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Future Risk Assessment in the Genome

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I found the following research quite intriguing. It has far reaching implications of interest to IDists. One implication requires a front-loading IDist to appreciate. Basically what the researchers found is that there are risk assessments in the promoter regions of genes. If a gene is critical and random mutations to it would be bad news it is marked as high risk and isn’t subject to mutation. If it’s not so critical it is marked low risk and exposed to experimentation.

How does this apply to front-loading? A major problem for front-loading is no known mechanism for conservation of genomic information other than natural selection. Information stored for a distant future that isn’t used in the present is ostensibly destroyed by deep time and random mutation. Other research we’ve blogged here showed compelling evidence that a mechanism for conserving unexpressed information exists. This is even more compelling – tags saying “conserve this”. Now all we need to find is the enhanced error detection and correction mechanism that is employed to conserve information tagged for conservation and there’s our mechanism for presevation of front-loaded genomic information over deep time.

Evolution: When Are Genes ‘Adventurous’ And When Are They Conservative?

ScienceDaily (Nov. 8, 2007) — Taking a chance on an experiment – this is one of the impulses that drive evolution. Living cells are, from this angle, great subjects for experimentation: Changes in one molecule can have all sorts of interesting consequences for many other molecules in the cell. Such experiments on genes and proteins have led the cell, and indeed all life, on a long and fascinating evolutionary journey.

Prof. Naama Barkai of the Weizmann Institute’s Molecular Genetics Department recently took a look at gene expression – the process in which the encoded instructions are translated into proteins – and the evolution of mechanisms in the cell for controlling that expression. Changes in genes, and thus in protein structure, are a double-edged sword: They can give cells new abilities or advantages for survival, but they can also spell disease or death for the organism. Not all genes evolve at the same rate. Indeed, some have been conserved through long stretches of evolution: Similar versions of some genes are found in yeast, plants, worms, flies, and humans.

When do cells hold on to specific gene sequences, and when do they allow evolution to experiment with them? Clearly, highly conserved genes fulfill some basic, universal function for all life, and changes in their sequences have drastic consequences, involving death or the inability to multiply. How does evolution “decide” which genes need to be conserved, and which it can change freely? What keeps these genes safe from the ongoing experimentation that’s constantly carried out on other genes?

Barkai and her team discovered a sort of “risk distribution law” for evolution. They found that a genetic “phrase” that regularly shows up in the promoter region of genes (the bit of genetic code responsible for activating the gene) contains a key to gene conservation: The expression of a gene that contains the sequence TATA in its promoter is more likely to have evolved than that of a gene that does not have TATA in its promoter.

In other words, the level of risk appears to written in the gene code, in a way that’s similar to financial risk analysis: When the cost of error is high, an investor’s willingness to chance the risk is low, but if the cost of a mistake is negligible, even if the chance of making one is high, the possibility of gain may make the risk worthwhile. Evolution, it seems, discovered this principle millions of years before Wall Street.

Read the rest of the article at the source here

Comments
In response to comment #16 by bornagain77: As Niles Eldredge and Stephen Jay Gould pointed out almost three decades ago, the general pattern for the evolution of diversity (as shown by the fossil record) follows precisely this pattern: a burst of rapid diversity following a major ecological change, and then a gradual decline in diversity over relatively long periods of time. This is clearly the case among east African cichlid fish, such as those in Lake Malawi and Lake Victoria. As numerous studies have pointed out, Lake Victoria is only a little over 12,000 years old, while Lake Malawi is approximately 1.5 million years old. Lake Victoria has (or had, until the introduction of the Nile perch) over 600 species of cichlids, while Lake Malawi has many, many fewer (the exact numbers are not known, due to rapid species turnover and the difficulty of sampling fish species in these lakes). In other words, the older the lake, the lower the species diversity. This general pattern is also observable among the arthropod phyla in the "Cambrian explosion", the vertebrate tetrapod taxa following the Permian-Triassic mass extinction, and the mammalian phyla following the Cretaceous-Teritary mass extinction. This is precisely what macroevolutionary theory predicts: adaptive radiation, followed by species "pruning", caused mostly by increasing niche specialization and the squeezing out of marginally adaptive taxa. Over deep evolutionary time, however, species diversity has shown a steady increase: there are more species of animals alive today than at any time in the preceding 600 million years. That is, although species diversity declines within taxa, the overall number of higher taxa increases over time. This is because macroevolution includes a kind of "rachet": mass extinctions rarely if even eliminate an entire set of higher taxa. Even the Permian-Triassic mass extinction didn't kill all of the multicellular organisms on Earth (only about 99% of them). And then, as the surviving taxa rapidly diversified into the now-vacant adaptive zones, the new taxa were added to the survivors. Is this version of macroevolutionary theory non-falsifiable? On the contrary, it could easily be falsified by showing (in the fossil record) that intra-taxonomic diversification increases steadily over deep evolutionary time. This finding would verify the gradual diversification model that Eldredge and Gould called "phlogenetic gradualism" and falsify their alternative hypothesis of "punctuated equilibrium." However, as more and more evidence has accumulated about the adaptive radiation of various taxa following major extinctions, it is clear that Eldredge and Gould's model has more empirical evidence supporting it. Now, just how much empirical evidence has ID going for it? The only published books and papers that I'm aware of (and I've read almost all of them, and assigned them as required reading in my evolution/design seminar last summer) are theoretical models and alternative interpretations of already existing evidence, virtually all of it collected and published by evolutionary biologists. Until IDers start doing actual empirical science of their own, their "theories" will remain untested hypotheses, and their ideas will consist virtually entirely of airy speculation. Want to have your ideas respected by other scientists? Get your hands dirty...Allen_MacNeill
November 9, 2007
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Adam Rutherford, (the "impartial" reviewer of the NOVA PBS production "Judgement Day" in Nature http://www.nature.com/nature/journal/v450/n7167/full/450170a.html ), can perhaps help enlighten us on why not much overt ID research gets done in our universities. "Guillermo Gonzalez has been denied a physics post by his university. Quite right: you cannot believe in ID and call yourself a scientist. So farewell, I hope, to the scientific career of Guillermo Gonzalez. ... I know that, were I in a position to offer Guillermo Gonzalez tenure, I would deny it for the precise reason that his, yes, religious views about purpose in the universe explicitly mean he is a crap scientist, regardless of his ability to generate valid data. ... As a vocal supporter of the demonstrably unscientific guff that is intelligent design, Gonzalez displays ignorance of the scientific process, and appears to wilfully [sic] defy it. And for that reason, he neither deserves the use of the facilities of a university to conduct scientific research, nor the privilege of teaching the next generation of scientists." http://commentisfree.guardian.co.uk/adam_rutherford/2007/07/wrong_by_design.htmlidnet.com.au
November 9, 2007
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Who is the “we” that Patrick refers to?
I was referring to all scientists, whatever their personal stance on this issue may be. Personally I'd love to see Darwinists and ID proponents working together. The major problem is procuring funding. I hate to see it when Darwinists are demanding that ID proponents produce more research and then at the same time advocating closing any potential avenues for this research to take place. If they want to be consistent and if they take these questions seriously they should be helping ID proponents receive a decent level of funding even if they do believe in general that ID is a waste of time. At the very least these research projects may discover the limitations of certain mechanisms and in the process discover information that could advance medical technology. Who knows, maybe it would be an ID proponent who does the actual gruntwork and manages to find positive evidence for some Darwinian mechanisms being capable of producing CSI.Patrick
November 9, 2007
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Allen_MacNeill you stated: However, the only way to answer this question is to do the relevant empirical research, testing falsifiable hypotheses that distinguish clearly between the two. So far this has not been done, especially by IDers. I take issue with that statement. Since Patrick already pointed to Dr. Behe's work, in which malaria was subjected to extreme pressure to evolve complexity and failed to generate even one novel protein/protein binding site. I will refer you to my post on #7, it is one of many studies verifying the principle of Genetic Entropy (the marriage of the second law with conservation of information) (The exact opposite of the evolutionary theory). This study is unique in that it clearly demonstrates loss of variability over approximately 250 million years for trilobites: I maintain that over 250 million years severe environmental pressure would have been introduced at some time for the trilobites to evolve more complexity not less! Thus your assertions are found wanting in only this first study I've collected for long time span analysis of a species! http://www.terradaily.com/reports/The_Cambrian_Many_Forms_999.html Of special note: So for his Science study, Webster combed through 68 previously published studies of trilobites, searching for descriptions of evolving characteristics that could be incorporated into his analysis. After eliminating studies that were inappropriate for inclusion, 49 still remained. He focused on actively evolving characteristics. The trilobite head alone, for example, displays many such characteristics. These include differences in ornamentation, number and placement of spines, and the shape of head segments. His findings: Overall, approximately 35 percent of the 982 trilobite species exhibited some variation in some aspect of their appearance that was evolving. But more than 70 percent of early and middle Cambrian species exhibited variation, while only 13 percent of later trilobite species did so. “There’s hardly any variation in the post-Cambrian,” he said. “Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn’t vary in the post-Cambrian trilobites.” Allen_MacNeill, what do you want to bet that every long term analysis of a species I can get my hands on will fall into this loss of variability category, thus conforming to Genetic Entropy,,,,Thus, I am making a clear prediction that can clearly be falsified,,,Indeed if variability is found to increase over long periods of time in the fossil record then Genetic Entropy will be tentatively falsified...That is a lot more than I can say for evolution for, from what I've seen, evolution can never be falsified!bornagain77
November 9, 2007
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Hi, I'm new here, and I find the information very enlightening. I've been confused a bit by one thing that Patrick brings up in #14 above, namely his statement that "...we should continue researching." While a believer myself, and being a strong adherent to the design inference, I'm troubled by what seems to be a dearth of actual research on the part of ID advocates. Who is the "we" that Patrick refers to?Stanton Rockwell
November 9, 2007
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Do the currently identified mechanisms of genetic and phenotypic variation produce enough variation to get from there to here or not? the only way to answer this question is to do the relevant empirical research, testing falsifiable hypotheses that distinguish clearly between the two. So far this has not been done, especially by IDers.
I was under the impression that Behe's EoE was intended to analyze this exact question. My understanding is that, no, we do not have positive evidence these mechanisms are capable to the extent required for them to be responsible for everything since OOL but at the same time we should continue researching.Patrick
November 9, 2007
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In case some of your readers might be interested in more on this topic, here is a link to a discussion of it on my blog. In that blogpost, I ask the following question: • Is the rate of generation of genetic and phenotypic variation a constant? I then point out that if the answer is "no," then a new question immediately follows: • Is the increased rate of generation of variations correlated with any identifiable factor in either the genetics/development or the environment of organisms in which such variable rates of variation are observed? If the answer to this question is "no," then we may safely assume that the underlying "engines of variation" are probably random, insofar as we can observe phenotypes changing randomly over time. However, if the answer is "yes" (and the research report that is the sutbject of this blogpost strongly suggests that it is), then this suggests another question: • Via what mechanism(s) is the increased rate of variation generated, and are the "triggers" for such increased variation endogenous, exogenous, or some combination of the two? According to the article, the answer is (not surprisingly) a combination of the two. That is, the TATA box provides a switch that responds to a signal from the environment; • If the environment is becoming more variable, the switch throttles up the rate of production of variation • If the environment is becoming more stable, the switch throttles down the rate of production of variation If evolutionary theory is a reasonable explanation for the origin of biological diversity, then the "engines of variation" are prodigious, as they have been able over time to modify something as simple as a mycoplasm into an oak tree or a blue whale. Some supporters of "intelligent design" (ID) would dispute this statement, of course, claiming (without any empirical evidence) that "you can't get here from there." However, as Michael Behe, MikeGene, and other ID supporters have clearly asserted, we have gotten here from there; the real question is "how?" There are logically at least two possibilities: • The processes by which the "engines of variation" have produced the necessary variation have operated endogenously by means of a prodigious (and undirected) "random variation generator," the products of which have been sorted over time by natural selection (i.e. the Darwinian hypothesis) or • The processed by which the "engines of variation" have produced the necessary variation have operated endogenously by means of a series of equally prodigious "non-random variation generators," the products of which have been sorted over time by natural selection (i.e. the ID hypothesis). Notice that in both cases, natural selection is what finally determines what exists and what doesn't. The intelligent designer of ID theory, in other words, works virtually exclusively through modification of variation, allowing natural selection to preserve those variations that it has intelligently designed. Noticing that the only difference between these two possibilities is the amount of variation and its source also immediately suggests a way of testing the two hypotheses: • Do the currently identified mechanisms of genetic and phenotypic variation produce enough variation to get from there to here or not? If the answer is "yes," then the ID hypothesis is unnecessary, and therefore irrelevent to science. If the answer is "no", then ID may have something very significant to contribute to science. However, the only way to answer this question is to do the relevant empirical research, testing falsifiable hypotheses that distinguish clearly between the two. So far this has not been done, especially by IDers. Therefore, it is clearly not yet time for either side to declare that this is a settled question. To declare otherwise is not science but propaganda. –Allen ********************************* Allen D. MacNeill, Senior Lecturer The Biology Learning Skills Center G-24 Stimson Hall, Cornell University Ithaca, New York 14853 ********************************* phone: 607-255-3357 (Allen’s office) email: adm6@cornell.edu website: http://evolutionlist.blogspot.com/ ********************************* “I had at last got a theory by which to work” -The Autobiography of Charles Darwin *********************************Allen_MacNeill
November 9, 2007
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"You don’t seem to get it even though people keeping correcting you…universal common descent does not add even one dark speck to “All complex biological systems are generated by intelligent agents.”" Feel free to pop back to the P.falciparum thread to discuss it. I'm just pointing out that comparison between closely related species of Plasmodium suggests hundreds of genes have appeared since divergence, with complex new functions associated with the genes. But this information (and the TATA stuff) is only valid if common descent is accepted.Pantrog
November 9, 2007
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Allen_MacNeill, Please list your source for CSI (complex specified information) generation i.e. What genetic mutational study lays the foundational framework for your latter assertions? i.e. Why should your your hypothesis be considered viable as far as generating the required information (CSI) it absolutely needs exactly when it needs to when all mutational studies, I know of, rule out your scenario from first principles even in the most favorable of circumstances?bornagain77
November 9, 2007
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This assumes common descent (…apply that approach to Plasmoidum vivax and Plasmodium falciparum - and one gets a few dark grey swans).
You don't seem to get it even though people keeping correcting you...universal common descent does not add even one dark speck to "All complex biological systems are generated by intelligent agents." Also:
I think a lot of folks get confused because they think that all events have to be assigned en masse to either the category of chance or to that of design. I disagree. We live in a universe containing both real chance and real design. Chance events do happen (and can be useful historical markers of common descent), but they don’t explain the background elegance and functional complexity of nature. That required design.
Patrick
November 9, 2007
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I note from the rest of the article that Prof. Barkai is studying evolutionary events (such as genome doubling) by comparisons between distantly related species. This assumes common descent (...apply that approach to Plasmoidum vivax and Plasmodium falciparum - and one gets a few dark grey swans). The other key point is causality - there's an association between TATA binding sites in promoters and conservation of the gene, but does this just reflect the physiological role of TATA binding sites - e.g. not being infront of house-keeping genes and therefore not subject to purifying selection i.e. the presense of TATA is an epiphenomenon, rather than a cue for non-conservation. Thirdly this finding is associated with conservation (or not) of expressed genes - rather than a mechanism to conserve unused front-loaded information.Pantrog
November 9, 2007
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Hi, Dave: As I pointed out on my own blog, this is relatively easily explained as a consequence of stabilizing selection. During a transition from one stable phenotype to another, the "engines of variation" (listed here) produce a population of individuals with a range of modified phenotypes, some of which survive and reproduce more often than others. The preservation and resulting increase in frequency of such modified individuals over time constitutes directional selection. However, once an evolving population reaches a state in which the mean phenotypic type has the highest relative fitness, then stabilizing selection replaces directional selection and the population stops changing significantly. This stasis then persists as long as the ecological niche of the stable population doesn't change significantly. Under such conditions, any mechanism that might increase the stability of the evolved phenotype in a stable ecological niche would have a higher relative fitness than one that was continually producing new variations at a rate equivalent to that during the evolutionary transition to the new stable state. Therefore, modifications of the promoters to the genes undergoing selection would be selected for in organisms that have undergone one or more periods of evolutionary stasis (as defined by Eldredge and Gould). Indeed, this finding strongly suggests that the "engines of variation" that I listed in my own blog have a throttle: that is, the amount of variation that can be produced in any given gene is not fixed (i.e. it is not really "random"), but rather can increase or decrease as the result of selection. This possibility presents the very exciting possibility that we will be able to explain the apparent bursts of variation that accompany major ecological changes, such as the major adaptive radiations that have accompanied the five major mass extinctions on Earth. Far from being a problem for evolutionary biology, this finding is in fact a potentially major advance in our understanding of what G. G. Simpson called "tempo and mode" in evolution.Allen_MacNeill
November 9, 2007
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DaveScot off topic sort of: In regards to verifying Genetic Entropy, I found this research interesting: http://www.terradaily.com/reports/The_Cambrian_Many_Forms_999.html of special note: "That led me into thinking there's something weird about these very primitive Cambrian trilobites that you don't see in other (more recent) ones," he said. The only way to verify his hunch was to conduct an analysis that combined the data compiled in previously published reports. "It's too much for one person to look at a thousand trilobite species," Webster said. So for his Science study, Webster combed through 68 previously published studies of trilobites, searching for descriptions of evolving characteristics that could be incorporated into his analysis. After eliminating studies that were inappropriate for inclusion, 49 still remained. He focused on actively evolving characteristics. The trilobite head alone, for example, displays many such characteristics. These include differences in ornamentation, number and placement of spines, and the shape of head segments. His findings: Overall, approximately 35 percent of the 982 trilobite species exhibited some variation in some aspect of their appearance that was evolving. But more than 70 percent of early and middle Cambrian species exhibited variation, while only 13 percent of later trilobite species did so. "There's hardly any variation in the post-Cambrian," he said. "Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn't vary in the post-Cambrian trilobites." Paleontologists have proposed two ideas to account for why variation within species declined through time. One is ecological. In the very early Cambrian seas, fewer organisms existed than today, which meant that they faced less competition for food. "You didn't really have to be tightly specialized to make a living in the Cambrian," Webster said. But as evolution gave rise to more varieties of organisms, ecological communities became more diverse. "You had to be very fine-tuned to your particular niche to make a living and to beat out competitors for a limited resource." The genomic hypothesis offers a second explanation for the decline of within-species variation over time. According to this idea, internal processes in the organism were the key factors. Various developmental processes interact with one another to control the growth and formation of body parts as any organism progresses from egg to . "It's been suggested that early on in evolutionary history, in the Cambrian Period, the degree to which these different developmental processes interacted with each other within the organism was a lot less," Webster said. "As a result, the constraints on what the final organism looked like were relatively low." Well Dave, what do you think? I bet this pattern will hold across the board for all species that have exceeding long spans in the fossil record, and I also think it is directly attributable to loss of genetic diversity and clearly conforming to the principle of Genetic Entropy. It is the most reasonable explanation. When I think about no matter how they dress it up it is in direct opposition to what evolutionary theory would predict...i.e. We see a culling of variety, not a searching for new pathways to take advantage of!bornagain77
November 9, 2007
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This has deep implications for genetic entropy as well. If the core code of an organism is protected then the rest can carry a high mutation load. There's also an opportunity for a "reboot" if things get bad - the genome can be cleaned up and restored to a previously known working state. Stuff like this is hard to anticipate or imagine under the rubric of blind evolution but not so for intelligent design. Researchers wouldn't keep being so surprised by what they find if they just bit the bullet and worked under the assumption that life is here by design not by chance.DaveScot
November 9, 2007
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(Slightly) off topic. Speaking about Specified Complexity, I just saw this remarkable documentary: "Rivers and Tides" (links at bottom). It is about artist Andy Goldsworthy who creates art works in nature using natural materials. For example, he might create a work in the forest using leaves. For this reason, his works are often (but not always) transient. What got my brain it a twist is that you could be walking in the forest, see a "thing" made out of the same things that the rest of the forest was made out of, but be able to immediately recognize it as "art": it had specified complexity whereas the rest of the forest does not (or at least has a different kind of specified complexity). It is reminiscent of the Mount Rushmore example, But that example only makes sense if you know what a human face looks like. That requirement is removed when viewing Andy Goldsworthy's art. You would say that it is both in nature and of nature. But it is not natural. It uses a more abstract level of specificity than, say, Mount Rushmore. I would heartily invite anyone who is thinking deeply about specified complexity to view this film. I think it will give you a whole new perspective. Here are some links: http://www.imdb.com/title/tt0307385/ http://www.amazon.com/Andy-Goldsworthys-Rivers-Tides-Goldsworthy/dp/B0002JL9N6 http://www.netflix.com/Movie/Rivers_and_Tides/60027273EndoplasmicMessenger
November 9, 2007
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DaveScot in regards to this, When the cost of error is high, an investor’s willingness to chance the risk is low, but if the cost of a mistake is negligible, even if the chance of making one is high, the possibility of gain may make the risk worthwhile. Evolution, it seems, discovered this principle millions of years before Wall Street. Seems to me there is a huge amount of "insider trading" going on in the Genome in this scenario, as far as future information is concerned that would be of benefit to future life forms. And that's illegal in science as well as on Wall Street!bornagain77
November 9, 2007
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You need this unprecedented level of protection against mutation in deep time. That is untill you realize that "deep time" is another one of the stories that was necessary for the Darwinists story to have any plausibility.Latemarch
November 9, 2007
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It's surprising that this is not presented as a challenge to Darwinism in the article. Somebody has to do the marking; somebody has to say to this gene, "you need some bodacious TATAs." :-)getawitness
November 9, 2007
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This is also yet another level of unexpected specified complexity to be explained. It is clear that random mutation is not as random as we thought. Why is this so? I do not think, in the standard model of evolution, the important genes need to be marked as important. Would it not be OK for natural selection to do the work of preserving the important genes? Even if they do need to be marked, who is there to mark them? No designer allowed, where does the marking come from?idnet.com.au
November 9, 2007
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