger population yet the problem of generating useful information is still very large for you!! Plus you run into problems with Gould's punctuated equilibrium, since he requires small populations rapidly evolving to explain the gaps in the fossil record! Not to mention the problems you have for inherent small population sizes for animals! To me it seems like you are trying to have your cake and eat it too. So I ask what exactly what is going to be the exact differentiating factor for your wild natural selection for a species as opposed to the artificial selection imposed by man on a species? Is complex new information going to magically appear in the Genome of the species in the wild thus violating Dembski's CSI. I truly would like to know how you can dare differentiate the two and claim that one is not similar to the other. Are you saying that a species under selection is not a species under selection? This is absurd! As stated before reproductive isolation is most likely, from the best evidence available, due to the fact that information for variability is being lost and thus the sub species has demonstratively less information for variation than the original parent species did. This principle includes your wheat example; i.e. your wheat example by no means escapes this principle of genetic entropy!!bornagain77_{September 11, 2007
September
09
Sep
11
11
2007
07:19 AM
7
07
19
AM
PDT}

Bob O'H you stated: Although it appears that the bacteria have changed: Yet researchers stated: These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the approximately 59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies. I would also like to point out that Vreeland is adamant that His test are faultless and that his results are accurate. Whereas the molecular clock and relative rest rates used to refute him are themselves subject to suspicion and are based on assumptions rather than rock solid evidence. Also this test of Vreeland's is not an anomaly for many other test have been done on other ancient bacteria recovered from amber crystals and also show "very little" change in the DNA...That is to say, that the change that is consistently found for ancient bacteria's DNA is always way below Darwinian predictions. Again I point out this is observationally direct evidence whereas the supposed refutation is based on indirect evidence and assumption. I believe direct evidence still carries more weight in science than indirect assumption, thus I find Vreeland's findings much more persuasive than the obviously weak attempts at refutation.bornagain77_{September 11, 2007
September
09
Sep
11
11
2007
06:36 AM
6
06
36
AM
PDT}

ex-xian: As far as I know, Michael Behe has never speculated about this. If the SETI (Search for Extraterrestial Intelligence) researchers ever receive the type of signal they are looking for, they will conclude there are intelligent beings out there, despite the fact that they probably will not be able to tell us anything else about these beings.Granville Sewell_{September 11, 2007
September
09
Sep
11
11
2007
06:01 AM
6
06
01
AM
PDT}

As to how to extrapolate this basic fact for color information to the genome I do not know right now.
Wiki has a nice page on this. It also links to a paper that shows that lighter skin is due to different genes in different areas of the world. If you want to get empirical support for your theory, you should go through the CEPH data and show that all of the genetic variants are present in the East African populations. BobBob O'H_{September 10, 2007
September
09
Sep
10
10
2007
11:20 PM
11
11
20
PM
PDT}

Patrick -
So perhaps genetic entropy isnÃ¢â‚¬â„¢t much of an issue with high replicators such as bacteria.?
That's my understanding - IIRC Mike Lynch showed that the rate of mutational meltdown depends on population size. A related issue is the evolution of sex, which is favoured more in small populations (I recently blogged about Sally Otto's talk on this at ESEB), and hence can be seen as a mechanism to escape these problems. Bob BobBob O'H_{September 10, 2007
September
09
Sep
10
10
2007
11:09 PM
11
11
09
PM
PDT}

Yes Bob OÃ¢â‚¬â„¢H here is the reference: http://www.nature.com/nature/j.....897a0.html
Ah, thanks. Although it appears that the bacteria have changed:
Thus the bottleneck you refer to is not a artificial phenomena but an inherent part of the genome when selection is placed on the genome and will and does occur in the wild!
The bottleneck wasn't a result of natural (or artificial) selection. It was a result of domestication starting from a small base population - the plants that happened to be in the right place at the right time (the story is clearer with bread wheat, which is a hybrid, so the parents in the hybridisation form a small base).
Do you think the younger races have more information for skin color than the younger races?
Well, as I don't know what you mean by information in this context, I'll repeat my questions: How exactly is the Ã¢â‚¬Å“less informationÃ¢â‚¬Â in Ã¢â‚¬Å“young racesÃ¢â‚¬Â measured? And how was it measured/estimated for a population 50 000 years ago? BobBob O'H_{September 10, 2007
September
09
Sep
10
10
2007
11:04 PM
11
11
04
PM
PDT}

Yes Bob O'H here is the reference: http://www.nature.com/nature/journal/v407/n6806/abs/407897a0.html You allude to a bottleneck, then why should Dawkins use dog breeding as an example of evolution when information is in fact being lost? Exactly why would artificial selection by men be vastly different that natural selection in the wild since the natural selection would ultimately be a random occurrence of selection for a desired trait, when taken into total context of how the selection operates? Thus the bottleneck you refer to is not a artificial phenomena but an inherent part of the genome when selection is placed on the genome and will and does occur in the wild! Do you think the younger races have more information for skin color than the younger races? I think it is fairly obvious that the East Africans have all the inherent traits of all the races in their genomes! Whereas it is also obvious that Europeans are much more deficient of the raw material to "make" other color races. To me it is clear that more information for skin color resides in the East Africans! It is commonly known that the black color is really a mixture of all the other colors when referring to materials, whereas white contains all the other colors when referring to light! As to how to extrapolate this basic fact for color information to the genome I do not know right now. As well you can clearly see genetic entropy in the wild with the sub-species of "horses" such as donkey and zebra. It is very easy to see which is closer to the parent species that was originally created by God and to see which has been "naturally selected" for to produce the "very limited variability" we can easily see in the sub-species! As far as front loading goes, I believe that "beneficial adaptations" will occur from preexisting information such as what we see in the polar bear from the grizzly bear but that the adaptation , though beneficial, will result in the loss of information from the original parent species. Such as the loss of information for hair color. As well the highly touted Lactase Persistence mutation that is offerred as conclusive proof of evolution in humans is actually the loss of a preexisting instruction to turn the Lactase Enzyme off. Thus, even in evolutionists "hardest proof" once again Genetic Entropy is obeyed and no new information was created in the genome!bornagain77_{September 10, 2007
September
09
Sep
10
10
2007
01:46 PM
1
01
46
PM
PDT}

When it comes to degeneration, a population on average is receiving so many deleterious mutations per individual, so each bacterium would have to be reproducing X amount to provide sufficient population resources to purge the deleterious mutations out of the population. Might be making a boneheaded comment but I'm assuming that bacterium reproduce often enough to avoid such problems as Nachman's U-Paradox in humans? So perhaps genetic entropy isn't much of an issue with high replicators such as bacteria.? Or am I missing something... "Observed baseline mutation ratesin bacteria are low: DRAKE et al. (1998) estimate the per base pair, per generation, mutation rate to be ubp = 5.4 x 10Ã¢â‚¬â€œ10 in Escherichia coli "well adapted to laboratory conditions."...They estimate the genomic rate of deleterious mutation to be ug = 2 x 10Ã¢â‚¬â€œ4, as a lower bound." linkPatrick_{September 10, 2007
September
09
Sep
10
10
2007
01:37 PM
1
01
37
PM
PDT}

bornagain77 - I assume then that you would disagree with DaveScot about front-loading. Can you give a reference to the PCR on the 250m year old bacterium - did they really extract DNA from something that old? The reason why corn (I assume you mean maize, although similar results would be seen for wheat and other agricultural cereals) lacks diversity is because the process of domestication introduced a huge bottleneck, and this has become worse with breeding. It has nothing to do with entropy. Your example of human skin colour is confusing - how exactly is the "less information" in "young races" measured? And how was it measured/estimated for a population 50 000 years ago? BobBob O'H_{September 10, 2007
September
09
Sep
10
10
2007
12:16 PM
12
12
16
PM
PDT}

Bob O'H, Genetic degradation for single celled bacteria is still pretty much up in the air,,In fact I remember a PCR (Poly-merase Chain reaction) study of some 250 million year old bacteria that caused quite a stir for the study showed very little change in the genome of the bacteria when compared to its modern day descendants. Yet bacteria still display adherence to the overall principle of Genetic Entropy for they are commonly known to lose fitness for survival the further away from their original state they are selected for! As well in crops such corn we can see the principle of Genetic Entropy being adhered to, for it is easy to see that corn crops have much less variability (information) than the parent species of corn has..As well even the human species is clearly shown to obey the principle of genetic entropy for the younger races of humans (Chinese, Europeans, American Indians etc..) all have less information for skin color than the original race of humans that is thought to have migrated out of Africa 50,000 years ago. Degradation of the particular genomes of different species or phyla is still very much only in the rough outline phase, yet the principle of Genetic entropy is very strong in empirical validation for it lines up with many other lines of evidence such as the over 90% of mysterious extinctions in the fossil record that have no connection to any natural disasters. Plus it lines up with what is known about CSI generating by chance. And lines up with the strength of observed data for mutation rates to DNA. Genetic Entropy has some refining to go through but it has definitely asserted itself with more solid proof than Neo_Darwinism has at this point. If I were a betting man, all my money would definitely ride on Genetic Entropy being validated as the foundational law of biology in the not to distant future!bornagain77_{September 10, 2007
September
09
Sep
10
10
2007
11:45 AM
11
11
45
AM
PDT}

Bob An obvious question arises - why doesnÃ¢â‚¬â„¢t an organism degrade before its terminal point? Observation has revealed great variation in the level of protection and repair of genetic code both from one organism to the next and from one stretch of code to the next in the same organism. From an engineering perspective it's trivial to protect some memory regions better than others. It's all a matter of how much protection you need and how much overhead you're willing to use to protect it. Code that needs to be maintained without error for geologic timespans gets better error detection/correction applied to it.DaveScot_{September 10, 2007
September
09
Sep
10
10
2007
11:17 AM
11
11
17
AM
PDT}

I agree that Sanford doesn't discuss front-loading (or at least I'm not aware of him discussing it), but his claims about degradation are relevant to front-loading, so I'm interested in how the two can be squared. An obvious question arises - why doesn't an organism degrade before its terminal point? BobBob O'H_{September 10, 2007
September
09
Sep
10
10
2007
11:00 AM
11
11
00
AM
PDT}

I don't think Sanford claims front loading millions of years ago. And I don't think the degrading of the genome is really a hypothesis of Sanfords, it is just an observation. However, the typical front loading scenerio is that after an organism reaches its terminal point is starts to degrade. Front loaders like Davison find support for this in the paleontology of Schindenwolf. They also see the patern in ontongeny. What begins as a single cell becomes a complex organism and then degrades.Jehu_{September 10, 2007
September
09
Sep
10
10
2007
10:55 AM
10
10
55
AM
PDT}

If I understand Sanford's genetic entropy hypothesis (and I admit I haven't read his book), he's arguing that genomes are degrading, because mutations reduce fitness. But then how can front-loading work? If sequences that are under selection are degrading, surely sequences that are neutral (i.e. those that are waiting to be activated) must also be degrading, at least as fast as functional sequences. So the will probably have no function by the time they are called into action. Anyone care to make a refutation? BobBob O'H_{September 10, 2007
September
09
Sep
10
10
2007
10:18 AM
10
10
18
AM
PDT}

The weak point in this argument (for both evolutionists and ID Frontloaders) is that beneficial mutations would still have to occur at the proper time in the proper place. Thus the assumption of beneficial mutations is at its core of these beliefs...Yet it hasn't been clearly demonstrated, in the least, that the DNA itself has any beneficial flexibility to mutations in it. This one point of evidence, the actual flexibility of DNA to any random mutations, which happens to be a foundational piece of evidence, has not even been decisively proven to be true yet. Though it is commonly presumed to be true. This is very shabby science to say the % How can anyone dare judge the genetic data accurately if the foundational paradigm is not even set in stone yet!?! Point blank fact,,IF the DNA is in fact not flexible to mutations then intelligent design is most likely true by default. This one piece of evidence (Beneficial Flexibility of DNA) should easily be within science's grasp at this present time. Indeed, Sanford in his book "Genetic Entropy" lists several studies that could find no beneficial flexibility to DNA (Spetner "NOT By Chance" list some studies as well). If rigorously proven true then analysis of genetic data would take on the appropriate engineering posture to deduce design instead of the "vainly" searching for natural explanations posture. This seems simple to me yet even in ID circles I find many people blindly gloss over the fact that they are vainly depending on some sort of beneficial mutations to occur that have not even been proven true in the first place.bornagain77_{September 10, 2007
September
09
Sep
10
10
2007
06:33 AM
6
06
33
AM
PDT}

I am afraid that Michael Sherman (Associate Professor Biochem) does not seem to be a materialist. I fear he will quickly be branded a neo-creationist. I admire his courage in seriously proposing such a novel idea. I am worried that the editor of Cell Cycle may soon get Sternberged for publishing this.idnet.com.au_{September 10, 2007
September
09
Sep
10
10
2007
04:38 AM
4
04
38
AM
PDT}

I am no biologist but ever since I read about the mechanism of genetic code, I realized that shared genetic traits of species that is placed very far apart on the "Tree of Life", must be traced back to an ancestor with vast amounts of genetic information ready to share with the rest of "the Tree" (i.e I deduced front loading). This was a logical conclusion that excluded the very small probability that, for instance, something like the eye can have several completely independent evolutionary emergences that is so strikingly similar for so many species on so many location on the "Tree of Life". The eye is just a simple example of a plethora of similarities that has to relate back as far as logically necessary. Trying to account for the Cambrian Explosion force this reality through a logical bottleneck. It will be interesting to see more attempts to get through this bottleneck. We should also expect evo-biology to start to derelict their trusted geological coulomb if more of these results are "logically forced" into peer reviewed papers. This article seems to support my intuitive deduction. Thank you for sharing - it makes great academic discussions open to ID skeptics.mullerpr_{September 10, 2007
September
09
Sep
10
10
2007
12:04 AM
12
12
04
AM
PDT}

Let's notice that one of the proposals---turning on in lower taxon higher complexity latent programs--is every bit as proof-positive as lac-operon genes in bacteria. If they are able to do "turn these programs on", then we can say that "front-loading" is a "fact"!! As Jackie Gleason used to say: "How sweet it issss!!!"PaV_{September 9, 2007
September
09
Sep
9
09
2007
04:42 PM
4
04
42
PM
PDT}

Cell Cycle paper: "This model has two major predictions, first that a significant fraction of genetic information in lower taxons must be functionally useless but becomes useful in higher taxons, and second that one should be able to turn on in lower taxons some of the complex latent developmental programs, e.g., a program of eye development or antibody synthesis in sea urchin." I don't see how this could have gotten past peer review. The clear implication is that all the complex developmental programs such as for eye development and antibody synthesis evolved in "a unicellular or a primitive multicellular organism shortly before the Cambrian period". Such a primitive organism would have not had anything like complex eyes or immune systems, or so it would seem. So it is precarious to say they came about by RM & NS. Then where did they come from?magnan_{September 9, 2007
September
09
Sep
9
09
2007
04:09 PM
4
04
09
PM
PDT}

In reading The God Theory, Bernard Haisch, a book I mostly don't agree with, and mostly because of his undying pro-evolution stance, he makes an interesting argument centered around light. It basically goes like this. To make an image with pure white light, you must start subtracting portions of that light in order to create an image. If you are familiar with slides, or have Photoshop where you can view an image as made up of it's different color components, you'll see what he means. You're removing purity from the source in order to create something. Well I read this post and it got me thinking. What if God does this with DNA. What if God started off with the purest form of DNA, containing infinite possibility and to create things, He masks or even chops away portions in order to create images. Us. Image of God. Interesting thought? Israel AndersonGods iPod_{September 9, 2007
September
09
Sep
9
09
2007
10:53 AM
10
10
53
AM
PDT}

And so it goes,,,They find the genetic data that is nothing like Darwinism predicted yet Darwinism must be true thus the genetic complexity we find in simple life must have purpose for a future evolutionary scenario since we know evolution to be true. Don't bother with pesky how did the original information get there in the first place! They state: This has two major predictions, first that a significant fraction of genetic information in lower taxons must be functionally useless but becomes useful in higher taxons, and second that one should be able to turn on in lower taxons some of the complex latent developmental programs, e.g., a program of eye development or antibody synthesis in sea urchin. Thus the ID weak position of front loading is their most tenable position for materialistic evolution,,,Yet ID predicted this scenario years ago!!! I would like to think that the #1 major prediction of the ID strong position (my favorite) would be that the complexity of the Genetic code of these lower life forms is really barely understood by us right now and that the entire code will be found to have some type of function though we have not yet deduced its entire function as of now. IOW, The intelligent design that is found in the genetic code of simple life forms is so complex that it is currently beyond our ability to fully comprehend right now. To me this seems the strongest position and most reasonable position so far since it is truly the position that best reflects the evidence and the repeated failure of Darwinian predictions for the genome complexity we are finding. As well I am very weary of being burnt by my false presumptions I had from my Neo-Darwinism education. Thus I think when deciphering the function of a Genetic Code, scientists should wipe the blackboard totally clean of any Darwinists/materialists presumptions and then basic foundational engineering questions should seek to lay a new foundation for scientists to work with for deciphering the sheer complexity we are actually dealing with!bornagain77_{September 9, 2007
September
09
Sep
9
09
2007
10:27 AM
10
10
27
AM
PDT}

Oh, my mistake. Looks like it has already appeared.Granville Sewell_{September 9, 2007
September
09
Sep
9
09
2007
09:56 AM
9
09
56
AM
PDT}

Very interesting abstract. This is the kind of paper I expect to see more and more of in the coming years, which avoid the word "design" but which have obvious design implications. The evidence for design is just too overwhelming to ignore indefinitely. But Dave, I would have been reluctant to post this until the paper actually appeared; aren't you concerned that an anonymous Baylor student or faculty member will alert the editor that this paper may have ID implications. It could still disappear suddenly.Granville Sewell_{September 9, 2007
September
09
Sep
9
09
2007
09:53 AM
9
09
53
AM
PDT}

Side note to whoever is in charge of the theme for this site: please make the font for the quoted text darker. It is way too light for easy reading. Instead of using 888, perhaps something like 333 would work. ThanksJack Krebs_{September 9, 2007
September
09
Sep
9
09
2007
09:17 AM
9
09
17
AM
PDT}

So much for the saying that early, ie the first, population(s) of living organisms (single-celled) were "simple" compared with today's single-celled organisms. There isn't any justification for that now. However I still think that in order to use this data for front-loading or universal common descent someone needs to be able to account for the physiological and anatomical differences observed.Joseph_{September 9, 2007
September
09
Sep
9
09
2007
08:31 AM
8
08
31
AM
PDT}

Sounds like front loading from the abstract, but what does the full paper say? What is the mechanism responsible for this "program" being in place? Is it blind watchmaker programming? A dash of luck, and a pinch of chance? Nothing is beyond belief in the world of Darwin, which is why I ask.shaner74_{September 9, 2007
September
09
Sep
9
09
2007
08:20 AM
8
08
20
AM
PDT}

Prev 1 2

You must be logged in to post a comment.

Leave a Reply