A prominent ID supporter at UD, gpuccio, has this to say:
My simple point is: reasoning in terms of design, intention and plans is a true science promoter which can help give new perspective to our approach to biology. Questions simply change. The question is no more:
how did this sequence evolve by some non existent neo darwinian mechanism giving reproductive advantage?
but rather:
why was this functional information introduced at this stage? what is the plan? what functions (even completely unrelated to sheer survival and reproduction) are being engineered here?
Gpuccio references actual biology in his writings and is one of the few at UD that do, and as such I’m prepared to take him at his word that the ID project is now ready to move from simply determining design to answering the questions he posed:
- why was this functional information introduced at this stage?
- what is the plan?
- what functions (even completely unrelated to sheer survival and reproduction) are being engineered here?
If any ID supporter would like to provide a specific example with answers for those 3 points for discussion that would be perfect.
Gpuccio’s OP concludes:
The transition to vertebrates was a highly engineered process. The necessary functional information was added by design.
In response I simply repeat back the question what is the plan?
Part of me agrees. But I don’t like to tar everyone at UD because of the childish behaviour of a few. I have had several good discussions with many of them (Heks, VividBleu and others). Unfortunately, I invariably run afoul of Barry, William, Gordon Mulllings or cut-and-pasta BA77, and don’t heed my own advice and keep my mouth shut.
Sadly, the 90% of them who are smug, closed-minded, and reactionary against anything that questions their beliefs, give a bad reputation to all of the rest.
Glen Davidson
I’m too scared to post at UD. They allus get the better of me.
I agree with petrushka with the added point that, apart from conversation being arbitrarily curtailed by a quixotic blog owner without notice or explanation, there is the added risk that an investment in comments can yield zero return when the whole set is disappeared at the push of a button.
Here at TSZ, we try to maintain a full record of comments and contributions. Apart from obvious spam, porn and legally defamatory stuff, the worst that happens is a comment gets moved to guano. And there are no members, none at all, who are currently banned from posting here.
Following links above, I see gpuccio is looking in.
Hi, gpuccio! *waves*
Indeed. Doctor Liddle’s ambition in creating and maintaining this blog was to enable conversations that were curtailed at UD to continue in a venue where discussion could ensue without favour or rancour.
I happen to agree with you that the hardest nut to crack regarding life on earth is its origin. Then the biochemical evolution of prokaryotes that continued for two billion years prior to the emergence of anything more complex* can only be considered with circumstantial evidence. (Anything from Mars or SETI and all bets are off.)
Though that the biochemistry is common across all Earth life is the killer argument for me that we all share a common ancestor.
Once you have eukaryotes, for which there is a very satisfying explanation in symbiogenesis, it gets much easier. Evolve sex, multicellularity, cell specialisation… you’re home free.
ETA *as far as we know!
Gpuccio agrees!
Quantum handwaving it is, then.
So God not only plays dice; He cheats.
He mocks the evolutionary mechanisms, dismisses them despite of the huge amounts of evidence, claims that there’s no relation between natural selection and reproductive advantage… and his proposed mechanism is “quantum interface”, as if that was testable or had any kind of explanatory power. In fact he thinks the lack of explanatory power is a strenght of ID:
He sees explanatory power as a “limitation”, and ID is much better since it explains anything really.
A true paradigm shift in science, one that dispenses with science entirely. Praise the Lord!
Alan Fox,
How do you explain the differences in biochemistry across life?
How do you explain the parts of the eukaryotic cell that cannot be accounted for by endosymbiosis i.e. spliceosome, nuclear pore complex and chromosome structure?
If gpuccio finds it tiresome, he is more than welcome to join us here. Unlike UD, no participants are banned for dissenting views, no comments are deleted, and all are protected by the same set of equally applied rules. If gpuccio has the minimal daring required to venture out of the intelligent design creationist haven of UD, I assure him that I’ll pay special attention to ensure that he is not subject to rule-violating personal abuse.
That being said, I will not give that anti-science, censorious cesspool any traffic.
A friendly word to gpuccio (Hi!), Barry does not like his flock mingling here:
I doubt it can ever be known what the chemistry of the earliest organisms was precisely, though Nick Lane in his book The Vital Question gives a plausible (if optimistic) account. I’m sure others have recommended it before as well as me. But we can examine the whole panoply of extant organisms and examine their biochemistry and compare DNA sequences.
The most staggering fact to witness is that there is one DNA code for all organisms apart from a few interesting slight differences in some micro-organisms. This one fact is overwhelming evidence for common descent in my view.
I can’t offhand as I’m not a professional biochemist with expertise in the field of spliceosome chemistry. A quick glance at the literature indicates that both major and minor spliceosomes are ubiquitous in all Eukaryota that have been studied which suggest an early origin.
I could find a little time to lend a helping hand on that score if need be too. 😉
So Barry wants to get the flock out?
Gpuccio confirms that he accepts common descent in a response to me, that deserves a detailed response. I have errands to run but should find time later.
I wonder if he also accepts that mutations happen, and that mutations alter the DNA sequence and in turn, protein sequence too. Because comparing protein sequences and rejecting the roll of mutation seems self-refuting. Maybe his “quantum interface” is responsible for those mutations instead of being truly random?
Can someone please ask gpuccio if he can share the FASTA files he used?
He’s reading this thread, so I’m sure he’ll spot your request.
Pasting in gpuccio’s comment at UD
Well, all that goes out of the window, if you consider RNA world a plausible precursor to DNA and proteins. I used to be skeptical of RNA world, mainly due to the influence of the late Professor Robert Shapiro but I’ve come around due to persuasive arguments by fellow members here (notably Allan Miller) and also as it answers Upright Bipeds “semiotic” argument, RNA being able to double up on both information storage and catalytic function.
But this argument is only convincing if functional proteins are rare in sequence space. Evolutionary search only needs to stumble on a solution, not the solution. There is plenty of new research since Keefe and Szostak showed ATP binding is common in a random sequence library.
Well, the point I would like to emphasize is “two billion years”, short generation times and huge populations. A lot of opportunity to get your biochemical ducks in a row
Good! 😉
Once you have life, as the earliest possible and simplest possible self-sustaining replicators, you have all the elements in place for evolutionary processes to go to work. And whilst the idea that every single living and formerly living organism on Earth must have parents and ancestors linking back in an unbroken chain to the LUCA is daunting, arguments from incredulity and gap arguments seem constantly to retreat in the face of new discoveries, new research and new evidence.
I honestly think that evolutionary pathways from, say the first clear evidence of diverse multicellular organisms, some grazers, some hunters, are much easier to propose. The biochemistry, for the most part, is in place. The concepts of evo-devo and regulatory genes, cell differentiation and so on is much more variation on a common theme.
colewd,
What, all of ’em? A vague question deserves a vague answer: divergence.
Allan Miller,
Similarities are 50% of the vague analysis that Alan based his opinion on:-)
colewd,
And the similarities are explained by common descent. Next!
Colewd
Don’t you think it unfair. You demand details for evolutionary processes at every turn. The big picture may not be complete but the pattern is there. Some questions relating to the 2 billion years of evolution prior to eukaryotes bursting on the scene may never be answered satisfactorily.
Yet you seem to think that there are plausible alternatives offered by the Creationist/ID movement. I and others keep saying, there is no other scientific theory that explains the evidence we have.
You don’t have to look at that evidence if you don’t want to or you can keep maintaining that holes exist therefore ID/Creationism gets a shoo-in. It’s up to you, I guess.
Surely someone needs to mention that LUCA is the oldest species that had two or more living descendant species. It is not the organism at the origin of life, which could be much earlier
Is it just me, or has ID/creationism become the most boring, repetitiously simple minded act on the internet?
There was a time when Dembski and Behe were freshly minted, and acronyms like IC and FSCI stirred up actual debate.
Now its all mindless god of the gaps stuff. Paley warmed over.
LUCA, not FUCA.
Glen Davidson
Joe Felsenstein,
To be fair, I have mentioned this on numerous occasions. I live in hope of getting through.
You’re not wrong. If the SOBs didn’t vote based on this and related nonsense there’d be no reason to pay them any attention.
Unfortunately, even some scientists seem to forget that: http://www.nytimes.com/2016/07/26/science/last-universal-ancestor.html
🙂 🙂
Then it makes no sense to posit a hypothesis like “design” and a mechanism like “quantum interfacing” that don’t even mention random mutation.
So you accept common descent, random mutation, drift, natural selection at the “microevolutionary” level… the key to your theory seems to be that there’s some sort of intelligent entity designing life by deliberately introducing beneficial mutations. Since you reject that natural selection leads to reproductive advantage, I guess this intelligent agent must also actively select which individuals reproduce more to preserve the information.
This looks exactly like the modern evolutionary synthesis to me, only that some mutations are designed and (some?) selection is artificial.
This to me fails on many levels.
1. Parsimony. As mentioned by others before here, all you do is to posit an imaginary barrier to evolution, and then an undetectable agent to overcome the barrier you just imagined, and once he’s done his job, the result is indistinguishable from evolution by RM+NS.
2. You haven’t event tried to show where this barrier is, what kind of evolution is possible by RM+NS and what requires the designer’s intervention.
3. If you accept common descent, and that beneficial mutations can accumulate over time to produce macroevolutionary changes, why can only “designed” beneficial mutations and not random ones accumulate to produce the same variation? How can we tell a designed mutation from a random one?
4. There are multiple experiments showing that beneficial mutations give organisms a reproductive advantage. Denying it is absurd. Also, deleterious mutations produce differential reproduction. I don’t think you would contend that lethal mutations don’t give a relative reproductive advantage to those without it.
5. (This is more of a philosophical objection) It makes no sense whatsoever to design things this way, in particular if you allow your designs to drift after (and while) you keep painstakingly adding beneficial mutations one at a time during millions of years
6. As already noted, your hypothesis and mechanism lack any kind of explanatory power. All the heavy lifting is still done by the evolutionary concepts that you accept (mutation producing variation, common descent). For example, there’s no reason why the designer couldn’t inject the mutations needed to make a cat give birth to a crocoduck. Anything goes under your hypothesis. All you can do is to affirm after the fact that anything we see was designed that way just because.
You’re exactly where ID has always been and it’s nowhere near science
I think the last time we went round on this topic (which recurs in identical form every year or two) I mentioned Phenomenon of Man by Chardin.
Gpuccio will correct me if I’m wrong, but the one thing that seems to bind all versions of ID is the necessity of producing humans.
The actual historical path is not always contested. Evolution: fine. Common descent: fine. Mutation and selection: fine.
But all versions of ID seem to hold that evolution has a direction, that it is steered.
ETA: In some versions, indistinguishable from Deism, the steering is done up front. Front loading.
gpuccio: “Those “reproductive advantages”, which should evoke NS, remain in the realm of myth, just like the famous intermediates which have all gone extinct.”
I don’t get it. If you accept common descent, what’s the issue with intermediates?
Perhaps he’s saying that big innovations must arise all at once, from identical macromutations being given to all the members of some population. So we go from theropod (terrestrial, no feathers, no wings) to bird (aerial, feathers, wings) in one generation with no intermediates to be fossilized. Wait, there are intermediates? Never mind, then.
The article does seem to conflate LUCA with the Origins Of Life (OOL). But later in the article the distinction is made:
All unclearly, however. This morning my wife passed the New York Times on to me, saying “Here’s today’s paper. I could write it better than they did.”
Thanks, I already had the human ones but been struggling to find the rest. Well, I found the ASTN1 for humans, mouse, danio rerio (bony fish) and Branchiostoma floridae (Cephalochordates)
http://www.uniprot.org/uniprot/C3ZHZ3
http://www.uniprot.org/uniprot/F1Q5X4
http://www.uniprot.org/uniprot/Q61137
http://www.uniprot.org/uniprot/O14525
I’m missing:
Non chordate metazoa
Echinoderms
Tunicates
Cartilaginous fish
The ASTN1 ones would do
dazz,
I don’t see the point. All he’s doing is comparing sequence similarity (crudely) to humans. Well of course we expect some taxa to be more similar to us than others. And that big jump he makes a big deal out of is just the big slice of time separating the human-shark common ancestor from the human-cephalochordate common ancestor. Nobody should expect the time-intervals to be even between points. I wonder what it would look like if he did attempt to show the time-intervals on the x axis, rather than just evenly spaced points.
And why is similarity to humans an index of increased information content?
Because we are the epitome of Creation, and obviously got passed The Word, unlike those benighted animals and plants.
gpuccio’s response to this is:
This doesn’t make any sense to me because the match for ASTN2 for example, between humans and sharks is 73%. That doesn’t look so conserved to me. It’s also hard to reconcile the idea that a single fold can diverge more than 25% and still perform the same basic function if “islands of function” was true. And that’s just one pair comparison
BLAST Screenshot
https://drive.google.com/open?id=0Bx4m0vhzxbGIbVMzbjZ0aFFVenc
In fact, even if it was an entirely different function in my book that would also falsify the “islands of function” hypothesis
The fact that Gordon (LackOfFocus) Mullings beats the drum for “islands of function” is enough to raise serious doubts about it in my mind. 🙂
It doesn’t make sense to me for quite different reasons. I would consider 73% after 300 million years to be quite conserved. But why should “conservation” refer to matching humans? Why not sharks? Why not fruit flies? And what does that have to do with information?
Alan Fox,
I understand the limitations of the ID approach. It is interesting but only answers an inference and is therefor limited. It does not answer the how question.
I think the current evolutionary has evidence for and against. The evidence against is currently more compelling to me. I think the theory needs to be re worked and built on a house of bricks vs a house of cards. If you just answer the high level inference of UCD without the details (how does a specie with unique genes emerge from a common ancestor) then ID becomes a real alternative and at this point is a better fit for the evidence we currently have.
colewd,
You’re trying very hard to ignore the evidence for — hence your refusal to read Theobald and Wagner.
Why the fear? (Rhetorical question.)
What evidence against evolutionary theory would that be? “Science doesn’t know every last detail” isn’t evidence against.
ID offers no mechanisms, no timeline, not the slightest bit of detail on anything yet it’s supposed to be the better idea? You sure have a screwed up sense of reality.
Give an example (of a unique gene not present in a “common ancestor”).
colewd,
So you are basically saying that you can’t conceive of a reason for a gene with no detectable homologues in nearby taxa other than the rather vague ‘an entity or entities unknown must have stuck it there’. I don’t see how that is a better fit. Because there are mechanisms by which novel genes can arise, or appear to arise, and there are reasons why homology can be difficult to detect.
I probably don’t need to clarify that I’m not a biologist and not a particularly knowledgeable layman either. I wasn’t using conservation in that sense, although I don’t get to redefine terms, so that’s on me. I appreciate corrections wherever they come from.
John Harshman already clarified that 73% over such a time span represents quite a bit of conservation.
This raises a few questions though. If there’s conservation, then there’s selective pressure to keep the sequence relatively similar and to retain some level of functionality. You can’t possibly maintain that differential reproduction wouldn’t play a key roll in this process.
On your methodology:
Obviously our LCA with sharks had to have more similarity in the sequence with humans than humans have with sharks, because humans and sharks have been diverging independently from that LCA. This applies to every common ancestor of humans and any other species. If you measure “functional information” by comparing sequence similarities with humans, you’re essentially saying that every branch in the tree starts losing “functional information” as soon as it diverges from the human lineage. This is absurd IMHO. It means for example that birds had to lose “functional information” to evolve the ability to fly, and it doesn’t matter where you think that information comes from.
And if you take any other species other than humans to do the same calculations, you end up with conflicting results in measuring information.
Do you mean to tell me that the function remains exactly the same in that particular system between sharks and humans? But my point was that, if a protein can change a 1%, 10%, 25%, 50%, 60%, …73% and even more and still retain some function, it obviously means that these are not islands of function, because they’re clearly interconnected.
Yes, I understand that some proteins are more flexible to variation. But your metric is still bogus and I don’t think it shows what you claim it shows. Highly conserved proteins may be close to a local fitness maxima. But when those proteins were undergoing faster variation they clearly weren’t under so much selective pressure to remain relatively unchanged, and yet they managed to diversify in a myriad of vastly different sequences millions of years later which would be impossible if the sequence space was so scarce.
Also gpuccio, you claim that you can measure functional information by comparing protein sequences that retain the same exact function. So if you have a large difference in sequence but the same function, then there’s a large increase in “functional information”. This looks like an oxymoron to me. How can “functional information” be tied to retaining the same (exact) function? At best you’re begging the question that proteins can’t evolve new functions