The Human Genome and Evolution

Given that this point is still under great contest in the other thread, I find it bad form to start propagating it as if you won. Add to that the fact that your impact is mostly relegated to textbooks rather than the mainstream scientific literature.Science allows itself the freedom to be wrong and correct itself. No such thing can be said for any kind of religious fundamentalism.

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No problem. I've never been one to argue that we are practising 'pure-science' all the time. However, most of the time we are IMO. But we're influenced by the Bible and our faith. Even mainstream science is influenced by funding, ah . . funding, and . . funding (I was trying to list all the different things science is influenced by but they all came down to fnding whether government/old boys/start-ups etc)! My only criticism of evolution is the extrapolation from observed small-scale evolution to evolution of eveything. Creationists have been limited to primarily theoretical, simulation and reanalysing data due to funding issues.In terms of new data collection I would cite helium retneiton, the new multiple dating method field studies, the recolonization group's work and the Mt St Helen's stuff. Biologically the closest thing I can think of are the early recolonization studies and some fairly extensive attempts to identify the biblical kinds (barimins). If the data peg back to a couple of hundred (or thousand) anscestral genomes then that is suggestive of creaiton of original genomic material. I dont' expect to get back that far. Our proposal is falsifiable due to claims of non-common desent at *approximately* the family level. This is changing but I basically agree. Fortunately in many instances there is simply no need to change the nomenclature and whne there is it is often only a 'label' change. Well, you tell me what we should call hroizontal transfer in our model? In our model it is also descriptively a horizontal transfer. RATE is producing a lot of radiodating work *beyond* the helium retention work:Error | The Institute for Creation Research
Error | The Institute for Creation Research
Error | The Institute for Creation Research
Error | The Institute for Creation Research
Error | The Institute for Creation Research It's starting as I demonstrated above. Read my definition again. I'm clearly stating that animals which are related by common descent are 'kinds'. Common decent doesn't have to be universal. Creaitonists beleive that the horse family and cat family, for example, are related by common descent (within). I'm prepared to concede now that 'Creationists are generating new data sets' should have 'beginning to' inserted so you may not want to bother debating that one.Do you really want to debate the biblical kind one given my comments in this post on it? All we're saying is that some groups are undeniably related by common descent. In the gray area we would claim some others as well. I'll conceded now that it is a proposal that has some supporting data but is not proven. Is this worth debating? Do we have enough genomes for this yet to bother?So how does a great debate work? Can we limit it to three sessions each of 1000 words or something so it's not endless? I'll consider it but it seems to me the only one worth debating is the pseudoscience one?

That, in my view, is a pre-determined bias that is incompatible with a truly objective scientific approach. No argument there. But a lot of mainstream science does get accomplished without direct funding. Even as a post-doc, most of my best work was never directly funded - I accomplished it on the side with leftover funds from other work that was funded - what we called 'bootleg' projects. I repeat, theory, however elegant, is only as good as the empirical observations on which it is premised. That is only one possible inference and definitely a debatable topic. Again, here is a topic that is definitely contestable, but first I would like to see it phrased in *specific terms* as a falsifiable hypothesis. Fine. But doesn't HG transfer decrease, rather than increase, the chance that there might be definitive and immutable 'kinds' of organisms? It would seem to be yet one more line of evidence against the creationist view. Absolutely. You still haven't come up with a rigorous definition, and I would contend that it is not possible. Sounds like you are trying to be as slippery as possible on this one, but I aim to pin you down. Yes, it is. And we don't need to sequence every single genome to debate the concept of a 'kind'. It is merely a biblical abstraction and completely unscientific. You bear the burden of demonstrating that it is. As I understand it, the moderators oversee the debate and make a decision at some point. It would not be endless, and certainly I don't have time for that either. No, that one is the least specific and the hardest to demonstrate incontrovertably. I would say the existence of a biological 'kind' is perhaps the best of the 3 to debate. Let me research your references - I am away from my fast connection but I want to verify if these authors have published anything credible outside of ICR. I already see the first three articles are by the same author, Andrew Snelling, and none of your references are published in accredited geology journals. Also, I am not a geologist, so I am not qualified to critique radio-dating of volcanic rock and such. I would be seeking a debate on issues relating specifically to evolutionary *biology*. I will respond further in a day or two.

EZ For the purpose of scientific discussion I'm happy to simply state a minimum of these creation inputs and treat them as postulates to be tested by their natual consequences. How scientific are the postualtes of QM? Not at all in themsleves. I know the feeling. We use the same empirical data. The same sea-level curves, the same fossil record, the same genomes . . It's at least a potential compatability. I guess here I mean things like retroviral inserts etc which can potentially falsify our claims. But we're comfortable with created kinds transferring genomica material. OU claim is about the origin of the origina lgenomes. We're not claiming God has protected them since! I stand by definition. What's wrong with it? It's simply an admission that the data is not always easily interpretable. When is a gene gained or lost? A 'gain' in one genome can be considered a loss from another. Well perhaps that's the problem. You're trying to make our identification of the Biblical kinds in biology as stronger tha nwe claim. Our expectation is that life is a set of Biblical kinds that have since evolved. I don't claim to be able to prove it.But I will argue that it's consistent with the data and theoretical expectations of evolution. Great. Do you still want to debate the kind given the limited claim I make about the concept (in this post)? I agree they have not published much creation-funded work in mainstream journals (but their non-creaiton stuff is of course). Gentry has published creation-relevant stuff mainstream and the RATE results were presented at a recent AGU conference.This message has been edited by Tranquility Base, 07-03-2005 09:36 PM

Now there is a slippery concept.Lets hope it is more relvant than the papers the ID proponents regularly trot out to bolster their claims that ID related work is being published mainstream.TTFN,WK

Although I can't speak for EZ, I want to see it debated precisely because the definition is always so vague and you (or any creationist for that matter) seem reluctant to define it better. You are so adamant that the kind of theorising you are describing is not pseudoscience and yet I haven't seen you present anything scientific about it.For example, "*approximately* family level" may sound reasuringly empirical to some people but it's more or less nonsense as a useable, (and vitally) falsifiable definition. If you do start a "great debate" on the subject (or an open general debate for that matter) then here are a few things that I think need to be addressed:

But you use it selectively. You guys sift through mountains of data, seemingly ignoring the implications of 98 % of it, looking for tiny shreds that you can hold up and say "Look - this is consistent with the biblical account!". So how many did he create and how can this be objectively quantified at all? We can't debate final origins - only the process of evolutionary change and its boundaries. Are you not suggesting that such a boundary exists with your concept of 'kind'? There are no boundary conditions defined. If things can evolve and change with families (the taxonomic level you mentioned) but no further, what mechanism prevents higher level divergence? I see no basis for recognizing a 'kind' as a valid taxonomic distinction whatsoever. And even if it does correspond approximately to 'family', why not just use 'family'? What scientific understanding is to be gained by introducing this nebulous, biblically-derived concept? And you are trying to make it as cloudy and indefinable as possible. So you can only trace evolution back so far and then it magically breaks down at some imaginary, undetermined point corresponding to the 'poof' of creation? Why 'of course'? Surely independent peer-review is the litmus test of the scientific validity of these ideas? So you're saying that these guys have managed to achieve some credentials by publishing some 'conventional' research in their discipline, only to turn around and use those credentials to flog other stuff that could never pass peer review anywhere outside the ICR ? Seems a little disingenous to me.
That would be like me taking a big crappy data set from an entomological study with all kinds of methodological flaws and saying, hmmmm... this will never fly in a good journal, but look - it makes this new pesticide look like it works really well. I bet Monsanto would like to publish it as a promotional flyer...

EZ Can you list some data you thnk we don't use. In advance I will say that IF I claim it to be 'anomolous', I will demonstrate in what sense it is anomolous in the context of the rest of the data that I will - in advance - claim we do use. There are creationists working on this:http://www.noahsarkzoofarm.co.uk/research/animals.shtmlCheck out the links at the bootom of the pages to see tentatively assigned kinds for mammals etc. E.g. 100 mammal kinds, 49 reptile/dinosaur kinds and 42 bird kinds. The amphibian list (3) is under construction and only includes extant representatives but the other vertebrate orders cover the extinct kinds. It is based on the identificaiton of whether novelty (i) requires the addition of new systems and (ii) is gained or lost. This means it will not be a straight forward identification in all cases.So, for example, let's look at the fly and the mosquito (genomes/biology). They clearly have a core overlapping genome that represents about 80% of gene types (by memory).But there are thousands of genes that are *completely* unique to each genome - that contribute to their unique biologies of course.Does this mean that they are not the one biblical kind? Not necesarily (unfortnately from the point of view of distinguishing our models). Because we do not ahve a problem with there being an early fly/mosquito hybrid that d-evolved into these two variants. Yes it's a lot of genetic change (ie relative losses), but it's quite possible given what we know about genomic plasticity. It's easy to lose entire swags of genetic material as we know with extremeophiles.So, simply because this means our models are not always easily distinguishabel does that mean that our model is irrelevant or does not make predictions.No, our model is consistent with the data and does make predictions. For example, we would predict that there MAY have been an anscestral form of the fly/mosquito. Our model doesn't require it, but it allows it. If we find that in the fossil record we would see that as consistent wiht our model and IMO a prediciton.Now, when we come to predictions that are differnet to the mainstream scenario I agree there are less differences. I'll put my thinking cap on and see if I can make some predicitons that are different. We do make a prediction on how much change can occur. We do not expect - given the time-frame - for new gene types to regualraly arise and certainly not entire cellular sub-systems to arise. That is a bona fide prediction.The problem of distinguishing the models is, as highlighted with my mosquito/fly example, that when you claim - aha, the mosquito added an entire blood-sucking apparatus tha tthe fly doesn't - we will, of course, claim - quite rightly so - that that appartus may have been present in the original - created - common anscestor - and has since been lost by the fly.I hope this clarifies our position and that there is a lot of common ground although we do provide a very different framework. As I'm sure you're aware there is great debate mainstream as to the evolutioanry m,eaning of these categorizations. Using genomic data we will, over time, ceom to firmer conclusions of where we expect the boundaries to be. I have give examples above of predictions. That they do not necesaarily differ from mainstream expectaitons is not per se a problem with the model.OK, here's a genuine prediction that *potentially* differs from mainstream theory.If we claim a kind, then in principle we should be able to find examples where there is evidence that functions were *lost* rather than gained.However, the problem with this still is that in those cases you will agree that these are losses, not gains!It seems to me we are stuck on being unable to come up with clear diagnostic differences. And I am well aware of this but will give it continued thought.I'd appreciate it if you would follow my logic in this post and not jump on any single point. It might seem like that to you. However, given* Genomic plasticity
* Limited time
* But ecological shocks to the system (eg Flood/recolonization)these are our clear expectations not us being 'indefinable' IMO. Yes. And it has consequences which are testable as discussed above. Sure, but let's move back in to the real world. Creaitonists publishing material in mainstream journals are free to interperet results mainstream in the 'discussion' section but not according to creaiontist points of view. There are well known cases (eg Gentry) where this occurred. I myself would have liked to insert a creationist interpretation of convergent evoltuion in one of my bioinformatics papers but I didn't even bother becasue I am a realist. It's not a good analogy because - for a start the data set is the same as you're using as I'v mentioned.This message has been edited by Tranquility Base, 07-06-2005 12:31 AM

What do you mean by '*completely* unique'? Are you suggesting that these genes have no homologues outside of the fly/mosquito? How can you possibly know that simply by comparing 2 genomes, you would have to compare all of the closely related genomes of both species before you could justifiably say that any gene is '*completely* unique'.The current comparisons of the genomes identify about 1437 proteins in Anopheles and 2570 in Drosophila with no homologues in any of the other species whose genomes have been fully sequenced (Zdobnov, et al., 2002). But even this does not show that these proteins are '*completely* unique'.TTFN,WK

Is is possible that humans and chimpanzees belong to the same kind?

Or Neanderthals , for that matter?I guess maybe we'll find out when old TB gets his posting privilidges restored. He's been suspended (again).

EZsays validly-Below are some of my notes on how to reach this boundary IN PLANTS. It would if working remand kinds even with mutiple origins of life in the galaxy. If the specifics were prooved then implications for the starting conditions in human monophyly would be apparent.
Dr. Gladyshev @
http://www.endeav.org/evolut/
has well writ,
"Probably, the lack of our knowledge on actual complex systems may be partly attributed to the changes in entropy during this transition, because the entropy cannot be measured directly."I have not been able to think this outside the green stuff so far.
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As the static dielectric constant can sign a systematic entropic thickness independently of temperature provided an equilibrium is entrained in some attractor of its causal environs the free energy of such a biological dielectric if so polarizable as is a quasi-equilibrium transition temporally coincident/(congruently) with the equilibrium biometrically is in truth actual. If biology correlates a temperature dependence in this volume of material constituents, it may be that the dielectric moment contributes to the thermostat parameters no matter how the macrothermodynamics of capacitive self-energy is measured. It is probable however that physical teleology remands a logic of differences in electrotonic sources and sinks in the variance once quantum mechanical lexicology is invested in the collections responsible for the phenomena.It is important to notice GG’s We may only discuss the accuracy of the Gibbs thermodynamics as applied to, e.g., quasi-closed systems the processes in which are close to equilibrium. In accord with the very essence of full differential (its mathematical meaning), as well as the first law of thermodynamics, the change in the function of state of the system accompanying the transition from one equilibrium state to another is independent of the way or mechanisms of this transition. Probably, the lack of our knowledge on actual complex systems may be partly attributed to the changes in entropy during this transition, because the entropy cannot be measured directly. The changes in phenomenological entropy accompanying transformations in both simple and complex systems may be calculated only if one has studied the corresponding thermal processes.The temperature independences might be relatable through the principle of substance stability if the thermostat is not thermostatically strongly correlated transitively across levels.The equilibration would occur through the process of elastic displacement. Frolich, Equation A 3.4 finds its main application in the case of dielectrics in which polarization is connected with elastic displacement of charges (case (i) of &4). The most general displacement of the dielectric material in a sphere may then be developed in terms of is normal vibrations (cf. van Vleck, V3), and it is then found that the polarizablility alpha is a constant independent of temperature if the density of the substance is kept constant. This procedure is of importance because it shows in a very general way that the assumption of elastic displacement leads to a temperature-independent dielectric constant.What is at stake is the relative formatting influence of the reductionist(aggregation/aggluntination) vs the holist (differentiation/fragmentation) evolution of the world as presented by Salthe pp143in Evolving Hierarchical Systems. As soon as it is known how the thermostat states are related to phenotypes the differences in relative genetypic frequencies can be assoicatied with the smallest prior fragment fragmentable (due to temporal availability of force) no matter what the figure being formatted is and becomes. If the thermostat is only a property of genetic units, no mater how differentiated the physical means of permitting transitivity across levels will be only that much more determinate and less uncertain. In that case gene expression would be required before one could be most certain of the possible transitions between forms both available and those canalized/constrained. The distinction bears on further functions of action at a distance ultimately. Thus one would have available the form and position of the inducteous body and the nature of the interposed medium (niche construction would have to be defined by then) and it is required to find the changeable distribution of electricity in the inductric. All of this had to do with the resistance that a prior aggreagation bears on a future differentitation.Elastic Displacment 1/4pie(EdD) (if the displacement D is increased by a small amount dD) (Frohlich 3.4)Free Energy differnences in the horizontal line below work differences in displacements represented in the vertical below without work of expansion. dU = dQ + E/4pie (dD) (dQ is heat influx) (Frohlich 3.5) Free Energy = U-TS (3.3)Substance stability(OR EQUIVALENT) l-2Substance stability l-1
I -3 I-2 I-1 Inititating conditions FOCAL level B+1 B+2 B+3 Boundary conditionsSubstance stability l+1Substance stability l+2
--------------numbers above(+/-) refer to levels of organization------------The equations are from Frohlich's book on Dielectrics, previously cited on EVC.This message has been edited by Brad McFall, 07-08-2005 10:09 AM

Wounded King Yes. However, I fully agree some will turn out to be well known protein folds. I'm not saying you wont get hits with PHI-BLAST or PSI-BLAST, but the comparison papers make it clear you don't get robust plain old BLAST hits. The fly and mosquito are very similar organisms. If these genes are not shared here, and we already know they are not present in the other major taxa already seqeunced, then they're very unlikely to turn up elsewhere (other than in ones and twos). It means they're unrecognizable and thus if they do turn up elsewhere you wont be able to distinguish between convergent and divergent evolution.This message has been edited by Tranquility Base, 07-07-2005 10:55 PM

sfsYes, using my definition of kinds one could try to put man and the chimpanzee into the one kind.As a *postulate* we would of course state that this was not the case. Empirically, human-specific genes aside, one then has to note that the millions of SNPs in coding and regulatory regions that distinguish man and chimpanzee are doing something very important (to human intelligence for example). One cannot argue that this combination of SNPs could evolved easily unless one assumes evolution a priori.

EZI have little doubt that Neanderthal and Erectus were fully human.